diff --git a/doc/Makefile b/doc/Makefile index a3c4906cec..82c099ff70 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -3,7 +3,6 @@ SHELL = /bin/bash BUILDDIR = ${CURDIR} RSTDIR = $(BUILDDIR)/src -TXTDIR = $(BUILDDIR)/txt VENV = $(BUILDDIR)/docenv TXT2RST = $(VENV)/bin/txt2rst ANCHORCHECK = $(VENV)/bin/rst_anchor_check @@ -28,8 +27,6 @@ HAS_VIRTUALENV = YES endif SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') -SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt)) -OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst) .PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check style_check @@ -61,9 +58,9 @@ clean: clean-spelling: rm -rf spelling -rst: clean $(OBJECTS) $(ANCHORCHECK) +rst: clean $(ANCHORCHECK) -html: $(OBJECTS) $(ANCHORCHECK) +html: $(ANCHORCHECK) @(\ . $(VENV)/bin/activate ;\ sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\ @@ -86,7 +83,7 @@ html: $(OBJECTS) $(ANCHORCHECK) @rm -rf html/USER/*/*.[sg]* @echo "Build finished. The HTML pages are in doc/html." -spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt +spelling: utils/sphinx-config/false_positives.txt @(\ . $(VENV)/bin/activate ;\ pip install sphinxcontrib-spelling ;\ @@ -96,7 +93,7 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt ) @echo "Spell check finished." -epub: $(OBJECTS) +epub: @mkdir -p epub/JPG @rm -f LAMMPS.epub @cp src/JPG/lammps-logo.png epub/ @@ -115,7 +112,7 @@ mobi: epub @ebook-convert LAMMPS.epub LAMMPS.mobi @echo "Conversion finished. The MOBI manual file is created." -pdf: $(OBJECTS) $(ANCHORCHECK) +pdf: $(ANCHORCHECK) @(\ cd src/Developer; \ pdflatex developer; \ @@ -167,7 +164,7 @@ fetch: anchor_check : $(ANCHORCHECK) @(\ . $(VENV)/bin/activate ;\ - rst_anchor_check src/*.txt ;\ + rst_anchor_check src/*.rst ;\ deactivate ;\ ) @@ -180,14 +177,6 @@ style_check : # ------------------------------------------ -$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST) - @(\ - mkdir -p $(RSTDIR) ; \ - . $(VENV)/bin/activate ;\ - txt2rst -v $< > $@ ;\ - deactivate ;\ - ) - $(VENV): @if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi @if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 20d846fb7e..951e094c12 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -177,7 +177,7 @@ KIM package To build with this package, the KIM library with API v2 must be downloaded and built on your system. It must include the KIM models that you want to -use with LAMMPS. If you want to use the :doc:`kim\_query ` +use with LAMMPS. If you want to use the :doc:`kim_query ` command, you also need to have libcurl installed with the matching development headers and the curl-config tool. diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index b76e902033..cdb8016f57 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -5,11 +5,11 @@ LAMMPS can be built with several optional settings. Each sub-section explain how to do this for building both with CMake and make. | :ref:`C++11 standard compliance test ` when building all of LAMMPS -| :ref:`FFT library ` for use with the :doc:`kspace\_style pppm ` command +| :ref:`FFT library ` for use with the :doc:`kspace_style pppm ` command | :ref:`Size of LAMMPS data types ` | :ref:`Read or write compressed files ` | :ref:`Output of JPG and PNG files ` via the :doc:`dump image ` command -| :ref:`Output of movie files ` via the :doc:`dump\_movie ` command +| :ref:`Output of movie files ` via the :doc:`dump_movie ` command | :ref:`Memory allocation alignment ` | :ref:`Workaround for long long integers ` | :ref:`Error handling exceptions ` when using LAMMPS as a library @@ -72,7 +72,7 @@ FFT library --------------------- When the KSPACE package is included in a LAMMPS build, the -:doc:`kspace\_style pppm ` command performs 3d FFTs which +:doc:`kspace_style pppm ` command performs 3d FFTs which require use of an FFT library to compute 1d FFTs. The KISS FFT library is included with LAMMPS but other libraries can be faster. LAMMPS can use them if they are available on your system. @@ -251,7 +251,7 @@ support 8-byte integers. It allows for: Atom IDs are not required for atomic systems which do not store bond topology information, though IDs are enabled by default. The -:doc:`atom\_modify id no ` command will turn them off. Atom +:doc:`atom_modify id no ` command will turn them off. Atom IDs are required for molecular systems with bond topology (bonds, angles, dihedrals, etc). Thus if you model a molecular system with more than 2 billion atoms, you need the "bigbig" setting. @@ -357,7 +357,7 @@ Read or write compressed files If this option is enabled, large files can be read or written with gzip compression by several LAMMPS commands, including -:doc:`read\_data `, :doc:`rerun `, and :doc:`dump `. +:doc:`read_data `, :doc:`rerun `, and :doc:`dump `. **CMake variables**\ : diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index 5412675ee4..19be6d8cbc 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -131,7 +131,7 @@ OPT. Improper_style potentials ========================= -All LAMMPS :doc:`improper\_style ` commands. Some styles +All LAMMPS :doc:`improper_style ` commands. Some styles have accelerated versions. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. diff --git a/doc/src/Commands_category.rst b/doc/src/Commands_category.rst index b1b0e0cadc..6476c73bbb 100644 --- a/doc/src/Commands_category.rst +++ b/doc/src/Commands_category.rst @@ -18,73 +18,73 @@ Setup simulation box: * :doc:`boundary `, * :doc:`box `, -* :doc:`change\_box `, -* :doc:`create\_box `, +* :doc:`change_box `, +* :doc:`create_box `, * :doc:`dimension `, * :doc:`lattice `, * :doc:`region ` Setup atoms: -* :doc:`atom\_modify `, -* :doc:`atom\_style `, +* :doc:`atom_modify `, +* :doc:`atom_style `, * :doc:`balance `, -* :doc:`create\_atoms `, -* :doc:`create\_bonds `, -* :doc:`delete\_atoms `, -* :doc:`delete\_bonds `, -* :doc:`displace\_atoms `, +* :doc:`create_atoms `, +* :doc:`create_bonds `, +* :doc:`delete_atoms `, +* :doc:`delete_bonds `, +* :doc:`displace_atoms `, * :doc:`group `, * :doc:`mass `, * :doc:`molecule `, -* :doc:`read\_data `, -* :doc:`read\_dump `, -* :doc:`read\_restart `, +* :doc:`read_data `, +* :doc:`read_dump `, +* :doc:`read_restart `, * :doc:`replicate `, * :doc:`set `, * :doc:`velocity ` Force fields: -* :doc:`angle\_coeff `, -* :doc:`angle\_style `, -* :doc:`bond\_coeff `, -* :doc:`bond\_style `, -* :doc:`bond\_write `, +* :doc:`angle_coeff `, +* :doc:`angle_style `, +* :doc:`bond_coeff `, +* :doc:`bond_style `, +* :doc:`bond_write `, * :doc:`dielectric `, -* :doc:`dihedral\_coeff `, -* :doc:`dihedral\_style `, -* :doc:`improper\_coeff `, -* :doc:`improper\_style `, -* :doc:`kspace\_modify `, -* :doc:`kspace\_style `, -* :doc:`pair\_coeff `, -* :doc:`pair\_modify `, -* :doc:`pair\_style `, -* :doc:`pair\_write `, -* :doc:`special\_bonds ` +* :doc:`dihedral_coeff `, +* :doc:`dihedral_style `, +* :doc:`improper_coeff `, +* :doc:`improper_style `, +* :doc:`kspace_modify `, +* :doc:`kspace_style `, +* :doc:`pair_coeff `, +* :doc:`pair_modify `, +* :doc:`pair_style `, +* :doc:`pair_write `, +* :doc:`special_bonds ` Settings: -* :doc:`comm\_modify `, -* :doc:`comm\_style `, +* :doc:`comm_modify `, +* :doc:`comm_style `, * :doc:`info `, -* :doc:`min\_modify `, -* :doc:`min\_style `, -* :doc:`neigh\_modify `, +* :doc:`min_modify `, +* :doc:`min_style `, +* :doc:`neigh_modify `, * :doc:`neighbor `, * :doc:`partition `, -* :doc:`reset\_timestep `, -* :doc:`run\_style `, +* :doc:`reset_timestep `, +* :doc:`run_style `, * :doc:`timer `, * :doc:`timestep ` Operations within timestepping (fixes) and diagnostics (computes): * :doc:`compute `, -* :doc:`compute\_modify `, +* :doc:`compute_modify `, * :doc:`fix `, -* :doc:`fix\_modify `, +* :doc:`fix_modify `, * :doc:`uncompute `, * :doc:`unfix ` @@ -93,22 +93,22 @@ Output: * :doc:`dump image `, * :doc:`dump movie `, * :doc:`dump `, -* :doc:`dump\_modify `, +* :doc:`dump_modify `, * :doc:`restart `, * :doc:`thermo `, -* :doc:`thermo\_modify `, -* :doc:`thermo\_style `, +* :doc:`thermo_modify `, +* :doc:`thermo_style `, * :doc:`undump `, -* :doc:`write\_coeff `, -* :doc:`write\_data `, -* :doc:`write\_dump `, -* :doc:`write\_restart ` +* :doc:`write_coeff `, +* :doc:`write_data `, +* :doc:`write_dump `, +* :doc:`write_restart ` Actions: * :doc:`minimize `, * :doc:`neb `, -* :doc:`neb\_spin `, +* :doc:`neb_spin `, * :doc:`prd `, * :doc:`rerun `, * :doc:`run `, diff --git a/doc/src/Commands_input.rst b/doc/src/Commands_input.rst index c66b530dd0..69d3393d08 100644 --- a/doc/src/Commands_input.rst +++ b/doc/src/Commands_input.rst @@ -45,7 +45,7 @@ belong to the group. (3) Sometimes command B will use values that can be set by command A. This means command A must precede command B in the input script if it is to have the desired effect. For example, the -:doc:`read\_data ` command initializes the system by setting +:doc:`read_data ` command initializes the system by setting up the simulation box and assigning atoms to processors. If default values are not desired, the :doc:`processors ` and :doc:`boundary ` commands need to be used before read\_data to diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst index be953c5277..18fa5b5442 100644 --- a/doc/src/Commands_kspace.rst +++ b/doc/src/Commands_kspace.rst @@ -14,7 +14,7 @@ KSpace solvers ============== -All LAMMPS :doc:`kspace\_style ` solvers. Some styles have +All LAMMPS :doc:`kspace_style ` solvers. Some styles have accelerated versions. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index ee87296863..b7f48a9c36 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -57,8 +57,8 @@ restart2data tool The functionality of the restart2data tool has been folded into the LAMMPS executable directly instead of having a separate tool. A -combination of the commands :doc:`read\_restart ` and -:doc:`write\_data ` can be used to the same effect. For added +combination of the commands :doc:`read_restart ` and +:doc:`write_data ` can be used to the same effect. For added convenience this conversion can also be triggered by :doc:`command line flags ` diff --git a/doc/src/Commands_structure.rst b/doc/src/Commands_structure.rst index b419074212..cd96007bf2 100644 --- a/doc/src/Commands_structure.rst +++ b/doc/src/Commands_structure.rst @@ -26,23 +26,23 @@ read-in from a file. The relevant commands are :doc:`units `, :doc:`dimension `, :doc:`newton `, :doc:`processors `, :doc:`boundary `, -:doc:`atom\_style `, :doc:`atom\_modify `. +:doc:`atom_style `, :doc:`atom_modify `. If force-field parameters appear in the files that will be read, these commands tell LAMMPS what kinds of force fields are being used: -:doc:`pair\_style `, :doc:`bond\_style `, -:doc:`angle\_style `, :doc:`dihedral\_style `, -:doc:`improper\_style `. +:doc:`pair_style `, :doc:`bond_style `, +:doc:`angle_style `, :doc:`dihedral_style `, +:doc:`improper_style `. (2) Atom definition There are 3 ways to define atoms in LAMMPS. Read them in from a data -or restart file via the :doc:`read\_data ` or -:doc:`read\_restart ` commands. These files can contain +or restart file via the :doc:`read_data ` or +:doc:`read_restart ` commands. These files can contain molecular topology information. Or create atoms on a lattice (with no molecular topology), using these commands: :doc:`lattice `, -:doc:`region `, :doc:`create\_box `, -:doc:`create\_atoms `. The entire set of atoms can be +:doc:`region `, :doc:`create_box `, +:doc:`create_atoms `. The entire set of atoms can be duplicated to make a larger simulation using the :doc:`replicate ` command. @@ -53,25 +53,25 @@ can be specified: force field coefficients, simulation parameters, output options, etc. Force field coefficients are set by these commands (they can also be -set in the read-in files): :doc:`pair\_coeff `, -:doc:`bond\_coeff `, :doc:`angle\_coeff `, -:doc:`dihedral\_coeff `, -:doc:`improper\_coeff `, -:doc:`kspace\_style `, :doc:`dielectric `, -:doc:`special\_bonds `. +set in the read-in files): :doc:`pair_coeff `, +:doc:`bond_coeff `, :doc:`angle_coeff `, +:doc:`dihedral_coeff `, +:doc:`improper_coeff `, +:doc:`kspace_style `, :doc:`dielectric `, +:doc:`special_bonds `. Various simulation parameters are set by these commands: -:doc:`neighbor `, :doc:`neigh\_modify `, +:doc:`neighbor `, :doc:`neigh_modify `, :doc:`group `, :doc:`timestep `, -:doc:`reset\_timestep `, :doc:`run\_style `, -:doc:`min\_style `, :doc:`min\_modify `. +:doc:`reset_timestep `, :doc:`run_style `, +:doc:`min_style `, :doc:`min_modify `. Fixes impose a variety of boundary conditions, time integration, and diagnostic options. The :doc:`fix ` command comes in many flavors. Various computations can be specified for execution during a simulation using the :doc:`compute `, -:doc:`compute\_modify `, and :doc:`variable ` +:doc:`compute_modify `, and :doc:`variable ` commands. Output options are set by the :doc:`thermo `, :doc:`dump `, diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst index 8137c64e96..2da3e623dc 100644 --- a/doc/src/Errors_common.rst +++ b/doc/src/Errors_common.rst @@ -18,7 +18,7 @@ the two simulations will rapidly diverge. See the discussion of the *loop* option in the :doc:`velocity ` command for details and options that avoid this issue. -Similarly, the :doc:`create\_atoms ` command generates a +Similarly, the :doc:`create_atoms ` command generates a lattice of atoms. For the same physical system, the ordering and numbering of atoms by atom ID may be different depending on the number of processors. diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 22a4facdd0..8c457bba83 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -6194,7 +6194,7 @@ keyword to allow for additional bonds to be formed rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the - :doc:`neigh\_modify ` command. The safest settings are + :doc:`neigh_modify ` command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly @@ -6209,7 +6209,7 @@ keyword to allow for additional bonds to be formed rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the - :doc:`neigh\_modify ` command. The safest settings are + :doc:`neigh_modify ` command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly @@ -6224,7 +6224,7 @@ keyword to allow for additional bonds to be formed rebuilt and atoms being migrated to new processors. This also means you may be missing pairwise interactions that need to be computed. The solution is to change the re-neighboring criteria via the - :doc:`neigh\_modify ` command. The safest settings are + :doc:`neigh_modify ` command. The safest settings are "delay 0 every 1 check yes". Second, it may mean that an atom has moved far outside a processor's sub-domain or even the entire simulation box. This indicates bad physics, e.g. due to highly diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index 2b2f88204b..7b8f85dc9a 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -118,10 +118,10 @@ Doc page with :doc:`ERROR messages ` *Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost* The communication cutoff defaults to the maximum of what is inferred from pair and bond styles (will be zero, if none are defined) and what is specified - via :doc:`comm\_modify cutoff ` (defaults to 0.0). If this results + via :doc:`comm_modify cutoff ` (defaults to 0.0). If this results to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use incorrect periodic images of atoms in interaction lists. To avoid, either use - :doc:`pair style zero ` with a suitable cutoff or use :doc:`comm\_modify cutoff `. + :doc:`pair style zero ` with a suitable cutoff or use :doc:`comm_modify cutoff `. *Communication cutoff is too small for SNAP micro load balancing, increased to %lf* Self-explanatory. diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst index ee978f3521..d4fce71230 100644 --- a/doc/src/Howto_2d.rst +++ b/doc/src/Howto_2d.rst @@ -33,7 +33,7 @@ are for 2d models. .. note:: Some models in LAMMPS treat particles as finite-size spheres, as - opposed to point particles. See the :doc:`atom\_style sphere ` and :doc:`fix nve/sphere ` + opposed to point particles. See the :doc:`atom_style sphere ` and :doc:`fix nve/sphere ` commands for details. By default, for 2d simulations, such particles will still be modeled as 3d spheres, not 2d discs (circles), meaning their moment of inertia will be that of a sphere. If you wish to diff --git a/doc/src/Howto_barostat.rst b/doc/src/Howto_barostat.rst index 0c46c696c7..7f016e0c14 100644 --- a/doc/src/Howto_barostat.rst +++ b/doc/src/Howto_barostat.rst @@ -38,7 +38,7 @@ the kinetic component of the pressure. The barostatting fixes can also use temperature computes that remove bias for the purpose of computing the kinetic component which contributes to the current pressure. See the doc pages for the individual fixes and for the -:doc:`fix\_modify ` command for instructions on how to assign +:doc:`fix_modify ` command for instructions on how to assign a temperature or pressure compute to a barostatting fix. .. note:: @@ -49,16 +49,16 @@ a temperature or pressure compute to a barostatting fix. fixes. Thermodynamic output, which can be setup via the -:doc:`thermo\_style ` command, often includes pressure +:doc:`thermo_style ` command, often includes pressure values. As explained on the doc page for the -:doc:`thermo\_style ` command, the default pressure is +:doc:`thermo_style ` command, the default pressure is setup by the thermo command itself. It is NOT the pressure associated with any barostatting fix you have defined or with any compute you have defined that calculates a pressure. The doc pages for the barostatting fixes explain the ID of the pressure compute they create. Thus if you want to view these pressures, you need to specify them -explicitly via the :doc:`thermo\_style custom ` command. -Or you can use the :doc:`thermo\_modify ` command to +explicitly via the :doc:`thermo_style custom ` command. +Or you can use the :doc:`thermo_modify ` command to re-define what pressure compute is used for default thermodynamic output. diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index 0ec0c16be8..fe8f6482aa 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -6,9 +6,9 @@ coefficients used for a particular system. Here we only discuss formulas implemented in LAMMPS that correspond to formulas commonly used in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting coefficients is done either from special sections in an input data file -via the :doc:`read\_data ` command or in the input script with -commands like :doc:`pair\_coeff ` or -:doc:`bond\_coeff ` and so on. See the :doc:`Tools ` doc +via the :doc:`read_data ` command or in the input script with +commands like :doc:`pair_coeff ` or +:doc:`bond_coeff ` and so on. See the :doc:`Tools ` doc page for additional tools that can use CHARMM, AMBER, or Materials Studio generated files to assign force field coefficients and convert their output into LAMMPS input. @@ -30,18 +30,18 @@ The interaction styles listed below compute force field formulas that are consistent with common options in CHARMM or AMBER. See each command's documentation for the formula it computes. -* :doc:`bond\_style ` harmonic -* :doc:`angle\_style ` charmm -* :doc:`dihedral\_style ` charmmfsh -* :doc:`dihedral\_style ` charmm -* :doc:`pair\_style ` lj/charmmfsw/coul/charmmfsh -* :doc:`pair\_style ` lj/charmmfsw/coul/long -* :doc:`pair\_style ` lj/charmm/coul/charmm -* :doc:`pair\_style ` lj/charmm/coul/charmm/implicit -* :doc:`pair\_style ` lj/charmm/coul/long +* :doc:`bond_style ` harmonic +* :doc:`angle_style ` charmm +* :doc:`dihedral_style ` charmmfsh +* :doc:`dihedral_style ` charmm +* :doc:`pair_style ` lj/charmmfsw/coul/charmmfsh +* :doc:`pair_style ` lj/charmmfsw/coul/long +* :doc:`pair_style ` lj/charmm/coul/charmm +* :doc:`pair_style ` lj/charmm/coul/charmm/implicit +* :doc:`pair_style ` lj/charmm/coul/long -* :doc:`special\_bonds ` charmm -* :doc:`special\_bonds ` amber +* :doc:`special_bonds ` charmm +* :doc:`special_bonds ` amber .. note:: @@ -66,16 +66,16 @@ These interaction styles listed below compute force field formulas that are consistent with the COMPASS force field. See each command's documentation for the formula it computes. -* :doc:`bond\_style ` class2 -* :doc:`angle\_style ` class2 -* :doc:`dihedral\_style ` class2 -* :doc:`improper\_style ` class2 +* :doc:`bond_style ` class2 +* :doc:`angle_style ` class2 +* :doc:`dihedral_style ` class2 +* :doc:`improper_style ` class2 -* :doc:`pair\_style ` lj/class2 -* :doc:`pair\_style ` lj/class2/coul/cut -* :doc:`pair\_style ` lj/class2/coul/long +* :doc:`pair_style ` lj/class2 +* :doc:`pair_style ` lj/class2/coul/cut +* :doc:`pair_style ` lj/class2/coul/long -* :doc:`special\_bonds ` lj/coul 0 0 1 +* :doc:`special_bonds ` lj/coul 0 0 1 DREIDING is a generic force field developed by the `Goddard group `_ at Caltech and is useful for predicting structures and dynamics of organic, biological and main-group @@ -92,27 +92,27 @@ The interaction styles listed below compute force field formulas that are consistent with the DREIDING force field. See each command's documentation for the formula it computes. -* :doc:`bond\_style ` harmonic -* :doc:`bond\_style ` morse +* :doc:`bond_style ` harmonic +* :doc:`bond_style ` morse -* :doc:`angle\_style ` harmonic -* :doc:`angle\_style ` cosine -* :doc:`angle\_style ` cosine/periodic +* :doc:`angle_style ` harmonic +* :doc:`angle_style ` cosine +* :doc:`angle_style ` cosine/periodic -* :doc:`dihedral\_style ` charmm -* :doc:`improper\_style ` umbrella +* :doc:`dihedral_style ` charmm +* :doc:`improper_style ` umbrella -* :doc:`pair\_style ` buck -* :doc:`pair\_style ` buck/coul/cut -* :doc:`pair\_style ` buck/coul/long -* :doc:`pair\_style ` lj/cut -* :doc:`pair\_style ` lj/cut/coul/cut -* :doc:`pair\_style ` lj/cut/coul/long +* :doc:`pair_style ` buck +* :doc:`pair_style ` buck/coul/cut +* :doc:`pair_style ` buck/coul/long +* :doc:`pair_style ` lj/cut +* :doc:`pair_style ` lj/cut/coul/cut +* :doc:`pair_style ` lj/cut/coul/long -* :doc:`pair\_style ` hbond/dreiding/lj -* :doc:`pair\_style ` hbond/dreiding/morse +* :doc:`pair_style ` hbond/dreiding/lj +* :doc:`pair_style ` hbond/dreiding/morse -* :doc:`special\_bonds ` dreiding +* :doc:`special_bonds ` dreiding ---------- diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index 4819ea97df..f929b9f439 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -12,10 +12,10 @@ as spheres, ellipsoids, line segments, and triangles, but they are simpler entities that body particles. See the :doc:`Howto spherical ` doc page for a general overview of all these particle types. -Body particles are used via the :doc:`atom\_style body ` +Body particles are used via the :doc:`atom_style body ` command. It takes a body style as an argument. The current body styles supported by LAMMPS are as follows. The name in the first -column is used as the *bstyle* argument for the :doc:`atom\_style body ` command. +column is used as the *bstyle* argument for the :doc:`atom_style body ` command. +----------------------+---------------------------------------------------+ | *nparticle* | rigid body with N sub-particles | @@ -129,7 +129,7 @@ arguments: The Nmin and Nmax arguments are used to bound the size of data structures used internally by each particle. -When the :doc:`read\_data ` command reads a data file for this +When the :doc:`read_data ` command reads a data file for this body style, the following information must be provided for each entry in the *Bodies* section of the data file: @@ -149,7 +149,7 @@ particle. The integer line has a single value N. The floating point line(s) list 6 moments of inertia followed by the coordinates of the N sub-particles (x1 to zN) as 3N values. These values can be listed on -as many lines as you wish; see the :doc:`read\_data ` command +as many lines as you wish; see the :doc:`read_data ` command for more details. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the @@ -163,7 +163,7 @@ center-of-mass position of the particle is specified by the x,y,z values in the *Atoms* section of the data file, as is the total mass of the body particle. -The :doc:`pair\_style body/nparticle ` command can be used +The :doc:`pair_style body/nparticle ` command can be used with this body style to compute body/body and body/non-body interactions. For output purposes via the :doc:`compute body/local ` and :doc:`dump local ` @@ -217,7 +217,7 @@ this body style takes two additional arguments: The Nmin and Nmax arguments are used to bound the size of data structures used internally by each particle. -When the :doc:`read\_data ` command reads a data file for this +When the :doc:`read_data ` command reads a data file for this body style, the following information must be provided for each entry in the *Bodies* section of the data file: @@ -243,7 +243,7 @@ vertices (x1 to zN) as 3N values (with z = 0.0 for each), followed by followed by a single diameter value = the rounded diameter of the circle that surrounds each vertex. The diameter value can be different for each body particle. These floating-point values can be listed on -as many lines as you wish; see the :doc:`read\_data ` command +as many lines as you wish; see the :doc:`read_data ` command for more details. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the @@ -302,7 +302,7 @@ A disk, whose diameter is 3.0, mass 1.0, is specified as follows: 0 0 0 3.0 -The :doc:`pair\_style body/rounded/polygon ` +The :doc:`pair_style body/rounded/polygon ` command can be used with this body style to compute body/body interactions. The :doc:`fix wall/body/polygon ` command can be used with this body style to compute the interaction of @@ -340,7 +340,7 @@ for this body style takes two additional arguments: The Nmin and Nmax arguments are used to bound the size of data structures used internally by each particle. -When the :doc:`read\_data ` command reads a data file for this +When the :doc:`read_data ` command reads a data file for this body style, the following information must be provided for each entry in the *Bodies* section of the data file: @@ -375,7 +375,7 @@ faces. The last value is the diameter value = the rounded diameter of the sphere that surrounds each vertex. The diameter value can be different for each body particle. These floating-point values can be listed on as many lines as you wish; see the -:doc:`read\_data ` command for more details. Because the +:doc:`read_data ` command for more details. Because the maximum number of vertices per face is hard-coded to be 4 (i.e. quadrilaterals), faces with more than 4 vertices need to be split into triangles or quadrilaterals. For triangular faces, the @@ -459,7 +459,7 @@ A sphere whose diameter is 3.0 and mass 1.0, is specified as follows: 0 0 0 3.0 -The :doc:`pair\_style body/rounded/polhedron ` command can +The :doc:`pair_style body/rounded/polhedron ` command can be used with this body style to compute body/body interactions. The :doc:`fix wall/body/polyhedron ` command can be used with this body style to compute the interaction of body particles @@ -489,7 +489,7 @@ For images created by the :doc:`dump image ` command, if the *body* keyword is set, then each body particle is drawn as a polygon consisting of N line segments. Note that the line segments are drawn between the N vertices, which does not correspond exactly to the -physical extent of the body (because the :doc:`pair\_style rounded/polygon ` defines finite-size +physical extent of the body (because the :doc:`pair_style rounded/polygon ` defines finite-size spheres at those point and the line segments between the spheres are tangent to the spheres). The drawn diameter of each line segment is determined by the *bflag1* parameter for the *body* keyword. The diff --git a/doc/src/Howto_coreshell.rst b/doc/src/Howto_coreshell.rst index c39f87fac2..8b2ba38306 100644 --- a/doc/src/Howto_coreshell.rst +++ b/doc/src/Howto_coreshell.rst @@ -17,7 +17,7 @@ alpha = q(shell)\^2 / k. In a similar fashion the mass of the ion is distributed on the core and the shell with the core having the larger mass. -To run this model in LAMMPS, :doc:`atom\_style ` *full* can +To run this model in LAMMPS, :doc:`atom_style ` *full* can be used since atom charge and bonds are needed. Each kind of core/shell pair requires two atom types and a bond type. The core and shell of a core/shell pair should be bonded to each other with a @@ -63,12 +63,12 @@ defined between the shells. Coulombic interactions are defined between all cores and shells. If desired, additional bonds can be specified between cores. -The :doc:`special\_bonds ` command should be used to +The :doc:`special_bonds ` command should be used to turn-off the Coulombic interaction within core/shell pairs, since that interaction is set by the bond spring. This is done using the -:doc:`special\_bonds ` command with a 1-2 weight = 0.0, +:doc:`special_bonds ` command with a 1-2 weight = 0.0, which is the default value. It needs to be considered whether one has -to adjust the :doc:`special\_bonds ` weighting according +to adjust the :doc:`special_bonds ` weighting according to the molecular topology since the interactions of the shells are bypassed over an extra bond. @@ -81,7 +81,7 @@ core and shell, a pair style with a "cs" suffix needs to be used to implement a valid long-range Coulombic correction. Several such pair styles are provided in the CORESHELL package. See :doc:`this doc page ` for details. All of the core/shell enabled pair styles require the use of a long-range Coulombic solver, as specified -by the :doc:`kspace\_style ` command. Either the PPPM or +by the :doc:`kspace_style ` command. Either the PPPM or Ewald solvers can be used. For the NaCL example problem, these pair style and bond style settings @@ -126,7 +126,7 @@ groups can be defined using the :doc:`group *type*\ ` command. Note that to perform thermostatting using this definition of temperature, the :doc:`fix modify temp ` command should be used to assign the compute to the thermostat fix. Likewise the -:doc:`thermo\_modify temp ` command can be used to make +:doc:`thermo_modify temp ` command can be used to make this temperature be output for the overall system. For the NaCl example, this can be done as follows: @@ -148,7 +148,7 @@ as well as for the application of a barostat, it is necessary to use an additional :doc:`pressure ` compute based on the default :doc:`temperature ` and specifying it as a second argument in :doc:`fix modify ` and -:doc:`thermo\_modify ` resulting in: +:doc:`thermo_modify ` resulting in: .. parsed-literal:: @@ -204,7 +204,7 @@ the molecule ID can be used to define the chunks. If cores are bonded to each other to form larger molecules, the chunks can be identified by the :doc:`fix property/atom ` via assigning a core/shell ID to each atom using a special field in the data file read -by the :doc:`read\_data ` command. This field can then be +by the :doc:`read_data ` command. This field can then be accessed by the :doc:`compute property/atom ` command, to use as input to the :doc:`compute chunk/atom ` command to define the core/shell pairs as chunks. diff --git a/doc/src/Howto_drude.rst b/doc/src/Howto_drude.rst index d786c66ef8..78eb7ba49f 100644 --- a/doc/src/Howto_drude.rst +++ b/doc/src/Howto_drude.rst @@ -39,19 +39,19 @@ specified via the :doc:`fix drude ` command. The special list of neighbors is automatically refactored to account for the equivalence of core and Drude particles as regards special 1-2 to 1-4 screening. It may be necessary to use the *extra/special/per/atom* -keyword of the :doc:`read\_data ` command. If using :doc:`fix shake `, make sure no Drude particle is in this fix +keyword of the :doc:`read_data ` command. If using :doc:`fix shake `, make sure no Drude particle is in this fix group. There are two ways to thermostat the Drude particles at a low temperature: use either :doc:`fix langevin/drude ` for a Langevin thermostat, or :doc:`fix drude/transform/\* ` for a Nose-Hoover -thermostat. The former requires use of the command :doc:`comm\_modify vel yes `. The latter requires two separate integration +thermostat. The former requires use of the command :doc:`comm_modify vel yes `. The latter requires two separate integration fixes like *nvt* or *npt*\ . The correct temperatures of the reduced degrees of freedom can be calculated using the :doc:`compute temp/drude `. This requires also to use the command *comm\_modify vel yes*. Short-range damping of the induced dipole interactions can be achieved -using Thole functions through the :doc:`pair style thole ` in :doc:`pair\_style hybrid/overlay ` +using Thole functions through the :doc:`pair style thole ` in :doc:`pair_style hybrid/overlay ` with a Coulomb pair style. It may be useful to use *coul/long/cs* or similar from the CORESHELL package if the core and Drude particle come too close, which can cause numerical issues. diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index baf9a38f08..e1572df6c6 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -159,7 +159,7 @@ DC-DP pairs and will treat DP as equivalent to their DC in the *special bonds* relations. It may be necessary to extend the space for storing such special relations. In this case extra space should be reserved by using the *extra/special/per/atom* keyword of either -the :doc:`read\_data ` or :doc:`create\_box ` +the :doc:`read_data ` or :doc:`create_box ` command. With our phenol, there is 1 more special neighbor for which space is required. Otherwise LAMMPS crashes and gives the required value. diff --git a/doc/src/Howto_elastic.rst b/doc/src/Howto_elastic.rst index f249ea2df7..389c8e19de 100644 --- a/doc/src/Howto_elastic.rst +++ b/doc/src/Howto_elastic.rst @@ -16,7 +16,7 @@ most 7\*6/2 = 21 distinct elements. At zero temperature, it is easy to estimate these derivatives by deforming the simulation box in one of the six directions using the -:doc:`change\_box ` command and measuring the change in the +:doc:`change_box ` command and measuring the change in the stress tensor. A general-purpose script that does this is given in the examples/elastic directory described on the :doc:`Examples ` doc page. diff --git a/doc/src/Howto_granular.rst b/doc/src/Howto_granular.rst index d6c983efe1..0bd4fa0349 100644 --- a/doc/src/Howto_granular.rst +++ b/doc/src/Howto_granular.rst @@ -8,7 +8,7 @@ velocity and torque can be imparted to them to cause them to rotate. To run a simulation of a granular model, you will want to use the following commands: -* :doc:`atom\_style sphere ` +* :doc:`atom_style sphere ` * :doc:`fix nve/sphere ` * :doc:`fix gravity ` @@ -21,9 +21,9 @@ calculates rotational kinetic energy which can be :doc:`output with thermodynami Use one of these 3 pair potentials, which compute forces and torques between interacting pairs of particles: -* :doc:`pair\_style ` gran/history -* :doc:`pair\_style ` gran/no\_history -* :doc:`pair\_style ` gran/hertzian +* :doc:`pair_style ` gran/history +* :doc:`pair_style ` gran/no\_history +* :doc:`pair_style ` gran/hertzian These commands implement fix options specific to granular systems: @@ -39,7 +39,7 @@ atoms, and should be used for granular system instead of the fix style For computational efficiency, you can eliminate needless pairwise computations between frozen atoms by using this command: -* :doc:`neigh\_modify ` exclude +* :doc:`neigh_modify ` exclude .. note:: diff --git a/doc/src/Howto_output.rst b/doc/src/Howto_output.rst index 6a5788cab3..617447fc04 100644 --- a/doc/src/Howto_output.rst +++ b/doc/src/Howto_output.rst @@ -88,21 +88,21 @@ Thermodynamic output --------------------------------- The frequency and format of thermodynamic output is set by the -:doc:`thermo `, :doc:`thermo\_style `, and -:doc:`thermo\_modify ` commands. The -:doc:`thermo\_style ` command also specifies what values +:doc:`thermo `, :doc:`thermo_style `, and +:doc:`thermo_modify ` commands. The +:doc:`thermo_style ` command also specifies what values are calculated and written out. Pre-defined keywords can be specified (e.g. press, etotal, etc). Three additional kinds of keywords can also be specified (c\_ID, f\_ID, v\_name), where a :doc:`compute ` or :doc:`fix ` or :doc:`variable ` provides the value to be output. In each case, the compute, fix, or variable must generate -global values for input to the :doc:`thermo\_style custom ` +global values for input to the :doc:`thermo_style custom ` command. Note that thermodynamic output values can be "extensive" or "intensive". The former scale with the number of atoms in the system (e.g. total energy), the latter do not (e.g. temperature). The -setting for :doc:`thermo\_modify norm ` determines whether +setting for :doc:`thermo_modify norm ` determines whether extensive quantities are normalized or not. Computes and fixes produce either extensive or intensive values; see their individual doc pages for details. :doc:`Equal-style variables ` produce only @@ -116,7 +116,7 @@ Dump file output --------------------------- Dump file output is specified by the :doc:`dump ` and -:doc:`dump\_modify ` commands. There are several +:doc:`dump_modify ` commands. There are several pre-defined formats (dump atom, dump xtc, etc). There is also a :doc:`dump custom ` format where the user @@ -151,7 +151,7 @@ specifies one or more quantities as input. These can be global :doc:`compute ` values, global :doc:`fix ` values, or :doc:`variables ` of any style except the atom style which produces per-atom values. Since a variable can refer to keywords used -by the :doc:`thermo\_style custom ` command (like temp or +by the :doc:`thermo_style custom ` command (like temp or press) and individual per-atom values, a wide variety of quantities can be time averaged and/or output in this way. If the inputs are one or more scalar values, then the fix generate a global scalar or vector @@ -304,7 +304,7 @@ vector input could be a column of an array. +--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ | Command | Input | Output | +--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`thermo\_style custom ` | global scalars | screen, log file | +| :doc:`thermo_style custom ` | global scalars | screen, log file | +--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ | :doc:`dump custom ` | per-atom vectors | dump file | +--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ diff --git a/doc/src/Howto_replica.rst b/doc/src/Howto_replica.rst index 49150ae985..885cdf050e 100644 --- a/doc/src/Howto_replica.rst +++ b/doc/src/Howto_replica.rst @@ -9,7 +9,7 @@ periodically. These are the relevant commands: * :doc:`neb ` for nudged elastic band calculations -* :doc:`neb\_spin ` for magnetic nudged elastic band calculations +* :doc:`neb_spin ` for magnetic nudged elastic band calculations * :doc:`prd ` for parallel replica dynamics * :doc:`tad ` for temperature accelerated dynamics * :doc:`temper ` for parallel tempering diff --git a/doc/src/Howto_restart.rst b/doc/src/Howto_restart.rst index 608246ccbc..c6dc818816 100644 --- a/doc/src/Howto_restart.rst +++ b/doc/src/Howto_restart.rst @@ -6,16 +6,16 @@ There are 3 ways to continue a long LAMMPS simulation. Multiple run will continue from where the previous run left off. Or binary restart files can be saved to disk using the :doc:`restart ` command. At a later time, these binary files can be read via a -:doc:`read\_restart ` command in a new script. Or they can -be converted to text data files using the :doc:`-r command-line switch ` and read by a :doc:`read\_data ` +:doc:`read_restart ` command in a new script. Or they can +be converted to text data files using the :doc:`-r command-line switch ` and read by a :doc:`read_data ` command in a new script. Here we give examples of 2 scripts that read either a binary restart file or a converted data file and then issue a new run command to continue where the previous run left off. They illustrate what settings must be made in the new script. Details are discussed in the -documentation for the :doc:`read\_restart ` and -:doc:`read\_data ` commands. +documentation for the :doc:`read_restart ` and +:doc:`read_data ` commands. Look at the *in.chain* input script provided in the *bench* directory of the LAMMPS distribution to see the original script that these 2 @@ -95,7 +95,7 @@ Then, this script could be used to re-run the last 50 steps: Note that nearly all the settings specified in the original *in.chain* script must be repeated, except the *pair\_coeff* and *bond\_coeff* commands since the new data file lists the force field coefficients. -Also, the :doc:`reset\_timestep ` command is used to tell +Also, the :doc:`reset_timestep ` command is used to tell LAMMPS the current timestep. This value is stored in restart files, but not in data files. diff --git a/doc/src/Howto_spherical.rst b/doc/src/Howto_spherical.rst index 23ea6435f8..ec199c859b 100644 --- a/doc/src/Howto_spherical.rst +++ b/doc/src/Howto_spherical.rst @@ -45,7 +45,7 @@ like This is because when dipoles interact with each other, they induce torques, and a particle must be finite-size (i.e. have a moment of -inertia) in order to respond and rotate. See the :doc:`atom\_style dipole ` command for details. The "set" command can be +inertia) in order to respond and rotate. See the :doc:`atom_style dipole ` command for details. The "set" command can be used to modify the orientation and length of the dipole moment of individual particles, after then are created. @@ -71,7 +71,7 @@ particles with a triangulated surface. The peri style is used with :doc:`Peridynamic models ` and defines particles as having a volume, that is used internally in the -:doc:`pair\_style peri ` potentials. +:doc:`pair_style peri ` potentials. The body style allows for definition of particles which can represent complex entities, such as surface meshes of discrete points, @@ -80,7 +80,7 @@ is discussed in more detail on the :doc:`Howto body ` doc page. Note that if one of these atom styles is used (or multiple styles via -the :doc:`atom\_style hybrid ` command), not all particles in +the :doc:`atom_style hybrid ` command), not all particles in the system are required to be finite-size or aspherical. For example, in the ellipsoid style, if the 3 shape parameters are set @@ -94,7 +94,7 @@ Some of the pair styles used to compute pairwise interactions between finite-size particles also compute the correct interaction with point particles as well, e.g. the interaction between a point particle and a finite-size particle or between two point particles. If necessary, -:doc:`pair\_style hybrid ` can be used to insure the correct +:doc:`pair_style hybrid ` can be used to insure the correct interactions are computed for the appropriate style of interactions. Likewise, using groups to partition particles (ellipsoids versus spheres versus point particles) will allow you to use the appropriate @@ -114,17 +114,17 @@ When a system with finite-size particles is defined, the particles will only rotate and experience torque if the force field computes such interactions. These are the various :doc:`pair styles ` that generate torque: -* :doc:`pair\_style gran/history ` -* :doc:`pair\_style gran/hertzian ` -* :doc:`pair\_style gran/no\_history ` -* :doc:`pair\_style dipole/cut ` -* :doc:`pair\_style gayberne ` -* :doc:`pair\_style resquared ` -* :doc:`pair\_style brownian ` -* :doc:`pair\_style lubricate ` -* :doc:`pair\_style line/lj ` -* :doc:`pair\_style tri/lj ` -* :doc:`pair\_style body/nparticle ` +* :doc:`pair_style gran/history ` +* :doc:`pair_style gran/hertzian ` +* :doc:`pair_style gran/no\_history ` +* :doc:`pair_style dipole/cut ` +* :doc:`pair_style gayberne ` +* :doc:`pair_style resquared ` +* :doc:`pair_style brownian ` +* :doc:`pair_style lubricate ` +* :doc:`pair_style line/lj ` +* :doc:`pair_style tri/lj ` +* :doc:`pair_style body/nparticle ` The granular pair styles are used with spherical particles. The dipole pair style is used with the dipole atom style, which could be @@ -187,10 +187,10 @@ These include rotational degrees of freedom in their computation. If you wish the thermodynamic output of temperature or pressure to use one of these computes (e.g. for a system entirely composed of finite-size particles), then the compute can be defined and the -:doc:`thermo\_modify ` command used. Note that by default +:doc:`thermo_modify ` command used. Note that by default thermodynamic quantities will be calculated with a temperature that only includes translational degrees of freedom. See the -:doc:`thermo\_style ` command for details. +:doc:`thermo_style ` command for details. These commands can be used to output various attributes of finite-size particles: @@ -235,7 +235,7 @@ Also note that body particles cannot be modeled with the :doc:`fix rigid `. Interactions between pairs of body -particles are computed via a command like :doc:`pair\_style body/nparticle `. +particles are computed via a command like :doc:`pair_style body/nparticle `. .. _lws: http://lammps.sandia.gov diff --git a/doc/src/Howto_thermostat.rst b/doc/src/Howto_thermostat.rst index 89d0c7b693..273876c9fd 100644 --- a/doc/src/Howto_thermostat.rst +++ b/doc/src/Howto_thermostat.rst @@ -23,7 +23,7 @@ can be invoked via the *dpd/tstat* pair style: * :doc:`fix temp/csvr ` * :doc:`fix langevin ` * :doc:`fix temp/rescale ` -* :doc:`pair\_style dpd/tstat ` +* :doc:`pair_style dpd/tstat ` :doc:`Fix nvt ` only thermostats the translational velocity of particles. :doc:`Fix nvt/sllod ` also does this, except @@ -49,7 +49,7 @@ bias removed. Second, the thermostat adjusts only the thermal temperature component of the particle's velocities, which are the velocities with the bias removed. The removed bias is then added back to the adjusted velocities. See the doc pages for the individual -fixes and for the :doc:`fix\_modify ` command for +fixes and for the :doc:`fix_modify ` command for instructions on how to assign a temperature compute to a thermostatting fix. For example, you can apply a thermostat to only the x and z components of velocity by using it in conjunction with @@ -70,16 +70,16 @@ particles without affecting the streaming velocity, by using :doc:`compute temp/ * :doc:`fix nve/asphere ` Thermodynamic output, which can be setup via the -:doc:`thermo\_style ` command, often includes temperature +:doc:`thermo_style ` command, often includes temperature values. As explained on the doc page for the -:doc:`thermo\_style ` command, the default temperature is +:doc:`thermo_style ` command, the default temperature is setup by the thermo command itself. It is NOT the temperature associated with any thermostatting fix you have defined or with any compute you have defined that calculates a temperature. The doc pages for the thermostatting fixes explain the ID of the temperature compute they create. Thus if you want to view these temperatures, you need to -specify them explicitly via the :doc:`thermo\_style custom ` command. Or you can use the -:doc:`thermo\_modify ` command to re-define what +specify them explicitly via the :doc:`thermo_style custom ` command. Or you can use the +:doc:`thermo_modify ` command to re-define what temperature compute is used for default thermodynamic output. diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index 449aa8e9f7..c55e22ba60 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -11,12 +11,12 @@ angle style of *harmonic* or *charmm* should also be used. A TIP4P model is run with LAMMPS using either this command for a cutoff model: -:doc:`pair\_style lj/cut/tip4p/cut ` +:doc:`pair_style lj/cut/tip4p/cut ` or these two commands for a long-range model: -* :doc:`pair\_style lj/cut/tip4p/long ` -* :doc:`kspace\_style pppm/tip4p ` +* :doc:`pair_style lj/cut/tip4p/long ` +* :doc:`kspace_style pppm/tip4p ` For both models, the bond lengths and bond angles should be held fixed using the :doc:`fix shake ` command. @@ -24,7 +24,7 @@ using the :doc:`fix shake ` command. These are the additional parameters (in real units) to set for O and H atoms and the water molecule to run a rigid TIP4P model with a cutoff :ref:`(Jorgensen) `. Note that the OM distance is specified in -the :doc:`pair\_style ` command, not as part of the pair +the :doc:`pair_style ` command, not as part of the pair coefficients. | O mass = 15.9994 @@ -95,7 +95,7 @@ typically best in an efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2\*(OM distance), to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. The OM distance and the LJ -and Coulombic cutoffs are set in the :doc:`pair\_style lj/cut/tip4p/long ` command. +and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long ` command. Wikipedia also has a nice article on `water models `_. diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index 6e341907a8..6667e9cf66 100644 --- a/doc/src/Howto_triclinic.rst +++ b/doc/src/Howto_triclinic.rst @@ -22,11 +22,11 @@ box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting from the origin given by **a** = (xhi-xlo,0,0); **b** = (0,yhi-ylo,0); **c** = (0,0,zhi-zlo). The 6 parameters (xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box -is created, e.g. by the :doc:`create\_box ` or -:doc:`read\_data ` or :doc:`read\_restart ` +is created, e.g. by the :doc:`create_box ` or +:doc:`read_data ` or :doc:`read_restart ` commands. Additionally, LAMMPS defines box size parameters lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions. The 6 -parameters, as well as lx,ly,lz, can be output via the :doc:`thermo\_style custom ` command. +parameters, as well as lx,ly,lz, can be output via the :doc:`thermo_style custom ` command. LAMMPS also allows simulations to be performed in triclinic (non-orthogonal) simulation boxes shaped as a parallelepiped with @@ -90,14 +90,14 @@ for details. The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the time the simulation box is created. This happens in one of 3 ways. -If the :doc:`create\_box ` command is used with a region of +If the :doc:`create_box ` command is used with a region of style *prism*\ , then a triclinic box is setup. See the :doc:`region ` command for details. If the -:doc:`read\_data ` command is used to define the simulation +:doc:`read_data ` command is used to define the simulation box, and the header of the data file contains a line with the "xy xz yz" keyword, then a triclinic box is setup. See the -:doc:`read\_data ` command for details. Finally, if the -:doc:`read\_restart ` command reads a restart file which +:doc:`read_data ` command for details. Finally, if the +:doc:`read_restart ` command reads a restart file which was written from a simulation using a triclinic box, then a triclinic box will be setup for the restarted simulation. @@ -105,20 +105,20 @@ Note that you can define a triclinic box with all 3 tilt factors = 0.0, so that it is initially orthogonal. This is necessary if the box will become non-orthogonal, e.g. due to the :doc:`fix npt ` or :doc:`fix deform ` commands. Alternatively, you can use the -:doc:`change\_box ` command to convert a simulation box from +:doc:`change_box ` command to convert a simulation box from orthogonal to triclinic and vice versa. As with orthogonal boxes, LAMMPS defines triclinic box size parameters lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions. The 9 parameters, as well as lx,ly,lz, can be output via the -:doc:`thermo\_style custom ` command. +:doc:`thermo_style custom ` command. To avoid extremely tilted boxes (which would be computationally inefficient), LAMMPS normally requires that no tilt factor can skew the box more than half the distance of the parallel box length, which is the 1st dimension in the tilt factor (x for xz). This is required both when the simulation box is created, e.g. via the -:doc:`create\_box ` or :doc:`read\_data ` commands, +:doc:`create_box ` or :doc:`read_data ` commands, as well as when the box shape changes dynamically during a simulation, e.g. via the :doc:`fix deform ` or :doc:`fix npt ` commands. @@ -173,7 +173,7 @@ The inverse relationship can be written as follows: The values of *a*\ , *b*\ , *c* , *alpha*\ , *beta* , and *gamma* can be printed out or accessed by computes using the -:doc:`thermo\_style custom ` keywords +:doc:`thermo_style custom ` keywords *cella*\ , *cellb*\ , *cellc*\ , *cellalpha*\ , *cellbeta*\ , *cellgamma*\ , respectively. @@ -213,7 +213,7 @@ One use of triclinic simulation boxes is to model solid-state crystals with triclinic symmetry. The :doc:`lattice ` command can be used with non-orthogonal basis vectors to define a lattice that will tile a triclinic simulation box via the -:doc:`create\_atoms ` command. +:doc:`create_atoms ` command. A second use is to run Parrinello-Rahman dynamics via the :doc:`fix npt ` command, which will adjust the xy, xz, yz tilt factors to compensate for off-diagonal components of the pressure diff --git a/doc/src/Howto_walls.rst b/doc/src/Howto_walls.rst index f04b7f1057..eed28f2ed1 100644 --- a/doc/src/Howto_walls.rst +++ b/doc/src/Howto_walls.rst @@ -11,8 +11,8 @@ tangential direction. Rough walls, built of particles, can be created in various ways. The particles themselves can be generated like any other particle, via the -:doc:`lattice ` and :doc:`create\_atoms ` commands, -or read in via the :doc:`read\_data ` command. +:doc:`lattice ` and :doc:`create_atoms ` commands, +or read in via the :doc:`read_data ` command. Their motion can be constrained by many different commands, so that they do not move at all, move together as a group at constant velocity @@ -34,7 +34,7 @@ the motion of individual particles can be specified with particle position. For rough walls, it may be useful to turn off pairwise interactions -between wall particles via the :doc:`neigh\_modify exclude ` command. +between wall particles via the :doc:`neigh_modify exclude ` command. Rough walls can also be created by specifying frozen particles that do not move and do not interact with mobile particles, and then tethering @@ -47,11 +47,11 @@ granular particles; all the other commands create smooth walls. * :doc:`fix wall/reflect ` - reflective flat walls * :doc:`fix wall/lj93 ` - flat walls, with Lennard-Jones 9/3 potential * :doc:`fix wall/lj126 ` - flat walls, with Lennard-Jones 12/6 potential -* :doc:`fix wall/colloid ` - flat walls, with :doc:`pair\_style colloid ` potential +* :doc:`fix wall/colloid ` - flat walls, with :doc:`pair_style colloid ` potential * :doc:`fix wall/harmonic ` - flat walls, with repulsive harmonic spring potential * :doc:`fix wall/morse ` - flat walls, with Morse potential * :doc:`fix wall/region ` - use region surface as wall -* :doc:`fix wall/gran ` - flat or curved walls with :doc:`pair\_style granular ` potential +* :doc:`fix wall/gran ` - flat or curved walls with :doc:`pair_style granular ` potential The *lj93*\ , *lj126*\ , *colloid*\ , *harmonic*\ , and *morse* styles all allow the flat walls to move with a constant velocity, or oscillate in diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst index 67d37b917a..d8dd0a0531 100644 --- a/doc/src/Intro_features.rst +++ b/doc/src/Intro_features.rst @@ -96,9 +96,9 @@ commands) Atom creation -------------------------- -(:doc:`read\_data `, :doc:`lattice `, -:doc:`create\_atoms `, :doc:`delete\_atoms `, -:doc:`displace\_atoms `, :doc:`replicate ` commands) +(:doc:`read_data `, :doc:`lattice `, +:doc:`create_atoms `, :doc:`delete_atoms `, +:doc:`displace_atoms `, :doc:`replicate ` commands) * read in atom coords from files * create atoms on one or more lattices (e.g. grain boundaries) @@ -133,7 +133,7 @@ Ensembles, constraints, and boundary conditions Integrators --------------------------- -(:doc:`run `, :doc:`run\_style `, :doc:`minimize ` commands) +(:doc:`run `, :doc:`run_style `, :doc:`minimize ` commands) * velocity-Verlet integrator * Brownian dynamics diff --git a/doc/src/Modify_fix.rst b/doc/src/Modify_fix.rst index cafde08af6..d4c4fa046f 100644 --- a/doc/src/Modify_fix.rst +++ b/doc/src/Modify_fix.rst @@ -146,7 +146,7 @@ implementing the grow\_arrays, copy\_arrays, pack\_exchange, and unpack\_exchange methods. Similarly, the pack\_restart and unpack\_restart methods can be implemented to store information about the fix in restart files. If you wish an integrator or force -constraint fix to work with rRESPA (see the :doc:`run\_style ` +constraint fix to work with rRESPA (see the :doc:`run_style ` command), the initial\_integrate, post\_force\_integrate, and final\_integrate\_respa methods can be implemented. The thermo method enables a fix to contribute values to thermodynamic output, as printed diff --git a/doc/src/Modify_thermo.rst b/doc/src/Modify_thermo.rst index f3a3f00e2f..d95b98ab40 100644 --- a/doc/src/Modify_thermo.rst +++ b/doc/src/Modify_thermo.rst @@ -7,7 +7,7 @@ to the screen and log file; see the file thermo.cpp. There are two styles defined in thermo.cpp: "one" and "multi". There is also a flexible "custom" style which allows the user to explicitly list keywords for quantities to print when thermodynamic info is -output. See the :doc:`thermo\_style ` command for a list +output. See the :doc:`thermo_style ` command for a list of defined quantities. The thermo styles (one, multi, etc) are simply lists of keywords. @@ -20,7 +20,7 @@ for output. Search for the word "customize" with references to "keyword" in thermo.cpp to see the several locations where code will need to be added. -Note that the :doc:`thermo\_style custom ` command already allows +Note that the :doc:`thermo_style custom ` command already allows for thermo output of quantities calculated by :doc:`fixes `, :doc:`computes `, and :doc:`variables `. Thus, it may be simpler to compute what you wish via one of those constructs, than diff --git a/doc/src/Modify_variable.rst b/doc/src/Modify_variable.rst index bd3f70588b..40e2e9e6a3 100644 --- a/doc/src/Modify_variable.rst +++ b/doc/src/Modify_variable.rst @@ -5,7 +5,7 @@ There is one class that computes and stores :doc:`variable ` information in LAMMPS; see the file variable.cpp. The value associated with a variable can be periodically printed to the screen via the :doc:`print `, :doc:`fix print `, or -:doc:`thermo\_style custom ` commands. Variables of style +:doc:`thermo_style custom ` commands. Variables of style "equal" can compute complex equations that involve the following types of arguments: @@ -19,7 +19,7 @@ of arguments: atom values = x[123], y[3], vx[34], ... compute values = c_mytemp[0], c_thermo_press[3], ... -Adding keywords for the :doc:`thermo\_style custom ` +Adding keywords for the :doc:`thermo_style custom ` command (which can then be accessed by variables) is discussed on the :doc:`Modify thermo ` doc page. diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 376bc0acda..efdd222cf1 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -72,8 +72,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles. * src/ASPHERE: filenames -> commands * :doc:`Howto spherical ` -* :doc:`pair\_style gayberne ` -* :doc:`pair\_style resquared ` +* :doc:`pair_style gayberne ` +* :doc:`pair_style resquared ` * `doc/PDF/pair\_gayberne\_extra.pdf `_ * `doc/PDF/pair\_resquared\_extra.pdf `_ * examples/ASPHERE @@ -101,9 +101,9 @@ overview. * src/BODY filenames -> commands * :doc:`Howto\_body ` -* :doc:`atom\_style body ` +* :doc:`atom_style body ` * :doc:`fix nve/body ` -* :doc:`pair\_style body/nparticle ` +* :doc:`pair_style body/nparticle ` * examples/body @@ -123,11 +123,11 @@ CLASS2 molecular force field. **Supporting info:** * src/CLASS2: filenames -> commands -* :doc:`bond\_style class2 ` -* :doc:`angle\_style class2 ` -* :doc:`dihedral\_style class2 ` -* :doc:`improper\_style class2 ` -* :doc:`pair\_style lj/class2 ` +* :doc:`bond_style class2 ` +* :doc:`angle_style class2 ` +* :doc:`dihedral_style class2 ` +* :doc:`improper_style class2 ` +* :doc:`pair_style lj/class2 ` ---------- @@ -153,11 +153,11 @@ Higdon's group at UIUC. * src/COLLOID: filenames -> commands * :doc:`fix wall/colloid ` -* :doc:`pair\_style colloid ` -* :doc:`pair\_style yukawa/colloid ` -* :doc:`pair\_style brownian ` -* :doc:`pair\_style lubricate ` -* :doc:`pair\_style lubricateU ` +* :doc:`pair_style colloid ` +* :doc:`pair_style yukawa/colloid ` +* :doc:`pair_style brownian ` +* :doc:`pair_style lubricate ` +* :doc:`pair_style lubricateU ` * examples/colloid * examples/srd @@ -219,9 +219,9 @@ this package. * :doc:`Howto coreshell ` * :doc:`Howto polarizable ` * :doc:`compute temp/cs ` -* :doc:`pair\_style born/coul/long/cs ` -* :doc:`pair\_style buck/coul/long/cs ` -* :doc:`pair\_style lj/cut/coul/long/cs ` +* :doc:`pair_style born/coul/long/cs ` +* :doc:`pair_style buck/coul/long/cs ` +* :doc:`pair_style lj/cut/coul/long/cs ` * examples/coreshell @@ -241,10 +241,10 @@ short-range or long-range interactions. **Supporting info:** * src/DIPOLE: filenames -> commands -* :doc:`atom\_style dipole ` -* :doc:`pair\_style lj/cut/dipole/cut ` -* :doc:`pair\_style lj/cut/dipole/long ` -* :doc:`pair\_style lj/long/dipole/long ` +* :doc:`atom_style dipole ` +* :doc:`pair_style lj/cut/dipole/cut ` +* :doc:`pair_style lj/cut/dipole/long ` +* :doc:`pair_style lj/long/dipole/long ` * examples/dipole @@ -309,8 +309,8 @@ potentials. * :doc:`Howto granular ` * :doc:`fix pour ` * :doc:`fix wall/gran ` -* :doc:`pair\_style gran/hooke ` -* :doc:`pair\_style gran/hertz/history ` +* :doc:`pair_style gran/hooke ` +* :doc:`pair_style gran/hertz/history ` * examples/granregion * examples/pour * bench/in.chute @@ -335,13 +335,13 @@ This package contains a set of commands that serve as a wrapper on the `Open Knowledgebase of Interatomic Models (OpenKIM) `_ repository of interatomic models (IMs) enabling compatible ones to be used in LAMMPS simulations. -This includes :doc:`kim\_init and kim\_interactions ` +This includes :doc:`kim_init and kim\_interactions ` commands to select, initialize and instantiate the IM, and a -:doc:`kim\_query ` command to perform web queries +:doc:`kim_query ` command to perform web queries for material property predictions of OpenKIM IMs. Support for KIM IMs that conform to the `KIM Application Programming Interface (API) `_ -is provided by the :doc:`pair\_style kim ` command. +is provided by the :doc:`pair_style kim ` command. .. note:: @@ -361,7 +361,7 @@ and is funded by the `National Science Foundation `_. **Authors:** Ryan Elliott (U Minnesota) is the main developer for the KIM API and the *pair\_style kim* command. Axel Kohlmeyer (Temple U) and -Ellad Tadmor (U Minnesota) contributed to the :doc:`kim\_commands ` +Ellad Tadmor (U Minnesota) contributed to the :doc:`kim_commands ` interface in close collaboration with Ryan Elliott. **Install:** @@ -370,8 +370,8 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu **Supporting info:** -* :doc:`kim\_commands ` -* :doc:`pair\_style kim ` +* :doc:`kim_commands ` +* :doc:`pair_style kim ` * src/KIM: filenames -> commands * src/KIM/README * lib/kim/README @@ -458,12 +458,12 @@ different FFT options for your LAMPMS build. **Supporting info:** * src/KSPACE: filenames -> commands -* :doc:`kspace\_style ` +* :doc:`kspace_style ` * `doc/PDF/kspace.pdf `_ * :doc:`Howto tip3p ` * :doc:`Howto tip4p ` * :doc:`Howto spc ` -* :doc:`pair\_style coul ` +* :doc:`pair_style coul ` * :doc:`Commands pair ` page for styles with "long" or "msm" in name * examples/peptide * bench/in.rhodo @@ -558,7 +558,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC * :doc:`fix bond/create ` * :doc:`fix bond/swap ` * :doc:`fix gcmc ` -* :doc:`pair\_style dsmc ` +* :doc:`pair_style dsmc ` * http://lammps.sandia.gov/movies.html#gcmc @@ -642,13 +642,13 @@ force fields, and a TIP4P water model. **Supporting info:** * src/MOLECULE: filenames -> commands -* :doc:`atom\_style ` -* :doc:`bond\_style ` -* :doc:`angle\_style ` -* :doc:`dihedral\_style ` -* :doc:`improper\_style ` -* :doc:`pair\_style hbond/dreiding/lj ` -* :doc:`pair\_style lj/charmm/coul/charmm ` +* :doc:`atom_style ` +* :doc:`bond_style ` +* :doc:`angle_style ` +* :doc:`dihedral_style ` +* :doc:`improper_style ` +* :doc:`pair_style hbond/dreiding/lj ` +* :doc:`pair_style lj/charmm/coul/charmm ` * :doc:`Howto bioFF ` * examples/cmap * examples/dreiding @@ -678,8 +678,8 @@ written and read in parallel. * src/MPIIO: filenames -> commands * :doc:`dump ` * :doc:`restart ` -* :doc:`write\_restart ` -* :doc:`read\_restart ` +* :doc:`write_restart ` +* :doc:`read_restart ` ---------- @@ -779,8 +779,8 @@ Foster (UTSA). * `doc/PDF/PDLammps\_overview.pdf `_ * `doc/PDF/PDLammps\_EPS.pdf `_ * `doc/PDF/PDLammps\_VES.pdf `_ -* :doc:`atom\_style peri ` -* :doc:`pair\_style peri/\* ` +* :doc:`atom_style peri ` +* :doc:`pair_style peri/\* ` * :doc:`compute damage/atom ` * :doc:`compute plasticity/atom ` * examples/peri @@ -902,7 +902,7 @@ another set. * :doc:`prd ` * :doc:`tad ` * :doc:`temper `, -* :doc:`run\_style verlet/split ` +* :doc:`run_style verlet/split ` * examples/neb * examples/prd * examples/tad @@ -981,7 +981,7 @@ computes which analyze attributes of the potential. **Supporting info:** * src/SNAP: filenames -> commands -* :doc:`pair\_style snap ` +* :doc:`pair_style snap ` * :doc:`compute sna/atom ` * :doc:`compute snad/atom ` * :doc:`compute snav/atom ` @@ -1007,12 +1007,12 @@ the usual manner via MD. Various pair, fix, and compute styles. * src/SPIN: filenames -> commands * :doc:`Howto spins ` -* :doc:`pair\_style spin/dipole/cut ` -* :doc:`pair\_style spin/dipole/long ` -* :doc:`pair\_style spin/dmi ` -* :doc:`pair\_style spin/exchange ` -* :doc:`pair\_style spin/magelec ` -* :doc:`pair\_style spin/neel ` +* :doc:`pair_style spin/dipole/cut ` +* :doc:`pair_style spin/dipole/long ` +* :doc:`pair_style spin/dmi ` +* :doc:`pair_style spin/exchange ` +* :doc:`pair_style spin/magelec ` +* :doc:`pair_style spin/neel ` * :doc:`fix nve/spin ` * :doc:`fix precession/spin ` * :doc:`compute spin ` @@ -1172,7 +1172,7 @@ This package has :ref:`specific installation instructions ` on the : * src/USER-AWPMD: filenames -> commands * src/USER-AWPMD/README -* :doc:`pair\_style awpmd/cut ` +* :doc:`pair_style awpmd/cut ` * examples/USER/awpmd @@ -1233,10 +1233,10 @@ stability. * src/USER-CGDNA: filenames -> commands * /src/USER-CGDNA/README -* :doc:`pair\_style oxdna/\* ` -* :doc:`pair\_style oxdna2/\* ` -* :doc:`bond\_style oxdna/\* ` -* :doc:`bond\_style oxdna2/\* ` +* :doc:`pair_style oxdna/\* ` +* :doc:`pair_style oxdna2/\* ` +* :doc:`bond_style oxdna/\* ` +* :doc:`bond_style oxdna2/\* ` * :doc:`fix nve/dotc/langevin ` @@ -1261,8 +1261,8 @@ acids. * src/USER-CGSDK: filenames -> commands * src/USER-CGSDK/README -* :doc:`pair\_style lj/sdk/\* ` -* :doc:`angle\_style sdk ` +* :doc:`pair_style lj/sdk/\* ` +* :doc:`angle_style sdk ` * examples/USER/cgsdk * http://lammps.sandia.gov/pictures.html#cg @@ -1397,12 +1397,12 @@ Brennan (ARL). * :doc:`fix eos/table/rx ` * :doc:`fix shardlow ` * :doc:`fix rx ` -* :doc:`pair\_style table/rx ` -* :doc:`pair\_style dpd/fdt ` -* :doc:`pair\_style dpd/fdt/energy ` -* :doc:`pair\_style exp6/rx ` -* :doc:`pair\_style multi/lucy ` -* :doc:`pair\_style multi/lucy/rx ` +* :doc:`pair_style table/rx ` +* :doc:`pair_style dpd/fdt ` +* :doc:`pair_style dpd/fdt/energy ` +* :doc:`pair_style exp6/rx ` +* :doc:`pair_style multi/lucy ` +* :doc:`pair_style multi/lucy/rx ` * examples/USER/dpd @@ -1434,8 +1434,8 @@ Devemy (CNRS), and Agilio Padua (U Blaise Pascal). * :doc:`fix drude ` * :doc:`fix drude/transform/\* ` * :doc:`compute temp/drude ` -* :doc:`pair\_style thole ` -* :doc:`pair\_style lj/cut/thole/long ` +* :doc:`pair_style thole ` +* :doc:`pair_style lj/cut/thole/long ` * examples/USER/drude * tools/drude @@ -1464,14 +1464,14 @@ tools/eff; see its README file. * src/USER-EFF: filenames -> commands * src/USER-EFF/README -* :doc:`atom\_style electron ` +* :doc:`atom_style electron ` * :doc:`fix nve/eff ` * :doc:`fix nvt/eff ` * :doc:`fix npt/eff ` * :doc:`fix langevin/eff ` * :doc:`compute temp/eff ` -* :doc:`pair\_style eff/cut ` -* :doc:`pair\_style eff/inline ` +* :doc:`pair_style eff/cut ` +* :doc:`pair_style eff/inline ` * examples/USER/eff * tools/eff/README * tools/eff @@ -1501,7 +1501,7 @@ for using this package in tools/fep; see its README file. * src/USER-FEP/README * :doc:`fix adapt/fep ` * :doc:`compute fep ` -* :doc:`pair\_style \*/soft ` +* :doc:`pair_style \*/soft ` * examples/USER/fep * tools/fep/README * tools/fep @@ -1644,7 +1644,7 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. * src/USER-MGPT: filenames -> commands * src/USER-MGPT/README -* :doc:`pair\_style mgpt ` +* :doc:`pair_style mgpt ` * examples/USER/mgpt @@ -1729,7 +1729,7 @@ Sandia. * src/USER-MEAMC: filenames -> commands * src/USER-MEAMC/README -* :doc:`pair\_style meam/c ` +* :doc:`pair_style meam/c ` * examples/meamc @@ -1757,10 +1757,10 @@ algorithm. * src/USER-MESO: filenames -> commands * src/USER-MESO/README -* :doc:`atom\_style edpd ` -* :doc:`pair\_style edpd ` -* :doc:`pair\_style mdpd ` -* :doc:`pair\_style tdpd ` +* :doc:`atom_style edpd ` +* :doc:`pair_style edpd ` +* :doc:`pair_style mdpd ` +* :doc:`pair_style tdpd ` * :doc:`fix mvv/dpd ` * examples/USER/meso * http://lammps.sandia.gov/movies.html#mesodpd @@ -1796,10 +1796,10 @@ Rochus Schmid (Ruhr-University Bochum). * src/USER-MOFFF: filenames -> commands * src/USER-MOFFF/README -* :doc:`pair\_style buck6d/coul/gauss ` -* :doc:`angle\_style class2 ` -* :doc:`angle\_style cosine/buck6d ` -* :doc:`improper\_style inversion/harmonic ` +* :doc:`pair_style buck6d/coul/gauss ` +* :doc:`angle_style class2 ` +* :doc:`angle_style cosine/buck6d ` +* :doc:`improper_style inversion/harmonic ` * examples/USER/mofff @@ -1965,8 +1965,8 @@ USER-PHONON package A :doc:`fix phonon ` command that calculates dynamical matrices, which can then be used to compute phonon dispersion relations, directly from molecular dynamics simulations. -And a :doc:`dynamical\_matrix ` as well as a -:doc:`third\_order ` command to compute the dynamical matrix +And a :doc:`dynamical_matrix ` as well as a +:doc:`third_order ` command to compute the dynamical matrix and third order tensor from finite differences. **Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon" @@ -1977,8 +1977,8 @@ and Charlie Sievers (UC Davis) for "dynamical\_matrix" and "third\_order" * src/USER-PHONON: filenames -> commands * src/USER-PHONON/README * :doc:`fix phonon ` -* :doc:`dynamical\_matrix ` -* :doc:`third\_order ` +* :doc:`dynamical_matrix ` +* :doc:`third_order ` * examples/USER/phonon @@ -2088,7 +2088,7 @@ USER-QUIP package **Contents:** -A :doc:`pair\_style quip ` command which wraps the `QUIP libAtoms library `_, which includes a variety of interatomic +A :doc:`pair_style quip ` command which wraps the `QUIP libAtoms library `_, which includes a variety of interatomic potentials, including Gaussian Approximation Potential (GAP) models developed by the Cambridge University group. @@ -2109,7 +2109,7 @@ This package has :ref:`specific installation instructions ` on the :d * src/USER-QUIP: filenames -> commands * src/USER-QUIP/README -* :doc:`pair\_style quip ` +* :doc:`pair_style quip ` * examples/USER/quip @@ -2134,7 +2134,7 @@ for monitoring molecules as bonds are created and destroyed. * src/USER-REAXC: filenames -> commands * src/USER-REAXC/README -* :doc:`pair\_style reax/c ` +* :doc:`pair_style reax/c ` * :doc:`fix reax/c/bonds ` * :doc:`fix reax/c/species ` * examples/reax @@ -2172,8 +2172,8 @@ This package has :ref:`specific installation instructions ` on th * src/USER-SCAFACOS: filenames -> commands * src/USER-SCAFACOS/README -* :doc:`kspace\_style scafacos ` -* :doc:`kspace\_modify ` +* :doc:`kspace_style scafacos ` +* :doc:`kspace_modify ` * examples/USER/scafacos @@ -2201,7 +2201,7 @@ Sciences, Iran). * src/USER-SDPD: filenames -> commands * src/USER-SDPD/README -* :doc:`pair\_style sdpd/taitwater/isothermal ` +* :doc:`pair_style sdpd/taitwater/isothermal ` * :doc:`fix meso/move ` * :doc:`fix rigid/meso ` * examples/USER/sdpd @@ -2268,7 +2268,7 @@ Tetot (LAAS-CNRS, France). * src/USER-SMTBQ: filenames -> commands * src/USER-SMTBQ/README -* :doc:`pair\_style smtbq ` +* :doc:`pair_style smtbq ` * examples/USER/smtbq @@ -2438,13 +2438,13 @@ which discuss the `QuickFF `_ methodology. **Supporting info:** * src/USER-YAFF/README -* :doc:`angle\_style cross ` -* :doc:`angle\_style mm3 ` -* :doc:`bond\_style mm3 ` -* :doc:`improper\_style distharm ` -* :doc:`improper\_style sqdistharm ` -* :doc:`pair\_style mm3/switch3/coulgauss/long ` -* :doc:`pair\_style lj/switch3/coulgauss/long ` +* :doc:`angle_style cross ` +* :doc:`angle_style mm3 ` +* :doc:`bond_style mm3 ` +* :doc:`improper_style distharm ` +* :doc:`improper_style sqdistharm ` +* :doc:`pair_style mm3/switch3/coulgauss/long ` +* :doc:`pair_style lj/switch3/coulgauss/long ` * examples/USER/yaff diff --git a/doc/src/Packages_standard.rst b/doc/src/Packages_standard.rst index c234f8198d..c7993cf947 100644 --- a/doc/src/Packages_standard.rst +++ b/doc/src/Packages_standard.rst @@ -29,29 +29,29 @@ package: +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`BODY ` | body-style particles | :doc:`Howto body ` | body | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`CLASS2 ` | class 2 force fields | :doc:`pair\_style lj/class2 ` | n/a | no | +| :ref:`CLASS2 ` | class 2 force fields | :doc:`pair_style lj/class2 ` | n/a | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`COLLOID ` | colloidal particles | :doc:`atom\_style colloid ` | colloid | no | +| :ref:`COLLOID ` | colloidal particles | :doc:`atom_style colloid ` | colloid | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`COMPRESS ` | I/O compression | :doc:`dump \*/gz ` | n/a | sys | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`CORESHELL ` | adiabatic core/shell model | :doc:`Howto coreshell ` | coreshell | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`DIPOLE ` | point dipole particles | :doc:`pair\_style dipole/cut ` | dipole | no | +| :ref:`DIPOLE ` | point dipole particles | :doc:`pair_style dipole/cut ` | dipole | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`GPU ` | GPU-enabled styles | :doc:`Section gpu ` | `Benchmarks `_ | int | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`GRANULAR ` | granular systems | :doc:`Howto granular ` | pour | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`KIM ` | OpenKIM wrapper | :doc:`pair\_style kim ` | kim | ext | +| :ref:`KIM ` | OpenKIM wrapper | :doc:`pair_style kim ` | kim | ext | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`KOKKOS ` | Kokkos-enabled styles | :doc:`Speed kokkos ` | `Benchmarks `_ | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`KSPACE ` | long-range Coulombic solvers | :doc:`kspace\_style ` | peptide | no | +| :ref:`KSPACE ` | long-range Coulombic solvers | :doc:`kspace_style ` | peptide | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`LATTE ` | quantum DFTB forces via LATTE | :doc:`fix latte ` | latte | ext | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`MANYBODY ` | many-body potentials | :doc:`pair\_style tersoff ` | shear | no | +| :ref:`MANYBODY ` | many-body potentials | :doc:`pair_style tersoff ` | shear | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`MC ` | Monte Carlo options | :doc:`fix gcmc ` | n/a | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ @@ -67,7 +67,7 @@ package: +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`OPT ` | optimized pair styles | :doc:`Speed opt ` | `Benchmarks `_ | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`PERI ` | Peridynamics models | :doc:`pair\_style peri ` | peri | no | +| :ref:`PERI ` | Peridynamics models | :doc:`pair_style peri ` | peri | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`POEMS ` | coupled rigid body motion | :doc:`fix poems ` | rigid | int | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ @@ -81,7 +81,7 @@ package: +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`SHOCK ` | shock loading methods | :doc:`fix msst ` | n/a | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`SNAP ` | quantum-fitted potential | :doc:`pair\_style snap ` | snap | no | +| :ref:`SNAP ` | quantum-fitted potential | :doc:`pair_style snap ` | snap | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`SPIN ` | magnetic atomic spin dynamics | :doc:`Howto spins ` | SPIN | no | +----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 702d014c57..d705c8273d 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -35,13 +35,13 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-ATC ` | Atom-to-Continuum coupling | :doc:`fix atc ` | USER/atc | int | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-AWPMD ` | wave packet MD | :doc:`pair\_style awpmd/cut ` | USER/awpmd | int | +| :ref:`USER-AWPMD ` | wave packet MD | :doc:`pair_style awpmd/cut ` | USER/awpmd | int | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-BOCS ` | BOCS bottom up coarse graining | :doc:`fix bocs ` | USER/bocs | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-CGDNA ` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-CGSDK ` | SDK coarse-graining model | :doc:`pair\_style lj/sdk ` | USER/cgsdk | no | +| :ref:`USER-CGSDK ` | SDK coarse-graining model | :doc:`pair_style lj/sdk ` | USER/cgsdk | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-COLVARS ` | collective variables library | :doc:`fix colvars ` | USER/colvars | int | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ @@ -51,7 +51,7 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-DRUDE ` | Drude oscillators | :doc:`Howto drude ` | USER/drude | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-EFF ` | electron force field | :doc:`pair\_style eff/cut ` | USER/eff | no | +| :ref:`USER-EFF ` | electron force field | :doc:`pair_style eff/cut ` | USER/eff | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-FEP ` | free energy perturbation | :doc:`compute fep ` | USER/fep | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ @@ -63,15 +63,15 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-MANIFOLD ` | motion on 2d surfaces | :doc:`fix manifoldforce ` | USER/manifold | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair\_style meam/c ` | meamc | no | +| :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair_style meam/c ` | meamc | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MESO ` | mesoscale DPD models | :doc:`pair\_style edpd ` | USER/meso | no | +| :ref:`USER-MESO ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/meso | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair\_style mgpt ` | USER/mgpt | no | +| :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt ` | USER/mgpt | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-MISC ` | single-file contributions | USER-MISC/README | USER/misc | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MOFFF ` | styles for `MOF-FF `_ force field | :doc:`pair\_style buck6d/coul/gauss ` | USER/mofff | no | +| :ref:`USER-MOFFF ` | styles for `MOF-FF `_ force field | :doc:`pair_style buck6d/coul/gauss ` | USER/mofff | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-MOLFILE ` | `VMD `_ molfile plug-ins | :doc:`dump molfile ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ @@ -89,17 +89,17 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-QTB ` | quantum nuclear effects | :doc:`fix qtb ` :doc:`fix qbmsst ` | qtb | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair\_style quip ` | USER/quip | ext | +| :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-REAXC ` | ReaxFF potential (C/C++) | :doc:`pair\_style reaxc ` | reax | no | +| :ref:`USER-REAXC ` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc ` | reax | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SCAFACOS ` | wrapper on ScaFaCoS solver | :doc:`kspace\_style scafacos ` | USER/scafacos | ext | +| :ref:`USER-SCAFACOS ` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos ` | USER/scafacos | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SDPD ` | smoothed dissipative particle dynamics | :doc:`pair\_style sdpd/taitwater/isothermal ` | USER/sdpd | no | +| :ref:`USER-SDPD ` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal ` | USER/sdpd | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-SMD ` | smoothed Mach dynamics | `SMD User Guide `_ | USER/smd | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SMTBQ ` | second moment tight binding QEq potential | :doc:`pair\_style smtbq ` | USER/smtbq | no | +| :ref:`USER-SMTBQ ` | second moment tight binding QEq potential | :doc:`pair_style smtbq ` | USER/smtbq | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-SPH ` | smoothed particle hydrodynamics | `SPH User Guide `_ | USER/sph | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ @@ -109,18 +109,12 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-VTK ` | dump output via VTK | :doc:`compute vtk ` | n/a | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-YAFF ` | additional styles implemented in YAFF | :doc:`angle\_style cross ` | USER/yaff | no | +| :ref:`USER-YAFF ` | additional styles implemented in YAFF | :doc:`angle_style cross ` | USER/yaff | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ .. _MOFplus: https://www.mofplus.org/content/show/MOF-FF - - - .. _PLUMED: http://www.plumed.org - - - .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Commands_all.html diff --git a/doc/src/Python_call.rst b/doc/src/Python_call.rst index 6b53b263c3..2ce0b88cb5 100644 --- a/doc/src/Python_call.rst +++ b/doc/src/Python_call.rst @@ -7,7 +7,7 @@ code directly from an input script: * :doc:`python ` * :doc:`variable python ` * :doc:`fix python/invoke ` -* :doc:`pair\_style python ` +* :doc:`pair_style python ` The :doc:`python ` command which can be used to define and execute a Python function that you write the code for. The Python @@ -51,7 +51,7 @@ and callbacks to LAMMPS. The :doc:`fix python/invoke ` command can execute Python code at selected timesteps during a simulation run. -The :doc:`pair\_style python ` command allows you to define +The :doc:`pair_style python ` command allows you to define pairwise potentials as python code which encodes a single pairwise interaction. This is useful for rapid development and debugging of a new potential. diff --git a/doc/src/Python_install.rst b/doc/src/Python_install.rst index 29d9964c64..83b9a4dd9d 100644 --- a/doc/src/Python_install.rst +++ b/doc/src/Python_install.rst @@ -20,7 +20,12 @@ python module and the shared library into the python site-packages folders; either the system-wide ones, or the local users ones (in case of insufficient permissions for the global install). Python will then find the module and shared library file automatically. The exact location of these folders -depends on your python version and your operating system. +depends on your python version and your operating system. When using +the CMake build system, you can set the python executable to use during +the CMake configuration process. Details are given in the build instructions +for the :ref:`PYTHON ` package. When using the conventional make +system, you can override the python version to version x.y when calling +make with PYTHON=pythonx.y. If you set the paths to these files as environment variables, you only have to do it once. For the csh or tcsh shells, add something like diff --git a/doc/src/Python_mpi.rst b/doc/src/Python_mpi.rst index ec5ec35ceb..b72a0161a2 100644 --- a/doc/src/Python_mpi.rst +++ b/doc/src/Python_mpi.rst @@ -5,15 +5,17 @@ If you wish to run LAMMPS in parallel from Python, you need to extend your Python with an interface to MPI. This also allows you to make MPI calls directly from Python in your script, if you desire. -We recommend use of mpi4py: +We have tested this with mpi4py and pypar: -* `PyPar `_ +* `MPI for Python `_ +* `pypar `_ -As of version 2.0.0 it allows passing a custom MPI communicator to -the LAMMPS constructor, which means one can easily run one or more +We recommend the use of mpi4py as it is the more complete MPI interface, +and as of version 2.0.0 mpi4py allows passing a custom MPI communicator +to the LAMMPS constructor, which means one can easily run one or more LAMMPS instances on subsets of the total MPI ranks. -To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it +To install mpi4py (version mpi4py-3.0.3 as of Nov 2019), unpack it and from its main directory, type diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index 1e0091f057..e45a4d3053 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -354,14 +354,14 @@ all P processors from 0 to P-1. The mapping of these ranks to physical processors is done by MPI before LAMMPS begins. It may be useful in some cases to alter the rank order. E.g. to insure that cores within each node are ranked in a desired order. Or when using -the :doc:`run\_style verlet/split ` command with 2 partitions +the :doc:`run_style verlet/split ` command with 2 partitions to insure that a specific Kspace processor (in the 2nd partition) is matched up with a specific set of processors in the 1st partition. See the :doc:`Speed tips ` doc page for more details. If the keyword *nth* is used with a setting *N*\ , then it means every Nth processor will be moved to the end of the ranking. This is useful -when using the :doc:`run\_style verlet/split ` command with 2 +when using the :doc:`run_style verlet/split ` command with 2 partitions via the -partition command-line switch. The first set of processors will be in the first partition, the 2nd set in the 2nd partition. The -reorder command-line switch can alter this so that @@ -446,7 +446,7 @@ run: The specified restartfile and/or datafile name may contain the wild-card character "\*". The restartfile name may also contain the wild-card character "%". The meaning of these characters is explained on the -:doc:`read\_restart ` and :doc:`write\_data ` doc +:doc:`read_restart ` and :doc:`write_data ` doc pages. The use of "%" means that a parallel restart file can be read. Note that a filename such as file.\* may need to be enclosed in quotes or the "\*" character prefixed with a backslash ("\") to avoid shell @@ -454,7 +454,7 @@ expansion of the "\*" character. Following restartfile argument, the optional word "remap" may be used. This has the same effect like adding it to a -:doc:`read\_restart ` command, and operates as explained on +:doc:`read_restart ` command, and operates as explained on its doc page. This is useful if reading the restart file triggers an error that atoms have been lost. In that case, use of the remap flag should allow the data file to still be produced. @@ -466,7 +466,7 @@ The syntax following restartfile (or remap), namely datafile keyword value ... -is identical to the arguments of the :doc:`write\_data ` +is identical to the arguments of the :doc:`write_data ` command. See its doc page for details. This includes its optional keyword/value settings. @@ -490,7 +490,7 @@ run: Note that the specified restartfile and dumpfile names may contain wild-card characters ("\*","%") as explained on the -:doc:`read\_restart ` and :doc:`write\_dump ` doc +:doc:`read_restart ` and :doc:`write_dump ` doc pages. The use of "%" means that a parallel restart file and/or parallel dump file can be read and/or written. Note that a filename such as file.\* may need to be enclosed in quotes or the "\*" character @@ -499,7 +499,7 @@ character. Note that following the restartfile argument, the optional word "remap" can be used. This has the effect as adding it to the -:doc:`read\_restart ` command, as explained on its doc page. +:doc:`read_restart ` command, as explained on its doc page. This is useful if reading the restart file triggers an error that atoms have been lost. In that case, use of the remap flag should allow the dump file to still be produced. @@ -511,12 +511,12 @@ The syntax following restartfile (or remap), namely group-ID dumpstyle dumpfile arg1 arg2 ... -is identical to the arguments of the :doc:`write\_dump ` +is identical to the arguments of the :doc:`write_dump ` command. See its doc page for details. This includes what per-atom fields are written to the dump file and optional dump\_modify settings, including ones that affect how parallel dump files are written, e.g. the *nfile* and *fileper* keywords. See the -:doc:`dump\_modify ` doc page for details. +:doc:`dump_modify ` doc page for details. ---------- @@ -566,7 +566,7 @@ Along with the "-package" command-line switch, this is a convenient mechanism for invoking accelerator packages and their options without having to edit an input script. -As an example, all of the packages provide a :doc:`pair\_style lj/cut ` variant, with style names lj/cut/gpu, +As an example, all of the packages provide a :doc:`pair_style lj/cut ` variant, with style names lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A variant style can be specified explicitly in your input script, e.g. pair\_style lj/cut/gpu. If the -suffix switch is used the specified suffix diff --git a/doc/src/Run_output.rst b/doc/src/Run_output.rst index 41a6dcd4f3..b8cdf6cc29 100644 --- a/doc/src/Run_output.rst +++ b/doc/src/Run_output.rst @@ -125,10 +125,10 @@ number of histogram counts is equal to the number of processors. The last section gives aggregate statistics (across all processors) for pair-wise neighbors and special neighbors that LAMMPS keeps track -of (see the :doc:`special\_bonds ` command). The number +of (see the :doc:`special_bonds ` command). The number of times neighbor lists were rebuilt is tallied, as is the number of potentially *dangerous* rebuilds. If atom movement triggered neighbor -list rebuilding (see the :doc:`neigh\_modify ` command), +list rebuilding (see the :doc:`neigh_modify ` command), then dangerous reneighborings are those that were triggered on the first timestep atom movement was checked for. If this count is non-zero you may wish to reduce the delay factor to insure no force @@ -171,7 +171,7 @@ perform a 1d line minimization in the search direction. See the ---------- -If a :doc:`kspace\_style ` long-range Coulombics solver +If a :doc:`kspace_style ` long-range Coulombics solver that performs FFTs was used during the run (PPPM, Ewald), then additional information is printed, e.g. diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index dca32f1bb1..f9ade13401 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -4,7 +4,7 @@ GPU package The GPU package was developed by Mike Brown while at SNL and ORNL and his collaborators, particularly Trung Nguyen (now at Northwestern). It provides GPU versions of many pair styles and for parts of the -:doc:`kspace\_style pppm ` for long-range Coulombics. +:doc:`kspace_style pppm ` for long-range Coulombics. It has the following general features: * It is designed to exploit common GPU hardware configurations where one diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst index f70852701b..95a7ef9e6b 100644 --- a/doc/src/Speed_intel.rst +++ b/doc/src/Speed_intel.rst @@ -385,7 +385,7 @@ follow in the input script. The USER-INTEL package will perform better with modifications to the input script when :doc:`PPPM ` is used: - :doc:`kspace\_modify diff ad ` should be added to the + :doc:`kspace_modify diff ad ` should be added to the input script. Long-Range Thread (LRT) mode is an option to the :doc:`package intel ` command that can improve performance when using @@ -537,7 +537,7 @@ supported with offload, however, the same effect can often be accomplished by setting cutoffs for excluded atom types to 0. None of the pair styles in the USER-INTEL package currently support the "inner", "middle", "outer" options for rRESPA integration via the -:doc:`run\_style respa ` command; only the "pair" option is +:doc:`run_style respa ` command; only the "pair" option is supported. **References:** diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index fab7f671d7..1b9a1caaf5 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -129,14 +129,14 @@ circumstances: where MPI parallelism is maxed out. For example, this can happen when using the :doc:`PPPM solver ` for long-range electrostatics on large numbers of nodes. The scaling of the KSpace - calculation (see the :doc:`kspace\_style ` command) becomes + calculation (see the :doc:`kspace_style ` command) becomes the performance-limiting factor. Using multi-threading allows less MPI tasks to be invoked and can speed-up the long-range solver, while increasing overall performance by parallelizing the pairwise and bonded calculations via OpenMP. Likewise additional speedup can be sometimes be achieved by increasing the length of the Coulombic cutoff and thus reducing the work done by the long-range solver. Using the - :doc:`run\_style verlet/split ` command, which is compatible + :doc:`run_style verlet/split ` command, which is compatible with the USER-OMP package, is an alternative way to reduce the number of MPI tasks assigned to the KSpace calculation. diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst index 3ec76d4de2..6c62d40706 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -1,7 +1,7 @@ Accelerator packages ==================== -Accelerated versions of various :doc:`pair\_style `, +Accelerated versions of various :doc:`pair_style `, :doc:`fixes `, :doc:`computes `, and other commands have been added to LAMMPS, which will typically run faster than the standard non-accelerated versions. Some require appropriate hardware @@ -62,13 +62,13 @@ the same, and the numerical results it produces should also be the same, except for precision and round-off effects. For example, all of these styles are accelerated variants of the -Lennard-Jones :doc:`pair\_style lj/cut `: +Lennard-Jones :doc:`pair_style lj/cut `: -* :doc:`pair\_style lj/cut/gpu ` -* :doc:`pair\_style lj/cut/intel ` -* :doc:`pair\_style lj/cut/kk ` -* :doc:`pair\_style lj/cut/omp ` -* :doc:`pair\_style lj/cut/opt ` +* :doc:`pair_style lj/cut/gpu ` +* :doc:`pair_style lj/cut/intel ` +* :doc:`pair_style lj/cut/kk ` +* :doc:`pair_style lj/cut/omp ` +* :doc:`pair_style lj/cut/opt ` To see what accelerate styles are currently available for a particular style, find the style name in the `Commands\_all `_ diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index baee955201..1f9661191f 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -60,7 +60,7 @@ Post-processing tools +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ | :ref:`amber2lmp ` | :ref:`binary2txt ` | :ref:`ch2lmp ` | :ref:`colvars ` | :ref:`eff ` | :ref:`fep ` | +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ -| :ref:`lmp2arc ` | :ref:`lmp2cfg ` | :ref:`matlab ` | :ref:`phonon ` | :ref:`pymol\_asphere ` | :ref:`python ` | +| :ref:`lmp2arc ` | :ref:`lmp2cfg ` | :ref:`matlab ` | :ref:`phonon ` | :ref:`pymol_asphere ` | :ref:`python ` | +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ | :ref:`reax ` | :ref:`replica ` | :ref:`smd ` | :ref:`spin ` | :ref:`xmgrace ` | | +--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+ @@ -268,7 +268,7 @@ eam database tool The tools/eam\_database directory contains a Fortran program that will generate EAM alloy setfl potential files for any combination of 16 elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti, -Zr. The files can then be used with the :doc:`pair\_style eam/alloy ` command. +Zr. The files can then be used with the :doc:`pair_style eam/alloy ` command. The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov, and is based on his paper: @@ -288,7 +288,7 @@ eam generate tool The tools/eam\_generate directory contains several one-file C programs that convert an analytic formula into a tabulated :doc:`embedded atom method (EAM) ` setfl potential file. The potentials they produce are in the potentials directory, and can be used with the -:doc:`pair\_style eam/alloy ` command. +:doc:`pair_style eam/alloy ` command. The source files and potentials were provided by Gerolf Ziegenhain (gerolf at ziegenhain.com). diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index 92ab8b5ea3..34843fe855 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -48,9 +48,9 @@ See :ref:`(MacKerell) ` for a description of the CHARMM force field. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/radian\^2) * :math:`\theta_0` (degrees) @@ -97,7 +97,7 @@ for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst index 9d1ff8e8e7..ae5330d964 100644 --- a/doc/src/angle_class2.rst +++ b/doc/src/angle_class2.rst @@ -51,9 +51,9 @@ the equilibrium bond lengths. See :ref:`(Sun) ` for a description of the COMPASS class2 force field. Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for -each angle type via the :doc:`angle\_coeff ` command as in +each angle type via the :doc:`angle_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands. These are the 4 coefficients for the :math:`E_a` formula: @@ -66,7 +66,7 @@ These are the 4 coefficients for the :math:`E_a` formula: :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the units of the various :math:`K` are in per-radian. -For the :math:`E_{bb}` formula, each line in a :doc:`angle\_coeff ` +For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff ` command in the input script lists 4 coefficients, the first of which is "bb" to indicate they are BondBond coefficients. In a data file, these coefficients should be listed under a "BondBond Coeffs" heading @@ -78,7 +78,7 @@ the angle type. * :math:`r_1` (distance) * :math:`r_2` (distance) -For the :math:`E_{ba}` formula, each line in a :doc:`angle\_coeff ` +For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff ` command in the input script lists 5 coefficients, the first of which is "ba" to indicate they are BondAngle coefficients. In a data file, these coefficients should be listed under a "BondAngle Coeffs" heading @@ -154,7 +154,7 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_cosine.rst b/doc/src/angle_cosine.rst index 68bfdbb82b..583f43bc40 100644 --- a/doc/src/angle_cosine.rst +++ b/doc/src/angle_cosine.rst @@ -39,9 +39,9 @@ The *cosine* angle style uses the potential where :math:`K` is defined for each angle type. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy) @@ -82,6 +82,6 @@ for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_cosine_buck6d.rst b/doc/src/angle_cosine_buck6d.rst index 2d00863b02..bb024c3474 100644 --- a/doc/src/angle_cosine_buck6d.rst +++ b/doc/src/angle_cosine_buck6d.rst @@ -33,9 +33,9 @@ where :math:`K` is the energy constant, :math:`n` is the periodic multiplicity a :math:`\theta_0` is the equilibrium angle. The coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands in the following order: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands in the following order: * :math:`K` (energy) * :math:`n` @@ -49,7 +49,7 @@ the short range (vdW) interaction belonging to the :doc:`pair\_buck6d ` between the end atoms of the angle. For this reason this angle style only works in combination with the :doc:`pair\_buck6d ` styles and needs -the :doc:`special\_bonds ` 1-3 interactions to be weighted +the :doc:`special_bonds ` 1-3 interactions to be weighted 0.0 to prevent double counting. @@ -62,7 +62,7 @@ Restrictions *cosine/buck6d* can only be used in combination with the :doc:`pair\_buck6d ` style and with a -:doc:`special\_bonds ` 0.0 weighting of 1-3 interactions. +:doc:`special_bonds ` 0.0 weighting of 1-3 interactions. This angle style can only be used if LAMMPS was built with the USER-MOFFF package. See the :doc:`Build package ` doc @@ -71,6 +71,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst index 9af93cb06a..f83b03b36d 100644 --- a/doc/src/angle_cosine_delta.rst +++ b/doc/src/angle_cosine_delta.rst @@ -37,9 +37,9 @@ where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy) * :math:`\theta_0` (degrees) @@ -84,6 +84,6 @@ for more info. Related commands """""""""""""""" -:doc:`angle\_coeff `, :doc:`angle\_style cosine/squared ` +:doc:`angle_coeff `, :doc:`angle_style cosine/squared ` **Default:** none diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index caaf15007a..c8ede7e03d 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -42,9 +42,9 @@ where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle See :ref:`(Mayo) ` for a description of the DREIDING force field The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`C` (energy) * :math:`B` = 1 or -1 @@ -92,7 +92,7 @@ for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_cosine_shift.rst b/doc/src/angle_cosine_shift.rst index bd7b6416c7..00b494bc08 100644 --- a/doc/src/angle_cosine_shift.rst +++ b/doc/src/angle_cosine_shift.rst @@ -39,9 +39,9 @@ between :math:`-U_{\text{min}}` and zero. In the neighborhood of the minimum the spring constant is :math:`\frac{U_{\text{min}}}{2}`. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`U_{\text{min}}` (energy) * :math:`\theta` (angle) @@ -82,7 +82,7 @@ USER-MISC package. Related commands """""""""""""""" -:doc:`angle\_coeff `, +:doc:`angle_coeff `, :doc:`angle\_cosine\_shift\_exp ` **Default:** none diff --git a/doc/src/angle_cosine_shift_exp.rst b/doc/src/angle_cosine_shift_exp.rst index 331ccb9da7..ae810f9f33 100644 --- a/doc/src/angle_cosine_shift_exp.rst +++ b/doc/src/angle_cosine_shift_exp.rst @@ -48,9 +48,9 @@ order in :math:`a` for :math:`a < 0.001`. In this limit the potential reduces to cosineshifted potential. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`U_min` (energy) * :math:`\theta` (angle) @@ -93,7 +93,7 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff `, +:doc:`angle_coeff `, :doc:`angle\_cosine\_shift `, :doc:`dihedral\_cosine\_shift\_exp ` diff --git a/doc/src/angle_cosine_squared.rst b/doc/src/angle_cosine_squared.rst index b1a516880d..ee9258dda8 100644 --- a/doc/src/angle_cosine_squared.rst +++ b/doc/src/angle_cosine_squared.rst @@ -37,9 +37,9 @@ where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy) * :math:`\theta_0` (degrees) @@ -84,6 +84,6 @@ for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_cross.rst b/doc/src/angle_cross.rst index 7dcff0264f..eb5865c060 100644 --- a/doc/src/angle_cross.rst +++ b/doc/src/angle_cross.rst @@ -37,9 +37,9 @@ the bond stretch-bond stretch term and :math:`K_{BS0}` and :math:`K_{BS1}` are t of the bond stretch-angle stretch terms. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K_{SS}` (energy/distance\^2) * :math:`K_{BS0}` (energy/distance/rad) @@ -62,6 +62,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_dipole.rst b/doc/src/angle_dipole.rst index 351572cc22..cfa4313b30 100644 --- a/doc/src/angle_dipole.rst +++ b/doc/src/angle_dipole.rst @@ -79,9 +79,9 @@ where :math:`\vec{F_i}` and :math:`\vec{F_j}` are applied on atoms :math:`i` and :math:`j`, respectively. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy) * :math:`\gamma_0` (degrees) @@ -136,7 +136,7 @@ This angle style should not be used with SHAKE. Related commands """""""""""""""" -:doc:`angle\_coeff `, :doc:`angle\_hybrid ` +:doc:`angle_coeff `, :doc:`angle_hybrid ` **Default:** none diff --git a/doc/src/angle_fourier.rst b/doc/src/angle_fourier.rst index c814b7224e..d290e2d1f7 100644 --- a/doc/src/angle_fourier.rst +++ b/doc/src/angle_fourier.rst @@ -33,9 +33,9 @@ The *fourier* angle style uses the potential The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy) * :math:`C_0` (real) @@ -79,6 +79,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_fourier_simple.rst b/doc/src/angle_fourier_simple.rst index 5ad8b386d0..d19dd19753 100644 --- a/doc/src/angle_fourier_simple.rst +++ b/doc/src/angle_fourier_simple.rst @@ -33,9 +33,9 @@ The *fourier/simple* angle style uses the potential The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy) * :math:`c` (real) @@ -78,6 +78,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_harmonic.rst b/doc/src/angle_harmonic.rst index 1066621729..6b9ed776f5 100644 --- a/doc/src/angle_harmonic.rst +++ b/doc/src/angle_harmonic.rst @@ -43,9 +43,9 @@ where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/radian\^2) * :math:`\theta_0` (degrees) @@ -90,6 +90,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_mm3.rst b/doc/src/angle_mm3.rst index 7cf7f9e720..6d6c6d874c 100644 --- a/doc/src/angle_mm3.rst +++ b/doc/src/angle_mm3.rst @@ -36,9 +36,9 @@ prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example :math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ... The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/radian\^2) * :math:`\theta_0` (degrees) @@ -57,6 +57,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_quartic.rst b/doc/src/angle_quartic.rst index 104c0be802..bbf1dd618e 100644 --- a/doc/src/angle_quartic.rst +++ b/doc/src/angle_quartic.rst @@ -37,9 +37,9 @@ where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`\theta_0` (degrees) * :math:`K_2` (energy/radian\^2) @@ -86,6 +86,6 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index 0af22a5372..9f9b1ee532 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -39,12 +39,12 @@ where :math:`\theta_0` is the equilibrium value of the angle and :math:`K` a pre with the *repulsive* part of the non-bonded *lj/sdk* pair style between the atoms 1 and 3. This angle potential is intended for coarse grained MD simulations with the CMM parameterization using the -:doc:`pair\_style lj/sdk `. Relative to the pair\_style +:doc:`pair_style lj/sdk `. Relative to the pair\_style *lj/sdk*\ , however, the energy is shifted by *epsilon*\ , to avoid sudden jumps. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above: +:doc:`angle_coeff ` command as in the example above: * :math:`K` (energy/radian\^2) * :math:`\theta_0` (degrees) @@ -91,7 +91,7 @@ page for more info. Related commands """""""""""""""" -:doc:`angle\_coeff `, :doc:`angle\_style harmonic `, :doc:`pair\_style lj/sdk `, -:doc:`pair\_style lj/sdk/coul/long ` +:doc:`angle_coeff `, :doc:`angle_style harmonic `, :doc:`pair_style lj/sdk `, +:doc:`pair_style lj/sdk/coul/long ` **Default:** none diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index ac2720d4f2..147727dd66 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -39,14 +39,14 @@ Description """"""""""" Modify certain attributes of atoms defined and stored within LAMMPS, -in addition to what is specified by the :doc:`atom\_style ` +in addition to what is specified by the :doc:`atom_style ` command. The *id* and *map* keywords must be specified before a simulation box is defined; other keywords can be specified any time. The *id* keyword determines whether non-zero atom IDs can be assigned to each atom. If the value is *yes*\ , which is the default, IDs are assigned, whether you use the :doc:`create atoms ` or -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands to initialize atoms. If the value is *no* the IDs for all atoms are assumed to be 0. @@ -77,7 +77,7 @@ efficiently by creating a "map", which is either an *array* or *hash* table, as described below. When the *map* keyword is not specified in your input script, LAMMPS -only creates a map for :doc:`atom\_styles ` for molecular +only creates a map for :doc:`atom_styles ` for molecular systems which have permanent bonds (angles, etc). No map is created for atomic systems, since it is normally not needed. However some LAMMPS commands require a map, even for atomic systems, and will @@ -103,7 +103,7 @@ of owned atoms. This in only useful when the specified group is a small fraction of all the atoms, and there are other operations LAMMPS is performing that will be sped-up significantly by being able to loop over the smaller set of atoms. Otherwise the reordering required by -this option will be a net slow-down. The :doc:`neigh\_modify include ` and :doc:`comm\_modify group ` +this option will be a net slow-down. The :doc:`neigh_modify include ` and :doc:`comm_modify group ` commands are two examples of commands that require this setting to work efficiently. Several :doc:`fixes `, most notably time integration fixes like :doc:`fix nve `, also take advantage of diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index d2ebc220d6..d0707559d7 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -50,8 +50,8 @@ Description Define what style of atoms to use in a simulation. This determines what attributes are associated with the atoms. This command must be -used before a simulation is setup via a :doc:`read\_data `, -:doc:`read\_restart `, or :doc:`create\_box ` +used before a simulation is setup via a :doc:`read_data `, +:doc:`read_restart `, or :doc:`create_box ` command. .. note:: @@ -68,12 +68,12 @@ style more general than needed, though it may be slightly inefficient. The choice of style affects what quantities are stored by each atom, what quantities are communicated between processors to enable forces to be computed, and what quantities are listed in the data file read -by the :doc:`read\_data ` command. +by the :doc:`read_data ` command. These are the additional attributes of each style and the typical kinds of physical systems they are used to model. All styles store coordinates, velocities, atom IDs and types. See the -:doc:`read\_data `, :doc:`create\_atoms `, and +:doc:`read_data `, :doc:`create_atoms `, and :doc:`set ` commands for info on how to set these various quantities. @@ -173,7 +173,7 @@ per-particle mass and volume. The *dpd* style is for dissipative particle dynamics (DPD) particles. Note that it is part of the USER-DPD package, and is not for use with -the :doc:`pair\_style dpd or dpd/stat ` commands, which can +the :doc:`pair_style dpd or dpd/stat ` commands, which can simply use atom\_style atomic. Atom\_style dpd extends DPD particle properties with internal temperature (dpdTheta), internal conductive energy (uCond), internal mechanical energy (uMech), and internal @@ -240,7 +240,7 @@ can be advantageous for large-scale coarse-grained systems. another CO2, then you probably do not want each molecule file to define 2 atom types and a single bond type, because they will conflict with each other when a mixture system of H2O and CO2 molecules is - defined, e.g. by the :doc:`read\_data ` command. Rather the + defined, e.g. by the :doc:`read_data ` command. Rather the H2O molecule should define atom types 1 and 2, and bond type 1. And the CO2 molecule should define atom types 3 and 4 (or atom types 3 and 2 if a single oxygen type is desired), and bond type 2. @@ -317,7 +317,7 @@ Restrictions This command cannot be used after the simulation box is defined by a -:doc:`read\_data ` or :doc:`create\_box ` command. +:doc:`read_data ` or :doc:`create_box ` command. Many of the styles listed above are only enabled if LAMMPS was built with a specific package, as listed below. See the :doc:`Build package ` doc page for more info. @@ -354,7 +354,7 @@ The *wavepacket* style is part of the USER-AWPMD package for the Related commands """""""""""""""" -:doc:`read\_data `, :doc:`pair\_style ` +:doc:`read_data `, :doc:`pair_style ` Default """"""" diff --git a/doc/src/balance.rst b/doc/src/balance.rst index 67146b2ba9..9da86342ec 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -132,8 +132,8 @@ forced even if the current balance is perfect (1.0) be specifying a exceed the *thresh* parameter if a "grid" style is specified when the current partitioning is "tiled". The meaning of "grid" vs "tiled" is explained below. This is to allow forcing of the partitioning to - "grid" so that the :doc:`comm\_style brick ` command can then - be used to replace a current :doc:`comm\_style tiled ` + "grid" so that the :doc:`comm_style brick ` command can then + be used to replace a current :doc:`comm_style tiled ` setting. When the balance command completes, it prints statistics about the @@ -151,7 +151,7 @@ fractions of the box length) are also printed. create a logical 3d grid cannot achieve perfect balance for many irregular distributions of particles. Likewise, if a portion of the system is a perfect lattice, e.g. the initial system is generated by - the :doc:`create\_atoms ` command, then "grid" methods may + the :doc:`create_atoms ` command, then "grid" methods may be unable to achieve exact balance. This is because entire lattice planes will be owned or not owned by a single processor. @@ -165,7 +165,7 @@ fractions of the box length) are also printed. proportional to particle count, and changing the relative size and shape of processor sub-domains may lead to additional computational and communication overheads, e.g. in the PPPM solver used via the - :doc:`kspace\_style ` command. Thus you should benchmark + :doc:`kspace_style ` command. Thus you should benchmark the run times of a simulation before and after balancing. @@ -201,9 +201,9 @@ fashion so as to have equal numbers of particles (or weight) in each sub-box, as in the rightmost diagram above. The "grid" methods can be used with either of the -:doc:`comm\_style ` command options, *brick* or *tiled*\ . The -"tiling" methods can only be used with :doc:`comm\_style tiled `. Note that it can be useful to use a "grid" -method with :doc:`comm\_style tiled ` to return the domain +:doc:`comm_style ` command options, *brick* or *tiled*\ . The +"tiling" methods can only be used with :doc:`comm_style tiled `. Note that it can be useful to use a "grid" +method with :doc:`comm_style tiled ` to return the domain partitioning to a logical 3d grid of processors so that "comm\_style brick" can afterwords be specified for subsequent :doc:`run ` commands. @@ -384,7 +384,7 @@ multiple groups, its weight is the product of the weight factors. This weight style is useful in combination with pair style :doc:`hybrid `, e.g. when combining a more costly many-body potential with a fast pair-wise potential. It is also useful when -using :doc:`run\_style respa ` where some portions of the +using :doc:`run_style respa ` where some portions of the system have many bonded interactions and others none. It assumes that the computational cost for each group remains constant over time. This is a purely empirical weighting, so a series test runs to tune @@ -555,13 +555,13 @@ For 2d simulations, the *z* style cannot be used. Nor can a "z" appear in *dimstr* for the *shift* style. Balancing through recursive bisectioning (\ *rcb* style) requires -:doc:`comm\_style tiled ` +:doc:`comm_style tiled ` Related commands """""""""""""""" :doc:`group `, :doc:`processors `, -:doc:`fix balance `, :doc:`comm\_style ` +:doc:`fix balance `, :doc:`comm_style ` .. _pizza: http://pizza.sandia.gov diff --git a/doc/src/bond_class2.rst b/doc/src/bond_class2.rst index e3098ef6dc..7b07c8a69a 100644 --- a/doc/src/bond_class2.rst +++ b/doc/src/bond_class2.rst @@ -41,9 +41,9 @@ where :math:`r_0` is the equilibrium bond distance. See :ref:`(Sun) ` for a description of the COMPASS class2 force field. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`r_0` (distance) * :math:`K_2` (energy/distance\^2) @@ -87,7 +87,7 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_coeff.rst b/doc/src/bond_coeff.rst index 281dfc7095..157403a301 100644 --- a/doc/src/bond_coeff.rst +++ b/doc/src/bond_coeff.rst @@ -31,7 +31,7 @@ Description Specify the bond force field coefficients for one or more bond types. The number and meaning of the coefficients depends on the bond style. Bond coefficients can also be set in the data file read by the -:doc:`read\_data ` command or in a restart file. +:doc:`read_data ` command or in a restart file. N can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be @@ -69,7 +69,7 @@ corresponds to the 1st example above would be listed as The list of all bond styles defined in LAMMPS is given on the -:doc:`bond\_style ` doc page. They are also listed in more +:doc:`bond_style ` doc page. They are also listed in more compact form on the :doc:`Commands bond ` doc page. On either of those pages, click on the style to display the formula it @@ -85,8 +85,8 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. A bond style must be defined before any bond coefficients are set, either in the input script or in a data file. @@ -94,6 +94,6 @@ either in the input script or in a data file. Related commands """""""""""""""" -:doc:`bond\_style ` +:doc:`bond_style ` **Default:** none diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index d952321c20..a36db3a170 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -46,9 +46,9 @@ first term extends to :math:`R_0`, the maximum extent of the bond. The 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^2) * :math:`R_0` (distance) @@ -89,14 +89,14 @@ This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. -You typically should specify :doc:`special\_bonds fene ` -or :doc:`special\_bonds lj/coul 0 1 1 ` to use this bond +You typically should specify :doc:`special_bonds fene ` +or :doc:`special_bonds lj/coul 0 1 1 ` to use this bond style. LAMMPS will issue a warning it that's not the case. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_fene_expand.rst b/doc/src/bond_fene_expand.rst index 5b5b858330..8a05e141d7 100644 --- a/doc/src/bond_fene_expand.rst +++ b/doc/src/bond_fene_expand.rst @@ -43,9 +43,9 @@ effectively change the bead size of the bonded atoms. The first term now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^2) * :math:`R_0` (distance) @@ -87,14 +87,14 @@ This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. -You typically should specify :doc:`special\_bonds fene ` -or :doc:`special\_bonds lj/coul 0 1 1 ` to use this bond +You typically should specify :doc:`special_bonds fene ` +or :doc:`special_bonds lj/coul 0 1 1 ` to use this bond style. LAMMPS will issue a warning it that's not the case. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_gromos.rst b/doc/src/bond_gromos.rst index 5d0a4ab1c6..3b935568bb 100644 --- a/doc/src/bond_gromos.rst +++ b/doc/src/bond_gromos.rst @@ -37,9 +37,9 @@ where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/4 factor is included in :math:`K`. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^4) * :math:`r_0` (distance) @@ -81,6 +81,6 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index d65f0337f0..06af4037f6 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -43,9 +43,9 @@ where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^2) * :math:`r_0` (distance) @@ -87,6 +87,6 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst index cc39bda7a7..26373790a2 100644 --- a/doc/src/bond_harmonic_shift.rst +++ b/doc/src/bond_harmonic_shift.rst @@ -39,9 +39,9 @@ The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`U_{\text{min}}` (energy) @@ -86,7 +86,7 @@ page for more info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds `, -:doc:`bond\_harmonic ` +:doc:`bond_coeff `, :doc:`delete_bonds `, +:doc:`bond_harmonic ` **Default:** none diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst index 459acfdbfb..6b7e7d4fbb 100644 --- a/doc/src/bond_harmonic_shift_cut.rst +++ b/doc/src/bond_harmonic_shift_cut.rst @@ -39,9 +39,9 @@ The bond potential is zero for distances :math:`r > r_c`. The potential is :math at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`U_{\text{min}}` (energy) * :math:`r_0` (distance) @@ -84,8 +84,8 @@ page for more info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds `, -:doc:`bond\_harmonic `, +:doc:`bond_coeff `, :doc:`delete_bonds `, +:doc:`bond_harmonic `, :doc:`bond\_harmonic\_shift ` **Default:** none diff --git a/doc/src/bond_mm3.rst b/doc/src/bond_mm3.rst index 5794592ce4..e7baa78ea0 100644 --- a/doc/src/bond_mm3.rst +++ b/doc/src/bond_mm3.rst @@ -39,9 +39,9 @@ Note that the MM3 papers contains an error in Eq (1): (7/12)2.55 should be replaced with (7/12)2.55\^2 The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^2) * :math:`r_0` (distance) @@ -57,7 +57,7 @@ page for more info. Related commands """""""""""""""" -:doc:`bond\_coeff ` +:doc:`bond_coeff ` **Default:** none diff --git a/doc/src/bond_morse.rst b/doc/src/bond_morse.rst index 26471424c5..13f24855f3 100644 --- a/doc/src/bond_morse.rst +++ b/doc/src/bond_morse.rst @@ -37,9 +37,9 @@ where :math:`r_0` is the equilibrium bond distance, :math:`\alpha` is a stiffnes parameter, and :math:`D` determines the depth of the potential well. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`D` (energy) * :math:`\alpha` (inverse distance) @@ -82,6 +82,6 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_nonlinear.rst b/doc/src/bond_nonlinear.rst index 0003257e0b..4f8a0c881e 100644 --- a/doc/src/bond_nonlinear.rst +++ b/doc/src/bond_nonlinear.rst @@ -37,9 +37,9 @@ to define an anharmonic spring :ref:`(Rector) ` of equilibrium length :math:`r_0` and maximum extension lamda. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`\epsilon` (energy) * :math:`r_0` (distance) @@ -82,7 +82,7 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 03863eb5cf..2b7ba54708 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -52,9 +52,9 @@ phosphate backbone in the oxDNA/oxRNA force field for coarse-grained modelling of DNA/RNA. The following coefficients must be defined for the bond type via the -:doc:`bond\_coeff ` command as given in the above example, or +:doc:`bond_coeff ` command as given in the above example, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * :math:`\epsilon` (energy) @@ -68,7 +68,7 @@ commands: *oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and coaxial stacking interaction *oxdna/coaxstk* as well as hydrogen-bonding interaction *oxdna/hbond* (see also documentation of - :doc:`pair\_style oxdna/excv `). For the oxDNA2 + :doc:`pair_style oxdna/excv `). For the oxDNA2 :ref:`(Snodin) ` bond style the analogous pair styles *oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* , *oxdna2/hbond* and an additional Debye-Hueckel pair style @@ -111,8 +111,8 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the Related commands """""""""""""""" -:doc:`pair\_style oxdna/excv `, :doc:`pair\_style oxdna2/excv `, :doc:`pair\_style oxrna2/excv `, -:doc:`bond\_coeff `, :doc:`fix nve/dotc/langevin ` +:doc:`pair_style oxdna/excv `, :doc:`pair_style oxdna2/excv `, :doc:`pair_style oxrna2/excv `, +:doc:`bond_coeff `, :doc:`fix nve/dotc/langevin ` **Default:** diff --git a/doc/src/bond_quartic.rst b/doc/src/bond_quartic.rst index 898aa9315a..89b1a0a131 100644 --- a/doc/src/bond_quartic.rst +++ b/doc/src/bond_quartic.rst @@ -37,9 +37,9 @@ due to a polymer being stretched). The :math:`\sigma` and :math:`\epsilon` used LJ portion of the formula are both set equal to 1.0 by LAMMPS. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * :math:`K` (energy/distance\^4) * :math:`B_1` (distance) @@ -75,12 +75,12 @@ LAMMPS does the second task via a computational sleight-of-hand. It subtracts the pairwise interaction as part of the bond computation. When the bond breaks, the subtraction stops. For this to work, the pairwise interaction must always be computed by the -:doc:`pair\_style ` command, whether the bond is broken or -not. This means that :doc:`special\_bonds ` must be set +:doc:`pair_style ` command, whether the bond is broken or +not. This means that :doc:`special_bonds ` must be set to 1,1,1, as indicated as a restriction below. Note that when bonds are dumped to a file via the :doc:`dump local ` command, bonds with type 0 are not included. The -:doc:`delete\_bonds ` command can also be used to query the +:doc:`delete_bonds ` command can also be used to query the status of broken bonds or permanently delete them, e.g.: @@ -123,13 +123,13 @@ This bond style can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more info. -The *quartic* style requires that :doc:`special\_bonds ` +The *quartic* style requires that :doc:`special_bonds ` parameters be set to 1,1,1. Three- and four-body interactions (angle, dihedral, etc) cannot be used with *quartic* bonds. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index dd3acb6833..a0908606e4 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -32,12 +32,12 @@ Description Set the formula(s) LAMMPS uses to compute bond interactions between pairs of atoms. In LAMMPS, a bond differs from a pairwise -interaction, which are set via the :doc:`pair\_style ` +interaction, which are set via the :doc:`pair_style ` command. Bonds are defined between specified pairs of atoms and remain in force for the duration of the simulation (unless the bond breaks which is possible in some bond potentials). The list of bonded -atoms is read in by a :doc:`read\_data ` or -:doc:`read\_restart ` command from a data or restart file. +atoms is read in by a :doc:`read_data ` or +:doc:`read_restart ` command from a data or restart file. By contrast, pair potentials are typically defined between all pairs of atoms within a cutoff distance and the set of active interactions changes over time. @@ -46,12 +46,12 @@ Hybrid models where bonds are computed using different bond potentials can be setup using the *hybrid* bond style. The coefficients associated with a bond style can be specified in a -data or restart file or via the :doc:`bond\_coeff ` command. +data or restart file or via the :doc:`bond_coeff ` command. All bond potentials store their coefficient data in binary restart -files which means bond\_style and :doc:`bond\_coeff ` commands +files which means bond\_style and :doc:`bond_coeff ` commands do not need to be re-specified in an input script that restarts a -simulation. See the :doc:`read\_restart ` command for +simulation. See the :doc:`read_restart ` command for details on how to do this. The one exception is that bond\_style *hybrid* only stores the list of sub-styles in the restart file; bond coefficients need to be re-specified. @@ -59,7 +59,7 @@ coefficients need to be re-specified. .. note:: When both a bond and pair style is defined, the - :doc:`special\_bonds ` command often needs to be used to + :doc:`special_bonds ` command often needs to be used to turn off (or weight) the pairwise interaction that would otherwise exist between 2 bonded atoms. @@ -122,7 +122,7 @@ individual bond potentials tell if it is part of a package. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` Default """"""" diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index 5378df3cff..79ad429222 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -90,7 +90,7 @@ keyword followed by one or more numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`bond\_style table ` command. Let +specified in the :doc:`bond_style table ` command. Let Ntable = *N* in the bond_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It diff --git a/doc/src/bond_zero.rst b/doc/src/bond_zero.rst index 43a0af33e2..329cd9d13a 100644 --- a/doc/src/bond_zero.rst +++ b/doc/src/bond_zero.rst @@ -31,14 +31,14 @@ commands. As an example, the :doc:`compute bond/local ` command can be used to compute distances for the list of pairs of bond -atoms listed in the data file read by the :doc:`read\_data ` +atoms listed in the data file read by the :doc:`read_data ` command. If no bond style is defined, this command cannot be used. The optional *nocoeff* flag allows to read data files with a BondCoeff section for any bond style. Similarly, any bond\_coeff commands will only be checked for the bond type number and the rest ignored. -Note that the :doc:`bond\_coeff ` command must be used for +Note that the :doc:`bond_coeff ` command must be used for all bond types. If specified, there can be only one value, which is going to be used to assign an equilibrium distance, e.g. for use with :doc:`fix shake `. @@ -50,6 +50,6 @@ Restrictions Related commands """""""""""""""" -:doc:`bond\_style none ` +:doc:`bond_style none ` **Default:** none diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst index 909ee3b446..2a9896c2c8 100644 --- a/doc/src/boundary.rst +++ b/doc/src/boundary.rst @@ -39,8 +39,8 @@ Set the style of boundaries for the global simulation box in each dimension. A single letter assigns the same style to both the lower and upper face of the box. Two letters assigns the first style to the lower face and the second style to the upper face. The initial size -of the simulation box is set by the :doc:`read\_data `, -:doc:`read\_restart `, or :doc:`create\_box ` +of the simulation box is set by the :doc:`read_data `, +:doc:`read_restart `, or :doc:`create_box ` commands. The style *p* means the box is periodic, so that particles interact @@ -56,7 +56,7 @@ side of the box to the other. For style *f*\ , the position of the face is fixed. If an atom moves outside the face it will be deleted on the next timestep that reneighboring occurs. This will typically generate an error unless -you have set the :doc:`thermo\_modify lost ` option to +you have set the :doc:`thermo_modify lost ` option to allow for lost atoms. For style *s*\ , the position of the face is set so as to encompass the @@ -73,7 +73,7 @@ shrink-wrapped dimensions more closely, by using *m* style boundaries For style *m*\ , shrink-wrapping occurs, but is bounded by the value specified in the data or restart file or set by the -:doc:`create\_box ` command. For example, if the upper z +:doc:`create_box ` command. For example, if the upper z face has a value of 50.0 in the data file, the face will always be positioned at 50.0 or above, even if the maximum z-extent of all the atoms becomes less than 50.0. This can be useful if you start a @@ -99,9 +99,9 @@ Restrictions This command cannot be used after the simulation box is defined by a -:doc:`read\_data ` or :doc:`create\_box ` command or -:doc:`read\_restart ` command. See the -:doc:`change\_box ` command for how to change the simulation +:doc:`read_data ` or :doc:`create_box ` command or +:doc:`read_restart ` command. See the +:doc:`change_box ` command for how to change the simulation box boundaries after it has been defined. For 2d simulations, the z dimension must be periodic. @@ -109,7 +109,7 @@ For 2d simulations, the z dimension must be periodic. Related commands """""""""""""""" -See the :doc:`thermo\_modify ` command for a discussion +See the :doc:`thermo_modify ` command for a discussion of lost atoms. Default diff --git a/doc/src/box.rst b/doc/src/box.rst index 3338e138fb..9ef8316dae 100644 --- a/doc/src/box.rst +++ b/doc/src/box.rst @@ -36,8 +36,8 @@ Set attributes of the simulation box. For triclinic (non-orthogonal) simulation boxes, the *tilt* keyword allows simulation domains to be created with arbitrary tilt factors, -e.g. via the :doc:`create\_box ` or -:doc:`read\_data ` commands. Tilt factors determine how +e.g. via the :doc:`create_box ` or +:doc:`read_data ` commands. Tilt factors determine how skewed the triclinic box is; see the :doc:`Howto triclinic ` doc page for a discussion of triclinic boxes in LAMMPS. @@ -60,8 +60,8 @@ Restrictions This command cannot be used after the simulation box is defined by a -:doc:`read\_data ` or :doc:`create\_box ` command or -:doc:`read\_restart ` command. +:doc:`read_data ` or :doc:`create_box ` command or +:doc:`read_restart ` command. **Related commands:** none diff --git a/doc/src/change_box.rst b/doc/src/change_box.rst index bc34db9262..3430d25c72 100644 --- a/doc/src/change_box.rst +++ b/doc/src/change_box.rst @@ -77,12 +77,12 @@ conditions for the simulation box, similar to the :doc:`boundary ` command. The size and shape of the initial simulation box are specified by the -:doc:`create\_box ` or :doc:`read\_data ` or -:doc:`read\_restart ` command used to setup the simulation. +:doc:`create_box ` or :doc:`read_data ` or +:doc:`read_restart ` command used to setup the simulation. The size and shape may be altered by subsequent runs, e.g. by use of the :doc:`fix npt ` or :doc:`fix deform ` commands. -The :doc:`create\_box `, :doc:`read data `, and -:doc:`read\_restart ` commands also determine whether the +The :doc:`create_box `, :doc:`read data `, and +:doc:`read_restart ` commands also determine whether the simulation box is orthogonal or triclinic and their doc pages explain the meaning of the xy,xz,yz tilt factors. @@ -108,7 +108,7 @@ new owning processors. This means that you cannot use the change\_box command to enlarge a shrink-wrapped box, e.g. to make room to insert more atoms via the - :doc:`create\_atoms ` command, because the simulation box + :doc:`create_atoms ` command, because the simulation box will be re-shrink-wrapped before the change\_box command completes. Instead you could do something like this, assuming the simulation box is non-periodic and atoms extend from 0 to 20 in all dimensions: @@ -289,11 +289,11 @@ smaller. See the :doc:`boundary ` command for more explanation of these style options. Note that the "boundary" command itself can only be used before the -simulation box is defined via a :doc:`read\_data ` or -:doc:`create\_box ` or :doc:`read\_restart ` +simulation box is defined via a :doc:`read_data ` or +:doc:`create_box ` or :doc:`read_restart ` command. This command allows the boundary conditions to be changed later in your input script. Also note that the -:doc:`read\_restart ` will change boundary conditions to +:doc:`read_restart ` will change boundary conditions to match what is stored in the restart file. So if you wish to change them, you should use the change\_box command after the read\_restart command. @@ -306,8 +306,8 @@ The *ortho* and *triclinic* keywords convert the simulation box to be orthogonal or triclinic (non-orthogonal). The simulation box is defined as either orthogonal or triclinic when -it is created via the :doc:`create\_box `, -:doc:`read\_data `, or :doc:`read\_restart ` +it is created via the :doc:`create_box `, +:doc:`read_data `, or :doc:`read_restart ` commands. These keywords allow you to toggle the existing simulation box from diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 9375bd60c9..5526646261 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -50,8 +50,8 @@ processors and stored as properties of ghost atoms. .. note:: These options apply to the currently defined comm style. When - you specify a :doc:`comm\_style ` or - :doc:`read\_restart ` command, all communication settings + you specify a :doc:`comm_style ` or + :doc:`read_restart ` command, all communication settings are restored to their default or stored values, including those previously reset by a comm\_modify command. Thus if your input script specifies a comm\_style or read\_restart command, you should use the @@ -138,17 +138,17 @@ find the needed atoms. side of the simulation box, across a periodic boundary. This will typically lead to bad dynamics (i.e. the bond length is now the simulation box length). To detect if this is happening, see the - :doc:`neigh\_modify cluster ` command. + :doc:`neigh_modify cluster ` command. The *group* keyword will limit communication to atoms in the specified group. This can be useful for models where no ghost atoms are needed for some kinds of particles. All atoms (not just those in the specified group) will still migrate to new processors as they move. The group specified with this option must also be specified via the -:doc:`atom\_modify first ` command. +:doc:`atom_modify first ` command. The *vel* keyword enables velocity information to be communicated with -ghost particles. Depending on the :doc:`atom\_style `, +ghost particles. Depending on the :doc:`atom_style `, velocity info includes the translational velocity, angular velocity, and angular momentum of a particle. If the *vel* option is set to *yes*\ , then ghost atoms store these quantities; if *no* then they do @@ -167,12 +167,12 @@ Restrictions Communication mode *multi* is currently only available for -:doc:`comm\_style ` *brick*\ . +:doc:`comm_style ` *brick*\ . Related commands """""""""""""""" -:doc:`comm\_style `, :doc:`neighbor ` +:doc:`comm_style `, :doc:`neighbor ` Default """"""" diff --git a/doc/src/comm_style.rst b/doc/src/comm_style.rst index 1d733b7c40..528f05ecf1 100644 --- a/doc/src/comm_style.rst +++ b/doc/src/comm_style.rst @@ -46,11 +46,11 @@ Note that this command does not actually define a partitioning of the simulation box (a domain decomposition), rather it determines what kinds of decompositions are allowed and the pattern of communication used to enable the decomposition. A decomposition is created when the -simulation box is first created, via the :doc:`create\_box ` -or :doc:`read\_data ` or :doc:`read\_restart ` +simulation box is first created, via the :doc:`create_box ` +or :doc:`read_data ` or :doc:`read_restart ` commands. For both the *brick* and *tiled* styles, the initial decomposition will be the same, as described by -:doc:`create\_box ` and :doc:`processors ` +:doc:`create_box ` and :doc:`processors ` commands. The decomposition can be changed via the :doc:`balance ` or :doc:`fix balance ` commands. @@ -64,7 +64,7 @@ cells. Related commands """""""""""""""" -:doc:`comm\_modify `, :doc:`processors `, +:doc:`comm_modify `, :doc:`processors `, :doc:`balance `, :doc:`fix balance ` Default diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 9c66c58bd9..56de4f4225 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -106,7 +106,7 @@ ways: * The results of computes that calculate a global temperature or pressure can be used by fixes that do thermostatting or barostatting or when atom velocities are created. -* Global values can be output via the :doc:`thermo\_style custom ` or :doc:`fix ave/time ` command. +* Global values can be output via the :doc:`thermo_style custom ` or :doc:`fix ave/time ` command. Or the values can be referenced in a :doc:`variable equal ` or :doc:`variable atom ` command. * Per-atom values can be output via the :doc:`dump custom ` command. @@ -147,7 +147,7 @@ in the input script: Additional computes for other quantities are created if the thermo style requires it. See the documentation for the -:doc:`thermo\_style ` command. +:doc:`thermo_style ` command. Fixes that calculate temperature or pressure, i.e. for thermostatting or barostatting, may also create computes. These are discussed in the @@ -155,10 +155,10 @@ documentation for specific :doc:`fix ` commands. In all these cases, the default computes LAMMPS creates can be replaced by computes defined by the user in the input script, as -described by the :doc:`thermo\_modify ` and :doc:`fix modify ` commands. +described by the :doc:`thermo_modify ` and :doc:`fix modify ` commands. Properties of either a default or user-defined compute can be modified -via the :doc:`compute\_modify ` command. +via the :doc:`compute_modify ` command. Computes can be deleted with the :doc:`uncompute ` command. @@ -329,7 +329,7 @@ Restrictions Related commands """""""""""""""" -:doc:`uncompute `, :doc:`compute\_modify `, :doc:`fix ave/atom `, :doc:`fix ave/time `, :doc:`fix ave/histo ` +:doc:`uncompute `, :doc:`compute_modify `, :doc:`fix ave/atom `, :doc:`fix ave/time `, :doc:`fix ave/histo ` **Default:** none diff --git a/doc/src/compute_adf.rst b/doc/src/compute_adf.rst index 3c8af03b10..363091a033 100644 --- a/doc/src/compute_adf.rst +++ b/doc/src/compute_adf.rst @@ -60,9 +60,9 @@ neighbor atom in each requested ADF. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses a neighbor list, it also means those pairs will not be included in the ADF. This does not apply when @@ -72,7 +72,7 @@ neighbor atom in each requested ADF. zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to compute the ADF for snapshots in the dump file. The rerun script can use a - :doc:`special\_bonds ` command that includes all pairs in + :doc:`special_bonds ` command that includes all pairs in the neighbor list. .. note:: @@ -81,7 +81,7 @@ neighbor atom in each requested ADF. pair style is defined, e.g. the :doc:`rerun ` command is being used to post-process a dump file of snapshots you must insure ghost atom information out to the largest value of *Router* + *skin* is communicated, via the - :doc:`comm\_modify cutoff ` command, else the ADF computation + :doc:`comm_modify cutoff ` command, else the ADF computation cannot be performed, and LAMMPS will give an error message. The *skin* value is what is specified with the :doc:`neighbor ` command. @@ -221,7 +221,7 @@ your model. Related commands """""""""""""""" -:doc:`compute rdf `, :doc:`fix ave/time `, :doc:`compute\_modify ` +:doc:`compute rdf `, :doc:`fix ave/time `, :doc:`compute_modify ` Default """"""" diff --git a/doc/src/compute_angle.rst b/doc/src/compute_angle.rst index 2b025ea217..49b9849f05 100644 --- a/doc/src/compute_angle.rst +++ b/doc/src/compute_angle.rst @@ -31,13 +31,13 @@ hybrid" angle\_hybrid.html command. These values are made accessible for output or further processing by other commands. The group specified for this command is ignored. -This compute is useful when using :doc:`angle\_style hybrid ` if you want to know the portion of the total +This compute is useful when using :doc:`angle_style hybrid ` if you want to know the portion of the total energy contributed by one or more of the hybrid sub-styles. **Output info:** This compute calculates a global vector of length N where N is the -number of sub\_styles defined by the :doc:`angle\_style hybrid ` command, which can be accessed by indices +number of sub\_styles defined by the :doc:`angle_style hybrid ` command, which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_angle_local.rst b/doc/src/compute_angle_local.rst index 15b484a3bc..e6efe50b42 100644 --- a/doc/src/compute_angle_local.rst +++ b/doc/src/compute_angle_local.rst @@ -90,7 +90,7 @@ and output the statistics in various ways: The :doc:`dump local ` command will output the energy, angle, cosine(angle), cosine\^2(angle) for every angle in the system. The -:doc:`thermo\_style ` command will print the average of +:doc:`thermo_style ` command will print the average of those quantities via the :doc:`compute reduce ` command with thermo output. And the :doc:`fix ave/histo ` command will histogram the cosine(angle) values and write them to a @@ -104,8 +104,8 @@ The local data stored by this command is generated by looping over all the atoms owned on a processor and their angles. An angle will only be included if all 3 atoms in the angle are in the specified compute group. Any angles that have been broken (see the -:doc:`angle\_style ` command) by setting their angle type to -0 are not included. Angles that have been turned off (see the :doc:`fix shake ` or :doc:`delete\_bonds ` commands) by +:doc:`angle_style ` command) by setting their angle type to +0 are not included. Angles that have been turned off (see the :doc:`fix shake ` or :doc:`delete_bonds ` commands) by setting their angle type negative are written into the file, but their energy will be 0.0. diff --git a/doc/src/compute_angmom_chunk.rst b/doc/src/compute_angmom_chunk.rst index 5da4adecac..2637e4774a 100644 --- a/doc/src/compute_angmom_chunk.rst +++ b/doc/src/compute_angmom_chunk.rst @@ -56,7 +56,7 @@ non-zero chunk IDs. momentum in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the - :doc:`read\_data ` command for a discussion of image flags and + :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_body_local.rst b/doc/src/compute_body_local.rst index eb431aafc2..5d6a492c66 100644 --- a/doc/src/compute_body_local.rst +++ b/doc/src/compute_body_local.rst @@ -64,7 +64,7 @@ group. For a body particle, the *integer* keywords refer to fields calculated by the body style for each sub-particle. The body style, as specified -by the :doc:`atom\_style body `, determines how many fields +by the :doc:`atom_style body `, determines how many fields exist and what they are. See the :doc:`Howto\_body ` doc page for details of the different styles. diff --git a/doc/src/compute_bond.rst b/doc/src/compute_bond.rst index 74c1ccb262..43e9a64cbb 100644 --- a/doc/src/compute_bond.rst +++ b/doc/src/compute_bond.rst @@ -26,18 +26,18 @@ Description """"""""""" Define a computation that extracts the bond energy calculated by each -of the bond sub-styles used in the :doc:`bond\_style hybrid ` command. These values are made accessible +of the bond sub-styles used in the :doc:`bond_style hybrid ` command. These values are made accessible for output or further processing by other commands. The group specified for this command is ignored. -This compute is useful when using :doc:`bond\_style hybrid ` +This compute is useful when using :doc:`bond_style hybrid ` if you want to know the portion of the total energy contributed by one or more of the hybrid sub-styles. **Output info:** This compute calculates a global vector of length N where N is the -number of sub\_styles defined by the :doc:`bond\_style hybrid ` command, which can be accessed by indices 1-N. +number of sub\_styles defined by the :doc:`bond_style hybrid ` command, which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_bond_local.rst b/doc/src/compute_bond_local.rst index 23d052c734..9559dd0f35 100644 --- a/doc/src/compute_bond_local.rst +++ b/doc/src/compute_bond_local.rst @@ -143,7 +143,7 @@ output the statistics in various ways: The :doc:`dump local ` command will output the energy, distance, distance\^2 for every bond in the system. The -:doc:`thermo\_style ` command will print the average of +:doc:`thermo_style ` command will print the average of those quantities via the :doc:`compute reduce ` command with thermo output. And the :doc:`fix ave/histo ` command will histogram the distance\^2 values and write them to a file. @@ -155,10 +155,10 @@ command will histogram the distance\^2 values and write them to a file. The local data stored by this command is generated by looping over all the atoms owned on a processor and their bonds. A bond will only be included if both atoms in the bond are in the specified compute group. -Any bonds that have been broken (see the :doc:`bond\_style ` +Any bonds that have been broken (see the :doc:`bond_style ` command) by setting their bond type to 0 are not included. Bonds that have been turned off (see the :doc:`fix shake ` or -:doc:`delete\_bonds ` commands) by setting their bond type +:doc:`delete_bonds ` commands) by setting their bond type negative are written into the file, but their energy will be 0.0. Note that as atoms migrate from processor to processor, there will be diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst index 4cead81df8..a88d5fa61b 100644 --- a/doc/src/compute_chunk_atom.rst +++ b/doc/src/compute_chunk_atom.rst @@ -247,7 +247,7 @@ assigned to the atom. The *type* style uses the atom type as the chunk ID. *Nchunk* is set to the number of atom types defined for the simulation, e.g. via the -:doc:`create\_box ` or :doc:`read\_data ` commands. +:doc:`create_box ` or :doc:`read_data ` commands. ---------- diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst index df1614858c..cab2e60ecc 100644 --- a/doc/src/compute_cluster_atom.rst +++ b/doc/src/compute_cluster_atom.rst @@ -47,7 +47,7 @@ cluster. A fragment is similarly defined as a set of atoms, each of which has an explicit bond (i.e. defined via a :doc:`data file `, -the :doc:`create\_bonds ` command, or through fixes like +the :doc:`create_bonds ` command, or through fixes like :doc:`fix bond/create `, :doc:`fix bond/swap `, or :doc:`fix bond/break `). The cluster ID or fragment ID of every atom in the cluster will be set to the smallest atom ID of any atom @@ -76,9 +76,9 @@ multiple compute/dump commands, each of a *cluster/atom* or .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included when computing the clusters. This @@ -88,7 +88,7 @@ multiple compute/dump commands, each of a *cluster/atom* or zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to compute the clusters for snapshots in the dump file. The rerun script can use a - :doc:`special\_bonds ` command that includes all pairs in + :doc:`special_bonds ` command that includes all pairs in the neighbor list. **Output info:** diff --git a/doc/src/compute_com.rst b/doc/src/compute_com.rst index 8a9381e37e..ac20b3cb73 100644 --- a/doc/src/compute_com.rst +++ b/doc/src/compute_com.rst @@ -38,7 +38,7 @@ are the x,y,z coordinates of the center of mass. "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the - :doc:`read\_data ` command for a discussion of image flags and + :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_com_chunk.rst b/doc/src/compute_com_chunk.rst index d143f911f6..15cf528517 100644 --- a/doc/src/compute_com_chunk.rst +++ b/doc/src/compute_com_chunk.rst @@ -54,7 +54,7 @@ non-zero chunk IDs. center-of-mass in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of - the :doc:`read\_data ` command for a discussion of image flags + the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_contact_atom.rst b/doc/src/compute_contact_atom.rst index 0d8563d2ce..c6c58a5ea4 100644 --- a/doc/src/compute_contact_atom.rst +++ b/doc/src/compute_contact_atom.rst @@ -51,7 +51,7 @@ Restrictions This compute requires that atoms store a radius as defined by the -:doc:`atom\_style sphere ` command. +:doc:`atom_style sphere ` command. Related commands """""""""""""""" diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index 2e55d3a673..db87284cc2 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -101,16 +101,16 @@ too frequently. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included in the coordination count. One way to get around this, is to write a dump file, and use the :doc:`rerun ` command to compute the coordination for snapshots in the dump file. The rerun script can use a - :doc:`special\_bonds ` command that includes all pairs in + :doc:`special_bonds ` command that includes all pairs in the neighbor list. **Output info:** diff --git a/doc/src/compute_dihedral.rst b/doc/src/compute_dihedral.rst index 087b25c393..695031e05e 100644 --- a/doc/src/compute_dihedral.rst +++ b/doc/src/compute_dihedral.rst @@ -26,17 +26,17 @@ Description """"""""""" Define a computation that extracts the dihedral energy calculated by -each of the dihedral sub-styles used in the :doc:`dihedral\_style hybrid ` command. These values are made +each of the dihedral sub-styles used in the :doc:`dihedral_style hybrid ` command. These values are made accessible for output or further processing by other commands. The group specified for this command is ignored. -This compute is useful when using :doc:`dihedral\_style hybrid ` if you want to know the portion of the +This compute is useful when using :doc:`dihedral_style hybrid ` if you want to know the portion of the total energy contributed by one or more of the hybrid sub-styles. **Output info:** This compute calculates a global vector of length N where N is the -number of sub\_styles defined by the :doc:`dihedral\_style hybrid ` command. which can be accessed by indices +number of sub\_styles defined by the :doc:`dihedral_style hybrid ` command. which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst index 18c268a70f..ce7a9ede84 100644 --- a/doc/src/compute_dihedral_local.rst +++ b/doc/src/compute_dihedral_local.rst @@ -51,7 +51,7 @@ processors, equals the number of dihedral angles in the system, modified by the group parameter as explained below. The value *phi* is the dihedral angle, as defined in the diagram on -the :doc:`dihedral\_style ` doc page. +the :doc:`dihedral_style ` doc page. The value *v\_name* can be used together with the *set* keyword to compute a user-specified function of the dihedral angle phi. The @@ -88,7 +88,7 @@ the system and output the statistics in various ways: The :doc:`dump local ` command will output the angle, cosine(angle), cosine\^2(angle) for every dihedral in the system. The -:doc:`thermo\_style ` command will print the average of +:doc:`thermo_style ` command will print the average of those quantities via the :doc:`compute reduce ` command with thermo output. And the :doc:`fix ave/histo ` command will histogram the cosine(angle) values and write them to a diff --git a/doc/src/compute_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst index 5c80b62faa..8d70f1ef13 100644 --- a/doc/src/compute_dipole_chunk.rst +++ b/doc/src/compute_dipole_chunk.rst @@ -59,7 +59,7 @@ non-zero chunk IDs. dipole in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of - the :doc:`read\_data ` command for a discussion of image flags + the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst index 57e2037305..797e132480 100644 --- a/doc/src/compute_displace_atom.rst +++ b/doc/src/compute_displace_atom.rst @@ -51,7 +51,7 @@ the compute command was issued. The value of the displacement will be Initial coordinates are stored in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. - See the Atoms section of the :doc:`read\_data ` command for a + See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. @@ -100,7 +100,7 @@ something like the following commands: dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} & refresh c_dsp delay 100 -The :doc:`dump\_modify thresh ` command will only output +The :doc:`dump_modify thresh ` command will only output atoms that have displaced more than 0.6 Angstroms on each snapshot (assuming metal units). The dump\_modify *refresh* option triggers a call to this compute at the end of every dump. @@ -121,7 +121,7 @@ atoms is 0.0. If an initial dump snapshot is desired, containing the initial reference positions of all atoms, one way to do this is illustrated above. An initial write\_dump command can be used before the first run. It will contain the positions of all the atoms, -Options in the :doc:`dump\_modify ` command above will +Options in the :doc:`dump_modify ` command above will append new output to that same file and delay the output until a later timestep. The *delay* setting avoids a second time = 0 snapshot which would be empty. @@ -140,7 +140,7 @@ for an overview of LAMMPS output options. The per-atom array values will be in distance :doc:`units `. This compute supports the *refresh* option as explained above, for use -in conjunction with :doc:`dump\_modify refresh ` to generate +in conjunction with :doc:`dump_modify refresh ` to generate incremental dump files. Restrictions diff --git a/doc/src/compute_dpd.rst b/doc/src/compute_dpd.rst index f85c0259f8..39b07865c2 100644 --- a/doc/src/compute_dpd.rst +++ b/doc/src/compute_dpd.rst @@ -60,14 +60,14 @@ Restrictions This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This command also requires use of the :doc:`atom\_style dpd ` +This command also requires use of the :doc:`atom_style dpd ` command. Related commands """""""""""""""" :doc:`compute dpd/atom `, -:doc:`thermo\_style ` +:doc:`thermo_style ` **Default:** none diff --git a/doc/src/compute_dpd_atom.rst b/doc/src/compute_dpd_atom.rst index 2970141a19..a517f572be 100644 --- a/doc/src/compute_dpd_atom.rst +++ b/doc/src/compute_dpd_atom.rst @@ -50,7 +50,7 @@ Restrictions This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This command also requires use of the :doc:`atom\_style dpd ` +This command also requires use of the :doc:`atom_style dpd ` command. Related commands diff --git a/doc/src/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst index 03dd4e9af5..ce9a4e26b2 100644 --- a/doc/src/compute_edpd_temp_atom.rst +++ b/doc/src/compute_edpd_temp_atom.rst @@ -52,7 +52,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_style edpd ` +:doc:`pair_style edpd ` **Default:** none diff --git a/doc/src/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst index c50d21df99..be17f8bedc 100644 --- a/doc/src/compute_erotate_asphere.rst +++ b/doc/src/compute_erotate_asphere.rst @@ -28,7 +28,7 @@ Description Define a computation that calculates the rotational kinetic energy of a group of aspherical particles. The aspherical particles can be ellipsoids, or line segments, or triangles. See the -:doc:`atom\_style ` and :doc:`read\_data ` commands +:doc:`atom_style ` and :doc:`read_data ` commands for descriptions of these options. For all 3 types of particles, the rotational kinetic energy is @@ -58,14 +58,14 @@ Restrictions This compute requires that ellipsoidal particles atoms store a shape and quaternion orientation and angular momentum as defined by the -:doc:`atom\_style ellipsoid ` command. +:doc:`atom_style ellipsoid ` command. This compute requires that line segment particles atoms store a length -and orientation and angular velocity as defined by the :doc:`atom\_style line ` command. +and orientation and angular velocity as defined by the :doc:`atom_style line ` command. This compute requires that triangular particles atoms store a size and shape and quaternion orientation and angular momentum as defined by -the :doc:`atom\_style tri ` command. +the :doc:`atom_style tri ` command. All particles in the group must be finite-size. They cannot be point particles. diff --git a/doc/src/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst index fa1396681c..d1df476435 100644 --- a/doc/src/compute_erotate_sphere.rst +++ b/doc/src/compute_erotate_sphere.rst @@ -52,7 +52,7 @@ Restrictions This compute requires that atoms store a radius and angular velocity -(omega) as defined by the :doc:`atom\_style sphere ` command. +(omega) as defined by the :doc:`atom_style sphere ` command. All particles in the group must be finite-size spheres or point particles. They cannot be aspherical. Point particles will not diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index c54d0ee8fa..0f2fdc18c1 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -140,7 +140,7 @@ lengths or other internal coordinates :ref:`(Boresch, Karplus) ` The *pair* attribute enables various parameters of potentials defined -by the :doc:`pair\_style ` and :doc:`pair\_coeff ` +by the :doc:`pair_style ` and :doc:`pair_coeff ` commands to be changed, if the pair style supports it. The *pstyle* argument is the name of the pair style. For example, @@ -212,7 +212,7 @@ Note that it is easy to add new potentials and their parameters to this list. All it typically takes is adding an extract() method to the pair\_\*.cpp file associated with the potential. -Similar to the :doc:`pair\_coeff ` command, I and J can be +Similar to the :doc:`pair_coeff ` command, I and J can be specified in one of two ways. Explicit numeric values can be used for each, as in the 1st example above. I <= J is required. LAMMPS sets the coefficients for the symmetric J,I interaction to the same @@ -226,10 +226,10 @@ means all types from 1 to N. A leading asterisk means all types from (inclusive). Note that only type pairs with I <= J are considered; if asterisks imply type pairs where J < I, they are ignored. -If :doc:`pair\_style hybrid or hybrid/overlay ` is being +If :doc:`pair_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will be a sub-style name. You must specify I,J arguments that correspond to type pair values defined (via the -:doc:`pair\_coeff ` command) for that sub-style. +:doc:`pair_coeff ` command) for that sub-style. The *v\_name* argument for keyword *pair* is the name of an :doc:`equal-style variable ` which will be evaluated each time @@ -257,7 +257,7 @@ is the variable name. The *tail* keyword controls the calculation of the tail correction to "van der Waals" pair energies beyond the cutoff, if this has been -activated via the :doc:`pair\_modify ` command. If the +activated via the :doc:`pair_modify ` command. If the perturbation is small, the tail contribution to the energy difference between the reference and perturbed systems should be negligible. diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst index 7345bd1031..390f4f7c6a 100644 --- a/doc/src/compute_group_group.rst +++ b/doc/src/compute_group_group.rst @@ -55,7 +55,7 @@ interactions with atoms in the specified group2. The energies computed by the *pair* keyword do not include tail corrections, even if they are enabled via the - :doc:`pair\_modify ` command. + :doc:`pair_modify ` command. If the *molecule* keyword is set to *inter* or *intra* than an additional check is made based on the molecule IDs of the two atoms in @@ -65,7 +65,7 @@ molecules. For the *intra* setting, the two atoms must be in the same molecule. If the *kspace* keyword is set to *yes*\ , which is not the default, and -if a :doc:`kspace\_style ` is defined, then the interaction +if a :doc:`kspace_style ` is defined, then the interaction energy will include a Kspace component which is the long-range Coulombic energy between all the atoms in the first group and all the atoms in the 2nd group. Likewise, the interaction force calculated by @@ -107,9 +107,9 @@ frequently. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this compute uses a neighbor list, it also means those pairs will not be included in the group/group interaction. @@ -119,7 +119,7 @@ frequently. numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to compute the group/group interactions for snapshots in the dump file. - The rerun script can use a :doc:`special\_bonds ` command + The rerun script can use a :doc:`special_bonds ` command that includes all pairs in the neighbor list. If you desire a breakdown of the interactions into a pairwise and diff --git a/doc/src/compute_gyration.rst b/doc/src/compute_gyration.rst index 15636a9275..89d11799e0 100644 --- a/doc/src/compute_gyration.rst +++ b/doc/src/compute_gyration.rst @@ -51,7 +51,7 @@ and taking a sqrt() would be invalid. The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. - See the Atoms section of the :doc:`read\_data ` command for a + See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_gyration_chunk.rst b/doc/src/compute_gyration_chunk.rst index 4726a14d0e..7ed70e0968 100644 --- a/doc/src/compute_gyration_chunk.rst +++ b/doc/src/compute_gyration_chunk.rst @@ -78,7 +78,7 @@ ordered xx, yy, zz, xy, xz, yz. The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. - See the Atoms section of the :doc:`read\_data ` command for a + See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst index 5461825923..bfabd48132 100644 --- a/doc/src/compute_gyration_shape.rst +++ b/doc/src/compute_gyration_shape.rst @@ -57,7 +57,7 @@ is bounded between zero (if all points are spherically symmetric) and one The coordinates of an atom contribute to the gyration tensor in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" - coordinates. See the Atoms section of the :doc:`read\_data ` + coordinates. See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst index fa839aea35..5b88cbd4dc 100644 --- a/doc/src/compute_gyration_shape_chunk.rst +++ b/doc/src/compute_gyration_shape_chunk.rst @@ -58,7 +58,7 @@ The tensor keyword must be specified in the compute gyration/chunk command. The coordinates of an atom contribute to the gyration tensor in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" - coordinates. See the Atoms section of the :doc:`read\_data ` + coordinates. See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst index 3b7058d3d3..cb36d30da4 100644 --- a/doc/src/compute_heat_flux.rst +++ b/doc/src/compute_heat_flux.rst @@ -111,7 +111,7 @@ to the thermal conductivity :math:`\kappa`: The heat flux can be output every so many timesteps (e.g. via the -:doc:`thermo\_style custom ` command). Then as a +:doc:`thermo_style custom ` command). Then as a post-processing operation, an auto-correlation can be performed, its integral estimated, and the Green-Kubo formula above evaluated. diff --git a/doc/src/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst index 0807f2ff7f..16ecaf5b41 100644 --- a/doc/src/compute_hexorder_atom.rst +++ b/doc/src/compute_hexorder_atom.rst @@ -87,16 +87,16 @@ too frequently. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included in the order parameter. This difficulty can be circumvented by writing a dump file, and using the :doc:`rerun ` command to compute the order parameter for snapshots in the dump file. The rerun script can use a - :doc:`special\_bonds ` command that includes all pairs in + :doc:`special_bonds ` command that includes all pairs in the neighbor list. **Output info:** diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index d8e7a6b31a..61e598948e 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -58,8 +58,8 @@ restricted to simulations in the NVT ensemble. While this compute may be used with any potential in LAMMPS, it will provide inaccurate results for potentials that do not go to 0 at the truncation distance; :doc:`pair\_lj\_smooth\_linear ` and Ewald summation should -work fine, while :doc:`pair\_lj ` will perform poorly unless -the potential is shifted (via :doc:`pair\_modify ` shift) or the cutoff is large. Furthermore, computation of the heat capacity with +work fine, while :doc:`pair_lj ` will perform poorly unless +the potential is shifted (via :doc:`pair_modify ` shift) or the cutoff is large. Furthermore, computation of the heat capacity with this compute is restricted to those that implement the single\_hessian method in Pair. Implementing single\_hessian in additional pair styles is simple. Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at @@ -127,7 +127,7 @@ The *anharmonic* keyword will instruct the compute to return anharmonic properties rather than the full properties, which include lattice, harmonic and anharmonic contributions. When using this keyword, the compute must be first active (it must be included -via a :doc:`thermo\_style custom ` command) while the atoms are +via a :doc:`thermo_style custom ` command) while the atoms are still at their lattice sites (before equilibration). The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover (:doc:`fix nvt `) or @@ -156,7 +156,7 @@ The following example illustrates the placement of this command in the input scr .. note:: - The :doc:`fix\_modify energy yes ` command must also be specified if a fix is to contribute potential energy to this command. + The :doc:`fix_modify energy yes ` command must also be specified if a fix is to contribute potential energy to this command. An example input script that uses this compute is included in examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA diff --git a/doc/src/compute_improper.rst b/doc/src/compute_improper.rst index 27cd5f5902..aec2bfbbf5 100644 --- a/doc/src/compute_improper.rst +++ b/doc/src/compute_improper.rst @@ -26,17 +26,17 @@ Description """"""""""" Define a computation that extracts the improper energy calculated by -each of the improper sub-styles used in the :doc:`improper\_style hybrid ` command. These values are made +each of the improper sub-styles used in the :doc:`improper_style hybrid ` command. These values are made accessible for output or further processing by other commands. The group specified for this command is ignored. -This compute is useful when using :doc:`improper\_style hybrid ` if you want to know the portion of the +This compute is useful when using :doc:`improper_style hybrid ` if you want to know the portion of the total energy contributed by one or more of the hybrid sub-styles. **Output info:** This compute calculates a global vector of length N where N is the -number of sub\_styles defined by the :doc:`improper\_style hybrid ` command. which can be accessed by indices +number of sub\_styles defined by the :doc:`improper_style hybrid ` command. which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or vector values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_improper_local.rst b/doc/src/compute_improper_local.rst index 6daad705b5..fc651d324a 100644 --- a/doc/src/compute_improper_local.rst +++ b/doc/src/compute_improper_local.rst @@ -40,7 +40,7 @@ the group parameter as explained below. The value *chi* is the improper angle, as defined in the doc pages for the individual improper styles listed on -:doc:`improper\_style ` doc page. +:doc:`improper_style ` doc page. The local data stored by this command is generated by looping over all the atoms owned on a processor and their impropers. An improper will diff --git a/doc/src/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst index 029245d883..a60c98b3c3 100644 --- a/doc/src/compute_inertia_chunk.rst +++ b/doc/src/compute_inertia_chunk.rst @@ -55,7 +55,7 @@ non-zero chunk IDs. tensor in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the - :doc:`read\_data ` command for a discussion of image flags and + :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_ke.rst b/doc/src/compute_ke.rst index 8d7fd3e5f4..baccf848b5 100644 --- a/doc/src/compute_ke.rst +++ b/doc/src/compute_ke.rst @@ -34,7 +34,7 @@ and v are the mass and velocity of the particle. There is a subtle difference between the quantity calculated by this compute and the kinetic energy calculated by the *ke* or *etotal* keyword used in thermodynamic output, as specified by the -:doc:`thermo\_style ` command. For this compute, kinetic +:doc:`thermo_style ` command. For this compute, kinetic energy is "translational" kinetic energy, calculated by the simple formula above. For thermodynamic output, the *ke* keyword infers kinetic energy from the temperature of the system with 1/2 Kb T of diff --git a/doc/src/compute_ke_atom_eff.rst b/doc/src/compute_ke_atom_eff.rst index db08516b61..bbe7aa1013 100644 --- a/doc/src/compute_ke_atom_eff.rst +++ b/doc/src/compute_ke_atom_eff.rst @@ -39,7 +39,7 @@ electron, and s to its radial velocity, respectively. There is a subtle difference between the quantity calculated by this compute and the kinetic energy calculated by the *ke* or *etotal* keyword used in thermodynamic output, as specified by the -:doc:`thermo\_style ` command. For this compute, kinetic +:doc:`thermo_style ` command. For this compute, kinetic energy is "translational" plus electronic "radial" kinetic energy, calculated by the simple formula above. For thermodynamic output, the *ke* keyword infers kinetic energy from the temperature of the system @@ -49,7 +49,7 @@ eFF. .. note:: The temperature in eFF should be monitored via the :doc:`compute temp/eff ` command, which can be printed with - thermodynamic output by using the :doc:`thermo\_modify ` + thermodynamic output by using the :doc:`thermo_modify ` command, as shown in the following example: diff --git a/doc/src/compute_ke_eff.rst b/doc/src/compute_ke_eff.rst index c635b9fecc..981e238bbe 100644 --- a/doc/src/compute_ke_eff.rst +++ b/doc/src/compute_ke_eff.rst @@ -38,7 +38,7 @@ radial velocity of the electron, respectively. There is a subtle difference between the quantity calculated by this compute and the kinetic energy calculated by the *ke* or *etotal* keyword used in thermodynamic output, as specified by the -:doc:`thermo\_style ` command. For this compute, kinetic +:doc:`thermo_style ` command. For this compute, kinetic energy is "translational" and "radial" (only for electrons) kinetic energy, calculated by the simple formula above. For thermodynamic output, the *ke* keyword infers kinetic energy from the temperature of @@ -51,7 +51,7 @@ degrees of freedom. IMPRORTANT NOTE: The temperature in eFF models should be monitored via the :doc:`compute temp/eff ` command, which can be printed with thermodynamic output by using the -:doc:`thermo\_modify ` command, as shown in the following +:doc:`thermo_modify ` command, as shown in the following example: diff --git a/doc/src/compute_msd.rst b/doc/src/compute_msd.rst index 4d47d58cd0..4b472566e7 100644 --- a/doc/src/compute_msd.rst +++ b/doc/src/compute_msd.rst @@ -80,7 +80,7 @@ solids undergoing thermal motion. Initial coordinates are stored in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. - See the Atoms section of the :doc:`read\_data ` command for a + See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst index 18d1ae4440..f8a2ee1dc1 100644 --- a/doc/src/compute_msd_chunk.rst +++ b/doc/src/compute_msd_chunk.rst @@ -84,7 +84,7 @@ compute command was first invoked. "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the - :doc:`read\_data ` command for a discussion of image flags and + :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_omega_chunk.rst b/doc/src/compute_omega_chunk.rst index bd0b8f91de..dd8a3be806 100644 --- a/doc/src/compute_omega_chunk.rst +++ b/doc/src/compute_omega_chunk.rst @@ -56,7 +56,7 @@ non-zero chunk IDs. velocity in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the - :doc:`read\_data ` command for a discussion of image flags and + :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index b7a1442a62..70b96a9fc5 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -115,16 +115,16 @@ too frequently. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included in the order parameter. This difficulty can be circumvented by writing a dump file, and using the :doc:`rerun ` command to compute the order parameter for snapshots in the dump file. The rerun script can use a - :doc:`special\_bonds ` command that includes all pairs in + :doc:`special_bonds ` command that includes all pairs in the neighbor list. **Output info:** diff --git a/doc/src/compute_pair.rst b/doc/src/compute_pair.rst index 924ddc7cca..03da8acddb 100644 --- a/doc/src/compute_pair.rst +++ b/doc/src/compute_pair.rst @@ -41,7 +41,7 @@ by other commands. The group specified for this command is **ignored**\ . The specified *pstyle* must be a pair style used in your simulation -either by itself or as a sub-style in a :doc:`pair\_style hybrid or hybrid/overlay ` command. If the sub-style is +either by itself or as a sub-style in a :doc:`pair_style hybrid or hybrid/overlay ` command. If the sub-style is used more than once, an additional number *nsub* has to be specified in order to choose which instance of the sub-style will be used by the compute. Not specifying the number in this case will cause the @@ -55,7 +55,7 @@ be tallied in *ecoul*\ . Everything else (whether it is a Lennard-Jones style van der Waals interaction or not) is tallied in *evdwl*\ . If *evalue* is blank or specified as *epair*\ , then *epair* is stored as a global scalar by this compute. This is useful when using -:doc:`pair\_style hybrid ` if you want to know the portion +:doc:`pair_style hybrid ` if you want to know the portion of the total energy contributed by one sub-style. If *evalue* is specified as *evdwl* or *ecoul*\ , then just that portion of the energy is stored as a global scalar. @@ -64,10 +64,10 @@ is stored as a global scalar. The energy returned by the *evdwl* keyword does not include tail corrections, even if they are enabled via the - :doc:`pair\_modify ` command. + :doc:`pair_modify ` command. Some pair styles tally additional quantities, e.g. a breakdown of -potential energy into 14 components is tallied by the :doc:`pair\_style reax/c ` command. These values (1 or more) +potential energy into 14 components is tallied by the :doc:`pair_style reax/c ` command. These values (1 or more) are stored as a global vector by this compute. See the doc page for :doc:`individual pair styles ` for info on these values. diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst index 4e61852f2c..39abd67f6c 100644 --- a/doc/src/compute_pair_local.rst +++ b/doc/src/compute_pair_local.rst @@ -56,7 +56,7 @@ pairwise neighbor list. Info about an individual pairwise interaction will only be included if both atoms in the pair are in the specified compute group, and if the current pairwise distance is less than the force cutoff distance for that interaction, as defined by the -:doc:`pair\_style ` and :doc:`pair\_coeff ` +:doc:`pair_style ` and :doc:`pair_coeff ` commands. The value *dist* is the distance between the pair of atoms. @@ -100,7 +100,7 @@ will be in whatever units the pair style defines. The optional *cutoff* keyword determines how the force cutoff distance for an interaction is determined. For the default setting of *type*\ , -the pairwise cutoff defined by the :doc:`pair\_style ` +the pairwise cutoff defined by the :doc:`pair_style ` command for the types of the two atoms is used. For the *radius* setting, the sum of the radii of the two particles is used as a cutoff. For example, this is appropriate for granular particles which @@ -135,9 +135,9 @@ Here is an example of how to do this: specifically, this will be true of I,J pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are included. The weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set - by the :doc:`special\_bonds ` command. An exception is if + by the :doc:`special_bonds ` command. An exception is if long-range Coulombics are being computed via the - :doc:`kspace\_style ` command, then atom pairs with + :doc:`kspace_style ` command, then atom pairs with weighting factors of zero are still included in the neighbor list, so that a portion of the long-range interaction contribution can be computed in the pair style. Hence in that case, those atom pairs will diff --git a/doc/src/compute_pe.rst b/doc/src/compute_pe.rst index 88f6b5f7f6..d3d23e590c 100644 --- a/doc/src/compute_pe.rst +++ b/doc/src/compute_pe.rst @@ -42,7 +42,7 @@ keywords were listed. If any extra keywords are listed, then only those components are summed to compute the potential energy. The Kspace contribution requires 1 extra FFT each timestep the energy -is calculated, if using the PPPM solver via the :doc:`kspace\_style pppm ` command. Thus it can increase the cost of the +is calculated, if using the PPPM solver via the :doc:`kspace_style pppm ` command. Thus it can increase the cost of the PPPM calculation if it is needed on a large fraction of the simulation timesteps. @@ -53,7 +53,7 @@ potential energy. .. note:: - The :doc:`fix\_modify energy yes ` command must also be + The :doc:`fix_modify energy yes ` command must also be specified if a fix is to contribute potential energy to this command. A compute of this style with the ID of "thermo\_pe" is created when diff --git a/doc/src/compute_pe_atom.rst b/doc/src/compute_pe_atom.rst index bedc508d71..bd4dcd2d57 100644 --- a/doc/src/compute_pe_atom.rst +++ b/doc/src/compute_pe_atom.rst @@ -48,13 +48,13 @@ atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that energy is assigned in equal portions to each atom in the set. E.g. 1/4 of the dihedral energy to each of the 4 atoms. -The :doc:`dihedral\_style charmm ` style calculates +The :doc:`dihedral_style charmm ` style calculates pairwise interactions between 1-4 atoms. The energy contribution of these terms is included in the pair energy, not the dihedral energy. The KSpace contribution is calculated using the method in :ref:`(Heyes) ` for the Ewald method and a related method for PPPM, -as specified by the :doc:`kspace\_style pppm ` command. +as specified by the :doc:`kspace_style pppm ` command. For PPPM, the calculation requires 1 extra FFT each timestep that per-atom energy is calculated. This `document `_ describes how the long-range per-atom energy calculation is performed. @@ -66,7 +66,7 @@ per-atom potential energy. .. note:: - The :doc:`fix\_modify energy yes ` command must also be + The :doc:`fix_modify energy yes ` command must also be specified if a fix is to contribute per-atom potential energy to this command. @@ -84,7 +84,7 @@ in the last 2 columns of thermo output: .. note:: The per-atom energy does not include any Lennard-Jones tail - corrections to the energy added by the :doc:`pair\_modify tail yes ` command, since those are contributions to the + corrections to the energy added by the :doc:`pair_modify tail yes ` command, since those are contributions to the global system energy. **Output info:** diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index d708b88ab0..3ee7f86fbd 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -156,7 +156,7 @@ Related commands """""""""""""""" :doc:`compute temp `, :doc:`compute stress/atom `, -:doc:`thermo\_style `, +:doc:`thermo_style `, **Default:** none diff --git a/doc/src/compute_pressure_cylinder.rst b/doc/src/compute_pressure_cylinder.rst index d2ffb275ca..8d5cbb7b25 100644 --- a/doc/src/compute_pressure_cylinder.rst +++ b/doc/src/compute_pressure_cylinder.rst @@ -76,7 +76,7 @@ Related commands """""""""""""""" :doc:`compute temp `, :doc:`compute stress/atom `, -:doc:`thermo\_style `, +:doc:`thermo_style `, **Default:** none diff --git a/doc/src/compute_pressure_uef.rst b/doc/src/compute_pressure_uef.rst index f5a3d47945..59f7608f44 100644 --- a/doc/src/compute_pressure_uef.rst +++ b/doc/src/compute_pressure_uef.rst @@ -38,7 +38,7 @@ value of the pressure. A :doc:`compute pressure ` may be used for that purpose. The keywords and output information are documented in -:doc:`compute\_pressure `. +:doc:`compute_pressure `. Restrictions """""""""""" diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index d388b4fc09..ff4388f989 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -82,13 +82,13 @@ atom pairs in the neighbor list are considered (out to the neighbor cutoff = force cutoff + :doc:`neighbor skin `). For *patom1* and *patom2*\ , the distance between the atoms must be less than the force cutoff distance for that pair to be included, as defined by the -:doc:`pair\_style ` and :doc:`pair\_coeff ` +:doc:`pair_style ` and :doc:`pair_coeff ` commands. The optional *cutoff* keyword determines how the force cutoff distance for an interaction is determined for the *patom1* and *patom2* attributes. For the default setting of *type*\ , the pairwise cutoff -defined by the :doc:`pair\_style ` command for the types of +defined by the :doc:`pair_style ` command for the types of the two atoms is used. For the *radius* setting, the sum of the radii of the two particles is used as a cutoff. For example, this is appropriate for granular particles which only interact when they are @@ -106,7 +106,7 @@ specified compute group. Likewise for angles, dihedrals, etc. For bonds and angles, a bonds/angles that have been broken by setting their bond/angle type to 0 will not be included. Bonds/angles that have been turned off (see the :doc:`fix shake ` or -:doc:`delete\_bonds ` commands) by setting their bond/angle +:doc:`delete_bonds ` commands) by setting their bond/angle type negative are written into the file. This is consistent with the :doc:`compute bond/local ` and :doc:`compute angle/local ` commands @@ -120,7 +120,7 @@ atom indices from this command and output by the :doc:`dump local ` comman The *natom1* and *natom2*\ , or *patom1* and *patom2* attributes refer to the atom IDs of the 2 atoms in each pairwise interaction computed -by the :doc:`pair\_style ` command. The *ntype1* and +by the :doc:`pair_style ` command. The *ntype1* and *ntype2*\ , or *ptype1* and *ptype2* attributes refer to the atom types of the 2 atoms in each pairwise interaction. @@ -133,13 +133,13 @@ of the 2 atoms in each pairwise interaction. specifically, this may be true of I,J pairs with a weighting factor of 0.0; pairs with a non-zero weighting factor are included. The weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set - by the :doc:`special\_bonds ` command. + by the :doc:`special_bonds ` command. The *batom1* and *batom2* attributes refer to the atom IDs of the 2 atoms in each :doc:`bond `. The *btype* attribute refers to the type of the bond, from 1 to Nbtypes = # of bond types. The number of bond types is defined in the data file read by the -:doc:`read\_data ` command. +:doc:`read_data ` command. The attributes that start with "a", "d", "i", refer to similar values for :doc:`angles `, :doc:`dihedrals `, and diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index 19ab21475a..a11e1a1c97 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -45,7 +45,7 @@ Define a computation that calculates the radial distribution function (RDF), also called g(r), and the coordination number for a group of particles. Both are calculated in histogram form by binning pairwise distances into *Nbin* bins from 0.0 to the maximum force cutoff -defined by the :doc:`pair\_style ` command or the cutoff +defined by the :doc:`pair_style ` command or the cutoff distance *Rcut* specified via the *cutoff* keyword. The bins are of uniform size in radial distance. Thus a single bin encompasses a thin shell of distances in 3d and a thin ring of distances in 2d. @@ -53,9 +53,9 @@ shell of distances in 3d and a thin ring of distances in 2d. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses a neighbor list, it also means those pairs will not be included in the RDF. This does not apply when @@ -65,11 +65,11 @@ shell of distances in 3d and a thin ring of distances in 2d. zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the :doc:`rerun ` command to compute the RDF for snapshots in the dump file. The rerun script can use a - :doc:`special\_bonds ` command that includes all pairs in + :doc:`special_bonds ` command that includes all pairs in the neighbor list. By default the RDF is computed out to the maximum force cutoff defined -by the :doc:`pair\_style ` command. If the *cutoff* keyword +by the :doc:`pair_style ` command. If the *cutoff* keyword is used, then the RDF is computed accurately out to the *Rcut* > 0.0 distance specified. @@ -87,7 +87,7 @@ distance specified. timestep, whichever is less frequent), which is inefficient. LAMMPS will warn you if this is the case. If you specify a *Rcut* > force cutoff, you must insure ghost atom information out to *Rcut* + *skin* - is communicated, via the :doc:`comm\_modify cutoff ` + is communicated, via the :doc:`comm_modify cutoff ` command, else the RDF computation cannot be performed, and LAMMPS will give an error message. The *skin* value is what is specified with the :doc:`neighbor ` command. In this case, you are forcing a @@ -120,7 +120,7 @@ by *itypeN* are the central atom, and atoms of any of the range of types represented by *jtypeN* are the distribution atom. Pairwise distances are generated by looping over a pairwise neighbor -list, just as they would be in a :doc:`pair\_style ` +list, just as they would be in a :doc:`pair_style ` computation. The distance between two atoms I and J is included in a specific histogram if the following criteria are met: @@ -205,12 +205,12 @@ change from zero to one at the location of the spike in g(r). parallel efficiency and scaling. For systems, where only the type of atoms changes (e.g. when using :doc:`fix atom/swap `), you need to explicitly request the dynamic normalization updates - via :doc:`compute\_modify dynamic yes ` + via :doc:`compute_modify dynamic yes ` Related commands """""""""""""""" -:doc:`fix ave/time `, :doc:`compute\_modify `, +:doc:`fix ave/time `, :doc:`compute_modify `, :doc:`compute adf ` Default diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index ff67fa9651..283c5da95d 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -203,7 +203,7 @@ inputs specified. As discussed below, for the *sum* and *sumsq* modes, the value(s) produced by this compute are all "extensive", meaning their value scales linearly with the number of atoms involved. If normalized -values are desired, this compute can be accessed by the :doc:`thermo\_style custom ` command with :doc:`thermo\_modify norm yes ` set as an option. Or it can be accessed by a +values are desired, this compute can be accessed by the :doc:`thermo_style custom ` command with :doc:`thermo_modify norm yes ` set as an option. Or it can be accessed by a :doc:`variable ` that divides by the appropriate atom count. diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 8556b3971b..2bcd983237 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -222,15 +222,15 @@ ordered in which they are listed. .. note:: If you have a bonded system, then the settings of - :doc:`special\_bonds ` command can remove pairwise + :doc:`special_bonds ` command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This - is the default setting for the :doc:`special\_bonds ` + is the default setting for the :doc:`special_bonds ` command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included in the calculation. One way to get around this, is to write a dump file, and use the :doc:`rerun ` command to compute the bispectrum components for snapshots in the dump - file. The rerun script can use a :doc:`special\_bonds ` + file. The rerun script can use a :doc:`special_bonds ` command that includes all pairs in the neighbor list. ;line @@ -320,7 +320,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_style snap ` +:doc:`pair_style snap ` Default """"""" diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index c37a8cc52d..45d6027871 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -152,14 +152,14 @@ i.e. computed values for contributions from bonds and two-body pair styles, such as :doc:`Lennard-Jones `, will be the same, while contributions from angles, dihedrals and impropers will be different. -The :doc:`dihedral\_style charmm ` style calculates +The :doc:`dihedral_style charmm ` style calculates pairwise interactions between 1-4 atoms. The virial contribution of these terms is included in the pair virial, not the dihedral virial. The KSpace contribution is calculated using the method in :ref:`(Heyes) ` for the Ewald method and by the methodology described in :ref:`(Sirk) ` for PPPM. The choice of KSpace solver is specified -by the :doc:`kspace\_style pppm ` command. Note that for +by the :doc:`kspace_style pppm ` command. Note that for PPPM, the calculation requires 6 extra FFTs each timestep that per-atom stress is calculated. Thus it can significantly increase the cost of the PPPM calculation if it is needed on a large fraction of @@ -210,7 +210,7 @@ result. I.e. the last 2 columns of thermo output will be the same: .. note:: The per-atom stress does not include any Lennard-Jones tail - corrections to the pressure added by the :doc:`pair\_modify tail yes ` command, since those are contributions to the + corrections to the pressure added by the :doc:`pair_modify tail yes ` command, since those are contributions to the global system pressure. **Output info:** diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index aadc78050c..892924575d 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -67,7 +67,7 @@ configurational stress (conf), and/or total stress (total). NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID. NOTE 2: The local stress does not include any Lennard-Jones tail -corrections to the pressure added by the :doc:`pair\_modify tail yes ` command, since those are contributions to the global system pressure. +corrections to the pressure added by the :doc:`pair_modify tail yes ` command, since those are contributions to the global system pressure. **Output info:** diff --git a/doc/src/compute_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst index ed7af54d2a..b6e5497f2d 100644 --- a/doc/src/compute_tdpd_cc_atom.rst +++ b/doc/src/compute_tdpd_cc_atom.rst @@ -54,7 +54,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_style tdpd ` +:doc:`pair_style tdpd ` **Default:** none diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index 052da705ac..b9b00c7469 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -31,7 +31,7 @@ Description Define a computation that calculates the temperature of a group of atoms. A compute of this style can be used by any command that -computes a temperature, e.g. :doc:`thermo\_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. +computes a temperature, e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. The temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2), @@ -47,14 +47,14 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. A compute of this style with the ID of "thermo\_temp" is created when LAMMPS starts up, as if this command were in the input script: diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index 46743c780e..499065ca5c 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -59,7 +59,7 @@ rotational). use a combination of interaction potentials and fixes that induce no torque or otherwise constrain some of all of your particles so that this is not the case. Then there are less dof and you should use the - :doc:`compute\_modify extra ` command to adjust the dof + :doc:`compute_modify extra ` command to adjust the dof accordingly. For example, an aspherical particle with all three of its shape @@ -94,14 +94,14 @@ vector are ordered xx, yy, zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. This compute subtracts out translational degrees-of-freedom due to fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the -:doc:`compute\_modify ` command. +:doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform @@ -153,7 +153,7 @@ This compute is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute requires that atoms store angular momentum and a -quaternion as defined by the :doc:`atom\_style ellipsoid ` +quaternion as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst index e17227fe3e..3464a584b1 100644 --- a/doc/src/compute_temp_body.rst +++ b/doc/src/compute_temp_body.rst @@ -57,7 +57,7 @@ rotational). rotational dof. It is possible to use a combination of interaction potentials and fixes that induce no torque or otherwise constrain some of all of your particles so that this is not the case. Then there are - less dof and you should use the :doc:`compute\_modify extra ` command to adjust the dof accordingly. + less dof and you should use the :doc:`compute_modify extra ` command to adjust the dof accordingly. The translational kinetic energy is computed the same as is described by the :doc:`compute temp ` command. The rotational @@ -74,14 +74,14 @@ vector are ordered xx, yy, zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. This compute subtracts out translational degrees-of-freedom due to fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the -:doc:`compute\_modify ` command. +:doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform @@ -133,7 +133,7 @@ This compute is part of the BODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This compute requires that atoms store angular momentum and a -quaternion as defined by the :doc:`atom\_style body ` +quaternion as defined by the :doc:`atom_style body ` command. Related commands diff --git a/doc/src/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst index cc9e70a0c5..37b6a05264 100644 --- a/doc/src/compute_temp_chunk.rst +++ b/doc/src/compute_temp_chunk.rst @@ -89,7 +89,7 @@ Note that the number of atoms contributing to the temperature is calculated each time the temperature is evaluated since it is assumed the atoms may be dynamically assigned to chunks. Thus there is no need to use the *dynamic* option of the -:doc:`compute\_modify ` command for this compute style. +:doc:`compute_modify ` command for this compute style. If any optional values are specified, then per-chunk quantities are also calculated and stored in a global array, as described below. diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index 083e9f652c..d81ede2e43 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -31,7 +31,7 @@ atoms, after subtracting out the center-of-mass velocity of the group. This is useful if the group is expected to have a non-zero net velocity for some reason. A compute of this style can be used by any command that computes a temperature, -e.g. :doc:`thermo\_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. After the center-of-mass velocity has been subtracted from each atom, the temperature is calculated by the formula KE = dim/2 N k T, where @@ -48,7 +48,7 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. The removal of the center-of-mass velocity by this fix is essentially computing the temperature after a "bias" has been removed from the @@ -63,7 +63,7 @@ constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index 7d5843e1db..e735a79b6f 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -38,7 +38,7 @@ enables correct temperature calculation and thermostatting of core/shell pairs where it is desirable for the internal degrees of freedom of the core/shell pairs to not be influenced by a thermostat. A compute of this style can be used by any command that computes a -temperature via :doc:`fix\_modify ` e.g. :doc:`fix temp/rescale `, :doc:`fix npt `, etc. +temperature via :doc:`fix_modify ` e.g. :doc:`fix temp/rescale `, :doc:`fix npt `, etc. Note that this compute does not require all ions to be polarized, hence defined as core/shell pairs. One can mix core/shell pairs and diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index 88dbc62422..779ce2de71 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -33,7 +33,7 @@ induced by use of the :doc:`fix deform ` command. A compute of this style is created by the :doc:`fix nvt/sllod ` command to compute the thermal temperature of atoms for thermostatting purposes. A compute of this style can also be used by any command -that computes a temperature, e.g. :doc:`thermo\_modify `, +that computes a temperature, e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. The deformation fix changes the box size and/or shape over time, so @@ -74,7 +74,7 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. The removal of the box deformation velocity component by this fix is essentially computing the temperature after a "bias" has been removed @@ -104,7 +104,7 @@ constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst index 98b28aa76a..fab6275f0a 100644 --- a/doc/src/compute_temp_deform_eff.rst +++ b/doc/src/compute_temp_deform_eff.rst @@ -34,7 +34,7 @@ induced by use of the :doc:`fix deform ` command. A compute of this style is created by the :doc:`fix nvt/sllod/eff ` command to compute the thermal temperature of atoms for thermostatting purposes. A compute of this style can also be used by any command that computes a temperature, -e.g. :doc:`thermo\_modify `, :doc:`fix npt/eff `, +e.g. :doc:`thermo_modify `, :doc:`fix npt/eff `, etc. The calculation performed by this compute is exactly like that diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index fbebf02ea9..fc45a5ba2b 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -77,7 +77,7 @@ assumed to be constant for the duration of the run unless the Related commands """""""""""""""" -:doc:`fix drude `, :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`pair\_style thole `, :doc:`compute temp ` +:doc:`fix drude `, :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`pair_style thole `, :doc:`compute temp ` **Default:** none diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst index b83a9cbec9..e15832a25b 100644 --- a/doc/src/compute_temp_eff.rst +++ b/doc/src/compute_temp_eff.rst @@ -29,14 +29,14 @@ Description Define a computation that calculates the temperature of a group of nuclei and electrons in the :doc:`electron force field ` model. A compute of this style can be used by commands that compute a -temperature, e.g. :doc:`thermo\_modify `, :doc:`fix npt/eff `, etc. +temperature, e.g. :doc:`thermo_modify `, :doc:`fix npt/eff `, etc. The temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2 for nuclei and sum of 1/2 (m v\^2 + 3/4 m s\^2) for electrons, where s includes the radial electron velocity contributions), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms (only total -number of nuclei in the eFF (see the :doc:`pair\_eff ` +number of nuclei in the eFF (see the :doc:`pair_eff ` command) in the group, k = Boltzmann constant, and T = temperature. This expression is summed over all nuclear and electronic degrees of freedom, essentially by setting the kinetic contribution to the heat @@ -50,7 +50,7 @@ densities two to five times the density of liquid H2 ranges from For eFF models, in order to override the default temperature reported by LAMMPS in the thermodynamic quantities reported via the :doc:`thermo ` command, the user should apply a - :doc:`thermo\_modify ` command, as shown in the following + :doc:`thermo_modify ` command, as shown in the following example: @@ -68,14 +68,14 @@ again, the radial electronic velocities are also considered. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. This compute subtracts out degrees-of-freedom due to fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst index 51e92dc4c4..ce493802d6 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -29,7 +29,7 @@ Description Define a computation that calculates the temperature of a group of atoms, after excluding one or more velocity components. A compute of this style can be used by any command that computes a temperature, -e.g. :doc:`thermo\_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. The temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2), @@ -48,7 +48,7 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. The removal of velocity components by this fix is essentially computing the temperature after a "bias" has been removed from the @@ -63,7 +63,7 @@ constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index 67dcf3fd49..d7bbc74aea 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -55,7 +55,7 @@ velocity field, before computing the kinetic energy. This can be useful for thermostatting a collection of atoms undergoing a complex flow, e.g. via a profile-unbiased thermostat (PUT) as described in :ref:`(Evans) `. A compute of this style can be used by any command -that computes a temperature, e.g. :doc:`thermo\_modify `, +that computes a temperature, e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. The *xflag*\ , *yflag*\ , *zflag* settings determine which components of @@ -107,7 +107,7 @@ bin. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. The removal of the spatially-averaged velocity field by this fix is essentially computing the temperature after a "bias" has been removed @@ -122,7 +122,7 @@ constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. .. note:: diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index a4fc86d541..b2161c53d7 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -40,7 +40,7 @@ Define a computation that calculates the temperature of a group of atoms, after subtracting out an ramped velocity profile before computing the kinetic energy. A compute of this style can be used by any command that computes a temperature, -e.g. :doc:`thermo\_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. The meaning of the arguments for this command which define the velocity ramp are the same as for the :doc:`velocity ramp ` @@ -70,7 +70,7 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. The removal of the ramped velocity component by this fix is essentially computing the temperature after a "bias" has been removed @@ -85,7 +85,7 @@ constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index 284b38d3b1..38432a18ca 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -31,7 +31,7 @@ atoms in a geometric region. This can be useful for thermostatting one portion of the simulation box. E.g. a McDLT simulation where one side is cooled, and the other side is heated. A compute of this style can be used by any command that computes a temperature, -e.g. :doc:`thermo\_modify `, :doc:`fix temp/rescale `, etc. +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, etc. Note that a *region*\ -style temperature can be used to thermostat with :doc:`fix temp/rescale ` or :doc:`fix langevin `, but should probably not be used with @@ -54,7 +54,7 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is calculated each time the temperature is evaluated since it is assumed atoms can enter/leave the region. Thus there is no need to use the *dynamic* -option of the :doc:`compute\_modify ` command for this +option of the :doc:`compute_modify ` command for this compute style. The removal of atoms outside the region by this fix is essentially @@ -77,7 +77,7 @@ motion, such as :doc:`fix shake ` and :doc:`fix rigid `. the region boundary, and hence the concept is somewhat ill-defined. If needed the number of subtracted degrees-of-freedom can be set explicitly using the *extra* option of the -:doc:`compute\_modify ` command. +:doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index b09752a4e2..37d690848e 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -30,7 +30,7 @@ Define a computation that calculates the temperature of a group of nuclei and electrons in the :doc:`electron force field ` model, within a geometric region using the electron force field. A compute of this style can be used by commands that compute a -temperature, e.g. :doc:`thermo\_modify `. +temperature, e.g. :doc:`thermo_modify `. The operation of this compute is exactly like that described by the :doc:`compute temp/region ` command, except that diff --git a/doc/src/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst index 75912482d8..47a94b3923 100644 --- a/doc/src/compute_temp_rotate.rst +++ b/doc/src/compute_temp_rotate.rst @@ -30,7 +30,7 @@ atoms, after subtracting out the center-of-mass velocity and angular velocity of This is useful if the group is expected to have a non-zero net velocity and/or global rotation motion for some reason. A compute of this style can be used by any command that computes a temperature, -e.g. :doc:`thermo\_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. After the center-of-mass velocity and angular velocity has been subtracted from each atom, the temperature is calculated by the formula KE = dim/2 N k T, where @@ -47,7 +47,7 @@ zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. The removal of the center-of-mass velocity and angular velocity by this fix is essentially computing the temperature after a "bias" has been removed from the @@ -62,7 +62,7 @@ constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the -*extra* option of the :doc:`compute\_modify ` command. +*extra* option of the :doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst index 6008874ce4..285a232d56 100644 --- a/doc/src/compute_temp_sphere.rst +++ b/doc/src/compute_temp_sphere.rst @@ -59,7 +59,7 @@ each has 3 degrees of freedom (2 translational, 1 rotational). combination of interaction potentials and fixes that induce no torque or otherwise constrain some of all of your particles so that this is not the case. Then there are less dof and you should use the - :doc:`compute\_modify extra ` command to adjust the dof + :doc:`compute_modify extra ` command to adjust the dof accordingly. The translational kinetic energy is computed the same as is described @@ -81,14 +81,14 @@ the vector are ordered xx, yy, zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the *dynamic* option of the -:doc:`compute\_modify ` command if this is not the case. +:doc:`compute_modify ` command if this is not the case. This compute subtracts out translational degrees-of-freedom due to fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the temperature of groups of atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the *extra* option of the -:doc:`compute\_modify ` command. +:doc:`compute_modify ` command. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform @@ -137,7 +137,7 @@ Restrictions This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the :doc:`atom\_style sphere ` +and a radius as defined by the :doc:`atom_style sphere ` command. All particles in the group must be finite-size spheres, or point diff --git a/doc/src/compute_ti.rst b/doc/src/compute_ti.rst index e21e6caf6d..6c0b04e3bb 100644 --- a/doc/src/compute_ti.rst +++ b/doc/src/compute_ti.rst @@ -54,7 +54,7 @@ described in :ref:`Eike `. Typically this compute will be used in conjunction with the :doc:`fix adapt ` command which can perform alchemical transformations by adjusting the strength of an interaction potential as a simulation runs, as defined by one or more -:doc:`pair\_style ` or :doc:`kspace\_style ` +:doc:`pair_style ` or :doc:`kspace_style ` commands. This scaling is done via a prefactor on the energy, forces, virial calculated by the pair or K-Space style. The prefactor is often a function of a *lambda* parameter which may be adjusted from 0 @@ -100,7 +100,7 @@ lambda. Note that the *name1* variable is also typically given as an argument to the :doc:`fix adapt ` command. An alchemical simulation may use several pair potentials together, -invoked via the :doc:`pair\_style hybrid or hybrid/overlay ` +invoked via the :doc:`pair_style hybrid or hybrid/overlay ` command. The total dUs/dlambda for the overall system is calculated as the sum of each contributing term as listed by the keywords in the compute ti command. Individual pair potentials can be listed, which diff --git a/doc/src/compute_torque_chunk.rst b/doc/src/compute_torque_chunk.rst index d673aee13e..b9b5fd82bf 100644 --- a/doc/src/compute_torque_chunk.rst +++ b/doc/src/compute_torque_chunk.rst @@ -55,7 +55,7 @@ non-zero chunk IDs. "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the - :doc:`read\_data ` command for a discussion of image flags and + :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index 7474fe1a25..2f25339c21 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -178,8 +178,8 @@ Voro++ software in the src/VORONOI/README file. systems, but may lead to underestimation of Voronoi volumes in low density systems. By default, the set of ghost atoms stored by each processor is determined by the cutoff used for - :doc:`pair\_style ` interactions. The cutoff can be set - explicitly via the :doc:`comm\_modify cutoff ` command. The + :doc:`pair_style ` interactions. The cutoff can be set + explicitly via the :doc:`comm_modify cutoff ` command. The Voronoi cells for atoms adjacent to empty regions will extend into those regions up to the communication cutoff in x, y, or z. In that situation, an exterior face is created at the cutoff distance normal @@ -198,7 +198,7 @@ Voro++ software in the src/VORONOI/README file. Voronoi cell can be obtained by dividing its volume by the z extent of the simulation box. Note that you define the z extent of the simulation box for 2d simulations when using the - :doc:`create\_box ` or :doc:`read\_data ` commands. + :doc:`create_box ` or :doc:`read_data ` commands. **Output info:** diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 595095e213..ea49d99ab1 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -75,9 +75,9 @@ Description This command creates atoms (or molecules) on a lattice, or a single atom (or molecule), or a random collection of atoms (or molecules), as an alternative to reading in their coordinates explicitly via a -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` command. A simulation box must already exist, which is typically -created via the :doc:`create\_box ` command. Before using +created via the :doc:`create_box ` command. Before using this command, a lattice must also be defined using the :doc:`lattice ` command, unless you specify the *single* style with units = box or the *random* style. For the remainder of this doc @@ -145,13 +145,13 @@ used multiple times, to add multiple sets of particles to the simulation. For example, grain boundaries can be created, by interleaving create\_atoms with :doc:`lattice ` commands specifying different orientations. By using the create\_atoms command -in conjunction with the :doc:`delete\_atoms ` command, +in conjunction with the :doc:`delete_atoms ` command, reasonably complex geometries can be created, or a protein can be solvated with a surrounding box of water molecules. In all these cases, care should be taken to insure that new atoms do not overlap existing atoms inappropriately, especially if molecules -are being added. The :doc:`delete\_atoms ` command can be +are being added. The :doc:`delete_atoms ` command can be used to remove overlapping atoms or molecules. .. note:: @@ -160,10 +160,10 @@ used to remove overlapping atoms or molecules. that are outside the simulation box; they will just be ignored by LAMMPS. This is true even if you are using shrink-wrapped box boundaries, as specified by the :doc:`boundary ` command. - However, you can first use the :doc:`change\_box ` command to + However, you can first use the :doc:`change_box ` command to temporarily expand the box, then add atoms via create\_atoms, then finally use change\_box command again if needed to re-shrink-wrap the - new atoms. See the :doc:`change\_box ` doc page for an + new atoms. See the :doc:`change_box ` doc page for an example of how to do this, using the create\_atoms *single* style to insert a new atom outside the current simulation box. @@ -200,12 +200,12 @@ not overlap, regardless of their relative orientations. .. note:: - If the :doc:`create\_box ` command is used to create + If the :doc:`create_box ` command is used to create the simulation box, followed by the create\_atoms command with its *mol* option for adding molecules, then you typically need to use the - optional keywords allowed by the :doc:`create\_box ` command + optional keywords allowed by the :doc:`create_box ` command for extra bonds (angles,etc) or extra special neighbors. This is - because by default, the :doc:`create\_box ` command sets up a + because by default, the :doc:`create_box ` command sets up a non-molecular system which doesn't allow molecules to be added. @@ -264,7 +264,7 @@ create a sinusoidal surface. Note that the surface is "rough" due to individual lattice points being "above" or "below" the mathematical expression for the sinusoidal curve. If a finer lattice were used, the sinusoid would appear to be "smoother". Also note the use of the -"xlat" and "ylat" :doc:`thermo\_style ` keywords which +"xlat" and "ylat" :doc:`thermo_style ` keywords which converts lattice spacings to distance. Click on the image for a larger version. @@ -366,7 +366,7 @@ Restrictions """""""""""" -An :doc:`atom\_style ` must be previously defined to use this +An :doc:`atom_style ` must be previously defined to use this command. A rotation vector specified for a single molecule must be in @@ -375,8 +375,8 @@ the z-direction for a 2d model. Related commands """""""""""""""" -:doc:`lattice `, :doc:`region `, :doc:`create\_box `, -:doc:`read\_data `, :doc:`read\_restart ` +:doc:`lattice `, :doc:`region `, :doc:`create_box `, +:doc:`read_data `, :doc:`read_restart ` Default """"""" diff --git a/doc/src/create_bonds.rst b/doc/src/create_bonds.rst index 185c1ebfd7..9b9c814c9a 100644 --- a/doc/src/create_bonds.rst +++ b/doc/src/create_bonds.rst @@ -66,15 +66,15 @@ or 4 specified atoms. The new bond (angle, dihedral, improper) interactions will then be computed during a simulation by the bond (angle, dihedral, improper) potential defined by -the :doc:`bond\_style `, :doc:`bond\_coeff `, -:doc:`angle\_style `, :doc:`angle\_coeff `, -:doc:`dihedral\_style `, -:doc:`dihedral\_coeff `, :doc:`improper\_style `, -:doc:`improper\_coeff ` commands. +the :doc:`bond_style `, :doc:`bond_coeff `, +:doc:`angle_style `, :doc:`angle_coeff `, +:doc:`dihedral_style `, +:doc:`dihedral_coeff `, :doc:`improper_style `, +:doc:`improper_coeff ` commands. The *many* style is useful for adding bonds to a system, e.g. between nearest neighbors in a lattice of atoms, without having to enumerate -all the bonds in the data file read by the :doc:`read\_data ` +all the bonds in the data file read by the :doc:`read_data ` command. The *single* styles are useful for adding bonds, angles, dihedrals, impropers @@ -97,10 +97,10 @@ data file for a complex system of molecules. bonds per atom are set to large enough values. And similarly for angles, dihedrals and impropers. Otherwise an error may occur when too many bonds (angles, dihedrals, impropers) are added to an atom. If the - :doc:`read\_data ` command is used to define the system, these + :doc:`read_data ` command is used to define the system, these parameters can be set via the "bond types" and "extra bond per atom" fields in the header section of the data file. If the - :doc:`create\_box ` command is used to define the system, + :doc:`create_box ` command is used to define the system, these 2 parameters can be set via its optional "bond/types" and "extra/bond/per/atom" arguments. And similarly for angles, dihedrals and impropers. See the doc pages for these 2 commands for details. @@ -122,9 +122,9 @@ The following settings must have been made in an input script before this style is used: * special\_bonds weight for 1-2 interactions must be 0.0 -* a :doc:`pair\_style ` must be defined -* no :doc:`kspace\_style ` defined -* minimum :doc:`pair\_style ` cutoff + :doc:`neighbor ` skin >= *rmax* +* a :doc:`pair_style ` must be defined +* no :doc:`kspace_style ` defined +* minimum :doc:`pair_style ` cutoff + :doc:`neighbor ` skin >= *rmax* These settings are required so that a neighbor list can be created to search for nearby atoms. Pairs of atoms that are already bonded @@ -134,8 +134,8 @@ a distance that encompasses the *rmax* for new bonds to create. An additional requirement for this style is that your system must be ready to perform a simulation. This means, for example, that all -:doc:`pair\_style ` coefficients be set via the -:doc:`pair\_coeff ` command. A :doc:`bond\_style ` +:doc:`pair_style ` coefficients be set via the +:doc:`pair_coeff ` command. A :doc:`bond_style ` command and all bond coefficients must also be set, even if no bonds exist before this command is invoked. This is because the building of neighbor list requires initialization and setup of a simulation, @@ -143,7 +143,7 @@ similar to what a :doc:`run ` command would require. Note that you can change any of these settings after this command executes, e.g. if you wish to use long-range Coulombic interactions -via the :doc:`kspace\_style ` command for your subsequent +via the :doc:`kspace_style ` command for your subsequent simulation. @@ -157,7 +157,7 @@ between 1 and the number of bond types defined. The *single/angle* style creates a single angle of type *atype* between three atoms with IDs *aatom1*\ , *aatom2*\ , and *aatom3*\ . The ordering of the atoms is the same as in the *Angles* section of a data -file read by the :doc:`read\_data ` command. I.e. the 3 atoms are +file read by the :doc:`read_data ` command. I.e. the 3 atoms are ordered linearly within the angle; the central atom is *aatom2*\ . *Atype* must be a value between 1 and the number of angle types defined. @@ -165,14 +165,14 @@ defined. The *single/dihedral* style creates a single dihedral of type *dtype* between four atoms with IDs *datom1*\ , *datom2*\ , *datom3*\ , and *datom4*\ . The ordering of the atoms is the same as in the *Dihedrals* section of a data file -read by the :doc:`read\_data ` command. I.e. the 4 atoms are ordered +read by the :doc:`read_data ` command. I.e. the 4 atoms are ordered linearly within the dihedral. *dtype* must be a value between 1 and the number of dihedral types defined. The *single/improper* style creates a single improper of type *itype* between four atoms with IDs *iatom1*\ , *iatom2*\ , *iatom3*\ , and *iatom4*\ . The ordering of the atoms is the same as in the *Impropers* section of a data file -read by the :doc:`read\_data ` command. I.e. the 4 atoms are ordered +read by the :doc:`read_data ` command. I.e. the 4 atoms are ordered linearly within the improper. *itype* must be a value between 1 and the number of improper types defined. @@ -190,7 +190,7 @@ with the *many* style. This is an expensive operation since the bond topology for the system must be walked to find all 1-2, 1-3, 1-4 interactions to store in an internal list, which is used when pairwise interactions are weighted; -see the :doc:`special\_bonds ` command for details. +see the :doc:`special_bonds ` command for details. Thus if you are adding a few bonds or a large list of angles all at the same time, by using this command repeatedly, it is more efficient @@ -221,12 +221,12 @@ Restrictions This command cannot be used with molecular systems defined using molecule template files via the :doc:`molecule ` and -:doc:`atom\_style template ` commands. +:doc:`atom_style template ` commands. Related commands """""""""""""""" -:doc:`create\_atoms `, :doc:`delete\_bonds ` +:doc:`create_atoms `, :doc:`delete_bonds ` Default """"""" diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index 1bffab90b5..4e19def87d 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -108,7 +108,7 @@ using the :doc:`change box ` command with its *ortho* and not make the lo/hi box dimensions (as defined in your :doc:`region ` command) radically smaller/larger than the extent of the atoms you eventually plan to create, e.g. via the - :doc:`create\_atoms ` command. For example, if your atoms + :doc:`create_atoms ` command. For example, if your atoms extend from 0 to 50, you should not specify the box bounds as -10000 and 10000. This is because as described above, LAMMPS uses the specified box size to layout the 3d grid of processors. A huge @@ -128,13 +128,13 @@ bond (angle, dihedral, improper) interactions, or for molecules with special 1-2,1-3,1-4 neighbors to be added later. These optional keywords serve the same purpose as the analogous keywords that can be used in a data file which are recognized by the -:doc:`read\_data ` command when it sets up a system. +:doc:`read_data ` command when it sets up a system. Note that if these keywords are not used, then the create\_box command creates an atomic (non-molecular) simulation that does not allow bonds between pairs of atoms to be defined, or a :doc:`bond potential ` to be specified, or for molecules with special neighbors to be added to the system by commands such as -:doc:`create\_atoms mol `, :doc:`fix deposit ` +:doc:`create_atoms mol `, :doc:`fix deposit ` or :doc:`fix pour `. As an example, see the examples/deposit/in.deposit.molecule script, @@ -153,13 +153,13 @@ Restrictions """""""""""" -An :doc:`atom\_style ` and :doc:`region ` must have +An :doc:`atom_style ` and :doc:`region ` must have been previously defined to use this command. Related commands """""""""""""""" -:doc:`read\_data `, :doc:`create\_atoms `, +:doc:`read_data `, :doc:`create_atoms `, :doc:`region ` **Default:** none diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index f2db9aeb3a..ca684b4a11 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -90,24 +90,24 @@ different numbers of processors. If the *compress* keyword is set to *yes*\ , then after atoms are deleted, then atom IDs are re-assigned so that they run from 1 to the number of atoms in the system. Note that this is not done for -molecular systems (see the :doc:`atom\_style ` command), +molecular systems (see the :doc:`atom_style ` command), regardless of the *compress* setting, since it would foul up the bond connectivity that has already been assigned. However, the -:doc:`reset\_ids ` command can be used after this command to +:doc:`reset_ids ` command can be used after this command to accomplish the same thing. Note that the re-assignment of IDs is not really a compression, where gaps in atom IDs are removed by decrementing atom IDs that are larger. Instead the IDs for all atoms are erased, and new IDs are assigned so that the atoms owned by individual processors have consecutive IDs, as -the :doc:`create\_atoms ` command explains. +the :doc:`create_atoms ` command explains. A molecular system with fixed bonds, angles, dihedrals, or improper interactions, is one where the topology of the interactions is typically defined in the data file read by the -:doc:`read\_data ` command, and where the interactions -themselves are defined with the :doc:`bond\_style `, -:doc:`angle\_style `, etc commands. If you delete atoms +:doc:`read_data ` command, and where the interactions +themselves are defined with the :doc:`bond_style `, +:doc:`angle_style `, etc commands. If you delete atoms from such a system, you must be careful not to end up with bonded interactions that are stored by remaining atoms but which include deleted atoms. This will cause LAMMPS to generate a "missing atoms" @@ -149,7 +149,7 @@ find overlapping atom pairs, it also means that you must define a between any pair of atoms types (plus the :doc:`neighbor ` skin) >= the specified overlap cutoff. -If the :doc:`special\_bonds ` command is used with a +If the :doc:`special_bonds ` command is used with a setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not appear in the neighbor list, and thus will not be considered for deletion by the *overlap* styles. You probably don't want to be @@ -157,12 +157,12 @@ deleting one atom in a bonded pair anyway. The *bond yes* option cannot be used with molecular systems defined using molecule template files via the :doc:`molecule ` and -:doc:`atom\_style template ` commands. +:doc:`atom_style template ` commands. Related commands """""""""""""""" -:doc:`create\_atoms `, :doc:`reset\_ids ` +:doc:`create_atoms `, :doc:`reset_ids ` Default """"""" diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index f964d059a6..7a12376eee 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -48,7 +48,7 @@ dihedrals, impropers. This command is useful for deleting interactions that have been previously turned off by bond-breaking potentials. It is also useful for turning off topology interactions between frozen or rigid atoms. Pairwise interactions can be turned -off via the :doc:`neigh\_modify exclude ` command. The +off via the :doc:`neigh_modify exclude ` command. The :doc:`fix shake ` command also effectively turns off certain bond and angle interactions. @@ -83,7 +83,7 @@ must also be of the specified type. Styles *angle*\ , *dihedral*\ , and For style *bond*\ , you can set the type to 0 to delete bonds that have been previously broken by a bond-breaking potential (which sets the -bond type to 0 when a bond is broken); e.g. see the :doc:`bond\_style quartic ` command. +bond type to 0 when a bond is broken); e.g. see the :doc:`bond_style quartic ` command. For style *stats* no interactions are turned off (or on); the status of all interactions in the specified group is simply reported. This @@ -96,7 +96,7 @@ permanently remove the interaction. E.g. a bond\_type of 2 is set to -2. The neighbor list creation routines will not include such an interaction in their interaction lists. The default is also to not alter the list of 1-2, 1-3, 1-4 neighbors computed by the -:doc:`special\_bonds ` command and used to weight pairwise +:doc:`special_bonds ` command and used to weight pairwise force and energy calculations. This means that pairwise computations will proceed as if the bond (or angle, etc) were still turned on. @@ -144,7 +144,7 @@ shared by multiple processors. This means that your system must be ready to perform a simulation before using this command (force fields setup, atom masses set, etc). Just as would be needed to run dynamics, the force field you define should define a cutoff -(e.g. through a :doc:`pair\_style ` command) which is long +(e.g. through a :doc:`pair_style ` command) which is long enough for a processor to acquire the ghost atoms its needs to compute bond, angle, etc interactions. @@ -157,8 +157,8 @@ which case you probably should be recomputing the weighting list. Related commands """""""""""""""" -:doc:`neigh\_modify ` exclude, -:doc:`special\_bonds `, :doc:`fix shake ` +:doc:`neigh_modify ` exclude, +:doc:`special_bonds `, :doc:`fix shake ` **Default:** none diff --git a/doc/src/dielectric.rst b/doc/src/dielectric.rst index 96fc861d97..44a8f4176c 100644 --- a/doc/src/dielectric.rst +++ b/doc/src/dielectric.rst @@ -29,7 +29,7 @@ long-range) to this value. The constant is unitless, since it is used to reduce the strength of the interactions. The value is used in the denominator of the formulas for Coulombic interactions - e.g. a value of 4.0 reduces the Coulombic interactions to 25% of their default -strength. See the :doc:`pair\_style ` command for more +strength. See the :doc:`pair_style ` command for more details. Restrictions @@ -39,7 +39,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_style ` +:doc:`pair_style ` Default """"""" diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst index 52e636dd75..46da2f9458 100644 --- a/doc/src/dihedral_charmm.rst +++ b/doc/src/dihedral_charmm.rst @@ -56,15 +56,15 @@ field. The newer *charmmfsw* style was released in March 2017. We recommend it be used instead of the older *charmm* style when running a simulation with the CHARMM force field, either with long-range - Coulombics or a Coulombic cutoff, via the :doc:`pair\_style lj/charmmfsw/coul/long ` and :doc:`pair\_style lj/charmmfsw/coul/charmmfsh ` commands respectively. + Coulombics or a Coulombic cutoff, via the :doc:`pair_style lj/charmmfsw/coul/long ` and :doc:`pair_style lj/charmmfsw/coul/charmmfsh ` commands respectively. Otherwise the older *charmm* style is fine to use. See the discussion - below and more details on the :doc:`pair\_style charmm ` doc + below and more details on the :doc:`pair_style charmm ` doc page. The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * K (energy) * n (integer >= 0) @@ -78,8 +78,8 @@ With the CHARMM dihedral style, interactions between the 1st and 4th atoms in a dihedral are skipped during the normal non-bonded force computation and instead evaluated as part of the dihedral using special epsilon and sigma values specified with the -:doc:`pair\_coeff ` command of pair styles that contain -"lj/charmm" (e.g. :doc:`pair\_style lj/charmm/coul/long `) +:doc:`pair_coeff ` command of pair styles that contain +"lj/charmm" (e.g. :doc:`pair_style lj/charmm/coul/long `) In 6-membered rings, the same 1-4 interaction would be computed twice (once for the clockwise 1-4 pair in dihedral 1-2-3-4 and once in the counterclockwise dihedral 1-6-5-4) and thus the weighting factor has @@ -107,9 +107,9 @@ distance between the two atoms is within the switching region of the pairwise potential defined by the corresponding CHARMM pair style, i.e. within the outer cutoff specified for the pair style. The *charmmfsw* style should only be used when using the corresponding -:doc:`pair\_style lj/charmmfsw/coul/charmmfsw ` or -:doc:`pair\_style lj/charmmfsw/coul/long ` commands. Use -the *charmm* style with the older :doc:`pair\_style ` +:doc:`pair_style lj/charmmfsw/coul/charmmfsw ` or +:doc:`pair_style lj/charmmfsw/coul/long ` commands. Use +the *charmm* style with the older :doc:`pair_style ` commands that have just "charmm" in their style name. See the discussion on the :doc:`CHARMM pair\_style ` doc page for details. @@ -158,7 +158,7 @@ When using run\_style :doc:`respa `, these dihedral styles must be assigned to the same r-RESPA level as *pair* or *outer*\ . When used in combination with CHARMM pair styles, the 1-4 -:doc:`special\_bonds ` scaling factors must be set to 0.0. +:doc:`special_bonds ` scaling factors must be set to 0.0. Otherwise non-bonded contributions for these 1-4 pairs will be computed multiple times. @@ -169,7 +169,7 @@ for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_class2.rst b/doc/src/dihedral_class2.rst index f8f6a01bc4..fd26167f65 100644 --- a/doc/src/dihedral_class2.rst +++ b/doc/src/dihedral_class2.rst @@ -50,9 +50,9 @@ See :ref:`(Sun) ` for a description of the COMPASS class2 force fi Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, +:doc:`dihedral_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands. These are the 6 coefficients for the Ed formula: @@ -65,7 +65,7 @@ These are the 6 coefficients for the Ed formula: * phi3 (degrees) For the Embt formula, each line in a -:doc:`dihedral\_coeff ` command in the input script lists +:doc:`dihedral_coeff ` command in the input script lists 5 coefficients, the first of which is "mbt" to indicate they are MiddleBondTorsion coefficients. In a data file, these coefficients should be listed under a "MiddleBondTorsion Coeffs" heading and you @@ -79,7 +79,7 @@ dihedral type. * r2 (distance) For the Eebt formula, each line in a -:doc:`dihedral\_coeff ` command in the input script lists +:doc:`dihedral_coeff ` command in the input script lists 9 coefficients, the first of which is "ebt" to indicate they are EndBondTorsion coefficients. In a data file, these coefficients should be listed under a "EndBondTorsion Coeffs" heading and you must @@ -97,7 +97,7 @@ type. * r3 (distance) For the Eat formula, each line in a -:doc:`dihedral\_coeff ` command in the input script lists +:doc:`dihedral_coeff ` command in the input script lists 9 coefficients, the first of which is "at" to indicate they are AngleTorsion coefficients. In a data file, these coefficients should be listed under a "AngleTorsion Coeffs" heading and you must leave out @@ -118,7 +118,7 @@ to radians internally; hence the units of D and E are in energy/radian. For the Eaat formula, each line in a -:doc:`dihedral\_coeff ` command in the input script lists +:doc:`dihedral_coeff ` command in the input script lists 4 coefficients, the first of which is "aat" to indicate they are AngleAngleTorsion coefficients. In a data file, these coefficients should be listed under a "AngleAngleTorsion Coeffs" heading and you @@ -134,7 +134,7 @@ Theta1 and theta2 are specified in degrees, but LAMMPS converts them to radians internally; hence the units of M are in energy/radian\^2. For the Ebb13 formula, each line in a -:doc:`dihedral\_coeff ` command in the input script lists +:doc:`dihedral_coeff ` command in the input script lists 4 coefficients, the first of which is "bb13" to indicate they are BondBond13 coefficients. In a data file, these coefficients should be listed under a "BondBond13 Coeffs" heading and you must leave out the @@ -182,7 +182,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_coeff.rst b/doc/src/dihedral_coeff.rst index a2cddfa6e9..4a3f0cd487 100644 --- a/doc/src/dihedral_coeff.rst +++ b/doc/src/dihedral_coeff.rst @@ -30,7 +30,7 @@ Description Specify the dihedral force field coefficients for one or more dihedral types. The number and meaning of the coefficients depends on the dihedral style. Dihedral coefficients can also be set in the data file read by the -:doc:`read\_data ` command or in a restart file. +:doc:`read_data ` command or in a restart file. N can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be @@ -63,7 +63,7 @@ corresponds to the 1st example above would be listed as 1 80.0 1 3 -The :doc:`dihedral\_style class2 ` is an exception to +The :doc:`dihedral_style class2 ` is an exception to this rule, in that an additional argument is used in the input script to allow specification of the cross-term coefficients. See its doc page for details. @@ -84,7 +84,7 @@ page for details. The list of all dihedral styles defined in LAMMPS is given on the -:doc:`dihedral\_style ` doc page. They are also listed +:doc:`dihedral_style ` doc page. They are also listed in more compact form on the :ref:`Commands dihedral ` doc page. On either of those pages, click on the style to display the formula it @@ -100,8 +100,8 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. A dihedral style must be defined before any dihedral coefficients are set, either in the input script or in a data file. @@ -109,7 +109,7 @@ set, either in the input script or in a data file. Related commands """""""""""""""" -:doc:`dihedral\_style ` +:doc:`dihedral_style ` **Default:** none diff --git a/doc/src/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst index 7a2f2bf2db..2a9aadc99e 100644 --- a/doc/src/dihedral_cosine_shift_exp.rst +++ b/doc/src/dihedral_cosine_shift_exp.rst @@ -45,9 +45,9 @@ behaved in the limit a->0, where it has been implemented to linear order in a for a < 0.001. The following coefficients must be defined for each dihedral type via -the :doc:`dihedral\_coeff ` command as in the example +the :doc:`dihedral_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * umin (energy) @@ -91,7 +91,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff `, +:doc:`dihedral_coeff `, :doc:`angle\_cosine\_shift\_exp ` **Default:** none diff --git a/doc/src/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst index 83f2349cd5..0156cdce26 100644 --- a/doc/src/dihedral_fourier.rst +++ b/doc/src/dihedral_fourier.rst @@ -35,9 +35,9 @@ The *fourier* dihedral style uses the potential: :align: center The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * m (integer >=1) * K1 (energy) @@ -85,7 +85,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_harmonic.rst b/doc/src/dihedral_harmonic.rst index bdcfbf38ae..8f711f0f63 100644 --- a/doc/src/dihedral_harmonic.rst +++ b/doc/src/dihedral_harmonic.rst @@ -38,9 +38,9 @@ The *harmonic* dihedral style uses the potential :align: center The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * K (energy) * d (+1 or -1) @@ -97,7 +97,7 @@ for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst index d348bf03de..19086e1aeb 100644 --- a/doc/src/dihedral_helix.rst +++ b/doc/src/dihedral_helix.rst @@ -40,9 +40,9 @@ so as to balance secondary (largely driven by local interactions) and tertiary structure (driven by long-range interactions). The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * A (energy) * B (energy) @@ -85,7 +85,7 @@ for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_hybrid.rst b/doc/src/dihedral_hybrid.rst index c878cbb9ca..f67b1185fe 100644 --- a/doc/src/dihedral_hybrid.rst +++ b/doc/src/dihedral_hybrid.rst @@ -32,7 +32,7 @@ example, dihedrals in a polymer flow (of dihedral type 1) could be computed with a *harmonic* potential and dihedrals in the wall boundary (of dihedral type 2) could be computed with a *helix* potential. The assignment of dihedral type to style is made via the -:doc:`dihedral\_coeff ` command or in the data file. +:doc:`dihedral_coeff ` command or in the data file. In the dihedral\_coeff commands, the name of a dihedral style must be added after the dihedral type, with the remaining coefficients being @@ -43,7 +43,7 @@ K, d, n. All other dihedral types (2-N) are computed with a *helix* potential with coefficients 10, 10, 10 for A, B, C. If dihedral coefficients are specified in the data file read via the -:doc:`read\_data ` command, then the same rule applies. +:doc:`read_data ` command, then the same rule applies. E.g. "harmonic" or "helix", must be added after the dihedral type, for each line in the "Dihedral Coeffs" section, e.g. @@ -101,7 +101,7 @@ restart file, you need to re-specify dihedral\_coeff commands. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_multi_harmonic.rst b/doc/src/dihedral_multi_harmonic.rst index bd66014bd7..e304685a68 100644 --- a/doc/src/dihedral_multi_harmonic.rst +++ b/doc/src/dihedral_multi_harmonic.rst @@ -32,9 +32,9 @@ The *multi/harmonic* dihedral style uses the potential :align: center The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * A1 (energy) * A2 (energy) @@ -79,7 +79,7 @@ for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst index 51ddd6a109..ceb87e4651 100644 --- a/doc/src/dihedral_nharmonic.rst +++ b/doc/src/dihedral_nharmonic.rst @@ -32,9 +32,9 @@ The *nharmonic* dihedral style uses the potential: :align: center The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * n (integer >=1) * A1 (energy) @@ -79,7 +79,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_none.rst b/doc/src/dihedral_none.rst index ebae5c32d6..8955323bb5 100644 --- a/doc/src/dihedral_none.rst +++ b/doc/src/dihedral_none.rst @@ -24,9 +24,9 @@ Description Using a dihedral style of none means dihedral forces and energies are not computed, even if quadruplets of dihedral atoms were listed in the -data file read by the :doc:`read\_data ` command. +data file read by the :doc:`read_data ` command. -See the :doc:`dihedral\_style zero ` command for a way to +See the :doc:`dihedral_style zero ` command for a way to calculate dihedral statistics, but compute no dihedral interactions. Restrictions @@ -36,7 +36,7 @@ Restrictions Related commands """""""""""""""" -:doc:`dihedral\_style zero ` +:doc:`dihedral_style zero ` **Default:** none diff --git a/doc/src/dihedral_opls.rst b/doc/src/dihedral_opls.rst index 4cd21423a2..5edbcd870b 100644 --- a/doc/src/dihedral_opls.rst +++ b/doc/src/dihedral_opls.rst @@ -45,9 +45,9 @@ This dihedral potential is used in the OPLS force field and is described in :ref:`(Watkins) `. The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * K1 (energy) * K2 (energy) @@ -91,7 +91,7 @@ for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst index d145d596ba..9634e729e9 100644 --- a/doc/src/dihedral_quadratic.rst +++ b/doc/src/dihedral_quadratic.rst @@ -35,9 +35,9 @@ This dihedral potential can be used to keep a dihedral in a predefined value (cis=zero, right-hand convention is used). The following coefficients must be defined for each dihedral type via -the :doc:`dihedral\_coeff ` command as in the example +the :doc:`dihedral_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy/radian\^2) @@ -80,7 +80,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_spherical.rst b/doc/src/dihedral_spherical.rst index 4c59e7297f..ef5a3801e2 100644 --- a/doc/src/dihedral_spherical.rst +++ b/doc/src/dihedral_spherical.rst @@ -52,9 +52,9 @@ The coefficient 69.3 is the harmonic spring constant for phi after division by sin(74.4)\*sin(48.1) (the minima positions for theta1 and theta2). The following coefficients must be defined for each dihedral type via the -:doc:`dihedral\_coeff ` command as in the example above, or in +:doc:`dihedral_coeff ` command as in the example above, or in the Dihedral Coeffs section of a data file read by the -:doc:`read\_data ` command: +:doc:`read_data ` command: * n (integer >= 1) * C1 (energy) @@ -94,7 +94,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_style.rst b/doc/src/dihedral_style.rst index 553cfbde7c..81d1ddabdd 100644 --- a/doc/src/dihedral_style.rst +++ b/doc/src/dihedral_style.rst @@ -29,21 +29,21 @@ Description Set the formula(s) LAMMPS uses to compute dihedral interactions between quadruplets of atoms, which remain in force for the duration of the simulation. The list of dihedral quadruplets is read in by a -:doc:`read\_data ` or :doc:`read\_restart ` command +:doc:`read_data ` or :doc:`read_restart ` command from a data or restart file. Hybrid models where dihedrals are computed using different dihedral potentials can be setup using the *hybrid* dihedral style. The coefficients associated with a dihedral style can be specified in -a data or restart file or via the :doc:`dihedral\_coeff ` +a data or restart file or via the :doc:`dihedral_coeff ` command. All dihedral potentials store their coefficient data in binary restart files which means dihedral\_style and -:doc:`dihedral\_coeff ` commands do not need to be +:doc:`dihedral_coeff ` commands do not need to be re-specified in an input script that restarts a simulation. See the -:doc:`read\_restart ` command for details on how to do +:doc:`read_restart ` command for details on how to do this. The one exception is that dihedral\_style *hybrid* only stores the list of sub-styles in the restart file; dihedral coefficients need to be re-specified. @@ -51,7 +51,7 @@ to be re-specified. .. note:: When both a dihedral and pair style is defined, the - :doc:`special\_bonds ` command often needs to be used to + :doc:`special_bonds ` command often needs to be used to turn off (or weight) the pairwise interaction that would otherwise exist between 4 bonded atoms. @@ -79,7 +79,7 @@ coefficients you specify. bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed dihedral equation applies to each individual dihedral. Thus you need to define *K* appropriately via the - :doc:`dihedral\_coeff ` command to account for this + :doc:`dihedral_coeff ` command to account for this difference if necessary. @@ -88,11 +88,11 @@ coefficients you specify. Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients -specified by the associated :doc:`dihedral\_coeff ` command. +specified by the associated :doc:`dihedral_coeff ` command. Click on the style to display the formula it computes, any additional arguments specified in the dihedral\_style command, and coefficients -specified by the associated :doc:`dihedral\_coeff ` +specified by the associated :doc:`dihedral_coeff ` command. There are also additional accelerated pair styles included in the @@ -137,7 +137,7 @@ individual dihedral potentials tell if it is part of a package. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` Default """"""" diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index 03c05f7893..fb3e620adc 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -34,7 +34,7 @@ Description The *table* dihedral style creates interpolation tables of length *Ntable* from dihedral potential and derivative values listed in a file(s) as a function of the dihedral angle "phi". The files are read -by the :doc:`dihedral\_coeff ` command. +by the :doc:`dihedral_coeff ` command. The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and derivative values at each of @@ -54,7 +54,7 @@ coefficients are chosen from this list, and a cubic polynomial is used to compute the energy and the derivative at this angle. The following coefficients must be defined for each dihedral type via -the :doc:`dihedral\_coeff ` command as in the example +the :doc:`dihedral_coeff ` command as in the example above. * filename @@ -102,7 +102,7 @@ A section begins with a non-blank line whose 1st character is not a between sections. The first line begins with a keyword which identifies the section. The line can contain additional text, but the initial text must match the argument specified in the -:doc:`dihedral\_coeff ` command. The next line lists (in +:doc:`dihedral_coeff ` command. The next line lists (in any order) one or more parameters for the table. Each parameter is a keyword followed by one or more numeric values. @@ -131,7 +131,7 @@ strange numerical behavior can occur in the large remaining gap. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the N -specified in the :doc:`dihedral\_style table ` command. +specified in the :doc:`dihedral_style table ` command. Let *Ntable* is the number of table entries requested dihedral\_style command, and let *Nfile* be the parameter following "N" in the tabulated file ("30" in the sparse example above). What LAMMPS does @@ -223,7 +223,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff ` +:doc:`dihedral_coeff ` **Default:** none diff --git a/doc/src/dihedral_table_cut.rst b/doc/src/dihedral_table_cut.rst index 78b9346e61..809a858f00 100644 --- a/doc/src/dihedral_table_cut.rst +++ b/doc/src/dihedral_table_cut.rst @@ -33,7 +33,7 @@ The *table/cut* dihedral style creates interpolation tables of length file(s) as a function of the dihedral angle "phi". In addition, an analytic cutoff that is quadratic in the bond-angle (theta) is applied in order to regularize the dihedral interaction. The dihedral table -files are read by the :doc:`dihedral\_coeff ` command. +files are read by the :doc:`dihedral_coeff ` command. The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and derivative values at each of @@ -53,7 +53,7 @@ coefficients are chosen from this list, and a cubic polynomial is used to compute the energy and the derivative at this angle. The following coefficients must be defined for each dihedral type via -the :doc:`dihedral\_coeff ` command as in the example +the :doc:`dihedral_coeff ` command as in the example above. * style (aat) @@ -121,7 +121,7 @@ A section begins with a non-blank line whose 1st character is not a between sections. The first line begins with a keyword which identifies the section. The line can contain additional text, but the initial text must match the argument specified in the -:doc:`dihedral\_coeff ` command. The next line lists (in +:doc:`dihedral_coeff ` command. The next line lists (in any order) one or more parameters for the table. Each parameter is a keyword followed by one or more numeric values. @@ -150,7 +150,7 @@ strange numerical behavior can occur in the large remaining gap. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the N -specified in the :doc:`dihedral\_style table ` command. +specified in the :doc:`dihedral_style table ` command. Let *Ntable* is the number of table entries requested dihedral\_style command, and let *Nfile* be the parameter following "N" in the tabulated file ("30" in the sparse example above). What LAMMPS does @@ -220,7 +220,7 @@ page for more info. Related commands """""""""""""""" -:doc:`dihedral\_coeff `, :doc:`dihedral\_style table ` +:doc:`dihedral_coeff `, :doc:`dihedral_style table ` **Default:** none diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst index 7edf15e213..38715735ce 100644 --- a/doc/src/dihedral_zero.rst +++ b/doc/src/dihedral_zero.rst @@ -30,7 +30,7 @@ accessible to other commands. As an example, the :doc:`compute dihedral/local ` command can be used to compute the theta values for the list of quadruplets of dihedral atoms -listed in the data file read by the :doc:`read\_data ` +listed in the data file read by the :doc:`read_data ` command. If no dihedral style is defined, this command cannot be used. @@ -38,7 +38,7 @@ The optional *nocoeff* flag allows to read data files with a DihedralCoeff section for any dihedral style. Similarly, any dihedral\_coeff commands will only be checked for the dihedral type number and the rest ignored. -Note that the :doc:`dihedral\_coeff ` command must be +Note that the :doc:`dihedral_coeff ` command must be used for all dihedral types, though no additional values are specified. @@ -48,7 +48,7 @@ Restrictions **Related commands:** none -:doc:`dihedral\_style none ` +:doc:`dihedral_style none ` **Default:** none diff --git a/doc/src/dimension.rst b/doc/src/dimension.rst index c50d92c5f8..1ccb3930d6 100644 --- a/doc/src/dimension.rst +++ b/doc/src/dimension.rst @@ -27,7 +27,7 @@ Description Set the dimensionality of the simulation. By default LAMMPS runs 3d simulations. To run a 2d simulation, this command should be used prior to setting up a simulation box via the -:doc:`create\_box ` or :doc:`read\_data ` commands. +:doc:`create_box ` or :doc:`read_data ` commands. Restart files also store this setting. See the discussion on the :doc:`Howto 2d ` doc page for @@ -45,7 +45,7 @@ Restrictions This command must be used before the simulation box is defined by a -:doc:`read\_data ` or :doc:`create\_box ` command. +:doc:`read_data ` or :doc:`create_box ` command. Related commands """""""""""""""" diff --git a/doc/src/displace_atoms.rst b/doc/src/displace_atoms.rst index 2cf5849a10..2764940dde 100644 --- a/doc/src/displace_atoms.rst +++ b/doc/src/displace_atoms.rst @@ -69,7 +69,7 @@ displacement(s). The scale factor implied by the *units* keyword will also be applied to the variable result. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Atom-style variables can specify the same formulas as equal-style variables but can also include per-atom values, such as @@ -100,7 +100,7 @@ rotation axis is consistent with the right-hand rule: if your right-hand thumb points along *R*\ , then your fingers wrap around the axis in the direction of positive theta. -If the defined :doc:`atom\_style ` assigns an orientation to +If the defined :doc:`atom_style ` assigns an orientation to each atom (:doc:`atom styles ` ellipsoid, line, tri, body), then that property is also updated appropriately to correspond to the atom's rotation. @@ -125,7 +125,7 @@ define the lattice spacing. :doc:`boundary ` command) are enforced which may change the box size. Other than this effect, this command does not change the size or shape of the simulation box. See the - :doc:`change\_box ` command if that effect is desired. + :doc:`change_box ` command if that effect is desired. .. note:: @@ -153,7 +153,7 @@ the z-axis are allowed. Related commands """""""""""""""" -:doc:`lattice `, :doc:`change\_box `, +:doc:`lattice `, :doc:`change_box `, :doc:`fix move ` Default diff --git a/doc/src/dump.rst b/doc/src/dump.rst index c76b8efbad..833575debc 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -154,12 +154,12 @@ of the atom configuration every N timesteps while the *movie* style combines and compresses them into a movie file; both are discussed in detail on the :doc:`dump image ` doc page. The timesteps on which dump output is written can also be controlled by a variable. -See the :doc:`dump\_modify every ` command. +See the :doc:`dump_modify every ` command. Only information for atoms in the specified group is dumped. The -:doc:`dump\_modify thresh and region and refresh ` commands +:doc:`dump_modify thresh and region and refresh ` commands can also alter what atoms are included. Not all styles support -these options; see details on the :doc:`dump\_modify ` doc +these options; see details on the :doc:`dump_modify ` doc page. As described below, the filename determines the kind of output (text @@ -172,16 +172,16 @@ or multiple smaller files). timesteps when neighbor lists are rebuilt, the coordinates of an atom written to a dump file may be slightly outside the simulation box. Re-neighbor timesteps will not typically coincide with the timesteps - dump snapshots are written. See the :doc:`dump\_modify pbc ` command if you with to force coordinates to be + dump snapshots are written. See the :doc:`dump_modify pbc ` command if you with to force coordinates to be strictly inside the simulation box. .. note:: - Unless the :doc:`dump\_modify sort ` option is + Unless the :doc:`dump_modify sort ` option is invoked, the lines of atom information written to dump files (typically one line per atom) will be in an indeterminate order for each snapshot. This is even true when running on a single processor, - if the :doc:`atom\_modify sort ` option is on, which it is + if the :doc:`atom_modify sort ` option is on, which it is by default. In this case atoms are re-ordered periodically during a simulation, due to spatial sorting. It is also true when running in parallel, because data for a single snapshot is collected from @@ -189,7 +189,7 @@ or multiple smaller files). For the *atom*\ , *custom*\ , *cfg*\ , and *local* styles, sorting is off by default. For the *dcd*\ , *xtc*\ , *xyz*\ , and *molfile* styles, sorting by -atom ID is on by default. See the :doc:`dump\_modify ` doc +atom ID is on by default. See the :doc:`dump_modify ` doc page for details. The *atom/gz*\ , *cfg/gz*\ , *custom/gz*\ , and *xyz/gz* styles are identical @@ -213,7 +213,7 @@ be inter-changeable. The one exception is how the filename is specified for the MPI-IO styles, as explained below. The precision of values output to text-based dump files can be -controlled by the :doc:`dump\_modify format ` command and +controlled by the :doc:`dump_modify format ` command and its options. @@ -222,7 +222,7 @@ its options. The *style* keyword determines what atom quantities are written to the file and in what format. Settings made via the -:doc:`dump\_modify ` command can also alter the format of +:doc:`dump_modify ` command can also alter the format of individual values and the file itself. The *atom*\ , *local*\ , and *custom* styles create files in a simple text @@ -288,7 +288,7 @@ the atom ID and atom type. By default, atom coords are written in a scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom is at a location 1/4 of the distance from xlo to xhi of the box boundaries. The format can be changed to unscaled coords via the -:doc:`dump\_modify ` settings. Image flags can also be +:doc:`dump_modify ` settings. Image flags can also be added for each atom via dump\_modify. Style *custom* allows you to specify a list of atom attributes to be @@ -310,7 +310,7 @@ of the possible dump local attributes is given below. Note that by using input from the :doc:`compute property/local ` command with dump local, it is possible to generate information on bonds, angles, etc that can be cut and pasted directly into a data file read by the -:doc:`read\_data ` command. +:doc:`read_data ` command. Style *cfg* has the same command syntax as style *custom* and writes extended CFG format files, as used by the @@ -323,7 +323,7 @@ since these quantities are needed to write the CFG files in the appropriate format (though the "mass" and "type" fields do not appear explicitly in the file). Any remaining attributes will be stored as "auxiliary properties" in the CFG files. Note that you will typically -want to use the :doc:`dump\_modify element ` command with +want to use the :doc:`dump_modify element ` command with CFG-formatted files, to associate element names with atom types, so that AtomEye can render atoms appropriately. When unwrapped coordinates *xsu*\ , *ysu*\ , and *zsu* are requested, the nominal AtomEye @@ -339,7 +339,7 @@ The *dcd* style writes DCD files, a standard atomic trajectory format used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD files are binary and thus may not be portable to different machines. The number of atoms per snapshot cannot change with the *dcd* style. -The *unwrap* option of the :doc:`dump\_modify ` command +The *unwrap* option of the :doc:`dump_modify ` command allows DCD coordinates to be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed through a periodic boundary one or more times, the value is printed for what @@ -351,12 +351,12 @@ The *xtc* style writes XTC files, a compressed trajectory format used by the GROMACS molecular dynamics package, and described `here `_. The precision used in XTC files can be adjusted via the -:doc:`dump\_modify ` command. The default value of 1000 +:doc:`dump_modify ` command. The default value of 1000 means that coordinates are stored to 1/1000 nanometer accuracy. XTC files are portable binary files written in the NFS XDR data format, so that any machine which supports XDR should be able to read them. The number of atoms per snapshot cannot change with the *xtc* style. -The *unwrap* option of the :doc:`dump\_modify ` command allows +The *unwrap* option of the :doc:`dump_modify ` command allows XTC coordinates to be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed through a periodic boundary one or more times, the value is printed for what the @@ -369,7 +369,7 @@ coordinate format that many codes can read. Specifically it has a line with the number of atoms, then a comment line that is usually ignored followed by one line per atom with the atom type and the x-, y-, and z-coordinate of that atom. You can use the -:doc:`dump\_modify element ` option to change the output +:doc:`dump_modify element ` option to change the output from using the (numerical) atom type to an element name (or some other label). This will help many visualization programs to guess bonds and colors. @@ -387,15 +387,15 @@ timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be performed on the initial timestep after the dump command is invoked, if the current timestep is not a multiple of N. This behavior can be -changed via the :doc:`dump\_modify first ` command, which +changed via the :doc:`dump_modify first ` command, which can also be useful if the dump command is invoked after a minimization ended on an arbitrary timestep. N can be changed between runs by -using the :doc:`dump\_modify every ` command (not allowed -for *dcd* style). The :doc:`dump\_modify every ` command +using the :doc:`dump_modify every ` command (not allowed +for *dcd* style). The :doc:`dump_modify every ` command also allows a variable to be used to determine the sequence of timesteps on which dump files are written. In this mode a dump on the first timestep of a run will also not be written unless the -:doc:`dump\_modify first ` command is used. +:doc:`dump_modify first ` command is used. The specified filename determines how the dump file(s) is written. The default is to write one large text file, which is opened when the @@ -408,7 +408,7 @@ character appears in the filename, then one file per snapshot is written and the "\*" character is replaced with the timestep value. For example, tmp.dump.\* becomes tmp.dump.0, tmp.dump.10000, tmp.dump.20000, etc. This option is not available for the *dcd* and -*xtc* styles. Note that the :doc:`dump\_modify pad ` +*xtc* styles. Note that the :doc:`dump_modify pad ` command can be used to insure all timestep numbers are the same length (e.g. 00010), which can make it easier to read a series of dump files in order with some post-processing tools. @@ -423,7 +423,7 @@ support parallel I/O for output. This option is not available for the By default, P = the number of processors meaning one file per processor, but P can be set to a smaller value via the *nfile* or -*fileper* keywords of the :doc:`dump\_modify ` command. +*fileper* keywords of the :doc:`dump_modify ` command. These options can be the most efficient way of writing out dump files when running on large numbers of processors. @@ -448,7 +448,7 @@ Unlike MPI-IO restart files, which must be both written and read using MPI-IO, the dump files produced by these MPI-IO styles are identical in format to the files produced by their non-MPI-IO style counterparts. This means you can write a dump file using MPI-IO and -use the :doc:`read\_dump ` command or perform other +use the :doc:`read_dump ` command or perform other post-processing, just as if the dump file was not written using MPI-IO. @@ -529,7 +529,7 @@ bonds and angles. Note that computes which calculate global or per-atom quantities, as opposed to local quantities, cannot be output in a dump local command. -Instead, global quantities can be output by the :doc:`thermo\_style custom ` command, and per-atom quantities can be +Instead, global quantities can be output by the :doc:`thermo_style custom ` command, and per-atom quantities can be output by the dump custom command. If *c\_ID* is used as a attribute, then the local vector calculated by @@ -577,7 +577,7 @@ Nprocs-1) that currently owns the atom. *Procp1* is the proc ID+1, which can be convenient in place of a *type* attribute (1 to Ntypes) for coloring atoms in a visualization program. *Type* is the atom type (1 to Ntypes). *Element* is typically the chemical name of an -element, which you must assign to each type via the :doc:`dump\_modify element ` command. More generally, it can be any +element, which you must assign to each type via the :doc:`dump_modify element ` command. More generally, it can be any string you wish to associated with an atom type. *Mass* is the atom mass. *Vx*\ , *vy*\ , *vz*\ , *fx*\ , *fy*\ , *fz*\ , and *q* are components of atom velocity and force and atomic charge. @@ -643,7 +643,7 @@ and coordination number of individual atoms. Note that computes which calculate global or local quantities, as opposed to per-atom quantities, cannot be output in a dump custom command. Instead, global quantities can be output by the -:doc:`thermo\_style custom ` command, and local quantities +:doc:`thermo_style custom ` command, and local quantities can be output by the dump local command. If *c\_ID* is used as a attribute, then the per-atom vector calculated @@ -718,7 +718,7 @@ Related commands :doc:`dump atom/adios `, :doc:`dump custom/adios `, :doc:`dump h5md `, :doc:`dump image `, -:doc:`dump molfile `, :doc:`dump\_modify `, +:doc:`dump molfile `, :doc:`dump_modify `, :doc:`undump ` Default diff --git a/doc/src/dump_adios.rst b/doc/src/dump_adios.rst index e3cb74e978..1cd2e81c9b 100644 --- a/doc/src/dump_adios.rst +++ b/doc/src/dump_adios.rst @@ -50,7 +50,7 @@ ADIOS-BP files are binary, portable and self-describing. **Use from write\_dump:** It is possible to use these dump styles with the -:doc:`write\_dump ` command. In this case, the sub-intervals +:doc:`write_dump ` command. In this case, the sub-intervals must not be set at all. The write\_dump command can be used to create a new file at each individual dump. @@ -84,7 +84,7 @@ See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" -:doc:`dump `, :doc:`dump\_modify `, :doc:`undump ` +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` ---------- diff --git a/doc/src/dump_h5md.rst b/doc/src/dump_h5md.rst index 85a80e7d12..e0a22a846a 100644 --- a/doc/src/dump_h5md.rst +++ b/doc/src/dump_h5md.rst @@ -91,7 +91,7 @@ every N steps. **Use from write\_dump:** It is possible to use this dump style with the -:doc:`write\_dump ` command. In this case, the sub-intervals +:doc:`write_dump ` command. In this case, the sub-intervals must not be set at all. The write\_dump command can be used either to create a new file or to add current data to an existing dump file by using the *file\_from* keyword. @@ -137,7 +137,7 @@ provided by the HDF5 library. Related commands """""""""""""""" -:doc:`dump `, :doc:`dump\_modify `, :doc:`undump ` +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` ---------- diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index 84be993724..938b11c356 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -104,7 +104,7 @@ Description Dump a high-quality rendered image of the atom configuration every N timesteps and save the images either as a sequence of JPEG or PNG or PPM files, or as a single movie file. The options for this command as -well as the :doc:`dump\_modify ` command control what is +well as the :doc:`dump_modify ` command control what is included in the image or movie and how it appears. A series of such images can easily be manually converted into an animated movie of your simulation or the process can be automated without writing the @@ -136,7 +136,7 @@ to see the full-size images: Only atoms in the specified group are rendered in the image. The -:doc:`dump\_modify region and thresh ` commands can also +:doc:`dump_modify region and thresh ` commands can also alter what atoms are included in the image. The filename suffix determines whether a JPEG, PNG, or PPM file is created with the *image* dump style. If the suffix is ".jpg" or @@ -153,7 +153,7 @@ Similarly, the format of the resulting movie is chosen with the and thus details have to be looked up in the FFmpeg documentation. Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie compression like bitrate and -framerate can be set using the :doc:`dump\_modify ` command. +framerate can be set using the :doc:`dump_modify ` command. To write out JPEG and PNG format files, you must build LAMMPS with support for the corresponding JPEG or PNG library. To convert images @@ -176,16 +176,16 @@ timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be performed on the initial timestep after the dump command is invoked, if the current timestep is not a multiple of N. This behavior can be -changed via the :doc:`dump\_modify first ` command, which +changed via the :doc:`dump_modify first ` command, which can be useful if the dump command is invoked after a minimization ended on an arbitrary timestep. N can be changed between runs by -using the :doc:`dump\_modify every ` command. +using the :doc:`dump_modify every ` command. Dump *image* filenames must contain a wildcard character "\*", so that one image file per snapshot is written. The "\*" character is replaced with the timestep value. For example, tmp.dump.\*.jpg becomes tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note -that the :doc:`dump\_modify pad ` command can be used to +that the :doc:`dump_modify pad ` command can be used to insure all timestep numbers are the same length (e.g. 00010), which can make it easier to convert a series of images into a movie in the correct ordering. @@ -219,11 +219,11 @@ to colors is as follows: * type 6 = cyan and repeats itself for types > 6. This mapping can be changed by the -:doc:`dump\_modify acolor ` command. +:doc:`dump_modify acolor ` command. If *type* is specified for the *diameter* setting then the diameter of each atom is determined by its atom type. By default all types have -diameter 1.0. This mapping can be changed by the :doc:`dump\_modify adiam ` command. +diameter 1.0. This mapping can be changed by the :doc:`dump_modify adiam ` command. If *element* is specified for the *color* and/or *diameter* setting, then the color and/or diameter of each atom is determined by which @@ -244,7 +244,7 @@ If "vx", for example, is used as the *color* setting, then the color of the atom will depend on the x-component of its velocity. The association of a per-atom value with a specific color is determined by a "color map", which can be specified via the -:doc:`dump\_modify ` command. The basic idea is that the +:doc:`dump_modify ` command. The basic idea is that the atom-attribute will be within a range of values, and every value within the range is mapped to a specific color. Depending on how the color map is defined, that mapping can take place via interpolation so @@ -255,7 +255,7 @@ If "vx", for example, is used as the *diameter* setting, then the atom will be rendered using the x-component of its velocity as the diameter. If the per-atom value <= 0.0, them the atom will not be drawn. Note that finite-size spherical particles, as defined by -:doc:`atom\_style sphere ` define a per-particle radius or +:doc:`atom_style sphere ` define a per-particle radius or diameter, which can be used as the *diameter* setting. @@ -291,9 +291,9 @@ The *bond* keyword allows to you to alter how bonds are drawn. A bond is only drawn if both atoms in the bond are being drawn due to being in the specified group and due to other selection criteria (e.g. region, threshold settings of the -:doc:`dump\_modify ` command). By default, bonds are drawn +:doc:`dump_modify ` command). By default, bonds are drawn if they are defined in the input data file as read by the -:doc:`read\_data ` command. Using *none* for both the bond +:doc:`read_data ` command. Using *none* for both the bond *color* and *width* value will turn off the drawing of all bonds. If *atom* is specified for the bond *color* value, then each bond is @@ -312,7 +312,7 @@ types to colors is as follows: * type 6 = cyan and repeats itself for bond types > 6. This mapping can be changed by -the :doc:`dump\_modify bcolor ` command. +the :doc:`dump_modify bcolor ` command. The bond *width* value can be a numeric value or *atom* or *type* (or *none* as indicated above). @@ -327,13 +327,13 @@ of the 2 atoms in the bond. If *type* is specified for the *width* value then the diameter of each bond is determined by its bond type. By default all types have -diameter 0.5. This mapping can be changed by the :doc:`dump\_modify bdiam ` command. +diameter 0.5. This mapping can be changed by the :doc:`dump_modify bdiam ` command. ---------- -The *line* keyword can be used when :doc:`atom\_style line ` +The *line* keyword can be used when :doc:`atom_style line ` is used to define particles as line segments, and will draw them as lines. If this keyword is not used, such particles will be drawn as spheres, the same as if they were regular atoms. The only setting @@ -349,7 +349,7 @@ mapping of types to colors is as follows: * type 6 = cyan and repeats itself for types > 6. There is not yet an option to -change this via the :doc:`dump\_modify ` command. +change this via the :doc:`dump_modify ` command. The line *width* can only be a numeric value, which specifies that all lines will be drawn as cylinders with that diameter, e.g. 1.0, which @@ -360,7 +360,7 @@ e.g. Angstroms. ---------- -The *tri* keyword can be used when :doc:`atom\_style tri ` is +The *tri* keyword can be used when :doc:`atom_style tri ` is used to define particles as triangles, and will draw them as triangles or edges (3 lines) or both, depending on the setting for *tflag*\ . If edges are drawn, the *width* setting determines the diameters of the @@ -378,13 +378,13 @@ default the mapping of types to colors is as follows: * type 6 = cyan and repeats itself for types > 6. There is not yet an option to -change this via the :doc:`dump\_modify ` command. +change this via the :doc:`dump_modify ` command. ---------- -The *body* keyword can be used when :doc:`atom\_style body ` +The *body* keyword can be used when :doc:`atom_style body ` is used to define body particles with internal state (e.g. sub-particles), and will drawn them in a manner specific to the body style. If this keyword is not used, such particles will be drawn @@ -413,7 +413,7 @@ particle. By default the mapping of types to colors is as follows: * type 6 = cyan and repeats itself for types > 6. There is not yet an option to -change this via the :doc:`dump\_modify ` command. +change this via the :doc:`dump_modify ` command. ---------- @@ -439,7 +439,7 @@ the mapping of types to colors is as follows: * type 6 = cyan and repeats itself for types > 6. There is not yet an option to -change this via the :doc:`dump\_modify ` command. +change this via the :doc:`dump_modify ` command. ---------- @@ -532,7 +532,7 @@ are rendered as thin cylinders in the image. If *no* is set, then the box boundaries are not drawn and the *diam* setting is ignored. If *yes* is set, the 12 edges of the box are drawn, with a diameter that is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for -2d). The color of the box boundaries can be set with the :doc:`dump\_modify boxcolor ` command. +2d). The color of the box boundaries can be set with the :doc:`dump_modify boxcolor ` command. The *axes* keyword determines if and how the coordinate axes are rendered as thin cylinders in the image. If *no* is set, then the @@ -551,7 +551,7 @@ set (default), then the sub-domain boundaries are not drawn and the *diam* setting is ignored. If *yes* is set, the 12 edges of each processor sub-domain are drawn, with a diameter that is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color -of the sub-domain boundaries can be set with the :doc:`dump\_modify boxcolor ` command. +of the sub-domain boundaries can be set with the :doc:`dump_modify boxcolor ` command. ---------- @@ -722,7 +722,7 @@ mp4). Related commands """""""""""""""" -:doc:`dump `, :doc:`dump\_modify `, :doc:`undump ` +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` Default """"""" diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 1aa09c6092..8d42a7acab 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -546,7 +546,7 @@ commands: The :doc:`compute displace/atom ` command calculates the displacement of each atom from its reference position. The "4" index is the scalar displacement; 1,2,3 are the xyz components -of the displacement. The :doc:`dump\_modify thresh ` +of the displacement. The :doc:`dump_modify thresh ` command will cause only atoms that have displaced more than 0.6 Angstroms to be output on a given snapshot (assuming metal units). However, note that when an atom is output, we also need to update the @@ -621,7 +621,7 @@ most effective when the typical magnitude of position data is between The *sort* keyword determines whether lines of per-atom output in a snapshot are sorted or not. A sort value of *off* means they will typically be written in indeterminate order, either in serial or -parallel. This is the case even in serial if the :doc:`atom\_modify sort ` option is turned on, which it is by default, to +parallel. This is the case even in serial if the :doc:`atom_modify sort ` option is turned on, which it is by default, to improve performance. A sort value of *id* means sort the output by atom ID. A sort value of N or -N means sort the output by the value in the Nth column of per-atom info in either ascending or descending @@ -647,7 +647,7 @@ performed. The *thermo* keyword only applies the dump *netcdf* style. It triggers writing of :doc:`thermo ` information to the dump file alongside per-atom data. The values included in the dump file are -identical to the values specified by :doc:`thermo\_style `. +identical to the values specified by :doc:`thermo_style `. ---------- diff --git a/doc/src/dump_molfile.rst b/doc/src/dump_molfile.rst index 4c03def9b7..69347840b5 100644 --- a/doc/src/dump_molfile.rst +++ b/doc/src/dump_molfile.rst @@ -63,7 +63,7 @@ must be sorted, outside of the coordinates no change in atom properties The *format* keyword determines what format is used to write out the dump. For this to work, LAMMPS must be able to find and load a compatible molfile plugin that supports this format. Settings made via -the :doc:`dump\_modify ` command can alter per atom properties +the :doc:`dump_modify ` command can alter per atom properties like element names. The *path* keyword determines which in directories. This is a "path" @@ -71,7 +71,7 @@ like other search paths, i.e. it can contain multiple directories separated by a colon (or semi-colon on windows). This keyword is optional and default to ".", the current directory. -The *unwrap* option of the :doc:`dump\_modify ` command allows +The *unwrap* option of the :doc:`dump_modify ` command allows coordinates to be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed through a periodic boundary one or more times, the value is printed for what the coordinate would be @@ -88,10 +88,10 @@ timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be performed on the initial timestep after the dump command is invoked, if the current timestep is not a multiple of N. This behavior can be -changed via the :doc:`dump\_modify first ` command, which can +changed via the :doc:`dump_modify first ` command, which can be useful if the dump command is invoked after a minimization ended on an arbitrary timestep. N can be changed between runs by using the -:doc:`dump\_modify every ` command. The :doc:`dump\_modify every ` command also allows a variable to be used to +:doc:`dump_modify every ` command. The :doc:`dump_modify every ` command also allows a variable to be used to determine the sequence of timesteps on which dump files are written. @@ -132,7 +132,7 @@ application itself. The plugins are installed in the directory: Related commands """""""""""""""" -:doc:`dump `, :doc:`dump\_modify `, :doc:`undump ` +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` Default """"""" diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst index f89faff0ca..9f98cd9824 100644 --- a/doc/src/dump_netcdf.rst +++ b/doc/src/dump_netcdf.rst @@ -20,7 +20,7 @@ Syntax * *netcdf* or *netcdf/mpiio* = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump ` doc page) * N = dump every this many timesteps * file = name of file to write dump info to -* args = list of atom attributes, same as for :doc:`dump\_style custom ` +* args = list of atom attributes, same as for :doc:`dump_style custom ` Examples """""""" @@ -59,7 +59,7 @@ all extensions of this dump style. In addition to per-atom data, :doc:`thermo ` data can be included in the dump file. The data included in the dump file is identical to the data specified -by :doc:`thermo\_style `. +by :doc:`thermo_style `. .. _netcdf-home: http://www.unidata.ucar.edu/software/netcdf/ @@ -89,7 +89,7 @@ more info. Related commands """""""""""""""" -:doc:`dump `, :doc:`dump\_modify `, :doc:`undump ` +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` .. _lws: http://lammps.sandia.gov diff --git a/doc/src/dump_vtk.rst b/doc/src/dump_vtk.rst index 2f229aaccc..6624820a4f 100644 --- a/doc/src/dump_vtk.rst +++ b/doc/src/dump_vtk.rst @@ -16,7 +16,7 @@ Syntax * vtk = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump ` doc page) * N = dump every this many timesteps * file = name of file to write dump info to -* args = same as arguments for :doc:`dump\_style custom ` +* args = same as arguments for :doc:`dump_style custom ` Examples """""""" @@ -34,20 +34,20 @@ Dump a snapshot of atom quantities to one or more files every N timesteps in a format readable by the `VTK visualization toolkit `_ or other visualization tools that use it, e.g. `ParaView `_. The timesteps on which dump output is written can also be controlled by a variable; see the -:doc:`dump\_modify every ` command for details. +:doc:`dump_modify every ` command for details. -This dump style is similar to :doc:`dump\_style custom ` but uses +This dump style is similar to :doc:`dump_style custom ` but uses the VTK library to write data to VTK simple legacy or XML format depending on the filename extension specified for the dump file. This can be either *\*.vtk* for the legacy format or *\*.vtp* and *\*.vtu*, respectively, for XML format; see the `VTK homepage `_ for a detailed description of these formats. Since this naming convention conflicts with the way binary output is usually specified (see below), the -:doc:`dump\_modify binary ` command allows setting of a +:doc:`dump_modify binary ` command allows setting of a binary option for this dump style explicitly. Only information for atoms in the specified group is dumped. The -:doc:`dump\_modify thresh and region ` commands can also +:doc:`dump_modify thresh and region ` commands can also alter what atoms are included; see details below. As described below, special characters ("\*", "%") in the filename @@ -62,17 +62,17 @@ determine the kind of output. .. warning:: - Unless the :doc:`dump\_modify sort ` option + Unless the :doc:`dump_modify sort ` option is invoked, the lines of atom information written to dump files will be in an indeterminate order for each snapshot. This is even true - when running on a single processor, if the :doc:`atom\_modify sort ` option is on, which it is by default. In this + when running on a single processor, if the :doc:`atom_modify sort ` option is on, which it is by default. In this case atoms are re-ordered periodically during a simulation, due to spatial sorting. It is also true when running in parallel, because data for a single snapshot is collected from multiple processors, each of which owns a subset of the atoms. For the *vtk* style, sorting is off by default. See the -:doc:`dump\_modify ` doc page for details. +:doc:`dump_modify ` doc page for details. ---------- @@ -91,7 +91,7 @@ hexahedrons in either legacy .vtk or .vtu XML format. Style *vtk* allows you to specify a list of atom attributes to be written to the dump file for each atom. The list of possible attributes -is the same as for the :doc:`dump\_style custom ` command; see +is the same as for the :doc:`dump_style custom ` command; see its doc page for a listing and an explanation of each attribute. .. note:: @@ -118,21 +118,21 @@ timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be performed on the initial timestep after the dump command is invoked, if the current timestep is not a multiple of N. This behavior can be -changed via the :doc:`dump\_modify first ` command, which +changed via the :doc:`dump_modify first ` command, which can also be useful if the dump command is invoked after a minimization ended on an arbitrary timestep. N can be changed between runs by -using the :doc:`dump\_modify every ` command. -The :doc:`dump\_modify every ` command +using the :doc:`dump_modify every ` command. +The :doc:`dump_modify every ` command also allows a variable to be used to determine the sequence of timesteps on which dump files are written. In this mode a dump on the first timestep of a run will also not be written unless the -:doc:`dump\_modify first ` command is used. +:doc:`dump_modify first ` command is used. Dump filenames can contain two wildcard characters. If a "\*" character appears in the filename, then one file per snapshot is written and the "\*" character is replaced with the timestep value. For example, tmp.dump\*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk, -tmp.dump20000.vtk, etc. Note that the :doc:`dump\_modify pad ` +tmp.dump20000.vtk, etc. Note that the :doc:`dump_modify pad ` command can be used to insure all timestep numbers are the same length (e.g. 00010), which can make it easier to read a series of dump files in order with some post-processing tools. @@ -146,7 +146,7 @@ mode of output on parallel machines that support parallel I/O for output. By default, P = the number of processors meaning one file per processor, but P can be set to a smaller value via the *nfile* or -*fileper* keywords of the :doc:`dump\_modify ` command. +*fileper* keywords of the :doc:`dump_modify ` command. These options can be the most efficient way of writing out dump files when running on large numbers of processors. @@ -185,7 +185,7 @@ Related commands """""""""""""""" :doc:`dump `, :doc:`dump image `, -:doc:`dump\_modify `, :doc:`undump ` +:doc:`dump_modify `, :doc:`undump ` Default """"""" diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index 4d5cf59a39..723cbd4618 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -107,13 +107,13 @@ initial values after the run. The *pair* keyword enables various parameters of potentials defined by -the :doc:`pair\_style ` command to be changed, if the pair -style supports it. Note that the :doc:`pair\_style ` and -:doc:`pair\_coeff ` commands must be used in the usual manner +the :doc:`pair_style ` command to be changed, if the pair +style supports it. Note that the :doc:`pair_style ` and +:doc:`pair_coeff ` commands must be used in the usual manner to specify these parameters initially; the fix adapt command simply overrides the parameters. -The *pstyle* argument is the name of the pair style. If :doc:`pair\_style hybrid or hybrid/overlay ` is used, *pstyle* should be +The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay ` is used, *pstyle* should be a sub-style name. If there are multiple sub-styles using the same pair style, then *pstyle* should be specified as "style:N" where N is which instance of the pair style you wish to adapt, e.g. the first, @@ -213,9 +213,9 @@ meaning of these parameters: the pair\_\*.cpp file associated with the potential. Some parameters are global settings for the pair style, e.g. the -viscosity setting "mu" for :doc:`pair\_style lubricate `. +viscosity setting "mu" for :doc:`pair_style lubricate `. Other parameters apply to atom type pairs within the pair style, -e.g. the prefactor "a" for :doc:`pair\_style soft `. +e.g. the prefactor "a" for :doc:`pair_style soft `. Note that for many of the potentials, the parameter that can be varied is effectively a prefactor on the entire energy expression for the @@ -233,7 +233,7 @@ be specified to indicate which type pairs to apply it to. If a global parameter is specified, the *I* and *J* settings still need to be specified, but are ignored. -Similar to the :doc:`pair\_coeff command `, I and J can be +Similar to the :doc:`pair_coeff command `, I and J can be specified in one of two ways. Explicit numeric values can be used for each, as in the 1st example above. I <= J is required. LAMMPS sets the coefficients for the symmetric J,I interaction to the same values. @@ -248,9 +248,9 @@ all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). Note that only type pairs with I <= J are considered; if asterisks imply type pairs where J < I, they are ignored. -IMPROTANT NOTE: If :doc:`pair\_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will +IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will be a sub-style name. You must specify I,J arguments that correspond -to type pair values defined (via the :doc:`pair\_coeff ` +to type pair values defined (via the :doc:`pair_coeff ` command) for that sub-style. The *v\_name* argument for keyword *pair* is the name of an @@ -258,16 +258,16 @@ The *v\_name* argument for keyword *pair* is the name of an this fix is invoked to set the parameter to a new value. It should be specified as v\_name, where name is the variable name. Equal-style variables can specify formulas with various mathematical functions, -and include :doc:`thermo\_style ` command keywords for the +and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify parameters that change as a function of time or span consecutive runs in a continuous fashion. For the latter, see the *start* and *stop* keywords of the :doc:`run ` command and the -*elaplong* keyword of :doc:`thermo\_style custom ` for +*elaplong* keyword of :doc:`thermo_style custom ` for details. For example, these commands would change the prefactor coefficient of -the :doc:`pair\_style soft ` potential from 10.0 to 30.0 in a +the :doc:`pair_style soft ` potential from 10.0 to 30.0 in a linear fashion over the course of a simulation: @@ -309,7 +309,7 @@ working with fix\_adapt are The *kspace* keyword used the specified variable as a scale factor on the energy, forces, virial calculated by whatever K-Space solver is -defined by the :doc:`kspace\_style ` command. If the +defined by the :doc:`kspace_style ` command. If the variable has a value of 1.0, then the solver is unaltered. The *kspace* keyword works this way whether the *scale* keyword @@ -341,7 +341,7 @@ for all atoms in the fix group. by the *atom* keyword. If the atom parameter is *diameter* and per-atom density and per-atom -mass are defined for particles (e.g. :doc:`atom\_style granular `), then the mass of each particle is also +mass are defined for particles (e.g. :doc:`atom_style granular `), then the mass of each particle is also changed when the diameter changes (density is assumed to stay constant). @@ -361,7 +361,7 @@ over the course of a 1000-step simulation: **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index 60c05ec796..2cc3a59191 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -111,13 +111,13 @@ the same values of the parameters. The *pair* keyword enables various parameters of potentials defined by -the :doc:`pair\_style ` command to be changed, if the pair -style supports it. Note that the :doc:`pair\_style ` and -:doc:`pair\_coeff ` commands must be used in the usual manner +the :doc:`pair_style ` command to be changed, if the pair +style supports it. Note that the :doc:`pair_style ` and +:doc:`pair_coeff ` commands must be used in the usual manner to specify these parameters initially; the fix adapt command simply overrides the parameters. -The *pstyle* argument is the name of the pair style. If :doc:`pair\_style hybrid or hybrid/overlay ` is used, *pstyle* should be +The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay ` is used, *pstyle* should be a sub-style name. For example, *pstyle* could be specified as "soft" or "lubricate". The *pparam* argument is the name of the parameter to change. This is the current list of pair styles and parameters that @@ -204,7 +204,7 @@ be specified to indicate which type pairs to apply it to. If a global parameter is specified, the *I* and *J* settings still need to be specified, but are ignored. -Similar to the :doc:`pair\_coeff command `, I and J can be +Similar to the :doc:`pair_coeff command `, I and J can be specified in one of two ways. Explicit numeric values can be used for each, as in the 1st example above. I <= J is required. LAMMPS sets the coefficients for the symmetric J,I interaction to the same values. @@ -219,9 +219,9 @@ all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). Note that only type pairs with I <= J are considered; if asterisks imply type pairs where J < I, they are ignored. -IMPROTANT NOTE: If :doc:`pair\_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will +IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will be a sub-style name. You must specify I,J arguments that correspond -to type pair values defined (via the :doc:`pair\_coeff ` +to type pair values defined (via the :doc:`pair_coeff ` command) for that sub-style. The *v\_name* argument for keyword *pair* is the name of an @@ -229,16 +229,16 @@ The *v\_name* argument for keyword *pair* is the name of an this fix is invoked to set the parameter to a new value. It should be specified as v\_name, where name is the variable name. Equal-style variables can specify formulas with various mathematical functions, -and include :doc:`thermo\_style ` command keywords for the +and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify parameters that change as a function of time or span consecutive runs in a continuous fashion. For the latter, see the *start* and *stop* keywords of the :doc:`run ` command and the -*elaplong* keyword of :doc:`thermo\_style custom ` for +*elaplong* keyword of :doc:`thermo_style custom ` for details. For example, these commands would change the prefactor coefficient of -the :doc:`pair\_style soft ` potential from 10.0 to 30.0 in a +the :doc:`pair_style soft ` potential from 10.0 to 30.0 in a linear fashion over the course of a simulation: @@ -253,7 +253,7 @@ linear fashion over the course of a simulation: The *kspace* keyword used the specified variable as a scale factor on the energy, forces, virial calculated by whatever K-Space solver is -defined by the :doc:`kspace\_style ` command. If the +defined by the :doc:`kspace_style ` command. If the variable has a value of 1.0, then the solver is unaltered. The *kspace* keyword works this way whether the *scale* keyword @@ -283,7 +283,7 @@ variables. The new value is assigned to the corresponding attribute for all atoms in the fix group. If the atom parameter is *diameter* and per-atom density and per-atom -mass are defined for particles (e.g. :doc:`atom\_style granular `), then the mass of each particle is also +mass are defined for particles (e.g. :doc:`atom_style granular `), then the mass of each particle is also changed when the diameter changes (density is assumed to stay constant). @@ -306,7 +306,7 @@ parameters on the outermost rRESPA level. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index 91134eac12..971abdc682 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -59,7 +59,7 @@ will be evaluated each timestep, and its value(s) used to determine the force component. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent force field. @@ -145,7 +145,7 @@ instructions on how to use the accelerated styles effectively. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential "energy" inferred by the added force to the system's potential energy as part of :doc:`thermodynamic output `. This is a fictitious quantity but is needed so that the :doc:`minimize ` command can include the @@ -153,12 +153,12 @@ forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added force. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the added forces on atoms to the system's virial as part of :doc:`thermodynamic output `. The default is *virial no* -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -184,7 +184,7 @@ the iteration count during the minimization. If you want the fictitious potential energy associated with the added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the - :doc:`fix\_modify ` *energy* option for this fix. + :doc:`fix_modify ` *energy* option for this fix. Restrictions """""""""""" diff --git a/doc/src/fix_addtorque.rst b/doc/src/fix_addtorque.rst index 26493624ec..75636d5abf 100644 --- a/doc/src/fix_addtorque.rst +++ b/doc/src/fix_addtorque.rst @@ -48,7 +48,7 @@ will be evaluated each timestep, and its value used to determine the torque component. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent torque. @@ -60,7 +60,7 @@ time. Thus it is easy to specify a time-dependent torque. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential "energy" inferred by the added forces to the system's potential energy as part of :doc:`thermodynamic output `. This is a fictitious quantity but is needed so that the :doc:`minimize ` command can include the @@ -68,7 +68,7 @@ forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added forces. -The :doc:`fix\_modify ` *respa* option is supported by +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its torque. Default is the outermost level. diff --git a/doc/src/fix_append_atoms.rst b/doc/src/fix_append_atoms.rst index 977e96a53a..29ef20342a 100644 --- a/doc/src/fix_append_atoms.rst +++ b/doc/src/fix_append_atoms.rst @@ -57,7 +57,7 @@ This fix creates atoms on a lattice, appended on the zhi edge of the system box. This can be useful when a shock or wave is propagating from zlo. This allows the system to grow with time to accommodate an expanding wave. A simulation box must already exist, which is -typically created via the :doc:`create\_box ` command. +typically created via the :doc:`create_box ` command. Before using this command, a lattice must also be defined using the :doc:`lattice ` command. @@ -94,7 +94,7 @@ define the lattice spacings. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index b765efb30c..2c2f474c93 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -122,7 +122,7 @@ Note coupling and post-processing can be combined in the same simulations using **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. The :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. The :doc:`fix_modify ` options relevant to this fix are listed below. No global scalar or vector or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be @@ -141,7 +141,7 @@ Thermal and two\_temperature (coupling) types use a Verlet time-integration algo Related commands """""""""""""""" -After specifying this fix in your input script, several other :doc:`fix\_modify ` commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions. +After specifying this fix in your input script, several other :doc:`fix_modify ` commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions. fix\_modify commands for setup: diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index e5851db353..420a490c15 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -141,7 +141,7 @@ include: :doc:`efield `, :doc:`gravity `, :doc:`temp/rescale `, and :doc:`wall fixes `. For that energy to be included in the total potential energy of the system (the quantity used when performing GCMC moves), -you MUST enable the :doc:`fix\_modify ` *energy* option for +you MUST enable the :doc:`fix_modify ` *energy* option for that fix. The doc pages for individual :doc:`fix ` commands specify if this should be done. @@ -150,17 +150,17 @@ specify if this should be done. This fix writes the state of the fix to :doc:`binary restart files `. This includes information about the random number generator seed, the next timestep for MC exchanges, the number of exchange attempts and successes etc. See -the :doc:`read\_restart ` command for info on how to +the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. .. note:: For this to work correctly, the timestep must **not** be changed - after reading the restart with :doc:`reset\_timestep `. + after reading the restart with :doc:`reset_timestep `. The fix will try to detect it and stop with an error. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global vector of length 2, which can be accessed @@ -188,7 +188,7 @@ Related commands :doc:`fix nvt `, :doc:`neighbor `, :doc:`fix deposit `, :doc:`fix evaporate `, -:doc:`delete\_atoms `, :doc:`fix gcmc ` +:doc:`delete_atoms `, :doc:`fix gcmc ` Default """"""" diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index 3a066ab55b..a9878887d8 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -162,7 +162,7 @@ per-atom quantities to time average. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global scalar or vector quantities are stored by this fix for access by various :doc:`output commands `. diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index ff317bf15e..92fe47bfb5 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -102,7 +102,7 @@ Use one or more per-atom vectors as inputs every few timesteps, sum the values over the atoms in each chunk at each timestep, then average the per-chunk values over longer timescales. The resulting chunk averages can be used by other :doc:`output commands ` such -as :doc:`thermo\_style custom `, and can also be written to +as :doc:`thermo_style custom `, and can also be written to a file. In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom @@ -474,7 +474,7 @@ dimensions. Those values are always in distance :doc:`units `. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global array of values which can be accessed by diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 9c7d27b761..c5b422ef6e 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -79,7 +79,7 @@ Use one or more global scalar values as inputs every few timesteps, calculate time correlations between them at varying time intervals, and average the correlation data over longer timescales. The resulting correlation values can be time integrated by -:doc:`variables ` or used by other :doc:`output commands ` such as :doc:`thermo\_style custom `, and can also be written to a file. See the +:doc:`variables ` or used by other :doc:`output commands ` such as :doc:`thermo_style custom `, and can also be written to a file. See the :doc:`fix ave/correlate/long ` command for an alternate method for computing correlation functions efficiently over very long time windows. @@ -332,7 +332,7 @@ included in the variable formula or via the *prefactor* keyword. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global array of values which can be accessed by diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 4a2e73d7df..176e4b51db 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -345,7 +345,7 @@ the histogram. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a global vector and global array which can be diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index 3774379f19..39fa1746e4 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -76,7 +76,7 @@ Description Use one or more global values as inputs every few timesteps, and average them over longer timescales. The resulting averages can be used by other :doc:`output commands ` such as -:doc:`thermo\_style custom `, and can also be written to a +:doc:`thermo_style custom `, and can also be written to a file. Note that if no time averaging is done, this command can be used as a convenient way to simply output one or more global values to a file. @@ -321,7 +321,7 @@ appropriate fields from the fix ave/time command. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a global scalar or global vector or global array diff --git a/doc/src/fix_aveforce.rst b/doc/src/fix_aveforce.rst index f786c043c9..07d2e3b0f0 100644 --- a/doc/src/fix_aveforce.rst +++ b/doc/src/fix_aveforce.rst @@ -65,7 +65,7 @@ evaluated each timestep, and its value used to determine the average force. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent average force. @@ -103,7 +103,7 @@ instructions on how to use the accelerated styles effectively. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 93c2a5b33c..db2bf9e64b 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -130,7 +130,7 @@ forced even if the current balance is perfect (1.0) be specifying a create a logical 3d grid cannot achieve perfect balance for many irregular distributions of particles. Likewise, if a portion of the system is a perfect lattice, e.g. the initial system is generated by - the :doc:`create\_atoms ` command, then "grid" methods may + the :doc:`create_atoms ` command, then "grid" methods may be unable to achieve exact balance. This is because entire lattice planes will be owned or not owned by a single processor. @@ -144,7 +144,7 @@ forced even if the current balance is perfect (1.0) be specifying a proportional to particle count, and changing the relative size and shape of processor sub-domains may lead to additional computational and communication overheads, e.g. in the PPPM solver used via the - :doc:`kspace\_style ` command. Thus you should benchmark + :doc:`kspace_style ` command. Thus you should benchmark the run times of a simulation before and after balancing. @@ -180,8 +180,8 @@ fashion so as to have equal numbers of particles (or weight) in each sub-box, as in the rightmost diagram above. The "grid" methods can be used with either of the -:doc:`comm\_style ` command options, *brick* or *tiled*\ . The -"tiling" methods can only be used with :doc:`comm\_style tiled `. +:doc:`comm_style ` command options, *brick* or *tiled*\ . The +"tiling" methods can only be used with :doc:`comm_style tiled `. When a "grid" method is specified, the current domain partitioning can be either a logical 3d grid or a tiled partitioning. In the former @@ -208,7 +208,7 @@ The *Nfreq* setting determines how often a re-balance is performed. If time a re-balance occurs, a reneighboring is triggered, so *Nfreq* should not be too small. If *Nfreq* = 0, then re-balancing will be done every time reneighboring normally occurs, as determined by the -the :doc:`neighbor ` and :doc:`neigh\_modify ` +the :doc:`neighbor ` and :doc:`neigh_modify ` command settings. On re-balance steps, re-balancing will only be attempted if the current @@ -377,7 +377,7 @@ each processor, instead of 4, and "SQUARES" replaced by "CUBES". **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which is the imbalance factor @@ -411,13 +411,13 @@ For 2d simulations, the *z* style cannot be used. Nor can a "z" appear in *dimstr* for the *shift* style. Balancing through recursive bisectioning (\ *rcb* style) requires -:doc:`comm\_style tiled ` +:doc:`comm_style tiled ` Related commands """""""""""""""" :doc:`group `, :doc:`processors `, :doc:`balance `, -:doc:`comm\_style ` +:doc:`comm_style ` .. _pizza: http://pizza.sandia.gov diff --git a/doc/src/fix_bond_break.rst b/doc/src/fix_bond_break.rst index fa7aba3c6b..57bd3d39a8 100644 --- a/doc/src/fix_bond_break.rst +++ b/doc/src/fix_bond_break.rst @@ -43,7 +43,7 @@ Break bonds between pairs of atoms as a simulation runs according to specified criteria. This can be used to model the dissolution of a polymer network due to stretching of the simulation box or other deformations. In this context, a bond means an interaction between a -pair of atoms computed by the :doc:`bond\_style ` command. +pair of atoms computed by the :doc:`bond_style ` command. Once the bond is broken it will be permanently deleted, as will all angle, dihedral, and improper interactions that bond is part of. @@ -100,7 +100,7 @@ neighbor lists must be immediately updated on the same timestep. This is to insure that any pairwise interactions that should be turned "on" due to a bond breaking, because they are no longer excluded by the presence of the bond and the settings of the -:doc:`special\_bonds ` command, will be immediately +:doc:`special_bonds ` command, will be immediately recognized. All of these operations increase the cost of a timestep. Thus you should be cautious about invoking this fix too frequently. @@ -123,7 +123,7 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes two statistics which it stores in a global vector of @@ -150,7 +150,7 @@ Related commands """""""""""""""" :doc:`fix bond/create `, :doc:`fix bond/react `, :doc:`fix bond/swap `, -:doc:`dump local `, :doc:`special\_bonds ` +:doc:`dump local `, :doc:`special_bonds ` Default """"""" diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index 9a11558e83..dbf1234582 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -57,7 +57,7 @@ Create bonds between pairs of atoms as a simulation runs according to specified criteria. This can be used to model cross-linking of polymers, the formation of a percolation network, etc. In this context, a bond means an interaction between a pair of atoms computed -by the :doc:`bond\_style ` command. Once the bond is created +by the :doc:`bond_style ` command. Once the bond is created it will be permanently in place. Optionally, the creation of a bond can also create angle, dihedral, and improper interactions that bond is part of. See the discussion of the *atype*\ , *dtype*\ , and *itype* @@ -92,7 +92,7 @@ a bond on this timestep, even if it has other possible bond partners. It is permissible to have *itype* = *jtype*\ . *Rmin* must be <= the pairwise cutoff distance between *itype* and *jtype* atoms, as defined -by the :doc:`pair\_style ` command. +by the :doc:`pair_style ` command. The *iparam* and *jparam* keywords can be used to limit the bonding functionality of the participating atoms. Each atom keeps track of @@ -106,7 +106,7 @@ The *newtype* value for *iparam* and *jparam* can be used to change the atom type of atom I or J when it reaches *maxbond* number of bonds of type *bondtype*\ . This means it can now interact in a pairwise fashion with other atoms in a different way by specifying different -:doc:`pair\_coeff ` coefficients. If you do not wish the +:doc:`pair_coeff ` coefficients. If you do not wish the atom type to change, simply specify *newtype* as *itype* or *jtype*\ . The *prob* keyword can also effect whether an eligible bond is @@ -132,10 +132,10 @@ of new bonds, angles, etc. molecule retain their original molecule IDs. If the *atype* keyword is used and if an angle potential is defined -via the :doc:`angle\_style ` command, then any new 3-body +via the :doc:`angle_style ` command, then any new 3-body interactions inferred by the creation of a bond will create new angles of type *angletype*\ , with parameters assigned by the corresponding -:doc:`angle\_coeff ` command. Likewise, the *dtype* and +:doc:`angle_coeff ` command. Likewise, the *dtype* and *itype* keywords will create new dihedrals and impropers of type *dihedraltype* and *impropertype*\ . @@ -149,8 +149,8 @@ of type *angletype*\ , with parameters assigned by the corresponding "extra bond per atom" parameter must be set to allow for it. Ditto for "extra angle per atom", "extra dihedral per atom", and "extra improper per atom" if angles, dihedrals, or impropers are being added - when bonds are created. See the :doc:`read\_data ` or - :doc:`create\_box ` command for more details. Note that a + when bonds are created. See the :doc:`read_data ` or + :doc:`create_box ` command for more details. Note that a data file with no atoms can be used if you wish to add non-bonded atoms via the :doc:`create atoms ` command, e.g. for a percolation simulation. @@ -165,8 +165,8 @@ of type *angletype*\ , with parameters assigned by the corresponding molecular topology of your system. The "extra special per atom" parameter must typically be set to allow for the new maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 2 - ways to do this. See the :doc:`read\_data ` or - :doc:`create\_box ` commands for details. + ways to do this. See the :doc:`read_data ` or + :doc:`create_box ` commands for details. .. note:: @@ -174,20 +174,20 @@ of type *angletype*\ , with parameters assigned by the corresponding keywords, the list of topological neighbors is updated for atoms affected by the new bond. This in turn affects which neighbors are considered for pairwise interactions, using the weighting rules set by - the :doc:`special\_bonds ` command. Consider a new bond + the :doc:`special_bonds ` command. Consider a new bond created between atoms I,J. If J has a bonded neighbor K, then K becomes a 2nd neighbor of I. Even if the *atype* keyword is not used to create angle I-J-K, the pairwise interaction between I and K will be potentially turned off or weighted by the 1-3 weighting specified - by the :doc:`special\_bonds ` command. This is the case + by the :doc:`special_bonds ` command. This is the case even if the "angle yes" option was used with that command. The same is true for 3rd neighbors (1-4 interactions), the *dtype* keyword, and the "dihedral yes" option used with the - :doc:`special\_bonds ` command. + :doc:`special_bonds ` command. Note that even if your simulation starts with no bonds, you must -define a :doc:`bond\_style ` and use the -:doc:`bond\_coeff ` command to specify coefficients for the +define a :doc:`bond_style ` and use the +:doc:`bond_coeff ` command to specify coefficients for the *bondtype*\ . Similarly, if new atom types are specified by the *iparam* or *jparam* keywords, they must be within the range of atom types allowed by the simulation and pairwise coefficients must be @@ -201,7 +201,7 @@ created, neighbor lists must be immediately updated on the same timestep. This is to insure that any pairwise interactions that should be turned "off" due to a bond creation, because they are now excluded by the presence of the bond and the settings of the -:doc:`special\_bonds ` command, will be immediately +:doc:`special_bonds ` command, will be immediately recognized. All of these operations increase the cost of a timestep. Thus you should be cautious about invoking this fix too frequently. @@ -224,7 +224,7 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes two statistics which it stores in a global vector of @@ -251,7 +251,7 @@ Related commands """""""""""""""" :doc:`fix bond/break `, :doc:`fix bond/react `, :doc:`fix bond/swap `, -:doc:`dump local `, :doc:`special\_bonds ` +:doc:`dump local `, :doc:`special_bonds ` Default """"""" diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index b2866eb9c7..ec9533788e 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -248,7 +248,7 @@ A discussion of correctly handling this is also provided on the the existing system and reaction templates. As when inserting molecules, enough space for this increased topology/atom must be reserved by using the relevant "extra" keywords to the - :doc:`read\_data ` or :doc:`create\_box ` commands. + :doc:`read_data ` or :doc:`create_box ` commands. The map file is a text document with the following format: @@ -492,7 +492,7 @@ local command. Cumulative reaction counts for each reaction are written to :doc:`binary restart files `. These values are associated with the reaction name (react-ID). Additionally, internally-created per-atom properties are stored to allow for smooth restarts. None of the -:doc:`fix\_modify ` options are relevant to this fix. +:doc:`fix_modify ` options are relevant to this fix. This fix computes one statistic for each *react* argument that it stores in a global vector, of length 'number of react arguments', that @@ -524,7 +524,7 @@ Related commands :doc:`fix bond/create `, :doc:`fix bond/break `, :doc:`fix bond/swap `, -:doc:`dump local `, :doc:`special\_bonds ` +:doc:`dump local `, :doc:`special_bonds ` Default """"""" diff --git a/doc/src/fix_bond_swap.rst b/doc/src/fix_bond_swap.rst index c4eb2a16b5..b341fea35b 100644 --- a/doc/src/fix_bond_swap.rst +++ b/doc/src/fix_bond_swap.rst @@ -41,7 +41,7 @@ gyration. It is designed for use with systems of :doc:`FENE ` or :doc:`harmonic ` bead-spring polymer chains where each polymer is a linear chain of monomers, but LAMMPS does not enforce this requirement, i.e. any -:doc:`bond\_style ` can be used. +:doc:`bond_style ` can be used. A schematic of the kinds of bond swaps that can occur is shown here: @@ -86,7 +86,7 @@ by this processor on this timestep. The criterion for matching molecule IDs is how bond swaps performed by this fix conserve chain length. To use this features you must setup the molecule IDs for your polymer chains in a certain way, typically -in the data file, read by the :doc:`read\_data ` command. +in the data file, read by the :doc:`read_data ` command. Consider a system of 6-mer chains. You have 2 choices. If the molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then swaps will conserve chain length. For a particular monomer there will @@ -134,11 +134,11 @@ appended and the group for the new compute is "all", so that the temperature of the entire system is used. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -157,7 +157,7 @@ each processor generates possible swaps independently of other processors. Thus if you repeat the same simulation on a different number of processors, the specific swaps performed will be different. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have defined to this fix which will be used to compute the temperature for the Boltzmann criterion. diff --git a/doc/src/fix_box_relax.rst b/doc/src/fix_box_relax.rst index 315846a943..02e5f97736 100644 --- a/doc/src/fix_box_relax.rst +++ b/doc/src/fix_box_relax.rst @@ -67,7 +67,7 @@ varied together during the minimization. Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable -dimensions (x,y,z,xy,xz,yz). The :doc:`create\_box `, :doc:`read data `, and :doc:`read\_restart ` commands +dimensions (x,y,z,xy,xz,yz). The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. @@ -315,11 +315,11 @@ as the fix group. Also note that the pressure compute does not include a kinetic component. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -331,7 +331,7 @@ It also means that changing attributes of *thermo\_temp* or No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its temperature and pressure calculation, as described above. Note @@ -357,7 +357,7 @@ energy, plus the strain energy, if it exists, as described above. The energy values reported at the end of a minimization run under "Minimization stats" include this energy, and so differ from what LAMMPS normally reports as potential energy. This fix does not support -the :doc:`fix\_modify ` *energy* option, because that would +the :doc:`fix_modify ` *energy* option, because that would result in double-counting of the fix energy in the minimization energy. Instead, the fix energy can be explicitly added to the potential energy using one of these two variants: @@ -385,8 +385,8 @@ Only dimensions that are available can be adjusted by this fix. Non-periodic dimensions are not available. *z*\ , *xz*\ , and *yz*\ , are not available for 2D simulations. *xy*\ , *xz*\ , and *yz* are only available if the simulation domain is non-orthogonal. The -:doc:`create\_box `, :doc:`read data `, and -:doc:`read\_restart ` commands specify whether the +:doc:`create_box `, :doc:`read data `, and +:doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. diff --git a/doc/src/fix_client_md.rst b/doc/src/fix_client_md.rst index d935144cc0..01539b6d68 100644 --- a/doc/src/fix_client_md.rst +++ b/doc/src/fix_client_md.rst @@ -53,8 +53,8 @@ that LAMMPS exchanges with the server code is defined on the :doc:`server md `, :doc:`bond\_style `, or -:doc:`kspace\_style ` command. However it is possible for +:doc:`pair_style `, :doc:`bond_style `, or +:doc:`kspace_style ` command. However it is possible for a server code to only compute a portion of the full force-field, while LAMMPS computes the remaining part. Your LAMMPS script can also specify boundary conditions or force constraints in the usual way, @@ -74,11 +74,11 @@ LAMMPS and another code in tandem to perform a coupled simulation. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential energy computed by the server application to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the server application's contribution to the system's virial as part of :doc:`thermodynamic output `. The default is *virial yes* diff --git a/doc/src/fix_cmap.rst b/doc/src/fix_cmap.rst index abdf095959..70e1dd5987 100644 --- a/doc/src/fix_cmap.rst +++ b/doc/src/fix_cmap.rst @@ -76,7 +76,7 @@ remaining 5 columns are the atom IDs of the atoms in the two 4-atom dihedrals that overlap to create the CMAP 5-body interaction. Note that the "crossterm" and "CMAP" keywords for the header and body sections match those specified in the read\_data command following the -data file name; see the :doc:`read\_data ` doc page for +data file name; see the :doc:`read_data ` doc page for more details. A data file containing CMAP cross-terms can be generated from a PDB @@ -88,7 +88,7 @@ more information. The potential energy associated with CMAP interactions can be output as described below. It can also be included in the total potential energy of the system, as output by the -:doc:`thermo\_style ` command, if the :doc:`fix\_modify energy ` command is used, as in the example above. See +:doc:`thermo_style ` command, if the :doc:`fix_modify energy ` command is used, as in the example above. See the note below about how to include the CMAP energy when performing an :doc:`energy minimization `. @@ -98,16 +98,16 @@ the note below about how to include the CMAP energy when performing an **Restart, fix\_modify, output, run start/stop, minimize info:** -This fix writes the list of CMAP cross-terms to :doc:`binary restart files `. See the :doc:`read\_restart ` command +This fix writes the list of CMAP cross-terms to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential "energy" of the CMAP interactions system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the interaction between atoms to the system's virial as part of :doc:`thermodynamic output `. The default is *virial yes* @@ -128,15 +128,15 @@ invoked by the :doc:`minimize ` command. If you want the potential energy associated with the CMAP terms forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the - :doc:`fix\_modify ` *energy* option for this fix. + :doc:`fix_modify ` *energy* option for this fix. Restrictions """""""""""" To function as expected this fix command must be issued *before* a -:doc:`read\_data ` command but *after* a -:doc:`read\_restart ` command. +:doc:`read_data ` command but *after* a +:doc:`read_restart ` command. This fix can only be used if LAMMPS was built with the MOLECULE package. See the :doc:`Build package ` doc page for more @@ -145,7 +145,7 @@ info. Related commands """""""""""""""" -:doc:`fix\_modify `, :doc:`read\_data ` +:doc:`fix_modify `, :doc:`read_data ` **Default:** none diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst index bd29a394cb..eac0e21d76 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -74,7 +74,7 @@ no restriction to functionality by limiting the number of colvars fixes. The *input* keyword allows to specify a state file that would contain the restart information required in order to continue a calculation from a prerecorded state. Fix colvars records it state in :doc:`binary restart ` -files, so when using the :doc:`read\_restart ` command, +files, so when using the :doc:`read_restart ` command, this is usually not needed. The *output* keyword allows to specify the output prefix. All output @@ -103,7 +103,7 @@ This fix writes the current status of the colvars module into mode status file that is written by the colvars module itself and the kind of information in both files is identical. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change from the biasing force added by the fix to the system's potential energy as part of :doc:`thermodynamic output `. diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst index 906be7ca7c..55be294df8 100644 --- a/doc/src/fix_controller.rst +++ b/doc/src/fix_controller.rst @@ -194,7 +194,7 @@ equal-style versus internal-style variable interchangeably. **Restart, fix\_modify, output, run start/stop, minimize info:** -Currently, no information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +Currently, no information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a global vector with 3 values which can be accessed diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index dc0b566678..fe1b0925d6 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -114,10 +114,10 @@ unspecified parameters can also be controlled by a :doc:`fix npt ` or :d The size and shape of the simulation box at the beginning of the simulation run were either specified by the -:doc:`create\_box ` or :doc:`read\_data ` or -:doc:`read\_restart ` command used to setup the simulation +:doc:`create_box ` or :doc:`read_data ` or +:doc:`read_restart ` command used to setup the simulation initially if it is the first run, or they are the values from the end -of the previous run. The :doc:`create\_box `, :doc:`read data `, and :doc:`read\_restart ` commands +of the previous run. The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. If fix deform changes the xy,xz,yz tilt factors, then the simulation box @@ -578,7 +578,7 @@ been previously used to define the lattice spacing. Note that the units choice also affects the *vel* style parameters since it is defined in terms of distance/time. Also note that the units keyword does not affect the *variable* style. You should use the *xlat*\ , -*ylat*\ , *zlat* keywords of the :doc:`thermo\_style ` +*ylat*\ , *zlat* keywords of the :doc:`thermo_style ` command if you want to include lattice spacings in a variable formula. @@ -607,7 +607,7 @@ instructions on how to use the accelerated styles effectively. This fix will restore the initial box settings from :doc:`binary restart files `, which allows the fix to be properly continue deformation, when using the start/stop options of the :doc:`run ` -command. None of the :doc:`fix\_modify ` options are +command. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. @@ -630,7 +630,7 @@ xy) that is shrink-wrapped via the :doc:`boundary ` command. Related commands """""""""""""""" -:doc:`change\_box ` +:doc:`change_box ` Default """"""" diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index 29b4381441..c076d80ed4 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -100,7 +100,7 @@ default group "all" and the group specified in the fix deposit command If you are computing temperature values which include inserted particles, you will want to use the -:doc:`compute\_modify ` dynamic option, which insures the +:doc:`compute_modify ` dynamic option, which insures the current number of atoms is used as a normalizing factor each time the temperature is computed. @@ -115,7 +115,7 @@ prevent this behavior. Note that if a shrink-wrap boundary is used, it is OK to insert the new particle outside the box, however the box will immediately be expanded to include the new particle. When simulating a sputtering experiment it is probably more realistic to -ignore those atoms using the :doc:`thermo\_modify ` +ignore those atoms using the :doc:`thermo_modify ` command with the *lost ignore* option and a fixed :doc:`boundary `. @@ -272,7 +272,7 @@ units of distance or velocity. If you are monitoring the temperature of a system where the atom count is changing due to adding particles, you typically should use - the :doc:`compute\_modify dynamic yes ` command for the + the :doc:`compute_modify dynamic yes ` command for the temperature compute you are using. **Restart, fix\_modify, output, run start/stop, minimize info:** @@ -280,17 +280,17 @@ units of distance or velocity. This fix writes the state of the deposition to :doc:`binary restart files `. This includes information about how many particles have been deposited, the random number generator seed, the next timestep for deposition, etc. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. .. note:: For this to work correctly, the timestep must **not** be changed - after reading the restart with :doc:`reset\_timestep `. + after reading the restart with :doc:`reset_timestep `. The fix will try to detect it and stop with an error. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index e2cedd0d9f..09fc23ac66 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -39,10 +39,10 @@ the particle internal energy through a mesoparticle equation of state. An additional fix must be specified that defines the equation of state for each particle, e.g. :doc:`fix eos/cv `. -This fix must be used with the :doc:`pair\_style dpd/fdt/energy ` command. +This fix must be used with the :doc:`pair_style dpd/fdt/energy ` command. Note that numerous variants of DPD can be specified by choosing an -appropriate combination of the integrator and :doc:`pair\_style dpd/fdt/energy ` command. DPD under isoenergetic conditions +appropriate combination of the integrator and :doc:`pair_style dpd/fdt/energy ` command. DPD under isoenergetic conditions can be specified by using fix *dpd/energy*\ , fix *nve* and pair\_style *dpd/fdt/energy*\ . DPD under isoenthalpic conditions can be specified by using fix *dpd/energy*\ , fix *nph* and pair\_style @@ -85,7 +85,7 @@ LAMMPS was built with that package. See the :doc:`Build package This fix must be used with an additional fix that specifies time integration, e.g. :doc:`fix nve `. -The fix *dpd/energy* requires the *dpd* :doc:`atom\_style ` +The fix *dpd/energy* requires the *dpd* :doc:`atom_style ` to be used in order to properly account for the particle internal energies and temperature. diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 66895f2538..d23fbff1c9 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -72,7 +72,7 @@ cuboid domain to apply the source flux to. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -85,13 +85,13 @@ Restrictions This fix is part of the USER-MESO package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -Fix *edpd/source* must be used with the :doc:`pair\_style edpd ` command. Fix *tdpd/source* must be used with the -:doc:`pair\_style tdpd ` command. +Fix *edpd/source* must be used with the :doc:`pair_style edpd ` command. Fix *tdpd/source* must be used with the +:doc:`pair_style tdpd ` command. Related commands """""""""""""""" -:doc:`pair\_style edpd `, :doc:`pair\_style tdpd `, +:doc:`pair_style edpd `, :doc:`pair_style tdpd `, :doc:`compute edpd/temp/atom `, :doc:`compute tdpd/cc/atom ` **Default:** none diff --git a/doc/src/fix_drag.rst b/doc/src/fix_drag.rst index 9490f58f01..bc1476301a 100644 --- a/doc/src/fix_drag.rst +++ b/doc/src/fix_drag.rst @@ -44,7 +44,7 @@ in the simulation. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. diff --git a/doc/src/fix_drude.rst b/doc/src/fix_drude.rst index 4a39c7abc8..d58d1c6d6a 100644 --- a/doc/src/fix_drude.rst +++ b/doc/src/fix_drude.rst @@ -44,12 +44,12 @@ Restrictions This fix should be invoked before any other commands that implement -the Drude oscillator model, such as :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair\_style thole `. +the Drude oscillator model, such as :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair_style thole `. Related commands """""""""""""""" -:doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair\_style thole ` +:doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair_style thole ` **Default:** None diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index 58c3628dce..f54fce6a43 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -211,7 +211,7 @@ Related commands :doc:`fix drude `, :doc:`fix langevin/drude `, :doc:`compute temp/drude `, -:doc:`pair\_style thole ` +:doc:`pair_style thole ` **Default:** none diff --git a/doc/src/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst index b99161934f..ba34dee50b 100644 --- a/doc/src/fix_dt_reset.rst +++ b/doc/src/fix_dt_reset.rst @@ -81,11 +81,11 @@ outer loop (largest) timestep, which is the same timestep that the Note that the cumulative simulation time (in time units), which accounts for changes in the timestep size as a simulation proceeds, -can be accessed by the :doc:`thermo\_style time ` keyword. +can be accessed by the :doc:`thermo_style time ` keyword. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which can be accessed by various diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst index c5228a0cc3..faf4d9c81a 100644 --- a/doc/src/fix_efield.rst +++ b/doc/src/fix_efield.rst @@ -58,7 +58,7 @@ gradients of the field are required for the force and torque on dipoles. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent E-field. @@ -126,7 +126,7 @@ minimization will not converge properly. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential "energy" inferred by the added force due to the electric field to the system's potential energy as part of :doc:`thermodynamic output `. This is a fictitious @@ -135,12 +135,12 @@ can include the forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added force due to the electric field. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the added forces on atoms to the system's virial as part of :doc:`thermodynamic output `. The default is *virial no* -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix adding its forces. Default is the outermost level. @@ -164,7 +164,7 @@ the iteration count during the minimization. If you want the fictitious potential energy associated with the added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the - :doc:`fix\_modify ` *energy* option for this fix. + :doc:`fix_modify ` *energy* option for this fix. Restrictions """""""""""" diff --git a/doc/src/fix_ehex.rst b/doc/src/fix_ehex.rst index 4c4487b11b..2a8a4c8f67 100644 --- a/doc/src/fix_ehex.rst +++ b/doc/src/fix_ehex.rst @@ -118,7 +118,7 @@ cool continuously. heat is added/subtracted less frequently but in larger portions. The resulting temperature profile will therefore be the same. -This fix will default to :doc:`fix\_heat ` (HEX algorithm) if +This fix will default to :doc:`fix_heat ` (HEX algorithm) if the keyword *hex* is specified. @@ -166,7 +166,7 @@ constraints will be satisfied. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst index 3329681333..6589d4b69d 100644 --- a/doc/src/fix_electron_stopping.rst +++ b/doc/src/fix_electron_stopping.rst @@ -68,7 +68,7 @@ its velocity and :math:`S_e` is the stopping power of the ion. :doc:`fix dt/reset `) and the repulsive ZBL potential (see :doc:`ZBL ` potential) or similar. Without these settings the interaction between the ion and the target atoms will be faulty. It is also - common to use in such simulations a thermostat (:doc:`fix\_nvt `) in + common to use in such simulations a thermostat (:doc:`fix_nvt `) in the borders of the simulation cell. .. note:: @@ -79,7 +79,7 @@ its velocity and :math:`S_e` is the stopping power of the ion. e.g. simulations of Swift Heavy Ions (energy per nucleon of 100 keV/amu or higher) or multiple projectiles. You could compensate energy loss by coupling bulk atoms with some thermostat or control heat transfer between electronic and - atomic subsystems with the two-temperature model (:doc:`fix\_ttm `). + atomic subsystems with the two-temperature model (:doc:`fix_ttm `). At low velocities the electronic stopping is negligible. The electronic friction is not applied to atoms whose kinetic energy is smaller than *Ecut*\ , @@ -141,7 +141,7 @@ to derive the stopping power. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` options are not supported. +The :doc:`fix_modify ` options are not supported. This fix computes a global scalar, which can be accessed by various :doc:`output commands `. The scalar is the total energy diff --git a/doc/src/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst index bef732a82d..7c4934d223 100644 --- a/doc/src/fix_enforce2d.rst +++ b/doc/src/fix_enforce2d.rst @@ -60,7 +60,7 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_eos_cv.rst b/doc/src/fix_eos_cv.rst index 850d0ecde3..7c309ec135 100644 --- a/doc/src/fix_eos_cv.rst +++ b/doc/src/fix_eos_cv.rst @@ -50,7 +50,7 @@ Restrictions This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This command also requires use of the :doc:`atom\_style dpd ` +This command also requires use of the :doc:`atom_style dpd ` command. Related commands diff --git a/doc/src/fix_eos_table.rst b/doc/src/fix_eos_table.rst index 3953d31f2d..d1cb88edf4 100644 --- a/doc/src/fix_eos_table.rst +++ b/doc/src/fix_eos_table.rst @@ -113,7 +113,7 @@ Restrictions This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This command also requires use of the :doc:`atom\_style dpd ` +This command also requires use of the :doc:`atom_style dpd ` command. The equation of state must be a monotonically increasing function. diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index 622e24dd79..8b94ef9459 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -206,7 +206,7 @@ Restrictions This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This command also requires use of the :doc:`atom\_style dpd ` +This command also requires use of the :doc:`atom_style dpd ` command. The equation of state must be a monotonically increasing function. diff --git a/doc/src/fix_evaporate.rst b/doc/src/fix_evaporate.rst index 24954ec3da..75c6b2bcbe 100644 --- a/doc/src/fix_evaporate.rst +++ b/doc/src/fix_evaporate.rst @@ -73,12 +73,12 @@ incur overhead due to the cost of building neighbor lists. If you are monitoring the temperature of a system where the atom count is changing due to evaporation, you typically should use the - :doc:`compute\_modify dynamic yes ` command for the + :doc:`compute_modify dynamic yes ` command for the temperature compute you are using. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar, which can be accessed by various diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst index fcd283ccc2..8e7ca5b2e1 100644 --- a/doc/src/fix_external.rst +++ b/doc/src/fix_external.rst @@ -144,7 +144,7 @@ insure this energy setting is used appropriately in a minimization. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential "energy" set by the external driver to the system's potential energy as part of :doc:`thermodynamic output `. This is a fictitious quantity but is needed so that the :doc:`minimize ` command can include the @@ -152,7 +152,7 @@ forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added force. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the interactions computed by the external program to the system's virial as part of :doc:`thermodynamic output `. The default is *virial yes* @@ -171,7 +171,7 @@ invoked by the :doc:`minimize ` command. If you want the fictitious potential energy associated with the added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the - :doc:`fix\_modify ` *energy* option for this fix. + :doc:`fix_modify ` *energy* option for this fix. Restrictions """""""""""" diff --git a/doc/src/fix_ffl.rst b/doc/src/fix_ffl.rst index b914c23940..67e386c26f 100644 --- a/doc/src/fix_ffl.rst +++ b/doc/src/fix_ffl.rst @@ -95,7 +95,7 @@ This fix can ramp its target temperature over multiple runs, using the *start* and *stop* keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Langevin thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -119,7 +119,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair\_style dpd/tstat `, :doc:`fix gld `, :doc:`fix gle ` +:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair_style dpd/tstat `, :doc:`fix gld `, :doc:`fix gle ` ---------- diff --git a/doc/src/fix_filter_corotate.rst b/doc/src/fix_filter_corotate.rst index 50db945a37..b6765c25b4 100644 --- a/doc/src/fix_filter_corotate.rst +++ b/doc/src/fix_filter_corotate.rst @@ -44,7 +44,7 @@ method. In biomolecular simulations, it allows the usage of larger timesteps for long-range electrostatic interactions. For details, see :ref:`(Fath) `. -When using :doc:`run\_style respa ` for a biomolecular +When using :doc:`run_style respa ` for a biomolecular simulation with high-frequency covalent bonds, the outer time-step is restricted to below ~ 4fs due to resonance problems. This fix filters the outer stage of the respa and thus a larger (outer) time-step can @@ -60,7 +60,7 @@ is slightly modified only for the computation of long-range forces. A good cluster decomposition constitutes in building clusters which contain the fastest covalent bonds inside clusters. -If the clusters are chosen suitably, the :doc:`run\_style respa ` is stable for outer time-steps of at least 8fs. +If the clusters are chosen suitably, the :doc:`run_style respa ` is stable for outer time-steps of at least 8fs. ---------- @@ -68,7 +68,7 @@ If the clusters are chosen suitably, the :doc:`run\_style respa ` is **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about these fixes is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about these fixes is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to these fixes. No global or per-atom quantities are stored by these fixes for access by various :doc:`output commands `. No parameter of these fixes can be used with the *start/stop* keywords of the :doc:`run ` command. These diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst index fa1d65c999..728ef17387 100644 --- a/doc/src/fix_flow_gauss.rst +++ b/doc/src/fix_flow_gauss.rst @@ -93,7 +93,7 @@ fluctuating in time, the work cannot be computed from a potential. As a result, computing the work is slightly more computationally expensive than usual, so it is not performed by default. To invoke the work calculation, use the *energy* keyword. The -:doc:`fix\_modify ` *energy* option also invokes the work +:doc:`fix_modify ` *energy* option also invokes the work calculation, and overrides an *energy no* setting here. If neither *energy yes* or *fix\_modify energy yes* are set, the global scalar computed by the fix will return zero. @@ -109,7 +109,7 @@ If this fix is used in a simulation with the :doc:`rRESPA ` integrator, the applied acceleration must be computed and applied at the same rRESPA level as the interactions between the flowing fluid and the obstacle. The rRESPA level at which the acceleration is applied can be changed using -the :doc:`fix\_modify ` *respa* option discussed below. If the +the :doc:`fix_modify ` *respa* option discussed below. If the flowing fluid and the obstacle interact through multiple interactions that are computed at different rRESPA levels, then there must be a separate flow/gauss fix for each level. For example, if the flowing fluid and obstacle interact @@ -129,11 +129,11 @@ LAMMPS was built with that package. See the :doc:`Build package No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to subtract the work done from the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows the user to set at which level of the :doc:`rRESPA ` integrator the fix computes and adds the external acceleration. Default is the outermost level. diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst index 773eacf509..cc67f969df 100644 --- a/doc/src/fix_freeze.rst +++ b/doc/src/fix_freeze.rst @@ -64,7 +64,7 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global 3-vector of forces, which can be accessed @@ -91,7 +91,7 @@ this fix is applied. Related commands """""""""""""""" -:doc:`atom\_style sphere `, :doc:`fix setforce ` +:doc:`atom_style sphere `, :doc:`fix setforce ` **Default:** none diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst index 9f64be8699..6b6af93fdc 100644 --- a/doc/src/fix_gcmc.rst +++ b/doc/src/fix_gcmc.rst @@ -343,7 +343,7 @@ include: :doc:`efield `, :doc:`gravity `, For that energy to be included in the total potential energy of the system (the quantity used when performing GCMC exchange and MC moves), you MUST enable -the :doc:`fix\_modify ` *energy* option for that fix. The +the :doc:`fix_modify ` *energy* option for that fix. The doc pages for individual :doc:`fix ` commands specify if this should be done. @@ -355,7 +355,7 @@ about simulating non-neutral systems with kspace on. Use of this fix typically will cause the number of atoms to fluctuate, therefore, you will want to use the -:doc:`compute\_modify dynamic/dof ` command to insure that the +:doc:`compute_modify dynamic/dof ` command to insure that the current number of atoms is used as a normalizing factor each time temperature is computed. A simple example of this is: @@ -403,17 +403,17 @@ adds all inserted atoms of the specified type to the This fix writes the state of the fix to :doc:`binary restart files `. This includes information about the random number generator seed, the next timestep for MC exchanges, the number of MC step attempts and successes etc. See -the :doc:`read\_restart ` command for info on how to +the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. .. note:: For this to work correctly, the timestep must **not** be changed - after reading the restart with :doc:`reset\_timestep `. + after reading the restart with :doc:`reset_timestep `. The fix will try to detect it and stop with an error. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global vector of length 8, which can be accessed @@ -471,7 +471,7 @@ Related commands :doc:`fix atom/swap `, :doc:`fix nvt `, :doc:`neighbor `, :doc:`fix deposit `, :doc:`fix evaporate `, -:doc:`delete\_atoms ` +:doc:`delete_atoms ` Default """"""" diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst index 03b5aa418b..4826ce07ff 100644 --- a/doc/src/fix_gld.rst +++ b/doc/src/fix_gld.rst @@ -137,7 +137,7 @@ do "exact" restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. @@ -158,7 +158,7 @@ Related commands """""""""""""""" :doc:`fix langevin `, :doc:`fix viscous `, -:doc:`pair\_style dpd/tstat ` +:doc:`pair_style dpd/tstat ` Default """"""" diff --git a/doc/src/fix_gle.rst b/doc/src/fix_gle.rst index ecb03618f5..53efdf91a5 100644 --- a/doc/src/fix_gle.rst +++ b/doc/src/fix_gle.rst @@ -121,7 +121,7 @@ This fix can ramp its target temperature over multiple runs, using the *start* and *stop* keywords of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Langevin thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -150,7 +150,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair\_style dpd/tstat `, :doc:`fix gld ` +:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair_style dpd/tstat `, :doc:`fix gld ` ---------- diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index e8aae5a910..87ed196a90 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -93,7 +93,7 @@ insure that the variable calculates a result in the appropriate units, e.g. force/mass or degrees. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent gravitational field. @@ -128,11 +128,11 @@ instructions on how to use the accelerated styles effectively. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the gravitational potential energy of the system to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -153,7 +153,7 @@ Restrictions Related commands """""""""""""""" -:doc:`atom\_style sphere `, :doc:`fix addforce ` +:doc:`atom_style sphere `, :doc:`fix addforce ` **Default:** none diff --git a/doc/src/fix_grem.rst b/doc/src/fix_grem.rst index 598131a935..68e143b1ad 100644 --- a/doc/src/fix_grem.rst +++ b/doc/src/fix_grem.rst @@ -90,7 +90,7 @@ temperature changes. Replicas are easily added where needed. No information about this fix is written to :doc:`binary restart files `. -The :doc:`thermo\_modify ` *press* option is supported +The :doc:`thermo_modify ` *press* option is supported by this fix to add the rescaled kinetic pressure as part of :doc:`thermodynamic output `. @@ -104,7 +104,7 @@ LAMMPS was built with that package. See the :doc:`Build package ` Related commands """""""""""""""" -:doc:`temper/grem `, :doc:`fix nvt `, :doc:`fix npt `, :doc:`thermo\_modify ` +:doc:`temper/grem `, :doc:`fix nvt `, :doc:`fix npt `, :doc:`thermo_modify ` **Default:** none diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst index 4eaa75abb8..e020ea7e26 100644 --- a/doc/src/fix_halt.rst +++ b/doc/src/fix_halt.rst @@ -128,8 +128,8 @@ If its value is *soft*\ , LAMMPS will exit the current run, but continue to execute subsequent commands in the input script. However, additional :doc:`run ` or :doc:`minimize ` commands will be skipped. For example, this allows a script to output the current -state of the system, e.g. via a :doc:`write\_dump ` or -:doc:`write\_restart ` command. +state of the system, e.g. via a :doc:`write_dump ` or +:doc:`write_restart ` command. If its value is *continue*\ , the behavior is the same as for *soft*\ , except subsequent :doc:`run ` or :doc:`minimize ` commands @@ -148,7 +148,7 @@ files. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_heat.rst b/doc/src/fix_heat.rst index 1972eb2b03..c96a88ee35 100644 --- a/doc/src/fix_heat.rst +++ b/doc/src/fix_heat.rst @@ -82,7 +82,7 @@ name. In this case, the variable will be evaluated each timestep, and its value(s) used to determine the flux. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent flux. @@ -114,7 +114,7 @@ by another fix - e.g. :doc:`fix nvt ` or :doc:`fix langevin `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which can be accessed by various diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst index 7aa5891e25..579d6cc681 100644 --- a/doc/src/fix_hyper_global.rst +++ b/doc/src/fix_hyper_global.rst @@ -210,7 +210,7 @@ algorithm. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy of the bias potential to the system's potential energy as part of :doc:`thermodynamic output `. diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst index 31c606380a..6758c747b6 100644 --- a/doc/src/fix_hyper_local.rst +++ b/doc/src/fix_hyper_local.rst @@ -249,7 +249,7 @@ well for many solid-state systems. atoms move (between quenched states) to be considered an "event". It is an argument to the "compute event/displace" command used to detect events. By default the ghost communication distance is set by the - pair\_style cutoff, which will typically be < *Dcut*\ . The :doc:`comm\_modify cutoff ` command should be used to override the ghost + pair\_style cutoff, which will typically be < *Dcut*\ . The :doc:`comm_modify cutoff ` command should be used to override the ghost cutoff explicitly, e.g. @@ -378,7 +378,7 @@ enabled by these keywords. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy of the bias potential to the system's potential energy as part of :doc:`thermodynamic output `. @@ -475,7 +475,7 @@ the communication cutoff for ghosts is too close to *Dcut* leading to many not-found ghost atoms before the next event. This may lead to a reduced number of bonds being selected for biasing, since the code assumes those atoms are part of highly strained bonds. As explained -above, the :doc:`comm\_modify cutoff ` command can be used +above, the :doc:`comm_modify cutoff ` command can be used to set a longer cutoff. For value 22, no two bonds should be biased if they are within a diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index b688316546..75c5ccc741 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -150,7 +150,7 @@ screen output is active. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst index c130ede009..ea8aa28b41 100644 --- a/doc/src/fix_indent.rst +++ b/doc/src/fix_indent.rst @@ -110,12 +110,12 @@ will be evaluated each timestep, and its value used to define the indenter geometry. Note that equal-style variables can specify formulas with various -mathematical functions, and include :doc:`thermo\_style ` +mathematical functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify indenter properties that change as a function of time or span consecutive runs in a continuous fashion. For the latter, see the *start* and *stop* keywords of the -:doc:`run ` command and the *elaplong* keyword of :doc:`thermo\_style custom ` for details. +:doc:`run ` command and the *elaplong* keyword of :doc:`thermo_style custom ` for details. For example, if a spherical indenter's x-position is specified as v\_x, then this variable definition will keep it's center at a relative @@ -169,7 +169,7 @@ cylindrical indenter is scaled by the x lattice spacing. Note that the units keyword only affects indenter geometry parameters specified directly with numbers, not those specified as variables. In the latter case, you should use the *xlat*\ , *ylat*\ , *zlat* keywords of -the :doc:`thermo\_style ` command if you want to include +the :doc:`thermo_style ` command if you want to include lattice spacings in a variable formula. The force constant *K* is not affected by the *units* keyword. It is @@ -177,7 +177,7 @@ always in force/distance\^2 units where force and distance are defined by the :doc:`units ` command. If you wish K to be scaled by the lattice spacing, you can define K with a variable whose formula contains *xlat*\ , *ylat*\ , *zlat* keywords of the -:doc:`thermo\_style ` command, e.g. +:doc:`thermo_style ` command, e.g. .. parsed-literal:: @@ -189,12 +189,12 @@ contains *xlat*\ , *ylat*\ , *zlat* keywords of the No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy of interaction between atoms and the indenter to the system's potential energy as part of :doc:`thermodynamic output `. The energy of each particle interacting with the indenter is K/3 (r - R)\^3. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -214,7 +214,7 @@ check if you have done this. If you want the atom/indenter interaction energy to be included in the total potential energy of the system (the quantity being - minimized), you must enable the :doc:`fix\_modify ` *energy* + minimized), you must enable the :doc:`fix_modify ` *energy* option for this fix. Restrictions diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index d6f52084f5..429e831a11 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -74,11 +74,11 @@ will have the form: Fr is proportional to sqrt(Kb T m / (dt damp)) Fc is the conservative force computed via the usual inter-particle -interactions (:doc:`pair\_style `, -:doc:`bond\_style `, etc). +interactions (:doc:`pair_style `, +:doc:`bond_style `, etc). The Ff and Fr terms are added by this fix on a per-particle basis. -See the :doc:`pair\_style dpd/tstat ` command for a +See the :doc:`pair_style dpd/tstat ` command for a thermostatting option that adds similar terms on a pairwise basis to pairs of interacting particles. @@ -131,7 +131,7 @@ will be evaluated each timestep, and its value used to determine the target temperature. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. @@ -145,7 +145,7 @@ with :doc:`compute commands ` that remove a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or removing the x-component of velocity from the calculation. This is not done by default, but only if the -:doc:`fix\_modify ` command is used to assign a temperature +:doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following @@ -304,13 +304,13 @@ restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by this fix and by the compute should be the same. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Langevin thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. Note that use of this option requires setting the *tally* keyword to *yes*\ . @@ -337,7 +337,7 @@ with run\_style respa. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair\_style dpd/tstat ` +:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair_style dpd/tstat ` Default """"""" diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index 16de2eba8b..32546f69b0 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -152,7 +152,7 @@ specify the Drude status of each atom type. .. note:: Ghost atoms need to know their velocity for this fix to act - correctly. You must use the :doc:`comm\_modify ` command to + correctly. You must use the :doc:`comm_modify ` command to enable this, e.g. @@ -174,7 +174,7 @@ the variable will be evaluated each timestep, and its value used to determine the target temperature. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. @@ -182,7 +182,7 @@ Like other fixes that perform thermostatting, this fix can be used with :doc:`compute commands ` that remove a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms. This is not done by default, but only if the -:doc:`fix\_modify ` command is used to assign a temperature +:doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following @@ -283,7 +283,7 @@ restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by the @@ -302,7 +302,7 @@ Related commands :doc:`fix drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, -:doc:`pair\_style thole ` +:doc:`pair_style thole ` Default """"""" diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst index 0de23c65ab..d9f00a76ea 100644 --- a/doc/src/fix_langevin_eff.rst +++ b/doc/src/fix_langevin_eff.rst @@ -62,7 +62,7 @@ each atom will have the form: Fr is proportional to sqrt(Kb T m / (dt damp)) Fc is the conservative force computed via the usual inter-particle -interactions (:doc:`pair\_style `). +interactions (:doc:`pair_style `). The Ff and Fr terms are added by this fix on a per-particle basis. @@ -78,13 +78,13 @@ restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by this fix and by the compute should be the same. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Langevin thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. Note that use of this option requires setting the *tally* keyword to *yes*\ . diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index a13df3f40a..d30b911e7f 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -114,11 +114,11 @@ larger system sizes and longer time scales No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential energy computed by LATTE to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the LATTE DFTB contribution to the system's virial as part of :doc:`thermodynamic output `. The default is *virial yes* @@ -139,7 +139,7 @@ energy minimization, invoked by the :doc:`minimize ` command. If you want the potential energy associated with the DFTB forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the - :doc:`fix\_modify ` *energy* option for this fix. + :doc:`fix_modify ` *energy* option for this fix. Restrictions """""""""""" diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst index cd177b7f32..c0d924078c 100644 --- a/doc/src/fix_lb_fluid.rst +++ b/doc/src/fix_lb_fluid.rst @@ -324,7 +324,7 @@ binary restart files, if requested, independent of the main LAMMPS :doc:`binary restart files `; no information about *lb\_fluid* is written to the main LAMMPS :doc:`binary restart files `. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the diff --git a/doc/src/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst index 2f1b953db3..cfc5c07d8d 100644 --- a/doc/src/fix_lb_momentum.rst +++ b/doc/src/fix_lb_momentum.rst @@ -56,7 +56,7 @@ dimension. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_lb_pc.rst b/doc/src/fix_lb_pc.rst index f490b82981..039e315be1 100644 --- a/doc/src/fix_lb_pc.rst +++ b/doc/src/fix_lb_pc.rst @@ -33,7 +33,7 @@ algorithm if the force coupling constant has been set by default. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_lb_viscous.rst b/doc/src/fix_lb_viscous.rst index ee962dfd75..36f33037bf 100644 --- a/doc/src/fix_lb_viscous.rst +++ b/doc/src/fix_lb_viscous.rst @@ -58,7 +58,7 @@ research. As described in the :doc:`fix viscous ` documentation: -"No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +"No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -67,7 +67,7 @@ the :doc:`run ` command. The forces due to this fix are imposed during an energy minimization, invoked by the :doc:`minimize ` command. This fix should only be used with damped dynamics minimizers that allow for -non-conservative forces. See the :doc:`min\_style ` command +non-conservative forces. See the :doc:`min_style ` command for details." Restrictions diff --git a/doc/src/fix_lineforce.rst b/doc/src/fix_lineforce.rst index ef365eb75c..e317348a5e 100644 --- a/doc/src/fix_lineforce.rst +++ b/doc/src/fix_lineforce.rst @@ -36,7 +36,7 @@ it should continue to move along the line thereafter. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_manifoldforce.rst b/doc/src/fix_manifoldforce.rst index 58f98762dc..5dfdd70150 100644 --- a/doc/src/fix_manifoldforce.rst +++ b/doc/src/fix_manifoldforce.rst @@ -38,7 +38,7 @@ adequately though. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_meso.rst b/doc/src/fix_meso.rst index 6be247101e..e28514f8ea 100644 --- a/doc/src/fix_meso.rst +++ b/doc/src/fix_meso.rst @@ -35,7 +35,7 @@ LAMMPS. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_meso_move.rst b/doc/src/fix_meso_move.rst index 79d9f499e5..62804aa75c 100644 --- a/doc/src/fix_meso_move.rst +++ b/doc/src/fix_meso_move.rst @@ -83,7 +83,7 @@ internal energy and extrapolated velocity are also updated. are stored by the fix in "unwrapped" form, by using the image flags associated with each particle. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of - the :doc:`read\_data ` command for a discussion of image flags + the :doc:`read_data ` command for a discussion of image flags and how they are set for each particle. You can reset the image flags (e.g. to 0) before invoking this fix by using the :doc:`set image ` command. @@ -220,7 +220,7 @@ spacings can be different in x,y,z. This fix writes the original coordinates of moving particles to :doc:`binary restart files `, as well as the initial timestep, so that the motion can be continuous in a restarted simulation. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. @@ -231,7 +231,7 @@ operation of the fix continues in an uninterrupted fashion. different value after reading a restart file, if you expect a fix move command to work in an uninterrupted fashion. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a per-atom array which can be accessed by various @@ -252,7 +252,7 @@ This fix is part of the USER-SDPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store density and internal energy as -defined by the :doc:`atom\_style meso ` command. +defined by the :doc:`atom_style meso ` command. All particles in the group must be mesoscopic SPH/SDPD particles. @@ -260,7 +260,7 @@ Related commands """""""""""""""" :doc:`fix move `, :doc:`fix meso `, -:doc:`displace\_atoms ` +:doc:`displace_atoms ` Default """"""" diff --git a/doc/src/fix_meso_stationary.rst b/doc/src/fix_meso_stationary.rst index 5a39661cb6..5a7d53e55b 100644 --- a/doc/src/fix_meso_stationary.rst +++ b/doc/src/fix_meso_stationary.rst @@ -36,7 +36,7 @@ LAMMPS. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index ed9f82988e..baa31338ed 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -67,7 +67,7 @@ The *energy* keyword can be used with fixes that support it. *energy yes* adds a contribution to the potential energy of the system. The fix's global and per-atom energy is included in the calculation performed by the :doc:`compute pe ` or :doc:`compute pe/atom ` -commands. See the :doc:`thermo\_style ` command for info +commands. See the :doc:`thermo_style ` command for info on how potential energy is output. For fixes that tally a global energy, it can be printed by using the keyword f\_ID in the thermo\_style custom command, where ID is the fix-ID of the appropriate @@ -85,7 +85,7 @@ The *virial* keyword can be used with fixes that support it. system. The fix's global and per-atom virial is included in the calculation performed by the :doc:`compute pressure ` or :doc:`compute stress/atom ` -commands. See the :doc:`thermo\_style ` command for info +commands. See the :doc:`thermo_style ` command for info on how pressure is output. .. note:: @@ -129,7 +129,7 @@ normalized. Other thermostatting fixes, such as :doc:`fix nvt `, do not use the *dynamic/dof* keyword because they use a temperature - compute to calculate temperature. See the :doc:`compute\_modify dynamic/dof ` command for a similar way to insure + compute to calculate temperature. See the :doc:`compute_modify dynamic/dof ` command for a similar way to insure correct temperature normalization for those thermostats. The *bodyforces* keyword determines whether the forces and torques @@ -159,7 +159,7 @@ Restrictions Related commands """""""""""""""" -:doc:`fix `, :doc:`compute temp `, :doc:`compute pressure `, :doc:`thermo\_style ` +:doc:`fix `, :doc:`compute temp `, :doc:`compute pressure `, :doc:`thermo_style ` Default """"""" diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst index e3ace5a60e..e8194143d6 100644 --- a/doc/src/fix_momentum.rst +++ b/doc/src/fix_momentum.rst @@ -94,7 +94,7 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst index 6994d9aa7c..036b156630 100644 --- a/doc/src/fix_move.rst +++ b/doc/src/fix_move.rst @@ -78,7 +78,7 @@ whose movement can influence nearby atoms. are stored by the fix in "unwrapped" form, by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of - the :doc:`read\_data ` command for a discussion of image flags + the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this fix by using the :doc:`set image ` command. @@ -159,7 +159,7 @@ around the axis in the direction of rotation. This style also sets the velocity of each atom to (omega cross Rperp) where omega is its angular velocity around the rotation axis and Rperp is a perpendicular vector from the rotation axis to the atom. If the -defined :doc:`atom\_style ` assigns an angular velocity or +defined :doc:`atom_style ` assigns an angular velocity or angular momentum or orientation to each atom (:doc:`atom styles ` sphere, ellipsoid, line, tri, body), then those properties are also updated appropriately to correspond to the atom's motion and rotation over time. @@ -219,7 +219,7 @@ spacings can be different in x,y,z. This fix writes the original coordinates of moving atoms to :doc:`binary restart files `, as well as the initial timestep, so that the motion can be continuous in a restarted simulation. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. @@ -230,7 +230,7 @@ operation of the fix continues in an uninterrupted fashion. different value after reading a restart file, if you expect a fix move command to work in an uninterrupted fashion. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a per-atom array which can be accessed by various @@ -251,7 +251,7 @@ Restrictions Related commands """""""""""""""" -:doc:`fix nve `, :doc:`displace\_atoms ` +:doc:`fix nve `, :doc:`displace_atoms ` **Default:** none diff --git a/doc/src/fix_msst.rst b/doc/src/fix_msst.rst index 85fb9049c3..b22aedde7a 100644 --- a/doc/src/fix_msst.rst +++ b/doc/src/fix_msst.rst @@ -132,7 +132,7 @@ timestepping. DFTB+ will communicate its info to LAMMPS via that fix. **Restart, fix\_modify, output, run start/stop, minimize info:** -This fix writes the state of all internal variables to :doc:`binary restart files `. See the :doc:`read\_restart ` command +This fix writes the state of all internal variables to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. @@ -142,11 +142,11 @@ scalar and global vector quantities computed by the fix. The scalar is the cumulative energy change due to the fix. This is also the energy added to the potential energy by the -:doc:`fix\_modify ` *energy* command. With this command, the +:doc:`fix_modify ` *energy* command. With this command, the thermo keyword *etotal* prints the conserved quantity of the MSST dynamic equations. This can be used to test if the MD timestep is sufficiently small for accurate integration of the dynamic -equations. See also :doc:`thermo\_style ` command. +equations. See also :doc:`thermo_style ` command. The global vector contains four values in this order: diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index 9c9471fd71..e42dc84115 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -62,15 +62,15 @@ standard velocity-Verlet (VV) scheme. For more details, see :ref:`Groot `. Fix *mvv/dpd* updates the position and velocity of each atom. It can -be used with the :doc:`pair\_style mdpd ` command or other +be used with the :doc:`pair_style mdpd ` command or other pair styles such as :doc:`pair dpd `. Fix *mvv/edpd* updates the per-atom temperature, in addition to -position and velocity, and must be used with the :doc:`pair\_style edpd ` command. +position and velocity, and must be used with the :doc:`pair_style edpd ` command. Fix *mvv/tdpd* updates the per-atom chemical concentration, in addition to position and velocity, and must be used with the -:doc:`pair\_style tdpd ` command. +:doc:`pair_style tdpd ` command. ---------- @@ -78,7 +78,7 @@ addition to position and velocity, and must be used with the **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -94,8 +94,8 @@ LAMMPS was built with that package. See the :doc:`Build package ` Related commands """""""""""""""" -:doc:`pair\_style mdpd `, :doc:`pair\_style edpd `, -:doc:`pair\_style tdpd ` +:doc:`pair_style mdpd `, :doc:`pair_style edpd `, +:doc:`pair_style tdpd ` Default """"""" diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst index 5dded81f55..4d84e5d0b6 100644 --- a/doc/src/fix_neb.rst +++ b/doc/src/fix_neb.rst @@ -219,7 +219,7 @@ target energy. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_neb_spin.rst b/doc/src/fix_neb_spin.rst index 5b316f0009..859ae5ad79 100644 --- a/doc/src/fix_neb_spin.rst +++ b/doc/src/fix_neb_spin.rst @@ -48,7 +48,7 @@ See this reference for more explanation about their expression. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -69,7 +69,7 @@ page for more info. Related commands """""""""""""""" -:doc:`neb\_spin ` +:doc:`neb_spin ` Default """"""" diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 0f75125058..50abc247a1 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -181,7 +181,7 @@ Other barostat-related keywords are *pchain*\ , *mtk*\ , *ploop*\ , Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable -dimensions (x,y,z,xy,xz,yz). The :doc:`create\_box `, :doc:`read data `, and :doc:`read\_restart ` commands +dimensions (x,y,z,xy,xz,yz). The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. @@ -389,7 +389,7 @@ If the *update* keyword is used with the *dipole* value, then the orientation of the dipole moment of each particle is also updated during the time integration. This option should be used for models where a dipole moment is assigned to finite-size particles, -e.g. spheroids via use of the :doc:`atom\_style hybrid sphere dipole ` command. +e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole ` command. The default dipole orientation integrator can be changed to the Dullweber-Leimkuhler-McLachlan integration scheme @@ -478,12 +478,12 @@ commands for details. Note that the IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID + underscore + "press". Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of these fix's temperature or pressure via the -:doc:`compute\_modify ` command. Or you can print this +:doc:`compute_modify ` command. Or you can print this temperature or pressure during thermodynamic output via the -:doc:`thermo\_style custom ` command using the appropriate +:doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -493,7 +493,7 @@ temperature after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not -done by default, but only if the :doc:`fix\_modify ` command +done by default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -577,11 +577,11 @@ instructions on how to use the accelerated styles effectively. These fixes writes the state of all the thermostat and barostat variables to :doc:`binary restart files `. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by these fixes. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure, as described above. @@ -602,7 +602,7 @@ compute temperature on a subset of atoms. specified by the *press* keyword will be unaffected by the *temp* setting. -The :doc:`fix\_modify ` *energy* option is supported by these +The :doc:`fix_modify ` *energy* option is supported by these fixes to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -663,8 +663,8 @@ Restrictions periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the simulation domain is triclinic and the 2nd dimension in the keyword (\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be -barostatted for 2D simulations. The :doc:`create\_box `, -:doc:`read data `, and :doc:`read\_restart ` +barostatted for 2D simulations. The :doc:`create_box `, +:doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. @@ -690,8 +690,8 @@ over time or the atom count becomes very small. Related commands """""""""""""""" -:doc:`fix nve `, :doc:`fix\_modify `, -:doc:`run\_style ` +:doc:`fix nve `, :doc:`fix_modify `, +:doc:`run_style ` Default """"""" diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index cf6a65352f..58ed3e41cd 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -138,7 +138,7 @@ Related commands """""""""""""""" :doc:`fix nvt `, :doc:`fix nph `, :doc:`fix npt `, -:doc:`fix\_modify `, :doc:`run\_style ` +:doc:`fix_modify `, :doc:`run_style ` Default """"""" diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 35110d9cce..7c15f5ffcb 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -187,7 +187,7 @@ or fix\_ID + underscore + "press". **Restart, fix\_modify, output, run start/stop, minimize info:** The fix writes the state of all the thermostat and barostat variables, -as well as the cumulative strain applied, to :doc:`binary restart files `. See the :doc:`read\_restart ` command +as well as the cumulative strain applied, to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. @@ -199,7 +199,7 @@ uninterrupted fashion. not contain the cumulative applied strain, will this keyword be necessary. -This fix can be used with the :doc:`fix\_modify ` *temp* and +This fix can be used with the :doc:`fix_modify ` *temp* and *press* options. The temperature and pressure computes used must be of type *temp/uef* and *pressure/uef*\ . @@ -217,7 +217,7 @@ was built with that package. See the :doc:`Build package ` doc pa Due to requirements of the boundary conditions, when the *strain* keyword is set to zero (or unset), the initial simulation box must be cubic and have style triclinic. If the box is initially of type ortho, -use :doc:`change\_box ` before invoking the fix. +use :doc:`change_box ` before invoking the fix. .. note:: diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst index cea1ee71b3..88d8052a5a 100644 --- a/doc/src/fix_nph_asphere.rst +++ b/doc/src/fix_nph_asphere.rst @@ -77,11 +77,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -109,12 +109,12 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** -This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read\_restart ` +This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note @@ -123,7 +123,7 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -144,7 +144,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style ellipsoid ` +quaternion as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point @@ -154,7 +154,7 @@ shape attribute. Related commands """""""""""""""" -:doc:`fix nph `, :doc:`fix nve\_asphere `, :doc:`fix nvt\_asphere `, :doc:`fix npt\_asphere `, :doc:`fix\_modify ` +:doc:`fix nph `, :doc:`fix nve\_asphere `, :doc:`fix nvt\_asphere `, :doc:`fix npt\_asphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nph_body.rst b/doc/src/fix_nph_body.rst index 8ce3009700..25416bfa11 100644 --- a/doc/src/fix_nph_body.rst +++ b/doc/src/fix_nph_body.rst @@ -74,11 +74,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -106,12 +106,12 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** -This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read\_restart ` +This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note @@ -120,7 +120,7 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -141,13 +141,13 @@ This fix is part of the BODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style body ` +quaternion as defined by the :doc:`atom_style body ` command. Related commands """""""""""""""" -:doc:`fix nph `, :doc:`fix nve\_body `, :doc:`fix nvt\_body `, :doc:`fix npt\_body `, :doc:`fix\_modify ` +:doc:`fix nph `, :doc:`fix nve\_body `, :doc:`fix nvt\_body `, :doc:`fix npt\_body `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst index af45b6babc..de8fb71944 100644 --- a/doc/src/fix_nph_sphere.rst +++ b/doc/src/fix_nph_sphere.rst @@ -90,11 +90,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -122,12 +122,12 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** -This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read\_restart ` +This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note @@ -136,7 +136,7 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -154,7 +154,7 @@ Restrictions This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the :doc:`atom\_style sphere ` +and a radius as defined by the :doc:`atom_style sphere ` command. All particles in the group must be finite-size spheres. They cannot @@ -167,7 +167,7 @@ Related commands """""""""""""""" :doc:`fix nph `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_sphere `, :doc:`fix npt\_sphere `, -:doc:`fix\_modify ` +:doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst index be0a28b8b4..070192207f 100644 --- a/doc/src/fix_nphug.rst +++ b/doc/src/fix_nphug.rst @@ -143,11 +143,11 @@ the new computes is "all" since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -182,18 +182,18 @@ instructions on how to use the accelerated styles effectively. This fix writes the values of E0, V0, and P0, as well as the state of all the thermostat and barostat variables to :doc:`binary restart files `. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *e0*\ , *v0* and *p0* keywords +The :doc:`fix_modify ` *e0*\ , *v0* and *p0* keywords can be used to define the values of E0, V0, and P0. Note the the values for *e0* and *v0* are extensive, and so must correspond to the total energy and volume of the entire system, not energy and volume per atom. If any of these quantities are not specified, then the instantaneous value in the system at the start of the simulation is used. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by these fixes. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure, as described above. @@ -202,7 +202,7 @@ temperature should be consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by these +The :doc:`fix_modify ` *energy* option is supported by these fixes to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of :doc:`thermodynamic output `. Either way, this energy is \*not\* @@ -236,7 +236,7 @@ plus the additional ones mentioned above. Related commands """""""""""""""" -:doc:`fix msst `, :doc:`fix npt `, :doc:`fix\_modify ` +:doc:`fix msst `, :doc:`fix npt `, :doc:`fix_modify ` Default """"""" diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst index a728128aa3..ee3a81892e 100644 --- a/doc/src/fix_npt_asphere.rst +++ b/doc/src/fix_npt_asphere.rst @@ -85,11 +85,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -99,7 +99,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -133,11 +133,11 @@ instructions on how to use the accelerated styles effectively. This fix writes the state of the Nose/Hoover thermostat and barostat to :doc:`binary restart files `. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note @@ -146,7 +146,7 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -169,7 +169,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style ellipsoid ` +quaternion as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point @@ -179,7 +179,7 @@ shape attribute. Related commands """""""""""""""" -:doc:`fix npt `, :doc:`fix nve\_asphere `, :doc:`fix nvt\_asphere `, :doc:`fix\_modify ` +:doc:`fix npt `, :doc:`fix nve\_asphere `, :doc:`fix nvt\_asphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_npt_body.rst b/doc/src/fix_npt_body.rst index 64ae261e31..bfc743d923 100644 --- a/doc/src/fix_npt_body.rst +++ b/doc/src/fix_npt_body.rst @@ -82,11 +82,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -96,7 +96,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -130,11 +130,11 @@ instructions on how to use the accelerated styles effectively. This fix writes the state of the Nose/Hoover thermostat and barostat to :doc:`binary restart files `. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note @@ -143,7 +143,7 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -166,13 +166,13 @@ This fix is part of the BODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style body ` +quaternion as defined by the :doc:`atom_style body ` command. Related commands """""""""""""""" -:doc:`fix npt `, :doc:`fix nve\_body `, :doc:`fix nvt\_body `, :doc:`fix\_modify ` +:doc:`fix npt `, :doc:`fix nve\_body `, :doc:`fix nvt\_body `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst index 9d0e04b0c0..3a660c5c4f 100644 --- a/doc/src/fix_npt_cauchy.rst +++ b/doc/src/fix_npt_cauchy.rst @@ -136,7 +136,7 @@ Other barostat-related keywords are *pchain*\ , *mtk*\ , *ploop*\ , Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable -dimensions (x,y,z,xy,xz,yz). The :doc:`create\_box `, :doc:`read data `, and :doc:`read\_restart ` commands +dimensions (x,y,z,xy,xz,yz). The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. @@ -411,12 +411,12 @@ commands for details. Note that the IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID + underscore + "press". Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of these fix's temperature or pressure via the -:doc:`compute\_modify ` command. Or you can print this +:doc:`compute_modify ` command. Or you can print this temperature or pressure during thermodynamic output via the -:doc:`thermo\_style custom ` command using the appropriate +:doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -426,7 +426,7 @@ temperature after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not -done by default, but only if the :doc:`fix\_modify ` command +done by default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -476,11 +476,11 @@ of the underlying non-Hamiltonian equations of motion. This fix writes the state of all the thermostat and barostat variables to :doc:`binary restart files `. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure, as described above. @@ -501,7 +501,7 @@ compute temperature on a subset of atoms. specified by the *press* keyword will be unaffected by the *temp* setting. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -565,8 +565,8 @@ LAMMPS was built with that package. See the :doc:`Build package periodic. *Xy*\ , *xz*\ , and *yz* can only be barostatted if the simulation domain is triclinic and the 2nd dimension in the keyword (\ *y* dimension in *xy*\ ) is periodic. *Z*\ , *xz*\ , and *yz*\ , cannot be -barostatted for 2D simulations. The :doc:`create\_box `, -:doc:`read data `, and :doc:`read\_restart ` +barostatted for 2D simulations. The :doc:`create_box `, +:doc:`read data `, and :doc:`read_restart ` commands specify whether the simulation box is orthogonal or non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz tilt factors. @@ -625,8 +625,8 @@ over time or the atom count becomes very small. Related commands """""""""""""""" -:doc:`fix nve `, :doc:`fix\_modify `, -:doc:`run\_style ` +:doc:`fix nve `, :doc:`fix_modify `, +:doc:`run_style ` Default """"""" diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst index 9fe7b93633..0c4b79d616 100644 --- a/doc/src/fix_npt_sphere.rst +++ b/doc/src/fix_npt_sphere.rst @@ -98,11 +98,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID since pressure is computed for the entire system. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -112,7 +112,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -146,11 +146,11 @@ instructions on how to use the accelerated styles effectively. This fix writes the state of the Nose/Hoover thermostat and barostat to :doc:`binary restart files `. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting or barostatting procedure. If you do this, note @@ -159,7 +159,7 @@ consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -179,7 +179,7 @@ Restrictions This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the :doc:`atom\_style sphere ` +and a radius as defined by the :doc:`atom_style sphere ` command. All particles in the group must be finite-size spheres. They cannot @@ -191,7 +191,7 @@ defined by the :doc:`dimension ` keyword. Related commands """""""""""""""" -:doc:`fix npt `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_sphere `, :doc:`fix npt\_asphere `, :doc:`fix\_modify ` +:doc:`fix npt `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_sphere `, :doc:`fix npt\_asphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst index bae6f8a95c..9c8b5dcf33 100644 --- a/doc/src/fix_nve.rst +++ b/doc/src/fix_nve.rst @@ -67,7 +67,7 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst index 4ac734c468..688792058d 100644 --- a/doc/src/fix_nve_asphere.rst +++ b/doc/src/fix_nve_asphere.rst @@ -38,7 +38,7 @@ assumes point particles and only updates their position and velocity. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -78,7 +78,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style ellipsoid ` +quaternion as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point diff --git a/doc/src/fix_nve_asphere_noforce.rst b/doc/src/fix_nve_asphere_noforce.rst index 309928f582..b175b769e8 100644 --- a/doc/src/fix_nve_asphere_noforce.rst +++ b/doc/src/fix_nve_asphere_noforce.rst @@ -30,7 +30,7 @@ angular momenta are used to update their positions and orientation. This is useful as an implicit time integrator for Fast Lubrication Dynamics, since the velocity and angular momentum are updated by the -:doc:`pair\_style lubricuteU ` command. +:doc:`pair_style lubricuteU ` command. ---------- @@ -38,7 +38,7 @@ Dynamics, since the velocity and angular momentum are updated by the **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -52,7 +52,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style ellipsoid ` +quaternion as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point diff --git a/doc/src/fix_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst index e44f78c25c..8aeb6969b2 100644 --- a/doc/src/fix_nve_awpmd.rst +++ b/doc/src/fix_nve_awpmd.rst @@ -39,7 +39,7 @@ the electron wave functions are also updated. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nve_body.rst b/doc/src/fix_nve_body.rst index 1d75b3ac34..5410ddb8ee 100644 --- a/doc/src/fix_nve_body.rst +++ b/doc/src/fix_nve_body.rst @@ -36,7 +36,7 @@ assumes point particles and only updates their position and velocity. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -50,7 +50,7 @@ This fix is part of the BODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style body ` +quaternion as defined by the :doc:`atom_style body ` command. All particles in the group must be body particles. They cannot be diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst index 3143db968f..6b210b7150 100644 --- a/doc/src/fix_nve_dotc_langevin.rst +++ b/doc/src/fix_nve_dotc_langevin.rst @@ -68,8 +68,8 @@ The total force on each atom will have the form: Fr is proportional to sqrt(Kb T m / (dt damp)) Fc is the conservative force computed via the usual inter-particle -interactions (:doc:`pair\_style `, -:doc:`bond\_style `, etc). +interactions (:doc:`pair_style `, +:doc:`bond_style `, etc). The Ff and Fr terms are implicitly taken into account by this fix on a per-particle basis. @@ -146,7 +146,7 @@ See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" -:doc:`fix nve `, :doc:`fix langevin `, :doc:`fix nve/dot `, :doc:`bond\_style oxdna/fene `, :doc:`bond\_style oxdna2/fene `, :doc:`pair\_style oxdna/excv `, :doc:`pair\_style oxdna2/excv ` +:doc:`fix nve `, :doc:`fix langevin `, :doc:`fix nve/dot `, :doc:`bond_style oxdna/fene `, :doc:`bond_style oxdna2/fene `, :doc:`pair_style oxdna/excv `, :doc:`pair_style oxdna2/excv ` **Default:** none diff --git a/doc/src/fix_nve_eff.rst b/doc/src/fix_nve_eff.rst index a7346f1ed2..a1d10cb484 100644 --- a/doc/src/fix_nve_eff.rst +++ b/doc/src/fix_nve_eff.rst @@ -34,7 +34,7 @@ of electrons are also updated. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nve_limit.rst b/doc/src/fix_nve_limit.rst index f637db54d1..684016959b 100644 --- a/doc/src/fix_nve_limit.rst +++ b/doc/src/fix_nve_limit.rst @@ -42,7 +42,7 @@ in a single timestep. *Xmax* is specified in distance units; see the consistent with the neighbor skin distance and the frequency of neighbor list re-building, so that pairwise interactions are not missed on successive timesteps as atoms move. See the -:doc:`neighbor ` and :doc:`neigh\_modify ` commands +:doc:`neighbor ` and :doc:`neigh_modify ` commands for details. Note that if a velocity reset occurs the integrator will not conserve @@ -64,7 +64,7 @@ very large for overlapped configurations. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which can be accessed by various @@ -88,7 +88,7 @@ Related commands """""""""""""""" :doc:`fix nve `, :doc:`fix nve/noforce `, -:doc:`pair\_style soft ` +:doc:`pair_style soft ` **Default:** none diff --git a/doc/src/fix_nve_line.rst b/doc/src/fix_nve_line.rst index 8f77e8481e..e92f529542 100644 --- a/doc/src/fix_nve_line.rst +++ b/doc/src/fix_nve_line.rst @@ -36,7 +36,7 @@ assumes point particles and only updates their position and velocity. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -50,7 +50,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that particles be line segments as defined by the -:doc:`atom\_style line ` command. +:doc:`atom_style line ` command. Related commands """""""""""""""" diff --git a/doc/src/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst index 5836dc005c..f4215f2abe 100644 --- a/doc/src/fix_nve_manifold_rattle.rst +++ b/doc/src/fix_nve_manifold_rattle.rst @@ -78,7 +78,7 @@ conserved. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nve_noforce.rst b/doc/src/fix_nve_noforce.rst index 07caefca16..bacc4a9908 100644 --- a/doc/src/fix_nve_noforce.rst +++ b/doc/src/fix_nve_noforce.rst @@ -41,7 +41,7 @@ fcm() group function to compute the total force on the group of atoms. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst index 1789a9e119..855ea0f916 100644 --- a/doc/src/fix_nve_sphere.rst +++ b/doc/src/fix_nve_sphere.rst @@ -57,7 +57,7 @@ If the *update* keyword is used with the *dipole* value, then the orientation of the dipole moment of each particle is also updated during the time integration. This option should be used for models where a dipole moment is assigned to finite-size particles, -e.g. spheroids via use of the :doc:`atom\_style hybrid sphere dipole ` command. +e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole ` command. The default dipole orientation integrator can be changed to the Dullweber-Leimkuhler-McLachlan integration scheme @@ -100,7 +100,7 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -111,9 +111,9 @@ Restrictions This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the :doc:`atom\_style sphere ` +and a radius as defined by the :doc:`atom_style sphere ` command. If the *dipole* keyword is used, then they must also store a -dipole moment as defined by the :doc:`atom\_style dipole ` +dipole moment as defined by the :doc:`atom_style dipole ` command. All particles in the group must be finite-size spheres. They cannot diff --git a/doc/src/fix_nve_spin.rst b/doc/src/fix_nve_spin.rst index 5f1b1a648f..65f235bd3f 100644 --- a/doc/src/fix_nve_spin.rst +++ b/doc/src/fix_nve_spin.rst @@ -82,7 +82,7 @@ instead of "array" is also valid. Related commands """""""""""""""" -:doc:`atom\_style spin `, :doc:`fix nve ` +:doc:`atom_style spin `, :doc:`fix nve ` Default """"""" diff --git a/doc/src/fix_nve_tri.rst b/doc/src/fix_nve_tri.rst index 4e71a69c5a..c5e5aa99d6 100644 --- a/doc/src/fix_nve_tri.rst +++ b/doc/src/fix_nve_tri.rst @@ -37,7 +37,7 @@ assumes point particles and only updates their position and velocity. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -51,7 +51,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that particles be triangles as defined by the -:doc:`atom\_style tri ` command. +:doc:`atom_style tri ` command. Related commands """""""""""""""" diff --git a/doc/src/fix_nvk.rst b/doc/src/fix_nvk.rst index c153ab6ff2..a3f3928339 100644 --- a/doc/src/fix_nvk.rst +++ b/doc/src/fix_nvk.rst @@ -45,7 +45,7 @@ energy prior to this fix. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst index 9df4c9e84f..a3ad145405 100644 --- a/doc/src/fix_nvt_asphere.rst +++ b/doc/src/fix_nvt_asphere.rst @@ -66,11 +66,11 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -80,7 +80,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -112,17 +112,17 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** -This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read\_restart ` +This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -143,7 +143,7 @@ This fix is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style ellipsoid ` +quaternion as defined by the :doc:`atom_style ellipsoid ` command. All particles in the group must be finite-size. They cannot be point @@ -153,7 +153,7 @@ shape attribute. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix nve\_asphere `, :doc:`fix npt\_asphere `, :doc:`fix\_modify ` +:doc:`fix nvt `, :doc:`fix nve\_asphere `, :doc:`fix npt\_asphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nvt_body.rst b/doc/src/fix_nvt_body.rst index f94c1850da..92819b26ca 100644 --- a/doc/src/fix_nvt_body.rst +++ b/doc/src/fix_nvt_body.rst @@ -63,11 +63,11 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -77,7 +77,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -109,17 +109,17 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** -This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read\_restart ` +This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -140,13 +140,13 @@ This fix is part of the BODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the :doc:`atom\_style body ` +quaternion as defined by the :doc:`atom_style body ` command. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix nve\_body `, :doc:`fix npt\_body `, :doc:`fix\_modify ` +:doc:`fix nvt `, :doc:`fix nve\_body `, :doc:`fix npt\_body `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst index 4b9c063caf..438c11fe7e 100644 --- a/doc/src/fix_nvt_manifold_rattle.rst +++ b/doc/src/fix_nvt_manifold_rattle.rst @@ -54,7 +54,7 @@ parameters, see the :doc:`Howto manifold ` doc page. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_nvt_sllod.rst b/doc/src/fix_nvt_sllod.rst index aa4197e19b..cd8f529c83 100644 --- a/doc/src/fix_nvt_sllod.rst +++ b/doc/src/fix_nvt_sllod.rst @@ -98,11 +98,11 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -112,7 +112,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -144,17 +144,17 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** -This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read\_restart ` +This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -179,7 +179,7 @@ Related commands """""""""""""""" :doc:`fix nve `, :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix langevin `, -:doc:`fix\_modify `, :doc:`compute temp/deform ` +:doc:`fix_modify `, :doc:`compute temp/deform ` Default """"""" diff --git a/doc/src/fix_nvt_sllod_eff.rst b/doc/src/fix_nvt_sllod_eff.rst index 0e8b005176..f1dc60c88f 100644 --- a/doc/src/fix_nvt_sllod_eff.rst +++ b/doc/src/fix_nvt_sllod_eff.rst @@ -42,17 +42,17 @@ velocity. **Restart, fix\_modify, output, run start/stop, minimize info:** -This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read\_restart ` +This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -79,7 +79,7 @@ equilibration. Related commands """""""""""""""" -:doc:`fix nve/eff `, :doc:`fix nvt/eff `, :doc:`fix langevin/eff `, :doc:`fix nvt/sllod `, :doc:`fix\_modify `, :doc:`compute temp/deform/eff ` +:doc:`fix nve/eff `, :doc:`fix nvt/eff `, :doc:`fix langevin/eff `, :doc:`fix nvt/sllod `, :doc:`fix_modify `, :doc:`compute temp/deform/eff ` Default """"""" diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst index eedf21f69b..3275114a03 100644 --- a/doc/src/fix_nvt_sphere.rst +++ b/doc/src/fix_nvt_sphere.rst @@ -80,11 +80,11 @@ underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -94,7 +94,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -126,17 +126,17 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** -This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read\_restart ` +This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change induced by Nose/Hoover thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. @@ -154,7 +154,7 @@ Restrictions This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the :doc:`atom\_style sphere ` +and a radius as defined by the :doc:`atom_style sphere ` command. All particles in the group must be finite-size spheres. They cannot @@ -166,7 +166,7 @@ defined by the :doc:`dimension ` keyword. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_asphere `, :doc:`fix npt\_sphere `, :doc:`fix\_modify ` +:doc:`fix nvt `, :doc:`fix nve\_sphere `, :doc:`fix nvt\_asphere `, :doc:`fix npt\_sphere `, :doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_oneway.rst b/doc/src/fix_oneway.rst index 9d1f40ef5f..cc57989a53 100644 --- a/doc/src/fix_oneway.rst +++ b/doc/src/fix_oneway.rst @@ -46,7 +46,7 @@ membrane, or as an implementation of Maxwell's demon. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index dcce12eb91..7ac297b064 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -130,12 +130,12 @@ writing the orientation files is given in :ref:`(Wicaksono2) ` No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential energy of atom interactions with the grain boundary driving force to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by these +The :doc:`fix_modify ` *respa* option is supported by these fixes. This allows to set at which level of the :doc:`r-RESPA ` integrator a fix is adding its forces. Default is the outermost level. @@ -164,7 +164,7 @@ This fix should only be used with fcc or bcc lattices. Related commands """""""""""""""" -:doc:`fix\_modify ` +:doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst index ca71595664..f331f3ebb4 100644 --- a/doc/src/fix_phonon.rst +++ b/doc/src/fix_phonon.rst @@ -164,7 +164,7 @@ corresponding reciprocal lattice. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to change the temperature compute from thermo\_temp to the one that reflects the true temperature of atoms in the group. @@ -200,7 +200,7 @@ Related commands """""""""""""""" :doc:`compute msd `, -:doc:`dynamical\_matrix ` +:doc:`dynamical_matrix ` Default """"""" diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index 2639150bd4..cdbdf33d2b 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -161,7 +161,7 @@ This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. A PIMD simulation can be initialized with a single data file read via -the :doc:`read\_data ` command. However, this means all +the :doc:`read_data ` command. However, this means all quasi-beads in a ring polymer will have identical positions and velocities, resulting in identical trajectories for all quasi-beads. To avoid this, users can simply initialize velocities with different diff --git a/doc/src/fix_planeforce.rst b/doc/src/fix_planeforce.rst index 1cac0f8be8..2a406f5da5 100644 --- a/doc/src/fix_planeforce.rst +++ b/doc/src/fix_planeforce.rst @@ -36,7 +36,7 @@ should continue to move in the plane thereafter. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst index 93a3ac0638..26f66d4ac7 100644 --- a/doc/src/fix_plumed.rst +++ b/doc/src/fix_plumed.rst @@ -90,7 +90,7 @@ dependent bias potentials that were accumulated in previous calculations will be read in when the RESTART command is included in the PLUMED input. -The :doc:`fix\_modify ` *energy* option is not supported by +The :doc:`fix_modify ` *energy* option is not supported by this fix. Nothing is computed by this fix that can be accessed by any of the diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst index 816568b537..da690030f6 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -115,7 +115,7 @@ off, and there is only a single fix poems defined. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *bodyforces* option is supported by +The :doc:`fix_modify ` *bodyforces* option is supported by this fix style to set whether per-body forces and torques are computed early or late in a timestep, i.e. at the post-force stage or at the final-integrate stage, respectively. @@ -136,8 +136,8 @@ built and linked with LAMMPS. See the :doc:`Build package ` doc Related commands """""""""""""""" -:doc:`fix rigid `, :doc:`delete\_bonds `, -:doc:`neigh\_modify ` exclude +:doc:`fix rigid `, :doc:`delete_bonds `, +:doc:`neigh_modify ` exclude **Default:** none diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst index 8deeb6e885..dab9fa601d 100644 --- a/doc/src/fix_pour.rst +++ b/doc/src/fix_pour.rst @@ -154,7 +154,7 @@ many timesteps until the desired # of particles has been inserted. If you are monitoring the temperature of a system where the particle count is changing due to adding particles, you typically - should use the :doc:`compute\_modify dynamic yes ` + should use the :doc:`compute_modify dynamic yes ` command for the temperature compute you are using. @@ -220,7 +220,7 @@ successively higher height over time. The *ignore* option is useful when running a simulation that used line segment (2d) or triangle (3d) particles, typically to define boundaries for spherical granular particles to interact with. See the -:doc:`atom\_style line or tri ` command for details. Lines +:doc:`atom_style line or tri ` command for details. Lines and triangles store their size, and if the size is large it may overlap (in a spherical sense) with the insertion region, even if the line/triangle is oriented such that there is no actual overlap. This @@ -249,7 +249,7 @@ place. However, in a statistical sense, a restarted simulation should produce the same behavior if you adjust the fix pour parameters appropriately. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the diff --git a/doc/src/fix_precession_spin.rst b/doc/src/fix_precession_spin.rst index 2c84eaa304..b81d0a8bf8 100644 --- a/doc/src/fix_precession_spin.rst +++ b/doc/src/fix_precession_spin.rst @@ -142,7 +142,7 @@ Those styles can be combined within one single command line. By default, the energy associated to this fix is not added to the potential energy of the system. -The :doc:`fix\_modify ` *energy* option is supported by this fix +The :doc:`fix_modify ` *energy* option is supported by this fix to add this magnetic potential energy to the potential energy of the system, @@ -167,7 +167,7 @@ atom\_style "spin" was declared. See the :doc:`Build package ` d Related commands """""""""""""""" -:doc:`atom\_style spin ` +:doc:`atom_style spin ` **Default:** diff --git a/doc/src/fix_press_berendsen.rst b/doc/src/fix_press_berendsen.rst index 4237d06228..17338048b0 100644 --- a/doc/src/fix_press_berendsen.rst +++ b/doc/src/fix_press_berendsen.rst @@ -197,11 +197,11 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix\_ID as the fix group. Note that these are NOT the computes used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp* +the :doc:`thermo_style ` command) with ID = *thermo\_temp* and *thermo\_press*. This means you can change the attributes of this fix's temperature or pressure via the -:doc:`compute\_modify ` command or print this temperature -or pressure during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* or *thermo\_press* will have no effect on this fix. @@ -209,7 +209,7 @@ It also means that changing attributes of *thermo\_temp* or No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by this fix. You can use them to assign a :doc:`compute ` you have defined to this fix which will be used in its temperature and pressure calculations. If you do this, note @@ -237,7 +237,7 @@ Related commands """""""""""""""" :doc:`fix nve `, :doc:`fix nph `, :doc:`fix npt `, :doc:`fix temp/berendsen `, -:doc:`fix\_modify ` +:doc:`fix_modify ` Default """"""" diff --git a/doc/src/fix_print.rst b/doc/src/fix_print.rst index 865d3d9741..72d231a15c 100644 --- a/doc/src/fix_print.rst +++ b/doc/src/fix_print.rst @@ -97,7 +97,7 @@ where ID is replaced with the fix-ID. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index 645bc13452..f13c6239cd 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -53,8 +53,8 @@ about atoms and to use during a simulation. The specified *group-ID* is ignored by this fix. The atom style used for a simulation defines a set of per-atom -properties, as explained on the :doc:`atom\_style ` and -:doc:`read\_data ` doc pages. The latter command allows these +properties, as explained on the :doc:`atom_style ` and +:doc:`read_data ` doc pages. The latter command allows these properties to be defined for each atom in the system when a data file is read. This fix will augment the set of properties with new custom ones. This can be useful in several scenarios. @@ -113,7 +113,7 @@ new properties are also defined for the ghost atoms. If you use this command with the *mol*\ , *q* or *rmass* vectors, then you most likely want to set *ghost* yes, since these properties - are stored with ghost atoms if you use an :doc:`atom\_style ` + are stored with ghost atoms if you use an :doc:`atom_style ` that defines them, and many LAMMPS operations that use molecule IDs or charge, such as neighbor lists and pair styles, will expect ghost atoms to have these values. LAMMPS will issue a warning it you define @@ -142,14 +142,14 @@ new properties are also defined for the ghost atoms. This fix is one of a small number that can be defined in an input script before the simulation box is created or atoms are defined. -This is so it can be used with the :doc:`read\_data ` command +This is so it can be used with the :doc:`read_data ` command as described below. Per-atom properties that are defined by the :doc:`atom style ` are initialized when atoms are created, e.g. by -the :doc:`read\_data ` or :doc:`create\_atoms ` +the :doc:`read_data ` or :doc:`create_atoms ` commands. The per-atom properties defined by this fix are not. So you need to initialize them explicitly. This can be done by the -:doc:`read\_data ` command, using its *fix* keyword and +:doc:`read_data ` command, using its *fix* keyword and passing it the fix-ID of this fix. Thus these commands: @@ -258,7 +258,7 @@ this to using per-atom masses: set type 1 mass 15.9994 set type 2 mass 1.008 -When writing out the system data with the :doc:`write\_data ` +When writing out the system data with the :doc:`write_data ` command, there will be a new section named with the fix-ID (i.e. *Isotopes* in this case). Alternatively, you can take an existing data file and just add this *Isotopes* section with @@ -312,12 +312,12 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** This fix writes the per-atom values it stores to :doc:`binary restart files `, so that the values can be restored when a -simulation is restarted. See the :doc:`read\_restart ` +simulation is restarted. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the @@ -330,7 +330,7 @@ Restrictions Related commands """""""""""""""" -:doc:`read\_data `, :doc:`set `, :doc:`compute property/atom ` +:doc:`read_data `, :doc:`set `, :doc:`compute property/atom ` Default """"""" diff --git a/doc/src/fix_python_move.rst b/doc/src/fix_python_move.rst index 0d59cf82c0..e188c096af 100644 --- a/doc/src/fix_python_move.rst +++ b/doc/src/fix_python_move.rst @@ -91,7 +91,7 @@ Examples for how to do this are in the *examples/python* folder. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst index 84ab2abc91..6156c65041 100644 --- a/doc/src/fix_qbmsst.rst +++ b/doc/src/fix_qbmsst.rst @@ -176,9 +176,9 @@ vector contains five values in this order: To print these quantities to the log file with descriptive column headers, the following LAMMPS commands are suggested. Here the -:doc:`fix\_modify ` energy command is also enabled to allow +:doc:`fix_modify ` energy command is also enabled to allow the thermo keyword *etotal* to print the quantity etot. See -also the :doc:`thermo\_style ` command. +also the :doc:`thermo_style ` command. .. parsed-literal:: @@ -195,7 +195,7 @@ also the :doc:`thermo\_style ` command. The global scalar under the entry f\_fix\_id is the quantity of thermo energy as an extra part of etot. This global scalar and the vector of 5 quantities can be accessed by various :doc:`output commands `. It is worth noting that the temp keyword -under the :doc:`thermo\_style ` command print the +under the :doc:`thermo_style ` command print the instantaneous classical temperature Tcl as described in the command :doc:`fix qtb `. diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index 8875c22af6..77ce447fed 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -137,7 +137,7 @@ point charges, but uses a shielded Coulomb potential to describe the interaction between a pair of charged particles. Interaction through the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force field ` paper. The shielding accounts for charge overlap between charged particles at small separation. This style is the same -as :doc:`fix qeq/reax `, and can be used with :doc:`pair\_style reax/c `. Only the *chi*\ , *eta*\ , and *gamma* +as :doc:`fix qeq/reax `, and can be used with :doc:`pair_style reax/c `. Only the *chi*\ , *eta*\ , and *gamma* parameters from the *qfile* file are used. When using the string *reax/c* as filename, these parameters are extracted directly from an active *reax/c* pair style. This style solves partial diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst index 35eb514a75..b5da7142fa 100644 --- a/doc/src/fix_qeq_comb.rst +++ b/doc/src/fix_qeq_comb.rst @@ -97,7 +97,7 @@ instructions on how to use the accelerated styles effectively. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is performing charge equilibration. Default is the outermost level. @@ -121,7 +121,7 @@ This fix command currently only supports :doc:`pair style *comb*\ `. Related commands """""""""""""""" -:doc:`pair\_style comb ` +:doc:`pair_style comb ` Default """"""" diff --git a/doc/src/fix_qeq_reax.rst b/doc/src/fix_qeq_reax.rst index 4371e7a1a1..e39c0eb590 100644 --- a/doc/src/fix_qeq_reax.rst +++ b/doc/src/fix_qeq_reax.rst @@ -39,7 +39,7 @@ Description Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) ` and formulated in :ref:`(Nakano) `. It is typically used in conjunction with the ReaxFF force field model as -implemented in the :doc:`pair\_style reax/c ` command, but +implemented in the :doc:`pair_style reax/c ` command, but it can be used with any potential in LAMMPS, so long as it defines and uses charges on each atom. The :doc:`fix qeq/comb ` command should be used to perform charge equilibration with the :doc:`COMB potential `. For more technical details about the @@ -50,7 +50,7 @@ The QEq method minimizes the electrostatic energy of the system by adjusting the partial charge on individual atoms based on interactions with their neighbors. It requires some parameters for each atom type. If the *params* setting above is the word "reax/c", then these are -extracted from the :doc:`pair\_style reax/c ` command and +extracted from the :doc:`pair_style reax/c ` command and the ReaxFF force field file it reads in. If a file name is specified for *params*\ , then the parameters are taken from the specified file and the file must contain one line for each atom type. The latter @@ -122,7 +122,7 @@ be used for periodic cell dimensions less than 10 angstroms. Related commands """""""""""""""" -:doc:`pair\_style reax/c ` +:doc:`pair_style reax/c ` **Default:** none diff --git a/doc/src/fix_qmmm.rst b/doc/src/fix_qmmm.rst index ee08cd1d15..6166efbada 100644 --- a/doc/src/fix_qmmm.rst +++ b/doc/src/fix_qmmm.rst @@ -45,7 +45,7 @@ description of the QM/MM interface code itself in lib/qmmm/README. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This diff --git a/doc/src/fix_reaxc_bonds.rst b/doc/src/fix_reaxc_bonds.rst index b6c15a2dd3..fcd788cff0 100644 --- a/doc/src/fix_reaxc_bonds.rst +++ b/doc/src/fix_reaxc_bonds.rst @@ -31,7 +31,7 @@ Description """"""""""" Write out the bond information computed by the ReaxFF potential specified -by :doc:`pair\_style reax/c ` in the exact same format as the +by :doc:`pair_style reax/c ` in the exact same format as the original stand-alone ReaxFF code of Adri van Duin. The bond information is written to *filename* on timesteps that are multiples of *Nevery*\ , including timestep 0. For time-averaged chemical species analysis, @@ -64,7 +64,7 @@ version, but will also take longer to write. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of @@ -101,7 +101,7 @@ Restrictions """""""""""" -The fix reax/c/bonds command requires that the :doc:`pair\_style reax/c ` is invoked. This fix is part of the +The fix reax/c/bonds command requires that the :doc:`pair_style reax/c ` is invoked. This fix is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -112,7 +112,7 @@ To write gzipped bond files, you must compile LAMMPS with the Related commands """""""""""""""" -:doc:`pair\_style reax/c `, :doc:`fix reax/c/species ` +:doc:`pair_style reax/c `, :doc:`fix reax/c/species ` **Default:** none diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst index 210f6fe5cc..ebcae065ee 100644 --- a/doc/src/fix_reaxc_species.rst +++ b/doc/src/fix_reaxc_species.rst @@ -49,7 +49,7 @@ Description """"""""""" Write out the chemical species information computed by the ReaxFF -potential specified by :doc:`pair\_style reax/c `. +potential specified by :doc:`pair_style reax/c `. Bond-order values (either averaged or instantaneous, depending on value of *Nrepeat*\ ) are used to determine chemical bonds. Every *Nfreq* timesteps, chemical species information is written to @@ -122,7 +122,7 @@ average bond-order for the species analysis output on timestep 100. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes both a global vector of length 2 and a per-atom @@ -174,7 +174,7 @@ Restrictions """""""""""" -The "fix reax/c/species" currently only works with :doc:`pair\_style reax/c ` and it requires that the :doc:`pair\_style reax/c ` be invoked. This fix is part of the +The "fix reax/c/species" currently only works with :doc:`pair_style reax/c ` and it requires that the :doc:`pair_style reax/c ` be invoked. This fix is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -189,7 +189,7 @@ It should be possible to extend it to other reactive pair\_styles (such as Related commands """""""""""""""" -:doc:`pair\_style reax/c `, :doc:`fix reax/c/bonds ` +:doc:`pair_style reax/c `, :doc:`fix reax/c/bonds ` Default """"""" diff --git a/doc/src/fix_recenter.rst b/doc/src/fix_recenter.rst index 0a33bbaea3..d6895b0874 100644 --- a/doc/src/fix_recenter.rst +++ b/doc/src/fix_recenter.rst @@ -99,7 +99,7 @@ velocities with zero aggregate linear and/or angular momentum. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which can be accessed by various @@ -124,7 +124,7 @@ This fix should not be used with an x,y,z setting that causes a large shift in the system on the 1st timestep, due to the requested COM being very different from the initial COM. This could cause atoms to be lost, especially in parallel. Instead, use the -:doc:`displace\_atoms ` command, which can be used to +:doc:`displace_atoms ` command, which can be used to move atoms a large distance. Related commands diff --git a/doc/src/fix_restrain.rst b/doc/src/fix_restrain.rst index 0fc0ccee77..04d7a01c07 100644 --- a/doc/src/fix_restrain.rst +++ b/doc/src/fix_restrain.rst @@ -53,7 +53,7 @@ Restrain the motion of the specified sets of atoms by making them part of a bond or angle or dihedral interaction whose strength can vary over time during a simulation. This is functionally similar to creating a bond or angle or dihedral for the same atoms in a data -file, as specified by the :doc:`read\_data ` command, albeit +file, as specified by the :doc:`read_data ` command, albeit with a time-varying pre-factor coefficient, and except for exclusion rules, as explained below. @@ -68,9 +68,9 @@ data file. Adding a bond/angle/dihedral with this command does not apply the exclusion rules and weighting factors specified by the - :doc:`special\_bonds ` command to atoms in the restraint + :doc:`special_bonds ` command to atoms in the restraint that are now bonded (1-2,1-3,1-4 neighbors) as a result. If they are - close enough to interact in a :doc:`pair\_style ` sense + close enough to interact in a :doc:`pair_style ` sense (non-bonded interaction), then the bond/angle/dihedral restraint interaction will simply be superposed on top of that interaction. @@ -131,7 +131,7 @@ as the following may be useful: The *bond* keyword applies a bond restraint to the specified atoms -using the same functional form used by the :doc:`bond\_style harmonic ` command. The potential associated with +using the same functional form used by the :doc:`bond_style harmonic ` command. The potential associated with the restraint is .. math:: @@ -152,7 +152,7 @@ is included in :math:`K`. The *angle* keyword applies an angle restraint to the specified atoms -using the same functional form used by the :doc:`angle\_style harmonic ` command. The potential associated with +using the same functional form used by the :doc:`angle_style harmonic ` command. The potential associated with the restraint is .. math:: @@ -173,7 +173,7 @@ factor is included in :math:`K`. The *dihedral* keyword applies a dihedral restraint to the specified atoms using a simplified form of the function used by the -:doc:`dihedral\_style charmm ` command. The potential +:doc:`dihedral_style charmm ` command. The potential associated with the restraint is .. math:: @@ -201,11 +201,11 @@ current dihedral angle :math:`\phi` is equal to :math:`\phi_0`. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the potential energy associated with this fix to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -214,7 +214,7 @@ integrator the fix is adding its forces. Default is the outermost level. If you want the fictitious potential energy associated with the added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the - :doc:`fix\_modify ` *energy* option for this fix. + :doc:`fix_modify ` *energy* option for this fix. This fix computes a global scalar and a global vector of length 3, which can be accessed by various :doc:`output commands `. diff --git a/doc/src/fix_rhok.rst b/doc/src/fix_rhok.rst index 7f18b03966..25acb09f0b 100644 --- a/doc/src/fix_rhok.rst +++ b/doc/src/fix_rhok.rst @@ -51,7 +51,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`thermo\_style ` +:doc:`thermo_style ` **Default:** none diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index 1f16d33a19..9e9c65dd19 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -204,8 +204,8 @@ processors when ghost atom info is accumulated. large enough to span the distance between the atom that owns the body and every other atom in the body. This distance value is printed out when the rigid bodies are defined. If the - :doc:`pair\_style ` cutoff plus neighbor skin does not span - this distance, then you should use the :doc:`comm\_modify cutoff ` command with a setting epsilon larger than + :doc:`pair_style ` cutoff plus neighbor skin does not span + this distance, then you should use the :doc:`comm_modify cutoff ` command with a setting epsilon larger than the distance. Which of the two variants is faster for a particular problem is hard @@ -254,7 +254,7 @@ differences may accumulate to produce divergent trajectories. could displace the atoms in a body or add a large velocity to each atom in a body to make it move in a desired direction before a 2nd run is performed, using the :doc:`set ` or - :doc:`displace\_atoms ` or :doc:`velocity ` + :doc:`displace_atoms ` or :doc:`velocity ` commands. But these commands will not affect the internal attributes of the body unless *reinit* is set to *yes*\ . With *reinit* set to *no* (or using the *infile* option, which implies *reinit* *no*\ ) the position @@ -353,7 +353,7 @@ settings from the final keyword are used. For computational efficiency, you may wish to turn off pairwise and bond interactions within each rigid body, as they no longer - contribute to the motion. The :doc:`neigh\_modify exclude ` and :doc:`delete\_bonds ` + contribute to the motion. The :doc:`neigh_modify exclude ` and :doc:`delete_bonds ` commands are used to do this. If the rigid bodies have strongly overlapping atoms, you may need to turn off these interactions to avoid numerical problems due to large equal/opposite intra-body forces @@ -370,7 +370,7 @@ is more expensive. The constituent particles within a rigid body can be point particles (the default in LAMMPS) or finite-size particles, such as spheres or -ellipsoids or line segments or triangles. See the :doc:`atom\_style sphere and ellipsoid and line and tri ` commands for more +ellipsoids or line segments or triangles. See the :doc:`atom_style sphere and ellipsoid and line and tri ` commands for more details on these kinds of particles. Finite-size particles contribute differently to the moment of inertia of a rigid body than do point particles. Finite-size particles can also experience torque (e.g. due @@ -380,7 +380,7 @@ orientation. These contributions are accounted for by these fixes. Forces between particles within a body do not contribute to the external force or torque on the body. Thus for computational efficiency, you may wish to turn off pairwise and bond interactions -between particles within each rigid body. The :doc:`neigh\_modify exclude ` and :doc:`delete\_bonds ` +between particles within each rigid body. The :doc:`neigh_modify exclude ` and :doc:`delete_bonds ` commands are used to do this. For finite-size particles this also means the particles can be highly overlapped when creating the rigid body. @@ -792,27 +792,27 @@ with rigid body information each time a restart file is written, as explained above for the *infile* keyword. For the 2 NVT rigid styles, the state of the Nose/Hoover thermostat is written to :doc:`binary restart files `. Ditto for the 4 NPT and NPH rigid styles, and the state of the Nose/Hoover barostat. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *energy* option is supported by the 6 +The :doc:`fix_modify ` *energy* option is supported by the 6 NVT, NPT, NPH rigid styles to add the energy change induced by the thermostatting to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to keeping the objects rigid to the system's virial as part of :doc:`thermodynamic output `. The default is *virial yes* -The :doc:`fix\_modify ` *temp* and *press* options are +The :doc:`fix_modify ` *temp* and *press* options are supported by the 4 NPT and NPH rigid styles to change the computes used to calculate the instantaneous pressure tensor. Note that the 2 NVT rigid fixes do not use any external compute to compute instantaneous temperature. -The :doc:`fix\_modify ` *bodyforces* option is supported by +The :doc:`fix_modify ` *bodyforces* option is supported by all rigid styles to set whether per-body forces and torques are computed early or late in a timestep, i.e. at the post-force stage or at the final-integrate stage or the timestep, respectively. @@ -906,7 +906,7 @@ example: Related commands """""""""""""""" -:doc:`delete\_bonds `, :doc:`neigh\_modify ` +:doc:`delete_bonds `, :doc:`neigh_modify ` exclude, :doc:`fix shake ` Default diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst index c7835e83fb..964d414c70 100644 --- a/doc/src/fix_rigid_meso.rst +++ b/doc/src/fix_rigid_meso.rst @@ -112,7 +112,7 @@ internal energy and extrapolated velocity are also updated. could displace the particles in a body or add a large velocity to each particle in a body to make it move in a desired direction before a 2nd run is performed, using the :doc:`set ` or - :doc:`displace\_atoms ` or :doc:`velocity ` + :doc:`displace_atoms ` or :doc:`velocity ` commands. But these commands will not affect the internal attributes of the body unless *reinit* is set to *yes*\ . With *reinit* set to *no* (or using the *infile* option, which implies *reinit* *no*\ ) the position @@ -306,7 +306,7 @@ If the *infile* keyword is used, an auxiliary file is written out with rigid body information each time a restart file is written, as explained above for the *infile* keyword. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global array of values which can be accessed by @@ -362,7 +362,7 @@ package. It is only enabled if LAMMPS was built with both packages. See the :doc:`Build package ` doc page for more info. This fix requires that atoms store density and internal energy as -defined by the :doc:`atom\_style meso ` command. +defined by the :doc:`atom_style meso ` command. All particles in the group must be mesoscopic SPH/SDPD particles. @@ -370,7 +370,7 @@ Related commands """""""""""""""" :doc:`fix meso/move `, :doc:`fix rigid `, -:doc:`neigh\_modify exclude ` +:doc:`neigh_modify exclude ` Default """"""" diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index b9df24f5a9..79809b7fc6 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -193,7 +193,7 @@ define the thermodynamic properties of each species. Furthermore, the number of species molecules (i.e., concentration) can be specified either with the :doc:`set ` command using the "d\_" prefix or by reading directly the concentrations from a data file. For the latter -case, the :doc:`read\_data ` command with the fix keyword +case, the :doc:`read_data ` command with the fix keyword should be specified, where the fix-ID will be the "fix rx`ID with a `_ suffix, e.g. fix foo all rx reaction.file ... @@ -232,7 +232,7 @@ Restrictions This command is part of the USER-DPD package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. -This command also requires use of the :doc:`atom\_style dpd ` +This command also requires use of the :doc:`atom_style dpd ` command. This command can only be used with a constant energy or constant diff --git a/doc/src/fix_saed_vtk.rst b/doc/src/fix_saed_vtk.rst index 8b11f71e62..2aa3960efb 100644 --- a/doc/src/fix_saed_vtk.rst +++ b/doc/src/fix_saed_vtk.rst @@ -179,7 +179,7 @@ output. This option can only be used with the *ave running* setting. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No parameter of this fix can be used with the *start/stop* keywords of @@ -190,12 +190,12 @@ Restrictions The attributes for fix\_saed\_vtk must match the values assigned in the -associated :doc:`compute\_saed ` command. +associated :doc:`compute_saed ` command. Related commands """""""""""""""" -:doc:`compute\_saed ` +:doc:`compute_saed ` Default """"""" diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst index a01fb7dc00..39a51e0f7b 100644 --- a/doc/src/fix_setforce.rst +++ b/doc/src/fix_setforce.rst @@ -64,7 +64,7 @@ will be evaluated each timestep, and its value used to determine the force component. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent force field. @@ -125,7 +125,7 @@ instructions on how to use the accelerated styles effectively. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *respa* option is supported by +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is setting the forces to the desired values; on all other levels, the force is set to 0.0 for the atoms in the fix group, diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 28a50e6754..ce875b18cf 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -211,12 +211,12 @@ LAMMPS closely follows (:ref:`Andersen (1983) `). **Restart, fix\_modify, output, run start/stop, minimize info:** -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to keeping the constraints to the system's virial as part of :doc:`thermodynamic output `. The default is *virial yes* -No information about these fixes is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about these fixes is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to these fixes. No global or per-atom quantities are stored by these fixes for access by various :doc:`output commands `. No parameter of these fixes can be used with the *start/stop* keywords of the :doc:`run ` command. These diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index b1f3cb0745..20bd2273d4 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -38,12 +38,12 @@ the deterministic integration of the conservative force. Further details regarding the method are provided in :ref:`(Lisal) ` and :ref:`(Larentzos1) `. -The fix *shardlow* must be used with the :doc:`pair\_style dpd/fdt ` or :doc:`pair\_style dpd/fdt/energy ` command to properly initialize the +The fix *shardlow* must be used with the :doc:`pair_style dpd/fdt ` or :doc:`pair_style dpd/fdt/energy ` command to properly initialize the fluctuation-dissipation theorem parameter(s) sigma (and kappa, if necessary). Note that numerous variants of DPD can be specified by choosing an -appropriate combination of the integrator and :doc:`pair\_style dpd/fdt ` command. DPD under isothermal conditions can +appropriate combination of the integrator and :doc:`pair_style dpd/fdt ` command. DPD under isothermal conditions can be specified by using fix *shardlow*\ , fix *nve* and pair\_style *dpd/fdt*\ . DPD under isoenergetic conditions can be specified by using fix *shardlow*\ , fix *nve* and pair\_style *dpd/fdt/energy*\ . DPD @@ -100,7 +100,7 @@ requested. Related commands """""""""""""""" -:doc:`pair\_style dpd/fdt `, :doc:`fix eos/cv ` +:doc:`pair_style dpd/fdt `, :doc:`fix eos/cv ` **Default:** none diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst index 7473cb07a9..e9ea27e61f 100644 --- a/doc/src/fix_smd.rst +++ b/doc/src/fix_smd.rst @@ -107,16 +107,16 @@ pulling path. The fix stores the direction of the spring, current pulling target distance and the running PMF to :doc:`binary restart files `. -See the :doc:`read\_restart ` command for info on how to +See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the added forces on atoms to the system's virial as part of :doc:`thermodynamic output `. The default is *virial no* -The :doc:`fix\_modify ` *respa* option is supported by +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. diff --git a/doc/src/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst index 6a8eb80ade..22cf1dff53 100644 --- a/doc/src/fix_smd_setvel.rst +++ b/doc/src/fix_smd_setvel.rst @@ -53,7 +53,7 @@ will be evaluated each timestep, and its value used to determine the force component. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent velocity field. @@ -72,7 +72,7 @@ specified geometric :doc:`region ` in order to have its velocity set by **Restart, fix\_modify, output, run start/stop, minimize info:** Currently, no part of USER-SMD supports restarting nor minimization -None of the :doc:`fix\_modify ` options +None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global 3-vector of forces, which can be accessed diff --git a/doc/src/fix_spring.rst b/doc/src/fix_spring.rst index 2d874e4b23..c3621cab3f 100644 --- a/doc/src/fix_spring.rst +++ b/doc/src/fix_spring.rst @@ -105,11 +105,11 @@ last example holds the ion a distance 5 away from the pore axis No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy stored in the spring to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -140,7 +140,7 @@ invoked by the :doc:`minimize ` command. If you want the spring energy to be included in the total potential energy of the system (the quantity being minimized), you - MUST enable the :doc:`fix\_modify ` *energy* option for this + MUST enable the :doc:`fix_modify ` *energy* option for this fix. Restrictions diff --git a/doc/src/fix_spring_chunk.rst b/doc/src/fix_spring_chunk.rst index 9f6182df8e..d645519add 100644 --- a/doc/src/fix_spring_chunk.rst +++ b/doc/src/fix_spring_chunk.rst @@ -54,11 +54,11 @@ atom. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy stored in all the springs to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -78,7 +78,7 @@ invoked by the :doc:`minimize ` command. If you want the spring energies to be included in the total potential energy of the system (the quantity being minimized), you - MUST enable the :doc:`fix\_modify ` *energy* option for this + MUST enable the :doc:`fix_modify ` *energy* option for this fix. Restrictions diff --git a/doc/src/fix_spring_rg.rst b/doc/src/fix_spring_rg.rst index b2573483e0..59007b6cb6 100644 --- a/doc/src/fix_spring_rg.rst +++ b/doc/src/fix_spring_rg.rst @@ -57,13 +57,13 @@ the time the fix is specified, and that value is used as the target. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. diff --git a/doc/src/fix_spring_self.rst b/doc/src/fix_spring_self.rst index d061c96eba..d9720f0e7c 100644 --- a/doc/src/fix_spring_self.rst +++ b/doc/src/fix_spring_self.rst @@ -47,15 +47,15 @@ plane, respectively. This fix writes the original coordinates of tethered atoms to :doc:`binary restart files `, so that the spring effect will be the same in a restarted simulation. See the -:doc:`read\_restart ` command for info on how to re-specify +:doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy stored in the per-atom springs to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *respa* option is supported by +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -75,7 +75,7 @@ invoked by the :doc:`minimize ` command. If you want the per-atom spring energy to be included in the total potential energy of the system (the quantity being minimized), - you MUST enable the :doc:`fix\_modify ` *energy* option for + you MUST enable the :doc:`fix_modify ` *energy* option for this fix. Restrictions diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst index 51c1b25930..6232c345a1 100644 --- a/doc/src/fix_srd.rst +++ b/doc/src/fix_srd.rst @@ -333,12 +333,12 @@ one of the operations and off for the other. Three other input script commands will largely overcome this effect, speeding up an SRD simulation by a significant amount. These are the -:doc:`atom\_modify first `, :doc:`neigh\_modify include `, and :doc:`comm\_modify group ` +:doc:`atom_modify first `, :doc:`neigh_modify include `, and :doc:`comm_modify group ` commands. Each takes a group-ID as an argument, which in this case should be the group-ID of the big solute particles. -Additionally, when a :doc:`pair\_style ` for big/big particle -interactions is specified, the :doc:`pair\_coeff ` command +Additionally, when a :doc:`pair_style ` for big/big particle +interactions is specified, the :doc:`pair_coeff ` command should be used to turn off big/SRD interactions, e.g. by setting their epsilon or cutoff length to 0.0. @@ -352,7 +352,7 @@ particles. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix tabulates several SRD statistics which are stored in a vector diff --git a/doc/src/fix_store_force.rst b/doc/src/fix_store_force.rst index 4578f39f87..5d96ee26fe 100644 --- a/doc/src/fix_store_force.rst +++ b/doc/src/fix_store_force.rst @@ -53,7 +53,7 @@ potentially modify the force on each atom. Examples of such fixes are **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a per-atom array which can be accessed by various diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst index 131ba5d0b1..15cad5bc81 100644 --- a/doc/src/fix_store_state.rst +++ b/doc/src/fix_store_state.rst @@ -110,12 +110,12 @@ group. **Restart, fix\_modify, output, run start/stop, minimize info:** This fix writes the per-atom values it stores to :doc:`binary restart files `, so that the values can be restored when a -simulation is restarted. See the :doc:`read\_restart ` +simulation is restarted. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. If a single input is specified, this fix produces a per-atom vector. diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst index 8d0959cd96..f378d5dac7 100644 --- a/doc/src/fix_temp_berendsen.rst +++ b/doc/src/fix_temp_berendsen.rst @@ -64,7 +64,7 @@ its value used to determine the target temperature. zero temperature. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. @@ -97,11 +97,11 @@ that the ID of the new compute is the fix-ID + underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -111,7 +111,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -127,13 +127,13 @@ thermal degrees of freedom, and the bias is added back in. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by this fix and by the compute should be the same. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change implied by a velocity rescaling to the system's potential energy as part of :doc:`thermodynamic output `. @@ -164,7 +164,7 @@ Related commands """""""""""""""" :doc:`fix nve `, :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix langevin `, -:doc:`fix\_modify `, :doc:`compute temp `, +:doc:`fix_modify `, :doc:`compute temp `, :doc:`fix press/berendsen ` **Default:** none diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index 6494c9e981..27aabaab1d 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -74,7 +74,7 @@ name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. @@ -107,11 +107,11 @@ that the ID of the new compute is the fix-ID + underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -121,7 +121,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -137,7 +137,7 @@ thermal degrees of freedom, and the bias is added back in. No information about these fixes are written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* option is supported by these +The :doc:`fix_modify ` *temp* option is supported by these fixes. You can use it to assign a temperature :doc:`compute ` you have defined to these fixes which will be used in its thermostatting procedure, as described above. For consistency, the group used by @@ -172,7 +172,7 @@ Related commands """""""""""""""" :doc:`fix nve `, :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix langevin `, -:doc:`fix\_modify `, :doc:`compute temp `, +:doc:`fix_modify `, :doc:`compute temp `, :doc:`fix temp/berendsen ` **Default:** none diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst index 80f03a3018..13858f6043 100644 --- a/doc/src/fix_temp_rescale.rst +++ b/doc/src/fix_temp_rescale.rst @@ -64,7 +64,7 @@ name. In this case, the variable will be evaluated each timestep, and its value used to determine the target temperature. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. @@ -104,11 +104,11 @@ ID of the new compute is the fix-ID + underscore + "temp", and the group for the new compute is the same as the fix group. Note that this is NOT the compute used by thermodynamic output (see -the :doc:`thermo\_style ` command) with ID = *thermo\_temp*. +the :doc:`thermo_style ` command) with ID = *thermo\_temp*. This means you can change the attributes of this fix's temperature (e.g. its degrees-of-freedom) via the -:doc:`compute\_modify ` command or print this temperature -during thermodynamic output via the :doc:`thermo\_style custom ` command using the appropriate compute-ID. +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. It also means that changing attributes of *thermo\_temp* will have no effect on this fix. @@ -118,7 +118,7 @@ after removing a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by -default, but only if the :doc:`fix\_modify ` command is used +default, but only if the :doc:`fix_modify ` command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In this case, the thermostat works in the following manner: the current @@ -134,13 +134,13 @@ thermal degrees of freedom, and the bias is added back in. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by this fix and by the compute should be the same. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change implied by a velocity rescaling to the system's potential energy as part of :doc:`thermodynamic output `. @@ -163,7 +163,7 @@ Related commands """""""""""""""" :doc:`fix langevin `, :doc:`fix nvt `, -:doc:`fix\_modify ` +:doc:`fix_modify ` **Default:** none diff --git a/doc/src/fix_temp_rescale_eff.rst b/doc/src/fix_temp_rescale_eff.rst index e60459a29b..ef7cf8f42a 100644 --- a/doc/src/fix_temp_rescale_eff.rst +++ b/doc/src/fix_temp_rescale_eff.rst @@ -41,13 +41,13 @@ particles. No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *temp* option is supported by this +The :doc:`fix_modify ` *temp* option is supported by this fix. You can use it to assign a temperature :doc:`compute ` you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by this fix and by the compute should be the same. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy change implied by a velocity rescaling to the system's potential energy as part of :doc:`thermodynamic output `. @@ -72,7 +72,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`fix langevin/eff `, :doc:`fix nvt/eff `, :doc:`fix\_modify `, +:doc:`fix langevin/eff `, :doc:`fix nvt/eff `, :doc:`fix_modify `, :doc:`fix temp rescale `, **Default:** none diff --git a/doc/src/fix_tfmc.rst b/doc/src/fix_tfmc.rst index ab407ba7b1..a5d37136ef 100644 --- a/doc/src/fix_tfmc.rst +++ b/doc/src/fix_tfmc.rst @@ -126,7 +126,7 @@ rotational component of the tfMC displacements after every iteration. No information about this fix is written to :doc:`binary restart files `. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. This fix is not invoked during :doc:`energy minimization `. diff --git a/doc/src/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst index 05552c1b37..9682adf76a 100644 --- a/doc/src/fix_thermal_conductivity.rst +++ b/doc/src/fix_thermal_conductivity.rst @@ -115,7 +115,7 @@ fluid, in appropriate units. See the :ref:`Muller-Plathe paper **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which can be accessed by various diff --git a/doc/src/fix_tmd.rst b/doc/src/fix_tmd.rst index ed31733196..416ab877ab 100644 --- a/doc/src/fix_tmd.rst +++ b/doc/src/fix_tmd.rst @@ -61,7 +61,7 @@ the atoms to follow. If image flags are included with the atoms, the 1st 3 lo/hi lines must appear in the file. If image flags are not included, the 1st 3 lines should not appear. The 3 lines contain the simulation box dimensions for the atom coordinates, in the same format -as in a LAMMPS data file (see the :doc:`read\_data ` command). +as in a LAMMPS data file (see the :doc:`read_data ` command). The remaining lines each contain an atom ID and its target x,y,z coordinates. The atom lines (all or none of them) can optionally be @@ -94,7 +94,7 @@ For more information about TMD, see :ref:`(Schlitter1) ` and **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index b6bc43ecd3..8833e0f471 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -285,7 +285,7 @@ ignored. The lines with the even numbers are treated as follows: **Restart, fix\_modify, output, run start/stop, minimize info:** These fixes write the state of the electronic subsystem and the energy -exchange between the subsystems to :doc:`binary restart files `. See the :doc:`read\_restart ` command +exchange between the subsystems to :doc:`binary restart files `. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. @@ -296,7 +296,7 @@ fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior. -None of the :doc:`fix\_modify ` options are relevant to these +None of the :doc:`fix_modify ` options are relevant to these fixes. Both fixes compute 2 output quantities stored in a vector of length 2, diff --git a/doc/src/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst index 1dc6c2befd..8424418988 100644 --- a/doc/src/fix_tune_kspace.rst +++ b/doc/src/fix_tune_kspace.rst @@ -70,11 +70,11 @@ to use this fix only to discover the optimal parameter set for a given setup that can then be used on subsequent production runs. This fix starts with kspace parameters that are set by the user with the -:doc:`kspace\_style ` and :doc:`kspace\_modify ` +:doc:`kspace_style ` and :doc:`kspace_modify ` commands. The prescribed accuracy will be maintained by this fix throughout the simulation. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No parameter of this fix can be used with the *start/stop* keywords of @@ -96,9 +96,9 @@ TIP4P water support, or long-range point dipole support. Related commands """""""""""""""" -:doc:`kspace\_style `, :doc:`boundary ` -:doc:`kspace\_modify `, :doc:`pair\_style lj/cut/coul/long `, :doc:`pair\_style lj/charmm/coul/long `, :doc:`pair\_style lj/long `, :doc:`pair\_style lj/long/coul/long `, -:doc:`pair\_style buck/coul/long ` +:doc:`kspace_style `, :doc:`boundary ` +:doc:`kspace_modify `, :doc:`pair_style lj/cut/coul/long `, :doc:`pair_style lj/charmm/coul/long `, :doc:`pair_style lj/long `, :doc:`pair_style lj/long/coul/long `, +:doc:`pair_style buck/coul/long ` Default """"""" diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index 3d7fb85274..a2c7c87cd5 100644 --- a/doc/src/fix_vector.rst +++ b/doc/src/fix_vector.rst @@ -134,7 +134,7 @@ quantities to be stored by fix vector. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix produces a global vector or global array which can be diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst index 637551b1e4..27250f2c85 100644 --- a/doc/src/fix_viscosity.rst +++ b/doc/src/fix_viscosity.rst @@ -120,7 +120,7 @@ box orthogonal; thus it does not suffer from this limitation. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global scalar which can be accessed by various diff --git a/doc/src/fix_viscous.rst b/doc/src/fix_viscous.rst index 247600db93..0c8338048a 100644 --- a/doc/src/fix_viscous.rst +++ b/doc/src/fix_viscous.rst @@ -89,20 +89,20 @@ easily be used as a thermostat. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is modifying forces. Default is the outermost level. The forces due to this fix are imposed during an energy minimization, invoked by the :doc:`minimize ` command. This fix should only be used with damped dynamics minimizers that allow for -non-conservative forces. See the :doc:`min\_style ` command +non-conservative forces. See the :doc:`min_style ` command for details. Restrictions diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index b31ee4a663..a14cf423b0 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -118,7 +118,7 @@ For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: :align: center For style *wall/colloid*\ , the energy E is given by an integrated form -of the :doc:`pair\_style colloid ` potential: +of the :doc:`pair_style colloid ` potential: .. image:: Eqs/fix_wall_colloid.jpg :align: center @@ -157,7 +157,7 @@ where name is an :doc:`equal-style variable ` name. In this case the variable is evaluated each timestep and the result becomes the current position of the reflecting wall. Equal-style variables can specify formulas with various mathematical functions, and include -:doc:`thermo\_style ` command keywords for the simulation +:doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent wall position. See examples below. @@ -213,7 +213,7 @@ specified as v\_name, where name is the variable name. As with a variable wall position, the variable is evaluated each timestep and the result becomes the current epsilon or sigma of the wall. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent wall interaction. @@ -247,7 +247,7 @@ define the lattice spacings. The *fld* keyword can be used with a *yes* setting to invoke the wall constraint before pairwise interactions are computed. This allows an -implicit FLD model using :doc:`pair\_style lubricateU ` +implicit FLD model using :doc:`pair_style lubricateU ` to include the wall force in its calculations. If the setting is *no*\ , wall forces are imposed after pairwise interactions, in the usual manner. @@ -321,15 +321,15 @@ perturbation on the particles: No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy of interaction between atoms and each wall to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the interaction between atoms and each wall to the system's virial as part of :doc:`thermodynamic output `. The default is *virial no* -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -353,7 +353,7 @@ invoked by the :doc:`minimize ` command. If you want the atom/wall interaction energy to be included in the total potential energy of the system (the quantity being - minimized), you MUST enable the :doc:`fix\_modify ` *energy* + minimized), you MUST enable the :doc:`fix_modify ` *energy* option for this fix. diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst index 840338db5c..2ecbb2e911 100644 --- a/doc/src/fix_wall_body_polygon.rst +++ b/doc/src/fix_wall_body_polygon.rst @@ -56,7 +56,7 @@ the :doc:`Howto body ` doc page for more details on using body particles. The parameters *k\_n*, *c\_n*, *c\_t* have the same meaning and units as -those specified with the :doc:`pair\_style body/rounded/polygon ` command. +those specified with the :doc:`pair_style body/rounded/polygon ` command. The *wallstyle* can be planar or cylindrical. The 2 planar options specify a pair of walls in a dimension. Wall positions are given by @@ -91,7 +91,7 @@ to the derivative of this expression. **Restart, fix\_modify, output, run start/stop, minimize info:** -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the @@ -109,7 +109,7 @@ Any dimension (xy) that has a wall must be non-periodic. Related commands """""""""""""""" -:doc:`atom\_style body `, :doc:`pair\_style body/rounded/polygon ` +:doc:`atom_style body `, :doc:`pair_style body/rounded/polygon ` **Default:** none diff --git a/doc/src/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst index 6c3e3f5e6d..fd58c16c44 100644 --- a/doc/src/fix_wall_body_polyhedron.rst +++ b/doc/src/fix_wall_body_polyhedron.rst @@ -56,7 +56,7 @@ the :doc:`Howto body ` doc page for more details on using body particles. The parameters *k\_n*, *c\_n*, *c\_t* have the same meaning and units as -those specified with the :doc:`pair\_style body/rounded/polyhedron ` command. +those specified with the :doc:`pair_style body/rounded/polyhedron ` command. The *wallstyle* can be planar or cylindrical. The 3 planar options specify a pair of walls in a dimension. Wall positions are given by @@ -90,7 +90,7 @@ to the derivative of this expression. **Restart, fix\_modify, output, run start/stop, minimize info:** -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the @@ -108,7 +108,7 @@ Any dimension (xyz) that has a wall must be non-periodic. Related commands """""""""""""""" -:doc:`atom\_style body `, :doc:`pair\_style body/rounded/polyhedron ` +:doc:`atom_style body `, :doc:`pair_style body/rounded/polyhedron ` **Default:** none diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index 559f1958d9..873811110c 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -116,7 +116,7 @@ This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This fix requires that atoms be ellipsoids as defined by the -:doc:`atom\_style ellipsoid ` command. +:doc:`atom_style ellipsoid ` command. Related commands """""""""""""""" diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index 5c9c476a44..0db5a3e5ac 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -83,12 +83,12 @@ close enough to touch it. The nature of the wall/particle interactions are determined by the *fstyle* setting. It can be any of the styles defined by the -:doc:`pair\_style gran/\* ` or the more general `pair\_style granular `_ commands. Currently the options are +:doc:`pair_style gran/\* ` or the more general `pair\_style granular `_ commands. Currently the options are *hooke*\ , *hooke/history*\ , or *hertz/history* for the former, and *granular* with all the possible options of the associated *pair\_coeff* command for the latter. The equation for the force between the wall and particles touching it is the same as the -corresponding equation on the :doc:`pair\_style gran/\* ` and +corresponding equation on the :doc:`pair_style gran/\* ` and :doc:`pair\_style\_granular ` doc pages, in the limit of one of the two particles going to infinite radius and mass (flat wall). Specifically, delta = radius - r = overlap of particle with @@ -97,16 +97,16 @@ RiRj/Ri+Rj is set to the radius of the particle. The parameters *Kn*\ , *Kt*\ , *gamma\_n*, *gamma\_t*, *xmu* and *dampflag* have the same meaning and units as those specified with the -:doc:`pair\_style gran/\* ` commands. This means a NULL can be +:doc:`pair_style gran/\* ` commands. This means a NULL can be used for either *Kt* or *gamma\_t* as described on that page. If a NULL is used for *Kt*\ , then a default value is used where *Kt* = 2/7 *Kn*\ . If a NULL is used for *gamma\_t*, then a default value is used where *gamma\_t* = 1/2 *gamma\_n*. All the model choices for cohesion, tangential friction, rolling -friction and twisting friction supported by the :doc:`pair\_style granular ` through its *pair\_coeff* command are also +friction and twisting friction supported by the :doc:`pair_style granular ` through its *pair\_coeff* command are also supported for walls. These are discussed in greater detail on the doc -page for :doc:`pair\_style granular `. +page for :doc:`pair_style granular `. Note that you can choose a different force styles and/or different values for the wall/particle coefficients than for particle/particle @@ -115,7 +115,7 @@ material. .. note:: - As discussed on the doc page for :doc:`pair\_style gran/\* `, versions of LAMMPS before 9Jan09 used a + As discussed on the doc page for :doc:`pair_style gran/\* `, versions of LAMMPS before 9Jan09 used a different equation for Hertzian interactions. This means Hertizian wall/particle interactions have also changed. They now include a sqrt(radius) term which was not present before. Also the previous @@ -128,7 +128,7 @@ material. Kt, gamma\_n, and gamma\_s should be set sqrt(2.0) larger than they were previously. -The effective mass *m\_eff* in the formulas listed on the :doc:`pair\_style granular ` doc page is the mass of the particle for +The effective mass *m\_eff* in the formulas listed on the :doc:`pair_style granular ` doc page is the mass of the particle for particle/wall interactions (mass of wall is infinite). If the particle is part of a rigid body, its mass is replaced by the mass of the rigid body in those formulas. This is determined by searching for @@ -180,12 +180,12 @@ the wall at whatever *radius* has been defined. This fix writes the shear friction state of atoms interacting with the wall to :doc:`binary restart files `, so that a simulation can continue correctly if granular potentials with shear "history" effects -are being used. See the :doc:`read\_restart ` command for +are being used. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the @@ -205,8 +205,8 @@ Related commands :doc:`fix move `, :doc:`fix wall/gran/region `, -:doc:`pair\_style gran/\* ` -:doc:`pair\_style granular ` +:doc:`pair_style gran/\* ` +:doc:`pair_style granular ` **Default:** none diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index cdd6c7445b..3ca17aa440 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -81,7 +81,7 @@ wall exerts on the particle is along the direction between that point and the particle center, which is the direction normal to the surface at that point. Note that if the region surface is comprised of multiple "faces", then each face can exert a force on the particle if -it is close enough. E.g. for :doc:`region\_style block `, a +it is close enough. E.g. for :doc:`region_style block `, a particle in the interior, near a corner of the block, could feel wall forces from 1, 2, or 3 faces of the block. @@ -154,12 +154,12 @@ corresponding manner. The nature of the wall/particle interactions are determined by the *fstyle* setting. It can be any of the styles defined by the -:doc:`pair\_style gran/\* ` or the more general `pair\_style granular `_ commands. Currently the options are +:doc:`pair_style gran/\* ` or the more general `pair\_style granular `_ commands. Currently the options are *hooke*\ , *hooke/history*\ , or *hertz/history* for the former, and *granular* with all the possible options of the associated *pair\_coeff* command for the latter. The equation for the force between the wall and particles touching it is the same as the -corresponding equation on the :doc:`pair\_style gran/\* ` and +corresponding equation on the :doc:`pair_style gran/\* ` and :doc:`pair\_style\_granular ` doc pages, but the effective radius is calculated using the radius of the particle and the radius of curvature of the wall at the contact point. @@ -175,16 +175,16 @@ particle. The parameters *Kn*\ , *Kt*\ , *gamma\_n*, *gamma\_t*, *xmu* and *dampflag* have the same meaning and units as those specified with the -:doc:`pair\_style gran/\* ` commands. This means a NULL can be +:doc:`pair_style gran/\* ` commands. This means a NULL can be used for either *Kt* or *gamma\_t* as described on that page. If a NULL is used for *Kt*\ , then a default value is used where *Kt* = 2/7 *Kn*\ . If a NULL is used for *gamma\_t*, then a default value is used where *gamma\_t* = 1/2 *gamma\_n*. All the model choices for cohesion, tangential friction, rolling -friction and twisting friction supported by the :doc:`pair\_style granular ` through its *pair\_coeff* command are also +friction and twisting friction supported by the :doc:`pair_style granular ` through its *pair\_coeff* command are also supported for walls. These are discussed in greater detail on the doc -page for :doc:`pair\_style granular `. +page for :doc:`pair_style granular `. Note that you can choose a different force styles and/or different values for the 6 wall/particle coefficients than for particle/particle @@ -197,7 +197,7 @@ Similar to :doc:`fix wall/gran ` command, this fix writes the shear friction state of atoms interacting with the wall to :doc:`binary restart files `, so that a simulation can continue correctly if granular potentials with shear "history" effects are being used. This fix also includes info about a moving region in the -restart file. See the :doc:`read\_restart ` command for +restart file. See the :doc:`read_restart ` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. @@ -205,7 +205,7 @@ uninterrupted fashion. .. note:: Information about region definitions is NOT included in restart - files, as discussed on the :doc:`read\_restart ` doc page. + files, as discussed on the :doc:`read_restart ` doc page. So you must re-define your region and if it is a moving region, define its motion attributes in a way that is consistent with the simulation that wrote the restart file. In particular, if you want to change the @@ -219,7 +219,7 @@ uninterrupted fashion. use the same fix ID for fix wall/gran/region, but assign it a region with a different region ID. -None of the :doc:`fix\_modify ` options are relevant to this +None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the @@ -235,10 +235,10 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`fix\_move `, +:doc:`fix_move `, :doc:`fix wall/gran `, :doc:`fix wall/region `, -:doc:`pair\_style granular `, +:doc:`pair_style granular `, :doc:`region ` **Default:** none diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst index c38057915b..863fb2bd86 100644 --- a/doc/src/fix_wall_piston.rst +++ b/doc/src/fix_wall_piston.rst @@ -98,7 +98,7 @@ define the lattice spacings. **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index 464ae3b4a5..c6807eee94 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/doc/src/fix_wall_reflect.rst @@ -59,7 +59,7 @@ put back inside the face by the same delta, and the sign of the corresponding component of its velocity is flipped. When used in conjunction with :doc:`fix nve ` and -:doc:`run\_style verlet `, the resultant time-integration +:doc:`run_style verlet `, the resultant time-integration algorithm is equivalent to the primitive splitting algorithm (PSA) described by :ref:`Bond `. Because each reflection event divides the corresponding timestep asymmetrically, energy conservation @@ -83,7 +83,7 @@ where name is an :doc:`equal-style variable ` name. In this case the variable is evaluated each timestep and the result becomes the current position of the reflecting wall. Equal-style variables can specify formulas with various mathematical functions, and include -:doc:`thermo\_style ` command keywords for the simulation +:doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent wall position. @@ -177,7 +177,7 @@ instructions on how to use the accelerated styles effectively. **Restart, fix\_modify, output, run start/stop, minimize info:** No information about this fix is written to :doc:`binary restart files -`. None of the :doc:`fix\_modify ` options are +`. None of the :doc:`fix_modify ` options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst index 36b2dffde9..069221df9d 100644 --- a/doc/src/fix_wall_region.rst +++ b/doc/src/fix_wall_region.rst @@ -56,7 +56,7 @@ particle is along the direction between that point and the particle, which is the direction normal to the surface at that point. Note that if the region surface is comprised of multiple "faces", then each face can exert a force on the particle if it is close enough. E.g. for -:doc:`region\_style block `, a particle in the interior, near a +:doc:`region_style block `, a particle in the interior, near a corner of the block, could feel wall forces from 1, 2, or 3 faces of the block. @@ -146,7 +146,7 @@ For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential: :align: center For style *colloid*\ , the energy E is given by an integrated form of -the :doc:`pair\_style colloid ` potential: +the :doc:`pair_style colloid ` potential: .. image:: Eqs/fix_wall_colloid.jpg :align: center @@ -178,15 +178,15 @@ For a full description of these wall styles, see fix\_style No information about this fix is written to :doc:`binary restart files `. -The :doc:`fix\_modify ` *energy* option is supported by this +The :doc:`fix_modify ` *energy* option is supported by this fix to add the energy of interaction between atoms and the wall to the system's potential energy as part of :doc:`thermodynamic output `. -The :doc:`fix\_modify ` *virial* option is supported by this +The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the interaction between atoms and each wall to the system's virial as part of :doc:`thermodynamic output `. The default is *virial no* -The :doc:`fix\_modify ` *respa* option is supported by this +The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the outermost level. @@ -207,7 +207,7 @@ invoked by the :doc:`minimize ` command. If you want the atom/wall interaction energy to be included in the total potential energy of the system (the quantity being - minimized), you MUST enable the :doc:`fix\_modify ` *energy* + minimized), you MUST enable the :doc:`fix_modify ` *energy* option for this fix. Restrictions diff --git a/doc/src/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst index c302539f3c..8a4fd22176 100644 --- a/doc/src/fix_wall_srd.rst +++ b/doc/src/fix_wall_srd.rst @@ -93,7 +93,7 @@ where name is an :doc:`equal-style variable ` name. In this case the variable is evaluated each timestep and the result becomes the current position of the reflecting wall. Equal-style variables can specify formulas with various mathematical functions, and include -:doc:`thermo\_style ` command keywords for the simulation +:doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent wall position. @@ -190,7 +190,7 @@ perturbation on the particles: **Restart, fix\_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix\_modify ` options +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options are relevant to this fix. This fix computes a global array of values which can be accessed by diff --git a/doc/src/hyper.rst b/doc/src/hyper.rst index bf1e884cda..90268a2c90 100644 --- a/doc/src/hyper.rst +++ b/doc/src/hyper.rst @@ -115,9 +115,9 @@ is performed by quenching the system and comparing the resulting atom coordinates to the coordinates from the previous basin. A quench is an energy minimization and is performed by whichever -algorithm has been defined by the :doc:`min\_style ` command. +algorithm has been defined by the :doc:`min_style ` command. Minimization parameters may be set via the -:doc:`min\_modify ` command and by the *min* keyword of the +:doc:`min_modify ` command and by the *min* keyword of the hyper command. The latter are the settings that would be used with the :doc:`minimize ` command. Note that typically, you do not need to perform a highly-converged minimization to detect a transition diff --git a/doc/src/improper_class2.rst b/doc/src/improper_class2.rst index d6f23e761c..ed120acb58 100644 --- a/doc/src/improper_class2.rst +++ b/doc/src/improper_class2.rst @@ -39,7 +39,7 @@ where Ei is the improper term and Eaa is an angle-angle term. The 3 X terms in Ei are an average over 3 out-of-plane angles. The 4 atoms in an improper quadruplet (listed in the data file read by -the :doc:`read\_data ` command) are ordered I,J,K,L. X\_IJKL +the :doc:`read_data ` command) are ordered I,J,K,L. X\_IJKL refers to the angle between the plane of I,J,K and the plane of J,K,L, and the bond JK lies in both planes. Similarly for X\_KJLI and X\_LJIK. Note that atom J appears in the common bonds (JI, JK, JL) of all 3 X @@ -60,9 +60,9 @@ this is not required. See :ref:`(Sun) ` for a description of the COMPASS class2 force field. Coefficients for the Ei and Eaa formulas must be defined for each -improper type via the :doc:`improper\_coeff ` command as +improper type via the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands. These are the 2 coefficients for the Ei formula: @@ -74,7 +74,7 @@ X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian\^2. For the Eaa formula, each line in a -:doc:`improper\_coeff ` command in the input script lists +:doc:`improper_coeff ` command in the input script lists 7 coefficients, the first of which is "aa" to indicate they are AngleAngle coefficients. In a data file, these coefficients should be listed under a "AngleAngle Coeffs" heading and you must leave out the @@ -128,7 +128,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_coeff.rst b/doc/src/improper_coeff.rst index b71469523f..3c50f9bf58 100644 --- a/doc/src/improper_coeff.rst +++ b/doc/src/improper_coeff.rst @@ -30,7 +30,7 @@ Description Specify the improper force field coefficients for one or more improper types. The number and meaning of the coefficients depends on the improper style. Improper coefficients can also be set in the data -file read by the :doc:`read\_data ` command or in a restart +file read by the :doc:`read_data ` command or in a restart file. N can be specified in one of two ways. An explicit numeric value can @@ -65,7 +65,7 @@ corresponds to the 1st example above would be listed as 1 300.0 0.0 -The :doc:`improper\_style class2 ` is an exception to +The :doc:`improper_style class2 ` is an exception to this rule, in that an additional argument is used in the input script to allow specification of the cross-term coefficients. See its doc page for details. @@ -75,7 +75,7 @@ page for details. The list of all improper styles defined in LAMMPS is given on the -:doc:`improper\_style ` doc page. They are also listed +:doc:`improper_style ` doc page. They are also listed in more compact form on the :ref:`Commands improper ` doc page. On either of those pages, click on the style to display the formula it @@ -91,8 +91,8 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. An improper style must be defined before any improper coefficients are set, either in the input script or in a data file. @@ -100,7 +100,7 @@ set, either in the input script or in a data file. Related commands """""""""""""""" -:doc:`improper\_style ` +:doc:`improper_style ` **Default:** none diff --git a/doc/src/improper_cossq.rst b/doc/src/improper_cossq.rst index 803f6d9e6a..b8f0c33c29 100644 --- a/doc/src/improper_cossq.rst +++ b/doc/src/improper_cossq.rst @@ -35,7 +35,7 @@ where x is the improper angle, x0 is its equilibrium value, and K is a prefactor. If the 4 atoms in an improper quadruplet (listed in the data file read -by the :doc:`read\_data ` command) are ordered I,J,K,L then X +by the :doc:`read_data ` command) are ordered I,J,K,L then X is the angle between the plane of I,J,K and the plane of J,K,L. Alternatively, you can think of atoms J,K,L as being in a plane, and atom I above the plane, and X as a measure of how far out-of-plane I @@ -47,9 +47,9 @@ linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an improper to be defined between the 4 atoms. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy) @@ -92,7 +92,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_cvff.rst b/doc/src/improper_cvff.rst index 43cd36f60a..e661d3b84a 100644 --- a/doc/src/improper_cvff.rst +++ b/doc/src/improper_cvff.rst @@ -37,11 +37,11 @@ The *cvff* improper style uses the potential where phi is the improper dihedral angle. If the 4 atoms in an improper quadruplet (listed in the data file read -by the :doc:`read\_data ` command) are ordered I,J,K,L then +by the :doc:`read_data ` command) are ordered I,J,K,L then the improper dihedral angle is between the plane of I,J,K and the plane of J,K,L. Note that because this is effectively a dihedral angle, the formula for this improper style is the same as for -:doc:`dihedral\_style harmonic `. +:doc:`dihedral_style harmonic `. Note that defining 4 atoms to interact in this way, does not mean that bonds necessarily exist between I-J, J-K, or K-L, as they would in a @@ -49,9 +49,9 @@ linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an improper to be defined between the 4 atoms. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy) @@ -95,7 +95,7 @@ for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_distance.rst b/doc/src/improper_distance.rst index 4efc9a2261..72643a05bd 100644 --- a/doc/src/improper_distance.rst +++ b/doc/src/improper_distance.rst @@ -27,7 +27,7 @@ The *distance* improper style uses the potential where d is the distance between the central atom and the plane formed by the other three atoms. If the 4 atoms in an improper quadruplet -(listed in the data file read by the :doc:`read\_data ` +(listed in the data file read by the :doc:`read_data ` command) are ordered I,J,K,L then the I-atom is assumed to be the central atom. @@ -61,7 +61,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_distharm.rst b/doc/src/improper_distharm.rst index 8fb74129ec..dcbdfbc656 100644 --- a/doc/src/improper_distharm.rst +++ b/doc/src/improper_distharm.rst @@ -27,7 +27,7 @@ The *distharm* improper style uses the potential where d is the oriented distance between the central atom and the plane formed by the other three atoms. If the 4 atoms in an improper quadruplet -(listed in the data file read by the :doc:`read\_data ` +(listed in the data file read by the :doc:`read_data ` command) are ordered I,J,K,L then the L-atom is assumed to be the central atom. Note that this is different from the convention used in the improper\_style distance. The distance d is oriented and can take @@ -55,7 +55,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index 227b02d275..23988a49ad 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -40,9 +40,9 @@ and omega is the angle between the IL axis and the IJK plane: If all parameter (see below) is not zero, the all the three possible angles will taken in account. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy) @@ -88,7 +88,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst index 6eb205f8e7..d3332c816c 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -41,7 +41,7 @@ where X is the improper angle, X0 is its equilibrium value, and K is a prefactor. Note that the usual 1/2 factor is included in K. If the 4 atoms in an improper quadruplet (listed in the data file read -by the :doc:`read\_data ` command) are ordered I,J,K,L then X +by the :doc:`read_data ` command) are ordered I,J,K,L then X is the angle between the plane of I,J,K and the plane of J,K,L. Alternatively, you can think of atoms J,K,L as being in a plane, and atom I above the plane, and X as a measure of how far out-of-plane I @@ -53,9 +53,9 @@ linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an improper to be defined between the 4 atoms. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy/radian\^2) @@ -101,7 +101,7 @@ for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_hybrid.rst b/doc/src/improper_hybrid.rst index 7272cb2abc..5b170749cc 100644 --- a/doc/src/improper_hybrid.rst +++ b/doc/src/improper_hybrid.rst @@ -32,7 +32,7 @@ example, impropers in a polymer flow (of improper type 1) could be computed with a *harmonic* potential and impropers in the wall boundary (of improper type 2) could be computed with a *cvff* potential. The assignment of improper type to style is made via the -:doc:`improper\_coeff ` command or in the data file. +:doc:`improper_coeff ` command or in the data file. In the improper\_coeff command, the first coefficient sets the improper style and the remaining coefficients are those appropriate to that @@ -73,7 +73,7 @@ restart file, you need to re-specify improper\_coeff commands. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_inversion_harmonic.rst b/doc/src/improper_inversion_harmonic.rst index 11832d2754..ecdcad7136 100644 --- a/doc/src/improper_inversion_harmonic.rst +++ b/doc/src/improper_inversion_harmonic.rst @@ -37,13 +37,13 @@ the IL axis and the IJK plane omega looks as follows: :align: center Note that the *inversion/harmonic* angle term evaluation differs to -the :doc:`improper\_umbrella ` due to the cyclic +the :doc:`improper_umbrella ` due to the cyclic evaluation of all possible angles omega. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy) @@ -68,7 +68,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_none.rst b/doc/src/improper_none.rst index 83622b4f11..b348f3aab2 100644 --- a/doc/src/improper_none.rst +++ b/doc/src/improper_none.rst @@ -24,9 +24,9 @@ Description Using an improper style of none means improper forces and energies are not computed, even if quadruplets of improper atoms were listed in the -data file read by the :doc:`read\_data ` command. +data file read by the :doc:`read_data ` command. -See the :doc:`improper\_style zero ` command for a way to +See the :doc:`improper_style zero ` command for a way to calculate improper statistics, but compute no improper interactions. Restrictions @@ -36,7 +36,7 @@ Restrictions Related commands """""""""""""""" -:doc:`improper\_style zero ` +:doc:`improper_style zero ` **Default:** none diff --git a/doc/src/improper_ring.rst b/doc/src/improper_ring.rst index 374b64fcd7..6cc14ea15a 100644 --- a/doc/src/improper_ring.rst +++ b/doc/src/improper_ring.rst @@ -35,7 +35,7 @@ where K is a prefactor, theta is the angle formed by the atoms specified by (i,j,k,l) indices and theta0 its equilibrium value. If the 4 atoms in an improper quadruplet (listed in the data file read -by the :doc:`read\_data ` command) are ordered i,j,k,l then +by the :doc:`read_data ` command) are ordered i,j,k,l then theta\_\ *ijl* is the angle between atoms i,j and l, theta\_\ *ijk* is the angle between atoms i,j and k, theta\_\ *kjl* is the angle between atoms j,k, and l. @@ -51,9 +51,9 @@ data file four atoms: i, j, k and l are specified with i,j and l lying on the backbone of the chain and k specifying the chirality of j. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy) @@ -96,7 +96,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` .. _Destree: diff --git a/doc/src/improper_sqdistharm.rst b/doc/src/improper_sqdistharm.rst index 94e9c12fca..f54e610c80 100644 --- a/doc/src/improper_sqdistharm.rst +++ b/doc/src/improper_sqdistharm.rst @@ -27,7 +27,7 @@ The *sqdistharm* improper style uses the potential where d is the distance between the central atom and the plane formed by the other three atoms. If the 4 atoms in an improper quadruplet -(listed in the data file read by the :doc:`read\_data ` +(listed in the data file read by the :doc:`read_data ` command) are ordered I,J,K,L then the L-atom is assumed to be the central atom. Note that this is different from the convention used in the improper\_style distance. @@ -56,7 +56,7 @@ page for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_style.rst b/doc/src/improper_style.rst index e49818981a..ee8b75ed3f 100644 --- a/doc/src/improper_style.rst +++ b/doc/src/improper_style.rst @@ -29,7 +29,7 @@ Description Set the formula(s) LAMMPS uses to compute improper interactions between quadruplets of atoms, which remain in force for the duration of the simulation. The list of improper quadruplets is read in by a -:doc:`read\_data ` or :doc:`read\_restart ` command +:doc:`read_data ` or :doc:`read_restart ` command from a data or restart file. Note that the ordering of the 4 atoms in an improper quadruplet determines the definition of the improper angle used in the formula for each style. See the doc pages of @@ -39,14 +39,14 @@ Hybrid models where impropers are computed using different improper potentials can be setup using the *hybrid* improper style. The coefficients associated with an improper style can be specified in -a data or restart file or via the :doc:`improper\_coeff ` +a data or restart file or via the :doc:`improper_coeff ` command. All improper potentials store their coefficient data in binary restart files which means improper\_style and -:doc:`improper\_coeff ` commands do not need to be +:doc:`improper_coeff ` commands do not need to be re-specified in an input script that restarts a simulation. See the -:doc:`read\_restart ` command for details on how to do +:doc:`read_restart ` command for details on how to do this. The one exception is that improper\_style *hybrid* only stores the list of sub-styles in the restart file; improper coefficients need to be re-specified. @@ -54,7 +54,7 @@ to be re-specified. .. note:: When both an improper and pair style is defined, the - :doc:`special\_bonds ` command often needs to be used to + :doc:`special_bonds ` command often needs to be used to turn off (or weight) the pairwise interaction that would otherwise exist between a group of 4 bonded atoms. @@ -64,12 +64,12 @@ to be re-specified. Here is an alphabetic list of improper styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients -specified by the associated :doc:`improper\_coeff ` +specified by the associated :doc:`improper_coeff ` command. Click on the style to display the formula it computes, any additional arguments specified in the improper\_style command, and coefficients -specified by the associated :doc:`improper\_coeff ` +specified by the associated :doc:`improper_coeff ` command. There are also additional accelerated pair styles included in the @@ -112,7 +112,7 @@ individual improper potentials tell if it is part of a package. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` Default """"""" diff --git a/doc/src/improper_umbrella.rst b/doc/src/improper_umbrella.rst index 785d3ce7dd..66f3112fe7 100644 --- a/doc/src/improper_umbrella.rst +++ b/doc/src/improper_umbrella.rst @@ -46,9 +46,9 @@ in between. See :ref:`(Mayo) ` for a description of the DREIDING force field. The following coefficients must be defined for each improper type via -the :doc:`improper\_coeff ` command as in the example +the :doc:`improper_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * K (energy) @@ -91,7 +91,7 @@ for more info. Related commands """""""""""""""" -:doc:`improper\_coeff ` +:doc:`improper_coeff ` **Default:** none diff --git a/doc/src/improper_zero.rst b/doc/src/improper_zero.rst index 145146e6f6..5714749596 100644 --- a/doc/src/improper_zero.rst +++ b/doc/src/improper_zero.rst @@ -30,7 +30,7 @@ accessible to other commands. As an example, the :doc:`compute improper/local ` command can be used to compute the chi values for the list of quadruplets of improper atoms -listed in the data file read by the :doc:`read\_data ` +listed in the data file read by the :doc:`read_data ` command. If no improper style is defined, this command cannot be used. @@ -38,7 +38,7 @@ The optional *nocoeff* flag allows to read data files with a ImproperCoeff section for any improper style. Similarly, any improper\_coeff commands will only be checked for the improper type number and the rest ignored. -Note that the :doc:`improper\_coeff ` command must be +Note that the :doc:`improper_coeff ` command must be used for all improper types, though no additional values are specified. @@ -48,7 +48,7 @@ Restrictions **Related commands:** none -:doc:`improper\_style none ` +:doc:`improper_style none ` **Default:** none diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index 9f0b5a6775..ea2f768e7c 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -195,7 +195,7 @@ the simulation box is created (normally at the top of the file). This command sets the OpenKIM IM that will be used and may issue additional commands changing LAMMPS default settings that are required for using the selected IM (such as :doc:`units ` or -:doc:`atom\_style `). If needed, those settings can be overridden, +:doc:`atom_style `). If needed, those settings can be overridden, however, typically a script containing a *kim\_init* command would not include *units* and *atom\_style* commands. @@ -216,7 +216,7 @@ printed to help diagnose any incompatible changes to input script or command syntax between the two LAMMPS versions. Based on the selected model *kim\_init* may modify the -:doc:`atom\_style `. +:doc:`atom_style `. Some SMs have requirements for this setting. If this is the case, then *atom\_style* will be set to the required style. Otherwise, the value is left unchanged (which in the absence of an *atom\_style* command in the input script @@ -316,7 +316,7 @@ will work correctly for any IM for Al (KIM PM or SM) selected by the Care must be taken to apply unit conversion to dimensional variables read in from a file. For example, if a configuration of atoms is read in from a -dump file using the :doc:`read\_dump ` command, the following can +dump file using the :doc:`read_dump ` command, the following can be done to convert the box and all atomic positions to the correct units: @@ -345,7 +345,7 @@ OpenKIM IM Execution (*kim\_interactions*) The second and final step in using an OpenKIM IM is to execute the *kim\_interactions* command. This command must be preceded by a *kim\_init* command and a command that defines the number of atom types *N* (such as -:doc:`create\_box `). +:doc:`create_box `). The *kim\_interactions* command has one argument *typeargs*\ . This argument contains either a list of *N* chemical species, which defines a mapping between atom types in LAMMPS to the available species in the OpenKIM IM, or the @@ -374,7 +374,7 @@ Alternatively, for a model with a fixed mapping the command would be: The *kim\_interactions* command performs all the necessary steps to set up the OpenKIM IM selected in the *kim\_init* command. The specific actions depend on whether the IM is a KIM PM or a KIM SM. For a KIM PM, -a :doc:`pair\_style kim ` command is executed followed by +a :doc:`pair_style kim ` command is executed followed by the appropriate *pair\_coeff* command. For example, for the Ercolessi and Adams (1994) KIM PM for Al set by the following commands: @@ -894,7 +894,7 @@ must be installed. Related commands """""""""""""""" -:doc:`pair\_style kim ` +:doc:`pair_style kim ` ---------- diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index 5f4dad4dcd..c79b9ceb09 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -72,7 +72,7 @@ Description """"""""""" Set parameters used by the kspace solvers defined by the -:doc:`kspace\_style ` command. Not all parameters are +:doc:`kspace_style ` command. Not all parameters are relevant to all kspace styles. @@ -92,12 +92,12 @@ collective operations and adequate hardware. The *compute* keyword allows Kspace computations to be turned off, -even though a :doc:`kspace\_style ` is defined. This is +even though a :doc:`kspace_style ` is defined. This is not useful for running a real simulation, but can be useful for debugging purposes or for computing only partial forces that do not include the Kspace contribution. You can also do this by simply not -defining a :doc:`kspace\_style `, but a Kspace-compatible -:doc:`pair\_style ` requires a kspace style to be defined. +defining a :doc:`kspace_style `, but a Kspace-compatible +:doc:`pair_style ` requires a kspace style to be defined. This keyword gives you that option. @@ -179,7 +179,7 @@ are different. The *force* keyword overrides the relative accuracy parameter set by -the :doc:`kspace\_style ` command with an absolute +the :doc:`kspace_style ` command with an absolute accuracy. The accuracy determines the RMS error in per-atom forces calculated by the long-range solver and is thus specified in force units. A negative value for the accuracy setting means to use the @@ -272,7 +272,7 @@ MSM. The *mix/disp* keyword selects the mixing rule for the dispersion coefficients. With *pair*\ , the dispersion coefficients of unlike -types are computed as indicated with :doc:`pair\_modify `. +types are computed as indicated with :doc:`pair_modify `. With *geom*\ , geometric mixing is enforced on the dispersion coefficients in the kspace coefficients. When using the arithmetic mixing rule, this will speed-up the simulations but introduces some @@ -361,10 +361,10 @@ or with suffix kspace/pair styles of MSM, like OMP or GPU. The *scafacos* keyword is used for settings that are passed to the -ScaFaCoS library when using :doc:`kspace\_style scafacos `. +ScaFaCoS library when using :doc:`kspace_style scafacos `. The *tolerance* option affects how the *accuracy* specified with the -:doc:`kspace\_style ` command is interpreted by ScaFaCoS. +:doc:`kspace_style ` command is interpreted by ScaFaCoS. The following values may be used: * energy = absolute accuracy in total Coulombic energy @@ -394,7 +394,7 @@ field\_rel tolerance types set a tolerance based on the electric field values computed by ScaFaCoS. Since per-atom forces are derived from the per-atom electric field, this effectively sets a tolerance on the forces, similar to other LAMMPS KSpace styles, as explained on the -:doc:`kspace\_style ` doc page. +:doc:`kspace_style ` doc page. Note that not all ScaFaCoS solvers support all tolerance types. These are the allowed values for each method: @@ -444,7 +444,7 @@ boundaries can be set using :doc:`boundary ` (the slab approximation in not needed). The *slab* keyword is not currently supported by Ewald or PPPM when using a triclinic simulation cell. The slab correction has also been extended to point dipole interactions -:ref:`(Klapp) ` in :doc:`kspace\_style ` *ewald/disp*\ , +:ref:`(Klapp) ` in :doc:`kspace_style ` *ewald/disp*\ , *ewald/dipole*\ , and *pppm/dipole*\ . .. note:: @@ -488,7 +488,7 @@ Restrictions Related commands """""""""""""""" -:doc:`kspace\_style `, :doc:`boundary ` +:doc:`kspace_style `, :doc:`boundary ` Default """"""" diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 4dfcf2fe73..5142734f19 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -212,7 +212,7 @@ that Lennard-Jones or Buckingham potentials can be used without a cutoff, i.e. they become full long-range potentials. For these styles, you will possibly want to adjust the default choice -of parameters by using the :doc:`kspace\_modify ` command. +of parameters by using the :doc:`kspace_modify ` command. This can be done by either choosing the Ewald and grid parameters, or by specifying separate accuracies for the real and kspace calculations. When not making any settings, the simulation will stop @@ -256,7 +256,7 @@ angstroms instead of 10 angstroms) provides better MSM accuracy for both the real space and grid computed forces. Currently calculation of the full pressure tensor in MSM is expensive. -Using the :doc:`kspace\_modify ` *pressure/scalar yes* +Using the :doc:`kspace_modify ` *pressure/scalar yes* command provides a less expensive way to compute the scalar pressure (Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example, to run an isotropic barostat. If the full pressure tensor is needed, @@ -320,9 +320,9 @@ ScaFaCoS library the *accuracy* is treated as a tolerance level (either absolute or relative) for the chosen quantity, where the quantity can be either the Columic field values, the per-atom Columic energy or the total Columic energy. To select from these options, see -the :doc:`kspace\_modify scafacos accuracy ` doc page. +the :doc:`kspace_modify scafacos accuracy ` doc page. -The :doc:`kspace\_modify scafacos ` command also explains +The :doc:`kspace_modify scafacos ` command also explains other ScaFaCoS options currently exposed to LAMMPS. @@ -346,7 +346,7 @@ Note that style *pppm* only computes the grid size at the beginning of a simulation, so if the length or triclinic tilt of the simulation cell increases dramatically during the course of the simulation, the accuracy of the simulation may degrade. Likewise, if the -:doc:`kspace\_modify slab ` option is used with +:doc:`kspace_modify slab ` option is used with shrink-wrap boundaries in the z-dimension, and the box size changes dramatically in z. For example, for a triclinic system with all three tilt factors set to the maximum limit, the PPPM grid should be @@ -359,7 +359,7 @@ works because the grid size is re-computed at the beginning of each run. Another way to ensure the described accuracy requirement is met is to run a short simulation at the maximum expected tilt or length, note the required grid size, and then use the -:doc:`kspace\_modify ` *mesh* command to manually set the +:doc:`kspace_modify ` *mesh* command to manually set the PPPM grid size to this value for the long run. The simulation then will be "too accurate" for some portion of the run. @@ -378,7 +378,7 @@ or *ewald/dipole* are estimated using equations 33 and 46 of :ref:`(Wang) `. The RMS force errors for *pppm/dipole* are estimated using the equations in :ref:`(Cerda) `. -See the :doc:`kspace\_modify ` command for additional +See the :doc:`kspace_modify ` command for additional options of the K-space solvers that can be set, including a *force* option for setting an absolute RMS error in forces, as opposed to a relative RMS error. @@ -441,7 +441,7 @@ the :doc:`boundary ` command). For Ewald and PPPM, a simulation must be 3d and periodic in all dimensions. The only exception is if the slab option is set with -:doc:`kspace\_modify `, in which case the xy dimensions +:doc:`kspace_modify `, in which case the xy dimensions must be periodic and the z dimension must be non-periodic. The scafacos KSpace style will only be enabled if LAMMPS is built with @@ -451,7 +451,7 @@ doc page for more info. The use of ScaFaCos in LAMMPS does not yet support molecular charged systems where the short-range Coulombic interactions between atoms in the same bond/angle/dihedral are weighted by the -:doc:`special\_bonds ` command. Likewise it does not +:doc:`special_bonds ` command. Likewise it does not support the "TIP4P water style" where a fictitious charge site is introduced in each water molecule. Finally, the methods *p3m* and *ewald* do not support computing the @@ -460,7 +460,7 @@ virial, so this contribution is not included. Related commands """""""""""""""" -:doc:`kspace\_modify `, :doc:`pair\_style lj/cut/coul/long `, :doc:`pair\_style lj/charmm/coul/long `, :doc:`pair\_style lj/long/coul/long `, :doc:`pair\_style buck/coul/long ` +:doc:`kspace_modify `, :doc:`pair_style lj/cut/coul/long `, :doc:`pair_style lj/charmm/coul/long `, :doc:`pair_style lj/long/coul/long `, :doc:`pair_style buck/coul/long ` Default """"""" diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index bf5dec5453..a26060d7c0 100644 --- a/doc/src/lattice.rst +++ b/doc/src/lattice.rst @@ -61,13 +61,13 @@ of the lattice command can be used to define a wide variety of crystallographic lattices. A lattice is used by LAMMPS in two ways. First, the -:doc:`create\_atoms ` command creates atoms on the lattice +:doc:`create_atoms ` command creates atoms on the lattice points inside the simulation box. Note that the -:doc:`create\_atoms ` command allows different atom types +:doc:`create_atoms ` command allows different atom types to be assigned to different basis atoms of the lattice. Second, the lattice spacing in the x,y,z dimensions implied by the lattice, can be used by other commands as distance units -(e.g. :doc:`create\_box `, :doc:`region ` and +(e.g. :doc:`create_box `, :doc:`region ` and :doc:`velocity `), which are often convenient to use when the underlying problem geometry is atoms on a lattice. @@ -89,7 +89,7 @@ Note that the lattice command can be used multiple times in an input script. Each time it is invoked, the lattice attributes are re-defined and are used for all subsequent commands (that use lattice attributes). For example, a sequence of lattice, -:doc:`region `, and :doc:`create\_atoms ` commands +:doc:`region `, and :doc:`create_atoms ` commands can be repeated multiple times to build a poly-crystalline model with different geometric regions populated with atoms in different lattice orientations. @@ -99,7 +99,7 @@ orientations. A lattice of style *none* does not define a unit cell and basis set, -so it cannot be used with the :doc:`create\_atoms ` +so it cannot be used with the :doc:`create_atoms ` command. However it does define a lattice spacing via the specified scale parameter. As explained above the lattice spacings in x,y,z can be used by other commands as distance units. No additional @@ -242,7 +242,7 @@ factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and of the periodicity of the lattice in that direction. Thus, if you create an orthogonal periodic simulation box whose size in a dimension is a multiple of the lattice spacing, and then fill it with atoms via - the :doc:`create\_atoms ` command, you will NOT necessarily + the :doc:`create_atoms ` command, you will NOT necessarily create a periodic system. I.e. atoms may overlap incorrectly at the faces of the simulation box. @@ -314,7 +314,7 @@ The *a1,a2,a3,basis* keywords can only be used with style *custom*\ . Related commands """""""""""""""" -:doc:`dimension `, :doc:`create\_atoms `, +:doc:`dimension `, :doc:`create_atoms `, :doc:`region ` Default diff --git a/doc/src/mass.rst b/doc/src/mass.rst index 05cef2e3b2..0431b8f65b 100644 --- a/doc/src/mass.rst +++ b/doc/src/mass.rst @@ -28,7 +28,7 @@ Description """"""""""" Set the mass for all atoms of one or more atom types. Per-type mass -values can also be set in the :doc:`read\_data ` data file +values can also be set in the :doc:`read_data ` data file using the "Masses" keyword. See the :doc:`units ` command for what mass units to use. @@ -57,12 +57,12 @@ Note that the mass command can only be used if the :doc:`atom style Currently, all but the *sphere* and *ellipsoid* and *peri* styles do. They require mass to be set for individual particles, not types. Per-atom masses are defined in the data file read by the -:doc:`read\_data ` command, or set to default values by the -:doc:`create\_atoms ` command. Per-atom masses can also be +:doc:`read_data ` command, or set to default values by the +:doc:`create_atoms ` command. Per-atom masses can also be set to new values by the :doc:`set mass ` or :doc:`set density ` commands. -Also note that :doc:`pair\_style eam ` and :doc:`pair\_style bop ` commands define the masses of atom types in their +Also note that :doc:`pair_style eam ` and :doc:`pair_style bop ` commands define the masses of atom types in their respective potential files, in which case the mass command is normally not used. @@ -77,8 +77,8 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. All masses must be defined before a simulation is run. They must also all be defined before a :doc:`velocity ` or :doc:`fix shake ` command is used. diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst index 6b25a1d32d..b90354deb0 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -43,7 +43,7 @@ Description """"""""""" This command sets parameters that affect the energy minimization -algorithms selected by the :doc:`min\_style ` command. The +algorithms selected by the :doc:`min_style ` command. The various settings may affect the convergence rate and overall number of force evaluations required by a minimization, so users can experiment with these parameters to tune their minimizations. @@ -107,13 +107,13 @@ For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force norm is replaced by the spin-torque norm. Keywords *alpha\_damp* and *discrete\_factor* only make sense when -a :doc:`min\_spin ` command is declared. +a :doc:`min_spin ` command is declared. Keyword *alpha\_damp* defines an analog of a magnetic Gilbert damping. It defines a relaxation rate toward an equilibrium for a given magnetic system. Keyword *discrete\_factor* defines a discretization factor for the adaptive timestep used in the *spin* minimization. -See :doc:`min\_spin ` for more information about those +See :doc:`min_spin ` for more information about those quantities. The choice of a line search algorithm for the *spin/cg* and @@ -138,7 +138,7 @@ See :doc:`neb/spin ` for more explanation. Related commands """""""""""""""" -:doc:`min\_style `, :doc:`minimize ` +:doc:`min_style `, :doc:`minimize ` Default """"""" diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst index 1535a1067f..96053fda98 100644 --- a/doc/src/min_spin.rst +++ b/doc/src/min_spin.rst @@ -43,7 +43,7 @@ timestep, according to: with lambda a damping coefficient (similar to a Gilbert damping). Lambda can be defined by setting the *alpha\_damp* keyword with the -:doc:`min\_modify ` command. +:doc:`min_modify ` command. The minimization procedure solves this equation using an adaptive timestep. The value of this timestep is defined @@ -59,12 +59,12 @@ spin/neb calculation is performed). Kappa defines a discretization factor *discrete\_factor* for the definition of this timestep. -*discrete\_factor* can be defined with the :doc:`min\_modify ` +*discrete\_factor* can be defined with the :doc:`min_modify ` command. Style *spin/cg* defines an orthogonal spin optimization (OSO) combined to a conjugate gradient (CG) algorithm. -The :doc:`min\_modify ` command can be used to +The :doc:`min_modify ` command can be used to couple the *spin/cg* to a line search procedure, and to modify the discretization factor *discrete\_factor*. By default, style *spin/cg* does not employ the line search procedure @@ -80,7 +80,7 @@ The default value for Kappa is 10. The *spin\_cubic* line search can improve the convergence of the *spin/lbfgs* algorithm. -The :doc:`min\_modify ` command can be used to +The :doc:`min_modify ` command can be used to activate the line search procedure, and to modify the discretization factor *discrete\_factor*. @@ -108,8 +108,8 @@ freedom for a frozen lattice configuration. Related commands """""""""""""""" -:doc:`min\_style `, :doc:`minimize `, -:doc:`min\_modify ` +:doc:`min_style `, :doc:`minimize `, +:doc:`min_modify ` Default """"""" diff --git a/doc/src/min_style.rst b/doc/src/min_style.rst index 91accc7967..b9e896df3e 100644 --- a/doc/src/min_style.rst +++ b/doc/src/min_style.rst @@ -46,7 +46,7 @@ derivative. When close to an energy minimum, the algorithm behaves like a Newton method and exhibits a quadratic convergence rate to high accuracy. In most cases the behavior of *hftn* is similar to *cg*\ , but it offers an alternative if *cg* seems to perform poorly. This -style is not affected by the :doc:`min\_modify ` command. +style is not affected by the :doc:`min_modify ` command. Style *sd* is a steepest descent algorithm. At each iteration, the search direction is set to the downhill direction corresponding to the @@ -135,7 +135,7 @@ Restrictions Related commands """""""""""""""" -:doc:`min\_modify `, :doc:`minimize `, :doc:`neb ` +:doc:`min_modify `, :doc:`minimize `, :doc:`neb ` Default """"""" diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index 668759401e..d9aba3eda0 100644 --- a/doc/src/minimize.rst +++ b/doc/src/minimize.rst @@ -39,8 +39,8 @@ configuration should approximate a critical point for the objective function (see below), which may or may not be a local minimum. The minimization algorithm used is set by the -:doc:`min\_style ` command. Other options are set by the -:doc:`min\_modify ` command. Minimize commands can be +:doc:`min_style ` command. Other options are set by the +:doc:`min_modify ` command. Minimize commands can be interspersed with :doc:`run ` commands to alternate between relaxation and dynamics. The minimizers bound the distance atoms move in one iteration, so that you can relax systems with highly overlapped @@ -50,7 +50,7 @@ other. Alternate means of relaxing a system are to run dynamics with a small or :doc:`limited timestep `. Or dynamics can be run using :doc:`fix viscous ` to impose a damping force that -slowly drains all kinetic energy from the system. The :doc:`pair\_style soft ` potential can be used to un-overlap atoms while +slowly drains all kinetic energy from the system. The :doc:`pair_style soft ` potential can be used to un-overlap atoms while running dynamics. Note that you can minimize some atoms in the system while holding the @@ -155,7 +155,7 @@ During a minimization, the outer iteration count is treated as a timestep. Output is triggered by this timestep, e.g. thermodynamic output or dump and restart files. -Using the :doc:`thermo\_style custom ` command with the +Using the :doc:`thermo_style custom ` command with the *fmax* or *fnorm* keywords can be useful for monitoring the progress of the minimization. Note that these outputs will be calculated only from forces on the atoms, and will not include any extra degrees of @@ -228,14 +228,14 @@ The iterations and force evaluation values are what is checked by the Note that a cutoff Lennard-Jones potential (and others) can be shifted so that its energy is 0.0 at the cutoff via the -:doc:`pair\_modify ` command. See the doc pages for +:doc:`pair_modify ` command. See the doc pages for individual :doc:`pair styles ` for details. Note that Coulombic potentials always have a cutoff, unless versions with a -long-range component are used (e.g. :doc:`pair\_style lj/cut/coul/long `). The CHARMM potentials go to 0.0 at -the cutoff (e.g. :doc:`pair\_style lj/charmm/coul/charmm `), -as do the GROMACS potentials (e.g. :doc:`pair\_style lj/gromacs `). +long-range component are used (e.g. :doc:`pair_style lj/cut/coul/long `). The CHARMM potentials go to 0.0 at +the cutoff (e.g. :doc:`pair_style lj/charmm/coul/charmm `), +as do the GROMACS potentials (e.g. :doc:`pair_style lj/gromacs `). -If a soft potential (:doc:`pair\_style soft `) is used the +If a soft potential (:doc:`pair_style soft `) is used the Astop value is used for the prefactor (no time dependence). The :doc:`fix box/relax ` command can be used to apply an @@ -266,7 +266,7 @@ that can be used include: Some fixes which are invoked during minimization have an associated potential energy. For that energy to be included in the total potential energy of the system (the quantity being minimized), - you MUST enable the :doc:`fix\_modify ` *energy* option for + you MUST enable the :doc:`fix_modify ` *energy* option for that fix. The doc pages for individual :doc:`fix ` commands specify if this should be done. @@ -321,7 +321,7 @@ algorithm. is not an error to have it defined, but the energy minimization will not keep the defined body(s) rigid during the minimization. Note that if bonds, angles, etc internal to a rigid body have been turned off -(e.g. via :doc:`neigh\_modify exclude `), they will not +(e.g. via :doc:`neigh_modify exclude `), they will not contribute to the potential energy which is probably not what is desired. @@ -333,8 +333,8 @@ system will not fully relax. Related commands """""""""""""""" -:doc:`min\_modify `, :doc:`min\_style `, -:doc:`run\_style ` +:doc:`min_modify `, :doc:`min_style `, +:doc:`run_style ` **Default:** none diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst index e4a8a40468..6a36636d9c 100644 --- a/doc/src/molecule.rst +++ b/doc/src/molecule.rst @@ -64,8 +64,8 @@ templates include: * :doc:`fix rigid/small ` * :doc:`fix shake ` * :doc:`fix gcmc ` -* :doc:`create\_atoms ` -* :doc:`atom\_style template ` +* :doc:`create_atoms ` +* :doc:`atom_style template ` The ID of a molecule template can only contain alphanumeric characters and underscores. @@ -73,7 +73,7 @@ and underscores. A single template can contain multiple molecules, listed one per file. Some of the commands listed above currently use only the first molecule in the template, and will issue a warning if the template -contains multiple molecules. The :doc:`atom\_style template ` command allows multiple-molecule templates +contains multiple molecules. The :doc:`atom_style template ` command allows multiple-molecule templates to define a system with more than one templated molecule. Each filename can be followed by optional keywords which are applied @@ -109,16 +109,16 @@ molecule (header keyword = inertia). to your simulation, via one or more of the commands listed above. Since this topology-related information requires that suitable storage is reserved when LAMMPS creates the simulation box (e.g. when using - the :doc:`create\_box ` command or the - :doc:`read\_data ` command) suitable space has to be reserved + the :doc:`create_box ` command or the + :doc:`read_data ` command) suitable space has to be reserved so you do not overflow those pre-allocated data structures when adding - molecules later. Both the :doc:`create\_box ` command and - the :doc:`read\_data ` command have "extra" options which + molecules later. Both the :doc:`create_box ` command and + the :doc:`read_data ` command have "extra" options which insure space is allocated for storing topology info for molecules that are added later. The format of an individual molecule file is similar but -(not identical) to the data file read by the :doc:`read\_data ` +(not identical) to the data file read by the :doc:`read_data ` commands, and is as follows. A molecule file has a header and a body. The header appears first. @@ -182,7 +182,7 @@ details below). This is optional since if these sections are not included, LAMMPS will auto-generate this information. Note that LAMMPS uses this info to properly exclude or weight bonded pairwise interactions between bonded atoms. See the -:doc:`special\_bonds ` command for more details. One +:doc:`special_bonds ` command for more details. One reason to list the special bond info explicitly is for the :doc:`thermalized Drude oscillator model ` which treats the bonds between nuclear cores and Drude electrons in a different manner. @@ -350,7 +350,7 @@ the doc pages for individual styles for details. N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of this atom within the topology of the molecule. See the -:doc:`special\_bonds ` doc page for more discussion of +:doc:`special_bonds ` doc page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds section must also appear. @@ -373,7 +373,7 @@ A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3, Natoms, where Natoms = # of atoms in the molecule. The first N1 values should be the 1-2 neighbors, the next N2 should be the 1-3 neighbors, the last N3 should be the 1-4 neighbors. No atom ID should -appear more than once. See the :doc:`special\_bonds ` doc +appear more than once. See the :doc:`special_bonds ` doc page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bond Counts section must also appear. @@ -498,8 +498,8 @@ Restrictions This command must come after the simulation box is define by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. Related commands """""""""""""""" diff --git a/doc/src/neb.rst b/doc/src/neb.rst index ef14739301..713179b02c 100644 --- a/doc/src/neb.rst +++ b/doc/src/neb.rst @@ -171,8 +171,8 @@ For a *file-style* setting of *none*\ , no filename is specified. Each replica is assumed to already be in its initial configuration at the time the neb command is issued. This allows each replica to define its own configuration by reading a replica-specific data or restart or -dump file, via the :doc:`read\_data `, -:doc:`read\_restart `, or :doc:`read\_dump ` +dump file, via the :doc:`read_data `, +:doc:`read_restart `, or :doc:`read_dump ` commands. The replica-specific names of these files can be specified as in the discussion above for the *each* file-style. Also see the section below for how a NEB calculation can produce restart files, so @@ -192,7 +192,7 @@ that a long calculation can be restarted if needed. A NEB calculation proceeds in two stages, each of which is a minimization procedure, performed via damped dynamics. To enable this, you must first define a damped dynamics -:doc:`min\_style `, such as *quickmin* or *fire*\ . The *cg*\ , +:doc:`min_style `, such as *quickmin* or *fire*\ . The *cg*\ , *sd*\ , and *hftn* styles cannot be used, since they perform iterative line searches in their inner loop, which cannot be easily synchronized across multiple replicas. @@ -254,7 +254,7 @@ A few other settings in your input script are required or advised to perform a NEB calculation. See the NOTE about the choice of timestep at the beginning of this doc page. -An atom map must be defined which it is not by default for :doc:`atom\_style atomic ` problems. The :doc:`atom\_modify map ` command can be used to do this. +An atom map must be defined which it is not by default for :doc:`atom_style atomic ` problems. The :doc:`atom_modify map ` command can be used to do this. The minimizers in LAMMPS operate on all atoms in your system, even non-NEB atoms, as defined above. To prevent non-NEB atoms from moving diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst index 161348e97c..74c46ff58e 100644 --- a/doc/src/neb_spin.rst +++ b/doc/src/neb_spin.rst @@ -171,8 +171,8 @@ For a *file-style* setting of *none*\ , no filename is specified. Each replica is assumed to already be in its initial configuration at the time the neb command is issued. This allows each replica to define its own configuration by reading a replica-specific data or restart or -dump file, via the :doc:`read\_data `, -:doc:`read\_restart `, or :doc:`read\_dump ` +dump file, via the :doc:`read_data `, +:doc:`read_restart `, or :doc:`read_dump ` commands. The replica-specific names of these files can be specified as in the discussion above for the *each* file-style. Also see the section below for how a NEB calculation can produce restart files, so @@ -192,9 +192,9 @@ that a long calculation can be restarted if needed. A NEB calculation proceeds in two stages, each of which is a minimization procedure. To enable this, you must first define a -:doc:`min\_style `, using either the *spin*\ , +:doc:`min_style `, using either the *spin*\ , *spin/cg*\ , or *spin/lbfgs* style (see -:doc:`min\_spin ` for more information). +:doc:`min_spin ` for more information). The other styles cannot be used, since they relax the lattice degrees of freedom instead of the spins. @@ -253,7 +253,7 @@ profile of the transition along the MEP. ---------- -An atom map must be defined which it is not by default for :doc:`atom\_style atomic ` problems. The :doc:`atom\_modify map ` command can be used to do this. +An atom map must be defined which it is not by default for :doc:`atom_style atomic ` problems. The :doc:`atom_modify map ` command can be used to do this. An initial value can be defined for the timestep. Although, the *spin* minimization algorithm is an adaptive timestep methodology, so that diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 9035690a00..2ab119193c 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -92,7 +92,7 @@ move far enough that the neighbor list should be rebuilt, e.g. running a simulation of a cold crystal. Note that it is not that expensive to check if neighbor lists should be rebuilt. -When the rRESPA integrator is used (see the :doc:`run\_style ` +When the rRESPA integrator is used (see the :doc:`run_style ` command), the *every* and *delay* parameters refer to the longest (outermost) timestep. @@ -107,7 +107,7 @@ nearby periodic images. The only way this should happen is if the pairwise cutoff is so short that atoms that are part of the same interaction are not communicated as ghost atoms. This is an unusual model (e.g. no pair interactions at all) and the problem can be fixed -by use of the :doc:`comm\_modify cutoff ` command. Note +by use of the :doc:`comm_modify cutoff ` command. Note that to save time, the default *cluster* setting is *no*\ , so that this check is not performed. @@ -116,7 +116,7 @@ atoms in the specified group. This can be useful for models where a large portion of the simulation is particles that do not interact with other particles or with each other via pairwise interactions. The group specified with this option must also be specified via the -:doc:`atom\_modify first ` command. Note that specifying +:doc:`atom_modify first ` command. Note that specifying "all" as the group-ID effectively turns off the *include* option. The *exclude* option turns off pairwise interactions between certain @@ -150,20 +150,20 @@ The other exclude options are more expensive if specified multiple times; they require one check for each time they have been specified. Note that the exclude options only affect pairwise interactions; see -the :doc:`delete\_bonds ` command for information on +the :doc:`delete_bonds ` command for information on turning off bond interactions. .. note:: Excluding pairwise interactions will not work correctly when also using a long-range solver via the - :doc:`kspace\_style ` command. LAMMPS will give a warning + :doc:`kspace_style ` command. LAMMPS will give a warning to this effect. This is because the short-range pairwise interaction needs to subtract off a term from the total energy for pairs whose short-range interaction is excluded, to compensate for how the long-range solver treats the interaction. This is done correctly for pairwise interactions that are excluded (or weighted) via the - :doc:`special\_bonds ` command. But it is not done for + :doc:`special_bonds ` command. But it is not done for interactions that are excluded via these neigh\_modify exclude options. The *page* and *one* options affect how memory is allocated for the @@ -219,7 +219,7 @@ space. Related commands """""""""""""""" -:doc:`neighbor `, :doc:`delete\_bonds ` +:doc:`neighbor `, :doc:`delete_bonds ` Default """"""" diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index ae21232609..3869723202 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -37,7 +37,7 @@ default values below. The *skin* distance is also used to determine how often atoms migrate to new processors if the *check* option of the -:doc:`neigh\_modify ` command is set to *yes*\ . Atoms are +:doc:`neigh_modify ` command is set to *yes*\ . Atoms are migrated (communicated) to new processors on the same timestep that neighbor lists are re-built. @@ -59,10 +59,10 @@ other type pairs have a much shorter cutoff. For style *multi* the bin size is set to 1/2 of the shortest cutoff distance and multiple sets of bins are defined to search over for different atom types. This imposes some extra setup overhead, but the searches themselves -may be much faster for the short-cutoff cases. See the :doc:`comm\_modify mode multi ` command for a communication option +may be much faster for the short-cutoff cases. See the :doc:`comm_modify mode multi ` command for a communication option that may also be beneficial for simulations of this kind. -The :doc:`neigh\_modify ` command has additional options +The :doc:`neigh_modify ` command has additional options that control how often neighbor lists are built and which pairs are stored in the list. @@ -77,8 +77,8 @@ Restrictions Related commands """""""""""""""" -:doc:`neigh\_modify `, :doc:`units `, -:doc:`comm\_modify ` +:doc:`neigh_modify `, :doc:`units `, +:doc:`comm_modify ` Default """"""" diff --git a/doc/src/newton.rst b/doc/src/newton.rst index 6c1f600224..eb7a2250c7 100644 --- a/doc/src/newton.rst +++ b/doc/src/newton.rst @@ -46,7 +46,7 @@ processor. LAMMPS should produce the same answers for any newton flag settings, except for round-off issues. -With :doc:`run\_style ` *respa* and only bonded interactions +With :doc:`run_style ` *respa* and only bonded interactions (bond, angle, etc) computed in the innermost timestep, it may be faster to turn newton *off* for bonded interactions, to avoid extra communication in the innermost loop. @@ -56,13 +56,13 @@ Restrictions The newton bond setting cannot be changed after the simulation box is -defined by a :doc:`read\_data ` or -:doc:`create\_box ` command. +defined by a :doc:`read_data ` or +:doc:`create_box ` command. Related commands """""""""""""""" -:doc:`run\_style ` respa +:doc:`run_style ` respa Default """"""" diff --git a/doc/src/package.rst b/doc/src/package.rst index 06cebea6c4..368caf63fb 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -387,7 +387,7 @@ process. LAMMPS will generate a warning in the case that more threads are used than available in SMT hardware on a node. If the PPPM solver from the USER-INTEL package is not used, then the LRT setting is ignored and no extra threads are generated. Enabling LRT will replace -the :doc:`run\_style ` with the *verlet/lrt/intel* style that +the :doc:`run_style ` with the *verlet/lrt/intel* style that is identical to the default *verlet* style aside from supporting the LRT feature. This feature requires setting the pre-processor flag -DLMP\_INTEL\_USELRT in the makefile when compiling LAMMPS. @@ -483,7 +483,7 @@ CPUs a value of *on* is the default since it can often be faster, just as it is for non-accelerated pair styles The *binsize* keyword sets the size of bins used to bin atoms in -neighbor list builds. The same value can be set by the :doc:`neigh\_modify binsize ` command. Making it an option in the package +neighbor list builds. The same value can be set by the :doc:`neigh_modify binsize ` command. Making it an option in the package kokkos command allows it to be set from the command line. The default value for CPUs is 0.0, which means the LAMMPS default will be used, which is bins = 1/2 the size of the pairwise cutoff + neighbor skin @@ -622,7 +622,7 @@ Restrictions This command cannot be used after the simulation box is defined by a -:doc:`read\_data ` or :doc:`create\_box ` command. +:doc:`read_data ` or :doc:`create_box ` command. The gpu style of this command can only be invoked if LAMMPS was built with the GPU package. See the :doc:`Build package ` doc diff --git a/doc/src/pair_adp.rst b/doc/src/pair_adp.rst index 36311f738d..b6fba9e960 100644 --- a/doc/src/pair_adp.rst +++ b/doc/src/pair_adp.rst @@ -54,7 +54,7 @@ command to specify them. Note that ADP potentials obtained from NIST must be converted into the extended DYNAMO *setfl* format discussed below. * The OpenKIM Project at https://openkim.org/browse/models/by-type provides - ADP potentials that can be used directly in LAMMPS with the :doc:`kim\_commands interface `. + ADP potentials that can be used directly in LAMMPS with the :doc:`kim_commands interface `. ---------- @@ -68,7 +68,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of extended *setfl* elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways to +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, the potentials/AlCu.adp file, included in the @@ -99,7 +99,7 @@ that will be used with other potentials. have an ".adp" suffix. A DYNAMO *setfl* file extended for ADP is formatted as follows. Basically it is the standard *setfl* format with additional tabulated functions u and w added to the file after -the tabulated pair potentials. See the :doc:`pair\_eam ` +the tabulated pair potentials. See the :doc:`pair_eam ` command for further details on the *setfl* format. * lines 1,2,3 = comments (ignored) @@ -159,7 +159,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, no special mixing rules are needed, since the ADP potential files specify alloy interactions explicitly. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in tabulated potential files. @@ -167,7 +167,7 @@ Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -184,7 +184,7 @@ if LAMMPS was built with that package. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_eam ` +:doc:`pair_coeff `, :doc:`pair_eam ` **Default:** none diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index 96bcf5eccd..d7088a7eae 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -51,7 +51,7 @@ pair\_coeff command, where N is the number of LAMMPS atom types: * filename * N element names = mapping of AGNI elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the force field file. An AGNI force field is fully specified by the filename which contains the @@ -85,7 +85,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -93,7 +93,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -125,7 +125,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index 66dc56c7a6..2a742d8ee2 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -147,7 +147,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of AIREBO elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, if your LAMMPS simulation has 4 atom types and you want @@ -228,7 +228,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -These pair styles do not support the :doc:`pair\_modify ` +These pair styles do not support the :doc:`pair_modify ` mix, shift, table, and tail options. These pair styles do not write their information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -236,7 +236,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -259,7 +259,7 @@ doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_atm.rst b/doc/src/pair_atm.rst index 1f22ca01c3..7043de0041 100644 --- a/doc/src/pair_atm.rst +++ b/doc/src/pair_atm.rst @@ -53,7 +53,7 @@ the same for all those permutations of the atom types of I,J,K and needs to be specified only once, as discussed below. The *atm* potential is typically used in combination with a two-body -potential using the :doc:`pair\_style hybrid/overlay ` +potential using the :doc:`pair_style hybrid/overlay ` command as in the example above. The potential for a triplet of atom is calculated only if all 3 @@ -63,9 +63,9 @@ cutoff\_triple\^3 is required, which excludes from calculation the triplets with small contribution to the interaction. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the restart files read by the -:doc:`read\_restart ` commands: +:doc:`read_restart ` commands: * K = atom type of the third atom (1 to Ntypes) * nu = prefactor (energy/distance\^9 units) @@ -147,18 +147,18 @@ combinations, else an error will result. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair styles do not support the :doc:`pair\_modify ` +This pair styles do not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. However, if the *atm* potential is used in combination with other -potentials using the :doc:`pair\_style hybrid/overlay ` +potentials using the :doc:`pair_style hybrid/overlay ` command then pair\_coeff commands need to be re-specified in the restart input script. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -175,7 +175,7 @@ if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_awpmd.rst b/doc/src/pair_awpmd.rst index 0076f50684..ecf6cc7c30 100644 --- a/doc/src/pair_awpmd.rst +++ b/doc/src/pair_awpmd.rst @@ -84,13 +84,13 @@ details needed. If the *flex\_press* keyword is used, then a contribution from the electrons is added to the total virial and pressure of the system. -This potential is designed to be used with :doc:`atom\_style wavepacket ` definitions, in order to handle the +This potential is designed to be used with :doc:`atom_style wavepacket ` definitions, in order to handle the description of systems with interacting nuclei and explicit electrons. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutoff (distance units) @@ -105,14 +105,14 @@ specified in the pair\_style command is used. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -The :doc:`pair\_modify ` mix, shift, table, and tail options +The :doc:`pair_modify ` mix, shift, table, and tail options are not relevant for this pair style. This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -126,7 +126,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` Default """"""" diff --git a/doc/src/pair_beck.rst b/doc/src/pair_beck.rst index 96f6d5d3f5..15bd126ac2 100644 --- a/doc/src/pair_beck.rst +++ b/doc/src/pair_beck.rst @@ -40,9 +40,9 @@ includes truncation at a cutoff distance Rc. :align: center The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands. * A (energy units) @@ -86,20 +86,20 @@ instructions on how to use the accelerated styles effectively. For atom type pairs I,J and I != J, coefficients must be specified. No default mixing rules are used. -This pair style does not support the :doc:`pair\_modify ` shift +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections. This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -113,7 +113,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_body_nparticle.rst b/doc/src/pair_body_nparticle.rst index 5d6b2a500b..1ebb6a3b47 100644 --- a/doc/src/pair_body_nparticle.rst +++ b/doc/src/pair_body_nparticle.rst @@ -74,9 +74,9 @@ where Rc is the cutoff. As explained above, an interaction involving one or two body sub-particles may be computed even for r > Rc. For style *body*\ , the following coefficients must be defined for each -pair of atoms types via the :doc:`pair\_coeff ` command as in +pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * epsilon (energy units) @@ -97,13 +97,13 @@ and cutoff distance for all of this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -118,12 +118,12 @@ This style is part of the BODY package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Defining particles to be bodies so they participate in body/body or -body/particle interactions requires the use of the :doc:`atom\_style body ` command. +body/particle interactions requires the use of the :doc:`atom_style body ` command. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix rigid ` +:doc:`pair_coeff `, :doc:`fix rigid ` **Default:** none diff --git a/doc/src/pair_body_rounded_polygon.rst b/doc/src/pair_body_rounded_polygon.rst index 237a792344..7fee589b9f 100644 --- a/doc/src/pair_body_rounded_polygon.rst +++ b/doc/src/pair_body_rounded_polygon.rst @@ -95,8 +95,8 @@ that gross sliding takes place as soon as two particles are in contact. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above, -or in the data file read by the :doc:`read\_data ` command: +via the :doc:`pair_coeff ` command as in the examples above, +or in the data file read by the :doc:`read_data ` command: * k\_n (energy/distance\^2 units) * k\_na (energy/distance\^2 units) @@ -107,14 +107,14 @@ above for force versus surface separation, for \delta\_n < 0 and 0 < **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -130,7 +130,7 @@ for pair interactions. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_body_rounded_polyhedron.rst b/doc/src/pair_body_rounded_polyhedron.rst index 1334756908..010e346f30 100644 --- a/doc/src/pair_body_rounded_polyhedron.rst +++ b/doc/src/pair_body_rounded_polyhedron.rst @@ -90,8 +90,8 @@ that gross sliding takes place as soon as two particles are in contact. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above, -or in the data file read by the :doc:`read\_data ` command: +via the :doc:`pair_coeff ` command as in the examples above, +or in the data file read by the :doc:`read_data ` command: * k\_n (energy/distance\^2 units) * k\_na (energy/distance\^2 units) @@ -102,14 +102,14 @@ above for force versus surface separation, for \delta\_n < 0 and 0 < **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -125,7 +125,7 @@ for pair interactions. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_bop.rst b/doc/src/pair_bop.rst index 75446ded3c..3c45e2cf2f 100644 --- a/doc/src/pair_bop.rst +++ b/doc/src/pair_bop.rst @@ -105,7 +105,7 @@ incorporation of dihedral angles effects. potentials with hydrogen, you will likely want to set the mass of H atoms to be 10x or 20x larger to avoid having to use a tiny timestep. You can do this by using the :doc:`mass ` command after using the - :doc:`pair\_coeff ` command to read the BOP potential + :doc:`pair_coeff ` command to read the BOP potential file. One option can be specified as a keyword with the pair\_style command. @@ -388,7 +388,7 @@ The rest of the table has the same structure as the previous section (see above) **Mixing, shift, table tail correction, restart**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -396,7 +396,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -422,7 +422,7 @@ appropriate units if your simulation does not use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` Default """"""" diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index 3a9191cfd7..7aeed58d48 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -111,7 +111,7 @@ ionic-pair dependent length parameter, and Rc is the cutoff. The styles with *coul/long* or *coul/msm* add a Coulombic term as described for the :doc:`lj/cut ` pair styles. An additional damping factor is applied to the Coulombic term so it can be used in -conjunction with the :doc:`kspace\_style ` command and its +conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* of *msm* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in @@ -132,9 +132,9 @@ damped shifted force model as in the :doc:`coul/dsf ` style. Note that these potentials are related to the :doc:`Buckingham potential `. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * A (energy units) @@ -185,12 +185,12 @@ instructions on how to use the accelerated styles effectively. These pair styles do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -These styles support the :doc:`pair\_modify ` shift option +These styles support the :doc:`pair_modify ` shift option for the energy of the exp(), 1/r\^6, and 1/r\^8 portion of the pair interaction. The *born/coul/long* pair style supports the -:doc:`pair\_modify ` table option to tabulate the +:doc:`pair_modify ` table option to tabulate the short-range portion of the long-range Coulombic interaction. These styles support the pair\_modify tail option for adding long-range @@ -200,7 +200,7 @@ Thess styles writes thei information to binary :doc:`restart ` files, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. -These styles can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. They do not support the *inner*\ , +These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -217,7 +217,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package `, :doc:`pair\_style buck ` +:doc:`pair_coeff `, :doc:`pair_style buck ` **Default:** none diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst index a05043d141..4286818c74 100644 --- a/doc/src/pair_brownian.rst +++ b/doc/src/pair_brownian.rst @@ -49,7 +49,7 @@ torques on finite-size spherical particles. The former requires monodisperse spherical particles; the latter allows for polydisperse spherical particles. -These pair styles are designed to be used with either the :doc:`pair\_style lubricate ` or :doc:`pair\_style lubricateU ` commands to provide thermostatting +These pair styles are designed to be used with either the :doc:`pair_style lubricate ` or :doc:`pair_style lubricateU ` commands to provide thermostatting when dissipative lubrication forces are acting. Thus the parameters *mu*\ , *flaglog*\ , *flagfld*\ , *cutinner*\ , and *cutoff* should be specified consistent with the settings in the lubrication pair styles. @@ -67,9 +67,9 @@ used, or both must be defined. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutinner (distance units) @@ -111,13 +111,13 @@ For atom type pairs I,J and I != J, the two cutoff distances for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -125,7 +125,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -147,7 +147,7 @@ Only spherical particles are allowed for pair\_style brownian/poly. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style lubricate `, :doc:`pair\_style lubricateU ` +:doc:`pair_coeff `, :doc:`pair_style lubricate `, :doc:`pair_style lubricateU ` Default """"""" diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index 7c559001b8..c3b5458ba1 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -119,7 +119,7 @@ The styles with *coul/cut* or *coul/long* or *coul/msm* add a Coulombic term as described for the :doc:`lj/cut ` pair styles. For *buck/coul/long* and *buc/coul/msm*\ , an additional damping factor is applied to the Coulombic term so it can be used in conjunction with -the :doc:`kspace\_style ` command and its *ewald* or *pppm* +the :doc:`kspace_style ` command and its *ewald* or *pppm* or *msm* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. @@ -138,12 +138,12 @@ Note that these potentials are related to the :doc:`Born-Mayer-Huggins potential cutoff. The additional Coulombic term can be cutoff or long-range (no cutoff) depending on whether the style name includes coul/cut or coul/long or coul/msm. If you wish the C/r\^6 term to be long-range - (no cutoff), then see the :doc:`pair\_style buck/long/coul/long ` command. + (no cutoff), then see the :doc:`pair_style buck/long/coul/long ` command. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * A (energy units) @@ -199,11 +199,11 @@ instructions on how to use the accelerated styles effectively. These pair styles do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -These styles support the :doc:`pair\_modify ` shift option +These styles support the :doc:`pair_modify ` shift option for the energy of the exp() and 1/r\^6 portion of the pair interaction. The *buck/coul/long* pair style supports the -:doc:`pair\_modify ` table option to tabulate the +:doc:`pair_modify ` table option to tabulate the short-range portion of the long-range Coulombic interaction. These styles support the pair\_modify tail option for adding long-range @@ -213,7 +213,7 @@ pair interaction. These styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. -These styles can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. They do not support the *inner*\ , +These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -226,7 +226,7 @@ only enabled if LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style born ` +:doc:`pair_coeff `, :doc:`pair_style born ` **Default:** none diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst index 94351f5152..3bf9fa53a2 100644 --- a/doc/src/pair_buck6d_coul_gauss.rst +++ b/doc/src/pair_buck6d_coul_gauss.rst @@ -92,7 +92,7 @@ via the damped shifted force model described in :ref:`(Fennell) ` approximating an Ewald sum similar to the :doc:`pair coul/dsf ` styles. In *buck6d/coul/gauss/long* an additional damping factor is applied to the Coulombic term so it can be used in conjunction with the -:doc:`kspace\_style ` command and its *ewald* or *pppm* +:doc:`kspace_style ` command and its *ewald* or *pppm* options. The Coulombic cutoff in this case separates the real and reciprocal space evaluation of the Ewald sum. @@ -101,9 +101,9 @@ terms. If two cutoffs are specified, the first is used as the cutoff for the vdW terms, and the second is the cutoff for the Coulombic term. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * A (energy units) @@ -126,7 +126,7 @@ is used. These pair styles do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -These styles do not support the :doc:`pair\_modify ` shift +These styles do not support the :doc:`pair_modify ` shift option for the energy. Instead the smoothing function should be applied by setting the global smoothing parameter to a value < 1.0. @@ -143,7 +143,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst index 3871e554ce..332f15b4f9 100644 --- a/doc/src/pair_buck_long.rst +++ b/doc/src/pair_buck_long.rst @@ -70,16 +70,16 @@ potential. If *flag\_buck* is set to *long*\ , no cutoff is used on the Buckingham 1/r\^6 dispersion term. The long-range portion can be calculated by -using the :doc:`kspace\_style ewald/disp or pppm/disp ` +using the :doc:`kspace_style ewald/disp or pppm/disp ` commands. The specified Buckingham cutoff then determines which portion of the Buckingham interactions are computed directly by the pair potential versus which part is computed in reciprocal space via the Kspace style. If *flag\_buck* is set to *cut*\ , the Buckingham -interactions are simply cutoff, as with :doc:`pair\_style buck `. +interactions are simply cutoff, as with :doc:`pair_style buck `. If *flag\_coul* is set to *long*\ , no cutoff is used on the Coulombic interactions. The long-range portion can calculated by using any of -several :doc:`kspace\_style ` command options such as +several :doc:`kspace_style ` command options such as *pppm* or *ewald*\ . Note that if *flag\_buck* is also set to long, then the *ewald/disp* or *pppm/disp* Kspace style needs to be used to perform the long-range calculations for both the Buckingham and @@ -87,9 +87,9 @@ Coulombic interactions. If *flag\_coul* is set to *off*\ , Coulombic interactions are not computed. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * A (energy units) @@ -143,15 +143,15 @@ instructions on how to use the accelerated styles effectively. This pair styles does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the exp() and 1/r\^6 portion of the pair interaction, assuming *flag\_buck* is *cut*\ . -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the Buckingham portion of the pair interaction. -This pair style supports the :doc:`pair\_modify ` table and +This pair style supports the :doc:`pair_modify ` table and table/disp options since they can tabulate the short-range portion of the long-range Coulombic and dispersion interactions. @@ -159,9 +159,9 @@ This pair style write its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , and *outer* -keywords of the :doc:`run\_style respa ` command, meaning the +keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of -the rRESPA hierarchy. See the :doc:`run\_style ` command for +the rRESPA hierarchy. See the :doc:`run_style ` command for details. @@ -178,7 +178,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index cd3e5dbc70..16a9a80223 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -145,7 +145,7 @@ artifacts. The newer *charmmfsw* or *charmmfsh* styles were released in March 2017. We recommend they be used instead of the older *charmm* - styles. This includes the newer :doc:`dihedral\_style charmmfsw ` command. Eventually code from the new + styles. This includes the newer :doc:`dihedral_style charmmfsw ` command. Eventually code from the new styles will propagate into the related pair styles (e.g. implicit, accelerator, free energy variants). @@ -194,7 +194,7 @@ formulas as style *lj/charmm/coul/charmm* and style *lj/charmmfsw/coul/long* computes the same formulas as style *lj/charmmfsw/coul/charmmfsh*\ , except that an additional damping factor is applied to the Coulombic term, so it can be used in -conjunction with the :doc:`kspace\_style ` command and its +conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* or *msm* option. Only one Coulombic cutoff is specified for these styles; if only 2 arguments are used in the pair\_style command, then the outer LJ cutoff is used as the single @@ -204,9 +204,9 @@ directly; interactions outside that distance are computed in reciprocal space. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -260,16 +260,16 @@ usual settings for the CHARMM force field. See the "pair\_modify" command for details. None of the *lj/charmm* or *lj/charmmfsw* pair styles support the -:doc:`pair\_modify ` shift option, since the Lennard-Jones +:doc:`pair_modify ` shift option, since the Lennard-Jones portion of the pair interaction is smoothed to 0.0 at the cutoff. The *lj/charmm/coul/long* and *lj/charmmfsw/coul/long* styles support -the :doc:`pair\_modify ` table option since they can +the :doc:`pair_modify ` table option since they can tabulate the short-range portion of the long-range Coulombic interaction. None of the *lj/charmm* or *lj/charmmfsw* pair styles support the -:doc:`pair\_modify ` tail option for adding long-range tail +:doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure, since the Lennard-Jones portion of the pair interaction is smoothed to 0.0 at the cutoff. @@ -280,10 +280,10 @@ that reads a restart file. The *lj/charmm/coul/long* and *lj/charmmfsw/coul/long* pair styles support the use of the *inner*\ , *middle*\ , and *outer* keywords of the -:doc:`run\_style respa ` command, meaning the pairwise forces +:doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the *pair* keyword of -run\_style respa. See the :doc:`run\_style ` command for +run\_style respa. See the :doc:`run_style ` command for details. @@ -303,7 +303,7 @@ page for more info. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index 985e6688f3..01c442176f 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -93,9 +93,9 @@ Coulombic term as described for the :doc:`lj/cut ` pair styles. See :ref:`(Sun) ` for a description of the COMPASS class2 force field. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -123,7 +123,7 @@ specified in the pair\_style command. If the pair\_coeff command is not used to define coefficients for a particular I != J type pair, the mixing rule for epsilon and sigma for all class2 potentials is to use the *sixthpower* formulas documented -by the :doc:`pair\_modify ` command. The :doc:`pair\_modify mix ` setting is thus ignored for class2 potentials +by the :doc:`pair_modify ` command. The :doc:`pair_modify mix ` setting is thus ignored for class2 potentials for epsilon and sigma. However it is still followed for mixing the cutoff distance. @@ -172,15 +172,15 @@ command (default = geometric). See the "pair\_modify" command for details. All of the lj/class2 pair styles support the -:doc:`pair\_modify ` shift option for the energy of the +:doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction. The *lj/class2/coul/long* pair style does not support the -:doc:`pair\_modify ` table option since a tabulation +:doc:`pair_modify ` table option since a tabulation capability has not yet been added to this potential. All of the lj/class2 pair styles support the -:doc:`pair\_modify ` tail option for adding a long-range +:doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure of the Lennard-Jones portion of the pair interaction. @@ -188,10 +188,10 @@ All of the lj/class2 pair styles write their information to :doc:`binary restart not need to be specified in an input script that reads a restart file. Only the *lj/class2* and *lj/class2/coul/long* pair styles support the use of the -*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run\_style respa ` command, meaning the pairwise forces can be +*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the *pair* keyword of run\_style respa. -See the :doc:`run\_style ` command for details. +See the :doc:`run_style ` command for details. Restrictions """""""""""" @@ -203,7 +203,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_fep\_soft ` +:doc:`pair_coeff `, :doc:`pair\_fep\_soft ` **Default:** none diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index 424b8c3242..a7eac2b6e6 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -34,7 +34,7 @@ Description Specify the pairwise force field coefficients for one or more pairs of atom types. The number and meaning of the coefficients depends on the pair style. Pair coefficients can also be set in the data file read -by the :doc:`read\_data ` command or in a restart file. +by the :doc:`read_data ` command or in a restart file. I and J can be specified in one of two ways. Explicit numeric values can be used for each, as in the 1st example above. I <= J is @@ -80,7 +80,7 @@ as For many potentials, if coefficients for type pairs with I != J are not set explicitly by a pair\_coeff command, the values are inferred from the I,I and J,J settings by mixing rules; see the -:doc:`pair\_modify ` command for a discussion. Details on +:doc:`pair_modify ` command for a discussion. Details on this option as it pertains to individual potentials are described on the doc page for the potential. @@ -132,7 +132,7 @@ Windows: The alphabetic list of pair styles defined in LAMMPS is given on the -:doc:`pair\_style ` doc page. They are also listed in more +:doc:`pair_style ` doc page. They are also listed in more compact form on the :doc:`Commands pair ` doc page. Click on the style to display the formula it computes and its @@ -147,15 +147,15 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. Related commands """""""""""""""" -:doc:`pair\_style `, :doc:`pair\_modify `, -:doc:`read\_data `, :doc:`read\_restart `, -:doc:`pair\_write ` +:doc:`pair_style `, :doc:`pair_modify `, +:doc:`read_data `, :doc:`read_restart `, +:doc:`pair_write ` **Default:** none diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst index fb9c92989f..3893d2113a 100644 --- a/doc/src/pair_colloid.rst +++ b/doc/src/pair_colloid.rst @@ -69,14 +69,14 @@ Lennard-Jones formula with A\_ss set appropriately, which results from letting both particle sizes go to zero. -When used in combination with :doc:`pair\_style yukawa/colloid `, the two terms become the so-called +When used in combination with :doc:`pair_style yukawa/colloid `, the two terms become the so-called DLVO potential, which combines electrostatic repulsion and van der Waals attraction. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * A (energy units) @@ -132,7 +132,7 @@ colloid-solvent cutoff in this case. widely different particles sizes (e.g. sigma=10 colloids in a background sigma=1 LJ fluid), you will likely want to use these commands for efficiency: :doc:`neighbor multi ` and - :doc:`comm\_modify multi `. + :doc:`comm_modify multi `. ---------- @@ -168,13 +168,13 @@ is an energy value mixed like a LJ epsilon. D1 and d2 are distance values and are mixed like sigma. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -182,7 +182,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -197,7 +197,7 @@ This style is part of the COLLOID package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Normally, this pair style should be used with finite-size particles -which have a diameter, e.g. see the :doc:`atom\_style sphere ` command. However, this is not a requirement, +which have a diameter, e.g. see the :doc:`atom_style sphere ` command. However, this is not a requirement, since the only definition of particle size is via the pair\_coeff parameters for each type. In other words, the physical radius of the particle is ignored. Thus you should insure that the d1,d2 parameters @@ -210,7 +210,7 @@ only per-type polydispersity is enabled via the pair\_coeff parameters. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index ece536a011..0dc15dcd89 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -112,7 +112,7 @@ file, *lib.comb3*\ , that is exclusively used for C/O/H systems, will be automatically loaded if carbon atom is detected in LAMMPS input structure. This file must be in your working directory or in the directory pointed to by the environment variable LAMMPS\_POTENTIALS, as -described on the :doc:`pair\_coeff ` command doc page. +described on the :doc:`pair_coeff ` command doc page. Keyword *polar* indicates whether the force field includes the atomic polarization. Since the equilibration of the polarization @@ -155,7 +155,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above from values in the potential file. -These pair styles does not support the :doc:`pair\_modify ` +These pair styles does not support the :doc:`pair_modify ` shift, table, and tail options. These pair styles do not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -163,7 +163,7 @@ need to re-specify the pair\_style, pair\_coeff, and :doc:`fix qeq/comb ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -190,7 +190,7 @@ doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_style `, :doc:`pair\_coeff `, +:doc:`pair_style `, :doc:`pair_coeff `, :doc:`fix qeq/comb ` **Default:** none diff --git a/doc/src/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst index f08ddc38e0..4031a9741c 100644 --- a/doc/src/pair_cosine_squared.rst +++ b/doc/src/pair_cosine_squared.rst @@ -94,7 +94,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -111,8 +111,8 @@ enabled if LAMMPS is build with that package. See the :doc:`Build package `, -:doc:`pair\_style lj/cut ` +:doc:`pair_coeff `, +:doc:`pair_style lj/cut ` **Default:** none diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index fda9ae4069..735b52cb6e 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -209,9 +209,9 @@ of the Streitz-Mintmire potential, as described in :ref:`this paper `, as a Slater 1\ *s* orbital. More details can be found in the referenced paper. To fully reproduce the published Streitz-Mintmire potential, which is a variable charge potential, style *coul/streitz* must be -used with :doc:`pair\_style eam/alloy ` (or some other +used with :doc:`pair_style eam/alloy ` (or some other short-range potential that has been parameterized appropriately) via -the :doc:`pair\_style hybrid/overlay ` command. Likewise, +the :doc:`pair_style hybrid/overlay ` command. Likewise, charge equilibration must be performed via the :doc:`fix qeq/slater ` command. For example: @@ -235,7 +235,7 @@ be computed via an Ewald summation. For example: kspace_style ewald 1e-6 Keyword *ewald* does not need a damping parameter, but a -:doc:`kspace\_style ` must be defined, which can be style +:doc:`kspace_style ` must be defined, which can be style *ewald* or *pppm*\ . The Ewald method was used in Streitz and Mintmire's original paper, but a Wolf summation offers a speed-up in some cases. @@ -264,7 +264,7 @@ Streitz-Mintmire parameterization for the material being modeled. Styles *coul/long* and *coul/msm* compute the same Coulombic interactions as style *coul/cut* except that an additional damping factor is applied so it can be used in conjunction with the -:doc:`kspace\_style ` command and its *ewald* or *pppm* +:doc:`kspace_style ` command and its *ewald* or *pppm* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. @@ -303,16 +303,16 @@ your model. Note that these potentials are designed to be combined with other pair -potentials via the :doc:`pair\_style hybrid/overlay ` +potentials via the :doc:`pair_style hybrid/overlay ` command. This is because they have no repulsive core. Hence if they are used by themselves, there will be no repulsion to keep two oppositely charged particles from moving arbitrarily close to each other. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutoff (distance units) @@ -358,14 +358,14 @@ For atom type pairs I,J and I != J, the cutoff distance for the *coul/cut* style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -The :doc:`pair\_modify ` shift option is not relevant +The :doc:`pair_modify ` shift option is not relevant for these pair styles. -The *coul/long* style supports the :doc:`pair\_modify ` +The *coul/long* style supports the :doc:`pair_modify ` table option for tabulation of the short-range portion of the long-range Coulombic interaction. -These pair styles do not support the :doc:`pair\_modify ` +These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -373,7 +373,7 @@ These pair styles write their information to :doc:`binary restart files ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -392,7 +392,7 @@ info. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style, hybrid/overlay `, :doc:`kspace\_style ` +:doc:`pair_coeff `, :doc:`pair\_style, hybrid/overlay `, :doc:`kspace_style ` **Default:** none diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index 2e86ab41b4..0d98a22dc7 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -58,9 +58,9 @@ and in combination with coul/cut or coul/long. It is also usually combined with gauss/cut, see :ref:`(Lenart) ` or :ref:`(Jusufi) `. The following coefficients must be defined for each pair of atom -types via the :doc:`pair\_coeff ` command as in the example +types via the :doc:`pair_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * epsilon (no units) @@ -78,19 +78,19 @@ The global cutoff (r\_c) specified in the pair\_style command is used. This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the Gauss-potential portion of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -103,8 +103,8 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` -:doc:`pair\_style gauss/cut ` +:doc:`pair_coeff ` +:doc:`pair_style gauss/cut ` **Default:** none diff --git a/doc/src/pair_coul_shield.rst b/doc/src/pair_coul_shield.rst index c6d306b2eb..dff5869649 100644 --- a/doc/src/pair_coul_shield.rst +++ b/doc/src/pair_coul_shield.rst @@ -50,9 +50,9 @@ eliminates the short-range singularity of the classical mono-polar electrostatic interaction expression :ref:`(Maaravi) `. The shielding parameter *lambda* (1/distance units) must be defined for -each pair of atom types via the :doc:`pair\_coeff ` command as +each pair of atom types via the :doc:`pair_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` commands: +:doc:`read_data ` or :doc:`read_restart ` commands: The global cutoff (r\_c) specified in the pair\_style command is used. @@ -65,15 +65,15 @@ The global cutoff (r\_c) specified in the pair\_style command is used. This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs. -The :doc:`pair\_modify ` *table* option is not relevant +The :doc:`pair_modify ` *table* option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` *tail* option for adding long-range tail corrections to energy and pressure. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -86,8 +86,8 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` -:doc:`pair\_style ilp/graphene/hbn ` +:doc:`pair_coeff ` +:doc:`pair_style ilp/graphene/hbn ` **Default:** tap\_flag = 1 diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index 3667aa6e2f..000f8df3eb 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -111,26 +111,26 @@ the model as implemented in LAMMPS. All the styles are identical to the corresponding pair style without the "/cs" in the name: -* :doc:`pair\_style born/coul/dsf ` -* :doc:`pair\_style born/coul/long ` -* :doc:`pair\_style born/coul/wolf ` -* :doc:`pair\_style buck/coul/long ` -* :doc:`pair\_style coul/long ` -* :doc:`pair\_style coul/wolf ` -* :doc:`pair\_style lj/cut/coul/long ` +* :doc:`pair_style born/coul/dsf ` +* :doc:`pair_style born/coul/long ` +* :doc:`pair_style born/coul/wolf ` +* :doc:`pair_style buck/coul/long ` +* :doc:`pair_style coul/long ` +* :doc:`pair_style coul/wolf ` +* :doc:`pair_style lj/cut/coul/long ` except that they correctly treat the special case where the distance between two charged core and shell atoms in the same core/shell pair approach r = 0.0. Styles with a "/long" in the name are used with a long-range solver -for Coulombic interactions via the :doc:`kspace\_style ` +for Coulombic interactions via the :doc:`kspace_style ` command. They require special treatment of the short-range Coulombic interactions within the cor/shell model. Specifically, the short-range Coulomb interaction between a core and its shell should be turned off using the -:doc:`special\_bonds ` command by setting the 1-2 weight +:doc:`special_bonds ` command by setting the 1-2 weight to 0.0, which works because the core and shell atoms are bonded to each other. This induces a long-range correction approximation which fails at small distances (~< 10e-8). Therefore, the Coulomb term which @@ -196,8 +196,8 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package `, :doc:`pair\_style born `, -:doc:`pair\_style buck ` +:doc:`pair_coeff `, :doc:`pair_style born `, +:doc:`pair_style buck ` **Default:** none diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index fc7de92900..9b9d969215 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -154,8 +154,8 @@ Style *lj/cut/dipole/long* computes long-range point-dipole interactions as discussed in :ref:`(Toukmaji) `. Dipole-dipole, dipole-charge, and charge-charge interactions are all supported, along with the standard 12/6 Lennard-Jones interactions, which are computed -with a cutoff. A :doc:`kspace\_style ` must be defined to -use this pair style. Currently, only :doc:`kspace\_style ewald/disp ` support long-range point-dipole +with a cutoff. A :doc:`kspace_style ` must be defined to +use this pair style. Currently, only :doc:`kspace_style ewald/disp ` support long-range point-dipole interactions. Style *lj/long/dipole/long* also computes point-dipole interactions as @@ -166,16 +166,16 @@ can be cutoff or long-ranged. For style *lj/long/dipole/long*\ , if *flag\_lj* is set to *long*\ , no cutoff is used on the LJ 1/r\^6 dispersion term. The long-range -portion is calculated by using the :doc:`kspace\_style ewald\_disp ` command. The specified LJ cutoff then +portion is calculated by using the :doc:`kspace_style ewald\_disp ` command. The specified LJ cutoff then determines which portion of the LJ interactions are computed directly by the pair potential versus which part is computed in reciprocal space via the Kspace style. If *flag\_lj* is set to *cut*\ , the LJ -interactions are simply cutoff, as with :doc:`pair\_style lj/cut `. If *flag\_lj* is set to *off*\ , LJ interactions +interactions are simply cutoff, as with :doc:`pair_style lj/cut `. If *flag\_lj* is set to *off*\ , LJ interactions are not computed at all. If *flag\_coul* is set to *long*\ , no cutoff is used on the Coulombic or dipole interactions. The long-range portion is calculated by using -*ewald\_disp* of the :doc:`kspace\_style ` command. If +*ewald\_disp* of the :doc:`kspace_style ` command. If *flag\_coul* is set to *off*\ , Coulombic and dipole interactions are not computed at all. @@ -183,16 +183,16 @@ Atoms with dipole moments should be integrated using the :doc:`fix nve/sphere up dipole moments. The *omega* option on the :doc:`fix langevin ` command can be used to thermostat the rotational motion. The :doc:`compute temp/sphere ` command can be used to monitor the temperature, since it includes -rotational degrees of freedom. The :doc:`atom\_style hybrid dipole sphere ` command should be used since +rotational degrees of freedom. The :doc:`atom_style hybrid dipole sphere ` command should be used since it defines the point dipoles and their rotational state. The magnitude and orientation of the dipole moment for each particle can be defined by the :doc:`set ` command or in the "Atoms" section -of the data file read in by the :doc:`read\_data ` command. +of the data file read in by the :doc:`read_data ` command. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -245,14 +245,14 @@ is an energy value mixed like a LJ epsilon. D1 and d2 are distance values and are mixed like sigma. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction; such energy goes to zero at the cutoff by construction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -260,7 +260,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -280,7 +280,7 @@ currently supported. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`set `, :doc:`read\_data `, +:doc:`pair_coeff `, :doc:`set `, :doc:`read_data `, :doc:`fix nve/sphere `, :doc:`fix nvt/sphere ` **Default:** none diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index 439e41d93b..aceef23179 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -61,7 +61,7 @@ field. This pair-wise thermostat can be used in conjunction with any :doc:`pair style `, and in leiu of per-particle thermostats like :doc:`fix langevin ` or ensemble thermostats like Nose Hoover as implemented by :doc:`fix nvt `. To use -*dpd/tstat* as a thermostat for another pair style, use the :doc:`pair\_style hybrid/overlay ` command to compute both the desired +*dpd/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay ` command to compute both the desired pair interaction and the thermostat for each pair of particles. For style *dpd*\ , the force on atom I due to atom J is given as a sum @@ -91,9 +91,9 @@ all 3 terms. For style *dpd/tstat* there is no pairwise energy, but the last two terms of the formula make a contribution to the virial. For style *dpd*\ , the following coefficients must be defined for each -pair of atoms types via the :doc:`pair\_coeff ` command as in +pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * A (force units) @@ -102,11 +102,11 @@ commands: The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that sigma is set equal to sqrt(2 T gamma), -where T is the temperature set by the :doc:`pair\_style ` +where T is the temperature set by the :doc:`pair_style ` command so it does not need to be specified. For style *dpd/tstat*\ , the coefficients defined for each pair of -atoms types via the :doc:`pair\_coeff ` command is the same, +atoms types via the :doc:`pair_coeff ` command is the same, except that A is not included. The GPU-accelerated versions of these styles are implemented based on @@ -115,7 +115,7 @@ the work of :ref:`(Afshar) ` and :ref:`(Phillips) `. .. note:: If you are modeling DPD polymer chains, you may want to use the - :doc:`pair\_style srp ` command in conjunction with these pair + :doc:`pair_style srp ` command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other. @@ -156,15 +156,15 @@ instructions on how to use the accelerated styles effectively. These pair styles do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -These pair styles do not support the :doc:`pair\_modify ` +These pair styles do not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative Fc term is already shifted to be 0.0 at the cutoff distance Rc. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for these pair styles. -These pair style do not support the :doc:`pair\_modify ` +These pair style do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -178,7 +178,7 @@ be the same as they would have been if the original simulation had continued past the restart time. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. The *dpd/tstat* style can ramp its target temperature over multiple @@ -195,26 +195,26 @@ Restrictions The default frequency for rebuilding neighbor lists is every 10 steps -(see the :doc:`neigh\_modify ` command). This may be too +(see the :doc:`neigh_modify ` command). This may be too infrequent for style *dpd* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of "dangerous" reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. -These pair styles requires you to use the :doc:`comm\_modify vel yes ` command so that velocities are stored by ghost +These pair styles requires you to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the -:doc:`read\_restart ` command, though they should provide +:doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the -:doc:`read\_restart ` command for more details. +:doc:`read_restart ` command for more details. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix nvt `, :doc:`fix langevin `, :doc:`pair\_style srp ` +:doc:`pair_coeff `, :doc:`fix nvt `, :doc:`fix langevin `, :doc:`pair_style srp ` **Default:** none diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index c0d4f8c0c4..91de642ddb 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -75,9 +75,9 @@ For style *dpd/fdt*\ , the fluctuation-dissipation theorem defines gamma to be set equal to sigma\*sigma/(2 T), where T is the set point temperature specified as a pair style parameter in the above examples. The following coefficients must be defined for each pair of atoms types -via the :doc:`pair\_coeff ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` commands: +:doc:`read_data ` or :doc:`read_restart ` commands: * A (force units) * sigma (force\*time\^(1/2) units) @@ -108,9 +108,9 @@ variance that is used to compute the internal conductive energy. The fluctuation-dissipation theorem defines alpha\*alpha to be set equal to 2\*kB\*kappa, where kappa is the mesoparticle thermal conductivity parameter. The following coefficients must be defined for -each pair of atoms types via the :doc:`pair\_coeff ` +each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files -read by the :doc:`read\_data ` or :doc:`read\_restart ` +read by the :doc:`read_data ` or :doc:`read_restart ` commands: * A (force units) @@ -174,17 +174,17 @@ These commands are part of the USER-DPD package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Pair styles *dpd/fdt* and *dpd/fdt/energy* require use of the -:doc:`comm\_modify vel yes ` option so that velocities are +:doc:`comm_modify vel yes ` option so that velocities are stored by ghost atoms. -Pair style *dpd/fdt/energy* requires :doc:`atom\_style dpd ` +Pair style *dpd/fdt/energy* requires :doc:`atom_style dpd ` to be used in order to properly account for the particle internal energies and temperatures. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix shardlow ` +:doc:`pair_coeff `, :doc:`fix shardlow ` **Default:** none diff --git a/doc/src/pair_drip.rst b/doc/src/pair_drip.rst index 270afb8dbd..abc65900a0 100644 --- a/doc/src/pair_drip.rst +++ b/doc/src/pair_drip.rst @@ -67,13 +67,13 @@ potentials (e.g. 2 Angstrom for :doc:`REBO `) is much smaller than the equilibrium layer distance of graphene layers (about 3.4 Angstrom). If you want, you can enforce this by assigning different atom types to atoms in different layers, and apply an intralayer potential to one atom type. -See :doc:`pair\_hybrid ` for details. +See :doc:`pair_hybrid ` for details. ---------- -The :doc:`pair\_coeff ` command for DRIP takes *4+N* arguments, where +The :doc:`pair_coeff ` command for DRIP takes *4+N* arguments, where *N* is the number of LAMMPS atom types. The fist three arguments must be fixed to be *\* \* drip*, the fourth argument is the path to the DRIP parameter file, and the remaining N arguments specifying the mapping between element in the @@ -139,10 +139,10 @@ simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_style lebedeva\_z `, -:doc:`pair\_style kolmogorov/crespi/z `, -:doc:`pair\_style kolmogorov/crespi/full `, -:doc:`pair\_style ilp/graphene/hbn `. +:doc:`pair_style lebedeva\_z `, +:doc:`pair_style kolmogorov/crespi/z `, +:doc:`pair_style kolmogorov/crespi/full `, +:doc:`pair_style ilp/graphene/hbn `. ---------- diff --git a/doc/src/pair_dsmc.rst b/doc/src/pair_dsmc.rst index 38093d00e8..1b76efd3a2 100644 --- a/doc/src/pair_dsmc.rst +++ b/doc/src/pair_dsmc.rst @@ -48,9 +48,9 @@ There is no pairwise energy or virial contributions associated with this pair style. The following coefficient must be defined for each pair of atoms types -via the :doc:`pair\_coeff ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * sigma (area units, i.e. distance-squared) @@ -118,13 +118,13 @@ as in the following: This pair style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -138,7 +138,7 @@ be the same as they would have been if the original simulation had continued past the restart time. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -155,9 +155,9 @@ was built with that package. See the :doc:`Build package ` doc p Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix nve/noforce `, -:doc:`neigh\_modify `, :doc:`neighbor `, -:doc:`comm\_modify ` +:doc:`pair_coeff `, :doc:`fix nve/noforce `, +:doc:`neigh_modify `, :doc:`neighbor `, +:doc:`comm_modify ` **Default:** none diff --git a/doc/src/pair_e3b.rst b/doc/src/pair_e3b.rst index 73afdd7f53..320090b8ca 100644 --- a/doc/src/pair_e3b.rst +++ b/doc/src/pair_e3b.rst @@ -111,7 +111,7 @@ See the examples/USER/e3b directory for a complete example script. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. Thus, you @@ -143,7 +143,7 @@ The *preset* keyword currently only works with real, metal, si, and cgs :doc:`un Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`compute pair ` +:doc:`pair_coeff `, :doc:`compute pair ` Default """"""" diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index b367f00eb5..0f6840bbe4 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -114,7 +114,7 @@ within the cutoff distance. The cutoff distance and the tabulated values of the functionals F, rho, and phi are listed in one or more files which are specified by -the :doc:`pair\_coeff ` command. These are ASCII text files +the :doc:`pair_coeff ` command. These are ASCII text files in a DYNAMO-style format which is described below. DYNAMO was the original serial EAM MD code, written by the EAM originators. Several DYNAMO potential files for different metals are included in the @@ -185,7 +185,7 @@ Thus the following command will read the cuu3 potential file and use the tabulated Cu values for F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs -1,2 and 2,1 are ignored). See the :doc:`pair\_coeff ` doc +1,2 and 2,1 are ignored). See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. In effect, this makes atom types 1 and 2 in LAMMPS be Cu atoms. Different single-element files can be assigned to different atom types @@ -242,7 +242,7 @@ where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms. Style *eam/alloy* computes pairwise interactions using the same formula as style *eam*\ . However the associated -:doc:`pair\_coeff ` command reads a DYNAMO *setfl* file +:doc:`pair_coeff ` command reads a DYNAMO *setfl* file instead of a *funcfl* file. *Setfl* files can be used to model a single-element or alloy system. In the alloy case, as explained above, *setfl* files contain explicit tabulated values for alloy @@ -267,7 +267,7 @@ where N is the number of LAMMPS atom types: As an example, the potentials/NiAlH\_jea.eam.alloy file is a *setfl* file which has tabulated EAM values for 3 elements and their alloy -interactions: Ni, Al, and H. See the :doc:`pair\_coeff ` doc +interactions: Ni, Al, and H. See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Ni, and the 4th to be Al, you would use the following pair\_coeff @@ -380,7 +380,7 @@ so that different elements can contribute differently to the total electron density at an atomic site depending on the identity of the element at that atomic site. -The associated :doc:`pair\_coeff ` command for style *eam/fs* +The associated :doc:`pair_coeff ` command for style *eam/fs* reads a DYNAMO *setfl* file that has been extended to include additional rho\_alpha\_beta arrays of tabulated values. A discussion of how FS EAM differs from conventional EAM alloy potentials is given in @@ -400,7 +400,7 @@ same as for style *eam/alloy*\ , e.g. pair_coeff \* \* NiAlH_jea.eam.fs Ni Ni Ni Al where there are N additional arguments after the filename, where N is -the number of LAMMPS atom types. See the :doc:`pair\_coeff ` +the number of LAMMPS atom types. See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. The N values determine the mapping of LAMMPS atom types to EAM elements in the file, as described above for style *eam/alloy*\ . As @@ -477,7 +477,7 @@ two different element types, mixing is performed by LAMMPS as described above with the individual styles. You never need to specify a pair\_coeff command with I != J arguments for the eam styles. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The eam pair styles do not write their information to :doc:`binary restart files `, since it is stored in tabulated potential files. @@ -485,7 +485,7 @@ Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. The eam pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -502,7 +502,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index a976baaf61..68b54a16fe 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -56,7 +56,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of EDIP elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine a file Si.edip has EDIP values for Si. @@ -139,7 +139,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -147,7 +147,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -174,7 +174,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_eff.rst b/doc/src/pair_eff.rst index 438ced6785..235090cd39 100644 --- a/doc/src/pair_eff.rst +++ b/doc/src/pair_eff.rst @@ -126,7 +126,7 @@ r\_ij to the distances between electrons. For additional details see The overall electrostatics energy is given in Hartree units of energy by default and can be modified by an energy-conversion constant, -according to the units chosen (see :doc:`electron\_units `). The +according to the units chosen (see :doc:`electron_units `). The cutoff Rc, given in Bohrs (by default), truncates the interaction distance. The recommended cutoff for this pair style should follow the minimum image criterion, i.e. half of the minimum unit cell @@ -135,18 +135,18 @@ length. Style *eff/long* (not yet available) computes the same interactions as style *eff/cut* except that an additional damping factor is applied so it can be used in conjunction with the -:doc:`kspace\_style ` command and its *ewald* or *pppm* +:doc:`kspace_style ` command and its *ewald* or *pppm* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. -This potential is designed to be used with :doc:`atom\_style electron ` definitions, in order to handle the +This potential is designed to be used with :doc:`atom_style electron ` definitions, in order to handle the description of systems with interacting nuclei and explicit electrons. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutoff (distance units) @@ -156,7 +156,7 @@ For *eff/cut*\ , the cutoff coefficient is optional. If it is not used in the pair\_style command is used. For *eff/long* (not yet available) no cutoff will be specified for an -individual I,J type pair via the :doc:`pair\_coeff ` command. +individual I,J type pair via the :doc:`pair_coeff ` command. All type pairs use the same global cutoff specified in the pair\_style command. @@ -283,14 +283,14 @@ For atom type pairs I,J and I != J, the cutoff distance for the *eff/cut* style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -The :doc:`pair\_modify ` shift option is not relevant for +The :doc:`pair_modify ` shift option is not relevant for these pair styles. The *eff/long* (not yet available) style supports the -:doc:`pair\_modify ` table option for tabulation of the +:doc:`pair_modify ` table option for tabulation of the short-range portion of the long-range Coulombic interaction. -These pair styles do not support the :doc:`pair\_modify ` +These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -298,7 +298,7 @@ These pair styles write their information to :doc:`binary restart files ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -316,16 +316,16 @@ more info. These pair styles require that particles store electron attributes such as radius, radial velocity, and radial force, as defined by the -:doc:`atom\_style `. The *electron* atom style does all of +:doc:`atom_style `. The *electron* atom style does all of this. -Thes pair styles require you to use the :doc:`comm\_modify vel yes ` command so that velocities are stored by ghost +Thes pair styles require you to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` Default """"""" diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst index 001f314443..bdaa8733bb 100644 --- a/doc/src/pair_eim.rst +++ b/doc/src/pair_eim.rst @@ -63,7 +63,7 @@ atoms in the atomic pair. .. note:: Even though the EIM potential is treating atoms as charged ions, - you should not use a LAMMPS :doc:`atom\_style ` that stores a + you should not use a LAMMPS :doc:`atom_style ` that stores a charge on each atom and thus requires you to assign a charge to each atom, e.g. the *charge* or *full* atom styles. This is because the EIM potential infers the charge on an atom from the equation above for @@ -74,7 +74,7 @@ atoms in the atomic pair. All the EIM parameters are listed in a potential file which is -specified by the :doc:`pair\_coeff ` command. This is an +specified by the :doc:`pair_coeff ` command. This is an ASCII text file in a format described below. The "ffield.eim" file included in the "potentials" directory of the LAMMPS distribution currently includes nine elements Li, Na, K, Rb, Cs, F, Cl, Br, and I. @@ -97,7 +97,7 @@ command, where N is the number of LAMMPS atom types: * EIM potential file * N element names = mapping of EIM elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example like one of those above, suppose you want to model a @@ -183,7 +183,7 @@ LAMMPS was built with that package. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index d8262e0712..01ef5ad9d1 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -50,7 +50,7 @@ where the *epsilon* parameter determines the depth of the potential minimum located at *Rm*\ , and *alpha* determines the softness of the repulsion. The coefficients must be defined for each species in a given particle -type via the :doc:`pair\_coeff ` command as in the examples +type via the :doc:`pair_coeff ` command as in the examples above, where the first argument is the filename that includes the exponential-6 parameters for each species. The file includes the species tag followed by the *alpha*\ , *epsilon* and *Rm* @@ -161,7 +161,7 @@ comprise the gas mixture. This pair style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` shift option +This style does not support the :doc:`pair_modify ` shift option for the energy of the exp() and 1/r\^6 portion of the pair interaction. This style does not support the pair\_modify tail option for adding long-range @@ -204,7 +204,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** fractional weighting diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index 90dbfeb612..d1e64ae5df 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -212,7 +212,7 @@ order to avoid singularities in potential energy and forces when sites are created or annihilated and can overlap :ref:`(Beutler) `. The parameters n, alpha\_LJ and alpha\_C are set in the -:doc:`pair\_style ` command, before the cutoffs. Usual choices for the +:doc:`pair_style ` command, before the cutoffs. Usual choices for the exponent are n = 2 or n = 1. For the remaining coefficients alpha\_LJ = 0.5 and alpha\_C = 10 Angstrom\^2 are appropriate choices. Plots of the 12/6 LJ and Coulomb terms are shown below, for lambda ranging from 1 to 0 every 0.1. @@ -223,9 +223,9 @@ Coulomb terms are shown below, for lambda ranging from 1 to 0 every 0.1. For the *lj/cut/coul/cut/soft* or *lj/cut/coul/long/soft* pair styles, as well as for the equivalent *class2* versions, the following coefficients must be -defined for each pair of atoms types via the :doc:`pair\_coeff ` +defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by -the :doc:`read\_data ` or :doc:`read\_restart ` commands, or +the :doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -246,31 +246,31 @@ specified. Style *lj/cut/tip4p/long/soft* implements a soft-core version of the TIP4P water model. The usage of the TIP4P pair style is documented in the -:doc:`pair\_lj ` styles. In the soft version the parameters n, alpha\_LJ -and alpha\_C are set in the :doc:`pair\_style ` command, after the +:doc:`pair_lj ` styles. In the soft version the parameters n, alpha\_LJ +and alpha\_C are set in the :doc:`pair_style ` command, after the specific parameters of the TIP4P water model and before the cutoffs. The activation parameter lambda is supplied as an argument of the -:doc:`pair\_coeff ` command, after epsilon and sigma and before the +:doc:`pair_coeff ` command, after epsilon and sigma and before the optional cutoffs. Style *lj/charmm/coul/long/soft* implements a soft-core version of the modified 12-6 LJ potential used in CHARMM and documented in the :doc:`pair\_lj\_charmm ` style. In the soft version the parameters n, -alpha\_LJ and alpha\_C are set in the :doc:`pair\_style ` command, before +alpha\_LJ and alpha\_C are set in the :doc:`pair_style ` command, before the global cutoffs. The activation parameter lambda is introduced as an argument -of the :doc:`pair\_coeff ` command, after epsilon and sigma and +of the :doc:`pair_coeff ` command, after epsilon and sigma and before the optional eps14 and sigma14. Style *lj/class2/soft* implements a soft-core version of the 9-6 potential in :doc:`pair\_class2 `. In the soft version the parameters n, alpha\_LJ -and alpha\_C are set in the :doc:`pair\_style ` command, before the +and alpha\_C are set in the :doc:`pair_style ` command, before the global cutoffs. The activation parameter lambda is introduced as an argument of -the the :doc:`pair\_coeff ` command, after epsilon and sigma and before +the the :doc:`pair_coeff ` command, after epsilon and sigma and before the optional cutoffs. The *coul/cut/soft*\ , *coul/long/soft* and *tip4p/long/soft* sub-styles are designed to be combined with other pair potentials via the -:doc:`pair\_style hybrid/overlay ` command. This is because +:doc:`pair_style hybrid/overlay ` command. This is because they have no repulsive core. Hence, if used by themselves, there will be no repulsion to keep two oppositely charged particles from overlapping each other. In this case, if lambda = 1, a singularity may @@ -299,13 +299,13 @@ in several water models). related styles; use the lambda parameter instead to activate/deactivate interactions, or use epsilon = 0 and sigma = 1. Alternatively, when sites do not interact though the Lennard-Jones term the *coul/long/soft* or similar sub-style - can be used via the :doc:`pair\_style hybrid/overlay ` command. + can be used via the :doc:`pair_style hybrid/overlay ` command. ---------- -The *morse/soft* variant modifies the :doc:`pair\_morse ` style at +The *morse/soft* variant modifies the :doc:`pair_morse ` style at short range to have a soft core. The functional form differs from that of the *lj/soft* styles, and is instead given by: @@ -357,20 +357,20 @@ distance for these pair style can be mixed. The default mix value is *geometric* for 12-6 styles. The mixing rule for epsilon and sigma for *lj/class2/soft* 9-6 potentials is to use the -*sixthpower* formulas. The :doc:`pair\_modify mix ` setting is thus +*sixthpower* formulas. The :doc:`pair_modify mix ` setting is thus ignored for class2 potentials for epsilon and sigma. However it is still -followed for mixing the cutoff distance. See the :doc:`pair\_modify ` +followed for mixing the cutoff distance. See the :doc:`pair_modify ` command for details. The *morse/soft* pair style does not support mixing. Thus, coefficients for all LJ pairs must be specified explicitly. -All of the pair styles with soft core support the :doc:`pair\_modify ` +All of the pair styles with soft core support the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction. The different versions of the *lj/cut/soft* pair styles support the -:doc:`pair\_modify ` tail option for adding a long-range tail +:doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure for the Lennard-Jones portion of the pair interaction. @@ -387,7 +387,7 @@ interaction. other approximations, namely that the system is homogeneous (local density equal the average density) beyond the cutoff. -The *morse/soft* pair style does not support the :doc:`pair\_modify ` +The *morse/soft* pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. All of these pair styles write information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be @@ -411,7 +411,7 @@ info. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix adapt `, +:doc:`pair_coeff `, :doc:`fix adapt `, :doc:`fix adapt/fep `, :doc:`compute fep ` **Default:** none diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst index e5252afe2b..cb687ff487 100644 --- a/doc/src/pair_gauss.rst +++ b/doc/src/pair_gauss.rst @@ -51,9 +51,9 @@ between an atom and its corresponding tether site which will typically be a frozen atom in the simulation. Rc is the cutoff. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * A (energy units) @@ -79,9 +79,9 @@ barrier is located at r\_mh and has a width of sigma\_h. The prefactor determines the height of the potential barrier. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the example above, +via the :doc:`pair_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * H (energy \* distance units) @@ -146,22 +146,22 @@ before mixing, and converted back after mixing This way, if either particle is repulsive (if Ai<0 or Aj<0), then the default interaction between both particles will be repulsive. -The *gauss* style does not support the :doc:`pair\_modify ` +The *gauss* style does not support the :doc:`pair_modify ` shift option. There is no effect due to the Gaussian well beyond the cutoff; hence reasonable cutoffs need to be specified. -The *gauss/cut* style supports the :doc:`pair\_modify ` shift +The *gauss/cut* style supports the :doc:`pair_modify ` shift option for the energy of the Gauss-potential portion of the pair interaction. -The :doc:`pair\_modify ` table and tail options are not +The :doc:`pair_modify ` table and tail options are not relevant for these pair styles. These pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. The *gauss* pair style tallies an "occupancy" count of how many Gaussian-well @@ -192,8 +192,8 @@ enabled if LAMMPS is build with that package. See the :doc:`Build package `, -:doc:`pair\_style coul/diel ` +:doc:`pair_coeff `, +:doc:`pair_style coul/diel ` **Default:** none diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index 47b7b5564e..8db0e6edc2 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -71,13 +71,13 @@ listed below and in `this supplementary document `_ Use of this pair style requires the NVE, NVT, or NPT fixes with the *asphere* extension (e.g. :doc:`fix nve/asphere `) in -order to integrate particle rotation. Additionally, :doc:`atom\_style ellipsoid ` should be used since it defines the +order to integrate particle rotation. Additionally, :doc:`atom_style ellipsoid ` should be used since it defines the rotational state and the size and shape of each ellipsoidal particle. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon = well depth (energy units) @@ -96,7 +96,7 @@ cutoff specified in the pair\_style command is used. It is typical with the Gay-Berne potential to define *sigma* as the minimum of the 3 shape diameters of the particles involved in an I,I interaction, though this is not required. Note that this is a -different meaning for *sigma* than the :doc:`pair\_style resquared ` potential uses. +different meaning for *sigma* than the :doc:`pair_style resquared ` potential uses. The epsilon\_i and epsilon\_j coefficients are actually defined for atom types, not for pairs of atom types. Thus, in a series of pair\_coeff @@ -114,7 +114,7 @@ J, you should insure they are consistent with their values in other pair\_coeff commands, since only the last setting will be in effect. Note that if this potential is being used as a sub-style of -:doc:`pair\_style hybrid `, and there is no "pair\_coeff I I" +:doc:`pair_style hybrid `, and there is no "pair\_coeff I I" setting made for Gay-Berne for a particular type I (because I-I interactions are computed by another hybrid pair potential), then you still need to insure the epsilon a,b,c coefficients are assigned to @@ -171,16 +171,16 @@ For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair styles supports the :doc:`pair\_modify ` shift +This pair styles supports the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction, but only for sphere-sphere interactions. There is no shifting performed for ellipsoidal interactions due to the anisotropic dependence of the interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -188,7 +188,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -204,12 +204,12 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package `. It also require they store a per-type +:doc:`atom_style `. It also require they store a per-type :doc:`shape `. The particles cannot store a per-particle diameter. This pair style requires that atoms be ellipsoids as defined by the -:doc:`atom\_style ellipsoid ` command. +:doc:`atom_style ellipsoid ` command. Particles acted on by the potential can be finite-size aspherical or spherical particles, or point particles. Spherical particles have all @@ -224,8 +224,8 @@ ratio ellipsoids are used. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix nve/asphere `, -:doc:`compute temp/asphere `, :doc:`pair\_style resquared ` +:doc:`pair_coeff `, :doc:`fix nve/asphere `, +:doc:`compute temp/asphere `, :doc:`pair_style resquared ` **Default:** none diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 7f03519f35..20ab3b3cab 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -184,9 +184,9 @@ This is determined by searching for a :doc:`fix rigid ` command (or its variants). For granular styles there are no additional coefficients to set for -each pair of atom types via the :doc:`pair\_coeff ` command. +each pair of atom types via the :doc:`pair_coeff ` command. All settings are global and are made via the pair\_style command. -However you must still use the :doc:`pair\_coeff ` for all +However you must still use the :doc:`pair_coeff ` for all pairs of granular atom types. For example the command @@ -196,7 +196,7 @@ pairs of granular atom types. For example the command should be used if all atoms in the simulation interact via a granular potential (i.e. one of the pair styles above is used). If a granular -potential is used as a sub-style of :doc:`pair\_style hybrid `, then specific atom types can be used in the +potential is used as a sub-style of :doc:`pair_style hybrid `, then specific atom types can be used in the pair\_coeff command to determine which atoms interact via a granular potential. @@ -228,14 +228,14 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -The :doc:`pair\_modify ` mix, shift, table, and tail options +The :doc:`pair_modify ` mix, shift, table, and tail options are not relevant for granular pair styles. These pair styles write their information to :doc:`binary restart files `, so a pair\_style command does not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. The single() function of these pair styles returns 0.0 for the energy @@ -265,23 +265,23 @@ All the granular pair styles are part of the GRANULAR package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. These pair styles require that atoms store torque and angular velocity -(omega) as defined by the :doc:`atom\_style `. They also +(omega) as defined by the :doc:`atom_style `. They also require a per-particle radius is stored. The *sphere* atom style does all of this. -This pair style requires you to use the :doc:`comm\_modify vel yes ` command so that velocities are stored by ghost +This pair style requires you to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the -:doc:`read\_restart ` command, though they should provide +:doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the -:doc:`read\_restart ` command for more details. +:doc:`read_restart ` command for more details. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index 294bec9b8c..a22e6b233a 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -50,10 +50,10 @@ and torques are the sum of various models selected for the normal, tangential, rolling and twisting modes of motion. All model choices and parameters are entered in the -:doc:`pair\_coeff ` command, as described below. Unlike +:doc:`pair_coeff ` command, as described below. Unlike e.g. :doc:`pair gran/hooke `, coefficient values are not global, but can be set to different values for different combinations -of particle types, as determined by the :doc:`pair\_coeff ` +of particle types, as determined by the :doc:`pair_coeff ` command. If the contact model choice is the same for two particle types, the mixing for the cross-coefficients can be carried out automatically. This is shown in the last example, where model @@ -674,7 +674,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -The :doc:`pair\_modify ` mix, shift, table, and tail options +The :doc:`pair_modify ` mix, shift, table, and tail options are not relevant for granular pair styles. Mixing of coefficients is carried out using geometric averaging for @@ -711,7 +711,7 @@ These pair styles write their information to :doc:`binary restart files ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. The single() function of these pair styles returns 0.0 for the energy @@ -743,23 +743,23 @@ All the granular pair styles are part of the GRANULAR package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. These pair styles require that atoms store torque and angular velocity -(omega) as defined by the :doc:`atom\_style `. They also +(omega) as defined by the :doc:`atom_style `. They also require a per-particle radius is stored. The *sphere* atom style does all of this. -This pair style requires you to use the :doc:`comm\_modify vel yes ` command so that velocities are stored by ghost +This pair style requires you to use the :doc:`comm_modify vel yes ` command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the -:doc:`read\_restart ` command, though they should provide +:doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the -:doc:`read\_restart ` command for more details. +:doc:`read_restart ` command for more details. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` :doc:`pair gran/\* ` Default diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index 9bc803bc55..d80e8a794b 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -86,9 +86,9 @@ the pair\_style command. The inner LJ cutoff must be > 0, but the inner Coulombic cutoff can be >= 0. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -143,15 +143,15 @@ The default mix value is *geometric*\ . See the "pair\_modify" command for details. None of the GROMACS pair styles support the -:doc:`pair\_modify ` shift option, since the Lennard-Jones +:doc:`pair_modify ` shift option, since the Lennard-Jones portion of the pair interaction is already smoothed to 0.0 at the cutoff. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. None of the GROMACS pair styles support the -:doc:`pair\_modify ` tail option for adding long-range tail +:doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure, since there are no corrections for a potential that goes to 0.0 at the cutoff. @@ -159,7 +159,7 @@ All of the GROMACS pair styles write their information to :doc:`binary restart f not need to be specified in an input script that reads a restart file. All of the GROMACS pair styles can only be used via the *pair* -keyword of the :doc:`run\_style respa ` command. They do not +keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -173,7 +173,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst index d1c89eaee8..cb17e581e1 100644 --- a/doc/src/pair_gw.rst +++ b/doc/src/pair_gw.rst @@ -52,7 +52,7 @@ command, where N is the number of LAMMPS atom types: * filename * N element names = mapping of GW elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.gw has Gao-Weber values for Si and C. @@ -90,7 +90,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above from values in the potential file. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -98,7 +98,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -124,7 +124,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index f87f0c45e2..e202cb4293 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -64,9 +64,9 @@ These 3-body interactions can be defined for pairs of acceptor and donor atoms, based on atom types. For each donor/acceptor atom pair, the 3rd atom in the interaction is a hydrogen permanently bonded to the donor atom, e.g. in a bond list read in from a data file via the -:doc:`read\_data ` command. The atom types of possible +:doc:`read_data ` command. The atom types of possible hydrogen atoms for each donor/acceptor type pair are specified by the -:doc:`pair\_coeff ` command (see below). +:doc:`pair_coeff ` command (see below). Style *hbond/dreiding/lj* is the original DREIDING potential of :ref:`(Mayo) `. It uses a LJ 12/10 functional for the Donor-Acceptor @@ -84,16 +84,16 @@ on the DREIDING force field. Because the Dreiding hydrogen bond potential is only one portion of an overall force field which typically includes other pairwise - interactions, it is common to use it as a sub-style in a :doc:`pair\_style hybrid/overlay ` command, where another pair style + interactions, it is common to use it as a sub-style in a :doc:`pair_style hybrid/overlay ` command, where another pair style provides the repulsive core interaction between pairs of atoms, e.g. a 1/r\^12 Lennard-Jones repulsion. .. note:: - When using the hbond/dreiding pair styles with :doc:`pair\_style hybrid/overlay `, you should explicitly define pair + When using the hbond/dreiding pair styles with :doc:`pair_style hybrid/overlay `, you should explicitly define pair interactions between the donor atom and acceptor atoms, (as well as between these atoms and ALL other atoms in your system). Whenever - :doc:`pair\_style hybrid/overlay ` is used, ordinary mixing + :doc:`pair_style hybrid/overlay ` is used, ordinary mixing rules are not applied to atoms like the donor and acceptor atoms because they are typically referenced in multiple pair styles. Neglecting to do this can cause difficult-to-detect physics problems. @@ -110,20 +110,20 @@ on the DREIDING force field. The following coefficients must be defined for pairs of eligible -donor/acceptor types via the :doc:`pair\_coeff ` command as +donor/acceptor types via the :doc:`pair_coeff ` command as in the examples above. .. note:: Unlike other pair styles and their associated - :doc:`pair\_coeff ` commands, you do not need to specify + :doc:`pair_coeff ` commands, you do not need to specify pair\_coeff settings for all possible I,J type pairs. Only I,J type pairs for atoms which act as joint donors/acceptors need to be specified; all other type pairs are assumed to be inactive. .. note:: - A :doc:`pair\_coeff ` command can be specified multiple + A :doc:`pair_coeff ` command can be specified multiple times for the same donor/acceptor type pair. This enables multiple hydrogen types to be assigned to the same donor/acceptor type pair. For other pair\_styles, if the pair\_coeff command is re-used for the @@ -160,14 +160,14 @@ follows: A single hydrogen atom type K can be specified, or a wild-card asterisk can be used in place of or in conjunction with the K arguments to select multiple types as hydrogen atoms. This takes the form -"\*" or "\*n" or "n\*" or "m\*n". See the :doc:`pair\_coeff ` +"\*" or "\*n" or "n\*" or "m\*n". See the :doc:`pair_coeff ` command doc page for details. If the donor flag is *i*\ , then the atom of type I in the pair\_coeff command is treated as the donor, and J is the acceptor. If the donor flag is *j*\ , then the atom of type J in the pair\_coeff command is treated as the donor and I is the donor. This option is required -because the :doc:`pair\_coeff ` command requires that I <= J. +because the :doc:`pair_coeff ` command requires that I <= J. Epsilon and sigma are settings for the hydrogen bond potential based on a Lennard-Jones functional form. Note that sigma is defined as the @@ -214,13 +214,13 @@ instructions on how to use the accelerated styles effectively. These pair styles do not support mixing. You must explicitly identify each donor/acceptor type pair. -These styles do not support the :doc:`pair\_modify ` shift +These styles do not support the :doc:`pair_modify ` shift option for the energy of the interactions. -The :doc:`pair\_modify ` table option is not relevant for +The :doc:`pair_modify ` table option is not relevant for these pair styles. -These pair styles do not support the :doc:`pair\_modify ` +These pair styles do not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -228,7 +228,7 @@ These pair styles do not write their information to :doc:`binary restart files < re-specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. These pair styles tally a count of how many hydrogen bonding @@ -258,7 +258,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index 3ee9c19428..2ede99b35a 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -46,7 +46,7 @@ pair styles in one simulation. With the *hybrid* style, exactly one pair style is assigned to each pair of atom types. With the *hybrid/overlay* style, one or more pair styles can be assigned to each pair of atom types. The assignment of pair styles to type pairs -is made via the :doc:`pair\_coeff ` command. +is made via the :doc:`pair_coeff ` command. Here are two examples of hybrid simulations. The *hybrid* style could be used for a simulation of a metal droplet on a LJ surface. The @@ -122,7 +122,7 @@ with Tersoff, and the cross-interactions with Lennard-Jones: pair_coeff 1 2 lj/cut 1.0 1.5 If pair coefficients are specified in the data file read via the -:doc:`read\_data ` command, then the same rule applies. +:doc:`read_data ` command, then the same rule applies. E.g. "eam/alloy" or "lj/cut" must be added after the atom type, for each line in the "Pair Coeffs" section, e.g. @@ -135,7 +135,7 @@ each line in the "Pair Coeffs" section, e.g. ... Note that the pair\_coeff command for some potentials such as -:doc:`pair\_style eam/alloy ` includes a mapping specification +:doc:`pair_style eam/alloy ` includes a mapping specification of elements to all atom types, which in the hybrid case, can include atom types not assigned to the *eam/alloy* potential. The NULL keyword is used by many such potentials (eam/alloy, Tersoff, AIREBO, @@ -170,20 +170,20 @@ commands are the same: pair_coeff 2 2 lj/cut 1.5 0.8 Coefficients must be defined for each pair of atoms types via the -:doc:`pair\_coeff ` command as described above, or in the -data file or restart files read by the :doc:`read\_data ` or -:doc:`read\_restart ` commands, or by mixing as described +:doc:`pair_coeff ` command as described above, or in the +data file or restart files read by the :doc:`read_data ` or +:doc:`read_restart ` commands, or by mixing as described below. For both the *hybrid* and *hybrid/overlay* styles, every atom type pair I,J (where I <= J) must be assigned to at least one sub-style via -the :doc:`pair\_coeff ` command as in the examples above, or -in the data file read by the :doc:`read\_data `, or by mixing +the :doc:`pair_coeff ` command as in the examples above, or +in the data file read by the :doc:`read_data `, or by mixing as described below. If you want there to be no interactions between a particular pair of atom types, you have 3 choices. You can assign the type pair to some -sub-style and use the :doc:`neigh\_modify exclude type ` +sub-style and use the :doc:`neigh_modify exclude type ` command. You can assign it to some sub-style and set the coefficients so that there is effectively no interaction (e.g. epsilon = 0.0 in a LJ potential). Or, for *hybrid* and *hybrid/overlay* simulations, you @@ -205,7 +205,7 @@ If an assignment to *none* is made in a simulation with the *hybrid/overlay* pair style, it wipes out all previous assignments of that atom type pair to sub-styles. -Note that you may need to use an :doc:`atom\_style ` hybrid +Note that you may need to use an :doc:`atom_style ` hybrid command in your input script, if atoms in the simulation will need attributes from several atom styles, due to using multiple pair potentials. @@ -218,8 +218,8 @@ Different force fields (e.g. CHARMM vs AMBER) may have different rules for applying weightings that change the strength of pairwise interactions between pairs of atoms that are also 1-2, 1-3, and 1-4 neighbors in the molecular bond topology, as normally set by the -:doc:`special\_bonds ` command. Different weights can be -assigned to different pair hybrid sub-styles via the :doc:`pair\_modify special ` command. This allows multiple force fields +:doc:`special_bonds ` command. Different weights can be +assigned to different pair hybrid sub-styles via the :doc:`pair_modify special ` command. This allows multiple force fields to be used in a model of a hybrid system, however, there is no consistent approach to determine parameters automatically for the interactions between the two force fields, this is only recommended when particles @@ -261,12 +261,12 @@ effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA: pair_modify pair tersoff special lj/coul 1.0 1.0 1.0 For use with the various :doc:`compute \*/tally ` -computes, the :doc:`pair\_modify compute/tally ` +computes, the :doc:`pair_modify compute/tally ` command can be used to selectively turn off processing of the compute tally styles, for example, if those pair styles (e.g. many-body styles) do not support this feature. -See the :doc:`pair\_modify ` doc page for details on +See the :doc:`pair_modify ` doc page for details on the specific syntax, requirements and restrictions. @@ -288,7 +288,7 @@ individual sub-style can be accessed and output via the :doc:`compute pair ` command, using "\* \*" to include +single :doc:`pair_coeff ` command, using "\* \*" to include all types and the NULL keywords described above to exclude specific types not assigned to that potential. If types 1,3,4 were assigned in that way (but not type 2), this means that all many-body interactions @@ -309,7 +309,7 @@ to think of excluding an interaction between a particular pair of atoms when the potential computes 3-body or 4-body interactions. However, you can still use the pair\_coeff none setting or the -:doc:`neigh\_modify exclude ` command to exclude certain +:doc:`neigh_modify exclude ` command to exclude certain type pairs from the neighbor list that will be passed to a many-body sub-style. This will alter the calculations made by a many-body potential, since it builds its list of 3-body, 4-body, etc @@ -390,7 +390,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : Any pair potential settings made via the -:doc:`pair\_modify ` command are passed along to all +:doc:`pair_modify ` command are passed along to all sub-styles of the hybrid potential. For atom type pairs I,J and I != J, if the sub-style assigned to I,I @@ -405,19 +405,19 @@ sub-style. See the "pair\_modify" command for details of mixing rules. See the See the doc page for the sub-style to see if allows for mixing. -The hybrid pair styles supports the :doc:`pair\_modify ` +The hybrid pair styles supports the :doc:`pair_modify ` shift, table, and tail options for an I,J pair interaction, if the associated sub-style supports it. For the hybrid pair styles, the list of sub-styles and their -respective settings are written to :doc:`binary restart files `, so a :doc:`pair\_style ` command does +respective settings are written to :doc:`binary restart files `, so a :doc:`pair_style ` command does not need to specified in an input script that reads a restart file. However, the coefficient information is not stored in the restart file. Thus, pair\_coeff commands need to be re-specified in the restart input script. These pair styles support the use of the *inner*\ , *middle*\ , and -*outer* keywords of the :doc:`run\_style respa ` command, if +*outer* keywords of the :doc:`run_style respa ` command, if their sub-styles do. Restrictions @@ -425,7 +425,7 @@ Restrictions When using a long-range Coulombic solver (via the -:doc:`kspace\_style ` command) with a hybrid pair\_style, +:doc:`kspace_style ` command) with a hybrid pair\_style, one or more sub-styles will be of the "long" variety, e.g. *lj/cut/coul/long* or *buck/coul/long*\ . You must insure that the short-range Coulombic cutoff used by each of these long pair styles is @@ -434,7 +434,7 @@ the same or else LAMMPS will generate an error. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst index b18ebb341b..74937bd0fb 100644 --- a/doc/src/pair_ilp_graphene_hbn.rst +++ b/doc/src/pair_ilp_graphene_hbn.rst @@ -146,14 +146,14 @@ units, if your simulation does not use *metal* units. Related commands """""""""""""""" -:doc:`pair\_coeff `, -:doc:`pair\_none `, -:doc:`pair\_style hybrid/overlay `, -:doc:`pair\_style drip `, -:doc:`pair\_style pair\_kolmogorov\_crespi\_z `, -:doc:`pair\_style pair\_kolmogorov\_crespi\_full `, -:doc:`pair\_style pair\_lebedeva\_z `, -:doc:`pair\_style pair\_coul\_shield `. +:doc:`pair_coeff `, +:doc:`pair_none `, +:doc:`pair_style hybrid/overlay `, +:doc:`pair_style drip `, +:doc:`pair_style pair\_kolmogorov\_crespi\_z `, +:doc:`pair_style pair\_kolmogorov\_crespi\_full `, +:doc:`pair_style pair\_lebedeva\_z `, +:doc:`pair_style pair\_coul\_shield `. **Default:** tap\_flag = 1 diff --git a/doc/src/pair_kim.rst b/doc/src/pair_kim.rst index 768ac3fa9b..56232a3e92 100644 --- a/doc/src/pair_kim.rst +++ b/doc/src/pair_kim.rst @@ -29,14 +29,14 @@ This pair style is a wrapper on the `Open Knowledgebase of Interatomic Models (O potentials to enable their use in LAMMPS scripts. The preferred interface for using interatomic models archived in -OpenKIM is the :doc:`kim\_commands interface `. That +OpenKIM is the :doc:`kim_commands interface `. That interface supports both "KIM Portable Models" (PMs) that conform to the KIM API Portable Model Interface (PMI) and can be used by any simulation code that conforms to the KIM API/PMI, and "KIM Simulator Models" that are natively implemented within a single simulation code (like LAMMPS) and can only be used with it. The *pair\_style kim* command is limited to KIM PMs. It is -used by the :doc:`kim\_commands interface ` as needed. +used by the :doc:`kim_commands interface ` as needed. .. note:: @@ -49,7 +49,7 @@ used by the :doc:`kim\_commands interface ` as needed. The argument *model* is the name of the KIM PM. For potentials archived in OpenKIM -this is the extended KIM ID (see :doc:`kim\_commands ` +this is the extended KIM ID (see :doc:`kim_commands ` for details). LAMMPS can invoke any KIM PM, however there can be incompatibilities (for example due to unit matching issues). In the event of an incompatibility, the code will terminate with @@ -97,7 +97,7 @@ in *examples/kim*\ . **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since KIM stores the potential parameters. @@ -105,7 +105,7 @@ Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -117,7 +117,7 @@ Restrictions This pair style is part of the KIM package. See details on -restrictions in :doc:`kim\_commands `. +restrictions in :doc:`kim_commands `. This current version of pair\_style kim is compatible with the kim-api package version 2.0.0 and higher. @@ -125,7 +125,7 @@ kim-api package version 2.0.0 and higher. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`kim\_commands ` +:doc:`pair_coeff `, :doc:`kim_commands ` **Default:** none diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst index 1faf271497..a9dcbcbda9 100644 --- a/doc/src/pair_kolmogorov_crespi_full.rst +++ b/doc/src/pair_kolmogorov_crespi_full.rst @@ -134,13 +134,13 @@ units. Related commands """""""""""""""" -:doc:`pair\_coeff `, -:doc:`pair\_none `, -:doc:`pair\_style hybrid/overlay `, -:doc:`pair\_style drip `, -:doc:`pair\_style pair\_lebedeva\_z `, -:doc:`pair\_style kolmogorov/crespi/z `, -:doc:`pair\_style ilp/graphene/hbn `. +:doc:`pair_coeff `, +:doc:`pair_none `, +:doc:`pair_style hybrid/overlay `, +:doc:`pair_style drip `, +:doc:`pair_style pair\_lebedeva\_z `, +:doc:`pair_style kolmogorov/crespi/z `, +:doc:`pair_style ilp/graphene/hbn `. **Default:** tap\_flag = 0 diff --git a/doc/src/pair_kolmogorov_crespi_z.rst b/doc/src/pair_kolmogorov_crespi_z.rst index a1e6c1afad..f9c116e15a 100644 --- a/doc/src/pair_kolmogorov_crespi_z.rst +++ b/doc/src/pair_kolmogorov_crespi_z.rst @@ -63,13 +63,13 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff `, -:doc:`pair\_none `, -:doc:`pair\_style hybrid/overlay `, -:doc:`pair\_style drip `, -:doc:`pair\_style ilp/graphene/hbn `. -:doc:`pair\_style kolmogorov/crespi/full `, -:doc:`pair\_style lebedeva/z ` +:doc:`pair_coeff `, +:doc:`pair_none `, +:doc:`pair_style hybrid/overlay `, +:doc:`pair_style drip `, +:doc:`pair_style ilp/graphene/hbn `. +:doc:`pair_style kolmogorov/crespi/full `, +:doc:`pair_style lebedeva/z ` **Default:** none diff --git a/doc/src/pair_lcbop.rst b/doc/src/pair_lcbop.rst index 8f667bf918..49a0ba0a4b 100644 --- a/doc/src/pair_lcbop.rst +++ b/doc/src/pair_lcbop.rst @@ -36,7 +36,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of LCBOP elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, if your LAMMPS simulation has 4 atom types and you want @@ -65,7 +65,7 @@ carefully. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -73,7 +73,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -95,7 +95,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_airebo `, :doc:`pair\_coeff ` +:doc:`pair_airebo `, :doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lebedeva_z.rst b/doc/src/pair_lebedeva_z.rst index 78e21ca616..08a88450b5 100644 --- a/doc/src/pair_lebedeva_z.rst +++ b/doc/src/pair_lebedeva_z.rst @@ -57,13 +57,13 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff `, -:doc:`pair\_style none `, -:doc:`pair\_style hybrid/overlay `, -:doc:`pair\_style drip `, -:doc:`pair\_style ilp/graphene/hbd `, -:doc:`pair\_style kolmogorov/crespi/z `, -:doc:`pair\_style kolmogorov/crespi/full `. +:doc:`pair_coeff `, +:doc:`pair_style none `, +:doc:`pair_style hybrid/overlay `, +:doc:`pair_style drip `, +:doc:`pair_style ilp/graphene/hbd `, +:doc:`pair_style kolmogorov/crespi/z `, +:doc:`pair_style kolmogorov/crespi/full `. **Default:** none diff --git a/doc/src/pair_line_lj.rst b/doc/src/pair_line_lj.rst index e8b1a9850f..3b7af38fd1 100644 --- a/doc/src/pair_line_lj.rst +++ b/doc/src/pair_line_lj.rst @@ -33,7 +33,7 @@ explained below. Interactions between two line segments, each with N1 and N2 spherical particles, are calculated as the pairwise sum of N1\*N2 Lennard-Jones interactions. Interactions between a line segment with N spherical particles and a point particle are treated as the -pairwise sum of N Lennard-Jones interactions. See the :doc:`pair\_style lj/cut ` doc page for the definition of Lennard-Jones +pairwise sum of N Lennard-Jones interactions. See the :doc:`pair_style lj/cut ` doc page for the definition of Lennard-Jones interactions. The set of non-overlapping spherical sub-particles that represent a @@ -79,9 +79,9 @@ the pair of particles to be included in the neighbor list. are using and the sub-particle cutoff settings. For style *line/lj*\ , the following coefficients must be defined for -each pair of atom types via the :doc:`pair\_coeff ` command +each pair of atom types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by -the :doc:`read\_data ` or :doc:`read\_restart ` +the :doc:`read_data ` or :doc:`read_restart ` commands: * sizeI (distance units) @@ -122,13 +122,13 @@ cutoff is used. For atom type pairs I,J and I != J, coefficients must be specified. No default mixing rules are used. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -144,12 +144,12 @@ LAMMPS was built with that package. See the :doc:`Build package Defining particles to be line segments so they participate in line/line or line/particle interactions requires the use the -:doc:`atom\_style line ` command. +:doc:`atom_style line ` command. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style tri/lj ` +:doc:`pair_coeff `, :doc:`pair_style tri/lj ` **Default:** none diff --git a/doc/src/pair_list.rst b/doc/src/pair_list.rst index b74070c4d3..2dd5ec44de 100644 --- a/doc/src/pair_list.rst +++ b/doc/src/pair_list.rst @@ -122,17 +122,17 @@ Note that the usual 1/2 factor is included in :math:`K`. This pair style does not support mixing since all parameters are explicit for each pair. -The :doc:`pair\_modify ` shift option is supported by this +The :doc:`pair_modify ` shift option is supported by this pair style. -The :doc:`pair\_modify ` table and tail options are not +The :doc:`pair_modify ` table and tail options are not relevant for this pair style. This pair style does not write its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -159,10 +159,10 @@ LAMMPS is build with that package. See the :doc:`Build package ` Related commands """""""""""""""" -:doc:`pair\_coeff `, -:doc:`pair\_style hybrid/overlay `, -:doc:`pair\_style lj/cut `, -:doc:`pair\_style morse `, -:doc:`bond\_style harmonic ` +:doc:`pair_coeff `, +:doc:`pair_style hybrid/overlay `, +:doc:`pair_style lj/cut `, +:doc:`pair_style morse `, +:doc:`bond_style harmonic ` **Default:** none diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index cfc56ecb5e..3fa1cb0bca 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -258,7 +258,7 @@ setting *alpha* to a small non-zero value. Styles *lj/cut/coul/long* and *lj/cut/coul/msm* compute the same Coulombic interactions as style *lj/cut/coul/cut* except that an additional damping factor is applied to the Coulombic term so it can -be used in conjunction with the :doc:`kspace\_style ` +be used in conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are @@ -314,9 +314,9 @@ your model. For all of the *lj/cut* pair styles, the following coefficients must be defined for each pair of atoms types via the -:doc:`pair\_coeff ` command as in the examples above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands, or by mixing as +:doc:`pair_coeff ` command as in the examples above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -385,15 +385,15 @@ The default mix value is *geometric*\ . See the "pair\_modify" command for details. All of the *lj/cut* pair styles support the -:doc:`pair\_modify ` shift option for the energy of the +:doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction. The *lj/cut/coul/long* and *lj/cut/tip4p/long* pair styles support the -:doc:`pair\_modify ` table option since they can tabulate +:doc:`pair_modify ` table option since they can tabulate the short-range portion of the long-range Coulombic interaction. All of the *lj/cut* pair styles support the -:doc:`pair\_modify ` tail option for adding a long-range +:doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure for the Lennard-Jones portion of the pair interaction. @@ -401,10 +401,10 @@ All of the *lj/cut* pair styles write their information to :doc:`binary restart not need to be specified in an input script that reads a restart file. The *lj/cut* and *lj/cut/coul/long* pair styles support the use of the -*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run\_style respa ` command, meaning the pairwise forces can be +*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. The other styles only support the *pair* keyword of run\_style respa. -See the :doc:`run\_style ` command for details. +See the :doc:`run_style ` command for details. ---------- @@ -423,7 +423,7 @@ more info. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst index 814eac69f9..e71627a364 100644 --- a/doc/src/pair_lj96.rst +++ b/doc/src/pair_lj96.rst @@ -41,9 +41,9 @@ of the standard 12/6 potential, given by Rc is the cutoff. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -86,13 +86,13 @@ and cutoff distance for all of the lj/cut pair styles can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style supports the :doc:`pair\_modify ` tail +This pair style supports the :doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure of the pair interaction. @@ -100,9 +100,9 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , and *outer* -keywords of the :doc:`run\_style respa ` command, meaning the +keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of -the rRESPA hierarchy. See the :doc:`run\_style ` command for +the rRESPA hierarchy. See the :doc:`run_style ` command for details. @@ -116,7 +116,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst index e03e70cb6b..dcfcc7167c 100644 --- a/doc/src/pair_lj_cubic.rst +++ b/doc/src/pair_lj_cubic.rst @@ -54,9 +54,9 @@ This potential is commonly used to study the shock mechanics of FCC solids, as in Ravelo et al. :ref:`(Ravelo) `. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the example above, +via the :doc:`pair_coeff ` command as in the example above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -101,15 +101,15 @@ The default mix value is *geometric*\ . See the "pair\_modify" command for details. The lj/cubic pair style does not support the -:doc:`pair\_modify ` shift option, +:doc:`pair_modify ` shift option, since pair interaction is already smoothed to 0.0 at the cutoff. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. The lj/cubic pair style does not support the -:doc:`pair\_modify ` tail option for adding long-range tail +:doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure, since there are no corrections for a potential that goes to 0.0 at the cutoff. @@ -117,7 +117,7 @@ The lj/cubic pair style writes its information to :doc:`binary restart files ` command. It does not +keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -131,7 +131,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst index 45a56219c4..606cead480 100644 --- a/doc/src/pair_lj_expand.rst +++ b/doc/src/pair_lj_expand.rst @@ -59,9 +59,9 @@ actual force cutoff is the sum of cutoff + delta. For all of the *lj/expand* pair styles, the following coefficients must be defined for each pair of atoms types via the -:doc:`pair\_coeff ` command as in the examples above, or in -the data file or restart files read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands, or by mixing as +:doc:`pair_coeff ` command as in the examples above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -112,13 +112,13 @@ coefficients are mixed according to the pair\_modify mix value. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style supports the :doc:`pair\_modify ` tail +This pair style supports the :doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure of the pair interaction. @@ -126,7 +126,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -140,7 +140,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index c6f17e2eb8..40d5688a33 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -125,16 +125,16 @@ calculation, so you can test the trade-off for your model. If *flag\_lj* is set to *long*\ , no cutoff is used on the LJ 1/r\^6 dispersion term. The long-range portion can be calculated by using -the :doc:`kspace\_style ewald/disp or pppm/disp ` commands. +the :doc:`kspace_style ewald/disp or pppm/disp ` commands. The specified LJ cutoff then determines which portion of the LJ interactions are computed directly by the pair potential versus which part is computed in reciprocal space via the Kspace style. If *flag\_lj* is set to *cut*\ , the LJ interactions are simply cutoff, as -with :doc:`pair\_style lj/cut `. +with :doc:`pair_style lj/cut `. If *flag\_coul* is set to *long*\ , no cutoff is used on the Coulombic interactions. The long-range portion can calculated by using any of -several :doc:`kspace\_style ` command options such as +several :doc:`kspace_style ` command options such as *pppm* or *ewald*\ . Note that if *flag\_lj* is also set to long, then the *ewald/disp* or *pppm/disp* Kspace style needs to be used to perform the long-range calculations for both the LJ and Coulombic @@ -142,9 +142,9 @@ interactions. If *flag\_coul* is set to *off*\ , Coulombic interactions are not computed. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -216,15 +216,15 @@ and cutoff distance for all of the lj/long pair styles can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -These pair styles support the :doc:`pair\_modify ` shift +These pair styles support the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction, assuming *flag\_lj* is *cut*\ . -These pair styles support the :doc:`pair\_modify ` table and +These pair styles support the :doc:`pair_modify ` table and table/disp options since they can tabulate the short-range portion of the long-range Coulombic and dispersion interactions. -Thes pair styles do not support the :doc:`pair\_modify ` +Thes pair styles do not support the :doc:`pair_modify ` tail option for adding a long-range tail correction to the Lennard-Jones portion of the energy and pressure. @@ -232,10 +232,10 @@ These pair styles write their information to :doc:`binary restart files ` +*middle*\ , and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of the rRESPA hierarchy. See the -:doc:`run\_style ` command for details. +:doc:`run_style ` command for details. ---------- @@ -251,7 +251,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index 6120faa24a..4b3c206ef5 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -50,12 +50,12 @@ and its 1st derivative will be 0.0. The inner cutoff cannot be 0.0. in its values and 1st derivative. This can lead to poor energy conservation and may require the use of a thermostat. Plot the energy and force resulting from this formula via the - :doc:`pair\_write ` command to see the effect. + :doc:`pair_write ` command to see the effect. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -101,13 +101,13 @@ coefficients are mixed according to the pair\_modify mix option. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure, since the energy of the pair interaction is smoothed to 0.0 at the cutoff. @@ -116,7 +116,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -130,7 +130,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair lj/smooth/linear ` +:doc:`pair_coeff `, :doc:`pair lj/smooth/linear ` **Default:** none diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst index 13dc334719..d400552ca1 100644 --- a/doc/src/pair_lj_smooth_linear.rst +++ b/doc/src/pair_lj_smooth_linear.rst @@ -39,9 +39,9 @@ continuously to zero at the cutoff Rc :ref:`(Toxvaerd) `: :align: center The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -83,14 +83,14 @@ For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance can be mixed. The default mix value is geometric. See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction, since it goes to 0.0 at the cutoff by construction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure, since the energy of the pair interaction is smoothed to 0.0 at the cutoff. @@ -99,7 +99,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -113,7 +113,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair lj/smooth ` +:doc:`pair_coeff `, :doc:`pair lj/smooth ` **Default:** none diff --git a/doc/src/pair_lj_switch3_coulgauss_long.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst index dd4040c595..3a885784a3 100644 --- a/doc/src/pair_lj_switch3_coulgauss_long.rst +++ b/doc/src/pair_lj_switch3_coulgauss_long.rst @@ -59,16 +59,16 @@ where qi and qj are the charges on the 2 atoms, epsilon is the dielectric constant which can be set by the :doc:`dielectric ` command, gamma\_i and gamma\_j are the widths of the Gaussian charge distribution and erf() is the error-function. -This style has to be used in conjunction with the :doc:`kspace\_style ` command +This style has to be used in conjunction with the :doc:`kspace_style ` command If one cutoff is specified it is used for both the vdW and Coulomb terms. If two cutoffs are specified, the first is used as the cutoff for the vdW terms, and the second is the cutoff for the Coulombic term. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * epsilon (energy) @@ -94,7 +94,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_local_density.rst b/doc/src/pair_local_density.rst index 2a9d4068b7..7cea5ef807 100644 --- a/doc/src/pair_local_density.rst +++ b/doc/src/pair_local_density.rst @@ -201,7 +201,7 @@ types (alpha, beta) and (beta, alpha) if need be (Here, the notation (alpha, beta) means that alpha is the central atom to which the LD potential is applied and beta is the neighbor atom which contributes to the LD potential on alpha). -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The local/density pair style does not write its information to :doc:`binary restart files `, since it is stored in tabulated potential files. @@ -222,7 +222,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index b9033be48d..c6aa16fe00 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -98,7 +98,7 @@ as long as *flagVF* is set to 1 (default). When using the FLD terms, these pair styles are designed to be used with explicit time integration and a correspondingly small timestep. Thus either :doc:`fix nve/sphere ` or :doc:`fix nve/asphere ` should be used for time integration. - To perform implicit FLD, see the :doc:`pair\_style lubricateU ` command. + To perform implicit FLD, see the :doc:`pair_style lubricateU ` command. Style *lubricate* requires monodisperse spherical particles; style *lubricate/poly* allows for polydisperse spherical particles. @@ -129,7 +129,7 @@ boundaries. Since lubrication forces are dissipative, it is usually desirable to thermostat the system at a constant temperature. If Brownian motion (at a constant temperature) is desired, it can be set using the -:doc:`pair\_style brownian ` command. These pair styles +:doc:`pair_style brownian ` command. These pair styles and the brownian style should use consistent parameters for *mu*\ , *flaglog*\ , *flagfld*\ , *cutinner*\ , *cutoff*\ , *flagHI* and *flagVF*\ . @@ -138,9 +138,9 @@ and the brownian style should use consistent parameters for *mu*\ , The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutinner (distance units) @@ -182,13 +182,13 @@ For atom type pairs I,J and I != J, the two cutoff distances for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -196,7 +196,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -216,15 +216,15 @@ lubricate. Only spherical particles are allowed for pair\_style lubricate/poly. These pair styles will not restart exactly when using the -:doc:`read\_restart ` command, though they should provide +:doc:`read_restart ` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the -:doc:`read\_restart ` command for more details. +:doc:`read_restart ` command for more details. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style lubricateU ` +:doc:`pair_coeff `, :doc:`pair_style lubricateU ` Default """"""" diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst index bf0a39c56e..b50eb18467 100644 --- a/doc/src/pair_lubricateU.rst +++ b/doc/src/pair_lubricateU.rst @@ -105,8 +105,8 @@ computed. When using these styles, the these pair styles are designed to be used with implicit time integration and a correspondingly larger timestep. Thus either :doc:`fix nve/noforce ` should - be used for spherical particles defined via :doc:`atom\_style sphere ` or :doc:`fix nve/asphere/noforce ` should be used for - spherical particles defined via :doc:`atom\_style ellipsoid `. This is because the velocity and angular + be used for spherical particles defined via :doc:`atom_style sphere ` or :doc:`fix nve/asphere/noforce ` should be used for + spherical particles defined via :doc:`atom_style ellipsoid `. This is because the velocity and angular momentum of each particle is set by the pair style, and should not be reset by the time integration fix. @@ -134,7 +134,7 @@ fix wall command. Since lubrication forces are dissipative, it is usually desirable to thermostat the system at a constant temperature. If Brownian motion (at a constant temperature) is desired, it can be set using the -:doc:`pair\_style brownian ` command. These pair styles +:doc:`pair_style brownian ` command. These pair styles and the brownian style should use consistent parameters for *mu*\ , *flaglog*\ , *flagfld*\ , *cutinner*\ , *cutoff*\ , *flagHI* and *flagVF*\ . @@ -143,9 +143,9 @@ and the brownian style should use consistent parameters for *mu*\ , The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutinner (distance units) @@ -165,13 +165,13 @@ For atom type pairs I,J and I != J, the two cutoff distances for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -179,7 +179,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -212,7 +212,7 @@ velocity-gradient direction. In this case, one must use :doc:`fix deform `, :doc:`pair\_style lubricate ` +:doc:`pair_coeff `, :doc:`pair_style lubricate ` Default """"""" diff --git a/doc/src/pair_mdf.rst b/doc/src/pair_mdf.rst index 181b7929a7..4174a516d3 100644 --- a/doc/src/pair_mdf.rst +++ b/doc/src/pair_mdf.rst @@ -90,7 +90,7 @@ standard 12-6 Lennard-Jones written in the epsilon/sigma form: Either the first two or all of the following coefficients must be defined for each pair of atoms types via the pair\_coeff command as in the examples above, or in the data file read by the -:doc:`read\_data `. The two cutoffs default to the global +:doc:`read_data `. The two cutoffs default to the global values and epsilon and sigma can also be determined by mixing as described below: @@ -152,13 +152,13 @@ support mixing, so all I,J pairs of coefficients must be specified explicitly. None of the lj/mdf, buck/mdf, or lennard/mdf pair styles supports -the :doc:`pair\_modify ` shift option or long-range +the :doc:`pair_modify ` shift option or long-range tail corrections to pressure and energy. These styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. -These styles can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. They do not support the *inner*\ , +These styles can only be used via the *pair* keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -176,7 +176,7 @@ page for more info. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index 68ccc829c9..d8cf53a66d 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -56,7 +56,7 @@ element. The cutoffs and the coefficients for these spline functions are listed in a parameter file which is specified by the -:doc:`pair\_coeff ` command. Parameter files for different +:doc:`pair_coeff ` command. Parameter files for different elements are included in the "potentials" directory of the LAMMPS distribution and have a ".meam.spline" file suffix. All of these files are parameterized in terms of LAMMPS :doc:`metal units `. @@ -79,7 +79,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of spline-based MEAM elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine the Ti.meam.spline file has values for Ti (old style). If @@ -143,7 +143,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The *meam/spline* pair style does not write its information to :doc:`binary restart files `, since it is stored in an external @@ -151,7 +151,7 @@ potential parameter file. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. The *meam/spline* pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -172,7 +172,7 @@ info. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style meam/c ` +:doc:`pair_coeff `, :doc:`pair_style meam/c ` **Default:** none diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst index 9331b5f36a..847ce797a1 100644 --- a/doc/src/pair_meam_sw_spline.rst +++ b/doc/src/pair_meam_sw_spline.rst @@ -41,7 +41,7 @@ Phi, F, G, U, rho, f, and g are represented by cubic splines. The cutoffs and the coefficients for these spline functions are listed in a parameter file which is specified by the -:doc:`pair\_coeff ` command. Parameter files for different +:doc:`pair_coeff ` command. Parameter files for different elements are included in the "potentials" directory of the LAMMPS distribution and have a ".meam.sw.spline" file suffix. All of these files are parameterized in terms of LAMMPS :doc:`metal units `. @@ -64,7 +64,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of spline-based MEAM+SW elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine the Ti.meam.sw.spline file has values for Ti. @@ -100,7 +100,7 @@ in the examples/USER/misc/meam\_sw\_spline directory. The pair style does not support multiple element types or mixing. It has been designed for pure elements only. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The *meam/sw/spline* pair style does not write its information to @@ -109,7 +109,7 @@ potential parameter file. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. The *meam/sw/spline* pair style can only be used via the *pair* -keyword of the :doc:`run\_style respa ` command. They do not +keyword of the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -130,8 +130,8 @@ info. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style meam/c `, -:doc:`pair\_style meam/spline ` +:doc:`pair_coeff `, :doc:`pair_style meam/c `, +:doc:`pair_style meam/spline ` **Default:** none diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meamc.rst index ac858ce24b..0240e683da 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meamc.rst @@ -58,7 +58,7 @@ computation of the embedding and pair energies, as implemented in LAMMPS, are given in :ref:`(Gullet) ` and references therein. The various parameters in the MEAM formulas are listed in two files -which are specified by the :doc:`pair\_coeff ` command. +which are specified by the :doc:`pair_coeff ` command. These are ASCII text files in a format consistent with other MD codes that implement MEAM potentials, such as the serial DYNAMO code and Warp. Several MEAM potential files with parameters for different @@ -81,7 +81,7 @@ command, where N is the number of LAMMPS atom types: * MEAM parameter file * N element names = mapping of MEAM elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential files. As an example, the potentials/library.meam file has generic MEAM @@ -382,7 +382,7 @@ two different element types, mixing is performed by LAMMPS with user-specifiable parameters as described above. You never need to specify a pair\_coeff command with I != J arguments for this style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -390,7 +390,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -415,8 +415,8 @@ limit on the number of atoms types. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style eam `, -:doc:`pair\_style meam/spline ` +:doc:`pair_coeff `, :doc:`pair_style eam `, +:doc:`pair_style meam/spline ` **Default:** none diff --git a/doc/src/pair_meso.rst b/doc/src/pair_meso.rst index b4a945409d..d645c4ab03 100644 --- a/doc/src/pair_meso.rst +++ b/doc/src/pair_meso.rst @@ -99,7 +99,7 @@ with υ being the kinematic viscosity. For more details, see Eq.(15) in :ref:`(Li2014\_JCP) `. The following coefficients must be defined in eDPD system for each -pair of atom types via the :doc:`pair\_coeff ` command as in +pair of atom types via the :doc:`pair_coeff ` command as in the examples above. * A (force units) @@ -133,7 +133,7 @@ The *mdpd/rhosum* style computes the local particle mass density rho for mDPD particles by kernel function interpolation. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above. +via the :doc:`pair_coeff ` command as in the examples above. * cutoff (distance units) @@ -157,7 +157,7 @@ term with B > 0 is the density-dependent repulsive force within an interaction range rd. The following coefficients must be defined for each pair of atom types via the -:doc:`pair\_coeff ` command as in the examples above. +:doc:`pair_coeff ` command as in the examples above. * A (force units) * B (force units) @@ -201,7 +201,7 @@ a tDPD particle m. For more details, see :ref:`(Li2015\_JCP) `. The following coefficients must be defined for each pair of atom types via the -:doc:`pair\_coeff ` command as in the examples above. +:doc:`pair_coeff ` command as in the examples above. * A (force units) * gamma (force/velocity units) @@ -272,7 +272,7 @@ The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not support -the :doc:`pair\_modify ` shift, table, and tail options. +the :doc:`pair_modify ` shift, table, and tail options. The styles *edpd*\ , *mdpd*\ , *mdpd/rhosum* and *tdpd* do not write information to :doc:`binary restart files `. Thus, you need @@ -291,7 +291,7 @@ more info. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix mvv/dpd `, +:doc:`pair_coeff `, :doc:`fix mvv/dpd `, :doc:`fix mvv/edpd `, :doc:`fix mvv/tdpd `, :doc:`fix edpd/source `, :doc:`fix tdpd/source `, :doc:`compute edpd/temp/atom `, diff --git a/doc/src/pair_mesocnt.rst b/doc/src/pair_mesocnt.rst index 30de8a07aa..566a6125c1 100644 --- a/doc/src/pair_mesocnt.rst +++ b/doc/src/pair_mesocnt.rst @@ -51,7 +51,7 @@ original papers :ref:`(Volkov1) ` and :ref:`(Volkov2) `. The potential requires tabulated data provided in a single ASCII -text file specified in the :doc:`pair\_coeff ` command. +text file specified in the :doc:`pair_coeff ` command. The first line of the file provides a time stamp and general information. The second line lists four integers giving the number of data points provided in the subsequent four @@ -105,7 +105,7 @@ Communications. This pair style does not support mixing. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. The *mesocnt* pair style do not write their information to :doc:`binary restart files `, @@ -114,7 +114,7 @@ Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -134,7 +134,7 @@ This pair potential requires the :doc:`newton ` setting to be Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst index 1c43d47b00..0981502635 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -64,7 +64,7 @@ algorithms have been developed independently by Glosli The *mgpt* pair style calculates forces, energies, and the total energy per atom, E\_tot/N, using the Oppelstrup matrix-MGPT algorithm. Input potential and control data are entered through the -:doc:`pair\_coeff ` command. Each material treated requires +:doc:`pair_coeff ` command. Each material treated requires input parmin and potin potential files, as shown in the above examples, as well as specification by the user of the initial atomic volume Omega through pair\_coeff. At the beginning of a time step in @@ -83,7 +83,7 @@ time step, and then respecified at the new value of Omega. In all simulations, Omega must remain within the defined volume range for E\_vol and the potentials for the given material. -The default option volpress yes in the :doc:`pair\_coeff ` +The default option volpress yes in the :doc:`pair_coeff ` command includes all volume derivatives of E\_tot required to calculate the stress tensor and pressure correctly. The option volpress no disregards the pressure contribution resulting from the volume term @@ -109,7 +109,7 @@ routines. For x-86 machines, there is a provided Makefile.mgptfast which enables the fast algebra routines, i.e. build LAMMPS with "make mgptfast". The user will be informed in the output files of the matrix kernels in use. To further improve speed, on x86 the option -precision single can be added to the :doc:`pair\_coeff ` +precision single can be added to the :doc:`pair_coeff ` command line, which improves speed (up to a factor of two) at the cost of doing matrix calculations with 7 digit precision instead of the default 16. For consistency the default option can be specified @@ -151,7 +151,7 @@ before proceeding to more complex simulations. **Mixing, shift, table tail correction, restart**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -159,7 +159,7 @@ needs to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -201,12 +201,12 @@ such cases will be added over time. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` Default """"""" -The options defaults for the :doc:`pair\_coeff ` command are +The options defaults for the :doc:`pair_coeff ` command are volpress yes, nbody 1234, and precision double. diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst index ba94830475..a516bdd3c0 100644 --- a/doc/src/pair_mie.rst +++ b/doc/src/pair_mie.rst @@ -45,9 +45,9 @@ Note that for 12/6 exponents, C is equal to 4 and the formula is the same as the standard Lennard-Jones potential. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -72,10 +72,10 @@ exponents for different atoms will be calculated following the same mixing rule defined for distances. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -This pair style supports the :doc:`pair\_modify ` tail +This pair style supports the :doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure of the pair interaction. @@ -83,9 +83,9 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , and *outer* -keywords of the :doc:`run\_style respa ` command, meaning the +keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be partitioned by distance at different levels of -the rRESPA hierarchy. See the :doc:`run\_style ` command for +the rRESPA hierarchy. See the :doc:`run_style ` command for details. @@ -99,7 +99,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst index 3f3a7cbc72..f100f9202d 100644 --- a/doc/src/pair_mm3_switch3_coulgauss_long.rst +++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst @@ -59,16 +59,16 @@ where qi and qj are the charges on the 2 atoms, epsilon is the dielectric constant which can be set by the :doc:`dielectric ` command, gamma\_i and gamma\_j are the widths of the Gaussian charge distribution and erf() is the error-function. -This style has to be used in conjunction with the :doc:`kspace\_style ` command +This style has to be used in conjunction with the :doc:`kspace_style ` command If one cutoff is specified it is used for both the vdW and Coulomb terms. If two cutoffs are specified, the first is used as the cutoff for the vdW terms, and the second is the cutoff for the Coulombic term. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * epsilon (energy) @@ -96,7 +96,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index b45a50573a..dee1390234 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -66,7 +66,7 @@ following parameters will only be modified for the specified sub-style. If the sub-style is defined multiple times, then an additional numeric argument *N* must also be specified, which is a number from 1 to M where M is the number of times the sub-style was -listed in the :doc:`pair\_style hybrid ` command. The extra +listed in the :doc:`pair_style hybrid ` command. The extra number indicates which instance of the sub-style the remaining keywords will be applied to. Note that if the *pair* keyword is not used, and the pair style is *hybrid* or *hybrid/overlay*\ , then all the @@ -75,7 +75,7 @@ specified keywords will be applied to all sub-styles. The *special* and *compute/tally* keywords can **only** be used in conjunction with the *pair* keyword and must directly follow it. *special* allows to override the -:doc:`special\_bonds ` settings for the specified sub-style. +:doc:`special_bonds ` settings for the specified sub-style. *compute/tally* allows to disable or enable registering :doc:`compute \*/tally ` computes for a given sub-style. More details are given below. @@ -93,7 +93,7 @@ In each case, the cutoff distance is mixed the same way as sigma. Note that not all pair styles support mixing. Also, some mix options are not available for certain pair styles. See the doc page for individual pair styles for those restrictions. Note also that the -:doc:`pair\_coeff ` command also can be to directly set +:doc:`pair_coeff ` command also can be to directly set coefficients for a specific I != J pairing, in which case no mixing is performed. @@ -168,7 +168,7 @@ These corrections are bookkeeping terms which do not affect dynamics, unless a constant-pressure simulation is being performed. See the doc page for individual styles to see which support this option. These corrections are included in the calculation and printing of -thermodynamic quantities (see the :doc:`thermo\_style ` +thermodynamic quantities (see the :doc:`thermo_style ` command). Their effect will also be included in constant NPT or NPH simulations where the pressure influences the simulation box dimensions (e.g. the :doc:`fix npt ` and :doc:`fix nph ` @@ -214,19 +214,19 @@ including the following: The *compute* keyword allows pairwise computations to be turned off, -even though a :doc:`pair\_style ` is defined. This is not +even though a :doc:`pair_style ` is defined. This is not useful for running a real simulation, but can be useful for debugging purposes or for performing a :doc:`rerun ` simulation, when you only wish to compute partial forces that do not include the pairwise contribution. Two examples are as follows. First, this option allows you to perform -a simulation with :doc:`pair\_style hybrid ` with only a +a simulation with :doc:`pair_style hybrid ` with only a subset of the hybrid sub-styles enabled. Second, this option allows you to perform a simulation with only long-range interactions but no short-range pairwise interactions. Doing this by simply not defining a pair style will not work, because the -:doc:`kspace\_style ` command requires a Kspace-compatible +:doc:`kspace_style ` command requires a Kspace-compatible pair style be defined. The *nofdotr* keyword allows to disable an optimization that computes @@ -240,7 +240,7 @@ than from summing forces between individual pairs of atoms. The *special* keyword allows to override the 1-2, 1-3, and 1-4 exclusion settings for individual sub-styles of a :doc:`hybrid pair style `. It requires 4 arguments similar -to the :doc:`special\_bonds ` command, *which* and +to the :doc:`special_bonds ` command, *which* and wt1,wt2,wt3. The *which* argument can be *lj* to change the Lennard-Jones settings, *coul* to change the Coulombic settings, or *lj/coul* to change both to the same set of 3 values. The wt1,wt2,wt3 @@ -254,7 +254,7 @@ it will cause an error. .. note:: The global settings specified by the - :doc:`special\_bonds ` command affect the construction of + :doc:`special_bonds ` command affect the construction of neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors) exclude those pairs from the neighbor list entirely. Weights of 1.0 store the neighbor with no weighting applied. Thus only global values @@ -289,8 +289,8 @@ USER-INTEL package. Related commands """""""""""""""" -:doc:`pair\_style `, :doc:`pair\_style hybrid `, -pair\_coeff"_pair\_coeff.html, :doc:`thermo\_style `, +:doc:`pair_style `, :doc:`pair_style hybrid `, +pair\_coeff"_pair\_coeff.html, :doc:`thermo_style `, :doc:`compute \*/tally ` Default diff --git a/doc/src/pair_momb.rst b/doc/src/pair_momb.rst index e318d285a3..0bc3e41310 100644 --- a/doc/src/pair_momb.rst +++ b/doc/src/pair_momb.rst @@ -40,9 +40,9 @@ dispersion in density functional theory calculations. :align: center For the *momb* pair style, the following coefficients must be defined -for each pair of atoms types via the :doc:`pair\_coeff ` +for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files -read by the :doc:`read\_data ` as described below: +read by the :doc:`read_data ` as described below: * D0 (energy units) * alpha (1/distance units) @@ -64,7 +64,7 @@ LAMMPS is built with that package. See the :doc:`Build package ` Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style morse ` +:doc:`pair_coeff `, :doc:`pair_style morse ` **Default:** none diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index 61f2e08904..ac1c106b06 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -62,9 +62,9 @@ Style *morse* computes pairwise interactions with the formula Rc is the cutoff. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * D0 (energy units) @@ -129,13 +129,13 @@ instructions on how to use the accelerated styles effectively. None of these pair styles support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -All of these pair styles support the :doc:`pair\_modify ` +All of these pair styles support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table options is not relevant for +The :doc:`pair_modify ` table options is not relevant for the Morse pair styles. -None of these pair styles support the :doc:`pair\_modify ` +None of these pair styles support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -143,7 +143,7 @@ All of these pair styles write their information to :doc:`binary restart files < to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -160,7 +160,7 @@ built with the USER-MISC package. See the :doc:`Build package ` Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_fep\_soft ` +:doc:`pair_coeff `, :doc:`pair\_fep\_soft ` **Default:** none diff --git a/doc/src/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst index cd2032c799..512ce07bd7 100644 --- a/doc/src/pair_multi_lucy.rst +++ b/doc/src/pair_multi_lucy.rst @@ -70,7 +70,7 @@ table values from which the density-dependent energy and force are computed by linear interpolation. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * filename @@ -117,7 +117,7 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`pair\_style multi/lucy ` command. +specified in the :doc:`pair_style multi/lucy ` command. Let Ntable = *N* in the pair\_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It @@ -174,7 +174,7 @@ one that matches the specified keyword. This pair style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -The :doc:`pair\_modify ` shift, table, and tail options are +The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. This pair style writes the settings for the "pair\_style multi/lucy" command @@ -185,7 +185,7 @@ file, since it is tabulated in the potential files. Thus, pair\_coeff commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -202,7 +202,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index 977309e311..7a7f5cbb47 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -83,7 +83,7 @@ table values from which the density-dependent energy and force are computed by linear interpolation. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * filename @@ -145,7 +145,7 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`pair\_style multi/lucy/rx ` +specified in the :doc:`pair_style multi/lucy/rx ` command. Let Ntable = *N* in the pair\_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as @@ -203,7 +203,7 @@ one that matches the specified keyword. This pair style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -The :doc:`pair\_modify ` shift, table, and tail options are +The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. This pair style writes the settings for the "pair\_style multi/lucy/rx" command @@ -214,7 +214,7 @@ file, since it is tabulated in the potential files. Thus, pair\_coeff commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -253,7 +253,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** fractional weighting diff --git a/doc/src/pair_nb3b_harmonic.rst b/doc/src/pair_nb3b_harmonic.rst index ef00dec25a..bc26e9b5ae 100644 --- a/doc/src/pair_nb3b_harmonic.rst +++ b/doc/src/pair_nb3b_harmonic.rst @@ -43,7 +43,7 @@ number of LAMMPS atom types: * filename * N element names = mapping of elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.nb3b.harmonic has potential values @@ -109,7 +109,7 @@ info. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst index e188ce1d1f..d0ef9efdf5 100644 --- a/doc/src/pair_nm.rst +++ b/doc/src/pair_nm.rst @@ -88,7 +88,7 @@ cutoffs for the NM and Coulombic terms respectively. Styles *nm/cut/coul/long* compute the same Coulombic interactions as style *nm/cut/coul/cut* except that an additional damping factor is applied to the Coulombic term so it can -be used in conjunction with the :doc:`kspace\_style ` +be used in conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are @@ -96,9 +96,9 @@ computed in reciprocal space. For all of the *nm* pair styles, the following coefficients must be defined for each pair of atoms types -via the :doc:`pair\_coeff ` command as in the +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands. * E0 (energy units) @@ -131,14 +131,14 @@ These pair styles do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. All of the *nm* pair styles supports the -:doc:`pair\_modify ` shift option for the energy of the pair +:doc:`pair_modify ` shift option for the energy of the pair interaction. The *nm/cut/coul/long* pair styles support the -:doc:`pair\_modify ` table option since they can tabulate +:doc:`pair_modify ` table option since they can tabulate the short-range portion of the long-range Coulombic interaction. -All of the *nm* pair styles support the :doc:`pair\_modify ` +All of the *nm* pair styles support the :doc:`pair_modify ` tail option for adding a long-range tail correction to the energy and pressure for the NM portion of the pair interaction. @@ -146,7 +146,7 @@ All of the *nm* pair styles write their information to :doc:`binary restart file to be specified in an input script that reads a restart file. All of the *nm* pair styles can only be used via the *pair* keyword of -the :doc:`run\_style respa ` command. They do not support the +the :doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -181,7 +181,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_none.rst b/doc/src/pair_none.rst index 080bb1168a..04a763b8e0 100644 --- a/doc/src/pair_none.rst +++ b/doc/src/pair_none.rst @@ -38,7 +38,7 @@ distance is small, then these data structures can consume a large amount of memory. So you should either set the neighbor style to *nsq* or set the skin distance to a larger value. -See the :doc:`pair\_style zero ` for a way to trigger the +See the :doc:`pair_style zero ` for a way to trigger the building of a neighbor lists, but compute no pairwise interactions. Restrictions @@ -48,7 +48,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_style zero ` +:doc:`pair_style zero ` **Default:** none diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index 727f19c327..2f6be35608 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -82,7 +82,7 @@ for a detailed description of the oxDNA force field. These pair styles have to be used together with the related oxDNA bond style *oxdna/fene* for the connectivity of the phosphate backbone (see also documentation of - :doc:`bond\_style oxdna/fene `). Most of the coefficients + :doc:`bond_style oxdna/fene `). Most of the coefficients in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. Exceptions are the first four coefficients after *oxdna/stk* (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example) and the first coefficient after *oxdna/hbond* (seq=seqdep in the above example). @@ -118,9 +118,9 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the Related commands """""""""""""""" -:doc:`bond\_style oxdna/fene `, :doc:`pair\_coeff `, -:doc:`bond\_style oxdna2/fene `, :doc:`pair\_style oxdna2/excv `, -:doc:`bond\_style oxrna2/fene `, :doc:`pair\_style oxrna2/excv `, +:doc:`bond_style oxdna/fene `, :doc:`pair_coeff `, +:doc:`bond_style oxdna2/fene `, :doc:`pair_style oxdna2/excv `, +:doc:`bond_style oxrna2/fene `, :doc:`pair_style oxrna2/excv `, :doc:`fix nve/dotc/langevin ` **Default:** none diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index 77052da666..c57eb86c1d 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -90,7 +90,7 @@ and :ref:`(Ouldridge) ` for a detailed description of the oxDNA2 fo These pair styles have to be used together with the related oxDNA2 bond style *oxdna2/fene* for the connectivity of the phosphate backbone (see also documentation of - :doc:`bond\_style oxdna2/fene `). Most of the coefficients + :doc:`bond_style oxdna2/fene `). Most of the coefficients in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. Exceptions are the first four coefficients after *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example), the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients @@ -124,9 +124,9 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the Related commands """""""""""""""" -:doc:`bond\_style oxdna2/fene `, :doc:`pair\_coeff `, -:doc:`bond\_style oxdna/fene `, :doc:`pair\_style oxdna/excv `, -:doc:`bond\_style oxrna2/fene `, :doc:`pair\_style oxrna2/excv `, +:doc:`bond_style oxdna2/fene `, :doc:`pair_coeff `, +:doc:`bond_style oxdna/fene `, :doc:`pair_style oxdna/excv `, +:doc:`bond_style oxrna2/fene `, :doc:`pair_style oxrna2/excv `, :doc:`fix nve/dotc/langevin ` **Default:** none diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index 3cc6e7f4a6..38e77e3368 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -91,7 +91,7 @@ and :ref:`(Ouldridge) ` for a detailed description of the oxRNA2 fo These pair styles have to be used together with the related oxDNA2 bond style *oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of - :doc:`bond\_style oxrna2/fene `). Most of the coefficients + :doc:`bond_style oxrna2/fene `). Most of the coefficients in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. Exceptions are the first four coefficients after *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 in the above example), the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients @@ -125,9 +125,9 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the Related commands """""""""""""""" -:doc:`bond\_style oxrna2/fene `, :doc:`pair\_coeff `, -:doc:`bond\_style oxdna/fene `, :doc:`pair\_style oxdna/excv `, -:doc:`bond\_style oxdna2/fene `, :doc:`pair\_style oxdna2/excv `, +:doc:`bond_style oxrna2/fene `, :doc:`pair_coeff `, +:doc:`bond_style oxdna/fene `, :doc:`pair_style oxdna/excv `, +:doc:`bond_style oxdna2/fene `, :doc:`pair_style oxdna2/excv `, :doc:`fix nve/dotc/langevin ` **Default:** diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst index 284f3de32a..c618aeccca 100644 --- a/doc/src/pair_peri.rst +++ b/doc/src/pair_peri.rst @@ -81,9 +81,9 @@ regarding the VES and EPS models in LAMMPS you can contact R. Rahman (rezwanur.rahman at utsa.edu). The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below. For the *peri/pmb* style: @@ -177,17 +177,17 @@ instructions on how to use the accelerated styles effectively. These pair styles do not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -These pair styles do not support the :doc:`pair\_modify ` +These pair styles do not support the :doc:`pair_modify ` shift option. -The :doc:`pair\_modify ` table and tail options are not +The :doc:`pair_modify ` table and tail options are not relevant for these pair styles. These pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. These pair styles can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. They do not support the +:doc:`run_style respa ` command. They do not support the *inner*\ , *middle*\ , *outer* keywords. @@ -204,7 +204,7 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index e9ab595011..ff522ae6b0 100644 --- a/doc/src/pair_polymorphic.rst +++ b/doc/src/pair_polymorphic.rst @@ -205,7 +205,7 @@ for the F(X) functions. **Mixing, shift, table tail correction, restart**\ : -This pair styles does not support the :doc:`pair\_modify ` +This pair styles does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write their information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -238,7 +238,7 @@ files. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` ---------- diff --git a/doc/src/pair_python.rst b/doc/src/pair_python.rst index 53480ff286..a962bdb7ca 100644 --- a/doc/src/pair_python.rst +++ b/doc/src/pair_python.rst @@ -38,7 +38,7 @@ interpreted language, however, the performance of this pair style is going to be significantly slower (often between 20x and 100x) than corresponding compiled code. This penalty can be significantly reduced through generating tabulations from the python code through the -:doc:`pair\_write ` command, which is supported by this style. +:doc:`pair_write ` command, which is supported by this style. Only a single pair\_coeff command is used with the *python* pair style which specifies a python class inside a python module or file that @@ -177,7 +177,7 @@ the *LJCutMelt* example, here are the two functions: computation pair-wise interactions quite significantly. However, this can be largely worked around through using the python pair style not for the actual simulation, but to generate tabulated potentials on the - fly using the :doc:`pair\_write ` command. Please see below + fly using the :doc:`pair_write ` command. Please see below for an example LAMMPS input of how to build a table file: @@ -219,7 +219,7 @@ energy computation can be correctly performed for all pairs of atom types as they are mapped to the atom type labels inside the python potential class. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -227,7 +227,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -244,7 +244,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_write `, +:doc:`pair_coeff `, :doc:`pair_write `, :doc:`pair style table ` **Default:** none diff --git a/doc/src/pair_quip.rst b/doc/src/pair_quip.rst index 3e953afebc..293d76443e 100644 --- a/doc/src/pair_quip.rst +++ b/doc/src/pair_quip.rst @@ -44,7 +44,7 @@ number of LAMMPS atom types: * QUIP initialization string * N atomic numbers = mapping of QUIP elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. A QUIP potential is fully specified by the filename which contains the @@ -62,7 +62,7 @@ directory. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -70,7 +70,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -84,7 +84,7 @@ QUIP potentials are parameterized in electron-volts and Angstroms and therefore should be used with LAMMPS metal :doc:`units `. QUIP potentials are generally not designed to work with the scaling -factors set by the :doc:`special\_bonds ` command. The +factors set by the :doc:`special_bonds ` command. The recommended setting in molecular systems is to include all interactions, i.e. to use *special\_bonds lj/coul 1.0 1.0 1.0*. Scaling factors > 0.0 will be ignored and treated as 1.0. The only exception @@ -98,7 +98,7 @@ required. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` ---------- diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxc.rst index b670711e8c..6040b78a77 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxc.rst @@ -116,8 +116,8 @@ Examples using *pair\_style reax/c* are provided in the examples/reax sub-directory. Use of this pair style requires that a charge be defined for every -atom. See the :doc:`atom\_style ` and -:doc:`read\_data ` commands for details on how to specify +atom. See the :doc:`atom_style ` and +:doc:`read_data ` commands for details on how to specify charges. The ReaxFF parameter files provided were created using a charge @@ -309,7 +309,7 @@ angle\_info: 1 prints angles in the trajectory file (default = 0) **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -317,7 +317,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -362,7 +362,7 @@ appropriate units if your simulation doesn't use "real" units. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix qeq/reax `, :doc:`fix reax/c/bonds `, :doc:`fix reax/c/species ` +:doc:`pair_coeff `, :doc:`fix qeq/reax `, :doc:`fix reax/c/bonds `, :doc:`fix reax/c/species ` Default """"""" diff --git a/doc/src/pair_resquared.rst b/doc/src/pair_resquared.rst index 2ddf7fb24d..b996ae1189 100644 --- a/doc/src/pair_resquared.rst +++ b/doc/src/pair_resquared.rst @@ -44,13 +44,13 @@ in `this supplementary document `_. Use of this pair style requires the NVE, NVT, or NPT fixes with the *asphere* extension (e.g. :doc:`fix nve/asphere `) in -order to integrate particle rotation. Additionally, :doc:`atom\_style ellipsoid ` should be used since it defines the +order to integrate particle rotation. Additionally, :doc:`atom_style ellipsoid ` should be used since it defines the rotational state and the size and shape of each ellipsoidal particle. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands: * A12 = Energy Prefactor/Hamaker constant (energy units) @@ -113,7 +113,7 @@ When one of both of the interacting particles are ellipsoids, then *sigma* specifies the diameter of the continuous distribution of constituent particles within each ellipsoid used to model the RE-squared potential. Note that this is a different meaning for -*sigma* than the :doc:`pair\_style gayberne ` potential +*sigma* than the :doc:`pair_style gayberne ` potential uses. The epsilon\_i and epsilon\_j coefficients are defined for atom types, @@ -132,7 +132,7 @@ J, you should insure they are consistent with their values in other pair\_coeff commands. Note that if this potential is being used as a sub-style of -:doc:`pair\_style hybrid `, and there is no "pair\_coeff I I" +:doc:`pair_style hybrid `, and there is no "pair\_coeff I I" setting made for RE-squared for a particular type I (because I-I interactions are computed by another hybrid pair potential), then you still need to insure the epsilon a,b,c coefficients are assigned to @@ -188,16 +188,16 @@ equation for the Hamaker constant presented here. Mixing of sigma and epsilon followed by calculation of the energy prefactors using the equations above is recommended. -This pair styles supports the :doc:`pair\_modify ` shift +This pair styles supports the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction, but only for sphere-sphere interactions. There is no shifting performed for ellipsoidal interactions due to the anisotropic dependence of the interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -205,8 +205,8 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the -*inner*\ , *middle*\ , *outer* keywords of the :doc:`run\_style command `. +:doc:`run_style respa ` command. It does not support the +*inner*\ , *middle*\ , *outer* keywords of the :doc:`run_style command `. ---------- @@ -220,7 +220,7 @@ This style is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This pair style requires that atoms be ellipsoids as defined by the -:doc:`atom\_style ellipsoid ` command. +:doc:`atom_style ellipsoid ` command. Particles acted on by the potential can be finite-size aspherical or spherical particles, or point particles. Spherical particles have all @@ -233,8 +233,8 @@ less accurate when high-aspect ratio ellipsoids are used. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix nve/asphere `, -:doc:`compute temp/asphere `, :doc:`pair\_style gayberne ` +:doc:`pair_coeff `, :doc:`fix nve/asphere `, +:doc:`compute temp/asphere `, :doc:`pair_style gayberne ` **Default:** none diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 17694067c8..1ad9bd9c59 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -78,16 +78,16 @@ as required for the SDK Coarse-grained MD parameterization discussed in Style *lj/sdk/coul/long* computes the adds Coulombic interactions with an additional damping factor applied so it can be used in -conjunction with the :doc:`kspace\_style ` command and +conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* or *pppm/cg* option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cg\_type (lj9\_6, lj12\_4, or lj12\_6) @@ -147,18 +147,18 @@ command. Defining then in a data file is also not supported, due to limitations of that file format. All of the lj/sdk pair styles support the -:doc:`pair\_modify ` shift option for the energy of the +:doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction. The *lj/sdk/coul/long* pair styles support the -:doc:`pair\_modify ` table option since they can tabulate +:doc:`pair_modify ` table option since they can tabulate the short-range portion of the long-range Coulombic interaction. All of the lj/sdk pair styles write their information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. The lj/sdk and lj/cut/coul/long pair styles do not support -the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run\_style respa ` command. +the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa ` command. ---------- @@ -177,7 +177,7 @@ doc page for more info. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`angle\_style sdk ` +:doc:`pair_coeff `, :doc:`angle_style sdk ` **Default:** none diff --git a/doc/src/pair_sdpd_taitwater_isothermal.rst b/doc/src/pair_sdpd_taitwater_isothermal.rst index ec4ada108b..5d970d382d 100644 --- a/doc/src/pair_sdpd_taitwater_isothermal.rst +++ b/doc/src/pair_sdpd_taitwater_isothermal.rst @@ -72,7 +72,7 @@ to formulas described in :ref:`(Espanol and Revenga) `. different MPI tasks have distinct seeds. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * rho0 reference density (mass/volume units) @@ -88,13 +88,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions diff --git a/doc/src/pair_smd_hertz.rst b/doc/src/pair_smd_hertz.rst index 5af530aabb..a7b004830f 100644 --- a/doc/src/pair_smd_hertz.rst +++ b/doc/src/pair_smd_hertz.rst @@ -59,7 +59,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_smd_tlsph.rst b/doc/src/pair_smd_tlsph.rst index 02343b678f..20fbbf86dc 100644 --- a/doc/src/pair_smd_tlsph.rst +++ b/doc/src/pair_smd_tlsph.rst @@ -75,7 +75,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst index 07b08a95f2..e531a7a2ec 100644 --- a/doc/src/pair_smd_triangulated_surface.rst +++ b/doc/src/pair_smd_triangulated_surface.rst @@ -60,7 +60,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst index cd97a799a3..f09f2d829e 100644 --- a/doc/src/pair_smd_ulsph.rst +++ b/doc/src/pair_smd_ulsph.rst @@ -90,7 +90,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_smtbq.rst b/doc/src/pair_smtbq.rst index cb57f6ba98..14f836bd52 100644 --- a/doc/src/pair_smtbq.rst +++ b/doc/src/pair_smtbq.rst @@ -191,7 +191,7 @@ For each cations (metal): 7) Charge initialization mode: -* Keyword (\ *QInitMode*\ ) and initial oxygen charge (\ *Qinit*\ ). If keyword = 'true', all oxygen charges are initially set equal to *Qinit*\ . The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create\_atom"#create\_atom command or the charge specified in the file structure using :doc:`read\_data ` command. +* Keyword (\ *QInitMode*\ ) and initial oxygen charge (\ *Qinit*\ ). If keyword = 'true', all oxygen charges are initially set equal to *Qinit*\ . The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create\_atom"#create\_atom command or the charge specified in the file structure using :doc:`read_data ` command. * Divided line 8) Mode for the electronegativity equalization (Qeq) @@ -217,7 +217,7 @@ For each cations (metal): **Mixing, shift, table, tail correction, restart, rRESPA info:** -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` mix, shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -225,7 +225,7 @@ needs to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 1b0fb0f385..d1137eb586 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -93,7 +93,7 @@ LAMMPS mapping list. The name of the SNAP parameter file usually ends in the ".snapparam" extension. It contains a small number of parameters that define the overall form of the SNAP potential. -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for these files. Quite commonly, @@ -171,7 +171,7 @@ two different element types, mixing is performed by LAMMPS with user-specifiable parameters as described above. You never need to specify a pair\_coeff command with I != J arguments for this style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -179,7 +179,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index 9e81b26c10..384f7e1cc3 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -50,9 +50,9 @@ interactions over time. Rc is the cutoff. See the :doc:`fix nve/limit ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * A (energy units) @@ -63,7 +63,7 @@ cutoff is used. .. note:: - The syntax for :doc:`pair\_coeff ` with a single A + The syntax for :doc:`pair_coeff ` with a single A coeff is different in the current version of LAMMPS than in older versions which took two values, Astart and Astop, to ramp between them. This functionality is now available in a more general form @@ -124,17 +124,17 @@ distance for this pair style can be mixed. A is always mixed via a mix value. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option, since the pair interaction goes to 0.0 at the cutoff. -The :doc:`pair\_modify ` table and tail options are not +The :doc:`pair_modify ` table and tail options are not relevant for this pair style. This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -148,7 +148,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix nve/limit `, :doc:`fix adapt ` +:doc:`pair_coeff `, :doc:`fix nve/limit `, :doc:`fix adapt ` **Default:** none diff --git a/doc/src/pair_sph_heatconduction.rst b/doc/src/pair_sph_heatconduction.rst index 741cfe4368..6e468aaf1d 100644 --- a/doc/src/pair_sph_heatconduction.rst +++ b/doc/src/pair_sph_heatconduction.rst @@ -30,7 +30,7 @@ See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * D diffusion coefficient (length\^2/time units) @@ -45,13 +45,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -64,7 +64,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair\_sph/rhosum **Default:** none diff --git a/doc/src/pair_sph_idealgas.rst b/doc/src/pair_sph_idealgas.rst index 9267186e7d..bd21a3cf5b 100644 --- a/doc/src/pair_sph_idealgas.rst +++ b/doc/src/pair_sph_idealgas.rst @@ -38,7 +38,7 @@ See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * nu artificial viscosity (no units) @@ -53,13 +53,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -72,7 +72,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair\_sph/rhosum **Default:** none diff --git a/doc/src/pair_sph_lj.rst b/doc/src/pair_sph_lj.rst index cf9d145121..1911e4f1b8 100644 --- a/doc/src/pair_sph_lj.rst +++ b/doc/src/pair_sph_lj.rst @@ -34,7 +34,7 @@ See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * nu artificial viscosity (no units) @@ -49,13 +49,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -71,7 +71,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair\_sph/rhosum **Default:** none diff --git a/doc/src/pair_sph_rhosum.rst b/doc/src/pair_sph_rhosum.rst index 2ba1ad010a..65a0840ef5 100644 --- a/doc/src/pair_sph_rhosum.rst +++ b/doc/src/pair_sph_rhosum.rst @@ -32,7 +32,7 @@ See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * h (distance units) @@ -46,13 +46,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -65,7 +65,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/taitwater +:doc:`pair_coeff `, pair\_sph/taitwater **Default:** none diff --git a/doc/src/pair_sph_taitwater.rst b/doc/src/pair_sph_taitwater.rst index ede4d4b115..3bb085b5bd 100644 --- a/doc/src/pair_sph_taitwater.rst +++ b/doc/src/pair_sph_taitwater.rst @@ -39,7 +39,7 @@ See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * rho0 reference density (mass/volume units) @@ -56,13 +56,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -75,7 +75,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair\_sph/rhosum **Default:** none diff --git a/doc/src/pair_sph_taitwater_morris.rst b/doc/src/pair_sph_taitwater_morris.rst index 8637faf188..91f79a1ac5 100644 --- a/doc/src/pair_sph_taitwater_morris.rst +++ b/doc/src/pair_sph_taitwater_morris.rst @@ -38,7 +38,7 @@ See `this PDF guide `_ to using SPH in LAMMPS. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * rho0 reference density (mass/volume units) @@ -55,13 +55,13 @@ above. This style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -This style does not support the :doc:`pair\_modify ` +This style does not support the :doc:`pair_modify ` shift, table, and tail options. This style does not write information to :doc:`binary restart files `. Thus, you need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. -This style can only be used via the *pair* keyword of the :doc:`run\_style respa ` command. It does not support the *inner*\ , +This style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. Restrictions @@ -74,7 +74,7 @@ if LAMMPS was built with that package. See the :doc:`Build package `, pair\_sph/rhosum +:doc:`pair_coeff `, pair\_sph/rhosum **Default:** none diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index 87a3f7e424..8b2112e34a 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -52,18 +52,18 @@ is the direction vector between the two particles. Style *spin/dipole/long* computes long-range magnetic dipole-dipole interaction. -A :doc:`kspace\_style ` must be defined to -use this pair style. Currently, :doc:`kspace\_style ewald/dipole/spin ` and :doc:`kspace\_style pppm/dipole/spin ` support long-range magnetic +A :doc:`kspace_style ` must be defined to +use this pair style. Currently, :doc:`kspace_style ewald/dipole/spin ` and :doc:`kspace_style pppm/dipole/spin ` support long-range magnetic dipole-dipole interactions. ---------- -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -85,7 +85,7 @@ currently supported. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`kspace\_style ` +:doc:`pair_coeff `, :doc:`kspace_style ` :doc:`fix nve/spin ` **Default:** none diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst index 166885d29d..98205e8d6e 100644 --- a/doc/src/pair_spin_dmi.rst +++ b/doc/src/pair_spin_dmi.rst @@ -55,9 +55,9 @@ More details about the derivation of these torques/forces are reported in :ref:`(Tranchida) `. For the *spin/dmi* pair style, the following coefficients must be defined for -each pair of atoms types via the :doc:`pair\_coeff ` command as in +each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` commands, and +:doc:`read_data ` or :doc:`read_restart ` commands, and set in the following order: * rc (distance units) @@ -85,8 +85,8 @@ atom\_style "spin" was declared. See the :doc:`Build package ` d Related commands """""""""""""""" -:doc:`atom\_style spin `, :doc:`pair\_coeff `, -:doc:`pair\_eam `, +:doc:`atom_style spin `, :doc:`pair_coeff `, +:doc:`pair_eam `, **Default:** none diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst index 3bbbed421b..b232649f95 100644 --- a/doc/src/pair_spin_exchange.rst +++ b/doc/src/pair_spin_exchange.rst @@ -72,9 +72,9 @@ More details about the derivation of these torques/forces are reported in :ref:`(Tranchida) `. For the *spin/exchange* pair style, the following coefficients must be defined -for each pair of atoms types via the :doc:`pair\_coeff ` command as in +for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` commands, and +:doc:`read_data ` or :doc:`read_restart ` commands, and set in the following order: * :math:`R_c` (distance units) @@ -104,8 +104,8 @@ atom\_style "spin" was declared. See the :doc:`Build package ` d Related commands """""""""""""""" -:doc:`atom\_style spin `, :doc:`pair\_coeff `, -:doc:`pair\_eam `, +:doc:`atom_style spin `, :doc:`pair_coeff `, +:doc:`pair_eam `, **Default:** diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index 679e13e628..bd5ff51650 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -67,8 +67,8 @@ atom\_style "spin" was declared. See the :doc:`Build package ` d Related commands """""""""""""""" -:doc:`atom\_style spin `, :doc:`pair\_coeff `, -:doc:`pair\_spin\_exchange `, :doc:`pair\_eam `, +:doc:`atom_style spin `, :doc:`pair_coeff `, +:doc:`pair\_spin\_exchange `, :doc:`pair_eam `, **Default:** none diff --git a/doc/src/pair_spin_neel.rst b/doc/src/pair_spin_neel.rst index ecdb8f30f6..872b40d522 100644 --- a/doc/src/pair_spin_neel.rst +++ b/doc/src/pair_spin_neel.rst @@ -91,8 +91,8 @@ atom\_style "spin" was declared. See the :doc:`Build package ` d Related commands """""""""""""""" -:doc:`atom\_style spin `, :doc:`pair\_coeff `, -:doc:`pair\_eam `, +:doc:`atom_style spin `, :doc:`pair_coeff `, +:doc:`pair_eam `, **Default:** diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index 1b4e6d3031..057b09e427 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -75,9 +75,9 @@ closest approach of bond *i* and *j*\ . The *mid* option takes *L* as 0.5 for each interaction as described in :ref:`(Sirk) `. The following coefficients must be defined via the -:doc:`pair\_coeff ` command as in the examples above, or in -the data file or restart file read by the :doc:`read\_data ` -or :doc:`read\_restart ` commands: +:doc:`pair_coeff ` command as in the examples above, or in +the data file or restart file read by the :doc:`read_data ` +or :doc:`read_restart ` commands: * *C* (force units) * *rc* (distance units) @@ -93,15 +93,15 @@ is used. Any actual existing particles with this atom type will be deleted at the beginning of a run. This means you must specify the number of types in your system accordingly; usually to be one larger than what - would normally be the case, e.g. via the :doc:`create\_box ` + would normally be the case, e.g. via the :doc:`create_box ` or by changing the header in your :doc:`data file `. The fictitious "bond particles" are inserted at the beginning of the run, and serve as placeholders that define the position of the bonds. This allows neighbor lists to be constructed and pairwise interactions to be computed in almost the same way as is done for actual particles. - Because bonds interact only with other bonds, :doc:`pair\_style hybrid ` should be used to turn off interactions + Because bonds interact only with other bonds, :doc:`pair_style hybrid ` should be used to turn off interactions between atom type *bptype* and all other types of atoms. An error - will be flagged if :doc:`pair\_style hybrid ` is not used. + will be flagged if :doc:`pair_style hybrid ` is not used. The optional *exclude* keyword determines if forces are computed between first neighbor (directly connected) bonds. For a setting of @@ -111,7 +111,7 @@ distance calculation because the minimum distance between directly connected bonds is zero. Pair style *srp* turns off normalization of thermodynamic properties -by particle number, as if the command :doc:`thermo\_modify norm no ` had been issued. +by particle number, as if the command :doc:`thermo_modify norm no ` had been issued. The pairwise energy associated with style *srp* is shifted to be zero at the cutoff distance *rc*\ . @@ -124,23 +124,23 @@ at the cutoff distance *rc*\ . This pair styles does not support mixing. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. Note that as discussed above, the energy term is already shifted to be 0.0 at the cutoff distance *rc*\ . -The :doc:`pair\_modify ` table option is not relevant for +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. -This pair style writes global and per-atom information to :doc:`binary restart files `. Pair srp should be used with :doc:`pair\_style hybrid `, thus the pair\_coeff commands need to be +This pair style writes global and per-atom information to :doc:`binary restart files `. Pair srp should be used with :doc:`pair_style hybrid `, thus the pair\_coeff commands need to be specified in the input script when reading a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -155,7 +155,7 @@ This pair style is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info. -This pair style must be used with :doc:`pair\_style hybrid `. +This pair style must be used with :doc:`pair_style hybrid `. This pair style requires the :doc:`newton ` command to be *on* for non-bonded interactions. @@ -165,7 +165,7 @@ This pair style is not compatible with :doc:`rigid body integrators ` Related commands """""""""""""""" -:doc:`pair\_style hybrid `, :doc:`pair\_coeff `, +:doc:`pair_style hybrid `, :doc:`pair_coeff `, :doc:`pair dpd ` Default diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index ae09daf919..abd551cffb 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -55,7 +55,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of SW elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.sw has Stillinger-Weber values for @@ -192,7 +192,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above from values in the potential file. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -200,7 +200,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -226,7 +226,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index 202832dfe7..9607f2ab77 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -78,7 +78,7 @@ to index into the table via a fast bit-mapping technique due to adjacent table values. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * filename @@ -95,12 +95,12 @@ table. The format of this file is described below. If your tabulated potential(s) are designed to be used as the short-range part of one of the long-range solvers specified by the -:doc:`kspace\_style ` command, then you must use one or +:doc:`kspace_style ` command, then you must use one or more of the optional keywords listed above for the pair\_style command. These are *ewald* or *pppm* or *msm* or *dispersion* or *tip4p*\ . This is so LAMMPS can insure the short-range potential and long-range solver are compatible with each other, as it does for other -short-range pair styles, such as :doc:`pair\_style lj/cut/coul/long `. Note that it is up to you to insure +short-range pair styles, such as :doc:`pair_style lj/cut/coul/long `. Note that it is up to you to insure the tabulated values for each pair of atom types has the correct functional form to be compatible with the matching long-range solver. @@ -113,7 +113,7 @@ best effect: * Vary the number of table points; you may need to use more than you think to get good resolution. -* Always use the :doc:`pair\_write ` command to produce a plot +* Always use the :doc:`pair_write ` command to produce a plot of what the final interpolated potential looks like. This can show up interpolation "features" you may not like. * Start with the linear style; it's the style least likely to have problems. @@ -158,7 +158,7 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`pair\_style table ` command. Let +specified in the :doc:`pair_style table ` command. Let Ntable = *N* in the pair\_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It @@ -200,7 +200,7 @@ If used, the parameter "BITMAP" is also followed by 2 values *rlo* and *rhi*\ . These values, along with the "N" value determine the ordering of the N lines that follow and what distance is associated with each. This ordering is complex, so it is not documented here, since this -file is typically produced by the :doc:`pair\_write ` command +file is typically produced by the :doc:`pair_write ` command with its *bitmap* option. When the table is in BITMAP format, the "N" parameter in the file must be equal to 2\^M where M is the value specified in the pair\_style command. Also, a cutoff parameter cannot @@ -256,7 +256,7 @@ instructions on how to use the accelerated styles effectively. This pair style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -The :doc:`pair\_modify ` shift, table, and tail options are +The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. This pair style writes the settings for the "pair\_style table" command @@ -267,7 +267,7 @@ file, since it is tabulated in the potential files. Thus, pair\_coeff commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -281,7 +281,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_write ` +:doc:`pair_coeff `, :doc:`pair_write ` **Default:** none diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst index e04f12e715..616dbb3da0 100644 --- a/doc/src/pair_table_rx.rst +++ b/doc/src/pair_table_rx.rst @@ -42,7 +42,7 @@ one CG particle can interact with a species in a neighboring CG particle through a site-site interaction potential model. Style *table/rx* creates interpolation tables of length *N* from pair potential and force values listed in a file(s) as a function of -distance. The files are read by the :doc:`pair\_coeff ` +distance. The files are read by the :doc:`pair_coeff ` command. The interpolation tables are created by fitting cubic splines to the @@ -69,7 +69,7 @@ table via a fast bit-mapping technique :ref:`(Wolff) ` and a linear interpolation is performed between adjacent table values. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above. * filename @@ -108,7 +108,7 @@ best effect: * Vary the number of table points; you may need to use more than you think to get good resolution. -* Always use the :doc:`pair\_write ` command to produce a plot +* Always use the :doc:`pair_write ` command to produce a plot of what the final interpolated potential looks like. This can show up interpolation "features" you may not like. * Start with the linear style; it's the style least likely to have problems. @@ -152,7 +152,7 @@ numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`pair\_style table/rx ` command. Let +specified in the :doc:`pair_style table/rx ` command. Let Ntable = *N* in the pair\_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It @@ -184,7 +184,7 @@ If used, the parameter "BITMAP" is also followed by 2 values *rlo* and *rhi*\ . These values, along with the "N" value determine the ordering of the N lines that follow and what distance is associated with each. This ordering is complex, so it is not documented here, since this -file is typically produced by the :doc:`pair\_write ` command +file is typically produced by the :doc:`pair_write ` command with its *bitmap* option. When the table is in BITMAP format, the "N" parameter in the file must be equal to 2\^M where M is the value specified in the pair\_style command. Also, a cutoff parameter cannot @@ -218,7 +218,7 @@ one that matches the specified keyword. This pair style does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly. -The :doc:`pair\_modify ` shift, table, and tail options are +The :doc:`pair_modify ` shift, table, and tail options are not relevant for this pair style. This pair style writes the settings for the "pair\_style table/rx" command @@ -229,7 +229,7 @@ file, since it is tabulated in the potential files. Thus, pair\_coeff commands do need to be specified in the restart input script. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -268,7 +268,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** fractional weighting diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index 773ee649df..071fc6c084 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -72,7 +72,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of Tersoff elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine the SiC.tersoff file has Tersoff values for Si @@ -227,7 +227,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above from values in the potential file. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -235,7 +235,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -261,7 +261,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst index 15cce523f7..d0ba8770be 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -173,7 +173,7 @@ instructions on how to use the accelerated styles effectively. **Mixing, shift, table, tail correction, restart, rRESPA info**\ : -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -181,7 +181,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -207,7 +207,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index fecc22c31a..4b9fc25918 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -70,7 +70,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of Tersoff/ZBL elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values @@ -231,7 +231,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above from values in the potential file. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -239,7 +239,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -266,7 +266,7 @@ units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index 8f4bac0182..9f8cb67714 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -103,14 +103,14 @@ is not applied to the full charge of the core particle :math:`q_i`, but only to the :math:`-q_{D,i}` part of it. The interactions between core charges are subject to the weighting -factors set by the :doc:`special\_bonds ` command. The +factors set by the :doc:`special_bonds ` command. The interactions between Drude particles and core charges or non-polarizable atoms are also subject to these weighting factors. The Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from their respective cores. For pair\_style *thole*\ , the following coefficients must be defined for -each pair of atoms types via the :doc:`pair\_coeff ` command +each pair of atoms types via the :doc:`pair_coeff ` command as in the example above. * alpha (distance units\^3) @@ -123,7 +123,7 @@ command are used. In order to specify a cutoff (third argument) a damp parameter (second argument) must also be specified. For pair style *lj/cut/thole/long*\ , the following coefficients must be -defined for each pair of atoms types via the :doc:`pair\_coeff ` +defined for each pair of atoms types via the :doc:`pair_coeff ` command. * epsilon (energy units) @@ -194,7 +194,7 @@ Related commands """""""""""""""" :doc:`fix drude `, :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude ` -:doc:`pair\_style lj/cut/coul/long ` +:doc:`pair_style lj/cut/coul/long ` **Default:** none diff --git a/doc/src/pair_tri_lj.rst b/doc/src/pair_tri_lj.rst index 350f9c0617..b9590a02a8 100644 --- a/doc/src/pair_tri_lj.rst +++ b/doc/src/pair_tri_lj.rst @@ -32,7 +32,7 @@ Interactions between two triangles, each with N1 and N2 spherical particles, are calculated as the pairwise sum of N1\*N2 Lennard-Jones interactions. Interactions between a triangle with N spherical particles and a point particle are treated as the pairwise sum of N -Lennard-Jones interactions. See the :doc:`pair\_style lj/cut ` +Lennard-Jones interactions. See the :doc:`pair_style lj/cut ` doc page for the definition of Lennard-Jones interactions. The cutoff distance for an interaction between 2 triangles, or between @@ -69,9 +69,9 @@ means that any specified sigma\_IJ values (for I != J) are effectively ignored. For style *tri/lj*\ , the following coefficients must be defined for -each pair of atoms types via the :doc:`pair\_coeff ` command +each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by -the :doc:`read\_data ` or :doc:`read\_restart ` +the :doc:`read_data ` or :doc:`read_restart ` commands: * epsilon (energy units) @@ -92,13 +92,13 @@ and cutoff distance for all of this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -113,12 +113,12 @@ This style is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. Defining particles to be triangles so they participate in tri/tri or -tri/particle interactions requires the use the :doc:`atom\_style tri ` command. +tri/particle interactions requires the use the :doc:`atom_style tri ` command. Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`pair\_style line/lj ` +:doc:`pair_coeff `, :doc:`pair_style line/lj ` **Default:** none diff --git a/doc/src/pair_ufm.rst b/doc/src/pair_ufm.rst index 318762bb4b..1656720fd1 100644 --- a/doc/src/pair_ufm.rst +++ b/doc/src/pair_ufm.rst @@ -50,9 +50,9 @@ to control the softness of the interactions :ref:`(Paula Leite2017) `. This model is useful as a reference system for fluid-phase free-energy calculations :ref:`(Paula Leite2016) `. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * epsilon (energy units) @@ -112,18 +112,18 @@ distance for this pair style can be mixed. A is always mixed via a mix value. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style support the :doc:`pair\_modify ` shift option for the energy of the pair interaction. +This pair style support the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table and tail are not relevant for this +The :doc:`pair_modify ` table and tail are not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` tail option for adding long-range tail corrections to energy and pressure. +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -137,7 +137,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff `, :doc:`fix adapt ` +:doc:`pair_coeff `, :doc:`fix adapt ` **Default:** none diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index c4c8a6c9f5..58baf53143 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -95,7 +95,7 @@ where N is the number of LAMMPS atom types: * filename * N element names = mapping of Vashishta elements to atom types -See the :doc:`pair\_coeff ` doc page for alternate ways +See the :doc:`pair_coeff ` doc page for alternate ways to specify the path for the potential file. As an example, imagine a file SiC.vashishta has parameters for @@ -220,7 +220,7 @@ For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as described above from values in the potential file. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you @@ -228,7 +228,7 @@ need to re-specify the pair\_style and pair\_coeff commands in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -254,7 +254,7 @@ appropriate units if your simulation doesn't use "metal" units. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst index 17be08f29a..eff77b4d68 100644 --- a/doc/src/pair_write.rst +++ b/doc/src/pair_write.rst @@ -40,7 +40,7 @@ file. The energy and force values are computed at distances from inner to outer for 2 interacting atoms of type itype and jtype, using the -appropriate :doc:`pair\_coeff ` coefficients. If the style +appropriate :doc:`pair_coeff ` coefficients. If the style is *r*\ , then N distances are used, evenly spaced in r; if the style is *rsq*\ , N distances are used, evenly spaced in r\^2. @@ -49,7 +49,7 @@ values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0. If the style is *bitmap*\ , then 2\^N values are written to the file in a format and order consistent with how they are read in by the -:doc:`pair\_coeff ` command for pair style *table*\ . For +:doc:`pair_coeff ` command for pair style *table*\ . For reasonable accuracy in a bitmapped table, choose N >= 12, an *inner* value that is smaller than the distance of closest approach of 2 atoms, and an *outer* value <= cutoff of the potential. @@ -59,7 +59,7 @@ of the pair of interacting atoms can optionally be specified. If not specified, values of Qi = Qj = 1.0 are used. The file is written in the format used as input for the -:doc:`pair\_style ` *table* option with *keyword* as the +:doc:`pair_style ` *table* option with *keyword* as the section name. Each line written to the file lists an index number (1-N), a distance (in distance units), an energy (in energy units), and a force (in force units). @@ -80,8 +80,8 @@ pairwise portion of the potential, not the embedding portion. Related commands """""""""""""""" -:doc:`pair\_style table `, -:doc:`pair\_style `, :doc:`pair\_coeff ` +:doc:`pair_style table `, +:doc:`pair_style `, :doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst index 14cec88d2e..a4a96b15c3 100644 --- a/doc/src/pair_yukawa.rst +++ b/doc/src/pair_yukawa.rst @@ -44,9 +44,9 @@ Style *yukawa* computes pairwise interactions with the formula Rc is the cutoff. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * A (energy\*distance units) @@ -88,13 +88,13 @@ distance for this pair style can be mixed. A is an energy value mixed like a LJ epsilon. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -102,7 +102,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -116,7 +116,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst index b46f8fc704..74fa1e7e78 100644 --- a/doc/src/pair_yukawa_colloid.rst +++ b/doc/src/pair_yukawa_colloid.rst @@ -41,7 +41,7 @@ Style *yukawa/colloid* computes pairwise interactions with the formula where Ri and Rj are the radii of the two particles and Rc is the cutoff. -In contrast to :doc:`pair\_style yukawa `, this functional +In contrast to :doc:`pair_style yukawa `, this functional form arises from the Coulombic interaction between two colloid particles, screened due to the presence of an electrolyte, see the book by :ref:`Safran ` for a derivation in the context of DLVO @@ -52,14 +52,14 @@ This potential applies to nearby particle pairs for which the Derjagin approximation holds, meaning h << Ri + Rj, where h is the surface-to-surface separation of the two particles. -When used in combination with :doc:`pair\_style colloid `, +When used in combination with :doc:`pair_style colloid `, the two terms become the so-called DLVO potential, which combines electrostatic repulsion and van der Waals attraction. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * A (energy/distance units) @@ -68,7 +68,7 @@ commands, or by mixing as described below: The prefactor A is determined from the relationship between surface charge and surface potential due to the presence of electrolyte. Note that the A for this potential style has different units than the A -used in :doc:`pair\_style yukawa `. For low surface +used in :doc:`pair_style yukawa `. For low surface potentials, i.e. less than about 25 mV, A can be written as: @@ -120,13 +120,13 @@ distance for this pair style can be mixed. A is an energy value mixed like a LJ epsilon. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style supports the :doc:`pair\_modify ` shift +This pair style supports the :doc:`pair_modify ` shift option for the energy of the pair interaction. -The :doc:`pair\_modify ` table option is not relevant +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. @@ -134,7 +134,7 @@ This pair style writes its information to :doc:`binary restart files `, to be specified in an input script that reads a restart file. This pair style can only be used via the *pair* keyword of the -:doc:`run\_style respa ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -149,7 +149,7 @@ This style is part of the COLLOID package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. This pair style requires that atoms be finite-size spheres with a -diameter, as defined by the :doc:`atom\_style sphere ` +diameter, as defined by the :doc:`atom_style sphere ` command. Per-particle polydispersity is not yet supported by this pair style; @@ -160,7 +160,7 @@ diameter. Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index 6bb485ee8a..4d08418ce8 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -49,11 +49,11 @@ energy due to a pair of atoms at a distance r\_ij is given by: where e is the electron charge, epsilon\_0 is the electrical permittivity of vacuum, and Z\_i and Z\_j are the nuclear charges of the two atoms. The switching function S(r) is identical to that used by -:doc:`pair\_style lj/gromacs `. Here, the inner and outer +:doc:`pair_style lj/gromacs `. Here, the inner and outer cutoff are the same for all pairs of atom types. The following coefficients must be defined for each pair of atom types -via the :doc:`pair\_coeff ` command as in the examples above, +via the :doc:`pair_coeff ` command as in the examples above, or in the LAMMPS data file. * Z\_i (atomic number for first atom type, e.g. 13.0 for aluminum) @@ -115,17 +115,17 @@ with :doc:`hybrid/overlay ` and pairs are assigned to more than one sub-style, the mixing rule is not used and each pair of types interacting with the ZBL sub-style must be included in a pair\_coeff command. -The :doc:`pair\_modify ` mix option has no effect on +The :doc:`pair_modify ` mix option has no effect on the mixing behavior -The ZBL pair style does not support the :doc:`pair\_modify ` +The ZBL pair style does not support the :doc:`pair_modify ` shift option, since the ZBL interaction is already smoothed to 0.0 at the cutoff. -The :doc:`pair\_modify ` table option is not relevant for +The :doc:`pair_modify ` table option is not relevant for this pair style. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure, since there are no corrections for a potential that goes to 0.0 at the cutoff. @@ -134,7 +134,7 @@ This pair style does not write information to :doc:`binary restart files ` command. It does not support the +:doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. @@ -148,7 +148,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_coeff ` +:doc:`pair_coeff ` **Default:** none diff --git a/doc/src/pair_zero.rst b/doc/src/pair_zero.rst index 6afafc2017..18afdbf355 100644 --- a/doc/src/pair_zero.rst +++ b/doc/src/pair_zero.rst @@ -38,7 +38,7 @@ to enumerate pairs of atoms within some cutoff distance, but when pairwise forces are not otherwise needed. Examples are the :doc:`fix bond/create `, :doc:`compute rdf `, :doc:`compute voronoi/atom ` commands. -Note that the :doc:`comm\_modify cutoff ` command can be +Note that the :doc:`comm_modify cutoff ` command can be used to insure communication of ghost atoms even when a pair style is not defined, but it will not trigger neighbor list generation. @@ -48,9 +48,9 @@ will only be checked for the atom type numbers and the rest ignored. In this case, only the global cutoff will be used. The following coefficients must be defined for each pair of atoms -types via the :doc:`pair\_coeff ` command as in the examples +types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the -:doc:`read\_data ` or :doc:`read\_restart ` +:doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutoff (distance units) @@ -69,14 +69,14 @@ pair coefficient is ignored. The cutoff distance for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair\_modify" command for details. -This pair style does not support the :doc:`pair\_modify ` +This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. This pair style writes its information to :doc:`binary restart files `, so pair\_style and pair\_coeff commands do not need to be specified in an input script that reads a restart file. This pair style supports the use of the *inner*\ , *middle*\ , -and *outer* keywords of the :doc:`run\_style respa ` command. +and *outer* keywords of the :doc:`run_style respa ` command. ---------- @@ -89,7 +89,7 @@ Restrictions Related commands """""""""""""""" -:doc:`pair\_style none ` +:doc:`pair_style none ` **Default:** none diff --git a/doc/src/partition.rst b/doc/src/partition.rst index e238e7c60d..7ee6d76f3c 100644 --- a/doc/src/partition.rst +++ b/doc/src/partition.rst @@ -72,7 +72,7 @@ Restrictions Related commands """""""""""""""" -:doc:`run\_style verlet/split ` +:doc:`run_style verlet/split ` **Default:** none diff --git a/doc/src/prd.rst b/doc/src/prd.rst index 5ea3db6121..a53f8d561e 100644 --- a/doc/src/prd.rst +++ b/doc/src/prd.rst @@ -145,9 +145,9 @@ The first time through the PRD loop, the "previous basin" is the set of quenched coordinates from the initial state of the system. A quench is an energy minimization and is performed by whichever -algorithm has been defined by the :doc:`min\_style ` command. +algorithm has been defined by the :doc:`min_style ` command. Minimization parameters may be set via the -:doc:`min\_modify ` command and by the *min* keyword of the +:doc:`min_modify ` command and by the *min* keyword of the PRD command. The latter are the settings that would be used with the :doc:`minimize ` command. Note that typically, you do not need to perform a highly-converged minimization to detect a transition @@ -337,8 +337,8 @@ Related commands """""""""""""""" :doc:`compute event/displace `, -:doc:`min\_modify `, :doc:`min\_style `, -:doc:`run\_style `, :doc:`minimize `, +:doc:`min_modify `, :doc:`min_style `, +:doc:`run_style `, :doc:`minimize `, :doc:`velocity `, :doc:`temper `, :doc:`neb `, :doc:`tad `, :doc:`hyper ` diff --git a/doc/src/processors.rst b/doc/src/processors.rst index a13b44330c..6f593ffc6a 100644 --- a/doc/src/processors.rst +++ b/doc/src/processors.rst @@ -107,11 +107,11 @@ different processor grids for different partitions, e.g. This command only affects the initial regular 3d grid created when the simulation box is first specified via a - :doc:`create\_box ` or :doc:`read\_data ` or - :doc:`read\_restart ` command. Or if the simulation box is + :doc:`create_box ` or :doc:`read_data ` or + :doc:`read_restart ` command. Or if the simulation box is re-created via the :doc:`replicate ` command. The same regular grid is initially created, regardless of which - :doc:`comm\_style ` command is in effect. + :doc:`comm_style ` command is in effect. If load-balancing is never invoked via the :doc:`balance ` or :doc:`fix balance ` commands, then the initial regular grid @@ -120,7 +120,7 @@ the methods invoked by those commands retain the logical topology of the initial 3d grid, and the mapping of processors to the grid specified by the processors command. However the grid spacings in different dimensions may change, so that processors own sub-domains of -different sizes. If the :doc:`comm\_style tiled ` command is +different sizes. If the :doc:`comm_style tiled ` command is used, methods invoked by the balancing commands may discard the 3d grid of processors and tile the simulation domain with sub-domains of different sizes and shapes which no longer have a logical 3d @@ -274,7 +274,7 @@ styles are not supported, so an *xyz* style is used in their place. The *part* keyword affects the factorization of P into Px,Py,Pz. It can be useful when running in multi-partition mode, e.g. with the -:doc:`run\_style verlet/split ` command. It specifies a +:doc:`run_style verlet/split ` command. It specifies a dependency between a sending partition *Psend* and a receiving partition *Precv* which is enforced when each is setting up their own mapping of their processors to the simulation box. Each of *Psend* @@ -292,7 +292,7 @@ constraint. The nature of the constraint is determined by the For a *cstyle* of *multiple*\ , each dimension of the sender's processor grid is required to be an integer multiple of the corresponding dimension in the receiver's processor grid. This is a requirement of -the :doc:`run\_style verlet/split ` command. +the :doc:`run_style verlet/split ` command. For example, assume the sending partition creates a 4x6x10 grid = 240 processor grid. If the receiving partition is running on 80 @@ -358,7 +358,7 @@ Restrictions This command cannot be used after the simulation box is defined by a -:doc:`read\_data ` or :doc:`create\_box ` command. +:doc:`read_data ` or :doc:`create_box ` command. It can be used before a restart file is read to change the 3d processor grid from what is specified in the restart file. diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 798f95e5ec..59ce92ca34 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -68,8 +68,8 @@ Description Read in a data file containing information LAMMPS needs to run a simulation. The file can be ASCII text or a gzipped text file (detected by a .gz suffix). This is one of 3 ways to specify initial -atom coordinates; see the :doc:`read\_restart ` and -:doc:`create\_atoms ` commands for alternative methods. +atom coordinates; see the :doc:`read_restart ` and +:doc:`create_atoms ` commands for alternative methods. Also see the explanation of the :doc:`-restart command-line switch ` which can convert a restart file to a data file. @@ -83,7 +83,7 @@ specified group-ID. The group will be created if it does not already exist. This is useful if you are reading multiple data files and wish to put sets of atoms into different groups so they can be operated on later. E.g. a group of added atoms can be moved to new positions via -the :doc:`displace\_atoms ` command. Note that atoms +the :doc:`displace_atoms ` command. Note that atoms read from the data file are also always added to the "all" group. The :doc:`group ` command discusses atom groups, as used in LAMMPS. @@ -107,7 +107,7 @@ contained in individual data files. For example one data file could contain fluid in a confined domain; a second could contain wall atoms, and the second file could be read a third time to create a wall on the other side of the fluid. The third set of atoms could be rotated to -an opposing direction using the :doc:`displace\_atoms ` +an opposing direction using the :doc:`displace_atoms ` command, after the third read\_data command is used. The *add*\ , *offset*\ , *shift*\ , *extra*\ , and *group* keywords are @@ -116,7 +116,7 @@ useful in this context. If a simulation box does not yet exist, the *add* keyword cannot be used; the read\_data command is being used for the first time. If a simulation box does exist, due to using the -:doc:`create\_box ` command, or a previous read\_data command, +:doc:`create_box ` command, or a previous read\_data command, then the *add* keyword must be used. .. note:: @@ -175,9 +175,9 @@ for a 2d simulation. This is a mechanism for adding structured collections of atoms at different locations within the simulation box, to build up a complex geometry. It is up to you to insure atoms do not end up overlapping unphysically which would lead to bad dynamics. -Note that the :doc:`displace\_atoms ` command can be used +Note that the :doc:`displace_atoms ` command can be used to move a subset of atoms after they have been read from a data file. -Likewise, the :doc:`delete\_atoms ` command can be used to +Likewise, the :doc:`delete_atoms ` command can be used to remove overlapping atoms. Note that the shift values (Sx, Sy, Sz) are also added to the simulation box information (xlo, xhi, ylo, yhi, zlo, zhi) in the data file to shift its boundaries. E.g. xlo\_new = xlo + @@ -212,7 +212,7 @@ interactions in your input script to have a complete pairwise interaction model. An alternative to using the *extra* keywords with the read\_data -command, is to use the :doc:`create\_box ` command to +command, is to use the :doc:`create_box ` command to initialize the simulation box and all the various type limits you need via its *extra* keywords. Then use the read\_data command one or more times to populate the system with atoms, bonds, angles, etc, using the @@ -408,7 +408,7 @@ molecules defined in the data file. Using this header flag is deprecated; please use the *extra/special/per/atom* keyword instead. Using this setting will pre-allocate space in the LAMMPS data structures for storing these neighbors. See the -:doc:`special\_bonds ` and :doc:`molecule ` doc +:doc:`special_bonds ` and :doc:`molecule ` doc pages for more discussion of 1-2,1-3,1-4 neighbors. .. note:: @@ -421,7 +421,7 @@ pages for more discussion of 1-2,1-3,1-4 neighbors. If they appear in later data files, they are ignored. The "ellipsoids" and "lines" and "triangles" and "bodies" settings are -only used with :doc:`atom\_style ellipsoid or line or tri or body ` and specify how many of the atoms are +only used with :doc:`atom_style ellipsoid or line or tri or body ` and specify how many of the atoms are finite-size ellipsoids or lines or triangles or bodies; the remainder are point particles. See the discussion of ellipsoidflag and the *Ellipsoids* section below. See the discussion of lineflag and the @@ -431,7 +431,7 @@ are point particles. See the discussion of ellipsoidflag and the .. note:: - For :doc:`atom\_style template `, the molecular + For :doc:`atom_style template `, the molecular topology (bonds,angles,etc) is contained in the molecule templates read-in by the :doc:`molecule ` command. This means you cannot set the *bonds*\ , *angles*\ , etc header keywords in the data @@ -466,8 +466,8 @@ For example, these lines: Atoms # sphere Pair Coeffs # lj/cut -will check if the currently-defined :doc:`atom\_style ` is -*sphere*\ , and the current :doc:`pair\_style ` is *lj/cut*\ . +will check if the currently-defined :doc:`atom_style ` is +*sphere*\ , and the current :doc:`pair_style ` is *lj/cut*\ . If not, LAMMPS will issue a warning to indicate that the data file section likely does not contain the correct number or type of parameters expected for the currently-defined style. @@ -508,9 +508,9 @@ Atoms section: The number and meaning of the coefficients are specific to the defined -angle style. See the :doc:`angle\_style ` and -:doc:`angle\_coeff ` commands for details. Coefficients can -also be set via the :doc:`angle\_coeff ` command in the +angle style. See the :doc:`angle_style ` and +:doc:`angle_coeff ` commands for details. Coefficients can +also be set via the :doc:`angle_coeff ` command in the input script. @@ -702,7 +702,7 @@ in dump files. Normally, it is a unique value from 1 to Natoms for each atom. Unique values larger than Natoms can be used, but they will cause extra memory to be allocated on each processor, if an atom map array is used, but not if an atom map hash is used; see the -:doc:`atom\_modify ` command for details. If an atom map is +:doc:`atom_modify ` command for details. If an atom map is not used (e.g. an atomic system with no bonds), and you don't care if unique atom IDs appear in dump files, then the atom-IDs can all be set to 0. @@ -723,7 +723,7 @@ triangle, or body in the corresponding *Ellipsoids*\ , *Lines*\ , *Triangles*\ , or *Bodies* section. The *template-index* and *template-atom* are only defined used by -:doc:`atom\_style template `. In this case the +:doc:`atom_style template `. In this case the :doc:`molecule ` command is used to define a molecule template which contains one or more molecules. If an atom belongs to one of those molecules, its *template-index* and *template-atom* are both set @@ -757,7 +757,7 @@ discs (not 3d spheres), by changing their moment of inertia. For atom\_style hybrid, following the 5 initial values (ID,type,x,y,z), specific values for each sub-style must be listed. The order of the sub-styles is the same as they were listed in the -:doc:`atom\_style ` command. The sub-style specific values +:doc:`atom_style ` command. The sub-style specific values are those that are not the 5 standard ones (ID,type,x,y,z). For example, for the "charge" sub-style, a "q" value would appear. For the "full" sub-style, a "molecule-ID" and "q" would appear. These are @@ -875,7 +875,7 @@ script. -The *Bodies* section must appear if :doc:`atom\_style body ` +The *Bodies* section must appear if :doc:`atom_style body ` is used and any atoms listed in the *Atoms* section have a bodyflag = 1. The number of bodies should be specified in the header section via the "bodies" keyword. @@ -883,7 +883,7 @@ the "bodies" keyword. Each body can have a variable number of integer and/or floating-point values. The number and meaning of the values is defined by the body style, as described in the :doc:`Howto body ` doc page. The -body style is given as an argument to the :doc:`atom\_style body ` command. +body style is given as an argument to the :doc:`atom_style body ` command. The Ninteger and Ndouble values determine how many integer and floating-point values are specified for this particle. Ninteger and @@ -919,9 +919,9 @@ The *Bodies* section must appear after the *Atoms* section. The number and meaning of the coefficients are specific to the defined -bond style. See the :doc:`bond\_style ` and -:doc:`bond\_coeff ` commands for details. Coefficients can -also be set via the :doc:`bond\_coeff ` command in the input +bond style. See the :doc:`bond_style ` and +:doc:`bond_coeff ` commands for details. Coefficients can +also be set via the :doc:`bond_coeff ` command in the input script. @@ -1021,10 +1021,10 @@ in this section must be integers (1, not 1.0). The number and meaning of the coefficients are specific to the defined -dihedral style. See the :doc:`dihedral\_style ` and -:doc:`dihedral\_coeff ` commands for details. +dihedral style. See the :doc:`dihedral_style ` and +:doc:`dihedral_coeff ` commands for details. Coefficients can also be set via the -:doc:`dihedral\_coeff ` command in the input script. +:doc:`dihedral_coeff ` command in the input script. ---------- @@ -1076,7 +1076,7 @@ section must be integers (1, not 1.0). -The *Ellipsoids* section must appear if :doc:`atom\_style ellipsoid ` is used and any atoms are listed in the +The *Ellipsoids* section must appear if :doc:`atom_style ellipsoid ` is used and any atoms are listed in the *Atoms* section with an ellipsoidflag = 1. The number of ellipsoids should be specified in the header section via the "ellipsoids" keyword. @@ -1138,10 +1138,10 @@ The *Ellipsoids* section must appear after the *Atoms* section. The number and meaning of the coefficients are specific to the defined -improper style. See the :doc:`improper\_style ` and -:doc:`improper\_coeff ` commands for details. +improper style. See the :doc:`improper_style ` and +:doc:`improper_coeff ` commands for details. Coefficients can also be set via the -:doc:`improper\_coeff ` command in the input script. +:doc:`improper_coeff ` command in the input script. ---------- @@ -1196,7 +1196,7 @@ values in this section must be integers (1, not 1.0). -The *Lines* section must appear if :doc:`atom\_style line ` +The *Lines* section must appear if :doc:`atom_style line ` is used and any atoms are listed in the *Atoms* section with a lineflag = 1. The number of lines should be specified in the header section via the "lines" keyword. @@ -1235,7 +1235,7 @@ The *Lines* section must appear after the *Atoms* section. This defines the mass of each atom type. This can also be set via the :doc:`mass ` command in the input script. This section cannot be used for atom styles that define a mass for individual atoms - -e.g. :doc:`atom\_style sphere `. +e.g. :doc:`atom_style sphere `. ---------- @@ -1276,12 +1276,12 @@ e.g. :doc:`atom\_style sphere `. The number and meaning of the coefficients are specific to the defined -pair style. See the :doc:`pair\_style ` and -:doc:`pair\_coeff ` commands for details. Since pair +pair style. See the :doc:`pair_style ` and +:doc:`pair_coeff ` commands for details. Since pair coefficients for types I != J are not specified, these will be generated automatically by the pair style's mixing rule. See the -individual pair\_style doc pages and the :doc:`pair\_modify mix ` command for details. Pair coefficients can also -be set via the :doc:`pair\_coeff ` command in the input +individual pair\_style doc pages and the :doc:`pair_modify mix ` command for details. Pair coefficients can also +be set via the :doc:`pair_coeff ` command in the input script. @@ -1310,12 +1310,12 @@ script. This section must have N\*(N+1)/2 lines where N = # of atom types. The number and meaning of the coefficients are specific to the defined -pair style. See the :doc:`pair\_style ` and -:doc:`pair\_coeff ` commands for details. Since pair +pair style. See the :doc:`pair_style ` and +:doc:`pair_coeff ` commands for details. Since pair coefficients for types I != J are all specified, these values will turn off the default mixing rule defined by the pair style. See the -individual pair\_style doc pages and the :doc:`pair\_modify mix ` command for details. Pair coefficients can also -be set via the :doc:`pair\_coeff ` command in the input +individual pair\_style doc pages and the :doc:`pair_modify mix ` command for details. Pair coefficients can also +be set via the :doc:`pair_coeff ` command in the input script. @@ -1342,7 +1342,7 @@ script. -The *Triangles* section must appear if :doc:`atom\_style tri ` is used and any atoms are listed in the *Atoms* +The *Triangles* section must appear if :doc:`atom_style tri ` is used and any atoms are listed in the *Atoms* section with a triangleflag = 1. The number of lines should be specified in the header section via the "triangles" keyword. @@ -1394,7 +1394,7 @@ Wz are in units of angular velocity (radians/time). For atom\_style hybrid, following the 4 initial values (ID,vx,vy,vz), specific values for each sub-style must be listed. The order of the sub-styles is the same as they were listed in the -:doc:`atom\_style ` command. The sub-style specific values +:doc:`atom_style ` command. The sub-style specific values are those that are not the 5 standard ones (ID,vx,vy,vz). For example, for the "sphere" sub-style, "wx", "wy", "wz" values would appear. These are listed in the same order they appear as listed @@ -1431,8 +1431,8 @@ doc page for details. Related commands """""""""""""""" -:doc:`read\_dump `, :doc:`read\_restart `, -:doc:`create\_atoms `, :doc:`write\_data ` +:doc:`read_dump `, :doc:`read_restart `, +:doc:`create_atoms `, :doc:`write_data ` Default """"""" diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index de81a98276..030d55f25a 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -78,15 +78,15 @@ Read atom information from a dump file to overwrite the current atom coordinates, and optionally the atom velocities and image flags and the simulation box dimensions. This is useful for restarting a run from a particular snapshot in a dump file. See the -:doc:`read\_restart ` and :doc:`read\_data ` +:doc:`read_restart ` and :doc:`read_data ` commands for alternative methods to do this. Also see the :doc:`rerun ` command for a means of reading multiple snapshots from a dump file. Note that a simulation box must already be defined before using the read\_dump command. This can be done by the -:doc:`create\_box `, :doc:`read\_data `, or -:doc:`read\_restart ` commands. The read\_dump command can +:doc:`create_box `, :doc:`read_data `, or +:doc:`read_restart ` commands. The read\_dump command can reset the simulation box dimensions, as explained below. Also note that reading per-atom information from a dump snapshot is @@ -95,7 +95,7 @@ explained below. Other atom properties, which may be necessary to run a valid simulation, such as atom charge, or bond topology information for a molecular system, are not read from (or even contained in) dump files. Thus this auxiliary information should be defined in the usual -way, e.g. in a data file read in by a :doc:`read\_data ` +way, e.g. in a data file read in by a :doc:`read_data ` command, before using the read\_dump command, or by the :doc:`set ` command, after the dump snapshot is read. @@ -247,7 +247,7 @@ supported. The dump file does not store atom IDs, so these are assigned consecutively to the atoms as they appear in the dump file, starting from 1. Thus you should insure that order of atoms is consistent from snapshot to snapshot in the XYZ dump file. See -the :doc:`dump\_modify sort ` command if the XYZ dump file +the :doc:`dump_modify sort ` command if the XYZ dump file was written by LAMMPS. For dump files in *molfile* format, the *x*\ , *y*\ , *z*\ , *vx*\ , *vy*\ , and @@ -257,7 +257,7 @@ velocities. The molfile dump files do not store atom IDs, so these are assigned consecutively to the atoms as they appear in the dump file, starting from 1. Thus you should insure that order of atoms are consistent from snapshot to snapshot in the molfile dump file. -See the :doc:`dump\_modify sort ` command if the dump file +See the :doc:`dump_modify sort ` command if the dump file was written by LAMMPS. The *adios* format supports all fields that the *native* format supports @@ -282,7 +282,7 @@ for how this is done, determined by the specified fields and optional keywords. The timestep of the snapshot becomes the current timestep for the -simulation. See the :doc:`reset\_timestep ` command if +simulation. See the :doc:`reset_timestep ` command if you wish to change this after the dump snapshot is read. If the *box* keyword is specified with a *yes* value, then the current @@ -312,7 +312,7 @@ added to the system. They are simply ignored. If a *yes* value is specified, the atoms with new IDs are added to the system but their atom IDs are not preserved. Instead, after all the atoms are added, new IDs are assigned to them in the same manner as is -described for the :doc:`create\_atoms ` command. Basically +described for the :doc:`create_atoms ` command. Basically the largest existing atom ID in the system is identified, and all the added atoms are assigned IDs that consecutively follow the largest ID. @@ -328,7 +328,7 @@ type, so this value must appear in the dump file. Any other attributes (e.g. charge or particle diameter for spherical particles) will be set to default values, the same as if the -:doc:`create\_atoms ` command were used. +:doc:`create_atoms ` command were used. ---------- @@ -406,7 +406,7 @@ Related commands :doc:`dump `, :doc:`dump molfile `, :doc:`dump adios `, -:doc:`read\_data `, :doc:`read\_restart `, +:doc:`read_data `, :doc:`read_restart `, :doc:`rerun ` Default diff --git a/doc/src/read_restart.rst b/doc/src/read_restart.rst index 44210a3a70..321b533acb 100644 --- a/doc/src/read_restart.rst +++ b/doc/src/read_restart.rst @@ -44,7 +44,7 @@ changed by the :doc:`balance ` or :doc:`fix balance ` comm .. note:: Normally, restart files are written by the - :doc:`restart ` or :doc:`write\_restart ` commands + :doc:`restart ` or :doc:`write_restart ` commands so that all atoms in the restart file are inside the simulation box. If this is not the case, the read\_restart command will print an error that atoms were "lost" when the file is read. This error should be @@ -86,7 +86,7 @@ Because restart files are binary, they may not be portable to other machines. In this case, you can use the :doc:`-restart command-line switch ` to convert a restart file to a data file. Similar to how restart files are written (see the -:doc:`write\_restart ` and :doc:`restart ` +:doc:`write_restart ` and :doc:`restart ` commands), the restart filename can contain two wild-card characters. If a "\*" appears in the filename, the directory is searched for all filenames that match the pattern where "\*" is replaced with a timestep @@ -98,7 +98,7 @@ the run command so it doesn't need to be changed either. If a "%" character appears in the restart filename, LAMMPS expects a set of multiple files to exist. The :doc:`restart ` and -:doc:`write\_restart ` commands explain how such sets are +:doc:`write_restart ` commands explain how such sets are created. Read\_restart will first read a filename where "%" is replaced by "base". This file tells LAMMPS how many processors created the set and how many files are in it. Read\_restart then reads @@ -110,7 +110,7 @@ processors that created the restart file. Note that P could be the total number of processors in the previous simulation, or some subset of those processors, if the *fileper* or *nfile* options were used when the restart file was written; see the -:doc:`restart ` and :doc:`write\_restart ` commands +:doc:`restart ` and :doc:`write_restart ` commands for details. The processors in the current LAMMPS simulation share the work of reading these files; each reads a roughly equal subset of the files. The number of processors which created the set can be @@ -146,8 +146,8 @@ these settings after the restart file is read. * :doc:`units ` * :doc:`newton bond ` (see discussion of newton command below) -* :doc:`atom style ` and :doc:`atom\_modify ` settings id, map, sort -* :doc:`comm style ` and :doc:`comm\_modify ` settings mode, cutoff, vel +* :doc:`atom style ` and :doc:`atom_modify ` settings id, map, sort +* :doc:`comm style ` and :doc:`comm_modify ` settings mode, cutoff, vel * :doc:`timestep ` * simulation box size and shape and :doc:`boundary ` settings * atom :doc:`group ` definitions @@ -155,8 +155,8 @@ these settings after the restart file is read. * per-atom attributes including their group assignments and molecular topology attributes (bonds, angles, etc) * force field styles (:doc:`pair `, :doc:`bond `, :doc:`angle `, etc) * force field coefficients (:doc:`pair `, :doc:`bond `, :doc:`angle `, etc) in some cases (see below) -* :doc:`pair\_modify ` settings, except the compute option -* :doc:`special\_bonds ` settings +* :doc:`pair_modify ` settings, except the compute option +* :doc:`special_bonds ` settings Here is a list of information not stored in a restart file, which means you must re-issue these commands in your input script, after @@ -167,8 +167,8 @@ reading the restart file. * :doc:`compute ` commands (see below) * :doc:`variable ` commands * :doc:`region ` commands -* :doc:`neighbor list ` criteria including :doc:`neigh\_modify ` settings -* :doc:`kspace\_style ` and :doc:`kspace\_modify ` settings +* :doc:`neighbor list ` criteria including :doc:`neigh_modify ` settings +* :doc:`kspace_style ` and :doc:`kspace_modify ` settings * info for :doc:`thermodynamic `, :doc:`dump `, or :doc:`restart ` output The :doc:`newton ` command has two settings, one for pairwise @@ -185,10 +185,10 @@ Note that some force field styles (pair, bond, angle, etc) do not store their coefficient info in restart files. Typically these are many-body or tabulated potentials which read their parameters from separate files. In these cases you will need to re-specify the -:doc:`pair\_coeff `, :doc:`bond\_coeff `, etc +:doc:`pair_coeff `, :doc:`bond_coeff `, etc commands in your restart input script. The doc pages for individual force field styles mention if this is the case. This is also true of -:doc:`pair\_style hybrid ` (bond hybrid, angle hybrid, etc) +:doc:`pair_style hybrid ` (bond hybrid, angle hybrid, etc) commands; they do not store coefficient info. As indicated in the above list, the :doc:`fixes ` used for a @@ -250,7 +250,7 @@ LAMMPS allows bond interactions (angle, etc) to be turned off or deleted in various ways, which can affect how their info is stored in a restart file. -If bonds (angles, etc) have been turned off by the :doc:`fix shake ` or :doc:`delete\_bonds ` command, +If bonds (angles, etc) have been turned off by the :doc:`fix shake ` or :doc:`delete_bonds ` command, their info will be written to a restart file as if they are turned on. This means they will need to be turned off again in a new run after the restart file is read. @@ -277,8 +277,8 @@ package must be installed. Related commands """""""""""""""" -:doc:`read\_data `, :doc:`read\_dump `, -:doc:`write\_restart `, :doc:`restart ` +:doc:`read_data `, :doc:`read_dump `, +:doc:`write_restart `, :doc:`restart ` **Default:** none diff --git a/doc/src/region.rst b/doc/src/region.rst index 3eaaae30ac..81e247a8e2 100644 --- a/doc/src/region.rst +++ b/doc/src/region.rst @@ -91,11 +91,11 @@ Description This command defines a geometric region of space. Various other commands use regions. For example, the region can be filled with -atoms via the :doc:`create\_atoms ` command. Or a bounding +atoms via the :doc:`create_atoms ` command. Or a bounding box around the region, can be used to define the simulation box via -the :doc:`create\_box ` command. Or the atoms in the region +the :doc:`create_box ` command. Or the atoms in the region can be identified as a group via the :doc:`group ` command, or -deleted via the :doc:`delete\_atoms ` command. Or the +deleted via the :doc:`delete_atoms ` command. Or the surface of the region can be used as a boundary wall via the :doc:`fix wall/region ` command. Commands which use regions typically test whether an atom's position @@ -127,8 +127,8 @@ box boundary; if the box changes size during a simulation, the region does not. INF means a large negative or positive number (1.0e20), so it should encompass the simulation box even if it changes size. If a region is defined before the simulation box has been created (via -:doc:`create\_box ` or :doc:`read\_data ` or -:doc:`read\_restart ` commands), then an EDGE or INF +:doc:`create_box ` or :doc:`read_data ` or +:doc:`read_restart ` commands), then an EDGE or INF parameter cannot be used. For a *prism* region, a non-zero tilt factor in any pair of dimensions cannot be used if both the lo/hi values in either of those dimensions are INF. E.g. if the xy tilt is @@ -176,7 +176,7 @@ and are called "tilt factors" because they are the amount of displacement applied to faces of an originally orthogonal box to transform it into the parallelepiped. -A prism region that will be used with the :doc:`create\_box ` +A prism region that will be used with the :doc:`create_box ` command to define a triclinic simulation box must have tilt factors (xy,xz,yz) that do not skew the box more than half the distance of corresponding the parallel box length. For example, if xlo = 2 and @@ -198,7 +198,7 @@ the cylinder axes can be a variable with the same kind of effect and requirements than for the radius. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent radius or have a time dependent position of the sphere or cylinder region. @@ -285,12 +285,12 @@ three variables can be specified as NULL, in which case no displacement is calculated in that dimension. Note that equal-style variables can specify formulas with various -mathematical functions, and include :doc:`thermo\_style ` +mathematical functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a region displacement that change as a function of time or spans consecutive runs in a continuous fashion. For the latter, see the *start* and *stop* keywords of the -:doc:`run ` command and the *elaplong* keyword of :doc:`thermo\_style custom ` for details. +:doc:`run ` command and the *elaplong* keyword of :doc:`thermo_style custom ` for details. For example, these commands would displace a region from its initial position, in the positive x direction, effectively at a constant @@ -420,8 +420,8 @@ parameters must be 0.0. Related commands """""""""""""""" -:doc:`lattice `, :doc:`create\_atoms `, -:doc:`delete\_atoms `, :doc:`group ` +:doc:`lattice `, :doc:`create_atoms `, +:doc:`delete_atoms `, :doc:`group ` Default """"""" diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index 65d05265c0..6563ef7dd0 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -73,7 +73,7 @@ initial simulation produced the dump file: Conceptually, using the rerun command is like running an input script that has a loop in it (see the :doc:`next ` and :doc:`jump ` commands). Each iteration of the loop reads one snapshot from the -dump file via the :doc:`read\_dump ` command, sets the +dump file via the :doc:`read_dump ` command, sets the timestep to the appropriate value, and then invokes a :doc:`run ` command for zero timesteps to simply compute energy and forces, and any other :doc:`thermodynamic output ` or diagnostic info @@ -81,18 +81,18 @@ you have defined. This computation also invokes any fixes you have defined that apply constraints to the system, such as :doc:`fix shake ` or :doc:`fix indent `. Note that a simulation box must already be defined before using the -rerun command. This can be done by the :doc:`create\_box `, -:doc:`read\_data `, or :doc:`read\_restart ` +rerun command. This can be done by the :doc:`create_box `, +:doc:`read_data `, or :doc:`read_restart ` commands. Also note that reading per-atom information from dump snapshots is limited to the atom coordinates, velocities and image flags as -explained in the :doc:`read\_dump ` command. Other atom +explained in the :doc:`read_dump ` command. Other atom properties, which may be necessary to compute energies and forces, such as atom charge, or bond topology information for a molecular system, are not read from (or even contained in) dump files. Thus this auxiliary information should be defined in the usual way, e.g. in -a data file read in by a :doc:`read\_data ` command, before +a data file read in by a :doc:`read_data ` command, before using the rerun command. Also note that the frequency of thermodynamic or dump output from the @@ -154,10 +154,10 @@ dump file with a timestep value larger than the *stop* setting you have specified. The *dump* keyword is required and must be the last keyword specified. -Its arguments are passed internally to the :doc:`read\_dump ` +Its arguments are passed internally to the :doc:`read_dump ` command. The first argument following the *dump* keyword should be -the *field1* argument of the :doc:`read\_dump ` command. See -the :doc:`read\_dump ` doc page for details on the various +the *field1* argument of the :doc:`read_dump ` command. See +the :doc:`read_dump ` doc page for details on the various options it allows for extracting information from the dump file snapshots, and for using that information to alter the LAMMPS simulation. @@ -181,12 +181,12 @@ in which you are reprocessing the dump snapshots. If you only want the rerun script to perform an analysis that does not involve pair interactions, such as use compute msd to calculated displacements over time, you do not need to define a :doc:`pair style `, which may also mean neighbor lists will not -need to be calculated which saves time. The :doc:`comm\_modify cutoff ` command can also be used to insure ghost +need to be calculated which saves time. The :doc:`comm_modify cutoff ` command can also be used to insure ghost atoms are acquired from far enough away for operations like bond and angle evaluations, if no pair style is being used. Every time a snapshot is read, the timestep for the simulation is -reset, as if the :doc:`reset\_timestep ` command were +reset, as if the :doc:`reset_timestep ` command were used. This command has some restrictions as to what fixes can be defined. See its doc page for details. For example, the :doc:`fix deposit ` and :doc:`fix dt/reset ` fixes are in this category. They also make no sense to use with a rerun @@ -201,7 +201,7 @@ are read from the dump file(s). If an averaging fix is not invoked on a timestep it expects to be, LAMMPS will flag an error. The various forms of LAMMPS output, as defined by the -:doc:`thermo\_style `, :doc:`thermo `, +:doc:`thermo_style `, :doc:`thermo `, :doc:`dump `, and :doc:`restart ` commands occur with specified frequency, e.g. every N steps. If the timestep for a dump snapshot is not a multiple of N, then it will be read and processed, @@ -224,7 +224,7 @@ doc page for details. Related commands """""""""""""""" -:doc:`read\_dump ` +:doc:`read_dump ` Default """"""" diff --git a/doc/src/reset_ids.rst b/doc/src/reset_ids.rst index 774b9d4628..e41745fa52 100644 --- a/doc/src/reset_ids.rst +++ b/doc/src/reset_ids.rst @@ -39,7 +39,7 @@ Note that the resetting of IDs is not really a compression, where gaps in atom IDs are removed by decrementing atom IDs that are larger. Instead the IDs for all atoms are erased, and new IDs are assigned so that the atoms owned by an individual processor have consecutive IDs, -as the :doc:`create\_atoms ` command explains. +as the :doc:`create_atoms ` command explains. .. note:: @@ -47,7 +47,7 @@ as the :doc:`create\_atoms ` command explains. defined, an error about bond topology atom IDs not being found may result. This is because the cutoff distance for ghost atom communication was not sufficient to find atoms in bonds, angles, etc - that are owned by other processors. The :doc:`comm\_modify cutoff ` command can be used to correct this issue. + that are owned by other processors. The :doc:`comm_modify cutoff ` command can be used to correct this issue. Or you can define a pair style before using this command. If you do the former, you should unset the comm\_modify cutoff after using reset\_ids so that subsequent communication is not inefficient. @@ -59,7 +59,7 @@ Restrictions Related commands """""""""""""""" -:doc:`delete\_atoms ` +:doc:`delete_atoms ` **Default:** none diff --git a/doc/src/reset_timestep.rst b/doc/src/reset_timestep.rst index f898bf2453..e9f8818653 100644 --- a/doc/src/reset_timestep.rst +++ b/doc/src/reset_timestep.rst @@ -27,11 +27,11 @@ Description Set the timestep counter to the specified value. This command normally comes after the timestep has been set by reading a restart -file via the :doc:`read\_restart ` command, or a previous +file via the :doc:`read_restart ` command, or a previous simulation advanced the timestep. -The :doc:`read\_data ` and :doc:`create\_box ` -commands set the timestep to 0; the :doc:`read\_restart ` +The :doc:`read_data ` and :doc:`create_box ` +commands set the timestep to 0; the :doc:`read_restart ` command sets the timestep to the value it had when the restart file was written. diff --git a/doc/src/restart.rst b/doc/src/restart.rst index e061adece3..6cfbdec475 100644 --- a/doc/src/restart.rst +++ b/doc/src/restart.rst @@ -102,7 +102,7 @@ written and read using MPI-IO. Restart files are written on timesteps that are a multiple of N but not on the first timestep of a run or minimization. You can use the -:doc:`write\_restart ` command to write a restart file +:doc:`write_restart ` command to write a restart file before a run begins. A restart file is not written on the last timestep of a run unless it is a multiple of N. A restart file is written on the last timestep of a minimization if N > 0 and the @@ -132,10 +132,10 @@ a simulation where something goes wrong at step 1163: ---------- -See the :doc:`read\_restart ` command for information about +See the :doc:`read_restart ` command for information about what is stored in a restart file. -Restart files can be read by a :doc:`read\_restart ` +Restart files can be read by a :doc:`read_restart ` command to restart a simulation from a particular state. Because the file is binary (to enable exact restarts), it may not be readable on another machine. In this case, you can use the :doc:`-r command-line switch ` to convert a restart file to a data file. @@ -149,7 +149,7 @@ another machine. In this case, you can use the :doc:`-r command-line switch ` + to re-use that information. See the :doc:`read_restart ` command for information about what is stored in a restart file. @@ -188,7 +188,7 @@ package must be installed. Related commands """""""""""""""" -:doc:`write\_restart `, :doc:`read\_restart ` +:doc:`write_restart `, :doc:`read_restart ` Default """"""" diff --git a/doc/src/run.rst b/doc/src/run.rst index 1399c6a963..0cf9f3de1d 100644 --- a/doc/src/run.rst +++ b/doc/src/run.rst @@ -226,7 +226,7 @@ successive runs to run a simulation for any number of steps (ok, up to Related commands """""""""""""""" -:doc:`minimize `, :doc:`run\_style `, +:doc:`minimize `, :doc:`run_style `, :doc:`temper `, :doc:`fix halt ` Default diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index 5dd51f7f1a..b320c57ea8 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -83,10 +83,10 @@ processors. See the :doc:`-partition command-line switch ` for info on how to run LAMMPS with multiple partitions. Specifically, this style performs all computation except the -:doc:`kspace\_style ` portion of the force field on the 1st +:doc:`kspace_style ` portion of the force field on the 1st partition. This include the :doc:`pair style `, :doc:`bond style `, :doc:`neighbor list building `, :doc:`fixes ` including time integration, and output. The -:doc:`kspace\_style ` portion of the calculation is +:doc:`kspace_style ` portion of the calculation is performed on the 2nd partition. This is most useful for the PPPM kspace\_style when its performance on @@ -163,7 +163,7 @@ outermost rRESPA level. Thus if the 3 loop factors are "2 2 2" for 4-level rRESPA, and the outer timestep is set to 4.0 fmsec, then the inner timestep would be 8x smaller or 0.5 fmsec. All other LAMMPS commands that specify number of timesteps (e.g. :doc:`thermo ` -for thermo output every N steps, :doc:`neigh\_modify delay/every ` parameters, :doc:`dump ` every N +for thermo output every N steps, :doc:`neigh_modify delay/every ` parameters, :doc:`dump ` every N steps, etc) refer to the outermost timesteps. The rRESPA keywords enable you to specify at what level of the @@ -176,7 +176,7 @@ outermost level, and kspace forces are computed where pair forces are. The inner, middle, outer forces have no defaults. For fixes that support it, the rRESPA level at which a given fix is -active, can be selected through the :doc:`fix\_modify ` command. +active, can be selected through the :doc:`fix_modify ` command. The *inner* and *middle* keywords take additional arguments for cutoffs that are used by the pairwise force computations. If the 2 @@ -200,7 +200,7 @@ are computed at the same rRESPA level. See the doc pages for individual pair styles for details. Another option for using pair potentials with rRESPA is with the -*hybrid* keyword, which requires the use of the :doc:`pair\_style hybrid or hybrid/overlay ` command. In this scenario, different +*hybrid* keyword, which requires the use of the :doc:`pair_style hybrid or hybrid/overlay ` command. In this scenario, different sub-styles of the hybrid pair style are evaluated at different rRESPA levels. This can be useful, for example, to set different timesteps for hybrid coarse-grained/all-atom models. The *hybrid* keyword diff --git a/doc/src/set.rst b/doc/src/set.rst index 087c3487e5..613c19bcca 100644 --- a/doc/src/set.rst +++ b/doc/src/set.rst @@ -141,11 +141,11 @@ Description """"""""""" Set one or more properties of one or more atoms. Since atom -properties are initially assigned by the :doc:`read\_data `, -:doc:`read\_restart ` or :doc:`create\_atoms ` +properties are initially assigned by the :doc:`read_data `, +:doc:`read_restart ` or :doc:`create_atoms ` commands, this command changes those assignments. This can be useful for overriding the default values assigned by the -:doc:`create\_atoms ` command (e.g. charge = 0.0). It can +:doc:`create_atoms ` command (e.g. charge = 0.0). It can be useful for altering pairwise and molecular force interactions, since force-field coefficients are defined in terms of types. It can be used to change the labeling of atoms by atom type or molecule ID @@ -204,7 +204,7 @@ the variable to reset a property for all atoms is to use style *atom* with *ID* = "\*"; this selects all atom IDs. Atom-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters and timestep and elapsed time. They can also include per-atom values, such as atom coordinates. Thus it is easy to specify a time-dependent or @@ -223,8 +223,8 @@ from a file. Keyword *type* sets the atom type for all selected atoms. The specified value must be from 1 to ntypes, where ntypes was set by the -:doc:`create\_box ` command or the *atom types* field in the -header of the data file read by the :doc:`read\_data ` +:doc:`create_box ` command or the *atom types* field in the +header of the data file read by the :doc:`read_data ` command. Keyword *type/fraction* sets the atom type for a fraction of the @@ -281,8 +281,8 @@ Keyword *quat* uses the specified values to create a quaternion (4-vector) that represents the orientation of the selected atoms. The particles must define a quaternion for their orientation (e.g. ellipsoids, triangles, body particles) as defined by the -:doc:`atom\_style ` command. Note that particles defined by -:doc:`atom\_style ellipsoid ` have 3 shape parameters. The 3 +:doc:`atom_style ` command. Note that particles defined by +:doc:`atom_style ellipsoid ` have 3 shape parameters. The 3 values must be non-zero for each particle set by this command. They are used to specify the aspect ratios of an ellipsoidal particle, which is oriented by default with its x-axis along the simulation @@ -298,7 +298,7 @@ ignored, since a rotation vector of (0,0,1) is the only valid choice. Keyword *quat/random* randomizes the orientation of the quaternion for the selected atoms. The particles must define a quaternion for their orientation (e.g. ellipsoids, triangles, body particles) as defined by -the :doc:`atom\_style ` command. Random numbers are used in +the :doc:`atom_style ` command. Random numbers are used in such a way that the orientation of a particular atom is the same, regardless of how many processors are being used. For 2d systems, only orientations in the xy plane are generated. As with keyword @@ -307,32 +307,32 @@ for each particle set by this command. This keyword does not allow use of an atom-style variable. Keyword *diameter* sets the size of the selected atoms. The particles -must be finite-size spheres as defined by the :doc:`atom\_style sphere ` command. The diameter of a particle can be +must be finite-size spheres as defined by the :doc:`atom_style sphere ` command. The diameter of a particle can be set to 0.0, which means they will be treated as point particles. Note that this command does not adjust the particle mass, even if it was -defined with a density, e.g. via the :doc:`read\_data ` +defined with a density, e.g. via the :doc:`read_data ` command. Keyword *shape* sets the size and shape of the selected atoms. The -particles must be ellipsoids as defined by the :doc:`atom\_style ellipsoid ` command. The *Sx*\ , *Sy*\ , *Sz* settings are +particles must be ellipsoids as defined by the :doc:`atom_style ellipsoid ` command. The *Sx*\ , *Sy*\ , *Sz* settings are the 3 diameters of the ellipsoid in each direction. All 3 can be set to the same value, which means the ellipsoid is effectively a sphere. They can also all be set to 0.0 which means the particle will be treated as a point particle. Note that this command does not adjust the particle mass, even if it was defined with a density, e.g. via the -:doc:`read\_data ` command. +:doc:`read_data ` command. Keyword *length* sets the length of selected atoms. The particles -must be line segments as defined by the :doc:`atom\_style line ` command. If the specified value is non-zero the +must be line segments as defined by the :doc:`atom_style line ` command. If the specified value is non-zero the line segment is (re)set to a length = the specified value, centered around the particle position, with an orientation along the x-axis. If the specified value is 0.0, the particle will become a point particle. Note that this command does not adjust the particle mass, even if it was defined with a density, e.g. via the -:doc:`read\_data ` command. +:doc:`read_data ` command. Keyword *tri* sets the size of selected atoms. The particles must be -triangles as defined by the :doc:`atom\_style tri ` command. +triangles as defined by the :doc:`atom_style tri ` command. If the specified value is non-zero the triangle is (re)set to be an equilateral triangle in the xy plane with side length = the specified value, with a centroid at the particle position, with its base @@ -340,22 +340,22 @@ parallel to the x axis, and the y-axis running from the center of the base to the top point of the triangle. If the specified value is 0.0, the particle will become a point particle. Note that this command does not adjust the particle mass, even if it was defined with a -density, e.g. via the :doc:`read\_data ` command. +density, e.g. via the :doc:`read_data ` command. Keyword *theta* sets the orientation of selected atoms. The particles -must be line segments as defined by the :doc:`atom\_style line ` command. The specified value is used to set the +must be line segments as defined by the :doc:`atom_style line ` command. The specified value is used to set the orientation angle of the line segments with respect to the x axis. Keyword *theta/random* randomizes the orientation of theta for the selected atoms. The particles must be line segments as defined by the -:doc:`atom\_style line ` command. Random numbers are used in +:doc:`atom_style line ` command. Random numbers are used in such a way that the orientation of a particular atom is the same, regardless of how many processors are being used. This keyword does not allow use of an atom-style variable. Keyword *angmom* sets the angular momentum of selected atoms. The -particles must be ellipsoids as defined by the :doc:`atom\_style ellipsoid ` command or triangles as defined by the -:doc:`atom\_style tri ` command. The angular momentum vector +particles must be ellipsoids as defined by the :doc:`atom_style ellipsoid ` command or triangles as defined by the +:doc:`atom_style tri ` command. The angular momentum vector of the particles is set to the 3 specified components. Keyword *omega* sets the angular velocity of selected atoms. The @@ -365,13 +365,13 @@ is set to the 3 specified components. Keyword *mass* sets the mass of all selected particles. The particles must have a per-atom mass attribute, as defined by the -:doc:`atom\_style ` command. See the "mass" command for how +:doc:`atom_style ` command. See the "mass" command for how to set mass values on a per-type basis. Keyword *density* or *density/disc* also sets the mass of all selected particles, but in a different way. The particles must have a per-atom -mass attribute, as defined by the :doc:`atom\_style ` -command. If the atom has a radius attribute (see :doc:`atom\_style sphere `) and its radius is non-zero, its mass is set +mass attribute, as defined by the :doc:`atom_style ` +command. If the atom has a radius attribute (see :doc:`atom_style sphere `) and its radius is non-zero, its mass is set from the density and particle volume for 3d systems (the input density is assumed to be in mass/distance\^3 units). For 2d, the default is for LAMMPS to model particles with a radius attribute as spheres. @@ -380,16 +380,16 @@ modeled as 2d discs (circles). Their mass is set from the density and particle area (the input density is assumed to be in mass/distance\^2 units). -If the atom has a shape attribute (see :doc:`atom\_style ellipsoid `) and its 3 shape parameters are non-zero, +If the atom has a shape attribute (see :doc:`atom_style ellipsoid `) and its 3 shape parameters are non-zero, then its mass is set from the density and particle volume (the input density is assumed to be in mass/distance\^3 units). The *density/disc* keyword has no effect; it does not (yet) treat 3d ellipsoids as 2d ellipses. -If the atom has a length attribute (see :doc:`atom\_style line `) and its length is non-zero, then its mass is +If the atom has a length attribute (see :doc:`atom_style line `) and its length is non-zero, then its mass is set from the density and line segment length (the input density is assumed to be in mass/distance units). If the atom has an area -attribute (see :doc:`atom\_style tri `) and its area is +attribute (see :doc:`atom_style tri `) and its area is non-zero, then its mass is set from the density and triangle area (the input density is assumed to be in mass/distance\^2 units). @@ -397,7 +397,7 @@ If none of these cases are valid, then the mass is set to the density value directly (the input density is assumed to be in mass units). Keyword *volume* sets the volume of all selected particles. -Currently, only the :doc:`atom\_style peri ` command defines +Currently, only the :doc:`atom_style peri ` command defines particles with a volume attribute. Note that this command does not adjust the particle mass. @@ -428,7 +428,7 @@ the specified value from 1 to nbondtypes (nangletypes, etc). All atoms in a particular bond (angle, etc) must be selected atoms in order for the change to be made. The value of nbondtype (nangletypes, etc) was set by the *bond types* (\ *angle types*\ , etc) field in the -header of the data file read by the :doc:`read\_data ` +header of the data file read by the :doc:`read_data ` command. These keywords do not allow use of an atom-style variable. Keywords *meso/e*\ , *meso/cv*\ , and *meso/rho* set the energy, heat @@ -463,13 +463,13 @@ temperature is set to that value. Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric heat capacity of an eDPD particle as defined by the USER-MESO package. -Currently, only :doc:`atom\_style edpd ` defines particles +Currently, only :doc:`atom_style edpd ` defines particles with these attributes. The values for the temperature and heat capacity must be positive. Keyword *cc* sets the chemical concentration of a tDPD particle for a specified species as defined by the USER-MESO package. Currently, only -:doc:`atom\_style tdpd ` defines particles with this +:doc:`atom_style tdpd ` defines particles with this attribute. An integer for "index" selects a chemical species (1 to Nspecies) where Nspecies is set by the atom\_style command. The value for the chemical concentration must be >= 0.0. @@ -485,7 +485,7 @@ Restrictions You cannot set an atom attribute (e.g. *mol* or *q* or *volume*\ ) if -the :doc:`atom\_style ` does not have that attribute. +the :doc:`atom_style ` does not have that attribute. This command requires inter-processor communication to coordinate the setting of bond types (angle types, etc). This means that your system @@ -502,8 +502,8 @@ coordinates outside the simulation box if they are ghost atoms. Related commands """""""""""""""" -:doc:`create\_box `, :doc:`create\_atoms `, -:doc:`read\_data ` +:doc:`create_box `, :doc:`create_atoms `, +:doc:`read_data ` **Default:** none diff --git a/doc/src/special_bonds.rst b/doc/src/special_bonds.rst index 1e30dc2761..824ed5ead0 100644 --- a/doc/src/special_bonds.rst +++ b/doc/src/special_bonds.rst @@ -51,8 +51,8 @@ either directly or via one or two intermediate bonds. These weighting factors are used by nearly all :doc:`pair styles ` in LAMMPS that compute simple pairwise interactions. Permanent bonds between atoms are specified by defining the bond topology in the data file -read by the :doc:`read\_data ` command. Typically a -:doc:`bond\_style ` command is also used to define a bond +read by the :doc:`read_data ` command. Typically a +:doc:`bond_style ` command is also used to define a bond potential. The rationale for using these weighting factors is that the interaction between a pair of bonded atoms is all (or mostly) specified by the bond, angle, dihedral potentials, and thus the @@ -68,7 +68,7 @@ atoms should be excluded (or reduced by a weighting factor). Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no sense to define permanent bonds between atoms that interact via these potentials, though such bonds may exist elsewhere in your system, - e.g. when using the :doc:`pair\_style hybrid ` command. + e.g. when using the :doc:`pair_style hybrid ` command. Thus LAMMPS ignores special\_bonds settings when many-body potentials are calculated. Please note, that the existence of explicit bonds for atoms that are described by a many-body potential will alter the @@ -112,8 +112,8 @@ that interaction will be at full strength. and 1-4 interactions are not defined from the list of angles or dihedrals used by the simulation. Rather, they are inferred topologically from the set of bonds specified when the simulation is - defined from a data or restart file (see :doc:`read\_data ` or - :doc:`read\_restart ` commands). Thus the set of + defined from a data or restart file (see :doc:`read_data ` or + :doc:`read_restart ` commands). Thus the set of 1-2,1-3,1-4 interactions that the weights apply to is the same whether angle and dihedral potentials are computed or not, and remains the same even if bonds are constrained, or turned off, or removed during a @@ -121,9 +121,9 @@ that interaction will be at full strength. The two exceptions to this rule are (a) if the *angle* or *dihedral* keywords are set to *yes* (see below), or (b) if the -:doc:`delete\_bonds ` command is used with the *special* +:doc:`delete_bonds ` command is used with the *special* option that re-computes the 1-2,1-3,1-4 topologies after bonds are -deleted; see the :doc:`delete\_bonds ` command for more +deleted; see the :doc:`delete_bonds ` command for more details. The *amber* keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ @@ -138,7 +138,7 @@ used version of the CHARMM force field. Note that in pair styles *lj/charmm/coul/charmm* and *lj/charmm/coul/long* the 1-4 coefficients are defined explicitly, and these pairwise contributions are computed as part of the charmm dihedral style - see the -:doc:`pair\_coeff ` and :doc:`dihedral\_style ` +:doc:`pair_coeff ` and :doc:`dihedral_style ` commands for more information. See :ref:`(MacKerell) ` for a description of the CHARMM force field. @@ -200,7 +200,7 @@ default, then the 2,5 interaction will also be weighted by 0.5. grow. Note that adding a single bond always adds a new 1st neighbor but may also induce \*many\* new 2nd and 3rd neighbors, depending on the molecular topology of your system. Using the *extra/special/per/atom* - keyword to either :doc:`read\_data ` or :doc:`create\_box ` + keyword to either :doc:`read_data ` or :doc:`create_box ` reserves empty space in the list for this N additional 1st, 2nd, or 3rd neighbors to be added. If you do not do this, you may get an error when bonds (or molecules) are added. @@ -255,7 +255,7 @@ Restrictions Related commands """""""""""""""" -:doc:`delete\_bonds `, :doc:`fix bond/create ` +:doc:`delete_bonds `, :doc:`fix bond/create ` Default """"""" diff --git a/doc/src/suffix.rst b/doc/src/suffix.rst index 263b83187c..f7737b00d9 100644 --- a/doc/src/suffix.rst +++ b/doc/src/suffix.rst @@ -60,7 +60,7 @@ These are the variants these packages provide: * HYBRID = a combination of two packages can be specified (see below) -As an example, all of the packages provide a :doc:`pair\_style lj/cut ` variant, with style names lj/cut/opt, lj/cut/omp, +As an example, all of the packages provide a :doc:`pair_style lj/cut ` variant, with style names lj/cut/opt, lj/cut/omp, lj/cut/gpu, lj/cut/intel, or lj/cut/kk. A variant styles can be specified explicitly in your input script, e.g. pair\_style lj/cut/gpu. If the suffix command is used with the appropriate style, @@ -93,7 +93,7 @@ commands in your input script. .. note:: - The default :doc:`run\_style ` verlet is invoked prior to + The default :doc:`run_style ` verlet is invoked prior to reading the input script and is therefore not affected by a suffix command in the input script. The KOKKOS package requires "run\_style verlet/kk", so when using the KOKKOS package it is necessary to either use the command diff --git a/doc/src/tad.rst b/doc/src/tad.rst index 5322251ed5..d74fb2e8fb 100644 --- a/doc/src/tad.rst +++ b/doc/src/tad.rst @@ -129,7 +129,7 @@ check is performed by quenching the system and comparing the resulting atom coordinates to the coordinates from the previous basin. A quench is an energy minimization and is performed by whichever -algorithm has been defined by the :doc:`min\_style ` command; +algorithm has been defined by the :doc:`min_style ` command; its default is the CG minimizer. The tolerances and limits for each quench can be set by the *min* keyword. Note that typically, you do not need to perform a highly-converged minimization to detect a @@ -304,8 +304,8 @@ Related commands """""""""""""""" :doc:`compute event/displace `, -:doc:`min\_modify `, :doc:`min\_style `, -:doc:`run\_style `, :doc:`minimize `, +:doc:`min_modify `, :doc:`min_style `, +:doc:`run_style `, :doc:`minimize `, :doc:`temper `, :doc:`neb `, :doc:`prd ` diff --git a/doc/src/temper_npt.rst b/doc/src/temper_npt.rst index 8140989189..847d91fb1b 100644 --- a/doc/src/temper_npt.rst +++ b/doc/src/temper_npt.rst @@ -66,7 +66,7 @@ isothermal-isobaric (NPT) ensemble. Related commands """""""""""""""" -:doc:`temper `, :doc:`variable `, :doc:`fix\_npt ` +:doc:`temper `, :doc:`variable `, :doc:`fix_npt ` **Default:** none diff --git a/doc/src/thermo.rst b/doc/src/thermo.rst index 8b11ff9078..503ef84f6d 100644 --- a/doc/src/thermo.rst +++ b/doc/src/thermo.rst @@ -31,8 +31,8 @@ and end of a simulation. A value of 0 will only print thermodynamics at the beginning and end. The content and format of what is printed is controlled by the -:doc:`thermo\_style ` and -:doc:`thermo\_modify ` commands. +:doc:`thermo_style ` and +:doc:`thermo_modify ` commands. Instead of a numeric value, N can be specified as an :doc:`equal-style variable `, which should be specified as v\_name, where name is the variable name. In this case, the variable is evaluated at @@ -60,7 +60,7 @@ Restrictions Related commands """""""""""""""" -:doc:`thermo\_style `, :doc:`thermo\_modify ` +:doc:`thermo_style `, :doc:`thermo_modify ` Default """"""" diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index f0b27d2bc6..c0ec18b465 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -49,7 +49,7 @@ by LAMMPS. .. note:: These options apply to the currently defined thermo style. When - you specify a :doc:`thermo\_style ` command, all + you specify a :doc:`thermo_style ` command, all thermodynamic settings are restored to their default values, including those previously reset by a thermo\_modify command. Thus if your input script specifies a thermo\_style command, you should use the @@ -86,12 +86,12 @@ different defaults for this setting (see below). Even if *norm* is set to *yes*\ , a value is only normalized if it is an "extensive" quantity, meaning that it scales with the number of atoms in the system. For the thermo keywords described by the doc page for the -:doc:`thermo\_style ` command, all energy-related keywords +:doc:`thermo_style ` command, all energy-related keywords are extensive, such as *pe* or *ebond* or *enthalpy*\ . Other keywords such as *temp* or *press* are "intensive" meaning their value is independent (in a statistical sense) of the number of atoms in the system and thus are never normalized. For thermodynamic output values -extracted from fixes and computes in a :doc:`thermo\_style custom ` command, the doc page for the individual +extracted from fixes and computes in a :doc:`thermo_style custom ` command, the doc page for the individual :doc:`fix ` or :doc:`compute ` lists whether the value is "extensive" or "intensive" and thus whether it is normalized. Thermodynamic output values calculated by a variable formula are @@ -111,7 +111,7 @@ containing the timestep and CPU time. This modify option overrides the *one* and *multi* thermo\_style settings. The *format* keyword can be used to change the default numeric format -of any of quantities the :doc:`thermo\_style ` command +of any of quantities the :doc:`thermo_style ` command outputs. All the specified format strings are C-style formats, e.g. as used by the C/C++ printf() command. The *line* keyword takes a single argument which is the format string for the entire line of @@ -147,7 +147,7 @@ temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx", etc). The specified compute ID must have been previously defined by the user via the :doc:`compute ` command and it must be a style of compute that calculates a temperature. As described in the -:doc:`thermo\_style ` command, thermo output uses a default +:doc:`thermo_style ` command, thermo output uses a default compute for temperature with ID = *thermo\_temp*. This option allows the user to override the default. @@ -157,7 +157,7 @@ pressure ("press", "enthalpy", "pxx", etc). The specified compute ID must have been previously defined by the user via the :doc:`compute ` command and it must be a style of compute that calculates a pressure. As described in the -:doc:`thermo\_style ` command, thermo output uses a default +:doc:`thermo_style ` command, thermo output uses a default compute for pressure with ID = *thermo\_press*. This option allows the user to override the default. @@ -180,7 +180,7 @@ Restrictions Related commands """""""""""""""" -:doc:`thermo `, :doc:`thermo\_style ` +:doc:`thermo `, :doc:`thermo_style ` Default """"""" diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 480b14ae63..0aa401dd96 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -131,7 +131,7 @@ include values from previous timesteps, can be output by using the f\_ID keyword and accessing a fix that does time-averaging such as the :doc:`fix ave/time ` command. -Options invoked by the :doc:`thermo\_modify ` command can +Options invoked by the :doc:`thermo_modify ` command can be used to set the one- or multi-line format of the print-out, the normalization of thermodynamic output (total values versus per-atom values for extensive quantities (ones which scale with the number of @@ -141,7 +141,7 @@ atoms in the system), and the numeric precision of each printed value. When you use a "thermo\_style" command, all thermodynamic settings are restored to their default values, including those - previously set by a :doc:`thermo\_modify ` command. Thus + previously set by a :doc:`thermo_modify ` command. Thus if your input script specifies a thermo\_style command, you should use the thermo\_modify command after it. @@ -162,11 +162,11 @@ when LAMMPS starts up, as if this command had been issued: See the :doc:`compute temp ` command for details. Note that the ID of this compute is *thermo\_temp* and the group is *all*\ . You can change the attributes of this temperature (e.g. its -degrees-of-freedom) via the :doc:`compute\_modify ` +degrees-of-freedom) via the :doc:`compute_modify ` command. Alternatively, you can directly assign a new compute (that calculates temperature) which you have defined, to be used for calculating any thermodynamic quantity that requires a temperature. -This is done via the :doc:`thermo\_modify ` command. +This is done via the :doc:`thermo_modify ` command. Several of the thermodynamic quantities require a pressure to be computed: "press", "enthalpy", "pxx", etc. By default this is done by @@ -181,11 +181,11 @@ if this command had been issued: See the :doc:`compute pressure ` command for details. Note that the ID of this compute is *thermo\_press* and the group is *all*\ . You can change the attributes of this pressure via the -:doc:`compute\_modify ` command. Alternatively, you can +:doc:`compute_modify ` command. Alternatively, you can directly assign a new compute (that calculates pressure) which you have defined, to be used for calculating any thermodynamic quantity that requires a pressure. This is done via the -:doc:`thermo\_modify ` command. +:doc:`thermo_modify ` command. Several of the thermodynamic quantities require a potential energy to be computed: "pe", "etotal", "ebond", etc. This is done by using a @@ -200,7 +200,7 @@ command had been issued: See the :doc:`compute pe ` command for details. Note that the ID of this compute is *thermo\_pe* and the group is *all*\ . You can change the attributes of this potential energy via the -:doc:`compute\_modify ` command. +:doc:`compute_modify ` command. ---------- @@ -209,20 +209,20 @@ change the attributes of this potential energy via the The kinetic energy of the system *ke* is inferred from the temperature of the system with 1/2 Kb T of energy for each degree of freedom. Thus, using different :doc:`compute commands ` for calculating -temperature, via the :doc:`thermo\_modify temp ` command, +temperature, via the :doc:`thermo_modify temp ` command, may yield different kinetic energies, since different computes that calculate temperature can subtract out different non-thermal components of velocity and/or include different degrees of freedom (translational, rotational, etc). The potential energy of the system *pe* will include contributions -from fixes if the :doc:`fix\_modify thermo ` option is set +from fixes if the :doc:`fix_modify thermo ` option is set for a fix that calculates such a contribution. For example, the :doc:`fix wall/lj93 ` fix calculates the energy of atoms interacting with the wall. See the doc pages for "individual fixes" to see which ones contribute. A long-range tail correction *etail* for the VanderWaal pairwise -energy will be non-zero only if the :doc:`pair\_modify tail ` option is turned on. The *etail* contribution +energy will be non-zero only if the :doc:`pair_modify tail ` option is turned on. The *etail* contribution is included in *evdwl*\ , *epair*\ , *pe*\ , and *etotal*\ , and the corresponding tail correction to the pressure is included in *press* and *pxx*\ , *pyy*\ , etc. @@ -302,7 +302,7 @@ printed with the end-of-run statistics. The *nbuild* keyword is the number of re-builds during the current run. The *ndanger* keyword is the number of re-builds that LAMMPS considered potentially "dangerous". If atom movement triggered neighbor list rebuilding (see -the :doc:`neigh\_modify ` command), then dangerous +the :doc:`neigh_modify ` command), then dangerous reneighborings are those that were triggered on the first timestep atom movement was checked for. If this count is non-zero you may wish to reduce the delay factor to insure no force interactions are missed @@ -372,7 +372,7 @@ kinetic energy that are summed over all atoms in the compute group. Intensive quantities are printed directly without normalization by thermo\_style custom. Extensive quantities may be normalized by the total number of atoms in the simulation (NOT the number of atoms in -the compute group) when output, depending on the :doc:`thermo\_modify norm ` option being used. +the compute group) when output, depending on the :doc:`thermo_modify norm ` option being used. The *f\_ID* and *f\_ID[I]* and *f\_ID[I][J]* keywords allow global values calculated by a fix to be output. As discussed on the @@ -396,7 +396,7 @@ energy that are summed over all atoms in the fix group. Intensive quantities are printed directly without normalization by thermo\_style custom. Extensive quantities may be normalized by the total number of atoms in the simulation (NOT the number of atoms in the fix group) -when output, depending on the :doc:`thermo\_modify norm ` +when output, depending on the :doc:`thermo_modify norm ` option being used. The *v\_name* keyword allow the current value of a variable to be @@ -427,14 +427,14 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. Related commands """""""""""""""" -:doc:`thermo `, :doc:`thermo\_modify `, -:doc:`fix\_modify `, :doc:`compute temp `, +:doc:`thermo `, :doc:`thermo_modify `, +:doc:`fix_modify `, :doc:`compute temp `, :doc:`compute pressure ` Default diff --git a/doc/src/third_order.rst b/doc/src/third_order.rst index 13a230d511..d49f790812 100644 --- a/doc/src/third_order.rst +++ b/doc/src/third_order.rst @@ -66,7 +66,7 @@ LAMMPS was built with that package. See the :doc:`Build package Related commands """""""""""""""" -:doc:`fix phonon ` :doc:`dynamical\_matrix ` +:doc:`fix phonon ` :doc:`dynamical_matrix ` Default """"""" diff --git a/doc/src/timer.rst b/doc/src/timer.rst index c36b436b06..a5ef8ca137 100644 --- a/doc/src/timer.rst +++ b/doc/src/timer.rst @@ -122,7 +122,7 @@ Restrictions Related commands """""""""""""""" -:doc:`run post no `, :doc:`kspace\_modify fftbench ` +:doc:`run post no `, :doc:`kspace_modify fftbench ` Default """"""" diff --git a/doc/src/timestep.rst b/doc/src/timestep.rst index da1a132a32..ddbe33a9d2 100644 --- a/doc/src/timestep.rst +++ b/doc/src/timestep.rst @@ -43,7 +43,7 @@ Related commands """""""""""""""" :doc:`fix dt/reset `, :doc:`run `, -:doc:`run\_style ` respa, :doc:`units ` +:doc:`run_style ` respa, :doc:`units ` Default """"""" diff --git a/doc/src/uncompute.rst b/doc/src/uncompute.rst index e27a5fcc34..941a7b7b38 100644 --- a/doc/src/uncompute.rst +++ b/doc/src/uncompute.rst @@ -27,7 +27,7 @@ Description Delete a compute that was previously defined with a :doc:`compute ` command. This also wipes out any additional changes made to the compute -via the :doc:`compute\_modify ` command. +via the :doc:`compute_modify ` command. Restrictions """""""""""" diff --git a/doc/src/unfix.rst b/doc/src/unfix.rst index dcd4e58c3d..016ac211aa 100644 --- a/doc/src/unfix.rst +++ b/doc/src/unfix.rst @@ -27,7 +27,7 @@ Description Delete a fix that was previously defined with a :doc:`fix ` command. This also wipes out any additional changes made to the fix -via the :doc:`fix\_modify ` command. +via the :doc:`fix_modify ` command. Restrictions """""""""""" diff --git a/doc/src/units.rst b/doc/src/units.rst index 6c0815f302..57558a4f53 100644 --- a/doc/src/units.rst +++ b/doc/src/units.rst @@ -80,12 +80,12 @@ results from a unitless LJ simulation into physical quantities. * density = mass/volume, where rho\* = rho sigma\^dim Note that for LJ units, the default mode of thermodynamic output via -the :doc:`thermo\_style ` command is to normalize all +the :doc:`thermo_style ` command is to normalize all extensive quantities by the number of atoms. E.g. potential energy is extensive because it is summed over atoms, so it is output as energy/atom. Temperature is intensive since it is already normalized by the number of atoms, so it is output as-is. This behavior can be -changed via the :doc:`thermo\_modify norm ` command. +changed via the :doc:`thermo_modify norm ` command. For style *real*\ , these are the units: @@ -220,7 +220,7 @@ Restrictions This command cannot be used after the simulation box is defined by a -:doc:`read\_data ` or :doc:`create\_box ` command. +:doc:`read_data ` or :doc:`create_box ` command. **Related commands:** none diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 99413ce96c..3e44b56f37 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -113,7 +113,7 @@ strings, the :doc:`next ` command can be used to increment which string is assigned to the variable. Variables of style *equal* store a formula which when evaluated produces a single numeric value which can be output either directly (see the :doc:`print `, :doc:`fix print `, and :doc:`run every ` commands) or as part -of thermodynamic output (see the :doc:`thermo\_style ` +of thermodynamic output (see the :doc:`thermo_style ` command), or used as input to an averaging fix (see the :doc:`fix ave/time ` command). Variables of style *vector* store a formula which produces a vector of such values which can be used as input to various averaging fixes, or elements of which can be @@ -425,7 +425,7 @@ For the *internal* style a numeric value is provided. This value will be assigned to the variable until a LAMMPS command sets it to a new value. There are currently only two LAMMPS commands that require *internal* variables as inputs, because they reset them: -:doc:`create\_atoms ` and :doc:`fix controller `. As mentioned above, an +:doc:`create_atoms ` and :doc:`fix controller `. As mentioned above, an internal-style variable can be used in place of an equal-style variable anywhere else in an input script, e.g. as an argument to another command that allows for equal-style variables. @@ -557,10 +557,10 @@ will not work, since the *version* has been introduced more recently): if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes" The thermo keywords allowed in a formula are those defined by the -:doc:`thermo\_style custom ` command. Thermo keywords that +:doc:`thermo_style custom ` command. Thermo keywords that require a :doc:`compute ` to calculate their values such as "temp" or "press", use computes stored and invoked by the -:doc:`thermo\_style ` command. This means that you can +:doc:`thermo_style ` command. This means that you can only use those keywords in a variable if the style you are using with the thermo\_style command (and the thermo keywords associated with that style) also define and use the needed compute. Note that some thermo @@ -688,7 +688,7 @@ timestep. X,y > 0 and x > y are required. The generated timesteps increase in a staggered fashion, as the sequence x,x+y,2x,2x+y,3x,3x+y,etc. For any current timestep, the next timestep in the sequence is returned. Thus if stagger(1000,100) is -used in a variable by the :doc:`dump\_modify every ` +used in a variable by the :doc:`dump_modify every ` command, it will generate the sequence of output timesteps: @@ -703,7 +703,7 @@ y value is how many of the z-1 possible timesteps within one logarithmic interval are generated. I.e. the timesteps follow the sequence x,2x,3x,...y\*x,x\*z,2x\*z,3x\*z,...y\*x\*z,x\*z\^2,2x\*z\^2,etc. For any current timestep, the next timestep in the sequence is returned. -Thus if logfreq(100,4,10) is used in a variable by the :doc:`dump\_modify every ` command, it will generate this sequence of +Thus if logfreq(100,4,10) is used in a variable by the :doc:`dump_modify every ` command, it will generate this sequence of output timesteps: @@ -714,7 +714,7 @@ output timesteps: The logfreq2(x,y,z) function is similar to logfreq, except a single logarithmic interval is divided into y equally-spaced timesteps and all of them are output. Y < z is not required. Thus, if -logfreq2(100,18,10) is used in a variable by the :doc:`dump\_modify every ` command, then the interval between 100 and +logfreq2(100,18,10) is used in a variable by the :doc:`dump_modify every ` command, then the interval between 100 and 1000 is divided as 900/18 = 50 steps, and it will generate the sequence of output timesteps: @@ -743,7 +743,7 @@ the sequence x,x+z,x+2z,...,y. If y-x is not a multiple of z, then similar to the way a for loop operates, the last value will be one that does not exceed y. For any current timestep, the next timestep in the sequence is returned. Thus if stride(1000,2000,100) is used -in a variable by the :doc:`dump\_modify every ` command, it +in a variable by the :doc:`dump_modify every ` command, it will generate the sequence of output timesteps: @@ -763,7 +763,7 @@ that point the timestep increases in increments of c, from a to b, then after b, increments by z are resumed until y is reached. For any current timestep, the next timestep in the sequence is returned. Thus if stride2(1000,2000,100,1350,1360,1) is used in a variable by the -:doc:`dump\_modify every ` command, it will generate the +:doc:`dump_modify every ` command, it will generate the sequence of output timesteps: @@ -786,7 +786,7 @@ where dt = the timestep size. The run begins on startstep. Startstep can span multiple runs, using the *start* keyword of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. Note that the -:doc:`thermo\_style ` keyword elaplong = +:doc:`thermo_style ` keyword elaplong = timestep-startstep. The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments: @@ -805,7 +805,7 @@ where dt = the timestep size. The run begins on startstep. Startstep can span multiple runs, using the *start* keyword of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. Note that the -:doc:`thermo\_style ` keyword elaplong = +:doc:`thermo_style ` keyword elaplong = timestep-startstep. @@ -1045,7 +1045,7 @@ evaluating the variable. The meaning of the different atom values and vectors is mostly self-explanatory. *Mol* refers to the molecule ID of an atom, and is -only defined if an :doc:`atom\_style ` is being used that +only defined if an :doc:`atom_style ` is being used that defines molecule IDs. Note that many other atom attributes can be used as inputs to a @@ -1260,7 +1260,7 @@ the string between the parenthesis as an equal-style variable formula. Referencing a variable with a leading "v\_" is an optional or required kind of argument for some commands (e.g. the :doc:`fix ave/chunk ` or :doc:`dump custom ` or -:doc:`thermo\_style ` commands) if you wish it to evaluate +:doc:`thermo_style ` commands) if you wish it to evaluate a variable periodically during a run. It can also be used in a variable formula if you wish to reference a second variable. The second variable will be evaluated whenever the first variable is @@ -1333,7 +1333,7 @@ bond, etc) on timesteps that the variable will need the values. LAMMPS keeps track of all of this during a :doc:`run ` or :doc:`energy minimization `. An error will be generated if you attempt to evaluate a variable on timesteps when it cannot produce -accurate values. For example, if a :doc:`thermo\_style custom ` command prints a variable which accesses +accurate values. For example, if a :doc:`thermo_style custom ` command prints a variable which accesses values stored by a :doc:`fix ave/time ` command and the timesteps on which thermo output is generated are not multiples of the averaging frequency used in the fix command, then an error will occur. @@ -1423,10 +1423,10 @@ commands: print "Final potential energy = $e" The first run is performed using one setting for the pairwise -potential defined by the :doc:`pair\_style ` and -:doc:`pair\_coeff ` commands. The potential energy is +potential defined by the :doc:`pair_style ` and +:doc:`pair_coeff ` commands. The potential energy is evaluated on the final timestep and stored by the :doc:`compute pe ` compute (this is done by the -:doc:`thermo\_style ` command). Then a pair coefficient is +:doc:`thermo_style ` command). Then a pair coefficient is changed, altering the potential energy of the system. When the potential energy is printed via the "e" variable, LAMMPS will use the potential energy value stored by the :doc:`compute pe ` @@ -1461,7 +1461,7 @@ Restrictions Indexing any formula element by global atom ID, such as an atom value, requires the :doc:`atom style ` to use a global mapping in order to look up the vector indices. By default, only atom styles -with molecular information create global maps. The :doc:`atom\_modify map ` command can override the default, e.g. for +with molecular information create global maps. The :doc:`atom_modify map ` command can override the default, e.g. for atomic-style atom styles. All *universe*\ - and *uloop*\ -style variables defined in an input script diff --git a/doc/src/velocity.rst b/doc/src/velocity.rst index 5a4bb33d0c..314a5681e5 100644 --- a/doc/src/velocity.rst +++ b/doc/src/velocity.rst @@ -85,7 +85,7 @@ variable is used, the velocity it calculates must be in box units, not lattice units; see the discussion of the *units* keyword below. Equal-style variables can specify formulas with various mathematical -functions, and include :doc:`thermo\_style ` command +functions, and include :doc:`thermo_style ` command keywords for the simulation box parameters or other parameters. Atom-style variables can specify the same formulas as equal-style @@ -202,7 +202,7 @@ it owns. This can be a slow loop for a large simulation. If atoms were read from a data file, the velocity assigned to a particular atom will be the same, independent of how many processors are being used. This will not be the case if atoms were created using the -:doc:`create\_atoms ` command, since atom IDs will likely +:doc:`create_atoms ` command, since atom IDs will likely be assigned to atoms differently. If loop = local, then each processor loops over only its atoms to diff --git a/doc/src/write_coeff.rst b/doc/src/write_coeff.rst index 4b452d7928..4a293f7e3f 100644 --- a/doc/src/write_coeff.rst +++ b/doc/src/write_coeff.rst @@ -27,7 +27,7 @@ Description Write a text format file with the currently defined force field coefficients in a way, that it can be read by LAMMPS with the :doc:`include ` command. In combination with the nocoeff -option of :doc:`write\_data ` this can be used to move +option of :doc:`write_data ` this can be used to move the Coeffs sections from a data file into a separate file. .. note:: @@ -49,8 +49,8 @@ none Related commands """""""""""""""" -:doc:`read\_data `, :doc:`write\_restart `, -:doc:`write\_data ` +:doc:`read_data `, :doc:`write_restart `, +:doc:`write_data ` .. _lws: http://lammps.sandia.gov diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst index 63e15c45f3..3ff9f155b0 100644 --- a/doc/src/write_data.rst +++ b/doc/src/write_data.rst @@ -39,7 +39,7 @@ Description Write a data file in text format of the current state of the simulation. Data files can be read by the :doc:`read data ` -command to begin a simulation. The :doc:`read\_data ` command +command to begin a simulation. The :doc:`read_data ` command also describes their format. Similar to :doc:`dump ` files, the data filename can contain a "\*" @@ -52,7 +52,7 @@ value. respects. First, most pair styles do not yet write their coefficient information into the data file. This means you will need to specify that information in your input script that reads the data file, via - the :doc:`pair\_coeff ` command. Second, a few of the :doc:`atom styles ` (body, ellipsoid, line, tri) that store + the :doc:`pair_coeff ` command. Second, a few of the :doc:`atom styles ` (body, ellipsoid, line, tri) that store auxiliary "bonus" information about aspherical particles, do not yet write the bonus info into the data file. Both these functionalities will be added to the write\_data command later. @@ -66,8 +66,8 @@ thus typically diverge from a simulation that continued in the original input script. If you want to do more exact restarts, using binary files, see the -:doc:`restart `, :doc:`write\_restart `, and -:doc:`read\_restart ` commands. You can also convert +:doc:`restart `, :doc:`write_restart `, and +:doc:`read_restart ` commands. You can also convert binary restart files to text data files, after a simulation has run, using the :doc:`-r command-line switch `. @@ -78,7 +78,7 @@ using the :doc:`-r command-line switch `. :doc:`fixes ` are stored. :doc:`Binary restart files ` store more information. -Bond interactions (angle, etc) that have been turned off by the :doc:`fix shake ` or :doc:`delete\_bonds ` command will +Bond interactions (angle, etc) that have been turned off by the :doc:`fix shake ` or :doc:`delete_bonds ` command will be written to a data file as if they are turned on. This means they will need to be turned off again in a new run after the data file is read. @@ -98,7 +98,7 @@ are read in separately anyway, e.g. from an include file. The *nofix* keyword requests that no extra sections read by fixes should be written to the data file (see the *fix* option of the -:doc:`read\_data ` command for details). For example, this +:doc:`read_data ` command for details). For example, this option excludes sections for user-created per-atom properties from :doc:`fix property/atom `. @@ -108,9 +108,9 @@ is specified as *ii*\ , then one line per atom type is written, to specify the coefficients for each of the I=J interactions. This means that no cross-interactions for I != J will be specified in the data file and the pair style will apply its mixing rule, as documented on -individual :doc:`pair\_style ` doc pages. Of course this +individual :doc:`pair_style ` doc pages. Of course this behavior can be overridden in the input script after reading the data -file, by specifying additional :doc:`pair\_coeff ` commands +file, by specifying additional :doc:`pair_coeff ` commands for any desired I,J pairs. If the value is specified as *ij*\ , then one line of coefficients is @@ -120,7 +120,7 @@ point. The presence of these I != J coefficients in the data file will effectively turn off the default mixing rule for the pair style. Again, the coefficient values in the data file can be overridden in the input script after reading the data file, by specifying -additional :doc:`pair\_coeff ` commands for any desired I,J +additional :doc:`pair_coeff ` commands for any desired I,J pairs. @@ -139,7 +139,7 @@ setup, atom masses initialized, etc). Related commands """""""""""""""" -:doc:`read\_data `, :doc:`write\_restart ` +:doc:`read_data `, :doc:`write_restart ` Default """"""" diff --git a/doc/src/write_dump.rst b/doc/src/write_dump.rst index e894406a22..afd7470ce8 100644 --- a/doc/src/write_dump.rst +++ b/doc/src/write_dump.rst @@ -15,8 +15,8 @@ Syntax * style = any of the supported :doc:`dump styles ` * file = name of file to write dump info to * dump-args = any additional args needed for a particular :doc:`dump style ` -* modify = all args after this keyword are passed to :doc:`dump\_modify ` (optional) -* dump-modify-args = args for :doc:`dump\_modify ` (optional) +* modify = all args after this keyword are passed to :doc:`dump_modify ` (optional) +* dump-modify-args = args for :doc:`dump_modify ` (optional) Examples @@ -45,11 +45,11 @@ dump style to write out snapshots periodically during a running simulation. The syntax for this command is mostly identical to that of the -:doc:`dump ` and :doc:`dump\_modify ` commands as if +:doc:`dump ` and :doc:`dump_modify ` commands as if they were concatenated together, with the following exceptions: There is no need for a dump ID or dump frequency and the keyword *modify* is added. The latter is so that the full range of -:doc:`dump\_modify ` options can be specified for the single +:doc:`dump_modify ` options can be specified for the single snapshot, just as they can be for multiple snapshots. The *modify* keyword separates the arguments that would normally be passed to the *dump* command from those that would be given the *dump\_modify*. Both @@ -71,7 +71,7 @@ Restrictions All restrictions for the :doc:`dump ` and -:doc:`dump\_modify ` commands apply to this command as well, +:doc:`dump_modify ` commands apply to this command as well, with the exception of the :doc:`dump image ` filename not requiring a wildcard "\*" character, as noted above. @@ -90,13 +90,13 @@ Related commands """""""""""""""" :doc:`dump `, :doc:`dump image `, -:doc:`dump\_modify ` +:doc:`dump_modify ` Default """"""" The defaults are listed on the doc pages for the :doc:`dump ` and -:doc:`dump image ` and :doc:`dump\_modify ` +:doc:`dump image ` and :doc:`dump_modify ` commands. diff --git a/doc/src/write_restart.rst b/doc/src/write_restart.rst index 853a046ed9..734bbb3a44 100644 --- a/doc/src/write_restart.rst +++ b/doc/src/write_restart.rst @@ -73,7 +73,7 @@ does not have to end in ".mpiio", just contain those characters. Unlike MPI-IO dump files, a particular restart file must be both written and read using MPI-IO. -Restart files can be read by a :doc:`read\_restart ` +Restart files can be read by a :doc:`read_restart ` command to restart a simulation from a particular state. Because the file is binary (to enable exact restarts), it may not be readable on another machine. In this case, you can use the :doc:`-r command-line switch ` to convert a restart file to a data file. @@ -89,7 +89,7 @@ another machine. In this case, you can use the :doc:`-r command-line switch ` command for general information about + :doc:`read_restart ` command for general information about what is stored in a restart file. @@ -133,8 +133,8 @@ package must be installed. Related commands """""""""""""""" -:doc:`restart `, :doc:`read\_restart `, -:doc:`write\_data ` +:doc:`restart `, :doc:`read_restart `, +:doc:`write_data ` **Default:** none diff --git a/doc/txt/Build.txt b/doc/txt/Build.txt deleted file mode 100644 index 8906549350..0000000000 --- a/doc/txt/Build.txt +++ /dev/null @@ -1,51 +0,0 @@ -"Previous Section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Run_head.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Build LAMMPS :h2 - -LAMMPS can be built as an executable or library from source code via -either traditional makefiles (which may require manual editing) -for use with GNU make or gmake, or a build environment generated by CMake -(Unix Makefiles, Xcode, Visual Studio, KDevelop or more). As an -alternative you can download a package with pre-built executables -as described on the "Install"_Install.html doc page. - - - - - -"Build LAMMPS with CMake"_Build_cmake.html -"Build LAMMPS with make"_Build_make.html -"Link LAMMPS as a library to another code"_Build_link.html -"Basic build options"_Build_basics.html -"Optional build settings"_Build_settings.html -"Include packages in build"_Build_package.html -"Packages with extra build options"_Build_extras.html -"Notes for building LAMMPS on Windows"_Build_windows.html -"Development build options (CMake only)"_Build_development.html :all(b) - -If you have problems building LAMMPS, it is often due to software -issues on your local machine. If you can, find a local expert to -help. If you're still stuck, send an email to the "LAMMPS mail -list"_http://lammps.sandia.gov/mail.html. diff --git a/doc/txt/Build_basics.txt b/doc/txt/Build_basics.txt deleted file mode 100644 index cde1055419..0000000000 --- a/doc/txt/Build_basics.txt +++ /dev/null @@ -1,359 +0,0 @@ -"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Basic build options :h3 - -The following topics are covered on this page, for building both with -CMake and make: - -"Serial vs parallel build"_#serial -"Choice of compiler and compile/link options"_#compile -"Build LAMMPS as an executable or a library"_#exe -"Build the LAMMPS documentation"_#doc -"Install LAMMPS after a build"_#install :ul - -:line - -Serial vs parallel build :h4,link(serial) - -LAMMPS can be built to run in parallel using the ubiquitous "MPI -(message-passing -interface)"_https://en.wikipedia.org/wiki/Message_Passing_Interface -library. Or it can built to run on a single processor (serial) -without MPI. It can also be built with support for OpenMP threading -(see more discussion below). - -[CMake variables]: - --D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI, else no --D BUILD_OMP=value # yes or no (default) --D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc - # no default value :pre - -The executable created by CMake (after running make) is lmp_name. If -the LAMMPS_MACHINE variable is not specified, the executable is just -lmp. Using BUILD_MPI=no will produce a serial executable. - -[Traditional make]: - -cd lammps/src -make mpi # parallel build, produces lmp_mpi using Makefile.mpi -make serial # serial build, produces lmp_serial using Makefile/serial -make mybox :pre # uses Makefile.mybox to produce lmp_mybox :pre - -Serial build (see src/MAKE/Makefile.serial): - -MPI_INC = -I../STUBS -MPI_PATH = -L../STUBS -MPI_LIB = -lmpi_stubs :pre - -For a parallel build, if MPI is installed on your system in the usual -place (e.g. under /usr/local), you do not need to specify the 3 -variables MPI_INC, MPI_PATH, MPI_LIB. The MPI wrapper on the compiler -(e.g. mpicxx, mpiCC) knows where to find the needed include and -library files. Failing this, these 3 variables can be used to specify -where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH) -are found, and the name of the library files (MPI_LIB). - -For a serial build, you need to specify the 3 variables, as shown -above. - -For a serial LAMMPS build, use the dummy MPI library provided in -src/STUBS. You also need to build the STUBS library for your platform -before making LAMMPS itself. A "make serial" build does this for. -Otherwise, type "make mpi-stubs" from the src directory, or "make" -from the src/STUBS dir. If the build fails, you will need to edit the -STUBS/Makefile for your platform. - -The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime() -that calls gettimeofday() . If your system doesn't support -gettimeofday() , you'll need to insert code to call another timer. -Note that the ANSI-standard function clock() rolls over after an hour -or so, and is therefore insufficient for timing long LAMMPS -simulations. - -[CMake and make info]: - -If you are installing MPI yourself, we recommend MPICH2 from Argonne -National Laboratory or OpenMPI. MPICH can be downloaded from the -"Argonne MPI site"_http://www.mcs.anl.gov/research/projects/mpich2/. -OpenMPI can be downloaded from the "OpenMPI -site"_http://www.open-mpi.org. Other MPI packages should also work. -If you are running on a large parallel machine, your system admins or -the vendor should have already installed a version of MPI, which is -likely to be faster than a self-installed MPICH or OpenMPI, so find -out how to build and link with it. - -The majority of OpenMP (threading) support in LAMMPS is provided by -the USER-OMP package; see the "Speed omp"_Speed_omp.html doc page for -details. The USER-INTEL package also provides OpenMP support (it is -compatible with USER-OMP) and adds vectorization support when compiled -with the Intel compilers on top of that. Also, the KOKKOS package can -be compiled for using OpenMP threading. - -However, there are a few commands in LAMMPS that have native OpenMP -support. These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and -USER-DPD packages. In addition some packages support OpenMP threading -indirectly through the libraries they interface to: e.g. LATTE and -USER-COLVARS. See the "Packages details"_Packages_details.html doc -page for more info on these packages and the doc pages for their -respective commands for OpenMP threading info. - -For CMake, if you use BUILD_OMP=yes, you can use these packages and -turn on their native OpenMP support and turn on their native OpenMP -support at run time, by setting the OMP_NUM_THREADS environment -variable before you launch LAMMPS. - -For building via conventional make, the CCFLAGS and LINKFLAGS -variables in Makefile.machine need to include the compiler flag that -enables OpenMP. For GNU compilers it is -fopenmp. For (recent) Intel -compilers it is -qopenmp. If you are using a different compiler, -please refer to its documentation. - -[OpenMP Compiler compatibility info]: :link(default-none-issues) - -Some compilers do not fully support the 'default(none)' directive -and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0 -semantics, which are incompatible with the OpenMP 3.1 directives used -in LAMMPS (for maximal compatibility with compiler versions in use). -In those case, all 'default(none)' directives (which aid in detecting -incorrect and unwanted sharing) can be replaced with 'default(shared)' -while dropping all 'shared()' directives. The script -'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate -this conversion. - -:line - -Choice of compiler and compile/link options :h4,link(compile) - -The choice of compiler and compiler flags can be important for -performance. Vendor compilers can produce faster code than -open-source compilers like GNU. On boxes with Intel CPUs, we suggest -trying the "Intel C++ compiler"_intel. - -:link(intel,https://software.intel.com/en-us/intel-compilers) - -On parallel clusters or supercomputers which use "modules" for their -compile/link environments, you can often access different compilers by -simply loading the appropriate module before building LAMMPS. - -[CMake variables]: - --D CMAKE_CXX_COMPILER=name # name of C++ compiler --D CMAKE_C_COMPILER=name # name of C compiler --D CMAKE_Fortran_COMPILER=name # name of Fortran compiler :pre - --D CMAKE_CXX_FLAGS=string # flags to use with C++ compiler --D CMAKE_C_FLAGS=string # flags to use with C compiler --D CMAKE_Fortran_FLAGS=string # flags to use with Fortran compiler :pre - -By default CMake will use a compiler it finds and it will add -optimization flags appropriate to that compiler and any "accelerator -packages"_Speed_packages.html you have included in the build. - -You can tell CMake to look for a specific compiler with these variable -settings. Likewise you can specify the FLAGS variables if you want to -experiment with alternate optimization flags. You should specify all -3 compilers, so that the small number of LAMMPS source files written -in C or Fortran are built with a compiler consistent with the one used -for all the C++ files: - -Building with GNU Compilers: -cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran -Building with Intel Compilers: -cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort -Building with LLVM/Clang Compilers: -cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang :pre - -NOTE: When the cmake command completes, it prints info to the screen -as to which compilers it is using, and what flags will be used in the -compilation. Note that if the top-level compiler is mpicxx, it is -simply a wrapper on a real compiler. The underlying compiler info is -what will be listed in the CMake output. You should check to insure -you are using the compiler and optimization flags are the ones you -want. - -[Makefile.machine settings]: - -Parallel build (see src/MAKE/Makefile.mpi): - -CC = mpicxx -CCFLAGS = -g -O3 -LINK = mpicxx -LINKFLAGS = -g -O :pre - -Serial build (see src/MAKE/Makefile.serial): - -CC = g++ -CCFLAGS = -g -O3 -LINK = g++ -LINKFLAGS = -g -O :pre - -The "compiler/linker settings" section of a Makefile.machine lists -compiler and linker settings for your C++ compiler, including -optimization flags. You should always use mpicxx or mpiCC for -a parallel build, since these compiler wrappers will include -a variety of settings appropriate for your MPI installation. - -NOTE: If you build LAMMPS with any "accelerator -packages"_Speed_packages.html included, they have specific -optimization flags that are either required or recommended for optimal -performance. You need to include these in the CCFLAGS and LINKFLAGS -settings above. For details, see the individual package doc pages -listed on the "Speed packages"_Speed_packages.html doc page. Or -examine these files in the src/MAKE/OPTIONS directory. They -correspond to each of the 5 accelerator packages and their hardware -variants: - -Makefile.opt # OPT package -Makefile.omp # USER-OMP package -Makefile.intel_cpu # USER-INTEL package for CPUs -Makefile.intel_coprocessor # USER-INTEL package for KNLs -Makefile.gpu # GPU package -Makefile.kokkos_cuda_mpi # KOKKOS package for GPUs -Makefile.kokkos_omp # KOKKOS package for CPUs (OpenMP) -Makefile.kokkos_phi # KOKKOS package for KNLs (OpenMP) :pre - -:line - -Build LAMMPS as an executable or a library :h4,link(exe) - -LAMMPS can be built as either an executable or as a static or shared -library. The LAMMPS library can be called from another application or -a scripting language. See the "Howto couple"_Howto_couple.html doc -page for more info on coupling LAMMPS to other codes. See the -"Python"_Python_head.html doc page for more info on wrapping and -running LAMMPS from Python via its library interface. - -[CMake variables]: - --D BUILD_EXE=value # yes (default) or no --D BUILD_LIB=value # yes or no (default) --D BUILD_SHARED_LIBS=value # yes or no (default) --D LAMMPS_LIB_SUFFIX=name # name = mpi, serial, mybox, titan, laptop, etc - # no default value :pre - - -Setting BUILD_EXE=no will not produce an executable. Setting -BUILD_LIB=yes will produce a static library named liblammps.a. -Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a -shared library named liblammps.so. If LAMMPS_LIB_SUFFIX is set the generated -libraries will be named liblammps_name.a or liblammps_name.so instead. - -[Traditional make]: - -cd lammps/src -make machine # build LAMMPS executable lmp_machine -make mode=lib machine # build LAMMPS static lib liblammps_machine.a -make mode=shlib machine # build LAMMPS shared lib liblammps_machine.so :pre - -The two library builds also create generic soft links, named -liblammps.a and liblammps.so, which point to the liblammps_machine -files. - -[CMake and make info]: - -Note that for a shared library to be usable by a calling program, all -the auxiliary libraries it depends on must also exist as shared -libraries. This will be the case for libraries included with LAMMPS, -such as the dummy MPI library in src/STUBS or any package libraries in -the lib/packages directory, since they are always built as shared -libraries using the -fPIC switch. However, if a library like MPI or -FFTW does not exist as a shared library, the shared library build will -generate an error. This means you will need to install a shared -library version of the auxiliary library. The build instructions for -the library should tell you how to do this. - -As an example, here is how to build and install the "MPICH -library"_mpich, a popular open-source version of MPI, distributed by -Argonne National Lab, as a shared library in the default -/usr/local/lib location: - -:link(mpich,http://www-unix.mcs.anl.gov/mpi) - -./configure --enable-shared -make -make install :pre - -You may need to use "sudo make install" in place of the last line if -you do not have write privileges for /usr/local/lib. The end result -should be the file /usr/local/lib/libmpich.so. - -:line - -Build the LAMMPS documentation :h4,link(doc) - -[CMake variable]: - --D BUILD_DOC=value # yes or no (default) :pre - -This will create the HTML doc pages within the CMake build directory. -The reason to do this is if you want to "install" LAMMPS on a system -after the CMake build via "make install", and include the doc pages in -the install. - -[Traditional make]: - -cd lammps/doc -make html # html doc pages -make pdf # single Manual.pdf file :pre - -This will create a lammps/doc/html dir with the HTML doc pages so that -you can browse them locally on your system. Type "make" from the -lammps/doc dir to see other options. - -NOTE: You can also download a tarball of the documentation for the -current LAMMPS version (HTML and PDF files), from the website -"download page"_http://lammps.sandia.gov/download.html. - -:line - -Build LAMMPS tools :h4,link(tools) - -Some tools described in "Auxiliary tools"_Tools.html can be built directly -using CMake or Make. - -[CMake variable]: - --D BUILD_TOOLS=value # yes or no (default) :pre - -The generated binaries will also become part of the LAMMPS installation (see below) - -[Traditional make]: - -cd lammps/tools -make all # build all binaries of tools -make binary2txt # build only binary2txt tool -make chain # build only chain tool -make micelle2d # build only micelle2d tool -make thermo_extract # build only thermo_extract tool -:pre - -:line - - -Install LAMMPS after a build :h4,link(install) - -After building LAMMPS, you may wish to copy the LAMMPS executable of -library, along with other LAMMPS files (library header, doc files) to -a globally visible place on your system, for others to access. Note -that you may need super-user privileges (e.g. sudo) if the directory -you want to copy files to is protected. - -[CMake variable]: - -cmake -D CMAKE_INSTALL_PREFIX=path \[options ...\] ../cmake -make # perform make after CMake command -make install # perform the installation into prefix :pre - -[Traditional make]: - -There is no "install" option in the src/Makefile for LAMMPS. If you -wish to do this you will need to first build LAMMPS, then manually -copy the desired LAMMPS files to the appropriate system directories. diff --git a/doc/txt/Build_cmake.txt b/doc/txt/Build_cmake.txt deleted file mode 100644 index b2411272eb..0000000000 --- a/doc/txt/Build_cmake.txt +++ /dev/null @@ -1,212 +0,0 @@ -"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Build LAMMPS with CMake :h3 - -This page is a short summary of how to use CMake to build LAMMPS. -Details on CMake variables that enable specific LAMMPS build options -are given on the pages linked to from the "Build"_Build.html doc page. - -Richard Berger (Temple U) has also written a "more comprehensive -guide"_https://github.com/lammps/lammps/blob/master/cmake/README.md -for how to use CMake to build LAMMPS. If you are new to CMake it is a -good place to start. - -:line - -Building LAMMPS with CMake is a two-step process. First you use CMake -to create a build environment in a new directory. On Linux systems, -this will be based on makefiles for use with make. Then you use the -make command to build LAMMPS, which uses the created -Makefile(s). Example: - -cd lammps # change to the LAMMPS distribution directory -mkdir build; cd build # create a new directory (folder) for build -cmake \[options ...\] ../cmake # configuration with (command-line) cmake -make # compilation :pre - -The cmake command will detect available features, enable selected -packages and options, and will generate the build environment. By default -this build environment will be created for "Unix Makefiles" on most -platforms and particularly on Linux. However, alternate build tools -(e.g. Ninja) and support files for Integrated Development Environments -(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is -selected via the "-G" command line flag. For the rest of the documentation -we will assume that the build environment is generated for makefiles -and thus the make command will be used to compile and link LAMMPS as -indicated above, producing (by default) an executable called "lmp" and -a library called "liblammps.a" in the "build" folder. When generating -a build environment for the "Ninja" build tool, the build command would -be "ninja" instead of "make". - -If your machine has multiple CPU cores (most do these days), using a -command like "make -jN" (with N being the number of available local -CPU cores) can be much faster. If you plan to do development on -LAMMPS or need to re-compile LAMMPS repeatedly, installation of the -ccache (= Compiler Cache) software may speed up repeated compilation -even more. - -After compilation, you may optionally install the LAMMPS executable into -your system with: - -make install # optional, copy LAMMPS executable & library elsewhere :pre - -This will install the lammps executable and library (if requested), some -tools (if configured) and additional files like library API headers, -manpages, potential and force field files. The location of the installation -tree is set by the CMake variable "CMAKE_INSTALL_PREFIX" which defaults -to $\{HOME\}/.local - -:line - -There are 3 variants of CMake: a command-line version (cmake), a text mode -UI version (ccmake), and a graphical GUI version (cmake-GUI). You can use -any of them interchangeably to configure and create the LAMMPS build -environment. On Linux all the versions produce a Makefile as their -output. See more details on each below. - -You can specify a variety of options with any of the 3 versions, which -affect how the build is performed and what is included in the LAMMPS -executable. Links to pages explaining all the options are listed on -the "Build"_Build.html doc page. - -You must perform the CMake build system generation and compilation in -a new directory you create. It can be anywhere on your local machine. -In these Build pages we assume that you are building in a directory -called "lammps/build". You can perform separate builds independently -with different options, so long as you perform each of them in a -separate directory you create. All the auxiliary files created by one -build process (executable, object files, log files, etc) are stored in -this directory or sub-directories within it that CMake creates. - -NOTE: To perform a CMake build, no packages can be installed or a -build been previously attempted in the LAMMPS src directory by using -"make" commands to "perform a conventional LAMMPS -build"_Build_make.html. CMake detects if this is the case and -generates an error, telling you to type "make no-all purge" in the src -directory to un-install all packages. The purge removes all the *.h -files auto-generated by make. - -You must have CMake version 2.8 or later on your system to build -LAMMPS. A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a -later version. CMake will print a message telling you if a later -version is required. Installation instructions for CMake are below. - -After the initial build, if you edit LAMMPS source files, or add your -own new files to the source directory, you can just re-type make from -your build directory and it will re-compile only the files that have -changed. If you want to change CMake options you can run cmake (or -ccmake or cmake-gui) again from the same build directory and alter -various options; see details below. Or you can remove the entire build -folder, recreate the directory and start over. - -:line - -[Command-line version of CMake]: - -cmake \[options ...\] /path/to/lammps/cmake # build from any dir -cmake \[options ...\] ../cmake # build from lammps/build :pre - -The cmake command takes one required argument, which is the LAMMPS -cmake directory which contains the CMakeLists.txt file. - -The argument can be preceeded or followed by various CMake -command-line options. Several useful ones are: - --D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired --D CMAKE_BUILD_TYPE=type # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug --G output # style of output CMake generates --DVARIABLE=value # setting for a LAMMPS feature to enable --D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir --C path/to/preset/file # load some CMake settings before configuring :pre - -All the LAMMPS-specific -D variables that a LAMMPS build supports are -described on the pages linked to from the "Build"_Build.html doc page. -All of these variable names are upper-case and their values are -lower-case, e.g. -D LAMMPS_SIZES=smallbig. For boolean values, any of -these forms can be used: yes/no, on/off, 1/0. - -On Unix/Linux machines, CMake generates a Makefile by default to -perform the LAMMPS build. Alternate forms of build info can be -generated via the -G switch, e.g. Visual Studio on a Windows machine, -Xcode on MacOS, or KDevelop on Linux. Type "cmake --help" to see the -"Generator" styles of output your system supports. - -NOTE: When CMake runs, it prints configuration info to the screen. -You should review this to verify all the features you requested were -enabled, including packages. You can also see what compilers and -compile options will be used for the build. Any errors in CMake -variable syntax will also be flagged, e.g. mis-typed variable names or -variable values. - -CMake creates a CMakeCache.txt file when it runs. This stores all the -settings, so that when running CMake again you can use the current -folder '.' instead of the path to the LAMMPS cmake folder as the -required argument to the CMake command. Either way the existing -settings will be inherited unless the CMakeCache.txt file is removed. - -If you later want to change a setting you can rerun cmake in the build -directory with different setting. Please note that some automatically -detected variables will not change their value when you rerun cmake. -In these cases it is usually better to first remove all the -files/directories in the build directory, or start with a fresh build -directory. - -:line - -[Curses version (terminal-style menu) of CMake]: - -ccmake ../cmake :pre - -You initiate the configuration and build environment generation steps -separately. For the first you have to type [c], for the second you -have to type [g]. You may need to type [c] multiple times, and may be -required to edit some of the entries of CMake configuration variables -in between. Please see the "ccmake -manual"_https://cmake.org/cmake/help/latest/manual/ccmake.1.html for -more information. - -:line - -[GUI version of CMake]: - -cmake-gui ../cmake :pre - -You initiate the configuration and build environment generation steps -separately. For the first you have to click on the [Configure] button, -for the second you have to click on the [Generate] button. You may -need to click on [Configure] multiple times, and may be required to -edit some of the entries of CMake configuration variables in between. -Please see the "cmake-gui -manual"_https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html -for more information. - -:line - -[Installing CMake] - -Check if your machine already has CMake installed: - -which cmake # do you have it? -which cmake3 # version 3 may have this name -cmake --version # what specific version you have :pre - -On clusters or supercomputers which use environment modules to manage -software packages, do this: - -module list # is a cmake module already loaded? -module avail # is a cmake module available? -module load cmake3 # load cmake module with appropriate name :pre - -Most Linux distributions offer pre-compiled cmake packages through -their package management system. If you do not have CMake or a new -enough version, you can download the latest version at -"https://cmake.org/download/"_https://cmake.org/download/. -Instructions on how to install it on various platforms can be found -"on this page"_https://cmake.org/install/. diff --git a/doc/txt/Build_development.txt b/doc/txt/Build_development.txt deleted file mode 100644 index bd3897fba6..0000000000 --- a/doc/txt/Build_development.txt +++ /dev/null @@ -1,86 +0,0 @@ -"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Development build options (CMake only) :h3 - -The CMake build of LAMMPS has a few extra options which are useful during -development, testing or debugging. - -:line - -Verify compilation flags :h4,link(compilation) - -Sometimes it is necessary to verify the complete sequence of compilation flags -generated by the CMake build. To enable a more verbose output during -compilation you can use the following option. - --D CMAKE_VERBOSE_MAKEFILE=value # value = no (default) or yes :pre - -Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1: - -make VERBOSE=1 :pre - -:line - -Address, Undefined Behavior, and Thread Sanitizer Support :h4,link(sanitizer) - -Compilers such as GCC and Clang support generating binaries which use different -sanitizers to detect problems in code during run-time. They can detect "memory leaks"_https://clang.llvm.org/docs/AddressSanitizer.html, -code that runs into "undefined behavior"_https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html of the -language and "data races"_https://clang.llvm.org/docs/ThreadSanitizer.html in threaded code. - -The following settings allow you enable these features if your compiler supports -it. Please note that they come with a performance hit. However, they are -usually faster than using tools like Valgrind. - --D ENABLE_SANITIZE_ADDRESS=value # enable Address Sanitizer, value = no (default) or yes --D ENABLE_SANITIZE_UNDEFINED=value # enable Undefined Behaviour Sanitizer, value = no (default) or yes --D ENABLE_SANITIZE_THREAD=value # enable Thread Sanitizer, value = no (default) or yes -:pre - -:line - -Code Coverage and Testing :h4,link(testing) - -We do extensive regression testing of the LAMMPS code base on a continuous -basis. Some of the logic to do this has been added to the CMake build so -developers can run the tests directly on their workstation. - -NOTE: this is incomplete and only represents a small subset of tests that we run - --D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes --D LAMMPS_TESTING_SOURCE_DIR=path # path to lammps-testing repository (option if in custom location) --D LAMMPS_TESTING_GIT_TAG=value # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag -:pre - -If you enable testing in the CMake build it will create an additional target called "test". You can run them with: - -make test -:pre - -The test cases used come from the lammps-testing repository. They are -derivatives of the examples folder with some modifications to make the run -faster. - -You can also collect code coverage metrics while running the tests by enabling -coverage support during building. - --D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes :pre - -This will also add the following targets to generate coverage reports after running the LAMMPS executable: - -make test # run tests first! -make gen_coverage_html # generate coverage report in HTML format -make gen_coverage_xml # generate coverage report in XML format -:pre - -These reports require GCOVR to be installed. The easiest way to do this to install it via pip: - -pip install git+https://github.com/gcovr/gcovr.git :pre -:pre diff --git a/doc/txt/Build_extras.txt b/doc/txt/Build_extras.txt deleted file mode 100644 index 4cf40bbee4..0000000000 --- a/doc/txt/Build_extras.txt +++ /dev/null @@ -1,1170 +0,0 @@ -"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Packages with extra build options :h3 - -When building with some packages, additional steps may be required, -in addition to: - --D PKG_NAME=yes # CMake -make yes-name # make :pre - -as described on the "Build_package"_Build_package.html doc page. - -For a CMake build there may be additional optional or required -variables to set. For a build with make, a provided library under the -lammps/lib directory may need to be built first. Or an external -library may need to exist on your system or be downloaded and built. -You may need to tell LAMMPS where it is found on your system. - -This is the list of packages that may require additional steps. - -"COMPRESS"_#compress, -"GPU"_#gpu, -"KIM"_#kim, -"KOKKOS"_#kokkos, -"LATTE"_#latte, -"MESSAGE"_#message, -"MSCG"_#mscg, -"OPT"_#opt, -"POEMS"_#poems, -"PYTHON"_#python, -"VORONOI"_#voronoi, -"USER-ADIOS"_#user-adios, -"USER-ATC"_#user-atc, -"USER-AWPMD"_#user-awpmd, -"USER-COLVARS"_#user-colvars, -"USER-H5MD"_#user-h5md, -"USER-INTEL"_#user-intel, -"USER-MOLFILE"_#user-molfile, -"USER-NETCDF"_#user-netcdf, -"USER-PLUMED"_#user-plumed, -"USER-OMP"_#user-omp, -"USER-QMMM"_#user-qmmm, -"USER-QUIP"_#user-quip, -"USER-SCAFACOS"_#user-scafacos, -"USER-SMD"_#user-smd, -"USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l) - -:line - -COMPRESS package :h4,link(compress) - -To build with this package you must have the zlib compression library -available on your system. - -[CMake build]: - -If CMake cannot find the library, you can set these variables: - --D ZLIB_INCLUDE_DIR=path # path to zlib.h header file --D ZLIB_LIBRARIES=path # path to libz.a (.so) file :pre - -[Traditional make]: - -If make cannot find the library, you can edit the -lib/compress/Makefile.lammps file to specify the paths and library -name. - -:line - -GPU package :h4,link(gpu) - -To build with this package, you must choose options for precision and -which GPU hardware to build for. - -[CMake build]: - --D GPU_API=value # value = opencl (default) or cuda --D GPU_PREC=value # precision setting - # value = double or mixed (default) or single --D OCL_TUNE=value # hardware choice for GPU_API=opencl - # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA) --D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda - # value = sm_XX, see below - # default is sm_30 --D CUDPP_OPT=value # optimization setting for GPU_API=cuda - # enables CUDA Performance Primitives Optimizations - # value = yes (default) or no --D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon - # value = yes or no (default) :pre - -GPU_ARCH settings for different GPU hardware is as follows: - -sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5) -sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5) -sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5) -sm_50 or sm_52 for Maxwell (supported since CUDA 6) -sm_60 or sm_61 for Pascal (supported since CUDA 8) -sm_70 for Volta (supported since CUDA 9) -sm_75 for Turing (supported since CUDA 10) :ul - -A more detailed list can be found, for example, -at "Wikipedia's CUDA article"_https://en.wikipedia.org/wiki/CUDA#GPUs_supported - -CMake can detect which version of the CUDA toolkit is used and thus can -include support for [all] major GPU architectures supported by this toolkit. -Thus the GPU_ARCH setting is merely an optimization, to have code for -the preferred GPU architecture directly included rather than having to wait -for the JIT compiler of the CUDA driver to translate it. - -[Traditional make]: - -Before building LAMMPS, you must build the GPU library in lib/gpu. -You can do this manually if you prefer; follow the instructions in -lib/gpu/README. Note that the GPU library uses MPI calls, so you must -use the same MPI library (or the STUBS library) settings as the main -LAMMPS code. This also applies to the -DLAMMPS_BIGBIG, --DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL settings in whichever -Makefile you use. - -You can also build the library in one step from the lammps/src dir, -using a command like these, which simply invoke the lib/gpu/Install.py -script with the specified args: - -make lib-gpu # print help message -make lib-gpu args="-b" # build GPU library with default Makefile.linux -make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision -make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi :pre - -Note that this procedure starts with a Makefile.machine in lib/gpu, as -specified by the "-m" switch. For your convenience, machine makefiles -for "mpi" and "serial" are provided, which have the same settings as -the corresponding machine makefiles in the main LAMMPS source -folder. In addition you can alter 4 important settings in the -Makefile.machine you start from via the corresponding -c, -a, -p, -e -switches (as in the examples above), and also save a copy of the new -Makefile if desired: - -CUDA_HOME = where NVIDIA CUDA software is installed on your system -CUDA_ARCH = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above -CUDA_PRECISION = precision (double, mixed, single) -EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul - -The file Makefile.linux_multi is set up to include support for multiple -GPU architectures as supported by the CUDA toolkit in use. This is done -through using the "--gencode " flag, which can be used multiple times and -thus support all GPU architectures supported by your CUDA compiler. - -If the library build is successful, 3 files should be created: -lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and -lib/gpu/Makefile.lammps. The latter has settings that enable LAMMPS -to link with CUDA libraries. If the settings in Makefile.lammps for -your machine are not correct, the LAMMPS build will fail, and -lib/gpu/Makefile.lammps may need to be edited. - -NOTE: If you re-build the GPU library in lib/gpu, you should always -un-install the GPU package in lammps/src, then re-install it and -re-build LAMMPS. This is because the compilation of files in the GPU -package uses the library settings from the lib/gpu/Makefile.machine -used to build the GPU library. - - -:line - -KIM package :h4,link(kim) - -To build with this package, the KIM library with API v2 must be downloaded -and built on your system. It must include the KIM models that you want to -use with LAMMPS. If you want to use the "kim_query"_kim_commands.html -command, you also need to have libcurl installed with the matching -development headers and the curl-config tool. - -See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to -learn how to install a pre-build binary of the OpenKIM Repository of Models. -See the list of all KIM models here: https://openkim.org/browse/models - -(Also note that when downloading and installing from source -the KIM API library with all its models, may take a long time (tens of -minutes to hours) to build. Of course you only need to do that once.) - -[CMake build]: - --D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes --D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off, value = off (default) or on --D LMP_NO_SSL_CHECK=value # tell libcurl to not verify the peer, value = no (default) or yes -:pre - -If DOWNLOAD_KIM is set, the KIM library will be downloaded and built -inside the CMake build directory. If the KIM library is already on -your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH -environment variable so that libkim-api can be found. - -For using OpenKIM web queries in LAMMPS. - -If LMP_DEBUG_CURL is set, the libcurl verbose mode will be on, and any -libcurl calls within the KIM web query display a lot of information about -libcurl operations. You hardly ever want this set in production use, you will -almost always want this when you debug/report problems. - -The libcurl performs peer SSL certificate verification by default. This -verification is done using a CA certificate store that the SSL library can -use to make sure the peer's server certificate is valid. If SSL reports an -error ("certificate verify failed") during the handshake and thus refuses -further communication with that server, you can set LMP_NO_SSL_CHECK. -If LMP_NO_SSL_CHECK is set, libcurl does not verify the peer and connection -succeeds regardless of the names in the certificate. This option is insecure. -As an alternative, you can specify your own CA cert path by setting the -environment variable CURL_CA_BUNDLE to the path of your choice. A call to the -KIM web query would get this value from the environmental variable. - -[Traditional make]: - -You can download and build the KIM library manually if you prefer; -follow the instructions in lib/kim/README. You can also do it in one -step from the lammps/src dir, using a command like these, which simply -invoke the lib/kim/Install.py script with the specified args. - -make lib-kim # print help message -make lib-kim args="-b " # (re-)install KIM API lib with only example models -make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model -make lib-kim args="-b -a everything" # install KIM API lib with all models -make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver -make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location -make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre - -:line - -KOKKOS package :h4,link(kokkos) - -To build with this package, you must choose which hardware you want to -build for, either CPUs (multi-threading via OpenMP) or KNLs (OpenMP) -or GPUs (NVIDIA Cuda). - -For a CMake or make build, these are the possible choices for the -KOKKOS_ARCH settings described below. Note that for CMake, these are -really Kokkos variables, not LAMMPS variables. Hence you must use -case-sensitive values, e.g. BDW, not bdw. - -ARMv80 = ARMv8.0 Compatible CPU -ARMv81 = ARMv8.1 Compatible CPU -ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU -BGQ = IBM Blue Gene/Q CPUs -Power8 = IBM POWER8 CPUs -Power9 = IBM POWER9 CPUs -SNB = Intel Sandy/Ivy Bridge CPUs -HSW = Intel Haswell CPUs -BDW = Intel Broadwell Xeon E-class CPUs -SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512) -KNC = Intel Knights Corner Xeon Phi -KNL = Intel Knights Landing Xeon Phi -Kepler30 = NVIDIA Kepler generation CC 3.0 -Kepler32 = NVIDIA Kepler generation CC 3.2 -Kepler35 = NVIDIA Kepler generation CC 3.5 -Kepler37 = NVIDIA Kepler generation CC 3.7 -Maxwell50 = NVIDIA Maxwell generation CC 5.0 -Maxwell52 = NVIDIA Maxwell generation CC 5.2 -Maxwell53 = NVIDIA Maxwell generation CC 5.3 -Pascal60 = NVIDIA Pascal generation CC 6.0 -Pascal61 = NVIDIA Pascal generation CC 6.1 -Volta70 = NVIDIA Volta generation CC 7.0 -Volta72 = NVIDIA Volta generation CC 7.2 -Turing75 = NVIDIA Turing generation CC 7.5 :ul - -[CMake build]: - -For multicore CPUs using OpenMP, set these 2 variables. - --D KOKKOS_ARCH=archCPU # archCPU = CPU from list above --D KOKKOS_ENABLE_OPENMP=yes :pre - -For Intel KNLs using OpenMP, set these 2 variables: - --D KOKKOS_ARCH=KNL --D KOKKOS_ENABLE_OPENMP=yes :pre - -For NVIDIA GPUs using CUDA, set these 4 variables: - --D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU - # archGPU = GPU from list above --D KOKKOS_ENABLE_CUDA=yes --D KOKKOS_ENABLE_OPENMP=yes --D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper :pre - -The wrapper value is the Cuda nvcc compiler wrapper provided in the -Kokkos library: lib/kokkos/bin/nvcc_wrapper. The setting should -include the full path name to the wrapper, e.g. - --D CMAKE_CXX_COMPILER=/home/username/lammps/lib/kokkos/bin/nvcc_wrapper :pre - -[Traditional make]: - -Choose which hardware to support in Makefile.machine via -KOKKOS_DEVICES and KOKKOS_ARCH settings. See the -src/MAKE/OPTIONS/Makefile.kokkos* files for examples. - -For multicore CPUs using OpenMP: - -KOKKOS_DEVICES = OpenMP -KOKKOS_ARCH = archCPU # archCPU = CPU from list above :pre - -For Intel KNLs using OpenMP: - -KOKKOS_DEVICES = OpenMP -KOKKOS_ARCH = KNL :pre - -For NVIDIA GPUs using CUDA: - -KOKKOS_DEVICES = Cuda -KOKKOS_ARCH = archCPU,archGPU # archCPU = CPU from list above that is hosting the GPU - # archGPU = GPU from list above :pre - -For GPUs, you also need these 2 lines in your Makefile.machine before -the CC line is defined, in this case for use with OpenMPI mpicxx. The -2 lines define a nvcc wrapper compiler, which will use nvcc for -compiling CUDA files and use a C++ compiler for non-Kokkos, non-CUDA -files. - -KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd) -export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper -CC = mpicxx :pre - -:line - -LATTE package :h4,link(latte) - -To build with this package, you must download and build the LATTE -library. - -[CMake build]: - --D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes --D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location) :pre - -If DOWNLOAD_LATTE is set, the LATTE library will be downloaded and -built inside the CMake build directory. If the LATTE library is -already on your system (in a location CMake cannot find it), -LATTE_LIBRARY is the filename (plus path) of the LATTE library file, -not the directory the library file is in. - -[Traditional make]: - -You can download and build the LATTE library manually if you prefer; -follow the instructions in lib/latte/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invokes the lib/latte/Install.py script with the specified -args: - -make lib-latte # print help message -make lib-latte args="-b" # download and build in lib/latte/LATTE-master -make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte -make lib-latte args="-b -m gfortran" # download and build in lib/latte and - # copy Makefile.lammps.gfortran to Makefile.lammps -:pre - -Note that 3 symbolic (soft) links, "includelink" and "liblink" and -"filelink.o", are created in lib/latte to point into the LATTE home -dir. When LAMMPS itself is built it will use these links. You should -also check that the Makefile.lammps file you create is appropriate for -the compiler you use on your system to build LATTE. - -:line - -MESSAGE package :h4,link(message) - -This package can optionally include support for messaging via sockets, -using the open-source "ZeroMQ library"_http://zeromq.org, which must -be installed on your system. - -[CMake build]: - --D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes --D ZMQ_LIBRARY=path # ZMQ library file (only needed if a custom location) --D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location) -:pre - -[Traditional make]: - -Before building LAMMPS, you must build the CSlib library in -lib/message. You can build the CSlib library manually if you prefer; -follow the instructions in lib/message/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invoke the lib/message/Install.py script with the specified args: - -make lib-message # print help message -make lib-message args="-m -z" # build with MPI and socket (ZMQ) support -make lib-message args="-s" # build as serial lib with no ZMQ support -:pre - -The build should produce two files: lib/message/cslib/src/libmessage.a -and lib/message/Makefile.lammps. The latter is copied from an -existing Makefile.lammps.* and has settings to link with the ZeroMQ -library if requested in the build. - -:line - -MSCG package :h4,link(mscg) - -To build with this package, you must download and build the MS-CG -library. Building the MS-CG library and using it from LAMMPS requires -a C++11 compatible compiler and that the GSL (GNU Scientific Library) -headers and libraries are installed on your machine. See the -lib/mscg/README and MSCG/Install files for more details. - -[CMake build]: - --D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes --D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location) --D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location) :pre - -If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built -inside the CMake build directory. If the MSCG library is already on -your system (in a location CMake cannot find it), MSCG_LIBRARY is the -filename (plus path) of the MSCG library file, not the directory the -library file is in. MSCG_INCLUDE_DIR is the directory the MSCG -include file is in. - -[Traditional make]: - -You can download and build the MS-CG library manually if you prefer; -follow the instructions in lib/mscg/README. You can also do it in one -step from the lammps/src dir, using a command like these, which simply -invoke the lib/mscg/Install.py script with the specified args: - -make lib-mscg # print help message -make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master - # with the settings compatible with "make serial" -make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master - # with the settings compatible with "make mpi" -make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre - -Note that 2 symbolic (soft) links, "includelink" and "liblink", will -be created in lib/mscg to point to the MS-CG src/installation dir. -When LAMMPS is built in src it will use these links. You should not -need to edit the lib/mscg/Makefile.lammps file. - -:line - -OPT package :h4,link(opt) - -[CMake build]: - -No additional settings are needed besides "-D PKG_OPT=yes". - -[Traditional make]: - -The compile flag "-restrict" must be used to build LAMMPS with the OPT -package when using Intel compilers. It should be added to the CCFLAGS -line of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.opt for -an example. - -:line - -POEMS package :h4,link(poems) - -[CMake build]: - -No additional settings are needed besides "-D PKG_OPT=yes". - -[Traditional make]: - -Before building LAMMPS, you must build the POEMS library in lib/poems. -You can do this manually if you prefer; follow the instructions in -lib/poems/README. You can also do it in one step from the lammps/src -dir, using a command like these, which simply invoke the -lib/poems/Install.py script with the specified args: - -make lib-poems # print help message -make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial") -make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi") -make lib-poems args="-m icc" # build with Intel icc compiler :pre - -The build should produce two files: lib/poems/libpoems.a and -lib/poems/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -POEMS library (though typically the settings are just blank). If -necessary, you can edit/create a new lib/poems/Makefile.machine file -for your system, which should define an EXTRAMAKE variable to specify -a corresponding Makefile.lammps.machine file. - -:line - -PYTHON package :h4,link(python) - -Building with the PYTHON package requires you have a Python shared -library available on your system, which needs to be a Python 2 -version, 2.6 or later. Python 3 is not yet supported. See -lib/python/README for more details. - -[CMake build]: - --D PYTHON_EXECUTABLE=path # path to Python executable to use :pre - -Without this setting, CMake will guess the default Python on your -system. To use a different Python version, you can either create a -virtualenv, activate it and then run cmake. Or you can set the -PYTHON_EXECUTABLE variable to specify which Python interpreter should -be used. Note note that you will also need to have the development -headers installed for this version, e.g. python2-devel. - -[Traditional make]: - -The build uses the lib/python/Makefile.lammps file in the compile/link -process to find Python. You should only need to create a new -Makefile.lammps.* file (and copy it to Makefile.lammps) if the LAMMPS -build fails. - -:line - -VORONOI package :h4,link(voronoi) - -To build with this package, you must download and build the "Voro++ -library"_voro-home. - -:link(voro-home,http://math.lbl.gov/voro++) - -[CMake build]: - --D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes --D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location) --D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location) :pre - -If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and -built inside the CMake build directory. If the Voro++ library is -already on your system (in a location CMake cannot find it), -VORO_LIBRARY is the filename (plus path) of the Voro++ library file, -not the directory the library file is in. VORO_INCLUDE_DIR is the -directory the Voro++ include file is in. - -[Traditional make]: - -You can download and build the Voro++ library manually if you prefer; -follow the instructions in lib/voronoi/README. You can also do it in -one step from the lammps/src dir, using a command like these, which -simply invoke the lib/voronoi/Install.py script with the specified -args: - -make lib-voronoi # print help message -make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++- -make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++ -make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre - -Note that 2 symbolic (soft) links, "includelink" and "liblink", are -created in lib/voronoi to point to the Voro++ src dir. When LAMMPS -builds in src it will use these links. You should not need to edit -the lib/voronoi/Makefile.lammps file. - -:line - -USER-ADIOS package :h4,link(user-adios) - -The USER-ADIOS package requires the "ADIOS I/O library"_https://github.com/ornladios/ADIOS2, -version 2.3.1 or newer. Make sure that you have ADIOS built either with or -without MPI to match if you build LAMMPS with or without MPI. -ADIOS compilation settings for LAMMPS are automatically detected, if the PATH -and LD_LIBRARY_PATH environment variables have been updated for the local ADIOS -installation and the instructions below are followed for the respective build systems. - -[CMake build]: - --D ADIOS2_DIR=path # path is where ADIOS 2.x is installed --D PKG_USER-ADIOS=yes :pre - -[Traditional make]: - -Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do: - -make yes-user-adios :pre - -otherwise, set ADIOS2_DIR environment variable when turning on the package: - -ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed :pre - -:line - -USER-ATC package :h4,link(user-atc) - -The USER-ATC package requires the MANYBODY package also be installed. - -[CMake build]: - -No additional settings are needed besides "-D PKG_USER-ATC=yes" -and "-D PKG_MANYBODY=yes". - -[Traditional make]: - -Before building LAMMPS, you must build the ATC library in lib/atc. -You can do this manually if you prefer; follow the instructions in -lib/atc/README. You can also do it in one step from the lammps/src -dir, using a command like these, which simply invoke the -lib/atc/Install.py script with the specified args: - -make lib-atc # print help message -make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") -make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi") -make lib-atc args="-m icc" # build with Intel icc compiler :pre - -The build should produce two files: lib/atc/libatc.a and -lib/atc/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the ATC -library. If necessary, you can edit/create a new -lib/atc/Makefile.machine file for your system, which should define an -EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine -file. - -Note that the Makefile.lammps file has settings for the BLAS and -LAPACK linear algebra libraries. As explained in lib/atc/README these -can either exist on your system, or you can use the files provided in -lib/linalg. In the latter case you also need to build the library in -lib/linalg with a command like these: - -make lib-linalg # print help message -make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") -make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") -make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre - -:line - -USER-AWPMD package :h4,link(user-awpmd) - -[CMake build]: - -No additional settings are needed besides "-D PKG_USER-AQPMD=yes". - -[Traditional make]: - -Before building LAMMPS, you must build the AWPMD library in lib/awpmd. -You can do this manually if you prefer; follow the instructions in -lib/awpmd/README. You can also do it in one step from the lammps/src -dir, using a command like these, which simply invoke the -lib/awpmd/Install.py script with the specified args: - -make lib-awpmd # print help message -make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") -make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi") -make lib-awpmd args="-m icc" # build with Intel icc compiler :pre - -The build should produce two files: lib/awpmd/libawpmd.a and -lib/awpmd/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -AWPMD library. If necessary, you can edit/create a new -lib/awpmd/Makefile.machine file for your system, which should define -an EXTRAMAKE variable to specify a corresponding -Makefile.lammps.machine file. - -Note that the Makefile.lammps file has settings for the BLAS and -LAPACK linear algebra libraries. As explained in lib/awpmd/README -these can either exist on your system, or you can use the files -provided in lib/linalg. In the latter case you also need to build the -library in lib/linalg with a command like these: - -make lib-linalg # print help message -make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") -make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") -make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre - -:line - -USER-COLVARS package :h4,link(user-colvars) - -This package includes into the LAMMPS distribution the Colvars library, which -can be built for the most part with all major versions of the C++ language. - -A few of the most recent features require C++11 support. In particular, the -library is optionally built together with the -"Lepton"_https://simtk.org/projects/lepton library, a copy of which is also -included in the LAMMPS distribution. Lepton implements the -"customFunction"_http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction -feature, and requires C++11 support. - -See "here"_https://colvars.github.io/README-c++11.html for a detailed list of -C++11-only features. - -[CMake build]: - -This is the recommended build recipe: no additional settings are normally -needed besides "-D PKG_USER-COLVARS=yes". - -Building and linking of Lepton (or other C++11-only features) is enabled -automatically when compilation is carried out with C++11 support, and disabled -otherwise. Optionally, Lepton build may be manually controlled with the flag -"-D COLVARS_LEPTON=yes|no". - -[Traditional make]: - -Before building LAMMPS, one must build the Colvars library in lib/colvars. - -This can be done manually in the same folder by using or adapting one of the -provided Makefiles: for example, Makefile.g++ for the GNU compiler. - -In general, it is safer to use build setting consistent with the rest of -LAMMPS. This is best carried out from the LAMMPS src directory using a -command like these, which simply invoke the lib/colvars/Install.py script with -the specified args: - -make lib-colvars # print help message -make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") -make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi") -make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre - -The "machine" argument of the "-m" flag is used to find a Makefile.machine to -use as build recipe. If it does not already exist in lib/colvars, it will be -auto-generated by using compiler flags consistent with those parsed from the -core LAMMPS makefiles. - -Optional flags may be specified as environment variables: - -COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower) -COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise) - -The build should produce two files: the library lib/colvars/libcolvars.a -(which also includes Lepton objects if enabled) and the specification file -lib/colvars/Makefile.lammps. The latter is auto-generated, and normally does -not need to be edited. - - -:line - -USER-PLUMED package :h4,link(user-plumed) - -Before building LAMMPS with this package, you must first build PLUMED. -PLUMED can be built as part of the LAMMPS build or installed separately -from LAMMPS using the generic "plumed installation instructions"_plumedinstall. -:link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html) - -PLUMED can be linked into MD codes in three different modes: static, -shared, and runtime. With the "static" mode, all the code that PLUMED -requires is linked statically into LAMMPS. LAMMPS is then fully -independent from the PLUMED installation, but you have to rebuild/relink -it in order to update the PLUMED code inside it. With the "shared" -linkage mode, LAMMPS is linked to a shared library that contains the -PLUMED code. This library should preferably be installed in a globally -accessible location. When PLUMED is linked in this way the same library -can be used by multiple MD packages. Furthermore, the PLUMED library -LAMMPS uses can be updated without the need for a recompile of LAMMPS -for as long as the shared PLUMED library is ABI-compatible. - -The third linkage mode is "runtime" which allows the user to specify -which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL -environment variable. This variable should point to the location of the -libplumedKernel.so dynamical shared object, which is then loaded at -runtime. This mode of linking is particularly convenient for doing -PLUMED development and comparing multiple PLUMED versions as these sorts -of comparisons can be done without recompiling the hosting MD code. All -three linkage modes are supported by LAMMPS on selected operating -systems (e.g. Linux) and using either CMake or traditional make -build. The "static" mode should be the most portable, while the -"runtime" mode support in LAMMPS makes the most assumptions about -operating system and compiler environment. If one mode does not work, -try a different one, switch to a different build system, consider a -global PLUMED installation or consider downloading PLUMED during the -LAMMPS build. - -[CMake build]: - -When the "-D PKG_USER-PLUMED" flag is included in the cmake command you -must ensure that GSL is installed in locations that are specified in -your environment. There are then two additional commands that control -the manner in which PLUMED is obtained and linked into LAMMPS. - --D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes --D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre - -If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be -downloaded (the version of PLUMED that will be downloaded is hard-coded -to a vetted version of PLUMED, usually a recent stable release version) -and built inside the CMake build directory. If DOWNLOAD_PLUMED is set -to "no" (the default), CMake will try to detect and link to an installed -version of PLUMED. For this to work, the PLUMED library has to be -installed into a location where the pkg-config tool can find it or the -PKG_CONFIG_PATH environment variable has to be set up accordingly. -PLUMED should be installed in such a location if you compile it using -the default make; make install commands. - -The PLUMED_MODE setting determines the linkage mode for the PLUMED -library. The allowed values for this flag are "static" (default), -"shared", or "runtime". For a discussion of PLUMED linkage modes, -please see above. When DOWNLOAD_PLUMED is enabled the static linkage -mode is recommended. - -[Traditional make]: - -PLUMED needs to be installed before the USER-PLUMED package is installed -so that LAMMPS can find the right settings when compiling and linking -the LAMMPS executable. You can either download and build PLUMED inside -the LAMMPS plumed library folder or use a previously installed PLUMED -library and point LAMMPS to its location. You also have to choose the -linkage mode: "static" (default), "shared" or "runtime". For a -discussion of PLUMED linkage modes, please see above. - -Download/compilation/configuration of the plumed library can be done -from the src folder through the following make args: - -make lib-plumed # print help message -make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2 -make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local -make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in - # /usr/local and use shared linkage mode -:pre - -Note that 2 symbolic (soft) links, "includelink" and "liblink" are -created in lib/plumed that point to the location of the PLUMED build to -use. A new file lib/plumed/Makefile.lammps is also created with settings -suitable for LAMMPS to compile and link PLUMED using the desired linkage -mode. After this step is completed, you can install the USER-PLUMED -package and compile LAMMPS in the usual manner: - -make yes-user-plumed -make machine :pre - -Once this compilation completes you should be able to run LAMMPS in the -usual way. For shared linkage mode, libplumed.so must be found by the -LAMMPS executable, which on many operating systems means, you have to -set the LD_LIBRARY_PATH environment variable accordingly. - -Support for the different linkage modes in LAMMPS varies for different -operating systems, using the static linkage is expected to be the most -portable, and thus set to be the default. - -If you want to change the linkage mode, you have to re-run "make -lib-plumed" with the desired settings [and] do a re-install if the -USER-PLUMED package with "make yes-user-plumed" to update the required -makefile settings with the changes in the lib/plumed folder. - -:line - -USER-H5MD package :h4,link(user-h5md) - -To build with this package you must have the HDF5 software package -installed on your system, which should include the h5cc compiler and -the HDF5 library. - -[CMake build]: - -No additional settings are needed besides "-D PKG_USER-H5MD=yes". - -This should auto-detect the H5MD library on your system. Several -advanced CMake H5MD options exist if you need to specify where it is -installed. Use the ccmake (terminal window) or cmake-gui (graphical) -tools to see these options and set them interactively from their user -interfaces. - -[Traditional make]: - -Before building LAMMPS, you must build the CH5MD library in lib/h5md. -You can do this manually if you prefer; follow the instructions in -lib/h5md/README. You can also do it in one step from the lammps/src -dir, using a command like these, which simply invoke the -lib/h5md/Install.py script with the specified args: - -make lib-h5md # print help message -make lib-h5md args="-m h5cc" # build with h5cc compiler :pre - -The build should produce two files: lib/h5md/libch5md.a and -lib/h5md/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -system HDF5 library. If necessary, you can edit/create a new -lib/h5md/Makefile.machine file for your system, which should define an -EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine -file. - -:line - -USER-INTEL package :h4,link(user-intel) - -To build with this package, you must choose which hardware you want to -build for, either x86 CPUs or Intel KNLs in offload mode. You should -also typically "install the USER-OMP package"_#user-omp, as it can be -used in tandem with the USER-INTEL package to good effect, as explained -on the "Speed intel"_Speed_intel.html doc page. - -[CMake build]: - --D INTEL_ARCH=value # value = cpu (default) or knl --D INTEL_LRT_MODE=value # value = threads, none, or c++11 :pre - -In Long-range thread mode (LRT) a modified verlet style is used, that -operates the Kspace calculation in a separate thread concurrently to -other calculations. This has to be enabled in the "package intel"_package.html -command at runtime. With the setting "threads" it used the pthreads -library, while c++11 will use the built-in thread support of C++11 -compilers. The option "none" skips compilation of this feature. The -default is to use "threads" if pthreads is available and otherwise "none". - -Best performance is achieved with Intel hardware, Intel compilers, as well as -the Intel TBB and MKL libraries. However, the code also compiles, links, and -runs with other compilers and without TBB and MKL. - -[Traditional make]: - -Choose which hardware to compile for in Makefile.machine via the -following settings. See src/MAKE/OPTIONS/Makefile.intel_cpu* and -Makefile.knl files for examples. and src/USER-INTEL/README for -additional information. - -For CPUs: - -OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS) -LINKFLAGS = -g -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc :pre - -For KNLs: - -OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS) -LINKFLAGS = -g -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc :pre - -:line - -USER-MOLFILE package :h4,link(user-molfile) - -[CMake build]: - --D MOLFILE_INCLUDE_DIRS=path # (optional) path where VMD molfile plugin headers are installed --D PKG_USER-MOLFILE=yes :pre - - -Using "-D PKG_USER-MOLFILE=yes" enables the package, and setting -"-D MOLFILE_INCLUDE DIRS" allows to provide a custom location for -the molfile plugin header files. These should match the ABI of the -plugin files used, and thus one typically sets them to include -folder of the local VMD installation in use. LAMMPS ships with a -couple of default header files that correspond to a popular VMD -version, usually the latest release. - -[Traditional make]: - -The lib/molfile/Makefile.lammps file has a setting for a dynamic -loading library libdl.a that is typically present on all systems. It -is required for LAMMPS to link with this package. If the setting is -not valid for your system, you will need to edit the Makefile.lammps -file. See lib/molfile/README and lib/molfile/Makefile.lammps for -details. It is also possible to configure a different folder with -the VMD molfile plugin header files. LAMMPS ships with a couple of -default headers, but these are not compatible with all VMD versions, -so it is often best to change this setting to the location of the -same include files of the local VMD installation in use. - -:line - -USER-NETCDF package :h4,link(user-netcdf) - -To build with this package you must have the NetCDF library installed -on your system. - -[CMake build]: - -No additional settings are needed besides "-D PKG_USER-NETCDF=yes". - -This should auto-detect the NETCDF library if it is installed on your -system at standard locations. Several advanced CMake NETCDF options -exist if you need to specify where it was installed. Use the ccmake -(terminal window) or cmake-gui (graphical) tools to see these options -and set them interactively from their user interfaces. - -[Traditional make]: - -The lib/netcdf/Makefile.lammps file has settings for NetCDF include -and library files which LAMMPS needs to build with this package. If -the settings are not valid for your system, you will need to edit the -Makefile.lammps file. See lib/netcdf/README for details. - -:line - -USER-OMP package :h4,link(user-omp) - -[CMake build]: - -No additional settings are required besides "-D PKG_USER-OMP=yes". If -CMake detects OpenMP support, the USER-OMP code will be compiled with -multi-threading support enabled, otherwise as optimized serial code. - -[Traditional make]: - -To enable multi-threading support in the USER-OMP package (and other -styles supporting OpenMP) the following compile and link flags must -be added to your Makefile.machine file. -See src/MAKE/OPTIONS/Makefile.omp for an example. - -CCFLAGS: -fopenmp # for GNU Compilers -CCFLAGS: -qopenmp -restrict # for Intel compilers on Linux -LINKFLAGS: -fopenmp # for GNU Compilers -LINKFLAGS: -qopenmp # for Intel compilers on Linux :pre - -For other platforms and compilers, please consult the documentation -about OpenMP support for your compiler. Please see the note about -how to address compatibility "issues with the 'default(none)' -directive"_Build_basics.html#default-none-issues of some compilers. - -:line - -USER-QMMM package :h4,link(user-qmmm) - -NOTE: The LAMMPS executable these steps produce is not yet functional -for a QM/MM simulation. You must also build Quantum ESPRESSO and -create a new executable (pwqmmm.x) which links LAMMPS and Quantum -ESPRESSO together. These are steps 3 and 4 described in the -lib/qmmm/README file. Unfortunately, the Quantum ESPRESSO developers -have been breaking the interface that the QM/MM code in LAMMPS is using, -so that currently (Summer 2018) using this feature requires either -correcting the library interface feature in recent Quantum ESPRESSO -releases, or using an outdated version of QE. The last version of -Quantum ESPRESSO known to work with this QM/MM interface was version -5.4.1 from 2016. - -[CMake build]: - -The CMake build system currently does not support building the full -QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x. -You must use the traditional make build for this package. - -[Traditional make]: - -Before building LAMMPS, you must build the QMMM library in lib/qmmm. -You can do this manually if you prefer; follow the first two steps -explained in lib/qmmm/README. You can also do it in one step from the -lammps/src dir, using a command like these, which simply invoke the -lib/qmmm/Install.py script with the specified args: - -make lib-qmmm # print help message -make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial") -make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi") -make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre - -The build should produce two files: lib/qmmm/libqmmm.a and -lib/qmmm/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -QMMM library (though typically the settings are just blank). If -necessary, you can edit/create a new lib/qmmm/Makefile.machine file -for your system, which should define an EXTRAMAKE variable to specify -a corresponding Makefile.lammps.machine file. - -You can then install QMMM package and build LAMMPS in the usual -manner. After completing the LAMMPS build and compiling Quantum -ESPRESSO with external library support, go back to the lib/qmmm folder -and follow the instructions on the README file to build the combined -LAMMPS/QE QM/MM executable (pwqmmm.x) in the lib/qmmm folder. - -:line - -USER-QUIP package :h4,link(user-quip) - -To build with this package, you must download and build the QUIP -library. It can be obtained from GitHub. For support of GAP -potentials, additional files with specific licensing conditions need -to be downloaded and configured. See step 1 and step 1.1 in the -lib/quip/README file for details on how to do this. - -[CMake build]: - --D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) :pre - -CMake will not download and build the QUIP library. But once you have -done that, a CMake build of LAMMPS with "-D PKG_USER-QUIP=yes" should -work. Set QUIP_LIBRARY if CMake cannot find the QUIP library. - -[Traditional make]: - -The download/build procedure for the QUIP library, described in -lib/quip/README file requires setting two environment variables, -QUIP_ROOT and QUIP_ARCH. These are accessed by the -lib/quip/Makefile.lammps file which is used when you compile and link -LAMMPS with this package. You should only need to edit -Makefile.lammps if the LAMMPS build can not use its settings to -successfully build on your system. - -:line - -USER-SCAFACOS package :h4,link(user-scafacos) - -To build with this package, you must download and build the "ScaFaCoS -Coulomb solver library"_scafacos-home - -:link(scafacos-home,http://www.scafacos.de) - -[CMake build]: - --D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes --D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location) --D SCAFACOS_INCLUDE_DIR=path # ScaFaCoS include directory (only needed if at custom location) :pre - -If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded -and built inside the CMake build directory. If the ScaFaCoS library -is already on your system (in a location CMake cannot find it), -SCAFACOS_LIBRARY is the filename (plus path) of the ScaFaCoS library -file, not the directory the library file is in. SCAFACOS_INCLUDE_DIR -is the directory the ScaFaCoS include file is in. - -[Traditional make]: - -You can download and build the ScaFaCoS library manually if you -prefer; follow the instructions in lib/scafacos/README. You can also -do it in one step from the lammps/src dir, using a command like these, -which simply invoke the lib/scafacos/Install.py script with the -specified args: - -make lib-scafacos # print help message -make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos- -make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos - -Note that 2 symbolic (soft) links, "includelink" and "liblink", are -created in lib/scafacos to point to the ScaFaCoS src dir. When LAMMPS -builds in src it will use these links. You should not need to edit -the lib/scafacos/Makefile.lammps file. - -:line - -USER-SMD package :h4,link(user-smd) - -To build with this package, you must download the Eigen3 library. -Eigen3 is a template library, so you do not need to build it. - -[CMake build]: - --D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes --D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) :pre - -If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and -inside the CMake build directory. If the Eigen3 library is already on -your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR -is the directory the Eigen3++ include file is in. - -[Traditional make]: - -You can download the Eigen3 library manually if you prefer; follow the -instructions in lib/smd/README. You can also do it in one step from -the lammps/src dir, using a command like these, which simply invoke -the lib/smd/Install.py script with the specified args: - -make lib-smd # print help message -make lib-smd args="-b" # download to lib/smd/eigen3 -make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 :pre - -Note that a symbolic (soft) link named "includelink" is created in -lib/smd to point to the Eigen dir. When LAMMPS builds it will use -this link. You should not need to edit the lib/smd/Makefile.lammps -file. - -:line - -USER-VTK package :h4,link(user-vtk) - -To build with this package you must have the VTK library installed on -your system. - -[CMake build]: - -No additional settings are needed besides "-D PKG_USER-VTK=yes". - -This should auto-detect the VTK library if it is installed on your -system at standard locations. Several advanced VTK options exist if -you need to specify where it was installed. Use the ccmake (terminal -window) or cmake-gui (graphical) tools to see these options and set -them interactively from their user interfaces. - -[Traditional make]: - -The lib/vtk/Makefile.lammps file has settings for accessing VTK files -and its library, which LAMMPS needs to build with this package. If -the settings are not valid for your system, check if one of the other -lib/vtk/Makefile.lammps.* files is compatible and copy it to -Makefile.lammps. If none of the provided files work, you will need to -edit the Makefile.lammps file. See lib/vtk/README for details. diff --git a/doc/txt/Build_link.txt b/doc/txt/Build_link.txt deleted file mode 100644 index 706c51d6bc..0000000000 --- a/doc/txt/Build_link.txt +++ /dev/null @@ -1,85 +0,0 @@ -"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Link LAMMPS as a library to another code :h3 - -LAMMPS can be used as a library by another application, including -Python scripts. The files src/library.cpp and library.h define the -C-style API for using LAMMPS as a library. See the "Howto -library"_Howto_library.html doc page for a description of the -interface and how to extend it for your needs. - -The "Build basics"_Build_basics.html doc page explains how to build -LAMMPS as either a shared or static library. This results in one of -these 2 files: - -liblammps.so # shared library -liblammps.a # static library - -:line - -[Link with LAMMPS as a static library]: - -The calling application can link to LAMMPS as a static library with a -link command like this: - -g++ caller.o -L/home/sjplimp/lammps/src -llammps -o caller - -The -L argument is the path to where the liblammps.a file is. The --llammps argument is shorthand for the file liblammps.a. - -:line - -[Link with LAMMPS as a shared library]: - -If you wish to link to liblammps.so, the operating system finds shared -libraries to load at run-time using the environment variable -LD_LIBRARY_PATH. To enable this you can do one of two things: - -(1) Copy the liblammps.so file to a location the system can find it, -such as /usr/local/lib. I.e. a directory already listed in your -LD_LIBRARY_PATH variable. You can type - -printenv LD_LIBRARY_PATH :pre - -to see what directories are in that list. - -(2) Add the LAMMPS src directory (or the directory you perform CMake -build in) to your LD_LIBRARY_PATH, so that the current version of the -shared library is always available to programs that use it. - -For the csh or tcsh shells, you would add something like this to your -~/.cshrc file: - -setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre - -:line - -[Calling the LAMMPS library]: - -Either flavor of library (static or shared) allows one or more LAMMPS -objects to be instantiated from the calling program. - -When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS -namespace; you can safely use any of its classes and methods from -within the calling code, as needed. - -When used from a C or Fortran program, the library has a simple -C-style interface, provided in src/library.cpp and src/library.h. - -See the "Python library"_Python_library.html doc page for a -description of the Python interface to LAMMPS, which wraps the C-style -interface. - -See the sample codes in examples/COUPLE/simple for examples of C++ and -C and Fortran codes that invoke LAMMPS through its library interface. -Other examples in the COUPLE directory use coupling ideas discussed on -the "Howto couple"_Howto_couple.html doc page. - - diff --git a/doc/txt/Build_make.txt b/doc/txt/Build_make.txt deleted file mode 100644 index ad18695e46..0000000000 --- a/doc/txt/Build_make.txt +++ /dev/null @@ -1,85 +0,0 @@ -"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Build LAMMPS with make :h3 - -Building LAMMPS with traditional makefiles requires that you have a -Makefile."machine" file appropriate for your system in the src/MAKE, -src/MAKE/MACHINES, src/MAKE/OPTIONS, or src/MAKE/MINE directory (see -below). It can include various options for customizing your LAMMPS -build with a number of global compilation options and features. - -To include LAMMPS packages (i.e. optional commands and styles) you -must install them first, as discussed on the "Build -package"_Build_package.html doc page. If the packages require -provided or external libraries, you must build those libraries before -building LAMMPS. Building "LAMMPS with CMake"_Build_cmake.html can -automate all of this for many types of machines, especially -workstations, desktops and laptops, so we suggest you try it first. - -These commands perform a default LAMMPS build, producing the LAMMPS -executable lmp_serial or lmp_mpi in lammps/src: - -cd lammps/src -make serial # build a serial LAMMPS executable -make mpi # build a parallel LAMMPS executable with MPI -make # see a variety of make options :pre - -This initial compilation can take a long time, since LAMMPS is a large -project with many features. If your machine has multiple CPU cores -(most do these days), using a command like "make -jN mpi" (with N = -the number of available CPU cores) can be much faster. If you plan to -do development on LAMMPS or need to re-compile LAMMPS repeatedly, the -installation of the ccache (= Compiler Cache) software may speed up -compilation even more. - -After the initial build, whenever you edit LAMMPS source files, or add -or remove new files to the source directory (e.g. by installing or -uninstalling packages), you must re-compile and relink the LAMMPS -executable with the same "make" command. This makefiles dependencies -should insure that only the subset of files that need to be are -re-compiled. - -NOTE: When you build LAMMPS for the first time, a long list of *.d -files will be printed out rapidly. This is not an error; it is the -Makefile doing its normal creation of dependencies. - -:line - -The lammps/src/MAKE tree contains all the Makefile.machine files -included in the LAMMPS distribution. Typing "make machine" uses -Makefile.machine. Thus the "make serial" or "make mpi" lines above -use Makefile.serial and Makefile.mpi. Others are in these dirs: - -OPTIONS # Makefiles which enable specific options -MACHINES # Makefiles for specific machines -MINE # customized Makefiles you create (you may need to create this folder) :pre - -Typing "make" lists all the available Makefile.machine files. A file -with the same name can appear in multiple folders (not a good idea). -The order the dirs are searched is as follows: src/MAKE/MINE, -src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES. This gives preference -to a customized file you put in src/MAKE/MINE. - -Makefiles you may wish to try include these (some require a package -first be installed). Many of these include specific compiler flags -for optimized performance. Please note, however, that some of these -customized machine Makefile are contributed by users. Since both -compilers, OS configurations, and LAMMPS itself keep changing, their -settings may become outdated: - -make mac # build serial LAMMPS on a Mac -make mac_mpi # build parallel LAMMPS on a Mac -make intel_cpu # build with the USER-INTEL package optimized for CPUs -make knl # build with the USER-INTEL package optimized for KNLs -make opt # build with the OPT package optimized for CPUs -make omp # build with the USER-OMP package optimized for OpenMP -make kokkos_omp # build with the KOKKOS package for OpenMP -make kokkos_cuda_mpi # build with the KOKKOS package for GPUs -make kokkos_phi # build with the KOKKOS package for KNLs :pre diff --git a/doc/txt/Build_package.txt b/doc/txt/Build_package.txt deleted file mode 100644 index 869175e160..0000000000 --- a/doc/txt/Build_package.txt +++ /dev/null @@ -1,240 +0,0 @@ -"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Include packages in build :h3 - -In LAMMPS, a package is a group of files that enable a specific set of -features. For example, force fields for molecular systems or -rigid-body constraints are in packages. In the src directory, each -package is a sub-directory with the package name in capital letters. - -An overview of packages is given on the "Packages"_Packages.html doc -page. Brief overviews of each package are on the "Packages -details"_Packages_details.html doc page. - -When building LAMMPS, you can choose to include or exclude each -package. In general there is no need to include a package if you -never plan to use its features. - -If you get a run-time error that a LAMMPS command or style is -"Unknown", it is often because the command is contained in a package, -and your build did not include that package. Running LAMMPS with the -"-h command-line switch"_Run_options.html will print all the included -packages and commands for that executable. - -For the majority of packages, if you follow the single step below to -include it, you can then build LAMMPS exactly the same as you would -without any packages installed. A few packages may require additional -steps, as explained on the "Build extras"_Build_extras.html doc page. - -These links take you to the extra instructions for those select -packages: - -"COMPRESS"_Build_extras.html#compress, -"GPU"_Build_extras.html#gpu, -"KIM"_Build_extras.html#kim, -"KOKKOS"_Build_extras.html#kokkos, -"LATTE"_Build_extras.html#latte, -"MESSAGE"_Build_extras.html#message, -"MSCG"_Build_extras.html#mscg, -"OPT"_Build_extras.html#opt, -"POEMS"_Build_extras.html#poems, -"PYTHON"_Build_extras.html#python, -"VORONOI"_Build_extras.html#voronoi, -"USER-ADIOS"_Build_extras.html#user-adios, -"USER-ATC"_Build_extras.html#user-atc, -"USER-AWPMD"_Build_extras.html#user-awpmd, -"USER-COLVARS"_Build_extras.html#user-colvars, -"USER-H5MD"_Build_extras.html#user-h5md, -"USER-INTEL"_Build_extras.html#user-intel, -"USER-MOLFILE"_Build_extras.html#user-molfile, -"USER-NETCDF"_Build_extras.html#user-netcdf, -"USER-PLUMED"_Build_extras.html#user-plumed, -"USER-OMP"_Build_extras.html#user-omp, -"USER-QMMM"_Build_extras.html#user-qmmm, -"USER-QUIP"_Build_extras.html#user-quip, -"USER-SCAFACOS"_Build_extras.html#user-scafacos, -"USER-SMD"_Build_extras.html#user-smd, -"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l) - -The mechanism for including packages is simple but different for CMake -versus make. - -[CMake variables]: - --D PKG_NAME=value # yes or no (default) :pre - -Examples: - --D PKG_MANYBODY=yes --D PKG_USER-INTEL=yes :pre - -All standard and user packages are included the same way. Note that -USER packages have a hyphen between USER and the rest of the package -name, not an underscore. - -See the shortcut section below for how to install many packages at -once with CMake. - -NOTE: If you toggle back and forth between building with CMake vs -make, no packages in the src directory can be installed when you -invoke cmake. CMake will give an error if that is not the case, -indicating how you can un-install all packages in the src dir. - -[Traditional make]: - -cd lammps/src -make ps # check which packages are currently installed -make yes-name # install a package with name -make no-name # un-install a package with name -make mpi # build LAMMPS with whatever packages are now installed :pre - -Examples: - -make no-rigid -make yes-user-intel :pre - -All standard and user packages are included the same way. - -See the shortcut section below for how to install many packages at -once with make. - -NOTE: You must always re-build LAMMPS (via make) after installing or -un-installing a package, for the action to take effect. - -NOTE: You cannot install or un-install packages and build LAMMPS in a -single make command with multiple targets, e.g. make yes-colloid mpi. -This is because the make procedure creates a list of source files that -will be out-of-date for the build if the package configuration changes -within the same command. You can include or exclude multiple packages -in a single make command, e.g. make yes-colloid no-manybody. - -[CMake and make info]: - -Any package can be included or excluded in a LAMMPS build, independent -of all other packages. However, some packages include files derived -from files in other packages. LAMMPS checks for this and does the -right thing. Individual files are only included if their dependencies -are already included. Likewise, if a package is excluded, other files -dependent on that package are also excluded. - -When you download a LAMMPS tarball or download LAMMPS source files -from the Git or SVN repositories, no packages are pre-installed in the -src directory. - -NOTE: Prior to Aug 2018, if you downloaded a tarball, 3 packages -(KSPACE, MANYBODY, MOLECULE) were pre-installed in the src directory. -That is no longer the case, so that CMake will build as-is without the -need to un-install those packages. - -:line - -[CMake shortcuts for installing many packages]: - -Instead of specifying all the CMake options via the command-line, -CMake allows initializing the variable cache using script files. These -are regular CMake files which can manipulate and set variables, and -can also contain control flow constructs. - -LAMMPS includes several of these files to define configuration -"presets", similar to the options that exist for the Make based -system. Using these files you can enable/disable portions of the -available packages in LAMMPS. If you need a custom preset you can take -one of them as a starting point and customize it to your needs. - -cmake -C ../cmake/presets/all_on.cmake \[OPTIONS\] ../cmake | - enable all packages | -cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake | - disable all packages | -cmake -C ../cmake/presets/minimal.cmake \[OPTIONS\] ../cmake | - enable just a few core packages | -cmake -C ../cmake/presets/most.cmake \[OPTIONS\] ../cmake | - enable most common packages | -cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake | - disable packages that do require extra libraries or tools | -cmake -C ../cmake/presets/clang.cmake \[OPTIONS\] ../cmake | - change settings to use the Clang compilers by default | -cmake -C ../cmake/presets/mingw.cmake \[OPTIONS\] ../cmake | - enable all packages compatible with MinGW compilers :tb(c=2,s=|,a=l) - -NOTE: Running cmake this way manipulates the variable cache in your -current build directory. You can combine multiple presets and options -in a single cmake run, or change settings incrementally by running -cmake with new flags. - -[Example:] - -# build LAMMPS with most commonly used packages, but then remove -# those requiring additional library or tools, but still enable -# GPU package and configure it for using CUDA. You can run. -mkdir build -cd build -cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake :pre - -# to add another package, say BODY to the previous configuration you can run: -cmake -D PKG_BODY=on . :pre - -# to reset the package selection from above to the default of no packages -# but leaving all other settings untouched. You can run: -cmake -C ../cmake/presets/no_all.cmake . :pre -:line - -[Make shortcuts for installing many packages]: - -The following commands are useful for managing package source files -and their installation when building LAMMPS via traditional make. -Just type "make" in lammps/src to see a one-line summary. - -These commands install/un-install sets of packages: - -make yes-all | install all packages -make no-all | un-install all packages -make yes-standard or make yes-std | install standard packages -make no-standard or make no-std| un-install standard packages -make yes-user | install user packages -make no-user | un-install user packages -make yes-lib | install packages that require extra libraries -make no-lib | un-install packages that require extra libraries -make yes-ext | install packages that require external libraries -make no-ext | un-install packages that require external libraries :tb(s=|,a=l) - -which install/un-install various sets of packages. Typing "make -package" will list all the these commands. - -NOTE: Installing or un-installing a package works by simply copying -files back and forth between the main src directory and -sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC), -so that the files are included or excluded when LAMMPS is built. - -The following make commands help manage files that exist in both the -src directory and in package sub-directories. You do not normally -need to use these commands unless you are editing LAMMPS files or are -"installing a patch"_Install_patch.html downloaded from the LAMMPS web -site. - -Type "make package-status" or "make ps" to show which packages are -currently installed. For those that are installed, it will list any -files that are different in the src directory and package -sub-directory. - -Type "make package-installed" or "make pi" to show which packages are -currently installed, without listing the status of packages that are -not installed. - -Type "make package-update" or "make pu" to overwrite src files with -files from the package sub-directories if the package is installed. -It should be used after a "patch has been applied"_Install_patch.html, -since patches only update the files in the package sub-directory, but -not the src files. - -Type "make package-overwrite" to overwrite files in the package -sub-directories with src files. - -Type "make package-diff" to list all differences between pairs of -files in both the src dir and a package dir. diff --git a/doc/txt/Build_settings.txt b/doc/txt/Build_settings.txt deleted file mode 100644 index 730d779d63..0000000000 --- a/doc/txt/Build_settings.txt +++ /dev/null @@ -1,372 +0,0 @@ -"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Optional build settings :h3 - -LAMMPS can be built with several optional settings. Each sub-section -explain how to do this for building both with CMake and make. - -"C++11 standard compliance test"_#cxx11 when building all of LAMMPS -"FFT library"_#fft for use with the "kspace_style pppm"_kspace_style.html command -"Size of LAMMPS data types"_#size -"Read or write compressed files"_#gzip -"Output of JPG and PNG files"_#graphics via the "dump image"_dump_image.html command -"Output of movie files"_#graphics via the "dump_movie"_dump_image.html command -"Memory allocation alignment"_#align -"Workaround for long long integers"_#longlong -"Error handling exceptions"_#exceptions when using LAMMPS as a library :all(b) - -:line - -C++11 standard compliance test :h4,link(cxx11) - -The LAMMPS developers plan to transition to make the C++11 standard the -minimum requirement for compiling LAMMPS. Currently this only applies to -some packages like KOKKOS while the rest aims to be compatible with the C++98 -standard. Most currently used compilers are compatible with C++11; some need -to set extra flags to switch. To determine the impact of requiring C++11, -we have added a simple compliance test to the source code, that will cause -the compilation to abort, if C++11 compliance is not available or enabled. -To bypass this check, you need to change a setting in the makefile or -when calling CMake. - -[CMake variable]: - --D DISABLE_CXX11_REQUIREMENT=yes :pre - -You can set additional C++ compiler flags (beyond those selected by CMake) -through the CMAKE_CXX_FLAGS variable. Example for CentOS 7: - --D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11" :pre - -[Makefile.machine setting]: - -LMP_INC = -DLAMMPS_CXX98 :pre - -:line - -FFT library :h4,link(fft) - -When the KSPACE package is included in a LAMMPS build, the -"kspace_style pppm"_kspace_style.html command performs 3d FFTs which -require use of an FFT library to compute 1d FFTs. The KISS FFT -library is included with LAMMPS but other libraries can be faster. -LAMMPS can use them if they are available on your system. - -[CMake variables]: - --D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS --D FFT_SINGLE=value # yes or no (default), no = double precision --D FFT_PACK=value # array (default) or pointer or memcpy :pre - -NOTE: The values for the FFT variable must be in upper-case. This is -an exception to the rule that all CMake variables can be specified -with lower-case values. - -Usually these settings are all that is needed. If CMake cannot find -the FFT library, you can set these variables: - --D FFTW3_INCLUDE_DIRS=path # path to FFTW3 include files --D FFTW3_LIBRARIES=path # path to FFTW3 libraries --D MKL_INCLUDE_DIRS=path # ditto for Intel MKL library --D MKL_LIBRARIES=path :pre - -[Makefile.machine settings]: - -FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS - # default is KISS if not specified -FFT_INC = -DFFT_SINGLE # do not specify for double precision -FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY :pre - # default is FFT_PACK_ARRAY if not specified - -FFT_INC = -I/usr/local/include -FFT_PATH = -L/usr/local/lib -FFT_LIB = -lfftw3 # FFTW3 double precision -FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision -FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler -FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compier :pre - -As with CMake, you do not need to set paths in FFT_INC or FFT_PATH, if -make can find the FFT header and library files. You must specify -FFT_LIB with the appropriate FFT libraries to include in the link. - -[CMake and make info]: - -The "KISS FFT library"_http://kissfft.sf.net is included in the LAMMPS -distribution. It is portable across all platforms. Depending on the -size of the FFTs and the number of processors used, the other -libraries listed here can be faster. - -However, note that long-range Coulombics are only a portion of the -per-timestep CPU cost, FFTs are only a portion of long-range -Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel -communication can be costly). A breakdown of these timings is printed -to the screen at the end of a run using the "kspace_style -pppm"_kspace_style.html command. The "Run output"_Run_output.html -doc page gives more details. - -FFTW is a fast, portable FFT library that should also work on any -platform and can be faster than the KISS FFT library. You can -download it from "www.fftw.org"_http://www.fftw.org. LAMMPS requires -version 3.X; the legacy version 2.1.X is no longer supported. - -Building FFTW for your box should be as simple as ./configure; make; -make install. The install command typically requires root privileges -(e.g. invoke it via sudo), unless you specify a local directory with -the "--prefix" option of configure. Type "./configure --help" to see -various options. - -The Intel MKL math library is part of the Intel compiler suite. It -can be used with the Intel or GNU compiler (see FFT_LIB setting above). - -Performing 3d FFTs in parallel can be time consuming due to data -access and required communication. This cost can be reduced by -performing single-precision FFTs instead of double precision. Single -precision means the real and imaginary parts of a complex datum are -4-byte floats. Double precision means they are 8-byte doubles. Note -that Fourier transform and related PPPM operations are somewhat less -sensitive to floating point truncation errors and thus the resulting -error is less than the difference in precision. Using the -DFFT_SINGLE -setting trades off a little accuracy for reduced memory use and -parallel communication costs for transposing 3d FFT data. - -When using -DFFT_SINGLE with FFTW3 you may need to build the FFTW -library a second time with support for single-precision. - -For FFTW3, do the following, which should produce the additional -library libfftw3f.a - -make clean -./configure --enable-single; make; make install :pre - -Performing 3d FFTs requires communication to transpose the 3d FFT -grid. The data packing/unpacking for this can be done in one of 3 -modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above. -Depending on the machine, the size of the FFT grid, the number of -processors used, one option may be slightly faster. The default is -ARRAY mode. - -:line - -Size of LAMMPS data types :h4,link(size) - -LAMMPS has a few integer data types which can be defined as 4-byte or -8-byte integers. The default setting of "smallbig" is almost always -adequate. - -[CMake variable]: - --D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall :pre - -[Makefile.machine setting]: - -LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre - # default is LAMMPS_SMALLBIG if not specified -[CMake and make info]: - -The default "smallbig" setting allows for simulations with: - -total atom count = 2^63 atoms (about 9e18) -total timesteps = 2^63 (about 9e18) -atom IDs = 2^31 (about 2 billion) -image flags = roll over at 512 :ul - -The "bigbig" setting increases the latter two limits. It allows for: - -total atom count = 2^63 atoms (about 9e18) -total timesteps = 2^63 (about 9e18) -atom IDs = 2^63 (about 9e18) -image flags = roll over at about 1 million (2^20) :ul - -The "smallsmall" setting is only needed if your machine does not -support 8-byte integers. It allows for: - -total atom count = 2^31 atoms (about 2 billion) -total timesteps = 2^31 (about 2 billion) -atom IDs = 2^31 (about 2 billion) -image flags = roll over at 512 (2^9) :ul - -Atom IDs are not required for atomic systems which do not store bond -topology information, though IDs are enabled by default. The -"atom_modify id no"_atom_modify.html command will turn them off. Atom -IDs are required for molecular systems with bond topology (bonds, -angles, dihedrals, etc). Thus if you model a molecular system with -more than 2 billion atoms, you need the "bigbig" setting. - -Image flags store 3 values per atom which count the number of times an -atom has moved through the periodic box in each dimension. See the -"dump"_dump.html doc page for a discussion. If an atom moves through -the periodic box more than this limit, the value will "roll over", -e.g. from 511 to -512, which can cause diagnostics like the -mean-squared displacement, as calculated by the "compute -msd"_compute_msd.html command, to be faulty. - -Note that the USER-ATC package and the USER-INTEL package are currently -not compatible with the "bigbig" setting. Also, there are limitations -when using the library interface. Some functions with known issues -have been replaced by dummy calls printing a corresponding error rather -than crashing randomly or corrupting data. - -Also note that the GPU package requires its lib/gpu library to be -compiled with the same size setting, or the link will fail. A CMake -build does this automatically. When building with make, the setting -in whichever lib/gpu/Makefile is used must be the same as above. - -:line - -Output of JPG, PNG, and movie files :h4,link(graphics) - -The "dump image"_dump_image.html command has options to output JPEG or -PNG image files. Likewise the "dump movie"_dump_image.html command -outputs movie files in MPEG format. Using these options requires the -following settings: - -[CMake variables]: - --D WITH_JPEG=value # yes or no - # default = yes if CMake finds JPEG files, else no --D WITH_PNG=value # yes or no - # default = yes if CMake finds PNG and ZLIB files, else no --D WITH_FFMPEG=value # yes or no - # default = yes if CMake can find ffmpeg, else no :pre - -Usually these settings are all that is needed. If CMake cannot find -the graphics header, library, executable files, you can set these -variables: - --D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file --D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file --D PNG_INCLUDE_DIR=path # path to png.h header file --D PNG_LIBRARIES=path # path to libpng.a (.so) file --D ZLIB_INCLUDE_DIR=path # path to zlib.h header file --D ZLIB_LIBRARIES=path # path to libz.a (.so) file --D FFMPEG_EXECUTABLE=path # path to ffmpeg executable :pre - -[Makefile.machine settings]: - -LMP_INC = -DLAMMPS_JPEG -LMP_INC = -DLAMMPS_PNG -LMP_INC = -DLAMMPS_FFMPEG :pre - -JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them -JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them -JPG_LIB = -ljpeg -lpng -lz # library names :pre - -As with CMake, you do not need to set JPG_INC or JPG_PATH, if make can -find the graphics header and library files. You must specify JPG_LIB -with a list of graphics libraries to include in the link. You must -insure ffmpeg is in a directory where LAMMPS can find it at runtime, -i.e. a dir in your PATH environment variable. - -[CMake and make info]: - -Using ffmpeg to output movie files requires that your machine -supports the "popen" function in the standard runtime library. - -NOTE: On some clusters with high-speed networks, using the fork() -library calls (required by popen()) can interfere with the fast -communication library and lead to simulations using ffmpeg to hang or -crash. - -:line - -Read or write compressed files :h4,link(gzip) - -If this option is enabled, large files can be read or written with -gzip compression by several LAMMPS commands, including -"read_data"_read_data.html, "rerun"_rerun.html, and "dump"_dump.html. - -[CMake variables]: - --D WITH_GZIP=value # yes or no - # default is yes if CMake can find gzip, else no --D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it :pre - -[Makefile.machine setting]: - -LMP_INC = -DLAMMPS_GZIP :pre - -[CMake and make info]: - -This option requires that your machine supports the "popen()" function -in the standard runtime library and that a gzip executable can be -found by LAMMPS during a run. - -NOTE: On some clusters with high-speed networks, using the fork() -library calls (required by popen()) can interfere with the fast -communication library and lead to simulations using compressed output -or input to hang or crash. For selected operations, compressed file -I/O is also available using a compression library instead, which is -what the "COMPRESS package"_Packages_details.html#PKG-COMPRESS enables. - -:line - -Memory allocation alignment :h4,link(align) - -This setting enables the use of the posix_memalign() call instead of -malloc() when LAMMPS allocates large chunks or memory. This can make -vector instructions on CPUs more efficient, if dynamically allocated -memory is aligned on larger-than-default byte boundaries. -On most current systems, the malloc() implementation returns -pointers that are aligned to 16-byte boundaries. Using SSE vector -instructions efficiently, however, requires memory blocks being -aligned on 64-byte boundaries. - -[CMake variable]: - --D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default) :pre - -Use a LAMMPS_MEMALIGN value of 0 to disable using posix_memalign() -and revert to using the malloc() C-library function instead. When -compiling LAMMPS for Windows systems, malloc() will always be used -and this setting ignored. - -[Makefile.machine setting]: - -LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64 :pre - -Do not set -DLAMMPS_MEMALIGN, if you want to have memory allocated -with the malloc() function call instead. -DLAMMPS_MEMALIGN [cannot] -be used on Windows, as it does use different function calls for -allocating aligned memory, that are not compatible with how LAMMPS -manages its dynamical memory. - -:line - -Workaround for long long integers :h4,link(longlong) - -If your system or MPI version does not recognize "long long" data -types, the following setting will be needed. It converts "long long" -to a "long" data type, which should be the desired 8-byte integer on -those systems: - -[CMake variable]: - --D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default) :pre - -[Makefile.machine setting]: - -LMP_INC = -DLAMMPS_LONGLONG_TO_LONG :pre - -:line - -Exception handling when using LAMMPS as a library :h4,link(exceptions) - -This setting is useful when external codes drive LAMMPS as a library. -With this option enabled LAMMPS errors do not kill the caller. -Instead, the call stack is unwound and control returns to the caller, -e.g. to Python. - -[CMake variable]: - --D LAMMPS_EXCEPTIONS=value # yes or no (default) :pre - -[Makefile.machine setting]: - -LMP_INC = -DLAMMPS_EXCEPTIONS :pre diff --git a/doc/txt/Build_windows.txt b/doc/txt/Build_windows.txt deleted file mode 100644 index b3dbf775c9..0000000000 --- a/doc/txt/Build_windows.txt +++ /dev/null @@ -1,102 +0,0 @@ -"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Notes for building LAMMPS on Windows :h3 - -"General remarks"_#generic -"Running Linux on Windows"_#linux -"Using GNU GCC ported to Windows"_#gnu -"Using a cross-compiler"_#cross :ul - -:line - -General remarks :h4,link(generic) - -LAMMPS is developed and tested primarily on Linux machines. The vast -majority of HPC clusters and supercomputers today runs on Linux as well. -Thus portability to other platforms is desired, but not always achieved. -The LAMMPS developers strongly rely on LAMMPS users giving feedback and -providing assistance in resolving portability issues. This particularly -true for compiling LAMMPS on Windows, since this platform has significant -differences with some low-level functionality. - - -Running Linux on Windows :h4,link(linux) - -So before trying to build LAMMPS on Windows, please consider if using -the pre-compiled Windows binary packages are sufficient for your needs -(as an aside, those packages themselves are build on a Linux machine -using cross-compilers). If it is necessary for your to compile LAMMPS -on a Windows machine (e.g. because it is your main desktop), please also -consider using a virtual machine software and run a Linux virtual machine, -or - if have a recently updated Windows 10 installation - consider using -the Windows subsystem for Linux, which allows to run a bash shell from -Ubuntu and from there on, you can pretty much use that shell like you -are running on an Ubuntu Linux machine (e.g. installing software via -apt-get). For more details on that, please see "this tutorial"_Howto_bash.html - - -Using GNU GCC ported to Windows :h4,link(gnu) - -One option for compiling LAMMPS on Windows natively, that has been known -to work in the past is to install a bash shell, unix shell utilities, -perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package -provides a unix/linux interface to low-level Windows functions, so LAMMPS -can be compiled on Windows. The necessary (minor) modifications to LAMMPS -are included, but may not always up-to-date for recently added functionality -and the corresponding new code. A machine makefile for using cygwin for -the old build system is provided. Using CMake for this mode of compilation -is untested and not likely to work. - -When compiling for Windows do [not] set the -DLAMMPS_MEMALIGN define -in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker -flags in LIB makefile variable. Try adding -static-libgcc or -static or -both to the linker flags when your resulting LAMMPS Windows executable -complains about missing .dll files. The CMake configuration should set -this up automatically, but is untested. - -In case of problems, you are recommended to contact somebody with -experience in using cygwin. If you do come across portability problems -requiring changes to the LAMMPS source code, or figure out corrections -yourself, please report them on the lammps-users mailing list, or file -them as an issue or pull request on the LAMMPS GitHub project. - - -Using a cross-compiler :h4,link(cross) - -If you need to provide custom LAMMPS binaries for Windows, but do not -need to do the compilation on Windows, please consider using a Linux -to Windows cross-compiler. This is how currently the Windows binary -packages are created by the LAMMPS developers. Because of that, this is -probably the currently best tested and supported way to build LAMMPS -executables for Windows. There are makefiles provided for the -traditional build system, but CMake has also been successfully tested -using the mingw32-cmake and mingw64-cmake wrappers that are bundled -with the cross-compiler environment on Fedora machines. A CMake preset -selecting all packages compatible with this cross-compilation build -is provided. You likely need to disable the GPU package unless you -download and install the contents of the pre-compiled "OpenCL ICD loader -library"_https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz -into your MinGW64 cross-compiler environment. The cross-compilation -currently will only produce non-MPI serial binaries. - -Please keep in mind, though, that this only applies to compiling LAMMPS. -Whether the resulting binaries do work correctly is no tested by the -LAMMPS developers. We instead rely on the feedback of the users -of these pre-compiled LAMMPS packages for Windows. We will try to resolve -issues to the best of our abilities if we become aware of them. However -this is subject to time constraints and focus on HPC platforms. - - -Native Visual C++ support :h4,link(native) - -Support for the Visual C++ compilers is currently not available. The -CMake build system is capable of creating suitable a Visual Studio -style build environment, but the LAMMPS code itself is not fully ported -to support Visual C++. Volunteers to take on this task are welcome. diff --git a/doc/txt/Errors.txt b/doc/txt/Errors.txt deleted file mode 100644 index 0489d228bd..0000000000 --- a/doc/txt/Errors.txt +++ /dev/null @@ -1,38 +0,0 @@ -"Previous Section"_Python_head.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Manual.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Errors :h2 - -These doc pages describe the errors you can encounter when using -LAMMPS. The common problems include conceptual issues. The messages -and warnings doc pages give complete lists of all the messages the -code may generate (except those generated by USER packages), with -additional details for many of them. - - - - - -"Common problems"_Errors_common.html -"Reporting bugs"_Errors_bugs.html -"Error messages"_Errors_messages.html -"Warning messages"_Errors_warnings.html :all(b) - - diff --git a/doc/txt/Errors_bugs.txt b/doc/txt/Errors_bugs.txt deleted file mode 100644 index 4a8e62e775..0000000000 --- a/doc/txt/Errors_bugs.txt +++ /dev/null @@ -1,35 +0,0 @@ -"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Reporting bugs :h3 - -If you are confident that you have found a bug in LAMMPS, follow these -steps. - -Check the "New features and bug -fixes"_http://lammps.sandia.gov/bug.html section of the "LAMMPS WWW -site"_lws to see if the bug has already been reported or fixed or the -"Unfixed bug"_http://lammps.sandia.gov/unbug.html to see if a fix is -pending. - -Check the "mailing list"_http://lammps.sandia.gov/mail.html to see if -it has been discussed before. - -If not, send an email to the mailing list describing the problem with -any ideas you have as to what is causing it or where in the code the -problem might be. The developers will ask for more info if needed, -such as an input script or data files. - -The most useful thing you can do to help us fix the bug is to isolate -the problem. Run it on the smallest number of atoms and fewest number -of processors and with the simplest input script that reproduces the -bug and try to identify what command or combination of commands is -causing the problem. - -NOTE: this page needs to have GitHub issues info added diff --git a/doc/txt/Errors_common.txt b/doc/txt/Errors_common.txt deleted file mode 100644 index da90aad64b..0000000000 --- a/doc/txt/Errors_common.txt +++ /dev/null @@ -1,126 +0,0 @@ -"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Common problems :h3 - -If two LAMMPS runs do not produce the exact same answer on different -machines or different numbers of processors, this is typically not a -bug. In theory you should get identical answers on any number of -processors and on any machine. In practice, numerical round-off can -cause slight differences and eventual divergence of molecular dynamics -phase space trajectories within a few 100s or few 1000s of timesteps. -However, the statistical properties of the two runs (e.g. average -energy or temperature) should still be the same. - -If the "velocity"_velocity.html command is used to set initial atom -velocities, a particular atom can be assigned a different velocity -when the problem is run on a different number of processors or on -different machines. If this happens, the phase space trajectories of -the two simulations will rapidly diverge. See the discussion of the -{loop} option in the "velocity"_velocity.html command for details and -options that avoid this issue. - -Similarly, the "create_atoms"_create_atoms.html command generates a -lattice of atoms. For the same physical system, the ordering and -numbering of atoms by atom ID may be different depending on the number -of processors. - -Some commands use random number generators which may be setup to -produce different random number streams on each processor and hence -will produce different effects when run on different numbers of -processors. A commonly-used example is the "fix -langevin"_fix_langevin.html command for thermostatting. - -A LAMMPS simulation typically has two stages, setup and run. Most -LAMMPS errors are detected at setup time; others like a bond -stretching too far may not occur until the middle of a run. - -LAMMPS tries to flag errors and print informative error messages so -you can fix the problem. For most errors it will also print the last -input script command that it was processing. Of course, LAMMPS cannot -figure out your physics or numerical mistakes, like choosing too big a -timestep, specifying erroneous force field coefficients, or putting 2 -atoms on top of each other! If you run into errors that LAMMPS -doesn't catch that you think it should flag, please send an email to -the "developers"_http://lammps.sandia.gov/authors.html. - -If you get an error message about an invalid command in your input -script, you can determine what command is causing the problem by -looking in the log.lammps file or using the "echo command"_echo.html -to see it on the screen. If you get an error like "Invalid ... -style", with ... being fix, compute, pair, etc, it means that you -mistyped the style name or that the command is part of an optional -package which was not compiled into your executable. The list of -available styles in your executable can be listed by using "the -h -command-line swith"_Run_options.html. The installation and -compilation of optional packages is explained on the "Build -packages"_Build_package.html doc page. - -For a given command, LAMMPS expects certain arguments in a specified -order. If you mess this up, LAMMPS will often flag the error, but it -may also simply read a bogus argument and assign a value that is -valid, but not what you wanted. E.g. trying to read the string "abc" -as an integer value of 0. Careful reading of the associated doc page -for the command should allow you to fix these problems. In most cases, -where LAMMPS expects to read a number, either integer or floating point, -it performs a stringent test on whether the provided input actually -is an integer or floating-point number, respectively, and reject the -input with an error message (for instance, when an integer is required, -but a floating-point number 1.0 is provided): - -ERROR: Expected integer parameter instead of '1.0' in input script or data file :pre - -Some commands allow for using variable references in place of numeric -constants so that the value can be evaluated and may change over the -course of a run. This is typically done with the syntax {v_name} for a -parameter, where name is the name of the variable. On the other hand, -immediate variable expansion with the syntax ${name} is performed while -reading the input and before parsing commands, - -NOTE: Using a variable reference (i.e. {v_name}) is only allowed if -the documentation of the corresponding command explicitly says it is. -Otherwise, you will receive an error message of this kind: - -ERROR: Expected floating point parameter instead of 'v_name' in input script or data file :pre - -Generally, LAMMPS will print a message to the screen and logfile and -exit gracefully when it encounters a fatal error. Sometimes it will -print a WARNING to the screen and logfile and continue on; you can -decide if the WARNING is important or not. A WARNING message that is -generated in the middle of a run is only printed to the screen, not to -the logfile, to avoid cluttering up thermodynamic output. If LAMMPS -crashes or hangs without spitting out an error message first then it -could be a bug (see "this section"_Errors_bugs.html) or one of the following -cases: - -LAMMPS runs in the available memory a processor allows to be -allocated. Most reasonable MD runs are compute limited, not memory -limited, so this shouldn't be a bottleneck on most platforms. Almost -all large memory allocations in the code are done via C-style malloc's -which will generate an error message if you run out of memory. -Smaller chunks of memory are allocated via C++ "new" statements. If -you are unlucky you could run out of memory just when one of these -small requests is made, in which case the code will crash or hang (in -parallel), since LAMMPS doesn't trap on those errors. - -Illegal arithmetic can cause LAMMPS to run slow or crash. This is -typically due to invalid physics and numerics that your simulation is -computing. If you see wild thermodynamic values or NaN values in your -LAMMPS output, something is wrong with your simulation. If you -suspect this is happening, it is a good idea to print out -thermodynamic info frequently (e.g. every timestep) via the -"thermo"_thermo.html so you can monitor what is happening. -Visualizing the atom movement is also a good idea to insure your model -is behaving as you expect. - -In parallel, one way LAMMPS can hang is due to how different MPI -implementations handle buffering of messages. If the code hangs -without an error message, it may be that you need to specify an MPI -setting or two (usually via an environment variable) to enable -buffering or boost the sizes of messages that can be buffered. diff --git a/doc/txt/Examples.txt b/doc/txt/Examples.txt deleted file mode 100644 index 04c211cb1d..0000000000 --- a/doc/txt/Examples.txt +++ /dev/null @@ -1,159 +0,0 @@ -"Previous Section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Tools.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Example scripts :h3 - -The LAMMPS distribution includes an examples sub-directory with many -sample problems. Many are 2d models that run quickly and are -straightforward to visualize, requiring at most a couple of minutes to -run on a desktop machine. Each problem has an input script (in.*) and -produces a log file (log.*) when it runs. Some use a data file -(data.*) of initial coordinates as additional input. A few sample log -file run on different machines and different numbers of processors are -included in the directories to compare your answers to. E.g. a log -file like log.date.crack.foo.P means the "crack" example was run on P -processors of machine "foo" on that date (i.e. with that version of -LAMMPS). - -Many of the input files have commented-out lines for creating dump -files and image files. - -If you uncomment the "dump"_dump.html command in the input script, a -text dump file will be produced, which can be animated by various -"visualization programs"_http://lammps.sandia.gov/viz.html. - -If you uncomment the "dump image"_dump.html command in the input -script, and assuming you have built LAMMPS with a JPG library, JPG -snapshot images will be produced when the simulation runs. They can -be quickly post-processed into a movie using commands described on the -"dump image"_dump_image.html doc page. - -Animations of many of the examples can be viewed on the Movies section -of the "LAMMPS web site"_lws. - -There are two kinds of sub-directories in the examples dir. Lowercase -dirs contain one or a few simple, quick-to-run problems. Uppercase -dirs contain up to several complex scripts that illustrate a -particular kind of simulation method or model. Some of these run for -longer times, e.g. to measure a particular quantity. - -Lists of both kinds of directories are given below. - -:line - -Lowercase directories :h4 - -accelerate: run with various acceleration options (OpenMP, GPU, Phi) -airebo: polyethylene with AIREBO potential -atm: Axilrod-Teller-Muto potential example -balance: dynamic load balancing, 2d system -body: body particles, 2d system -cmap: CMAP 5-body contributions to CHARMM force field -colloid: big colloid particles in a small particle solvent, 2d system -comb: models using the COMB potential -controller: use of fix controller as a thermostat -coreshell: core/shell model using CORESHELL package -crack: crack propagation in a 2d solid -deposit: deposit atoms and molecules on a surface -dipole: point dipolar particles, 2d system -dreiding: methanol via Dreiding FF -eim: NaCl using the EIM potential -ellipse: ellipsoidal particles in spherical solvent, 2d system -flow: Couette and Poiseuille flow in a 2d channel -friction: frictional contact of spherical asperities between 2d surfaces -gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command -granregion: use of fix wall/region/gran as boundary on granular particles -hugoniostat: Hugoniostat shock dynamics -hyper: global and local hyperdynamics of diffusion on Pt surface -indent: spherical indenter into a 2d solid -kim: use of potentials from the "OpenKIM Repository"_openkim -latte: examples for using fix latte for DFTB via the LATTE library -meam: MEAM test for SiC and shear (same as shear examples) -melt: rapid melt of 3d LJ system -message: demos for LAMMPS client/server coupling with the MESSAGE package -micelle: self-assembly of small lipid-like molecules into 2d bilayers -min: energy minimization of 2d LJ melt -mscg: parameterize a multi-scale coarse-graining (MSCG) model -msst: MSST shock dynamics -nb3b: use of non-bonded 3-body harmonic pair style -neb: nudged elastic band (NEB) calculation for barrier finding -nemd: non-equilibrium MD of 2d sheared system -obstacle: flow around two voids in a 2d channel -peptide: dynamics of a small solvated peptide chain (5-mer) -peri: Peridynamic model of cylinder impacted by indenter -pour: pouring of granular particles into a 3d box, then chute flow -prd: parallel replica dynamics of vacancy diffusion in bulk Si -python: using embedded Python in a LAMMPS input script -qeq: use of the QEQ package for charge equilibration -rdf-adf: computing radial and angle distribution functions for water -reax: RDX and TATB models using the ReaxFF -rerun: use of rerun and read_dump commands -rigid: rigid bodies modeled as independent or coupled -shear: sideways shear applied to 2d solid, with and without a void -snap: NVE dynamics for BCC tantalum crystal using SNAP potential -srd: stochastic rotation dynamics (SRD) particles as solvent -streitz: use of Streitz/Mintmire potential with charge equilibration -tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si -threebody: regression test input for a variety of manybody potentials -vashishta: use of the Vashishta potential -voronoi: Voronoi tesselation via compute voronoi/atom command :tb(s=:) - -Here is how you can run and visualize one of the sample problems: - -cd indent -cp ../../src/lmp_linux . # copy LAMMPS executable to this dir -lmp_linux -in in.indent # run the problem :pre - -Running the simulation produces the files {dump.indent} and -{log.lammps}. You can visualize the dump file of snapshots with a -variety of 3rd-party tools highlighted on the -"Visualization"_http://lammps.sandia.gov/viz.html page of the LAMMPS -web site. - -If you uncomment the "dump image"_dump_image.html line(s) in the input -script a series of JPG images will be produced by the run (assuming -you built LAMMPS with JPG support; see the -"Build_settings"_Build_settings.html doc page for details). These can -be viewed individually or turned into a movie or animated by tools -like ImageMagick or QuickTime or various Windows-based tools. See the -"dump image"_dump_image.html doc page for more details. E.g. this -Imagemagick command would create a GIF file suitable for viewing in a -browser. - -% convert -loop 1 *.jpg foo.gif :pre - -:line - -Uppercase directories :h4 - -ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc -COUPLE: examples of how to use LAMMPS as a library -DIFFUSE: compute diffusion coefficients via several methods -ELASTIC: compute elastic constants at zero temperature -ELASTIC_T: compute elastic constants at finite temperature -HEAT: compute thermal conductivity for LJ and water via fix ehex -KAPPA: compute thermal conductivity via several methods -MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system -SPIN: examples for features of the SPIN package -UNITS: examples that run the same simulation in lj, real, metal units -USER: examples for USER packages and USER-contributed commands -VISCOSITY: compute viscosity via several methods :tb(s=:) - -Nearly all of these directories have README files which give more -details on how to understand and use their contents. - -The USER directory has a large number of sub-directories which -correspond by name to a USER package. They contain scripts that -illustrate how to use the command(s) provided in that package. Many -of the sub-directories have their own README files which give further -instructions. See the "Packages_details"_Packages_details.html doc -page for more info on specific USER packages. - -:link(openkim,https://openkim.org) diff --git a/doc/txt/Howto.txt b/doc/txt/Howto.txt deleted file mode 100644 index 0df417af75..0000000000 --- a/doc/txt/Howto.txt +++ /dev/null @@ -1,191 +0,0 @@ -"Previous Section"_Performance.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Examples.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands.html#comm) - -:line - -Howto discussions :h2 - -These doc pages describe how to perform various tasks with LAMMPS, -both for users and developers. The -"glossary"_http://lammps.sandia.gov website page also lists MD -terminology with links to corresponding LAMMPS manual pages. The -example input scripts included in the examples dir of the LAMMPS -distribution and highlighted on the "Examples"_Examples.html doc page -also show how to setup and run various kinds of simulations. - -Tutorials howto :h3 - - - - - -"Using GitHub with LAMMPS"_Howto_github.html -"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html -"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b) - - - -General howto :h3 - - - - - -"Restart a simulation"_Howto_restart.html -"Visualize LAMMPS snapshots"_Howto_viz.html -"Run multiple simulations from one input script"_Howto_multiple.html -"Multi-replica simulations"_Howto_replica.html -"Library interface to LAMMPS"_Howto_library.html -"Couple LAMMPS to other codes"_Howto_couple.html -"Using LAMMPS in client/server mode"_Howto_client_server.html :all(b) - - - -Settings howto :h3 - - - - - -"2d simulations"_Howto_2d.html -"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html -"Thermostats"_Howto_thermostat.html -"Barostats"_Howto_barostat.html -"Walls"_Howto_walls.html -"NEMD simulations"_Howto_nemd.html -"Long-range dispersion settings"_Howto_dispersion.html :all(b) - - - - -Analysis howto :h3 - - - - - -"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html -"Use chunks to calculate system properties"_Howto_chunk.html :all(b) -"Calculate temperature"_Howto_temperature.html -"Calculate elastic constants"_Howto_elastic.html -"Calculate thermal conductivity"_Howto_kappa.html -"Calculate viscosity"_Howto_viscosity.html -"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b) - - - -Force fields howto :h3 - - - - - -"CHARMM, AMBER, COMPASS, and DREIDING force fields"_Howto_bioFF.html -"TIP3P water model"_Howto_tip3p.html -"TIP4P water model"_Howto_tip4p.html -"SPC water model"_Howto_spc.html :all(b) - - - -Packages howto :h3 - - - - - - -"Finite-size spherical and aspherical particles"_Howto_spherical.html -"Granular models"_Howto_granular.html -"Body style particles"_Howto_body.html -"Polarizable models"_Howto_polarizable.html -"Adiabatic core/shell model"_Howto_coreshell.html -"Drude induced dipoles"_Howto_drude.html -"Drude induced dipoles (extended)"_Howto_drude2.html -"Manifolds (surfaces)"_Howto_manifold.html -"Magnetic spins"_Howto_spins.html :all(b) - - diff --git a/doc/txt/Howto_2d.txt b/doc/txt/Howto_2d.txt deleted file mode 100644 index e1758c05d5..0000000000 --- a/doc/txt/Howto_2d.txt +++ /dev/null @@ -1,48 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -2d simulations :h3 - -Use the "dimension"_dimension.html command to specify a 2d simulation. - -Make the simulation box periodic in z via the "boundary"_boundary.html -command. This is the default. - -If using the "create box"_create_box.html command to define a -simulation box, set the z dimensions narrow, but finite, so that the -create_atoms command will tile the 3d simulation box with a single z -plane of atoms - e.g. - -"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre - -If using the "read data"_read_data.html command to read in a file of -atom coordinates, set the "zlo zhi" values to be finite but narrow, -similar to the create_box command settings just described. For each -atom in the file, assign a z coordinate so it falls inside the -z-boundaries of the box - e.g. 0.0. - -Use the "fix enforce2d"_fix_enforce2d.html command as the last -defined fix to insure that the z-components of velocities and forces -are zeroed out every timestep. The reason to make it the last fix is -so that any forces induced by other fixes will be zeroed out. - -Many of the example input scripts included in the LAMMPS distribution -are for 2d models. - -NOTE: Some models in LAMMPS treat particles as finite-size spheres, as -opposed to point particles. See the "atom_style -sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html -commands for details. By default, for 2d simulations, such particles -will still be modeled as 3d spheres, not 2d discs (circles), meaning -their moment of inertia will be that of a sphere. If you wish to -model them as 2d discs, see the "set density/disc"_set.html command -and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html, -"fix nvt/sphere"_fix_nvt_sphere.html, "fix -nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html -commands. diff --git a/doc/txt/Howto_barostat.txt b/doc/txt/Howto_barostat.txt deleted file mode 100644 index 1fbfb14222..0000000000 --- a/doc/txt/Howto_barostat.txt +++ /dev/null @@ -1,75 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Barostats :h3 - -Barostatting means controlling the pressure in an MD simulation. -"Thermostatting"_Howto_thermostat.html means controlling the -temperature of the particles. Since the pressure includes a kinetic -component due to particle velocities, both these operations require -calculation of the temperature. Typically a target temperature (T) -and/or pressure (P) is specified by the user, and the thermostat or -barostat attempts to equilibrate the system to the requested T and/or -P. - -Barostatting in LAMMPS is performed by "fixes"_fix.html. Two -barostatting methods are currently available: Nose-Hoover (npt and -nph) and Berendsen: - -"fix npt"_fix_nh.html -"fix npt/sphere"_fix_npt_sphere.html -"fix npt/asphere"_fix_npt_asphere.html -"fix nph"_fix_nh.html -"fix press/berendsen"_fix_press_berendsen.html :ul - -The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat -and barostat. "Fix nph"_fix_nh.html is just a Nose/Hoover barostat; -it does no thermostatting. Both "fix nph"_fix_nh.html and "fix -press/berendsen"_fix_press_berendsen.html can be used in conjunction -with any of the thermostatting fixes. - -As with the "thermostats"_Howto_thermostat.html, "fix npt"_fix_nh.html -and "fix nph"_fix_nh.html only use translational motion of the -particles in computing T and P and performing thermo/barostatting. -"Fix npt/sphere"_fix_npt_sphere.html and "fix -npt/asphere"_fix_npt_asphere.html thermo/barostat using not only -translation velocities but also rotational velocities for spherical -and aspherical particles. - -All of the barostatting fixes use the "compute -pressure"_compute_pressure.html compute to calculate a current -pressure. By default, this compute is created with a simple "compute -temp"_compute_temp.html (see the last argument of the "compute -pressure"_compute_pressure.html command), which is used to calculated -the kinetic component of the pressure. The barostatting fixes can -also use temperature computes that remove bias for the purpose of -computing the kinetic component which contributes to the current -pressure. See the doc pages for the individual fixes and for the -"fix_modify"_fix_modify.html command for instructions on how to assign -a temperature or pressure compute to a barostatting fix. - -NOTE: As with the thermostats, the Nose/Hoover methods ("fix -npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration. -"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should -be used with one of the constant NVE fixes or with one of the NVT -fixes. - -Thermodynamic output, which can be setup via the -"thermo_style"_thermo_style.html command, often includes pressure -values. As explained on the doc page for the -"thermo_style"_thermo_style.html command, the default pressure is -setup by the thermo command itself. It is NOT the pressure associated -with any barostatting fix you have defined or with any compute you -have defined that calculates a pressure. The doc pages for the -barostatting fixes explain the ID of the pressure compute they create. -Thus if you want to view these pressures, you need to specify them -explicitly via the "thermo_style custom"_thermo_style.html command. -Or you can use the "thermo_modify"_thermo_modify.html command to -re-define what pressure compute is used for default thermodynamic -output. diff --git a/doc/txt/Howto_bioFF.txt b/doc/txt/Howto_bioFF.txt deleted file mode 100644 index d238e4024f..0000000000 --- a/doc/txt/Howto_bioFF.txt +++ /dev/null @@ -1,136 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -CHARMM, AMBER, COMPASS, and DREIDING force fields :h3 - -A force field has 2 parts: the formulas that define it and the -coefficients used for a particular system. Here we only discuss -formulas implemented in LAMMPS that correspond to formulas commonly -used in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting -coefficients is done either from special sections in an input data file -via the "read_data"_read_data.html command or in the input script with -commands like "pair_coeff"_pair_coeff.html or -"bond_coeff"_bond_coeff.html and so on. See the "Tools"_Tools.html doc -page for additional tools that can use CHARMM, AMBER, or Materials -Studio generated files to assign force field coefficients and convert -their output into LAMMPS input. - -See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force -field. See "(Cornell)"_#howto-Cornell for a description of the AMBER -force field. See "(Sun)"_#howto-Sun for a description of the COMPASS -force field. - -:link(charmm,http://www.scripps.edu/brooks) -:link(amber,http://amber.scripps.edu) - -The interaction styles listed below compute force field formulas that -are consistent with common options in CHARMM or AMBER. See each -command's documentation for the formula it computes. - -"bond_style"_bond_harmonic.html harmonic -"angle_style"_angle_charmm.html charmm -"dihedral_style"_dihedral_charmm.html charmmfsh -"dihedral_style"_dihedral_charmm.html charmm -"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh -"pair_style"_pair_charmm.html lj/charmmfsw/coul/long -"pair_style"_pair_charmm.html lj/charmm/coul/charmm -"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit -"pair_style"_pair_charmm.html lj/charmm/coul/long :ul - -"special_bonds"_special_bonds.html charmm -"special_bonds"_special_bonds.html amber :ul - -NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were released -in March 2017. We recommend they be used instead of the older {charmm} -styles. See discussion of the differences on the "pair -charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html doc -pages. - -COMPASS is a general force field for atomistic simulation of common -organic molecules, inorganic small molecules, and polymers which was -developed using ab initio and empirical parameterization techniques. -See the "Tools"_Tools.html doc page for the msi2lmp tool for creating -LAMMPS template input and data files from BIOVIA's Materials Studio -files. Please note that the msi2lmp tool is very old and largely -unmaintained, so it does not support all features of Materials Studio -provided force field files, especially additions during the last decade. -You should watch the output carefully and compare results, where -possible. See "(Sun)"_#howto-Sun for a description of the COMPASS force -field. - -These interaction styles listed below compute force field formulas that -are consistent with the COMPASS force field. See each command's -documentation for the formula it computes. - -"bond_style"_bond_class2.html class2 -"angle_style"_angle_class2.html class2 -"dihedral_style"_dihedral_class2.html class2 -"improper_style"_improper_class2.html class2 :ul - -"pair_style"_pair_class2.html lj/class2 -"pair_style"_pair_class2.html lj/class2/coul/cut -"pair_style"_pair_class2.html lj/class2/coul/long :ul - -"special_bonds"_special_bonds.html lj/coul 0 0 1 :ul - -DREIDING is a generic force field developed by the "Goddard -group"_http://www.wag.caltech.edu at Caltech and is useful for -predicting structures and dynamics of organic, biological and main-group -inorganic molecules. The philosophy in DREIDING is to use general force -constants and geometry parameters based on simple hybridization -considerations, rather than individual force constants and geometric -parameters that depend on the particular combinations of atoms involved -in the bond, angle, or torsion terms. DREIDING has an "explicit hydrogen -bond term"_pair_hbond_dreiding.html to describe interactions involving a -hydrogen atom on very electronegative atoms (N, O, F). - -See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field - -The interaction styles listed below compute force field formulas that -are consistent with the DREIDING force field. See each command's -documentation for the formula it computes. - -"bond_style"_bond_harmonic.html harmonic -"bond_style"_bond_morse.html morse :ul - -"angle_style"_angle_harmonic.html harmonic -"angle_style"_angle_cosine.html cosine -"angle_style"_angle_cosine_periodic.html cosine/periodic :ul - -"dihedral_style"_dihedral_charmm.html charmm -"improper_style"_improper_umbrella.html umbrella :ul - -"pair_style"_pair_buck.html buck -"pair_style"_pair_buck.html buck/coul/cut -"pair_style"_pair_buck.html buck/coul/long -"pair_style"_pair_lj.html lj/cut -"pair_style"_pair_lj.html lj/cut/coul/cut -"pair_style"_pair_lj.html lj/cut/coul/long :ul - -"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj -"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul - -"special_bonds"_special_bonds.html dreiding :ul - -:line - -:link(howto-MacKerell) -[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). - -:link(howto-Cornell) -[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, -Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). - -:link(howto-Sun) -[(Sun)] Sun, J. Phys. Chem. B, 102, 7338-7364 (1998). - -:link(howto-Mayo) -[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). diff --git a/doc/txt/Howto_body.txt b/doc/txt/Howto_body.txt deleted file mode 100644 index 7cbdf95315..0000000000 --- a/doc/txt/Howto_body.txt +++ /dev/null @@ -1,456 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Body particles :h3 - -[Overview:] - -In LAMMPS, body particles are generalized finite-size particles. -Individual body particles can represent complex entities, such as -surface meshes of discrete points, collections of sub-particles, -deformable objects, etc. Note that other kinds of finite-size -spherical and aspherical particles are also supported by LAMMPS, such -as spheres, ellipsoids, line segments, and triangles, but they are -simpler entities that body particles. See the "Howto -spherical"_Howto_spherical.html doc page for a general overview of all -these particle types. - -Body particles are used via the "atom_style body"_atom_style.html -command. It takes a body style as an argument. The current body -styles supported by LAMMPS are as follows. The name in the first -column is used as the {bstyle} argument for the "atom_style -body"_atom_style.html command. - -{nparticle} : rigid body with N sub-particles -{rounded/polygon} : 2d polygons with N vertices -{rounded/polyhedron} : 3d polyhedra with N vertices, E edges and F faces :tb(s=:) - -The body style determines what attributes are stored for each body and -thus how they can be used to compute pairwise body/body or -bond/non-body (point particle) interactions. More details of each -style are described below. - -More styles may be added in the future. See the "Modify -body"_Modify_body.html doc page for details on how to add a new body -style to the code. - -:line - -[When to use body particles:] - -You should not use body particles to model a rigid body made of -simpler particles (e.g. point, sphere, ellipsoid, line segment, -triangular particles), if the interaction between pairs of rigid -bodies is just the summation of pairwise interactions between the -simpler particles. LAMMPS already supports this kind of model via the -"fix rigid"_fix_rigid.html command. Any of the numerous pair styles -that compute interactions between simpler particles can be used. The -"fix rigid"_fix_rigid.html command time integrates the motion of the -rigid bodies. All of the standard LAMMPS commands for thermostatting, -adding constraints, performing output, etc will operate as expected on -the simple particles. - -By contrast, when body particles are used, LAMMPS treats an entire -body as a single particle for purposes of computing pairwise -interactions, building neighbor lists, migrating particles between -processors, output of particles to a dump file, etc. This means that -interactions between pairs of bodies or between a body and non-body -(point) particle need to be encoded in an appropriate pair style. If -such a pair style were to mimic the "fix rigid"_fix_rigid.html model, -it would need to loop over the entire collection of interactions -between pairs of simple particles within the two bodies, each time a -single body/body interaction was computed. - -Thus it only makes sense to use body particles and develop such a pair -style, when particle/particle interactions are more complex than what -the "fix rigid"_fix_rigid.html command can already calculate. For -example, consider particles with one or more of the following -attributes: - -represented by a surface mesh -represented by a collection of geometric entities (e.g. planes + spheres) -deformable -internal stress that induces fragmentation :ul - -For these models, the interaction between pairs of particles is likely -to be more complex than the summation of simple pairwise interactions. -An example is contact or frictional forces between particles with -planar surfaces that inter-penetrate. Likewise, the body particle may -store internal state, such as a stress tensor used to compute a -fracture criterion. - -These are additional LAMMPS commands that can be used with body -particles of different styles - -"fix nve/body"_fix_nve_body.html : integrate motion of a body particle in NVE ensemble -"fix nvt/body"_fix_nvt_body.html : ditto for NVT ensemble -"fix npt/body"_fix_npt_body.html : ditto for NPT ensemble -"fix nph/body"_fix_nph_body.html : ditto for NPH ensemble -"compute body/local"_compute_body_local.html : store sub-particle attributes of a body particle -"compute temp/body"_compute_temp_body.html : compute temperature of body particles -"dump local"_dump.html : output sub-particle attributes of a body particle -"dump image"_dump_image.html : output body particle attributes as an image :tb(s=:) - -The pair styles defined for use with specific body styles are listed -in the sections below. - -:line - -[Specifics of body style nparticle:] - -The {nparticle} body style represents body particles as a rigid body -with a variable number N of sub-particles. It is provided as a -vanilla, prototypical example of a body particle, although as -mentioned above, the "fix rigid"_fix_rigid.html command already -duplicates its functionality. - -The atom_style body command for this body style takes two additional -arguments: - -atom_style body nparticle Nmin Nmax -Nmin = minimum # of sub-particles in any body in the system -Nmax = maximum # of sub-particles in any body in the system :pre - -The Nmin and Nmax arguments are used to bound the size of data -structures used internally by each particle. - -When the "read_data"_read_data.html command reads a data file for this -body style, the following information must be provided for each entry -in the {Bodies} section of the data file: - -atom-ID 1 M -N -ixx iyy izz ixy ixz iyz -x1 y1 z1 -... -xN yN zN :pre - -where M = 6 + 3*N, and N is the number of sub-particles in the body -particle. - -The integer line has a single value N. The floating point line(s) -list 6 moments of inertia followed by the coordinates of the N -sub-particles (x1 to zN) as 3N values. These values can be listed on -as many lines as you wish; see the "read_data"_read_data.html command -for more details. - -The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the -values consistent with the current orientation of the rigid body -around its center of mass. The values are with respect to the -simulation box XYZ axes, not with respect to the principal axes of the -rigid body itself. LAMMPS performs the latter calculation internally. -The coordinates of each sub-particle are specified as its x,y,z -displacement from the center-of-mass of the body particle. The -center-of-mass position of the particle is specified by the x,y,z -values in the {Atoms} section of the data file, as is the total mass -of the body particle. - -The "pair_style body/nparticle"_pair_body_nparticle.html command can be used -with this body style to compute body/body and body/non-body interactions. - -For output purposes via the "compute -body/local"_compute_body_local.html and "dump local"_dump.html -commands, this body style produces one datum for each of the N -sub-particles in a body particle. The datum has 3 values: - -1 = x position of sub-particle -2 = y position of sub-particle -3 = z position of sub-particle :pre - -These values are the current position of the sub-particle within the -simulation domain, not a displacement from the center-of-mass (COM) of -the body particle itself. These values are calculated using the -current COM and orientation of the body particle. - -For images created by the "dump image"_dump_image.html command, if the -{body} keyword is set, then each body particle is drawn as a -collection of spheres, one for each sub-particle. The size of each -sphere is determined by the {bflag1} parameter for the {body} keyword. -The {bflag2} argument is ignored. - -:line - -[Specifics of body style rounded/polygon:] - -The {rounded/polygon} body style represents body particles as a 2d -polygon with a variable number of N vertices. This style can only be -used for 2d models; see the "boundary"_boundary.html command. See the -"pair_style body/rounded/polygon" doc page for a diagram of two -squares with rounded circles at the vertices. Special cases for N = 1 -(circle) and N = 2 (rod with rounded ends) can also be specified. - -One use of this body style is for 2d discrete element models, as -described in "Fraige"_#body-Fraige. - -Similar to body style {nparticle}, the atom_style body command for -this body style takes two additional arguments: - -atom_style body rounded/polygon Nmin Nmax -Nmin = minimum # of vertices in any body in the system -Nmax = maximum # of vertices in any body in the system :pre - -The Nmin and Nmax arguments are used to bound the size of data -structures used internally by each particle. - -When the "read_data"_read_data.html command reads a data file for this -body style, the following information must be provided for each entry -in the {Bodies} section of the data file: - -atom-ID 1 M -N -ixx iyy izz ixy ixz iyz -x1 y1 z1 -... -xN yN zN -i j j k k ... -diameter :pre - -where M = 6 + 3*N + 2*N + 1, and N is the number of vertices in the -body particle. - -The integer line has a single value N. The floating point line(s) -list 6 moments of inertia followed by the coordinates of the N -vertices (x1 to zN) as 3N values (with z = 0.0 for each), followed by -2N vertex indices corresponding to the end points of the N edges, -followed by a single diameter value = the rounded diameter of the -circle that surrounds each vertex. The diameter value can be different -for each body particle. These floating-point values can be listed on -as many lines as you wish; see the "read_data"_read_data.html command -for more details. - -The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the -values consistent with the current orientation of the rigid body -around its center of mass. The values are with respect to the -simulation box XYZ axes, not with respect to the principal axes of the -rigid body itself. LAMMPS performs the latter calculation internally. -The coordinates of each vertex are specified as its x,y,z displacement -from the center-of-mass of the body particle. The center-of-mass -position of the particle is specified by the x,y,z values in the -{Atoms} section of the data file. - -For example, the following information would specify a square particle -whose edge length is sqrt(2) and rounded diameter is 1.0. The -orientation of the square is aligned with the xy coordinate axes which -is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz = -1 1 4 0 0 0. Note that only Izz matters in 2D simulations. - -3 1 27 -4 -1 1 4 0 0 0 --0.7071 -0.7071 0 --0.7071 0.7071 0 -0.7071 0.7071 0 -0.7071 -0.7071 0 -0 1 -1 2 -2 3 -3 0 -1.0 :pre - -A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends -by circles of diameter 0.5, is specified as follows: - -1 1 13 -2 -1 1 1.33333 0 0 0 --2 0 0 -2 0 0 -0.5 :pre - -A disk, whose diameter is 3.0, mass 1.0, is specified as follows: - -1 1 10 -1 -1 1 4.5 0 0 0 -0 0 0 -3.0 :pre - -The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html -command can be used with this body style to compute body/body -interactions. The "fix wall/body/polygon"_fix_wall_body_polygon.html -command can be used with this body style to compute the interaction of -body particles with a wall. - -:line - -[Specifics of body style rounded/polyhedron:] - -The {rounded/polyhedron} body style represents body particles as a 3d -polyhedron with a variable number of N vertices, E edges and F faces. -This style can only be used for 3d models; see the -"boundary"_boundary.html command. See the "pair_style -body/rounded/polygon" doc page for a diagram of a two 2d squares with -rounded circles at the vertices. A 3d cube with rounded spheres at -the 8 vertices and 12 rounded edges would be similar. Special cases -for N = 1 (sphere) and N = 2 (rod with rounded ends) can also be -specified. - -This body style is for 3d discrete element models, as described in -"Wang"_#body-Wang. - -Similar to body style {rounded/polygon}, the atom_style body command -for this body style takes two additional arguments: - -atom_style body rounded/polyhedron Nmin Nmax -Nmin = minimum # of vertices in any body in the system -Nmax = maximum # of vertices in any body in the system :pre - -The Nmin and Nmax arguments are used to bound the size of data -structures used internally by each particle. - -When the "read_data"_read_data.html command reads a data file for this -body style, the following information must be provided for each entry -in the {Bodies} section of the data file: - -atom-ID 3 M -N E F -ixx iyy izz ixy ixz iyz -x1 y1 z1 -... -xN yN zN -0 1 -1 2 -2 3 -... -0 1 2 -1 -0 2 3 -1 -... -1 2 3 4 -diameter :pre - -where M = 6 + 3*N + 2*E + 4*F + 1, and N is the number of vertices in -the body particle, E = number of edges, F = number of faces. - -The integer line has three values: number of vertices (N), number of -edges (E) and number of faces (F). The floating point line(s) list 6 -moments of inertia followed by the coordinates of the N vertices (x1 -to zN) as 3N values, followed by 2N vertex indices corresponding to -the end points of the E edges, then 4*F vertex indices defining F -faces. The last value is the diameter value = the rounded diameter of -the sphere that surrounds each vertex. The diameter value can be -different for each body particle. These floating-point values can be -listed on as many lines as you wish; see the -"read_data"_read_data.html command for more details. Because the -maximum number of vertices per face is hard-coded to be 4 -(i.e. quadrilaterals), faces with more than 4 vertices need to be -split into triangles or quadrilaterals. For triangular faces, the -last vertex index should be set to -1. - -The ordering of the 4 vertices within a face should follow -the right-hand rule so that the normal vector of the face points -outwards from the center of mass. - -The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the -values consistent with the current orientation of the rigid body -around its center of mass. The values are with respect to the -simulation box XYZ axes, not with respect to the principal axes of the -rigid body itself. LAMMPS performs the latter calculation internally. -The coordinates of each vertex are specified as its x,y,z displacement -from the center-of-mass of the body particle. The center-of-mass -position of the particle is specified by the x,y,z values in the -{Atoms} section of the data file. - -For example, the following information would specify a cubic particle -whose edge length is 2.0 and rounded diameter is 0.5. -The orientation of the cube is aligned with the xyz coordinate axes -which is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz -iyz = 0.667 0.667 0.667 0 0 0. - -1 3 79 -8 12 6 -0.667 0.667 0.667 0 0 0 -1 1 1 -1 -1 1 --1 -1 1 --1 1 1 -1 1 -1 -1 -1 -1 --1 -1 -1 --1 1 -1 -0 1 -1 2 -2 3 -3 0 -4 5 -5 6 -6 7 -7 4 -0 4 -1 5 -2 6 -3 7 -0 1 2 3 -4 5 6 7 -0 1 5 4 -1 2 6 5 -2 3 7 6 -3 0 4 7 -0.5 :pre - -A rod in 3D, whose length is 4.0, mass 1.0 and rounded at two ends -by circles of diameter 0.5, is specified as follows: - -1 1 13 -2 -0 1.33333 1.33333 0 0 0 --2 0 0 -2 0 0 -0.5 :pre - -A sphere whose diameter is 3.0 and mass 1.0, is specified as follows: - -1 1 10 -1 -0.9 0.9 0.9 0 0 0 -0 0 0 -3.0 :pre - -The "pair_style -body/rounded/polhedron"_pair_body_rounded_polyhedron.html command can -be used with this body style to compute body/body interactions. The -"fix wall/body/polyhedron"_fix_wall_body_polygon.html command can be -used with this body style to compute the interaction of body particles -with a wall. - -:line - -For output purposes via the "compute -body/local"_compute_body_local.html and "dump local"_dump.html -commands, this body style produces one datum for each of the N -sub-particles in a body particle. The datum has 3 values: - -1 = x position of vertex -2 = y position of vertex -3 = z position of vertex :pre - -These values are the current position of the vertex within the -simulation domain, not a displacement from the center-of-mass (COM) of -the body particle itself. These values are calculated using the -current COM and orientation of the body particle. - -For images created by the "dump image"_dump_image.html command, if the -{body} keyword is set, then each body particle is drawn as a polygon -consisting of N line segments. Note that the line segments are drawn -between the N vertices, which does not correspond exactly to the -physical extent of the body (because the "pair_style -rounded/polygon"_pair_body_rounded_polygon.html defines finite-size -spheres at those point and the line segments between the spheres are -tangent to the spheres). The drawn diameter of each line segment is -determined by the {bflag1} parameter for the {body} keyword. The -{bflag2} argument is ignored. - -:line - -:link(body-Fraige) -[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, -Particuology, 6, 455 (2008). - -:link(body-Wang) -[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular -Matter, 13, 1 (2011). diff --git a/doc/txt/Howto_chunk.txt b/doc/txt/Howto_chunk.txt deleted file mode 100644 index ef9b49f87c..0000000000 --- a/doc/txt/Howto_chunk.txt +++ /dev/null @@ -1,205 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Use chunks to calculate system properties :h3 - -In LAMMS, "chunks" are collections of atoms, as defined by the -"compute chunk/atom"_compute_chunk_atom.html command, which assigns -each atom to a chunk ID (or to no chunk at all). The number of chunks -and the assignment of chunk IDs to atoms can be static or change over -time. Examples of "chunks" are molecules or spatial bins or atoms -with similar values (e.g. coordination number or potential energy). - -The per-atom chunk IDs can be used as input to two other kinds of -commands, to calculate various properties of a system: - -"fix ave/chunk"_fix_ave_chunk.html -any of the "compute */chunk"_compute.html commands :ul - -Here a brief overview for each of the 4 kinds of chunk-related commands -is provided. Then some examples are given of how to compute different -properties with chunk commands. - -Compute chunk/atom command: :h4 - -This compute can assign atoms to chunks of various styles. Only atoms -in the specified group and optional specified region are assigned to a -chunk. Here are some possible chunk definitions: - -atoms in same molecule | chunk ID = molecule ID | -atoms of same atom type | chunk ID = atom type | -all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom | -atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command | -atoms in same spatial bin | chunk ID = bin ID | -atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies | -atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html | -atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2) - -Note that chunk IDs are integer values, so for atom properties or -computes that produce a floating point value, they will be truncated -to an integer. You could also use the compute in a variable that -scales the floating point value to spread it across multiple integers. - -Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = -pencils, 3d bins = boxes, spherical bins, cylindrical bins. - -This compute also calculates the number of chunks {Nchunk}, which is -used by other commands to tally per-chunk data. {Nchunk} can be a -static value or change over time (e.g. the number of clusters). The -chunk ID for an individual atom can also be static (e.g. a molecule -ID), or dynamic (e.g. what spatial bin an atom is in as it moves). - -Note that this compute allows the per-atom output of other -"computes"_compute.html, "fixes"_fix.html, and -"variables"_variable.html to be used to define chunk IDs for each -atom. This means you can write your own compute or fix to output a -per-atom quantity to use as chunk ID. See the "Modify"_Modify.html -doc pages for info on how to do this. You can also define a "per-atom -variable"_variable.html in the input script that uses a formula to -generate a chunk ID for each atom. - -Fix ave/chunk command: :h4 - -This fix takes the ID of a "compute -chunk/atom"_compute_chunk_atom.html command as input. For each chunk, -it then sums one or more specified per-atom values over the atoms in -each chunk. The per-atom values can be any atom property, such as -velocity, force, charge, potential energy, kinetic energy, stress, -etc. Additional keywords are defined for per-chunk properties like -density and temperature. More generally any per-atom value generated -by other "computes"_compute.html, "fixes"_fix.html, and "per-atom -variables"_variable.html, can be summed over atoms in each chunk. - -Similar to other averaging fixes, this fix allows the summed per-chunk -values to be time-averaged in various ways, and output to a file. The -fix produces a global array as output with one row of values per -chunk. - -Compute */chunk commands: :h4 - -The following computes operate on chunks of atoms to produce per-chunk -values. Any compute whose style name ends in "/chunk" is in this -category: - -"compute com/chunk"_compute_com_chunk.html -"compute gyration/chunk"_compute_gyration_chunk.html -"compute inertia/chunk"_compute_inertia_chunk.html -"compute msd/chunk"_compute_msd_chunk.html -"compute property/chunk"_compute_property_chunk.html -"compute temp/chunk"_compute_temp_chunk.html -"compute torque/chunk"_compute_vcm_chunk.html -"compute vcm/chunk"_compute_vcm_chunk.html :ul - -They each take the ID of a "compute -chunk/atom"_compute_chunk_atom.html command as input. As their names -indicate, they calculate the center-of-mass, radius of gyration, -moments of inertia, mean-squared displacement, temperature, torque, -and velocity of center-of-mass for each chunk of atoms. The "compute -property/chunk"_compute_property_chunk.html command can tally the -count of atoms in each chunk and extract other per-chunk properties. - -The reason these various calculations are not part of the "fix -ave/chunk command"_fix_ave_chunk.html, is that each requires a more -complicated operation than simply summing and averaging over per-atom -values in each chunk. For example, many of them require calculation -of a center of mass, which requires summing mass*position over the -atoms and then dividing by summed mass. - -All of these computes produce a global vector or global array as -output, wih one or more values per chunk. The output can be used in -various ways: - -As input to the "fix ave/time"_fix_ave_time.html command, which can -write the values to a file and optionally time average them. :ulb,l - -As input to the "fix ave/histo"_fix_ave_histo.html command to -histogram values across chunks. E.g. a histogram of cluster sizes or -molecule diffusion rates. :l - -As input to special functions of "equal-style -variables"_variable.html, like sum() and max() and ave(). E.g. to -find the largest cluster or fastest diffusing molecule or average -radius-of-gyration of a set of molecules (chunks). :l,ule - -Other chunk commands: :h4 - -"compute chunk/spread/atom"_compute_chunk_spread_atom.html -"compute reduce/chunk"_compute_reduce_chunk.html :ul - -The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command -spreads per-chunk values to each atom in the chunk, producing per-atom -values as its output. This can be useful for outputting per-chunk -values to a per-atom "dump file"_dump.html. Or for using an atom's -associated chunk value in an "atom-style variable"_variable.html. Or -as input to the "fix ave/chunk"_fix_ave_chunk.html command to -spatially average per-chunk values calculated by a per-chunk compute. - -The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a -peratom value across the atoms in each chunk to produce a value per -chunk. When used with the "compute -chunk/spread/atom"_compute_chunk_spread_atom.html command it can -create peratom values that induce a new set of chunks with a second -"compute chunk/atom"_compute_chunk_atom.html command. - -Example calculations with chunks :h4 - -Here are examples using chunk commands to calculate various -properties: - -(1) Average velocity in each of 1000 2d spatial bins: - -compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced -fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre - -(2) Temperature in each spatial bin, after subtracting a flow -velocity: - -compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced -compute vbias all temp/profile 1 0 0 y 10 -fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre - -(3) Center of mass of each molecule: - -compute cc1 all chunk/atom molecule -compute myChunk all com/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre - -(4) Total force on each molecule and ave/max across all molecules: - -compute cc1 all chunk/atom molecule -fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out -variable xave equal ave(f_1\[2\]) -variable xmax equal max(f_1\[2\]) -thermo 1000 -thermo_style custom step temp v_xave v_xmax :pre - -(5) Histogram of cluster sizes: - -compute cluster all cluster/atom 1.0 -compute cc1 all chunk/atom c_cluster compress yes -compute size all property/chunk cc1 count -fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre - -(6) An example for using a per-chunk value to apply per-atom forces to -compress individual polymer chains (molecules) in a mixture, is -explained on the "compute -chunk/spread/atom"_compute_chunk_spread_atom.html command doc page. - -(7) An example for using one set of per-chunk values for molecule -chunks, to create a 2nd set of micelle-scale chunks (clustered -molecules, due to hydrophobicity), is explained on the "compute -chunk/reduce"_compute_reduce_chunk.html command doc page. - -(8) An example for using one set of per-chunk values (dipole moment -vectors) for molecule chunks, spreading the values to each atom in -each chunk, then defining a second set of chunks as spatial bins, and -using the "fix ave/chunk"_fix_ave_chunk.html command to calculate an -average dipole moment vector for each bin. This example is explained -on the "compute chunk/spread/atom"_compute_chunk_spread_atom.html -command doc page. diff --git a/doc/txt/Howto_coreshell.txt b/doc/txt/Howto_coreshell.txt deleted file mode 100644 index d3c320cb37..0000000000 --- a/doc/txt/Howto_coreshell.txt +++ /dev/null @@ -1,253 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Adiabatic core/shell model :h3 - -The adiabatic core-shell model by "Mitchell and -Fincham"_#MitchellFincham is a simple method for adding polarizability -to a system. In order to mimic the electron shell of an ion, a -satellite particle is attached to it. This way the ions are split into -a core and a shell where the latter is meant to react to the -electrostatic environment inducing polarizability. See the "Howto -polarizable"_Howto_polarizable.html doc page for a discussion of all -the polarizable models available in LAMMPS. - -Technically, shells are attached to the cores by a spring force f = -k*r where k is a parameterized spring constant and r is the distance -between the core and the shell. The charges of the core and the shell -add up to the ion charge, thus q(ion) = q(core) + q(shell). This -setup introduces the ion polarizability (alpha) given by -alpha = q(shell)^2 / k. In a -similar fashion the mass of the ion is distributed on the core and the -shell with the core having the larger mass. - -To run this model in LAMMPS, "atom_style"_atom_style.html {full} can -be used since atom charge and bonds are needed. Each kind of -core/shell pair requires two atom types and a bond type. The core and -shell of a core/shell pair should be bonded to each other with a -harmonic bond that provides the spring force. For example, a data file -for NaCl, as found in examples/coreshell, has this format: - -432 atoms # core and shell atoms -216 bonds # number of core/shell springs :pre - -4 atom types # 2 cores and 2 shells for Na and Cl -2 bond types :pre - -0.0 24.09597 xlo xhi -0.0 24.09597 ylo yhi -0.0 24.09597 zlo zhi :pre - -Masses # core/shell mass ratio = 0.1 :pre - -1 20.690784 # Na core -2 31.90500 # Cl core -3 2.298976 # Na shell -4 3.54500 # Cl shell :pre - -Atoms :pre - -1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1 -2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1 -3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2 -4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2 -(...) :pre - -Bonds # Bond topology for spring forces :pre - -1 2 1 2 # spring for core/shell pair 1 -2 2 3 4 # spring for core/shell pair 2 -(...) :pre - -Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only -defined between the shells. Coulombic interactions are defined -between all cores and shells. If desired, additional bonds can be -specified between cores. - -The "special_bonds"_special_bonds.html command should be used to -turn-off the Coulombic interaction within core/shell pairs, since that -interaction is set by the bond spring. This is done using the -"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0, -which is the default value. It needs to be considered whether one has -to adjust the "special_bonds"_special_bonds.html weighting according -to the molecular topology since the interactions of the shells are -bypassed over an extra bond. - -Note that this core/shell implementation does not require all ions to -be polarized. One can mix core/shell pairs and ions without a -satellite particle if desired. - -Since the core/shell model permits distances of r = 0.0 between the -core and shell, a pair style with a "cs" suffix needs to be used to -implement a valid long-range Coulombic correction. Several such pair -styles are provided in the CORESHELL package. See "this doc -page"_pair_cs.html for details. All of the core/shell enabled pair -styles require the use of a long-range Coulombic solver, as specified -by the "kspace_style"_kspace_style.html command. Either the PPPM or -Ewald solvers can be used. - -For the NaCL example problem, these pair style and bond style settings -are used: - -pair_style born/coul/long/cs 20.0 20.0 -pair_coeff * * 0.0 1.000 0.00 0.00 0.00 -pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na -pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl -pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre - -bond_style harmonic -bond_coeff 1 63.014 0.0 -bond_coeff 2 25.724 0.0 :pre - -When running dynamics with the adiabatic core/shell model, the -following issues should be considered. The relative motion of -the core and shell particles corresponds to the polarization, -hereby an instantaneous relaxation of the shells is approximated -and a fast core/shell spring frequency ensures a nearly constant -internal kinetic energy during the simulation. -Thermostats can alter this polarization behavior, by scaling the -internal kinetic energy, meaning the shell will not react freely to -its electrostatic environment. -Therefore it is typically desirable to decouple the relative motion of -the core/shell pair, which is an imaginary degree of freedom, from the -real physical system. To do that, the "compute -temp/cs"_compute_temp_cs.html command can be used, in conjunction with -any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix -langevin"_fix_langevin.html. This compute uses the center-of-mass velocity -of the core/shell pairs to calculate a temperature, and insures that -velocity is what is rescaled for thermostatting purposes. This -compute also works for a system with both core/shell pairs and -non-polarized ions (ions without an attached satellite particle). The -"compute temp/cs"_compute_temp_cs.html command requires input of two -groups, one for the core atoms, another for the shell atoms. -Non-polarized ions which might also be included in the treated system -should not be included into either of these groups, they are taken -into account by the {group-ID} (2nd argument) of the compute. The -groups can be defined using the "group {type}"_group.html command. -Note that to perform thermostatting using this definition of -temperature, the "fix modify temp"_fix_modify.html command should be -used to assign the compute to the thermostat fix. Likewise the -"thermo_modify temp"_thermo_modify.html command can be used to make -this temperature be output for the overall system. - -For the NaCl example, this can be done as follows: - -group cores type 1 2 -group shells type 3 4 -compute CSequ all temp/cs cores shells -fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system -fix thermostatequ all nve # integrator as needed for the berendsen thermostat -fix_modify thermoberendsen temp CSequ -thermo_modify temp CSequ # output of center-of-mass derived temperature :pre - -The pressure for the core/shell system is computed via the regular -LAMMPS convention by "treating the cores and shells as individual -particles"_#MitchellFincham2. For the thermo output of the pressure -as well as for the application of a barostat, it is necessary to -use an additional "pressure"_compute_pressure.html compute based on -the default "temperature"_compute_temp.html and specifying it as a -second argument in "fix modify"_fix_modify.html and -"thermo_modify"_thermo_modify.html resulting in: - -(...) -compute CSequ all temp/cs cores shells -compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles -thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure -fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4 -fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre - -If "compute temp/cs"_compute_temp_cs.html is used, the decoupled -relative motion of the core and the shell should in theory be -stable. However numerical fluctuation can introduce a small -momentum to the system, which is noticeable over long trajectories. -Therefore it is recommendable to use the "fix -momentum"_fix_momentum.html command in combination with "compute -temp/cs"_compute_temp_cs.html when equilibrating the system to -prevent any drift. - -When initializing the velocities of a system with core/shell pairs, it -is also desirable to not introduce energy into the relative motion of -the core/shell particles, but only assign a center-of-mass velocity to -the pairs. This can be done by using the {bias} keyword of the -"velocity create"_velocity.html command and assigning the "compute -temp/cs"_compute_temp_cs.html command to the {temp} keyword of the -"velocity"_velocity.html command, e.g. - -velocity all create 1427 134 bias yes temp CSequ -velocity all scale 1427 temp CSequ :pre - -To maintain the correct polarizability of the core/shell pairs, the -kinetic energy of the internal motion shall remain nearly constant. -Therefore the choice of spring force and mass ratio need to ensure -much faster relative motion of the 2 atoms within the core/shell pair -than their center-of-mass velocity. This allows the shells to -effectively react instantaneously to the electrostatic environment and -limits energy transfer to or from the core/shell oscillators. -This fast movement also dictates the timestep that can be used. - -The primary literature of the adiabatic core/shell model suggests that -the fast relative motion of the core/shell pairs only allows negligible -energy transfer to the environment. -The mentioned energy transfer will typically lead to a small drift -in total energy over time. This internal energy can be monitored -using the "compute chunk/atom"_compute_chunk_atom.html and "compute -temp/chunk"_compute_temp_chunk.html commands. The internal kinetic -energies of each core/shell pair can then be summed using the sum() -special function of the "variable"_variable.html command. Or they can -be time/averaged and output using the "fix ave/time"_fix_ave_time.html -command. To use these commands, each core/shell pair must be defined -as a "chunk". If each core/shell pair is defined as its own molecule, -the molecule ID can be used to define the chunks. If cores are bonded -to each other to form larger molecules, the chunks can be identified -by the "fix property/atom"_fix_property_atom.html via assigning a -core/shell ID to each atom using a special field in the data file read -by the "read_data"_read_data.html command. This field can then be -accessed by the "compute property/atom"_compute_property_atom.html -command, to use as input to the "compute -chunk/atom"_compute_chunk_atom.html command to define the core/shell -pairs as chunks. - -For example if core/shell pairs are the only molecules: - -read_data NaCl_CS_x0.1_prop.data -compute prop all property/atom molecule -compute cs_chunk all chunk/atom c_prop -compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs -fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre - -For example if core/shell pairs and other molecules are present: - -fix csinfo all property/atom i_CSID # property/atom command -read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file -compute prop all property/atom i_CSID -(...) :pre - -The additional section in the date file would be formatted like this: - -CS-Info # header of additional section :pre - -1 1 # column 1 = atom ID, column 2 = core/shell ID -2 1 -3 2 -4 2 -5 3 -6 3 -7 4 -8 4 -(...) :pre - -:line - -:link(MitchellFincham) -[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter, -5, 1031-1038 (1993). - -:link(MitchellFincham2) -[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter, -6, 393-404 (1994). diff --git a/doc/txt/Howto_couple.txt b/doc/txt/Howto_couple.txt deleted file mode 100644 index 6fa740d529..0000000000 --- a/doc/txt/Howto_couple.txt +++ /dev/null @@ -1,116 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Coupling LAMMPS to other codes :h3 - -LAMMPS is designed to allow it to be coupled to other codes. For -example, a quantum mechanics code might compute forces on a subset of -atoms and pass those forces to LAMMPS. Or a continuum finite element -(FE) simulation might use atom positions as boundary conditions on FE -nodal points, compute a FE solution, and return interpolated forces on -MD atoms. - -LAMMPS can be coupled to other codes in at least 4 ways. Each has -advantages and disadvantages, which you'll have to think about in the -context of your application. - -:line - -(1) Define a new "fix"_fix.html command that calls the other code. In -this scenario, LAMMPS is the driver code. During its timestepping, -the fix is invoked, and can make library calls to the other code, -which has been linked to LAMMPS as a library. This is the way the -"POEMS"_poems package that performs constrained rigid-body motion on -groups of atoms is hooked to LAMMPS. See the "fix -poems"_fix_poems.html command for more details. See the -"Modify"_Modify.html doc pages for info on how to add a new fix to -LAMMPS. - -:link(poems,http://www.rpi.edu/~anderk5/lab) - -:line - -(2) Define a new LAMMPS command that calls the other code. This is -conceptually similar to method (1), but in this case LAMMPS and the -other code are on a more equal footing. Note that now the other code -is not called during the timestepping of a LAMMPS run, but between -runs. The LAMMPS input script can be used to alternate LAMMPS runs -with calls to the other code, invoked via the new command. The -"run"_run.html command facilitates this with its {every} option, which -makes it easy to run a few steps, invoke the command, run a few steps, -invoke the command, etc. - -In this scenario, the other code can be called as a library, as in -(1), or it could be a stand-alone code, invoked by a system() call -made by the command (assuming your parallel machine allows one or more -processors to start up another program). In the latter case the -stand-alone code could communicate with LAMMPS through files that the -command writes and reads. - -See the "Modify command"_Modify_command.html doc page for info on how -to add a new command to LAMMPS. - -:line - -(3) Use LAMMPS as a library called by another code. In this case the -other code is the driver and calls LAMMPS as needed. Or a wrapper -code could link and call both LAMMPS and another code as libraries. -Again, the "run"_run.html command has options that allow it to be -invoked with minimal overhead (no setup or clean-up) if you wish to do -multiple short runs, driven by another program. - -Examples of driver codes that call LAMMPS as a library are included in -the examples/COUPLE directory of the LAMMPS distribution; see -examples/COUPLE/README for more details: - -simple: simple driver programs in C++ and C which invoke LAMMPS as a -library :ulb,l - -lammps_quest: coupling of LAMMPS and "Quest"_quest, to run classical -MD with quantum forces calculated by a density functional code :l - -lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple -a kinetic Monte Carlo model for grain growth using MD to calculate -strain induced across grain boundaries :l -:ule - -:link(quest,http://dft.sandia.gov/Quest) -:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html) - -The "Build basics"_Build_basics.html doc page describes how to build -LAMMPS as a library. Once this is done, you can interface with LAMMPS -either via C++, C, Fortran, or Python (or any other language that -supports a vanilla C-like interface). For example, from C++ you could -create one (or more) "instances" of LAMMPS, pass it an input script to -process, or execute individual commands, all by invoking the correct -class methods in LAMMPS. From C or Fortran you can make function -calls to do the same things. See the "Python"_Python_head.html doc -pages for a description of the Python wrapper provided with LAMMPS -that operates through the LAMMPS library interface. - -The files src/library.cpp and library.h contain the C-style interface -to LAMMPS. See the "Howto library"_Howto_library.html doc page for a -description of the interface and how to extend it for your needs. - -Note that the lammps_open() function that creates an instance of -LAMMPS takes an MPI communicator as an argument. This means that -instance of LAMMPS will run on the set of processors in the -communicator. Thus the calling code can run LAMMPS on all or a subset -of processors. For example, a wrapper script might decide to -alternate between LAMMPS and another code, allowing them both to run -on all the processors. Or it might allocate half the processors to -LAMMPS and half to the other code and run both codes simultaneously -before syncing them up periodically. Or it might instantiate multiple -instances of LAMMPS to perform different calculations. - -:line - -(4) Couple LAMMPS with another code in a client/server mode. This is -described on the "Howto client/server"_Howto_client_server.html doc -page. diff --git a/doc/txt/Howto_diffusion.txt b/doc/txt/Howto_diffusion.txt deleted file mode 100644 index 6b6eaf72ec..0000000000 --- a/doc/txt/Howto_diffusion.txt +++ /dev/null @@ -1,33 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Calculate diffusion coefficients :h3 - -The diffusion coefficient D of a material can be measured in at least -2 ways using various options in LAMMPS. See the examples/DIFFUSE -directory for scripts that implement the 2 methods discussed here for -a simple Lennard-Jones fluid model. - -The first method is to measure the mean-squared displacement (MSD) of -the system, via the "compute msd"_compute_msd.html command. The slope -of the MSD versus time is proportional to the diffusion coefficient. -The instantaneous MSD values can be accumulated in a vector via the -"fix vector"_fix_vector.html command, and a line fit to the vector to -compute its slope via the "variable slope"_variable.html function, and -thus extract D. - -The second method is to measure the velocity auto-correlation function -(VACF) of the system, via the "compute vacf"_compute_vacf.html -command. The time-integral of the VACF is proportional to the -diffusion coefficient. The instantaneous VACF values can be -accumulated in a vector via the "fix vector"_fix_vector.html command, -and time integrated via the "variable trap"_variable.html function, -and thus extract D. - -:line diff --git a/doc/txt/Howto_dispersion.txt b/doc/txt/Howto_dispersion.txt deleted file mode 100644 index 510e531d1f..0000000000 --- a/doc/txt/Howto_dispersion.txt +++ /dev/null @@ -1,108 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Long-range dispersion settings :h3 - -The PPPM method computes interactions by splitting the pair potential -into two parts, one of which is computed in a normal pairwise fashion, -the so-called real-space part, and one of which is computed using the -Fourier transform, the so called reciprocal-space or kspace part. For -both parts, the potential is not computed exactly but is approximated. -Thus, there is an error in both parts of the computation, the -real-space and the kspace error. The just mentioned facts are true -both for the PPPM for Coulomb as well as dispersion interactions. The -deciding difference - and also the reason why the parameters for -pppm/disp have to be selected with more care - is the impact of the -errors on the results: The kspace error of the PPPM for Coulomb and -dispersion interaction and the real-space error of the PPPM for -Coulomb interaction have the character of noise. In contrast, the -real-space error of the PPPM for dispersion has a clear physical -interpretation: the underprediction of cohesion. As a consequence, the -real-space error has a much stronger effect than the kspace error on -simulation results for pppm/disp. Parameters must thus be chosen in a -way that this error is much smaller than the kspace error. - -When using pppm/disp and not making any specifications on the PPPM -parameters via the kspace modify command, parameters will be tuned -such that the real-space error and the kspace error are equal. This -will result in simulations that are either inaccurate or slow, both of -which is not desirable. For selecting parameters for the pppm/disp -that provide fast and accurate simulations, there are two approaches, -which both have their up- and downsides. - -The first approach is to set desired real-space an kspace accuracies -via the {kspace_modify force/disp/real} and {kspace_modify -force/disp/kspace} commands. Note that the accuracies have to be -specified in force units and are thus dependent on the chosen unit -settings. For real units, 0.0001 and 0.002 seem to provide reasonable -accurate and efficient computations for the real-space and kspace -accuracies. 0.002 and 0.05 work well for most systems using lj -units. PPPM parameters will be generated based on the desired -accuracies. The upside of this approach is that it usually provides a -good set of parameters and will work for both the {kspace_modify diff -ad} and {kspace_modify diff ik} options. The downside of the method -is that setting the PPPM parameters will take some time during the -initialization of the simulation. - -The second approach is to set the parameters for the pppm/disp -explicitly using the {kspace_modify mesh/disp}, {kspace_modify -order/disp}, and {kspace_modify gewald/disp} commands. This approach -requires a more experienced user who understands well the impact of -the choice of parameters on the simulation accuracy and -performance. This approach provides a fast initialization of the -simulation. However, it is sensitive to errors: A combination of -parameters that will perform well for one system might result in -far-from-optimal conditions for other simulations. For example, -parameters that provide accurate and fast computations for -all-atomistic force fields can provide insufficient accuracy or -united-atomistic force fields (which is related to that the latter -typically have larger dispersion coefficients). - -To avoid inaccurate or inefficient simulations, the pppm/disp stops -simulations with an error message if no action is taken to control the -PPPM parameters. If the automatic parameter generation is desired and -real-space and kspace accuracies are desired to be equal, this error -message can be suppressed using the {kspace_modify disp/auto yes} -command. - -A reasonable approach that combines the upsides of both methods is to -make the first run using the {kspace_modify force/disp/real} and -{kspace_modify force/disp/kspace} commands, write down the PPPM -parameters from the output, and specify these parameters using the -second approach in subsequent runs (which have the same composition, -force field, and approximately the same volume). - -Concerning the performance of the pppm/disp there are two more things -to consider. The first is that when using the pppm/disp, the cutoff -parameter does no longer affect the accuracy of the simulation -(subject to that gewald/disp is adjusted when changing the cutoff). -The performance can thus be increased by examining different values -for the cutoff parameter. A lower bound for the cutoff is only set by -the truncation error of the repulsive term of pair potentials. - -The second is that the mixing rule of the pair style has an impact on -the computation time when using the pppm/disp. Fastest computations -are achieved when using the geometric mixing rule. Using the -arithmetic mixing rule substantially increases the computational cost. -The computational overhead can be reduced using the {kspace_modify -mix/disp geom} and {kspace_modify splittol} commands. The first -command simply enforces geometric mixing of the dispersion -coefficients in kspace computations. This introduces some error in -the computations but will also significantly speed-up the -simulations. The second keyword sets the accuracy with which the -dispersion coefficients are approximated using a matrix factorization -approach. This may result in better accuracy then using the first -command, but will usually also not provide an equally good increase of -efficiency. - -Finally, pppm/disp can also be used when no mixing rules apply. -This can be achieved using the {kspace_modify mix/disp none} command. -Note that the code does not check automatically whether any mixing -rule is fulfilled. If mixing rules do not apply, the user will have -to specify this command explicitly. diff --git a/doc/txt/Howto_drude.txt b/doc/txt/Howto_drude.txt deleted file mode 100644 index fdbbd19771..0000000000 --- a/doc/txt/Howto_drude.txt +++ /dev/null @@ -1,77 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Drude induced dipoles :h3 - -The thermalized Drude model represents induced dipoles by a pair of -charges (the core atom and the Drude particle) connected by a harmonic -spring. See the "Howto polarizable"_Howto_polarizable.html doc page -for a discussion of all the polarizable models available in LAMMPS. - -The Drude model has a number of features aimed at its use in -molecular systems ("Lamoureux and Roux"_#howto-Lamoureux): - -Thermostatting of the additional degrees of freedom associated with the -induced dipoles at very low temperature, in terms of the reduced -coordinates of the Drude particles with respect to their cores. This -makes the trajectory close to that of relaxed induced dipoles. :ulb,l - -Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle -pair represents a single (polarizable) atom, so the special screening -factors in a covalent structure should be the same for the core and -the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4 -special neighbor relations from their respective cores. :l - -Stabilization of the interactions between induced dipoles. Drude -dipoles on covalently bonded atoms interact too strongly due to the -short distances, so an atom may capture the Drude particle of a -neighbor, or the induced dipoles within the same molecule may align -too much. To avoid this, damping at short range can be done by Thole -functions (for which there are physical grounds). This Thole damping -is applied to the point charges composing the induced dipole (the -charge of the Drude particle and the opposite charge on the core, not -to the total charge of the core atom). :l,ule - -A detailed tutorial covering the usage of Drude induced dipoles in -LAMMPS is on the "Howto drude2e"_Howto_drude2.html doc page. - -As with the core-shell model, the cores and Drude particles should -appear in the data file as standard atoms. The same holds for the -springs between them, which are described by standard harmonic bonds. -The nature of the atoms (core, Drude particle or non-polarizable) is -specified via the "fix drude"_fix_drude.html command. The special -list of neighbors is automatically refactored to account for the -equivalence of core and Drude particles as regards special 1-2 to 1-4 -screening. It may be necessary to use the {extra/special/per/atom} -keyword of the "read_data"_read_data.html command. If using "fix -shake"_fix_shake.html, make sure no Drude particle is in this fix -group. - -There are two ways to thermostat the Drude particles at a low -temperature: use either "fix langevin/drude"_fix_langevin_drude.html -for a Langevin thermostat, or "fix -drude/transform/*"_fix_drude_transform.html for a Nose-Hoover -thermostat. The former requires use of the command "comm_modify vel -yes"_comm_modify.html. The latter requires two separate integration -fixes like {nvt} or {npt}. The correct temperatures of the reduced -degrees of freedom can be calculated using the "compute -temp/drude"_compute_temp_drude.html. This requires also to use the -command {comm_modify vel yes}. - -Short-range damping of the induced dipole interactions can be achieved -using Thole functions through the "pair style -thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html -with a Coulomb pair style. It may be useful to use {coul/long/cs} or -similar from the CORESHELL package if the core and Drude particle come -too close, which can cause numerical issues. - -:line - -:link(howto-Lamoureux) -[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003) diff --git a/doc/txt/Howto_drude2.txt b/doc/txt/Howto_drude2.txt deleted file mode 100644 index 376ecb0292..0000000000 --- a/doc/txt/Howto_drude2.txt +++ /dev/null @@ -1,472 +0,0 @@ - - - -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Tutorial for Thermalized Drude oscillators in LAMMPS :h3 - -This tutorial explains how to use Drude oscillators in LAMMPS to -simulate polarizable systems using the USER-DRUDE package. As an -illustration, the input files for a simulation of 250 phenol molecules -are documented. First of all, LAMMPS has to be compiled with the -USER-DRUDE package activated. Then, the data file and input scripts -have to be modified to include the Drude dipoles and how to handle -them. - -:line - -[Overview of Drude induced dipoles] - -Polarizable atoms acquire an induced electric dipole moment under the -action of an external electric field, for example the electric field -created by the surrounding particles. Drude oscillators represent -these dipoles by two fixed charges: the core (DC) and the Drude -particle (DP) bound by a harmonic potential. The Drude particle can be -thought of as the electron cloud whose center can be displaced from -the position of the corresponding nucleus. - -The sum of the masses of a core-Drude pair should be the mass of the -initial (unsplit) atom, \(m_C + m_D = m\). The sum of their charges -should be the charge of the initial (unsplit) atom, \(q_C + q_D = q\). -A harmonic potential between the core and Drude partners should be -present, with force constant \(k_D\) and an equilibrium distance of -zero. The (half-)stiffness of the "harmonic bond"_bond_harmonic.html -\(K_D = k_D/2\) and the Drude charge \(q_D\) are related to the atom -polarizability \(\alpha\) by - -\begin\{equation\} K_D = \frac 1 2\, \frac \{q_D^2\} \alpha -\end\{equation\} - -Ideally, the mass of the Drude particle should be small, and the -stiffness of the harmonic bond should be large, so that the Drude -particle remains close ot the core. The values of Drude mass, Drude -charge, and force constant can be chosen following different -strategies, as in the following examples of polarizable force -fields: - -"Lamoureux and Roux"_#Lamoureux2 suggest adopting a global half-stiffness, \ -\(K_D\) = 500 kcal/(mol Ang \(\{\}^2\)) - which corresponds to a force \ -constant \(k_D\) = 4184 kJ/(mol Ang \(\{\}^2\)) - for all types of \ -core-Drude bond, a global mass \(m_D\) = 0.4 g/mol (or u) for all types \ -of Drude particles, and to calculate the Drude charges for individual \ -atom types from the atom polarizabilities using equation (1). This \ -choice is followed in the polarizable CHARMM force field. :ulb,l -Alternately "Schroeder and Steinhauser"_#Schroeder suggest adopting a global \ -charge \(q_D\) = -1.0e and a global mass \(m_D\) = 0.1 g/mol (or u) \ -for all Drude particles, and to calculate the force constant for each \ -type of core-Drude bond from equation (1). The timesteps used by these \ -authors are between 0.5 and 2 fs, with the degrees of freedom of the \ -Drude oscillators kept cold at 1 K. :l -In both these force fields hydrogen atoms are treated as non-polarizable. :l -:ule - - -The motion of of the Drude particles can be calculated by minimizing -the energy of the induced dipoles at each timestep, by an iterative, -self-consistent procedure. The Drude particles can be massless and -therefore do not contribute to the kinetic energy. However, the -relaxed method is computational slow. An extended-lagrangian method -can be used to calculate the positions of the Drude particles, but -this requires them to have mass. It is important in this case to -decouple the degrees of freedom associated with the Drude oscillators -from those of the normal atoms. Thermalizing the Drude dipoles at -temperatures comparable to the rest of the simulation leads to several -problems (kinetic energy transfer, very short timestep, etc.), which -can be remedied by the "cold Drude" technique ("Lamoureux and -Roux"_#Lamoureux2). - -Two closely related models are used to represent polarization through -"charges on a spring": the core-shell model and the Drude -model. Although the basic idea is the same, the core-shell model is -normally used for ionic/crystalline materials, whereas the Drude model -is normally used for molecular systems and fluid states. In ionic -crystals the symmetry around each ion and the distance between them -are such that the core-shell model is sufficiently stable. But to be -applicable to molecular/covalent systems the Drude model includes two -important features: - -The possibility to thermostat the additional degrees of freedom \ -associated with the induced dipoles at very low temperature, in terms \ -of the reduced coordinates of the Drude particles with respect to \ -their cores. This makes the trajectory close to that of relaxed \ -induced dipoles. :olb,l -The Drude dipoles on covalently bonded atoms interact too strongly \ -due to the short distances, so an atom may capture the Drude particle \ -(shell) of a neighbor, or the induced dipoles within the same molecule \ -may align too much. To avoid this, damping at short of the \ -interactions between the point charges composing the induced dipole \ -can be done by "Thole"_#Thole2 functions. :l -:ole - - -:line - -[Preparation of the data file] - -The data file is similar to a standard LAMMPS data file for -{atom_style full}. The DPs and the {harmonic bonds} connecting them -to their DC should appear in the data file as normal atoms and bonds. - -You can use the {polarizer} tool (Python script distributed with the -USER-DRUDE package) to convert a non-polarizable data file (here -{data.102494.lmp}) to a polarizable data file ({data-p.lmp}) - -polarizer -q -f phenol.dff data.102494.lmp data-p.lmp :pre - -This will automatically insert the new atoms and bonds. -The masses and charges of DCs and DPs are computed -from {phenol.dff}, as well as the DC-DP bond constants. The file -{phenol.dff} contains the polarizabilities of the atom types -and the mass of the Drude particles, for instance: - -# units: kJ/mol, A, deg -# kforce is in the form k/2 r_D^2 -# type m_D/u q_D/e k_D alpha/A3 thole -OH 0.4 -1.0 4184.0 0.63 0.67 -CA 0.4 -1.0 4184.0 1.36 2.51 -CAI 0.4 -1.0 4184.0 1.09 2.51 :pre - -The hydrogen atoms are absent from this file, so they will be treated -as non-polarizable atoms. In the non-polarizable data file -{data.102494.lmp}, atom names corresponding to the atom type numbers -have to be specified as comments at the end of lines of the {Masses} -section. You probably need to edit it to add these names. It should -look like - -Masses :pre - -1 12.011 # CAI -2 12.011 # CA -3 15.999 # OH -4 1.008 # HA -5 1.008 # HO :pre - - -:line - -[Basic input file] - -The atom style should be set to (or derive from) {full}, so that you -can define atomic charges and molecular bonds, angles, dihedrals... - -The {polarizer} tool also outputs certain lines related to the input -script (the use of these lines will be explained below). In order for -LAMMPS to recognize that you are using Drude oscillators, you should -use the fix {drude}. The command is - -fix DRUDE all drude C C C N N D D D :pre - -The N, C, D following the {drude} keyword have the following meaning: -There is one tag for each atom type. This tag is C for DCs, D for DPs -and N for non-polarizable atoms. Here the atom types 1 to 3 (C and O -atoms) are DC, atom types 4 and 5 (H atoms) are non-polarizable and -the atom types 6 to 8 are the newly created DPs. - -By recognizing the fix {drude}, LAMMPS will find and store matching -DC-DP pairs and will treat DP as equivalent to their DC in the -{special bonds} relations. It may be necessary to extend the space -for storing such special relations. In this case extra space should -be reserved by using the {extra/special/per/atom} keyword of either -the "read_data"_read_data.html or "create_box"_create_box.html -command. With our phenol, there is 1 more special neighbor for which -space is required. Otherwise LAMMPS crashes and gives the required -value. - -read_data data-p.lmp extra/special/per/atom 1 :pre - -Let us assume we want to run a simple NVT simulation at 300 K. Note -that Drude oscillators need to be thermalized at a low temperature in -order to approximate a self-consistent field (SCF), therefore it is not -possible to simulate an NVE ensemble with this package. Since dipoles -are approximated by a charged DC-DP pair, the {pair_style} must -include Coulomb interactions, for instance {lj/cut/coul/long} with -{kspace_style pppm}. For example, with a cutoff of 10. and a precision -1.e-4: - -pair_style lj/cut/coul/long 10.0 -kspace_style pppm 1.0e-4 :pre - -As compared to the non-polarizable input file, {pair_coeff} lines need -to be added for the DPs. Since the DPs have no Lennard-Jones -interactions, their {epsilon} is 0. so the only {pair_coeff} line -that needs to be added is - -pair_coeff * 6* 0.0 0.0 # All-DPs :pre - -Now for the thermalization, the simplest choice is to use the "fix -langevin/drude"_fix_langevin_drude.html. - -fix LANG all langevin/drude 300. 100 12435 1. 20 13977 :pre - -This applies a Langevin thermostat at temperature 300. to the centers -of mass of the DC-DP pairs, with relaxation time 100 and with random -seed 12345. This fix applies also a Langevin thermostat at temperature -1. to the relative motion of the DPs around their DCs, with relaxation -time 20 and random seed 13977. Only the DCs and non-polarizable -atoms need to be in this fix's group. LAMMPS will thermostat the DPs -together with their DC. For this, ghost atoms need to know their -velocities. Thus you need to add the following command: - -comm_modify vel yes :pre - -In order to avoid that the center of mass of the whole system -drifts due to the random forces of the Langevin thermostat on DCs, you -can add the {zero yes} option at the end of the fix line. - -If the fix {shake} is used to constrain the C-H bonds, it should be -invoked after the fix {langevin/drude} for more accuracy. - -fix SHAKE ATOMS shake 0.0001 20 0 t 4 5 :pre - -NOTE: The group of the fix {shake} must not include the DPs. If the -group {ATOMS} is defined by non-DPs atom types, you could use - -Since the fix {langevin/drude} does not perform time integration (just -modification of forces but no position/velocity updates), the fix -{nve} should be used in conjunction. - -fix NVE all nve :pre - -Finally, do not forget to update the atom type elements if you use -them in a {dump_modify ... element ...} command, by adding the element -type of the DPs. Here for instance - -dump DUMP all custom 10 dump.lammpstrj id mol type element x y z ix iy iz -dump_modify DUMP element C C O H H D D D :pre - -The input file should now be ready for use! - -You will notice that the global temperature {thermo_temp} computed by -LAMMPS is not 300. K as wanted. This is because LAMMPS treats DPs as -standard atoms in his default compute. If you want to output the -temperatures of the DC-DP pair centers of mass and of the DPs relative -to their DCs, you should use the "compute -temp_drude"_compute_temp_drude.html - -compute TDRUDE all temp/drude :pre - -And then output the correct temperatures of the Drude oscillators -using {thermo_style custom} with respectively {c_TDRUDE\[1\]} and -{c_TDRUDE\[2\]}. These should be close to 300.0 and 1.0 on average. - -thermo_style custom step temp c_TDRUDE\[1\] c_TDRUDE\[2\] :pre - - -:line - -[Thole screening] - -Dipolar interactions represented by point charges on springs may not -be stable, for example if the atomic polarizability is too high for -instance, a DP can escape from its DC and be captured by another DC, -which makes the force and energy diverge and the simulation -crash. Even without reaching this extreme case, the correlation -between nearby dipoles on the same molecule may be exaggerated. Often, -special bond relations prevent bonded neighboring atoms to see the -charge of each other's DP, so that the problem does not always appear. -It is possible to use screened dipole-dipole interactions by using the -"{pair_style thole}"_pair_thole.html. This is implemented as a -correction to the Coulomb pair_styles, which dampens at short distance -the interactions between the charges representing the induced dipoles. -It is to be used as {hybrid/overlay} with any standard {coul} pair -style. In our example, we would use - -pair_style hybrid/overlay lj/cut/coul/long 10.0 thole 2.6 10.0 :pre - -This tells LAMMPS that we are using two pair_styles. The first one is -as above ({lj/cut/coul/long 10.0}). The second one is a {thole} -pair_style with default screening factor 2.6 ("Noskov"_#Noskov2) and -cutoff 10.0. - -Since {hybrid/overlay} does not support mixing rules, the interaction -coefficients of all the pairs of atom types with i < j should be -explicitly defined. The output of the {polarizer} script can be used -to complete the {pair_coeff} section of the input file. In our -example, this will look like: - -pair_coeff 1 1 lj/cut/coul/long 0.0700 3.550 -pair_coeff 1 2 lj/cut/coul/long 0.0700 3.550 -pair_coeff 1 3 lj/cut/coul/long 0.1091 3.310 -pair_coeff 1 4 lj/cut/coul/long 0.0458 2.985 -pair_coeff 2 2 lj/cut/coul/long 0.0700 3.550 -pair_coeff 2 3 lj/cut/coul/long 0.1091 3.310 -pair_coeff 2 4 lj/cut/coul/long 0.0458 2.985 -pair_coeff 3 3 lj/cut/coul/long 0.1700 3.070 -pair_coeff 3 4 lj/cut/coul/long 0.0714 2.745 -pair_coeff 4 4 lj/cut/coul/long 0.0300 2.420 -pair_coeff * 5 lj/cut/coul/long 0.0000 0.000 -pair_coeff * 6* lj/cut/coul/long 0.0000 0.000 -pair_coeff 1 1 thole 1.090 2.510 -pair_coeff 1 2 thole 1.218 2.510 -pair_coeff 1 3 thole 0.829 1.590 -pair_coeff 1 6 thole 1.090 2.510 -pair_coeff 1 7 thole 1.218 2.510 -pair_coeff 1 8 thole 0.829 1.590 -pair_coeff 2 2 thole 1.360 2.510 -pair_coeff 2 3 thole 0.926 1.590 -pair_coeff 2 6 thole 1.218 2.510 -pair_coeff 2 7 thole 1.360 2.510 -pair_coeff 2 8 thole 0.926 1.590 -pair_coeff 3 3 thole 0.630 0.670 -pair_coeff 3 6 thole 0.829 1.590 -pair_coeff 3 7 thole 0.926 1.590 -pair_coeff 3 8 thole 0.630 0.670 -pair_coeff 6 6 thole 1.090 2.510 -pair_coeff 6 7 thole 1.218 2.510 -pair_coeff 6 8 thole 0.829 1.590 -pair_coeff 7 7 thole 1.360 2.510 -pair_coeff 7 8 thole 0.926 1.590 -pair_coeff 8 8 thole 0.630 0.670 :pre - -For the {thole} pair style the coefficients are - -the atom polarizability in units of cubic length :olb,l -the screening factor of the Thole function (optional, default value -specified by the pair_style command) :l -the cutoff (optional, default value defined by the pair_style command) :l -:ole - -The special neighbors have charge-charge and charge-dipole -interactions screened by the {coul} factors of the {special_bonds} -command (0.0, 0.0, and 0.5 in the example above). Without using the -pair_style {thole}, dipole-dipole interactions are screened by the -same factor. By using the pair_style {thole}, dipole-dipole -interactions are screened by Thole's function, whatever their special -relationship (except within each DC-DP pair of course). Consider for -example 1-2 neighbors: using the pair_style {thole}, their dipoles -will see each other (despite the {coul} factor being 0.) and the -interactions between these dipoles will be damped by Thole's function. - - -:line - -[Thermostats and barostats] - -Using a Nose-Hoover barostat with the {langevin/drude} thermostat is -straightforward using fix {nph} instead of {nve}. For example: - -fix NPH all nph iso 1. 1. 500 :pre - -It is also possible to use a Nose-Hoover instead of a Langevin -thermostat. This requires to use "{fix -drude/transform}"_fix_drude_transform.html just before and after the -time integration fixes. The {fix drude/transform/direct} converts the -atomic masses, positions, velocities and forces into a reduced -representation, where the DCs transform into the centers of mass of -the DC-DP pairs and the DPs transform into their relative position -with respect to their DC. The {fix drude/transform/inverse} performs -the reverse transformation. For a NVT simulation, with the DCs and -atoms at 300 K and the DPs at 1 K relative to their DC one would use - -fix DIRECT all drude/transform/direct -fix NVT1 ATOMS nvt temp 300. 300. 100 -fix NVT2 DRUDES nvt temp 1. 1. 20 -fix INVERSE all drude/transform/inverse :pre - -For our phenol example, the groups would be defined as - -group ATOMS type 1 2 3 4 5 # DCs and non-polarizable atoms -group CORES type 1 2 3 # DCs -group DRUDES type 6 7 8 # DPs :pre - -Note that with the fixes {drude/transform}, it is not required to -specify {comm_modify vel yes} because the fixes do it anyway (several -times and for the forces also). To avoid the flying ice cube artifact -"(Lamoureux)"_#Lamoureux2, where the atoms progressively freeze and the -center of mass of the whole system drifts faster and faster, the {fix -momentum} can be used. For instance: - -fix MOMENTUM all momentum 100 linear 1 1 1 :pre - -It is a bit more tricky to run a NPT simulation with Nose-Hoover -barostat and thermostat. First, the volume should be integrated only -once. So the fix for DCs and atoms should be {npt} while the fix for -DPs should be {nvt} (or vice versa). Second, the {fix npt} computes a -global pressure and thus a global temperature whatever the fix group. -We do want the pressure to correspond to the whole system, but we want -the temperature to correspond to the fix group only. We must then use -the {fix_modify} command for this. In the end, the block of -instructions for thermostatting and barostatting will look like - -compute TATOMS ATOMS temp -fix DIRECT all drude/transform/direct -fix NPT ATOMS npt temp 300. 300. 100 iso 1. 1. 500 -fix_modify NPT temp TATOMS press thermo_press -fix NVT DRUDES nvt temp 1. 1. 20 -fix INVERSE all drude/transform/inverse :pre - - -:line - -[Rigid bodies] - -You may want to simulate molecules as rigid bodies (but polarizable). -Common cases are water models such as "SWM4-NDP"_#SWM4-NDP, which is a -kind of polarizable TIP4P water. The rigid bodies and the DPs should -be integrated separately, even with the Langevin thermostat. Let us -review the different thermostats and ensemble combinations. - -NVT ensemble using Langevin thermostat: - -comm_modify vel yes -fix LANG all langevin/drude 300. 100 12435 1. 20 13977 -fix RIGID ATOMS rigid/nve/small molecule -fix NVE DRUDES nve :pre - -NVT ensemble using Nose-Hoover thermostat: - -fix DIRECT all drude/transform/direct -fix RIGID ATOMS rigid/nvt/small molecule temp 300. 300. 100 -fix NVT DRUDES nvt temp 1. 1. 20 -fix INVERSE all drude/transform/inverse :pre - -NPT ensemble with Langevin thermostat: - -comm_modify vel yes -fix LANG all langevin/drude 300. 100 12435 1. 20 13977 -fix RIGID ATOMS rigid/nph/small molecule iso 1. 1. 500 -fix NVE DRUDES nve :pre - -NPT ensemble using Nose-Hoover thermostat: - -compute TATOM ATOMS temp -fix DIRECT all drude/transform/direct -fix RIGID ATOMS rigid/npt/small molecule temp 300. 300. 100 iso 1. 1. 500 -fix_modify RIGID temp TATOM press thermo_press -fix NVT DRUDES nvt temp 1. 1. 20 -fix INVERSE all drude/transform/inverse :pre - - -:line - -:link(Lamoureux2) -[(Lamoureux)] Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003) - -:link(Schroeder) -[(Schroeder)] Schroeder and Steinhauser, J Chem Phys, 133, -154511 (2010). - -:link(Jiang2) -[(Jiang)] Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, - J Phys Chem Lett, 2, 87-92 (2011). - -:link(Thole2) -[(Thole)] Chem Phys, 59, 341 (1981). - -:link(Noskov2) -[(Noskov)] Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005). - -:link(SWM4-NDP) -[(SWM4-NDP)] Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys -Let, 418, 245-249 (2006) - diff --git a/doc/txt/Howto_elastic.txt b/doc/txt/Howto_elastic.txt deleted file mode 100644 index ee8e7c26a4..0000000000 --- a/doc/txt/Howto_elastic.txt +++ /dev/null @@ -1,47 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Calculate elastic constants :h3 - -Elastic constants characterize the stiffness of a material. The formal -definition is provided by the linear relation that holds between the -stress and strain tensors in the limit of infinitesimal deformation. -In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where -the repeated indices imply summation. s_ij are the elements of the -symmetric stress tensor. e_kl are the elements of the symmetric strain -tensor. C_ijkl are the elements of the fourth rank tensor of elastic -constants. In three dimensions, this tensor has 3^4=81 elements. Using -Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij -is now the derivative of s_i w.r.t. e_j. Because s_i is itself a -derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at -most 7*6/2 = 21 distinct elements. - -At zero temperature, it is easy to estimate these derivatives by -deforming the simulation box in one of the six directions using the -"change_box"_change_box.html command and measuring the change in the -stress tensor. A general-purpose script that does this is given in the -examples/elastic directory described on the "Examples"_Examples.html -doc page. - -Calculating elastic constants at finite temperature is more -challenging, because it is necessary to run a simulation that performs -time averages of differential properties. One way to do this is to -measure the change in average stress tensor in an NVT simulations when -the cell volume undergoes a finite deformation. In order to balance -the systematic and statistical errors in this method, the magnitude of -the deformation must be chosen judiciously, and care must be taken to -fully equilibrate the deformed cell before sampling the stress -tensor. Another approach is to sample the triclinic cell fluctuations -that occur in an NPT simulation. This method can also be slow to -converge and requires careful post-processing "(Shinoda)"_#Shinoda1 - -:line - -:link(Shinoda1) -[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). diff --git a/doc/txt/Howto_github.txt b/doc/txt/Howto_github.txt deleted file mode 100644 index ef55653f37..0000000000 --- a/doc/txt/Howto_github.txt +++ /dev/null @@ -1,419 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -LAMMPS GitHub tutorial :h3 -[written by Stefan Paquay] - -:line - -This document describes the process of how to use GitHub to integrate -changes or additions you have made to LAMMPS into the official LAMMPS -distribution. It uses the process of updating this very tutorial as -an example to describe the individual steps and options. You need to -be familiar with git and you may want to have a look at the -"Git book"_http://git-scm.com/book/ to reacquaint yourself with some -of the more advanced git features used below. - -As of fall 2016, submitting contributions to LAMMPS via pull requests -on GitHub is the preferred option for integrating contributed features -or improvements to LAMMPS, as it significantly reduces the amount of -work required by the LAMMPS developers. Consequently, creating a pull -request will increase your chances to have your contribution included -and will reduce the time until the integration is complete. For more -information on the requirements to have your code included into LAMMPS -please see the "Modify contribute"_Modify_contribute.html doc page. - -:line - -[Making an account] - -First of all, you need a GitHub account. This is fairly simple, just -go to "GitHub"_https://github.com and create an account by clicking -the "Sign up for GitHub" button. Once your account is created, you -can sign in by clicking the button in the top left and filling in your -username or e-mail address and password. - -:line - -[Forking the repository] - -To get changes into LAMMPS, you need to first fork the `lammps/lammps` -repository on GitHub. At the time of writing, {master} is the preferred -target branch. Thus go to "LAMMPS on GitHub"_https://github.com/lammps/lammps -and make sure branch is set to "master", as shown in the figure below. - -:c,image(JPG/tutorial_branch.png) - -If it is not, use the button to change it to {master}. Once it is, use the -fork button to create a fork. - -:c,image(JPG/tutorial_fork.png) - - -This will create a fork (which is essentially a copy, but uses less -resources) of the LAMMPS repository under your own GitHub account. You -can make changes in this fork and later file {pull requests} to allow -the upstream repository to merge changes from your own fork into the one -we just forked from (or others that were forked from the same repository). -At the same time, you can set things up, so you can include changes from -upstream into your repository and thus keep it in sync with the ongoing -LAMMPS development. - -:line - -[Adding changes to your own fork] - -Additions to the upstream version of LAMMPS are handled using {feature -branches}. For every new feature, a so-called feature branch is -created, which contains only those modification relevant to one specific -feature. For example, adding a single fix would consist of creating a -branch with only the fix header and source file and nothing else. It is -explained in more detail here: "feature branch -workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow. - -[Feature branches] - -First of all, create a clone of your version on github on your local -machine via HTTPS: - - $ git clone https://github.com//lammps.git :pre - -or, if you have set up your GitHub account for using SSH keys, via SSH: - - $ git clone git@github.com:/lammps.git :pre - -You can find the proper URL by clicking the "Clone or download"-button: - -:c,image(JPG/tutorial_https_block.png) - -The above command copies ("clones") the git repository to your local -machine to a directory with the name you chose. If none is given, it will -default to "lammps". Typical names are "mylammps" or something similar. - -You can use this local clone to make changes and -test them without interfering with the repository on GitHub. - -To pull changes from upstream into this copy, you can go to the directory -and use git pull: - - $ cd mylammps - $ git checkout master - $ git pull https://github.com/lammps/lammps :pre - -You can also add this URL as a remote: - - $ git remote add lammps_upstream https://www.github.com/lammps/lammps :pre - -At this point, you typically make a feature branch from the updated master -branch for the feature you want to work on. This tutorial contains the -workflow that updated this tutorial, and hence we will call the branch -"github-tutorial-update": - - $ git checkout -b github-tutorial-update master :pre - -Now that we have changed branches, we can make our changes to our local -repository. Just remember that if you want to start working on another, -unrelated feature, you should switch branches! - -[After changes are made] - -After everything is done, add the files to the branch and commit them: - - $ git add doc/src/Howto_github.txt - $ git add doc/src/JPG/tutorial*.png :pre - -IMPORTANT NOTE: Do not use {git commit -a} (or {git add -A}). The -a -flag (or -A flag) will automatically include _all_ modified or new files -and that is rarely the behavior you want. It can easily lead to -accidentally adding unrelated and unwanted changes into the repository. -Instead it is preferable to explicitly use {git add}, {git rm}, {git mv} -for adding, removing, renaming individual files, respectively, and then -{git commit} to finalize the commit. Carefully check all pending -changes with {git status} before committing them. If you find doing -this on the command line too tedious, consider using a GUI, for example -the one included in git distributions written in Tk, i.e. use {git gui} -(on some Linux distributions it may be required to install an additional -package to use it). - -After adding all files, the change set can be committed with some -useful message that explains the change. - - $ git commit -m 'Finally updated the github tutorial' :pre - -After the commit, the changes can be pushed to the same branch on GitHub: - -$ git push :pre - -Git will ask you for your user name and password on GitHub if you have -not configured anything. If your local branch is not present on GitHub yet, -it will ask you to add it by running - - $ git push --set-upstream origin github-tutorial-update :pre - -If you correctly type your user name and -password, the feature branch should be added to your fork on GitHub. - -If you want to make really sure you push to the right repository -(which is good practice), you can provide it explicitly: - -$ git push origin :pre - -or using an explicit URL: - -$ git push git@github.com:Pakketeretet2/lammps.git :pre - -:line - -[Filing a pull request] - -Up to this point in the tutorial, all changes were to {your} clones of -LAMMPS. Eventually, however, you want this feature to be included into -the official LAMMPS version. To do this, you will want to file a pull -request by clicking on the "New pull request" button: - -:c,image(JPG/tutorial_new_pull_request.png) - -Make sure that the current branch is set to the correct one, which, in -this case, is "github-tutorial-update". If done correctly, the only -changes you will see are those that were made on this branch. - -This will open up a new window that lists changes made to the -repository. If you are just adding new files, there is not much to do, -but I suppose merge conflicts are to be resolved here if there are -changes in existing files. If all changes can automatically be merged, -green text at the top will say so and you can click the "Create pull -request" button, see image. - -:c,image(JPG/tutorial_create_new_pull_request1.png) - -Before creating the pull request, make sure the short title is accurate -and add a comment with details about your pull request. Here you write -what your modifications do and why they should be incorporated upstream. - -Note the checkbox that says "Allow edits from maintainers". -This is checked by default checkbox (although in my version of Firefox, only the checkmark is visible): - -:c,image(JPG/tutorial_edits_maintainers.png) - -If it is checked, maintainers can immediately add their own edits to the -pull request. This helps the inclusion of your branch significantly, as -simple/trivial changes can be added directly to your pull request branch -by the LAMMPS maintainers. The alternative would be that they make -changes on their own version of the branch and file a reverse pull -request to you. Just leave this box checked unless you have a very good -reason not to. - -Now just write some nice comments and click on "Create pull request". - -:c,image(JPG/tutorial_create_new_pull_request2.png) - -:line - -[After filing a pull request] - -NOTE: When you submit a pull request (or ask for a pull request) for the -first time, you will receive an invitation to become a LAMMPS project -collaborator. Please accept this invite as being a collaborator will -simplify certain administrative tasks and will probably speed up the -merging of your feature, too. - -You will notice that after filing the pull request, some checks are -performed automatically: - -:c,image(JPG/tutorial_automated_checks.png) - -If all is fine, you will see this: - -:c,image(JPG/tutorial_automated_checks_passed.png) - -If any of the checks are failing, your pull request will not be -processed, as your changes may break compilation for certain -configurations or may not merge cleanly. It is your responsibility -to remove the reason(s) for the failed test(s). If you need help -with this, please contact the LAMMPS developers by adding a comment -explaining your problems with resolving the failed tests. - -A few further interesting things (can) happen to pull requests before -they are included. - -[Additional changes] - -First of all, any additional changes you push into your branch in your -repository will automatically become part of the pull request: - -:c,image(JPG/tutorial_additional_changes.png) - -This means you can add changes that should be part of the feature after -filing the pull request, which is useful in case you have forgotten -them, or if a developer has requested that something needs to be changed -before the feature can be accepted into the official LAMMPS version. -After each push, the automated checks are run again. - -[Labels] - -LAMMPS developers may add labels to your pull request to assign it to -categories (mostly for bookkeeping purposes), but a few of them are -important: needs_work, work_in_progress, test-for-regression, and -full-regression-test. The first two indicate, that your pull request -is not considered to be complete. With "needs_work" the burden is on -exclusively on you; while "work_in_progress" can also mean, that a -LAMMPS developer may want to add changes. Please watch the comments -to the pull requests. The two "test" labels are used to trigger -extended tests before the code is merged. This is sometimes done by -LAMMPS developers, if they suspect that there may be some subtle -side effects from your changes. It is not done by default, because -those tests are very time consuming. - -[Reviews] - -As of Summer 2018, a pull request needs at least 1 approving review -from a LAMMPS developer with write access to the repository. -In case your changes touch code that certain developers are associated -with, they are auto-requested by the GitHub software. Those associations -are set in the file -".github/CODEOWNERS"_https://github.com/lammps/lammps/blob/master/.github/CODEOWNERS -Thus if you want to be automatically notified to review when anybody -changes files or packages, that you have contributed to LAMMPS, you can -add suitable patterns to that file, or a LAMMPS developer may add you. - -Otherwise, you can also manually request reviews from specific developers, -or LAMMPS developers - in their assessment of your pull request - may -determine who else should be reviewing your contribution and add that person. -Through reviews, LAMMPS developers also may request specific changes from you. -If those are not addressed, your pull requests cannot be merged. - -[Assignees] - -There is an assignee property for pull requests. If the request has not -been reviewed by any developer yet, it is not assigned to anyone. After -revision, a developer can choose to assign it to either a) you, b) a -LAMMPS developer (including him/herself) or c) Axel Kohlmeyer (akohlmey). - -Case a) happens if changes are required on your part :ulb,l -Case b) means that at the moment, it is being tested and reviewed by a -LAMMPS developer with the expectation that some changes would be required. -After the review, the developer can choose to implement changes directly -or suggest them to you. :l -Case c) means that the pull request has been assigned to the developer -overseeing the merging of pull requests into the master branch. :ule,l - -In this case, Axel assigned the tutorial to Steve: - -:c,image(JPG/tutorial_steve_assignee.png) - -[Edits from LAMMPS maintainers] - -If you allowed edits from maintainers (the default), any LAMMPS -maintainer can add changes to your pull request. In this case, both -Axel and Richard made changes to the tutorial: - -:c,image(JPG/tutorial_changes_others.png) - -[Reverse pull requests] - -Sometimes, however, you might not feel comfortable having other people -push changes into your own branch, or maybe the maintainers are not sure -their idea was the right one. In such a case, they can make changes, -reassign you as the assignee, and file a "reverse pull request", i.e. -file a pull request in your GitHub repository to include changes in the -branch, that you have submitted as a pull request yourself. In that -case, you can choose to merge their changes back into your branch, -possibly make additional changes or corrections and proceed from there. -It looks something like this: - -:c,image(JPG/tutorial_reverse_pull_request.png) - -For some reason, the highlighted button didn't work in my case, but I -can go to my own repository and merge the pull request from there: - -:c,image(JPG/tutorial_reverse_pull_request2.png) - -Be sure to check the changes to see if you agree with them by clicking -on the tab button: - -:c,image(JPG/tutorial_reverse_pull_request3.png) - -In this case, most of it is changes in the markup and a short rewrite of -Axel's explanation of the "git gui" and "git add" commands. - -:c,image(JPG/tutorial_reverse_pull_request4.png) - -Because the changes are OK with us, we are going to merge by clicking on -"Merge pull request". After a merge it looks like this: - -:c,image(JPG/tutorial_reverse_pull_request5.png) - -Now, since in the meantime our local text for the tutorial also changed, -we need to pull Axel's change back into our branch, and merge them: - - $ git add Howto_github.txt - $ git add JPG/tutorial_reverse_pull_request*.png - $ git commit -m "Updated text and images on reverse pull requests" - $ git pull :pre - -In this case, the merge was painless because git could auto-merge: - -:c,image(JPG/tutorial_reverse_pull_request6.png) - -With Axel's changes merged in and some final text updates, our feature -branch is now perfect as far as we are concerned, so we are going to -commit and push again: - - $ git add Howto_github.txt - $ git add JPG/tutorial_reverse_pull_request6.png - $ git commit -m "Merged Axel's suggestions and updated text" - $ git push git@github.com:Pakketeretet2/lammps :pre - -This merge also shows up on the lammps GitHub page: - -:c,image(JPG/tutorial_reverse_pull_request7.png) - -:line - -[After a merge] - -When everything is fine, the feature branch is merged into the master branch: - -:c,image(JPG/tutorial_merged.png) - -Now one question remains: What to do with the feature branch that got -merged into upstream? - -It is in principle safe to delete them from your own fork. This helps -keep it a bit more tidy. Note that you first have to switch to another -branch! - -$ git checkout master -$ git pull master -$ git branch -d github-tutorial-update :pre - -If you do not pull first, it is not really a problem but git will warn -you at the next statement that you are deleting a local branch that -was not yet fully merged into HEAD. This is because git does not yet -know your branch just got merged into LAMMPS upstream. If you -first delete and then pull, everything should still be fine. - -Finally, if you delete the branch locally, you might want to push this -to your remote(s) as well: - -$ git push origin :github-tutorial-update :pre - -[Recent changes in the workflow] - -Some changes to the workflow are not captured in this tutorial. For -example, in addition to the master branch, to which all new features -should be submitted, there is now also an "unstable" and a "stable" -branch; these have the same content as "master", but are only updated -after a patch release or stable release was made. -Furthermore, the naming of the patches now follow the pattern -"patch_" to simplify comparisons between releases. -Finally, all patches and submissions are subject to automatic testing -and code checks to make sure they at the very least compile. - -A discussion of the LAMMPS developer GitHub workflow can be found in the file -"doc/github-development-workflow.md"_https://github.com/lammps/lammps/blob/master/doc/github-development-workflow.md diff --git a/doc/txt/Howto_granular.txt b/doc/txt/Howto_granular.txt deleted file mode 100644 index 758b1cebee..0000000000 --- a/doc/txt/Howto_granular.txt +++ /dev/null @@ -1,57 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Granular models :h3 - -Granular system are composed of spherical particles with a diameter, -as opposed to point particles. This means they have an angular -velocity and torque can be imparted to them to cause them to rotate. - -To run a simulation of a granular model, you will want to use -the following commands: - -"atom_style sphere"_atom_style.html -"fix nve/sphere"_fix_nve_sphere.html -"fix gravity"_fix_gravity.html :ul - -This compute - -"compute erotate/sphere"_compute_erotate_sphere.html :ul - -calculates rotational kinetic energy which can be "output with -thermodynamic info"_Howto_output.html. - -Use one of these 3 pair potentials, which compute forces and torques -between interacting pairs of particles: - -"pair_style"_pair_style.html gran/history -"pair_style"_pair_style.html gran/no_history -"pair_style"_pair_style.html gran/hertzian :ul - -These commands implement fix options specific to granular systems: - -"fix freeze"_fix_freeze.html -"fix pour"_fix_pour.html -"fix viscous"_fix_viscous.html -"fix wall/gran"_fix_wall_gran.html :ul - -The fix style {freeze} zeroes both the force and torque of frozen -atoms, and should be used for granular system instead of the fix style -{setforce}. - -For computational efficiency, you can eliminate needless pairwise -computations between frozen atoms by using this command: - -"neigh_modify"_neigh_modify.html exclude :ul - -NOTE: By default, for 2d systems, granular particles are still modeled -as 3d spheres, not 2d discs (circles), meaning their moment of inertia -will be the same as in 3d. If you wish to model granular particles in -2d as 2d discs, see the note on this topic on the "Howto 2d"_Howto_2d.html -doc page, where 2d simulations are discussed. diff --git a/doc/txt/Howto_kappa.txt b/doc/txt/Howto_kappa.txt deleted file mode 100644 index b2a57ef49b..0000000000 --- a/doc/txt/Howto_kappa.txt +++ /dev/null @@ -1,90 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Calculate thermal conductivity :h3 - -The thermal conductivity kappa of a material can be measured in at -least 4 ways using various options in LAMMPS. See the examples/KAPPA -directory for scripts that implement the 4 methods discussed here for -a simple Lennard-Jones fluid model. Also, see the "Howto -viscosity"_Howto_viscosity.html doc page for an analogous discussion -for viscosity. - -The thermal conductivity tensor kappa is a measure of the propensity -of a material to transmit heat energy in a diffusive manner as given -by Fourier's law - -J = -kappa grad(T) - -where J is the heat flux in units of energy per area per time and -grad(T) is the spatial gradient of temperature. The thermal -conductivity thus has units of energy per distance per time per degree -K and is often approximated as an isotropic quantity, i.e. as a -scalar. - -The first method is to setup two thermostatted regions at opposite -ends of a simulation box, or one in the middle and one at the end of a -periodic box. By holding the two regions at different temperatures -with a "thermostatting fix"_Howto_thermostat.html, the energy added to -the hot region should equal the energy subtracted from the cold region -and be proportional to the heat flux moving between the regions. See -the papers by "Ikeshoji and Hafskjold"_#howto-Ikeshoji and -"Wirnsberger et al"_#howto-Wirnsberger for details of this idea. Note -that thermostatting fixes such as "fix nvt"_fix_nh.html, "fix -langevin"_fix_langevin.html, and "fix -temp/rescale"_fix_temp_rescale.html store the cumulative energy they -add/subtract. - -Alternatively, as a second method, the "fix heat"_fix_heat.html or -"fix ehex"_fix_ehex.html commands can be used in place of thermostats -on each of two regions to add/subtract specified amounts of energy to -both regions. In both cases, the resulting temperatures of the two -regions can be monitored with the "compute temp/region" command and -the temperature profile of the intermediate region can be monitored -with the "fix ave/chunk"_fix_ave_chunk.html and "compute -ke/atom"_compute_ke_atom.html commands. - -The third method is to perform a reverse non-equilibrium MD simulation -using the "fix thermal/conductivity"_fix_thermal_conductivity.html -command which implements the rNEMD algorithm of Muller-Plathe. -Kinetic energy is swapped between atoms in two different layers of the -simulation box. This induces a temperature gradient between the two -layers which can be monitored with the "fix -ave/chunk"_fix_ave_chunk.html and "compute -ke/atom"_compute_ke_atom.html commands. The fix tallies the -cumulative energy transfer that it performs. See the "fix -thermal/conductivity"_fix_thermal_conductivity.html command for -details. - -The fourth method is based on the Green-Kubo (GK) formula which -relates the ensemble average of the auto-correlation of the heat flux -to kappa. The heat flux can be calculated from the fluctuations of -per-atom potential and kinetic energies and per-atom stress tensor in -a steady-state equilibrated simulation. This is in contrast to the -two preceding non-equilibrium methods, where energy flows continuously -between hot and cold regions of the simulation box. - -The "compute heat/flux"_compute_heat_flux.html command can calculate -the needed heat flux and describes how to implement the Green_Kubo -formalism using additional LAMMPS commands, such as the "fix -ave/correlate"_fix_ave_correlate.html command to calculate the needed -auto-correlation. See the doc page for the "compute -heat/flux"_compute_heat_flux.html command for an example input script -that calculates the thermal conductivity of solid Ar via the GK -formalism. - -:line - -:link(howto-Ikeshoji) -[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 -(1994). - -:link(howto-Wirnsberger) -[(Wirnsberger)] Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 -(2015). diff --git a/doc/txt/Howto_library.txt b/doc/txt/Howto_library.txt deleted file mode 100644 index 0f805d69a6..0000000000 --- a/doc/txt/Howto_library.txt +++ /dev/null @@ -1,235 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Library interface to LAMMPS :h3 - -As described on the "Build basics"_Build_basics.html doc page, LAMMPS -can be built as a library, so that it can be called by another code, -used in a "coupled manner"_Howto_couple.html with other codes, or -driven through a "Python interface"_Python_head.html. - -All of these methodologies use a C-style interface to LAMMPS that is -provided in the files src/library.cpp and src/library.h. The -functions therein have a C-style argument list, but contain C++ code -you could write yourself in a C++ application that was invoking LAMMPS -directly. The C++ code in the functions illustrates how to invoke -internal LAMMPS operations. Note that LAMMPS classes are defined -within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ -application. - -The examples/COUPLE and python/examples directories have example C++ -and C and Python codes which show how a driver code can link to LAMMPS -as a library, run LAMMPS on a subset of processors, grab data from -LAMMPS, change it, and put it back into LAMMPS. - -Thread-safety :h4 - -LAMMPS has not initially been conceived as a thread-safe program, but -over the years changes have been applied to replace operations that -collide with creating multiple LAMMPS instances from multiple-threads -of the same process with thread-safe alternatives. This primarily -applies to the core LAMMPS code and less so on add-on packages, especially -when those packages require additional code in the {lib} folder, -interface LAMMPS to Fortran libraries, or the code uses static variables -(like the USER-COLVARS package. - -Another major issue to deal with is to correctly handle MPI. Creating -a LAMMPS instance requires passing an MPI communicator, or it assumes -the MPI_COMM_WORLD communicator, which spans all MPI processor ranks. -When creating multiple LAMMPS object instances from different threads, -this communicator has to be different for each thread or else collisions -can happen, or it has to be guaranteed, that only one thread at a time -is active. MPI communicators, however, are not a problem, if LAMMPS is -compiled with the MPI STUBS library, which implies that there is no MPI -communication and only 1 MPI rank. - -Provided APIs :h4 - -The file src/library.cpp contains the following functions for creating -and destroying an instance of LAMMPS and sending it commands to -execute. See the documentation in the src/library.cpp file for -details. - -NOTE: You can write code for additional functions as needed to define -how your code talks to LAMMPS and add them to src/library.cpp and -src/library.h, as well as to the "Python interface"_Python_head.html. -The added functions can access or change any internal LAMMPS data you -wish. - -void lammps_open(int, char **, MPI_Comm, void **) -void lammps_open_no_mpi(int, char **, void **) -void lammps_close(void *) -int lammps_version(void *) -void lammps_file(void *, char *) -char *lammps_command(void *, char *) -void lammps_commands_list(void *, int, char **) -void lammps_commands_string(void *, char *) -void lammps_free(void *) :pre - -The lammps_open() function is used to initialize LAMMPS, passing in a -list of strings as if they were "command-line -arguments"_Run_options.html when LAMMPS is run in stand-alone mode -from the command line, and a MPI communicator for LAMMPS to run under. -It returns a ptr to the LAMMPS object that is created, and which is -used in subsequent library calls. The lammps_open() function can be -called multiple times, to create multiple instances of LAMMPS. - -LAMMPS will run on the set of processors in the communicator. This -means the calling code can run LAMMPS on all or a subset of -processors. For example, a wrapper script might decide to alternate -between LAMMPS and another code, allowing them both to run on all the -processors. Or it might allocate half the processors to LAMMPS and -half to the other code and run both codes simultaneously before -syncing them up periodically. Or it might instantiate multiple -instances of LAMMPS to perform different calculations. - -The lammps_open_no_mpi() function is similar except that no MPI -communicator is passed from the caller. Instead, MPI_COMM_WORLD is -used to instantiate LAMMPS, and MPI is initialized if necessary. - -The lammps_close() function is used to shut down an instance of LAMMPS -and free all its memory. - -The lammps_version() function can be used to determined the specific -version of the underlying LAMMPS code. This is particularly useful -when loading LAMMPS as a shared library via dlopen(). The code using -the library interface can than use this information to adapt to -changes to the LAMMPS command syntax between versions. The returned -LAMMPS version code is an integer (e.g. 2 Sep 2015 results in -20150902) that grows with every new LAMMPS version. - -The lammps_file(), lammps_command(), lammps_commands_list(), and -lammps_commands_string() functions are used to pass one or more -commands to LAMMPS to execute, the same as if they were coming from an -input script. - -Via these functions, the calling code can read or generate a series of -LAMMPS commands one or multiple at a time and pass it through the library -interface to setup a problem and then run it in stages. The caller -can interleave the command function calls with operations it performs, -calls to extract information from or set information within LAMMPS, or -calls to another code's library. - -The lammps_file() function passes the filename of an input script. -The lammps_command() function passes a single command as a string. -The lammps_commands_list() function passes multiple commands in a -char** list. In both lammps_command() and lammps_commands_list(), -individual commands may or may not have a trailing newline. The -lammps_commands_string() function passes multiple commands -concatenated into one long string, separated by newline characters. -In both lammps_commands_list() and lammps_commands_string(), a single -command can be spread across multiple lines, if the last printable -character of all but the last line is "&", the same as if the lines -appeared in an input script. - -The lammps_free() function is a clean-up function to free memory that -the library allocated previously via other function calls. See -comments in src/library.cpp file for which other functions need this -clean-up. - -The file src/library.cpp also contains these functions for extracting -information from LAMMPS and setting value within LAMMPS. Again, see -the documentation in the src/library.cpp file for details, including -which quantities can be queried by name: - -int lammps_extract_setting(void *, char *) -void *lammps_extract_global(void *, char *) -void lammps_extract_box(void *, double *, double *, - double *, double *, double *, int *, int *) -void *lammps_extract_atom(void *, char *) -void *lammps_extract_compute(void *, char *, int, int) -void *lammps_extract_fix(void *, char *, int, int, int, int) -void *lammps_extract_variable(void *, char *, char *) :pre - -The extract_setting() function returns info on the size -of data types (e.g. 32-bit or 64-bit atom IDs) used -by the LAMMPS executable (a compile-time choice). - -The other extract functions return a pointer to various global or -per-atom quantities stored in LAMMPS or to values calculated by a -compute, fix, or variable. The pointer returned by the -extract_global() function can be used as a permanent reference to a -value which may change. For the extract_atom() method, see the -extract() method in the src/atom.cpp file for a list of valid per-atom -properties. New names could easily be added if the property you want -is not listed. For the other extract functions, the underlying -storage may be reallocated as LAMMPS runs, so you need to re-call the -function to assure a current pointer or returned value(s). - -double lammps_get_thermo(void *, char *) -int lammps_get_natoms(void *) :pre - -int lammps_set_variable(void *, char *, char *) -void lammps_reset_box(void *, double *, double *, double, double, double) :pre - -The lammps_get_thermo() function returns the current value of a thermo -keyword as a double precision value. - -The lammps_get_natoms() function returns the total number of atoms in -the system and can be used by the caller to allocate memory for the -lammps_gather_atoms() and lammps_scatter_atoms() functions. - -The lammps_set_variable() function can set an existing string-style -variable to a new string value, so that subsequent LAMMPS commands can -access the variable. - -The lammps_reset_box() function resets the size and shape of the -simulation box, e.g. as part of restoring a previously extracted and -saved state of a simulation. - -void lammps_gather_atoms(void *, char *, int, int, void *) -void lammps_gather_atoms_concat(void *, char *, int, int, void *) -void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *) -void lammps_scatter_atoms(void *, char *, int, int, void *) -void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre - -The gather functions collect peratom info of the requested type (atom -coords, atom types, forces, etc) from all processors, and returns the -same vector of values to each calling processor. The scatter -functions do the inverse. They distribute a vector of peratom values, -passed by all calling processors, to individual atoms, which may be -owned by different processors. - -IMPORTANT NOTE: These functions are not compatible with the --DLAMMPS_BIGBIG setting when compiling LAMMPS. Dummy functions -that result in an error message and abort will be substituted -instead of resulting in random crashes and memory corruption. - -The lammps_gather_atoms() function does this for all N atoms in the -system, ordered by atom ID, from 1 to N. The -lammps_gather_atoms_concat() function does it for all N atoms, but -simply concatenates the subset of atoms owned by each processor. The -resulting vector is not ordered by atom ID. Atom IDs can be requested -by the same function if the caller needs to know the ordering. The -lammps_gather_subset() function allows the caller to request values -for only a subset of atoms (identified by ID). -For all 3 gather function, per-atom image flags can be retrieved in 2 ways. -If the count is specified as 1, they are returned -in a packed format with all three image flags stored in a single integer. -If the count is specified as 3, the values are unpacked into xyz flags -by the library before returning them. - -The lammps_scatter_atoms() function takes a list of values for all N -atoms in the system, ordered by atom ID, from 1 to N, and assigns -those values to each atom in the system. The -lammps_scatter_atoms_subset() function takes a subset of IDs as an -argument and only scatters those values to the owning atoms. - -void lammps_create_atoms(void *, int, tagint *, int *, double *, double *, - imageint *, int) :pre - -The lammps_create_atoms() function takes a list of N atoms as input -with atom types and coords (required), an optionally atom IDs and -velocities and image flags. It uses the coords of each atom to assign -it as a new atom to the processor that owns it. This function is -useful to add atoms to a simulation or (in tandem with -lammps_reset_box()) to restore a previously extracted and saved state -of a simulation. Additional properties for the new atoms can then be -assigned via the lammps_scatter_atoms() or lammps_extract_atom() -functions. diff --git a/doc/txt/Howto_manifold.txt b/doc/txt/Howto_manifold.txt deleted file mode 100644 index 904432a946..0000000000 --- a/doc/txt/Howto_manifold.txt +++ /dev/null @@ -1,41 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Manifolds (surfaces) :h3 - -[Overview:] - -This doc page is not about a LAMMPS input script command, but about -manifolds, which are generalized surfaces, as defined and used by the -USER-MANIFOLD package, to track particle motion on the manifolds. See -the src/USER-MANIFOLD/README file for more details about the package -and its commands. - -Below is a list of currently supported manifolds by the USER-MANIFOLD -package, their parameters and a short description of them. The -parameters listed here are in the same order as they should be passed -to the relevant fixes. - -{manifold} @ {parameters} @ {equation} @ {description} -cylinder @ R @ x^2 + y^2 - R^2 = 0 @ Cylinder along z-axis, axis going through (0,0,0) -cylinder_dent @ R l a @ x^2 + y^2 - r(z)^2 = 0, r(x) = R if | z | > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise @ A cylinder with a dent around z = 0 -dumbbell @ a A B c @ -( x^2 + y^2 ) + (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 @ A dumbbell -ellipsoid @ a b c @ (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 @ An ellipsoid -gaussian_bump @ A l rc1 rc2 @ if( x < rc1) -z + A * exp( -x^2 / (2 l^2) ); else if( x < rc2 ) -z + a + b*x + c*x^2 + d*x^3; else z @ A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0. -plane @ a b c x0 y0 z0 @ a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 @ A plane with normal (a,b,c) going through point (x0,y0,z0) -plane_wiggle @ a w @ z - a*sin(w*x) = 0 @ A plane with a sinusoidal modulation on z along x. -sphere @ R @ x^2 + y^2 + z^2 - R^2 = 0 @ A sphere of radius R -supersphere @ R q @ | x |^q + | y |^q + | z |^q - R^q = 0 @ A supersphere of hyperradius R -spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ An approximation to a dendritic spine -spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ Another approximation to a dendritic spine -thylakoid @ wB LB lB @ Various, see "(Paquay)"_#Paquay1 @ A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB -torus @ R r @ (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2 @ A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=@) - -:link(Paquay1) -[(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016). -preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/. diff --git a/doc/txt/Howto_multiple.txt b/doc/txt/Howto_multiple.txt deleted file mode 100644 index 9ad872fedc..0000000000 --- a/doc/txt/Howto_multiple.txt +++ /dev/null @@ -1,94 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Run multiple simulations from one input script :h3 - -This can be done in several ways. See the documentation for -individual commands for more details on how these examples work. - -If "multiple simulations" means continue a previous simulation for -more timesteps, then you simply use the "run"_run.html command -multiple times. For example, this script - -units lj -atom_style atomic -read_data data.lj -run 10000 -run 10000 -run 10000 -run 10000 -run 10000 :pre - -would run 5 successive simulations of the same system for a total of -50,000 timesteps. - -If you wish to run totally different simulations, one after the other, -the "clear"_clear.html command can be used in between them to -re-initialize LAMMPS. For example, this script - -units lj -atom_style atomic -read_data data.lj -run 10000 -clear -units lj -atom_style atomic -read_data data.lj.new -run 10000 :pre - -would run 2 independent simulations, one after the other. - -For large numbers of independent simulations, you can use -"variables"_variable.html and the "next"_next.html and -"jump"_jump.html commands to loop over the same input script -multiple times with different settings. For example, this -script, named in.polymer - -variable d index run1 run2 run3 run4 run5 run6 run7 run8 -shell cd $d -read_data data.polymer -run 10000 -shell cd .. -clear -next d -jump in.polymer :pre - -would run 8 simulations in different directories, using a data.polymer -file in each directory. The same concept could be used to run the -same system at 8 different temperatures, using a temperature variable -and storing the output in different log and dump files, for example - -variable a loop 8 -variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15 -log log.$a -read data.polymer -velocity all create $t 352839 -fix 1 all nvt $t $t 100.0 -dump 1 all atom 1000 dump.$a -run 100000 -clear -next t -next a -jump in.polymer :pre - -All of the above examples work whether you are running on 1 or -multiple processors, but assumed you are running LAMMPS on a single -partition of processors. LAMMPS can be run on multiple partitions via -the "-partition command-line switch"_Run_options.html. - -In the last 2 examples, if LAMMPS were run on 3 partitions, the same -scripts could be used if the "index" and "loop" variables were -replaced with {universe}-style variables, as described in the -"variable"_variable.html command. Also, the "next t" and "next a" -commands would need to be replaced with a single "next a t" command. -With these modifications, the 8 simulations of each script would run -on the 3 partitions one after the other until all were finished. -Initially, 3 simulations would be started simultaneously, one on each -partition. When one finished, that partition would then start -the 4th simulation, and so forth, until all 8 were completed. diff --git a/doc/txt/Howto_nemd.txt b/doc/txt/Howto_nemd.txt deleted file mode 100644 index 1ec9c51f4e..0000000000 --- a/doc/txt/Howto_nemd.txt +++ /dev/null @@ -1,59 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -NEMD simulations :h3 - -Non-equilibrium molecular dynamics or NEMD simulations are typically -used to measure a fluid's rheological properties such as viscosity. -In LAMMPS, such simulations can be performed by first setting up a -non-orthogonal simulation box (see the preceding Howto section). - -A shear strain can be applied to the simulation box at a desired -strain rate by using the "fix deform"_fix_deform.html command. The -"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat -the sheared fluid and integrate the SLLOD equations of motion for the -system. Fix nvt/sllod uses "compute -temp/deform"_compute_temp_deform.html to compute a thermal temperature -by subtracting out the streaming velocity of the shearing atoms. The -velocity profile or other properties of the fluid can be monitored via -the "fix ave/chunk"_fix_ave_chunk.html command. - -NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-nemd -discusses use of the SLLOD method and non-equilibrium MD (NEMD) -thermostatting generally, for both simple and complex fluids, -e.g. molecular systems. The latter can be tricky to do correctly. - -As discussed in the previous section on non-orthogonal simulation -boxes, the amount of tilt or skew that can be applied is limited by -LAMMPS for computational efficiency to be 1/2 of the parallel box -length. However, "fix deform"_fix_deform.html can continuously strain -a box by an arbitrary amount. As discussed in the "fix -deform"_fix_deform.html command, when the tilt value reaches a limit, -the box is flipped to the opposite limit which is an equivalent tiling -of periodic space. The strain rate can then continue to change as -before. In a long NEMD simulation these box re-shaping events may -occur many times. - -In a NEMD simulation, the "remap" option of "fix -deform"_fix_deform.html should be set to "remap v", since that is what -"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity -profile consistent with the applied shear strain rate. - -An alternative method for calculating viscosities is provided via the -"fix viscosity"_fix_viscosity.html command. - -NEMD simulations can also be used to measure transport properties of a fluid -through a pore or channel. Simulations of steady-state flow can be performed -using the "fix flow/gauss"_fix_flow_gauss.html command. - -:line - -:link(Daivis-nemd) -[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book), -Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/txt/Howto_output.txt b/doc/txt/Howto_output.txt deleted file mode 100644 index a204a3cc96..0000000000 --- a/doc/txt/Howto_output.txt +++ /dev/null @@ -1,307 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Output from LAMMPS (thermo, dumps, computes, fixes, variables) :h3 - -There are four basic kinds of LAMMPS output: - -"Thermodynamic output"_thermo_style.html, which is a list -of quantities printed every few timesteps to the screen and logfile. :ulb,l - -"Dump files"_dump.html, which contain snapshots of atoms and various -per-atom values and are written at a specified frequency. :l - -Certain fixes can output user-specified quantities to files: "fix -ave/time"_fix_ave_time.html for time averaging, "fix -ave/chunk"_fix_ave_chunk.html for spatial or other averaging, and "fix -print"_fix_print.html for single-line output of -"variables"_variable.html. Fix print can also output to the -screen. :l - -"Restart files"_restart.html. :l -:ule - -A simulation prints one set of thermodynamic output and (optionally) -restart files. It can generate any number of dump files and fix -output files, depending on what "dump"_dump.html and "fix"_fix.html -commands you specify. - -As discussed below, LAMMPS gives you a variety of ways to determine -what quantities are computed and printed when the thermodynamics, -dump, or fix commands listed above perform output. Throughout this -discussion, note that users can also "add their own computes and fixes -to LAMMPS"_Modify.html which can then generate values that can then be -output with these commands. - -The following sub-sections discuss different LAMMPS command related -to output and the kind of data they operate on and produce: - -"Global/per-atom/local data"_#global -"Scalar/vector/array data"_#scalar -"Thermodynamic output"_#thermo -"Dump file output"_#dump -"Fixes that write output files"_#fixoutput -"Computes that process output quantities"_#computeoutput -"Fixes that process output quantities"_#fixprocoutput -"Computes that generate values to output"_#compute -"Fixes that generate values to output"_#fix -"Variables that generate values to output"_#variable -"Summary table of output options and data flow between commands"_#table :ul - -Global/per-atom/local data :h4,link(global) - -Various output-related commands work with three different styles of -data: global, per-atom, or local. A global datum is one or more -system-wide values, e.g. the temperature of the system. A per-atom -datum is one or more values per atom, e.g. the kinetic energy of each -atom. Local datums are calculated by each processor based on the -atoms it owns, but there may be zero or more per atom, e.g. a list of -bond distances. - -Scalar/vector/array data :h4,link(scalar) - -Global, per-atom, and local datums can each come in three kinds: a -single scalar value, a vector of values, or a 2d array of values. The -doc page for a "compute" or "fix" or "variable" that generates data -will specify both the style and kind of data it produces, e.g. a -per-atom vector. - -When a quantity is accessed, as in many of the output commands -discussed below, it can be referenced via the following bracket -notation, where ID in this case is the ID of a compute. The leading -"c_" would be replaced by "f_" for a fix, or "v_" for a variable: - -c_ID | entire scalar, vector, or array -c_ID\[I\] | one element of vector, one column of array -c_ID\[I\]\[J\] | one element of array :tb(s=|) - -In other words, using one bracket reduces the dimension of the data -once (vector -> scalar, array -> vector). Using two brackets reduces -the dimension twice (array -> scalar). Thus a command that uses -scalar values as input can typically also process elements of a vector -or array. - -Thermodynamic output :h4,link(thermo) - -The frequency and format of thermodynamic output is set by the -"thermo"_thermo.html, "thermo_style"_thermo_style.html, and -"thermo_modify"_thermo_modify.html commands. The -"thermo_style"_thermo_style.html command also specifies what values -are calculated and written out. Pre-defined keywords can be specified -(e.g. press, etotal, etc). Three additional kinds of keywords can -also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html -or "fix"_fix.html or "variable"_variable.html provides the value to be -output. In each case, the compute, fix, or variable must generate -global values for input to the "thermo_style custom"_dump.html -command. - -Note that thermodynamic output values can be "extensive" or -"intensive". The former scale with the number of atoms in the system -(e.g. total energy), the latter do not (e.g. temperature). The -setting for "thermo_modify norm"_thermo_modify.html determines whether -extensive quantities are normalized or not. Computes and fixes -produce either extensive or intensive values; see their individual doc -pages for details. "Equal-style variables"_variable.html produce only -intensive values; you can include a division by "natoms" in the -formula if desired, to make an extensive calculation produce an -intensive result. - -Dump file output :h4,link(dump) - -Dump file output is specified by the "dump"_dump.html and -"dump_modify"_dump_modify.html commands. There are several -pre-defined formats (dump atom, dump xtc, etc). - -There is also a "dump custom"_dump.html format where the user -specifies what values are output with each atom. Pre-defined atom -attributes can be specified (id, x, fx, etc). Three additional kinds -of keywords can also be specified (c_ID, f_ID, v_name), where a -"compute"_compute.html or "fix"_fix.html or "variable"_variable.html -provides the values to be output. In each case, the compute, fix, or -variable must generate per-atom values for input to the "dump -custom"_dump.html command. - -There is also a "dump local"_dump.html format where the user specifies -what local values to output. A pre-defined index keyword can be -specified to enumerate the local values. Two additional kinds of -keywords can also be specified (c_ID, f_ID), where a -"compute"_compute.html or "fix"_fix.html or "variable"_variable.html -provides the values to be output. In each case, the compute or fix -must generate local values for input to the "dump local"_dump.html -command. - -Fixes that write output files :h4,link(fixoutput) - -Several fixes take various quantities as input and can write output -files: "fix ave/time"_fix_ave_time.html, "fix -ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html, -"fix ave/correlate"_fix_ave_correlate.html, and "fix -print"_fix_print.html. - -The "fix ave/time"_fix_ave_time.html command enables direct output to -a file and/or time-averaging of global scalars or vectors. The user -specifies one or more quantities as input. These can be global -"compute"_compute.html values, global "fix"_fix.html values, or -"variables"_variable.html of any style except the atom style which -produces per-atom values. Since a variable can refer to keywords used -by the "thermo_style custom"_thermo_style.html command (like temp or -press) and individual per-atom values, a wide variety of quantities -can be time averaged and/or output in this way. If the inputs are one -or more scalar values, then the fix generate a global scalar or vector -of output. If the inputs are one or more vector values, then the fix -generates a global vector or array of output. The time-averaged -output of this fix can also be used as input to other output commands. - -The "fix ave/chunk"_fix_ave_chunk.html command enables direct output -to a file of chunk-averaged per-atom quantities like those output in -dump files. Chunks can represent spatial bins or other collections of -atoms, e.g. individual molecules. The per-atom quantities can be atom -density (mass or number) or atom attributes such as position, -velocity, force. They can also be per-atom quantities calculated by a -"compute"_compute.html, by a "fix"_fix.html, or by an atom-style -"variable"_variable.html. The chunk-averaged output of this fix can -also be used as input to other output commands. - -The "fix ave/histo"_fix_ave_histo.html command enables direct output -to a file of histogrammed quantities, which can be global or per-atom -or local quantities. The histogram output of this fix can also be -used as input to other output commands. - -The "fix ave/correlate"_fix_ave_correlate.html command enables direct -output to a file of time-correlated quantities, which can be global -values. The correlation matrix output of this fix can also be used as -input to other output commands. - -The "fix print"_fix_print.html command can generate a line of output -written to the screen and log file or to a separate file, periodically -during a running simulation. The line can contain one or more -"variable"_variable.html values for any style variable except the -vector or atom styles). As explained above, variables themselves can -contain references to global values generated by "thermodynamic -keywords"_thermo_style.html, "computes"_compute.html, -"fixes"_fix.html, or other "variables"_variable.html, or to per-atom -values for a specific atom. Thus the "fix print"_fix_print.html -command is a means to output a wide variety of quantities separate -from normal thermodynamic or dump file output. - -Computes that process output quantities :h4,link(computeoutput) - -The "compute reduce"_compute_reduce.html and "compute -reduce/region"_compute_reduce.html commands take one or more per-atom -or local vector quantities as inputs and "reduce" them (sum, min, max, -ave) to scalar quantities. These are produced as output values which -can be used as input to other output commands. - -The "compute slice"_compute_slice.html command take one or more global -vector or array quantities as inputs and extracts a subset of their -values to create a new vector or array. These are produced as output -values which can be used as input to other output commands. - -The "compute property/atom"_compute_property_atom.html command takes a -list of one or more pre-defined atom attributes (id, x, fx, etc) and -stores the values in a per-atom vector or array. These are produced -as output values which can be used as input to other output commands. -The list of atom attributes is the same as for the "dump -custom"_dump.html command. - -The "compute property/local"_compute_property_local.html command takes -a list of one or more pre-defined local attributes (bond info, angle -info, etc) and stores the values in a local vector or array. These -are produced as output values which can be used as input to other -output commands. - -Fixes that process output quantities :h4,link(fixprocoutput) - -The "fix vector"_fix_vector.html command can create global vectors as -output from global scalars as input, accumulating them one element at -a time. - -The "fix ave/atom"_fix_ave_atom.html command performs time-averaging -of per-atom vectors. The per-atom quantities can be atom attributes -such as position, velocity, force. They can also be per-atom -quantities calculated by a "compute"_compute.html, by a -"fix"_fix.html, or by an atom-style "variable"_variable.html. The -time-averaged per-atom output of this fix can be used as input to -other output commands. - -The "fix store/state"_fix_store_state.html command can archive one or -more per-atom attributes at a particular time, so that the old values -can be used in a future calculation or output. The list of atom -attributes is the same as for the "dump custom"_dump.html command, -including per-atom quantities calculated by a "compute"_compute.html, -by a "fix"_fix.html, or by an atom-style "variable"_variable.html. -The output of this fix can be used as input to other output commands. - -Computes that generate values to output :h4,link(compute) - -Every "compute"_compute.html in LAMMPS produces either global or -per-atom or local values. The values can be scalars or vectors or -arrays of data. These values can be output using the other commands -described in this section. The doc page for each compute command -describes what it produces. Computes that produce per-atom or local -values have the word "atom" or "local" in their style name. Computes -without the word "atom" or "local" produce global values. - -Fixes that generate values to output :h4,link(fix) - -Some "fixes"_fix.html in LAMMPS produces either global or per-atom or -local values which can be accessed by other commands. The values can -be scalars or vectors or arrays of data. These values can be output -using the other commands described in this section. The doc page for -each fix command tells whether it produces any output quantities and -describes them. - -Variables that generate values to output :h4,link(variable) - -"Variables"_variable.html defined in an input script can store one or -more strings. But equal-style, vector-style, and atom-style or -atomfile-style variables generate a global scalar value, global vector -or values, or a per-atom vector, respectively, when accessed. The -formulas used to define these variables can contain references to the -thermodynamic keywords and to global and per-atom data generated by -computes, fixes, and other variables. The values generated by -variables can be used as input to and thus output by the other -commands described in this section. - -Summary table of output options and data flow between commands :h4,link(table) - -This table summarizes the various commands that can be used for -generating output from LAMMPS. Each command produces output data of -some kind and/or writes data to a file. Most of the commands can take -data from other commands as input. Thus you can link many of these -commands together in pipeline form, where data produced by one command -is used as input to another command and eventually written to the -screen or to a file. Note that to hook two commands together the -output and input data types must match, e.g. global/per-atom/local -data and scalar/vector/array data. - -Also note that, as described above, when a command takes a scalar as -input, that could be an element of a vector or array. Likewise a -vector input could be a column of an array. - -Command: Input: Output: -"thermo_style custom"_thermo_style.html: global scalars: screen, log file: -"dump custom"_dump.html: per-atom vectors: dump file: -"dump local"_dump.html: local vectors: dump file: -"fix print"_fix_print.html: global scalar from variable: screen, file: -"print"_print.html: global scalar from variable: screen: -"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array: -"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array: -"variables"_variable.html: global scalars and vectors, per-atom vectors: global scalar and vector, per-atom vector: -"compute reduce"_compute_reduce.html: per-atom/local vectors: global scalar/vector: -"compute slice"_compute_slice.html: global vectors/arrays: global vector/array: -"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array: -"compute property/local"_compute_property_local.html: local vectors: local vector/array: -"fix vector"_fix_vector.html: global scalars: global vector: -"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array: -"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file: -"fix ave/chunk"_fix_ave_chunk.html: per-atom vectors: global array, file: -"fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file: -"fix ave/correlate"_fix_ave_correlate.html: global scalars: global array, file: -"fix store/state"_fix_store_state.html: per-atom vectors: per-atom vector/array :tb(c=3,s=:) diff --git a/doc/txt/Howto_polarizable.txt b/doc/txt/Howto_polarizable.txt deleted file mode 100644 index 00a73dddd3..0000000000 --- a/doc/txt/Howto_polarizable.txt +++ /dev/null @@ -1,81 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Polarizable models :h3 - -In polarizable force fields the charge distributions in molecules and -materials respond to their electrostatic environments. Polarizable -systems can be simulated in LAMMPS using three methods: - -the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html -package, :ulb,l -the adiabatic core-shell method, implemented in the -"CORESHELL"_Howto_coreshell.html package, :l -the thermalized Drude dipole method, implemented in the -"USER-DRUDE"_Howto_drude.html package. :l,ule - -The fluctuating charge method calculates instantaneous charges on -interacting atoms based on the electronegativity equalization -principle. It is implemented in the "fix qeq"_fix_qeq.html which is -available in several variants. It is a relatively efficient technique -since no additional particles are introduced. This method allows for -charge transfer between molecules or atom groups. However, because the -charges are located at the interaction sites, off-plane components of -polarization cannot be represented in planar molecules or atom groups. - -The two other methods share the same basic idea: polarizable atoms are -split into one core atom and one satellite particle (called shell or -Drude particle) attached to it by a harmonic spring. Both atoms bear -a charge and they represent collectively an induced electric dipole. -These techniques are computationally more expensive than the QEq -method because of additional particles and bonds. These two -charge-on-spring methods differ in certain features, with the -core-shell model being normally used for ionic/crystalline materials, -whereas the so-called Drude model is normally used for molecular -systems and fluid states. - -The core-shell model is applicable to crystalline materials where the -high symmetry around each site leads to stable trajectories of the -core-shell pairs. However, bonded atoms in molecules can be so close -that a core would interact too strongly or even capture the Drude -particle of a neighbor. The Drude dipole model is relatively more -complex in order to remedy this and other issues. Specifically, the -Drude model includes specific thermostatting of the core-Drude pairs -and short-range damping of the induced dipoles. - -The three polarization methods can be implemented through a -self-consistent calculation of charges or induced dipoles at each -timestep. In the fluctuating charge scheme this is done by the matrix -inversion method in "fix qeq/point"_fix_qeq.html, but for core-shell -or Drude-dipoles the relaxed-dipoles technique would require an slow -iterative procedure. These self-consistent solutions yield accurate -trajectories since the additional degrees of freedom representing -polarization are massless. An alternative is to attribute a mass to -the additional degrees of freedom and perform time integration using -an extended Lagrangian technique. For the fluctuating charge scheme -this is done by "fix qeq/dynamic"_fix_qeq.html, and for the -charge-on-spring models by the methods outlined in the next two -sections. The assignment of masses to the additional degrees of -freedom can lead to unphysical trajectories if care is not exerted in -choosing the parameters of the polarizable models and the simulation -conditions. - -In the core-shell model the vibration of the shells is kept faster -than the ionic vibrations to mimic the fast response of the -polarizable electrons. But in molecular systems thermalizing the -core-Drude pairs at temperatures comparable to the rest of the -simulation leads to several problems (kinetic energy transfer, too -short a timestep, etc.) In order to avoid these problems the relative -motion of the Drude particles with respect to their cores is kept -"cold" so the vibration of the core-Drude pairs is very slow, -approaching the self-consistent regime. In both models the -temperature is regulated using the velocities of the center of mass of -core+shell (or Drude) pairs, but in the Drude model the actual -relative core-Drude particle motion is thermostatted separately as -well. diff --git a/doc/txt/Howto_replica.txt b/doc/txt/Howto_replica.txt deleted file mode 100644 index 505967c1b8..0000000000 --- a/doc/txt/Howto_replica.txt +++ /dev/null @@ -1,61 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Multi-replica simulations :h3 - -Several commands in LAMMPS run multi-replica simulations, meaning -that multiple instances (replicas) of your simulation are run -simultaneously, with small amounts of data exchanged between replicas -periodically. - -These are the relevant commands: - -"neb"_neb.html for nudged elastic band calculations -"neb_spin"_neb_spin.html for magnetic nudged elastic band calculations -"prd"_prd.html for parallel replica dynamics -"tad"_tad.html for temperature accelerated dynamics -"temper"_temper.html for parallel tempering -"fix pimd"_fix_pimd.html for path-integral molecular dynamics (PIMD) :ul - -NEB is a method for finding transition states and barrier energies. -PRD and TAD are methods for performing accelerated dynamics to find -and perform infrequent events. Parallel tempering or replica exchange -runs different replicas at a series of temperature to facilitate -rare-event sampling. - -These commands can only be used if LAMMPS was built with the REPLICA -package. See the "Build package"_Build_package.html doc page for more -info. - -PIMD runs different replicas whose individual particles are coupled -together by springs to model a system or ring-polymers. - -This commands can only be used if LAMMPS was built with the USER-MISC -package. See the "Build package"_Build_package.html doc page for more -info. - -In all these cases, you must run with one or more processors per -replica. The processors assigned to each replica are determined at -run-time by using the "-partition command-line -switch"_Run_options.html to launch LAMMPS on multiple partitions, -which in this context are the same as replicas. E.g. these commands: - -mpirun -np 16 lmp_linux -partition 8x2 -in in.temper -mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre - -would each run 8 replicas, on either 16 or 8 processors. Note the use -of the "-in command-line switch"_Run_options.html to specify the input -script which is required when running in multi-replica mode. - -Also note that with MPI installed on a machine (e.g. your desktop), -you can run on more (virtual) processors than you have physical -processors. Thus the above commands could be run on a -single-processor (or few-processor) desktop so that you can run -a multi-replica simulation on more replicas than you have -physical processors. diff --git a/doc/txt/Howto_restart.txt b/doc/txt/Howto_restart.txt deleted file mode 100644 index bc67daa78e..0000000000 --- a/doc/txt/Howto_restart.txt +++ /dev/null @@ -1,97 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Restart a simulation :h3 - -There are 3 ways to continue a long LAMMPS simulation. Multiple -"run"_run.html commands can be used in the same input script. Each -run will continue from where the previous run left off. Or binary -restart files can be saved to disk using the "restart"_restart.html -command. At a later time, these binary files can be read via a -"read_restart"_read_restart.html command in a new script. Or they can -be converted to text data files using the "-r command-line -switch"_Run_options.html and read by a "read_data"_read_data.html -command in a new script. - -Here we give examples of 2 scripts that read either a binary restart -file or a converted data file and then issue a new run command to -continue where the previous run left off. They illustrate what -settings must be made in the new script. Details are discussed in the -documentation for the "read_restart"_read_restart.html and -"read_data"_read_data.html commands. - -Look at the {in.chain} input script provided in the {bench} directory -of the LAMMPS distribution to see the original script that these 2 -scripts are based on. If that script had the line - -restart 50 tmp.restart :pre - -added to it, it would produce 2 binary restart files (tmp.restart.50 -and tmp.restart.100) as it ran. - -This script could be used to read the 1st restart file and re-run the -last 50 timesteps: - -read_restart tmp.restart.50 :pre - -neighbor 0.4 bin -neigh_modify every 1 delay 1 :pre - -fix 1 all nve -fix 2 all langevin 1.0 1.0 10.0 904297 :pre - -timestep 0.012 :pre - -run 50 :pre - -Note that the following commands do not need to be repeated because -their settings are included in the restart file: {units, atom_style, -special_bonds, pair_style, bond_style}. However these commands do -need to be used, since their settings are not in the restart file: -{neighbor, fix, timestep}. - -If you actually use this script to perform a restarted run, you will -notice that the thermodynamic data match at step 50 (if you also put a -"thermo 50" command in the original script), but do not match at step -100. This is because the "fix langevin"_fix_langevin.html command -uses random numbers in a way that does not allow for perfect restarts. - -As an alternate approach, the restart file could be converted to a data -file as follows: - -lmp_g++ -r tmp.restart.50 tmp.restart.data :pre - -Then, this script could be used to re-run the last 50 steps: - -units lj -atom_style bond -pair_style lj/cut 1.12 -pair_modify shift yes -bond_style fene -special_bonds 0.0 1.0 1.0 :pre - -read_data tmp.restart.data :pre - -neighbor 0.4 bin -neigh_modify every 1 delay 1 :pre - -fix 1 all nve -fix 2 all langevin 1.0 1.0 10.0 904297 :pre - -timestep 0.012 :pre - -reset_timestep 50 -run 50 :pre - -Note that nearly all the settings specified in the original {in.chain} -script must be repeated, except the {pair_coeff} and {bond_coeff} -commands since the new data file lists the force field coefficients. -Also, the "reset_timestep"_reset_timestep.html command is used to tell -LAMMPS the current timestep. This value is stored in restart files, -but not in data files. diff --git a/doc/txt/Howto_spc.txt b/doc/txt/Howto_spc.txt deleted file mode 100644 index c0d4d77c5f..0000000000 --- a/doc/txt/Howto_spc.txt +++ /dev/null @@ -1,54 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -SPC water model :h3 - -The SPC water model specifies a 3-site rigid water molecule with -charges and Lennard-Jones parameters assigned to each of the 3 atoms. -In LAMMPS the "fix shake"_fix_shake.html command can be used to hold -the two O-H bonds and the H-O-H angle rigid. A bond style of -{harmonic} and an angle style of {harmonic} or {charmm} should also be -used. - -These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid SPC model. - -O mass = 15.9994 -H mass = 1.008 -O charge = -0.820 -H charge = 0.410 -LJ epsilon of OO = 0.1553 -LJ sigma of OO = 3.166 -LJ epsilon, sigma of OH, HH = 0.0 -r0 of OH bond = 1.0 -theta of HOH angle = 109.47 :all(b),p - -Note that as originally proposed, the SPC model was run with a 9 -Angstrom cutoff for both LJ and Coulombic terms. It can also be used -with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing -any of the parameters above, though it becomes a different model in -that mode of usage. - -The SPC/E (extended) water model is the same, except -the partial charge assignments change: - -O charge = -0.8476 -H charge = 0.4238 :all(b),p - -See the "(Berendsen)"_#howto-Berendsen reference for more details on both -the SPC and SPC/E models. - -Wikipedia also has a nice article on "water -models"_http://en.wikipedia.org/wiki/Water_model. - -:line - -:link(howto-Berendsen) -[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91, -6269-6271 (1987). diff --git a/doc/txt/Howto_spherical.txt b/doc/txt/Howto_spherical.txt deleted file mode 100644 index a0ff90c42d..0000000000 --- a/doc/txt/Howto_spherical.txt +++ /dev/null @@ -1,243 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Finite-size spherical and aspherical particles :h3 - -Typical MD models treat atoms or particles as point masses. Sometimes -it is desirable to have a model with finite-size particles such as -spheroids or ellipsoids or generalized aspherical bodies. The -difference is that such particles have a moment of inertia, rotational -energy, and angular momentum. Rotation is induced by torque coming -from interactions with other particles. - -LAMMPS has several options for running simulations with these kinds of -particles. The following aspects are discussed in turn: - -atom styles -pair potentials -time integration -computes, thermodynamics, and dump output -rigid bodies composed of finite-size particles :ul - -Example input scripts for these kinds of models are in the body, -colloid, dipole, ellipse, line, peri, pour, and tri directories of the -"examples directory"_Examples.html in the LAMMPS distribution. - -Atom styles :h4 - -There are several "atom styles"_atom_style.html that allow for -definition of finite-size particles: sphere, dipole, ellipsoid, line, -tri, peri, and body. - -The sphere style defines particles that are spheroids and each -particle can have a unique diameter and mass (or density). These -particles store an angular velocity (omega) and can be acted upon by -torque. The "set" command can be used to modify the diameter and mass -of individual particles, after then are created. - -The dipole style does not actually define finite-size particles, but -is often used in conjunction with spherical particles, via a command -like - -atom_style hybrid sphere dipole :pre - -This is because when dipoles interact with each other, they induce -torques, and a particle must be finite-size (i.e. have a moment of -inertia) in order to respond and rotate. See the "atom_style -dipole"_atom_style.html command for details. The "set" command can be -used to modify the orientation and length of the dipole moment of -individual particles, after then are created. - -The ellipsoid style defines particles that are ellipsoids and thus can -be aspherical. Each particle has a shape, specified by 3 diameters, -and mass (or density). These particles store an angular momentum and -their orientation (quaternion), and can be acted upon by torque. They -do not store an angular velocity (omega), which can be in a different -direction than angular momentum, rather they compute it as needed. -The "set" command can be used to modify the diameter, orientation, and -mass of individual particles, after then are created. It also has a -brief explanation of what quaternions are. - -The line style defines line segment particles with two end points and -a mass (or density). They can be used in 2d simulations, and they can -be joined together to form rigid bodies which represent arbitrary -polygons. - -The tri style defines triangular particles with three corner points -and a mass (or density). They can be used in 3d simulations, and they -can be joined together to form rigid bodies which represent arbitrary -particles with a triangulated surface. - -The peri style is used with "Peridynamic models"_pair_peri.html and -defines particles as having a volume, that is used internally in the -"pair_style peri"_pair_peri.html potentials. - -The body style allows for definition of particles which can represent -complex entities, such as surface meshes of discrete points, -collections of sub-particles, deformable objects, etc. The body style -is discussed in more detail on the "Howto body"_Howto_body.html doc -page. - -Note that if one of these atom styles is used (or multiple styles via -the "atom_style hybrid"_atom_style.html command), not all particles in -the system are required to be finite-size or aspherical. - -For example, in the ellipsoid style, if the 3 shape parameters are set -to the same value, the particle will be a sphere rather than an -ellipsoid. If the 3 shape parameters are all set to 0.0 or if the -diameter is set to 0.0, it will be a point particle. In the line or -tri style, if the lineflag or triflag is specified as 0, then it -will be a point particle. - -Some of the pair styles used to compute pairwise interactions between -finite-size particles also compute the correct interaction with point -particles as well, e.g. the interaction between a point particle and a -finite-size particle or between two point particles. If necessary, -"pair_style hybrid"_pair_hybrid.html can be used to insure the correct -interactions are computed for the appropriate style of interactions. -Likewise, using groups to partition particles (ellipsoids versus -spheres versus point particles) will allow you to use the appropriate -time integrators and temperature computations for each class of -particles. See the doc pages for various commands for details. - -Also note that for "2d simulations"_dimension.html, atom styles sphere -and ellipsoid still use 3d particles, rather than as circular disks or -ellipses. This means they have the same moment of inertia as the 3d -object. When temperature is computed, the correct degrees of freedom -are used for rotation in a 2d versus 3d system. - -Pair potentials :h4 - -When a system with finite-size particles is defined, the particles -will only rotate and experience torque if the force field computes -such interactions. These are the various "pair -styles"_pair_style.html that generate torque: - -"pair_style gran/history"_pair_gran.html -"pair_style gran/hertzian"_pair_gran.html -"pair_style gran/no_history"_pair_gran.html -"pair_style dipole/cut"_pair_dipole.html -"pair_style gayberne"_pair_gayberne.html -"pair_style resquared"_pair_resquared.html -"pair_style brownian"_pair_brownian.html -"pair_style lubricate"_pair_lubricate.html -"pair_style line/lj"_pair_line_lj.html -"pair_style tri/lj"_pair_tri_lj.html -"pair_style body/nparticle"_pair_body_nparticle.html :ul - -The granular pair styles are used with spherical particles. The -dipole pair style is used with the dipole atom style, which could be -applied to spherical or ellipsoidal particles. The GayBerne and -REsquared potentials require ellipsoidal particles, though they will -also work if the 3 shape parameters are the same (a sphere). The -Brownian and lubrication potentials are used with spherical particles. -The line, tri, and body potentials are used with line segment, -triangular, and body particles respectively. - -Time integration :h4 - -There are several fixes that perform time integration on finite-size -spherical particles, meaning the integrators update the rotational -orientation and angular velocity or angular momentum of the particles: - -"fix nve/sphere"_fix_nve_sphere.html -"fix nvt/sphere"_fix_nvt_sphere.html -"fix npt/sphere"_fix_npt_sphere.html :ul - -Likewise, there are 3 fixes that perform time integration on -ellipsoidal particles: - -"fix nve/asphere"_fix_nve_asphere.html -"fix nvt/asphere"_fix_nvt_asphere.html -"fix npt/asphere"_fix_npt_asphere.html :ul - -The advantage of these fixes is that those which thermostat the -particles include the rotational degrees of freedom in the temperature -calculation and thermostatting. The "fix langevin"_fix_langevin.html -command can also be used with its {omgea} or {angmom} options to -thermostat the rotational degrees of freedom for spherical or -ellipsoidal particles. Other thermostatting fixes only operate on the -translational kinetic energy of finite-size particles. - -These fixes perform constant NVE time integration on line segment, -triangular, and body particles: - -"fix nve/line"_fix_nve_line.html -"fix nve/tri"_fix_nve_tri.html -"fix nve/body"_fix_nve_body.html :ul - -Note that for mixtures of point and finite-size particles, these -integration fixes can only be used with "groups"_group.html which -contain finite-size particles. - -Computes, thermodynamics, and dump output :h4 - -There are several computes that calculate the temperature or -rotational energy of spherical or ellipsoidal particles: - -"compute temp/sphere"_compute_temp_sphere.html -"compute temp/asphere"_compute_temp_asphere.html -"compute erotate/sphere"_compute_erotate_sphere.html -"compute erotate/asphere"_compute_erotate_asphere.html :ul - -These include rotational degrees of freedom in their computation. If -you wish the thermodynamic output of temperature or pressure to use -one of these computes (e.g. for a system entirely composed of -finite-size particles), then the compute can be defined and the -"thermo_modify"_thermo_modify.html command used. Note that by default -thermodynamic quantities will be calculated with a temperature that -only includes translational degrees of freedom. See the -"thermo_style"_thermo_style.html command for details. - -These commands can be used to output various attributes of finite-size -particles: - -"dump custom"_dump.html -"compute property/atom"_compute_property_atom.html -"dump local"_dump.html -"compute body/local"_compute_body_local.html :ul - -Attributes include the dipole moment, the angular velocity, the -angular momentum, the quaternion, the torque, the end-point and -corner-point coordinates (for line and tri particles), and -sub-particle attributes of body particles. - -Rigid bodies composed of finite-size particles :h4 - -The "fix rigid"_fix_rigid.html command treats a collection of -particles as a rigid body, computes its inertia tensor, sums the total -force and torque on the rigid body each timestep due to forces on its -constituent particles, and integrates the motion of the rigid body. - -If any of the constituent particles of a rigid body are finite-size -particles (spheres or ellipsoids or line segments or triangles), then -their contribution to the inertia tensor of the body is different than -if they were point particles. This means the rotational dynamics of -the rigid body will be different. Thus a model of a dimer is -different if the dimer consists of two point masses versus two -spheroids, even if the two particles have the same mass. Finite-size -particles that experience torque due to their interaction with other -particles will also impart that torque to a rigid body they are part -of. - -See the "fix rigid" command for example of complex rigid-body models -it is possible to define in LAMMPS. - -Note that the "fix shake"_fix_shake.html command can also be used to -treat 2, 3, or 4 particles as a rigid body, but it always assumes the -particles are point masses. - -Also note that body particles cannot be modeled with the "fix -rigid"_fix_rigid.html command. Body particles are treated by LAMMPS -as single particles, though they can store internal state, such as a -list of sub-particles. Individual body particles are typically treated -as rigid bodies, and their motion integrated with a command like "fix -nve/body"_fix_nve_body.html. Interactions between pairs of body -particles are computed via a command like "pair_style -body/nparticle"_pair_body_nparticle.html. diff --git a/doc/txt/Howto_spins.txt b/doc/txt/Howto_spins.txt deleted file mode 100644 index c4bdc502ce..0000000000 --- a/doc/txt/Howto_spins.txt +++ /dev/null @@ -1,74 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Magnetic spins :h3 - -The magnetic spin simulations are enabled by the SPIN package, whose -implementation is detailed in "Tranchida"_#Tranchida. - -The model represents the simulation of atomic magnetic spins coupled -to lattice vibrations. The dynamics of those magnetic spins can be used -to simulate a broad range a phenomena related to magneto-elasticity, or -or to study the influence of defects on the magnetic properties of -materials. - -The magnetic spins are interacting with each others and with the -lattice via pair interactions. Typically, the magnetic exchange -interaction can be defined using the -"pair/spin/exchange"_pair_spin_exchange.html command. This exchange -applies a magnetic torque to a given spin, considering the orientation -of its neighboring spins and their relative distances. -It also applies a force on the atoms as a function of the spin -orientations and their associated inter-atomic distances. - -The command "fix precession/spin"_fix_precession_spin.html allows to -apply a constant magnetic torque on all the spins in the system. This -torque can be an external magnetic field (Zeeman interaction), or an -uniaxial magnetic anisotropy. - -A Langevin thermostat can be applied to those magnetic spins using -"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat -can be coupled to another Langevin thermostat applied to the atoms -using "fix langevin"_fix_langevin.html in order to simulate -thermostatted spin-lattice systems. - -The magnetic Gilbert damping can also be applied using "fix -langevin/spin"_fix_langevin_spin.html. It allows to either dissipate -the thermal energy of the Langevin thermostat, or to perform a -relaxation of the magnetic configuration toward an equilibrium state. - -The command "fix setforce/spin"_fix_setforce.html allows to set the -components of the magnetic precession vectors (while erasing and -replacing the previously computed magnetic precession vectors on -the atom). -This command can be used to freeze the magnetic moment of certain -atoms in the simulation by zeroing their precession vector. - -The command "fix nve/spin"_fix_nve_spin.html can be used to -perform a symplectic integration of the combined dynamics of spins -and atomic motions. - -The minimization style "min/spin"_min_spin.html can be applied -to the spins to perform a minimization of the spin configuration. - - -All the computed magnetic properties can be output by two main -commands. The first one is "compute spin"_compute_spin.html, that -enables to evaluate magnetic averaged quantities, such as the total -magnetization of the system along x, y, or z, the spin temperature, or -the magnetic energy. The second command is "compute -property/atom"_compute_property_atom.html. It enables to output all the -per atom magnetic quantities. Typically, the orientation of a given -magnetic spin, or the magnetic force acting on this spin. - -:line - -:link(Tranchida) -[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, -Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/txt/Howto_temperature.txt b/doc/txt/Howto_temperature.txt deleted file mode 100644 index 896cc96a40..0000000000 --- a/doc/txt/Howto_temperature.txt +++ /dev/null @@ -1,43 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Calculate temperature :h3 - -Temperature is computed as kinetic energy divided by some number of -degrees of freedom (and the Boltzmann constant). Since kinetic energy -is a function of particle velocity, there is often a need to -distinguish between a particle's advection velocity (due to some -aggregate motion of particles) and its thermal velocity. The sum of -the two is the particle's total velocity, but the latter is often what -is wanted to compute a temperature. - -LAMMPS has several options for computing temperatures, any of which -can be used in "thermostatting"_Howto_thermostat.html and -"barostatting"_Howto_barostat.html. These "compute -commands"_compute.html calculate temperature: - -"compute temp"_compute_temp.html -"compute temp/sphere"_compute_temp_sphere.html -"compute temp/asphere"_compute_temp_asphere.html -"compute temp/com"_compute_temp_com.html -"compute temp/deform"_compute_temp_deform.html -"compute temp/partial"_compute_temp_partial.html -"compute temp/profile"_compute_temp_profile.html -"compute temp/ramp"_compute_temp_ramp.html -"compute temp/region"_compute_temp_region.html :ul - -All but the first 3 calculate velocity biases directly (e.g. advection -velocities) that are removed when computing the thermal temperature. -"Compute temp/sphere"_compute_temp_sphere.html and "compute -temp/asphere"_compute_temp_asphere.html compute kinetic energy for -finite-size particles that includes rotational degrees of freedom. -They both allow for velocity biases indirectly, via an optional extra -argument which is another temperature compute that subtracts a -velocity bias. This allows the translational velocity of spherical or -aspherical particles to be adjusted in prescribed ways. diff --git a/doc/txt/Howto_thermostat.txt b/doc/txt/Howto_thermostat.txt deleted file mode 100644 index aebf4555a7..0000000000 --- a/doc/txt/Howto_thermostat.txt +++ /dev/null @@ -1,100 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Thermostats :h3 - -Thermostatting means controlling the temperature of particles in an MD -simulation. "Barostatting"_Howto_barostat.html means controlling the -pressure. Since the pressure includes a kinetic component due to -particle velocities, both these operations require calculation of the -temperature. Typically a target temperature (T) and/or pressure (P) -is specified by the user, and the thermostat or barostat attempts to -equilibrate the system to the requested T and/or P. - -Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one -case by a pair style. Several thermostatting fixes are available: -Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling -(temp/rescale). Dissipative particle dynamics (DPD) thermostatting -can be invoked via the {dpd/tstat} pair style: - -"fix nvt"_fix_nh.html -"fix nvt/sphere"_fix_nvt_sphere.html -"fix nvt/asphere"_fix_nvt_asphere.html -"fix nvt/sllod"_fix_nvt_sllod.html -"fix temp/berendsen"_fix_temp_berendsen.html -"fix temp/csvr"_fix_temp_csvr.html -"fix langevin"_fix_langevin.html -"fix temp/rescale"_fix_temp_rescale.html -"pair_style dpd/tstat"_pair_dpd.html :ul - -"Fix nvt"_fix_nh.html only thermostats the translational velocity of -particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except -that it subtracts out a velocity bias due to a deforming box and -integrates the SLLOD equations of motion. See the "Howto -nemd"_Howto_nemd.html doc page for further details. "Fix -nvt/sphere"_fix_nvt_sphere.html and "fix -nvt/asphere"_fix_nvt_asphere.html thermostat not only translation -velocities but also rotational velocities for spherical and aspherical -particles. - -NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-thermostat -discusses use of the SLLOD method and non-equilibrium MD (NEMD) -thermostatting generally, for both simple and complex fluids, -e.g. molecular systems. The latter can be tricky to do correctly. - -DPD thermostatting alters pairwise interactions in a manner analogous -to the per-particle thermostatting of "fix -langevin"_fix_langevin.html. - -Any of the thermostatting fixes can use "temperature -computes"_Howto_thermostat.html that remove bias which has two -effects. First, the current calculated temperature, which is compared -to the requested target temperature, is calculated with the velocity -bias removed. Second, the thermostat adjusts only the thermal -temperature component of the particle's velocities, which are the -velocities with the bias removed. The removed bias is then added back -to the adjusted velocities. See the doc pages for the individual -fixes and for the "fix_modify"_fix_modify.html command for -instructions on how to assign a temperature compute to a -thermostatting fix. For example, you can apply a thermostat to only -the x and z components of velocity by using it in conjunction with -"compute temp/partial"_compute_temp_partial.html. Of you could -thermostat only the thermal temperature of a streaming flow of -particles without affecting the streaming velocity, by using "compute -temp/profile"_compute_temp_profile.html. - -NOTE: Only the nvt fixes perform time integration, meaning they update -the velocities and positions of particles due to forces and velocities -respectively. The other thermostat fixes only adjust velocities; they -do NOT perform time integration updates. Thus they should be used in -conjunction with a constant NVE integration fix such as these: - -"fix nve"_fix_nve.html -"fix nve/sphere"_fix_nve_sphere.html -"fix nve/asphere"_fix_nve_asphere.html :ul - -Thermodynamic output, which can be setup via the -"thermo_style"_thermo_style.html command, often includes temperature -values. As explained on the doc page for the -"thermo_style"_thermo_style.html command, the default temperature is -setup by the thermo command itself. It is NOT the temperature -associated with any thermostatting fix you have defined or with any -compute you have defined that calculates a temperature. The doc pages -for the thermostatting fixes explain the ID of the temperature compute -they create. Thus if you want to view these temperatures, you need to -specify them explicitly via the "thermo_style -custom"_thermo_style.html command. Or you can use the -"thermo_modify"_thermo_modify.html command to re-define what -temperature compute is used for default thermodynamic output. - -:line - -:link(Daivis-thermostat) -[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book), -Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/txt/Howto_tip3p.txt b/doc/txt/Howto_tip3p.txt deleted file mode 100644 index a34577c5e1..0000000000 --- a/doc/txt/Howto_tip3p.txt +++ /dev/null @@ -1,73 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -TIP3P water model :h3 - -The TIP3P water model as implemented in CHARMM -"(MacKerell)"_#howto-tip3p specifies a 3-site rigid water molecule with -charges and Lennard-Jones parameters assigned to each of the 3 atoms. -In LAMMPS the "fix shake"_fix_shake.html command can be used to hold -the two O-H bonds and the H-O-H angle rigid. A bond style of -{harmonic} and an angle style of {harmonic} or {charmm} should also be -used. - -These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid TIP3P-CHARMM model with a -cutoff. The K values can be used if a flexible TIP3P model (without -fix shake) is desired. If the LJ epsilon and sigma for HH and OH are -set to 0.0, it corresponds to the original 1983 TIP3P model -"(Jorgensen)"_#Jorgensen1. - -O mass = 15.9994 -H mass = 1.008 -O charge = -0.834 -H charge = 0.417 -LJ epsilon of OO = 0.1521 -LJ sigma of OO = 3.1507 -LJ epsilon of HH = 0.0460 -LJ sigma of HH = 0.4000 -LJ epsilon of OH = 0.0836 -LJ sigma of OH = 1.7753 -K of OH bond = 450 -r0 of OH bond = 0.9572 -K of HOH angle = 55 -theta of HOH angle = 104.52 :all(b),p - -These are the parameters to use for TIP3P with a long-range Coulombic -solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for -details: - -O mass = 15.9994 -H mass = 1.008 -O charge = -0.830 -H charge = 0.415 -LJ epsilon of OO = 0.102 -LJ sigma of OO = 3.188 -LJ epsilon, sigma of OH, HH = 0.0 -K of OH bond = 450 -r0 of OH bond = 0.9572 -K of HOH angle = 55 -theta of HOH angle = 104.52 :all(b),p - -Wikipedia also has a nice article on "water -models"_http://en.wikipedia.org/wiki/Water_model. - -:line - -:link(howto-tip3p) -[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). - -:link(Jorgensen1) -[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem -Phys, 79, 926 (1983). - -:link(Price1) -[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004). - diff --git a/doc/txt/Howto_tip4p.txt b/doc/txt/Howto_tip4p.txt deleted file mode 100644 index 9f7f141314..0000000000 --- a/doc/txt/Howto_tip4p.txt +++ /dev/null @@ -1,112 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -TIP4P water model :h3 - -The four-point TIP4P rigid water model extends the traditional -three-point TIP3P model by adding an additional site, usually -massless, where the charge associated with the oxygen atom is placed. -This site M is located at a fixed distance away from the oxygen along -the bisector of the HOH bond angle. A bond style of {harmonic} and an -angle style of {harmonic} or {charmm} should also be used. - -A TIP4P model is run with LAMMPS using either this command -for a cutoff model: - -"pair_style lj/cut/tip4p/cut"_pair_lj.html - -or these two commands for a long-range model: - -"pair_style lj/cut/tip4p/long"_pair_lj.html -"kspace_style pppm/tip4p"_kspace_style.html :ul - -For both models, the bond lengths and bond angles should be held fixed -using the "fix shake"_fix_shake.html command. - -These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid TIP4P model with a cutoff -"(Jorgensen)"_#Jorgensen5. Note that the OM distance is specified in -the "pair_style"_pair_style.html command, not as part of the pair -coefficients. - -O mass = 15.9994 -H mass = 1.008 -O charge = -1.040 -H charge = 0.520 -r0 of OH bond = 0.9572 -theta of HOH angle = 104.52 -OM distance = 0.15 -LJ epsilon of O-O = 0.1550 -LJ sigma of O-O = 3.1536 -LJ epsilon, sigma of OH, HH = 0.0 -Coulombic cutoff = 8.5 :all(b),p - -For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005); -http://dx.doi.org/10.1063/1.1931662) these values can be used: - -O mass = 15.9994 -H mass = 1.008 -O charge = -1.1794 -H charge = 0.5897 -r0 of OH bond = 0.9572 -theta of HOH angle = 104.52 -OM distance = 0.1577 -LJ epsilon of O-O = 0.21084 -LJ sigma of O-O = 3.1668 -LJ epsilon, sigma of OH, HH = 0.0 -Coulombic cutoff = 8.5 :all(b),p - -For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005); -http://dx.doi.org/10.1063/1.2121687), these values can be used: - -O mass = 15.9994 -H mass = 1.008 -O charge = -1.1128 -H charge = 0.5564 -r0 of OH bond = 0.9572 -theta of HOH angle = 104.52 -OM distance = 0.1546 -LJ epsilon of O-O = 0.1852 -LJ sigma of O-O = 3.1589 -LJ epsilon, sigma of OH, HH = 0.0 -Coulombic cutoff = 8.5 :all(b),p - -These are the parameters to use for TIP4P with a long-range Coulombic -solver (e.g. Ewald or PPPM in LAMMPS): - -O mass = 15.9994 -H mass = 1.008 -O charge = -1.0484 -H charge = 0.5242 -r0 of OH bond = 0.9572 -theta of HOH angle = 104.52 -OM distance = 0.1250 -LJ epsilon of O-O = 0.16275 -LJ sigma of O-O = 3.16435 -LJ epsilon, sigma of OH, HH = 0.0 :all(b),p - -Note that the when using the TIP4P pair style, the neighbor list -cutoff for Coulomb interactions is effectively extended by a distance -2 * (OM distance), to account for the offset distance of the -fictitious charges on O atoms in water molecules. Thus it is -typically best in an efficiency sense to use a LJ cutoff >= Coulomb -cutoff + 2*(OM distance), to shrink the size of the neighbor list. -This leads to slightly larger cost for the long-range calculation, so -you can test the trade-off for your model. The OM distance and the LJ -and Coulombic cutoffs are set in the "pair_style -lj/cut/tip4p/long"_pair_lj.html command. - -Wikipedia also has a nice article on "water -models"_http://en.wikipedia.org/wiki/Water_model. - -:line - -:link(Jorgensen5) -[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem -Phys, 79, 926 (1983). diff --git a/doc/txt/Howto_triclinic.txt b/doc/txt/Howto_triclinic.txt deleted file mode 100644 index 2c5834a396..0000000000 --- a/doc/txt/Howto_triclinic.txt +++ /dev/null @@ -1,213 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -Triclinic (non-orthogonal) simulation boxes :h3 - -By default, LAMMPS uses an orthogonal simulation box to encompass the -particles. The "boundary"_boundary.html command sets the boundary -conditions of the box (periodic, non-periodic, etc). The orthogonal -box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors -starting from the origin given by [a] = (xhi-xlo,0,0); [b] = -(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters -(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box -is created, e.g. by the "create_box"_create_box.html or -"read_data"_read_data.html or "read_restart"_read_restart.html -commands. Additionally, LAMMPS defines box size parameters lx,ly,lz -where lx = xhi-xlo, and similarly in the y and z dimensions. The 6 -parameters, as well as lx,ly,lz, can be output via the "thermo_style -custom"_thermo_style.html command. - -LAMMPS also allows simulations to be performed in triclinic -(non-orthogonal) simulation boxes shaped as a parallelepiped with -triclinic symmetry. The parallelepiped has its "origin" at -(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the -origin given by [a] = (xhi-xlo,0,0); [b] = (xy,yhi-ylo,0); [c] = -(xz,yz,zhi-zlo). {xy,xz,yz} can be 0.0 or positive or negative values -and are called "tilt factors" because they are the amount of -displacement applied to faces of an originally orthogonal box to -transform it into the parallelepiped. In LAMMPS the triclinic -simulation box edge vectors [a], [b], and [c] cannot be arbitrary -vectors. As indicated, [a] must lie on the positive x axis. [b] must -lie in the xy plane, with strictly positive y component. [c] may have -any orientation with strictly positive z component. The requirement -that [a], [b], and [c] have strictly positive x, y, and z components, -respectively, ensures that [a], [b], and [c] form a complete -right-handed basis. These restrictions impose no loss of generality, -since it is possible to rotate/invert any set of 3 crystal basis -vectors so that they conform to the restrictions. - -For example, assume that the 3 vectors [A],[B],[C] are the edge -vectors of a general parallelepiped, where there is no restriction on -[A],[B],[C] other than they form a complete right-handed basis i.e. -[A] x [B] . [C] > 0. The equivalent LAMMPS [a],[b],[c] are a linear -rotation of [A], [B], and [C] and can be computed as follows: - -:c,image(Eqs/transform.jpg) - -where A = | [A] | indicates the scalar length of [A]. The hat symbol (^) -indicates the corresponding unit vector. {beta} and {gamma} are angles -between the vectors described below. Note that by construction, -[a], [b], and [c] have strictly positive x, y, and z components, respectively. -If it should happen that -[A], [B], and [C] form a left-handed basis, then the above equations -are not valid for [c]. In this case, it is necessary -to first apply an inversion. This can be achieved -by interchanging two basis vectors or by changing the sign of one of them. - -For consistency, the same rotation/inversion applied to the basis vectors -must also be applied to atom positions, velocities, -and any other vector quantities. -This can be conveniently achieved by first converting to -fractional coordinates in the -old basis and then converting to distance coordinates in the new basis. -The transformation is given by the following equation: - -:c,image(Eqs/rotate.jpg) - -where {V} is the volume of the box, [X] is the original vector quantity and -[x] is the vector in the LAMMPS basis. - -There is no requirement that a triclinic box be periodic in any -dimension, though it typically should be in at least the 2nd dimension -of the tilt (y in xy) if you want to enforce a shift in periodic -boundary conditions across that boundary. Some commands that work -with triclinic boxes, e.g. the "fix deform"_fix_deform.html and "fix -npt"_fix_nh.html commands, require periodicity or non-shrink-wrap -boundary conditions in specific dimensions. See the command doc pages -for details. - -The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the -time the simulation box is created. This happens in one of 3 ways. -If the "create_box"_create_box.html command is used with a region of -style {prism}, then a triclinic box is setup. See the -"region"_region.html command for details. If the -"read_data"_read_data.html command is used to define the simulation -box, and the header of the data file contains a line with the "xy xz -yz" keyword, then a triclinic box is setup. See the -"read_data"_read_data.html command for details. Finally, if the -"read_restart"_read_restart.html command reads a restart file which -was written from a simulation using a triclinic box, then a triclinic -box will be setup for the restarted simulation. - -Note that you can define a triclinic box with all 3 tilt factors = -0.0, so that it is initially orthogonal. This is necessary if the box -will become non-orthogonal, e.g. due to the "fix npt"_fix_nh.html or -"fix deform"_fix_deform.html commands. Alternatively, you can use the -"change_box"_change_box.html command to convert a simulation box from -orthogonal to triclinic and vice versa. - -As with orthogonal boxes, LAMMPS defines triclinic box size parameters -lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions. -The 9 parameters, as well as lx,ly,lz, can be output via the -"thermo_style custom"_thermo_style.html command. - -To avoid extremely tilted boxes (which would be computationally -inefficient), LAMMPS normally requires that no tilt factor can skew -the box more than half the distance of the parallel box length, which -is the 1st dimension in the tilt factor (x for xz). This is required -both when the simulation box is created, e.g. via the -"create_box"_create_box.html or "read_data"_read_data.html commands, -as well as when the box shape changes dynamically during a simulation, -e.g. via the "fix deform"_fix_deform.html or "fix npt"_fix_nh.html -commands. - -For example, if xlo = 2 and xhi = 12, then the x box length is 10 and -the xy tilt factor must be between -5 and 5. Similarly, both xz and -yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is -not a limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are geometrically all equivalent. If the box tilt exceeds this -limit during a dynamics run (e.g. via the "fix deform"_fix_deform.html -command), then the box is "flipped" to an equivalent shape with a tilt -factor within the bounds, so the run can continue. See the "fix -deform"_fix_deform.html doc page for further details. - -One exception to this rule is if the 1st dimension in the tilt -factor (x for xy) is non-periodic. In that case, the limits on the -tilt factor are not enforced, since flipping the box in that dimension -does not change the atom positions due to non-periodicity. In this -mode, if you tilt the system to extreme angles, the simulation will -simply become inefficient, due to the highly skewed simulation box. - -The limitation on not creating a simulation box with a tilt factor -skewing the box more than half the distance of the parallel box length -can be overridden via the "box"_box.html command. Setting the {tilt} -keyword to {large} allows any tilt factors to be specified. - -Box flips that may occur using the "fix deform"_fix_deform.html or -"fix npt"_fix_nh.html commands can be turned off using the {flip no} -option with either of the commands. - -Note that if a simulation box has a large tilt factor, LAMMPS will run -less efficiently, due to the large volume of communication needed to -acquire ghost atoms around a processor's irregular-shaped sub-domain. -For extreme values of tilt, LAMMPS may also lose atoms and generate an -error. - -Triclinic crystal structures are often defined using three lattice -constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and -{gamma}. Note that in this nomenclature, the a, b, and c lattice -constants are the scalar lengths of the edge vectors [a], [b], and [c] -defined above. The relationship between these 6 quantities -(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) = -(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows: - -:c,image(Eqs/box.jpg) - -The inverse relationship can be written as follows: - -:c,image(Eqs/box_inverse.jpg) - -The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed -out or accessed by computes using the -"thermo_style custom"_thermo_style.html keywords -{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma}, -respectively. - -As discussed on the "dump"_dump.html command doc page, when the BOX -BOUNDS for a snapshot is written to a dump file for a triclinic box, -an orthogonal bounding box which encloses the triclinic simulation box -is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic -box, formatted as follows: - -ITEM: BOX BOUNDS xy xz yz -xlo_bound xhi_bound xy -ylo_bound yhi_bound xz -zlo_bound zhi_bound yz :pre - -This bounding box is convenient for many visualization programs and is -calculated from the 9 triclinic box parameters -(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows: - -xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz) -xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz) -ylo_bound = ylo + MIN(0.0,yz) -yhi_bound = yhi + MAX(0.0,yz) -zlo_bound = zlo -zhi_bound = zhi :pre - -These formulas can be inverted if you need to convert the bounding box -back into the triclinic box parameters, e.g. xlo = xlo_bound - -MIN(0.0,xy,xz,xy+xz). - -One use of triclinic simulation boxes is to model solid-state crystals -with triclinic symmetry. The "lattice"_lattice.html command can be -used with non-orthogonal basis vectors to define a lattice that will -tile a triclinic simulation box via the -"create_atoms"_create_atoms.html command. - -A second use is to run Parrinello-Rahman dynamics via the "fix -npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt -factors to compensate for off-diagonal components of the pressure -tensor. The analog for an "energy minimization"_minimize.html is -the "fix box/relax"_fix_box_relax.html command. - -A third use is to shear a bulk solid to study the response of the -material. The "fix deform"_fix_deform.html command can be used for -this purpose. It allows dynamic control of the xy, xz, yz tilt -factors as a simulation runs. This is discussed in the next section -on non-equilibrium MD (NEMD) simulations. diff --git a/doc/txt/Howto_viscosity.txt b/doc/txt/Howto_viscosity.txt deleted file mode 100644 index c87c8a3b84..0000000000 --- a/doc/txt/Howto_viscosity.txt +++ /dev/null @@ -1,144 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Calculate viscosity :h3 - -The shear viscosity eta of a fluid can be measured in at least 5 ways -using various options in LAMMPS. See the examples/VISCOSITY directory -for scripts that implement the 5 methods discussed here for a simple -Lennard-Jones fluid model. Also, see the "Howto -kappa"_Howto_kappa.html doc page for an analogous discussion for -thermal conductivity. - -Eta is a measure of the propensity of a fluid to transmit momentum in -a direction perpendicular to the direction of velocity or momentum -flow. Alternatively it is the resistance the fluid has to being -sheared. It is given by - -J = -eta grad(Vstream) - -where J is the momentum flux in units of momentum per area per time. -and grad(Vstream) is the spatial gradient of the velocity of the fluid -moving in another direction, normal to the area through which the -momentum flows. Viscosity thus has units of pressure-time. - -The first method is to perform a non-equilibrium MD (NEMD) simulation -by shearing the simulation box via the "fix deform"_fix_deform.html -command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to -thermostat the fluid via the SLLOD equations of motion. -Alternatively, as a second method, one or more moving walls can be -used to shear the fluid in between them, again with some kind of -thermostat that modifies only the thermal (non-shearing) components of -velocity to prevent the fluid from heating up. - -NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-viscosity -discusses use of the SLLOD method and non-equilibrium MD (NEMD) -thermostatting generally, for both simple and complex fluids, -e.g. molecular systems. The latter can be tricky to do correctly. - -In both cases, the velocity profile setup in the fluid by this -procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html -command, which determines grad(Vstream) in the equation above. -E.g. the derivative in the y-direction of the Vx component of fluid -motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of -the pressure or stress tensor, as calculated by the "compute -pressure"_compute_pressure.html command, can also be monitored, which -is the J term in the equation above. See the "Howto -nemd"_Howto_nemd.html doc page for details on NEMD simulations. - -The third method is to perform a reverse non-equilibrium MD simulation -using the "fix viscosity"_fix_viscosity.html command which implements -the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is -swapped between atoms in two different layers of the simulation box in -a different dimension. This induces a velocity gradient which can be -monitored with the "fix ave/chunk"_fix_ave_chunk.html command. -The fix tallies the cumulative momentum transfer that it performs. -See the "fix viscosity"_fix_viscosity.html command for details. - -The fourth method is based on the Green-Kubo (GK) formula which -relates the ensemble average of the auto-correlation of the -stress/pressure tensor to eta. This can be done in a fully -equilibrated simulation which is in contrast to the two preceding -non-equilibrium methods, where momentum flows continuously through the -simulation box. - -Here is an example input script that calculates the viscosity of -liquid Ar via the GK formalism: - -# Sample LAMMPS input script for viscosity of liquid Ar :pre - -units real -variable T equal 86.4956 -variable V equal vol -variable dt equal 4.0 -variable p equal 400 # correlation length -variable s equal 5 # sample interval -variable d equal $p*$s # dump interval :pre - -# convert from LAMMPS real units to SI :pre - -variable kB equal 1.3806504e-23 # \[J/K\] Boltzmann -variable atm2Pa equal 101325.0 -variable A2m equal 1.0e-10 -variable fs2s equal 1.0e-15 -variable convert equal $\{atm2Pa\}*$\{atm2Pa\}*$\{fs2s\}*$\{A2m\}*$\{A2m\}*$\{A2m\} :pre - -# setup problem :pre - -dimension 3 -boundary p p p -lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 -region box block 0 4 0 4 0 4 -create_box 1 box -create_atoms 1 box -mass 1 39.948 -pair_style lj/cut 13.0 -pair_coeff * * 0.2381 3.405 -timestep $\{dt\} -thermo $d :pre - -# equilibration and thermalization :pre - -velocity all create $T 102486 mom yes rot yes dist gaussian -fix NVT all nvt temp $T $T 10 drag 0.2 -run 8000 :pre - -# viscosity calculation, switch to NVE if desired :pre - -#unfix NVT -#fix NVE all nve :pre - -reset_timestep 0 -variable pxy equal pxy -variable pxz equal pxz -variable pyz equal pyz -fix SS all ave/correlate $s $p $d & - v_pxy v_pxz v_pyz type auto file S0St.dat ave running -variable scale equal $\{convert\}/($\{kB\}*$T)*$V*$s*$\{dt\} -variable v11 equal trap(f_SS\[3\])*$\{scale\} -variable v22 equal trap(f_SS\[4\])*$\{scale\} -variable v33 equal trap(f_SS\[5\])*$\{scale\} -thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33 -run 100000 -variable v equal (v_v11+v_v22+v_v33)/3.0 -variable ndens equal count(all)/vol -print "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre - -The fifth method is related to the above Green-Kubo method, -but uses the Einstein formulation, analogous to the Einstein -mean-square-displacement formulation for self-diffusivity. The -time-integrated momentum fluxes play the role of Cartesian -coordinates, whose mean-square displacement increases linearly -with time at sufficiently long times. - -:line - -:link(Daivis-viscosity) -[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book), -Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/txt/Howto_viz.txt b/doc/txt/Howto_viz.txt deleted file mode 100644 index 00c329c50b..0000000000 --- a/doc/txt/Howto_viz.txt +++ /dev/null @@ -1,40 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Visualize LAMMPS snapshots :h3 - -LAMMPS itself does not do visualization, but snapshots from LAMMPS -simulations can be visualized (and analyzed) in a variety of ways. - -Mention dump image and dump movie. - -LAMMPS snapshots are created by the "dump"_dump.html command which can -create files in several formats. The native LAMMPS dump format is a -text file (see "dump atom" or "dump custom") which can be visualized -by several popular visualization tools. The "dump -image"_dump_image.html and "dump movie"_dump_image.html styles can -output internally rendered images and convert a sequence of them to a -movie during the MD run. Several programs included with LAMMPS as -auxiliary tools can convert between LAMMPS format files and other -formats. See the "Tools"_Tools.html doc page for details. - -A Python-based toolkit distributed by our group can read native LAMMPS -dump files, including custom dump files with additional columns of -user-specified atom information, and convert them to various formats -or pipe them into visualization software directly. See the "Pizza.py -WWW site"_pizza for details. Specifically, Pizza.py can convert -LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats. -Pizza.py can pipe LAMMPS dump files directly into the Raster3d and -RasMol visualization programs. Pizza.py has tools that do interactive -3d OpenGL visualization and one that creates SVG images of dump file -snapshots. - -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) -:link(ensight,http://www.ensight.com) -:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) diff --git a/doc/txt/Howto_walls.txt b/doc/txt/Howto_walls.txt deleted file mode 100644 index 4e4f0c5d6f..0000000000 --- a/doc/txt/Howto_walls.txt +++ /dev/null @@ -1,81 +0,0 @@ -"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Walls :h3 - -Walls in an MD simulation are typically used to bound particle motion, -i.e. to serve as a boundary condition. - -Walls in LAMMPS can be of rough (made of particles) or idealized -surfaces. Ideal walls can be smooth, generating forces only in the -normal direction, or frictional, generating forces also in the -tangential direction. - -Rough walls, built of particles, can be created in various ways. The -particles themselves can be generated like any other particle, via the -"lattice"_lattice.html and "create_atoms"_create_atoms.html commands, -or read in via the "read_data"_read_data.html command. - -Their motion can be constrained by many different commands, so that -they do not move at all, move together as a group at constant velocity -or in response to a net force acting on them, move in a prescribed -fashion (e.g. rotate around a point), etc. Note that if a time -integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html -is not used with the group that contains wall particles, their -positions and velocities will not be updated. - -"fix aveforce"_fix_aveforce.html - set force on particles to average value, so they move together -"fix setforce"_fix_setforce.html - set force on particles to a value, e.g. 0.0 -"fix freeze"_fix_freeze.html - freeze particles for use as granular walls -"fix nve/noforce"_fix_nve_noforce.html - advect particles by their velocity, but without force -"fix move"_fix_move.html - prescribe motion of particles by a linear velocity, oscillation, rotation, variable :ul - -The "fix move"_fix_move.html command offers the most generality, since -the motion of individual particles can be specified with -"variable"_variable.html formula which depends on time and/or the -particle position. - -For rough walls, it may be useful to turn off pairwise interactions -between wall particles via the "neigh_modify -exclude"_neigh_modify.html command. - -Rough walls can also be created by specifying frozen particles that do -not move and do not interact with mobile particles, and then tethering -other particles to the fixed particles, via a "bond"_bond_style.html. -The bonded particles do interact with other mobile particles. - -Idealized walls can be specified via several fix commands. "Fix -wall/gran"_fix_wall_gran.html creates frictional walls for use with -granular particles; all the other commands create smooth walls. - -"fix wall/reflect"_fix_wall_reflect.html - reflective flat walls -"fix wall/lj93"_fix_wall.html - flat walls, with Lennard-Jones 9/3 potential -"fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential -"fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential -"fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential -"fix wall/morse"_fix_wall.html - flat walls, with Morse potential -"fix wall/region"_fix_wall_region.html - use region surface as wall -"fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul - -The {lj93}, {lj126}, {colloid}, {harmonic}, and {morse} styles all -allow the flat walls to move with a constant velocity, or oscillate in -time. The "fix wall/region"_fix_wall_region.html command offers the -most generality, since the region surface is treated as a wall, and -the geometry of the region can be a simple primitive volume (e.g. a -sphere, or cube, or plane), or a complex volume made from the union -and intersection of primitive volumes. "Regions"_region.html can also -specify a volume "interior" or "exterior" to the specified primitive -shape or {union} or {intersection}. "Regions"_region.html can also be -"dynamic" meaning they move with constant velocity, oscillate, or -rotate. - -The only frictional idealized walls currently in LAMMPS are flat or -curved surfaces specified by the "fix wall/gran"_fix_wall_gran.html -command. At some point we plan to allow regoin surfaces to be used as -frictional walls, as well as triangulated surfaces. diff --git a/doc/txt/Install_git.txt b/doc/txt/Install_git.txt deleted file mode 100644 index 19decde516..0000000000 --- a/doc/txt/Install_git.txt +++ /dev/null @@ -1,113 +0,0 @@ -"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Download source via Git :h3 - -All LAMMPS development is coordinated through the "LAMMPS GitHub -site". If you clone the LAMMPS repository onto your local machine, it -has several advantages: - -You can stay current with changes to LAMMPS with a single git -command. :ulb,l - -You can create your own development branches to add code to LAMMPS. :l - -You can submit your new features back to GitHub for inclusion in -LAMMPS. :l,ule - -You must have "Git"_git installed on your system to communicate with -the public Git server for LAMMPS. - -IMPORTANT NOTE: As of Oct 2016, the official home of public LAMMPS -development is on GitHub. The previously advertised LAMMPS git -repositories on git.lammps.org and bitbucket.org are now deprecated, -may not be up-to-date, and may go away at any time. - -:link(git,http://git-scm.com) - -You can follow LAMMPS development on 3 different Git branches: - -[stable] : this branch is updated with every stable release -[unstable] : this branch is updated with every patch release -[master] : this branch continuously follows ongoing development :ul - -To access the Git repositories on your box, use the clone command to -create a local copy of the LAMMPS repository with a command like: - -git clone -b unstable https://github.com/lammps/lammps.git mylammps :pre - -where "mylammps" is the name of the directory you wish to create on -your machine and "unstable" is one of the 3 branches listed above. -(Note that you actually download all 3 branches; you can switch -between them at any time using "git checkout ".) - -Once the command completes, your directory will contain the same files -as if you unpacked a current LAMMPS tarball, with the exception, that -the HTML documentation files are not included. They can be fetched -from the LAMMPS website by typing "make fetch" in the doc directory. -Or they can be generated from the content provided in doc/src by -typing "make html" from the doc directory. - -After initial cloning, as bug fixes and new features are added to -LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay -up-to-date by typing the following Git commands from within the -"mylammps" directory: - -git checkout unstable # not needed if you always stay in this branch -git checkout stable # use one of the 3 checkout commands -git checkout master -git pull :pre - -Doing a "pull" will not change any files you have added to the LAMMPS -directory structure. It will also not change any existing LAMMPS -files you have edited, unless those files have changed in the -repository. In that case, Git will attempt to merge the new -repository file with your version of the file and tell you if there -are any conflicts. See the Git documentation for details. - -If you want to access a particular previous release version of LAMMPS, -you can instead "checkout" any version with a published tag. See the -output of "git tag -l" for the list of tags. The Git command to do -this is as follows. - -git checkout tagID :pre - -Stable versions and what tagID to use for a particular stable version -are discussed on "this page"_Errors_bugs.html. Note that this command -will print some warnings, because in order to get back to the latest -revision and to be able to update with "git pull" again, you first -will need to first type "git checkout unstable" (or check out any -other desired branch). - -Once you have updated your local files with a "git pull" (or "git -checkout"), you still need to re-build LAMMPS if any source files have -changed. To do this, you should cd to the src directory and type: - -make purge # remove any deprecated src files -make package-update # sync package files with src files -make foo # re-build for your machine (mpi, serial, etc) :pre - -just as described on the "Install patch"_Install_patch.html doc page, -after a patch has been installed. - -IMPORTANT NOTE: If you wish to edit/change a src file that is from a -package, you should edit the version of the file inside the package -sub-directory with src, then re-install the package. The version in -the src dir is merely a copy and will be wiped out if you type "make -package-update". - -IMPORTANT NOTE: The GitHub servers support both the "git://" and -"https://" access protocols for anonymous read-only access. If you -have a correspondingly configured GitHub account, you may also use SSH -with "git@github.com:/lammps/lammps.git". - -The LAMMPS GitHub project is managed by Christoph Junghans (LANL, -junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at -gmail.com) and Richard Berger (Temple U, richard.berger at -temple.edu). diff --git a/doc/txt/Install_linux.txt b/doc/txt/Install_linux.txt deleted file mode 100644 index 9aebd30c05..0000000000 --- a/doc/txt/Install_linux.txt +++ /dev/null @@ -1,199 +0,0 @@ -"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Download an executable for Linux :h3 - -Binaries are available for different versions of Linux: - -"Pre-built Ubuntu Linux executables"_#ubuntu -"Pre-built Fedora Linux executables"_#fedora -"Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel -"Pre-built OpenSuse Linux executables"_#opensuse -"Gentoo Linux executable"_#gentoo -"Arch Linux build-script"_#arch :all(b) - -:line - -Pre-built Ubuntu Linux executables :h4,link(ubuntu) - -A pre-built LAMMPS executable suitable for running on the latest -Ubuntu Linux versions, can be downloaded as a Debian package. This -allows you to install LAMMPS with a single command, and stay -up-to-date with the current version of LAMMPS by simply updating your -operating system. - -To install the appropriate personal-package archive (PPA), do the -following once: - -sudo add-apt-repository ppa:gladky-anton/lammps -sudo apt-get update :pre - -To install LAMMPS do the following once: - -sudo apt-get install lammps-daily :pre - -This downloads an executable named "lmp_daily" to your box, which -can then be used in the usual way to run input scripts: - -lmp_daily -in in.lj :pre - -To update LAMMPS to the most current version, do the following: - -sudo apt-get update :pre - -which will also update other packages on your system. - -To get a copy of the current documentation and examples: - -sudo apt-get install lammps-daily-doc :pre - -which will download the doc files in -/usr/share/doc/lammps-daily-doc/doc and example problems in -/usr/share/doc/lammps-doc/examples. - -Note that you may still wish to download the tarball to get potential -files and auxiliary tools. - -To un-install LAMMPS, do the following: - -sudo apt-get remove lammps-daily :pre - -Note that the lammps-daily executable is built with the following -sequence of make commands, as if you had done the same with the -unpacked tarball files in the src directory: - -make yes-all; make no-lib; make openmpi - -Thus it builds with FFTW3 and OpenMPI. - -Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this -Ubuntu package capability. - -:line - -Pre-built Fedora Linux executables :h4,link(fedora) - -Pre-built LAMMPS packages for stable releases are available -in the Fedora Linux distribution as of version 28. The packages -can be installed via the dnf package manager. There are 3 basic -varieties (lammps = no MPI, lammps-mpich = MPICH MPI library, -lammps-openmpi = OpenMPI MPI library) and for each support for -linking to the C library interface (lammps-devel, lammps-mpich-devel, -lammps-openmpi-devel), the header for compiling programs using -the C library interface (lammps-headers), and the LAMMPS python -module for Python 3. All packages can be installed at the same -time and the name of the LAMMPS executable is {lmp} and {lmp_openmpi} -or {lmp_mpich} respectively. By default, {lmp} will refer to the -serial executable, unless one of the MPI environment modules is loaded -("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64"). -Then the corresponding parallel LAMMPS executable can be used. -The same mechanism applies when loading the LAMMPS python module. - -To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do: - -dnf install lammps-openmpi -module load mpi/openmpi-x86_64 -mpirun -np 2 lmp -in in.lj :pre - -The "dnf install" command is needed only once. In case of a new LAMMPS -stable release, "dnf update" will automatically update to the newer -version as soon at the RPM files are built and uploaded to the download -mirrors. The "module load" command is needed once per (shell) session -or shell terminal instance, unless it is automatically loaded from the -shell profile. - -Please use "lmp -help" to see which compilation options, packages, -and styles are included in the binary. - -Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora. - -:line - -Pre-built EPEL Linux executable :h4,link(epel) - -Pre-built LAMMPS packages for stable releases are available -in the "Extra Packages for Enterprise Linux (EPEL) repository"_https://fedoraproject.org/wiki/EPEL -for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x -and compatible Linux distributions. Names of packages, executable, -and content are the same as described above for Fedora Linux. -But RHEL/CentOS 7.x uses the "yum" package manager instead of "dnf" -in Fedora 28. - -Please use "lmp -help" to see which compilation options, packages, -and styles are included in the binary. - -Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL. - -:line - -Pre-built OpenSuse Linux executable :h4,link(opensuse) - -A pre-built LAMMPS package for stable releases is available -in OpenSuse as of Leap 15.0. You can install the package with: - -zypper install lammps :pre - -This includes support for OpenMPI. The name of the LAMMPS executable -is {lmp}. Thus to run an input in parallel on 2 CPUs you would do: - -mpirun -np 2 lmp -in in.lj :pre - -Please use "lmp -help" to see which compilation options, packages, -and styles are included in the binary. - -Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse. - -:line - -Gentoo Linux executable :h4,link(gentoo) - -LAMMPS is part of Gentoo's main package tree and can be installed by -typing: - -% emerge --ask lammps :pre - -Note that in Gentoo the LAMMPS source is downloaded and the package is -built on the your machine. - -Certain LAMMPS packages can be enable via USE flags, type - -% equery uses lammps :pre - -for details. - -Thanks to Nicolas Bock and Christoph Junghans (LANL) for setting up -this Gentoo capability. - -:line - -Archlinux build-script :h4,link(arch) - -LAMMPS is available via Arch's unofficial Arch User repository (AUR). - -There are three scripts available, named lammps, lammps-beta and lammps-git. -They respectively package the stable, patch and git releases. - -To install, you will need to have the git package installed. You may use -any of the above names in-place of lammps. - -$ git clone https://aur.archlinux.org/lammps.git :pre -$ cd lammps :pre -$ makepkg -s :pre -# makepkg -i :pre - -To update, you may repeat the above, or change into the cloned directory, -and execute the following, after which, if there are any changes, you may -use makepkg as above. - -$ git pull :pre - -Alternatively, you may use an AUR helper to install these packages. - -Note that the AUR provides build-scripts that download the source and -the build the package on your machine. diff --git a/doc/txt/Install_patch.txt b/doc/txt/Install_patch.txt deleted file mode 100644 index 40c272d1c8..0000000000 --- a/doc/txt/Install_patch.txt +++ /dev/null @@ -1,68 +0,0 @@ -"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Applying patches :h3 - -It is easy to stay current with the most recent LAMMPS patch releases -if you use Git or SVN to track LAMMPS development. Instructions for -how to stay current are on the "Install git"_Install_git.html and -"Install svn"_Install_svn.html doc pages. - -If you prefer to download a tarball, as described on the "Install -git"_Install_tarball.html doc page, you can stay current by -downloading "patch files" when new patch releases are made. A link to -a patch file is posted on the "bug and feature -page"_http://lammps.sandia.gov/bug.html of the LAMMPS website, along -with a list of changed files and details about what is in the new patch -release. This page explains how to apply the patch file to your local -LAMMPS directory. - -NOTE: You should not apply patch files to a local Git or SVN repo of -LAMMPS, only to an unpacked tarball. Use Git and SVN commands to -update repo versions of LAMMPS. - -Here are the steps to apply a patch file. Note that if your version -of LAMMPS is several patch releases behind, you need to apply all the -intervening patch files in succession to bring your version of LAMMPS -up to date. - -Download the patch file. You may have to shift-click in your browser -to download the file instead of display it. Patch files have names -like patch.12Dec16. :ulb,l - -Put the patch file in your top-level LAMMPS directory, where the -LICENSE and README files are. :l - -Apply the patch by typing the following command from your top-level -LAMMPS directory, where the redirected file is the name of the patch -file. :l - -patch -bp1 < patch.12Dec16 :pre - -A list of updated files print out to the screen. The -b switch -creates backup files of your originals (e.g. src/force.cpp.orig), so -you can manually undo the patch if something goes wrong. :l - -Type the following from the src directory, to enforce consistency -between the src and package directories. This is OK to do even if you -don't use one or more packages. If you are applying several patches -successively, you only need to type this once at the end. The purge -command removes deprecated src files if any were removed by the patch -from package sub-directories. :l - -make purge -make package-update :pre - -Re-build LAMMPS via the "make" command. :l,ule - -IMPORTANT NOTE: If you wish to edit/change a src file that is from a -package, you should edit the version of the file inside the package -sub-dir of src, then re-install the package. The version in the src -dir is merely a copy and will be wiped out if you type "make -package-update". diff --git a/doc/txt/Install_svn.txt b/doc/txt/Install_svn.txt deleted file mode 100644 index b701c0b04d..0000000000 --- a/doc/txt/Install_svn.txt +++ /dev/null @@ -1,88 +0,0 @@ -"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Download source via SVN :h3 - -IMPORTANT NOTE: As of Oct 2016, SVN support is now implemented via a -git-to-subversion interface service on GitHub and no longer through a -mirror of the internal SVN repository at Sandia. - -You must have the "Subversion (SVN) client software"_svn installed on -your system to communicate with the Git server in this mode. - -:link(svn,http://subversion.apache.org) - -You can follow LAMMPS development on 3 different SVN branches: - -[stable] : this branch is updated with every stable release -[unstable] : this branch is updated with every patch release -[master] : this branch continuously follows ongoing development :ul - -The corresponding command lines to do an initial checkout are as -follows. (Note that unlike Git, you must perform a separate checkout -into a unique directory for each of the 3 branches.) - -svn checkout https://github.com/lammps/lammps.git/branches/unstable mylammps -svn checkout https://github.com/lammps/lammps.git/branches/stable mylammps -svn checkout https://github.com/lammps/lammps.git/trunk mylammps :pre - -where "mylammps" is the name of the directory you wish to create on -your machine. - -Once the command completes, your directory will contain the same files -as if you unpacked a current LAMMPS tarball, with the exception, that -the HTML documentation files are not included. They can be fetched -from the LAMMPS website by typing "make fetch" in the doc directory. -Or they can be generated from the content provided in doc/src by -typing "make html" from the doc directory. - -After initial checkout, as bug fixes and new features are added to -LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay -up-to-date by typing the following SVN commands from within the -"mylammps" directory: - -svn update :pre - -You can also check if there are any updates by typing: - -svn -qu status :pre - -Doing an "update" will not change any files you have added to the -LAMMPS directory structure. It will also not change any existing -LAMMPS files you have edited, unless those files have changed in the -repository. In that case, SVN will attempt to merge the new -repository file with your version of the file and tell you if there -are any conflicts. See the SVN documentation for details. - -Please refer to the "subversion client support help pages on -GitHub"_https://help.github.com/articles/support-for-subversion-clients -if you want to use advanced features like accessing particular -previous release versions via tags. - -Once you have updated your local files with an "svn update" (or "svn -co"), you still need to re-build LAMMPS if any source files have -changed. To do this, you should cd to the src directory and type: - -make purge # remove any deprecated src files -make package-update # sync package files with src files -make foo # re-build for your machine (mpi, serial, etc) :pre - -just as described on the "Install patch"_Install_patch.html doc page, -after a patch has been installed. - -IMPORTANT NOTE: If you wish to edit/change a src file that is from a -package, you should edit the version of the file inside the package -sub-directory with src, then re-install the package. The version in -the src dir is merely a copy and will be wiped out if you type "make -package-update". - -The LAMMPS GitHub project is managed by Christoph Junghans (LANL, -junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at -gmail.com) and Richard Berger (Temple U, richard.berger at -temple.edu). diff --git a/doc/txt/Install_tarball.txt b/doc/txt/Install_tarball.txt deleted file mode 100644 index 7ba5d15ac4..0000000000 --- a/doc/txt/Install_tarball.txt +++ /dev/null @@ -1,68 +0,0 @@ -"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Download source and documentation as a tarball :h3 - -You can download a current LAMMPS tarball from the "download page"_download -of the "LAMMPS website"_lws. - -:link(download,http://lammps.sandia.gov/download.html) -:link(bug,http://lammps.sandia.gov/bug.html) -:link(older,http://lammps.sandia.gov/tars) - -You have two choices of tarballs, either the most recent stable -release or the most current patch release. Stable releases occur a -few times per year, and undergo more testing before release. Patch -releases occur a couple times per month. The new contents in all -releases are listed on the "bug and feature page"_bug of the website. - -Both tarballs include LAMMPS documentation (HTML and PDF files) -corresponding to that version. The download page also has an option -to download the current-version LAMMPS documentation by itself. - -Older versions of LAMMPS can also be downloaded from "this -page"_older. - -Once you have a tarball, unzip and untar it with the following -command: - -tar -xzvf lammps*.tar.gz :pre - -This will create a LAMMPS directory with the version date -in its name, e.g. lammps-23Jun18. - -:line - -You can also download a zip file via the "Clone or download" button on -the "LAMMPS GitHub site"_git. The file name will be lammps-master.zip -which can be unzipped with the following command, to create -a lammps-master dir: - -unzip lammps*.zip :pre - -This version is the most up-to-date LAMMPS development version. It -will have the date of the most recent patch release (see the file -src/version.h). But it will also include any new bug-fixes or -features added since the last patch release. They will be included in -the next patch release tarball. - -:link(git,https://github.com/lammps/lammps) - -:line - -If you download a current LAMMPS tarball, one way to stay current as -new patch tarballs are released, is to download a patch file which you -can apply to your local directory to update it for each new patch -release. (Or of course you could just download the newest tarball -periodically.) - -The patch files are posted on the "bug and feature page"_bug of the -website, along with a list of changed files and details about what is -in the new patch release. Instructions for applying a patch file are -on the "Install patch"_Install_patch.html doc page. diff --git a/doc/txt/Install_windows.txt b/doc/txt/Install_windows.txt deleted file mode 100644 index 7d5aab34f5..0000000000 --- a/doc/txt/Install_windows.txt +++ /dev/null @@ -1,52 +0,0 @@ -"Higher level section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Download an executable for Windows :h3 - -Pre-compiled Windows installers which install LAMMPS executables on a -Windows system can be downloaded from this site: - -"http://packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html - -Note that each installer package has a date in its name, which -corresponds to the LAMMPS version of the same date. Installers for -current and older versions of LAMMPS are available. 32-bit and 64-bit -installers are available, and each installer contains both a serial -and parallel executable. The installer site also explains how to -install the Windows MPI package (MPICH2 from Argonne National Labs), -needed to run in parallel. - -The LAMMPS binaries contain all optional packages included in the -source distribution except: KIM, KOKKOS, USER-INTEL, and USER-QMMM. -The serial version also does not include the MPIIO and -USER-LB packages. GPU support is provided for OpenCL. - -The installer site also has instructions on how to run LAMMPS under -Windows, once it is installed, in both serial and parallel. - -When you download the installer package, you run it on your Windows -machine. It will then prompt you with a dialog, where you can choose -the installation directory, unpack and copy several executables, -potential files, documentation pdfs, selected example files, etc. It -will then update a few system settings (e.g. PATH, LAMMPS_POTENTIALS) -and add an entry into the Start Menu (with references to the -documentation, LAMMPS homepage and more). From that menu, there is -also a link to an uninstaller that removes the files and undoes the -environment manipulations. - -Note that to update to a newer version of LAMMPS, you should typically -uninstall the version you currently have, download a new installer, -and go through the install procedure described above. I.e. the same -procedure for installing/updating most Windows programs. You can -install multiple versions of LAMMPS (in different directories), but -only the executable for the last-installed package will be found -automatically, so this should only be done for debugging purposes. - -Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting -up this Windows capability. diff --git a/doc/txt/Intro.txt b/doc/txt/Intro.txt deleted file mode 100644 index c8725e0085..0000000000 --- a/doc/txt/Intro.txt +++ /dev/null @@ -1,39 +0,0 @@ -"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Install.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands.html#comm) - -:line - -Introduction :h2 - -These pages provide a brief introduction to LAMMPS. - - - - - -"Overview of LAMMPS"_Intro_overview.html -"LAMMPS features"_Intro_features.html -"LAMMPS non-features"_Intro_nonfeatures.html -"LAMMPS open-source license"_Intro_license.html -"LAMMPS authors"_Intro_authors.html -"Additional website links"_Intro_website.html :all(b) - - diff --git a/doc/txt/Intro_authors.txt b/doc/txt/Intro_authors.txt deleted file mode 100644 index 8f025df96d..0000000000 --- a/doc/txt/Intro_authors.txt +++ /dev/null @@ -1,66 +0,0 @@ -"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Authors of LAMMPS :h3 - -The primary LAMMPS developers are at Sandia National Labs and Temple -University: - -"Steve Plimpton"_sjp, sjplimp at sandia.gov -Aidan Thompson, athomps at sandia.gov -Stan Moore, stamoor at sandia.gov -Axel Kohlmeyer, akohlmey at gmail.com -Richard Berger, richard.berger at temple.edu :ul - -:link(sjp,http://www.cs.sandia.gov/~sjplimp) - -Past developers include Paul Crozier and Mark Stevens, both at Sandia, -and Ray Shan, now at Materials Design. - -:line - -The "Authors page"_http://lammps.sandia.gov/authors.html of the -"LAMMPS website"_lws has a comprehensive list of all the individuals -who have contributed code for a new feature or command or tool to -LAMMPS. - -:line - -The following folks deserve special recognition. Many of the packages -they have written are unique for an MD code and LAMMPS would not be as -general-purpose as it is without their expertise and efforts. - -Metin Aktulga (MSU), USER-REAXC package for C version of ReaxFF -Mike Brown (Intel), GPU and USER-INTEL packages -Colin Denniston (U Western Ontario), USER-LB package -Georg Ganzenmuller (EMI), USER-SMD and USER-SPH packages -Andres Jaramillo-Botero (Caltech), USER-EFF package for electron force field -Reese Jones (Sandia) and colleagues, USER-ATC package for atom/continuum coupling -Christoph Kloss (DCS Computing), LIGGGHTS code for granular materials, built on top of LAMMPS -Rudra Mukherjee (JPL), POEMS package for articulated rigid body motion -Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages -Mike Parks (Sandia), PERI package for Peridynamics -Roy Pollock (LLNL), Ewald and PPPM solvers -Christian Trott (Sandia), USER-CUDA and KOKKOS packages -Ilya Valuev (JIHT), USER-AWPMD package for wave packet MD -Greg Wagner (Northwestern U), MEAM package for MEAM potential :ul - -:line - -As discussed on the "History -page"_http://lammps.sandia.gov/history.html of the website, LAMMPS -originated as a cooperative project between DOE labs and industrial -partners. Folks involved in the design and testing of the original -version of LAMMPS were the following: - -John Carpenter (Mayo Clinic, formerly at Cray Research) -Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb) -Steve Lustig (Dupont) -Jim Belak and Roy Pollock (LLNL) :ul - diff --git a/doc/txt/Intro_features.txt b/doc/txt/Intro_features.txt deleted file mode 100644 index d133fd8064..0000000000 --- a/doc/txt/Intro_features.txt +++ /dev/null @@ -1,202 +0,0 @@ -"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -LAMMPS features :h3 - -LAMMPS is a classical molecular dynamics (MD) code with these general -classes of functionality: - -"General features"_#general -"Particle and model types"_#particle -"Interatomic potentials (force fields)"_#ff -"Atom creation"_#create -"Ensembles, constraints, and boundary conditions"_#ensemble -"Integrators"_#integrate -"Diagnostics"_#diag -"Output"_#output -"Multi-replica models"_#replica1 -"Pre- and post-processing"_#prepost -"Specialized features (beyond MD itself)"_#special :ul - -:line - -General features :h4,link(general) - - runs on a single processor or in parallel - distributed-memory message-passing parallelism (MPI) - spatial-decomposition of simulation domain for parallelism - open-source distribution - highly portable C++ - optional libraries used: MPI and single-processor FFT - GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features - easy to extend with new features and functionality - runs from an input script - syntax for defining and using variables and formulas - syntax for looping over runs and breaking out of loops - run one or multiple simulations simultaneously (in parallel) from one script - build as library, invoke LAMMPS through library interface or provided Python wrapper - couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul - -Particle and model types :h4,link(particle) -("atom style"_atom_style.html command) - - atoms - coarse-grained particles (e.g. bead-spring polymers) - united-atom polymers or organic molecules - all-atom polymers, organic molecules, proteins, DNA - metals - granular materials - coarse-grained mesoscale models - finite-size spherical and ellipsoidal particles - finite-size line segment (2d) and triangle (3d) particles - point dipole particles - rigid collections of particles - hybrid combinations of these :ul - -Interatomic potentials (force fields) :h4,link(ff) -("pair style"_pair_style.html, "bond style"_bond_style.html, -"angle style"_angle_style.html, "dihedral style"_dihedral_style.html, -"improper style"_improper_style.html, "kspace style"_kspace_style.html -commands) - - pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \ - Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated - charged pairwise potentials: Coulombic, point-dipole - many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \ - embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \ - REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic - long-range interactions for charge, point-dipoles, and LJ dispersion: \ - Ewald, Wolf, PPPM (similar to particle-mesh Ewald) - polarization models: "QEq"_fix_qeq.html, \ - "core/shell model"_Howto_coreshell.html, \ - "Drude dipole model"_Howto_drude.html - charge equilibration (QEq via dynamic, point, shielded, Slater methods) - coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO - mesoscopic potentials: granular, Peridynamics, SPH - electron force field (eFF, AWPMD) - bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \ - quartic (breakable) - angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \ - class 2 (COMPASS) - dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \ - class 2 (COMPASS), OPLS - improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS) - polymer potentials: all-atom, united-atom, bead-spring, breakable - water potentials: TIP3P, TIP4P, SPC - implicit solvent potentials: hydrodynamic lubrication, Debye - force-field compatibility with common CHARMM, AMBER, DREIDING, \ - OPLS, GROMACS, COMPASS options - access to the "OpenKIM Repository"_http://openkim.org of potentials via \ - "kim_init, kim_interactions, and kim_query"_kim_commands.html commands - hybrid potentials: multiple pair, bond, angle, dihedral, improper \ - potentials can be used in one simulation - overlaid potentials: superposition of multiple pair potentials :ul - -Atom creation :h4,link(create) -("read_data"_read_data.html, "lattice"_lattice.html, -"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html, -"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands) - - read in atom coords from files - create atoms on one or more lattices (e.g. grain boundaries) - delete geometric or logical groups of atoms (e.g. voids) - replicate existing atoms multiple times - displace atoms :ul - -Ensembles, constraints, and boundary conditions :h4,link(ensemble) -("fix"_fix.html command) - - 2d or 3d systems - orthogonal or non-orthogonal (triclinic symmetry) simulation domains - constant NVE, NVT, NPT, NPH, Parrinello/Rahman integrators - thermostatting options for groups and geometric regions of atoms - pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions - simulation box deformation (tensile and shear) - harmonic (umbrella) constraint forces - rigid body constraints - SHAKE bond and angle constraints - Monte Carlo bond breaking, formation, swapping - atom/molecule insertion and deletion - walls of various kinds - non-equilibrium molecular dynamics (NEMD) - variety of additional boundary conditions and constraints :ul - -Integrators :h4,link(integrate) -("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands) - - velocity-Verlet integrator - Brownian dynamics - rigid body integration - energy minimization via conjugate gradient or steepest descent relaxation - rRESPA hierarchical timestepping - rerun command for post-processing of dump files :ul - -Diagnostics :h4,link(diag) - - see various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul - -Output :h4,link(output) -("dump"_dump.html, "restart"_restart.html commands) - - log file of thermodynamic info - text dump files of atom coords, velocities, other per-atom quantities - binary restart files - parallel I/O of dump and restart files - per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc) - user-defined system-wide (log file) or per-atom (dump file) calculations - spatial and time averaging of per-atom quantities - time averaging of system-wide quantities - atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul - -Multi-replica models :h4,link(replica1) - -"nudged elastic band"_neb.html -"parallel replica dynamics"_prd.html -"temperature accelerated dynamics"_tad.html -"parallel tempering"_temper.html :ul - -Pre- and post-processing :h4,link(prepost) - -A handful of pre- and post-processing tools are packaged with LAMMPS, -some of which can convert input and output files to/from formats used -by other codes; see the "Toos"_Tools.html doc page. :ulb,l - -Our group has also written and released a separate toolkit called -"Pizza.py"_pizza which provides tools for doing setup, analysis, -plotting, and visualization for LAMMPS simulations. Pizza.py is -written in "Python"_python and is available for download from "the -Pizza.py WWW site"_pizza. :l,ule - -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) -:link(python,http://www.python.org) - -Specialized features :h4,link(special) - -LAMMPS can be built with optional packages which implement a variety -of additional capabilities. See the "Packages"_Packages.html doc -page for details. - -These are LAMMPS capabilities which you may not think of as typical -classical MD options: - -"static"_balance.html and "dynamic load-balancing"_fix_balance.html -"generalized aspherical particles"_Howto_body.html -"stochastic rotation dynamics (SRD)"_fix_srd.html -"real-time visualization and interactive MD"_fix_imd.html -calculate "virtual diffraction patterns"_compute_xrd.html -"atom-to-continuum coupling"_fix_atc.html with finite elements -coupled rigid body integration via the "POEMS"_fix_poems.html library -"QM/MM coupling"_fix_qmmm.html -Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_atom_swap.html -"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html -"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids -"Peridynamics mesoscale modeling"_pair_peri.html -"Lattice Boltzmann fluid"_fix_lb_fluid.html -"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics -"two-temperature electron model"_fix_ttm.html :ul diff --git a/doc/txt/Intro_nonfeatures.txt b/doc/txt/Intro_nonfeatures.txt deleted file mode 100644 index 22e827bb2d..0000000000 --- a/doc/txt/Intro_nonfeatures.txt +++ /dev/null @@ -1,100 +0,0 @@ -"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -LAMMPS non-features :h3 - -LAMMPS is designed to be a fast, parallel engine for molecular -dynamics (MD) simulations. It provides only a modest amount of -functionality for setting up simulations and analyzing their output. - -Specifically, LAMMPS was not conceived and designed for: - -being run through a GUI -building molecular systems, or building molecular topologies -assign force-field coefficients automagically -perform sophisticated analysis of your MD simulation -visualize your MD simulation interactively -plot your output data :ul - -Although over the years these limitations have been somewhat -reduced through features added to LAMMPS or external tools -that either closely interface with LAMMPS or extend LAMMPS. - -Here are suggestions on how to perform these tasks: - -[GUI:] LAMMPS can be built as a library and a Python wrapper that wraps -the library interface is provided. Thus, GUI interfaces can be -written in Python (or C or C++ if desired) that run LAMMPS and -visualize or plot its output. Examples of this are provided in the -python directory and described on the "Python"_Python_head.html doc -page. Also, there are several external wrappers or GUI front ends. :ulb,l - -[Builder:] Several pre-processing tools are packaged with LAMMPS. Some -of them convert input files in formats produced by other MD codes such -as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of them -are simple programs that will build simple molecular systems, such as -linear bead-spring polymer chains. The moltemplate program is a true -molecular builder that will generate complex molecular models. See -the "Tools"_Tools.html doc page for details on tools packaged with -LAMMPS. The "Pre/post processing -page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website -describes a variety of 3rd party tools for this task. Furthermore, -some LAMMPS internal commands allow to reconstruct, or selectively add -topology information, as well as provide the option to insert molecule -templates instead of atoms for building bulk molecular systems. :l - -[Force-field assignment:] The conversion tools described in the previous -bullet for CHARMM, AMBER, and Insight will also assign force field -coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER, -or BIOVIA (formerly Accelrys) force field files. The tools -"ParmEd"_https://parmed.github.io/ParmEd/html/index.html and -"InterMol"_https://github.com/shirtsgroup/InterMol are particularly -powerful and flexible in converting force field and topology data -between various MD simulation programs. :l - -[Simulation analysis:] If you want to perform analysis on-the-fly as -your simulation runs, see the "compute"_compute.html and -"fix"_fix.html doc pages, which list commands that can be used in a -LAMMPS input script. Also see the "Modify"_Modify.html doc page for -info on how to add your own analysis code or algorithms to LAMMPS. -For post-processing, LAMMPS output such as "dump file -snapshots"_dump.html can be converted into formats used by other MD or -post-processing codes. To some degree, that conversion can be done -directly inside of LAMMPS by interfacing to the VMD molfile plugins. -The "rerun"_rerun.html command also allows to do some post-processing -of existing trajectories, and through being able to read a variety -of file formats, this can also be used for analyzing trajectories -from other MD codes. Some post-processing tools packaged with -LAMMPS will do these conversions. Scripts provided in the -tools/python directory can extract and massage data in dump files to -make it easier to import into other programs. See the -"Tools"_Tools.html doc page for details on these various options. :l - -[Visualization:] LAMMPS can produce NETPBM, JPG or PNG snapshot images -on-the-fly via its "dump image"_dump_image.html command and pass -them to an external program, "FFmpeg"_https://www.ffmpeg.org to generate -movies from them. For high-quality, interactive visualization there are -many excellent and free tools available. See the "Other Codes -page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for -visualization packages that can use LAMMPS output data. :l - -[Plotting:] See the next bullet about Pizza.py as well as the -"Python"_Python_head.html doc page for examples of plotting LAMMPS -output. Scripts provided with the {python} tool in the tools -directory will extract and massage data in log and dump files to make -it easier to analyze and plot. See the "Tools"_Tools.html doc page -for more discussion of the various tools. :l - -[Pizza.py:] Our group has also written a separate toolkit called -"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of -setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS -simulations. It thus provides some functionality for several of the -above bullets. Pizza.py is written in "Python"_http://www.python.org -and is available for download from "this -page"_http://www.cs.sandia.gov/~sjplimp/download.html. :l,ule diff --git a/doc/txt/Intro_opensource.txt b/doc/txt/Intro_opensource.txt deleted file mode 100644 index e0d57f7ce1..0000000000 --- a/doc/txt/Intro_opensource.txt +++ /dev/null @@ -1,44 +0,0 @@ -"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -LAMMPS open-source license :h3 - -LAMMPS is a freely-available open-source code, distributed under the -terms of the "GNU Public License"_gnu, which means you can use or -modify the code however you wish. - -LAMMPS comes with no warranty of any kind. As each source file states -in its header, it is a copyrighted code that is distributed free-of- -charge, under the terms of the "GNU Public License"_gnu (GPL). This -is often referred to as open-source distribution - see -"www.gnu.org"_gnuorg or "www.opensource.org"_opensource. The legal -text of the GPL is in the LICENSE file included in the LAMMPS -distribution. - -:link(gnu,http://www.gnu.org/copyleft/gpl.html) -:link(gnuorg,http://www.gnu.org) -:link(opensource,http://www.opensource.org) - -Here is a summary of what the GPL means for LAMMPS users: - -(1) Anyone is free to use, modify, or extend LAMMPS in any way they -choose, including for commercial purposes. - -(2) If you distribute a modified version of LAMMPS, it must remain -open-source, meaning you distribute it under the terms of the GPL. -You should clearly annotate such a code as a derivative version of -LAMMPS. - -(3) If you release any code that includes LAMMPS source code, then it -must also be open-sourced, meaning you distribute it under the terms -of the GPL. - -(4) If you give LAMMPS files to someone else, the GPL LICENSE file and -source file headers (including the copyright and GPL notices) should -remain part of the code. diff --git a/doc/txt/Intro_overview.txt b/doc/txt/Intro_overview.txt deleted file mode 100644 index cd822c778f..0000000000 --- a/doc/txt/Intro_overview.txt +++ /dev/null @@ -1,58 +0,0 @@ -"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Overview of LAMMPS :h3 - -LAMMPS is a classical molecular dynamics (MD) code that models -ensembles of particles in a liquid, solid, or gaseous state. It can -model atomic, polymeric, biological, solid-state (metals, ceramics, -oxides), granular, coarse-grained, or macroscopic systems using a -variety of interatomic potentials (force fields) and boundary -conditions. It can model 2d or 3d systems with only a few particles -up to millions or billions. - -LAMMPS can be built and run on a laptop or desktop machine, but is -designed for parallel computers. It will run on any parallel machine -that supports the "MPI"_mpi message-passing library. This includes -shared-memory boxes and distributed-memory clusters and -supercomputers. - -:link(mpi,http://www-unix.mcs.anl.gov/mpi) - -LAMMPS is written in C++. Earlier versions were written in F77 and -F90. See the "History page"_http://lammps.sandia.gov/history.html of -the website for details. All versions can be downloaded from the -"LAMMPS website"_lws. - -LAMMPS is designed to be easy to modify or extend with new -capabilities, such as new force fields, atom types, boundary -conditions, or diagnostics. See the "Modify"_Modify.html doc page for -more details. - -In the most general sense, LAMMPS integrates Newton's equations of -motion for a collection of interacting particles. A single particle -can be an atom or molecule or electron, a coarse-grained cluster of -atoms, or a mesoscopic or macroscopic clump of material. The -interaction models that LAMMPS includes are mostly short-range in -nature; some long-range models are included as well. - -LAMMPS uses neighbor lists to keep track of nearby particles. The -lists are optimized for systems with particles that are repulsive at -short distances, so that the local density of particles never becomes -too large. This is in contrast to methods used for modeling plasma -or gravitational bodies (e.g. galaxy formation). - -On parallel machines, LAMMPS uses spatial-decomposition techniques to -partition the simulation domain into small sub-domains of equal -computational cost, one of which is assigned to each processor. -Processors communicate and store "ghost" atom information for atoms -that border their sub-domain. - - - diff --git a/doc/txt/Intro_website.txt b/doc/txt/Intro_website.txt deleted file mode 100644 index a8af94157c..0000000000 --- a/doc/txt/Intro_website.txt +++ /dev/null @@ -1,42 +0,0 @@ -"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Additional website links :h3 - -The "LAMMPS website"_lws has a variety of additional info about -LAMMPS, beyond what is in this manual. Some of the other pages in -this Intr are included in this list. - -"Brief intro and recently added significant features"_lws -"List of features"_http://lammps.sandia.gov/features.html -"List of non-features"_http://lammps.sandia.gov/non_features.html -"Recent bug fixes and new features"_http://lammps.sandia.gov/bug.html :ul - -"Download info"_http://lammps.sandia.gov/download.html -"GitHub site"_https://github.com/lammps/lammps -"SourceForge site"_https://sourceforge.net/projects/lammps -"LAMMPS open-source license"_http://lammps.sandia.gov/open_source.html :ul - -"Glossary of MD terms relevant to LAMMPS"_http://lammps.sandia.gov/glossary.html -"LAMMPS highlights with images"_http://lammps.sandia.gov/pictures.html -"LAMMPS highlights with movies"_http://lammps.sandia.gov/movies.html -"Mail list"_http://lammps.sandia.gov/mail.html -"Workshops"_http://lammps.sandia.gov/workshops.html -"Tutorials"_http://lammps.sandia.gov/tutorials.html -"Developer guide"_http://lammps.sandia.gov/Developer.pdf :ul - -"Pre- and post-processing tools for LAMMPS"_http://lammps.sandia.gov/prepost.html -"Other software usable with LAMMPS"_http://lammps.sandia.gov/offsite.html -"Viz tools usable with LAMMPS"_http://lammps.sandia.gov/viz.html :ul - -"Benchmark performance"_http://lammps.sandia.gov/bench.html -"Publications that have cited LAMMPS"_http://lammps.sandia.gov/papers.html -"Authors of LAMMPS"_http://lammps.sandia.gov/authors.html -"History of LAMMPS development"_http://lammps.sandia.gov/history.html -"Funding for LAMMPS"_http://lammps.sandia.gov/funding.html :ul diff --git a/doc/txt/Manual_version.txt b/doc/txt/Manual_version.txt deleted file mode 100644 index 436e531246..0000000000 --- a/doc/txt/Manual_version.txt +++ /dev/null @@ -1,33 +0,0 @@ -"Higher level section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -What does a LAMMPS version mean :h3 - -The LAMMPS "version" is the date when it was released, such as 1 May -2014. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it in the next {patch} release, which are -typically made every couple of weeks. Info on patch releases are on -"this website page"_http://lammps.sandia.gov/bug.html. Every few -months, the latest patch release is subjected to more thorough testing -and labeled as a {stable} version. - -Each version of LAMMPS contains all the features and bug-fixes up to -and including its version date. - -The version date is printed to the screen and logfile every time you -run LAMMPS. It is also in the file src/version.h and in the LAMMPS -directory name created when you unpack a tarball. And it is on the -first page of the "manual"_Manual.html. - -If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current patch release of LAMMPS. :ulb,l - -If you browse the HTML doc pages included in your tarball, they -describe the version you have, which may be older. :l,ule - diff --git a/doc/txt/Modify.txt b/doc/txt/Modify.txt deleted file mode 100644 index 38fbf17dd9..0000000000 --- a/doc/txt/Modify.txt +++ /dev/null @@ -1,70 +0,0 @@ -"Previous Section"_Tools.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Python_head.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Modify & extend LAMMPS :h2 - -LAMMPS is designed in a modular fashion so as to be easy to modify and -extend with new functionality. In fact, about 95% of its source code -is add-on files. These doc pages give basic instructions on how to do -this. - -If you add a new feature to LAMMPS and think it will be of interest to -general users, we encourage you to submit it for inclusion in LAMMPS -as a pull request on our "GitHub -site"_https://github.com/lammps/lammps, after reading the "Modify -contribute"_Modify_contribute.html doc page. - - - - - -"Overview"_Modify_overview.html -"Submitting new features for inclusion in LAMMPS"_Modify_contribute.html :all(b) - -"Atom styles"_Modify_atom.html -"Pair styles"_Modify_pair.html -"Bond, angle, dihedral, improper styles"_Modify_bond.html -"Compute styles"_Modify_compute.html -"Fix styles"_Modify_fix.html -"Input script command styles"_Modify_command.html -"Dump styles"_Modify_dump.html -"Kspace styles"_Modify_kspace.html -"Minimization styles"_Modify_min.html -"Region styles"_Modify_region.html -"Body styles"_Modify_body.html -"Thermodynamic output options"_Modify_thermo.html -"Variable options"_Modify_variable.html :all(b) - - diff --git a/doc/txt/Modify_atom.txt b/doc/txt/Modify_atom.txt deleted file mode 100644 index 60c7dccb29..0000000000 --- a/doc/txt/Modify_atom.txt +++ /dev/null @@ -1,90 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Atom styles :h3 - -Classes that define an "atom style"_atom_style.html are derived from -the AtomVec class and managed by the Atom class. The atom style -determines what attributes are associated with an atom. A new atom -style can be created if one of the existing atom styles does not -define all the attributes you need to store and communicate with -atoms. - -Atom_vec_atomic.cpp is a simple example of an atom style. - -Here is a brief description of methods you define in your new derived -class. See atom_vec.h for details. - -init: one time setup (optional) -grow: re-allocate atom arrays to longer lengths (required) -grow_reset: make array pointers in Atom and AtomVec classes consistent (required) -copy: copy info for one atom to another atom's array locations (required) -pack_comm: store an atom's info in a buffer communicated every timestep (required) -pack_comm_vel: add velocity info to communication buffer (required) -pack_comm_hybrid: store extra info unique to this atom style (optional) -unpack_comm: retrieve an atom's info from the buffer (required) -unpack_comm_vel: also retrieve velocity info (required) -unpack_comm_hybrid: retrieve extra info unique to this atom style (optional) -pack_reverse: store an atom's info in a buffer communicating partial forces (required) -pack_reverse_hybrid: store extra info unique to this atom style (optional) -unpack_reverse: retrieve an atom's info from the buffer (required) -unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional) -pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required) -pack_border_vel: add velocity info to buffer (required) -pack_border_hybrid: store extra info unique to this atom style (optional) -unpack_border: retrieve an atom's info from the buffer (required) -unpack_border_vel: also retrieve velocity info (required) -unpack_border_hybrid: retrieve extra info unique to this atom style (optional) -pack_exchange: store all an atom's info to migrate to another processor (required) -unpack_exchange: retrieve an atom's info from the buffer (required) -size_restart: number of restart quantities associated with proc's atoms (required) -pack_restart: pack atom quantities into a buffer (required) -unpack_restart: unpack atom quantities from a buffer (required) -create_atom: create an individual atom of this style (required) -data_atom: parse an atom line from the data file (required) -data_atom_hybrid: parse additional atom info unique to this atom style (optional) -data_vel: parse one line of velocity information from data file (optional) -data_vel_hybrid: parse additional velocity data unique to this atom style (optional) -memory_usage: tally memory allocated by atom arrays (required) :tb(s=:) - -The constructor of the derived class sets values for several variables -that you must set when defining a new atom style, which are documented -in atom_vec.h. New atom arrays are defined in atom.cpp. Search for -the word "customize" and you will find locations you will need to -modify. - -NOTE: It is possible to add some attributes, such as a molecule ID, to -atom styles that do not have them via the "fix -property/atom"_fix_property_atom.html command. This command also -allows new custom attributes consisting of extra integer or -floating-point values to be added to atoms. See the "fix -property/atom"_fix_property_atom.html doc page for examples of cases -where this is useful and details on how to initialize, access, and -output the custom values. - -New "pair styles"_pair_style.html, "fixes"_fix.html, or -"computes"_compute.html can be added to LAMMPS, as discussed below. -The code for these classes can use the per-atom properties defined by -fix property/atom. The Atom class has a find_custom() method that is -useful in this context: - -int index = atom->find_custom(char *name, int &flag); :pre - -The "name" of a custom attribute, as specified in the "fix -property/atom"_fix_property_atom.html command, is checked to verify -that it exists and its index is returned. The method also sets flag = -0/1 depending on whether it is an integer or floating-point attribute. -The vector of values associated with the attribute can then be -accessed using the returned index as - -int *ivector = atom->ivector\[index\]; -double *dvector = atom->dvector\[index\]; :pre - -Ivector or dvector are vectors of length Nlocal = # of owned atoms, -which store the attributes of individual atoms. diff --git a/doc/txt/Modify_body.txt b/doc/txt/Modify_body.txt deleted file mode 100644 index 0114ae10c8..0000000000 --- a/doc/txt/Modify_body.txt +++ /dev/null @@ -1,34 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Body styles :h3 - -Classes that define body particles are derived from the Body class. -Body particles can represent complex entities, such as surface meshes -of discrete points, collections of sub-particles, deformable objects, -etc. - -See the "Howto body"_Howto_body.html doc page for an overview of using -body particles and the various body styles LAMMPS supports. New -styles can be created to add new kinds of body particles to LAMMPS. - -Body_nparticle.cpp is an example of a body particle that is treated as -a rigid body containing N sub-particles. - -Here is a brief description of methods you define in your new derived -class. See body.h for details. - -data_body: process a line from the Bodies section of a data file -noutrow: number of sub-particles output is generated for -noutcol: number of values per-sub-particle output is generated for -output: output values for the Mth sub-particle -pack_comm_body: body attributes to communicate every timestep -unpack_comm_body: unpacking of those attributes -pack_border_body: body attributes to communicate when reneighboring is done -unpack_border_body: unpacking of those attributes :tb(s=:) diff --git a/doc/txt/Modify_bond.txt b/doc/txt/Modify_bond.txt deleted file mode 100644 index 7ceea3f910..0000000000 --- a/doc/txt/Modify_bond.txt +++ /dev/null @@ -1,33 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Bond, angle, dihedral, improper styles :h3 - -Classes that compute molecular interactions are derived from the Bond, -Angle, Dihedral, and Improper classes. New styles can be created to -add new potentials to LAMMPS. - -Bond_harmonic.cpp is the simplest example of a bond style. Ditto for -the harmonic forms of the angle, dihedral, and improper style -commands. - -Here is a brief description of common methods you define in your -new derived class. See bond.h, angle.h, dihedral.h, and improper.h -for details and specific additional methods. - -init: check if all coefficients are set, calls {init_style} (optional) -init_style: check if style specific conditions are met (optional) -compute: compute the molecular interactions (required) -settings: apply global settings for all types (optional) -coeff: set coefficients for one type (required) -equilibrium_distance: length of bond, used by SHAKE (required, bond only) -equilibrium_angle: opening of angle, used by SHAKE (required, angle only) -write & read_restart: writes/reads coeffs to restart files (required) -single: force and energy of a single bond or angle (required, bond or angle only) -memory_usage: tally memory allocated by the style (optional) :tb(s=:) diff --git a/doc/txt/Modify_command.txt b/doc/txt/Modify_command.txt deleted file mode 100644 index 4576f6c806..0000000000 --- a/doc/txt/Modify_command.txt +++ /dev/null @@ -1,27 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Input script command style :h3 - -New commands can be added to LAMMPS input scripts by adding new -classes that have a "command" method. For example, the create_atoms, -read_data, velocity, and run commands are all implemented in this -fashion. When such a command is encountered in the LAMMPS input -script, LAMMPS simply creates a class with the corresponding name, -invokes the "command" method of the class, and passes it the arguments -from the input script. The command method can perform whatever -operations it wishes on LAMMPS data structures. - -The single method your new class must define is as follows: - -command: operations performed by the new command :tb(s=:) - -Of course, the new class can define other methods and variables as -needed. - diff --git a/doc/txt/Modify_compute.txt b/doc/txt/Modify_compute.txt deleted file mode 100644 index 2f6481dbd5..0000000000 --- a/doc/txt/Modify_compute.txt +++ /dev/null @@ -1,49 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Compute styles :h3 - -Classes that compute scalar and vector quantities like temperature -and the pressure tensor, as well as classes that compute per-atom -quantities like kinetic energy and the centro-symmetry parameter -are derived from the Compute class. New styles can be created -to add new calculations to LAMMPS. - -Compute_temp.cpp is a simple example of computing a scalar -temperature. Compute_ke_atom.cpp is a simple example of computing -per-atom kinetic energy. - -Here is a brief description of methods you define in your new derived -class. See compute.h for details. - -init: perform one time setup (required) -init_list: neighbor list setup, if needed (optional) -compute_scalar: compute a scalar quantity (optional) -compute_vector: compute a vector of quantities (optional) -compute_peratom: compute one or more quantities per atom (optional) -compute_local: compute one or more quantities per processor (optional) -pack_comm: pack a buffer with items to communicate (optional) -unpack_comm: unpack the buffer (optional) -pack_reverse: pack a buffer with items to reverse communicate (optional) -unpack_reverse: unpack the buffer (optional) -remove_bias: remove velocity bias from one atom (optional) -remove_bias_all: remove velocity bias from all atoms in group (optional) -restore_bias: restore velocity bias for one atom after remove_bias (optional) -restore_bias_all: same as before, but for all atoms in group (optional) -pair_tally_callback: callback function for {tally}-style computes (optional). -memory_usage: tally memory usage (optional) :tb(s=:) - -Tally-style computes are a special case, as their computation is done -in two stages: the callback function is registered with the pair style -and then called from the Pair::ev_tally() function, which is called for -each pair after force and energy has been computed for this pair. Then -the tallied values are retrieved with the standard compute_scalar or -compute_vector or compute_peratom methods. The USER-TALLY package -provides {examples}_compute_tally.html for utilizing this mechanism. - diff --git a/doc/txt/Modify_contribute.txt b/doc/txt/Modify_contribute.txt deleted file mode 100644 index 31d459de1a..0000000000 --- a/doc/txt/Modify_contribute.txt +++ /dev/null @@ -1,216 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Submitting new features for inclusion in LAMMPS :h3 - -We encourage users to submit new features or modifications for LAMMPS -to "the core developers"_http://lammps.sandia.gov/authors.html so they -can be added to the LAMMPS distribution. The preferred way to manage -and coordinate this is as of Fall 2016 via the LAMMPS project on -"GitHub"_https://github.com/lammps/lammps. An alternative is to -contact the LAMMPS developers or the indicated developer of a package -or feature directly and send in your contribution via e-mail. - -For any larger modifications or programming project, you are -encouraged to contact the LAMMPS developers ahead of time, in order to -discuss implementation strategies and coding guidelines, that will -make it easier to integrate your contribution and result in less work -for everybody involved. You are also encouraged to search through the -list of "open issues on -GitHub"_https://github.com/lammps/lammps/issues and submit a new issue -for a planned feature, so you would not duplicate the work of others -(and possibly get scooped by them) or have your work duplicated by -others. - -How quickly your contribution will be integrated depends largely on -how much effort it will cause to integrate and test it, how much it -requires changes to the core codebase, and of how much interest it is -to the larger LAMMPS community. Please see below for a checklist of -typical requirements. Once you have prepared everything, see the -"Using GitHub with LAMMPS Howto"_Howto_github.html doc page for instructions on how to -submit your changes or new files through a GitHub pull request. If you -prefer to submit patches or full files, you should first make certain, -that your code works correctly with the latest patch-level version of -LAMMPS and contains all bug fixes from it. Then create a gzipped tar -file of all changed or added files or a corresponding patch file using -'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip -compression, as this works well on all platforms. - -If the new features/files are broadly useful we may add them as core -files to LAMMPS or as part of a "standard -package"_Packages_standard.html. Else we will add them as a -user-contributed file or "user package"_Packages_user.html. Examples -of user packages are in src sub-directories that start with USER. The -USER-MISC package is simply a collection of (mostly) unrelated single -files, which is the simplest way to have your contribution quickly -added to the LAMMPS distribution. All the standard and user packages -are listed and described on the "Packages -details"_Packages_details.html doc page. - -Note that by providing us files to release, you are agreeing to make -them open-source, i.e. we can release them under the terms of the GPL, -used as a license for the rest of LAMMPS. See the "Open -source"_http://lammps.sandia.gov/open_source.html page on the LAMMPS -website for details. - -With user packages and files, all we are really providing (aside from -the fame and fortune that accompanies having your name in the source -code and on the "Authors page"_http://lammps.sandia.gov/authors.html -of the "LAMMPS WWW site"_lws), is a means for you to distribute your -work to the LAMMPS user community, and a mechanism for others to -easily try out your new feature. This may help you find bugs or make -contact with new collaborators. Note that you're also implicitly -agreeing to support your code which means answer questions, fix bugs, -and maintain it if LAMMPS changes in some way that breaks it (an -unusual event). - -NOTE: If you prefer to actively develop and support your add-on -feature yourself, then you may wish to make it available for download -from your own website, as a user package that LAMMPS users can add to -their copy of LAMMPS. See the "Offsite LAMMPS packages and -tools"_http://lammps.sandia.gov/offsite.html page of the LAMMPS web -site for examples of groups that do this. We are happy to advertise -your package and web site from that page. Simply email the -"developers"_http://lammps.sandia.gov/authors.html with info about -your package and we will post it there. - -The previous sections of this doc page describe how to add new "style" -files of various kinds to LAMMPS. Packages are simply collections of -one or more new class files which are invoked as a new style within a -LAMMPS input script. If designed correctly, these additions typically -do not require changes to the main core of LAMMPS; they are simply -add-on files. If you think your new feature requires non-trivial -changes in core LAMMPS files, you'll need to "communicate with the -developers"_http://lammps.sandia.gov/authors.html, since we may or may -not want to make those changes. An example of a trivial change is -making a parent-class method "virtual" when you derive a new child -class from it. - -Here is a checklist of steps you need to follow to submit a single file -or user package for our consideration. Following these steps will save -both you and us time. See existing files in packages in the src dir for -examples. If you are uncertain, please ask. - -All source files you provide must compile with the most current -version of LAMMPS with multiple configurations. In particular you -need to test compiling LAMMPS from scratch with -DLAMMPS_BIGBIG -set in addition to the default -DLAMMPS_SMALLBIG setting. Your code -will need to work correctly in serial and in parallel using MPI. :ulb,l - -For consistency with the rest of LAMMPS and especially, if you want -your contribution(s) to be added to main LAMMPS code or one of its -standard packages, it needs to be written in a style compatible with -other LAMMPS source files. This means: 2-character indentation per -level, [no tabs], no lines over 80 characters. I/O is done via -the C-style stdio library (mixing of stdio and iostreams is generally -discouraged), class header files should not import any system headers -outside of , STL containers should be avoided in headers, -system header from the C library should use the C++-style names -(, , or ) instead of the C-style names -, , or ), and forward declarations -used where possible or needed to avoid including headers. -All added code should be placed into the LAMMPS_NS namespace or a -sub-namespace; global or static variables should be avoided, as they -conflict with the modular nature of LAMMPS and the C++ class structure. -Header files must [not] import namespaces with {using}. -This all is so the developers can more easily understand, integrate, -and maintain your contribution and reduce conflicts with other parts -of LAMMPS. This basically means that the code accesses data -structures, performs its operations, and is formatted similar to other -LAMMPS source files, including the use of the error class for error -and warning messages. :l - -If you want your contribution to be added as a user-contributed -feature, and it's a single file (actually a *.cpp and *.h file) it can -rapidly be added to the USER-MISC directory. Send us the one-line -entry to add to the USER-MISC/README file in that dir, along with the -2 source files. You can do this multiple times if you wish to -contribute several individual features. :l - -If you want your contribution to be added as a user-contribution and -it is several related features, it is probably best to make it a user -package directory with a name like USER-FOO. In addition to your new -files, the directory should contain a README text file. The README -should contain your name and contact information and a brief -description of what your new package does. If your files depend on -other LAMMPS style files also being installed (e.g. because your file -is a derived class from the other LAMMPS class), then an Install.sh -file is also needed to check for those dependencies. See other README -and Install.sh files in other USER directories as examples. Send us a -tarball of this USER-FOO directory. :l - -Your new source files need to have the LAMMPS copyright, GPL notice, -and your name and email address at the top, like other -user-contributed LAMMPS source files. They need to create a class -that is inside the LAMMPS namespace. If the file is for one of the - -USER packages, including USER-MISC, then we are not as picky about the -coding style (see above). I.e. the files do not need to be in the -same stylistic format and syntax as other LAMMPS files, though that -would be nice for developers as well as users who try to read your -code. :l - -You [must] also create a [documentation] file for each new command or -style you are adding to LAMMPS. For simplicity and convenience, the -documentation of groups of closely related commands or styles may be -combined into a single file. This will be one file for a single-file -feature. For a package, it might be several files. These are simple -text files with a specific markup language, that are then auto-converted -to HTML and PDF. The tools for this conversion are included in the -source distribution, and the translation can be as simple as doing -"make html pdf" in the doc folder. -Thus the documentation source files must be in the same format and -style as other *.txt files in the lammps/doc/src directory for similar -commands and styles; use one or more of them as a starting point. -A description of the markup can also be found in -lammps/doc/utils/txt2html/README.html -As appropriate, the text files can include links to equations -(see doc/Eqs/*.tex for examples, we auto-create the associated JPG -files), or figures (see doc/JPG for examples), or even additional PDF -files with further details (see doc/PDF for examples). The doc page -should also include literature citations as appropriate; see the -bottom of doc/fix_nh.txt for examples and the earlier part of the same -file for how to format the cite itself. The "Restrictions" section of -the doc page should indicate that your command is only available if -LAMMPS is built with the appropriate USER-MISC or USER-FOO package. -See other user package doc files for examples of how to do this. The -prerequisite for building the HTML format files are Python 3.x and -virtualenv, the requirement for generating the PDF format manual -is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least -"make html" and carefully inspect and proofread the resulting HTML format -doc page before submitting your code. :l - -For a new package (or even a single command) you should include one or -more example scripts demonstrating its use. These should run in no -more than a couple minutes, even on a single processor, and not require -large data files as input. See directories under examples/USER for -examples of input scripts other users provided for their packages. -These example inputs are also required for validating memory accesses -and testing for memory leaks with valgrind :l - -If there is a paper of yours describing your feature (either the -algorithm/science behind the feature itself, or its initial usage, or -its implementation in LAMMPS), you can add the citation to the *.cpp -source file. See src/USER-EFF/atom_vec_electron.cpp for an example. -A LaTeX citation is stored in a variable at the top of the file and a -single line of code that references the variable is added to the -constructor of the class. Whenever a user invokes your feature from -their input script, this will cause LAMMPS to output the citation to a -log.cite file and prompt the user to examine the file. Note that you -should only use this for a paper you or your group authored. -E.g. adding a cite in the code for a paper by Nose and Hoover if you -write a fix that implements their integrator is not the intended -usage. That kind of citation should just be in the doc page you -provide. :l -:ule - -Finally, as a general rule-of-thumb, the more clear and -self-explanatory you make your documentation and README files, and the -easier you make it for people to get started, e.g. by providing example -scripts, the more likely it is that users will try out your new feature. diff --git a/doc/txt/Modify_dump.txt b/doc/txt/Modify_dump.txt deleted file mode 100644 index cfe96f5d3d..0000000000 --- a/doc/txt/Modify_dump.txt +++ /dev/null @@ -1,35 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Dump styles :h3 - -Classes that dump per-atom info to files are derived from the Dump -class. To dump new quantities or in a new format, a new derived dump -class can be added, but it is typically simpler to modify the -DumpCustom class contained in the dump_custom.cpp file. - -Dump_atom.cpp is a simple example of a derived dump class. - -Here is a brief description of methods you define in your new derived -class. See dump.h for details. - -write_header: write the header section of a snapshot of atoms -count: count the number of lines a processor will output -pack: pack a proc's output data into a buffer -write_data: write a proc's data to a file :tb(s=:) - -See the "dump"_dump.html command and its {custom} style for a list of -keywords for atom information that can already be dumped by -DumpCustom. It includes options to dump per-atom info from Compute -classes, so adding a new derived Compute class is one way to calculate -new quantities to dump. - -Note that new keywords for atom properties are not typically -added to the "dump custom"_dump.html command. Instead they are added -to the "compute property/atom"_compute_property_atom.html command. diff --git a/doc/txt/Modify_fix.txt b/doc/txt/Modify_fix.txt deleted file mode 100644 index b095ebc4b5..0000000000 --- a/doc/txt/Modify_fix.txt +++ /dev/null @@ -1,107 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Fix styles :h3 - -In LAMMPS, a "fix" is any operation that is computed during -timestepping that alters some property of the system. Essentially -everything that happens during a simulation besides force computation, -neighbor list construction, and output, is a "fix". This includes -time integration (update of coordinates and velocities), force -constraints or boundary conditions (SHAKE or walls), and diagnostics -(compute a diffusion coefficient). New styles can be created to add -new options to LAMMPS. - -Fix_setforce.cpp is a simple example of setting forces on atoms to -prescribed values. There are dozens of fix options already in LAMMPS; -choose one as a template that is similar to what you want to -implement. - -Here is a brief description of methods you can define in your new -derived class. See fix.h for details. - -setmask: determines when the fix is called during the timestep (required) -init: initialization before a run (optional) -setup_pre_exchange: called before atom exchange in setup (optional) -setup_pre_force: called before force computation in setup (optional) -setup: called immediately before the 1st timestep and after forces are computed (optional) -min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional) -min_setup: like setup, but for minimizations instead of MD runs (optional) -initial_integrate: called at very beginning of each timestep (optional) -pre_exchange: called before atom exchange on re-neighboring steps (optional) -pre_neighbor: called before neighbor list build (optional) -pre_force: called before pair & molecular forces are computed (optional) -post_force: called after pair & molecular forces are computed and communicated (optional) -final_integrate: called at end of each timestep (optional) -end_of_step: called at very end of timestep (optional) -write_restart: dumps fix info to restart file (optional) -restart: uses info from restart file to re-initialize the fix (optional) -grow_arrays: allocate memory for atom-based arrays used by fix (optional) -copy_arrays: copy atom info when an atom migrates to a new processor (optional) -pack_exchange: store atom's data in a buffer (optional) -unpack_exchange: retrieve atom's data from a buffer (optional) -pack_restart: store atom's data for writing to restart file (optional) -unpack_restart: retrieve atom's data from a restart file buffer (optional) -size_restart: size of atom's data (optional) -maxsize_restart: max size of atom's data (optional) -setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional) -initial_integrate_respa: same as initial_integrate, but for rRESPA (optional) -post_integrate_respa: called after the first half integration step is done in rRESPA (optional) -pre_force_respa: same as pre_force, but for rRESPA (optional) -post_force_respa: same as post_force, but for rRESPA (optional) -final_integrate_respa: same as final_integrate, but for rRESPA (optional) -min_pre_force: called after pair & molecular forces are computed in minimizer (optional) -min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional) -min_store: store extra data for linesearch based minimization on a LIFO stack (optional) -min_pushstore: push the minimization LIFO stack one element down (optional) -min_popstore: pop the minimization LIFO stack one element up (optional) -min_clearstore: clear minimization LIFO stack (optional) -min_step: reset or move forward on line search minimization (optional) -min_dof: report number of degrees of freedom {added} by this fix in minimization (optional) -max_alpha: report maximum allowed step size during linesearch minimization (optional) -pack_comm: pack a buffer to communicate a per-atom quantity (optional) -unpack_comm: unpack a buffer to communicate a per-atom quantity (optional) -pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional) -unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional) -dof: report number of degrees of freedom {removed} by this fix during MD (optional) -compute_scalar: return a global scalar property that the fix computes (optional) -compute_vector: return a component of a vector property that the fix computes (optional) -compute_array: return a component of an array property that the fix computes (optional) -deform: called when the box size is changed (optional) -reset_target: called when a change of the target temperature is requested during a run (optional) -reset_dt: is called when a change of the time step is requested during a run (optional) -modify_param: called when a fix_modify request is executed (optional) -memory_usage: report memory used by fix (optional) -thermo: compute quantities for thermodynamic output (optional) :tb(s=:) - -Typically, only a small fraction of these methods are defined for a -particular fix. Setmask is mandatory, as it determines when the fix -will be invoked during the timestep. Fixes that perform time -integration ({nve}, {nvt}, {npt}) implement initial_integrate() and -final_integrate() to perform velocity Verlet updates. Fixes that -constrain forces implement post_force(). - -Fixes that perform diagnostics typically implement end_of_step(). For -an end_of_step fix, one of your fix arguments must be the variable -"nevery" which is used to determine when to call the fix and you must -set this variable in the constructor of your fix. By convention, this -is the first argument the fix defines (after the ID, group-ID, style). - -If the fix needs to store information for each atom that persists from -timestep to timestep, it can manage that memory and migrate the info -with the atoms as they move from processors to processor by -implementing the grow_arrays, copy_arrays, pack_exchange, and -unpack_exchange methods. Similarly, the pack_restart and -unpack_restart methods can be implemented to store information about -the fix in restart files. If you wish an integrator or force -constraint fix to work with rRESPA (see the "run_style"_run_style.html -command), the initial_integrate, post_force_integrate, and -final_integrate_respa methods can be implemented. The thermo method -enables a fix to contribute values to thermodynamic output, as printed -quantities and/or to be summed to the potential energy of the system. diff --git a/doc/txt/Modify_kspace.txt b/doc/txt/Modify_kspace.txt deleted file mode 100644 index d5f018411d..0000000000 --- a/doc/txt/Modify_kspace.txt +++ /dev/null @@ -1,25 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Kspace styles :h3 - -Classes that compute long-range Coulombic interactions via K-space -representations (Ewald, PPPM) are derived from the KSpace class. New -styles can be created to add new K-space options to LAMMPS. - -Ewald.cpp is an example of computing K-space interactions. - -Here is a brief description of methods you define in your new derived -class. See kspace.h for details. - -init: initialize the calculation before a run -setup: computation before the 1st timestep of a run -compute: every-timestep computation -memory_usage: tally of memory usage :tb(s=:) - diff --git a/doc/txt/Modify_min.txt b/doc/txt/Modify_min.txt deleted file mode 100644 index 8252a576f3..0000000000 --- a/doc/txt/Modify_min.txt +++ /dev/null @@ -1,23 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Minimization styles :h3 - -Classes that perform energy minimization derived from the Min class. -New styles can be created to add new minimization algorithms to -LAMMPS. - -Min_cg.cpp is an example of conjugate gradient minimization. - -Here is a brief description of methods you define in your new derived -class. See min.h for details. - -init: initialize the minimization before a run -run: perform the minimization -memory_usage: tally of memory usage :tb(s=:) diff --git a/doc/txt/Modify_overview.txt b/doc/txt/Modify_overview.txt deleted file mode 100644 index 4ab1eddf21..0000000000 --- a/doc/txt/Modify_overview.txt +++ /dev/null @@ -1,101 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Overview :h3 - -The best way to add a new feature to LAMMPS is to find a similar -feature and look at the corresponding source and header files to figure -out what it does. You will need some knowledge of C++ to be able to -understand the hi-level structure of LAMMPS and its class -organization, but functions (class methods) that do actual -computations are written in vanilla C-style code and operate on simple -C-style data structures (vectors and arrays). - -Most of the new features described on the "Modify"_Modify.html doc -page require you to write a new C++ derived class (except for -exceptions described below, where you can make small edits to existing -files). Creating a new class requires 2 files, a source code file -(*.cpp) and a header file (*.h). The derived class must provide -certain methods to work as a new option. Depending on how different -your new feature is compared to existing features, you can either -derive from the base class itself, or from a derived class that -already exists. Enabling LAMMPS to invoke the new class is as simple -as putting the two source files in the src dir and re-building LAMMPS. - -The advantage of C++ and its object-orientation is that all the code -and variables needed to define the new feature are in the 2 files you -write, and thus shouldn't make the rest of LAMMPS more complex or -cause side-effect bugs. - -Here is a concrete example. Suppose you write 2 files pair_foo.cpp -and pair_foo.h that define a new class PairFoo that computes pairwise -potentials described in the classic 1997 "paper"_#Foo by Foo, et al. -If you wish to invoke those potentials in a LAMMPS input script with a -command like - -pair_style foo 0.1 3.5 :pre - -then your pair_foo.h file should be structured as follows: - -#ifdef PAIR_CLASS -PairStyle(foo,PairFoo) -#else -... -(class definition for PairFoo) -... -#endif :pre - -where "foo" is the style keyword in the pair_style command, and -PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h -files. - -When you re-build LAMMPS, your new pairwise potential becomes part of -the executable and can be invoked with a pair_style command like the -example above. Arguments like 0.1 and 3.5 can be defined and -processed by your new class. - -As illustrated by this pairwise example, many kinds of options are -referred to in the LAMMPS documentation as the "style" of a particular -command. - -The "Modify page"_Modify.html lists all the common styles in LAMMPS, -and discusses the header file for the base class that these styles are -derived from. Public variables in that file are ones used and set by -the derived classes which are also used by the base class. Sometimes -they are also used by the rest of LAMMPS. Virtual functions in the -base class header file which are set = 0 are ones you must define in -your new derived class to give it the functionality LAMMPS expects. -Virtual functions that are not set to 0 are functions you can -optionally define. - -Additionally, new output options can be added directly to the -thermo.cpp, dump_custom.cpp, and variable.cpp files. These are also -listed on the "Modify page"_Modify.html. - -Here are additional guidelines for modifying LAMMPS and adding new -functionality: - -Think about whether what you want to do would be better as a pre- or -post-processing step. Many computations are more easily and more -quickly done that way. :ulb,l - -Don't do anything within the timestepping of a run that isn't -parallel. E.g. don't accumulate a bunch of data on a single processor -and analyze it. You run the risk of seriously degrading the parallel -efficiency. :l - -If your new feature reads arguments or writes output, make sure you -follow the unit conventions discussed by the "units"_units.html -command. :l -:ule - -:line - -:link(Foo) -[(Foo)] Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997). diff --git a/doc/txt/Modify_pair.txt b/doc/txt/Modify_pair.txt deleted file mode 100644 index 40806937d6..0000000000 --- a/doc/txt/Modify_pair.txt +++ /dev/null @@ -1,33 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Pair styles :h3 - -Classes that compute pairwise interactions are derived from the Pair -class. In LAMMPS, pairwise calculation include many-body potentials -such as EAM or Tersoff where particles interact without a static bond -topology. New styles can be created to add new pair potentials to -LAMMPS. - -Pair_lj_cut.cpp is a simple example of a Pair class, though it -includes some optional methods to enable its use with rRESPA. - -Here is a brief description of the class methods in pair.h: - -compute: workhorse routine that computes pairwise interactions -settings: reads the input script line with arguments you define -coeff: set coefficients for one i,j type pair -init_one: perform initialization for one i,j type pair -init_style: initialization specific to this pair style -write & read_restart: write/read i,j pair coeffs to restart files -write & read_restart_settings: write/read global settings to restart files -single: force and energy of a single pairwise interaction between 2 atoms -compute_inner/middle/outer: versions of compute used by rRESPA :tb(s=:) - -The inner/middle/outer routines are optional. diff --git a/doc/txt/Modify_region.txt b/doc/txt/Modify_region.txt deleted file mode 100644 index c7a56bd32a..0000000000 --- a/doc/txt/Modify_region.txt +++ /dev/null @@ -1,25 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Region styles :h3 - -Classes that define geometric regions are derived from the Region -class. Regions are used elsewhere in LAMMPS to group atoms, delete -atoms to create a void, insert atoms in a specified region, etc. New -styles can be created to add new region shapes to LAMMPS. - -Region_sphere.cpp is an example of a spherical region. - -Here is a brief description of methods you define in your new derived -class. See region.h for details. - -inside: determine whether a point is in the region -surface_interior: determine if a point is within a cutoff distance inside of surface -surface_exterior: determine if a point is within a cutoff distance outside of surface -shape_update : change region shape if set by time-dependent variable :tb(s=:) diff --git a/doc/txt/Modify_thermo.txt b/doc/txt/Modify_thermo.txt deleted file mode 100644 index 1772bae87a..0000000000 --- a/doc/txt/Modify_thermo.txt +++ /dev/null @@ -1,35 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Thermodynamic output options :h3 - -There is one class that computes and prints thermodynamic information -to the screen and log file; see the file thermo.cpp. - -There are two styles defined in thermo.cpp: "one" and "multi". There -is also a flexible "custom" style which allows the user to explicitly -list keywords for quantities to print when thermodynamic info is -output. See the "thermo_style"_thermo_style.html command for a list -of defined quantities. - -The thermo styles (one, multi, etc) are simply lists of keywords. -Adding a new style thus only requires defining a new list of keywords. -Search for the word "customize" with references to "thermo style" in -thermo.cpp to see the two locations where code will need to be added. - -New keywords can also be added to thermo.cpp to compute new quantities -for output. Search for the word "customize" with references to -"keyword" in thermo.cpp to see the several locations where code will -need to be added. - -Note that the "thermo_style custom"_thermo.html command already allows -for thermo output of quantities calculated by "fixes"_fix.html, -"computes"_compute.html, and "variables"_variable.html. Thus, it may -be simpler to compute what you wish via one of those constructs, than -by adding a new keyword to the thermo command. diff --git a/doc/txt/Modify_variable.txt b/doc/txt/Modify_variable.txt deleted file mode 100644 index b163272f3e..0000000000 --- a/doc/txt/Modify_variable.txt +++ /dev/null @@ -1,46 +0,0 @@ -"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Variable options :h3 - -There is one class that computes and stores "variable"_variable.html -information in LAMMPS; see the file variable.cpp. The value -associated with a variable can be periodically printed to the screen -via the "print"_print.html, "fix print"_fix_print.html, or -"thermo_style custom"_thermo_style.html commands. Variables of style -"equal" can compute complex equations that involve the following types -of arguments: - -thermo keywords = ke, vol, atoms, ... -other variables = v_a, v_myvar, ... -math functions = div(x,y), mult(x,y), add(x,y), ... -group functions = mass(group), xcm(group,x), ... -atom values = x\[123\], y\[3\], vx\[34\], ... -compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre - -Adding keywords for the "thermo_style custom"_thermo_style.html -command (which can then be accessed by variables) is discussed on the -"Modify thermo"_Modify_thermo.html doc page. - -Adding a new math function of one or two arguments can be done by -editing one section of the Variable::evaluate() method. Search for -the word "customize" to find the appropriate location. - -Adding a new group function can be done by editing one section of the -Variable::evaluate() method. Search for the word "customize" to find -the appropriate location. You may need to add a new method to the -Group class as well (see the group.cpp file). - -Accessing a new atom-based vector can be done by editing one section -of the Variable::evaluate() method. Search for the word "customize" -to find the appropriate location. - -Adding new "compute styles"_compute.html (whose calculated values can -then be accessed by variables) is discussed on the "Modify -compute"_Modify_compute.html doc page. diff --git a/doc/txt/Packages.txt b/doc/txt/Packages.txt deleted file mode 100644 index 231c8528e9..0000000000 --- a/doc/txt/Packages.txt +++ /dev/null @@ -1,40 +0,0 @@ -"Previous Section"_Commands.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Speed.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Optional packages :h2 - -This section gives an overview of the optional packages that extend -LAMMPS functionality. Packages are groups of files that enable a -specific set of features. For example, force fields for molecular -systems or rigid-body constraints are in packages. You can see the -list of all packages and "make" commands to manage them by typing -"make package" from within the src directory of the LAMMPS -distribution. The "Build package"_Build_package.html doc page gives -general info on how to install and un-install packages as part of the -LAMMPS build process. - - - - - -"Standard packages"_Packages_standard.html -"User packages"_Packages_user.html -"Details on each package"_Packages_details.html :ul - - diff --git a/doc/txt/Packages_standard.txt b/doc/txt/Packages_standard.txt deleted file mode 100644 index 7fb1d99174..0000000000 --- a/doc/txt/Packages_standard.txt +++ /dev/null @@ -1,65 +0,0 @@ -"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Standard packages :h3 - -This is the list of standard packages in LAMMPS. The link for each -package name gives more details. - -Standard packages are supported by the LAMMPS developers and are -written in a syntax and style consistent with the rest of LAMMPS. -This means the developers will answer questions about them, debug and -fix them if necessary, and keep them compatible with future changes to -LAMMPS. - -The "Example" column is a sub-directory in the examples directory of -the distribution which has an input script that uses the package. -E.g. "peptide" refers to the examples/peptide directory; USER/atc -refers to the examples/USER/atc directory. The "Library" column -indicates whether an extra library is needed to build and use the -package: - -no = no library -sys = system library: you likely have it on your machine -int = internal library: provided with LAMMPS, but you may need to build it -ext = external library: you will need to download and install it on your machine :ul - -Package, Description, Doc page, Example, Library -"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, no -"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, no -"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, n/a, no -"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, no -"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, n/a, sys -"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, no -"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, no -"GPU"_Packages_details.html#PKG-GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int -"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, no -"KIM"_Packages_details.html#PKG-KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext -"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no -"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, no -"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext -"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no -"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no -"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int -"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no -"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no -"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no -"MSCG"_Packages_details.html#PKG-MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext -"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no -"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, no -"POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int -"PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys -"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no -"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no -"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no -"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no -"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, no -"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, no -"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, no -"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, n/a, ext :tb(ea=c,ca1=l) diff --git a/doc/txt/Packages_user.txt b/doc/txt/Packages_user.txt deleted file mode 100644 index 4210f617ef..0000000000 --- a/doc/txt/Packages_user.txt +++ /dev/null @@ -1,83 +0,0 @@ -"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -User packages :h3 - -This is a list of user packages in LAMMPS. The link for each package -name gives more details. - -User packages have been contributed by users, and begin with the -"user" prefix. If a contribution is a single command (single file), -it is typically in the user-misc package. User packages don't -necessarily meet the requirements of the "standard -packages"_Packages_standard.html. This means the developers will try -to keep things working and usually can answer technical questions -about compiling the package. If you have problems using a specific -feature provided in a user package, you may need to contact the -contributor directly to get help. Information on how to submit -additions you make to LAMMPS as single files or as a standard or user -package is explained on the "Modify contribute"_Modify_contribute.html -doc page. - -The "Example" column is a sub-directory in the examples directory of -the distribution which has an input script that uses the package. -E.g. "peptide" refers to the examples/peptide directory; USER/atc -refers to the examples/USER/atc directory. The "Library" column -indicates whether an extra library is needed to build and use the -package: - -no = no library -sys = system library: you likely have it on your machine -int = internal library: provided with LAMMPS, but you may need to build it -ext = external library: you will need to download and install it on your machine :ul - -Package, Description, Doc page, Example, Library -"USER-ADIOS"_Packages_details.html#PKG-USER-ADIOS, dump output via ADIOS, "dump adios"_dump_adios.html, USER/adios, ext -"USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int -"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int -"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no -"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no -"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no -"USER-COLVARS"_Packages_details.html#PKG-USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int -"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, no -"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, no -"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, no -"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, no -"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, no -"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, n/a, ext -"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no -"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no -"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no -"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meamc.html, meamc, no -"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no -"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no -"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no -"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no -"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext -"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext -"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no -"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no -"USER-PLUMED"_Packages_details.html#PKG-USER-PLUMED, "PLUMED"_#PLUMED free energy library,"fix plumed"_fix_plumed.html, USER/plumed, ext -"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm_atom.html, n/a, no -"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext -"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no -"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext -"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no -"USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext -"USER-SDPD"_Packages_details.html#PKG-USER-SDPD, smoothed dissipative particle dynamics,"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html, USER/sdpd, no -"USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext -"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no -"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no -"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no -"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no -"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext -"USER-YAFF"_Packages_details.html#PKG-USER-YAFF, additional styles implemented in YAFF, "angle_style cross"_angle_cross.html, USER/yaff, no :tb(ea=c,ca1=l) - -:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF) -:link(PLUMED,http://www.plumed.org) diff --git a/doc/txt/Python_call.txt b/doc/txt/Python_call.txt deleted file mode 100644 index 34b04679d5..0000000000 --- a/doc/txt/Python_call.txt +++ /dev/null @@ -1,85 +0,0 @@ -"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Call Python from a LAMMPS input script :h3 - -LAMMPS has several commands which can be used to invoke Python -code directly from an input script: - -"python"_python.html -"variable python"_variable.html -"fix python/invoke"_fix_python_invoke.html -"pair_style python"_pair_python.html :ul - -The "python"_python.html command which can be used to define and -execute a Python function that you write the code for. The Python -function can also be assigned to a LAMMPS python-style variable via -the "variable"_variable.html command. Each time the variable is -evaluated, either in the LAMMPS input script itself, or by another -LAMMPS command that uses the variable, this will trigger the Python -function to be invoked. - -The Python code for the function can be included directly in the input -script or in an auxiliary file. The function can have arguments which -are mapped to LAMMPS variables (also defined in the input script) and -it can return a value to a LAMMPS variable. This is thus a mechanism -for your input script to pass information to a piece of Python code, -ask Python to execute the code, and return information to your input -script. - -Note that a Python function can be arbitrarily complex. It can import -other Python modules, instantiate Python classes, call other Python -functions, etc. The Python code that you provide can contain more -code than the single function. It can contain other functions or -Python classes, as well as global variables or other mechanisms for -storing state between calls from LAMMPS to the function. - -The Python function you provide can consist of "pure" Python code that -only performs operations provided by standard Python. However, the -Python function can also "call back" to LAMMPS through its -Python-wrapped library interface, in the manner described in the -"Python run"_Python_run.html doc page. This means it can issue LAMMPS -input script commands or query and set internal LAMMPS state. As an -example, this can be useful in an input script to create a more -complex loop with branching logic, than can be created using the -simple looping and branching logic enabled by the "next"_next.html and -"if"_if.html commands. - -See the "python"_python.html doc page and the "variable"_variable.html -doc page for its python-style variables for more info, including -examples of Python code you can write for both pure Python operations -and callbacks to LAMMPS. - -The "fix python/invoke"_fix_python_invoke.html command can execute -Python code at selected timesteps during a simulation run. - -The "pair_style python"_pair_python.html command allows you to define -pairwise potentials as python code which encodes a single pairwise -interaction. This is useful for rapid development and debugging of a -new potential. - -To use any of these commands, you only need to build LAMMPS with the -PYTHON package installed: - -make yes-python -make machine :pre - -Note that this will link LAMMPS with the Python library on your -system, which typically requires several auxiliary system libraries to -also be linked. The list of these libraries and the paths to find -them are specified in the lib/python/Makefile.lammps file. You need -to insure that file contains the correct information for your version -of Python and your machine to successfully build LAMMPS. See the -lib/python/README file for more info. - -If you want to write Python code with callbacks to LAMMPS, then you -must also follow the steps summarized in the "Python -run"_Python_run.html doc page. I.e. you must build LAMMPS as a shared -library and insure that Python can find the python/lammps.py file and -the shared library. diff --git a/doc/txt/Python_examples.txt b/doc/txt/Python_examples.txt deleted file mode 100644 index 181181dfb2..0000000000 --- a/doc/txt/Python_examples.txt +++ /dev/null @@ -1,81 +0,0 @@ -"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Example Python scripts that use LAMMPS :h3 - -These are the Python scripts included as demos in the python/examples -directory of the LAMMPS distribution, to illustrate the kinds of -things that are possible when Python wraps LAMMPS. If you create your -own scripts, send them to us and we can include them in the LAMMPS -distribution. - -trivial.py, read/run a LAMMPS input script through Python, -demo.py, invoke various LAMMPS library interface routines, -simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp, -split.py, same as simple.py but running in parallel on a subset of procs, -gui.py, GUI go/stop/temperature-slider to control LAMMPS, -plot.py, real-time temperature plot with GnuPlot via Pizza.py, -viz_tool.py, real-time viz via some viz package, -vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2) - -:line - -For the viz_tool.py and vizplotgui_tool.py commands, replace "tool" -with "gl" or "atomeye" or "pymol" or "vmd", depending on what -visualization package you have installed. - -Note that for GL, you need to be able to run the Pizza.py GL tool, -which is included in the pizza sub-directory. See the "Pizza.py doc -pages"_pizza for more info: - -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) - -Note that for AtomEye, you need version 3, and there is a line in the -scripts that specifies the path and name of the executable. See the -AtomEye WWW pages "here"_atomeye or "here"_atomeye3 for more details: - -http://mt.seas.upenn.edu/Archive/Graphics/A -http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre - -:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) -:link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html) - -The latter link is to AtomEye 3 which has the scripting -capability needed by these Python scripts. - -Note that for PyMol, you need to have built and installed the -open-source version of PyMol in your Python, so that you can import it -from a Python script. See the PyMol WWW pages "here"_pymolhome or -"here"_pymolopen for more details: - -http://www.pymol.org -http://sourceforge.net/scm/?type=svn&group_id=4546 :pre - -:link(pymolhome,http://www.pymol.org) -:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546) - -The latter link is to the open-source version. - -Note that for VMD, you need a fairly current version (1.8.7 works for -me) and there are some lines in the pizza/vmd.py script for 4 PIZZA -variables that have to match the VMD installation on your system. - -:line - -See the python/README file for instructions on how to run them and the -source code for individual scripts for comments about what they do. - -Here are screenshots of the vizplotgui_tool.py script in action for -different visualization package options. Click to see larger images: - -:image(JPG/screenshot_gl_small.jpg,JPG/screenshot_gl.jpg) -:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg) -:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg) -:image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg) - diff --git a/doc/txt/Python_head.txt b/doc/txt/Python_head.txt deleted file mode 100644 index 54f995c565..0000000000 --- a/doc/txt/Python_head.txt +++ /dev/null @@ -1,72 +0,0 @@ -"Previous Section"_Modify.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Errors.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Use Python with LAMMPS :h2 - -These doc pages describe various ways that LAMMPS and Python can be -used together. - - - - - -"Overview of Python and LAMMPS"_Python_overview.html -"Run LAMMPS from Python"_Python_run.html -"Build LAMMPS as a shared library"_Python_shlib.html -"Install LAMMPS in Python"_Python_install.html -"Extend Python to run in parallel"_Python_mpi.html -"Test the Python/LAMMPS interface"_Python_test.html -"Python library interface"_Python_library.html -"PyLammps interface"_Python_pylammps.html -"Example Python scripts that use LAMMPS"_Python_examples.html -"Call Python from a LAMMPS input script"_Python_call.html :all(b) - - - -If you're not familiar with "Python"_http://www.python.org, it's a -powerful scripting and programming language which can do most -everything that lower-level languages like C or C++ can do in fewer -lines of code. The only drawback is slower execution speed. Python -is also easy to use as a "glue" language to drive a program through -its library interface, or to hook multiple pieces of software -together, such as a simulation code plus a visualization tool, or to -run a coupled multiscale or multiphysics model. - -See the "Howto_couple"_Howto_couple.html doc page for more ideas about -coupling LAMMPS to other codes. See the "Howto -library"_Howto_library.html doc page for a description of the LAMMPS -library interface provided in src/library.h and src/library.h. That -interface is exposed to Python either when calling LAMMPS from Python -or when calling Python from a LAMMPS input script and then calling -back to LAMMPS from Python code. The library interface is designed to -be easy to add functionality to. Thus the Python interface to LAMMPS -is also easy to extend as well. - -If you create interesting Python scripts that run LAMMPS or -interesting Python functions that can be called from a LAMMPS input -script, that you think would be generally useful, please post them as -a pull request to our "GitHub site"_https://github.com/lammps/lammps, -and they can be added to the LAMMPS distribution or webpage. diff --git a/doc/txt/Python_install.txt b/doc/txt/Python_install.txt deleted file mode 100644 index 2c134974f5..0000000000 --- a/doc/txt/Python_install.txt +++ /dev/null @@ -1,67 +0,0 @@ -"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Installing LAMMPS in Python :h3 - -For Python to invoke LAMMPS, there are 2 files it needs to know about: - -python/lammps.py -liblammps.so or liblammps.dylib :ul - -The python source code in lammps.py is the Python wrapper on the -LAMMPS library interface. The liblammps.so or liblammps.dylib file -is the shared LAMMPS library that Python loads dynamically. - -You can achieve that Python can find these files in one of two ways: - -set two environment variables pointing to the location in the source tree -run "make install-python" or run the python/install.py script explicitly :ul - -When calling "make install-python" LAMMPS will try to install the -python module and the shared library into the python site-packages folders; -either the system-wide ones, or the local users ones (in case of insufficient -permissions for the global install). Python will then find the module -and shared library file automatically. The exact location of these folders -depends on your python version and your operating system. - -If you set the paths to these files as environment variables, you only -have to do it once. For the csh or tcsh shells, add something like -this to your ~/.cshrc file, one line for each of the two files: - -setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python -setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre - -On MacOSX you may also need to set DYLD_LIBRARY_PATH accordingly. -For Bourne/Korn shells accordingly into the corresponding files using -the "export" shell builtin. - -If you use "make install-python" or the python/install.py script, you need -to invoke it every time you rebuild LAMMPS (as a shared library) or -make changes to the python/lammps.py file, so that the site-packages -files are updated with the new version. - -If the default settings of "make install-python" are not what you want, -you can invoke install.py from the python directory manually as - -% python install.py -m \ -l -v \[-d \\] :pre - -The -m flag points to the lammps.py python module file to be installed, -the -l flag points to the LAMMPS shared library file to be installed, -the -v flag points to the version.h file in the LAMMPS source -and the optional -d flag to a custom (legacy) installation folder :ul - -If you use a legacy installation folder, you will need to set your -PYTHONPATH and LD_LIBRARY_PATH (and/or DYLD_LIBRARY_PATH) environment -variables accordingly, as described above. - -Note that if you want Python to be able to load different versions of -the LAMMPS shared library (see "this section"_Python_shlib.html), you will -need to manually copy files like liblammps_g++.so into the appropriate -system directory. This is not needed if you set the LD_LIBRARY_PATH -environment variable as described above. diff --git a/doc/txt/Python_mpi.txt b/doc/txt/Python_mpi.txt deleted file mode 100644 index 96c42e0d0f..0000000000 --- a/doc/txt/Python_mpi.txt +++ /dev/null @@ -1,67 +0,0 @@ -"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Extending Python to run in parallel :h3 - -If you wish to run LAMMPS in parallel from Python, you need to extend -your Python with an interface to MPI. This also allows you to -make MPI calls directly from Python in your script, if you desire. - -We recommend use of mpi4py: - -"PyPar"_https://github.com/daleroberts/pypar :ul - -As of version 2.0.0 it allows passing a custom MPI communicator to -the LAMMPS constructor, which means one can easily run one or more -LAMMPS instances on subsets of the total MPI ranks. - -To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it -and from its main directory, type - -python setup.py build -sudo python setup.py install :pre - -Again, the "sudo" is only needed if required to copy mpi4py files into -your Python distribution's site-packages directory. To install with -user privilege into the user local directory type - -python setup.py install --user :pre - -If you have successfully installed mpi4py, you should be able to run -Python and type - -from mpi4py import MPI :pre - -without error. You should also be able to run python in parallel -on a simple test script - -% mpirun -np 4 python test.py :pre - -where test.py contains the lines - -from mpi4py import MPI -comm = MPI.COMM_WORLD -print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) :pre - -and see one line of output for each processor you run on. - -NOTE: To use mpi4py and LAMMPS in parallel from Python, you must -insure both are using the same version of MPI. If you only have one -MPI installed on your system, this is not an issue, but it can be if -you have multiple MPIs. Your LAMMPS build is explicit about which MPI -it is using, since you specify the details in your lo-level -src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find -information about the MPI it uses to build against. And it tries to -load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find -the MPI library that LAMMPS is using. If you have problems running -both mpi4py and LAMMPS together, this is an issue you may need to -address, e.g. by moving other MPI installations so that mpi4py finds -the right one. - - diff --git a/doc/txt/Python_overview.txt b/doc/txt/Python_overview.txt deleted file mode 100644 index 0195ec2b20..0000000000 --- a/doc/txt/Python_overview.txt +++ /dev/null @@ -1,36 +0,0 @@ -"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Tools.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands.html#comm) - -:line - -Overview of Python and LAMMPS :h3 - -LAMMPS can work together with Python in three ways. First, Python can -wrap LAMMPS through the its "library interface"_Howto_library.html, so -that a Python script can create one or more instances of LAMMPS and -launch one or more simulations. In Python lingo, this is called -"extending" Python with a LAMMPS module. - -Second, a lower-level Python interface can be used indirectly through -the provided PyLammps and IPyLammps wrapper classes, written in Python. -These wrappers try to simplify the usage of LAMMPS in Python by -providing an object-based interface to common LAMMPS functionality. -They also reduces the amount of code necessary to parameterize LAMMPS -scripts through Python and make variables and computes directly -accessible. - -Third, LAMMPS can use the Python interpreter, so that a LAMMPS -input script or styles can invoke Python code directly, and pass -information back-and-forth between the input script and Python -functions you write. This Python code can also callback to LAMMPS -to query or change its attributes through the LAMMPS Python module -mentioned above. In Python lingo, this is "embedding" Python in -LAMMPS. When used in this mode, Python can perform script operations -that the simple LAMMPS input script syntax can not. - - diff --git a/doc/txt/Python_pylammps.txt b/doc/txt/Python_pylammps.txt deleted file mode 100644 index 303ac21a27..0000000000 --- a/doc/txt/Python_pylammps.txt +++ /dev/null @@ -1,14 +0,0 @@ -"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -PyLammps interface :h3 - -PyLammps is a Python wrapper class which can be created on its own or -use an existing lammps Python object. It has its own "Howto -pylammps"_Howto_pylammps.html doc page. diff --git a/doc/txt/Python_run.txt b/doc/txt/Python_run.txt deleted file mode 100644 index 8974d1469a..0000000000 --- a/doc/txt/Python_run.txt +++ /dev/null @@ -1,40 +0,0 @@ -"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Run LAMMPS from Python :h3 - -The LAMMPS distribution includes a python directory with all you need -to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS -library interface, with one wrapper function per LAMMPS library -function. This file makes it is possible to do the following either -from a Python script, or interactively from a Python prompt: create -one or more instances of LAMMPS, invoke LAMMPS commands or give it an -input script, run LAMMPS incrementally, extract LAMMPS results, an -modify internal LAMMPS variables. From a Python script you can do -this in serial or parallel. Running Python interactively in parallel -does not generally work, unless you have a version of Python that -extends Python to enable multiple instances of Python to read what you -type. - -To do all of this, you must first build LAMMPS as a shared library, -then insure that your Python can find the python/lammps.py file and -the shared library. - -Two advantages of using Python to run LAMMPS are how concise the -language is, and that it can be run interactively, enabling rapid -development and debugging. If you use it to mostly invoke costly -operations within LAMMPS, such as running a simulation for a -reasonable number of timesteps, then the overhead cost of invoking -LAMMPS through Python will be negligible. - -The Python wrapper for LAMMPS uses the "ctypes" package in Python, -which auto-generates the interface code needed between Python and a -set of C-style library functions. Ctypes is part of standard Python -for versions 2.5 and later. You can check which version of Python you -have by simply typing "python" at a shell prompt. diff --git a/doc/txt/Python_shlib.txt b/doc/txt/Python_shlib.txt deleted file mode 100644 index 91c90d9a8f..0000000000 --- a/doc/txt/Python_shlib.txt +++ /dev/null @@ -1,73 +0,0 @@ -"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Build LAMMPS as a shared library :h3 - -Build LAMMPS as a shared library using make :h4 - -Instructions on how to build LAMMPS as a shared library are given on -the "Build_basics"_Build_basics.html doc page. A shared library is -one that is dynamically loadable, which is what Python requires to -wrap LAMMPS. On Linux this is a library file that ends in ".so", not -".a". - -From the src directory, type - -make foo mode=shlib :pre - -where foo is the machine target name, such as mpi or serial. -This should create the file liblammps_foo.so in the src directory, as -well as a soft link liblammps.so, which is what the Python wrapper will -load by default. Note that if you are building multiple machine -versions of the shared library, the soft link is always set to the -most recently built version. - -NOTE: If you are building LAMMPS with an MPI or FFT library or other -auxiliary libraries (used by various packages), then all of these -extra libraries must also be shared libraries. If the LAMMPS -shared-library build fails with an error complaining about this, see -the "Build_basics"_Build_basics.html doc page. - -Build LAMMPS as a shared library using CMake :h4 - -When using CMake the following two options are necessary to generate the LAMMPS -shared library: - --D BUILD_LIB=on # enable building LAMMPS as a library --D BUILD_SHARED_LIBS=on # enable building of LAMMPS shared library (both options are needed!) :pre - -What this does is create a liblammps.so which contains the majority of LAMMPS -code. The generated lmp binary also dynamically links to this library. This -means that either this liblammps.so file has to be in the same directory, a system -library path (e.g. /usr/lib64/) or in the LD_LIBRARY_PATH. - -If you want to use the shared library with Python the recommended way is to create a virtualenv and use it as -CMAKE_INSTALL_PREFIX. - -# create virtualenv -virtualenv --python=$(which python3) myenv3 -source myenv3/bin/activate :pre - -# build library -mkdir build -cd build -cmake -D PKG_PYTHON=on -D BUILD_LIB=on -D BUILD_SHARED_LIBS=on -D CMAKE_INSTALL_PREFIX=$VIRTUAL_ENV ../cmake -make -j 4 :pre - -# install into prefix -make install :pre - -This will also install the Python module into your virtualenv. Since virtualenv -doesn't change your LD_LIBRARY_PATH, you still need to add its lib64 folder to -it, which contains the installed liblammps.so. - -export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib64:$LD_LIBRARY_PATH :pre - -Starting Python outside (!) of your build directory, but with the virtualenv -enabled and with the LD_LIBRARY_PATH set gives you access to LAMMPS via Python. diff --git a/doc/txt/Python_test.txt b/doc/txt/Python_test.txt deleted file mode 100644 index 3909ea9979..0000000000 --- a/doc/txt/Python_test.txt +++ /dev/null @@ -1,131 +0,0 @@ -"Higher level section"_Python_head.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Test the Python/LAMMPS interface :h3 - -To test if LAMMPS is callable from Python, launch Python interactively -and type: - ->>> from lammps import lammps ->>> lmp = lammps() :pre - -If you get no errors, you're ready to use LAMMPS from Python. If the -2nd command fails, the most common error to see is - -OSError: Could not load LAMMPS dynamic library :pre - -which means Python was unable to load the LAMMPS shared library. This -typically occurs if the system can't find the LAMMPS shared library or -one of the auxiliary shared libraries it depends on, or if something -about the library is incompatible with your Python. The error message -should give you an indication of what went wrong. - -You can also test the load directly in Python as follows, without -first importing from the lammps.py file: - ->>> from ctypes import CDLL ->>> CDLL("liblammps.so") :pre - -If an error occurs, carefully go through the steps on the -"Build_basics"_Build_basics.html doc page about building a shared -library and the "Python_install"_Python_install.html doc page about -insuring Python can find the necessary two files it needs. - -[Test LAMMPS and Python in serial:] :h4 - -To run a LAMMPS test in serial, type these lines into Python -interactively from the bench directory: - ->>> from lammps import lammps ->>> lmp = lammps() ->>> lmp.file("in.lj") :pre - -Or put the same lines in the file test.py and run it as - -% python test.py :pre - -Either way, you should see the results of running the in.lj benchmark -on a single processor appear on the screen, the same as if you had -typed something like: - -lmp_g++ -in in.lj :pre - -[Test LAMMPS and Python in parallel:] :h4 - -To run LAMMPS in parallel, assuming you have installed the -"PyPar"_https://github.com/daleroberts/pypar package as discussed -above, create a test.py file containing these lines: - -import pypar -from lammps import lammps -lmp = lammps() -lmp.file("in.lj") -print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp -pypar.finalize() :pre - -To run LAMMPS in parallel, assuming you have installed the -"mpi4py"_https://bitbucket.org/mpi4py/mpi4py package as discussed -above, create a test.py file containing these lines: - -from mpi4py import MPI -from lammps import lammps -lmp = lammps() -lmp.file("in.lj") -me = MPI.COMM_WORLD.Get_rank() -nprocs = MPI.COMM_WORLD.Get_size() -print "Proc %d out of %d procs has" % (me,nprocs),lmp -MPI.Finalize() :pre - -You can either script in parallel as: - -% mpirun -np 4 python test.py :pre - -and you should see the same output as if you had typed - -% mpirun -np 4 lmp_g++ -in in.lj :pre - -Note that if you leave out the 3 lines from test.py that specify PyPar -commands you will instantiate and run LAMMPS independently on each of -the P processors specified in the mpirun command. In this case you -should get 4 sets of output, each showing that a LAMMPS run was made -on a single processor, instead of one set of output showing that -LAMMPS ran on 4 processors. If the 1-processor outputs occur, it -means that PyPar is not working correctly. - -Also note that once you import the PyPar module, PyPar initializes MPI -for you, and you can use MPI calls directly in your Python script, as -described in the PyPar documentation. The last line of your Python -script should be pypar.finalize(), to insure MPI is shut down -correctly. - -[Running Python scripts:] :h4 - -Note that any Python script (not just for LAMMPS) can be invoked in -one of several ways: - -% python foo.script -% python -i foo.script -% foo.script :pre - -The last command requires that the first line of the script be -something like this: - -#!/usr/local/bin/python -#!/usr/local/bin/python -i :pre - -where the path points to where you have Python installed, and that you -have made the script file executable: - -% chmod +x foo.script :pre - -Without the "-i" flag, Python will exit when the script finishes. -With the "-i" flag, you will be left in the Python interpreter when -the script finishes, so you can type subsequent commands. As -mentioned above, you can only run Python interactively when running -Python on a single processor, not in parallel. diff --git a/doc/txt/Run_basics.txt b/doc/txt/Run_basics.txt deleted file mode 100644 index 1b7387b46b..0000000000 --- a/doc/txt/Run_basics.txt +++ /dev/null @@ -1,89 +0,0 @@ -"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Basics of running LAMMPS :h3 - -LAMMPS is run from the command line, reading commands from a -file via the -in command line flag, or from standard input. -Using the "-in in.file" variant is recommended: - -lmp_serial < in.file -lmp_serial -in in.file -/path/to/lammps/src/lmp_serial < in.file -mpirun -np 4 lmp_mpi -in in.file -mpirun -np 8 /path/to//lammps/src/lmp_mpi -in in.file -mpirun -np 6 /usr/local/bin/lmp -in in.file :pre - -You normally run the LAMMPS command in the directory where your -input script is located. That is also where output files are -produced by default, unless you provide specific other paths in -your input script or on the command line. As in some of the -examples above, the LAMMPS executable itself can be placed elsewhere. - -NOTE: The redirection operator "<" will not always work when running -in parallel with mpirun; for those systems the -in form is required. - -As LAMMPS runs it prints info to the screen and a logfile named -log.lammps. More info about output is given on the "Run -output"_Run_output.html doc page. - -If LAMMPS encounters errors in the input script or while running a -simulation it will print an ERROR message and stop or a WARNING -message and continue. See the "Errors"_Errors.html doc page for a -discussion of the various kinds of errors LAMMPS can or can't detect, -a list of all ERROR and WARNING messages, and what to do about them. - -:line - -LAMMPS can run the same problem on any number of processors, including -a single processor. In theory you should get identical answers on any -number of processors and on any machine. In practice, numerical -round-off can cause slight differences and eventual divergence of -molecular dynamics phase space trajectories. See the "Errors -common"_Errors_common.html doc page for discussion of this. - -LAMMPS can run as large a problem as will fit in the physical memory -of one or more processors. If you run out of memory, you must run on -more processors or define a smaller problem. - -If you run LAMMPS in parallel via mpirun, you should be aware of the -"processors"_processors.html command which controls how MPI tasks are -mapped to the simulation box, as well as mpirun options that control -how MPI tasks are assigned to physical cores of the node(s) of the -machine you are running on. These settings can improve performance, -though the defaults are often adequate. - -For example, it is often important to bind MPI tasks (processes) to -physical cores (processor affinity), so that the operating system does -not migrate them during a simulation. If this is not the default -behavior on your machine, the mpirun option "--bind-to core" (OpenMPI) -or "-bind-to core" (MPICH) can be used. - -If the LAMMPS command(s) you are using support multi-threading, you -can set the number of threads per MPI task via the environment -variable OMP_NUM_THREADS, before you launch LAMMPS: - -export OMP_NUM_THREADS=2 # bash -setenv OMP_NUM_THREADS 2 # csh or tcsh :pre - -This can also be done via the "package"_package.html command or via -the "-pk command-line switch"_Run_options.html which invokes the -package command. See the "package"_package.html command or -"Speed"_Speed.html doc pages for more details about which accelerator -packages and which commands support multi-threading. - -:line - -You can experiment with running LAMMPS using any of the input scripts -provided in the examples or bench directory. Input scripts are named -in.* and sample outputs are named log.*.P where P is the number of -processors it was run on. - -Some of the examples or benchmarks require LAMMPS to be built with -optional packages. diff --git a/doc/txt/Run_head.txt b/doc/txt/Run_head.txt deleted file mode 100644 index 5e2c0fe235..0000000000 --- a/doc/txt/Run_head.txt +++ /dev/null @@ -1,38 +0,0 @@ -"Previous Section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Commands.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Run LAMMPS :h2 - -These pages explain how to run LAMMPS once you have "installed an -executable"_Install.html or "downloaded the source code"_Install.html -and "built an executable"_Build.html. The "Commands"_Commands.html -doc page describes how input scripts are structured and the commands -they can contain. - - - - - -"Basics of running LAMMPS"_Run_basics.html -"Command-line options"_Run_options.html -"Screen and logfile output"_Run_output.html -"Running LAMMPS on Windows"_Run_windows.html :all(b) - - diff --git a/doc/txt/Run_options.txt b/doc/txt/Run_options.txt deleted file mode 100644 index df1a57421a..0000000000 --- a/doc/txt/Run_options.txt +++ /dev/null @@ -1,542 +0,0 @@ -"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Command-line options :h3 - -At run time, LAMMPS recognizes several optional command-line switches -which may be used in any order. Either the full word or a one-or-two -letter abbreviation can be used: - -"-e or -echo"_#echo -"-h or -help"_#help -"-i or -in"_#file -"-k or -kokkos"_#run-kokkos -"-l or -log"_#log -"-m or -mpicolor"_#mpicolor -"-nc or -nocite"_#nocite -"-pk or -package"_#package -"-p or -partition"_#partition -"-pl or -plog"_#plog -"-ps or -pscreen"_#pscreen -"-ro or -reorder"_#reorder -"-r2data or -restart2data"_#restart2data -"-r2dump or -restart2dump"_#restart2dump -"-sc or -screen"_#screen -"-sf or -suffix"_#suffix -"-v or -var"_#var :ul - -For example, the lmp_mpi executable might be launched as follows: - -mpirun -np 16 lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy -mpirun -np 16 lmp_mpi -var f tmp.out -log my.log -screen none -in in.alloy :pre - -:line - -[-echo style] :link(echo) - -Set the style of command echoing. The style can be {none} or {screen} -or {log} or {both}. Depending on the style, each command read from -the input script will be echoed to the screen and/or logfile. This -can be useful to figure out which line of your script is causing an -input error. The default value is {log}. The echo style can also be -set by using the "echo"_echo.html command in the input script itself. - -:line - -[-help] :link(help) - -Print a brief help summary and a list of options compiled into this -executable for each LAMMPS style (atom_style, fix, compute, -pair_style, bond_style, etc). This can tell you if the command you -want to use was included via the appropriate package at compile time. -LAMMPS will print the info and immediately exit if this switch is -used. - -:line - -[-in file] :link(file) - -Specify a file to use as an input script. This is an optional switch -when running LAMMPS in one-partition mode. If it is not specified, -LAMMPS reads its script from standard input, typically from a script -via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should -also work in parallel, but if it does not (in the unlikely case that -an MPI implementation does not support it), then use the -in flag. -Note that this is a required switch when running LAMMPS in -multi-partition mode, since multiple processors cannot all read from -stdin. - -:line - -[-kokkos on/off keyword/value ...] :link(run-kokkos) - -Explicitly enable or disable KOKKOS support, as provided by the KOKKOS -package. Even if LAMMPS is built with this package, as described -in "Speed kokkos"_Speed_kokkos.html, this switch must be set to enable -running with KOKKOS-enabled styles the package provides. If the -switch is not set (the default), LAMMPS will operate as if the KOKKOS -package were not installed; i.e. you can run standard LAMMPS or with -the GPU or USER-OMP packages, for testing or benchmarking purposes. - -Additional optional keyword/value pairs can be specified which -determine how Kokkos will use the underlying hardware on your -platform. These settings apply to each MPI task you launch via the -"mpirun" or "mpiexec" command. You may choose to run one or more MPI -tasks per physical node. Note that if you are running on a desktop -machine, you typically have one physical node. On a cluster or -supercomputer there may be dozens or 1000s of physical nodes. - -Either the full word or an abbreviation can be used for the keywords. -Note that the keywords do not use a leading minus sign. I.e. the -keyword is "t", not "-t". Also note that each of the keywords has a -default setting. Examples of when to use these options and what -settings to use on different platforms is given on the "Speed -kokkos"_Speed_kokkos.html doc page. - -d or device -g or gpus -t or threads -n or numa :ul - -device Nd :pre - -This option is only relevant if you built LAMMPS with CUDA=yes, you -have more than one GPU per node, and if you are running with only one -MPI task per node. The Nd setting is the ID of the GPU on the node to -run on. By default Nd = 0. If you have multiple GPUs per node, they -have consecutive IDs numbered as 0,1,2,etc. This setting allows you -to launch multiple independent jobs on the node, each with a single -MPI task per node, and assign each job to run on a different GPU. - -gpus Ng Ns :pre - -This option is only relevant if you built LAMMPS with CUDA=yes, you -have more than one GPU per node, and you are running with multiple MPI -tasks per node (up to one per GPU). The Ng setting is how many GPUs -you will use. The Ns setting is optional. If set, it is the ID of a -GPU to skip when assigning MPI tasks to GPUs. This may be useful if -your desktop system reserves one GPU to drive the screen and the rest -are intended for computational work like running LAMMPS. By default -Ng = 1 and Ns is not set. - -Depending on which flavor of MPI you are running, LAMMPS will look for -one of these 4 environment variables - -SLURM_LOCALID (various MPI variants compiled with SLURM support) -MPT_LRANK (HPE MPI) -MV2_COMM_WORLD_LOCAL_RANK (Mvapich) -OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) :pre - -which are initialized by the "srun", "mpirun" or "mpiexec" commands. -The environment variable setting for each MPI rank is used to assign a -unique GPU ID to the MPI task. - -threads Nt :pre - -This option assigns Nt number of threads to each MPI task for -performing work when Kokkos is executing in OpenMP or pthreads mode. -The default is Nt = 1, which essentially runs in MPI-only mode. If -there are Np MPI tasks per physical node, you generally want Np*Nt = -the number of physical cores per node, to use your available hardware -optimally. This also sets the number of threads used by the host when -LAMMPS is compiled with CUDA=yes. - -numa Nm :pre - -This option is only relevant when using pthreads with hwloc support. -In this case Nm defines the number of NUMA regions (typically sockets) -on a node which will be utilized by a single MPI rank. By default Nm -= 1. If this option is used the total number of worker-threads per -MPI rank is threads*numa. Currently it is always almost better to -assign at least one MPI rank per NUMA region, and leave numa set to -its default value of 1. This is because letting a single process span -multiple NUMA regions induces a significant amount of cross NUMA data -traffic which is slow. - -:line - -[-log file] :link(log) - -Specify a log file for LAMMPS to write status information to. In -one-partition mode, if the switch is not used, LAMMPS writes to the -file log.lammps. If this switch is used, LAMMPS writes to the -specified file. In multi-partition mode, if the switch is not used, a -log.lammps file is created with hi-level status information. Each -partition also writes to a log.lammps.N file where N is the partition -ID. If the switch is specified in multi-partition mode, the hi-level -logfile is named "file" and each partition also logs information to a -file.N. For both one-partition and multi-partition mode, if the -specified file is "none", then no log files are created. Using a -"log"_log.html command in the input script will override this setting. -Option -plog will override the name of the partition log files file.N. - -:line - -[-mpicolor] color :link(mpicolor) - -If used, this must be the first command-line argument after the LAMMPS -executable name. It is only used when LAMMPS is launched by an mpirun -command which also launches another executable(s) at the same time. -(The other executable could be LAMMPS as well.) The color is an -integer value which should be different for each executable (another -application may set this value in a different way). LAMMPS and the -other executable(s) perform an MPI_Comm_split() with their own colors -to shrink the MPI_COMM_WORLD communication to be the subset of -processors they are actually running on. - -Currently, this is only used in LAMMPS to perform client/server -messaging with another application. LAMMPS can act as either a client -or server (or both). More details are given on the "Howto -client/server"_Howto_client_server.html doc page. - -Specifically, this refers to the "mpi/one" mode of messaging provided -by the "message"_message.html command and the CSlib library LAMMPS -links with from the lib/message directory. See the -"message"_message.html command for more details. - -:line - -[-nocite] :link(nocite) - -Disable writing the log.cite file which is normally written to list -references for specific cite-able features used during a LAMMPS run. -See the "citation page"_http://lammps.sandia.gov/cite.html for more -details. - -:line - -[-package style args ....] :link(package) - -Invoke the "package"_package.html command with style and args. The -syntax is the same as if the command appeared at the top of the input -script. For example "-package gpu 2" or "-pk gpu 2" is the same as -"package gpu 2"_package.html in the input script. The possible styles -and args are documented on the "package"_package.html doc page. This -switch can be used multiple times, e.g. to set options for the -USER-INTEL and USER-OMP packages which can be used together. - -Along with the "-suffix" command-line switch, this is a convenient -mechanism for invoking accelerator packages and their options without -having to edit an input script. - -:line - -[-partition 8x2 4 5 ...] :link(partition) - -Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P -processors and this switch is not used, LAMMPS runs in one partition, -i.e. all P processors run a single simulation. If this switch is -used, the P processors are split into separate partitions and each -partition runs its own simulation. The arguments to the switch -specify the number of processors in each partition. Arguments of the -form MxN mean M partitions, each with N processors. Arguments of the -form N mean a single partition with N processors. The sum of -processors in all partitions must equal P. Thus the command -"-partition 8x2 4 5" has 10 partitions and runs on a total of 25 -processors. - -Running with multiple partitions can be useful for running -"multi-replica simulations"_Howto_replica.html, where each replica -runs on one or a few processors. Note that with MPI installed on a -machine (e.g. your desktop), you can run on more (virtual) processors -than you have physical processors. - -To run multiple independent simulations from one input script, using -multiple partitions, see the "Howto multiple"_Howto_multiple.html doc -page. World- and universe-style "variables"_variable.html are useful -in this context. - -:line - -[-plog file] :link(plog) - -Specify the base name for the partition log files, so partition N -writes log information to file.N. If file is none, then no partition -log files are created. This overrides the filename specified in the --log command-line option. This option is useful when working with -large numbers of partitions, allowing the partition log files to be -suppressed (-plog none) or placed in a sub-directory (-plog -replica_files/log.lammps) If this option is not used the log file for -partition N is log.lammps.N or whatever is specified by the -log -command-line option. - -:line - -[-pscreen file] :link(pscreen) - -Specify the base name for the partition screen file, so partition N -writes screen information to file.N. If file is none, then no -partition screen files are created. This overrides the filename -specified in the -screen command-line option. This option is useful -when working with large numbers of partitions, allowing the partition -screen files to be suppressed (-pscreen none) or placed in a -sub-directory (-pscreen replica_files/screen). If this option is not -used the screen file for partition N is screen.N or whatever is -specified by the -screen command-line option. - -:line - -[-reorder] :link(reorder) - -This option has 2 forms: - --reorder nth N --reorder custom filename :pre - -Reorder the processors in the MPI communicator used to instantiate -LAMMPS, in one of several ways. The original MPI communicator ranks -all P processors from 0 to P-1. The mapping of these ranks to -physical processors is done by MPI before LAMMPS begins. It may be -useful in some cases to alter the rank order. E.g. to insure that -cores within each node are ranked in a desired order. Or when using -the "run_style verlet/split"_run_style.html command with 2 partitions -to insure that a specific Kspace processor (in the 2nd partition) is -matched up with a specific set of processors in the 1st partition. -See the "Speed tips"_Speed_tips.html doc page for more details. - -If the keyword {nth} is used with a setting {N}, then it means every -Nth processor will be moved to the end of the ranking. This is useful -when using the "run_style verlet/split"_run_style.html command with 2 -partitions via the -partition command-line switch. The first set of -processors will be in the first partition, the 2nd set in the 2nd -partition. The -reorder command-line switch can alter this so that -the 1st N procs in the 1st partition and one proc in the 2nd partition -will be ordered consecutively, e.g. as the cores on one physical node. -This can boost performance. For example, if you use "-reorder nth 4" -and "-partition 9 3" and you are running on 12 processors, the -processors will be reordered from - -0 1 2 3 4 5 6 7 8 9 10 11 :pre - -to - -0 1 2 4 5 6 8 9 10 3 7 11 :pre - -so that the processors in each partition will be - -0 1 2 4 5 6 8 9 10 -3 7 11 :pre - -See the "processors" command for how to insure processors from each -partition could then be grouped optimally for quad-core nodes. - -If the keyword is {custom}, then a file that specifies a permutation -of the processor ranks is also specified. The format of the reorder -file is as follows. Any number of initial blank or comment lines -(starting with a "#" character) can be present. These should be -followed by P lines of the form: - -I J :pre - -where P is the number of processors LAMMPS was launched with. Note -that if running in multi-partition mode (see the -partition switch -above) P is the total number of processors in all partitions. The I -and J values describe a permutation of the P processors. Every I and -J should be values from 0 to P-1 inclusive. In the set of P I values, -every proc ID should appear exactly once. Ditto for the set of P J -values. A single I,J pairing means that the physical processor with -rank I in the original MPI communicator will have rank J in the -reordered communicator. - -Note that rank ordering can also be specified by many MPI -implementations, either by environment variables that specify how to -order physical processors, or by config files that specify what -physical processors to assign to each MPI rank. The -reorder switch -simply gives you a portable way to do this without relying on MPI -itself. See the "processors out"_processors.html command for how -to output info on the final assignment of physical processors to -the LAMMPS simulation domain. - -:line - -[-restart2data restartfile \[remap\] datafile keyword value ...] -:link(restart2data) - -Convert the restart file into a data file and immediately exit. This -is the same operation as if the following 2-line input script were -run: - -read_restart restartfile \[remap\] -write_data datafile keyword value ... :pre - -The specified restartfile and/or datafile name may contain the wild-card -character "*". The restartfile name may also contain the wild-card -character "%". The meaning of these characters is explained on the -"read_restart"_read_restart.html and "write_data"_write_data.html doc -pages. The use of "%" means that a parallel restart file can be read. -Note that a filename such as file.* may need to be enclosed in quotes or -the "*" character prefixed with a backslash ("\") to avoid shell -expansion of the "*" character. - -Following restartfile argument, the optional word "remap" may be used. -This has the same effect like adding it to a -"read_restart"_read_restart.html command, and operates as explained on -its doc page. This is useful if reading the restart file triggers an -error that atoms have been lost. In that case, use of the remap flag -should allow the data file to still be produced. - -The syntax following restartfile (or remap), namely - -datafile keyword value ... :pre - -is identical to the arguments of the "write_data"_write_data.html -command. See its doc page for details. This includes its -optional keyword/value settings. - -:line - -[-restart2dump restartfile \[remap\] group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump) - -Convert the restart file into a dump file and immediately exit. This -is the same operation as if the following 2-line input script were -run: - -read_restart restartfile \[remap\] -write_dump group-ID dumpstyle dumpfile arg1 arg2 ... :pre - -Note that the specified restartfile and dumpfile names may contain -wild-card characters ("*","%") as explained on the -"read_restart"_read_restart.html and "write_dump"_write_dump.html doc -pages. The use of "%" means that a parallel restart file and/or -parallel dump file can be read and/or written. Note that a filename -such as file.* may need to be enclosed in quotes or the "*" character -prefixed with a backslash ("\") to avoid shell expansion of the "*" -character. - -Note that following the restartfile argument, the optional word "remap" -can be used. This has the effect as adding it to the -"read_restart"_read_restart.html command, as explained on its doc page. -This is useful if reading the restart file triggers an error that atoms -have been lost. In that case, use of the remap flag should allow the -dump file to still be produced. - -The syntax following restartfile (or remap), namely - -group-ID dumpstyle dumpfile arg1 arg2 ... :pre - -is identical to the arguments of the "write_dump"_write_dump.html -command. See its doc page for details. This includes what per-atom -fields are written to the dump file and optional dump_modify settings, -including ones that affect how parallel dump files are written, e.g. -the {nfile} and {fileper} keywords. See the -"dump_modify"_dump_modify.html doc page for details. - -:line - -[-screen file] :link(screen) - -Specify a file for LAMMPS to write its screen information to. In -one-partition mode, if the switch is not used, LAMMPS writes to the -screen. If this switch is used, LAMMPS writes to the specified file -instead and you will see no screen output. In multi-partition mode, -if the switch is not used, hi-level status information is written to -the screen. Each partition also writes to a screen.N file where N is -the partition ID. If the switch is specified in multi-partition mode, -the hi-level screen dump is named "file" and each partition also -writes screen information to a file.N. For both one-partition and -multi-partition mode, if the specified file is "none", then no screen -output is performed. Option -pscreen will override the name of the -partition screen files file.N. - -:line - -[-suffix style args] :link(suffix) - -Use variants of various styles if they exist. The specified style can -be {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}. These -refer to optional packages that LAMMPS can be built with, as described -in "Accelerate performance"_Speed.html. The "gpu" style corresponds to the -GPU package, the "intel" style to the USER-INTEL package, the "kk" -style to the KOKKOS package, the "opt" style to the OPT package, and -the "omp" style to the USER-OMP package. The hybrid style is the only -style that accepts arguments. It allows for two packages to be -specified. The first package specified is the default and will be used -if it is available. If no style is available for the first package, -the style for the second package will be used if available. For -example, "-suffix hybrid intel omp" will use styles from the -USER-INTEL package if they are installed and available, but styles for -the USER-OMP package otherwise. - -Along with the "-package" command-line switch, this is a convenient -mechanism for invoking accelerator packages and their options without -having to edit an input script. - -As an example, all of the packages provide a "pair_style -lj/cut"_pair_lj.html variant, with style names lj/cut/gpu, -lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A variant style -can be specified explicitly in your input script, e.g. pair_style -lj/cut/gpu. If the -suffix switch is used the specified suffix -(gpu,intel,kk,omp,opt) is automatically appended whenever your input -script command creates a new "atom"_atom_style.html, -"pair"_pair_style.html, "fix"_fix.html, "compute"_compute.html, or -"run"_run_style.html style. If the variant version does not exist, -the standard version is created. - -For the GPU package, using this command-line switch also invokes the -default GPU settings, as if the command "package gpu 1" were used at -the top of your input script. These settings can be changed by using -the "-package gpu" command-line switch or the "package -gpu"_package.html command in your script. - -For the USER-INTEL package, using this command-line switch also -invokes the default USER-INTEL settings, as if the command "package -intel 1" were used at the top of your input script. These settings -can be changed by using the "-package intel" command-line switch or -the "package intel"_package.html command in your script. If the -USER-OMP package is also installed, the hybrid style with "intel omp" -arguments can be used to make the omp suffix a second choice, if a -requested style is not available in the USER-INTEL package. It will -also invoke the default USER-OMP settings, as if the command "package -omp 0" were used at the top of your input script. These settings can -be changed by using the "-package omp" command-line switch or the -"package omp"_package.html command in your script. - -For the KOKKOS package, using this command-line switch also invokes -the default KOKKOS settings, as if the command "package kokkos" were -used at the top of your input script. These settings can be changed -by using the "-package kokkos" command-line switch or the "package -kokkos"_package.html command in your script. - -For the OMP package, using this command-line switch also invokes the -default OMP settings, as if the command "package omp 0" were used at -the top of your input script. These settings can be changed by using -the "-package omp" command-line switch or the "package -omp"_package.html command in your script. - -The "suffix"_suffix.html command can also be used within an input -script to set a suffix, or to turn off or back on any suffix setting -made via the command line. - -:line - -[-var name value1 value2 ...] :link(var) - -Specify a variable that will be defined for substitution purposes when -the input script is read. This switch can be used multiple times to -define multiple variables. "Name" is the variable name which can be a -single character (referenced as $x in the input script) or a full -string (referenced as $\{abc\}). An "index-style -variable"_variable.html will be created and populated with the -subsequent values, e.g. a set of filenames. Using this command-line -option is equivalent to putting the line "variable name index value1 -value2 ..." at the beginning of the input script. Defining an index -variable as a command-line argument overrides any setting for the same -index variable in the input script, since index variables cannot be -re-defined. - -See the "variable"_variable.html command for more info on defining -index and other kinds of variables and the "Commands -parse"_Commands_parse.html page for more info on using variables in -input scripts. - -NOTE: Currently, the command-line parser looks for arguments that -start with "-" to indicate new switches. Thus you cannot specify -multiple variable values if any of them start with a "-", e.g. a -negative numeric value. It is OK if the first value1 starts with a -"-", since it is automatically skipped. diff --git a/doc/txt/Run_output.txt b/doc/txt/Run_output.txt deleted file mode 100644 index 70eecff20d..0000000000 --- a/doc/txt/Run_output.txt +++ /dev/null @@ -1,176 +0,0 @@ -"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Screen and logfile output :h3 - -As LAMMPS reads an input script, it prints information to both the -screen and a log file about significant actions it takes to setup a -simulation. When the simulation is ready to begin, LAMMPS performs -various initializations, and prints info about the run it is about to -perform, including the amount of memory (in MBytes per processor) that -the simulation requires. It also prints details of the initial -thermodynamic state of the system. During the run itself, -thermodynamic information is printed periodically, every few -timesteps. When the run concludes, LAMMPS prints the final -thermodynamic state and a total run time for the simulation. It also -appends statistics about the CPU time and storage requirements for the -simulation. An example set of statistics is shown here: - -Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre - -Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s -97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre - -MPI task timings breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.9808 | 2.0134 | 2.0318 | 1.4 | 71.60 -Bond | 0.0021894 | 0.0060319 | 0.010058 | 4.7 | 0.21 -Kspace | 0.3207 | 0.3366 | 0.36616 | 3.1 | 11.97 -Neigh | 0.28411 | 0.28464 | 0.28516 | 0.1 | 10.12 -Comm | 0.075732 | 0.077018 | 0.07883 | 0.4 | 2.74 -Output | 0.00030518 | 0.00042665 | 0.00078821 | 1.0 | 0.02 -Modify | 0.086606 | 0.086631 | 0.086668 | 0.0 | 3.08 -Other | | 0.007178 | | | 0.26 :pre - -Nlocal: 501 ave 508 max 490 min -Histogram: 1 0 0 0 0 0 1 1 0 1 -Nghost: 6586.25 ave 6628 max 6548 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Neighs: 177007 ave 180562 max 170212 min -Histogram: 1 0 0 0 0 0 0 1 1 1 :pre - -Total # of neighbors = 708028 -Ave neighs/atom = 353.307 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 26 -Dangerous builds = 0 :pre - -:line - -The first section provides a global loop timing summary. The {loop -time} is the total wall-clock time for the simulation to run. The -{Performance} line is provided for convenience to help predict how -long it will take to run a desired physical simulation. The {CPU use} -line provides the CPU utilization per MPI task; it should be close to -100% times the number of OpenMP threads (or 1 of not using OpenMP). -Lower numbers correspond to delays due to file I/O or insufficient -thread utilization. - -:line - -The {MPI task} section gives the breakdown of the CPU run time (in -seconds) into major categories: - -{Pair} = non-bonded force computations -{Bond} = bonded interactions: bonds, angles, dihedrals, impropers -{Kspace} = long-range interactions: Ewald, PPPM, MSM -{Neigh} = neighbor list construction -{Comm} = inter-processor communication of atoms and their properties -{Output} = output of thermodynamic info and dump files -{Modify} = fixes and computes invoked by fixes -{Other} = all the remaining time :ul - -For each category, there is a breakdown of the least, average and most -amount of wall time any processor spent on this category of -computation. The "%varavg" is the percentage by which the max or min -varies from the average. This is an indication of load imbalance. A -percentage close to 0 is perfect load balance. A large percentage is -imbalance. The final "%total" column is the percentage of the total -loop time is spent in this category. - -When using the "timer full"_timer.html setting, an additional column -is added that also prints the CPU utilization in percent. In addition, -when using {timer full} and the "package omp"_package.html command are -active, a similar timing summary of time spent in threaded regions to -monitor thread utilization and load balance is provided. A new {Thread -timings} section is also added, which lists the time spent in reducing -the per-thread data elements to the storage for non-threaded -computation. These thread timings are measured for the first MPI rank -only and thus, because the breakdown for MPI tasks can change from -MPI rank to MPI rank, this breakdown can be very different for -individual ranks. Here is an example output for this section: - -Thread timings breakdown (MPI rank 0): -Total threaded time 0.6846 / 90.6% -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18 -Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68 -Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89 -Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70 -Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55 :pre - -:line - -The third section above lists the number of owned atoms (Nlocal), -ghost atoms (Nghost), and pair-wise neighbors stored per processor. -The max and min values give the spread of these values across -processors with a 10-bin histogram showing the distribution. The total -number of histogram counts is equal to the number of processors. - -:line - -The last section gives aggregate statistics (across all processors) -for pair-wise neighbors and special neighbors that LAMMPS keeps track -of (see the "special_bonds"_special_bonds.html command). The number -of times neighbor lists were rebuilt is tallied, as is the number of -potentially {dangerous} rebuilds. If atom movement triggered neighbor -list rebuilding (see the "neigh_modify"_neigh_modify.html command), -then dangerous reneighborings are those that were triggered on the -first timestep atom movement was checked for. If this count is -non-zero you may wish to reduce the delay factor to insure no force -interactions are missed by atoms moving beyond the neighbor skin -distance before a rebuild takes place. - -:line - -If an energy minimization was performed via the -"minimize"_minimize.html command, additional information is printed, -e.g. - -Minimization stats: - Stopping criterion = linesearch alpha is zero - Energy initial, next-to-last, final = - -6372.3765206 -8328.46998942 -8328.46998942 - Force two-norm initial, final = 1059.36 5.36874 - Force max component initial, final = 58.6026 1.46872 - Final line search alpha, max atom move = 2.7842e-10 4.0892e-10 - Iterations, force evaluations = 701 1516 :pre - -The first line prints the criterion that determined minimization was -converged. The next line lists the initial and final energy, as well -as the energy on the next-to-last iteration. The next 2 lines give a -measure of the gradient of the energy (force on all atoms). The -2-norm is the "length" of this 3N-component force vector; the largest -component (x, y, or z) of force (infinity-norm) is also given. Then -information is provided about the line search and statistics on how -many iterations and force-evaluations the minimizer required. -Multiple force evaluations are typically done at each iteration to -perform a 1d line minimization in the search direction. See the -"minimize"_minimize.html doc page for more details. - -:line - -If a "kspace_style"_kspace_style.html long-range Coulombics solver -that performs FFTs was used during the run (PPPM, Ewald), then -additional information is printed, e.g. - -FFT time (% of Kspce) = 0.200313 (8.34477) -FFT Gflps 3d 1d-only = 2.31074 9.19989 :pre - -The first line is the time spent doing 3d FFTs (several per timestep) -and the fraction it represents of the total KSpace time (listed -above). Each 3d FFT requires computation (3 sets of 1d FFTs) and -communication (transposes). The total flops performed is 5Nlog_2(N), -where N is the number of points in the 3d grid. The FFTs are timed -with and without the communication and a Gflop rate is computed. The -3d rate is with communication; the 1d rate is without (just the 1d -FFTs). Thus you can estimate what fraction of your FFT time was spent -in communication, roughly 75% in the example above. diff --git a/doc/txt/Run_windows.txt b/doc/txt/Run_windows.txt deleted file mode 100644 index e9c3b60dbe..0000000000 --- a/doc/txt/Run_windows.txt +++ /dev/null @@ -1,73 +0,0 @@ -"Higher level section"_Run_head.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Running LAMMPS on Windows :h3 - -To run a serial (non-MPI) executable, follow these steps: - -Get a command prompt by going to Start->Run... , -then typing "cmd". :ulb,l - -Move to the directory where you have your input script, -(e.g. by typing: cd "Documents"). :l - -At the command prompt, type "lmp_serial -in in.file", where -in.file is the name of your LAMMPS input script. :l,ule - -Note that the serial executable includes support for multi-threading -parallelization from the styles in the USER-OMP packages. To run with -4 threads, you can type this: - -lmp_serial -in in.lj -pk omp 4 -sf omp :pre - -:line - -For the MPI executable, which allows you to run LAMMPS under Windows -in parallel, follow these steps. - -Download and install a compatible MPI library binary package: - -for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi -for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul - -The LAMMPS Windows installer packages will automatically adjust your -path for the default location of this MPI package. After the -installation of the MPICH2 software, it needs to be integrated into -the system. For this you need to start a Command Prompt in -{Administrator Mode} (right click on the icon and select it). Change -into the MPICH2 installation directory, then into the sub-directory -[bin] and execute [smpd.exe -install]. Exit the command window. - -Get a new, regular command prompt by going to Start->Run... , -then typing "cmd". :ulb,l - -Move to the directory where you have your input file -(e.g. by typing: cd "Documents"). :l,ule - -Then type something like this: - -mpiexec -localonly 4 lmp_mpi -in in.file -mpiexec -np 4 lmp_mpi -in in.file :pre - -where in.file is the name of your LAMMPS input script. For the latter -case, you may be prompted to enter your password. - -In this mode, output may not immediately show up on the screen, so if -your input script takes a long time to execute, you may need to be -patient before the output shows up. - -The parallel executable can also run on a single processor by typing -something like this: - -lmp_mpi -in in.lj :pre - -Note that the parallel executable also includes OpenMP -multi-threading, which can be combined with MPI using something like: - -mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp :pre diff --git a/doc/txt/Speed.txt b/doc/txt/Speed.txt deleted file mode 100644 index 28aef26a5d..0000000000 --- a/doc/txt/Speed.txt +++ /dev/null @@ -1,57 +0,0 @@ -"Previous Section"_Package.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Howto.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Accelerate performance :h2 - -This section describes various methods for improving LAMMPS -performance for different classes of problems running on different -kinds of machines. - -There are two thrusts to the discussion that follows. The first is -using code options that implement alternate algorithms that can -speed-up a simulation. The second is to use one of the several -accelerator packages provided with LAMMPS that contain code optimized -for certain kinds of hardware, including multi-core CPUs, GPUs, and -Intel Xeon Phi co-processors. - -The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS -web site gives performance results for the various accelerator -packages discussed on the "Speed packages"_Speed_packages.html doc -page, for several of the standard LAMMPS benchmark problems, as a -function of problem size and number of compute nodes, on different -hardware platforms. - - - - - -"Benchmarks"_Speed_bench.html -"Measuring performance"_Speed_measure.html -"General tips"_Speed_tips.html -"Accelerator packages"_Speed_packages.html -"GPU package"_Speed_gpu.html -"USER-INTEL package"_Speed_intel.html -"KOKKOS package"_Speed_kokkos.html -"USER-OMP package"_Speed_omp.html -"OPT package"_Speed_opt.html -"Comparison of accelerator packages"_Speed_compare.html :all(b) - - diff --git a/doc/txt/Speed_bench.txt b/doc/txt/Speed_bench.txt deleted file mode 100644 index a3d0bf4f46..0000000000 --- a/doc/txt/Speed_bench.txt +++ /dev/null @@ -1,88 +0,0 @@ -"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Benchmarks :h3 - -Current LAMMPS performance is discussed on the "Benchmarks -page"_http://lammps.sandia.gov/bench.html of the "LAMMPS website"_lws -where timings and parallel efficiency are listed. The page has -several sections, which are briefly described below: - -CPU performance on 5 standard problems, strong and weak scaling -GPU and Xeon Phi performance on same and related problems -Comparison of cost of interatomic potentials -Performance of huge, billion-atom problems :ul - -The 5 standard problems are as follow: - -LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 -neighbors per atom), NVE integration :olb,l - -Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ -pairwise interactions with a 2^(1/6) sigma cutoff (5 neighbors per -atom), NVE integration :l - -EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45 -neighbors per atom), NVE integration :l - -Chute = granular chute flow, frictional history potential with 1.1 -sigma cutoff (7 neighbors per atom), NVE integration :l - -Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force -field with a 10 Angstrom LJ cutoff (440 neighbors per atom), -particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT -integration :l -:ole - -Input files for these 5 problems are provided in the bench directory -of the LAMMPS distribution. Each has 32,000 atoms and runs for 100 -timesteps. The size of the problem (number of atoms) can be varied -using command-line switches as described in the bench/README file. -This is an easy way to test performance and either strong or weak -scalability on your machine. - -The bench directory includes a few log.* files that show performance -of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI -and bench/KEPLER dirs have input files and scripts and instructions -for running the same (or similar) problems using OpenMP or GPU or Xeon -Phi acceleration options. See the README files in those dirs and the -"Speed packages"_Speed_packages.html doc pages for instructions on how -to build LAMMPS and run on that kind of hardware. - -The bench/POTENTIALS directory has input files which correspond to the -table of results on the -"Potentials"_http://lammps.sandia.gov/bench.html#potentials section of -the Benchmarks web page. So you can also run those test problems on -your machine. - -The "billion-atom"_http://lammps.sandia.gov/bench.html#billion section -of the Benchmarks web page has performance data for very large -benchmark runs of simple Lennard-Jones (LJ) models, which use the -bench/in.lj input script. - -:line - -For all the benchmarks, a useful metric is the CPU cost per atom per -timestep. Since performance scales roughly linearly with problem size -and timesteps for all LAMMPS models (i.e. interatomic or coarse-grained -potentials), the run time of any problem using the same model (atom -style, force field, cutoff, etc) can then be estimated. - -Performance on a parallel machine can also be predicted from one-core -or one-node timings if the parallel efficiency can be estimated. The -communication bandwidth and latency of a particular parallel machine -affects the efficiency. On most machines LAMMPS will give a parallel -efficiency on these benchmarks above 50% so long as the number of -atoms/core is a few 100 or greater, and closer to 100% for large -numbers of atoms/core. This is for all-MPI mode with one MPI task per -core. For nodes with accelerator options or hardware (OpenMP, GPU, -Phi), you should first measure single node performance. Then you can -estimate parallel performance for multi-node runs using the same logic -as for all-MPI mode, except that now you will typically need many more -atoms/node to achieve good scalability. diff --git a/doc/txt/Speed_compare.txt b/doc/txt/Speed_compare.txt deleted file mode 100644 index c95af3cb22..0000000000 --- a/doc/txt/Speed_compare.txt +++ /dev/null @@ -1,116 +0,0 @@ -"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Comparison of various accelerator packages :h3 - -The next section compares and contrasts the various accelerator -options, since there are multiple ways to perform OpenMP threading, -run on GPUs, optimize for vector units on CPUs and run on Intel -Xeon Phi (co-)processors. - -All of these packages can accelerate a LAMMPS calculation taking -advantage of hardware features, but they do it in different ways -and acceleration is not always guaranteed. - -As a consequence, for a particular simulation on specific hardware, -one package may be faster than the other. We give some guidelines -below, but the best way to determine which package is faster for your -input script is to try multiple of them on your machine and experiment -with available performance tuning settings. See the benchmarking -section below for examples where this has been done. - -[Guidelines for using each package optimally:] - -Both, the GPU and the KOKKOS package allows you to assign multiple -MPI ranks (= CPU cores) to the same GPU. For the GPU package, this -can lead to a speedup through better utilization of the GPU (by -overlapping computation and data transfer) and more efficient -computation of the non-GPU accelerated parts of LAMMPS through MPI -parallelization, as all system data is maintained and updated on -the host. For KOKKOS, there is less to no benefit from this, due -to its different memory management model, which tries to retain -data on the GPU. - :ulb,l - -The GPU package moves per-atom data (coordinates, forces, and -(optionally) neighbor list data, if not computed on the GPU) between -the CPU and GPU at every timestep. The KOKKOS/CUDA package only does -this on timesteps when a CPU calculation is required (e.g. to invoke -a fix or compute that is non-GPU-ized). Hence, if you can formulate -your input script to only use GPU-ized fixes and computes, and avoid -doing I/O too often (thermo output, dump file snapshots, restart files), -then the data transfer cost of the KOKKOS/CUDA package can be very low, -causing it to run faster than the GPU package. :l - -The GPU package is often faster than the KOKKOS/CUDA package, when the -number of atoms per GPU is on the smaller side. The crossover point, -in terms of atoms/GPU at which the KOKKOS/CUDA package becomes faster -depends strongly on the pair style. For example, for a simple Lennard Jones -system the crossover (in single precision) is often about 50K-100K -atoms per GPU. When performing double precision calculations the -crossover point can be significantly smaller. :l - -Both KOKKOS and GPU package compute bonded interactions (bonds, angles, -etc) on the CPU. If the GPU package is running with several MPI processes -assigned to one GPU, the cost of computing the bonded interactions is -spread across more CPUs and hence the GPU package can run faster in these -cases. :l - -When using LAMMPS with multiple MPI ranks assigned to the same GPU, its -performance depends to some extent on the available bandwidth between -the CPUs and the GPU. This can differ significantly based on the -available bus technology, capability of the host CPU and mainboard, -the wiring of the buses and whether switches are used to increase the -number of available bus slots, or if GPUs are housed in an external -enclosure. This can become quite complex. :l - -To achieve significant acceleration through GPUs, both KOKKOS and GPU -package require capable GPUs with fast on-device memory and efficient -data transfer rates. This requests capable upper mid-level to high-end -(desktop) GPUs. Using lower performance GPUs (e.g. on laptops) may -result in a slowdown instead. :l - -For the GPU package, specifically when running in parallel with MPI, -if it often more efficient to exclude the PPPM kspace style from GPU -acceleration and instead run it - concurrently with a GPU accelerated -pair style - on the CPU. This can often be easily achieved with placing -a {suffix off} command before and a {suffix on} command after the -{kspace_style pppm} command. :l - -The KOKKOS/OpenMP and USER-OMP package have different thread management -strategies, which should result in USER-OMP being more efficient for a -small number of threads with increasing overhead as the number of threads -per MPI rank grows. The KOKKOS/OpenMP kernels have less overhead in that -case, but have lower performance with few threads. :l - -The USER-INTEL package contains many options and settings for achieving -additional performance on Intel hardware (CPU and accelerator cards), but -to unlock this potential, an Intel compiler is required. The package code -will compile with GNU gcc, but it will not be as efficient. :l -:ule - -[Differences between the GPU and KOKKOS packages:] - -The GPU package accelerates only pair force, neighbor list, and (parts -of) PPPM calculations. The KOKKOS package attempts to run most of the -calculation on the GPU, but can transparently support non-accelerated -code (with a performance penalty due to having data transfers between -host and GPU). :ulb,l - -The GPU package requires neighbor lists to be built on the CPU when using -exclusion lists, or a triclinic simulation box. :l - -The GPU package can be compiled for CUDA or OpenCL and thus supports -both, Nvidia and AMD GPUs well. On Nvidia hardware, using CUDA is typically -resulting in equal or better performance over OpenCL. :l - -OpenCL in the GPU package does theoretically also support Intel CPUs or -Intel Xeon Phi, but the native support for those in KOKKOS (or USER-INTEL) -is superior. :l -:ule diff --git a/doc/txt/Speed_gpu.txt b/doc/txt/Speed_gpu.txt deleted file mode 100644 index bddefc5031..0000000000 --- a/doc/txt/Speed_gpu.txt +++ /dev/null @@ -1,193 +0,0 @@ -"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -GPU package :h3 - -The GPU package was developed by Mike Brown while at SNL and ORNL -and his collaborators, particularly Trung Nguyen (now at Northwestern). -It provides GPU versions of many pair styles and for parts of the -"kspace_style pppm"_kspace_style.html for long-range Coulombics. -It has the following general features: - -It is designed to exploit common GPU hardware configurations where one -or more GPUs are coupled to many cores of one or more multi-core CPUs, -e.g. within a node of a parallel machine. :ulb,l - -Atom-based data (e.g. coordinates, forces) are moved back-and-forth -between the CPU(s) and GPU every timestep. :l - -Neighbor lists can be built on the CPU or on the GPU :l - -The charge assignment and force interpolation portions of PPPM can be -run on the GPU. The FFT portion, which requires MPI communication -between processors, runs on the CPU. :l - -Force computations of different style (pair vs. bond/angle/dihedral/improper) -can be performed concurrently on the GPU and CPU(s), respectively. :l - -It allows for GPU computations to be performed in single or double -precision, or in mixed-mode precision, where pairwise forces are -computed in single precision, but accumulated into double-precision -force vectors. :l - -LAMMPS-specific code is in the GPU package. It makes calls to a -generic GPU library in the lib/gpu directory. This library provides -NVIDIA support as well as more general OpenCL support, so that the -same functionality is supported on a variety of hardware. :l -:ule - -[Required hardware/software:] - -To compile and use this package in CUDA mode, you currently need -to have an NVIDIA GPU and install the corresponding NVIDIA CUDA -toolkit software on your system (this is primarily tested on Linux -and completely unsupported on Windows): - -Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/*/information :ulb,l -Go to http://www.nvidia.com/object/cuda_get.html :l -Install a driver and toolkit appropriate for your system (SDK is not necessary) :l -Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to -list supported devices and properties :ule,l - -To compile and use this package in OpenCL mode, you currently need -to have the OpenCL headers and the (vendor neutral) OpenCL library installed. -In OpenCL mode, the acceleration depends on having an "OpenCL Installable Client -Driver (ICD)"_https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader -installed. There can be multiple of them for the same or different hardware -(GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those -as 'platforms'. The GPU library will select the [first] suitable platform, -but this can be overridden using the device option of the "package"_package.html -command. run lammps/lib/gpu/ocl_get_devices to get a list of available -platforms and devices with a suitable ICD available. - -[Building LAMMPS with the GPU package:] - -See the "Build extras"_Build_extras.html#gpu doc page for -instructions. - -[Run with the GPU package from the command line:] - -The mpirun or mpiexec command sets the total number of MPI tasks used -by LAMMPS (one or multiple per compute node) and the number of MPI -tasks used per node. E.g. the mpirun command in MPICH does this via -its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. - -When using the GPU package, you cannot assign more than one GPU to a -single MPI task. However multiple MPI tasks can share the same GPU, -and in many cases it will be more efficient to run this way. Likewise -it may be more efficient to use less MPI tasks/node than the available -# of CPU cores. Assignment of multiple MPI tasks to a GPU will happen -automatically if you create more MPI tasks/node than there are -GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be -shared by 4 MPI tasks. - -Use the "-sf gpu" "command-line switch"_Run_options.html, which will -automatically append "gpu" to styles that support it. Use the "-pk -gpu Ng" "command-line switch"_Run_options.html to set Ng = # of -GPUs/node to use. - -lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU -mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node -mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # ditto on 4 16-core nodes :pre - -Note that if the "-sf gpu" switch is used, it also issues a default -"package gpu 1"_package.html command, which sets the number of -GPUs/node to 1. - -Using the "-pk" switch explicitly allows for setting of the number of -GPUs/node to use and additional options. Its syntax is the same as -same as the "package gpu" command. See the "package"_package.html -command doc page for details, including the default values used for -all its options if it is not specified. - -Note that the default for the "package gpu"_package.html command is to -set the Newton flag to "off" pairwise interactions. It does not -affect the setting for bonded interactions (LAMMPS default is "on"). -The "off" setting for pairwise interaction is currently required for -GPU package pair styles. - -[Or run with the GPU package by editing an input script:] - -The discussion above for the mpirun/mpiexec command, MPI tasks/node, -and use of multiple MPI tasks/GPU is the same. - -Use the "suffix gpu"_suffix.html command, or you can explicitly add an -"gpu" suffix to individual styles in your input script, e.g. - -pair_style lj/cut/gpu 2.5 :pre - -You must also use the "package gpu"_package.html command to enable the -GPU package, unless the "-sf gpu" or "-pk gpu" "command-line -switches"_Run_options.html were used. It specifies the number of -GPUs/node to use, as well as other options. - -[Speed-ups to expect:] - -The performance of a GPU versus a multi-core CPU is a function of your -hardware, which pair style is used, the number of atoms/GPU, and the -precision used on the GPU (double, single, mixed). Using the GPU package -in OpenCL mode on CPUs (which uses vectorization and multithreading) is -usually resulting in inferior performance compared to using LAMMPS' native -threading and vectorization support in the USER-OMP and USER-INTEL packages. - -See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the -LAMMPS web site for performance of the GPU package on various -hardware, including the Titan HPC platform at ORNL. - -You should also experiment with how many MPI tasks per GPU to use to -give the best performance for your problem and machine. This is also -a function of the problem size and the pair style being using. -Likewise, you should experiment with the precision setting for the GPU -library to see if single or mixed precision will give accurate -results, since they will typically be faster. - -[Guidelines for best performance:] - -Using multiple MPI tasks per GPU will often give the best performance, -as allowed my most multi-core CPU/GPU configurations. :ulb,l - -If the number of particles per MPI task is small (e.g. 100s of -particles), it can be more efficient to run with fewer MPI tasks per -GPU, even if you do not use all the cores on the compute node. :l - -The "package gpu"_package.html command has several options for tuning -performance. Neighbor lists can be built on the GPU or CPU. Force -calculations can be dynamically balanced across the CPU cores and -GPUs. GPU-specific settings can be made which can be optimized -for different hardware. See the "package"_package.html command -doc page for details. :l - -As described by the "package gpu"_package.html command, GPU -accelerated pair styles can perform computations asynchronously with -CPU computations. The "Pair" time reported by LAMMPS will be the -maximum of the time required to complete the CPU pair style -computations and the time required to complete the GPU pair style -computations. Any time spent for GPU-enabled pair styles for -computations that run simultaneously with "bond"_bond_style.html, -"angle"_angle_style.html, "dihedral"_dihedral_style.html, -"improper"_improper_style.html, and "long-range"_kspace_style.html -calculations will not be included in the "Pair" time. :l - -When the {mode} setting for the package gpu command is force/neigh, -the time for neighbor list calculations on the GPU will be added into -the "Pair" time, not the "Neigh" time. An additional breakdown of the -times required for various tasks on the GPU (data copy, neighbor -calculations, force computations, etc) are output only with the LAMMPS -screen output (not in the log file) at the end of each run. These -timings represent total time spent on the GPU for each routine, -regardless of asynchronous CPU calculations. :l - -The output section "GPU Time Info (average)" reports "Max Mem / Proc". -This is the maximum memory used at one time on the GPU for data -storage by a single MPI process. :l -:ule - -[Restrictions:] - -None. diff --git a/doc/txt/Speed_intel.txt b/doc/txt/Speed_intel.txt deleted file mode 100644 index 2688b43e6f..0000000000 --- a/doc/txt/Speed_intel.txt +++ /dev/null @@ -1,526 +0,0 @@ -"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -USER-INTEL package :h3 - -The USER-INTEL package is maintained by Mike Brown at Intel -Corporation. It provides two methods for accelerating simulations, -depending on the hardware you have. The first is acceleration on -Intel CPUs by running in single, mixed, or double precision with -vectorization. The second is acceleration on Intel Xeon Phi -co-processors via offloading neighbor list and non-bonded force -calculations to the Phi. The same C++ code is used in both cases. -When offloading to a co-processor from a CPU, the same routine is run -twice, once on the CPU and once with an offload flag. This allows -LAMMPS to run on the CPU cores and co-processor cores simultaneously. - -[Currently Available USER-INTEL Styles:] - -Angle Styles: charmm, harmonic :ulb,l -Bond Styles: fene, fourier, harmonic :l -Dihedral Styles: charmm, fourier, harmonic, opls :l -Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l -Improper Styles: cvff, harmonic :l -Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long, -buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, -lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, -rebo, sw, tersoff :l -K-Space Styles: pppm, pppm/disp :l -:ule - -IMPORTANT NOTE: None of the styles in the USER-INTEL package currently -support computing per-atom stress. If any compute or fix in your -input requires it, LAMMPS will abort with an error message. - -[Speed-ups to expect:] - -The speedups will depend on your simulation, the hardware, which -styles are used, the number of atoms, and the floating-point -precision mode. Performance improvements are shown compared to -LAMMPS {without using other acceleration packages} as these are -under active development (and subject to performance changes). The -measurements were performed using the input files available in -the src/USER-INTEL/TEST directory with the provided run script. -These are scalable in size; the results given are with 512K -particles (524K for Liquid Crystal). Most of the simulations are -standard LAMMPS benchmarks (indicated by the filename extension in -parenthesis) with modifications to the run length and to add a -warm-up run (for use with offload benchmarks). - -:c,image(JPG/user_intel.png) - -Results are speedups obtained on Intel Xeon E5-2697v4 processors -(code-named Broadwell), Intel Xeon Phi 7250 processors (code-named -Knights Landing), and Intel Xeon Gold 6148 processors (code-named -Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio -2017 update 2. Results are with 1 MPI task per physical core. See -{src/USER-INTEL/TEST/README} for the raw simulation rates and -instructions to reproduce. - -:line - -[Accuracy and order of operations:] - -In most molecular dynamics software, parallelization parameters -(# of MPI, OpenMP, and vectorization) can change the results due -to changing the order of operations with finite-precision -calculations. The USER-INTEL package is deterministic. This means -that the results should be reproducible from run to run with the -{same} parallel configurations and when using deterministic -libraries or library settings (MPI, OpenMP, FFT). However, there -are differences in the USER-INTEL package that can change the -order of operations compared to LAMMPS without acceleration: - -Neighbor lists can be created in a different order :ulb,l -Bins used for sorting atoms can be oriented differently :l -The default stencil order for PPPM is 7. By default, LAMMPS will -calculate other PPPM parameters to fit the desired accuracy with -this order :l -The {newton} setting applies to all atoms, not just atoms shared -between MPI tasks :l -Vectorization can change the order for adding pairwise forces :l -When using the -DLMP_USE_MKL_RNG define (all included intel optimized -makefiles do) at build time, the random number generator for -dissipative particle dynamics (pair style dpd/intel) uses the Mersenne -Twister generator included in the Intel MKL library (that should be -more robust than the default Masaglia random number generator) :l -:ule - -The precision mode (described below) used with the USER-INTEL -package can change the {accuracy} of the calculations. For the -default {mixed} precision option, calculations between pairs or -triplets of atoms are performed in single precision, intended to -be within the inherent error of MD simulations. All accumulation -is performed in double precision to prevent the error from growing -with the number of atoms in the simulation. {Single} precision -mode should not be used without appropriate validation. - -:line - -[Quick Start for Experienced Users:] - -LAMMPS should be built with the USER-INTEL package installed. -Simulations should be run with 1 MPI task per physical {core}, -not {hardware thread}. - -Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l -Set the environment variable KMP_BLOCKTIME=0 :l -"-pk intel 0 omp $t -sf intel" added to LAMMPS command-line :l -$t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l -For some of the simple 2-body potentials without long-range -electrostatics, performance and scalability can be better with -the "newton off" setting added to the input script :l -For simulations on higher node counts, add "processors * * * grid -numa" to the beginning of the input script for better scalability :l -If using {kspace_style pppm} in the input script, add -"kspace_modify diff ad" for better performance :l -:ule - -For Intel Xeon Phi CPUs: - -Runs should be performed using MCDRAM. :ulb,l -:ule - -For simulations using {kspace_style pppm} on Intel CPUs supporting -AVX-512: - -Add "kspace_modify diff ad" to the input script :ulb,l -The command-line option should be changed to -"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of -threads minus 1. :l -Do not use thread affinity (set KMP_AFFINITY=none) :l -The "newton off" setting may provide better scalability :l -:ule - -For Intel Xeon Phi co-processors (Offload): - -Edit src/MAKE/OPTIONS/Makefile.intel_co-processor as necessary :ulb,l -"-pk intel N omp 1" added to command-line where N is the number of -co-processors per node. :l -:ule - -:line - -[Required hardware/software:] - -In order to use offload to co-processors, an Intel Xeon Phi -co-processor and an Intel compiler are required. For this, the -recommended version of the Intel compiler is 14.0.1.106 or -versions 15.0.2.044 and higher. - -Although any compiler can be used with the USER-INTEL package, -currently, vectorization directives are disabled by default when -not using Intel compilers due to lack of standard support and -observations of decreased performance. The OpenMP standard now -supports directives for vectorization and we plan to transition the -code to this standard once it is available in most compilers. We -expect this to allow improved performance and support with other -compilers. - -For Intel Xeon Phi x200 series processors (code-named Knights -Landing), there are multiple configuration options for the hardware. -For best performance, we recommend that the MCDRAM is configured in -"Flat" mode and with the cluster mode set to "Quadrant" or "SNC4". -"Cache" mode can also be used, although the performance might be -slightly lower. - -[Notes about Simultaneous Multithreading:] - -Modern CPUs often support Simultaneous Multithreading (SMT). On -Intel processors, this is called Hyper-Threading (HT) technology. -SMT is hardware support for running multiple threads efficiently on -a single core. {Hardware threads} or {logical cores} are often used -to refer to the number of threads that are supported in hardware. -For example, the Intel Xeon E5-2697v4 processor is described -as having 36 cores and 72 threads. This means that 36 MPI processes -or OpenMP threads can run simultaneously on separate cores, but that -up to 72 MPI processes or OpenMP threads can be running on the CPU -without costly operating system context switches. - -Molecular dynamics simulations will often run faster when making use -of SMT. If a thread becomes stalled, for example because it is -waiting on data that has not yet arrived from memory, another thread -can start running so that the CPU pipeline is still being used -efficiently. Although benefits can be seen by launching a MPI task -for every hardware thread, for multinode simulations, we recommend -that OpenMP threads are used for SMT instead, either with the -USER-INTEL package, "USER-OMP package"_Speed_omp.html, or -"KOKKOS package"_Speed_kokkos.html. In the example above, up -to 36X speedups can be observed by using all 36 physical cores with -LAMMPS. By using all 72 hardware threads, an additional 10-30% -performance gain can be achieved. - -The BIOS on many platforms allows SMT to be disabled, however, we do -not recommend this on modern processors as there is little to no -benefit for any software package in most cases. The operating system -will report every hardware thread as a separate core allowing one to -determine the number of hardware threads available. On Linux systems, -this information can normally be obtained with: - -cat /proc/cpuinfo :pre - -[Building LAMMPS with the USER-INTEL package:] - -See the "Build extras"_Build_extras.html#user-intel doc page for -instructions. Some additional details are covered here. - -For building with make, several example Makefiles for building with -the Intel compiler are included with LAMMPS in the src/MAKE/OPTIONS/ -directory: - -Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload -Makefile.knl # Intel Compiler, Intel MPI, No Offload -Makefile.intel_cpu_mpich # Intel Compiler, MPICH, No Offload -Makefile.intel_cpu_openpmi # Intel Compiler, OpenMPI, No Offload -Makefile.intel_co-processor # Intel Compiler, Intel MPI, Offload :pre - -Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that -it explicitly specifies that vectorization should be for Intel Xeon -Phi x200 processors making it easier to cross-compile. For users with -recent installations of Intel Parallel Studio, the process can be as -simple as: - -make yes-user-intel -source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh -# or psxevars.csh for C-shell -make intel_cpu_intelmpi :pre - -Note that if you build with support for a Phi co-processor, the same -binary can be used on nodes with or without co-processors installed. -However, if you do not have co-processors on your system, building -without offload support will produce a smaller binary. - -The general requirements for Makefiles with the USER-INTEL package -are as follows. When using Intel compilers, "-restrict" is required -and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS. -CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads -are not supported in the build environment) and "-DLMP_USE_MKL_RNG" -(unless Intel Math Kernel Library (MKL) is not available in the build -environment). For Intel compilers, LIB should include "-ltbbmalloc" -or if the library is not available, "-DLMP_INTEL_NO_TBB" can be added -to CCFLAGS. For builds supporting offload, "-DLMP_INTEL_OFFLOAD" is -required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other -recommended CCFLAG options for best performance are "-O2 -fno-alias --ansi-alias -qoverride-limits fp-model fast=2 -no-prec-div". - -NOTE: See the src/USER-INTEL/README file for additional flags that -might be needed for best performance on Intel server processors -code-named "Skylake". - -NOTE: The vectorization and math capabilities can differ depending on -the CPU. For Intel compilers, the "-x" flag specifies the type of -processor for which to optimize. "-xHost" specifies that the compiler -should build for the processor used for compiling. For Intel Xeon Phi -x200 series processors, this option is "-xMIC-AVX512". For fourth -generation Intel Xeon (v4/Broadwell) processors, "-xCORE-AVX2" should -be used. For older Intel Xeon processors, "-xAVX" will perform best -in general for the different simulations in LAMMPS. The default -in most of the example Makefiles is to use "-xHost", however this -should not be used when cross-compiling. - -[Running LAMMPS with the USER-INTEL package:] - -Running LAMMPS with the USER-INTEL package is similar to normal use -with the exceptions that one should 1) specify that LAMMPS should use -the USER-INTEL package, 2) specify the number of OpenMP threads, and -3) optionally specify the specific LAMMPS styles that should use the -USER-INTEL package. 1) and 2) can be performed from the command-line -or by editing the input script. 3) requires editing the input script. -Advanced performance tuning options are also described below to get -the best performance. - -When running on a single node (including runs using offload to a -co-processor), best performance is normally obtained by using 1 MPI -task per physical core and additional OpenMP threads with SMT. For -Intel Xeon processors, 2 OpenMP threads should be used for SMT. -For Intel Xeon Phi CPUs, 2 or 4 OpenMP threads should be used -(best choice depends on the simulation). In cases where the user -specifies that LRT mode is used (described below), 1 or 3 OpenMP -threads should be used. For multi-node runs, using 1 MPI task per -physical core will often perform best, however, depending on the -machine and scale, users might get better performance by decreasing -the number of MPI tasks and using more OpenMP threads. For -performance, the product of the number of MPI tasks and OpenMP -threads should not exceed the number of available hardware threads in -almost all cases. - -NOTE: Setting core affinity is often used to pin MPI tasks and OpenMP -threads to a core or group of cores so that memory access can be -uniform. Unless disabled at build time, affinity for MPI tasks and -OpenMP threads on the host (CPU) will be set by default on the host -{when using offload to a co-processor}. In this case, it is unnecessary -to use other methods to control affinity (e.g. taskset, numactl, -I_MPI_PIN_DOMAIN, etc.). This can be disabled with the {no_affinity} -option to the "package intel"_package.html command or by disabling the -option at build time (by adding -DINTEL_OFFLOAD_NOAFFINITY to the -CCFLAGS line of your Makefile). Disabling this option is not -recommended, especially when running on a machine with Intel -Hyper-Threading technology disabled. - -[Run with the USER-INTEL package from the command line:] - -To enable USER-INTEL optimizations for all available styles used in -the input script, the "-sf intel" "command-line -switch"_Run_options.html can be used without any requirement for -editing the input script. This switch will automatically append -"intel" to styles that support it. It also invokes a default command: -"package intel 1"_package.html. This package command is used to set -options for the USER-INTEL package. The default package command will -specify that USER-INTEL calculations are performed in mixed precision, -that the number of OpenMP threads is specified by the OMP_NUM_THREADS -environment variable, and that if co-processors are present and the -binary was built with offload support, that 1 co-processor per node -will be used with automatic balancing of work between the CPU and the -co-processor. - -You can specify different options for the USER-INTEL package by using -the "-pk intel Nphi" "command-line switch"_Run_options.html with -keyword/value pairs as specified in the documentation. Here, Nphi = # -of Xeon Phi co-processors/node (ignored without offload -support). Common options to the USER-INTEL package include {omp} to -override any OMP_NUM_THREADS setting and specify the number of OpenMP -threads, {mode} to set the floating-point precision mode, and {lrt} to -enable Long-Range Thread mode as described below. See the "package -intel"_package.html command for details, including the default values -used for all its options if not specified, and how to set the number -of OpenMP threads via the OMP_NUM_THREADS environment variable if -desired. - -Examples (see documentation for your MPI/Machine for differences in -launching MPI applications): - -mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads -mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision :pre - -[Or run with the USER-INTEL package by editing an input script:] - -As an alternative to adding command-line arguments, the input script -can be edited to enable the USER-INTEL package. This requires adding -the "package intel"_package.html command to the top of the input -script. For the second example above, this would be: - -package intel 0 omp 2 mode double :pre - -To enable the USER-INTEL package only for individual styles, you can -add an "intel" suffix to the individual style, e.g.: - -pair_style lj/cut/intel 2.5 :pre - -Alternatively, the "suffix intel"_suffix.html command can be added to -the input script to enable USER-INTEL styles for the commands that -follow in the input script. - -[Tuning for Performance:] - -NOTE: The USER-INTEL package will perform better with modifications -to the input script when "PPPM"_kspace_style.html is used: -"kspace_modify diff ad"_kspace_modify.html should be added to the -input script. - -Long-Range Thread (LRT) mode is an option to the "package -intel"_package.html command that can improve performance when using -"PPPM"_kspace_style.html for long-range electrostatics on processors -with SMT. It generates an extra pthread for each MPI task. The thread -is dedicated to performing some of the PPPM calculations and MPI -communications. This feature requires setting the pre-processor flag --DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset -in the default makefiles ({Makefile.mpi} and {Makefile.serial}) but -it is set in all makefiles tuned for the USER-INTEL package. On Intel -Xeon Phi x200 series CPUs, the LRT feature will likely improve -performance, even on a single node. On Intel Xeon processors, using -this mode might result in better performance when using multiple nodes, -depending on the specific machine configuration. To enable LRT mode, -specify that the number of OpenMP threads is one less than would -normally be used for the run and add the "lrt yes" option to the "-pk" -command-line suffix or "package intel" command. For example, if a run -would normally perform best with "-pk intel 0 omp 4", instead use -"-pk intel 0 omp 3 lrt yes". When using LRT, you should set the -environment variable "KMP_AFFINITY=none". LRT mode is not supported -when using offload. - -NOTE: Changing the "newton"_newton.html setting to off can improve -performance and/or scalability for simple 2-body potentials such as -lj/cut or when using LRT mode on processors supporting AVX-512. - -Not all styles are supported in the USER-INTEL package. You can mix -the USER-INTEL package with styles from the "OPT"_Speed_opt.html -package or the "USER-OMP package"_Speed_omp.html. Of course, this -requires that these packages were installed at build time. This can -performed automatically by using "-sf hybrid intel opt" or "-sf hybrid -intel omp" command-line options. Alternatively, the "opt" and "omp" -suffixes can be appended manually in the input script. For the latter, -the "package omp"_package.html command must be in the input script or -the "-pk omp Nt" "command-line switch"_Run_options.html must be used -where Nt is the number of OpenMP threads. The number of OpenMP threads -should not be set differently for the different packages. Note that -the "suffix hybrid intel omp"_suffix.html command can also be used -within the input script to automatically append the "omp" suffix to -styles when USER-INTEL styles are not available. - -NOTE: For simulations on higher node counts, add "processors * * * -grid numa"_processors.html to the beginning of the input script for -better scalability. - -When running on many nodes, performance might be better when using -fewer OpenMP threads and more MPI tasks. This will depend on the -simulation and the machine. Using the "verlet/split"_run_style.html -run style might also give better performance for simulations with -"PPPM"_kspace_style.html electrostatics. Note that this is an -alternative to LRT mode and the two cannot be used together. - -Currently, when using Intel MPI with Intel Xeon Phi x200 series -CPUs, better performance might be obtained by setting the -environment variable "I_MPI_SHM_LMT=shm" for Linux kernels that do -not yet have full support for AVX-512. Runs on Intel Xeon Phi x200 -series processors will always perform better using MCDRAM. Please -consult your system documentation for the best approach to specify -that MPI runs are performed in MCDRAM. - -[Tuning for Offload Performance:] - -The default settings for offload should give good performance. - -When using LAMMPS with offload to Intel co-processors, best performance -will typically be achieved with concurrent calculations performed on -both the CPU and the co-processor. This is achieved by offloading only -a fraction of the neighbor and pair computations to the co-processor or -using "hybrid"_pair_hybrid.html pair styles where only one style uses -the "intel" suffix. For simulations with long-range electrostatics or -bond, angle, dihedral, improper calculations, computation and data -transfer to the co-processor will run concurrently with computations -and MPI communications for these calculations on the host CPU. This -is illustrated in the figure below for the rhodopsin protein benchmark -running on E5-2697v2 processors with a Intel Xeon Phi 7120p -co-processor. In this plot, the vertical access is time and routines -running at the same time are running concurrently on both the host and -the co-processor. - -:c,image(JPG/offload_knc.png) - -The fraction of the offloaded work is controlled by the {balance} -keyword in the "package intel"_package.html command. A balance of 0 -runs all calculations on the CPU. A balance of 1 runs all -supported calculations on the co-processor. A balance of 0.5 runs half -of the calculations on the co-processor. Setting the balance to -1 -(the default) will enable dynamic load balancing that continuously -adjusts the fraction of offloaded work throughout the simulation. -Because data transfer cannot be timed, this option typically produces -results within 5 to 10 percent of the optimal fixed balance. - -If running short benchmark runs with dynamic load balancing, adding a -short warm-up run (10-20 steps) will allow the load-balancer to find a -near-optimal setting that will carry over to additional runs. - -The default for the "package intel"_package.html command is to have -all the MPI tasks on a given compute node use a single Xeon Phi -co-processor. In general, running with a large number of MPI tasks on -each node will perform best with offload. Each MPI task will -automatically get affinity to a subset of the hardware threads -available on the co-processor. For example, if your card has 61 cores, -with 60 cores available for offload and 4 hardware threads per core -(240 total threads), running with 24 MPI tasks per node will cause -each MPI task to use a subset of 10 threads on the co-processor. Fine -tuning of the number of threads to use per MPI task or the number of -threads to use per core can be accomplished with keyword settings of -the "package intel"_package.html command. - -The USER-INTEL package has two modes for deciding which atoms will be -handled by the co-processor. This choice is controlled with the {ghost} -keyword of the "package intel"_package.html command. When set to 0, -ghost atoms (atoms at the borders between MPI tasks) are not offloaded -to the card. This allows for overlap of MPI communication of forces -with computation on the co-processor when the "newton"_newton.html -setting is "on". The default is dependent on the style being used, -however, better performance may be achieved by setting this option -explicitly. - -When using offload with CPU Hyper-Threading disabled, it may help -performance to use fewer MPI tasks and OpenMP threads than available -cores. This is due to the fact that additional threads are generated -internally to handle the asynchronous offload tasks. - -If pair computations are being offloaded to an Intel Xeon Phi -co-processor, a diagnostic line is printed to the screen (not to the -log file), during the setup phase of a run, indicating that offload -mode is being used and indicating the number of co-processor threads -per MPI task. Additionally, an offload timing summary is printed at -the end of each run. When offloading, the frequency for "atom -sorting"_atom_modify.html is changed to 1 so that the per-atom data is -effectively sorted at every rebuild of the neighbor lists. All the -available co-processor threads on each Phi will be divided among MPI -tasks, unless the {tptask} option of the "-pk intel" "command-line -switch"_Run_options.html is used to limit the co-processor threads per -MPI task. - -[Restrictions:] - -When offloading to a co-processor, "hybrid"_pair_hybrid.html styles -that require skip lists for neighbor builds cannot be offloaded. -Using "hybrid/overlay"_pair_hybrid.html is allowed. Only one intel -accelerated style may be used with hybrid styles when offloading. -"Special_bonds"_special_bonds.html exclusion lists are not currently -supported with offload, however, the same effect can often be -accomplished by setting cutoffs for excluded atom types to 0. None of -the pair styles in the USER-INTEL package currently support the -"inner", "middle", "outer" options for rRESPA integration via the -"run_style respa"_run_style.html command; only the "pair" option is -supported. - -[References:] - -Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l - -Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. "Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency."_http://dl.acm.org/citation.cfm?id=3014915 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). :l - -Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l -:ule - - - - diff --git a/doc/txt/Speed_kokkos.txt b/doc/txt/Speed_kokkos.txt deleted file mode 100644 index 66f8fab8d9..0000000000 --- a/doc/txt/Speed_kokkos.txt +++ /dev/null @@ -1,395 +0,0 @@ -"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -KOKKOS package :h3 - -Kokkos is a templated C++ library that provides abstractions to allow -a single implementation of an application kernel (e.g. a pair style) -to run efficiently on different kinds of hardware, such as GPUs, Intel -Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto -different back end languages such as CUDA, OpenMP, or Pthreads. The -Kokkos library also provides data abstractions to adjust (at compile -time) the memory layout of data structures like 2d and 3d arrays to -optimize performance on different hardware. For more information on -Kokkos, see "GitHub"_https://github.com/kokkos/kokkos. Kokkos is part -of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos -library was written primarily by Carter Edwards, Christian Trott, and -Dan Sunderland (all Sandia). - -The LAMMPS KOKKOS package contains versions of pair, fix, and atom -styles that use data structures and macros provided by the Kokkos -library, which is included with LAMMPS in /lib/kokkos. The KOKKOS -package was developed primarily by Christian Trott (Sandia) and Stan -Moore (Sandia) with contributions of various styles by others, -including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez -(Sandia). For more information on developing using Kokkos abstractions -see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf. - -Kokkos currently provides support for 3 modes of execution (per MPI -task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP -(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA -GPUs). You choose the mode at build time to produce an executable -compatible with specific hardware. - -NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible -compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or -Clang 3.5.2 or later is required. - -NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA -software version 7.5 or later must be installed on your system. See -the discussion for the "GPU package"_Speed_gpu.html for details of how -to check and do this. - -NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library -is CUDA-aware. This is not always the case, especially when using -pre-compiled MPI libraries provided by a Linux distribution. This is not -a problem when using only a single GPU with a single MPI rank. When -running with multiple MPI ranks, you may see segmentation faults without -CUDA-aware MPI support. These can be avoided by adding the flags "-pk -kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by -using the command "package kokkos cuda/aware off"_package.html in the -input file. - -[Building LAMMPS with the KOKKOS package:] - -See the "Build extras"_Build_extras.html#kokkos doc page for instructions. - -[Running LAMMPS with the KOKKOS package:] - -All Kokkos operations occur within the context of an individual MPI -task running on a single node of the machine. The total number of MPI -tasks used by LAMMPS (one or multiple per compute node) is set in the -usual manner via the mpirun or mpiexec commands, and is independent of -Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and --npernode switches. Ditto for MPICH via -np and -ppn. - -[Running on a multi-core CPU:] - -Here is a quick overview of how to use the KOKKOS package -for CPU acceleration, assuming one or more 16-core nodes. - -mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no multi-threading -mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task -mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task -mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre - -To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk -kokkos" "command-line switches"_Run_options.html in your mpirun -command. You must use the "-k on" "command-line -switch"_Run_options.html to enable the KOKKOS package. It takes -additional arguments for hardware settings appropriate to your system. -For OpenMP use: - --k on t Nt :pre - -The "t Nt" option specifies how many OpenMP threads per MPI task to -use with a node. The default is Nt = 1, which is MPI-only mode. Note -that the product of MPI tasks * OpenMP threads/task should not exceed -the physical number of cores (on a node), otherwise performance will -suffer. If Hyper-Threading (HT) is enabled, then the product of MPI -tasks * OpenMP threads/task should not exceed the physical number of -cores * hardware threads. The "-k on" switch also issues a -"package kokkos" command (with no additional arguments) which sets -various KOKKOS options to default values, as discussed on the -"package"_package.html command doc page. - -The "-sf kk" "command-line switch"_Run_options.html will automatically -append the "/kk" suffix to styles that support it. In this manner no -modification to the input script is needed. Alternatively, one can run -with the KOKKOS package by editing the input script as described -below. - -NOTE: When using a single OpenMP thread, the Kokkos Serial back end (i.e. -Makefile.kokkos_mpi_only) will give better performance than the OpenMP -back end (i.e. Makefile.kokkos_omp) because some of the overhead to make -the code thread-safe is removed. - -NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html to -change the default "package kokkos"_package.html options. See its doc -page for details and default settings. Experimenting with its options -can provide a speed-up for specific calculations. For example: - -mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre - -If the "newton"_newton.html command is used in the input -script, it can also override the Newton flag defaults. - -For half neighbor lists and OpenMP, the KOKKOS package uses data -duplication (i.e. thread-private arrays) by default to avoid -thread-level write conflicts in the force arrays (and other data -structures as necessary). Data duplication is typically fastest for -small numbers of threads (i.e. 8 or less) but does increase memory -footprint and is not scalable to large numbers of threads. An -alternative to data duplication is to use thread-level atomic operations -which do not require data duplication. The use of atomic operations can -be enforced by compiling LAMMPS with the "-DLMP_KOKKOS_USE_ATOMICS" -pre-processor flag. Most but not all Kokkos-enabled pair_styles support -data duplication. Alternatively, full neighbor lists avoid the need for -duplication or atomic operations but require more compute operations per -atom. When using the Kokkos Serial back end or the OpenMP back end with -a single thread, no duplication or atomic operations are used. For CUDA -and half neighbor lists, the KOKKOS package always uses atomic operations. - -[Core and Thread Affinity:] - -When using multi-threading, it is important for performance to bind -both MPI tasks to physical cores, and threads to physical cores, so -they do not migrate during a simulation. - -If you are not certain MPI tasks are being bound (check the defaults -for your MPI installation), binding can be forced with these flags: - -OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ... -Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... :pre - -For binding threads with KOKKOS OpenMP, use thread affinity -environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or -later, intel 12 or later) setting the environment variable -OMP_PROC_BIND=true should be sufficient. In general, for best -performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and -OMP_PLACES=threads. For binding threads with the KOKKOS pthreads -option, compile LAMMPS the KOKKOS HWLOC=yes option as described below. - -[Running on Knight's Landing (KNL) Intel Xeon Phi:] - -Here is a quick overview of how to use the KOKKOS package for the -Intel Knight's Landing (KNL) Xeon Phi: - -KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are -reserved for the OS, and only 64 or 66 cores are used. Each core has 4 -Hyper-Threads,so there are effectively N = 256 (4*64) or N = 264 (4*66) -cores to run on. The product of MPI tasks * OpenMP threads/task should -not exceed this limit, otherwise performance will suffer. Note that -with the KOKKOS package you do not need to specify how many KNLs there -are per node; each KNL is simply treated as running some number of MPI -tasks. - -Examples of mpirun commands that follow these rules are shown below. - -Intel KNL node with 68 cores (272 threads/node via 4x hardware threading): -mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 64 MPI tasks/node, 4 threads/task -mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 66 MPI tasks/node, 4 threads/task -mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj # 1 node, 32 MPI tasks/node, 8 threads/task -mpirun -np 512 -ppn 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 8 nodes, 64 MPI tasks/node, 4 threads/task :pre - -The -np setting of the mpirun command sets the number of MPI -tasks/node. The "-k on t Nt" command-line switch sets the number of -threads/task as Nt. The product of these two values should be N, i.e. -256 or 264. - -NOTE: The default for the "package kokkos"_package.html command when -running on KNL is to use "half" neighbor lists and set the Newton flag -to "on" for both pairwise and bonded interactions. This will typically -be best for many-body potentials. For simpler pair-wise potentials, it -may be faster to use a "full" neighbor list with Newton flag to "off". -Use the "-pk kokkos" "command-line switch"_Run_options.html to change -the default "package kokkos"_package.html options. See its doc page for -details and default settings. Experimenting with its options can provide -a speed-up for specific calculations. For example: - -mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax # Newton on, half neighbor list, threaded comm -mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj # Newton off, full neighbor list, non-threaded comm :pre - -NOTE: MPI tasks and threads should be bound to cores as described -above for CPUs. - -NOTE: To build with Kokkos support for Intel Xeon Phi co-processors -such as Knight's Corner (KNC), your system must be configured to use -them in "native" mode, not "offload" mode like the USER-INTEL package -supports. - -[Running on GPUs:] - -Use the "-k" "command-line switch"_Run_options.html to specify the -number of GPUs per node. Typically the -np setting of the mpirun command -should set the number of MPI tasks/node to be equal to the number of -physical GPUs on the node. You can assign multiple MPI tasks to the same -GPU with the KOKKOS package, but this is usually only faster if some -portions of the input script have not been ported to use Kokkos. In this -case, also packing/unpacking communication buffers on the host may give -speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS -is recommended in this scenario. - -Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be -avoided by using "-pk kokkos cuda/aware no"_package.html. As above for -multi-core CPUs (and no GPU), if N is the number of physical cores/node, -then the number of MPI tasks/node should not exceed N. - --k on g Ng :pre - -Here are examples of how to use the KOKKOS package for GPUs, assuming -one or more nodes, each with two GPUs: - -mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node -mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre - -NOTE: The default for the "package kokkos"_package.html command when -running on GPUs is to use "full" neighbor lists and set the Newton flag -to "off" for both pairwise and bonded interactions, along with threaded -communication. When running on Maxwell or Kepler GPUs, this will -typically be best. For Pascal GPUs, using "half" neighbor lists and -setting the Newton flag to "on" may be faster. For many pair styles, -setting the neighbor binsize equal to twice the CPU default value will -give speedup, which is the default when running on GPUs. Use the "-pk -kokkos" "command-line switch"_Run_options.html to change the default -"package kokkos"_package.html options. See its doc page for details and -default settings. Experimenting with its options can provide a speed-up -for specific calculations. For example: - -mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre - -NOTE: For good performance of the KOKKOS package on GPUs, you must -have Kepler generation GPUs (or later). The Kokkos library exploits -texture cache options not supported by Telsa generation GPUs (or -older). - -NOTE: When using a GPU, you will achieve the best performance if your -input script does not use fix or compute styles which are not yet -Kokkos-enabled. This allows data to stay on the GPU for multiple -timesteps, without being copied back to the host CPU. Invoking a -non-Kokkos fix or compute, or performing I/O for -"thermo"_thermo_style.html or "dump"_dump.html output will cause data -to be copied back to the CPU incurring a performance penalty. - -NOTE: To get an accurate timing breakdown between time spend in pair, -kspace, etc., you must set the environment variable CUDA_LAUNCH_BLOCKING=1. -However, this will reduce performance and is not recommended for production runs. - -[Run with the KOKKOS package by editing an input script:] - -Alternatively the effect of the "-sf" or "-pk" switches can be -duplicated by adding the "package kokkos"_package.html or "suffix -kk"_suffix.html commands to your input script. - -The discussion above for building LAMMPS with the KOKKOS package, the -mpirun/mpiexec command, and setting appropriate thread are the same. - -You must still use the "-k on" "command-line switch"_Run_options.html -to enable the KOKKOS package, and specify its additional arguments for -hardware options appropriate to your system, as documented above. - -You can use the "suffix kk"_suffix.html command, or you can explicitly add a -"kk" suffix to individual styles in your input script, e.g. - -pair_style lj/cut/kk 2.5 :pre - -You only need to use the "package kokkos"_package.html command if you -wish to change any of its option defaults, as set by the "-k on" -"command-line switch"_Run_options.html. - -[Using OpenMP threading and CUDA together (experimental):] - -With the KOKKOS package, both OpenMP multi-threading and GPUs can be -used together in a few special cases. In the Makefile, the -KOKKOS_DEVICES variable must include both "Cuda" and "OpenMP", as is -the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi - -KOKKOS_DEVICES=Cuda,OpenMP :pre - -The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA, -using the "-sf kk" in the command line gives the default CUDA version -everywhere. However, if the "/kk/host" suffix is added to a specific -style in the input script, the Kokkos OpenMP (CPU) version of that -specific style will be used instead. Set the number of OpenMP threads -as "t Nt" and the number of GPUs as "g Ng" - --k on t Nt g Ng :pre - -For example, the command to run with 1 GPU and 8 OpenMP threads is then: - -mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre - -Conversely, if the "-sf kk/host" is used in the command line and then -the "/kk" or "/kk/device" suffix is added to a specific style in your -input script, then only that specific style will run on the GPU while -everything else will run on the CPU in OpenMP mode. Note that the -execution of the CPU and GPU styles will NOT overlap, except for a -special case: - -A kspace style and/or molecular topology (bonds, angles, etc.) running -on the host CPU can overlap with a pair style running on the -GPU. First compile with "--default-stream per-thread" added to CCFLAGS -in the Kokkos CUDA Makefile. Then explicitly use the "/kk/host" -suffix for kspace and bonds, angles, etc. in the input file and the -"kk" suffix (equal to "kk/device") on the command line. Also make -sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1" -so CPU/GPU overlap can occur. - -[Speed-ups to expect:] - -The performance of KOKKOS running in different modes is a function of -your hardware, which KOKKOS-enable styles are used, and the problem -size. - -Generally speaking, the following rules of thumb apply: - -When running on CPUs only, with a single thread per MPI task, -performance of a KOKKOS style is somewhere between the standard -(un-accelerated) styles (MPI-only mode), and those provided by the -USER-OMP package. However the difference between all 3 is small (less -than 20%). :ulb,l - -When running on CPUs only, with multiple threads per MPI task, -performance of a KOKKOS style is a bit slower than the USER-OMP -package. :l - -When running large number of atoms per GPU, KOKKOS is typically faster -than the GPU package. :l - -When running on Intel hardware, KOKKOS is not as fast as -the USER-INTEL package, which is optimized for that hardware. :l -:ule - -See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the -LAMMPS web site for performance of the KOKKOS package on different -hardware. - -[Advanced Kokkos options:] - -There are other allowed options when building with the KOKKOS package. -As explained on the "Build extras"_Build_extras.html#kokkos doc page, -they can be set either as variables on the make command line or in -Makefile.machine, or they can be specified as CMake variables. Each -takes a value shown below. The default value is listed, which is set -in the lib/kokkos/Makefile.kokkos file. - -KOKKOS_DEBUG, values = {yes}, {no}, default = {no} -KOKKOS_USE_TPLS, values = {hwloc}, {librt}, {experimental_memkind}, default = {none} -KOKKOS_CXX_STANDARD, values = {c++11}, {c++1z}, default = {c++11} -KOKKOS_OPTIONS, values = {aggressive_vectorization}, {disable_profiling}, default = {none} -KOKKOS_CUDA_OPTIONS, values = {force_uvm}, {use_ldg}, {rdc}, {enable_lambda}, default = {enable_lambda} :ul - -KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not -migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be -used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not -necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP -provides alternative methods via environment variables for binding -threads to hardware cores. More info on binding threads to cores is -given on the "Speed omp"_Speed_omp.html doc page. - -KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism -on most Unix platforms. This library is not available on all -platforms. - -KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style -within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time -debugging information that can be useful. It also enables runtime -bounds checking on Kokkos data structures. - -KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when -building LAMMPS. - -KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS -package must be compiled with the {enable_lambda} option when using -GPUs. - -[Restrictions:] - -Currently, there are no precision options with the KOKKOS package. All -compilation and computation is performed in double precision. diff --git a/doc/txt/Speed_measure.txt b/doc/txt/Speed_measure.txt deleted file mode 100644 index dd12685dc5..0000000000 --- a/doc/txt/Speed_measure.txt +++ /dev/null @@ -1,55 +0,0 @@ -"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Measuring performance :h3 - -Before trying to make your simulation run faster, you should -understand how it currently performs and where the bottlenecks are. - -The best way to do this is run the your system (actual number of -atoms) for a modest number of timesteps (say 100 steps) on several -different processor counts, including a single processor if possible. -Do this for an equilibrium version of your system, so that the -100-step timings are representative of a much longer run. There is -typically no need to run for 1000s of timesteps to get accurate -timings; you can simply extrapolate from short runs. - -For the set of runs, look at the timing data printed to the screen and -log file at the end of each LAMMPS run. The -"Run_output"_Run_output.html doc page gives an overview. - -Running on one (or a few processors) should give a good estimate of -the serial performance and what portions of the timestep are taking -the most time. Running the same problem on a few different processor -counts should give an estimate of parallel scalability. I.e. if the -simulation runs 16x faster on 16 processors, its 100% parallel -efficient; if it runs 8x faster on 16 processors, it's 50% efficient. - -The most important data to look at in the timing info is the timing -breakdown and relative percentages. For example, trying different -options for speeding up the long-range solvers will have little impact -if they only consume 10% of the run time. If the pairwise time is -dominating, you may want to look at GPU or OMP versions of the pair -style, as discussed below. Comparing how the percentages change as -you increase the processor count gives you a sense of how different -operations within the timestep are scaling. Note that if you are -running with a Kspace solver, there is additional output on the -breakdown of the Kspace time. For PPPM, this includes the fraction -spent on FFTs, which can be communication intensive. - -Another important detail in the timing info are the histograms of -atoms counts and neighbor counts. If these vary widely across -processors, you have a load-imbalance issue. This often results in -inaccurate relative timing data, because processors have to wait when -communication occurs for other processors to catch up. Thus the -reported times for "Communication" or "Other" may be higher than they -really are, due to load-imbalance. If this is an issue, you can -uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile -LAMMPS, to obtain synchronized timings. - diff --git a/doc/txt/Speed_omp.txt b/doc/txt/Speed_omp.txt deleted file mode 100644 index 97aa251e9e..0000000000 --- a/doc/txt/Speed_omp.txt +++ /dev/null @@ -1,171 +0,0 @@ -"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -USER-OMP package :h3 - -The USER-OMP package was developed by Axel Kohlmeyer at Temple -University. It provides optimized and multi-threaded versions -of many pair styles, nearly all bonded styles (bond, angle, dihedral, -improper), several Kspace styles, and a few fix styles. It uses -the OpenMP interface for multi-threading, but can also be compiled -without OpenMP support, providing optimized serial styles in that case. - -[Required hardware/software:] - -To enable multi-threading, your compiler must support the OpenMP interface. -You should have one or more multi-core CPUs, as multiple threads can only be -launched by each MPI task on the local node (using shared memory). - -[Building LAMMPS with the USER-OMP package:] - -See the "Build extras"_Build_extras.html#user-omp doc page for -instructions. - -[Run with the USER-OMP package from the command line:] - -These examples assume one or more 16-core nodes. - -env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script # 1 MPI task, 16 threads according to OMP_NUM_THREADS -lmp_mpi -sf omp -in in.script # 1 MPI task, no threads, optimized kernels -mpirun -np 4 lmp_omp -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task -mpirun -np 32 -ppn 4 lmp_omp -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre - -The mpirun or mpiexec command sets the total number of MPI tasks used -by LAMMPS (one or multiple per compute node) and the number of MPI -tasks used per node. E.g. the mpirun command in MPICH does this via -its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. - -You need to choose how many OpenMP threads per MPI task will be used -by the USER-OMP package. Note that the product of MPI tasks * -threads/task should not exceed the physical number of cores (on a -node), otherwise performance will suffer. - -As in the lines above, use the "-sf omp" "command-line -switch"_Run_options.html, which will automatically append "omp" to -styles that support it. The "-sf omp" switch also issues a default -"package omp 0"_package.html command, which will set the number of -threads per MPI task via the OMP_NUM_THREADS environment variable. - -You can also use the "-pk omp Nt" "command-line -switch"_Run_options.html, to explicitly set Nt = # of OpenMP threads -per MPI task to use, as well as additional options. Its syntax is the -same as the "package omp"_package.html command whose doc page gives -details, including the default values used if it is not specified. It -also gives more details on how to set the number of threads via the -OMP_NUM_THREADS environment variable. - -[Or run with the USER-OMP package by editing an input script:] - -The discussion above for the mpirun/mpiexec command, MPI tasks/node, -and threads/MPI task is the same. - -Use the "suffix omp"_suffix.html command, or you can explicitly add an -"omp" suffix to individual styles in your input script, e.g. - -pair_style lj/cut/omp 2.5 :pre - -You must also use the "package omp"_package.html command to enable the -USER-OMP package. When you do this you also specify how many threads -per MPI task to use. The command doc page explains other options and -how to set the number of threads via the OMP_NUM_THREADS environment -variable. - -[Speed-ups to expect:] - -Depending on which styles are accelerated, you should look for a -reduction in the "Pair time", "Bond time", "KSpace time", and "Loop -time" values printed at the end of a run. - -You may see a small performance advantage (5 to 20%) when running a -USER-OMP style (in serial or parallel) with a single thread per MPI -task, versus running standard LAMMPS with its standard un-accelerated -styles (in serial or all-MPI parallelization with 1 task/core). This -is because many of the USER-OMP styles contain similar optimizations -to those used in the OPT package, described in "Section -5.3.5"_Speed_opt.html. - -With multiple threads/task, the optimal choice of number of MPI -tasks/node and OpenMP threads/task can vary a lot and should always be -tested via benchmark runs for a specific simulation running on a -specific machine, paying attention to guidelines discussed in the next -sub-section. - -A description of the multi-threading strategy used in the USER-OMP -package and some performance examples are "presented -here"_http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1 - -[Guidelines for best performance:] - -For many problems on current generation CPUs, running the USER-OMP -package with a single thread/task is faster than running with multiple -threads/task. This is because the MPI parallelization in LAMMPS is -often more efficient than multi-threading as implemented in the -USER-OMP package. The parallel efficiency (in a threaded sense) also -varies for different USER-OMP styles. - -Using multiple threads/task can be more effective under the following -circumstances: - -Individual compute nodes have a significant number of CPU cores but -the CPU itself has limited memory bandwidth, e.g. for Intel Xeon 53xx -(Clovertown) and 54xx (Harpertown) quad-core processors. Running one -MPI task per CPU core will result in significant performance -degradation, so that running with 4 or even only 2 MPI tasks per node -is faster. Running in hybrid MPI+OpenMP mode will reduce the -inter-node communication bandwidth contention in the same way, but -offers an additional speedup by utilizing the otherwise idle CPU -cores. :ulb,l - -The interconnect used for MPI communication does not provide -sufficient bandwidth for a large number of MPI tasks per node. For -example, this applies to running over gigabit ethernet or on Cray XT4 -or XT5 series supercomputers. As in the aforementioned case, this -effect worsens when using an increasing number of nodes. :l - -The system has a spatially inhomogeneous particle density which does -not map well to the "domain decomposition scheme"_processors.html or -"load-balancing"_balance.html options that LAMMPS provides. This is -because multi-threading achieves parallelism over the number of -particles, not via their distribution in space. :l - -A machine is being used in "capability mode", i.e. near the point -where MPI parallelism is maxed out. For example, this can happen when -using the "PPPM solver"_kspace_style.html for long-range -electrostatics on large numbers of nodes. The scaling of the KSpace -calculation (see the "kspace_style"_kspace_style.html command) becomes -the performance-limiting factor. Using multi-threading allows less -MPI tasks to be invoked and can speed-up the long-range solver, while -increasing overall performance by parallelizing the pairwise and -bonded calculations via OpenMP. Likewise additional speedup can be -sometimes be achieved by increasing the length of the Coulombic cutoff -and thus reducing the work done by the long-range solver. Using the -"run_style verlet/split"_run_style.html command, which is compatible -with the USER-OMP package, is an alternative way to reduce the number -of MPI tasks assigned to the KSpace calculation. :l -:ule - -Additional performance tips are as follows: - -The best parallel efficiency from {omp} styles is typically achieved -when there is at least one MPI task per physical CPU chip, i.e. socket -or die. :ulb,l - -It is usually most efficient to restrict threading to a single -socket, i.e. use one or more MPI task per socket. :l - -NOTE: By default, several current MPI implementations use a processor -affinity setting that restricts each MPI task to a single CPU core. -Using multi-threading in this mode will force all threads to share the -one core and thus is likely to be counterproductive. Instead, binding -MPI tasks to a (multi-core) socket, should solve this issue. :l -:ule - -[Restrictions:] - -None. diff --git a/doc/txt/Speed_opt.txt b/doc/txt/Speed_opt.txt deleted file mode 100644 index 7dd83a84bf..0000000000 --- a/doc/txt/Speed_opt.txt +++ /dev/null @@ -1,53 +0,0 @@ -"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -OPT package :h3 - -The OPT package was developed by James Fischer (High Performance -Technologies), David Richie, and Vincent Natoli (Stone Ridge -Technologies). It contains a handful of pair styles whose compute() -methods were rewritten in C++ templated form to reduce the overhead -due to if tests and other conditional code. - -[Required hardware/software:] - -None. - -[Building LAMMPS with the OPT package:] - -See the "Build extras"_Build_extras.html#opt doc page for instructions. - -[Run with the OPT package from the command line:] - -lmp_mpi -sf opt -in in.script # run in serial -mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel :pre - -Use the "-sf opt" "command-line switch"_Run_options.html, which will -automatically append "opt" to styles that support it. - -[Or run with the OPT package by editing an input script:] - -Use the "suffix opt"_suffix.html command, or you can explicitly add an -"opt" suffix to individual styles in your input script, e.g. - -pair_style lj/cut/opt 2.5 :pre - -[Speed-ups to expect:] - -You should see a reduction in the "Pair time" value printed at the end -of a run. On most machines for reasonable problem sizes, it will be a -5 to 20% savings. - -[Guidelines for best performance:] - -Just try out an OPT pair style to see how it performs. - -[Restrictions:] - -None. diff --git a/doc/txt/Speed_packages.txt b/doc/txt/Speed_packages.txt deleted file mode 100644 index 2f72a46b3a..0000000000 --- a/doc/txt/Speed_packages.txt +++ /dev/null @@ -1,192 +0,0 @@ -"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Accelerator packages :h3 - -Accelerated versions of various "pair_style"_pair_style.html, -"fixes"_fix.html, "computes"_compute.html, and other commands have -been added to LAMMPS, which will typically run faster than the -standard non-accelerated versions. Some require appropriate hardware -to be present on your system, e.g. GPUs or Intel Xeon Phi -co-processors. - -All of these commands are in packages provided with LAMMPS. An -overview of packages is give on the "Packages"_Packages.html doc -pages. - -These are the accelerator packages currently in LAMMPS, either as -standard or user packages: - -"GPU Package"_Speed_gpu.html : for NVIDIA GPUs as well as OpenCL support -"USER-INTEL Package"_Speed_intel.html : for Intel CPUs and Intel Xeon Phi -"KOKKOS Package"_Speed_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading -"USER-OMP Package"_Speed_omp.html : for OpenMP threading and generic CPU optimizations -"OPT Package"_Speed_opt.html : generic CPU optimizations :tb(s=:) - - - -Inverting this list, LAMMPS currently has acceleration support for -three kinds of hardware, via the listed packages: - -Many-core CPUs : "USER-INTEL"_Speed_intel.html, "KOKKOS"_Speed_kokkos.html, "USER-OMP"_Speed_omp.html, "OPT"_Speed_opt.html packages -NVIDIA GPUs : "GPU"_Speed_gpu.html, "KOKKOS"_Speed_kokkos.html packages -Intel Phi : "USER-INTEL"_Speed_intel.html, "KOKKOS"_Speed_kokkos.html packages :tb(s=:) - -Which package is fastest for your hardware may depend on the size -problem you are running and what commands (accelerated and -non-accelerated) are invoked by your input script. While these doc -pages include performance guidelines, there is no substitute for -trying out the different packages appropriate to your hardware. - -Any accelerated style has the same name as the corresponding standard -style, except that a suffix is appended. Otherwise, the syntax for -the command that uses the style is identical, their functionality is -the same, and the numerical results it produces should also be the -same, except for precision and round-off effects. - -For example, all of these styles are accelerated variants of the -Lennard-Jones "pair_style lj/cut"_pair_lj.html: - -"pair_style lj/cut/gpu"_pair_lj.html -"pair_style lj/cut/intel"_pair_lj.html -"pair_style lj/cut/kk"_pair_lj.html -"pair_style lj/cut/omp"_pair_lj.html -"pair_style lj/cut/opt"_pair_lj.html :ul - -To see what accelerate styles are currently available for a particular -style, find the style name in the "Commands_all"_lc -style pages (fix,compute,pair,etc) and see what suffixes are listed -(g,i,k,o,t) with it. The doc pages for individual commands -(e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list -any accelerated variants available for that style. - -To use an accelerator package in LAMMPS, and one or more of the styles -it provides, follow these general steps. Details vary from package to -package and are explained in the individual accelerator doc pages, -listed above: - -build the accelerator library | - only for GPU package | -install the accelerator package | - make yes-opt, make yes-user-intel, etc | -add compile/link flags to Makefile.machine in src/MAKE | - only for USER-INTEL, KOKKOS, USER-OMP, OPT packages | -re-build LAMMPS | - make machine | -prepare and test a regular LAMMPS simulation | - lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script | -enable specific accelerator support via '-k on' "command-line switch"_Run_options.html, | - only needed for KOKKOS package | -set any needed options for the package via "-pk" "command-line switch"_Run_options.html or "package"_package.html command, | - only if defaults need to be changed | -use accelerated styles in your input via "-sf" "command-line switch"_Run_options.html or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu -:tb(c=2,s=|) - -Note that the first 4 steps can be done as a single command with -suitable make command invocations. This is discussed on the -"Packages"_Packages.html doc pages, and its use is illustrated in the -individual accelerator sections. Typically these steps only need to -be done once, to create an executable that uses one or more -accelerator packages. - -The last 4 steps can all be done from the command-line when LAMMPS is -launched, without changing your input script, as illustrated in the -individual accelerator sections. Or you can add -"package"_package.html and "suffix"_suffix.html commands to your input -script. - -NOTE: With a few exceptions, you can build a single LAMMPS executable -with all its accelerator packages installed. Note however that the -USER-INTEL and KOKKOS packages require you to choose one of their -hardware options when building for a specific platform. I.e. CPU or -Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi -option for the KOKKOS package. - -These are the exceptions. You cannot build a single executable with: - -both the USER-INTEL Phi and KOKKOS Phi options -the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul - -See the examples/accelerate/README and make.list files for sample -Make.py commands that build LAMMPS with any or all of the accelerator -packages. As an example, here is a command that builds with all the -GPU related packages installed (GPU, KOKKOS with Cuda), including -settings to build the needed auxiliary GPU libraries for Kepler GPUs: - -Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \ - -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre - -The examples/accelerate directory also has input scripts that can be -used with all of the accelerator packages. See its README file for -details. - -Likewise, the bench directory has FERMI and KEPLER and PHI -sub-directories with Make.py commands and input scripts for using all -the accelerator packages on various machines. See the README files in -those dirs. - -As mentioned above, the "Benchmark -page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives -performance results for the various accelerator packages for several -of the standard LAMMPS benchmark problems, as a function of problem -size and number of compute nodes, on different hardware platforms. - -Here is a brief summary of what the various packages provide. Details -are in the individual accelerator sections. - -Styles with a "gpu" suffix are part of the GPU package, and can be run -on NVIDIA GPUs. The speed-up on a GPU depends on a variety of -factors, discussed in the accelerator sections. :ulb,l - -Styles with an "intel" suffix are part of the USER-INTEL -package. These styles support vectorized single and mixed precision -calculations, in addition to full double precision. In extreme cases, -this can provide speedups over 3.5x on CPUs. The package also -supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM) -co-processors. This can result in additional speedup over 2x depending -on the hardware configuration. :l - -Styles with a "kk" suffix are part of the KOKKOS package, and can be -run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel -Xeon Phi in "native" mode. The speed-up depends on a variety of -factors, as discussed on the KOKKOS accelerator page. :l - -Styles with an "omp" suffix are part of the USER-OMP package and allow -a pair-style to be run in multi-threaded mode using OpenMP. This can -be useful on nodes with high-core counts when using less MPI processes -than cores is advantageous, e.g. when running with PPPM so that FFTs -are run on fewer MPI processors or when the many MPI tasks would -overload the available bandwidth for communication. :l - -Styles with an "opt" suffix are part of the OPT package and typically -speed-up the pairwise calculations of your simulation by 5-25% on a -CPU. :l -:ule - -The individual accelerator package doc pages explain: - -what hardware and software the accelerated package requires -how to build LAMMPS with the accelerated package -how to run with the accelerated package either via command-line switches or modifying the input script -speed-ups to expect -guidelines for best performance -restrictions :ul - diff --git a/doc/txt/Speed_tips.txt b/doc/txt/Speed_tips.txt deleted file mode 100644 index 858b1d493f..0000000000 --- a/doc/txt/Speed_tips.txt +++ /dev/null @@ -1,59 +0,0 @@ -"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -General tips :h3 - -NOTE: this page is still a work in progress - -Here is a list of general ideas for improving simulation performance. -Most of them are only applicable to certain models and certain -bottlenecks in the current performance, so let the timing data you -generate be your guide. It is hard, if not impossible, to predict how -much difference these options will make, since it is a function of -problem size, number of processors used, and your machine. There is -no substitute for identifying performance bottlenecks, and trying out -various options. - -rRESPA -Two-FFT PPPM -Staggered PPPM -single vs double PPPM -partial charge PPPM -verlet/split run style -processor command for proc layout and numa layout -load-balancing: balance and fix balance :ul - -Two-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, -uses 2 FFTs instead of the 4 FFTs used by the default {ik -differentiation} PPPM. However, 2-FFT PPPM also requires a slightly -larger mesh size to achieve the same accuracy as 4-FFT PPPM. For -problems where the FFT cost is the performance bottleneck (typically -large problems running on many processors), 2-FFT PPPM may be faster -than 4-FFT PPPM. - -Staggered PPPM performs calculations using two different meshes, one -shifted slightly with respect to the other. This can reduce force -aliasing errors and increase the accuracy of the method, but also -doubles the amount of work required. For high relative accuracy, using -staggered PPPM allows one to half the mesh size in each dimension as -compared to regular PPPM, which can give around a 4x speedup in the -kspace time. However, for low relative accuracy, using staggered PPPM -gives little benefit and can be up to 2x slower in the kspace -time. For example, the rhodopsin benchmark was run on a single -processor, and results for kspace time vs. relative accuracy for the -different methods are shown in the figure below. For this system, -staggered PPPM (using ik differentiation) becomes useful when using a -relative accuracy of slightly greater than 1e-5 and above. - -:c,image(JPG/rhodo_staggered.jpg) - -NOTE: Using staggered PPPM may not give the same increase in accuracy -of energy and pressure as it does in forces, so some caution must be -used if energy and/or pressure are quantities of interest, such as -when using a barostat. diff --git a/doc/txt/Tools.txt b/doc/txt/Tools.txt deleted file mode 100644 index dccdf77dee..0000000000 --- a/doc/txt/Tools.txt +++ /dev/null @@ -1,578 +0,0 @@ -"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Modify.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Auxiliary tools :h2 - -LAMMPS is designed to be a computational kernel for performing -molecular dynamics computations. Additional pre- and post-processing -steps are often necessary to setup and analyze a simulation. A list -of such tools can be found on the "LAMMPS webpage"_lws at these links: - -"Pre/Post processing"_http://lammps.sandia.gov/prepost.html -"Offsite LAMMPS packages & tools"_http://lammps.sandia.gov/offsite.html -"Pizza.py toolkit"_pizza :ul - -The last link for "Pizza.py"_pizza is a Python-based tool developed at -Sandia which provides tools for doing setup, analysis, plotting, and -visualization for LAMMPS simulations. - -:link(pizza,http://pizza.sandia.gov) -:link(python,http://www.python.org) - -Additional tools included in the LAMMPS distribution are described on -this page. - -Note that many users write their own setup or analysis tools or use -other existing codes and convert their output to a LAMMPS input format -or vice versa. The tools listed here are included in the LAMMPS -distribution as examples of auxiliary tools. Some of them are not -actively supported by the LAMMPS developers, as they were contributed -by LAMMPS users. If you have problems using them, we can direct you -to the authors. - -The source code for each of these codes is in the tools sub-directory -of the LAMMPS distribution. There is a Makefile (which you may need -to edit for your platform) which will build several of the tools which -reside in that directory. Most of them are larger packages in their -own sub-directories with their own Makefiles and/or README files. - -:line - -Pre-processing tools :h3 - -"amber2lmp"_#amber, -"ch2lmp"_#charmm, -"chain"_#chain, -"createatoms"_#createatoms, -"drude"_#drude, -"eam database"_#eamdb, -"eam generate"_#eamgn, -"eff"_#eff, -"ipp"_#ipp, -"micelle2d"_#micelle, -"moltemplate"_#moltemplate, -"msi2lmp"_#msi, -"polybond"_#polybond :tb(c=6,ea=c,a=l) - -Post-processing tools :h3 - -"amber2lmp"_#amber, -"binary2txt"_#binary, -"ch2lmp"_#charmm, -"colvars"_#colvars, -"eff"_#eff, -"fep"_#fep, -"lmp2arc"_#arc, -"lmp2cfg"_#cfg, -"matlab"_#matlab, -"phonon"_#phonon, -"pymol_asphere"_#pymol, -"python"_#pythontools, -"reax"_#reax_tool, -"replica"_#replica, -"smd"_#smd, -"spin"_#spin, -"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l) - -Miscellaneous tools :h3 - -"doxygen"_#doxygen, -"emacs"_#emacs, -"i-pi"_#ipi, -"kate"_#kate, -"singularity"_#singularity_tool, -"vim"_#vim :tb(c=5,ea=c,a=l) - -:line - -Tool descriptions :h3 - -amber2lmp tool :h4,link(amber) - -The amber2lmp sub-directory contains two Python scripts for converting -files back-and-forth between the AMBER MD code and LAMMPS. See the -README file in amber2lmp for more information. - -These tools were written by Keir Novik while he was at Queen Mary -University of London. Keir is no longer there and cannot support -these tools which are out-of-date with respect to the current LAMMPS -version (and maybe with respect to AMBER as well). Since we don't use -these tools at Sandia, you'll need to experiment with them and make -necessary modifications yourself. - -:line - -binary2txt tool :h4,link(binary) - -The file binary2txt.cpp converts one or more binary LAMMPS dump file -into ASCII text files. The syntax for running the tool is - -binary2txt file1 file2 ... :pre - -which creates file1.txt, file2.txt, etc. This tool must be compiled -on a platform that can read the binary file created by a LAMMPS run, -since binary files are not compatible across all platforms. - -:line - -ch2lmp tool :h4,link(charmm) - -The ch2lmp sub-directory contains tools for converting files -back-and-forth between the CHARMM MD code and LAMMPS. - -They are intended to make it easy to use CHARMM as a builder and as a -post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a -PDB file with associated CHARMM info, including CHARMM force field -data, into its LAMMPS equivalent. Support for the CMAP correction of -CHARMM22 and later is available as an option. This tool can also add -solvent water molecules and Na+ or Cl- ions to the system. -Using lammps2pdb.pl you can convert LAMMPS atom dumps into PDB files. - -See the README file in the ch2lmp sub-directory for more information. - -These tools were created by Pieter in't Veld (pjintve at sandia.gov) -and Paul Crozier (pscrozi at sandia.gov) at Sandia. - -CMAP support added and tested by Xiaohu Hu (hux2 at ornl.gov) and -Robert A. Latour (latourr at clemson.edu), David Hyde-Volpe, and -Tigran Abramyan, (Clemson University) and -Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London. - -:line - -chain tool :h4,link(chain) - -The file chain.f creates a LAMMPS data file containing bead-spring -polymer chains and/or monomer solvent atoms. It uses a text file -containing chain definition parameters as an input. The created -chains and solvent atoms can strongly overlap, so LAMMPS needs to run -the system initially with a "soft" pair potential to un-overlap it. -The syntax for running the tool is - -chain < def.chain > data.file :pre - -See the def.chain or def.chain.ab files in the tools directory for -examples of definition files. This tool was used to create the system -for the "chain benchmark"_Speed_bench.html. - -:line - -colvars tools :h4,link(colvars) - -The colvars directory contains a collection of tools for post-processing -data produced by the colvars collective variable library. -To compile the tools, edit the makefile for your system and run "make". - -Please report problems and issues the colvars library and its tools -at: https://github.com/colvars/colvars/issues - -abf_integrate: - -MC-based integration of multidimensional free energy gradient -Version 20110511 - -Syntax: ./abf_integrate < filename > \[-n < nsteps >\] \[-t < temp >\] \[-m \[0|1\] (metadynamics)\] \[-h < hill_height >\] \[-f < variable_hill_factor >\] :pre - -The LAMMPS interface to the colvars collective variable library, as -well as these tools, were created by Axel Kohlmeyer (akohlmey at -gmail.com) at ICTP, Italy. - -:line - -createatoms tool :h4,link(createatoms) - -The tools/createatoms directory contains a Fortran program called -createAtoms.f which can generate a variety of interesting crystal -structures and geometries and output the resulting list of atom -coordinates in LAMMPS or other formats. - -See the included Manual.pdf for details. - -The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov. - -:line - -doxygen tool :h4,link(doxygen) - -The tools/doxygen directory contains a shell script called -doxygen.sh which can generate a call graph and API lists using -the "Doxygen software"_http://doxygen.org. - -See the included README file for details. - -The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com. - -:line - -drude tool :h4,link(drude) - -The tools/drude directory contains a Python script called -polarizer.py which can add Drude oscillators to a LAMMPS -data file in the required format. - -See the header of the polarizer.py file for details. - -The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua -at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr - -:line - -eam database tool :h4,link(eamdb) - -The tools/eam_database directory contains a Fortran program that will -generate EAM alloy setfl potential files for any combination of 16 -elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti, -Zr. The files can then be used with the "pair_style -eam/alloy"_pair_eam.html command. - -The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov, -and is based on his paper: - -X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, -144113 (2004). - -:line - -eam generate tool :h4,link(eamgn) - -The tools/eam_generate directory contains several one-file C programs -that convert an analytic formula into a tabulated "embedded atom -method (EAM)"_pair_eam.html setfl potential file. The potentials they -produce are in the potentials directory, and can be used with the -"pair_style eam/alloy"_pair_eam.html command. - -The source files and potentials were provided by Gerolf Ziegenhain -(gerolf at ziegenhain.com). - -:line - -eff tool :h4,link(eff) - -The tools/eff directory contains various scripts for generating -structures and post-processing output for simulations using the -electron force field (eFF). - -These tools were provided by Andres Jaramillo-Botero at CalTech -(ajaramil at wag.caltech.edu). - -:line - -emacs tool :h4,link(emacs) - -The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs -that enables a lammps-mode for editing input scripts when using GNU Emacs, -with various highlighting options set up. - -These tools were provided by Aidan Thompson at Sandia -(athomps at sandia.gov). - -:line - -fep tool :h4,link(fep) - -The tools/fep directory contains Python scripts useful for -post-processing results from performing free-energy perturbation -simulations using the USER-FEP package. - -The scripts were contributed by Agilio Padua (Universite Blaise -Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr. - -See README file in the tools/fep directory. - -:line - -i-pi tool :h4,link(ipi) - -The tools/i-pi directory contains a version of the i-PI package, with -all the LAMMPS-unrelated files removed. It is provided so that it can -be used with the "fix ipi"_fix_ipi.html command to perform -path-integral molecular dynamics (PIMD). - -The i-PI package was created and is maintained by Michele Ceriotti, -michele.ceriotti at gmail.com, to interface to a variety of molecular -dynamics codes. - -See the tools/i-pi/manual.pdf file for an overview of i-PI, and the -"fix ipi"_fix_ipi.html doc page for further details on running PIMD -calculations with LAMMPS. - -:line - -ipp tool :h4,link(ipp) - -The tools/ipp directory contains a Perl script ipp which can be used -to facilitate the creation of a complicated file (say, a lammps input -script or tools/createatoms input file) using a template file. - -ipp was created and is maintained by Reese Jones (Sandia), rjones at -sandia.gov. - -See two examples in the tools/ipp directory. One of them is for the -tools/createatoms tool's input file. - -:line - -kate tool :h4,link(kate) - -The file in the tools/kate directory is an add-on to the Kate editor -in the KDE suite that allow syntax highlighting of LAMMPS input -scripts. See the README.txt file for details. - -The file was provided by Alessandro Luigi Sellerio -(alessandro.sellerio at ieni.cnr.it). - -:line - -lmp2arc tool :h4,link(arc) - -The lmp2arc sub-directory contains a tool for converting LAMMPS output -files to the format for Accelrys' Insight MD code (formerly -MSI/Biosym and its Discover MD code). See the README file for more -information. - -This tool was written by John Carpenter (Cray), Michael Peachey -(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic -(jec at mayo.edu), but still fields questions about the tool. - -This tool was updated for the current LAMMPS C++ version by Jeff -Greathouse at Sandia (jagreat at sandia.gov). - -:line - -lmp2cfg tool :h4,link(cfg) - -The lmp2cfg sub-directory contains a tool for converting LAMMPS output -files into a series of *.cfg files which can be read into the -"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualizer. See -the README file for more information. - -This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). - -:line - -matlab tool :h4,link(matlab) - -The matlab sub-directory contains several "MATLAB"_matlabhome scripts for -post-processing LAMMPS output. The scripts include readers for log -and dump files, a reader for EAM potential files, and a converter that -reads LAMMPS dump files and produces CFG files that can be visualized -with the "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A -visualizer. - -See the README.pdf file for more information. - -These scripts were written by Arun Subramaniyan at Purdue Univ -(asubrama at purdue.edu). - -:link(matlabhome,http://www.mathworks.com) - -:line - -micelle2d tool :h4,link(micelle) - -The file micelle2d.f creates a LAMMPS data file containing short lipid -chains in a monomer solution. It uses a text file containing lipid -definition parameters as an input. The created molecules and solvent -atoms can strongly overlap, so LAMMPS needs to run the system -initially with a "soft" pair potential to un-overlap it. The syntax -for running the tool is - -micelle2d < def.micelle2d > data.file :pre - -See the def.micelle2d file in the tools directory for an example of a -definition file. This tool was used to create the system for the -"micelle example"_Examples.html. - -:line - -moltemplate tool :h4,link(moltemplate) - -The moltemplate sub-directory contains instructions for installing -moltemplate, a Python-based tool for building molecular systems based -on a text-file description, and creating LAMMPS data files that encode -their molecular topology as lists of bonds, angles, dihedrals, etc. -See the README.txt file for more information. - -This tool was written by Andrew Jewett (jewett.aij at gmail.com), who -supports it. It has its own WWW page at -"http://moltemplate.org"_http://moltemplate.org. -The latest sources can be found "on its GitHub page"_https://github.com/jewettaij/moltemplate/releases - -:line - -msi2lmp tool :h4,link(msi) - -The msi2lmp sub-directory contains a tool for creating LAMMPS template -input and data files from BIOVIA's Materias Studio files (formerly -Accelrys' Insight MD code, formerly MSI/Biosym and its Discover MD code). - -This tool was written by John Carpenter (Cray), Michael Peachey -(Cray), and Steve Lustig (Dupont). Several people contributed changes -to remove bugs and adapt its output to changes in LAMMPS. - -This tool has several known limitations and is no longer under active -development, so there are no changes except for the occasional bug fix. - -See the README file in the tools/msi2lmp folder for more information. - -:line - -phonon tool :h4,link(phonon) - -The phonon sub-directory contains a post-processing tool useful for -analyzing the output of the "fix phonon"_fix_phonon.html command in -the USER-PHONON package. - -See the README file for instruction on building the tool and what -library it needs. And see the examples/USER/phonon directory -for example problems that can be post-processed with this tool. - -This tool was written by Ling-Ti Kong at Shanghai Jiao Tong -University. - -:line - -polybond tool :h4,link(polybond) - -The polybond sub-directory contains a Python-based tool useful for -performing "programmable polymer bonding". The Python file -lmpsdata.py provides a "Lmpsdata" class with various methods which can -be invoked by a user-written Python script to create data files with -complex bonding topologies. - -See the Manual.pdf for details and example scripts. - -This tool was written by Zachary Kraus at Georgia Tech. - -:line - -pymol_asphere tool :h4,link(pymol) - -The pymol_asphere sub-directory contains a tool for converting a -LAMMPS dump file that contains orientation info for ellipsoidal -particles into an input file for the "PyMol visualization -package"_pymolhome or its "open source variant"_pymolopen. - -:link(pymolhome,http://www.pymol.org) -:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546) - -Specifically, the tool triangulates the ellipsoids so they can be -viewed as true ellipsoidal particles within PyMol. See the README and -examples directory within pymol_asphere for more information. - -This tool was written by Mike Brown at Sandia. - -:line - -python tool :h4,link(pythontools) - -The python sub-directory contains several Python scripts -that perform common LAMMPS post-processing tasks, such as: - -extract thermodynamic info from a log file as columns of numbers -plot two columns of thermodynamic info from a log file using GnuPlot -sort the snapshots in a dump file by atom ID -convert multiple "NEB"_neb.html dump files into one dump file for viz -convert dump files into XYZ, CFG, or PDB format for viz by other packages :ul - -These are simple scripts built on "Pizza.py"_pizza modules. See the -README for more info on Pizza.py and how to use these scripts. - -:line - -replica tool :h4,link(replica) - -The tools/replica directory contains the reorder_remd_traj python script which -can be used to reorder the replica trajectories (resulting from the use of the -temper command) according to temperature. This will produce discontinuous -trajectories with all frames at the same temperature in each trajectory. -Additional options can be used to calculate the canonical configurational -log-weight for each frame at each temperature using the pymbar package. See -the README.md file for further details. Try out the peptide example provided. - -This tool was written by (and is maintained by) Tanmoy Sanyal, -while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) - -:line - -reax tool :h4,link(reax_tool) - -The reax sub-directory contains stand-alone codes that can -post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html -command from a LAMMPS simulation using "ReaxFF"_pair_reaxc.html. See -the README.txt file for more info. - -These tools were written by Aidan Thompson at Sandia. - -:line - -smd tool :h4,link(smd) - -The smd sub-directory contains a C++ file dump2vtk_tris.cpp and -Makefile which can be compiled and used to convert triangle output -files created by the Smooth-Mach Dynamics (USER-SMD) package into a -VTK-compatible unstructured grid file. It could then be read in and -visualized by VTK. - -See the header of dump2vtk.cpp for more details. - -This tool was written by the USER-SMD package author, Georg -Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, -Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). - -:line - -spin tool :h4,link(spin) - -The spin sub-directory contains a C file interpolate.c which can -be compiled and used to perform a cubic polynomial interpolation of -the MEP following a GNEB calculation. - -See the README file in tools/spin/interpolate_gneb for more details. - -This tool was written by the SPIN package author, Julien -Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei -Ivanov, at University of Iceland (ali5 at hi.is). - -:line - -singularity tool :h4,link(singularity_tool) - -The singularity sub-directory contains container definitions files -that can be used to build container images for building and testing -LAMMPS on specific OS variants using the "Singularity"_https://sylabs.io -container software. Contributions for additional variants are welcome. - -:line - -vim tool :h4,link(vim) - -The files in the tools/vim directory are add-ons to the VIM editor -that allow easier editing of LAMMPS input scripts. See the README.txt -file for details. - -These files were provided by Gerolf Ziegenhain (gerolf at -ziegenhain.com) - -:line - -xmgrace tool :h4,link(xmgrace) - -The files in the tools/xmgrace directory can be used to plot the -thermodynamic data in LAMMPS log files via the xmgrace plotting -package. There are several tools in the directory that can be used in -post-processing mode. The lammpsplot.cpp file can be compiled and -used to create plots from the current state of a running LAMMPS -simulation. - -See the README file for details. - -These files were provided by Vikas Varshney (vv0210 at gmail.com) - diff --git a/doc/txt/balance.txt b/doc/txt/balance.txt deleted file mode 100644 index 2ca44203f6..0000000000 --- a/doc/txt/balance.txt +++ /dev/null @@ -1,522 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -balance command :h3 - -[Syntax:] - -balance thresh style args ... keyword args ... :pre - -thresh = imbalance threshold that must be exceeded to perform a re-balance :ulb,l -one style/arg pair can be used (or multiple for {x},{y},{z}) :l -style = {x} or {y} or {z} or {shift} or {rcb} :l - {x} args = {uniform} or Px-1 numbers between 0 and 1 - {uniform} = evenly spaced cuts between processors in x dimension - numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension - {x} can be specified together with {y} or {z} - {y} args = {uniform} or Py-1 numbers between 0 and 1 - {uniform} = evenly spaced cuts between processors in y dimension - numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension - {y} can be specified together with {x} or {z} - {z} args = {uniform} or Pz-1 numbers between 0 and 1 - {uniform} = evenly spaced cuts between processors in z dimension - numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension - {z} can be specified together with {x} or {y} - {shift} args = dimstr Niter stopthresh - dimstr = sequence of letters containing "x" or "y" or "z", each not more than once - Niter = # of times to iterate within each dimension of dimstr sequence - stopthresh = stop balancing when this imbalance threshold is reached - {rcb} args = none :pre -zero or more keyword/arg pairs may be appended :l -keyword = {weight} or {out} :l - {weight} style args = use weighted particle counts for the balancing - {style} = {group} or {neigh} or {time} or {var} or {store} - {group} args = Ngroup group1 weight1 group2 weight2 ... - Ngroup = number of groups with assigned weights - group1, group2, ... = group IDs - weight1, weight2, ... = corresponding weight factors - {neigh} factor = compute weight based on number of neighbors - factor = scaling factor (> 0) - {time} factor = compute weight based on time spend computing - factor = scaling factor (> 0) - {var} name = take weight from atom-style variable - name = name of the atom-style variable - {store} name = store weight in custom atom property defined by "fix property/atom"_fix_property_atom.html command - name = atom property name (without d_ prefix) - {out} arg = filename - filename = write each processor's sub-domain to a file :pre -:ule - -[Examples:] - -balance 0.9 x uniform y 0.4 0.5 0.6 -balance 1.2 shift xz 5 1.1 -balance 1.0 shift xz 5 1.1 -balance 1.1 rcb -balance 1.0 shift x 10 1.1 weight group 2 fast 0.5 slow 2.0 -balance 1.0 shift x 10 1.1 weight time 0.8 weight neigh 0.5 weight store balance -balance 1.0 shift x 20 1.0 out tmp.balance :pre - -[Description:] - -This command adjusts the size and shape of processor sub-domains -within the simulation box, to attempt to balance the number of atoms -or particles and thus indirectly the computational cost (load) more -evenly across processors. The load balancing is "static" in the sense -that this command performs the balancing once, before or between -simulations. The processor sub-domains will then remain static during -the subsequent run. To perform "dynamic" balancing, see the "fix -balance"_fix_balance.html command, which can adjust processor -sub-domain sizes and shapes on-the-fly during a "run"_run.html. - -Load-balancing is typically most useful if the particles in the -simulation box have a spatially-varying density distribution or when -the computational cost varies significantly between different -particles. E.g. a model of a vapor/liquid interface, or a solid with -an irregular-shaped geometry containing void regions, or "hybrid pair -style simulations"_pair_hybrid.html which combine pair styles with -different computational cost. In these cases, the LAMMPS default of -dividing the simulation box volume into a regular-spaced grid of 3d -bricks, with one equal-volume sub-domain per processor, may assign -numbers of particles per processor in a way that the computational -effort varies significantly. This can lead to poor performance when -the simulation is run in parallel. - -The balancing can be performed with or without per-particle weighting. -With no weighting, the balancing attempts to assign an equal number of -particles to each processor. With weighting, the balancing attempts -to assign an equal aggregate computational weight to each processor, -which typically induces a different number of atoms assigned to each -processor. Details on the various weighting options and examples for -how they can be used are "given below"_#weighted_balance. - -Note that the "processors"_processors.html command allows some control -over how the box volume is split across processors. Specifically, for -a Px by Py by Pz grid of processors, it allows choice of Px, Py, and -Pz, subject to the constraint that Px * Py * Pz = P, the total number -of processors. This is sufficient to achieve good load-balance for -some problems on some processor counts. However, all the processor -sub-domains will still have the same shape and same volume. - -The requested load-balancing operation is only performed if the -current "imbalance factor" in particles owned by each processor -exceeds the specified {thresh} parameter. The imbalance factor is -defined as the maximum number of particles (or weight) owned by any -processor, divided by the average number of particles (or weight) per -processor. Thus an imbalance factor of 1.0 is perfect balance. - -As an example, for 10000 particles running on 10 processors, if the -most heavily loaded processor has 1200 particles, then the factor is -1.2, meaning there is a 20% imbalance. Note that a re-balance can be -forced even if the current balance is perfect (1.0) be specifying a -{thresh} < 1.0. - -NOTE: Balancing is performed even if the imbalance factor does not -exceed the {thresh} parameter if a "grid" style is specified when the -current partitioning is "tiled". The meaning of "grid" vs "tiled" is -explained below. This is to allow forcing of the partitioning to -"grid" so that the "comm_style brick"_comm_style.html command can then -be used to replace a current "comm_style tiled"_comm_style.html -setting. - -When the balance command completes, it prints statistics about the -result, including the change in the imbalance factor and the change in -the maximum number of particles on any processor. For "grid" methods -(defined below) that create a logical 3d grid of processors, the -positions of all cutting planes in each of the 3 dimensions (as -fractions of the box length) are also printed. - -NOTE: This command attempts to minimize the imbalance factor, as -defined above. But depending on the method a perfect balance (1.0) -may not be achieved. For example, "grid" methods (defined below) that -create a logical 3d grid cannot achieve perfect balance for many -irregular distributions of particles. Likewise, if a portion of the -system is a perfect lattice, e.g. the initial system is generated by -the "create_atoms"_create_atoms.html command, then "grid" methods may -be unable to achieve exact balance. This is because entire lattice -planes will be owned or not owned by a single processor. - -NOTE: The imbalance factor is also an estimate of the maximum speed-up -you can hope to achieve by running a perfectly balanced simulation -versus an imbalanced one. In the example above, the 10000 particle -simulation could run up to 20% faster if it were perfectly balanced, -versus when imbalanced. However, computational cost is not strictly -proportional to particle count, and changing the relative size and -shape of processor sub-domains may lead to additional computational -and communication overheads, e.g. in the PPPM solver used via the -"kspace_style"_kspace_style.html command. Thus you should benchmark -the run times of a simulation before and after balancing. - -:line - -The method used to perform a load balance is specified by one of the -listed styles (or more in the case of {x},{y},{z}), which are -described in detail below. There are 2 kinds of styles. - -The {x}, {y}, {z}, and {shift} styles are "grid" methods which produce -a logical 3d grid of processors. They operate by changing the cutting -planes (or lines) between processors in 3d (or 2d), to adjust the -volume (area in 2d) assigned to each processor, as in the following 2d -diagram where processor sub-domains are shown and particles are -colored by the processor that owns them. The leftmost diagram is the -default partitioning of the simulation box across processors (one -sub-box for each of 16 processors); the middle diagram is after a -"grid" method has been applied. - -:image(JPG/balance_uniform_small.jpg,JPG/balance_uniform.jpg),image(JPG/balance_nonuniform_small.jpg,JPG/balance_nonuniform.jpg),image(JPG/balance_rcb_small.jpg,JPG/balance_rcb.jpg) -:c - -The {rcb} style is a "tiling" method which does not produce a logical -3d grid of processors. Rather it tiles the simulation domain with -rectangular sub-boxes of varying size and shape in an irregular -fashion so as to have equal numbers of particles (or weight) in each -sub-box, as in the rightmost diagram above. - -The "grid" methods can be used with either of the -"comm_style"_comm_style.html command options, {brick} or {tiled}. The -"tiling" methods can only be used with "comm_style -tiled"_comm_style.html. Note that it can be useful to use a "grid" -method with "comm_style tiled"_comm_style.html to return the domain -partitioning to a logical 3d grid of processors so that "comm_style -brick" can afterwords be specified for subsequent "run"_run.html -commands. - -When a "grid" method is specified, the current domain partitioning can -be either a logical 3d grid or a tiled partitioning. In the former -case, the current logical 3d grid is used as a starting point and -changes are made to improve the imbalance factor. In the latter case, -the tiled partitioning is discarded and a logical 3d grid is created -with uniform spacing in all dimensions. This becomes the starting -point for the balancing operation. - -When a "tiling" method is specified, the current domain partitioning -("grid" or "tiled") is ignored, and a new partitioning is computed -from scratch. - -:line - -The {x}, {y}, and {z} styles invoke a "grid" method for balancing, as -described above. Note that any or all of these 3 styles can be -specified together, one after the other, but they cannot be used with -any other style. This style adjusts the position of cutting planes -between processor sub-domains in specific dimensions. Only the -specified dimensions are altered. - -The {uniform} argument spaces the planes evenly, as in the left -diagrams above. The {numeric} argument requires listing Ps-1 numbers -that specify the position of the cutting planes. This requires -knowing Ps = Px or Py or Pz = the number of processors assigned by -LAMMPS to the relevant dimension. This assignment is made (and the -Px, Py, Pz values printed out) when the simulation box is created by -the "create_box" or "read_data" or "read_restart" command and is -influenced by the settings of the "processors"_processors.html -command. - -Each of the numeric values must be between 0 and 1, and they must be -listed in ascending order. They represent the fractional position of -the cutting place. The left (or lower) edge of the box is 0.0, and -the right (or upper) edge is 1.0. Neither of these values is -specified. Only the interior Ps-1 positions are specified. Thus is -there are 2 processors in the x dimension, you specify a single value -such as 0.75, which would make the left processor's sub-domain 3x -larger than the right processor's sub-domain. - -:line - -The {shift} style invokes a "grid" method for balancing, as -described above. It changes the positions of cutting planes between -processors in an iterative fashion, seeking to reduce the imbalance -factor, similar to how the "fix balance shift"_fix_balance.html -command operates. - -The {dimstr} argument is a string of characters, each of which must be -an "x" or "y" or "z". Eacn character can appear zero or one time, -since there is no advantage to balancing on a dimension more than -once. You should normally only list dimensions where you expect there -to be a density variation in the particles. - -Balancing proceeds by adjusting the cutting planes in each of the -dimensions listed in {dimstr}, one dimension at a time. For a single -dimension, the balancing operation (described below) is iterated on up -to {Niter} times. After each dimension finishes, the imbalance factor -is re-computed, and the balancing operation halts if the {stopthresh} -criterion is met. - -A re-balance operation in a single dimension is performed using a -recursive multisectioning algorithm, where the position of each -cutting plane (line in 2d) in the dimension is adjusted independently. -This is similar to a recursive bisectioning for a single value, except -that the bounds used for each bisectioning take advantage of -information from neighboring cuts if possible. At each iteration, the -count of particles on either side of each plane is tallied. If the -counts do not match the target value for the plane, the position of -the cut is adjusted to be halfway between a low and high bound. The -low and high bounds are adjusted on each iteration, using new count -information, so that they become closer together over time. Thus as -the recursion progresses, the count of particles on either side of the -plane gets closer to the target value. - -Once the re-balancing is complete and final processor sub-domains -assigned, particles are migrated to their new owning processor, and -the balance procedure ends. - -NOTE: At each re-balance operation, the bisectioning for each cutting -plane (line in 2d) typically starts with low and high bounds separated -by the extent of a processor's sub-domain in one dimension. The size -of this bracketing region shrinks by 1/2 every iteration. Thus if -{Niter} is specified as 10, the cutting plane will typically be -positioned to 1 part in 1000 accuracy (relative to the perfect target -position). For {Niter} = 20, it will be accurate to 1 part in a -million. Thus there is no need ot set {Niter} to a large value. -LAMMPS will check if the threshold accuracy is reached (in a -dimension) is less iterations than {Niter} and exit early. However, -{Niter} should also not be set too small, since it will take roughly -the same number of iterations to converge even if the cutting plane is -initially close to the target value. - -:line - -The {rcb} style invokes a "tiled" method for balancing, as described -above. It performs a recursive coordinate bisectioning (RCB) of the -simulation domain. The basic idea is as follows. - -The simulation domain is cut into 2 boxes by an axis-aligned cut in -one of the dimensions, leaving one new sub-box on either side of the -cut. Which dimension is chosen for the cut depends on the particle -(weight) distribution within the parent box. Normally the longest -dimension of the box is cut, but if all (or most) of the particles are -at one end of the box, a cut may be performed in another dimension to -induce sub-boxes that are more cube-ish (3d) or square-ish (2d) in -shape. - -After the cut is made, all the processors are also partitioned into 2 -groups, half assigned to the box on the lower side of the cut, and -half to the box on the upper side. (If the processor count is odd, -one side gets an extra processor.) The cut is positioned so that the -number of (weighted) particles in the lower box is exactly the number -that the processors assigned to that box should own for load balance -to be perfect. This also makes load balance for the upper box -perfect. The positioning of the cut is done iteratively, by a -bisectioning method (median search). Note that counting particles on -either side of the cut requires communication between all processors -at each iteration. - -That is the procedure for the first cut. Subsequent cuts are made -recursively, in exactly the same manner. The subset of processors -assigned to each box make a new cut in one dimension of that box, -splitting the box, the subset of processors, and the particles in the -box in two. The recursion continues until every processor is assigned -a sub-box of the entire simulation domain, and owns the (weighted) -particles in that sub-box. - -:line - -This sub-section describes how to perform weighted load balancing -using the {weight} keyword. :link(weighted_balance) - -By default, all particles have a weight of 1.0, which means each -particle is assumed to require the same amount of computation during a -timestep. There are, however, scenarios where this is not a good -assumption. Measuring the computational cost for each particle -accurately would be impractical and slow down the computation. -Instead the {weight} keyword implements several ways to influence the -per-particle weights empirically by properties readily available or -using the user's knowledge of the system. Note that the absolute -value of the weights are not important; only their relative ratios -affect which particle is assigned to which processor. A particle with -a weight of 2.5 is assumed to require 5x more computational than a -particle with a weight of 0.5. For all the options below the weight -assigned to a particle must be a positive value; an error will be be -generated if a weight is <= 0.0. - -Below is a list of possible weight options with a short description of -their usage and some example scenarios where they might be applicable. -It is possible to apply multiple weight flags and the weightings they -induce will be combined through multiplication. Most of the time, -however, it is sufficient to use just one method. - -The {group} weight style assigns weight factors to specified -"groups"_group.html of particles. The {group} style keyword is -followed by the number of groups, then pairs of group IDs and the -corresponding weight factor. If a particle belongs to none of the -specified groups, its weight is not changed. If it belongs to -multiple groups, its weight is the product of the weight factors. - -This weight style is useful in combination with pair style -"hybrid"_pair_hybrid.html, e.g. when combining a more costly many-body -potential with a fast pair-wise potential. It is also useful when -using "run_style respa"_run_style.html where some portions of the -system have many bonded interactions and others none. It assumes that -the computational cost for each group remains constant over time. -This is a purely empirical weighting, so a series test runs to tune -the assigned weight factors for optimal performance is recommended. - -The {neigh} weight style assigns the same weight to each particle -owned by a processor based on the total count of neighbors in the -neighbor list owned by that processor. The motivation is that more -neighbors means a higher computational cost. The style does not use -neighbors per atom to assign a unique weight to each atom, because -that value can vary depending on how the neighbor list is built. - -The {factor} setting is applied as an overall scale factor to the -{neigh} weights which allows adjustment of their impact on the -balancing operation. The specified {factor} value must be positive. -A value > 1.0 will increase the weights so that the ratio of max -weight to min weight increases by {factor}. A value < 1.0 will -decrease the weights so that the ratio of max weight to min weight -decreases by {factor}. In both cases the intermediate weight values -increase/decrease proportionally as well. A value = 1.0 has no effect -on the {neigh} weights. As a rule of thumb, we have found a {factor} -of about 0.8 often results in the best performance, since the number -of neighbors is likely to overestimate the ideal weight. - -This weight style is useful for systems where there are different -cutoffs used for different pairs of interactions, or the density -fluctuates, or a large number of particles are in the vicinity of a -wall, or a combination of these effects. If a simulation uses -multiple neighbor lists, this weight style will use the first suitable -neighbor list it finds. It will not request or compute a new list. A -warning will be issued if there is no suitable neighbor list available -or if it is not current, e.g. if the balance command is used before a -"run"_run.html or "minimize"_minimize.html command is used, in which -case the neighbor list may not yet have been built. In this case no -weights are computed. Inserting a "run 0 post no"_run.html command -before issuing the {balance} command, may be a workaround for this -case, as it will induce the neighbor list to be built. - -The {time} weight style uses "timer data"_timer.html to estimate -weights. It assigns the same weight to each particle owned by a -processor based on the total computational time spent by that -processor. See details below on what time window is used. It uses -the same timing information as is used for the "MPI task timing -breakdown"_Run_output.html, namely, for sections {Pair}, {Bond}, -{Kspace}, and {Neigh}. The time spent in those portions of the -timestep are measured for each MPI rank, summed, then divided by the -number of particles owned by that processor. I.e. the weight is an -effective CPU time/particle averaged over the particles on that -processor. - -The {factor} setting is applied as an overall scale factor to the -{time} weights which allows adjustment of their impact on the -balancing operation. The specified {factor} value must be positive. -A value > 1.0 will increase the weights so that the ratio of max -weight to min weight increases by {factor}. A value < 1.0 will -decrease the weights so that the ratio of max weight to min weight -decreases by {factor}. In both cases the intermediate weight values -increase/decrease proportionally as well. A value = 1.0 has no effect -on the {time} weights. As a rule of thumb, effective values to use -are typically between 0.5 and 1.2. Note that the timer quantities -mentioned above can be affected by communication which occurs in the -middle of the operations, e.g. pair styles with intermediate exchange -of data witin the force computation, and likewise for KSpace solves. - -When using the {time} weight style with the {balance} command, the -timing data is taken from the preceding run command, i.e. the timings -are for the entire previous run. For the {fix balance} command the -timing data is for only the timesteps since the last balancing -operation was performed. If timing information for the required -sections is not available, e.g. at the beginning of a run, or when the -"timer"_timer.html command is set to either {loop} or {off}, a warning -is issued. In this case no weights are computed. - -NOTE: The {time} weight style is the most generic option, and should -be tried first, unless the {group} style is easily applicable. -However, since the computed cost function is averaged over all -particles on a processor, the weights may not be highly accurate. -This style can also be effective as a secondary weight in combination -with either {group} or {neigh} to offset some of inaccuracies in -either of those heuristics. - -The {var} weight style assigns per-particle weights by evaluating an -"atom-style variable"_variable.html specified by {name}. This is -provided as a more flexible alternative to the {group} weight style, -allowing definition of a more complex heuristics based on information -(global and per atom) available inside of LAMMPS. For example, -atom-style variables can reference the position of a particle, its -velocity, the volume of its Voronoi cell, etc. - -The {store} weight style does not compute a weight factor. Instead it -stores the current accumulated weights in a custom per-atom property -specified by {name}. This must be a property defined as {d_name} via -the "fix property/atom"_fix_property_atom.html command. Note that -these custom per-atom properties can be output in a "dump"_dump.html -file, so this is a way to examine, debug, or visualize the -per-particle weights computed during the load-balancing operation. - -:line - -The {out} keyword writes a text file to the specified {filename} with -the results of the balancing operation. The file contains the bounds -of the sub-domain for each processor after the balancing operation -completes. The format of the file is compatible with the -"Pizza.py"_pizza {mdump} tool which has support for manipulating and -visualizing mesh files. An example is shown here for a balancing by 4 -processors for a 2d problem: - -ITEM: TIMESTEP -0 -ITEM: NUMBER OF NODES -16 -ITEM: BOX BOUNDS -0 10 -0 10 -0 10 -ITEM: NODES -1 1 0 0 0 -2 1 5 0 0 -3 1 5 5 0 -4 1 0 5 0 -5 1 5 0 0 -6 1 10 0 0 -7 1 10 5 0 -8 1 5 5 0 -9 1 0 5 0 -10 1 5 5 0 -11 1 5 10 0 -12 1 10 5 0 -13 1 5 5 0 -14 1 10 5 0 -15 1 10 10 0 -16 1 5 10 0 -ITEM: TIMESTEP -0 -ITEM: NUMBER OF SQUARES -4 -ITEM: SQUARES -1 1 1 2 3 4 -2 1 5 6 7 8 -3 1 9 10 11 12 -4 1 13 14 15 16 :pre - -The coordinates of all the vertices are listed in the NODES section, 5 -per processor. Note that the 4 sub-domains share vertices, so there -will be duplicate nodes in the list. - -The "SQUARES" section lists the node IDs of the 4 vertices in a -rectangle for each processor (1 to 4). - -For a 3d problem, the syntax is similar with 8 vertices listed for -each processor, instead of 4, and "SQUARES" replaced by "CUBES". - -:line - -[Restrictions:] - -For 2d simulations, the {z} style cannot be used. Nor can a "z" -appear in {dimstr} for the {shift} style. - -Balancing through recursive bisectioning ({rcb} style) requires -"comm_style tiled"_comm_style.html - -[Related commands:] - -"group"_group.html, "processors"_processors.html, -"fix balance"_fix_balance.html, "comm_style"_comm_style.html - -[Default:] none -:link(pizza,http://pizza.sandia.gov) diff --git a/doc/txt/boundary.txt b/doc/txt/boundary.txt deleted file mode 100644 index f9685433b2..0000000000 --- a/doc/txt/boundary.txt +++ /dev/null @@ -1,107 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -boundary command :h3 - -[Syntax:] - -boundary x y z :pre - -x,y,z = {p} or {s} or {f} or {m}, one or two letters :ulb,l - {p} is periodic - {f} is non-periodic and fixed - {s} is non-periodic and shrink-wrapped - {m} is non-periodic and shrink-wrapped with a minimum value :pre -:ule - -[Examples:] - -boundary p p f -boundary p fs p -boundary s f fm :pre - -[Description:] - -Set the style of boundaries for the global simulation box in each -dimension. A single letter assigns the same style to both the lower -and upper face of the box. Two letters assigns the first style to the -lower face and the second style to the upper face. The initial size -of the simulation box is set by the "read_data"_read_data.html, -"read_restart"_read_restart.html, or "create_box"_create_box.html -commands. - -The style {p} means the box is periodic, so that particles interact -across the boundary, and they can exit one end of the box and re-enter -the other end. A periodic dimension can change in size due to -constant pressure boundary conditions or box deformation (see the "fix -npt"_fix_nh.html and "fix deform"_fix_deform.html commands). The {p} -style must be applied to both faces of a dimension. - -The styles {f}, {s}, and {m} mean the box is non-periodic, so that -particles do not interact across the boundary and do not move from one -side of the box to the other. - -For style {f}, the position of the face is fixed. If an atom moves -outside the face it will be deleted on the next timestep that -reneighboring occurs. This will typically generate an error unless -you have set the "thermo_modify lost"_thermo_modify.html option to -allow for lost atoms. - -For style {s}, the position of the face is set so as to encompass the -atoms in that dimension (shrink-wrapping), no matter how far they -move. Note that when the difference between the current box dimensions -and the shrink-wrap box dimensions is large, this can lead to lost -atoms at the beginning of a run when running in parallel. This is due -to the large change in the (global) box dimensions also causing -significant changes in the individual sub-domain sizes. If these -changes are farther than the communication cutoff, atoms will be lost. -This is best addressed by setting initial box dimensions to match the -shrink-wrapped dimensions more closely, by using {m} style boundaries -(see below). - -For style {m}, shrink-wrapping occurs, but is bounded by the value -specified in the data or restart file or set by the -"create_box"_create_box.html command. For example, if the upper z -face has a value of 50.0 in the data file, the face will always be -positioned at 50.0 or above, even if the maximum z-extent of all the -atoms becomes less than 50.0. This can be useful if you start a -simulation with an empty box or if you wish to leave room on one side -of the box, e.g. for atoms to evaporate from a surface. - -For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension -of a tilt factor (e.g. y for xy) is periodic, then the periodicity is -enforced with the tilt factor offset. If the 1st dimension is -shrink-wrapped, then the shrink wrapping is applied to the tilted box -face, to encompass the atoms. E.g. for a positive xy tilt, the xlo -and xhi faces of the box are planes tilting in the +y direction as y -increases. These tilted planes are shrink-wrapped around the atoms to -determine the x extent of the box. - -See the "Howto triclinic"_Howto_triclinic.html doc page for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used -triclinic representations. - -[Restrictions:] - -This command cannot be used after the simulation box is defined by a -"read_data"_read_data.html or "create_box"_create_box.html command or -"read_restart"_read_restart.html command. See the -"change_box"_change_box.html command for how to change the simulation -box boundaries after it has been defined. - -For 2d simulations, the z dimension must be periodic. - -[Related commands:] - -See the "thermo_modify"_thermo_modify.html command for a discussion -of lost atoms. - -[Default:] - -boundary p p p :pre diff --git a/doc/txt/box.txt b/doc/txt/box.txt deleted file mode 100644 index 38c874fb78..0000000000 --- a/doc/txt/box.txt +++ /dev/null @@ -1,61 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -box command :h3 - -[Syntax:] - -box keyword value ... :pre - -one or more keyword/value pairs may be appended :ulb,l -keyword = {tilt} :l - {tilt} value = {small} or {large} :pre -:ule - -[Examples:] - -box tilt large -box tilt small :pre - -[Description:] - -Set attributes of the simulation box. - -For triclinic (non-orthogonal) simulation boxes, the {tilt} keyword -allows simulation domains to be created with arbitrary tilt factors, -e.g. via the "create_box"_create_box.html or -"read_data"_read_data.html commands. Tilt factors determine how -skewed the triclinic box is; see the "Howto -triclinic"_Howto_triclinic.html doc page for a discussion of triclinic -boxes in LAMMPS. - -LAMMPS normally requires that no tilt factor can skew the box more -than half the distance of the parallel box length, which is the 1st -dimension in the tilt factor (x for xz). If {tilt} is set to -{small}, which is the default, then an error will be -generated if a box is created which exceeds this limit. If {tilt} -is set to {large}, then no limit is enforced. You can create -a box with any tilt factors you wish. - -Note that if a simulation box has a large tilt factor, LAMMPS will run -less efficiently, due to the large volume of communication needed to -acquire ghost atoms around a processor's irregular-shaped sub-domain. -For extreme values of tilt, LAMMPS may also lose atoms and generate an -error. - -[Restrictions:] - -This command cannot be used after the simulation box is defined by a -"read_data"_read_data.html or "create_box"_create_box.html command or -"read_restart"_read_restart.html command. - -[Related commands:] none - -[Default:] - -The default value is tilt = small. diff --git a/doc/txt/change_box.txt b/doc/txt/change_box.txt deleted file mode 100644 index adc5d6bdcb..0000000000 --- a/doc/txt/change_box.txt +++ /dev/null @@ -1,329 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -change_box command :h3 - -[Syntax:] - -change_box group-ID parameter args ... keyword args ... :pre - -group-ID = ID of group of atoms to (optionally) displace :ulb,l -one or more parameter/arg pairs may be appended :l -parameter = {x} or {y} or {z} or {xy} or {xz} or {yz} or {boundary} or {ortho} or {triclinic} or {set} or {remap} - {x}, {y}, {z} args = style value(s) - style = {final} or {delta} or {scale} or {volume} - {final} values = lo hi - lo hi = box boundaries after displacement (distance units) - {delta} values = dlo dhi - dlo dhi = change in box boundaries after displacement (distance units) - {scale} values = factor - factor = multiplicative factor for change in box length after displacement - {volume} value = none = adjust this dim to preserve volume of system - {xy}, {xz}, {yz} args = style value - style = {final} or {delta} - {final} value = tilt - tilt = tilt factor after displacement (distance units) - {delta} value = dtilt - dtilt = change in tilt factor after displacement (distance units) - {boundary} args = x y z - x,y,z = {p} or {s} or {f} or {m}, one or two letters - {p} is periodic - {f} is non-periodic and fixed - {s} is non-periodic and shrink-wrapped - {m} is non-periodic and shrink-wrapped with a minimum value - {ortho} args = none = change box to orthogonal - {triclinic} args = none = change box to triclinic - {set} args = none = store state of current box - {remap} args = none = remap atom coords from last saved state to current box :pre - -zero or more keyword/value pairs may be appended :l -keyword = {units} :l - {units} value = {lattice} or {box} - lattice = distances are defined in lattice units - box = distances are defined in simulation box units :pre -:ule - -[Examples:] - -change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box -change_box all x scale 1.1 y volume z volume remap :pre - -[Description:] - -Change the volume and/or shape and/or boundary conditions for the -simulation box. Orthogonal simulation boxes have 3 adjustable size -parameters (x,y,z). Triclinic (non-orthogonal) simulation boxes have -6 adjustable size/shape parameters (x,y,z,xy,xz,yz). Any or all of -them can be adjusted independently by this command. Thus it can be -used to expand or contract a box, or to apply a shear strain to a -non-orthogonal box. It can also be used to change the boundary -conditions for the simulation box, similar to the -"boundary"_boundary.html command. - -The size and shape of the initial simulation box are specified by the -"create_box"_create_box.html or "read_data"_read_data.html or -"read_restart"_read_restart.html command used to setup the simulation. -The size and shape may be altered by subsequent runs, e.g. by use of -the "fix npt"_fix_nh.html or "fix deform"_fix_deform.html commands. -The "create_box"_create_box.html, "read data"_read_data.html, and -"read_restart"_read_restart.html commands also determine whether the -simulation box is orthogonal or triclinic and their doc pages explain -the meaning of the xy,xz,yz tilt factors. - -See the "Howto triclinic"_Howto_triclinic.html doc page for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used -triclinic representations. - -The keywords used in this command are applied sequentially to the -simulation box and the atoms in it, in the order specified. - -Before the sequence of keywords are invoked, the current box -size/shape is stored, in case a {remap} keyword is used to map the -atom coordinates from a previously stored box size/shape to the -current one. - -After all the keywords have been processed, any shrink-wrap boundary -conditions are invoked (see the "boundary"_boundary.html command) -which may change simulation box boundaries, and atoms are migrated to -new owning processors. - -NOTE: This means that you cannot use the change_box command to enlarge -a shrink-wrapped box, e.g. to make room to insert more atoms via the -"create_atoms"_create_atoms.html command, because the simulation box -will be re-shrink-wrapped before the change_box command completes. -Instead you could do something like this, assuming the simulation box -is non-periodic and atoms extend from 0 to 20 in all dimensions: - -change_box all x final -10 20 -create_atoms 1 single -5 5 5 # this will fail to insert an atom :pre - -change_box all x final -10 20 boundary f s s -create_atoms 1 single -5 5 5 -change_box all boundary s s s # this will work :pre - -NOTE: Unlike the earlier "displace_box" version of this command, atom -remapping is NOT performed by default. This command allows remapping -to be done in a more general way, exactly when you specify it (zero or -more times) in the sequence of transformations. Thus if you do not -use the {remap} keyword, atom coordinates will not be changed even if -the box size/shape changes. If a uniformly strained state is desired, -the {remap} keyword should be specified. - -NOTE: It is possible to lose atoms with this command. E.g. by -changing the box without remapping the atoms, and having atoms end up -outside of non-periodic boundaries. It is also possible to alter -bonds between atoms straddling a boundary in bad ways. E.g. by -converting a boundary from periodic to non-periodic. It is also -possible when remapping atoms to put them (nearly) on top of each -other. E.g. by converting a boundary from non-periodic to periodic. -All of these will typically lead to bad dynamics and/or generate error -messages. - -NOTE: The simulation box size/shape can be changed by arbitrarily -large amounts by this command. This is not a problem, except that the -mapping of processors to the simulation box is not changed from its -initial 3d configuration; see the "processors"_processors.html -command. Thus, if the box size/shape changes dramatically, the -mapping of processors to the simulation box may not end up as optimal -as the initial mapping attempted to be. - -NOTE: Because the keywords used in this command are applied one at a -time to the simulation box and the atoms in it, care must be taken -with triclinic cells to avoid exceeding the limits on skew after each -transformation in the sequence. If skew is exceeded before the final -transformation this can be avoided by changing the order of the -sequence, or breaking the transformation into two or more smaller -transformations. For more information on the allowed limits for box -skew see the discussion on triclinic boxes on "Howto -triclinic"_Howto_triclinic.html doc page. - -:line - -For the {x}, {y}, and {z} parameters, this is the meaning of their -styles and values. - -For style {final}, the final lo and hi box boundaries of a dimension -are specified. The values can be in lattice or box distance units. -See the discussion of the units keyword below. - -For style {delta}, plus or minus changes in the lo/hi box boundaries -of a dimension are specified. The values can be in lattice or box -distance units. See the discussion of the units keyword below. - -For style {scale}, a multiplicative factor to apply to the box length -of a dimension is specified. For example, if the initial box length -is 10, and the factor is 1.1, then the final box length will be 11. A -factor less than 1.0 means compression. - -The {volume} style changes the specified dimension in such a way that -the overall box volume remains constant with respect to the operation -performed by the preceding keyword. The {volume} style can only be -used following a keyword that changed the volume, which is any of the -{x}, {y}, {z} keywords. If the preceding keyword "key" had a {volume} -style, then both it and the current keyword apply to the keyword -preceding "key". I.e. this sequence of keywords is allowed: - -change_box all x scale 1.1 y volume z volume :pre - -The {volume} style changes the associated dimension so that the -overall box volume is unchanged relative to its value before the -preceding keyword was invoked. - -If the following command is used, then the z box length will shrink by -the same 1.1 factor the x box length was increased by: - -change_box all x scale 1.1 z volume :pre - -If the following command is used, then the y,z box lengths will each -shrink by sqrt(1.1) to keep the volume constant. In this case, the -y,z box lengths shrink so as to keep their relative aspect ratio -constant: - -change_box all"x scale 1.1 y volume z volume :pre - -If the following command is used, then the final box will be a factor -of 10% larger in x and y, and a factor of 21% smaller in z, so as to -keep the volume constant: - -change_box all x scale 1.1 z volume y scale 1.1 z volume :pre - -NOTE: For solids or liquids, when one dimension of the box is -expanded, it may be physically undesirable to hold the other 2 box -lengths constant since that implies a density change. For solids, -adjusting the other dimensions via the {volume} style may make -physical sense (just as for a liquid), but may not be correct for -materials and potentials whose Poisson ratio is not 0.5. - -For the {scale} and {volume} styles, the box length is expanded or -compressed around its mid point. - -:line - -For the {xy}, {xz}, and {yz} parameters, this is the meaning of their -styles and values. Note that changing the tilt factors of a triclinic -box does not change its volume. - -For style {final}, the final tilt factor is specified. The value -can be in lattice or box distance units. See the discussion of the -units keyword below. - -For style {delta}, a plus or minus change in the tilt factor is -specified. The value can be in lattice or box distance units. See -the discussion of the units keyword below. - -All of these styles change the xy, xz, yz tilt factors. In LAMMPS, -tilt factors (xy,xz,yz) for triclinic boxes are required to be no more -than half the distance of the parallel box length. For example, if -xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt -factor must be between -5 and 5. Similarly, both xz and yz must be -between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a -limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are all equivalent. Any tilt factor specified by this command -must be within these limits. - -:line - -The {boundary} keyword takes arguments that have exactly the same -meaning as they do for the "boundary"_boundary.html command. In each -dimension, a single letter assigns the same style to both the lower -and upper face of the box. Two letters assigns the first style to the -lower face and the second style to the upper face. - -The style {p} means the box is periodic; the other styles mean -non-periodic. For style {f}, the position of the face is fixed. For -style {s}, the position of the face is set so as to encompass the -atoms in that dimension (shrink-wrapping), no matter how far they -move. For style {m}, shrink-wrapping occurs, but is bounded by the -current box edge in that dimension, so that the box will become no -smaller. See the "boundary"_boundary.html command for more -explanation of these style options. - -Note that the "boundary" command itself can only be used before the -simulation box is defined via a "read_data"_read_data.html or -"create_box"_create_box.html or "read_restart"_read_restart.html -command. This command allows the boundary conditions to be changed -later in your input script. Also note that the -"read_restart"_read_restart.html will change boundary conditions to -match what is stored in the restart file. So if you wish to change -them, you should use the change_box command after the read_restart -command. - -:line - -The {ortho} and {triclinic} keywords convert the simulation box to be -orthogonal or triclinic (non-orthogonal). - -The simulation box is defined as either orthogonal or triclinic when -it is created via the "create_box"_create_box.html, -"read_data"_read_data.html, or "read_restart"_read_restart.html -commands. - -These keywords allow you to toggle the existing simulation box from -orthogonal to triclinic and vice versa. For example, an initial -equilibration simulation can be run in an orthogonal box, the box can -be toggled to triclinic, and then a "non-equilibrium MD (NEMD) -simulation"_Howto_nemd.html can be run with deformation via the "fix -deform"_fix_deform.html command. - -If the simulation box is currently triclinic and has non-zero tilt in -xy, yz, or xz, then it cannot be converted to an orthogonal box. - -:line - -The {set} keyword saves the current box size/shape. This can be -useful if you wish to use the {remap} keyword more than once or if you -wish it to be applied to an intermediate box size/shape in a sequence -of keyword operations. Note that the box size/shape is saved before -any of the keywords are processed, i.e. the box size/shape at the time -the create_box command is encountered in the input script. - -The {remap} keyword remaps atom coordinates from the last saved box -size/shape to the current box state. For example, if you stretch the -box in the x dimension or tilt it in the xy plane via the {x} and {xy} -keywords, then the {remap} command will dilate or tilt the atoms to -conform to the new box size/shape, as if the atoms moved with the box -as it deformed. - -Note that this operation is performed without regard to periodic -boundaries. Also, any shrink-wrapping of non-periodic boundaries (see -the "boundary"_boundary.html command) occurs after all keywords, -including this one, have been processed. - -Only atoms in the specified group are remapped. - -:line - -The {units} keyword determines the meaning of the distance units used -to define various arguments. A {box} value selects standard distance -units as defined by the "units"_units.html command, e.g. Angstroms for -units = real or metal. A {lattice} value means the distance units are -in lattice spacings. The "lattice"_lattice.html command must have -been previously used to define the lattice spacing. - -:line - -[Restrictions:] - -If you use the {ortho} or {triclinic} keywords, then at the point in -the input script when this command is issued, no "dumps"_dump.html can -be active, nor can a "fix deform"_fix_deform.html be active. This is -because these commands test whether the simulation box is orthogonal -when they are first issued. Note that these commands can be used in -your script before a change_box command is issued, so long as an -"undump"_undump.html or "unfix"_unfix.html command is also used to -turn them off. - -[Related commands:] - -"fix deform"_fix_deform.html, "boundary"_boundary.html - -[Default:] - -The option default is units = lattice. diff --git a/doc/txt/clear.txt b/doc/txt/clear.txt deleted file mode 100644 index c4ad4c4030..0000000000 --- a/doc/txt/clear.txt +++ /dev/null @@ -1,39 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -clear command :h3 - -[Syntax:] - -clear :pre - -[Examples:] - -(commands for 1st simulation) -clear -(commands for 2nd simulation) :pre - -[Description:] - -This command deletes all atoms, restores all settings to their default -values, and frees all memory allocated by LAMMPS. Once a clear -command has been executed, it is almost as if LAMMPS were starting -over, with only the exceptions noted below. This command enables -multiple jobs to be run sequentially from one input script. - -These settings are not affected by a clear command: the working -directory ("shell"_shell.html command), log file status -("log"_log.html command), echo status ("echo"_echo.html command), and -input script variables ("variable"_variable.html command). - -[Restrictions:] none - -[Related commands:] none - -[Default:] none - diff --git a/doc/txt/comm_modify.txt b/doc/txt/comm_modify.txt deleted file mode 100644 index 9a792f6cc6..0000000000 --- a/doc/txt/comm_modify.txt +++ /dev/null @@ -1,166 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -comm_modify command :h3 - -[Syntax:] - -comm_modify keyword value ... :pre - -zero or more keyword/value pairs may be appended :ulb,l -keyword = {mode} or {cutoff} or {cutoff/multi} or {group} or {vel} :l - {mode} value = {single} or {multi} = communicate atoms within a single or multiple distances - {cutoff} value = Rcut (distance units) = communicate atoms from this far away - {cutoff/multi} type value - type = atom type or type range (supports asterisk notation) - value = Rcut (distance units) = communicate atoms for selected types from this far away - {group} value = group-ID = only communicate atoms in the group - {vel} value = {yes} or {no} = do or do not communicate velocity info with ghost atoms :pre -:ule - -[Examples:] - -comm_modify mode multi -comm_modify mode multi group solvent -comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0 -comm_modify vel yes -comm_modify mode single cutoff 5.0 vel yes -comm_modify cutoff/multi * 0.0 :pre - -[Description:] - -This command sets parameters that affect the inter-processor -communication of atom information that occurs each timestep as -coordinates and other properties are exchanged between neighboring -processors and stored as properties of ghost atoms. - -NOTE: These options apply to the currently defined comm style. When -you specify a "comm_style"_comm_style.html or -"read_restart"_read_restart.html command, all communication settings -are restored to their default or stored values, including those -previously reset by a comm_modify command. Thus if your input script -specifies a comm_style or read_restart command, you should use the -comm_modify command after it. - -The {mode} keyword determines whether a single or multiple cutoff -distances are used to determine which atoms to communicate. - -The default mode is {single} which means each processor acquires -information for ghost atoms that are within a single distance from its -sub-domain. The distance is by default the maximum of the neighbor -cutoff across all atom type pairs. - -For many systems this is an efficient algorithm, but for systems with -widely varying cutoffs for different type pairs, the {multi} mode can -be faster. In this case, each atom type is assigned its own distance -cutoff for communication purposes, and fewer atoms will be -communicated. See the "neighbor multi"_neighbor.html command for a -neighbor list construction option that may also be beneficial for -simulations of this kind. - -The {cutoff} keyword allows you to extend the ghost cutoff distance -for communication mode {single}, which is the distance from the borders -of a processor's sub-domain at which ghost atoms are acquired from other -processors. By default the ghost cutoff = neighbor cutoff = pairwise -force cutoff + neighbor skin. See the "neighbor"_neighbor.html command -for more information about the skin distance. If the specified Rcut is -greater than the neighbor cutoff, then extra ghost atoms will be acquired. -If the provided cutoff is smaller, the provided value will be ignored, -the ghost cutoff is set to the neighbor cutoff and a warning will be -printed. Specifying a cutoff value of 0.0 will reset any previous value -to the default. If bonded interactions exist and equilibrium bond length -information is available, then also a heuristic based on that bond length -is computed. It is used as communication cutoff, if there is no pair -style present and no {comm_modify cutoff} command used. Otherwise a -warning is printed, if this bond based estimate is larger than the -communication cutoff used. A - -The {cutoff/multi} option is equivalent to {cutoff}, but applies to -communication mode {multi} instead. Since in this case the communication -cutoffs are determined per atom type, a type specifier is needed and -cutoff for one or multiple types can be extended. Also ranges of types -using the usual asterisk notation can be given. - -These are simulation scenarios in which it may be useful or even -necessary to set a ghost cutoff > neighbor cutoff: - -a single polymer chain with bond interactions, but no pairwise interactions -bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff -ghost atoms beyond the pairwise cutoff are needed for some computation :ul - -In the first scenario, a pairwise potential is not defined. Thus the -pairwise neighbor cutoff will be 0.0. But ghost atoms are still -needed for computing bond, angle, etc interactions between atoms on -different processors, or when the interaction straddles a periodic -boundary. - -The appropriate ghost cutoff depends on the "newton bond"_newton.html -setting. For newton bond {off}, the distance needs to be the furthest -distance between any two atoms in the bond, angle, etc. E.g. the -distance between 1-4 atoms in a dihedral. For newton bond {on}, the -distance between the central atom in the bond, angle, etc and any -other atom is sufficient. E.g. the distance between 2-4 atoms in a -dihedral. - -In the second scenario, a pairwise potential is defined, but its -neighbor cutoff is not sufficiently long enough to enable bond, angle, -etc terms to be computed. As in the previous scenario, an appropriate -ghost cutoff should be set. - -In the last scenario, a "fix"_fix.html or "compute"_compute.html or -"pairwise potential"_pair_style.html needs to calculate with ghost -atoms beyond the normal pairwise cutoff for some computation it -performs (e.g. locate neighbors of ghost atoms in a multibody pair -potential). Setting the ghost cutoff appropriately can insure it will -find the needed atoms. - -NOTE: In these scenarios, if you do not set the ghost cutoff long -enough, and if there is only one processor in a periodic dimension -(e.g. you are running in serial), then LAMMPS may "find" the atom it -is looking for (e.g. the partner atom in a bond), that is on the far -side of the simulation box, across a periodic boundary. This will -typically lead to bad dynamics (i.e. the bond length is now the -simulation box length). To detect if this is happening, see the -"neigh_modify cluster"_neigh_modify.html command. - -The {group} keyword will limit communication to atoms in the specified -group. This can be useful for models where no ghost atoms are needed -for some kinds of particles. All atoms (not just those in the -specified group) will still migrate to new processors as they move. -The group specified with this option must also be specified via the -"atom_modify first"_atom_modify.html command. - -The {vel} keyword enables velocity information to be communicated with -ghost particles. Depending on the "atom_style"_atom_style.html, -velocity info includes the translational velocity, angular velocity, -and angular momentum of a particle. If the {vel} option is set to -{yes}, then ghost atoms store these quantities; if {no} then they do -not. The {yes} setting is needed by some pair styles which require -the velocity state of both the I and J particles to compute a pairwise -I,J interaction, as well as by some compute and fix commands. - -Note that if the "fix deform"_fix_deform.html command is being used -with its "remap v" option enabled, then the velocities for ghost atoms -(in the fix deform group) mirrored across a periodic boundary will -also include components due to any velocity shift that occurs across -that boundary (e.g. due to dilation or shear). - -[Restrictions:] - -Communication mode {multi} is currently only available for -"comm_style"_comm_style.html {brick}. - -[Related commands:] - -"comm_style"_comm_style.html, "neighbor"_neighbor.html - -[Default:] - -The option defaults are mode = single, group = all, cutoff = 0.0, vel = -no. The cutoff default of 0.0 means that ghost cutoff = neighbor -cutoff = pairwise force cutoff + neighbor skin. diff --git a/doc/txt/comm_style.txt b/doc/txt/comm_style.txt deleted file mode 100644 index cd9631dd88..0000000000 --- a/doc/txt/comm_style.txt +++ /dev/null @@ -1,66 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -comm_style command :h3 - -[Syntax:] - -comm_style style :pre - -style = {brick} or {tiled} :ul - -[Examples:] - -comm_style brick -comm_style tiled :pre - -[Description:] - -This command sets the style of inter-processor communication of atom -information that occurs each timestep as coordinates and other -properties are exchanged between neighboring processors and stored as -properties of ghost atoms. - -For the default {brick} style, the domain decomposition used by LAMMPS -to partition the simulation box must be a regular 3d grid of bricks, -one per processor. Each processor communicates with its 6 Cartesian -neighbors in the grid to acquire information for nearby atoms. - -For the {tiled} style, a more general domain decomposition can be -used, as triggered by the "balance"_balance.html or "fix -balance"_fix_balance.html commands. The simulation box can be -partitioned into non-overlapping rectangular-shaped "tiles" or varying -sizes and shapes. Again there is one tile per processor. To acquire -information for nearby atoms, communication must now be done with a -more complex pattern of neighboring processors. - -Note that this command does not actually define a partitioning of the -simulation box (a domain decomposition), rather it determines what -kinds of decompositions are allowed and the pattern of communication -used to enable the decomposition. A decomposition is created when the -simulation box is first created, via the "create_box"_create_box.html -or "read_data"_read_data.html or "read_restart"_read_restart.html -commands. For both the {brick} and {tiled} styles, the initial -decomposition will be the same, as described by -"create_box"_create_box.html and "processors"_processors.html -commands. The decomposition can be changed via the -"balance"_balance.html or "fix balance"_fix_balance.html commands. - -[Restrictions:] - -Communication style {tiled} cannot be used with {triclinic} simulation -cells. - -[Related commands:] - -"comm_modify"_comm_modify.html, "processors"_processors.html, -"balance"_balance.html, "fix balance"_fix_balance.html - -[Default:] - -The default style is brick. diff --git a/doc/txt/commands_list.txt b/doc/txt/commands_list.txt deleted file mode 100644 index 714aedefed..0000000000 --- a/doc/txt/commands_list.txt +++ /dev/null @@ -1,125 +0,0 @@ -Commands :h1 - - diff --git a/doc/txt/compute.txt b/doc/txt/compute.txt deleted file mode 100644 index 7b6274d21a..0000000000 --- a/doc/txt/compute.txt +++ /dev/null @@ -1,324 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute command :h3 - -[Syntax:] - -compute ID group-ID style args :pre - -ID = user-assigned name for the computation -group-ID = ID of the group of atoms to perform the computation on -style = one of a list of possible style names (see below) -args = arguments used by a particular style :ul - -[Examples:] - -compute 1 all temp -compute newtemp flow temp/partial 1 1 0 -compute 3 all ke/atom :pre - -[Description:] - -Define a computation that will be performed on a group of atoms. -Quantities calculated by a compute are instantaneous values, meaning -they are calculated from information about atoms on the current -timestep or iteration, though a compute may internally store some -information about a previous state of the system. Defining a compute -does not perform a computation. Instead computes are invoked by other -LAMMPS commands as needed, e.g. to calculate a temperature needed for -a thermostat fix or to generate thermodynamic or dump file output. -See the "Howto output"_Howto_output.html doc page for a summary of -various LAMMPS output options, many of which involve computes. - -The ID of a compute can only contain alphanumeric characters and -underscores. - -:line - -Computes calculate one of three styles of quantities: global, -per-atom, or local. A global quantity is one or more system-wide -values, e.g. the temperature of the system. A per-atom quantity is -one or more values per atom, e.g. the kinetic energy of each atom. -Per-atom values are set to 0.0 for atoms not in the specified compute -group. Local quantities are calculated by each processor based on the -atoms it owns, but there may be zero or more per atom, e.g. a list of -bond distances. Computes that produce per-atom quantities have the -word "atom" in their style, e.g. {ke/atom}. Computes that produce -local quantities have the word "local" in their style, -e.g. {bond/local}. Styles with neither "atom" or "local" in their -style produce global quantities. - -Note that a single compute can produce either global or per-atom or -local quantities, but not both global and per-atom. It can produce -local quantities in tandem with global or per-atom quantities. The -compute doc page will explain. - -Global, per-atom, and local quantities each come in three kinds: a -single scalar value, a vector of values, or a 2d array of values. The -doc page for each compute describes the style and kind of values it -produces, e.g. a per-atom vector. Some computes produce more than one -kind of a single style, e.g. a global scalar and a global vector. - -When a compute quantity is accessed, as in many of the output commands -discussed below, it can be referenced via the following bracket -notation, where ID is the ID of the compute: - -c_ID | entire scalar, vector, or array -c_ID\[I\] | one element of vector, one column of array -c_ID\[I\]\[J\] | one element of array :tb(s=|) - -In other words, using one bracket reduces the dimension of the -quantity once (vector -> scalar, array -> vector). Using two brackets -reduces the dimension twice (array -> scalar). Thus a command that -uses scalar compute values as input can also process elements of a -vector or array. - -Note that commands and "variables"_variable.html which use compute -quantities typically do not allow for all kinds, e.g. a command may -require a vector of values, not a scalar. This means there is no -ambiguity about referring to a compute quantity as c_ID even if it -produces, for example, both a scalar and vector. The doc pages for -various commands explain the details. - -:line - -In LAMMPS, the values generated by a compute can be used in several -ways: - -The results of computes that calculate a global temperature or -pressure can be used by fixes that do thermostatting or barostatting -or when atom velocities are created. :ulb,l - -Global values can be output via the "thermo_style -custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command. -Or the values can be referenced in a "variable equal"_variable.html or -"variable atom"_variable.html command. :l - -Per-atom values can be output via the "dump custom"_dump.html command. -Or they can be time-averaged via the "fix ave/atom"_fix_ave_atom.html -command or reduced by the "compute reduce"_compute_reduce.html -command. Or the per-atom values can be referenced in an "atom-style -variable"_variable.html. :l - -Local values can be reduced by the "compute -reduce"_compute_reduce.html command, or histogrammed by the "fix -ave/histo"_fix_ave_histo.html command, or output by the "dump -local"_dump.html command. :l -:ule - -The results of computes that calculate global quantities can be either -"intensive" or "extensive" values. Intensive means the value is -independent of the number of atoms in the simulation, -e.g. temperature. Extensive means the value scales with the number of -atoms in the simulation, e.g. total rotational kinetic energy. -"Thermodynamic output"_thermo_style.html will normalize extensive -values by the number of atoms in the system, depending on the -"thermo_modify norm" setting. It will not normalize intensive values. -If a compute value is accessed in another way, e.g. by a -"variable"_variable.html, you may want to know whether it is an -intensive or extensive value. See the doc page for individual -computes for further info. - -:line - -LAMMPS creates its own computes internally for thermodynamic output. -Three computes are always created, named "thermo_temp", -"thermo_press", and "thermo_pe", as if these commands had been invoked -in the input script: - -compute thermo_temp all temp -compute thermo_press all pressure thermo_temp -compute thermo_pe all pe :pre - -Additional computes for other quantities are created if the thermo -style requires it. See the documentation for the -"thermo_style"_thermo_style.html command. - -Fixes that calculate temperature or pressure, i.e. for thermostatting -or barostatting, may also create computes. These are discussed in the -documentation for specific "fix"_fix.html commands. - -In all these cases, the default computes LAMMPS creates can be -replaced by computes defined by the user in the input script, as -described by the "thermo_modify"_thermo_modify.html and "fix -modify"_fix_modify.html commands. - -Properties of either a default or user-defined compute can be modified -via the "compute_modify"_compute_modify.html command. - -Computes can be deleted with the "uncompute"_uncompute.html command. - -Code for new computes can be added to LAMMPS; see the -"Modify"_Modify.html doc page for details. The results of their -calculations accessed in the various ways described above. - -:line - -Each compute style has its own doc page which describes its arguments -and what it does. Here is an alphabetic list of compute styles -available in LAMMPS. They are also listed in more compact form on the -"Commands compute"_Commands_compute.html doc page. - -There are also additional accelerated compute styles included in the -LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the "Commands -compute"_Commands_compute.html doc page are followed by one or more of -(g,i,k,o,t) to indicate which accelerated styles exist. - -"ackland/atom"_compute_ackland_atom.html - determines the local lattice structure based on the Ackland formulation -"adf"_compute_adf.html - angular distribution function of triples of atoms -"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom -"angle"_compute_angle.html - energy of each angle sub-style -"angle/local"_compute_angle_local.html - theta and energy of each angle -"angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk -"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed "c" lattice vector of each atom -"body/local"_compute_body_local.html - attributes of body sub-particles -"bond"_compute_bond.html - energy of each bond sub-style -"bond/local"_compute_bond_local.html - distance and energy of each bond -"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom -"centroid/stress/atom"_compute_stress_atom.html - centroid based stress tensor for each atom -"chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom -"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk -"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom -"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom -"cnp/atom"_compute_cnp_atom.html - common neighborhood parameter (CNP) for each atom -"com"_compute_com.html - center-of-mass of group of atoms -"com/chunk"_compute_com_chunk.html - center-of-mass for each chunk -"contact/atom"_compute_contact_atom.html - contact count for each spherical particle -"coord/atom"_compute_coord_atom.html - coordination number for each atom -"damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom -"dihedral"_compute_dihedral.html - energy of each dihedral sub-style -"dihedral/local"_compute_dihedral_local.html - angle of each dihedral -"dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom -"dipole/chunk"_compute_dipole_chunk.html - dipole vector and total dipole for each chunk -"displace/atom"_compute_displace_atom.html - displacement of each atom -"dpd"_compute_dpd.html - -"dpd/atom"_compute_dpd_atom.html - -"edpd/temp/atom"_compute_edpd_temp_atom.html - per-atom temperature for each eDPD particle in a group -"entropy/atom"_compute_entropy_atom.html - pair entropy fingerprint of each atom -"erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles -"erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies -"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles -"erotate/sphere/atom"_compute_erotate_sphere_atom.html - rotational energy for each spherical particle -"event/displace"_compute_event_displace.html - detect event on atom displacement -"fep"_compute_fep.html - -"force/tally"_compute_tally.html - -"fragment/atom"_compute_cluster_atom.html - fragment ID for each atom -"global/atom"_compute_global_atom.html - -"group/group"_compute_group_group.html - energy/force between two groups of atoms -"gyration"_compute_gyration.html - radius of gyration of group of atoms -"gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk -"gyration/shape"_compute_gyration_shape.html - shape parameters from gyration tensor -"gyration/shape/chunk"_compute_gyration_shape_chunk.html - shape parameters from gyration tensor for each chunk -"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms -"heat/flux/tally"_compute_tally.html - -"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6 -"hma"_compute_hma.html - harmonically mapped averaging for atomic crystals -"improper"_compute_improper.html - energy of each improper sub-style -"improper/local"_compute_improper_local.html - angle of each improper -"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk -"ke"_compute_ke.html - translational kinetic energy -"ke/atom"_compute_ke_atom.html - kinetic energy for each atom -"ke/atom/eff"_compute_ke_atom_eff.html - per-atom translational and radial kinetic energy in the electron force field model -"ke/eff"_compute_ke_eff.html - kinetic energy of a group of nuclei and electrons in the electron force field model -"ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies -"meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms -"meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms -"meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms -"momentum"_compute_momentum.html - translational momentum -"msd"_compute_msd.html - mean-squared displacement of group of atoms -"msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk -"msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms -"omega/chunk"_compute_omega_chunk.html - angular velocity for each chunk -"orientorder/atom"_compute_orientorder_atom.html - Steinhardt bond orientational order parameters Ql -"pair"_compute_pair.html - values computed by a pair style -"pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction -"pe"_compute_pe.html - potential energy -"pe/atom"_compute_pe_atom.html - potential energy for each atom -"pe/mol/tally"_compute_tally.html - -"pe/tally"_compute_tally.html - -"plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom -"pressure"_compute_pressure.html - total pressure and pressure tensor -"pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates -"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field -"property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays -"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes -"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays -"ptm/atom"_compute_ptm_atom.html - determines the local lattice structure based on the Polyhedral Template Matching method -"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms -"reduce"_compute_reduce.html - combine per-atom quantities into a single global value -"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk -"reduce/region"_compute_reduce.html - same as compute reduce, within a region -"rigid/local"_compute_rigid_local.html - extract rigid body attributes -"saed"_compute_saed.html - electron diffraction intensity on a mesh of reciprocal lattice nodes -"slice"_compute_slice.html - extract values from global vector or array -"smd/contact/radius"_compute_smd_contact_radius.html - -"smd/damage"_compute_smd_damage.html - damage status of SPH particles in Smooth Mach Dynamics -"smd/hourglass/error"_compute_smd_hourglass_error.html - -"smd/internal/energy"_compute_smd_internal_energy.html - per-particle enthalpy in Smooth Mach Dynamics -"smd/plastic/strain"_compute_smd_plastic_strain.html - equivalent plastic strain per particle in Smooth Mach Dynamics -"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - time rate of the equivalent plastic strain in Smooth Mach Dynamics -"smd/rho"_compute_smd_rho.html - per-particle mass density in Smooth Mach Dynamics -"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - deformation gradient in Smooth Mach Dynamics -"smd/tlsph/dt"_compute_smd_tlsph_dt.html - CFL-stable time increment per particle in Smooth Mach Dynamics -"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html - -"smd/tlsph/shape"_compute_smd_tlsph_shape.html - -"smd/tlsph/strain"_compute_smd_tlsph_strain.html - -"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html - -"smd/tlsph/stress"_compute_smd_tlsph_stress.html - per-particle Cauchy stress tensor for SPH particles -"smd/triangle/vertices"_compute_smd_triangle_vertices.html - -"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html - -"smd/ulsph/strain"_compute_smd_ulsph_strain.html - -"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html - -"smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics -"smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics -"snap"_compute_sna_atom.html - bispectrum components and related quantities for a group of atoms -"sna/atom"_compute_sna_atom.html - bispectrum components for each atom -"snad/atom"_compute_sna_atom.html - derivative of bispectrum components for each atom -"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum components for each atom -"spin"_compute_spin.html - magnetic quantities for a system of atoms having spins -"stress/atom"_compute_stress_atom.html - stress tensor for each atom -"stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes -"stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes -"stress/tally"_compute_tally.html - -"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle -"temp"_compute_temp.html - temperature of group of atoms -"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles -"temp/body"_compute_temp_body.html - temperature of body particles -"temp/chunk"_compute_temp_chunk.html - temperature of each chunk -"temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity -"temp/cs"_compute_temp_cs.html - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other -"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity -"temp/deform/eff"_compute_temp_deform_eff.html - temperature excluding box deformation velocity in the electron force field model -"temp/drude"_compute_temp_drude.html - temperature of Core-Drude pairs -"temp/eff"_compute_temp_eff.html - temperature of a group of nuclei and electrons in the electron force field model -"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity -"temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile -"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component -"temp/region"_compute_temp_region.html - temperature of a region of atoms -"temp/region/eff"_compute_temp_region_eff.html - temperature of a region of nuclei and electrons in the electron force field model -"temp/rotate"_compute_temp_rotate.html - temperature of a group of atoms after subtracting out their center-of-mass and angular velocities -"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles -"temp/uef"_compute_temp_uef.html - kinetic energy tensor in the reference frame of an applied flow field -"ti"_compute_ti.html - thermodynamic integration free energy values -"torque/chunk"_compute_torque_chunk.html - torque applied on each chunk -"vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms -"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk -"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom -"xrd"_compute_xrd.html - x-ray diffraction intensity on a mesh of reciprocal lattice nodes :ul - -[Restrictions:] none - -[Related commands:] - -"uncompute"_uncompute.html, "compute_modify"_compute_modify.html, "fix -ave/atom"_fix_ave_atom.html, "fix ave/time"_fix_ave_time.html, "fix -ave/histo"_fix_ave_histo.html - -[Default:] none diff --git a/doc/txt/compute_ackland_atom.txt b/doc/txt/compute_ackland_atom.txt deleted file mode 100644 index 46db81eb9e..0000000000 --- a/doc/txt/compute_ackland_atom.txt +++ /dev/null @@ -1,85 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute ackland/atom command :h3 - -[Syntax:] - -compute ID group-ID ackland/atom keyword/value :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -ackland/atom = style name of this compute command :l - -zero or more keyword/value pairs may be appended :l -keyword = {legacy} :l - {legacy} yes/no = use ({yes}) or do not use ({no}) legacy ackland algorithm implementation :pre -:ule - -[Examples:] - -compute 1 all ackland/atom -compute 1 all ackland/atom legacy yes :pre - -[Description:] - -Defines a computation that calculates the local lattice structure -according to the formulation given in "(Ackland)"_#Ackland. -Historically, LAMMPS had two, slightly different implementations of -the algorithm from the paper. With the {legacy} keyword, it is -possible to switch between the pre-2015 ({legacy yes}) and post-2015 -implementation ({legacy no}). The post-2015 variant is the default. - -In contrast to the "centro-symmetry -parameter"_compute_centro_atom.html this method is stable against -temperature boost, because it is based not on the distance between -particles but the angles. Therefore statistical fluctuations are -averaged out a little more. A comparison with the Common Neighbor -Analysis metric is made in the paper. - -The result is a number which is mapped to the following different -lattice structures: - -0 = UNKNOWN -1 = BCC -2 = FCC -3 = HCP -4 = ICO :ul - -The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently or to have multiple compute/dump commands, each of -which computes this quantity.- - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -[Restrictions:] - -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -The per-atom vector values will be unitless since they are the -integers defined above. - -[Related commands:] - -"compute centro/atom"_compute_centro_atom.html - -[Default:] -The keyword {legacy} defaults to {no}. - -:line - -:link(Ackland) -[(Ackland)] Ackland, Jones, Phys Rev B, 73, 054104 (2006). diff --git a/doc/txt/compute_adf.txt b/doc/txt/compute_adf.txt deleted file mode 100644 index 20b9fad3f6..0000000000 --- a/doc/txt/compute_adf.txt +++ /dev/null @@ -1,213 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -compute adf command :h3 - -[Syntax:] - -compute ID group-ID adf Nbin itype1 jtype1 ktype1 Rjinner1 Rjouter1 Rkinner1 Rkouter1 ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -adf = style name of this compute command :l -Nbin = number of ADF bins :l -itypeN = central atom type for Nth ADF histogram (see asterisk form below) :l -jtypeN = J atom type for Nth ADF histogram (see asterisk form below) :l -ktypeN = K atom type for Nth ADF histogram (see asterisk form below) :l -RjinnerN = inner radius of J atom shell for Nth ADF histogram (distance units) :l -RjouterN = outer radius of J atom shell for Nth ADF histogram (distance units) :l -RkinnerN = inner radius of K atom shell for Nth ADF histogram (distance units) :l -RkouterN = outer radius of K atom shell for Nth ADF histogram (distance units) :l - -zero or one keyword/value pairs may be appended :l -keyword = {ordinate} :l - {ordinate} value = {degree} or {radian} or {cosine} - Choose the ordinate parameter for the histogram :pre -:ule - -[Examples:] - -compute 1 fluid adf 32 1 1 1 0.0 1.2 0.0 1.2 & - 1 1 2 0.0 1.2 0.0 1.5 & - 1 2 2 0.0 1.5 0.0 1.5 & - 2 1 1 0.0 1.2 0.0 1.2 & - 2 1 2 0.0 1.5 2.0 3.5 & - 2 2 2 2.0 3.5 2.0 3.5 -compute 1 fluid adf 32 1*2 1*2 1*2 0.5 3.5 -compute 1 fluid adf 32 :pre - -[Description:] - -Define a computation that calculates one or more angular distribution functions -(ADF) for a group of particles. Each ADF is calculated in histogram form -by measuring the angle formed by a central atom and two neighbor atoms and -binning these angles into {Nbin} bins. -Only neighbors for which {Rinner} < {R} < {Router} are counted, where -{Rinner} and {Router} are specified separately for the first and second -neighbor atom in each requested ADF. - -NOTE: If you have a bonded system, then the settings of -"special_bonds"_special_bonds.html command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the "special_bonds"_special_bonds.html -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses a neighbor list, it also means -those pairs will not be included in the ADF. This does not apply when -using long-range coulomb interactions ({coul/long}, {coul/msm}, -{coul/wolf} or similar. One way to get around this would be to set -special_bond scaling factors to very tiny numbers that are not exactly -zero (e.g. 1.0e-50). Another workaround is to write a dump file, and -use the "rerun"_rerun.html command to compute the ADF for snapshots in -the dump file. The rerun script can use a -"special_bonds"_special_bonds.html command that includes all pairs in -the neighbor list. - -NOTE: If you request any outer cutoff {Router} > force cutoff, or if no -pair style is defined, e.g. the "rerun"_rerun.html command is being used to -post-process a dump file of snapshots you must insure ghost atom information -out to the largest value of {Router} + {skin} is communicated, via the -"comm_modify cutoff"_comm_modify.html command, else the ADF computation -cannot be performed, and LAMMPS will give an error message. The {skin} value -is what is specified with the "neighbor"_neighbor.html command. - -The {itypeN},{jtypeN},{ktypeN} settings can be specified in one of two -ways. An explicit numeric value can be used, as in the 1st example -above. Or a wild-card asterisk can be used to specify a range of atom -types as in the 2nd example above. -This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of atom types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). - -If {itypeN}, {jtypeN}, and {ktypeN} are single values, as in the 1st example -above, this means that the ADF is computed where atoms of type {itypeN} -are the central atom, and neighbor atoms of type {jtypeN} and {ktypeN} -are forming the angle. If any of {itypeN}, {jtypeN}, or {ktypeN} -represent a range of values via -the wild-card asterisk, as in the 2nd example above, this means that the -ADF is computed where atoms of any of the range of types represented -by {itypeN} are the central atom, and the angle is formed by two neighbors, -one neighbor in the range of types represented by {jtypeN} and another neighbor -in the range of types represented by {ktypeN}. - -If no {itypeN}, {jtypeN}, {ktypeN} settings are specified, then -LAMMPS will generate a single ADF for all atoms in the group. -The inner cutoff is set to zero and the outer cutoff is set -to the force cutoff. If no pair_style is specified, there is no -force cutoff and LAMMPS will give an error message. Note that -in most cases, generating an ADF for all atoms is not a good thing. -Such an ADF is both uninformative and -extremely expensive to compute. For example, with liquid water -with a 10 A force cutoff, there are 80,000 angles per atom. -In addition, most of the interesting angular structure occurs for -neighbors that are the closest to the central atom, involving -just a few dozen angles. - -Angles for each ADF are generated by double-looping over the list of -neighbors of each central atom I, -just as they would be in the force calculation for -a three-body potential such as "Stillinger-Weber"_pair_sw.html. -The angle formed by central atom I and neighbor atoms J and K is included in an -ADF if the following criteria are met: - -atoms I,J,K are all in the specified compute group -the distance between atoms I,J is between Rjinner and Rjouter -the distance between atoms I,K is between Rkinner and Rkouter -the type of the I atom matches itypeN (one or a range of types) -atoms I,J,K are distinct -the type of the J atom matches jtypeN (one or a range of types) -the type of the K atom matches ktypeN (one or a range of types) :ul - -Each unique angle satisfying the above criteria is counted only once, regardless -of whether either or both of the neighbor atoms making up the -angle appear in both the J and K lists. -It is OK if a particular angle is included in more than -one individual histogram, due to the way the {itypeN}, {jtypeN}, {ktypeN} -arguments are specified. - -The first ADF value for a bin is calculated from the histogram count by -dividing by the total number of triples satisfying the criteria, -so that the integral of the ADF w.r.t. angle is 1, i.e. the ADF -is a probability density function. - -The second ADF value is reported as a cumulative sum of -all bins up to the current bins, averaged -over atoms of type {itypeN}. It represents the -number of angles per central atom with angle less -than or equal to the angle of the current bin, -analogous to the coordination -number radial distribution function. - -The {ordinate} optional keyword determines -whether the bins are of uniform angular size from zero -to 180 ({degree}), zero to Pi ({radian}), or the -cosine of the angle uniform in the range \[-1,1\] ({cosine}). -{cosine} has the advantage of eliminating the {acos()} function -call, which speeds up the compute by 2-3x, and it is also preferred -on physical grounds, because the for uniformly distributed particles -in 3D, the angular probability density w.r.t dtheta is -sin(theta)/2, while for d(cos(theta)), it is 1/2, -Regardless of which ordinate is chosen, the first column of ADF -values is normalized w.r.t. the range of that ordinate, so that -the integral is 1. - -The simplest way to output the results of the compute adf calculation -to a file is to use the "fix ave/time"_fix_ave_time.html command, for -example: - -compute myADF all adf 32 2 2 2 0.5 3.5 0.5 3.5 -fix 1 all ave/time 100 1 100 c_myADF\[*\] file tmp.adf mode vector :pre - -[Output info:] - -This compute calculates a global array with the number of rows = -{Nbins}, and the number of columns = 1 + 2*Ntriples, where Ntriples is the -number of I,J,K triples specified. The first column has the bin -coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has -the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN}) -interactions, as described above. These values can be used -by any command that uses a global values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The array values calculated by this compute are all "intensive". - -The first column of array values is the angle-related ordinate, either -the angle in degrees or radians, or the cosine of the angle. Each -subsequent pair of columns gives the first and second kinds of ADF -for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values -in the first ADF column are normalized numbers >= 0.0, -whose integral w.r.t. the ordinate is 1, -i.e. the first ADF is a normalized probability distribution. -The values in the second ADF column are also numbers >= 0.0. -They are the cumulative density distribution of angles per atom. -By definition, this ADF is monotonically increasing from zero to -a maximum value equal to the average total number of -angles per atom satisfying the ADF criteria. - -[Restrictions:] - -The ADF is not computed for neighbors outside the force cutoff, -since processors (in parallel) don't know about atom coordinates for -atoms further away than that distance. If you want an ADF for larger -distances, you can use the "rerun"_rerun.html command to post-process -a dump file and set the cutoff for the potential to be longer in the -rerun script. Note that in the rerun context, the force cutoff is -arbitrary, since you aren't running dynamics and thus are not changing -your model. - -[Related commands:] - -"compute rdf"_compute_rdf.html, "fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html - -[Default:] - -The keyword default is ordinate = degree. - - diff --git a/doc/txt/compute_angle.txt b/doc/txt/compute_angle.txt deleted file mode 100644 index 64eb2f4bb1..0000000000 --- a/doc/txt/compute_angle.txt +++ /dev/null @@ -1,53 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute angle command :h3 - -[Syntax:] - -compute ID group-ID angle :pre - -ID, group-ID are documented in "compute"_compute.html command -angle = style name of this compute command :ul - -[Examples:] - -compute 1 all angle :pre - -[Description:] - -Define a computation that extracts the angle energy calculated by each -of the angle sub-styles used in the "angle_style -hybrid" angle_hybrid.html command. These values are made accessible -for output or further processing by other commands. The group -specified for this command is ignored. - -This compute is useful when using "angle_style -hybrid"_angle_hybrid.html if you want to know the portion of the total -energy contributed by one or more of the hybrid sub-styles. - -[Output info:] - -This compute calculates a global vector of length N where N is the -number of sub_styles defined by the "angle_style -hybrid"_angle_style.html command, which can be accessed by indices -1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The vector values are "extensive" and will be in energy -"units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute pe"_compute_pe.html, "compute pair"_compute_pair.html - -[Default:] none diff --git a/doc/txt/compute_angmom_chunk.txt b/doc/txt/compute_angmom_chunk.txt deleted file mode 100644 index f542ab51ab..0000000000 --- a/doc/txt/compute_angmom_chunk.txt +++ /dev/null @@ -1,88 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute angmom/chunk command :h3 - -[Syntax:] - -compute ID group-ID angmom/chunk chunkID :pre - -ID, group-ID are documented in "compute"_compute.html command -angmom/chunk = style name of this compute command -chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul - -[Examples:] - -compute 1 fluid angmom/chunk molchunk :pre - -[Description:] - -Define a computation that calculates the angular momentum of multiple -chunks of atoms. - -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. - -This compute calculates the 3 components of the angular momentum -vector for each chunk, due to the velocity/momentum of the individual -atoms in the chunk around the center-of-mass of the chunk. The -calculation includes all effects due to atoms passing through periodic -boundaries. - -Note that only atoms in the specified group contribute to the -calculation. The "compute chunk/atom"_compute_chunk_atom.html command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. - -NOTE: The coordinates of an atom contribute to the chunk's angular -momentum in "unwrapped" form, by using the image flags associated with -each atom. See the "dump custom"_dump.html command for a discussion -of "unwrapped" coordinates. See the Atoms section of the -"read_data"_read_data.html command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the "set -image"_set.html command. - -The simplest way to output the results of the compute angmom/chunk -calculation to a file is to use the "fix ave/time"_fix_ave_time.html -command, for example: - -compute cc1 all chunk/atom molecule -compute myChunk all angmom/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre - -[Output info:] - -This compute calculates a global array where the number of rows = the -number of chunks {Nchunk} as calculated by the specified "compute -chunk/atom"_compute_chunk_atom.html command. The number of columns = -3 for the 3 xyz components of the angular momentum for each chunk. -These values can be accessed by any command that uses global array -values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The array values are "intensive". The array values will be in -mass-velocity-distance "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"variable angmom() function"_variable.html - -[Default:] none diff --git a/doc/txt/compute_basal_atom.txt b/doc/txt/compute_basal_atom.txt deleted file mode 100644 index c74bd4342e..0000000000 --- a/doc/txt/compute_basal_atom.txt +++ /dev/null @@ -1,75 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute basal/atom command :h3 - -[Syntax:] - -compute ID group-ID basal/atom :pre - -ID, group-ID are documented in "compute"_compute.html command -basal/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all basal/atom :pre - -[Description:] - -Defines a computation that calculates the hexagonal close-packed "c" -lattice vector for each atom in the group. It does this by -calculating the normal unit vector to the basal plane for each atom. -The results enable efficient identification and characterization of -twins and grains in hexagonal close-packed structures. - -The output of the compute is thus the 3 components of a unit vector -associated with each atom. The components are set to 0.0 for -atoms not in the group. - -Details of the calculation are given in "(Barrett)"_#Barrett. - -The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently or to have multiple compute/dump commands, each of -which computes this quantity. - -An example input script that uses this compute is provided -in examples/USER/misc/basal. - -[Output info:] - -This compute calculates a per-atom array with 3 columns, which can be -accessed by indices 1-3 by any command that uses per-atom values from -a compute as input. See the "Howto output"_Howto_output.html doc page -for an overview of LAMMPS output options. - -The per-atom vector values are unitless since the 3 columns represent -components of a unit vector. - -[Restrictions:] - -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -The output of this compute will be meaningless unless the atoms are on -(or near) hcp lattice sites, since the calculation assumes a -well-defined basal plane. - -[Related commands:] - -"compute centro/atom"_compute_centro_atom.html, "compute -ackland/atom"_compute_ackland_atom.html - -[Default:] none - -:line - -:link(Barrett) -[(Barrett)] Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012). diff --git a/doc/txt/compute_body_local.txt b/doc/txt/compute_body_local.txt deleted file mode 100644 index 8ac3f00c55..0000000000 --- a/doc/txt/compute_body_local.txt +++ /dev/null @@ -1,92 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute body/local command :h3 - -[Syntax:] - -compute ID group-ID body/local input1 input2 ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -body/local = style name of this compute command :l -one or more keywords may be appended :l -keyword = {id} or {type} or {integer} :l - {id} = atom ID of the body particle - {type} = atom type of the body particle - {integer} = 1,2,3,etc = index of fields defined by body style :pre -:ule - -[Examples:] - -compute 1 all body/local type 1 2 3 -compute 1 all body/local 3 6 :pre - -[Description:] - -Define a computation that calculates properties of individual body -sub-particles. The number of datums generated, aggregated across all -processors, equals the number of body sub-particles plus the number of -non-body particles in the system, modified by the group parameter as -explained below. See the "Howto body"_Howto_body.html doc page for -more details on using body particles. - -The local data stored by this command is generated by looping over all -the atoms. An atom will only be included if it is in the group. If -the atom is a body particle, then its N sub-particles will be looped -over, and it will contribute N datums to the count of datums. If it -is not a body particle, it will contribute 1 datum. - -For both body particles and non-body particles, the {id} keyword -will store the ID of the particle. - -For both body particles and non-body particles, the {type} keyword -will store the type of the particle. - -The {integer} keywords mean different things for body and non-body -particles. If the atom is not a body particle, only its {x}, {y}, {z} -coordinates can be referenced, using the {integer} keywords 1,2,3. -Note that this means that if you want to access more fields than this -for body particles, then you cannot include non-body particles in the -group. - -For a body particle, the {integer} keywords refer to fields calculated -by the body style for each sub-particle. The body style, as specified -by the "atom_style body"_atom_style.html, determines how many fields -exist and what they are. See the "Howto_body"_Howto_body.html doc -page for details of the different styles. - -Here is an example of how to output body information using the "dump -local"_dump.html command with this compute. If fields 1,2,3 for the -body sub-particles are x,y,z coordinates, then the dump file will be -formatted similar to the output of a "dump atom or custom"_dump.html -command. - -compute 1 all body/local type 1 2 3 -dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] :pre - -[Output info:] - -This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of datums as described above. If a single keyword -is specified, a local vector is produced. If two or more keywords are -specified, a local array is produced where the number of columns = the -number of keywords. The vector or array can be accessed by any -command that uses local values from a compute as input. See the -"Howto output"_Howto_output.html doc page for an overview of LAMMPS -output options. - -The "units"_units.html for output values depend on the body style. - -[Restrictions:] none - -[Related commands:] - -"dump local"_dump.html - -[Default:] none diff --git a/doc/txt/compute_bond.txt b/doc/txt/compute_bond.txt deleted file mode 100644 index a87c510538..0000000000 --- a/doc/txt/compute_bond.txt +++ /dev/null @@ -1,53 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute bond command :h3 - -[Syntax:] - -compute ID group-ID bond :pre - -ID, group-ID are documented in "compute"_compute.html command -bond = style name of this compute command :ul - -[Examples:] - -compute 1 all bond :pre - -[Description:] - -Define a computation that extracts the bond energy calculated by each -of the bond sub-styles used in the "bond_style -hybrid"_bond_hybrid.html command. These values are made accessible -for output or further processing by other commands. The group -specified for this command is ignored. - -This compute is useful when using "bond_style hybrid"_bond_hybrid.html -if you want to know the portion of the total energy contributed by one -or more of the hybrid sub-styles. - -[Output info:] - -This compute calculates a global vector of length N where N is the -number of sub_styles defined by the "bond_style -hybrid"_bond_style.html command, which can be accessed by indices 1-N. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The vector values are "extensive" and will be in energy -"units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute pe"_compute_pe.html, "compute pair"_compute_pair.html - -[Default:] none diff --git a/doc/txt/compute_centro_atom.txt b/doc/txt/compute_centro_atom.txt deleted file mode 100644 index 183537690f..0000000000 --- a/doc/txt/compute_centro_atom.txt +++ /dev/null @@ -1,151 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute centro/atom command :h3 - -[Syntax:] - -compute ID group-ID centro/atom lattice keyword value ... :pre - -ID, group-ID are documented in "compute"_compute.html command -centro/atom = style name of this compute command -lattice = {fcc} or {bcc} or N = # of neighbors per atom to include :l -zero or more keyword/value pairs may be appended :l -keyword = {axes} :l - {axes} value = {no} or {yes} - {no} = do not calculate 3 symmetry axes - {yes} = calculate 3 symmetry axes :pre -:ule - -[Examples:] - -compute 1 all centro/atom fcc :pre -compute 1 all centro/atom 8 :pre - -[Description:] - -Define a computation that calculates the centro-symmetry parameter for -each atom in the group, for either FCC or BCC lattices, depending on -the choice of the {lattice} argument. In solid-state systems the -centro-symmetry parameter is a useful measure of the local lattice -disorder around an atom and can be used to characterize whether the -atom is part of a perfect lattice, a local defect (e.g. a dislocation -or stacking fault), or at a surface. - -The value of the centro-symmetry parameter will be 0.0 for atoms not -in the specified compute group. - -This parameter is computed using the following formula from -"(Kelchner)"_#Kelchner - -:c,image(Eqs/centro_symmetry.jpg) - -where the {N} nearest neighbors of each atom are identified and Ri and -Ri+N/2 are vectors from the central atom to a particular pair of -nearest neighbors. There are N*(N-1)/2 possible neighbor pairs that -can contribute to this formula. The quantity in the sum is computed -for each, and the N/2 smallest are used. This will typically be for -pairs of atoms in symmetrically opposite positions with respect to the -central atom; hence the i+N/2 notation. - -{N} is an input parameter, which should be set to correspond to the -number of nearest neighbors in the underlying lattice of atoms. If -the keyword {fcc} or {bcc} is used, {N} is set to 12 and 8 -respectively. More generally, {N} can be set to a positive, even -integer. - -For an atom on a lattice site, surrounded by atoms on a perfect -lattice, the centro-symmetry parameter will be 0. It will be near 0 -for small thermal perturbations of a perfect lattice. If a point -defect exists, the symmetry is broken, and the parameter will be a -larger positive value. An atom at a surface will have a large -positive parameter. If the atom does not have {N} neighbors (within -the potential cutoff), then its centro-symmetry parameter is set to -0.0. - -If the keyword {axes} has the setting {yes}, then this compute also -estimates three symmetry axes for each atom's local neighborhood. The -first two of these are the vectors joining the two pairs of neighbor -atoms with smallest contributions to the centrosymmetry parameter, -i.e. the two most symmetric pairs of atoms. The third vector is -normal to the first two by the right-hand rule. All three vectors are -normalized to unit length. For FCC crystals, the first two vectors -will lie along a <110> direction, while the third vector will lie -along either a <100> or <111> direction. For HCP crystals, the first -two vectors will lie along <1000> directions, while the third vector -will lie along <0001>. This provides a simple way to measure local -orientation in HCP structures. In general, the {axes} keyword can be -used to estimate the orientation of symmetry axes in the neighborhood -of any atom. - -Only atoms within the cutoff of the pairwise neighbor list are -considered as possible neighbors. Atoms not in the compute group are -included in the {N} neighbors used in this calculation. - -The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (e.g. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently or to have multiple compute/dump commands, each with a -{centro/atom} style. - -[Output info:] - -By default, this compute calculates the centrosymmetry value for each -atom as a per-atom vector, which can be accessed by any command that -uses per-atom values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -If the {axes} keyword setting is {yes}, then a per-atom array is -calculated. The first column is the centrosymmetry parameter. The -next three columns are the x, y, and z components of the first -symmetry axis, followed by the second, and third symmetry axes in -columns 5-7 and 8-10. - -The centrosymmetry values are unitless values >= 0.0. Their magnitude -depends on the lattice style due to the number of contributing neighbor -pairs in the summation in the formula above. And it depends on the -local defects surrounding the central atom, as described above. For -the {axes yes} case, the vector components are also unitless, since -they represent spatial directions. - -Here are typical centro-symmetry values, from a nanoindentation -simulation into gold (FCC). These were provided by Jon Zimmerman -(Sandia): - -Bulk lattice = 0 -Dislocation core ~ 1.0 (0.5 to 1.25) -Stacking faults ~ 5.0 (4.0 to 6.0) -Free surface ~ 23.0 :pre - -These values are *not* normalized by the square of the lattice -parameter. If they were, normalized values would be: - -Bulk lattice = 0 -Dislocation core ~ 0.06 (0.03 to 0.075) -Stacking faults ~ 0.3 (0.24 to 0.36) -Free surface ~ 1.38 :pre - -For BCC materials, the values for dislocation cores and free surfaces -would be somewhat different, due to their being only 8 neighbors instead -of 12. - -[Restrictions:] none - -[Related commands:] - -"compute cna/atom"_compute_cna_atom.html - -[Default:] - -The default value for the optional keyword is axes = no. - -:line - -:link(Kelchner) -[(Kelchner)] Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998). diff --git a/doc/txt/compute_chunk_atom.txt b/doc/txt/compute_chunk_atom.txt deleted file mode 100644 index c6dfddbd55..0000000000 --- a/doc/txt/compute_chunk_atom.txt +++ /dev/null @@ -1,665 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute chunk/atom command :h3 - -[Syntax:] - -compute ID group-ID chunk/atom style args keyword values ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -chunk/atom = style name of this compute command :l -style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} or c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name - {bin/1d} args = dim origin delta - dim = {x} or {y} or {z} - origin = {lower} or {center} or {upper} or coordinate value (distance units) - delta = thickness of spatial bins in dim (distance units) - {bin/2d} args = dim origin delta dim origin delta - dim = {x} or {y} or {z} - origin = {lower} or {center} or {upper} or coordinate value (distance units) - delta = thickness of spatial bins in dim (distance units) - {bin/3d} args = dim origin delta dim origin delta dim origin delta - dim = {x} or {y} or {z} - origin = {lower} or {center} or {upper} or coordinate value (distance units) - delta = thickness of spatial bins in dim (distance units) - {bin/sphere} args = xorig yorig zorig rmin rmax nsbin - xorig,yorig,zorig = center point of sphere - srmin,srmax = bin from sphere radius rmin to rmax - nsbin = # of spherical shell bins between rmin and rmax - {bin/cylinder} args = dim origin delta c1 c2 rmin rmax ncbin - dim = {x} or {y} or {z} = axis of cylinder axis - origin = {lower} or {center} or {upper} or coordinate value (distance units) - delta = thickness of spatial bins in dim (distance units) - c1,c2 = coords of cylinder axis in other 2 dimensions (distance units) - crmin,crmax = bin from cylinder radius rmin to rmax (distance units) - ncbin = # of concentric circle bins between rmin and rmax - {type} args = none - {molecule} args = none - c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name args = none - c_ID = per-atom vector calculated by a compute with ID - c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID - f_ID = per-atom vector calculated by a fix with ID - f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID - v_name = per-atom vector calculated by an atom-style variable with name :pre - -zero or more keyword/values pairs may be appended :l -keyword = {region} or {nchunk} or {static} or {compress} or {bound} or {discard} or {pbc} or {units} :l - {region} value = region-ID - region-ID = ID of region atoms must be in to be part of a chunk - {nchunk} value = {once} or {every} - once = only compute the number of chunks once - every = re-compute the number of chunks whenever invoked - {limit} values = 0 or Nc max or Nc exact - 0 = no limit on the number of chunks - Nc max = limit number of chunks to be <= Nc - Nc exact = set number of chunks to exactly Nc - {ids} value = {once} or {nfreq} or {every} - once = assign chunk IDs to atoms only once, they persist thereafter - nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by "fix ave/chunk"_fix_ave_chunk.html which sets Nfreq) - every = assign chunk IDs to atoms whenever invoked - {compress} value = {yes} or {no} - yes = compress chunk IDs to eliminate IDs with no atoms - no = do not compress chunk IDs even if some IDs have no atoms - {discard} value = {yes} or {no} or {mixed} - yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0 - no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID - mixed = keep or discard such atoms according to spatial binning rule - {bound} values = x/y/z lo hi - x/y/z = {x} or {y} or {z} to bound sptial bins in this dimension - lo = {lower} or coordinate value (distance units) - hi = {upper} or coordinate value (distance units) - {pbc} value = {no} or {yes} - yes = use periodic distance for bin/sphere and bin/cylinder styles - {units} value = {box} or {lattice} or {reduced} :pre -:ule - -[Examples:] - -compute 1 all chunk/atom type -compute 1 all chunk/atom bin/1d z lower 0.02 units reduced -compute 1 all chunk/atom bin/2d z lower 1.0 y 0.0 2.5 -compute 1 all chunk/atom molecule region sphere nchunk once ids once compress yes -compute 1 all chunk/atom bin/sphere 5 5 5 2.0 5.0 5 discard yes -compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes -compute 1 all chunk/atom c_cluster :pre - -[Description:] - -Define a computation that calculates an integer chunk ID from 1 to -Nchunk for each atom in the group. Values of chunk IDs are determined -by the {style} of chunk, which can be based on atom type or molecule -ID or spatial binning or a per-atom property or value calculated by -another "compute"_compute.html, "fix"_fix.html, or "atom-style -variable"_variable.html. Per-atom chunk IDs can be used by other -computes with "chunk" in their style name, such as "compute -com/chunk"_compute_com_chunk.html or "compute -msd/chunk"_compute_msd_chunk.html. Or they can be used by the "fix -ave/chunk"_fix_ave_chunk.html command to sum and time average a -variety of per-atom properties over the atoms in each chunk. Or they -can simply be accessed by any command that uses per-atom values from a -compute as input, as discussed on the "Howto output"_Howto_output.html -doc page. - -See the "Howto chunk"_Howto_chunk.html doc page for an overview of how -this compute can be used with a variety of other commands to tabulate -properties of a simulation. The page gives several examples of input -script commands that can be used to calculate interesting properties. - -Conceptually it is important to realize that this compute does two -simple things. First, it sets the value of {Nchunk} = the number of -chunks, which can be a constant value or change over time. Second, it -assigns each atom to a chunk via a chunk ID. Chunk IDs range from 1 -to {Nchunk} inclusive; some chunks may have no atoms assigned to them. -Atoms that do not belong to any chunk are assigned a value of 0. Note -that the two operations are not always performed together. For -example, spatial bins can be setup once (which sets {Nchunk}), and -atoms assigned to those bins many times thereafter (setting their -chunk IDs). - -All other commands in LAMMPS that use chunk IDs assume there are -{Nchunk} number of chunks, and that every atom is assigned to one of -those chunks, or not assigned to any chunk. - -There are many options for specifying for how and when {Nchunk} is -calculated, and how and when chunk IDs are assigned to atoms. The -details depend on the chunk {style} and its {args}, as well as -optional keyword settings. They can also depend on whether a "fix -ave/chunk"_fix_ave_chunk.html command is using this compute, since -that command requires {Nchunk} to remain static across windows of -timesteps it specifies, while it accumulates per-chunk averages. - -The details are described below. - -:line - -The different chunk styles operate as follows. For each style, how it -calculates {Nchunk} and assigns chunk IDs to atoms is explained. Note -that using the optional keywords can change both of those actions, as -described further below where the keywords are discussed. - -:line - -The {binning} styles perform a spatial binning of atoms, and assign an -atom the chunk ID corresponding to the bin number it is in. {Nchunk} -is set to the number of bins, which can change if the simulation box -size changes. This also depends on the setting of the {units} -keyword; e.g. for {reduced} units the number of chunks may not change -even if the box size does. - -The {bin/1d}, {bin/2d}, and {bin/3d} styles define bins as 1d layers -(slabs), 2d pencils, or 3d boxes. The {dim}, {origin}, and {delta} -settings are specified 1, 2, or 3 times. For 2d or 3d bins, there is -no restriction on specifying dim = x before dim = y or z, or dim = y -before dim = z. Bins in a particular {dim} have a bin size in that -dimension given by {delta}. In each dimension, bins are defined -relative to a specified {origin}, which may be the lower/upper edge of -the simulation box (in that dimension), or its center point, or a -specified coordinate value. Starting at the origin, sufficient bins -are created in both directions to completely span the simulation box -or the bounds specified by the optional {bounds} keyword. - -For orthogonal simulation boxes, the bins are layers, pencils, or -boxes aligned with the xyz coordinate axes. For triclinic -(non-orthogonal) simulation boxes, the bin faces are parallel to the -tilted faces of the simulation box. See the "Howto -triclinic"_Howto_triclinic.html doc page for a discussion of the -geometry of triclinic boxes in LAMMPS. As described there, a tilted -simulation box has edge vectors a,b,c. In that nomenclature, bins in -the x dimension have faces with normals in the "b" cross "c" -direction. Bins in y have faces normal to the "a" cross "c" -direction. And bins in z have faces normal to the "a" cross "b" -direction. Note that in order to define the size and position of -these bins in an unambiguous fashion, the {units} option must be set -to {reduced} when using a triclinic simulation box, as noted below. - -The meaning of {origin} and {delta} for triclinic boxes is as follows. -Consider a triclinic box with bins that are 1d layers or slabs in the -x dimension. No matter how the box is tilted, an {origin} of 0.0 -means start layers at the lower "b" cross "c" plane of the simulation -box and an {origin} of 1.0 means to start layers at the upper "b" -cross "c" face of the box. A {delta} value of 0.1 in {reduced} units -means there will be 10 layers from 0.0 to 1.0, regardless of the -current size or shape of the simulation box. - -The {bin/sphere} style defines a set of spherical shell bins around -the origin ({xorig},{yorig},{zorig}), using {nsbin} bins with radii -equally spaced between {srmin} and {srmax}. This is effectively a 1d -vector of bins. For example, if {srmin} = 1.0 and {srmax} = 10.0 and -{nsbin} = 9, then the first bin spans 1.0 < r < 2.0, and the last bin -spans 9.0 < r 10.0. The geometry of the bins is the same whether the -simulation box is orthogonal or triclinic; i.e. the spherical shells -are not tilted or scaled differently in different dimensions to -transform them into ellipsoidal shells. - -The {bin/cylinder} style defines bins for a cylinder oriented along -the axis {dim} with the axis coordinates in the other two radial -dimensions at ({c1},{c2}). For dim = x, c1/c2 = y/z; for dim = y, -c1/c2 = x/z; for dim = z, c1/c2 = x/y. This is effectively a 2d array -of bins. The first dimension is along the cylinder axis, the second -dimension is radially outward from the cylinder axis. The bin size -and positions along the cylinder axis are specified by the {origin} -and {delta} values, the same as for the {bin/1d}, {bin/2d}, and -{bin/3d} styles. There are {ncbin} concentric circle bins in the -radial direction from the cylinder axis with radii equally spaced -between {crmin} and {crmax}. For example, if {crmin} = 1.0 and -{crmax} = 10.0 and {ncbin} = 9, then the first bin spans 1.0 < r < -2.0, and the last bin spans 9.0 < r 10.0. The geometry of the bins in -the radial dimensions is the same whether the simulation box is -orthogonal or triclinic; i.e. the concentric circles are not tilted or -scaled differently in the two different dimensions to transform them -into ellipses. - -The created bins (and hence the chunk IDs) are numbered consecutively -from 1 to the number of bins = {Nchunk}. For {bin2d} and {bin3d}, the -numbering varies most rapidly in the first dimension (which could be -x, y, or z), next rapidly in the 2nd dimension, and most slowly in the -3rd dimension. For {bin/sphere}, the bin with smallest radii is chunk -1 and the bni with largest radii is chunk Nchunk = {ncbin}. For -{bin/cylinder}, the numbering varies most rapidly in the dimension -along the cylinder axis and most slowly in the radial direction. - -Each time this compute is invoked, each atom is mapped to a bin based -on its current position. Note that between reneighboring timesteps, -atoms can move outside the current simulation box. If the box is -periodic (in that dimension) the atom is remapping into the periodic -box for purposes of binning. If the box in not periodic, the atom may -have moved outside the bounds of all bins. If an atom is not inside -any bin, the {discard} keyword is used to determine how a chunk ID is -assigned to the atom. - -:line - -The {type} style uses the atom type as the chunk ID. {Nchunk} is set -to the number of atom types defined for the simulation, e.g. via the -"create_box"_create_box.html or "read_data"_read_data.html commands. - -:line - -The {molecule} style uses the molecule ID of each atom as its chunk -ID. {Nchunk} is set to the largest chunk ID. Note that this excludes -molecule IDs for atoms which are not in the specified group or -optional region. - -There is no requirement that all atoms in a particular molecule are -assigned the same chunk ID (zero or non-zero), though you probably -want that to be the case, if you wish to compute a per-molecule -property. LAMMPS will issue a warning if that is not the case, but -only the first time that {Nchunk} is calculated. - -Note that atoms with a molecule ID = 0, which may be non-molecular -solvent atoms, have an out-of-range chunk ID. These atoms are -discarded (not assigned to any chunk) or assigned to {Nchunk}, -depending on the value of the {discard} keyword. - -:line - -The {compute/fix/variable} styles set the chunk ID of each atom based -on a quantity calculated and stored by a compute, fix, or variable. -In each case, it must be a per-atom quantity. In each case the -referenced floating point values are converted to an integer chunk ID -as follows. The floating point value is truncated (rounded down) to -an integer value. If the integer value is <= 0, then a chunk ID of 0 -is assigned to the atom. If the integer value is > 0, it becomes the -chunk ID to the atom. {Nchunk} is set to the largest chunk ID. Note -that this excludes atoms which are not in the specified group or -optional region. - -If the style begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the compute is used. Users can also write code for -their own compute styles and "add them to LAMMPS"_Modify.html. - -If the style begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed integer is -appended, the per-atom vector calculated by the fix is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the fix is used. Note that some fixes only produce -their values on certain timesteps, which must be compatible with the -timestep on which this compute accesses the fix, else an error -results. Users can also write code for their own fix styles and "add -them to LAMMPS"_Modify.html. - -If a value begins with "v_", a variable name for an {atom} or -{atomfile} style "variable"_variable.html must follow which has been -previously defined in the input script. Variables of style {atom} can -reference thermodynamic keywords and various per-atom attributes, or -invoke other computes, fixes, or variables when they are evaluated, so -this is a very general means of generating per-atom quantities to -treat as a chunk ID. - -:line - -Normally, {Nchunk} = the number of chunks, is re-calculated every time -this fix is invoked, though the value may or may not change. As -explained below, the {nchunk} keyword can be set to {once} which means -{Nchunk} will never change. - -If a "fix ave/chunk"_fix_ave_chunk.html command uses this compute, it -can also turn off the re-calculation of {Nchunk} for one or more -windows of timesteps. The extent of the windows, during which Nchunk -is held constant, are determined by the {Nevery}, {Nrepeat}, {Nfreq} -values and the {ave} keyword setting that are used by the "fix -ave/chunk"_fix_ave_chunk.html command. - -Specifically, if {ave} = {one}, then for each span of {Nfreq} -timesteps, {Nchunk} is held constant between the first timestep when -averaging is done (within the Nfreq-length window), and the last -timestep when averaging is done (multiple of Nfreq). If {ave} = -{running} or {window}, then {Nchunk} is held constant forever, -starting on the first timestep when the "fix -ave/chunk"_fix_ave_chunk.html command invokes this compute. - -Note that multiple "fix ave/chunk"_fix_ave_chunk.html commands can use -the same compute chunk/atom compute. However, the time windows they -induce for holding {Nchunk} constant must be identical, else an error -will be generated. - -:line - -The various optional keywords operate as follows. Note that some of -them function differently or are ignored by different chunk styles. -Some of them also have different default values, depending on -the chunk style, as listed below. - -The {region} keyword applies to all chunk styles. If used, an atom -must be in both the specified group and the specified geometric -"region"_region.html to be assigned to a chunk. - -:line - -The {nchunk} keyword applies to all chunk styles. It specifies how -often {Nchunk} is recalculated, which in turn can affect the chunk IDs -assigned to individual atoms. - -If {nchunk} is set to {once}, then {Nchunk} is only calculated once, -the first time this compute is invoked. If {nchunk} is set to -{every}, then {Nchunk} is re-calculated every time the compute is -invoked. Note that, as described above, the use of this compute -by the "fix ave/chunk"_fix_ave_chunk.html command can override -the {every} setting. - -The default values for {nchunk} are listed below and depend on the -chunk style and other system and keyword settings. They attempt to -represent typical use cases for the various chunk styles. The -{nchunk} value can always be set explicitly if desired. - -:line - -The {limit} keyword can be used to limit the calculated value of -{Nchunk} = the number of chunks. The limit is applied each time -{Nchunk} is calculated, which also limits the chunk IDs assigned to -any atom. The {limit} keyword is used by all chunk styles except the -{binning} styles, which ignore it. This is because the number of bins -can be tailored using the {bound} keyword (described below) which -effectively limits the size of {Nchunk}. - -If {limit} is set to {Nc} = 0, then no limit is imposed on {Nchunk}, -though the {compress} keyword can still be used to reduce {Nchunk}, as -described below. - -If {Nc} > 0, then the effect of the {limit} keyword depends on whether -the {compress} keyword is also used with a setting of {yes}, and -whether the {compress} keyword is specified before the {limit} keyword -or after. - -In all cases, {Nchunk} is first calculated in the usual way for each -chunk style, as described above. - -First, here is what occurs if {compress yes} is not set. If {limit} -is set to {Nc max}, then {Nchunk} is reset to the smaller of {Nchunk} -and {Nc}. If {limit} is set to {Nc exact}, then {Nchunk} is reset to -{Nc}, whether the original {Nchunk} was larger or smaller than {Nc}. -If {Nchunk} shrank due to the {limit} setting, then atom chunk IDs > -{Nchunk} will be reset to 0 or {Nchunk}, depending on the setting of -the {discard} keyword. If {Nchunk} grew, there will simply be some -chunks with no atoms assigned to them. - -If {compress yes} is set, and the {compress} keyword comes before the -{limit} keyword, the compression operation is performed first, as -described below, which resets {Nchunk}. The {limit} keyword is then -applied to the new {Nchunk} value, exactly as described in the -preceding paragraph. Note that in this case, all atoms will end up -with chunk IDs <= {Nc}, but their original values (e.g. molecule ID or -compute/fix/variable) may have been > {Nc}, because of the compression -operation. - -If {compress yes} is set, and the {compress} keyword comes after the -{limit} keyword, then the {limit} value of {Nc} is applied first to -the uncompressed value of {Nchunk}, but only if {Nc} < {Nchunk} -(whether {Nc max} or {Nc exact} is used). This effectively means all -atoms with chunk IDs > {Nc} have their chunk IDs reset to 0 or {Nc}, -depending on the setting of the {discard} keyword. The compression -operation is then performed, which may shrink {Nchunk} further. If -the new {Nchunk} < {Nc} and {limit} = {Nc exact} is specified, then -{Nchunk} is reset to {Nc}, which results in extra chunks with no atoms -assigned to them. Note that in this case, all atoms will end up with -chunk IDs <= {Nc}, and their original values (e.g. molecule ID or -compute/fix/variable value) will also have been <= {Nc}. - -:line - -The {ids} keyword applies to all chunk styles. If the setting is -{once} then the chunk IDs assigned to atoms the first time this -compute is invoked will be permanent, and never be re-computed. - -If the setting is {nfreq} and if a "fix ave/chunk"_fix_ave_chunk.html -command is using this compute, then in each of the {Nchunk} = constant -time windows (discussed above), the chunk ID's assigned to atoms on -the first step of the time window will persist until the end of the -time window. - -If the setting is {every}, which is the default, then chunk IDs are -re-calculated on any timestep this compute is invoked. - -NOTE: If you want the persistent chunk-IDs calculated by this compute -to be continuous when running from a "restart file"_read_restart.html, -then you should use the same ID for this compute, as in the original -run. This is so that the fix this compute creates to store per-atom -quantities will also have the same ID, and thus be initialized -correctly with chunk IDs from the restart file. - -:line - -The {compress} keyword applies to all chunk styles and affects how -{Nchunk} is calculated, which in turn affects the chunk IDs assigned -to each atom. It is useful for converting a "sparse" set of chunk IDs -(with many IDs that have no atoms assigned to them), into a "dense" -set of IDs, where every chunk has one or more atoms assigned to it. - -Two possible use cases are as follows. If a large simulation box is -mostly empty space, then the {binning} style may produce many bins -with no atoms. If {compress} is set to {yes}, only bins with atoms -will be contribute to {Nchunk}. Likewise, the {molecule} or -{compute/fix/variable} styles may produce large {Nchunk} values. For -example, the "compute cluster/atom"_compute_cluster_atom.html command -assigns every atom an atom ID for one of the atoms it is clustered -with. For a million-atom system with 5 clusters, there would only be -5 unique chunk IDs, but the largest chunk ID might be 1 million, -resulting in {Nchunk} = 1 million. If {compress} is set to {yes}, -{Nchunk} will be reset to 5. - -If {compress} is set to {no}, which is the default, no compression is -done. If it is set to {yes}, all chunk IDs with no atoms are removed -from the list of chunk IDs, and the list is sorted. The remaining -chunk IDs are renumbered from 1 to {Nchunk} where {Nchunk} is the new -length of the list. The chunk IDs assigned to each atom reflect -the new renumbering from 1 to {Nchunk}. - -The original chunk IDs (before renumbering) can be accessed by the -"compute property/chunk"_compute_property_chunk.html command and its -{id} keyword, or by the "fix ave/chunk"_fix_ave_chunk.html command -which outputs the original IDs as one of the columns in its global -output array. For example, using the "compute cluster/atom" command -discussed above, the original 5 unique chunk IDs might be atom IDs -(27,4982,58374,857838,1000000). After compression, these will be -renumbered to (1,2,3,4,5). The original values (27,...,1000000) can -be output to a file by the "fix ave/chunk"_fix_ave_chunk.html command, -or by using the "fix ave/time"_fix_ave_time.html command in -conjunction with the "compute -property/chunk"_compute_property_chunk.html command. - -NOTE: The compression operation requires global communication across -all processors to share their chunk ID values. It can require large -memory on every processor to store them, even after they are -compressed, if there are a large number of unique chunk IDs with -atoms assigned to them. It uses a STL map to find unique chunk IDs -and store them in sorted order. Each time an atom is assigned a -compressed chunk ID, it must access the STL map. All of this means -that compression can be expensive, both in memory and CPU time. The -use of the {limit} keyword in conjunction with the {compress} keyword -can affect these costs, depending on which keyword is used first. So -use this option with care. - -:line - -The {discard} keyword applies to all chunk styles. It affects what -chunk IDs are assigned to atoms that do not match one of the valid -chunk IDs from 1 to {Nchunk}. Note that it does not apply to atoms -that are not in the specified group or optionally specified region. -Those atoms are always assigned a chunk ID = 0. - -If the calculated chunk ID for an atom is not within the range 1 to -{Nchunk} then it is a "discard" atom. Note that {Nchunk} may have -been shrunk by the {limit} keyword. Or the {compress} keyword may -have eliminated chunk IDs that were valid before the compression took -place, and are now not in the compressed list. Also note that for the -{molecule} chunk style, if new molecules are added to the system, -their chunk IDs may exceed a previously calculated {Nchunk}. -Likewise, evaluation of a compute/fix/variable on a later timestep may -return chunk IDs that are invalid for the previously calculated -{Nchunk}. - -All the chunk styles except the {binning} styles, must use {discard} -set to either {yes} or {no}. If {discard} is set to {yes}, which is -the default, then every "discard" atom has its chunk ID set to 0. If -{discard} is set to {no}, every "discard" atom has its chunk ID set to -{Nchunk}. I.e. it becomes part of the last chunk. - -The {binning} styles use the {discard} keyword to decide whether to -discard atoms outside the spatial domain covered by bins, or to assign -them to the bin they are nearest to. - -For the {bin/1d}, {bin/2d}, {bin/3d} styles the details are as -follows. If {discard} is set to {yes}, an out-of-domain atom will -have its chunk ID set to 0. If {discard} is set to {no}, the atom -will have its chunk ID set to the first or last bin in that dimension. -If {discard} is set to {mixed}, which is the default, it will only -have its chunk ID set to the first or last bin if bins extend to the -simulation box boundary in that dimension. This is the case if the -{bound} keyword settings are {lower} and {upper}, which is the -default. If the {bound} keyword settings are numeric values, then the -atom will have its chunk ID set to 0 if it is outside the bounds of -any bin. Note that in this case, it is possible that the first or -last bin extends beyond the numeric {bounds} settings, depending on -the specified {origin}. If this is the case, the chunk ID of the atom -is only set to 0 if it is outside the first or last bin, not if it is -simply outside the numeric {bounds} setting. - -For the {bin/sphere} style the details are as follows. If {discard} -is set to {yes}, an out-of-domain atom will have its chunk ID set to -0. If {discard} is set to {no} or {mixed}, the atom will have its -chunk ID set to the first or last bin, i.e. the innermost or outermost -spherical shell. If the distance of the atom from the origin is less -than {rmin}, it will be assigned to the first bin. If the distance of -the atom from the origin is greater than {rmax}, it will be assigned -to the last bin. - -For the {bin/cylinder} style the details are as follows. If {discard} -is set to {yes}, an out-of-domain atom will have its chunk ID set to -0. If {discard} is set to {no}, the atom will have its chunk ID set -to the first or last bin in both the radial and axis dimensions. If -{discard} is set to {mixed}, which is the default, the radial -dimension is treated the same as for {discard} = no. But for the axis -dimension, it will only have its chunk ID set to the first or last -bin if bins extend to the simulation box boundary in the axis -dimension. This is the case if the {bound} keyword settings are -{lower} and {upper}, which is the default. If the {bound} keyword -settings are numeric values, then the atom will have its chunk ID set -to 0 if it is outside the bounds of any bin. Note that in this case, -it is possible that the first or last bin extends beyond the numeric -{bounds} settings, depending on the specified {origin}. If this is -the case, the chunk ID of the atom is only set to 0 if it is outside -the first or last bin, not if it is simply outside the numeric -{bounds} setting. - -If {discard} is set to {no} or {mixed}, the atom will have its -chunk ID set to the first or last bin, i.e. the innermost or outermost -spherical shell. If the distance of the atom from the origin is less -than {rmin}, it will be assigned to the first bin. If the distance of -the atom from the origin is greater than {rmax}, it will be assigned -to the last bin. - -:line - -The {bound} keyword only applies to the {bin/1d}, {bin/2d}, {bin/3d} -styles and to the axis dimension of the {bin/cylinder} style; -otherwise it is ignored. It can be used one or more times to limit -the extent of bin coverage in a specified dimension, i.e. to only bin -a portion of the box. If the {lo} setting is {lower} or the {hi} -setting is {upper}, the bin extent in that direction extends to the -box boundary. If a numeric value is used for {lo} and/or {hi}, then -the bin extent in the {lo} or {hi} direction extends only to that -value, which is assumed to be inside (or at least near) the simulation -box boundaries, though LAMMPS does not check for this. Note that -using the {bound} keyword typically reduces the total number of bins -and thus the number of chunks {Nchunk}. - -The {pbc} keyword only applies to the {bin/sphere} and {bin/cylinder} -styles. If set to {yes}, the distance an atom is from the sphere -origin or cylinder axis is calculated in a minimum image sense with -respect to periodic dimensions, when determining which bin the atom is -in. I.e. if x is a periodic dimension and the distance between the -atom and the sphere center in the x dimension is greater than 0.5 * -simulation box length in x, then a box length is subtracted to give a -distance < 0.5 * simulation box length. This allosws the sphere or -cylinder center to be near a box edge, and atoms on the other side of -the periodic box will still be close to the center point/axis. Note -that with a setting of {yes}, the outer sphere or cylinder radius must -also be <= 0.5 * simulation box length in any periodic dimension -except for the cylinder axis dimension, or an error is generated. - -The {units} keyword only applies to the {binning} styles; otherwise it -is ignored. For the {bin/1d}, {bin/2d}, {bin/3d} styles, it -determines the meaning of the distance units used for the bin sizes -{delta} and for {origin} and {bounds} values if they are coordinate -values. For the {bin/sphere} style it determines the meaning of the -distance units used for {xorig},{yorig},{zorig} and the radii {srmin} -and {srmax}. For the {bin/cylinder} style it determines the meaning -of the distance units used for {delta},{c1},{c2} and the radii {crmin} -and {crmax}. - -For orthogonal simulation boxes, any of the 3 options may -be used. For non-orthogonal (triclinic) simulation boxes, only the -{reduced} option may be used. - -A {box} value selects standard distance units as defined by the -"units"_units.html command, e.g. Angstroms for units = real or metal. -A {lattice} value means the distance units are in lattice spacings. -The "lattice"_lattice.html command must have been previously used to -define the lattice spacing. A {reduced} value means normalized -unitless values between 0 and 1, which represent the lower and upper -faces of the simulation box respectively. Thus an {origin} value of -0.5 means the center of the box in any dimension. A {delta} value of -0.1 means 10 bins span the box in that dimension. - -Note that for the {bin/sphere} style, the radii {srmin} and {srmax} are -scaled by the lattice spacing or reduced value of the {x} dimension. - -Note that for the {bin/cylinder} style, the radii {crmin} and {crmax} -are scaled by the lattice spacing or reduced value of the 1st -dimension perpendicular to the cylinder axis. E.g. y for an x-axis -cylinder, x for a y-axis cylinder, and x for a z-axis cylinder. - -:line - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values are unitless chunk IDs, ranging from 1 to -{Nchunk} (inclusive) for atoms assigned to chunks, and 0 for atoms not -belonging to a chunk. - -[Restrictions:] - -Even if the {nchunk} keyword is set to {once}, the chunk IDs assigned -to each atom are not stored in a restart files. This means you cannot -expect those assignments to persist in a restarted simulation. -Instead you must re-specify this command and assign atoms to chunks when -the restarted simulation begins. - -[Related commands:] - -"fix ave/chunk"_fix_ave_chunk.html, -"compute global/atom"_compute_global_atom.html - -[Default:] - -The option defaults are as follows: - -region = none -nchunk = every, if compress is yes, overriding other defaults listed here -nchunk = once, for type style -nchunk = once, for mol style if region is none -nchunk = every, for mol style if region is set -nchunk = once, for binning style if the simulation box size is static or units = reduced -nchunk = every, for binning style if the simulation box size is dynamic and units is lattice or box -nchunk = every, for compute/fix/variable style -limit = 0 -ids = every -compress = no -discard = yes, for all styles except binning -discard = mixed, for binning styles -bound = lower and upper in all dimensions -pbc = no -units = lattice :ul diff --git a/doc/txt/compute_cluster_atom.txt b/doc/txt/compute_cluster_atom.txt deleted file mode 100644 index e6138fe1e8..0000000000 --- a/doc/txt/compute_cluster_atom.txt +++ /dev/null @@ -1,98 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute cluster/atom command :h3 -compute fragment/atom command :h3 -compute aggregate/atom command :h3 - -[Syntax:] - -compute ID group-ID cluster/atom cutoff -compute ID group-ID fragment/atom -compute ID group-ID aggregate/atom cutoff :pre - -ID, group-ID are documented in "compute"_compute.html command -{cluster/atom} or {fragment/atom} or {aggregate/atom} = style name of this compute command -cutoff = distance within which to label atoms as part of same cluster (distance units) :ul - -[Examples:] - -compute 1 all cluster/atom 3.5 -compute 1 all fragment/atom :pre -compute 1 all aggregate/atom 3.5 :pre - -[Description:] - -Define a computation that assigns each atom a cluster, fragment, -or aggregate ID. - -A cluster is defined as a set of atoms, each of which is within the -cutoff distance from one or more other atoms in the cluster. If an -atom has no neighbors within the cutoff distance, then it is a 1-atom -cluster. - -A fragment is similarly defined as a set of atoms, each of -which has an explicit bond (i.e. defined via a "data file"_read_data.html, -the "create_bonds"_create_bonds.html command, or through fixes like -"fix bond/create"_fix_bond_create.html, "fix bond/swap"_fix_bond_swap.html, -or "fix bond/break"_fix_bond_break.html). The cluster ID or fragment ID -of every atom in the cluster will be set to the smallest atom ID of any atom -in the cluster or fragment, respectively. - -An aggregate is defined by combining the rules for clusters and -fragments, i.e. a set of atoms, where each of it is within the cutoff -distance from one or more atoms within a fragment that is part of -the same cluster. This measure can be used to track molecular assemblies -like micelles. - -Only atoms in the compute group are clustered and assigned cluster -IDs. Atoms not in the compute group are assigned a cluster ID = 0. -For fragments, only bonds where [both] atoms of the bond are included -in the compute group are assigned to fragments, so that only fragments -are detected where [all] atoms are in the compute group. Thus atoms -may be included in the compute group, yes still have a fragment ID of 0. - -For computes {cluster/atom} and {aggregate/atom} the neighbor list needed -to compute this quantity is constructed each time the calculation is -performed (i.e. each time a snapshot of atoms is dumped). Thus it can be -inefficient to compute/dump this quantity too frequently or to have -multiple compute/dump commands, each of a {cluster/atom} or -{aggregate/atom} style. - -NOTE: If you have a bonded system, then the settings of -"special_bonds"_special_bonds.html command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the "special_bonds"_special_bonds.html -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included when computing the clusters. This -does not apply when using long-range coulomb ({coul/long}, {coul/msm}, -{coul/wolf} or similar. One way to get around this would be to set -special_bond scaling factors to very tiny numbers that are not exactly -zero (e.g. 1.0e-50). Another workaround is to write a dump file, and -use the "rerun"_rerun.html command to compute the clusters for -snapshots in the dump file. The rerun script can use a -"special_bonds"_special_bonds.html command that includes all pairs in -the neighbor list. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values will be an ID > 0, as explained above. - -[Restrictions:] none - -[Related commands:] - -"compute coord/atom"_compute_coord_atom.html - -[Default:] none diff --git a/doc/txt/compute_cna_atom.txt b/doc/txt/compute_cna_atom.txt deleted file mode 100644 index 56ad7dd715..0000000000 --- a/doc/txt/compute_cna_atom.txt +++ /dev/null @@ -1,97 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute cna/atom command :h3 - -[Syntax:] - -compute ID group-ID cna/atom cutoff :pre - -ID, group-ID are documented in "compute"_compute.html command -cna/atom = style name of this compute command -cutoff = cutoff distance for nearest neighbors (distance units) :ul - -[Examples:] - -compute 1 all cna/atom 3.08 :pre - -[Description:] - -Define a computation that calculates the CNA (Common Neighbor -Analysis) pattern for each atom in the group. In solid-state systems -the CNA pattern is a useful measure of the local crystal structure -around an atom. The CNA methodology is described in "(Faken)"_#Faken -and "(Tsuzuki)"_#Tsuzuki1. - -Currently, there are five kinds of CNA patterns LAMMPS recognizes: - -fcc = 1 -hcp = 2 -bcc = 3 -icosahedral = 4 -unknown = 5 :ul - -The value of the CNA pattern will be 0 for atoms not in the specified -compute group. Note that normally a CNA calculation should only be -performed on mono-component systems. - -The CNA calculation can be sensitive to the specified cutoff value. -You should insure the appropriate nearest neighbors of an atom are -found within the cutoff distance for the presumed crystal structure. -E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest -neighbors for perfect BCC crystals. These formulas can be used to -obtain a good cutoff distance: - -:c,image(Eqs/cna_cutoff1.jpg) - -where a is the lattice constant for the crystal structure concerned -and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a -for HCP crystals. - -Also note that since the CNA calculation in LAMMPS uses the neighbors -of an owned atom to find the nearest neighbors of a ghost atom, the -following relation should also be satisfied: - -:c,image(Eqs/cna_cutoff2.jpg) - -where Rc is the cutoff distance of the potential, Rs is the skin -distance as specified by the "neighbor"_neighbor.html command, and -cutoff is the argument used with the compute cna/atom command. LAMMPS -will issue a warning if this is not the case. - -The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (e.g. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently or to have multiple compute/dump commands, each with a -{cna/atom} style. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values will be a number from 0 to 5, as explained -above. - -[Restrictions:] none - -[Related commands:] - -"compute centro/atom"_compute_centro_atom.html - -[Default:] none - -:line - -:link(Faken) -[(Faken)] Faken, Jonsson, Comput Mater Sci, 2, 279 (1994). - -:link(Tsuzuki1) -[(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007). diff --git a/doc/txt/compute_cnp_atom.txt b/doc/txt/compute_cnp_atom.txt deleted file mode 100644 index 95dd59089f..0000000000 --- a/doc/txt/compute_cnp_atom.txt +++ /dev/null @@ -1,111 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute cnp/atom command :h3 - -[Syntax:] - -compute ID group-ID cnp/atom cutoff :pre - -ID, group-ID are documented in "compute"_compute.html command -cnp/atom = style name of this compute command -cutoff = cutoff distance for nearest neighbors (distance units) :ul - -[Examples:] - -compute 1 all cnp/atom 3.08 :pre - -[Description:] - -Define a computation that calculates the Common Neighborhood -Parameter (CNP) for each atom in the group. In solid-state systems -the CNP is a useful measure of the local crystal structure -around an atom and can be used to characterize whether the -atom is part of a perfect lattice, a local defect (e.g. a dislocation -or stacking fault), or at a surface. - -The value of the CNP parameter will be 0.0 for atoms not in the -specified compute group. Note that normally a CNP calculation should -only be performed on single component systems. - -This parameter is computed using the following formula from -"(Tsuzuki)"_#Tsuzuki2 - -:c,image(Eqs/cnp_eq.jpg) - -where the index {j} goes over the {n}i nearest neighbors of atom -{i}, and the index {k} goes over the {n}ij common nearest neighbors -between atom {i} and atom {j}. Rik and Rjk are the vectors connecting atom -{k} to atoms {i} and {j}. The quantity in the double sum is computed -for each atom. - -The CNP calculation is sensitive to the specified cutoff value. -You should ensure that the appropriate nearest neighbors of an atom are -found within the cutoff distance for the presumed crystal structure. -E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest -neighbors for perfect BCC crystals. These formulas can be used to -obtain a good cutoff distance: - -:c,image(Eqs/cnp_cutoff.jpg) - -where a is the lattice constant for the crystal structure concerned -and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a -for HCP crystals. - -Also note that since the CNP calculation in LAMMPS uses the neighbors -of an owned atom to find the nearest neighbors of a ghost atom, the -following relation should also be satisfied: - -:c,image(Eqs/cnp_cutoff2.jpg) - -where Rc is the cutoff distance of the potential, Rs is the skin -distance as specified by the "neighbor"_neighbor.html command, and -cutoff is the argument used with the compute cnp/atom command. LAMMPS -will issue a warning if this is not the case. - -The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (e.g. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently or to have multiple compute/dump commands, each with a -{cnp/atom} style. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values will be real positive numbers. Some typical CNP -values: - -FCC lattice = 0.0 -BCC lattice = 0.0 -HCP lattice = 4.4 :pre - -FCC (111) surface ~ 13.0 -FCC (100) surface ~ 26.5 -FCC dislocation core ~ 11 :pre - -[Restrictions:] - -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute cna/atom"_compute_cna_atom.html -"compute centro/atom"_compute_centro_atom.html - -[Default:] none - -:line - -:link(Tsuzuki2) -[(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007). diff --git a/doc/txt/compute_com.txt b/doc/txt/compute_com.txt deleted file mode 100644 index 35cdd37c4d..0000000000 --- a/doc/txt/compute_com.txt +++ /dev/null @@ -1,56 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute com command :h3 - -[Syntax:] - -compute ID group-ID com :pre - -ID, group-ID are documented in "compute"_compute.html command -com = style name of this compute command :ul - -[Examples:] - -compute 1 all com :pre - -[Description:] - -Define a computation that calculates the center-of-mass of the group -of atoms, including all effects due to atoms passing through periodic -boundaries. - -A vector of three quantities is calculated by this compute, which -are the x,y,z coordinates of the center of mass. - -NOTE: The coordinates of an atom contribute to the center-of-mass in -"unwrapped" form, by using the image flags associated with each atom. -See the "dump custom"_dump.html command for a discussion of -"unwrapped" coordinates. See the Atoms section of the -"read_data"_read_data.html command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the "set -image"_set.html command. - -[Output info:] - -This compute calculates a global vector of length 3, which can be -accessed by indices 1-3 by any command that uses global vector values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The vector values are "intensive". The vector values will be in -distance "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute com/chunk"_compute_com_chunk.html - -[Default:] none diff --git a/doc/txt/compute_com_chunk.txt b/doc/txt/compute_com_chunk.txt deleted file mode 100644 index 9c14a554d7..0000000000 --- a/doc/txt/compute_com_chunk.txt +++ /dev/null @@ -1,85 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute com/chunk command :h3 - -[Syntax:] - -compute ID group-ID com/chunk chunkID :pre - -ID, group-ID are documented in "compute"_compute.html command -com/chunk = style name of this compute command -chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul - -[Examples:] - -compute 1 fluid com/chunk molchunk :pre - -[Description:] - -Define a computation that calculates the center-of-mass for multiple -chunks of atoms. - -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. - -This compute calculates the x,y,z coordinates of the center-of-mass -for each chunk, which includes all effects due to atoms passing through -periodic boundaries. - -Note that only atoms in the specified group contribute to the -calculation. The "compute chunk/atom"_compute_chunk_atom.html command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. - -NOTE: The coordinates of an atom contribute to the chunk's -center-of-mass in "unwrapped" form, by using the image flags -associated with each atom. See the "dump custom"_dump.html command -for a discussion of "unwrapped" coordinates. See the Atoms section of -the "read_data"_read_data.html command for a discussion of image flags -and how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the "set -image"_set.html command. - -The simplest way to output the results of the compute com/chunk -calculation to a file is to use the "fix ave/time"_fix_ave_time.html -command, for example: - -compute cc1 all chunk/atom molecule -compute myChunk all com/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre - -[Output info:] - -This compute calculates a global array where the number of rows = the -number of chunks {Nchunk} as calculated by the specified "compute -chunk/atom"_compute_chunk_atom.html command. The number of columns = -3 for the x,y,z center-of-mass coordinates of each chunk. These -values can be accessed by any command that uses global array values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The array values are "intensive". The array values will be in -distance "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute com"_compute_com.html - -[Default:] none diff --git a/doc/txt/compute_contact_atom.txt b/doc/txt/compute_contact_atom.txt deleted file mode 100644 index efe524263a..0000000000 --- a/doc/txt/compute_contact_atom.txt +++ /dev/null @@ -1,54 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute contact/atom command :h3 - -[Syntax:] - -compute ID group-ID contact/atom :pre - -ID, group-ID are documented in "compute"_compute.html command -contact/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all contact/atom :pre - -[Description:] - -Define a computation that calculates the number of contacts -for each atom in a group. - -The contact number is defined for finite-size spherical particles as -the number of neighbor atoms which overlap the central particle, -meaning that their distance of separation is less than or equal to the -sum of the radii of the two particles. - -The value of the contact number will be 0.0 for atoms not in the -specified compute group. - -[Output info:] - -This compute calculates a per-atom vector, whose values can be -accessed by any command that uses per-atom values from a compute as -input. See the "Howto output"_Howto_output.html doc page for an -overview of LAMMPS output options. - -The per-atom vector values will be a number >= 0.0, as explained -above. - -[Restrictions:] - -This compute requires that atoms store a radius as defined by the -"atom_style sphere"_atom_style.html command. - -[Related commands:] - -"compute coord/atom"_compute_coord_atom.html - -[Default:] none diff --git a/doc/txt/compute_coord_atom.txt b/doc/txt/compute_coord_atom.txt deleted file mode 100644 index e4d57a5dc5..0000000000 --- a/doc/txt/compute_coord_atom.txt +++ /dev/null @@ -1,140 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute coord/atom command :h3 - -[Syntax:] - -compute ID group-ID coord/atom cstyle args ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -coord/atom = style name of this compute command :l -cstyle = {cutoff} or {orientorder} :l - {cutoff} args = cutoff \[group group2-ID\] typeN - cutoff = distance within which to count coordination neighbors (distance units) - group {group2-ID} = select group-ID to restrict which atoms to consider for coordination number (optional) - typeN = atom type for Nth coordination count (see asterisk form below) - {orientorder} args = orientorderID threshold - orientorderID = ID of an orientorder/atom compute - threshold = minimum value of the product of two "connected" atoms :pre -:ule - -[Examples:] - -compute 1 all coord/atom cutoff 2.0 -compute 1 all coord/atom cutoff 6.0 1 2 -compute 1 all coord/atom cutoff 6.0 2*4 5*8 * -compute 1 solute coord/atom cutoff 2.0 group solvent -compute 1 all coord/atom orientorder 2 0.5 :pre - -[Description:] - -This compute performs calculations between neighboring atoms to -determine a coordination value. The specific calculation and the -meaning of the resulting value depend on the {cstyle} keyword used. - -The {cutoff} cstyle calculates one or more traditional coordination -numbers for each atom. A coordination number is defined as the number -of neighbor atoms with specified atom type(s), and optionally within -the specified group, that are within the specified cutoff distance from -the central atom. The compute group selects only the central atoms; all -neighboring atoms, unless selected by type, type range, or group option, -are included in the coordination number tally. - -The optional {group} keyword allows to specify from which group atoms -contribute to the coordination number. Default setting is group 'all'. - -The {typeN} keywords allow specification of which atom types -contribute to each coordination number. One coordination number is -computed for each of the {typeN} keywords listed. If no {typeN} -keywords are listed, a single coordination number is calculated, which -includes atoms of all types (same as the "*" format, see below). - -The {typeN} keywords can be specified in one of two ways. An explicit -numeric value can be used, as in the 2nd example above. Or a -wild-card asterisk can be used to specify a range of atom types. This -takes the form "*" or "*n" or "n*" or "m*n". If N = the number of -atom types, then an asterisk with no numeric values means all types -from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). - -The {orientorder} cstyle calculates the number of "connected" neighbor -atoms J around each central atom I. For this {cstyle}, connected is -defined by the orientational order parameter calculated by the -"compute orientorder/atom"_compute_orientorder_atom.html command. -This {cstyle} thus allows one to apply the ten Wolde's criterion to -identify crystal-like atoms in a system, as discussed in "ten -Wolde"_#tenWolde1. - -The ID of the previously specified "compute -orientorder/atom"_compute_orientorder_atom.html command is specified as -{orientorderID}. The compute must invoke its {components} option to -calculate components of the {Ybar_lm} vector for each atoms, as -described in its documentation. Note that orientorder/atom compute -defines its own criteria for identifying neighboring atoms. If the -scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the -orientorder/atom compute is larger than the specified {threshold}, -then I and J are connected, and the coordination value of I is -incremented by one. - -For all {cstyle} settings, all coordination values will be 0.0 for -atoms not in the specified compute group. - -The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently. - -NOTE: If you have a bonded system, then the settings of -"special_bonds"_special_bonds.html command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the "special_bonds"_special_bonds.html -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included in the coordination count. One way -to get around this, is to write a dump file, and use the -"rerun"_rerun.html command to compute the coordination for snapshots -in the dump file. The rerun script can use a -"special_bonds"_special_bonds.html command that includes all pairs in -the neighbor list. - -[Output info:] - -For {cstyle} cutoff, this compute can calculate a per-atom vector or -array. If single {type1} keyword is specified (or if none are -specified), this compute calculates a per-atom vector. If multiple -{typeN} keywords are specified, this compute calculates a per-atom -array, with N columns. - -For {cstyle} orientorder, this compute calculates a per-atom vector. - -These values can be accessed by any command that uses per-atom values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The per-atom vector or array values will be a number >= 0.0, as -explained above. - -[Restrictions:] none - -[Related commands:] - -"compute cluster/atom"_compute_cluster_atom.html -"compute orientorder/atom"_compute_orientorder_atom.html - -[Default:] - -group = all - -:line - -:link(tenWolde1) -[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, -J. Chem. Phys. 104, 9932 (1996). diff --git a/doc/txt/compute_damage_atom.txt b/doc/txt/compute_damage_atom.txt deleted file mode 100644 index c3e822d79f..0000000000 --- a/doc/txt/compute_damage_atom.txt +++ /dev/null @@ -1,63 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute damage/atom command :h3 - -[Syntax:] - -compute ID group-ID damage/atom :pre - -ID, group-ID are documented in "compute"_compute.html command -damage/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all damage/atom :pre - -[Description:] - -Define a computation that calculates the per-atom damage for each atom -in a group. This is a quantity relevant for "Peridynamics -models"_pair_peri.html. See "this document"_PDF/PDLammps_overview.pdf -for an overview of LAMMPS commands for Peridynamics modeling. - -The "damage" of a Peridynamics particles is based on the bond breakage -between the particle and its neighbors. If all the bonds are broken -the particle is considered to be fully damaged. - -See the "PDLAMMPS user -guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for a formal -definition of "damage" and more details about Peridynamics as it is -implemented in LAMMPS. - -This command can be used with all the Peridynamic pair styles. - -The damage value will be 0.0 for atoms not in the specified compute -group. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values are unitless numbers (damage) >= 0.0. - -[Restrictions:] - -This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute dilatation/atom"_compute_dilatation_atom.html, -"compute plasticity/atom"_compute_plasticity_atom.html - -[Default:] none diff --git a/doc/txt/compute_dihedral.txt b/doc/txt/compute_dihedral.txt deleted file mode 100644 index aa25f9dd10..0000000000 --- a/doc/txt/compute_dihedral.txt +++ /dev/null @@ -1,53 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute dihedral command :h3 - -[Syntax:] - -compute ID group-ID dihedral :pre - -ID, group-ID are documented in "compute"_compute.html command -dihedral = style name of this compute command :ul - -[Examples:] - -compute 1 all dihedral :pre - -[Description:] - -Define a computation that extracts the dihedral energy calculated by -each of the dihedral sub-styles used in the "dihedral_style -hybrid"_dihedral_hybrid.html command. These values are made -accessible for output or further processing by other commands. The -group specified for this command is ignored. - -This compute is useful when using "dihedral_style -hybrid"_dihedral_hybrid.html if you want to know the portion of the -total energy contributed by one or more of the hybrid sub-styles. - -[Output info:] - -This compute calculates a global vector of length N where N is the -number of sub_styles defined by the "dihedral_style -hybrid"_dihedral_style.html command. which can be accessed by indices -1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The vector values are "extensive" and will be in energy -"units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute pe"_compute_pe.html, "compute pair"_compute_pair.html - -[Default:] none diff --git a/doc/txt/compute_dilatation_atom.txt b/doc/txt/compute_dilatation_atom.txt deleted file mode 100644 index 292638bdf5..0000000000 --- a/doc/txt/compute_dilatation_atom.txt +++ /dev/null @@ -1,67 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute dilatation/atom command :h3 - -[Syntax:] - -compute ID group-ID dilatation/atom :pre - -ID, group-ID are documented in compute command -dilation/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all dilatation/atom :pre - -[Description:] - -Define a computation that calculates the per-atom dilatation for each -atom in a group. This is a quantity relevant for "Peridynamics -models"_pair_peri.html. See "this document"_PDF/PDLammps_overview.pdf -for an overview of LAMMPS commands for Peridynamics modeling. - -For small deformation, dilatation of is the measure of the volumetric -strain. - -The dilatation "theta" for each peridynamic particle I is calculated -as a sum over its neighbors with unbroken bonds, where the -contribution of the IJ pair is a function of the change in bond length -(versus the initial length in the reference state), the volume -fraction of the particles and an influence function. See the -"PDLAMMPS user -guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for a formal -definition of dilatation. - -This command can only be used with a subset of the Peridynamic "pair -styles"_pair_peri.html: peri/lps, peri/ves and peri/eps. - -The dilatation value will be 0.0 for atoms not in the specified -compute group. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values are unitless numbers (theta) >= 0.0. - -[Restrictions:] - -This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute damage/atom"_compute_damage_atom.html, -"compute plasticity/atom"_compute_plasticity_atom.html - -[Default:] none diff --git a/doc/txt/compute_dipole_chunk.txt b/doc/txt/compute_dipole_chunk.txt deleted file mode 100644 index 2a3d1d9b56..0000000000 --- a/doc/txt/compute_dipole_chunk.txt +++ /dev/null @@ -1,91 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute dipole/chunk command :h3 - -[Syntax:] - -compute ID group-ID dipole/chunk chunkID charge-correction :pre - -ID, group-ID are documented in "compute"_compute.html command -dipole/chunk = style name of this compute command -chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command -charge-correction = {mass} or {geometry}, use COM or geometric center for charged chunk correction (optional) :ul - -[Examples:] - -compute 1 fluid dipole/chunk molchunk -compute dw water dipole/chunk 1 geometry :pre - -[Description:] - -Define a computation that calculates the dipole vector and total dipole -for multiple chunks of atoms. - -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. - -This compute calculates the x,y,z coordinates of the dipole vector -and the total dipole moment for each chunk, which includes all effects -due to atoms passing through periodic boundaries. For chunks with a net -charge the resulting dipole is made position independent by subtracting -the position vector of the center of mass or geometric center times the -net charge from the computed dipole vector. - -Note that only atoms in the specified group contribute to the -calculation. The "compute chunk/atom"_compute_chunk_atom.html command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. - -NOTE: The coordinates of an atom contribute to the chunk's -dipole in "unwrapped" form, by using the image flags -associated with each atom. See the "dump custom"_dump.html command -for a discussion of "unwrapped" coordinates. See the Atoms section of -the "read_data"_read_data.html command for a discussion of image flags -and how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the "set -image"_set.html command. - -The simplest way to output the results of the compute com/chunk -calculation to a file is to use the "fix ave/time"_fix_ave_time.html -command, for example: - -compute cc1 all chunk/atom molecule -compute myChunk all dipole/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre - -[Output info:] - -This compute calculates a global array where the number of rows = the -number of chunks {Nchunk} as calculated by the specified "compute -chunk/atom"_compute_chunk_atom.html command. The number of columns = -4 for the x,y,z dipole vector components and the total dipole of each -chunk. These values can be accessed by any command that uses global -array values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The array values are "intensive". The array values will be in -dipole units, i.e. charge units times distance "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute com/chunk"_compute_com_chunk.html - -[Default:] none diff --git a/doc/txt/compute_dpd.txt b/doc/txt/compute_dpd.txt deleted file mode 100644 index eccffee9b8..0000000000 --- a/doc/txt/compute_dpd.txt +++ /dev/null @@ -1,71 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute dpd command :h3 - -[Syntax:] - -compute ID group-ID dpd :pre - -ID, group-ID are documented in "compute"_compute.html command -dpd = style name of this compute command :ul - -[Examples:] - -compute 1 all dpd :pre - -[Description:] - -Define a computation that accumulates the total internal conductive -energy (U_cond), the total internal mechanical energy (U_mech), the -total chemical energy (U_chem) and the {harmonic} average of the internal -temperature (dpdTheta) for the entire system of particles. See the -"compute dpd/atom"_compute_dpd_atom.html command if you want -per-particle internal energies and internal temperatures. - -The system internal properties are computed according to the following -relations: - -:c,image(Eqs/compute_dpd.jpg) - -where N is the number of particles in the system - -:line - -[Output info:] - -This compute calculates a global vector of length 5 (U_cond, U_mech, -U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The vector values will be in energy and temperature "units"_units.html. - -[Restrictions:] - -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This command also requires use of the "atom_style dpd"_atom_style.html -command. - -[Related commands:] - -"compute dpd/atom"_compute_dpd_atom.html, -"thermo_style"_thermo_style.html - -[Default:] none - -:line - -:link(Larentzos1) -[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and -W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative -Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research -Laboratory, Aberdeen Proving Ground, MD (2014). diff --git a/doc/txt/compute_dpd_atom.txt b/doc/txt/compute_dpd_atom.txt deleted file mode 100644 index 2f9b4098cf..0000000000 --- a/doc/txt/compute_dpd_atom.txt +++ /dev/null @@ -1,66 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute dpd/atom command :h3 - -[Syntax:] - -compute ID group-ID dpd/atom :pre - -ID, group-ID are documented in "compute"_compute.html command -dpd/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all dpd/atom - -[Description:] - -Define a computation that accesses the per-particle internal -conductive energy (u_cond), internal mechanical energy (u_mech), -internal chemical energy (u_chem) and -internal temperatures (dpdTheta) for each particle in a group. See -the "compute dpd"_compute_dpd.html command if you want the total -internal conductive energy, the total internal mechanical energy, the -total chemical energy and -average internal temperature of the entire system or group of dpd -particles. - -[Output info:] - -This compute calculates a per-particle array with 4 columns (u_cond, -u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any -command that uses per-particle values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle array values will be in energy (u_cond, u_mech, u_chem) -and temperature (dpdTheta) "units"_units.html. - -[Restrictions:] - -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This command also requires use of the "atom_style dpd"_atom_style.html -command. - -[Related commands:] - -"dump custom"_dump.html, "compute dpd"_compute_dpd.html - -[Default:] none - -:line - -:link(Larentzos2) -[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and -W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative -Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research -Laboratory, Aberdeen Proving Ground, MD (2014). diff --git a/doc/txt/compute_edpd_temp_atom.txt b/doc/txt/compute_edpd_temp_atom.txt deleted file mode 100644 index ac3fb5e277..0000000000 --- a/doc/txt/compute_edpd_temp_atom.txt +++ /dev/null @@ -1,62 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute edpd/temp/atom command :h3 - -[Syntax:] - -compute ID group-ID edpd/temp/atom :pre - -ID, group-ID are documented in "compute"_compute.html command -edpd/temp/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all edpd/temp/atom :pre - -[Description:] - -Define a computation that calculates the per-atom temperature -for each eDPD particle in a group. - -The temperature is a local temperature derived from the internal energy -of each eDPD particle based on the local equilibrium hypothesis. -For more details please see "(Espanol1997)"_#Espanol1997 and -"(Li2014)"_#Li2014a. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See the -"Howto output"_Howto_output.html doc page for an overview of LAMMPS -output options. - -The per-atom vector values will be in temperature "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-MESO package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_style edpd"_pair_meso.html - -[Default:] none - -:line - -:link(Espanol1997) -[(Espanol1997)] Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI: -10.1209/epl/i1997-00515-8 - -:link(Li2014a) -[(Li2014)] Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: -113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003. - diff --git a/doc/txt/compute_entropy_atom.txt b/doc/txt/compute_entropy_atom.txt deleted file mode 100644 index cd90a9b590..0000000000 --- a/doc/txt/compute_entropy_atom.txt +++ /dev/null @@ -1,130 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute entropy/atom command :h3 - -[Syntax:] - -compute ID group-ID entropy/atom sigma cutoff keyword value ... :pre - -ID, group-ID are documented in "compute"_compute.html command :l -entropy/atom = style name of this compute command :l -sigma = width of gaussians used in the g(r) smoothing :l -cutoff = cutoff for the g(r) calculation :l -one or more keyword/value pairs may be appended :l -keyword = {avg} or {local} - {avg} values = {yes} or {no} cutoff2 - {yes} = average the pair entropy over neighbors - {no} = do not average the pair entropy over neighbors - cutoff2 = cutoff for the averaging over neighbors - {local} values = {yes} or {no} = use the local density around each atom to normalize the g(r) :pre -:ule - -[Examples:] - -compute 1 all entropy/atom 0.25 5. -compute 1 all entropy/atom 0.25 5. avg yes 5. -compute 1 all entropy/atom 0.125 7.3 avg yes 5.1 local yes :pre - -[Description:] - -Define a computation that calculates the pair entropy fingerprint for -each atom in the group. The fingerprint is useful to distinguish between -ordered and disordered environments, for instance liquid and solid-like -environments, or glassy and crystalline-like environments. Some -applications could be the identification of grain boundaries, a -melt-solid interface, or a solid cluster emerging from the melt. -The advantage of this parameter over others is that no a priori -information about the solid structure is required. - -This parameter for atom i is computed using the following formula from -"(Piaggi)"_#Piaggi and "(Nettleton)"_#Nettleton , - -:c,image(Eqs/pair_entropy.jpg) - -where r is a distance, g(r) is the radial distribution function of atom -i and rho is the density of the system. The g(r) computed for each -atom i can be noisy and therefore it is smoothed using: - -:c,image(Eqs/pair_entropy2.jpg) - -where the sum in j goes through the neighbors of atom i, and sigma is a -parameter to control the smoothing. - -The input parameters are {sigma} the smoothing parameter, and the -{cutoff} for the calculation of g(r). - -If the keyword {avg} has the setting {yes}, then this compute also -averages the parameter over the neighbors of atom i according to: - -:c,image(Eqs/pair_entropy3.jpg) - -where the sum j goes over the neighbors of atom i and N is the number -of neighbors. This procedure provides a sharper distinction between -order and disorder environments. In this case the input parameter -{cutoff2} is the cutoff for the averaging over the neighbors and -must also be specified. - -If the {avg yes} option is used, the effective cutoff of the neighbor -list should be {cutoff}+{cutoff2} and therefore it might be necessary -to increase the skin of the neighbor list with: - -neighbor skin bin :pre - -See "neighbor"_neighbor.html for details. - -If the {local yes} option is used, the g(r) is normalized by the -local density around each atom, that is to say the density around each -atom is the number of neighbors within the neighbor list cutoff divided -by the corresponding volume. This option can be useful when dealing with -inhomogeneous systems such as those that have surfaces. - -Here are typical input parameters for fcc aluminum (lattice -constant 4.05 Angstroms), - -compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 :pre - -and for bcc sodium (lattice constant 4.23 Angstroms), - -compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 :pre - - -[Output info:] - -By default, this compute calculates the pair entropy value for each -atom as a per-atom vector, which can be accessed by any command that -uses per-atom values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The pair entropy values have units of the Boltzmann constant. They are -always negative, and lower values (lower entropy) correspond to more -ordered environments. - -[Restrictions:] - -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute cna/atom"_compute_cna_atom.html -"compute centro/atom"_compute_centro_atom.html - -[Default:] - -The default values for the optional keywords are avg = no and local = no. - -:line - -:link(Piaggi) -[(Piaggi)] Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017). - -:link(Nettleton) -[(Nettleton)] Nettleton and Green, J Chem Phys, 29, 6 (1958). diff --git a/doc/txt/compute_erotate_asphere.txt b/doc/txt/compute_erotate_asphere.txt deleted file mode 100644 index 5cdc099782..0000000000 --- a/doc/txt/compute_erotate_asphere.txt +++ /dev/null @@ -1,70 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute erotate/asphere command :h3 - -[Syntax:] - -compute ID group-ID erotate/asphere :pre - -ID, group-ID are documented in "compute"_compute.html command -erotate/asphere = style name of this compute command :ul - -[Examples:] - -compute 1 all erotate/asphere :pre - -[Description:] - -Define a computation that calculates the rotational kinetic energy of -a group of aspherical particles. The aspherical particles can be -ellipsoids, or line segments, or triangles. See the -"atom_style"_atom_style.html and "read_data"_read_data.html commands -for descriptions of these options. - -For all 3 types of particles, the rotational kinetic energy is -computed as 1/2 I w^2, where I is the inertia tensor for the -aspherical particle and w is its angular velocity, which is computed -from its angular momentum if needed. - -NOTE: For "2d models"_dimension.html, ellipsoidal particles are -treated as ellipsoids, not ellipses, meaning their moments of inertia -will be the same as in 3d. - -[Output info:] - -This compute calculates a global scalar (the KE). This value can be -used by any command that uses a global scalar value from a compute as -input. See the "Howto output"_Howto_output.html doc page for an -overview of LAMMPS output options. - -The scalar value calculated by this compute is "extensive". The -scalar value will be in energy "units"_units.html. - -[Restrictions:] - -This compute requires that ellipsoidal particles atoms store a shape -and quaternion orientation and angular momentum as defined by the -"atom_style ellipsoid"_atom_style.html command. - -This compute requires that line segment particles atoms store a length -and orientation and angular velocity as defined by the "atom_style -line"_atom_style.html command. - -This compute requires that triangular particles atoms store a size and -shape and quaternion orientation and angular momentum as defined by -the "atom_style tri"_atom_style.html command. - -All particles in the group must be finite-size. They cannot be point -particles. - -[Related commands:] none - -"compute erotate/sphere"_compute_erotate_sphere.html - -[Default:] none diff --git a/doc/txt/compute_erotate_rigid.txt b/doc/txt/compute_erotate_rigid.txt deleted file mode 100644 index fa433c1c97..0000000000 --- a/doc/txt/compute_erotate_rigid.txt +++ /dev/null @@ -1,61 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute erotate/rigid command :h3 - -[Syntax:] - -compute ID group-ID erotate/rigid fix-ID :pre - -ID, group-ID are documented in "compute"_compute.html command -erotate/rigid = style name of this compute command -fix-ID = ID of rigid body fix :ul - -[Examples:] - -compute 1 all erotate/rigid myRigid :pre - -[Description:] - -Define a computation that calculates the rotational kinetic energy of -a collection of rigid bodies, as defined by one of the "fix -rigid"_fix_rigid.html command variants. - -The rotational energy of each rigid body is computed as 1/2 I Wbody^2, -where I is the inertia tensor for the rigid body, and Wbody is its -angular velocity vector. Both I and Wbody are in the frame of -reference of the rigid body, i.e. I is diagonalized. - -The {fix-ID} should be the ID of one of the "fix rigid"_fix_rigid.html -commands which defines the rigid bodies. The group specified in the -compute command is ignored. The rotational energy of all the rigid -bodies defined by the fix rigid command in included in the -calculation. - -[Output info:] - -This compute calculates a global scalar (the summed rotational energy -of all the rigid bodies). This value can be used by any command that -uses a global scalar value from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "extensive". The -scalar value will be in energy "units"_units.html. - -[Restrictions:] - -This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute ke/rigid"_compute_ke_rigid.html - -[Default:] none diff --git a/doc/txt/compute_erotate_sphere.txt b/doc/txt/compute_erotate_sphere.txt deleted file mode 100644 index d0c176b50e..0000000000 --- a/doc/txt/compute_erotate_sphere.txt +++ /dev/null @@ -1,57 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute erotate/sphere command :h3 - -[Syntax:] - -compute ID group-ID erotate/sphere :pre - -ID, group-ID are documented in "compute"_compute.html command -erotate/sphere = style name of this compute command :ul - -[Examples:] - -compute 1 all erotate/sphere :pre - -[Description:] - -Define a computation that calculates the rotational kinetic energy of -a group of spherical particles. - -The rotational energy is computed as 1/2 I w^2, where I is the moment -of inertia for a sphere and w is the particle's angular velocity. - -NOTE: For "2d models"_dimension.html, particles are treated as -spheres, not disks, meaning their moment of inertia will be the same -as in 3d. - -[Output info:] - -This compute calculates a global scalar (the KE). This value can be -used by any command that uses a global scalar value from a compute as -input. See the "Howto output"_Howto_output.html doc page for an -overview of LAMMPS output options. - -The scalar value calculated by this compute is "extensive". The -scalar value will be in energy "units"_units.html. - -[Restrictions:] - -This compute requires that atoms store a radius and angular velocity -(omega) as defined by the "atom_style sphere"_atom_style.html command. - -All particles in the group must be finite-size spheres or point -particles. They cannot be aspherical. Point particles will not -contribute to the rotational energy. - -[Related commands:] - -"compute erotate/asphere"_compute_erotate_asphere.html - -[Default:] none diff --git a/doc/txt/compute_erotate_sphere_atom.txt b/doc/txt/compute_erotate_sphere_atom.txt deleted file mode 100644 index fdd609a0e6..0000000000 --- a/doc/txt/compute_erotate_sphere_atom.txt +++ /dev/null @@ -1,53 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute erotate/sphere/atom command :h3 - -[Syntax:] - -compute ID group-ID erotate/sphere/atom :pre - -ID, group-ID are documented in "compute"_compute.html command -erotate/sphere/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all erotate/sphere/atom :pre - -[Description:] - -Define a computation that calculates the rotational kinetic energy for -each particle in a group. - -The rotational energy is computed as 1/2 I w^2, where I is the moment -of inertia for a sphere and w is the particle's angular velocity. - -NOTE: For "2d models"_dimension.html, particles are treated as -spheres, not disks, meaning their moment of inertia will be the same -as in 3d. - -The value of the rotational kinetic energy will be 0.0 for atoms not -in the specified compute group or for point particles with a radius = -0.0. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values will be in energy "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"dump custom"_dump.html - -[Default:] none diff --git a/doc/txt/compute_event_displace.txt b/doc/txt/compute_event_displace.txt deleted file mode 100644 index a36cf2c9c4..0000000000 --- a/doc/txt/compute_event_displace.txt +++ /dev/null @@ -1,62 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute event/displace command :h3 - -[Syntax:] - -compute ID group-ID event/displace threshold :pre - -ID, group-ID are documented in "compute"_compute.html command -event/displace = style name of this compute command -threshold = minimum distance any particle must move to trigger an event (distance units) :ul - -[Examples:] - -compute 1 all event/displace 0.5 :pre - -[Description:] - -Define a computation that flags an "event" if any particle in the -group has moved a distance greater than the specified threshold -distance when compared to a previously stored reference state -(i.e. the previous event). This compute is typically used in -conjunction with the "prd"_prd.html and "tad"_tad.html commands, -to detect if a transition -to a new minimum energy basin has occurred. - -This value calculated by the compute is equal to 0 if no particle has -moved far enough, and equal to 1 if one or more particles have moved -further than the threshold distance. - -NOTE: If the system is undergoing significant center-of-mass motion, -due to thermal motion, an external force, or an initial net momentum, -then this compute will not be able to distinguish that motion from -local atom displacements and may generate "false positives." - -[Output info:] - -This compute calculates a global scalar (the flag). This value can be -used by any command that uses a global scalar value from a compute as -input. See the "Howto output"_Howto_output.html doc page for an -overview of LAMMPS output options. - -The scalar value calculated by this compute is "intensive". The -scalar value will be a 0 or 1 as explained above. - -[Restrictions:] - -This command can only be used if LAMMPS was built with the REPLICA -package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"prd"_prd.html, "tad"_tad.html - -[Default:] none diff --git a/doc/txt/compute_fep.txt b/doc/txt/compute_fep.txt deleted file mode 100644 index a46ab5b8d3..0000000000 --- a/doc/txt/compute_fep.txt +++ /dev/null @@ -1,278 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute fep command :h3 - -[Syntax:] - -compute ID group-ID fep temp attribute args ... keyword value ... :pre - -ID, group-ID are documented in the "compute"_compute.html command :ulb,l -fep = name of this compute command :l -temp = external temperature (as specified for constant-temperature run) :l -one or more attributes with args may be appended :l -attribute = {pair} or {atom} :l - {pair} args = pstyle pparam I J v_delta - pstyle = pair style name, e.g. lj/cut - pparam = parameter to perturb - I,J = type pair(s) to set parameter for - v_delta = variable with perturbation to apply (in the units of the parameter) - {atom} args = aparam I v_delta - aparam = parameter to perturb - I = type to set parameter for - v_delta = variable with perturbation to apply (in the units of the parameter) :pre -zero or more keyword/value pairs may be appended :l -keyword = {tail} or {volume} :l - {tail} value = {no} or {yes} - {no} = ignore tail correction to pair energies (usually small in fep) - {yes} = include tail correction to pair energies - {volume} value = {no} or {yes} - {no} = ignore volume changes (e.g. in {NVE} or {NVT} trajectories) - {yes} = include volume changes (e.g. in {NpT} trajectories) :pre -:ule - -[Examples:] - -compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes -compute 1 all fep 300 atom charge 2 v_delta :pre - - -[Description:] - -Apply a perturbation to parameters of the interaction potential and -recalculate the pair potential energy without changing the atomic -coordinates from those of the reference, unperturbed system. This -compute can be used to calculate free energy differences using several -methods, such as free-energy perturbation (FEP), finite-difference -thermodynamic integration (FDTI) or Bennet's acceptance ratio method -(BAR). - -The potential energy of the system is decomposed in three terms: a -background term corresponding to interaction sites whose parameters -remain constant, a reference term \(U_0\) corresponding to the -initial interactions of the atoms that will undergo perturbation, and -a term \(U_1\) corresponding to the final interactions of -these atoms: - -:c,image(Eqs/compute_fep_u.jpg) - -A coupling parameter \(\lambda\) varying from 0 to 1 connects the -reference and perturbed systems: - -:c,image(Eqs/compute_fep_lambda.jpg) - -It is possible but not necessary that the coupling parameter (or a -function thereof) appears as a multiplication factor of the potential -energy. Therefore, this compute can apply perturbations to interaction -parameters that are not directly proportional to the potential energy -(e.g. \(\sigma\) in Lennard-Jones potentials). - -This command can be combined with "fix adapt"_fix_adapt.html to -perform multistage free-energy perturbation calculations along -stepwise alchemical transformations during a simulation run: - -:c,image(Eqs/compute_fep_fep.jpg) - -This compute is suitable for the finite-difference thermodynamic -integration (FDTI) method "(Mezei)"_#Mezei, which is based on an -evaluation of the numerical derivative of the free energy by a -perturbation method using a very small \(\delta\): - -:c,image(Eqs/compute_fep_fdti.jpg) - -where \(w_i\) are weights of a numerical quadrature. The "fix -adapt"_fix_adapt.html command can be used to define the stages of -\(\lambda\) at which the derivative is calculated and averaged. - -The compute fep calculates the exponential Boltzmann term and also the -potential energy difference \(U_1 -U_0\). By -choosing a very small perturbation \(\delta\) the thermodynamic -integration method can be implemented using a numerical evaluation of -the derivative of the potential energy with respect to \(\lambda\): - -:c,image(Eqs/compute_fep_ti.jpg) - -Another technique to calculate free energy differences is the -acceptance ratio method "(Bennet)"_#Bennet, which can be implemented -by calculating the potential energy differences with \(\delta\) = 1.0 on -both the forward and reverse routes: - -:c,image(Eqs/compute_fep_bar.jpg) - -The value of the free energy difference is determined by numerical -root finding to establish the equality. - -Concerning the choice of how the atomic parameters are perturbed in -order to setup an alchemical transformation route, several strategies -are available, such as single-topology or double-topology strategies -"(Pearlman)"_#Pearlman. The latter does not require modification of -bond lengths, angles or other internal coordinates. - -NOTES: This compute command does not take kinetic energy into account, -therefore the masses of the particles should not be modified between -the reference and perturbed states, or along the alchemical -transformation route. This compute command does not change bond -lengths or other internal coordinates "(Boresch, -Karplus)"_#BoreschKarplus. - -:line - -The {pair} attribute enables various parameters of potentials defined -by the "pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html -commands to be changed, if the pair style supports it. - -The {pstyle} argument is the name of the pair style. For example, -{pstyle} could be specified as "lj/cut". The {pparam} argument is the -name of the parameter to change. This is a list of -pair styles and parameters that can be used with this compute. See -the doc pages for individual pair styles and their energy formulas for -the meaning of these parameters: - -"born"_pair_born.html: a,b,c: type pairs: -"buck"_pair_buck.html: a,c: type pairs: -"buck/mdf"_pair_mdf.html: a,c: type pairs: -"coul/cut"_pair_coul.html: scale: type pairs: -"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs: -"coul/long, coul/msm"_pair_coul.html: scale: type pairs: -"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs: -"eam"_pair_eam.html: scale: type pairs: -"gauss"_pair_gauss.html: a: type pairs: -"lennard/mdf"_pair_mdf.html: a,b: type pairs: -"lj/class2"_pair_class2.html: epsilon,sigma: type pairs: -"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs: -"lj/cut"_pair_lj.html: epsilon,sigma: type pairs: -"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: -"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs: -"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: -"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs: -"lj/cut/tip4p/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: -"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs: -"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs: -"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs: -"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs: -"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs: -"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs: -"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs: -"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs: -"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs: -"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:) - -Note that it is easy to add new potentials and their parameters to -this list. All it typically takes is adding an extract() method to -the pair_*.cpp file associated with the potential. - -Similar to the "pair_coeff"_pair_coeff.html command, I and J can be -specified in one of two ways. Explicit numeric values can be used for -each, as in the 1st example above. I <= J is required. LAMMPS sets -the coefficients for the symmetric J,I interaction to the same -values. A wild-card asterisk can be used in place of or in conjunction -with the I,J arguments to set the coefficients for multiple pairs of -atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = -the number of atom types, then an asterisk with no numeric values -means all types from 1 to N. A leading asterisk means all types from -1 to n (inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). Note that only type pairs with I <= J are considered; if -asterisks imply type pairs where J < I, they are ignored. - -If "pair_style hybrid or hybrid/overlay"_pair_hybrid.html is being -used, then the {pstyle} will be a sub-style name. You must specify -I,J arguments that correspond to type pair values defined (via the -"pair_coeff"_pair_coeff.html command) for that sub-style. - -The {v_name} argument for keyword {pair} is the name of an -"equal-style variable"_variable.html which will be evaluated each time -this compute is invoked. It should be specified as v_name, where name -is the variable name. - -:line - -The {atom} attribute enables atom properties to be changed. The -{aparam} argument is the name of the parameter to change. This is the -current list of atom parameters that can be used with this compute: - -charge = charge on particle :ul - -The {v_name} argument for keyword {pair} is the name of an -"equal-style variable"_variable.html which will be evaluated each time -this compute is invoked. It should be specified as v_name, where name -is the variable name. - -:line - -The {tail} keyword controls the calculation of the tail correction to -"van der Waals" pair energies beyond the cutoff, if this has been -activated via the "pair_modify"_pair_modify.html command. If the -perturbation is small, the tail contribution to the energy difference -between the reference and perturbed systems should be negligible. - -If the keyword {volume} = {yes}, then the Boltzmann term is multiplied -by the volume so that correct ensemble averaging can be performed over -trajectories during which the volume fluctuates or changes "(Allen and -Tildesley)"_#AllenTildesley: - -:c,image(Eqs/compute_fep_vol.jpg) - - -:line - -[Output info:] - -This compute calculates a global vector of length 3 which contains the -energy difference ( \(U_1-U_0\) ) as c_ID\[1\], the -Boltzmann factor \(\exp(-(U_1-U_0)/kT)\), or -\(V \exp(-(U_1-U_0)/kT)\), as c_ID\[2\] and the -volume of the simulation box \(V\) as c_ID\[3\]. \(U_1\) is the -pair potential energy obtained with the perturbed parameters and -\(U_0\) is the pair potential energy obtained with the -unperturbed parameters. The energies include kspace terms if these -are used in the simulation. - -These output results can be used by any command that uses a global -scalar or vector from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. For example, the computed values can be averaged using "fix -ave/time"_fix_ave_time.html. - -The values calculated by this compute are "extensive". - - -[Restrictions:] - -This compute is distributed as the USER-FEP package. It is only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html, -"pair_fep_soft"_pair_fep_soft.html - -[Default:] - -The option defaults are {tail} = {no}, {volume} = {no}. - -:line - -:link(Pearlman) -[(Pearlman)] Pearlman, J Chem Phys, 98, 1487 (1994) - -:link(Mezei) -[(Mezei)] Mezei, J Chem Phys, 86, 7084 (1987) - -:link(Bennet) -[(Bennet)] Bennet, J Comput Phys, 22, 245 (1976) - -:link(BoreschKarplus) -[(BoreschKarplus)] Boresch and Karplus, J Phys Chem A, 103, 103 (1999) - -:link(AllenTildesley) -[(AllenTildesley)] Allen and Tildesley, Computer Simulation of -Liquids, Oxford University Press (1987) - - diff --git a/doc/txt/compute_global_atom.txt b/doc/txt/compute_global_atom.txt deleted file mode 100644 index a26dba72b0..0000000000 --- a/doc/txt/compute_global_atom.txt +++ /dev/null @@ -1,220 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute global/atom command :h3 - -[Syntax:] - -compute ID group-ID style index input1 input2 ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -global/atom = style name of this compute command :l -index = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l - c_ID = per-atom vector calculated by a compute with ID - c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID - f_ID = per-atom vector calculated by a fix with ID - f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID - v_name = per-atom vector calculated by an atom-style variable with name :pre -one or more inputs can be listed :l -input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l - c_ID = global vector calculated by a compute with ID - c_ID\[I\] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below) - f_ID = global vector calculated by a fix with ID - f_ID\[I\] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below) - v_name = global vector calculated by a vector-style variable with name :pre -:ule - -[Examples:] - -compute 1 all global/atom c_chunk c_com\[1\\] c_com\[2\\] c_com\[3\\] -compute 1 all global/atom c_chunk c_com\[*\\] :pre - -[Description:] - -Define a calculation that assigns global values to each atom from -vectors or arrays of global values. The specified {index} parameter -is used to determine which global value is assigned to each atom. - -The {index} parameter must reference a per-atom vector or array from a -"compute"_compute.html or "fix"_fix.html or the evaluation of an -atom-style "variable"_variable.html. Each {input} value must -reference a global vector or array from a "compute"_compute.html or -"fix"_fix.html or the evaluation of an vector-style -"variable"_variable.html. Details are given below. - -The {index} value for an atom is used as a index I (from 1 to N) into -the vector associated with each of the input values. The Ith value -from the input vector becomes one output value for that atom. If the -atom is not in the specified group, or the index I < 1 or I > M, where -M is the actual length of the input vector, then an output value of -0.0 is assigned to the atom. - -An example of how this command is useful, is in the context of -"chunks" which are static or dynamic subsets of atoms. The "compute -chunk/atom"_compute_chunk_atom.html command assigns unique chunk IDs -to each atom. It's output can be used as the {index} parameter for -this command. Various other computes with "chunk" in their style -name, such as "compute com/chunk"_compute_com_chunk.html or "compute -msd/chunk"_compute_msd_chunk.html, calculate properties for each -chunk. The output of these commands are global vectors or arrays, -with one or more values per chunk, and can be used as input values for -this command. This command will then assign the global chunk value to -each atom in the chunk, producing a per-atom vector or per-atom array -as output. The per-atom values can then be output to a dump file or -used by any command that uses per-atom values from a compute as input, -as discussed on the "Howto output"_Howto_output.html doc page. - -As a concrete example, these commands will calculate the displacement -of each atom from the center-of-mass of the molecule it is in, and -dump those values to a dump file. In this case, each molecule is a -chunk. - -compute cc1 all chunk/atom molecule -compute myChunk all com/chunk cc1 -compute prop all property/atom xu yu zu -compute glob all global/atom c_cc1 c_myChunk\[*\] -variable dx atom c_prop\[1\]-c_glob\[1\] -variable dy atom c_prop\[2\]-c_glob\[2\] -variable dz atom c_prop\[3\]-c_glob\[3\] -variable dist atom sqrt(v_dx*v_dx+v_dy*v_dy+v_dz*v_dz) -dump 1 all custom 100 tmp.dump id xu yu zu c_glob\[1\] c_glob\[2\] c_glob\[3\] & - v_dx v_dy v_dz v_dist -dump_modify 1 sort id :pre - -You can add these commands to the bench/in.chain script to see how -they work. - -:line - -Note that for input values from a compute or fix, the bracketed index -I can be specified using a wildcard asterisk with the index to -effectively specify multiple values. This takes the form "*" or "*n" -or "n*" or "m*n". If N = the size of the vector (for {mode} = scalar) -or the number of columns in the array (for {mode} = vector), then an -asterisk with no numeric values means all indices from 1 to N. A -leading asterisk means all indices from 1 to n (inclusive). A -trailing asterisk means all indices from n to N (inclusive). A middle -asterisk means all indices from m to n (inclusive). - -Using a wildcard is the same as if the individual columns of the array -had been listed one by one. E.g. these 2 compute global/atom commands -are equivalent, since the "compute com/chunk"_compute_com_chunk.html -command creates a global array with 3 columns: - -compute cc1 all chunk/atom molecule -compute com all com/chunk cc1 -compute 1 all global/atom c_cc1 c_com\[1\] c_com\[2\] c_com\[3\] -compute 1 all global/atom c_cc1 c_com\[*\] :pre - -:line - -This section explains the {index} parameter. Note that it must -reference per-atom values, as contrasted with the {input} values which -must reference global values. - -Note that all of these options generate floating point values. When -they are used as an index into the specified input vectors, they -simple rounded down to convert the value to integer indices. The -final values should range from 1 to N (inclusive), since they are used -to access values from N-length vectors. - -If {index} begins with "c_", a compute ID must follow which has been -previously defined in the input script. The compute must generate -per-atom quantities. See the individual "compute"_compute.html doc -page for details. If no bracketed integer is appended, the per-atom -vector calculated by the compute is used. If a bracketed integer is -appended, the Ith column of the per-atom array calculated by the -compute is used. Users can also write code for their own compute -styles and "add them to LAMMPS"_Modify.html. See the -discussion above for how I can be specified with a wildcard asterisk -to effectively specify multiple values. - -If {index} begins with "f_", a fix ID must follow which has been -previously defined in the input script. The Fix must generate -per-atom quantities. See the individual "fix"_fix.html doc page for -details. Note that some fixes only produce their values on certain -timesteps, which must be compatible with when compute global/atom -references the values, else an error results. If no bracketed integer -is appended, the per-atom vector calculated by the fix is used. If a -bracketed integer is appended, the Ith column of the per-atom array -calculated by the fix is used. Users can also write code for their -own fix style and "add them to LAMMPS"_Modify.html. See the -discussion above for how I can be specified with a wildcard asterisk -to effectively specify multiple values. - -If {index} begins with "v_", a variable name must follow which has -been previously defined in the input script. It must be an -"atom-style variable"_variable.html. Atom-style variables can -reference thermodynamic keywords and various per-atom attributes, or -invoke other computes, fixes, or variables when they are evaluated, so -this is a very general means of generating per-atom quantities to use -as {index}. - -:line - -This section explains the kinds of {input} values that can be used. -Note that inputs reference global values, as contrasted with the -{index} parameter which must reference per-atom values. - -If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. The compute must generate a -global vector or array. See the individual "compute"_compute.html doc -page for details. If no bracketed integer is appended, the vector -calculated by the compute is used. If a bracketed integer is -appended, the Ith column of the array calculated by the compute is -used. Users can also write code for their own compute styles and "add -them to LAMMPS"_Modify.html. See the discussion above for how -I can be specified with a wildcard asterisk to effectively specify -multiple values. - -If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. The fix must generate a -global vector or array. See the individual "fix"_fix.html doc page -for details. Note that some fixes only produce their values on -certain timesteps, which must be compatible with when compute -global/atom references the values, else an error results. If no -bracketed integer is appended, the vector calculated by the fix is -used. If a bracketed integer is appended, the Ith column of the array -calculated by the fix is used. Users can also write code for their -own fix style and "add them to LAMMPS"_Modify.html. See the -discussion above for how I can be specified with a wildcard asterisk -to effectively specify multiple values. - -If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. It must be a -"vector-style variable"_variable.html. Vector-style variables can -reference thermodynamic keywords and various other attributes of -atoms, or invoke other computes, fixes, or variables when they are -evaluated, so this is a very general means of generating a vector of -global quantities which the {index} parameter will reference for -assignment of global values to atoms. - -:line - -[Output info:] - -If a single input is specified this compute produces a per-atom -vector. If multiple inputs are specified, this compute produces a -per-atom array values, where the number of columns is equal to the -number of inputs specified. These values can be used by any command -that uses per-atom vector or array values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector or array values will be in whatever units the -corresponding input values are in. - -[Restrictions:] none - -[Related commands:] - -"compute"_compute.html, "fix"_fix.html, "variable"_variable.html, -"compute chunk/atom"_compute_chunk_atom.html, "compute -reduce"_compute_reduce.html - -[Default:] none diff --git a/doc/txt/compute_group_group.txt b/doc/txt/compute_group_group.txt deleted file mode 100644 index 5dfd8cf60b..0000000000 --- a/doc/txt/compute_group_group.txt +++ /dev/null @@ -1,157 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute group/group command :h3 - -[Syntax:] - -compute ID group-ID group/group group2-ID keyword value ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -group/group = style name of this compute command :l -group2-ID = group ID of second (or same) group :l -zero or more keyword/value pairs may be appended :l -keyword = {pair} or {kspace} or {boundary} or {molecule} :l - {pair} value = {yes} or {no} - {kspace} value = {yes} or {no} - {boundary} value = {yes} or {no} - {molecule} value = {off} or {inter} or {intra} :pre -:ule - -[Examples:] - -compute 1 lower group/group upper -compute 1 lower group/group upper kspace yes -compute mine fluid group/group wall :pre - -[Description:] - -Define a computation that calculates the total energy and force -interaction between two groups of atoms: the compute group and the -specified group2. The two groups can be the same. - -If the {pair} keyword is set to {yes}, which is the default, then the -the interaction energy will include a pair component which is defined -as the pairwise energy between all pairs of atoms where one atom in -the pair is in the first group and the other is in the second group. -Likewise, the interaction force calculated by this compute will -include the force on the compute group atoms due to pairwise -interactions with atoms in the specified group2. - -NOTE: The energies computed by the {pair} keyword do not include tail -corrections, even if they are enabled via the -"pair_modify"_pair_modify.html command. - -If the {molecule} keyword is set to {inter} or {intra} than an -additional check is made based on the molecule IDs of the two atoms in -each pair before including their pairwise interaction energy and -force. For the {inter} setting, the two atoms must be in different -molecules. For the {intra} setting, the two atoms must be in the same -molecule. - -If the {kspace} keyword is set to {yes}, which is not the default, and -if a "kspace_style"_kspace_style.html is defined, then the interaction -energy will include a Kspace component which is the long-range -Coulombic energy between all the atoms in the first group and all the -atoms in the 2nd group. Likewise, the interaction force calculated by -this compute will include the force on the compute group atoms due to -long-range Coulombic interactions with atoms in the specified group2. - -Normally the long-range Coulombic energy converges only when the net -charge of the unit cell is zero. However, one can assume the net -charge of the system is neutralized by a uniform background plasma, -and a correction to the system energy can be applied to reduce -artifacts. For more information see "(Bogusz)"_#Bogusz. If the -{boundary} keyword is set to {yes}, which is the default, and {kspace} -contributions are included, then this energy correction term will be -added to the total group-group energy. This correction term does not -affect the force calculation and will be zero if one or both of the -groups are charge neutral. This energy correction term is the same as -that included in the regular Ewald and PPPM routines. - -NOTE: The {molecule} setting only affects the group/group -contributions calculated by the {pair} keyword. It does not affect -the group/group contributions calculated by the {kspace} keyword. - -This compute does not calculate any bond or angle or dihedral or -improper interactions between atoms in the two groups. - -:line - -The pairwise contributions to the group-group interactions are -calculated by looping over a neighbor list. The Kspace contribution -to the group-group interactions require essentially the same amount of -work (FFTs, Ewald summation) as computing long-range forces for the -entire system. Thus it can be costly to invoke this compute too -frequently. - -NOTE: If you have a bonded system, then the settings of -"special_bonds"_special_bonds.html command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the "special_bonds"_special_bonds.html -command, and means those pairwise interactions do not appear in the -neighbor list. Because this compute uses a neighbor list, it also -means those pairs will not be included in the group/group interaction. -This does not apply when using long-range coulomb interactions -({coul/long}, {coul/msm}, {coul/wolf} or similar. One way to get -around this would be to set special_bond scaling factors to very tiny -numbers that are not exactly zero (e.g. 1.0e-50). Another workaround -is to write a dump file, and use the "rerun"_rerun.html command to -compute the group/group interactions for snapshots in the dump file. -The rerun script can use a "special_bonds"_special_bonds.html command -that includes all pairs in the neighbor list. - -If you desire a breakdown of the interactions into a pairwise and -Kspace component, simply invoke the compute twice with the appropriate -yes/no settings for the {pair} and {kspace} keywords. This is no more -costly than using a single compute with both keywords set to {yes}. -The individual contributions can be summed in a -"variable"_variable.html if desired. - -This "document"_PDF/kspace.pdf describes how the long-range -group-group calculations are performed. - -:line - -[Output info:] - -This compute calculates a global scalar (the energy) and a global -vector of length 3 (force), which can be accessed by indices 1-3. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -Both the scalar and vector values calculated by this compute are -"extensive". The scalar value will be in energy "units"_units.html. -The vector values will be in force "units"_units.html. - -[Restrictions:] - -Not all pair styles can be evaluated in a pairwise mode as required by -this compute. For example, 3-body and other many-body potentials, -such as "Tersoff"_pair_tersoff.html and -"Stillinger-Weber"_pair_sw.html cannot be used. "EAM"_pair_eam.html -potentials will re-use previously computed embedding term contributions, -so the computed pairwise forces and energies are based on the whole -system and not valid if particles have been moved since. - -Not all "Kspace styles"_kspace_style.html support the calculation of -group/group interactions. The regular {ewald} and {pppm} styles do. - -[Related commands:] none - -[Default:] - -The option defaults are pair = yes, kspace = no, boundary = yes, -molecule = off. - -:line - -:link(Bogusz) -Bogusz et al, J Chem Phys, 108, 7070 (1998) diff --git a/doc/txt/compute_gyration.txt b/doc/txt/compute_gyration.txt deleted file mode 100644 index 054ac02007..0000000000 --- a/doc/txt/compute_gyration.txt +++ /dev/null @@ -1,73 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute gyration command :h3 - -[Syntax:] - -compute ID group-ID gyration :pre - -ID, group-ID are documented in "compute"_compute.html command -gyration = style name of this compute command :ul - -[Examples:] - -compute 1 molecule gyration :pre - -[Description:] - -Define a computation that calculates the radius of gyration Rg of the -group of atoms, including all effects due to atoms passing through -periodic boundaries. - -Rg is a measure of the size of the group of atoms, and is computed as -the square root of the Rg^2 value in this formula - -:c,image(Eqs/compute_gyration.jpg) - -where M is the total mass of the group, Rcm is the center-of-mass -position of the group, and the sum is over all atoms in the group. - -A Rg^2 tensor, stored as a 6-element vector, is also calculated by -this compute. The formula for the components of the tensor is the -same as the above formula, except that (Ri - Rcm)^2 is replaced by -(Rix - Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6 -components of the vector are ordered xx, yy, zz, xy, xz, yz. Note -that unlike the scalar Rg, each of the 6 values of the tensor is -effectively a "squared" value, since the cross-terms may be negative -and taking a sqrt() would be invalid. - -NOTE: The coordinates of an atom contribute to Rg in "unwrapped" form, -by using the image flags associated with each atom. See the "dump -custom"_dump.html command for a discussion of "unwrapped" coordinates. -See the Atoms section of the "read_data"_read_data.html command for a -discussion of image flags and how they are set for each atom. You can -reset the image flags (e.g. to 0) before invoking this compute by -using the "set image"_set.html command. - -[Output info:] - -This compute calculates a global scalar (Rg) and a global vector of -length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These -values can be used by any command that uses a global scalar value or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar and vector values calculated by this compute are -"intensive". The scalar and vector values will be in distance and -distance^2 "units"_units.html respectively. - -[Restrictions:] none - -[Related commands:] - -"compute gyration/chunk"_compute_gyration_chunk.html, -"compute gyration/shape"_compute_gyration_shape.html - -[Default:] none diff --git a/doc/txt/compute_gyration_chunk.txt b/doc/txt/compute_gyration_chunk.txt deleted file mode 100644 index 4d2c30d9c7..0000000000 --- a/doc/txt/compute_gyration_chunk.txt +++ /dev/null @@ -1,109 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute gyration/chunk command :h3 - -[Syntax:] - -compute ID group-ID gyration/chunk chunkID keyword value ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -gyration/chunk = style name of this compute command :l -chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l -zero or more keyword/value pairs may be appended :l -keyword = {tensor} :l - {tensor} value = none :pre -:ule - -[Examples:] - -compute 1 molecule gyration/chunk molchunk -compute 2 molecule gyration/chunk molchunk tensor :pre - -[Description:] - -Define a computation that calculates the radius of gyration Rg for -multiple chunks of atoms. - -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. - -This compute calculates the radius of gyration Rg for each chunk, -which includes all effects due to atoms passing through periodic -boundaries. - -Rg is a measure of the size of a chunk, and is computed by this -formula - -:c,image(Eqs/compute_gyration.jpg) - -where M is the total mass of the chunk, Rcm is the center-of-mass -position of the chunk, and the sum is over all atoms in the -chunk. - -Note that only atoms in the specified group contribute to the -calculation. The "compute chunk/atom"_compute_chunk_atom.html command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. - -If the {tensor} keyword is specified, then the scalar Rg value is not -calculated, but an Rg tensor is instead calculated for each chunk. -The formula for the components of the tensor is the same as the above -formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy - -Rcmy) for the xy component, etc. The 6 components of the tensor are -ordered xx, yy, zz, xy, xz, yz. - -NOTE: The coordinates of an atom contribute to Rg in "unwrapped" form, -by using the image flags associated with each atom. See the "dump -custom"_dump.html command for a discussion of "unwrapped" coordinates. -See the Atoms section of the "read_data"_read_data.html command for a -discussion of image flags and how they are set for each atom. You can -reset the image flags (e.g. to 0) before invoking this compute by -using the "set image"_set.html command. - -The simplest way to output the results of the compute gyration/chunk -calculation to a file is to use the "fix ave/time"_fix_ave_time.html -command, for example: - -compute cc1 all chunk/atom molecule -compute myChunk all gyration/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre - -[Output info:] - -This compute calculates a global vector if the {tensor} keyword is not -specified and a global array if it is. The length of the vector or -number of rows in the array = the number of chunks {Nchunk} as -calculated by the specified "compute -chunk/atom"_compute_chunk_atom.html command. If the {tensor} keyword -is specified, the global array has 6 columns. The vector or array can -be accessed by any command that uses global values from a compute as -input. See the "Howto output"_Howto_output.html doc page for an -overview of LAMMPS output options. - -All the vector or array values calculated by this compute are -"intensive". The vector or array values will be in distance -"units"_units.html, since they are the square root of values -represented by the formula above. - -[Restrictions:] none - -[Related commands:] none - -"compute gyration"_compute_gyration.html - -[Default:] none diff --git a/doc/txt/compute_gyration_shape.txt b/doc/txt/compute_gyration_shape.txt deleted file mode 100644 index 5d97772544..0000000000 --- a/doc/txt/compute_gyration_shape.txt +++ /dev/null @@ -1,91 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute gyration/shape command :h3 - -[Syntax:] - -compute ID group-ID gyration/shape compute-ID :pre - -ID, group-ID are documented in "compute"_compute.html command -gyration/shape = style name of this compute command -compute-ID = ID of "compute gyration"_compute_gyration.html command :ul - -[Examples:] - -compute 1 molecule gyration/shape pe :pre - -[Description:] - -Define a computation that calculates the eigenvalues of the gyration tensor of a -group of atoms and three shape parameters. The computation includes all effects -due to atoms passing through periodic boundaries. - -The three computed shape parameters are the asphericity, b, the acylindricity, c, -and the relative shape anisotropy, k: - -:c,image(Eqs/compute_shape_parameters.jpg) - -where lx <= ly <= lz are the three eigenvalues of the gyration tensor. A general description -of these parameters is provided in "(Mattice)"_#Mattice1 while an application to polymer systems -can be found in "(Theodorou)"_#Theodorou1. -The asphericity is always non-negative and zero only when the three principal -moments are equal. This zero condition is met when the distribution of particles -is spherically symmetric (hence the name asphericity) but also whenever the particle -distribution is symmetric with respect to the three coordinate axes, e.g., -when the particles are distributed uniformly on a cube, tetrahedron or other Platonic -solid. The acylindricity is always non-negative and zero only when the two principal -moments are equal. This zero condition is met when the distribution of particles is -cylindrically symmetric (hence the name, acylindricity), but also whenever the particle -distribution is symmetric with respect to the two coordinate axes, e.g., when the -particles are distributed uniformly on a regular prism. the relative shape anisotropy -is bounded between zero (if all points are spherically symmetric) and one -(if all points lie on a line). - -NOTE: The coordinates of an atom contribute to the gyration tensor in -"unwrapped" form, by using the image flags associated with each atom. -See the "dump custom"_dump.html command for a discussion of "unwrapped" -coordinates. See the Atoms section of the "read_data"_read_data.html -command for a discussion of image flags and how they are set for each -atom. You can reset the image flags (e.g. to 0) before invoking this -compute by using the "set image"_set.html command. - -[Output info:] - -This compute calculates a global vector of -length 6, which can be accessed by indices 1-6. The first three values are the -eigenvalues of the gyration tensor followed by the asphericity, the acylindricity -and the relative shape anisotropy. The computed values can be used by any command -that uses global vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The vector values calculated by this compute are -"intensive". The first five vector values will be in -distance^2 "units"_units.html while the sixth one is dimensionless. - -[Restrictions:] - -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute gyration"_compute_gyration.html - -[Default:] none - -:line - -:link(Mattice1) -[(Mattice)] Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994. - -:link(Theodorou1) -[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985). - diff --git a/doc/txt/compute_hexorder_atom.txt b/doc/txt/compute_hexorder_atom.txt deleted file mode 100644 index 3c58c3f4dd..0000000000 --- a/doc/txt/compute_hexorder_atom.txt +++ /dev/null @@ -1,115 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute hexorder/atom command :h3 - -[Syntax:] - -compute ID group-ID hexorder/atom keyword values ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -hexorder/atom = style name of this compute command :l -one or more keyword/value pairs may be appended :l -keyword = {degree} or {nnn} or {cutoff} - {cutoff} value = distance cutoff - {nnn} value = number of nearest neighbors - {degree} value = degree {n} of order parameter :pre - -:ule - -[Examples:] - -compute 1 all hexorder/atom -compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2 :pre - -[Description:] - -Define a computation that calculates {qn} the bond-orientational -order parameter for each atom in a group. The hexatic ({n} = 6) order -parameter was introduced by "Nelson and Halperin"_#Nelson as a way to detect -hexagonal symmetry in two-dimensional systems. For each atom, {qn} -is a complex number (stored as two real numbers) defined as follows: - -:c,image(Eqs/hexorder.jpg) - -where the sum is over the {nnn} nearest neighbors -of the central atom. The angle theta -is formed by the bond vector rij and the {x} axis. theta is calculated -only using the {x} and {y} components, whereas the distance from the -central atom is calculated using all three -{x}, {y}, and {z} components of the bond vector. -Neighbor atoms not in the group -are included in the order parameter of atoms in the group. - -The optional keyword {cutoff} defines the distance cutoff -used when searching for neighbors. The default value, also -the maximum allowable value, is the cutoff specified -by the pair style. - -The optional keyword {nnn} defines the number of nearest -neighbors used to calculate {qn}. The default value is 6. -If the value is NULL, then all neighbors up to the -distance cutoff are used. - -The optional keyword {degree} sets the degree {n} of the order parameter. -The default value is 6. For a perfect hexagonal lattice with -{nnn} = 6, -{q}6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3 -depends only on the orientation of the lattice relative to the {x} axis. -In an isotropic liquid, local neighborhoods may still exhibit -weak hexagonal symmetry, but because the orientational correlation -decays quickly with distance, the value of phi will be different for -different atoms, and so when {q}6 is averaged over all the atoms -in the system, |<{q}6>| << 1. - -The value of {qn} is set to zero for atoms not in the -specified compute group, as well as for atoms that have less than -{nnn} neighbors within the distance cutoff. - -The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently. - -NOTE: If you have a bonded system, then the settings of -"special_bonds"_special_bonds.html command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the "special_bonds"_special_bonds.html -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included in the order parameter. This -difficulty can be circumvented by writing a dump file, and using the -"rerun"_rerun.html command to compute the order parameter for -snapshots in the dump file. The rerun script can use a -"special_bonds"_special_bonds.html command that includes all pairs in -the neighbor list. - -[Output info:] - -This compute calculates a per-atom array with 2 columns, giving the -real and imaginary parts {qn}, a complex number restricted to the -unit disk of the complex plane i.e. Re({qn})^2 + Im({qn})^2 <= 1 . - -These values can be accessed by any command that uses per-atom values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -[Restrictions:] none - -[Related commands:] - -"compute orientorder/atom"_compute_orientorder_atom.html, "compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html - -[Default:] - -The option defaults are {cutoff} = pair style cutoff, {nnn} = 6, {degree} = 6 - -:line - -:link(Nelson) -[(Nelson)] Nelson, Halperin, Phys Rev B, 19, 2457 (1979). diff --git a/doc/txt/compute_hma.txt b/doc/txt/compute_hma.txt deleted file mode 100644 index 289138eaa8..0000000000 --- a/doc/txt/compute_hma.txt +++ /dev/null @@ -1,184 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -compute hma command :h3 - -[Syntax:] - -compute ID group-ID hma temp-ID keyword ... :pre - -ID, group-ID are documented in "compute"_compute.html command :l -hma = style name of this compute command :l -temp-ID = ID of fix that specifies the set temperature during canonical simulation :l -keyword = {anharmonic} {u} {p Pharm} {cv} :l - {anharmonic} = compute will return anharmonic property values - {u} = compute will return potential energy - {p} = compute will return pressure. the following keyword must be the difference between the harmonic pressure and lattice pressure as described below - {cv} = compute will return the heat capacity :pre -:ule - -[Examples:] - -compute 2 all hma 1 u -compute 2 all hma 1 anharmonic u p 0.9 -compute 2 all hma 1 u cv :pre - - - -[Description:] - -Define a computation that calculates the properties of a solid (potential -energy, pressure or heat capacity), using the harmonically-mapped averaging -(HMA) method. -This command yields much higher precision than the equivalent compute commands -("compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html, etc.) -commands during a canonical simulation of an atomic crystal. Specifically, -near melting HMA can yield averages of a given precision an order of magnitude -faster than conventional methods, and this only improves as the temperatures is -lowered. This is particularly important for evaluating the free energy by -thermodynamic integration, where the low-temperature contributions are the -greatest source of statistical uncertainty. Moreover, HMA has other -advantages, including smaller potential-truncation effects, finite-size -effects, smaller timestep inaccuracy, faster equilibration and shorter -decorrelation time. - -HMA should not be used if atoms are expected to diffuse. It is also -restricted to simulations in the NVT ensemble. While this compute may be -used with any potential in LAMMPS, it will provide inaccurate results -for potentials that do not go to 0 at the truncation distance; -"pair_lj_smooth_linear"_pair_lj_smooth_linear.html and Ewald summation should -work fine, while "pair_lj"_pair_lj.html will perform poorly unless -the potential is shifted (via "pair_modify"_pair_modify.html shift) or the cutoff is large. Furthermore, computation of the heat capacity with -this compute is restricted to those that implement the single_hessian method -in Pair. Implementing single_hessian in additional pair styles is simple. -Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at -buffalo.edu) if your desired pair style does not have this method. This is -the list of pair styles that currently implement pair_hessian: - -"lj_smooth_linear"_pair_lj_smooth_linear.html :l -:ule - -In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble -averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination -by noise produced by the already-known harmonic behavior. -A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa). The potential energy is computed by the formula: - -\begin\{equation\} -\left< U\right>_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B T + \left< U + \frac\{1\}\{2\} F\bullet\Delta r \right> -\end\{equation\} - -where \(N\) is the number of atoms in the system, \(k_B\) is Boltzmann's -constant, \(T\) is the temperature, \(d\) is the -dimensionality of the system (2 or 3 for 2d/3d), \(F\bullet\Delta r\) is the sum of dot products of the -atomic force vectors and displacement (from lattice sites) vectors, and \(U\) is the sum of -pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies. - -The pressure is computed by the formula: - -\begin\{equation\} -\left< P\right>_\{HMA\} = \Delta \hat P + \left< P_\{vir\} + \frac\{\beta \Delta \hat P - \rho\}\{d(N-1)\} F\bullet\Delta r \right> -\end\{equation\} - -where \(\rho\) is the number density of the system, \(\Delta \hat P\) is the -difference between the harmonic and lattice pressure, \(P_\{vir\}\) is -the virial pressure computed as the sum of pair, bond, angle, dihedral, -improper, kspace (long-range), and fix contributions to the force on each -atom, and \(k_B=1/k_B T\). Although the method will work for any value of \(\Delta \hat P\) -specified (use pressure "units"_units.html), the precision of the resultant -pressure is sensitive to \(\Delta \hat P\); the precision tends to be -best when \(\Delta \hat P\) is the actual the difference between the lattice -pressure and harmonic pressure. - -\begin\{equation\} -\left_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B + \frac\{1\}\{k_B T^2\} \left( \left< -U_\{HMA\}^2 \right> - \left^2 \right) + \frac\{1\}\{4 T\} -\left< F\bullet\Delta r + \Delta r \bullet \Phi \bullet \Delta r \right> -\end\{equation\} - -where \(\Phi\) is the Hessian matrix. The compute hma command -computes the full expression for \(C_V\) except for the -\(\left^2\) in the variance term, which can be obtained by -passing the {u} keyword; you must add this extra contribution to the \(C_V\) -value reported by this compute. The variance term can cause significant -round-off error when computing \(C_V\). To address this, the {anharmonic} -keyword can be passed and/or the output format can be specified with more -digits. - -thermo_modify format float '%22.15e' :pre - -The {anharmonic} keyword will instruct the compute to return anharmonic -properties rather than the full properties, which include lattice, harmonic -and anharmonic contributions. -When using this keyword, the compute must be first active (it must be included -via a "thermo_style custom"_thermo_style.html command) while the atoms are -still at their lattice sites (before equilibration). - -The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover ("fix nvt"_fix_nh.html) or -Berendsen ("fix temp/berendsen"_fix_temp_berendsen.html) thermostat used for the simulation. While using this command, Langevin thermostat -("fix langevin"_fix_langevin.html) -should be avoided as its extra forces interfere with the HMA implementation. - - - -NOTE: Compute hma command should be used right after the energy minimization, when the atoms are at their lattice sites. -The simulation should not be started before this command has been used in the input script. - - -The following example illustrates the placement of this command in the input script: - - -min_style cg -minimize 1e-35 1e-15 50000 500000 -compute 1 all hma thermostatid u -fix thermostatid all nvt temp 600.0 600.0 100.0 :pre - - - -NOTE: Compute hma should be used when the atoms of the solid do not diffuse. Diffusion will reduce the precision in the potential energy computation. - - -NOTE: The "fix_modify energy yes"_fix_modify.html command must also be specified if a fix is to contribute potential energy to this command. - -An example input script that uses this compute is included in -examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA -properties fluctuate less than the corresponding conventional properties. - -[Output info:] - -This compute calculates a global vector that includes the n properties -requested as arguments to the command (the potential energy, pressure and/or heat -capacity). The elements of the vector can be accessed by indices 1-n by any -command that uses global vector values as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output options. - -The vector values calculated by this compute are "extensive". The -scalar value will be in energy "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-MISC package. It is enabled only -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Usage restricted to canonical (NVT) ensemble simulation only. - -[Related commands:] - -"compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html - -"dynamical matrix"_dynamical_matrix.html provides a finite difference -formulation of the hessian provided by Pair's single_hessian, which is used by -this compute. - -[Default:] none - -:line - -:link(hma-Moustafa) -[(Moustafa)] Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, {Very fast averaging of thermal properties of crystals by molecular simulation}, -"Phys. Rev. E \[92\], 043303 (2015)"_https://link.aps.org/doi/10.1103/PhysRevE.92.043303 diff --git a/doc/txt/compute_improper.txt b/doc/txt/compute_improper.txt deleted file mode 100644 index 867dd48cc1..0000000000 --- a/doc/txt/compute_improper.txt +++ /dev/null @@ -1,53 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute improper command :h3 - -[Syntax:] - -compute ID group-ID improper :pre - -ID, group-ID are documented in "compute"_compute.html command -improper = style name of this compute command :ul - -[Examples:] - -compute 1 all improper :pre - -[Description:] - -Define a computation that extracts the improper energy calculated by -each of the improper sub-styles used in the "improper_style -hybrid"_improper_hybrid.html command. These values are made -accessible for output or further processing by other commands. The -group specified for this command is ignored. - -This compute is useful when using "improper_style -hybrid"_improper_hybrid.html if you want to know the portion of the -total energy contributed by one or more of the hybrid sub-styles. - -[Output info:] - -This compute calculates a global vector of length N where N is the -number of sub_styles defined by the "improper_style -hybrid"_improper_style.html command. which can be accessed by indices -1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The vector values are "extensive" and will be in energy -"units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute pe"_compute_pe.html, "compute pair"_compute_pair.html - -[Default:] none diff --git a/doc/txt/compute_improper_local.txt b/doc/txt/compute_improper_local.txt deleted file mode 100644 index f340d5a03f..0000000000 --- a/doc/txt/compute_improper_local.txt +++ /dev/null @@ -1,79 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute improper/local command :h3 - -[Syntax:] - -compute ID group-ID improper/local value1 value2 ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -improper/local = style name of this compute command :l -one or more values may be appended :l -value = {chi} :l - {chi} = tabulate improper angles :pre -:ule - -[Examples:] - -compute 1 all improper/local chi :pre - -[Description:] - -Define a computation that calculates properties of individual improper -interactions. The number of datums generated, aggregated across all -processors, equals the number of impropers in the system, modified by -the group parameter as explained below. - -The value {chi} is the improper angle, as defined in the doc pages for -the individual improper styles listed on -"improper_style"_improper_style.html doc page. - -The local data stored by this command is generated by looping over all -the atoms owned on a processor and their impropers. An improper will -only be included if all 4 atoms in the improper are in the specified -compute group. - -Note that as atoms migrate from processor to processor, there will be -no consistent ordering of the entries within the local vector or array -from one timestep to the next. The only consistency that is -guaranteed is that the ordering on a particular timestep will be the -same for local vectors or arrays generated by other compute commands. -For example, improper output from the "compute -property/local"_compute_property_local.html command can be combined -with data from this command and output by the "dump local"_dump.html -command in a consistent way. - -Here is an example of how to do this: - -compute 1 all property/local itype iatom1 iatom2 iatom3 iatom4 -compute 2 all improper/local chi -dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\] c_2\[1\] :pre - -[Output info:] - -This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of impropers. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a -local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The output for {chi} will be in degrees. - -[Restrictions:] none - -[Related commands:] - -"dump local"_dump.html, "compute -property/local"_compute_property_local.html - -[Default:] none diff --git a/doc/txt/compute_inertia_chunk.txt b/doc/txt/compute_inertia_chunk.txt deleted file mode 100644 index 6ded3312c5..0000000000 --- a/doc/txt/compute_inertia_chunk.txt +++ /dev/null @@ -1,87 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute inertia/chunk command :h3 - -[Syntax:] - -compute ID group-ID inertia/chunk chunkID :pre - -ID, group-ID are documented in "compute"_compute.html command -inertia/chunk = style name of this compute command -chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul - -[Examples:] - -compute 1 fluid inertia/chunk molchunk :pre - -[Description:] - -Define a computation that calculates the inertia tensor for multiple -chunks of atoms. - -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. - -This compute calculates the 6 components of the symmetric inertia -tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The -calculation includes all effects due to atoms passing through periodic -boundaries. - -Note that only atoms in the specified group contribute to the -calculation. The "compute chunk/atom"_compute_chunk_atom.html command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. - -NOTE: The coordinates of an atom contribute to the chunk's inertia -tensor in "unwrapped" form, by using the image flags associated with -each atom. See the "dump custom"_dump.html command for a discussion -of "unwrapped" coordinates. See the Atoms section of the -"read_data"_read_data.html command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the "set -image"_set.html command. - -The simplest way to output the results of the compute inertia/chunk -calculation to a file is to use the "fix ave/time"_fix_ave_time.html -command, for example: - -compute cc1 all chunk/atom molecule -compute myChunk all inertia/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre - -[Output info:] - -This compute calculates a global array where the number of rows = the -number of chunks {Nchunk} as calculated by the specified "compute -chunk/atom"_compute_chunk_atom.html command. The number of columns = -6 for the 6 components of the inertia tensor for each chunk, ordered -as listed above. These values can be accessed by any command that -uses global array values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The array values are "intensive". The array values will be in -mass*distance^2 "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"variable inertia() function"_variable.html - -[Default:] none diff --git a/doc/txt/compute_ke.txt b/doc/txt/compute_ke.txt deleted file mode 100644 index 64ab83db48..0000000000 --- a/doc/txt/compute_ke.txt +++ /dev/null @@ -1,59 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute ke command :h3 - -[Syntax:] - -compute ID group-ID ke :pre - -ID, group-ID are documented in "compute"_compute.html command -ke = style name of this compute command :ul - -[Examples:] - -compute 1 all ke :pre - -[Description:] - -Define a computation that calculates the translational kinetic energy -of a group of particles. - -The kinetic energy of each particle is computed as 1/2 m v^2, where m -and v are the mass and velocity of the particle. - -There is a subtle difference between the quantity calculated by this -compute and the kinetic energy calculated by the {ke} or {etotal} -keyword used in thermodynamic output, as specified by the -"thermo_style"_thermo_style.html command. For this compute, kinetic -energy is "translational" kinetic energy, calculated by the simple -formula above. For thermodynamic output, the {ke} keyword infers -kinetic energy from the temperature of the system with 1/2 Kb T of -energy for each degree of freedom. For the default temperature -computation via the "compute temp"_compute_temp.html command, these -are the same. But different computes that calculate temperature can -subtract out different non-thermal components of velocity and/or -include different degrees of freedom (translational, rotational, etc). - -[Output info:] - -This compute calculates a global scalar (the summed KE). This value -can be used by any command that uses a global scalar value from a -compute as input. See the "Howto output"_Howto_output.html doc page -for an overview of LAMMPS output options. - -The scalar value calculated by this compute is "extensive". The -scalar value will be in energy "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute erotate/sphere"_compute_erotate_sphere.html - -[Default:] none diff --git a/doc/txt/compute_ke_atom.txt b/doc/txt/compute_ke_atom.txt deleted file mode 100644 index d288ab0236..0000000000 --- a/doc/txt/compute_ke_atom.txt +++ /dev/null @@ -1,48 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute ke/atom command :h3 - -[Syntax:] - -compute ID group-ID ke/atom :pre - -ID, group-ID are documented in "compute"_compute.html command -ke/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all ke/atom :pre - -[Description:] - -Define a computation that calculates the per-atom translational -kinetic energy for each atom in a group. - -The kinetic energy is simply 1/2 m v^2, where m is the mass and v is -the velocity of each atom. - -The value of the kinetic energy will be 0.0 for atoms not in the -specified compute group. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values will be in energy "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"dump custom"_dump.html - -[Default:] none diff --git a/doc/txt/compute_ke_atom_eff.txt b/doc/txt/compute_ke_atom_eff.txt deleted file mode 100644 index 29905f81d6..0000000000 --- a/doc/txt/compute_ke_atom_eff.txt +++ /dev/null @@ -1,76 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute ke/atom/eff command :h3 - -[Syntax:] - -compute ID group-ID ke/atom/eff :pre - -ID, group-ID are documented in "compute"_compute.html command -ke/atom/eff = style name of this compute command :ul - -[Examples:] - -compute 1 all ke/atom/eff :pre - -[Description:] - -Define a computation that calculates the per-atom translational -(nuclei and electrons) and radial kinetic energy (electron only) in a -group. The particles are assumed to be nuclei and electrons modeled -with the "electronic force field"_pair_eff.html. - -The kinetic energy for each nucleus is computed as 1/2 m v^2, where m -corresponds to the corresponding nuclear mass, and the kinetic energy -for each electron is computed as 1/2 (me v^2 + 3/4 me s^2), where me -and v correspond to the mass and translational velocity of each -electron, and s to its radial velocity, respectively. - -There is a subtle difference between the quantity calculated by this -compute and the kinetic energy calculated by the {ke} or {etotal} -keyword used in thermodynamic output, as specified by the -"thermo_style"_thermo_style.html command. For this compute, kinetic -energy is "translational" plus electronic "radial" kinetic energy, -calculated by the simple formula above. For thermodynamic output, the -{ke} keyword infers kinetic energy from the temperature of the system -with 1/2 Kb T of energy for each (nuclear-only) degree of freedom in -eFF. - -NOTE: The temperature in eFF should be monitored via the "compute -temp/eff"_compute_temp_eff.html command, which can be printed with -thermodynamic output by using the "thermo_modify"_thermo_modify.html -command, as shown in the following example: - -compute effTemp all temp/eff -thermo_style custom step etotal pe ke temp press -thermo_modify temp effTemp :pre - -The value of the kinetic energy will be 0.0 for atoms (nuclei or -electrons) not in the specified compute group. - -[Output info:] - -This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom computes as input. See the -"Howto output"_Howto_output.html doc page for an overview of LAMMPS -output options. - -The per-atom vector values will be in energy "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"dump custom"_dump.html - -[Default:] none diff --git a/doc/txt/compute_ke_eff.txt b/doc/txt/compute_ke_eff.txt deleted file mode 100644 index fa2c51a032..0000000000 --- a/doc/txt/compute_ke_eff.txt +++ /dev/null @@ -1,78 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute ke/eff command :h3 - -[Syntax:] - -compute ID group-ID ke/eff :pre - -ID, group-ID are documented in "compute"_compute.html command -ke/eff = style name of this compute command :ul - -[Examples:] - -compute 1 all ke/eff :pre - -[Description:] - -Define a computation that calculates the kinetic energy of motion of a -group of eFF particles (nuclei and electrons), as modeled with the -"electronic force field"_pair_eff.html. - -The kinetic energy for each nucleus is computed as 1/2 m v^2 and the -kinetic energy for each electron is computed as 1/2(me v^2 + 3/4 me -s^2), where m corresponds to the nuclear mass, me to the electron -mass, v to the translational velocity of each particle, and s to the -radial velocity of the electron, respectively. - -There is a subtle difference between the quantity calculated by this -compute and the kinetic energy calculated by the {ke} or {etotal} -keyword used in thermodynamic output, as specified by the -"thermo_style"_thermo_style.html command. For this compute, kinetic -energy is "translational" and "radial" (only for electrons) kinetic -energy, calculated by the simple formula above. For thermodynamic -output, the {ke} keyword infers kinetic energy from the temperature of -the system with 1/2 Kb T of energy for each degree of freedom. For -the eFF temperature computation via the "compute -temp_eff"_compute_temp_eff.html command, these are the same. But -different computes that calculate temperature can subtract out -different non-thermal components of velocity and/or include other -degrees of freedom. - -IMPRORTANT NOTE: The temperature in eFF models should be monitored via -the "compute temp/eff"_compute_temp_eff.html command, which can be -printed with thermodynamic output by using the -"thermo_modify"_thermo_modify.html command, as shown in the following -example: - -compute effTemp all temp/eff -thermo_style custom step etotal pe ke temp press -thermo_modify temp effTemp :pre - -See "compute temp/eff"_compute_temp_eff.html. - -[Output info:] - -This compute calculates a global scalar (the KE). This value can be -used by any command that uses a global scalar value from a compute as -input. See the "Howto output"_Howto_output.html doc page for an -overview of LAMMPS output options. - -The scalar value calculated by this compute is "extensive". The -scalar value will be in energy "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/compute_ke_rigid.txt b/doc/txt/compute_ke_rigid.txt deleted file mode 100644 index ad6baf567f..0000000000 --- a/doc/txt/compute_ke_rigid.txt +++ /dev/null @@ -1,60 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute ke/rigid command :h3 - -[Syntax:] - -compute ID group-ID ke/rigid fix-ID :pre - -ID, group-ID are documented in "compute"_compute.html command -ke = style name of this compute command -fix-ID = ID of rigid body fix :ul - -[Examples:] - -compute 1 all ke/rigid myRigid :pre - -[Description:] - -Define a computation that calculates the translational kinetic energy -of a collection of rigid bodies, as defined by one of the "fix -rigid"_fix_rigid.html command variants. - -The kinetic energy of each rigid body is computed as 1/2 M Vcm^2, -where M is the total mass of the rigid body, and Vcm is its -center-of-mass velocity. - -The {fix-ID} should be the ID of one of the "fix rigid"_fix_rigid.html -commands which defines the rigid bodies. The group specified in the -compute command is ignored. The kinetic energy of all the rigid -bodies defined by the fix rigid command in included in the -calculation. - -[Output info:] - -This compute calculates a global scalar (the summed KE of all the -rigid bodies). This value can be used by any command that uses a -global scalar value from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "extensive". The -scalar value will be in energy "units"_units.html. - -[Restrictions:] - -This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute erotate/rigid"_compute_erotate_rigid.html - -[Default:] none diff --git a/doc/txt/compute_meso_e_atom.txt b/doc/txt/compute_meso_e_atom.txt deleted file mode 100644 index 0f0cfda2d1..0000000000 --- a/doc/txt/compute_meso_e_atom.txt +++ /dev/null @@ -1,56 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute meso/e/atom command :h3 - -[Syntax:] - -compute ID group-ID meso/e/atom :pre - -ID, group-ID are documented in "compute"_compute.html command -meso/e/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all meso/e/atom :pre - -[Description:] - -Define a computation that calculates the per-atom internal energy -for each atom in a group. - -The internal energy is the energy associated with the internal degrees -of freedom of a mesoscopic particles, e.g. a Smooth-Particle -Hydrodynamics particle. - -See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in -LAMMPS. - -The value of the internal energy will be 0.0 for atoms not in the -specified compute group. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values will be in energy "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"dump custom"_dump.html - -[Default:] none diff --git a/doc/txt/compute_meso_rho_atom.txt b/doc/txt/compute_meso_rho_atom.txt deleted file mode 100644 index 5127ad2c48..0000000000 --- a/doc/txt/compute_meso_rho_atom.txt +++ /dev/null @@ -1,56 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute meso/rho/atom command :h3 - -[Syntax:] - -compute ID group-ID meso/rho/atom :pre - -ID, group-ID are documented in "compute"_compute.html command -meso/rho/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all meso/rho/atom :pre - -[Description:] - -Define a computation that calculates the per-atom mesoscopic density -for each atom in a group. - -The mesoscopic density is the mass density of a mesoscopic particle, -calculated by kernel function interpolation using "pair style -sph/rhosum". - -See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in -LAMMPS. - -The value of the mesoscopic density will be 0.0 for atoms not in the -specified compute group. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values will be in mass/volume "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"dump custom"_dump.html - -[Default:] none diff --git a/doc/txt/compute_meso_t_atom.txt b/doc/txt/compute_meso_t_atom.txt deleted file mode 100644 index f4ab869ec2..0000000000 --- a/doc/txt/compute_meso_t_atom.txt +++ /dev/null @@ -1,58 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute meso/t/atom command :h3 - -[Syntax:] - -compute ID group-ID meso/t/atom :pre - -ID, group-ID are documented in "compute"_compute.html command -meso/t/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all meso/t/atom :pre - -[Description:] - -Define a computation that calculates the per-atom internal temperature -for each atom in a group. - -The internal temperature is the ratio of internal energy over the heat -capacity associated with the internal degrees of freedom of a mesoscopic -particles, e.g. a Smooth-Particle Hydrodynamics particle. - -T_{int} = E_{int} / C_{V, int} - -See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in -LAMMPS. - -The value of the internal energy will be 0.0 for atoms not in the -specified compute group. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values will be in temperature "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"dump custom"_dump.html - -[Default:] none diff --git a/doc/txt/compute_modify.txt b/doc/txt/compute_modify.txt deleted file mode 100644 index 5ba2100fba..0000000000 --- a/doc/txt/compute_modify.txt +++ /dev/null @@ -1,73 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute_modify command :h3 - -[Syntax:] - -compute_modify compute-ID keyword value ... :pre - -compute-ID = ID of the compute to modify :ulb,l -one or more keyword/value pairs may be listed :l -keyword = {extra/dof} or {extra} or {dynamic/dof} or {dynamic} :l - {extra/dof} value = N - N = # of extra degrees of freedom to subtract - {extra} syntax is identical to {extra/dof}, will be disabled at some point - {dynamic/dof} value = {yes} or {no} - yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature - {dynamic} syntax is identical to {dynamic/dof}, will be disabled at some point :pre -:ule - -[Examples:] - -compute_modify myTemp extra/dof 0 -compute_modify newtemp dynamic/dof yes extra/dof 600 :pre - -[Description:] - -Modify one or more parameters of a previously defined compute. Not -all compute styles support all parameters. - -The {extra/dof} or {extra} keyword refers to how many -degrees-of-freedom are subtracted (typically from 3N) as a normalizing -factor in a temperature computation. Only computes that compute a -temperature use this option. The default is 2 or 3 for "2d or 3d -systems"_dimension.html which is a correction factor for an ensemble -of velocities with zero total linear momentum. For compute -temp/partial, if one or more velocity components are excluded, the -value used for {extra} is scaled accordingly. You can use a negative -number for the {extra} parameter if you need to add -degrees-of-freedom. See the "compute -temp/asphere"_compute_temp_asphere.html command for an example. - -The {dynamic/dof} or {dynamic} keyword determines whether the number -of atoms N in the compute group and their associated degrees of -freedom are re-computed each time a temperature is computed. Only -compute styles that calculate a temperature use this option. By -default, N and their DOF are assumed to be constant. If you are -adding atoms or molecules to the system (see the "fix -pour"_fix_pour.html, "fix deposit"_fix_deposit.html, and "fix -gcmc"_fix_gcmc.html commands) or expect atoms or molecules to be lost -(e.g. due to exiting the simulation box or via "fix -evaporate"_fix_evaporate.html), then this option should be used to -insure the temperature is correctly normalized. - -NOTE: The {extra} and {dynamic} keywords should not be used as they -are deprecated (March 2017) and will eventually be disabled. Instead, -use the equivalent {extra/dof} and {dynamic/dof} keywords. - -[Restrictions:] none - -[Related commands:] - -"compute"_compute.html - -[Default:] - -The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and -dynamic/dof = no. diff --git a/doc/txt/compute_momentum.txt b/doc/txt/compute_momentum.txt deleted file mode 100644 index 2c6ec78cf3..0000000000 --- a/doc/txt/compute_momentum.txt +++ /dev/null @@ -1,49 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute momentum command :h3 - -[Syntax:] - -compute ID group-ID momentum :pre - -ID, group-ID are documented in "compute"_compute.html command -momentum = style name of this compute command :ul - -[Examples:] - -compute 1 all momentum :pre - -[Description:] - -Define a computation that calculates the translational momentum -of a group of particles. - -The momentum of each particles is computed as m v, where m and v are -the mass and velocity of the particle. - -[Output info:] - -This compute calculates a global vector (the summed momentum) of -length 3. This value can be used by any command that uses a global -vector value from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The vector value calculated by this compute is "extensive". The vector -value will be in mass*velocity "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -[Default:] none diff --git a/doc/txt/compute_msd.txt b/doc/txt/compute_msd.txt deleted file mode 100644 index dbbe0d637d..0000000000 --- a/doc/txt/compute_msd.txt +++ /dev/null @@ -1,113 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute msd command :h3 - -[Syntax:] - -compute ID group-ID msd keyword values ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -msd = style name of this compute command :l -zero or more keyword/value pairs may be appended :l -keyword = {com} or {average} :l - {com} value = {yes} or {no} - {average} value = {yes} or {no} :pre -:ule - -[Examples:] - -compute 1 all msd -compute 1 upper msd com yes average yes :pre - -[Description:] - -Define a computation that calculates the mean-squared displacement -(MSD) of the group of atoms, including all effects due to atoms -passing through periodic boundaries. For computation of the non-Gaussian -parameter of mean-squared displacement, see the "compute -msd/nongauss"_compute_msd_nongauss.html command. - -A vector of four quantities is calculated by this compute. The first 3 -elements of the vector are the squared dx,dy,dz displacements, summed -and averaged over atoms in the group. The 4th element is the total -squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and -averaged over atoms in the group. - -The slope of the mean-squared displacement (MSD) versus time is -proportional to the diffusion coefficient of the diffusing atoms. - -The displacement of an atom is from its reference position. This is -normally the original position at the time -the compute command was issued, unless the {average} keyword is set to {yes}. -The value of the displacement will be -0.0 for atoms not in the specified compute group. - -If the {com} option is set to {yes} then the effect of any drift in -the center-of-mass of the group of atoms is subtracted out before the -displacement of each atom is calculated. - -If the {average} option is set to {yes} then the reference position of -an atom is based on the average position of that atom, corrected for -center-of-mass motion if requested. The average position is a running -average over all previous calls to the compute, including the current -call. So on the first call it is current position, on the second call -it is the arithmetic average of the current position and the position -on the first call, and so on. Note that when using this option, the -precise value of the mean square displacement will depend on the -number of times the compute is called. So, for example, changing the -frequency of thermo output may change the computed displacement. Also, -the precise values will be changed if a single simulation is broken up -into two parts, using either multiple run commands or a restart -file. It only makes sense to use this option if the atoms are not -diffusing, so that their average positions relative to the center of -mass of the system are stationary. The most common case is crystalline -solids undergoing thermal motion. - -NOTE: Initial coordinates are stored in "unwrapped" form, by using the -image flags associated with each atom. See the "dump -custom"_dump.html command for a discussion of "unwrapped" coordinates. -See the Atoms section of the "read_data"_read_data.html command for a -discussion of image flags and how they are set for each atom. You can -reset the image flags (e.g. to 0) before invoking this compute by -using the "set image"_set.html command. - -NOTE: If you want the quantities calculated by this compute to be -continuous when running from a "restart file"_read_restart.html, then -you should use the same ID for this compute, as in the original run. -This is so that the fix this compute creates to store per-atom -quantities will also have the same ID, and thus be initialized -correctly with atom reference positions from the restart file. When -{average} is set to yes, then the atom reference positions are -restored correctly, but not the number of samples used obtain them. As -a result, the reference positions from the restart file are combined -with subsequent positions as if they were from a single sample, -instead of many, which will change the values of msd somewhat. - -[Output info:] - -This compute calculates a global vector of length 4, which can be -accessed by indices 1-4 by any command that uses global vector values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The vector values are "intensive". The vector values will be in -distance^2 "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute msd/nongauss"_compute_msd_nongauss.html, "compute -displace_atom"_compute_displace_atom.html, "fix -store/state"_fix_store_state.html, "compute -msd/chunk"_compute_msd_chunk.html - -[Default:] - -The option default are com = no, average = no. diff --git a/doc/txt/compute_msd_chunk.txt b/doc/txt/compute_msd_chunk.txt deleted file mode 100644 index 12f54408d1..0000000000 --- a/doc/txt/compute_msd_chunk.txt +++ /dev/null @@ -1,120 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute msd/chunk command :h3 - -[Syntax:] - -compute ID group-ID msd/chunk chunkID :pre - -ID, group-ID are documented in "compute"_compute.html command -msd/chunk = style name of this compute command -chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul - -[Examples:] - -compute 1 all msd/chunk molchunk :pre - -[Description:] - -Define a computation that calculates the mean-squared displacement -(MSD) for multiple chunks of atoms. - -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. - -Four quantities are calculated by this compute for each chunk. The -first 3 quantities are the squared dx,dy,dz displacements of the -center-of-mass. The 4th component is the total squared displacement, -i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These -calculations include all effects due to atoms passing through periodic -boundaries. - -Note that only atoms in the specified group contribute to the -calculation. The "compute chunk/atom"_compute_chunk_atom.html command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. - -The slope of the mean-squared displacement (MSD) versus time is -proportional to the diffusion coefficient of the diffusing chunks. - -The displacement of the center-of-mass of the chunk is from its -original center-of-mass position, calculated on the timestep this -compute command was first invoked. - -NOTE: The number of chunks {Nchunk} calculated by the "compute -chunk/atom"_compute_chunk_atom.html command must remain constant each -time this compute is invoked, so that the displacement for each chunk -from its original position can be computed consistently. If {Nchunk} -does not remain constant, an error will be generated. If needed, you -can enforce a constant {Nchunk} by using the {nchunk once} or {ids -once} options when specifying the "compute -chunk/atom"_compute_chunk_atom.html command. - -NOTE: This compute stores the original position (of the -center-of-mass) of each chunk. When a displacement is calculated on a -later timestep, it is assumed that the same atoms are assigned to the -same chunk ID. However LAMMPS has no simple way to insure this is the -case, though you can use the {ids once} option when specifying the -"compute chunk/atom"_compute_chunk_atom.html command. Note that if -this is not the case, the MSD calculation does not have a sensible -meaning. - -NOTE: The initial coordinates of the atoms in each chunk are stored in -"unwrapped" form, by using the image flags associated with each atom. -See the "dump custom"_dump.html command for a discussion of -"unwrapped" coordinates. See the Atoms section of the -"read_data"_read_data.html command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the "set -image"_set.html command. - -NOTE: If you want the quantities calculated by this compute to be -continuous when running from a "restart file"_read_restart.html, then -you should use the same ID for this compute, as in the original run. -This is so that the fix this compute creates to store per-chunk -quantities will also have the same ID, and thus be initialized -correctly with chunk reference positions from the restart file. - -The simplest way to output the results of the compute msd/chunk -calculation to a file is to use the "fix ave/time"_fix_ave_time.html -command, for example: - -compute cc1 all chunk/atom molecule -compute myChunk all msd/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre - -[Output info:] - -This compute calculates a global array where the number of rows = the -number of chunks {Nchunk} as calculated by the specified "compute -chunk/atom"_compute_chunk_atom.html command. The number of columns = -4 for dx,dy,dz and the total displacement. These values can be -accessed by any command that uses global array values from a compute -as input. See the "Howto output"_Howto_output.html doc page for an -overview of LAMMPS output options. - -The array values are "intensive". The array values will be in -distance^2 "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute msd"_compute_msd.html - -[Default:] none diff --git a/doc/txt/compute_msd_nongauss.txt b/doc/txt/compute_msd_nongauss.txt deleted file mode 100644 index b745cf5a5b..0000000000 --- a/doc/txt/compute_msd_nongauss.txt +++ /dev/null @@ -1,79 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute msd/nongauss command :h3 - -[Syntax:] - -compute ID group-ID msd/nongauss keyword values ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -msd/nongauss = style name of this compute command :l -zero or more keyword/value pairs may be appended :l -keyword = {com} :l - {com} value = {yes} or {no} :pre -:ule - -[Examples:] - -compute 1 all msd/nongauss -compute 1 upper msd/nongauss com yes :pre - -[Description:] - -Define a computation that calculates the mean-squared displacement -(MSD) and non-Gaussian parameter (NGP) of the group of atoms, -including all effects due to atoms passing through periodic boundaries. - -A vector of three quantities is calculated by this compute. The first -element of the vector is the total squared dx,dy,dz displacements -drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the -fourth power of these displacements drfourth = (dx*dx + dy*dy + -dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the -group. The 3rd component is the nonGaussian diffusion parameter NGP = -3*drfourth/(5*drsquared*drsquared), i.e. - -:c,image(Eqs/compute_msd_nongauss.jpg) - -The NGP is a commonly used quantity in studies of dynamical -heterogeneity. Its minimum theoretical value (-0.4) occurs when all -atoms have the same displacement magnitude. NGP=0 for Brownian -diffusion, while NGP > 0 when some mobile atoms move faster than -others. - -If the {com} option is set to {yes} then the effect of any drift in -the center-of-mass of the group of atoms is subtracted out before the -displacement of each atom is calculated. - -See the "compute msd"_compute_msd.html doc page for further important -NOTEs, which also apply to this compute. - -[Output info:] - -This compute calculates a global vector of length 3, which can be -accessed by indices 1-3 by any command that uses global vector values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The vector values are "intensive". The first vector value will be in -distance^2 "units"_units.html, the second is in distance^4 units, and -the 3rd is dimensionless. - -[Restrictions:] - -This compute is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute msd"_compute_msd.html - -[Default:] - -The option default is com = no. diff --git a/doc/txt/compute_omega_chunk.txt b/doc/txt/compute_omega_chunk.txt deleted file mode 100644 index 393440759c..0000000000 --- a/doc/txt/compute_omega_chunk.txt +++ /dev/null @@ -1,88 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute omega/chunk command :h3 - -[Syntax:] - -compute ID group-ID omega/chunk chunkID :pre - -ID, group-ID are documented in "compute"_compute.html command -omega/chunk = style name of this compute command -chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul - -[Examples:] - -compute 1 fluid omega/chunk molchunk :pre - -[Description:] - -Define a computation that calculates the angular velocity (omega) of -multiple chunks of atoms. - -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. - -This compute calculates the 3 components of the angular velocity -vector for each chunk, via the formula L = Iw where L is the angular -momentum vector of the chunk, I is its moment of inertia tensor, and w -is omega = angular velocity of the chunk. The calculation includes -all effects due to atoms passing through periodic boundaries. - -Note that only atoms in the specified group contribute to the -calculation. The "compute chunk/atom"_compute_chunk_atom.html command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. - -NOTE: The coordinates of an atom contribute to the chunk's angular -velocity in "unwrapped" form, by using the image flags associated with -each atom. See the "dump custom"_dump.html command for a discussion -of "unwrapped" coordinates. See the Atoms section of the -"read_data"_read_data.html command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the "set -image"_set.html command. - -The simplest way to output the results of the compute omega/chunk -calculation to a file is to use the "fix ave/time"_fix_ave_time.html -command, for example: - -compute cc1 all chunk/atom molecule -compute myChunk all omega/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre - -[Output info:] - -This compute calculates a global array where the number of rows = the -number of chunks {Nchunk} as calculated by the specified "compute -chunk/atom"_compute_chunk_atom.html command. The number of columns = -3 for the 3 xyz components of the angular velocity for each chunk. -These values can be accessed by any command that uses global array -values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The array values are "intensive". The array values will be in -velocity/distance "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"variable omega() function"_variable.html - -[Default:] none diff --git a/doc/txt/compute_orientorder_atom.txt b/doc/txt/compute_orientorder_atom.txt deleted file mode 100644 index d59033f179..0000000000 --- a/doc/txt/compute_orientorder_atom.txt +++ /dev/null @@ -1,170 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute orientorder/atom command :h3 - -[Syntax:] - -compute ID group-ID orientorder/atom keyword values ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -orientorder/atom = style name of this compute command :l -one or more keyword/value pairs may be appended :l -keyword = {cutoff} or {nnn} or {degrees} or {components} - {cutoff} value = distance cutoff - {nnn} value = number of nearest neighbors - {degrees} values = nlvalues, l1, l2,... - {wl} value = yes or no - {wl/hat} value = yes or no - {components} value = ldegree :pre - -:ule - -[Examples:] - -compute 1 all orientorder/atom -compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 -compute 1 all orientorder/atom wl/hat yes -compute 1 all orientorder/atom components 6 :pre - -[Description:] - -Define a computation that calculates a set of bond-orientational -order parameters {Ql} for each atom in a group. These order parameters -were introduced by "Steinhardt et al."_#Steinhardt as a way to -characterize the local orientational order in atomic structures. -For each atom, {Ql} is a real number defined as follows: - -:c,image(Eqs/orientorder.jpg) - -The first equation defines the spherical harmonic order parameters. -These are complex number components of the 3D analog of the 2D order -parameter {qn}, which is implemented as LAMMPS compute -"hexorder/atom"_compute_hexorder_atom.html. -The summation is over the {nnn} nearest -neighbors of the central atom. -The angles theta and phi are the standard spherical polar angles -defining the direction of the bond vector {rij}. -The second equation defines {Ql}, which is a -rotationally invariant non-negative amplitude obtained by summing -over all the components of degree {l}. - -The optional keyword {cutoff} defines the distance cutoff -used when searching for neighbors. The default value, also -the maximum allowable value, is the cutoff specified -by the pair style. - -The optional keyword {nnn} defines the number of nearest -neighbors used to calculate {Ql}. The default value is 12. -If the value is NULL, then all neighbors up to the -specified distance cutoff are used. - -The optional keyword {degrees} defines the list of order parameters to -be computed. The first argument {nlvalues} is the number of order -parameters. This is followed by that number of non-negative integers giving the -degree of each order parameter. Because {Q}2 and all odd-degree order -parameters are zero for atoms in cubic crystals (see -"Steinhardt"_#Steinhardt), the default order parameters are {Q}4, -{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn} =12, {Q}4 -= sqrt(7/3)/8 = 0.19094.... The numerical values of all order -parameters up to {Q}12 for a range of commonly encountered -high-symmetry structures are given in Table I of "Mickel et -al."_#Mickel, and these can be reproduced with this compute - -The optional keyword {wl} will output the third-order invariants {Wl} -(see Eq. 1.4 in "Steinhardt"_#Steinhardt) for the same degrees as -for the {Ql} parameters. For the FCC crystal with {nnn} =12, -{W}4 = -sqrt(14/143).(49/4096)/Pi^1.5 = -0.0006722136... - -The optional keyword {wl/hat} will output the normalized third-order -invariants {Wlhat} (see Eq. 2.2 in "Steinhardt"_#Steinhardt) -for the same degrees as for the {Ql} parameters. For the FCC crystal -with {nnn} =12, {W}4hat = -7/3*sqrt(2/429) = -0.159317...The numerical -values of {Wlhat} for a range of commonly encountered high-symmetry -structures are given in Table I of "Steinhardt"_#Steinhardt, and these -can be reproduced with this keyword. - -The optional keyword {components} will output the components of the -normalized complex vector {Ybar_lm} of degree {ldegree}, which must be -explicitly included in the keyword {degrees}. This option can be used -in conjunction with "compute coord_atom"_compute_coord_atom.html to -calculate the ten Wolde's criterion to identify crystal-like -particles, as discussed in "ten Wolde"_#tenWolde2. - -The value of {Ql} is set to zero for atoms not in the -specified compute group, as well as for atoms that have less than -{nnn} neighbors within the distance cutoff, unless {nnn} is NULL. - -The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently. - -NOTE: If you have a bonded system, then the settings of -"special_bonds"_special_bonds.html command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the "special_bonds"_special_bonds.html -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included in the order parameter. This -difficulty can be circumvented by writing a dump file, and using the -"rerun"_rerun.html command to compute the order parameter for -snapshots in the dump file. The rerun script can use a -"special_bonds"_special_bonds.html command that includes all pairs in -the neighbor list. - -[Output info:] - -This compute calculates a per-atom array with {nlvalues} columns, -giving the {Ql} values for each atom, which are real numbers on the -range 0 <= {Ql} <= 1. - -If the keyword {wl} is set to yes, then the {Wl} values for each -atom will be added to the output array, which are real numbers. - -If the keyword {wl/hat} is set to yes, then the {Wl_hat} -values for each atom will be added to the output array, which are real numbers. - -If the keyword {components} is set, then the real and imaginary parts -of each component of (normalized) {Ybar_lm} will be added to the -output array in the following order: Re({Ybar_-m}) Im({Ybar_-m}) -Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}). This -way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1) -columns. - -These values can be accessed by any command that uses per-atom values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -[Restrictions:] none - -[Related commands:] - -"compute coord/atom"_compute_coord_atom.html, "compute -centro/atom"_compute_centro_atom.html, "compute -hexorder/atom"_compute_hexorder_atom.html - -[Default:] - -The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, -{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12, -{wl} = no, {wl/hat} = no, and {components} off - -:line - -:link(Steinhardt) -[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti, -Phys. Rev. B 28, 784 (1983). - -:link(Mickel) -[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, -J. Chem. Phys. 138, 044501 (2013). - -:link(tenWolde2) -[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, -J. Chem. Phys. 104, 9932 (1996). diff --git a/doc/txt/compute_pair.txt b/doc/txt/compute_pair.txt deleted file mode 100644 index c1bd4f74d9..0000000000 --- a/doc/txt/compute_pair.txt +++ /dev/null @@ -1,92 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute pair command :h3 - -[Syntax:] - -compute ID group-ID pair pstyle \[nstyle\] \[evalue\] :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -pair = style name of this compute command :l -pstyle = style name of a pair style that calculates additional values :l -nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a hybrid style :l -{evalue} = {epair} or {evdwl} or {ecoul} or blank (optional) :l -:ule - -[Examples:] - -compute 1 all pair gauss -compute 1 all pair lj/cut/coul/cut ecoul -compute 1 all pair tersoff 2 epair -compute 1 all pair reax/c :pre - -[Description:] - -Define a computation that extracts additional values calculated by a -pair style, and makes them accessible for output or further processing -by other commands. - -NOTE: The group specified for this command is [ignored]. - -The specified {pstyle} must be a pair style used in your simulation -either by itself or as a sub-style in a "pair_style hybrid or -hybrid/overlay"_pair_hybrid.html command. If the sub-style is -used more than once, an additional number {nsub} has to be specified -in order to choose which instance of the sub-style will be used by -the compute. Not specifying the number in this case will cause the -compute to fail. - -The {evalue} setting is optional. All -pair styles tally a potential energy {epair} which may be broken into -two parts: {evdwl} and {ecoul} such that {epair} = {evdwl} + {ecoul}. -If the pair style calculates Coulombic interactions, their energy will -be tallied in {ecoul}. Everything else (whether it is a Lennard-Jones -style van der Waals interaction or not) is tallied in {evdwl}. If -{evalue} is blank or specified as {epair}, then {epair} is stored -as a global scalar by this compute. This is useful when using -"pair_style hybrid"_pair_hybrid.html if you want to know the portion -of the total energy contributed by one sub-style. If {evalue} is -specified as {evdwl} or {ecoul}, then just that portion of the energy -is stored as a global scalar. - -NOTE: The energy returned by the {evdwl} keyword does not include tail -corrections, even if they are enabled via the -"pair_modify"_pair_modify.html command. - -Some pair styles tally additional quantities, e.g. a breakdown of -potential energy into 14 components is tallied by the "pair_style -reax/c"_pair_reaxc.html command. These values (1 or more) -are stored as a global vector by this compute. See the doc page for -"individual pair styles"_pair_style.html for info on these values. - -[Output info:] - -This compute calculates a global scalar which is {epair} or {evdwl} or -{ecoul}. If the pair style supports it, it also calculates a global -vector of length >= 1, as determined by the pair style. These values -can be used by any command that uses global scalar or vector values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The scalar and vector values calculated by this compute are -"extensive". - -The scalar value will be in energy "units"_units.html. The vector -values will typically also be in energy "units"_units.html, but see -the doc page for the pair style for details. - -[Restrictions:] none - -[Related commands:] - -"compute pe"_compute_pe.html, "compute bond"_compute_bond.html - -[Default:] - -The keyword defaults are {evalue} = {epair}, nsub = 0. diff --git a/doc/txt/compute_pair_local.txt b/doc/txt/compute_pair_local.txt deleted file mode 100644 index 10ff689582..0000000000 --- a/doc/txt/compute_pair_local.txt +++ /dev/null @@ -1,157 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute pair/local command :h3 - -[Syntax:] - -compute ID group-ID pair/local value1 value2 ... keyword args ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -pair/local = style name of this compute command :l -one or more values may be appended :l -value = {dist} or {eng} or {force} or {fx} or {fy} or {fz} or {pN} :l - {dist} = pairwise distance - {eng} = pairwise energy - {force} = pairwise force - {fx},{fy},{fz} = components of pairwise force - {pN} = pair style specific quantities for allowed N values :pre -zero or more keyword/arg pairs may be appended :l -keyword = {cutoff} :l - {cutoff} arg = {type} or {radius} :pre -:ule - -[Examples:] - -compute 1 all pair/local eng -compute 1 all pair/local dist eng force -compute 1 all pair/local dist eng fx fy fz -compute 1 all pair/local dist fx fy fz p1 p2 p3 :pre - -[Description:] - -Define a computation that calculates properties of individual pairwise -interactions. The number of datums generated, aggregated across all -processors, equals the number of pairwise interactions in the system. - -The local data stored by this command is generated by looping over the -pairwise neighbor list. Info about an individual pairwise interaction -will only be included if both atoms in the pair are in the specified -compute group, and if the current pairwise distance is less than the -force cutoff distance for that interaction, as defined by the -"pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html -commands. - -The value {dist} is the distance between the pair of atoms. - -The value {eng} is the interaction energy for the pair of atoms. - -The value {force} is the force acting between the pair of atoms, which -is positive for a repulsive force and negative for an attractive -force. The values {fx}, {fy}, and {fz} are the xyz components of -{force} on atom I. - -A pair style may define additional pairwise quantities which can be -accessed as {p1} to {pN}, where N is defined by the pair style. Most -pair styles do not define any additional quantities, so N = 0. An -example of ones that do are the "granular pair styles"_pair_gran.html -which calculate the tangential force between two particles and return -its components and magnitude acting on atom I for N = 1,2,3,4. See -individual pair styles for details. - -When using {pN} with pair style {hybrid}, the output will be the Nth -quantity from the sub-style that computes the pairwise interaction -(based on atom types). If that sub-style does not define a {pN}, -the output will be 0.0. The maximum allowed N is the maximum number -of quantities provided by any sub-style. - -When using {pN} with pair style {hybrid/overlay} the quantities -from all sub-styles that provide them are concatenated together -into one long list. For example, if there are 3 sub-styles and -2 of them have additional output (with 3 and 4 quantities, -respectively), then 7 values ({p1} up to {p7}) are defined. -The values {p1} to {p3} refer to quantities defined by the first -of the two sub-styles. Values {p4} to {p7} refer to quantities -from the second of the two sub-styles. If the referenced {pN} -is not computed for the specific pairwise interaction (based on -atom types), then the output will be 0.0. - -The value {dist} will be in distance "units"_units.html. The value -{eng} will be in energy "units"_units.html. The values {force}, {fx}, -{fy}, and {fz} will be in force "units"_units.html. The values {pN} -will be in whatever units the pair style defines. - -The optional {cutoff} keyword determines how the force cutoff distance -for an interaction is determined. For the default setting of {type}, -the pairwise cutoff defined by the "pair_style"_pair_style.html -command for the types of the two atoms is used. For the {radius} -setting, the sum of the radii of the two particles is used as a -cutoff. For example, this is appropriate for granular particles which -only interact when they are overlapping, as computed by "granular pair -styles"_pair_gran.html. Note that if a granular model defines atom -types such that all particles of a specific type are monodisperse -(same diameter), then the two settings are effectively identical. - -Note that as atoms migrate from processor to processor, there will be -no consistent ordering of the entries within the local vector or array -from one timestep to the next. The only consistency that is -guaranteed is that the ordering on a particular timestep will be the -same for local vectors or arrays generated by other compute commands. -For example, pair output from the "compute -property/local"_compute_property_local.html command can be combined -with data from this command and output by the "dump local"_dump.html -command in a consistent way. - -Here is an example of how to do this: - -compute 1 all property/local patom1 patom2 -compute 2 all pair/local dist eng force -dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_2\[1\] c_2\[2\] c_2\[3\] :pre - -NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4 -interactions within the molecular topology, their pairwise interaction -may be turned off, and thus they may not appear in the neighbor list, -and will not be part of the local data created by this command. More -specifically, this will be true of I,J pairs with a weighting factor -of 0.0; pairs with a non-zero weighting factor are included. The -weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set -by the "special_bonds"_special_bonds.html command. An exception is if -long-range Coulombics are being computed via the -"kspace_style"_kspace_style.html command, then atom pairs with -weighting factors of zero are still included in the neighbor list, so -that a portion of the long-range interaction contribution can be -computed in the pair style. Hence in that case, those atom pairs will -be part of the local data created by this command. - -[Output info:] - -This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of pairs. If a single keyword is specified, a -local vector is produced. If two or more keywords are specified, a -local array is produced where the number of columns = the number of -keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The output for {dist} will be in distance "units"_units.html. The -output for {eng} will be in energy "units"_units.html. The output for -{force}, {fx}, {fy}, and {fz} will be in force "units"_units.html. -The output for {pN} will be in whatever units the pair style defines. - -[Restrictions:] none - -[Related commands:] - -"dump local"_dump.html, "compute -property/local"_compute_property_local.html - -[Default:] - -The keyword default is cutoff = type. diff --git a/doc/txt/compute_pe.txt b/doc/txt/compute_pe.txt deleted file mode 100644 index 37655dfd48..0000000000 --- a/doc/txt/compute_pe.txt +++ /dev/null @@ -1,79 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute pe command :h3 - -[Syntax:] - -compute ID group-ID pe keyword ... :pre - -ID, group-ID are documented in "compute"_compute.html command -pe = style name of this compute command -zero or more keywords may be appended -keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} :ul - -[Examples:] - -compute 1 all pe -compute molPE all pe bond angle dihedral improper :pre - -[Description:] - -Define a computation that calculates the potential energy of the -entire system of atoms. The specified group must be "all". See the -"compute pe/atom"_compute_pe_atom.html command if you want per-atom -energies. These per-atom values could be summed for a group of atoms -via the "compute reduce"_compute_reduce.html command. - -The energy is calculated by the various pair, bond, etc potentials -defined for the simulation. If no extra keywords are listed, then the -potential energy is the sum of pair, bond, angle, dihedral, improper, -kspace (long-range), and fix energy. I.e. it is as if all the -keywords were listed. If any extra keywords are listed, then only -those components are summed to compute the potential energy. - -The Kspace contribution requires 1 extra FFT each timestep the energy -is calculated, if using the PPPM solver via the "kspace_style -pppm"_kspace_style.html command. Thus it can increase the cost of the -PPPM calculation if it is needed on a large fraction of the simulation -timesteps. - -Various fixes can contribute to the total potential energy of the -system if the {fix} contribution is included. See the doc pages for -"individual fixes"_fix.html for details of which ones compute a -potential energy. - -NOTE: The "fix_modify energy yes"_fix_modify.html command must also be -specified if a fix is to contribute potential energy to this command. - -A compute of this style with the ID of "thermo_pe" is created when -LAMMPS starts up, as if this command were in the input script: - -compute thermo_pe all pe :pre - -See the "thermo_style" command for more details. - -:line - -[Output info:] - -This compute calculates a global scalar (the potential energy). This -value can be used by any command that uses a global scalar value from -a compute as input. See the "Howto output"_Howto_output.html doc page -for an overview of LAMMPS output options. - -The scalar value calculated by this compute is "extensive". The -scalar value will be in energy "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute pe/atom"_compute_pe_atom.html - -[Default:] none diff --git a/doc/txt/compute_pe_atom.txt b/doc/txt/compute_pe_atom.txt deleted file mode 100644 index 400621f8df..0000000000 --- a/doc/txt/compute_pe_atom.txt +++ /dev/null @@ -1,101 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute pe/atom command :h3 - -[Syntax:] - -compute ID group-ID pe/atom keyword ... :pre - -ID, group-ID are documented in "compute"_compute.html command -pe/atom = style name of this compute command -zero or more keywords may be appended -keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} :ul - -[Examples:] - -compute 1 all pe/atom -compute 1 all pe/atom pair -compute 1 all pe/atom pair bond :pre - -[Description:] - -Define a computation that computes the per-atom potential energy for -each atom in a group. See the "compute pe"_compute_pe.html command if -you want the potential energy of the entire system. - -The per-atom energy is calculated by the various pair, bond, etc -potentials defined for the simulation. If no extra keywords are -listed, then the potential energy is the sum of pair, bond, angle, -dihedral,improper, kspace (long-range), and fix energy. I.e. it is as -if all the keywords were listed. If any extra keywords are listed, -then only those components are summed to compute the potential energy. - -Note that the energy of each atom is due to its interaction with all -other atoms in the simulation, not just with other atoms in the group. - -For an energy contribution produced by a small set of atoms (e.g. 4 -atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that -energy is assigned in equal portions to each atom in the set. -E.g. 1/4 of the dihedral energy to each of the 4 atoms. - -The "dihedral_style charmm"_dihedral_charmm.html style calculates -pairwise interactions between 1-4 atoms. The energy contribution of -these terms is included in the pair energy, not the dihedral energy. - -The KSpace contribution is calculated using the method in -"(Heyes)"_#Heyes1 for the Ewald method and a related method for PPPM, -as specified by the "kspace_style pppm"_kspace_style.html command. -For PPPM, the calculation requires 1 extra FFT each timestep that -per-atom energy is calculated. This "document"_PDF/kspace.pdf -describes how the long-range per-atom energy calculation is performed. - -Various fixes can contribute to the per-atom potential energy of the -system if the {fix} contribution is included. See the doc pages for -"individual fixes"_fix.html for details of which ones compute a -per-atom potential energy. - -NOTE: The "fix_modify energy yes"_fix_modify.html command must also be -specified if a fix is to contribute per-atom potential energy to this -command. - -As an example of per-atom potential energy compared to total potential -energy, these lines in an input script should yield the same result -in the last 2 columns of thermo output: - -compute peratom all pe/atom -compute pe all reduce sum c_peratom -thermo_style custom step temp etotal press pe c_pe :pre - -NOTE: The per-atom energy does not include any Lennard-Jones tail -corrections to the energy added by the "pair_modify tail -yes"_pair_modify.html command, since those are contributions to the -global system energy. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values will be in energy "units"_units.html. - -[Restrictions:] - -[Related commands:] - -"compute pe"_compute_pe.html, "compute -stress/atom"_compute_stress_atom.html - -[Default:] none - -:line - -:link(Heyes1) -[(Heyes)] Heyes, Phys Rev B 49, 755 (1994), diff --git a/doc/txt/compute_plasticity_atom.txt b/doc/txt/compute_plasticity_atom.txt deleted file mode 100644 index 6c21cecd6c..0000000000 --- a/doc/txt/compute_plasticity_atom.txt +++ /dev/null @@ -1,68 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute plasticity/atom command :h3 - -[Syntax:] - -compute ID group-ID plasticity/atom :pre - -ID, group-ID are documented in compute command -plasticity/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all plasticity/atom :pre - -[Description:] - -Define a computation that calculates the per-atom plasticity for each -atom in a group. This is a quantity relevant for "Peridynamics -models"_pair_peri.html. See "this document"_PDF/PDLammps_overview.pdf -for an overview of LAMMPS commands for Peridynamics modeling. - -The plasticity for a Peridynamic particle is the so-called consistency -parameter (lambda). For elastic deformation lambda = 0, otherwise -lambda > 0 for plastic deformation. For details, see -"(Mitchell)"_#Mitchell and the PDF doc included in the LAMMPS -distribution in "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf. - -This command can be invoked for one of the Peridynamic "pair -styles"_pair_peri.html: peri/eps. - -The plasticity value will be 0.0 for atoms not in the specified -compute group. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-atom vector values are unitless numbers (lambda) >= 0.0. - -[Restrictions:] - -This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute damage/atom"_compute_damage_atom.html, -"compute dilatation/atom"_compute_dilatation_atom.html - -[Default:] none - -:line - -:link(Mitchell) -[(Mitchell)] Mitchell, "A non-local, ordinary-state-based -viscoelasticity model for peridynamics", Sandia National Lab Report, -8064:1-28 (2011). diff --git a/doc/txt/compute_pressure.txt b/doc/txt/compute_pressure.txt deleted file mode 100644 index 9b27413cfc..0000000000 --- a/doc/txt/compute_pressure.txt +++ /dev/null @@ -1,157 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute pressure command :h3 - -[Syntax:] - -compute ID group-ID pressure temp-ID keyword ... :pre - -ID, group-ID are documented in "compute"_compute.html command -pressure = style name of this compute command -temp-ID = ID of compute that calculates temperature, can be NULL if not needed -zero or more keywords may be appended -keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} or {pair/hybrid} :ul - -[Examples:] - -compute 1 all pressure thermo_temp -compute 1 all pressure NULL pair bond -compute 1 all pressure NULL pair/hybrid lj/cut :pre - -[Description:] - -Define a computation that calculates the pressure of the entire system -of atoms. The specified group must be "all". See the "compute -stress/atom"_compute_stress_atom.html command if you want per-atom -pressure (stress). These per-atom values could be summed for a group -of atoms via the "compute reduce"_compute_reduce.html command. - -The pressure is computed by the formula - -:c,image(Eqs/pressure.jpg) - -where N is the number of atoms in the system (see discussion of DOF -below), Kb is the Boltzmann constant, T is the temperature, d is the -dimensionality of the system (2 or 3 for 2d/3d), and V is the system -volume (or area in 2d). The second term is the virial, equal to --dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body, -many-body, and long-range interactions, where r_i and f_i are the -position and force vector of atom i, and the black dot indicates a dot -product. When periodic boundary conditions are used, N' necessarily -includes periodic image (ghost) atoms outside the central box, and the -position and force vectors of ghost atoms are thus included in the -summation. When periodic boundary conditions are not used, N' = N = -the number of atoms in the system. "Fixes"_fix.html that impose -constraints (e.g. the "fix shake"_fix_shake.html command) also -contribute to the virial term. - -A symmetric pressure tensor, stored as a 6-element vector, is also -calculated by this compute. The 6 components of the vector are -ordered xx, yy, zz, xy, xz, yz. The equation for the I,J components -(where I and J = x,y,z) is similar to the above formula, except that -the first term uses components of the kinetic energy tensor and the -second term uses components of the virial tensor: - -:c,image(Eqs/pressure_tensor.jpg) - -If no extra keywords are listed, the entire equations above are -calculated. This includes a kinetic energy (temperature) term and the -virial as the sum of pair, bond, angle, dihedral, improper, kspace -(long-range), and fix contributions to the force on each atom. If any -extra keywords are listed, then only those components are summed to -compute temperature or ke and/or the virial. The {virial} keyword -means include all terms except the kinetic energy {ke}. - -The {pair/hybrid} keyword means to only include contribution -from a sub-style in a {hybrid} or {hybrid/overlay} pair style. - -Details of how LAMMPS computes the virial efficiently for the entire -system, including for many-body potentials and accounting for the -effects of periodic boundary conditions are discussed in -"(Thompson)"_#Thompson1. - -The temperature and kinetic energy tensor is not calculated by this -compute, but rather by the temperature compute specified with the -command. If the kinetic energy is not included in the pressure, than -the temperature compute is not used and can be specified as NULL. -Normally the temperature compute used by compute pressure should -calculate the temperature of all atoms for consistency with the virial -term, but any compute style that calculates temperature can be used, -e.g. one that excludes frozen atoms or other degrees of freedom. - -Note that if desired the specified temperature compute can be one that -subtracts off a bias to calculate a temperature using only the thermal -velocity of the atoms, e.g. by subtracting a background streaming -velocity. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. - -Also note that the N in the first formula above is really -degrees-of-freedom divided by d = dimensionality, where the DOF value -is calculated by the temperature compute. See the various "compute -temperature"_compute.html styles for details. - -A compute of this style with the ID of "thermo_press" is created when -LAMMPS starts up, as if this command were in the input script: - -compute thermo_press all pressure thermo_temp :pre - -where "thermo_temp" is the ID of a similarly defined compute of style -"temp". See the "thermo_style" command for more details. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Output info:] - -This compute calculates a global scalar (the pressure) and a global -vector of length 6 (pressure tensor), which can be accessed by indices -1-6. These values can be used by any command that uses global scalar -or vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar and vector values calculated by this compute are -"intensive". The scalar and vector values will be in pressure -"units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute temp"_compute_temp.html, "compute -stress/atom"_compute_stress_atom.html, -"thermo_style"_thermo_style.html, - -[Default:] none - -:line - -:link(Thompson1) -[(Thompson)] Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009). diff --git a/doc/txt/compute_pressure_cylinder.txt b/doc/txt/compute_pressure_cylinder.txt deleted file mode 100644 index 5cca9ea3a5..0000000000 --- a/doc/txt/compute_pressure_cylinder.txt +++ /dev/null @@ -1,81 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -compute pressure/cylinder command :h3 - -[Syntax:] - -compute ID group-ID pressure/cylinder zlo zhi Rmax bin_width :pre - -ID, group-ID are documented in "compute"_compute.html command -pressure/cylinder = style name of this compute command -zlo = minimum z-boundary for cylinder -zhi = maximum z-boundary for cylinder -Rmax = maximum radius to perform calculation to -bin_width = width of radial bins to use for calculation :ul - -[Examples:] - -compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25 :pre - -[Description:] - -Define a computation that calculates the pressure tensor of a system in -cylindrical coordinates, as discussed in "(Addington)"_#Addington1. -This is useful for systems with a single axis of rotational symmetry, -such as cylindrical micelles or carbon nanotubes. The compute splits the -system into radial, cylindrical-shell-type bins of width bin_width, -centered at x=0,y=0, and calculates the radial (P_rhorho), azimuthal -(P_phiphi), and axial (P_zz) components of the configurational pressure -tensor. The local density is also calculated for each bin, so that the -true pressure can be recovered as P_kin+P_conf=density*k*T+P_conf. The -output is a global array with 5 columns; one each for bin radius, local -number density, P_rhorho, P_phiphi, and P_zz. The number of rows is -governed by the values of Rmax and bin_width. Pressure tensor values are -output in pressure units. - -[Output info:] - -This compute calculates a global array with 5 columns and Rmax/bin_width -rows. The output columns are: R (distance units), number density (inverse -volume units), configurational radial pressure (pressure units), -configurational azimuthal pressure (pressure units), and configurational -axial pressure (pressure units). - -The values calculated by this compute are -"intensive". The pressure values will be in pressure -"units"_units.html. The number density values will be in -inverse volume "units"_units.html. - -[Restrictions:] - -This compute currently calculates the pressure tensor contributions -for pair styles only (i.e. no bond, angle, dihedral, etc. contributions -and in the presence of bonded interactions, the result will be incorrect -due to exclusions for special bonds) and requires pair-wise force -calculations not available for most many-body pair styles. K-space -calculations are also excluded. Note that this pressure compute outputs -the configurational terms only; the kinetic contribution is not included -and may be calculated from the number density output by P_kin=density*k*T. - -This compute is part of the USER-MISC package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute temp"_compute_temp.html, "compute -stress/atom"_compute_stress_atom.html, -"thermo_style"_thermo_style.html, - -[Default:] none - -:line - -:link(Addington1) -[(Addington)] Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018). diff --git a/doc/txt/compute_pressure_uef.txt b/doc/txt/compute_pressure_uef.txt deleted file mode 100644 index 72ed0ba5c4..0000000000 --- a/doc/txt/compute_pressure_uef.txt +++ /dev/null @@ -1,61 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute pressure/uef command :h3 - -[Syntax:] - -compute ID group-ID pressure/uef temp-ID keyword ... :pre - -ID, group-ID are documented in "compute"_compute.html command -pressure/uef = style name of this compute command -temp-ID = ID of compute that calculates temperature, can be NULL if not needed -zero or more keywords may be appended -keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul - -[Examples:] - -compute 1 all pressure/uef my_temp_uef -compute 2 all pressure/uef my_temp_uef virial :pre - -[Description:] - -This command is used to compute the pressure tensor in -the reference frame of the applied flow field when -"fix nvt/uef"_fix_nh_uef.html or -"fix npt/uef"_fix_nh_uef.html is used. -It is not necessary to use this command to compute the scalar -value of the pressure. A "compute pressure"_compute_pressure.html -may be used for that purpose. - -The keywords and output information are documented in -"compute_pressure"_compute_pressure.html. - -[Restrictions:] - -This fix is part of the USER-UEF package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This command can only be used when "fix nvt/uef"_fix_nh_uef.html -or "fix npt/uef"_fix_nh_uef.html is active. - -The kinetic contribution to the pressure tensor -will be accurate only when -the compute specified by {temp-ID} is a -"compute temp/uef"_compute_temp_uef.html. - -[Related commands:] - -"compute pressure"_compute_pressure.html, -"fix nvt/uef"_fix_nh_uef.html, -"compute temp/uef"_compute_temp_uef.html - -[Default:] none - - diff --git a/doc/txt/compute_property_atom.txt b/doc/txt/compute_property_atom.txt deleted file mode 100644 index a0c8579283..0000000000 --- a/doc/txt/compute_property_atom.txt +++ /dev/null @@ -1,172 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute property/atom command :h3 - -[Syntax:] - -compute ID group-ID property/atom input1 input2 ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -property/atom = style name of this compute command :l -input = one or more atom attributes :l - possible attributes = id, mol, proc, type, mass, - x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, - vx, vy, vz, fx, fy, fz, - q, mux, muy, muz, mu, - sp, spx, spy, spz, fmx, fmy, fmz, - radius, diameter, omegax, omegay, omegaz, - angmomx, angmomy, angmomz, - shapex,shapey, shapez, - quatw, quati, quatj, quatk, tqx, tqy, tqz, - end1x, end1y, end1z, end2x, end2y, end2z, - corner1x, corner1y, corner1z, - corner2x, corner2y, corner2z, - corner3x, corner3y, corner3z, - nbonds, - vfrac, s0, - spin, eradius, ervel, erforce, - rho, drho, e, de, cv, - i_name, d_name :pre - id = atom ID - mol = molecule ID - proc = ID of processor that owns atom - type = atom type - mass = atom mass - x,y,z = unscaled atom coordinates - xs,ys,zs = scaled atom coordinates - xu,yu,zu = unwrapped atom coordinates - ix,iy,iz = box image that the atom is in - vx,vy,vz = atom velocities - fx,fy,fz = forces on atoms - q = atom charge - mux,muy,muz = orientation of dipole moment of atom - mu = magnitude of dipole moment of atom - sp = atomic magnetic spin moment - spx, spy, spz = direction of the atomic magnetic spin - fmx, fmy, fmz = magnetic force - radius,diameter = radius,diameter of spherical particle - omegax,omegay,omegaz = angular velocity of spherical particle - angmomx,angmomy,angmomz = angular momentum of aspherical particle - shapex,shapey,shapez = 3 diameters of aspherical particle - quatw,quati,quatj,quatk = quaternion components for aspherical or body particles - tqx,tqy,tqz = torque on finite-size particles - end12x, end12y, end12z = end points of line segment - corner123x, corner123y, corner123z = corner points of triangle - nbonds = number of bonds assigned to an atom :pre - - PERI package per-atom properties: - vfrac = ??? - s0 = ??? :pre - - USER-EFF and USER-AWPMD package per-atom properties: - spin = electron spin - eradius = electron radius - ervel = electron radial velocity - erforce = electron radial force :pre - - USER-SPH package per-atom properties: - rho = ??? - drho = ??? - e = ??? - de = ??? - cv = ??? :pre - - "fix property/atom"_fix_property_atom.html per-atom properties: - i_name = custom integer vector with name - d_name = custom integer vector with name :pre -:ule - -[Examples:] - -compute 1 all property/atom xs vx fx mux -compute 2 all property/atom type -compute 1 all property/atom ix iy iz -compute 3 all property/atom sp spx spy spz :pre - -[Description:] - -Define a computation that simply stores atom attributes for each atom -in the group. This is useful so that the values can be used by other -"output commands"_Howto_output.html that take computes as inputs. See -for example, the "compute reduce"_compute_reduce.html, "fix -ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html, "fix -ave/chunk"_fix_ave_chunk.html, and "atom-style variable"_variable.html -commands. - -The list of possible attributes is the same as that used by the "dump -custom"_dump.html command, which describes their meaning, with some -additional quantities that are only defined for certain "atom -styles"_atom_style.html. Basically, this augmented list gives an -input script access to any per-atom quantity stored by LAMMPS. - -The values are stored in a per-atom vector or array as discussed -below. Zeroes are stored for atoms not in the specified group or for -quantities that are not defined for a particular particle in the group -(e.g. {shapex} if the particle is not an ellipsoid). - -The additional quantities only accessible via this command, and not -directly via the "dump custom"_dump.html command, are as follows. - -{Shapex}, {shapey}, and {shapez} are defined for ellipsoidal particles -and define the 3d shape of each particle. - -{Quatw}, {quati}, {quatj}, and {quatk} are defined for ellipsoidal -particles and body particles and store the 4-vector quaternion -representing the orientation of each particle. See the "set"_set.html -command for an explanation of the quaternion vector. - -{End1x}, {end1y}, {end1z}, {end2x}, {end2y}, {end2z}, are defined for -line segment particles and define the end points of each line segment. - -{Corner1x}, {corner1y}, {corner1z}, {corner2x}, {corner2y}, -{corner2z}, {corner3x}, {corner3y}, {corner3z}, are defined for -triangular particles and define the corner points of each triangle. - -{Nbonds} is available for all molecular atom styles and refers to the -number of explicit bonds assigned to an atom. Note that if the -"newton bond"_newton.html command is set to {on}, which is the -default, then every bond in the system is assigned to only one of the -two atoms in the bond. Thus a bond between atoms I,J may be tallied -for either atom I or atom J. If "newton bond off"_newton.html is set, -it will be tallied with both atom I and atom J. - -The {i_name} and {d_name} attributes refer to custom integer and -floating-point properties that have been added to each atom via the -"fix property/atom"_fix_property_atom.html command. When that command -is used specific names are given to each attribute which are what is -specified as the "name" portion of {i_name} or {d_name}. - -[Output info:] - -This compute calculates a per-atom vector or per-atom array depending -on the number of input values. If a single input is specified, a -per-atom vector is produced. If two or more inputs are specified, a -per-atom array is produced where the number of columns = the number of -inputs. The vector or array can be accessed by any command that uses -per-atom values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The vector or array values will be in whatever "units"_units.html the -corresponding attribute is in, e.g. velocity units for vx, charge -units for q, etc. - -For the spin quantities, sp is in the units of the Bohr magneton, spx, -spy, and spz are unitless quantities, and fmx, fmy and fmz are given -in rad/THz. - -[Restrictions:] none - -[Related commands:] - -"dump custom"_dump.html, "compute reduce"_compute_reduce.html, "fix -ave/atom"_fix_ave_atom.html, "fix ave/chunk"_fix_ave_chunk.html, -"fix property/atom"_fix_property_atom.html - -[Default:] none diff --git a/doc/txt/compute_property_chunk.txt b/doc/txt/compute_property_chunk.txt deleted file mode 100644 index a30b5a1f0a..0000000000 --- a/doc/txt/compute_property_chunk.txt +++ /dev/null @@ -1,117 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute property/chunk command :h3 - -[Syntax:] - -compute ID group-ID property/chunk chunkID input1 input2 ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -property/chunk = style name of this compute command :l -input = one or more attributes :l - attributes = count, id, coord1, coord2, coord3 - count = # of atoms in chunk - id = original chunk IDs before compression by "compute chunk/atom"_compute_chunk_atom.html - coord123 = coordinates for spatial bins calculated by "compute chunk/atom"_compute_chunk_atom.html :pre -:ule - -[Examples:] - -compute 1 all property/chunk count -compute 1 all property/chunk ID coord1 :pre - -[Description:] - -Define a computation that stores the specified attributes of chunks of -atoms. - -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. - -This compute calculates and stores the specified attributes of chunks -as global data so they can be accessed by other "output -commands"_Howto_output.html and used in conjunction with other -commands that generate per-chunk data, such as "compute -com/chunk"_compute_com_chunk.html or "compute -msd/chunk"_compute_msd_chunk.html. - -Note that only atoms in the specified group contribute to the -calculation of the {count} attribute. The "compute -chunk/atom"_compute_chunk_atom.html command defines its own group; -atoms will have a chunk ID = 0 if they are not in that group, -signifying they are not assigned to a chunk, and will thus also not -contribute to this calculation. You can specify the "all" group for -this command if you simply want to include atoms with non-zero chunk -IDs. - -The {count} attribute is the number of atoms in the chunk. - -The {id} attribute stores the original chunk ID for each chunk. It -can only be used if the {compress} keyword was set to {yes} for the -"compute chunk/atom"_compute_chunk_atom.html command referenced by -chunkID. This means that the original chunk IDs (e.g. molecule IDs) -will have been compressed to remove chunk IDs with no atoms assigned -to them. Thus a compressed chunk ID of 3 may correspond to an original -chunk ID (molecule ID in this case) of 415. The {id} attribute will -then be 415 for the 3rd chunk. - -The {coordN} attributes can only be used if a {binning} style was used -in the "compute chunk/atom"_compute_chunk_atom.html command referenced -by chunkID. For {bin/1d}, {bin/2d}, and {bin/3d} styles the attribute -is the center point of the bin in the corresponding dimension. Style -{bin/1d} only defines a {coord1} attribute. Style {bin/2d} adds a -{coord2} attribute. Style {bin/3d} adds a {coord3} attribute. - -Note that if the value of the {units} keyword used in the "compute -chunk/atom command"_compute_chunk_atom.html is {box} or {lattice}, the -{coordN} attributes will be in distance "units"_units.html. If the -value of the {units} keyword is {reduced}, the {coordN} attributes -will be in unitless reduced units (0-1). - -The simplest way to output the results of the compute property/chunk -calculation to a file is to use the "fix ave/time"_fix_ave_time.html -command, for example: - -compute cc1 all chunk/atom molecule -compute myChunk1 all property/chunk cc1 count -compute myChunk2 all com/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2\[*\] file tmp.out mode vector :pre - -[Output info:] - -This compute calculates a global vector or global array depending on -the number of input values. The length of the vector or number of -rows in the array is the number of chunks. - -This compute calculates a global vector or global array where the -number of rows = the number of chunks {Nchunk} as calculated by the -specified "compute chunk/atom"_compute_chunk_atom.html command. If a -single input is specified, a global vector is produced. If two or -more inputs are specified, a global array is produced where the number -of columns = the number of inputs. The vector or array can be -accessed by any command that uses global values from a compute as -input. See the "Howto output"_Howto_output.html doc page for an -overview of LAMMPS output options. - -The vector or array values are "intensive". The values will be -unitless or in the units discussed above. - -[Restrictions:] none - -[Related commands:] - -"fix ave/chunk"_fix_ave_chunk.html - -[Default:] none diff --git a/doc/txt/compute_property_local.txt b/doc/txt/compute_property_local.txt deleted file mode 100644 index c4ad0afc95..0000000000 --- a/doc/txt/compute_property_local.txt +++ /dev/null @@ -1,158 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute property/local command :h3 - -[Syntax:] - -compute ID group-ID property/local attribute1 attribute2 ... keyword args ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -property/local = style name of this compute command :l -one or more attributes may be appended :l - possible attributes = natom1 natom2 ntype1 ntype2 - patom1 patom2 ptype1 ptype2 - batom1 batom2 btype - aatom1 aatom2 aatom3 atype - datom1 datom2 datom3 datom4 dtype - iatom1 iatom2 iatom3 iatom4 itype :pre - - natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff) - ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff) - patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff) - ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff) - batom1, batom2 = IDs of 2 atoms in each bond - btype = bond type of each bond - aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle - atype = angle type of each angle - datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral - dtype = dihedral type of each dihedral - iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper - itype = improper type of each improper :pre -zero or more keyword/arg pairs may be appended :l -keyword = {cutoff} :l - {cutoff} arg = {type} or {radius} :pre -:ule - -[Examples:] - -compute 1 all property/local btype batom1 batom2 -compute 1 all property/local atype aatom2 :pre - -[Description:] - -Define a computation that stores the specified attributes as local -data so it can be accessed by other "output -commands"_Howto_output.html. If the input attributes refer to bond -information, then the number of datums generated, aggregated across -all processors, equals the number of bonds in the system. Ditto for -pairs, angles, etc. - -If multiple attributes are specified then they must all generate the -same amount of information, so that the resulting local array has the -same number of rows for each column. This means that only bond -attributes can be specified together, or angle attributes, etc. Bond -and angle attributes can not be mixed in the same compute -property/local command. - -If the inputs are pair attributes, the local data is generated by -looping over the pairwise neighbor list. Info about an individual -pairwise interaction will only be included if both atoms in the pair -are in the specified compute group. For {natom1} and {natom2}, all -atom pairs in the neighbor list are considered (out to the neighbor -cutoff = force cutoff + "neighbor skin"_neighbor.html). For {patom1} -and {patom2}, the distance between the atoms must be less than the -force cutoff distance for that pair to be included, as defined by the -"pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html -commands. - -The optional {cutoff} keyword determines how the force cutoff distance -for an interaction is determined for the {patom1} and {patom2} -attributes. For the default setting of {type}, the pairwise cutoff -defined by the "pair_style"_pair_style.html command for the types of -the two atoms is used. For the {radius} setting, the sum of the radii -of the two particles is used as a cutoff. For example, this is -appropriate for granular particles which only interact when they are -overlapping, as computed by "granular pair styles"_pair_gran.html. -Note that if a granular model defines atom types such that all -particles of a specific type are monodisperse (same diameter), then -the two settings are effectively identical. - -If the inputs are bond, angle, etc attributes, the local data is -generated by looping over all the atoms owned on a processor and -extracting bond, angle, etc info. For bonds, info about an individual -bond will only be included if both atoms in the bond are in the -specified compute group. Likewise for angles, dihedrals, etc. - -For bonds and angles, a bonds/angles that have been broken by setting -their bond/angle type to 0 will not be included. Bonds/angles that -have been turned off (see the "fix shake"_fix_shake.html or -"delete_bonds"_delete_bonds.html commands) by setting their bond/angle -type negative are written into the file. This is consistent with the -"compute bond/local"_compute_bond_local.html and "compute -angle/local"_compute_angle_local.html commands - -Note that as atoms migrate from processor to processor, there will be -no consistent ordering of the entries within the local vector or array -from one timestep to the next. The only consistency that is -guaranteed is that the ordering on a particular timestep will be the -same for local vectors or arrays generated by other compute commands. -For example, output from the "compute -bond/local"_compute_bond_local.html command can be combined with bond -atom indices from this command and output by the "dump -local"_dump.html command in a consistent way. - -The {natom1} and {natom2}, or {patom1} and {patom2} attributes refer -to the atom IDs of the 2 atoms in each pairwise interaction computed -by the "pair_style"_pair_style.html command. The {ntype1} and -{ntype2}, or {ptype1} and {ptype2} attributes refer to the atom types -of the 2 atoms in each pairwise interaction. - -NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4 -interactions within the molecular topology, their pairwise interaction -may be turned off, and thus they may not appear in the neighbor list, -and will not be part of the local data created by this command. More -specifically, this may be true of I,J pairs with a weighting factor of -0.0; pairs with a non-zero weighting factor are included. The -weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set -by the "special_bonds"_special_bonds.html command. - -The {batom1} and {batom2} attributes refer to the atom IDs of the 2 -atoms in each "bond"_bond_style.html. The {btype} attribute refers to -the type of the bond, from 1 to Nbtypes = # of bond types. The number -of bond types is defined in the data file read by the -"read_data"_read_data.html command. - -The attributes that start with "a", "d", "i", refer to similar values -for "angles"_angle_style.html, "dihedrals"_dihedral_style.html, and -"impropers"_improper_style.html. - -[Output info:] - -This compute calculates a local vector or local array depending on the -number of input values. The length of the vector or number of rows in -the array is the number of bonds, angles, etc. If a single input is -specified, a local vector is produced. If two or more inputs are -specified, a local array is produced where the number of columns = the -number of inputs. The vector or array can be accessed by any command -that uses local values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The vector or array values will be integers that correspond to the -specified attribute. - -[Restrictions:] none - -[Related commands:] - -"dump local"_dump.html, "compute reduce"_compute_reduce.html - -[Default:] - -The keyword default is cutoff = type. diff --git a/doc/txt/compute_ptm_atom.txt b/doc/txt/compute_ptm_atom.txt deleted file mode 100644 index dfe3afe970..0000000000 --- a/doc/txt/compute_ptm_atom.txt +++ /dev/null @@ -1,121 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -compute ptm/atom command :h3 - -[Syntax:] - -compute ID group-ID ptm/atom structures threshold :pre - -ID, group-ID are documented in "compute"_compute.html command -ptm/atom = style name of this compute command -structures = structure types to search for -threshold = lattice distortion threshold (RMSD) :ul - -[Examples:] - -compute 1 all ptm/atom default 0.1 -compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15 -compute 1 all ptm/atom all 0 :pre - -[Description:] - -Define a computation that determines the local lattice structure -around an atom using the PTM (Polyhedral Template Matching) method. -The PTM method is described in "(Larsen)"_#Larsen. - -Currently, there are seven lattice structures PTM recognizes: - -fcc = 1 -hcp = 2 -bcc = 3 -ico (icosahedral) = 4 -sc (simple cubic) = 5 -dcub (diamond cubic) = 6 -dhex (diamond hexagonal) = 7 -graphene = 8 :ul - -The value of the PTM structure will be 0 for unknown types and -1 for atoms not in the specified -compute group. The choice of structures to search for can be specified using the "structures" -argument, which is a hyphen-separated list of structure keywords. -Two convenient pre-set options are provided: - -default: fcc-hcp-bcc-ico -all: fcc-hcp-bcc-ico-sc-dcub-dhex-graphene :ul - -The 'default' setting detects the same structures as the Common Neighbor Analysis method. -The 'all' setting searches for all structure types. A performance penalty is -incurred for the diamond and graphene structures, so it is not recommended to use this option if -it is known that the simulation does not contain these structures. - - -PTM identifies structures using two steps. First, a graph isomorphism test is used -to identify potential structure matches. Next, the deviation is computed between the -local structure (in the simulation) and a template of the ideal lattice structure. -The deviation is calculated as: - -:c,image(Eqs/ptm_rmsd.jpg) - -Here, u and v contain the coordinates of the local and ideal structures respectively, -s is a scale factor, and Q is a rotation. The best match is identified by the -lowest RMSD value, using the optimal scaling, rotation, and correspondence between the -points. - -The 'threshold' keyword sets an upper limit on the maximum permitted deviation before -a local structure is identified as disordered. Typical values are in the range 0.1-0.15, -but larger values may be desirable at higher temperatures. -A value of 0 is equivalent to infinity and can be used if no threshold is desired. - - -The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (e.g. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently or to have multiple compute/dump commands, each with a -{ptm/atom} style. - -[Output info:] - -This compute calculates a per-atom array, which can be accessed by -any command that uses per-atom values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -Results are stored in the per-atom array in the following order: - -type -rmsd -interatomic distance -qw -qx -qy -qz :ul - -The type is a number from -1 to 8. The rmsd is a positive real number. -The interatomic distance is computed from the scale factor in the RMSD equation. -The (qw,qx,qy,qz) parameters represent the orientation of the local structure -in quaternion form. The reference coordinates for each template (from which the -orientation is determined) can be found in the {ptm_constants.h} file in the PTM source directory. - -[Restrictions:] - -This fix is part of the USER-PTM package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute centro/atom"_compute_centro_atom.html -"compute cna/atom"_compute_cna_atom.html - -[Default:] none - -:line - -:link(Larsen) -[(Larsen)] Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016). - diff --git a/doc/txt/compute_rdf.txt b/doc/txt/compute_rdf.txt deleted file mode 100644 index 17fa68e526..0000000000 --- a/doc/txt/compute_rdf.txt +++ /dev/null @@ -1,199 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute rdf command :h3 - -[Syntax:] - -compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ... keyword/value ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -rdf = style name of this compute command :l -Nbin = number of RDF bins :l -itypeN = central atom type for Nth RDF histogram (see asterisk form below) :l -jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) :l - -zero or more keyword/value pairs may be appended :l -keyword = {cutoff} :l - {cutoff} value = Rcut - Rcut = cutoff distance for RDF computation (distance units) :pre -:ule - -[Examples:] - -compute 1 all rdf 100 -compute 1 all rdf 100 1 1 -compute 1 all rdf 100 * 3 cutoff 5.0 -compute 1 fluid rdf 500 1 1 1 2 2 1 2 2 -compute 1 fluid rdf 500 1*3 2 5 *10 cutoff 3.5 :pre - -[Description:] - -Define a computation that calculates the radial distribution function -(RDF), also called g(r), and the coordination number for a group of -particles. Both are calculated in histogram form by binning pairwise -distances into {Nbin} bins from 0.0 to the maximum force cutoff -defined by the "pair_style"_pair_style.html command or the cutoff -distance {Rcut} specified via the {cutoff} keyword. The bins are of -uniform size in radial distance. Thus a single bin encompasses a thin -shell of distances in 3d and a thin ring of distances in 2d. - -NOTE: If you have a bonded system, then the settings of -"special_bonds"_special_bonds.html command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the "special_bonds"_special_bonds.html -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses a neighbor list, it also means -those pairs will not be included in the RDF. This does not apply when -using long-range coulomb interactions ({coul/long}, {coul/msm}, -{coul/wolf} or similar. One way to get around this would be to set -special_bond scaling factors to very tiny numbers that are not exactly -zero (e.g. 1.0e-50). Another workaround is to write a dump file, and -use the "rerun"_rerun.html command to compute the RDF for snapshots in -the dump file. The rerun script can use a -"special_bonds"_special_bonds.html command that includes all pairs in -the neighbor list. - -By default the RDF is computed out to the maximum force cutoff defined -by the "pair_style"_pair_style.html command. If the {cutoff} keyword -is used, then the RDF is computed accurately out to the {Rcut} > 0.0 -distance specified. - -NOTE: Normally, you should only use the {cutoff} keyword if no pair -style is defined, e.g. the "rerun"_rerun.html command is being used to -post-process a dump file of snapshots. Or if you really want the RDF -for distances beyond the pair_style force cutoff and cannot easily -post-process a dump file to calculate it. This is because using the -{cutoff} keyword incurs extra computation and possibly communication, -which may slow down your simulation. If you specify a {Rcut} <= force -cutoff, you will force an additional neighbor list to be built at -every timestep this command is invoked (or every reneighboring -timestep, whichever is less frequent), which is inefficient. LAMMPS -will warn you if this is the case. If you specify a {Rcut} > force -cutoff, you must insure ghost atom information out to {Rcut} + {skin} -is communicated, via the "comm_modify cutoff"_comm_modify.html -command, else the RDF computation cannot be performed, and LAMMPS will -give an error message. The {skin} value is what is specified with the -"neighbor"_neighbor.html command. In this case, you are forcing a -large neighbor list to be built just for the RDF computation, and -extra communication to be performed every timestep. - -The {itypeN} and {jtypeN} arguments are optional. These arguments -must come in pairs. If no pairs are listed, then a single histogram -is computed for g(r) between all atom types. If one or more pairs are -listed, then a separate histogram is generated for each -{itype},{jtype} pair. - -The {itypeN} and {jtypeN} settings can be specified in one of two -ways. An explicit numeric value can be used, as in the 4th example -above. Or a wild-card asterisk can be used to specify a range of atom -types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of atom types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). - -If both {itypeN} and {jtypeN} are single values, as in the 4th example -above, this means that a g(r) is computed where atoms of type {itypeN} -are the central atom, and atoms of type {jtypeN} are the distribution -atom. If either {itypeN} and {jtypeN} represent a range of values via -the wild-card asterisk, as in the 5th example above, this means that a -g(r) is computed where atoms of any of the range of types represented -by {itypeN} are the central atom, and atoms of any of the range of -types represented by {jtypeN} are the distribution atom. - -Pairwise distances are generated by looping over a pairwise neighbor -list, just as they would be in a "pair_style"_pair_style.html -computation. The distance between two atoms I and J is included in a -specific histogram if the following criteria are met: - -atoms I,J are both in the specified compute group -the distance between atoms I,J is less than the maximum force cutoff -the type of the I atom matches itypeN (one or a range of types) -the type of the J atom matches jtypeN (one or a range of types) :ul - -It is OK if a particular pairwise distance is included in more than -one individual histogram, due to the way the {itypeN} and {jtypeN} -arguments are specified. - -The g(r) value for a bin is calculated from the histogram count by -scaling it by the idealized number of how many counts there would be -if atoms of type {jtypeN} were uniformly distributed. Thus it -involves the count of {itypeN} atoms, the count of {jtypeN} atoms, the -volume of the entire simulation box, and the volume of the bin's thin -shell in 3d (or the area of the bin's thin ring in 2d). - -A coordination number coord(r) is also calculated, which is the number -of atoms of type {jtypeN} within the current bin or closer, averaged -over atoms of type {itypeN}. This is calculated as the area- or -volume-weighted sum of g(r) values over all bins up to and including -the current bin, multiplied by the global average volume density of -atoms of type jtypeN. - -The simplest way to output the results of the compute rdf calculation -to a file is to use the "fix ave/time"_fix_ave_time.html command, for -example: - -compute myRDF all rdf 50 -fix 1 all ave/time 100 1 100 c_myRDF\[*\] file tmp.rdf mode vector :pre - -[Output info:] - -This compute calculates a global array with the number of rows = -{Nbins}, and the number of columns = 1 + 2*Npairs, where Npairs is the -number of I,J pairings specified. The first column has the bin -coordinate (center of the bin), Each successive set of 2 columns has -the g(r) and coord(r) values for a specific set of {itypeN} versus -{jtypeN} interactions, as described above. These values can be used -by any command that uses a global values from a compute as input. See -the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The array values calculated by this compute are all "intensive". - -The first column of array values will be in distance -"units"_units.html. The g(r) columns of array values are normalized -numbers >= 0.0. The coordination number columns of array values are -also numbers >= 0.0. - -[Restrictions:] - -The RDF is not computed for distances longer than the force cutoff, -since processors (in parallel) don't know about atom coordinates for -atoms further away than that distance. If you want an RDF for larger -distances, you can use the "rerun"_rerun.html command to post-process -a dump file and set the cutoff for the potential to be longer in the -rerun script. Note that in the rerun context, the force cutoff is -arbitrary, since you aren't running dynamics and thus are not changing -your model. The definition of g(r) used by LAMMPS is only appropriate -for characterizing atoms that are uniformly distributed throughout the -simulation cell. In such cases, the coordination number is still -correct and meaningful. As an example, if a large simulation cell -contains only one atom of type {itypeN} and one of {jtypeN}, then g(r) -will register an arbitrarily large spike at whatever distance they -happen to be at, and zero everywhere else. Coord(r) will show a step -change from zero to one at the location of the spike in g(r). - -NOTE: compute rdf can handle dynamic groups and systems where atoms -are added or removed, but this causes that certain normalization -parameters need to be re-computed in every step and include collective -communication operations. This will reduce performance and limit -parallel efficiency and scaling. For systems, where only the type -of atoms changes (e.g. when using "fix atom/swap"_fix_atom_swap.html), -you need to explicitly request the dynamic normalization updates -via "compute_modify dynamic yes"_compute_modify.html - -[Related commands:] - -"fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html, -"compute adf"_compute_adf.html - -[Default:] - -The keyword defaults are cutoff = 0.0 (use the pairwise force cutoff). diff --git a/doc/txt/compute_reduce.txt b/doc/txt/compute_reduce.txt deleted file mode 100644 index 1e9cc651e1..0000000000 --- a/doc/txt/compute_reduce.txt +++ /dev/null @@ -1,212 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute reduce command :h3 -compute reduce/region command :h3 - -[Syntax:] - -compute ID group-ID style arg mode input1 input2 ... keyword args ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -style = {reduce} or {reduce/region} :l - {reduce} arg = none - {reduce/region} arg = region-ID - region-ID = ID of region to use for choosing atoms :pre -mode = {sum} or {min} or {max} or {ave} or {sumsq} or {avesq} :l -one or more inputs can be listed :l -input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l - x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) - c_ID = per-atom or local vector calculated by a compute with ID - c_ID\[I\] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below) - f_ID = per-atom or local vector calculated by a fix with ID - f_ID\[I\] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below) - v_name = per-atom vector calculated by an atom-style variable with name :pre - -zero or more keyword/args pairs may be appended :l -keyword = {replace} :l - {replace} args = vec1 vec2 - vec1 = reduced value from this input vector will be replaced - vec2 = replace it with vec1\[N\] where N is index of max/min value from vec2 :pre -:ule - -[Examples:] - -compute 1 all reduce sum c_force -compute 1 all reduce/region subbox sum c_force -compute 2 all reduce min c_press\[2\] f_ave v_myKE -compute 2 all reduce min c_press\[*\] f_ave v_myKE -compute 3 fluid reduce max c_index\[1\] c_index\[2\] c_dist replace 1 3 replace 2 3 :pre - -[Description:] - -Define a calculation that "reduces" one or more vector inputs into -scalar values, one per listed input. The inputs can be per-atom or -local quantities; they cannot be global quantities. Atom attributes -are per-atom quantities, "computes"_compute.html and "fixes"_fix.html -may generate any of the three kinds of quantities, and "atom-style -variables"_variable.html generate per-atom quantities. See the -"variable"_variable.html command and its special functions which can -perform the same operations as the compute reduce command on global -vectors. - -The reduction operation is specified by the {mode} setting. The {sum} -option adds the values in the vector into a global total. The {min} -or {max} options find the minimum or maximum value across all vector -values. The {ave} setting adds the vector values into a global total, -then divides by the number of values in the vector. The {sumsq} -option sums the square of the values in the vector into a global -total. The {avesq} setting does the same as {sumsq}, then divides the -sum of squares by the number of values. The last two options can be -useful for calculating the variance of some quantity, e.g. variance = -sumsq - ave^2. - -Each listed input is operated on independently. For per-atom inputs, -the group specified with this command means only atoms within the -group contribute to the result. For per-atom inputs, if the compute -reduce/region command is used, the atoms must also currently be within -the region. Note that an input that produces per-atom quantities may -define its own group which affects the quantities it returns. For -example, if a compute is used as an input which generates a per-atom -vector, it will generate values of 0.0 for atoms that are not in the -group specified for that compute. - -Each listed input can be an atom attribute (position, velocity, force -component) or can be the result of a "compute"_compute.html or -"fix"_fix.html or the evaluation of an atom-style -"variable"_variable.html. - -Note that for values from a compute or fix, the bracketed index I can -be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form "*" or "*n" or "n*" or -"m*n". If N = the size of the vector (for {mode} = scalar) or the -number of columns in the array (for {mode} = vector), then an asterisk -with no numeric values means all indices from 1 to N. A leading -asterisk means all indices from 1 to n (inclusive). A trailing -asterisk means all indices from n to N (inclusive). A middle asterisk -means all indices from m to n (inclusive). - -Using a wildcard is the same as if the individual columns of the array -had been listed one by one. E.g. these 2 compute reduce commands are -equivalent, since the "compute stress/atom"_compute_stress_atom.html -command creates a per-atom array with 6 columns: - -compute myPress all stress/atom NULL -compute 2 all reduce min c_myPress\[*\] -compute 2 all reduce min c_myPress\[1\] c_myPress\[2\] c_myPress\[3\] & - c_myPress\[4\] c_myPress\[5\] c_myPress\[6\] :pre - -:line - -The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are -self-explanatory. Note that other atom attributes can be used as -inputs to this fix by using the "compute -property/atom"_compute_property_atom.html command and then specifying -an input value from that compute. - -If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. Computes can generate -per-atom or local quantities. See the individual -"compute"_compute.html doc page for details. If no bracketed integer -is appended, the vector calculated by the compute is used. If a -bracketed integer is appended, the Ith column of the array calculated -by the compute is used. Users can also write code for their own -compute styles and "add them to LAMMPS"_Modify.html. See the -discussion above for how I can be specified with a wildcard asterisk -to effectively specify multiple values. - -If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. Fixes can generate per-atom -or local quantities. See the individual "fix"_fix.html doc page for -details. Note that some fixes only produce their values on certain -timesteps, which must be compatible with when compute reduce -references the values, else an error results. If no bracketed integer -is appended, the vector calculated by the fix is used. If a bracketed -integer is appended, the Ith column of the array calculated by the fix -is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Modify.html. See the discussion above for how I can -be specified with a wildcard asterisk to effectively specify multiple -values. - -If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. It must be an -"atom-style variable"_variable.html. Atom-style variables can -reference thermodynamic keywords and various per-atom attributes, or -invoke other computes, fixes, or variables when they are evaluated, so -this is a very general means of generating per-atom quantities to -reduce. - -:line - -If the {replace} keyword is used, two indices {vec1} and {vec2} are -specified, where each index ranges from 1 to the # of input values. -The replace keyword can only be used if the {mode} is {min} or {max}. -It works as follows. A min/max is computed as usual on the {vec2} -input vector. The index N of that value within {vec2} is also stored. -Then, instead of performing a min/max on the {vec1} input vector, the -stored index is used to select the Nth element of the {vec1} vector. - -Thus, for example, if you wish to use this compute to find the bond -with maximum stretch, you can do it as follows: - -compute 1 all property/local batom1 batom2 -compute 2 all bond/local dist -compute 3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3 -thermo_style custom step temp c_3\[1\] c_3\[2\] c_3\[3\] :pre - -The first two input values in the compute reduce command are vectors -with the IDs of the 2 atoms in each bond, using the "compute -property/local"_compute_property_local.html command. The last input -value is bond distance, using the "compute -bond/local"_compute_bond_local.html command. Instead of taking the -max of the two atom ID vectors, which does not yield useful -information in this context, the {replace} keywords will extract the -atom IDs for the two atoms in the bond of maximum stretch. These atom -IDs and the bond stretch will be printed with thermodynamic output. - -:line - -If a single input is specified this compute produces a global scalar -value. If multiple inputs are specified, this compute produces a -global vector of values, the length of which is equal to the number of -inputs specified. - -As discussed below, for the {sum} and {sumsq} modes, the value(s) -produced by this compute are all "extensive", meaning their value -scales linearly with the number of atoms involved. If normalized -values are desired, this compute can be accessed by the "thermo_style -custom"_thermo_style.html command with "thermo_modify norm -yes"_thermo_modify.html set as an option. Or it can be accessed by a -"variable"_variable.html that divides by the appropriate atom count. - -:line - -[Output info:] - -This compute calculates a global scalar if a single input value is -specified or a global vector of length N where N is the number of -inputs, and which can be accessed by indices 1 to N. These values can -be used by any command that uses global scalar or vector values from a -compute as input. See the "Howto output"_Howto_output.html doc page -for an overview of LAMMPS output options. - -All the scalar or vector values calculated by this compute are -"intensive", except when the {sum} or {sumsq} modes are used on -per-atom or local vectors, in which case the calculated values are -"extensive". - -The scalar or vector values will be in whatever "units"_units.html the -quantities being reduced are in. - -[Restrictions:] none - -[Related commands:] - -"compute"_compute.html, "fix"_fix.html, "variable"_variable.html - -[Default:] none diff --git a/doc/txt/compute_reduce_chunk.txt b/doc/txt/compute_reduce_chunk.txt deleted file mode 100644 index f19ed00c6a..0000000000 --- a/doc/txt/compute_reduce_chunk.txt +++ /dev/null @@ -1,177 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute reduce/chunk command :h3 - -[Syntax:] - -compute ID group-ID reduce/chunk chunkID mode input1 input2 ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -reduce/chunk = style name of this compute command :l -chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l -mode = {sum} or {min} or {max} :l -one or more inputs can be listed :l -input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_ID :l - c_ID = per-atom vector calculated by a compute with ID - c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) - f_ID = per-atom vector calculated by a fix with ID - f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) - v_name = per-atom vector calculated by an atom-style variable with name :pre -:ule - -[Examples:] - -compute 1 all reduce/chunk/atom mychunk min c_cluster :pre - -[Description:] - -Define a calculation that reduces one or more per-atom vectors into -per-chunk values. This can be useful for diagnostic output. Or when -used in conjunction with the "compute -chunk/spread/atom"_compute_chunk_spread_atom.html command it can be -used ot create per-atom values that induce a new set of chunks with a -second "compute chunk/atom"_compute_chunk_atom.html command. An -example is given below. - -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. - -For each atom, this compute accesses its chunk ID from the specified -{chunkID} compute. The per-atom value from an input contributes -to a per-chunk value corresponding the the chunk ID. - -The reduction operation is specified by the {mode} setting and is -performed over all the per-atom values from the atoms in each chunk. -The {sum} option adds the pre-atom values to a per-chunk total. The -{min} or {max} options find the minimum or maximum value of the -per-atom values for each chunk. - -Note that only atoms in the specified group contribute to the -reduction operation. If the {chunkID} compute returns a 0 for the -chunk ID of an atom (i.e. the atom is not in a chunk defined by the -"compute chunk/atom"_compute_chunk_atom.html command), that atom will -also not contribute to the reduction operation. An input that is a -compute or fix may define its own group which affects the quantities -it returns. For example, a compute with return a zero value for atoms -that are not in the group specified for that compute. - -Each listed input is operated on independently. Each input can be the -result of a "compute"_compute.html or "fix"_fix.html or the evaluation -of an atom-style "variable"_variable.html. - -Note that for values from a compute or fix, the bracketed index I can -be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form "*" or "*n" or "n*" or -"m*n". If N = the size of the vector (for {mode} = scalar) or the -number of columns in the array (for {mode} = vector), then an asterisk -with no numeric values means all indices from 1 to N. A leading -asterisk means all indices from 1 to n (inclusive). A trailing -asterisk means all indices from n to N (inclusive). A middle asterisk -means all indices from m to n (inclusive). - -Using a wildcard is the same as if the individual columns of the array -had been listed one by one. E.g. these 2 compute reduce/chunk -commands are equivalent, since the "compute -property/chunk"_compute_property_chunk.html command creates a per-atom -array with 3 columns: - -compute prop all property/atom vx vy vz -compute 10 all reduce/chunk mychunk max c_prop\[*\] -compute 10 all reduce/chunk mychunk max c_prop\[1\] c_prop\[2\] c_prop\[3\] :pre - -:line - -Here is an example of using this compute, in conjunction with the -compute chunk/spread/atom command to identify self-assembled micelles. -The commands below can be added to the examples/in.micelle script. - -Imagine a collection of polymer chains or small molecules with -hydrophobic end groups. All the hydrophobic (HP) atoms are assigned -to a group called "phobic". - -These commands will assign a unique cluster ID to all HP atoms within -a specified distance of each other. A cluster will contain all HP -atoms in a single molecule, but also the HP atoms in nearby molecules, -e.g. molecules that have clumped to form a micelle due to the -attraction induced by the hydrophobicity. The output of the -chunk/reduce command will be a cluster ID per chunk (molecule). -Molecules with the same cluster ID are in the same micelle. - -group phobic type 4 # specific to in.micelle model -compute cluster phobic cluster/atom 2.0 -compute cmol all chunk/atom molecule -compute reduce phobic reduce/chunk cmol min c_cluster :pre - -This per-chunk info could be output in at least two ways: - -fix 10 all ave/time 1000 1 1000 c_reduce file tmp.phobic mode vector :pre - -compute spread all chunk/spread/atom cmol c_reduce -dump 1 all custom 1000 tmp.dump id type mol x y z c_cluster c_spread -dump_modify 1 sort id :pre - -In the first case, each snapshot in the tmp.phobic file will contain -one line per molecule. Molecules with the same value are in the same -micelle. In the second case each dump snapshot contains all atoms, -each with a final field with the cluster ID of the micelle that the HP -atoms of that atom's molecule belong to. - -The result from compute chunk/spread/atom can be used to define a new -set of chunks, where all the atoms in all the molecules in the same -micelle are assigned to the same chunk, i.e. one chunk per micelle. - -compute micelle all chunk/atom c_spread compress yes :pre - -Further analysis on a per-micelle basis can now be performed using any -of the per-chunk computes listed on the "Howto chunk"_Howto_chunk.html -doc page. E.g. count the number of atoms in each micelle, calculate -its center or mass, shape (moments of inertia), radius of gyration, -etc. - -compute prop all property/chunk micelle count -fix 20 all ave/time 1000 1 1000 c_prop file tmp.micelle mode vector :pre - -Each snapshot in the tmp.micelle file will have one line per micelle -with its count of atoms, plus a first line for a chunk with all the -solvent atoms. By the time 50000 steps have elapsed there are a -handful of large micelles. - -:line - -[Output info:] - -This compute calculates a global vector if a single input value is -specified, otherwise a global array is output. The number of columns -in the array is the number of inputs provided. The length of the -vector or the number of vector elements or array rows = the number of -chunks {Nchunk} as calculated by the specified "compute -chunk/atom"_compute_chunk_atom.html command. The vector or array can -be accessed by any command that uses global values from a compute as -input. See the "Howto output"_Howto_output.html doc page for an -overview of LAMMPS output options. - -The per-atom values for the vector or each column of the array will be -in whatever "units"_units.html the corresponding input value is in. -The vector or array values are "intensive". - -[Restrictions:] none - -[Related commands:] - -"compute chunk/atom"_compute_chunk_atom.html, "compute -reduce"_compute_reduce.html, "compute -chunk/spread/atom"_compute_chunk_spread_atom.html - -[Default:] none diff --git a/doc/txt/compute_rigid_local.txt b/doc/txt/compute_rigid_local.txt deleted file mode 100644 index 73e9e4a609..0000000000 --- a/doc/txt/compute_rigid_local.txt +++ /dev/null @@ -1,185 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute rigid/local command :h3 - -[Syntax:] - -compute ID group-ID rigid/local rigidID input1 input2 ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -rigid/local = style name of this compute command :l -rigidID = ID of fix rigid/small command or one of its variants :l -input = one or more rigid body attributes :l - possible attributes = id, mol, mass, - x, y, z, xu, yu, zu, ix, iy, iz - vx, vy, vz, fx, fy, fz, - omegax, omegay, omegaz, - angmomx, angmomy, angmomz, - quatw, quati, quatj, quatk, - tqx, tqy, tqz, - inertiax, inertiay, inertiaz - id = atom ID of atom within body which owns body properties - mol = molecule ID used to define body in "fix rigid/small"_fix_rigid.html command - mass = total mass of body - x,y,z = center of mass coords of body - xu,yu,zu = unwrapped center of mass coords of body - ix,iy,iz = box image that the center of mass is in - vx,vy,vz = center of mass velocities - fx,fy,fz = force of center of mass - omegax,omegay,omegaz = angular velocity of body - angmomx,angmomy,angmomz = angular momentum of body - quatw,quati,quatj,quatk = quaternion components for body - tqx,tqy,tqz = torque on body - inertiax,inertiay,inertiaz = diagonalized moments of inertia of body :pre -:ule - -[Examples:] - -compute 1 all rigid/local myRigid mol x y z :pre - -[Description:] - -Define a computation that simply stores rigid body attributes for -rigid bodies defined by the "fix rigid/small"_fix_rigid.html command -or one of its NVE, NVT, NPT, NPH variants. The data is stored as -local data so it can be accessed by other "output -commands"_Howto_output.html that process local data, such as the -"compute reduce"_compute_reduce.html or "dump local"_dump.html -commands. - -Note that this command only works with the "fix -rigid/small"_fix_rigid.html command or its variants, not the fix rigid -command and its variants. The ID of the "fix -rigid/small"_fix_rigid.html command used to define rigid bodies must -be specified as {rigidID}. The "fix rigid"_fix_rigid.html command is -typically used to define a handful of (potentially very large) rigid -bodies. It outputs similar per-body information as this command -directly from the fix as global data; see the "fix -rigid"_fix_rigid.html doc page for details - -The local data stored by this command is generated by looping over all -the atoms owned on a processor. If the atom is not in the specified -{group-ID} or is not part of a rigid body it is skipped. If it is not -the atom within a body that is assigned to store the body information -it is skipped (only one atom per body is so assigned). If it is the -assigned atom, then the info for that body is output. This means that -information for N bodies is generated. N may be less than the # of -bodies defined by the fix rigid command, if the atoms in some bodies -are not in the {group-ID}. - -NOTE: Which atom in a body owns the body info is determined internal -to LAMMPS; it's the one nearest the geometric center of the body. -Typically you should avoid this complication, by defining the group -associated with this fix to include/exclude entire bodies. - -Note that as atoms and bodies migrate from processor to processor, -there will be no consistent ordering of the entries within the local -vector or array from one timestep to the next. - -Here is an example of how to use this compute to dump rigid body info -to a file: - -compute 1 all rigid/local myRigid mol x y z fx fy fz -dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\] c_1\[6\] c_1\[7\] :pre - -:line - -This section explains the rigid body attributes that can be specified. - -The {id} attribute is the atom-ID of the atom which owns the rigid body, which is -assigned by the "fix rigid/small"_fix_rigid.html command. - -The {mol} attribute is the molecule ID of the rigid body. It should -be the molecule ID which all of the atoms in the body belong to, since -that is how the "fix rigid/small"_fix_rigid.html command defines its -rigid bodies. - -The {mass} attribute is the total mass of the rigid body. - -There are two options for outputting the coordinates of the center of -mass (COM) of the body. The {x}, {y}, {z} attributes write the COM -"unscaled", in the appropriate distance "units"_units.html (Angstroms, -sigma, etc). Use {xu}, {yu}, {zu} if you want the COM "unwrapped" by -the image flags for each body. Unwrapped means that if the body -COM has passed through a periodic boundary one or more times, the value -is generated what the COM coordinate would be if it had not been -wrapped back into the periodic box. - -The image flags for the body can be generated directly using the {ix}, -{iy}, {iz} attributes. For periodic dimensions, they specify which -image of the simulation box the COM is considered to be in. An image -of 0 means it is inside the box as defined. A value of 2 means add 2 -box lengths to get the true value. A value of -1 means subtract 1 box -length to get the true value. LAMMPS updates these flags as the rigid -body COMs cross periodic boundaries during the simulation. - -The {vx}, {vy}, {vz}, {fx}, {fy}, {fz} attributes are components of -the COM velocity and force on the COM of the body. - -The {omegax}, {omegay}, and {omegaz} attributes are the angular -velocity components of the body around its COM. - -The {angmomx}, {angmomy}, and {angmomz} attributes are the angular -momentum components of the body around its COM. - -The {quatw}, {quati}, {quatj}, and {quatk} attributes are the -components of the 4-vector quaternion representing the orientation of -the rigid body. See the "set"_set.html command for an explanation of -the quaternion vector. - -The {angmomx}, {angmomy}, and {angmomz} attributes are the angular -momentum components of the body around its COM. - -The {tqx}, {tqy}, {tqz} attributes are components of the torque acting -on the body around its COM. - -The {inertiax}, {inertiay}, {inertiaz} attributes are components of -diagonalized inertia tensor for the body, i.e the 3 moments of inertia -for the body around its principal axes, as computed internally by -LAMMPS. - -:line - -[Output info:] - -This compute calculates a local vector or local array depending on the -number of keywords. The length of the vector or number of rows in the -array is the number of rigid bodies. If a single keyword is -specified, a local vector is produced. If two or more keywords are -specified, a local array is produced where the number of columns = the -number of keywords. The vector or array can be accessed by any -command that uses local values from a compute as input. See the -"Howto output"_Howto_output.html doc page for an overview of LAMMPS -output options. - -The vector or array values will be in whatever "units"_units.html the -corresponding attribute is in: - -id,mol = unitless -mass = mass units -x,y,z and xy,yu,zu = distance units -vx,vy,vz = velocity units -fx,fy,fz = force units -omegax,omegay,omegaz = radians/time units -angmomx,angmomy,angmomz = mass*distance^2/time units -quatw,quati,quatj,quatk = unitless -tqx,tqy,tqz = torque units -inertiax,inertiay,inertiaz = mass*distance^2 units :ul - -[Restrictions:] - -This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"dump local"_dump.html, "compute reduce"_compute_reduce.html - -[Default:] none diff --git a/doc/txt/compute_saed.txt b/doc/txt/compute_saed.txt deleted file mode 100644 index b27c36e318..0000000000 --- a/doc/txt/compute_saed.txt +++ /dev/null @@ -1,181 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute saed command :h3 - -[Syntax:] - -compute ID group-ID saed lambda type1 type2 ... typeN keyword value ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -saed = style name of this compute command :l -lambda = wavelength of incident radiation (length units) :l -type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) :l - -zero or more keyword/value pairs may be appended :l -keyword = {Kmax} or {Zone} or {dR_Ewald} or {c} or {manual} or {echo} :l - {Kmax} value = Maximum distance explored from reciprocal space origin - (inverse length units) - {Zone} values = z1 z2 z3 - z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all - reciprocal space will be meshed up to {Kmax} - {dR_Ewald} value = Thickness of Ewald sphere slice intercepting - reciprocal space (inverse length units) - {c} values = c1 c2 c3 - c1,c2,c3 = parameters to adjust the spacing of the reciprocal - lattice nodes in the h, k, and l directions respectively - {manual} = flag to use manual spacing of reciprocal lattice points - based on the values of the {c} parameters - {echo} = flag to provide extra output for debugging purposes :pre -:ule - -[Examples:] - -compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 -compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo :pre - -fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed -fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre - -[Description:] - -Define a computation that calculates electron diffraction intensity as -described in "(Coleman)"_#saed-Coleman on a mesh of reciprocal lattice nodes -defined by the entire simulation domain (or manually) using simulated -radiation of wavelength lambda. - -The electron diffraction intensity I at each reciprocal lattice point -is computed from the structure factor F using the equations: - -:c,image(Eqs/compute_saed1.jpg) -:c,image(Eqs/compute_saed2.jpg) - -Here, K is the location of the reciprocal lattice node, rj is the -position of each atom, fj are atomic scattering factors. - -Diffraction intensities are calculated on a three-dimensional mesh of -reciprocal lattice nodes. The mesh spacing is defined either (a) by -the entire simulation domain or (b) manually using selected values as -shown in the 2D diagram below. - -:c,image(JPG/saed_mesh_small.jpg,JPG/saed_mesh.jpg) - -For a mesh defined by the simulation domain, a rectilinear grid is -constructed with spacing {c}*inv(A) along each reciprocal lattice -axis. Where A are the vectors corresponding to the edges of the -simulation cell. If one or two directions has non-periodic boundary -conditions, then the spacing in these directions is defined from the -average of the (inversed) box lengths with periodic boundary conditions. -Meshes defined by the simulation domain must contain at least one periodic -boundary. - -If the {manual} flag is included, the mesh of reciprocal lattice nodes -will defined using the {c} values for the spacing along each reciprocal -lattice axis. Note that manual mapping of the reciprocal space mesh is -good for comparing diffraction results from multiple simulations; however -it can reduce the likelihood that Bragg reflections will be satisfied -unless small spacing parameters <0.05 Angstrom^(-1) are implemented. -Meshes with manual spacing do not require a periodic boundary. - -The limits of the reciprocal lattice mesh are determined by the use of -the {Kmax}, {Zone}, and {dR_Ewald} parameters. The rectilinear mesh -created about the origin of reciprocal space is terminated at the -boundary of a sphere of radius {Kmax} centered at the origin. If -{Zone} parameters z1=z2=z3=0 are used, diffraction intensities are -computed throughout the entire spherical volume - note this can -greatly increase the cost of computation. Otherwise, {Zone} -parameters will denote the z1=h, z2=k, and z3=l (in a global since) -zone axis of an intersecting Ewald sphere. Diffraction intensities -will only be computed at the intersection of the reciprocal lattice -mesh and a {dR_Ewald} thick surface of the Ewald sphere. See the -example 3D intensity data and the intersection of a \[010\] zone axis -in the below image. - -:c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg) - -The atomic scattering factors, fj, accounts for the reduction in -diffraction intensity due to Compton scattering. Compute saed uses -analytical approximations of the atomic scattering factors that vary -for each atom type (type1 type2 ... typeN) and angle of diffraction. -The analytic approximation is computed using the formula -"(Brown)"_#Brown: - -:c,image(Eqs/compute_saed3.jpg) - -Coefficients parameterized by "(Fox)"_#Fox are assigned for each -atom type designating the chemical symbol and charge of each atom -type. Valid chemical symbols for compute saed are: - -H: He: Li: Be: B: -C: N: O: F: Ne: -Na: Mg: Al: Si: P: -S: Cl: Ar: K: Ca: -Sc: Ti: V: Cr: Mn: -Fe: Co: Ni: Cu: Zn: -Ga: Ge: As: Se: Br: -Kr: Rb: Sr: Y: Zr: -Nb: Mo: Tc: Ru: Rh: -Pd: Ag: Cd: In: Sn: -Sb: Te: I: Xe: Cs: -Ba: La: Ce: Pr: Nd: -Pm: Sm: Eu: Gd: Tb: -Dy: Ho: Er: Tm: Yb: -Lu: Hf: Ta: W: Re: -Os: Ir: Pt: Au: Hg: -Tl: Pb: Bi: Po: At: -Rn: Fr: Ra: Ac: Th: -Pa: U: Np: Pu: Am: -Cm: Bk: Cf:tb(c=5,s=:) - - -If the {echo} keyword is specified, compute saed will provide extra -reporting information to the screen. - -[Output info:] - -This compute calculates a global vector. The length of the vector is -the number of reciprocal lattice nodes that are explored by the mesh. -The entries of the global vector are the computed diffraction -intensities as described above. - -The vector can be accessed by any command that uses global values from -a compute as input. See the "Howto output"_Howto_output.html doc page -for an overview of LAMMPS output options. - -All array values calculated by this compute are "intensive". - -[Restrictions:] - -This compute is part of the USER-DIFFRACTION package. It is only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -The compute_saed command does not work for triclinic cells. - -[Related commands:] - -"fix saed_vtk"_fix_saed_vtk.html, "compute xrd"_compute_xrd.html - -[Default:] - -The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald = -0.01. - -:line - -:link(saed-Coleman) -[(Coleman)] Coleman, Spearot, Capolungo, MSMSE, 21, 055020 -(2013). - -:link(Brown) -[(Brown)] Brown et al. International Tables for Crystallography -Volume C: Mathematical and Chemical Tables, 554-95 (2004). - -:link(Fox) -[(Fox)] Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93 -(1989). diff --git a/doc/txt/compute_slice.txt b/doc/txt/compute_slice.txt deleted file mode 100644 index 51031aeab3..0000000000 --- a/doc/txt/compute_slice.txt +++ /dev/null @@ -1,123 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute slice command :h3 - -[Syntax:] - -compute ID group-ID slice Nstart Nstop Nskip input1 input2 ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -slice = style name of this compute command :l -Nstart = starting index within input vector(s) :l -Nstop = stopping index within input vector(s) :l -Nskip = extract every Nskip elements from input vector(s) :l -input = c_ID, c_ID\[N\], f_ID, f_ID\[N\] :l - c_ID = global vector calculated by a compute with ID - c_ID\[I\] = Ith column of global array calculated by a compute with ID - f_ID = global vector calculated by a fix with ID - f_ID\[I\] = Ith column of global array calculated by a fix with ID - v_name = vector calculated by an vector-style variable with name :pre -:ule - -[Examples:] - -compute 1 all slice 1 100 10 c_msdmol\[4\] -compute 1 all slice 301 400 1 c_msdmol\[4\] v_myVec :pre - -[Description:] - -Define a calculation that "slices" one or more vector inputs into -smaller vectors, one per listed input. The inputs can be global -quantities; they cannot be per-atom or local quantities. -"Computes"_compute.html and "fixes"_fix.html and vector-style -"variables"_variable.html can generate such global quantities. The -group specified with this command is ignored. - -The values extracted from the input vector(s) are determined by the -{Nstart}, {Nstop}, and {Nskip} parameters. The elements of an input -vector of length N are indexed from 1 to N. Starting at element -{Nstart}, every Mth element is extracted, where M = {Nskip}, until -element {Nstop} is reached. The extracted quantities are stored as a -vector, which is typically shorter than the input vector. - -Each listed input is operated on independently to produce one output -vector. Each listed input must be a global vector or column of a -global array calculated by another "compute"_compute.html or -"fix"_fix.html. - -If an input value begins with "c_", a compute ID must follow which has -been previously defined in the input script and which generates a -global vector or array. See the individual "compute"_compute.html doc -page for details. If no bracketed integer is appended, the vector -calculated by the compute is used. If a bracketed integer is -appended, the Ith column of the array calculated by the compute is -used. Users can also write code for their own compute styles and "add -them to LAMMPS"_Modify.html. - -If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script and which generates a global -vector or array. See the individual "fix"_fix.html doc page for -details. Note that some fixes only produce their values on certain -timesteps, which must be compatible with when compute slice references -the values, else an error results. If no bracketed integer is -appended, the vector calculated by the fix is used. If a bracketed -integer is appended, the Ith column of the array calculated by the fix -is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Modify.html. - -If an input value begins with "v_", a variable name must follow which -has been previously defined in the input script. Only vector-style -variables can be referenced. See the "variable"_variable.html command -for details. Note that variables of style {vector} define a formula -which can reference individual atom properties or thermodynamic -keywords, or they can invoke other computes, fixes, or variables when -they are evaluated, so this is a very general means of specifying -quantities to slice. - -If a single input is specified this compute produces a global vector, -even if the length of the vector is 1. If multiple inputs are -specified, then a global array of values is produced, with the number -of columns equal to the number of inputs specified. - -:line - -[Output info:] - -This compute calculates a global vector if a single input value is -specified or a global array with N columns where N is the number of -inputs. The length of the vector or the number of rows in the array -is equal to the number of values extracted from each input vector. -These values can be used by any command that uses global vector or -array values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The vector or array values calculated by this compute are simply -copies of values generated by computes or fixes or variables that are -input vectors to this compute. If there is a single input vector of -intensive and/or extensive values, then each value in the vector of -values calculated by this compute will be "intensive" or "extensive", -depending on the corresponding input value. If there are multiple -input vectors, and all the values in them are intensive, then the -array values calculated by this compute are "intensive". If there are -multiple input vectors, and any value in them is extensive, then the -array values calculated by this compute are "extensive". Values -produced by a variable are treated as intensive. - -The vector or array values will be in whatever "units"_units.html the -input quantities are in. - -[Restrictions:] none - -[Related commands:] - -"compute"_compute.html, "fix"_fix.html, "compute -reduce"_compute_reduce.html - -[Default:] none diff --git a/doc/txt/compute_smd_contact_radius.txt b/doc/txt/compute_smd_contact_radius.txt deleted file mode 100644 index 4ab03e3738..0000000000 --- a/doc/txt/compute_smd_contact_radius.txt +++ /dev/null @@ -1,55 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/contact/radius command :h3 - -[Syntax:] - -compute ID group-ID smd/contact/radius :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/contact/radius = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/contact/radius :pre - -[Description:] - -Define a computation which outputs the contact radius, i.e., the -radius used to prevent particles from penetrating each other. The -contact radius is used only to prevent particles belonging to -different physical bodies from penetrating each other. It is used by -the contact pair styles, e.g., smd/hertz and smd/tri_surface. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth -Mach Dynamics in LAMMPS. - -The value of the contact radius will be 0.0 for particles not in the -specified compute group. - -[Output info:] - -This compute calculates a per-particle vector, which can be accessed -by any command that uses per-particle values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle vector values will be in distance "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"dump custom"_dump.html smd/hertz smd/tri_surface - -[Default:] none diff --git a/doc/txt/compute_smd_damage.txt b/doc/txt/compute_smd_damage.txt deleted file mode 100644 index 139fb3ec7b..0000000000 --- a/doc/txt/compute_smd_damage.txt +++ /dev/null @@ -1,48 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/damage command :h3 - -[Syntax:] - -compute ID group-ID smd/damage :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/damage = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/damage :pre - -[Description:] - -Define a computation that calculates the damage status of SPH particles -according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. - -[Output Info:] - -This compute calculates a per-particle vector, which can be accessed -by any command that uses per-particle values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle values are dimensionless an in the range of zero to one. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build - - -[Related commands:] - -"smd/plastic_strain"_compute_smd_plastic_strain.html, "smd/tlsph_stress"_compute_smd_tlsph_stress.html - -[Default:] none diff --git a/doc/txt/compute_smd_hourglass_error.txt b/doc/txt/compute_smd_hourglass_error.txt deleted file mode 100644 index 28f1f351a8..0000000000 --- a/doc/txt/compute_smd_hourglass_error.txt +++ /dev/null @@ -1,62 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/hourglass/error command :h3 - -[Syntax:] - -compute ID group-ID smd/hourglass/error :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/hourglass/error = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/hourglass/error :pre - -[Description:] - -Define a computation which outputs the error of the approximated -relative separation with respect to the actual relative separation of -the particles i and j. Ideally, if the deformation gradient is exact, -and there exists a unique mapping between all particles' positions -within the neighborhood of the central node and the deformation -gradient, the approximated relative separation will coincide with the -actual relative separation of the particles i and j in the deformed -configuration. This compute is only really useful for debugging the -hourglass control mechanism which is part of the Total-Lagrangian SPH -pair style. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth -Mach Dynamics in LAMMPS. - -[Output Info:] - -This compute calculates a per-particle vector, which can be accessed -by any command that uses per-particle values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle vector values will are dimensionless. See -"units"_units.html. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This quantity will be computed only for particles which interact with -tlsph pair style. - -[Related Commands:] - -"smd/tlsph_defgrad"_compute_smd_tlsph_defgrad.html - -[Default:] - diff --git a/doc/txt/compute_smd_internal_energy.txt b/doc/txt/compute_smd_internal_energy.txt deleted file mode 100644 index b9d18ce933..0000000000 --- a/doc/txt/compute_smd_internal_energy.txt +++ /dev/null @@ -1,49 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/internal/energy command :h3 - -[Syntax:] - -compute ID group-ID smd/internal/energy :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/smd/internal/energy = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/internal/energy :pre - -[Description:] - -Define a computation which outputs the per-particle enthalpy, i.e., -the sum of potential energy and heat. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth -Mach Dynamics in LAMMPS. - -[Output Info:] - -This compute calculates a per-particle vector, which can be accessed -by any command that uses per-particle values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle vector values will be given in "units"_units.html of energy. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. This compute can -only be used for particles which interact via the updated Lagrangian -or total Lagrangian SPH pair styles. - -[Related Commands:] - -[Default:] diff --git a/doc/txt/compute_smd_plastic_strain.txt b/doc/txt/compute_smd_plastic_strain.txt deleted file mode 100644 index d12be7222a..0000000000 --- a/doc/txt/compute_smd_plastic_strain.txt +++ /dev/null @@ -1,54 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/plastic/strain command :h3 - -[Syntax:] - -compute ID group-ID smd/plastic/strain :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/plastic/strain = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/plastic/strain :pre - -[Description:] - -Define a computation that outputs the equivalent plastic strain per -particle. This command is only meaningful if a material model with -plasticity is defined. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth -Mach Dynamics in LAMMPS. - -[Output Info:] - -This compute calculates a per-particle vector, which can be accessed -by any command that uses per-particle values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle values will be given dimensionless. See "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. This compute can -only be used for particles which interact via the updated Lagrangian -or total Lagrangian SPH pair styles. - -[Related commands:] - -"smd/plastic/strain/rate"_compute_smd_tlsph_strain.html, -"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, -"smd/tlsph/strain"_compute_smd_tlsph_strain.html - -[Default:] none diff --git a/doc/txt/compute_smd_plastic_strain_rate.txt b/doc/txt/compute_smd_plastic_strain_rate.txt deleted file mode 100644 index ffc009b2a7..0000000000 --- a/doc/txt/compute_smd_plastic_strain_rate.txt +++ /dev/null @@ -1,54 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/plastic/strain/rate command :h3 - -[Syntax:] - -compute ID group-ID smd/plastic/strain/rate :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/plastic/strain/rate = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/plastic/strain/rate :pre - -[Description:] - -Define a computation that outputs the time rate of the equivalent -plastic strain. This command is only meaningful if a material model -with plasticity is defined. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth -Mach Dynamics in LAMMPS. - -[Output Info:] - -This compute calculates a per-particle vector, which can be accessed -by any command that uses per-particle values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle values will be given in "units"_units.html of one over time. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. This compute can -only be used for particles which interact via the updated Lagrangian -or total Lagrangian SPH pair styles. - -[Related commands:] - -"smd/plastic/strain"_compute_smd_plastic_strain.html, -"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, -"smd/tlsph/strain"_compute_smd_tlsph_strain.html - -[Default:] none diff --git a/doc/txt/compute_smd_rho.txt b/doc/txt/compute_smd_rho.txt deleted file mode 100644 index 31d7351c92..0000000000 --- a/doc/txt/compute_smd_rho.txt +++ /dev/null @@ -1,51 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/rho command :h3 - -[Syntax:] - -compute ID group-ID smd/rho :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/rho = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/rho :pre - -[Description:] - -Define a computation that calculates the per-particle mass density. -The mass density is the mass of a particle which is constant during -the course of a simulation, divided by its volume, which can change -due to mechanical deformation. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute calculates a per-particle vector, which can be accessed -by any command that uses per-particle values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle values will be in "units"_units.html of mass over volume. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute smd/vol"_compute_smd_vol.html - -[Default:] none diff --git a/doc/txt/compute_smd_tlsph_defgrad.txt b/doc/txt/compute_smd_tlsph_defgrad.txt deleted file mode 100644 index bdd3a26a8f..0000000000 --- a/doc/txt/compute_smd_tlsph_defgrad.txt +++ /dev/null @@ -1,56 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/tlsph/defgrad command :h3 - -[Syntax:] - -compute ID group-ID smd/tlsph/defgrad :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/tlsph/defgrad = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/tlsph/defgrad :pre - -[Description:] - -Define a computation that calculates the deformation gradient. It is -only meaningful for particles which interact according to the -Total-Lagrangian SPH pair style. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute outputs a per-particle vector of vectors (tensors), -which can be accessed by any command that uses per-particle values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The per-particle vector values will be given dimensionless. See -"units"_units.html. The per-particle vector has 10 entries. The first -nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz -components of the asymmetric deformation gradient tensor. The tenth -entry is the determinant of the deformation gradient. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. TThis compute can -only be used for particles which interact via the total Lagrangian SPH -pair style. - -[Related commands:] - -"smd/hourglass/error"_compute_smd_hourglass_error.html - -[Default:] none diff --git a/doc/txt/compute_smd_tlsph_dt.txt b/doc/txt/compute_smd_tlsph_dt.txt deleted file mode 100644 index e9ff2e739b..0000000000 --- a/doc/txt/compute_smd_tlsph_dt.txt +++ /dev/null @@ -1,58 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/tlsph/dt command :h3 - -[Syntax:] - -compute ID group-ID smd/tlsph/dt :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/tlsph/dt = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/tlsph/dt :pre - -[Description:] - -Define a computation that outputs the CFL-stable time increment per -particle. This time increment is essentially given by the speed of -sound, divided by the SPH smoothing length. Because both the speed of -sound and the smoothing length typically change during the course of a -simulation, the stable time increment needs to be re-computed every -time step. This calculation is performed automatically in the -relevant SPH pair styles and this compute only serves to make the -stable time increment accessible for output purposes. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute calculates a per-particle vector, which can be accessed -by any command that uses per-particle values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle values will be given in "units"_units.html of time. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This compute can only be used for particles interacting with the -Total-Lagrangian SPH pair style. - -[Related commands:] - -"smd/adjust/dt"_fix_smd_adjust_dt.html - -[Default:] none diff --git a/doc/txt/compute_smd_tlsph_num_neighs.txt b/doc/txt/compute_smd_tlsph_num_neighs.txt deleted file mode 100644 index db977fe676..0000000000 --- a/doc/txt/compute_smd_tlsph_num_neighs.txt +++ /dev/null @@ -1,53 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/tlsph/num/neighs command :h3 - -[Syntax:] - -compute ID group-ID smd/tlsph/num/neighs :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/tlsph/num/neighs = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/tlsph/num/neighs :pre - -[Description:] - -Define a computation that calculates the number of particles inside of -the smoothing kernel radius for particles interacting via the -Total-Lagrangian SPH pair style. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute calculates a per-particle vector, which can be accessed -by any command that uses per-particle values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle values are dimensionless. See "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This quantity will be computed only for particles which interact with -the Total-Lagrangian pair style. - -[Related commands:] - -"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html - -[Default:] none diff --git a/doc/txt/compute_smd_tlsph_shape.txt b/doc/txt/compute_smd_tlsph_shape.txt deleted file mode 100644 index 0ecfec0187..0000000000 --- a/doc/txt/compute_smd_tlsph_shape.txt +++ /dev/null @@ -1,60 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/tlsph/shape command :h3 - -[Syntax:] - -compute ID group-ID smd/tlsph/shape :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/tlsph/shape = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/tlsph/shape :pre - -[Description:] - -Define a computation that outputs the current shape of the volume -associated with a particle as a rotated ellipsoid. It is only -meaningful for particles which interact according to the -Total-Lagrangian SPH pair style. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute calculates a per-particle vector of vectors, which can be -accessed by any command that uses per-particle values from a compute -as input. See the "Howto output"_Howto_output.html doc page for an -overview of LAMMPS output options. - -The per-particle vector has 7 entries. The first three entries -correspond to the lengths of the ellipsoid's axes and have units of -length. These axis values are computed as the contact radius times the -xx, yy, or zz components of the Green-Lagrange strain tensor -associated with the particle. The next 4 values are quaternions -(order: q, x, y, z) which describe the spatial rotation of the -particle relative to its initial state. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This quantity will be computed only for particles which interact with -the Total-Lagrangian SPH pair style. - -[Related commands:] - -"smd/contact/radius"_compute_smd_contact_radius.html - -[Default:] none diff --git a/doc/txt/compute_smd_tlsph_strain.txt b/doc/txt/compute_smd_tlsph_strain.txt deleted file mode 100644 index 70f996e206..0000000000 --- a/doc/txt/compute_smd_tlsph_strain.txt +++ /dev/null @@ -1,57 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/tlsph/strain command :h3 - -[Syntax:] - -compute ID group-ID smd/tlsph/strain :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/tlsph/strain = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/tlsph/strain :pre - -[Description:] - -Define a computation that calculates the Green-Lagrange strain tensor -for particles interacting via the Total-Lagrangian SPH pair style. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute calculates a per-particle vector of vectors (tensors), -which can be accessed by any command that uses per-particle values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The per-particle tensor values will be given dimensionless. See -"units"_units.html. - -The per-particle vector has 6 entries, corresponding to the xx, yy, -zz, xy, xz, yz components of the symmetric strain tensor. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This quantity will be computed only for particles which interact with -the Total-Lagrangian SPH pair style. - -[Related commands:] - -"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, -"smd/tlsph/stress"_compute_smd_tlsph_stress.html - -[Default:] none diff --git a/doc/txt/compute_smd_tlsph_strain_rate.txt b/doc/txt/compute_smd_tlsph_strain_rate.txt deleted file mode 100644 index e6d968c523..0000000000 --- a/doc/txt/compute_smd_tlsph_strain_rate.txt +++ /dev/null @@ -1,56 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/tlsph/strain/rate command :h3 - -[Syntax:] - -compute ID group-ID smd/tlsph/strain/rate :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/tlsph/strain/rate = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/tlsph/strain/rate :pre - -[Description:] - -Define a computation that calculates the rate of the strain tensor for -particles interacting via the Total-Lagrangian SPH pair style. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute calculates a per-particle vector of vectors (tensors), -which can be accessed by any command that uses per-particle values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The values will be given in "units"_units.html of one over time. - -The per-particle vector has 6 entries, corresponding to the xx, yy, -zz, xy, xz, yz components of the symmetric strain rate tensor. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This quantity will be computed only for particles which interact with -Total-Lagrangian SPH pair style. - -[Related commands:] - -"compute smd/tlsph/strain"_compute_smd_tlsph_strain.html, "compute -smd/tlsph/stress"_compute_smd_tlsph_stress.html - -[Default:] none diff --git a/doc/txt/compute_smd_tlsph_stress.txt b/doc/txt/compute_smd_tlsph_stress.txt deleted file mode 100644 index 8340e88536..0000000000 --- a/doc/txt/compute_smd_tlsph_stress.txt +++ /dev/null @@ -1,58 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/tlsph/stress command :h3 - -[Syntax:] - -compute ID group-ID smd/tlsph/stress :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/tlsph/stress = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/tlsph/stress :pre - -[Description:] - -Define a computation that outputs the Cauchy stress tensor for -particles interacting via the Total-Lagrangian SPH pair style. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute calculates a per-particle vector of vectors (tensors), -which can be accessed by any command that uses per-particle values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The values will be given in "units"_units.html of pressure. - -The per-particle vector has 7 entries. The first six entries -correspond to the xx, yy, zz, xy, xz and yz components of the -symmetric Cauchy stress tensor. The seventh entry is the second -invariant of the stress tensor, i.e., the von Mises equivalent stress. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This quantity will be computed only for particles which interact with -the Total-Lagrangian SPH pair style. - -[Related commands:] - -"compute smd/tlsph/strain"_compute_smd_tlsph_strain.html, "cmopute -smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html - -[Default:] none diff --git a/doc/txt/compute_smd_triangle_vertices.txt b/doc/txt/compute_smd_triangle_vertices.txt deleted file mode 100644 index 487b1b590b..0000000000 --- a/doc/txt/compute_smd_triangle_vertices.txt +++ /dev/null @@ -1,62 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/triangle/vertices command :h3 - -[Syntax:] - -compute ID group-ID smd/triangle/vertices :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/triangle/vertices = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/triangle/mesh/vertices :pre - -[Description:] - -Define a computation that returns the coordinates of the vertices -corresponding to the triangle-elements of a mesh created by the "fix -smd/wall_surface"_fix_smd_wall_surface.html. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute returns a per-particle vector of vectors, which can be -accessed by any command that uses per-particle values from a compute -as input. See the "Howto output"_Howto_output.html doc page for an -overview of LAMMPS output options. - -The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and -(x3/y3/z3) corresponding to the first, second, and third vertex of -each triangle. - -It is only meaningful to use this compute for a group of particles -which is created via the "fix smd/wall_surface"_fix_smd_wall_surface.html command. - -The output of this compute can be used with the dump2vtk_tris tool to -generate a VTK representation of the smd/wall_surface mesh for -visualization purposes. - -The values will be given in "units"_units.html of distance. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix smd/move/tri/surf"_fix_smd_move_triangulated_surface.html, -"fix smd/wall_surface"_fix_smd_wall_surface.html - -[Default:] none diff --git a/doc/txt/compute_smd_ulsph_num_neighs.txt b/doc/txt/compute_smd_ulsph_num_neighs.txt deleted file mode 100644 index 5157f17e57..0000000000 --- a/doc/txt/compute_smd_ulsph_num_neighs.txt +++ /dev/null @@ -1,52 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/ulsph/num/neighs command :h3 - -[Syntax:] - -compute ID group-ID smd/ulsph/num/neighs :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/ulsph/num/neighs = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/ulsph/num/neighs :pre - -[Description:] - -Define a computation that returns the number of neighbor particles -inside of the smoothing kernel radius for particles interacting via -the updated Lagrangian SPH pair style. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute returns a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle values will be given dimensionless, see "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. This compute can -only be used for particles which interact with the updated Lagrangian -SPH pair style. - -[Related commands:] - -"compute smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html - -[Default:] none diff --git a/doc/txt/compute_smd_ulsph_strain.txt b/doc/txt/compute_smd_ulsph_strain.txt deleted file mode 100644 index 3dc6bd5249..0000000000 --- a/doc/txt/compute_smd_ulsph_strain.txt +++ /dev/null @@ -1,55 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/ulsph/strain command :h3 - -[Syntax:] - -compute ID group-ID smd/ulsph/strain :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/ulsph/strain = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/ulsph/strain :pre - -[Description:] - -Define a computation that outputs the logarithmic strain tensor. for -particles interacting via the updated Lagrangian SPH pair style. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute calculates a per-particle tensor, which can be accessed -by any command that uses per-particle values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle vector has 6 entries, corresponding to the xx, yy, -zz, xy, xz, yz components of the symmetric strain rate tensor. - -The per-particle tensor values will be given dimensionless, see -"units"_units.html. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. This compute can -only be used for particles which interact with the updated Lagrangian -SPH pair style. - -[Related commands:] - -"compute smd/tlsph/strain"_compute_smd_tlsph_strain.html - -[Default:] none diff --git a/doc/txt/compute_smd_ulsph_strain_rate.txt b/doc/txt/compute_smd_ulsph_strain_rate.txt deleted file mode 100644 index 1ade5ac2d5..0000000000 --- a/doc/txt/compute_smd_ulsph_strain_rate.txt +++ /dev/null @@ -1,56 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/ulsph/strain/rate command :h3 - -[Syntax:] - -compute ID group-ID smd/ulsph/strain/rate :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/ulsph/strain/rate = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/ulsph/strain/rate :pre - -[Description:] - -Define a computation that outputs the rate of the logarithmic strain -tensor for particles interacting via the updated Lagrangian SPH pair -style. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute calculates a per-particle vector of vectors (tensors), -which can be accessed by any command that uses per-particle values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The values will be given in "units"_units.html of one over time. - -The per-particle vector has 6 entries, corresponding to the xx, yy, -zz, xy, xz, yz components of the symmetric strain rate tensor. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This compute can only be used for particles which interact with the -updated Lagrangian SPH pair style. - -[Related commands:] - -"compute smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html - -[Default:] none diff --git a/doc/txt/compute_smd_ulsph_stress.txt b/doc/txt/compute_smd_ulsph_stress.txt deleted file mode 100644 index ff53e777c5..0000000000 --- a/doc/txt/compute_smd_ulsph_stress.txt +++ /dev/null @@ -1,57 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/ulsph/stress command :h3 - -[Syntax:] - -compute ID group-ID smd/ulsph/stress :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/ulsph/stress = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/ulsph/stress :pre - -[Description:] - -Define a computation that outputs the Cauchy stress tensor. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute calculates a per-particle vector of vectors (tensors), -which can be accessed by any command that uses per-particle values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The values will be given in "units"_units.html of pressure. - -The per-particle vector has 7 entries. The first six entries -correspond to the xx, yy, zz, xy, xz, yz components of the symmetric -Cauchy stress tensor. The seventh entry is the second invariant of the -stress tensor, i.e., the von Mises equivalent stress. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. This compute can -only be used for particles which interact with the updated Lagrangian -SPH pair style. - -[Related commands:] - -"compute smd/ulsph/strain"_compute_smd_ulsph_strain.html, "compute -smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html "compute -smd/tlsph/stress"_compute_smd_tlsph_stress.html - -[Default:] none diff --git a/doc/txt/compute_smd_vol.txt b/doc/txt/compute_smd_vol.txt deleted file mode 100644 index 0edd61f624..0000000000 --- a/doc/txt/compute_smd_vol.txt +++ /dev/null @@ -1,53 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute smd/vol command :h3 - -[Syntax:] - -compute ID group-ID smd/vol :pre - -ID, group-ID are documented in "compute"_compute.html command -smd/vol = style name of this compute command :ul - -[Examples:] - -compute 1 all smd/vol :pre - -[Description:] - -Define a computation that provides the per-particle volume and the sum -of the per-particle volumes of the group for which the fix is defined. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth -Mach Dynamics in LAMMPS. - -[Output info:] - -This compute calculates a per-particle vector, which can be accessed -by any command that uses per-particle values from a compute as input. -See the "Howto output"_Howto_output.html doc page for an overview of -LAMMPS output options. - -The per-particle vector values will be given in "units"_units.html of -volume. - -Additionally, the compute returns a scalar, which is the sum of the -per-particle volumes of the group for which the fix is defined. - -[Restrictions:] - -This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute smd/rho"_compute_smd_rho.html - -[Default:] none diff --git a/doc/txt/compute_sna_atom.txt b/doc/txt/compute_sna_atom.txt deleted file mode 100644 index 0bf63019f9..0000000000 --- a/doc/txt/compute_sna_atom.txt +++ /dev/null @@ -1,312 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute sna/atom command :h3 -compute snad/atom command :h3 -compute snav/atom command :h3 -compute snap command :h3 - -[Syntax:] - -compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... -compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... -compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... -compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -sna/atom = style name of this compute command :l -rcutfac = scale factor applied to all cutoff radii (positive real) :l -rfac0 = parameter in distance to angle conversion (0 < rcutfac < 1) :l -twojmax = band limit for bispectrum components (non-negative integer) :l -R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l -w_1, w_2,... = list of neighbor weights, one for each type :l -zero or more keyword/value pairs may be appended :l -keyword = {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l - {rmin0} value = parameter in distance to angle conversion (distance units) - {switchflag} value = {0} or {1} - {0} = do not use switching function - {1} = use switching function - {bzeroflag} value = {0} or {1} - {0} = do not subtract B0 - {1} = subtract B0 - {quadraticflag} value = {0} or {1} - {0} = do not generate quadratic terms - {1} = generate quadratic terms :pre -:ule - -[Examples:] - -compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0 -compute db all sna/atom 1.4 0.95 6 2.0 1.0 -compute vb all sna/atom 1.4 0.95 6 2.0 1.0 -compute snap all snap 1.4 0.95 6 2.0 1.0 :pre - -[Description:] - -Define a computation that calculates a set of quantities related to the -bispectrum components of the atoms in a group. These computes are -used primarily for calculating the dependence of energy, force, and -stress components on the linear coefficients in the -"snap pair_style"_pair_snap.html, which is useful when training a -SNAP potential to match target data. - -Bispectrum components of an atom are order parameters characterizing -the radial and angular distribution of neighbor atoms. The detailed -mathematical definition is given in the paper by Thompson et -al. "(Thompson)"_#Thompson20141 - -The position of a neighbor atom {i'} relative to a central atom {i} is -a point within the 3D ball of radius {R_ii' = rcutfac*(R_i + R_i')} - -Bartok et al. "(Bartok)"_#Bartok20101, proposed mapping this 3D ball -onto the 3-sphere, the surface of the unit ball in a four-dimensional -space. The radial distance {r} within {R_ii'} is mapped on to a third -polar angle {theta0} defined by, - -:c,image(Eqs/compute_sna_atom1.jpg) - -In this way, all possible neighbor positions are mapped on to a subset -of the 3-sphere. Points south of the latitude {theta0max=rfac0*Pi} -are excluded. - -The natural basis for functions on the 3-sphere is formed by the 4D -hyperspherical harmonics {U^j_m,m'(theta, phi, theta0).} These -functions are better known as {D^j_m,m',} the elements of the Wigner -{D}-matrices "(Meremianin"_#Meremianin2006, -"Varshalovich)"_#Varshalovich1987. - -The density of neighbors on the 3-sphere can be written as a sum of -Dirac-delta functions, one for each neighbor, weighted by species and -radial distance. Expanding this density function as a generalized -Fourier series in the basis functions, we can write each Fourier -coefficient as - -:c,image(Eqs/compute_sna_atom2.jpg) - -The {w_i'} neighbor weights are dimensionless numbers that are chosen -to distinguish atoms of different types, while the central atom is -arbitrarily assigned a unit weight. The function {fc(r)} ensures that -the contribution of each neighbor atom goes smoothly to zero at -{R_ii'}: - -:c,image(Eqs/compute_sna_atom4.jpg) - -The expansion coefficients {u^j_m,m'} are complex-valued and they are -not directly useful as descriptors, because they are not invariant -under rotation of the polar coordinate frame. However, the following -scalar triple products of expansion coefficients can be shown to be -real-valued and invariant under rotation "(Bartok)"_#Bartok20101. - -:c,image(Eqs/compute_sna_atom3.jpg) - -The constants {H^jmm'_j1m1m1'_j2m2m2'} are coupling coefficients, -analogous to Clebsch-Gordan coefficients for rotations on the -2-sphere. These invariants are the components of the bispectrum and -these are the quantities calculated by the compute {sna/atom}. They -characterize the strength of density correlations at three points on -the 3-sphere. The j2=0 subset form the power spectrum, which -characterizes the correlations of two points. The lowest-order -components describe the coarsest features of the density function, -while higher-order components reflect finer detail. Note that the -central atom is included in the expansion, so three point-correlations -can be either due to three neighbors, or two neighbors and the central -atom. - -Compute {snad/atom} calculates the derivative of the bispectrum components -summed separately for each atom type: - -:c,image(Eqs/compute_sna_atom5.jpg) - -The sum is over all atoms {i'} of atom type {I}. For each atom {i}, -this compute evaluates the above expression for each direction, each -atom type, and each bispectrum component. See section below on output -for a detailed explanation. - -Compute {snav/atom} calculates the virial contribution due to the -derivatives: - -:c,image(Eqs/compute_sna_atom6.jpg) - -Again, the sum is over all atoms {i'} of atom type {I}. For each atom -{i}, this compute evaluates the above expression for each of the six -virial components, each atom type, and each bispectrum component. See -section below on output for a detailed explanation. - -Compute {snap} calculates a global array contains information related -to all three of the above per-atom computes {sna/atom}, {snad/atom}, -and {snav/atom}. The first row of the array contains the summation of -{sna/atom} over all atoms, but broken out by type. The last six rows -of the array contain the summation of {snav/atom} over all atoms, broken -out by type. In between these are 3*{N} rows containing the same values -computed by {snad/atom} (these are already summed over all atoms and -broken out by type). The element in the last column of each row contains -the potential energy, force, or stress, according to the row. -These quantities correspond to the user-specified reference potential -that must be subtracted from the target data when fitting SNAP. -The potential energy calculation uses the built in compute {thermo_pe}. -The stress calculation uses a compute called {snap_press} that is -automatically created behind the scenes, according to the following -command: - -compute snap_press all pressure NULL virial :pre - -See section below on output for a detailed explanation of the data -layout in the global array. - -The value of all bispectrum components will be zero for atoms not in -the group. Neighbor atoms not in the group do not contribute to the -bispectrum of atoms in the group. - -The neighbor list needed to compute this quantity is constructed each -time the calculation is performed (i.e. each time a snapshot of atoms -is dumped). Thus it can be inefficient to compute/dump this quantity -too frequently. - -The argument {rcutfac} is a scale factor that controls the ratio of -atomic radius to radial cutoff distance. - -The argument {rfac0} and the optional keyword {rmin0} define the -linear mapping from radial distance to polar angle {theta0} on the -3-sphere. - -The argument {twojmax} defines which -bispectrum components are generated. See section below on output for a -detailed explanation of the number of bispectrum components and the -ordered in which they are listed. - -The keyword {switchflag} can be used to turn off the switching -function. - -The keyword {bzeroflag} determines whether or not {B0}, the bispectrum -components of an atom with no neighbors, are subtracted from -the calculated bispectrum components. This optional keyword -normally only affects compute {sna/atom}. However, when -{quadraticflag} is on, it also affects {snad/atom} and {snav/atom}. - -The keyword {quadraticflag} determines whether or not the -quadratic analogs to the bispectrum quantities are generated. -These are formed by taking the outer product of the vector -of bispectrum components with itself. -See section below on output for a -detailed explanation of the number of quadratic terms and the -ordered in which they are listed. - -NOTE: If you have a bonded system, then the settings of -"special_bonds"_special_bonds.html command can remove pairwise -interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the "special_bonds"_special_bonds.html -command, and means those pairwise interactions do not appear in the -neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included in the calculation. One way to get -around this, is to write a dump file, and use the "rerun"_rerun.html -command to compute the bispectrum components for snapshots in the dump -file. The rerun script can use a "special_bonds"_special_bonds.html -command that includes all pairs in the neighbor list. - -;line - -[Output info:] - -Compute {sna/atom} calculates a per-atom array, each column -corresponding to a particular bispectrum component. The total number -of columns and the identity of the bispectrum component contained in -each column depend of the value of {twojmax}, as -described by the following piece of python code: - -for j1 in range(0,twojmax+1): - for j2 in range(0,j1+1): - for j in range(j1-j2,min(twojmax,j1+j2)+1,2): - if (j>=j1): print j1/2.,j2/2.,j/2. :pre - -NOTE: the {diagonal} keyword allowing other possible choices -for the number of bispectrum components was removed in 2019, -since all potentials use the value of 3, corresponding to the -above set of bispectrum components. - -Compute {snad/atom} evaluates a per-atom array. The columns are -arranged into {ntypes} blocks, listed in order of atom type {I}. Each -block contains three sub-blocks corresponding to the {x}, {y}, and {z} -components of the atom position. Each of these sub-blocks contains -one column for each bispectrum component, the same as for compute -{sna/atom} - -Compute {snav/atom} evaluates a per-atom array. The columns are -arranged into {ntypes} blocks, listed in order of atom type {I}. Each -block contains six sub-blocks corresponding to the {xx}, {yy}, {zz}, -{yz}, {xz}, and {xy} components of the virial tensor in Voigt -notation. Each of these sub-blocks contains one column for each -bispectrum component, the same as for compute {sna/atom} - -Compute {snap} evaluates a global array. -The columns are arranged into -{ntypes} blocks, listed in order of atom type {I}. Each block -contains one column for each bispectrum component, the same as for compute -{sna/atom}. A final column contains the corresponding energy, force component -on an atom, or virial stress component. The rows of the array appear -in the following order: - - 1 row: {sna/atom} quantities summed for all atoms of type {I} - 3*{N} rows: {snad/atom} quantities, with derivatives w.r.t. x, y, and z coordinate of atom {i} appearing in consecutive rows. The atoms are sorted based on atom ID. - 6 rows: {snav/atom} quantities summed for all atoms of type {I} :ul - -For example, if {K} =30 and ntypes=1, the number of columns in the per-atom -arrays generated by {sna/atom}, {snad/atom}, and {snav/atom} -are 30, 90, and 180, respectively. With {quadratic} value=1, -the numbers of columns are 930, 2790, and 5580, respectively. -The number of columns in the global array generated by {snap} -are 31, and 931, respectively, while the number of rows is -1+3*{N}+6, where {N} is the total number of atoms. - -If the {quadratic} keyword value is set to 1, then additional -columns are generated, corresponding to -the products of all distinct pairs of bispectrum components. If the -number of bispectrum components is {K}, then the number of distinct pairs -is {K}({K}+1)/2. -For compute {sna/atom} these columns are appended to existing {K} columns. -The ordering of quadratic terms is upper-triangular, -(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}). -For computes {snad/atom} and {snav/atom} each set of {K}({K}+1)/2 -additional columns is inserted directly after each of sub-block -of linear terms i.e. linear and quadratic terms are contiguous. -So the nesting order from inside to outside is bispectrum component, -linear then quadratic, vector/tensor component, type. - -These values can be accessed by any command that uses per-atom values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -[Restrictions:] - -These computes are part of the SNAP package. They are only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_style snap"_pair_snap.html - -[Default:] - -The optional keyword defaults are {rmin0} = 0, -{switchflag} = 1, {bzeroflag} = 1, {quadraticflag} = 0, - -:line - -:link(Thompson20141) -[(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint -available at "arXiv:1409.3880"_http://arxiv.org/abs/1409.3880 - -:link(Bartok20101) -[(Bartok)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010). - -:link(Meremianin2006) -[(Meremianin)] Meremianin, J. Phys. A, 39, 3099 (2006). - -:link(Varshalovich1987) -[(Varshalovich)] Varshalovich, Moskalev, Khersonskii, Quantum Theory -of Angular Momentum, World Scientific, Singapore (1987). diff --git a/doc/txt/compute_stress_mop.txt b/doc/txt/compute_stress_mop.txt deleted file mode 100644 index d97581afd5..0000000000 --- a/doc/txt/compute_stress_mop.txt +++ /dev/null @@ -1,111 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -compute stress/mop command :h3 -compute stress/mop/profile command :h3 - - -[Syntax:] - -compute ID group-ID style dir args keywords ... :pre - -ID, group-ID are documented in "compute"_compute.html command -style = {stress/mop} or {stress/mop/profile} -dir = {x} or {y} or {z} is the direction normal to the plane -args = argument specific to the compute style -keywords = {kin} or {conf} or {total} (one of more can be specified) :ul - {stress/mop} args = pos - pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane - {stress/mop/profile} args = origin delta - origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane - delta = value (distance units) is the distance between planes :pre - -compute 1 all stress/mop x lower total -compute 1 liquid stress/mop z 0.0 kin conf -fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time -fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre - -compute 1 all stress/mop/profile x lower 0.1 total -compute 1 liquid stress/mop/profile z 0.0 0.25 kin conf -fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre - - -[Description:] - -Compute {stress/mop} and compute {stress/mop/profile} define computations that -calculate components of the local stress tensor using the method of -planes "(Todd)"_#mop-todd. Specifically in compute {stress/mop} calculates 3 -components are computed in directions {dir},{x}; {dir},{y}; and -{dir},{z}; where {dir} is the direction normal to the plane, while -in compute {stress/mop/profile} the profile of the stress is computed. - -Contrary to methods based on histograms of atomic stress (i.e. using -"compute stress/atom"_compute_stress_atom.html), the method of planes is -compatible with mechanical balance in heterogeneous systems and at -interfaces "(Todd)"_#mop-todd. - -The stress tensor is the sum of a kinetic term and a configurational -term, which are given respectively by Eq. (21) and Eq. (16) in -"(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that -atoms have crossed the plane if their positions at times t-dt and t are -one on either side of the plane, and uses the velocity at time t-dt/2 -given by the velocity-Verlet algorithm. - -Between one and three keywords can be used to indicate which -contributions to the stress must be computed: kinetic stress (kin), -configurational stress (conf), and/or total stress (total). - -NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID. - -NOTE 2: The local stress does not include any Lennard-Jones tail -corrections to the pressure added by the "pair_modify tail -yes"_pair_modify.html command, since those are contributions to the global system pressure. - -[Output info:] - -Compute {stress/mop} calculates a global vector (indices starting at 1), with 3 -values for each declared keyword (in the order the keywords have been -declared). For each keyword, the stress tensor components are ordered as -follows: stress_dir,x, stress_dir,y, and stress_dir,z. - -Compute {stress/mop/profile} instead calculates a global array, with 1 column -giving the position of the planes where the stress tensor was computed, -and with 3 columns of values for each declared keyword (in the order the -keywords have been declared). For each keyword, the profiles of stress -tensor components are ordered as follows: stress_dir,x; stress_dir,y; -and stress_dir,z. - -The values are in pressure "units"_units.html. - -The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder. - -[Restrictions:] - -These styles are part of the USER-MISC package. They are only enabled if -LAMMPS is built with that package. See the "Build package"_Build_package.html -doc page on for more info. - -The method is only implemented for 3d orthogonal simulation boxes whose -size does not change in time, and axis-aligned planes. - -The method only works with two-body pair interactions, because it -requires the class method pair->single() to be implemented. In -particular, it does not work with more than two-body pair interactions, -intra-molecular interactions, and long range (kspace) interactions. - -[Related commands:] - -"compute stress/atom"_compute_stress_atom.html - -[Default:] none - -:line - -:link(mop-todd) -[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", -Phys. Rev. E 52, 1627 (1995). diff --git a/doc/txt/compute_tally.txt b/doc/txt/compute_tally.txt deleted file mode 100644 index 125eba1302..0000000000 --- a/doc/txt/compute_tally.txt +++ /dev/null @@ -1,99 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute force/tally command :h3 -compute heat/flux/tally command :h3 -compute pe/tally command :h3 -compute pe/mol/tally command :h3 -compute stress/tally command :h3 - -[Syntax:] - -compute ID group-ID style group2-ID :pre - -ID, group-ID are documented in "compute"_compute.html command -style = {force/tally} or {pe/tally} or {pe/mol/tally} or {stress/tally} -group2-ID = group ID of second (or same) group :ul - -[Examples:] - -compute 1 lower force/tally upper -compute 1 left pe/tally right -compute 1 lower stress/tally lower :pre - -[Description:] - -Define a computation that calculates properties between two groups of -atoms by accumulating them from pairwise non-bonded computations. The -two groups can be the same. This is similar to "compute -group/group"_compute_group_group.html only that the data is -accumulated directly during the non-bonded force computation. The -computes {force/tally}, {pe/tally}, {stress/tally}, and -{heat/flux/tally} are primarily provided as example how to program -additional, more sophisticated computes using the tally callback -mechanism. Compute {pe/mol/tally} is one such style, that can -- through using this mechanism - separately tally intermolecular -and intramolecular energies. Something that would otherwise be -impossible without integrating this as a core functionality into -the based classes of LAMMPS. - -:line - -The pairwise contributions are computing via a callback that the -compute registers with the non-bonded pairwise force computation. -This limits the use to systems that have no bonds, no Kspace, and no -many-body interactions. On the other hand, the computation does not -have to compute forces or energies a second time and thus can be much -more efficient. The callback mechanism allows to write more complex -pairwise property computations. - -:line - -[Output info:] - -Compute {pe/tally} calculates a global scalar (the energy) and a per -atom scalar (the contributions of the single atom to the global -scalar). Compute {pe/mol/tally} calculates a global 4-element vector -containing (in this order): {evdwl} and {ecoul} for intramolecular pairs -and {evdwl} and {ecoul} for intermolecular pairs. Since molecules are -identified by their molecule IDs, the partitioning does not have to be -related to molecules, but the energies are tallied into the respective -slots depending on whether the molecule IDs of a pair are the same or -different. Compute {force/tally} calculates a global scalar (the force -magnitude) and a per atom 3-element vector (force contribution from -each atom). Compute {stress/tally} calculates a global scalar -(average of the diagonal elements of the stress tensor) and a per atom -vector (the 6 elements of stress tensor contributions from the -individual atom). - -Both the scalar and vector values calculated by this compute are -"extensive". - -[Restrictions:] - -This compute is part of the USER-TALLY package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Not all pair styles can be evaluated in a pairwise mode as required by -this compute. For example, 3-body and other many-body potentials, -such as "Tersoff"_pair_tersoff.html and -"Stillinger-Weber"_pair_sw.html cannot be used. "EAM"_pair_eam.html -potentials only include the pair potential portion of the EAM -interaction when used by this compute, not the embedding term. Also -bonded or Kspace interactions do not contribute to this compute. - -The computes in this package are not compatible with dynamic groups. - -[Related commands:] - -{compute group/group}_compute_group_group.html, {compute -heat/flux}_compute_heat_flux.html - -[Default:] none - diff --git a/doc/txt/compute_tdpd_cc_atom.txt b/doc/txt/compute_tdpd_cc_atom.txt deleted file mode 100644 index d1f9c38319..0000000000 --- a/doc/txt/compute_tdpd_cc_atom.txt +++ /dev/null @@ -1,60 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute tdpd/cc/atom command :h3 - -[Syntax:] - -compute ID group-ID tdpd/cc/atom index :pre - -ID, group-ID are documented in "compute"_compute.html command -tdpd/cc/atom = style name of this compute command -index = index of chemical species (1 to Nspecies) :ul - -[Examples:] - -compute 1 all tdpd/cc/atom 2 :pre - -[Description:] - -Define a computation that calculates the per-atom chemical -concentration of a specified species for each tDPD particle in a -group. - -The chemical concentration of each species is defined as the number of -molecules carried by a tDPD particle for dilute solution. For more -details see "(Li2015)"_#Li2015a. - -[Output info:] - -This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See the -"Howto output"_Howto_output.html doc page for an overview of LAMMPS -output options. - -The per-atom vector values will be in the units of chemical species -per unit mass. - -[Restrictions:] - -This compute is part of the USER-MESO package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_style tdpd"_pair_meso.html - -[Default:] none - -:line - -:link(Li2015a) -[(Li2015)] Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: -014101 (2015). DOI: 10.1063/1.4923254 - diff --git a/doc/txt/compute_temp.txt b/doc/txt/compute_temp.txt deleted file mode 100644 index 757e00c4d2..0000000000 --- a/doc/txt/compute_temp.txt +++ /dev/null @@ -1,112 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp command :h3 -compute temp/kk command :h3 - -[Syntax:] - -compute ID group-ID temp :pre - -ID, group-ID are documented in "compute"_compute.html command -temp = style name of this compute command :ul - -[Examples:] - -compute 1 all temp -compute myTemp mobile temp :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -atoms. A compute of this style can be used by any command that -computes a temperature, e.g. "thermo_modify"_thermo_modify.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc. - -The temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = 2 or 3 = dimensionality of the simulation, N = number of atoms -in the group, k = Boltzmann constant, and T = temperature. - -A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. - -The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the {dynamic} option of the -"compute_modify"_compute_modify.html command if this is not the case. - -This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as "fix shake"_fix_shake.html and -"fix rigid"_fix_rigid.html. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -{extra} option of the "compute_modify"_compute_modify.html command. - -A compute of this style with the ID of "thermo_temp" is created when -LAMMPS starts up, as if this command were in the input script: - -compute thermo_temp all temp :pre - -See the "thermo_style" command for more details. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute temp/partial"_compute_temp_partial.html, "compute -temp/region"_compute_temp_region.html, "compute -pressure"_compute_pressure.html - -[Default:] none diff --git a/doc/txt/compute_temp_asphere.txt b/doc/txt/compute_temp_asphere.txt deleted file mode 100644 index 0b06ae0b48..0000000000 --- a/doc/txt/compute_temp_asphere.txt +++ /dev/null @@ -1,153 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/asphere command :h3 - -[Syntax:] - -compute ID group-ID temp/asphere keyword value ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -temp/asphere = style name of this compute command :l -zero or more keyword/value pairs may be appended :l -keyword = {bias} or {dof} :l - {bias} value = bias-ID - bias-ID = ID of a temperature compute that removes a velocity bias - {dof} value = {all} or {rotate} - all = compute temperature of translational and rotational degrees of freedom - rotate = compute temperature of just rotational degrees of freedom :pre -:ule - -[Examples:] - -compute 1 all temp/asphere -compute myTemp mobile temp/asphere bias tempCOM -compute myTemp mobile temp/asphere dof rotate :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -aspherical particles, including a contribution from both their -translational and rotational kinetic energy. This differs from the -usual "compute temp"_compute_temp.html command, which assumes point -particles with only translational kinetic energy. - -Only finite-size particles (aspherical or spherical) can be included -in the group. For 3d finite-size particles, each has 6 degrees of -freedom (3 translational, 3 rotational). For 2d finite-size -particles, each has 3 degrees of freedom (2 translational, 1 -rotational). - -NOTE: This choice for degrees of freedom (dof) assumes that all -finite-size aspherical or spherical particles in your model will -freely rotate, sampling all their rotational dof. It is possible to -use a combination of interaction potentials and fixes that induce no -torque or otherwise constrain some of all of your particles so that -this is not the case. Then there are less dof and you should use the -"compute_modify extra"_compute_modify.html command to adjust the dof -accordingly. - -For example, an aspherical particle with all three of its shape -parameters the same is a sphere. If it does not rotate, then it -should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A -uniaxial aspherical particle has two of its three shape parameters the -same. If it does not rotate around the axis perpendicular to its -circular cross section, then it should have 5 dof instead of 6 in 3d. -The latter is the case for uniaxial ellipsoids in a "GayBerne -model"_pair_gayberne.html since there is no induced torque around the -optical axis. It will also be the case for bi-axial ellipsoids when -exactly two of the semiaxes have the same length and the corresponding -relative well depths are equal. - -The translational kinetic energy is computed the same as is described -by the "compute temp"_compute_temp.html command. The rotational -kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor -for the aspherical particle and w is its angular velocity, which is -computed from its angular momentum. - -NOTE: For "2d models"_dimension.html, particles are treated as -ellipsoids, not ellipses, meaning their moments of inertia will be the -same as in 3d. - -A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute. The formula for the components of the -tensor is the same as the above formula, except that v^2 and w^2 are -replaced by vx*vy and wx*wy for the xy component, and the appropriate -elements of the inertia tensor are used. The 6 components of the -vector are ordered xx, yy, zz, xy, xz, yz. - -The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the {dynamic} option of the -"compute_modify"_compute_modify.html command if this is not the case. - -This compute subtracts out translational degrees-of-freedom due to -fixes that constrain molecular motion, such as "fix -shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the -temperature of groups of atoms that include these constraints will be -computed correctly. If needed, the subtracted degrees-of-freedom can -be altered using the {extra} option of the -"compute_modify"_compute_modify.html command. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -:line - -The keyword/value option pairs are used in the following ways. - -For the {bias} keyword, {bias-ID} refers to the ID of a temperature -compute that removes a "bias" velocity from each atom. This allows -compute temp/sphere to compute its thermal temperature after the -translational kinetic energy components have been altered in a -prescribed way, e.g. to remove a flow velocity profile. Thermostats -that use this compute will work with this bias term. See the doc -pages for individual computes that calculate a temperature and the doc -pages for fixes that perform thermostatting for more details. - -For the {dof} keyword, a setting of {all} calculates a temperature -that includes both translational and rotational degrees of freedom. A -setting of {rotate} calculates a temperature that includes only -rotational degrees of freedom. - -:line - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] - -This compute is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This compute requires that atoms store angular momentum and a -quaternion as defined by the "atom_style ellipsoid"_atom_style.html -command. - -All particles in the group must be finite-size. They cannot be point -particles, but they can be aspherical or spherical as defined by their -shape attribute. - -[Related commands:] - -"compute temp"_compute_temp.html - -[Default:] none diff --git a/doc/txt/compute_temp_body.txt b/doc/txt/compute_temp_body.txt deleted file mode 100644 index 341d6d7f79..0000000000 --- a/doc/txt/compute_temp_body.txt +++ /dev/null @@ -1,131 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/body command :h3 - -[Syntax:] - -compute ID group-ID temp/body keyword value ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -temp/body = style name of this compute command :l -zero or more keyword/value pairs may be appended :l -keyword = {bias} or {dof} :l - {bias} value = bias-ID - bias-ID = ID of a temperature compute that removes a velocity bias - {dof} value = {all} or {rotate} - all = compute temperature of translational and rotational degrees of freedom - rotate = compute temperature of just rotational degrees of freedom :pre -:ule - -[Examples:] - -compute 1 all temp/body -compute myTemp mobile temp/body bias tempCOM -compute myTemp mobile temp/body dof rotate :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -body particles, including a contribution from both their -translational and rotational kinetic energy. This differs from the -usual "compute temp"_compute_temp.html command, which assumes point -particles with only translational kinetic energy. - -Only body particles can be included in the group. For 3d particles, -each has 6 degrees of freedom (3 translational, 3 rotational). For 2d -body particles, each has 3 degrees of freedom (2 translational, 1 -rotational). - -NOTE: This choice for degrees of freedom (dof) assumes that all body -particles in your model will freely rotate, sampling all their -rotational dof. It is possible to use a combination of interaction -potentials and fixes that induce no torque or otherwise constrain some -of all of your particles so that this is not the case. Then there are -less dof and you should use the "compute_modify -extra"_compute_modify.html command to adjust the dof accordingly. - -The translational kinetic energy is computed the same as is described -by the "compute temp"_compute_temp.html command. The rotational -kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor -for the aspherical particle and w is its angular velocity, which is -computed from its angular momentum. - -A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute. The formula for the components of the -tensor is the same as the above formula, except that v^2 and w^2 are -replaced by vx*vy and wx*wy for the xy component, and the appropriate -elements of the inertia tensor are used. The 6 components of the -vector are ordered xx, yy, zz, xy, xz, yz. - -The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the {dynamic} option of the -"compute_modify"_compute_modify.html command if this is not the case. - -This compute subtracts out translational degrees-of-freedom due to -fixes that constrain molecular motion, such as "fix -shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the -temperature of groups of atoms that include these constraints will be -computed correctly. If needed, the subtracted degrees-of-freedom can -be altered using the {extra} option of the -"compute_modify"_compute_modify.html command. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -:line - -The keyword/value option pairs are used in the following ways. - -For the {bias} keyword, {bias-ID} refers to the ID of a temperature -compute that removes a "bias" velocity from each atom. This allows -compute temp/sphere to compute its thermal temperature after the -translational kinetic energy components have been altered in a -prescribed way, e.g. to remove a flow velocity profile. Thermostats -that use this compute will work with this bias term. See the doc -pages for individual computes that calculate a temperature and the doc -pages for fixes that perform thermostatting for more details. - -For the {dof} keyword, a setting of {all} calculates a temperature -that includes both translational and rotational degrees of freedom. A -setting of {rotate} calculates a temperature that includes only -rotational degrees of freedom. - -:line - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] - -This compute is part of the BODY package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This compute requires that atoms store angular momentum and a -quaternion as defined by the "atom_style body"_atom_style.html -command. - -[Related commands:] - -"compute temp"_compute_temp.html - -[Default:] none diff --git a/doc/txt/compute_temp_chunk.txt b/doc/txt/compute_temp_chunk.txt deleted file mode 100644 index 30dda79caf..0000000000 --- a/doc/txt/compute_temp_chunk.txt +++ /dev/null @@ -1,235 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/chunk command :h3 - -[Syntax:] - -compute ID group-ID temp/chunk chunkID value1 value2 ... keyword value ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -temp/chunk = style name of this compute command :l -chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l -zero or more values can be listed as value1,value2,etc :l -value = {temp} or {kecom} or {internal} :l - temp = temperature of each chunk - kecom = kinetic energy of each chunk based on velocity of center of mass - internal = internal kinetic energy of each chunk :pre -zero or more keyword/value pairs may be appended :l -keyword = {com} or {bias} or {adof} or {cdof} :l - {com} value = {yes} or {no} - yes = subtract center-of-mass velocity from each chunk before calculating temperature - no = do not subtract center-of-mass velocity - {bias} value = bias-ID - bias-ID = ID of a temperature compute that removes a velocity bias - {adof} value = dof_per_atom - dof_per_atom = define this many degrees-of-freedom per atom - {cdof} value = dof_per_chunk - dof_per_chunk = define this many degrees-of-freedom per chunk :pre -:ule - -[Examples:] - -compute 1 fluid temp/chunk molchunk -compute 1 fluid temp/chunk molchunk temp internal -compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0 :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -atoms that are also in chunks, after optionally subtracting out the -center-of-mass velocity of each chunk. By specifying optional values, -it can also calculate the per-chunk temperature or energies of the -multiple chunks of atoms. - -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. - -The temperature is calculated by the formula KE = DOF/2 k T, where KE = -total kinetic energy of all atoms assigned to chunks (sum of 1/2 m -v^2), DOF = the total number of degrees of freedom for those atoms, k -= Boltzmann constant, and T = temperature. - -The DOF is calculated as N*adof + Nchunk*cdof, where N = number of -atoms contributing to the KE, adof = degrees of freedom per atom, and -cdof = degrees of freedom per chunk. By default adof = 2 or 3 = -dimensionality of system, as set via the "dimension"_dimension.html -command, and cdof = 0.0. This gives the usual formula for -temperature. - -A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. - -Note that the number of atoms contributing to the temperature is -calculated each time the temperature is evaluated since it is assumed -the atoms may be dynamically assigned to chunks. Thus there is no -need to use the {dynamic} option of the -"compute_modify"_compute_modify.html command for this compute style. - -If any optional values are specified, then per-chunk quantities are -also calculated and stored in a global array, as described below. - -The {temp} value calculates the temperature for each chunk by the -formula KE = DOF/2 k T, where KE = total kinetic energy of the chunk -of atoms (sum of 1/2 m v^2), DOF = the total number of degrees of -freedom for all atoms in the chunk, k = Boltzmann constant, and T = -temperature. - -The DOF in this case is calculated as N*adof + cdof, where N = number -of atoms in the chunk, adof = degrees of freedom per atom, and cdof = -degrees of freedom per chunk. By default adof = 2 or 3 = -dimensionality of system, as set via the "dimension"_dimension.html -command, and cdof = 0.0. This gives the usual formula for -temperature. - -The {kecom} value calculates the kinetic energy of each chunk as if -all its atoms were moving with the velocity of the center-of-mass of -the chunk. - -The {internal} value calculates the internal kinetic energy of each -chunk. The interal KE is summed over the atoms in the chunk using an -internal "thermal" velocity for each atom, which is its velocity minus -the center-of-mass velocity of the chunk. - -:line - -Note that currently the global and per-chunk temperatures calculated -by this compute only include translational degrees of freedom for each -atom. No rotational degrees of freedom are included for finite-size -particles. Also no degrees of freedom are subtracted for any velocity -bias or constraints that are applied, such as "compute -temp/partial"_compute_temp_partial.html, or "fix shake"_fix_shake.html -or "fix rigid"_fix_rigid.html. This is because those degrees of -freedom (e.g. a constrained bond) could apply to sets of atoms that -are both included and excluded from a specific chunk, and hence the -concept is somewhat ill-defined. In some cases, you can use the -{adof} and {cdof} keywords to adjust the calculated degrees of freedom -appropriately, as explained below. - -Note that the per-chunk temperature calculated by this compute and the -"fix ave/chunk temp"_fix_ave_chunk.html command can be different. -This compute calculates the temperature for each chunk for a single -snapshot. Fix ave/chunk can do that but can also time average those -values over many snapshots, or it can compute a temperature as if the -atoms in the chunk on different timesteps were collected together as -one set of atoms to calculate their temperature. This compute allows -the center-of-mass velocity of each chunk to be subtracted before -calculating the temperature; fix ave/chunk does not. - -NOTE: Only atoms in the specified group contribute to the calculations -performed by this compute. The "compute -chunk/atom"_compute_chunk_atom.html command defines its own group; -atoms will have a chunk ID = 0 if they are not in that group, -signifying they are not assigned to a chunk, and will thus also not -contribute to this calculation. You can specify the "all" group for -this command if you simply want to include atoms with non-zero chunk -IDs. - -The simplest way to output the per-chunk results of the compute -temp/chunk calculation to a file is to use the "fix -ave/time"_fix_ave_time.html command, for example: - -compute cc1 all chunk/atom molecule -compute myChunk all temp/chunk cc1 temp -fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre - -:line - -The keyword/value option pairs are used in the following ways. - -The {com} keyword can be used with a value of {yes} to subtract the -velocity of the center-of-mass for each chunk from the velocity of the -atoms in that chunk, before calculating either the global or per-chunk -temperature. This can be useful if the atoms are streaming or -otherwise moving collectively, and you wish to calculate only the -thermal temperature. - -For the {bias} keyword, {bias-ID} refers to the ID of a temperature -compute that removes a "bias" velocity from each atom. This also -allows calculation of the global or per-chunk temperature using only -the thermal temperature of atoms in each chunk after the translational -kinetic energy components have been altered in a prescribed way, -e.g. to remove a velocity profile. It also applies to the calculation -of the other per-chunk values, such as {kecom} or {internal}, which -involve the center-of-mass velocity of each chunk, which is calculated -after the velocity bias is removed from each atom. Note that the -temperature compute will apply its bias globally to the entire system, -not on a per-chunk basis. - -The {adof} and {cdof} keywords define the values used in the degree of -freedom (DOF) formulas used for the global or per-chunk temperature, -as described above. They can be used to calculate a more appropriate -temperature for some kinds of chunks. Here are 3 examples: - -If spatially binned chunks contain some number of water molecules and -"fix shake"_fix_shake.html is used to make each molecule rigid, then -you could calculate a temperature with 6 degrees of freedom (DOF) (3 -translational, 3 rotational) per molecule by setting {adof} to 2.0. - -If "compute temp/partial"_compute_temp_partial.html is used with the -{bias} keyword to only allow the x component of velocity to contribute -to the temperature, then {adof} = 1.0 would be appropriate. - -If each chunk consists of a large molecule, with some number of its -bonds constrained by "fix shake"_fix_shake.html or the entire molecule -by "fix rigid/small"_fix_rigid.html, {adof} = 0.0 and {cdof} could be -set to the remaining degrees of freedom for the entire molecule -(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid -molecule. - -:line - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -This compute also optionally calculates a global array, if one or more -of the optional values are specified. The number of rows in the array -= the number of chunks {Nchunk} as calculated by the specified -"compute chunk/atom"_compute_chunk_atom.html command. The number of -columns is the number of specified values (1 or more). These values -can be accessed by any command that uses global array values from a -compute as input. Again, see the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". The array values are "intensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. The array values -will be in temperature "units"_units.html for the {temp} value, and in -energy "units"_units.html for the {kecom} and {internal} values. - -[Restrictions:] - -The {com} and {bias} keywords cannot be used together. - -[Related commands:] - -"compute temp"_compute_temp.html, "fix ave/chunk -temp"_fix_ave_chunk.html - -[Default:] - -The option defaults are com no, no bias, adof = dimensionality of the -system (2 or 3), and cdof = 0.0. diff --git a/doc/txt/compute_temp_com.txt b/doc/txt/compute_temp_com.txt deleted file mode 100644 index 12df694e38..0000000000 --- a/doc/txt/compute_temp_com.txt +++ /dev/null @@ -1,93 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/com command :h3 - -[Syntax:] - -compute ID group-ID temp/com :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/com = style name of this compute command :ul - -[Examples:] - -compute 1 all temp/com -compute myTemp mobile temp/com :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -atoms, after subtracting out the center-of-mass velocity of the group. -This is useful if the group is expected to have a non-zero net -velocity for some reason. A compute of this style can be used by any -command that computes a temperature, -e.g. "thermo_modify"_thermo_modify.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc. - -After the center-of-mass velocity has been subtracted from each atom, -the temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = 2 or 3 = dimensionality of the simulation, N = number of atoms -in the group, k = Boltzmann constant, and T = temperature. - -A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. - -The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the {dynamic} option of the -"compute_modify"_compute_modify.html command if this is not the case. - -The removal of the center-of-mass velocity by this fix is essentially -computing the temperature after a "bias" has been removed from the -velocity of the atoms. If this compute is used with a fix command -that performs thermostatting then this bias will be subtracted from -each atom, thermostatting of the remaining thermal velocity will be -performed, and the bias will be added back in. Thermostatting fixes -that work in this way include "fix nvt"_fix_nh.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen.html, and "fix -langevin"_fix_langevin.html. - -This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as "fix shake"_fix_shake.html and -"fix rigid"_fix_rigid.html. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -{extra} option of the "compute_modify"_compute_modify.html command. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute temp"_compute_temp.html - -[Default:] none diff --git a/doc/txt/compute_temp_cs.txt b/doc/txt/compute_temp_cs.txt deleted file mode 100644 index 5fc939e375..0000000000 --- a/doc/txt/compute_temp_cs.txt +++ /dev/null @@ -1,120 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/cs command :h3 - -[Syntax:] - -compute ID group-ID temp/cs group1 group2 :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/cs = style name of this compute command -group1 = group-ID of either cores or shells -group2 = group-ID of either shells or cores :ul - -[Examples:] - -compute oxygen_c-s all temp/cs O_core O_shell -compute core_shells all temp/cs cores shells :pre - -[Description:] - -Define a computation that calculates the temperature of a system based -on the center-of-mass velocity of atom pairs that are bonded to each -other. This compute is designed to be used with the adiabatic -core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham1. See -the "Howto coreshell"_Howto_coreshell.html doc page for an overview of -the model as implemented in LAMMPS. Specifically, this compute -enables correct temperature calculation and thermostatting of -core/shell pairs where it is desirable for the internal degrees of -freedom of the core/shell pairs to not be influenced by a thermostat. -A compute of this style can be used by any command that computes a -temperature via "fix_modify"_fix_modify.html e.g. "fix -temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc. - -Note that this compute does not require all ions to be polarized, -hence defined as core/shell pairs. One can mix core/shell pairs and -ions without a satellite particle if desired. The compute will -consider the non-polarized ions according to the physical system. - -For this compute, core and shell particles are specified by two -respective group IDs, which can be defined using the -"group"_group.html command. The number of atoms in the two groups -must be the same and there should be one bond defined between a pair -of atoms in the two groups. Non-polarized ions which might also be -included in the treated system should not be included into either of -these groups, they are taken into account by the {group-ID} (2nd -argument) of the compute. - -The temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = 2 or 3 = dimensionality of the simulation, N = number of atoms -in the group, k = Boltzmann constant, and T = temperature. Note that -the velocity of each core or shell atom used in the KE calculation is -the velocity of the center-of-mass (COM) of the core/shell pair the -atom is part of. - -A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. In contrast to the temperature, the velocity of -each core or shell atom is taken individually. - -The change this fix makes to core/shell atom velocities is essentially -computing the temperature after a "bias" has been removed from the -velocity of the atoms. This "bias" is the velocity of the atom -relative to the COM velocity of the core/shell pair. If this compute -is used with a fix command that performs thermostatting then this bias -will be subtracted from each atom, thermostatting of the remaining COM -velocity will be performed, and the bias will be added back in. This -means the thermostatting will effectively be performed on the -core/shell pairs, instead of on the individual core and shell atoms. -Thermostatting fixes that work in this way include "fix -nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen.html, and "fix -langevin"_fix_langevin.html. - -The internal energy of core/shell pairs can be calculated by the -"compute temp/chunk"_compute_temp_chunk.html command, if chunks are -defined as core/shell pairs. See the "Howto -coreshell"_Howto_coreshell.html doc page doc page for more discussion -on how to do this. - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] - -The number of core/shell pairs contributing to the temperature is -assumed to be constant for the duration of the run. No fixes should -be used which generate new molecules or atoms during a simulation. - -[Related commands:] - -"compute temp"_compute_temp.html, "compute -temp/chunk"_compute_temp_chunk.html - -[Default:] none - -:line - -:link(MitchellFinchham1) -[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter, -5, 1031-1038 (1993). diff --git a/doc/txt/compute_temp_deform.txt b/doc/txt/compute_temp_deform.txt deleted file mode 100644 index 26d322589e..0000000000 --- a/doc/txt/compute_temp_deform.txt +++ /dev/null @@ -1,134 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/deform command :h3 - -[Syntax:] - -compute ID group-ID temp/deform :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/deform = style name of this compute command :ul - -[Examples:] - -compute myTemp all temp/deform :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -atoms, after subtracting out a streaming velocity induced by the -simulation box changing size and/or shape, for example in a -non-equilibrium MD (NEMD) simulation. The size/shape change is -induced by use of the "fix deform"_fix_deform.html command. A compute -of this style is created by the "fix nvt/sllod"_fix_nvt_sllod.html -command to compute the thermal temperature of atoms for thermostatting -purposes. A compute of this style can also be used by any command -that computes a temperature, e.g. "thermo_modify"_thermo_modify.html, -"fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc. - -The deformation fix changes the box size and/or shape over time, so -each atom in the simulation box can be thought of as having a -"streaming" velocity. For example, if the box is being sheared in x, -relative to y, then atoms at the bottom of the box (low y) have a -small x velocity, while atoms at the top of the box (hi y) have a -large x velocity. This position-dependent streaming velocity is -subtracted from each atom's actual velocity to yield a thermal -velocity which is used to compute the temperature. - -NOTE: "Fix deform"_fix_deform.html has an option for remapping either -atom coordinates or velocities to the changing simulation box. When -using this compute in conjunction with a deforming box, fix deform -should NOT remap atom positions, but rather should let atoms respond -to the changing box by adjusting their own velocities (or let "fix -deform"_fix_deform.html remap the atom velocities, see it's remap -option). If fix deform does remap atom positions, then they appear to -move with the box but their velocity is not changed, and thus they do -NOT have the streaming velocity assumed by this compute. LAMMPS will -warn you if fix deform is defined and its remap setting is not -consistent with this compute. - -After the streaming velocity has been subtracted from each atom, the -temperature is calculated by the formula KE = dim/2 N k T, where KE = -total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 -or 3 = dimensionality of the simulation, N = number of atoms in the -group, k = Boltzmann constant, and T = temperature. Note that v in -the kinetic energy formula is the atom's thermal velocity. - -A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. - -The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the {dynamic} option of the -"compute_modify"_compute_modify.html command if this is not the case. - -The removal of the box deformation velocity component by this fix is -essentially computing the temperature after a "bias" has been removed -from the velocity of the atoms. If this compute is used with a fix -command that performs thermostatting then this bias will be subtracted -from each atom, thermostatting of the remaining thermal velocity will -be performed, and the bias will be added back in. Thermostatting -fixes that work in this way include "fix nvt"_fix_nh.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen.html, and "fix -langevin"_fix_langevin.html. - -NOTE: The temperature calculated by this compute is only accurate if -the atoms are indeed moving with a stream velocity profile that -matches the box deformation. If not, then the compute will subtract -off an incorrect stream velocity, yielding a bogus thermal -temperature. You should NOT assume that your atoms are streaming at -the same rate the box is deforming. Rather, you should monitor their -velocity profile, e.g. via the "fix ave/chunk"_fix_ave_chunk.html -command. And you can compare the results of this compute to "compute -temp/profile"_compute_temp_profile.html, which actually calculates the -stream profile before subtracting it. If the two computes do not give -roughly the same temperature, then your atoms are not streaming -consistent with the box deformation. See the "fix -deform"_fix_deform.html command for more details on ways to get atoms -to stream consistently with the box deformation. - -This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as "fix shake"_fix_shake.html and -"fix rigid"_fix_rigid.html. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -{extra} option of the "compute_modify"_compute_modify.html command. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute temp/ramp"_compute_temp_ramp.html, "compute -temp/profile"_compute_temp_profile.html, "fix deform"_fix_deform.html, -"fix nvt/sllod"_fix_nvt_sllod.html - -[Default:] none diff --git a/doc/txt/compute_temp_deform_eff.txt b/doc/txt/compute_temp_deform_eff.txt deleted file mode 100644 index 4af61dc918..0000000000 --- a/doc/txt/compute_temp_deform_eff.txt +++ /dev/null @@ -1,72 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/deform/eff command :h3 - -[Syntax:] - -compute ID group-ID temp/deform/eff :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/deform/eff = style name of this compute command :ul - -[Examples:] - -compute myTemp all temp/deform/eff :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -nuclei and electrons in the "electron force field"_pair_eff.html -model, after subtracting out a streaming velocity induced by the -simulation box changing size and/or shape, for example in a -non-equilibrium MD (NEMD) simulation. The size/shape change is -induced by use of the "fix deform"_fix_deform.html command. A -compute of this style is created by the "fix -nvt/sllod/eff"_fix_nvt_sllod_eff.html command to compute the thermal -temperature of atoms for thermostatting purposes. A compute of this -style can also be used by any command that computes a temperature, -e.g. "thermo_modify"_thermo_modify.html, "fix npt/eff"_fix_nh_eff.html, -etc. - -The calculation performed by this compute is exactly like that -described by the "compute temp/deform"_compute_temp_deform.html -command, except that the formula for the temperature includes the -radial electron velocity contributions, as discussed by the "compute -temp/eff"_compute_temp_eff.html command. Note that only the -translational degrees of freedom for each nuclei or electron are -affected by the streaming velocity adjustment. The radial velocity -component of the electrons is not affected. - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute temp/ramp"_compute_temp_ramp.html, "fix deform"_fix_deform.html, -"fix nvt/sllod/eff"_fix_nvt_sllod_eff.html - -[Default:] none diff --git a/doc/txt/compute_temp_drude.txt b/doc/txt/compute_temp_drude.txt deleted file mode 100644 index 20d9a5c056..0000000000 --- a/doc/txt/compute_temp_drude.txt +++ /dev/null @@ -1,81 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/drude command :h3 - -[Syntax:] - -compute ID group-ID temp/drude :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/drude = style name of this compute command :ul - -[Examples:] - -compute TDRUDE all temp/drude :pre - -[Description:] - -Define a computation that calculates the temperatures of core-Drude -pairs. This compute is designed to be used with the "thermalized Drude -oscillator model"_Howto_drude.html. Polarizable models in LAMMPS -are described on the "Howto polarizable"_Howto_polarizable.html doc -page. - -Drude oscillators consist of a core particle and a Drude particle -connected by a harmonic bond, and the relative motion of these Drude -oscillators is usually maintained cold by a specific thermostat that -acts on the relative motion of the core-Drude particle -pairs. Therefore, because LAMMPS considers Drude particles as normal -atoms in its default temperature compute ("compute -temp"_compute_temp.html command), the reduced temperature of the -core-Drude particle pairs is not calculated correctly. - -By contrast, this compute calculates the temperature of the cores -using center-of-mass velocities of the core-Drude pairs, and the -reduced temperature of the Drude particles using the relative -velocities of the Drude particles with respect to their cores. -Non-polarizable atoms are considered as cores. Their velocities -contribute to the temperature of the cores. - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6, which can be accessed by indices 1-6, whose components -are - -temperature of the centers of mass (temperature units) -temperature of the dipoles (temperature units) -number of degrees of freedom of the centers of mass -number of degrees of freedom of the dipoles -kinetic energy of the centers of mass (energy units) -kinetic energy of the dipoles (energy units) :ol - -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -Both the scalar value and the first two values of the vector -calculated by this compute are "intensive". The other 4 vector values -are "extensive". - -[Restrictions:] - -The number of degrees of freedom contributing to the temperature is -assumed to be constant for the duration of the run unless the -{fix_modify} command sets the option {dynamic yes}. - -[Related commands:] - -"fix drude"_fix_drude.html, "fix -langevin/drude"_fix_langevin_drude.html, "fix -drude/transform"_fix_drude_transform.html, "pair_style -thole"_pair_thole.html, "compute temp"_compute_temp.html - -[Default:] none diff --git a/doc/txt/compute_temp_eff.txt b/doc/txt/compute_temp_eff.txt deleted file mode 100644 index 415cb77595..0000000000 --- a/doc/txt/compute_temp_eff.txt +++ /dev/null @@ -1,95 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/eff command :h3 - -[Syntax:] - -compute ID group-ID temp/eff :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/eff = style name of this compute command :ul - -[Examples:] - -compute 1 all temp/eff -compute myTemp mobile temp/eff :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -nuclei and electrons in the "electron force field"_pair_eff.html -model. A compute of this style can be used by commands that compute a -temperature, e.g. "thermo_modify"_thermo_modify.html, "fix -npt/eff"_fix_nh_eff.html, etc. - -The temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for -nuclei and sum of 1/2 (m v^2 + 3/4 m s^2) for electrons, where s -includes the radial electron velocity contributions), dim = 2 or 3 = -dimensionality of the simulation, N = number of atoms (only total -number of nuclei in the eFF (see the "pair_eff"_pair_style.html -command) in the group, k = Boltzmann constant, and T = temperature. -This expression is summed over all nuclear and electronic degrees of -freedom, essentially by setting the kinetic contribution to the heat -capacity to 3/2k (where only nuclei contribute). This subtlety is -valid for temperatures well below the Fermi temperature, which for -densities two to five times the density of liquid H2 ranges from -86,000 to 170,000 K. - -NOTE: For eFF models, in order to override the default temperature -reported by LAMMPS in the thermodynamic quantities reported via the -"thermo"_thermo.html command, the user should apply a -"thermo_modify"_thermo_modify.html command, as shown in the following -example: - -compute effTemp all temp/eff -thermo_style custom step etotal pe ke temp press -thermo_modify temp effTemp :pre - -A 6-component kinetic energy tensor is also calculated by this compute -for use in the computation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. For the eFF, -again, the radial electronic velocities are also considered. - -The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the {dynamic} option of the -"compute_modify"_compute_modify.html command if this is not the case. - -This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as "fix shake"_fix_shake.html and -"fix rigid"_fix_rigid.html. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -{extra} option of the "compute_modify"_compute_modify.html command. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -[Output info:] - -The scalar value calculated by this compute is "intensive", meaning it -is independent of the number of atoms in the simulation. The vector -values are "extensive", meaning they scale with the number of atoms in -the simulation. - -[Restrictions:] - -This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute temp/partial"_compute_temp_partial.html, "compute -temp/region"_compute_temp_region.html, "compute -pressure"_compute_pressure.html - -[Default:] none diff --git a/doc/txt/compute_temp_partial.txt b/doc/txt/compute_temp_partial.txt deleted file mode 100644 index 14294842a1..0000000000 --- a/doc/txt/compute_temp_partial.txt +++ /dev/null @@ -1,119 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/partial command :h3 - -[Syntax:] - -compute ID group-ID temp/partial xflag yflag zflag :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/partial = style name of this compute command -xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension :ul - -[Examples:] - -compute newT flow temp/partial 1 1 0 :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -atoms, after excluding one or more velocity components. A compute of -this style can be used by any command that computes a temperature, -e.g. "thermo_modify"_thermo_modify.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc. - -The temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = dimensionality of the simulation, N = number of atoms in the -group, k = Boltzmann constant, and T = temperature. The calculation -of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag = -0. The dim parameter is adjusted to give the correct number of -degrees of freedom. - -A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the calculation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. - -The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the {dynamic} option of the -"compute_modify"_compute_modify.html command if this is not the case. - -The removal of velocity components by this fix is essentially -computing the temperature after a "bias" has been removed from the -velocity of the atoms. If this compute is used with a fix command -that performs thermostatting then this bias will be subtracted from -each atom, thermostatting of the remaining thermal velocity will be -performed, and the bias will be added back in. Thermostatting fixes -that work in this way include "fix nvt"_fix_nh.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen.html, and "fix -langevin"_fix_langevin.html. - -This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as "fix shake"_fix_shake.html and -"fix rigid"_fix_rigid.html. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -{extra} option of the "compute_modify"_compute_modify.html command. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute temp"_compute_temp.html, "compute -temp/region"_compute_temp_region.html, "compute -pressure"_compute_pressure.html - -[Default:] none diff --git a/doc/txt/compute_temp_profile.txt b/doc/txt/compute_temp_profile.txt deleted file mode 100644 index 4ed04ca67e..0000000000 --- a/doc/txt/compute_temp_profile.txt +++ /dev/null @@ -1,182 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/profile command :h3 - -[Syntax:] - -compute ID group-ID temp/profile xflag yflag zflag binstyle args :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -temp/profile = style name of this compute command :l -xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension :l -binstyle = {x} or {y} or {z} or {xy} or {yz} or {xz} or {xyz} :l - {x} arg = Nx - {y} arg = Ny - {z} arg = Nz - {xy} args = Nx Ny - {yz} args = Ny Nz - {xz} args = Nx Nz - {xyz} args = Nx Ny Nz - Nx,Ny,Nz = number of velocity bins in x,y,z dimensions :pre - -zero or more keyword/value pairs may be appended :l -keyword = {out} :l - {out} value = {tensor} or {bin} :pre -:ule - -[Examples:] - -compute myTemp flow temp/profile 1 1 1 x 10 -compute myTemp flow temp/profile 1 1 1 x 10 out bin -compute myTemp flow temp/profile 0 1 1 xyz 20 20 20 :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -atoms, after subtracting out a spatially-averaged center-of-mass -velocity field, before computing the kinetic energy. This can be -useful for thermostatting a collection of atoms undergoing a complex -flow, e.g. via a profile-unbiased thermostat (PUT) as described in -"(Evans)"_#Evans1. A compute of this style can be used by any command -that computes a temperature, e.g. "thermo_modify"_thermo_modify.html, -"fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc. - -The {xflag}, {yflag}, {zflag} settings determine which components of -average velocity are subtracted out. - -The {binstyle} setting and its {Nx}, {Ny}, {Nz} arguments determine -how bins are setup to perform spatial averaging. "Bins" can be 1d -slabs, 2d pencils, or 3d bricks depending on which {binstyle} is used. -The simulation box is partitioned conceptually into {Nx} by {Ny} by -{Nz} bins. Depending on the {binstyle}, you may only specify one or -two of these values; the others are effectively set to 1 (no binning -in that dimension). For non-orthogonal (triclinic) simulation boxes, -the bins are "tilted" slabs or pencils or bricks that are parallel to -the tilted faces of the box. See the "region prism"_region.html -command for a discussion of the geometry of tilted boxes in LAMMPS. - -When a temperature is computed, the center-of-mass velocity for the -set of atoms that are both in the compute group and in the same -spatial bin is calculated. This bias velocity is then subtracted from -the velocities of individual atoms in the bin to yield a thermal -velocity for each atom. Note that if there is only one atom in the -bin, its thermal velocity will thus be 0.0. - -After the spatially-averaged velocity field has been subtracted from -each atom, the temperature is calculated by the formula KE = (dim*N -- dim*Nx*Ny*Nz) k T/2, where KE = total kinetic energy of the group of -atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the -simulation, N = number of atoms in the group, k = Boltzmann constant, -and T = temperature. The dim*Nx*Ny*Nz term are degrees of freedom -subtracted to adjust for the removal of the center-of-mass velocity in -each of Nx*Ny*Nz bins, as discussed in the "(Evans)"_#Evans1 paper. - -If the {out} keyword is used with a {tensor} value, which is the -default, a kinetic energy tensor, stored as a 6-element vector, is -also calculated by this compute for use in the computation of a -pressure tensor. The formula for the components of the tensor is the -same as the above formula, except that v^2 is replaced by vx*vy for -the xy component, etc. The 6 components of the vector are ordered xx, -yy, zz, xy, xz, yz. - -If the {out} keyword is used with a {bin} value, the count of atoms -and computed temperature for each bin are stored for output, as an -array of values, as described below. The temperature of each bin is -calculated as described above, where the bias velocity is subtracted -and only the remaining thermal velocity of atoms in the bin -contributes to the temperature. See the note below for how the -temperature is normalized by the degrees-of-freedom of atoms in the -bin. - -The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the {dynamic} option of the -"compute_modify"_compute_modify.html command if this is not the case. - -The removal of the spatially-averaged velocity field by this fix is -essentially computing the temperature after a "bias" has been removed -from the velocity of the atoms. If this compute is used with a fix -command that performs thermostatting then this bias will be subtracted -from each atom, thermostatting of the remaining thermal velocity will -be performed, and the bias will be added back in. Thermostatting -fixes that work in this way include "fix nvt"_fix_nh.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen.html, and "fix -langevin"_fix_langevin.html. - -This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as "fix shake"_fix_shake.html and -"fix rigid"_fix_rigid.html. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -{extra} option of the "compute_modify"_compute_modify.html command. - -NOTE: When using the {out} keyword with a value of {bin}, the -calculated temperature for each bin does not include the -degrees-of-freedom adjustment described in the preceding paragraph, -for fixes that constrain molecular motion. It does include the -adjustment due to the {extra} option, which is applied to each bin. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. Using this compute in conjunction with a -thermostatting fix, as explained there, will effectively implement a -profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans1. - -[Output info:] - -This compute calculates a global scalar (the temperature). Depending -on the setting of the {out} keyword, it also calculates a global -vector or array. For {out} = {tensor}, it calculates a vector of -length 6 (KE tensor), which can be accessed by indices 1-6. For {out} -= {bin} it calculates a global array which has 2 columns and N rows, -where N is the number of bins. The first column contains the number -of atoms in that bin. The second contains the temperature of that -bin, calculated as described above. The ordering of rows in the array -is as follows. Bins in x vary fastest, then y, then z. Thus for a -10x10x10 3d array of bins, there will be 1000 rows. The bin with -indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10 -+ ix = 322, where the rows are numbered from 1 to 1000 and the bin -indices are numbered from 1 to 10 in each dimension. - -These values can be used by any command that uses global scalar or -vector or array values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". The array values are "intensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. The first column -of array values are counts; the values in the second column will be in -temperature "units"_units.html. - -[Restrictions:] - -You should not use too large a velocity-binning grid, especially in -3d. In the current implementation, the binned velocity averages are -summed across all processors, so this will be inefficient if the grid -is too large, and the operation is performed every timestep, as it -will be for most thermostats. - -[Related commands:] - -"compute temp"_compute_temp.html, "compute -temp/ramp"_compute_temp_ramp.html, "compute -temp/deform"_compute_temp_deform.html, "compute -pressure"_compute_pressure.html - -[Default:] - -The option default is out = tensor. - -:line - -:link(Evans1) -[(Evans)] Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986). diff --git a/doc/txt/compute_temp_ramp.txt b/doc/txt/compute_temp_ramp.txt deleted file mode 100644 index 15cad9c0cb..0000000000 --- a/doc/txt/compute_temp_ramp.txt +++ /dev/null @@ -1,116 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/ramp command :h3 - -[Syntax:] - -compute ID group-ID temp/ramp vdim vlo vhi dim clo chi keyword value ... :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/ramp = style name of this compute command -vdim = {vx} or {vy} or {vz} -vlo,vhi = subtract velocities between vlo and vhi (velocity units) -dim = {x} or {y} or {z} -clo,chi = lower and upper bound of domain to subtract from (distance units) -zero or more keyword/value pairs may be appended -keyword = {units} :ul - {units} value = {lattice} or {box} :pre - -[Examples:] - -compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -atoms, after subtracting out an ramped velocity profile before -computing the kinetic energy. A compute of this style can be used by -any command that computes a temperature, -e.g. "thermo_modify"_thermo_modify.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc. - -The meaning of the arguments for this command which define the -velocity ramp are the same as for the "velocity ramp"_velocity.html -command which was presumably used to impose the velocity. - -After the ramp velocity has been subtracted from the specified -dimension for each atom, the temperature is calculated by the formula -KE = dim/2 N k T, where KE = total kinetic energy of the group of -atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the -simulation, N = number of atoms in the group, k = Boltzmann constant, -and T = temperature. - -The {units} keyword determines the meaning of the distance units used -for coordinates (c1,c2) and velocities (vlo,vhi). A {box} value -selects standard distance units as defined by the "units"_units.html -command, e.g. Angstroms for units = real or metal. A {lattice} value -means the distance units are in lattice spacings; e.g. velocity = -lattice spacings / tau. The "lattice"_lattice.html command must have -been previously used to define the lattice spacing. - -A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. - -The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the {dynamic} option of the -"compute_modify"_compute_modify.html command if this is not the case. - -The removal of the ramped velocity component by this fix is -essentially computing the temperature after a "bias" has been removed -from the velocity of the atoms. If this compute is used with a fix -command that performs thermostatting then this bias will be subtracted -from each atom, thermostatting of the remaining thermal velocity will -be performed, and the bias will be added back in. Thermostatting -fixes that work in this way include "fix nvt"_fix_nh.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen.html, and "fix -langevin"_fix_langevin.html. - -This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as "fix shake"_fix_shake.html and -"fix rigid"_fix_rigid.html. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -{extra} option of the "compute_modify"_compute_modify.html command. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute temp"_compute_temp.html, "compute -temp/profie"_compute_temp_profile.html, "compute -temp/deform"_compute_temp_deform.html, "compute -pressure"_compute_pressure.html - -[Default:] - -The option default is units = lattice. diff --git a/doc/txt/compute_temp_region.txt b/doc/txt/compute_temp_region.txt deleted file mode 100644 index f23901af98..0000000000 --- a/doc/txt/compute_temp_region.txt +++ /dev/null @@ -1,110 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/region command :h3 - -[Syntax:] - -compute ID group-ID temp/region region-ID :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/region = style name of this compute command -region-ID = ID of region to use for choosing atoms :ul - -[Examples:] - -compute mine flow temp/region boundary :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -atoms in a geometric region. This can be useful for thermostatting -one portion of the simulation box. E.g. a McDLT simulation where one -side is cooled, and the other side is heated. A compute of this style -can be used by any command that computes a temperature, -e.g. "thermo_modify"_thermo_modify.html, "fix -temp/rescale"_fix_temp_rescale.html, etc. - -Note that a {region}-style temperature can be used to thermostat with -"fix temp/rescale"_fix_temp_rescale.html or "fix -langevin"_fix_langevin.html, but should probably not be used with -Nose/Hoover style fixes ("fix nvt"_fix_nh.html, "fix -npt"_fix_nh.html, or "fix nph"_fix_nh.html), if the -degrees-of-freedom included in the computed T varies with time. - -The temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = 2 or 3 = dimensionality of the simulation, N = number of atoms -in both the group and region, k = Boltzmann constant, and T = -temperature. - -A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. - -The number of atoms contributing to the temperature is calculated each -time the temperature is evaluated since it is assumed atoms can -enter/leave the region. Thus there is no need to use the {dynamic} -option of the "compute_modify"_compute_modify.html command for this -compute style. - -The removal of atoms outside the region by this fix is essentially -computing the temperature after a "bias" has been removed, which in -this case is the velocity of any atoms outside the region. If this -compute is used with a fix command that performs thermostatting then -this bias will be subtracted from each atom, thermostatting of the -remaining thermal velocity will be performed, and the bias will be -added back in. Thermostatting fixes that work in this way include -"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen.html, and "fix -langevin"_fix_langevin.html. This means that when this compute -is used to calculate the temperature for any of the thermostatting -fixes via the "fix modify temp"_fix_modify.html command, the thermostat -will operate only on atoms that are currently in the geometric -region. - -Unlike other compute styles that calculate temperature, this compute -does not subtract out degrees-of-freedom due to fixes that constrain -motion, such as "fix shake"_fix_shake.html and "fix -rigid"_fix_rigid.html. This is because those degrees of freedom -(e.g. a constrained bond) could apply to sets of atoms that straddle -the region boundary, and hence the concept is somewhat ill-defined. -If needed the number of subtracted degrees-of-freedom can be set -explicitly using the {extra} option of the -"compute_modify"_compute_modify.html command. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute temp"_compute_temp.html, "compute -pressure"_compute_pressure.html - -[Default:] none diff --git a/doc/txt/compute_temp_region_eff.txt b/doc/txt/compute_temp_region_eff.txt deleted file mode 100644 index f15f3155b0..0000000000 --- a/doc/txt/compute_temp_region_eff.txt +++ /dev/null @@ -1,64 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/region/eff command :h3 - -[Syntax:] - -compute ID group-ID temp/region/eff region-ID :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/region/eff = style name of this compute command -region-ID = ID of region to use for choosing atoms :ul - -[Examples:] - -compute mine flow temp/region/eff boundary :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -nuclei and electrons in the "electron force field"_pair_eff.html -model, within a geometric region using the electron force field. A -compute of this style can be used by commands that compute a -temperature, e.g. "thermo_modify"_thermo_modify.html. - -The operation of this compute is exactly like that described by the -"compute temp/region"_compute_temp_region.html command, except that -the formula for the temperature itself includes the radial electron -velocity contributions, as discussed by the "compute -temp/eff"_compute_temp_eff.html command. - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute temp/region"_compute_temp_region.html, "compute -temp/eff"_compute_temp_eff.html, "compute -pressure"_compute_pressure.html - -[Default:] none diff --git a/doc/txt/compute_temp_rotate.txt b/doc/txt/compute_temp_rotate.txt deleted file mode 100644 index 8dac0405b4..0000000000 --- a/doc/txt/compute_temp_rotate.txt +++ /dev/null @@ -1,96 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/rotate command :h3 - -[Syntax:] - -compute ID group-ID temp/rotate :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/rotate = style name of this compute command :ul - -[Examples:] - -compute Tbead bead temp/rotate :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -atoms, after subtracting out the center-of-mass velocity and angular velocity of the group. -This is useful if the group is expected to have a non-zero net -velocity and/or global rotation motion for some reason. A compute of this style can be used by any -command that computes a temperature, -e.g. "thermo_modify"_thermo_modify.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc. - -After the center-of-mass velocity and angular velocity has been subtracted from each atom, -the temperature is calculated by the formula KE = dim/2 N k T, where -KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), -dim = 2 or 3 = dimensionality of the simulation, N = number of atoms -in the group, k = Boltzmann constant, and T = temperature. - -A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute for use in the computation of a pressure -tensor. The formula for the components of the tensor is the same as -the above formula, except that v^2 is replaced by vx*vy for the xy -component, etc. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. - -The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the {dynamic} option of the -"compute_modify"_compute_modify.html command if this is not the case. - -The removal of the center-of-mass velocity and angular velocity by this fix is essentially -computing the temperature after a "bias" has been removed from the -velocity of the atoms. If this compute is used with a fix command -that performs thermostatting then this bias will be subtracted from -each atom, thermostatting of the remaining thermal velocity will be -performed, and the bias will be added back in. Thermostatting fixes -that work in this way include "fix nvt"_fix_nh.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen.html, and "fix -langevin"_fix_langevin.html. - -This compute subtracts out degrees-of-freedom due to fixes that -constrain molecular motion, such as "fix shake"_fix_shake.html and -"fix rigid"_fix_rigid.html. This means the temperature of groups of -atoms that include these constraints will be computed correctly. If -needed, the subtracted degrees-of-freedom can be altered using the -{extra} option of the "compute_modify"_compute_modify.html command. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] - -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute temp"_compute_temp.html - -[Default:] none diff --git a/doc/txt/compute_temp_sphere.txt b/doc/txt/compute_temp_sphere.txt deleted file mode 100644 index 5a55126d12..0000000000 --- a/doc/txt/compute_temp_sphere.txt +++ /dev/null @@ -1,137 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/sphere command :h3 - -[Syntax:] - -compute ID group-ID temp/sphere keyword value ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -temp/sphere = style name of this compute command :l -zero or more keyword/value pairs may be appended :l -keyword = {bias} or {dof} :l - {bias} value = bias-ID - bias-ID = ID of a temperature compute that removes a velocity bias - {dof} value = {all} or {rotate} - all = compute temperature of translational and rotational degrees of freedom - rotate = compute temperature of just rotational degrees of freedom :pre -:ule - -[Examples:] - -compute 1 all temp/sphere -compute myTemp mobile temp/sphere bias tempCOM -compute myTemp mobile temp/sphere dof rotate :pre - -[Description:] - -Define a computation that calculates the temperature of a group of -spherical particles, including a contribution from both their -translational and rotational kinetic energy. This differs from the -usual "compute temp"_compute_temp.html command, which assumes point -particles with only translational kinetic energy. - -Both point and finite-size particles can be included in the group. -Point particles do not rotate, so they have only 3 translational -degrees of freedom. For 3d spherical particles, each has 6 degrees of -freedom (3 translational, 3 rotational). For 2d spherical particles, -each has 3 degrees of freedom (2 translational, 1 rotational). - -NOTE: This choice for degrees of freedom (dof) assumes that all -finite-size spherical particles in your model will freely rotate, -sampling all their rotational dof. It is possible to use a -combination of interaction potentials and fixes that induce no torque -or otherwise constrain some of all of your particles so that this is -not the case. Then there are less dof and you should use the -"compute_modify extra"_compute_modify.html command to adjust the dof -accordingly. - -The translational kinetic energy is computed the same as is described -by the "compute temp"_compute_temp.html command. The rotational -kinetic energy is computed as 1/2 I w^2, where I is the moment of -inertia for a sphere and w is the particle's angular velocity. - -NOTE: For "2d models"_dimension.html, particles are treated as -spheres, not disks, meaning their moment of inertia will be the same -as in 3d. - -A kinetic energy tensor, stored as a 6-element vector, is also -calculated by this compute. The formula for the components of the -tensor is the same as the above formulas, except that v^2 and w^2 are -replaced by vx*vy and wx*wy for the xy component. The 6 components of -the vector are ordered xx, yy, zz, xy, xz, yz. - -The number of atoms contributing to the temperature is assumed to be -constant for the duration of the run; use the {dynamic} option of the -"compute_modify"_compute_modify.html command if this is not the case. - -This compute subtracts out translational degrees-of-freedom due to -fixes that constrain molecular motion, such as "fix -shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the -temperature of groups of atoms that include these constraints will be -computed correctly. If needed, the subtracted degrees-of-freedom can -be altered using the {extra} option of the -"compute_modify"_compute_modify.html command. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -:line - -The keyword/value option pairs are used in the following ways. - -For the {bias} keyword, {bias-ID} refers to the ID of a temperature -compute that removes a "bias" velocity from each atom. This allows -compute temp/sphere to compute its thermal temperature after the -translational kinetic energy components have been altered in a -prescribed way, e.g. to remove a flow velocity profile. Thermostats -that use this compute will work with this bias term. See the doc -pages for individual computes that calculate a temperature and the doc -pages for fixes that perform thermostatting for more details. - -For the {dof} keyword, a setting of {all} calculates a temperature -that includes both translational and rotational degrees of freedom. A -setting of {rotate} calculates a temperature that includes only -rotational degrees of freedom. - -:line - -[Output info:] - -This compute calculates a global scalar (the temperature) and a global -vector of length 6 (KE tensor), which can be accessed by indices 1-6. -These values can be used by any command that uses global scalar or -vector values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The scalar value calculated by this compute is "intensive". The -vector values are "extensive". - -The scalar value will be in temperature "units"_units.html. The -vector values will be in energy "units"_units.html. - -[Restrictions:] - -This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the "atom_style sphere"_atom_style.html -command. - -All particles in the group must be finite-size spheres, or point -particles with radius = 0.0. - -[Related commands:] - -"compute temp"_compute_temp.html, "compute -temp/asphere"_compute_temp.html - -[Default:] - -The option defaults are no bias and dof = all. diff --git a/doc/txt/compute_temp_uef.txt b/doc/txt/compute_temp_uef.txt deleted file mode 100644 index b9e6187533..0000000000 --- a/doc/txt/compute_temp_uef.txt +++ /dev/null @@ -1,52 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute temp/uef command :h3 - -[Syntax:] - -compute ID group-ID temp/uef :pre - -ID, group-ID are documented in "compute"_compute.html command -temp/uef = style name of this compute command :ul - -[Examples:] - -compute 1 all temp/uef -compute 2 sel temp/uef :pre - -[Description:] - -This command is used to compute the kinetic energy tensor in -the reference frame of the applied flow field when -"fix nvt/uef"_fix_nh_uef.html or -"fix npt/uef"_fix_nh_uef.html is used. -It is not necessary to use this command to compute the scalar -value of the temperature. A "compute temp"_compute_temp.html -may be used for that purpose. - -Output information for this command can be found in the -documentation for "compute temp"_compute_temp.html. - -[Restrictions:] - -This fix is part of the USER-UEF package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This command can only be used when "fix nvt/uef"_fix_nh_uef.html -or "fix npt/uef"_fix_nh_uef.html is active. - -[Related commands:] - -"compute temp"_compute_temp.html, -"fix nvt/uef"_fix_nh_uef.html, -"compute pressure/uef"_compute_pressure_uef.html - - -[Default:] none diff --git a/doc/txt/compute_ti.txt b/doc/txt/compute_ti.txt deleted file mode 100644 index 0dec297183..0000000000 --- a/doc/txt/compute_ti.txt +++ /dev/null @@ -1,136 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute ti command :h3 - -[Syntax:] - -compute ID group ti keyword args ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -ti = style name of this compute command :l -one or more attribute/arg pairs may be appended :l -keyword = pair style (lj/cut, gauss, born, etc) or {tail} or {kspace} :l - pair style args = atype v_name1 v_name2 - atype = atom type (see asterisk form below) - v_name1 = variable with name1 that is energy scale factor and function of lambda - v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda - {tail} args = atype v_name1 v_name2 - atype = atom type (see asterisk form below) - v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda - v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda - {kspace} args = atype v_name1 v_name2 - atype = atom type (see asterisk form below) - v_name1 = variable with name1 that is K-Space scale factor and function of lambda - v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda :pre -:ule - -[Examples:] - -compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks -compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks :pre - -[Description:] - -Define a computation that calculates the derivative of the interaction -potential with respect to {lambda}, the coupling parameter used in a -thermodynamic integration. This derivative can be used to infer a -free energy difference resulting from an alchemical simulation, as -described in "Eike"_#Eike. - -Typically this compute will be used in conjunction with the "fix -adapt"_fix_adapt.html command which can perform alchemical -transformations by adjusting the strength of an interaction potential -as a simulation runs, as defined by one or more -"pair_style"_pair_style.html or "kspace_style"_kspace_style.html -commands. This scaling is done via a prefactor on the energy, forces, -virial calculated by the pair or K-Space style. The prefactor is -often a function of a {lambda} parameter which may be adjusted from 0 -to 1 (or vice versa) over the course of a "run"_run.html. The -time-dependent adjustment is what the "fix adapt"_fix_adapt.html -command does. - -Assume that the unscaled energy of a pair_style or kspace_style is -given by U. Then the scaled energy is - -Us = f(lambda) U :pre - -where f() is some function of lambda. What this compute calculates is - -dUs / d(lambda) = U df(lambda)/dlambda = Us / f(lambda) df(lambda)/dlambda :pre - -which is the derivative of the system's scaled potential energy Us -with respect to {lambda}. - -To perform this calculation, you provide one or more atom types as -{atype}. {Atype} can be specified in one of two ways. An explicit -numeric values can be used, as in the 1st example above. Or a -wildcard asterisk can be used in place of or in conjunction with the -{atype} argument to select multiple atom types. This takes the form -"*" or "*n" or "n*" or "m*n". If N = the number of atom types, then -an asterisk with no numeric values means all types from 1 to N. A -leading asterisk means all types from 1 to n (inclusive). A trailing -asterisk means all types from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). - -You also specify two functions, as "equal-style -variables"_variable.html. The first is specified as {v_name1}, where -{name1} is the name of the variable, and is f(lambda) in the notation -above. The second is specified as {v_name2}, where {name2} is the -name of the variable, and is df(lambda) / dlambda in the notation -above. I.e. it is the analytic derivative of f() with respect to -lambda. Note that the {name1} variable is also typically given as an -argument to the "fix adapt"_fix_adapt.html command. - -An alchemical simulation may use several pair potentials together, -invoked via the "pair_style hybrid or hybrid/overlay"_pair_hybrid.html -command. The total dUs/dlambda for the overall system is calculated -as the sum of each contributing term as listed by the keywords in the -compute ti command. Individual pair potentials can be listed, which -will be sub-styles in the hybrid case. You can also include a K-space -term via the {kspace} keyword. You can also include a pairwise -long-range tail correction to the energy via the {tail} keyword. - -For each term you can specify a different (or the same) scale factor -by the two variables that you list. Again, these will typically -correspond toe the scale factors applied to these various potentials -and the K-Space contribution via the "fix adapt"_fix_adapt.html -command. - -More details about the exact functional forms for the computation of -du/dl can be found in the paper by "Eike"_#Eike. - -:line - -[Output info:] - -This compute calculates a global scalar, namely dUs/dlambda. This -value can be used by any command that uses a global scalar value from -a compute as input. See the "Howto output"_Howto_output.html doc page -for an overview of LAMMPS output options. - -The scalar value calculated by this compute is "extensive". - -The scalar value will be in energy "units"_units.html. - -[Restrictions:] - -This compute is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix adapt"_fix_adapt.html - -[Default:] none - -:line - -:link(Eike) -[(Eike)] Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006). diff --git a/doc/txt/compute_torque_chunk.txt b/doc/txt/compute_torque_chunk.txt deleted file mode 100644 index 8121c42781..0000000000 --- a/doc/txt/compute_torque_chunk.txt +++ /dev/null @@ -1,86 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute torque/chunk command :h3 - -[Syntax:] - -compute ID group-ID torque/chunk chunkID :pre - -ID, group-ID are documented in "compute"_compute.html command -torque/chunk = style name of this compute command -chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul - -[Examples:] - -compute 1 fluid torque/chunk molchunk :pre - -[Description:] - -Define a computation that calculates the torque on multiple chunks of -atoms. - -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. - -This compute calculates the 3 components of the torque vector for eqch -chunk, due to the forces on the individual atoms in the chunk around -the center-of-mass of the chunk. The calculation includes all effects -due to atoms passing through periodic boundaries. - -Note that only atoms in the specified group contribute to the -calculation. The "compute chunk/atom"_compute_chunk_atom.html command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. - -NOTE: The coordinates of an atom contribute to the chunk's torque in -"unwrapped" form, by using the image flags associated with each atom. -See the "dump custom"_dump.html command for a discussion of -"unwrapped" coordinates. See the Atoms section of the -"read_data"_read_data.html command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the "set -image"_set.html command. - -The simplest way to output the results of the compute torque/chunk -calculation to a file is to use the "fix ave/time"_fix_ave_time.html -command, for example: - -compute cc1 all chunk/atom molecule -compute myChunk all torque/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre - -[Output info:] - -This compute calculates a global array where the number of rows = the -number of chunks {Nchunk} as calculated by the specified "compute -chunk/atom"_compute_chunk_atom.html command. The number of columns = -3 for the 3 xyz components of the torque for each chunk. These values -can be accessed by any command that uses global array values from a -compute as input. See the "Howto output"_Howto_output.html doc page -for an overview of LAMMPS output options. - -The array values are "intensive". The array values will be in -force-distance "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"variable torque() function"_variable.html - -[Default:] none diff --git a/doc/txt/compute_vacf.txt b/doc/txt/compute_vacf.txt deleted file mode 100644 index 70f1e99490..0000000000 --- a/doc/txt/compute_vacf.txt +++ /dev/null @@ -1,70 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute vacf command :h3 - -[Syntax:] - -compute ID group-ID vacf :pre - -ID, group-ID are documented in "compute"_compute.html command -vacf = style name of this compute command :ul - -[Examples:] - -compute 1 all vacf -compute 1 upper vacf :pre - -[Description:] - -Define a computation that calculates the velocity auto-correlation -function (VACF), averaged over a group of atoms. Each atom's -contribution to the VACF is its current velocity vector dotted into -its initial velocity vector at the time the compute was specified. - -A vector of four quantities is calculated by this compute. The first 3 -elements of the vector are vx * vx0 (and similarly for the y and z -components), summed and averaged over atoms in the group. Vx is the -current x-component of velocity for the atom, vx0 is the initial -x-component of velocity for the atom. The 4th element of the vector -is the total VACF, i.e. (vx*vx0 + vy*vy0 + vz*vz0), summed and -averaged over atoms in the group. - -The integral of the VACF versus time is proportional to the diffusion -coefficient of the diffusing atoms. This can be computed in the -following manner, using the "variable trap()"_variable.html function: - -compute 2 all vacf -fix 5 all vector 1 c_2\[4\] -variable diff equal dt*trap(f_5) -thermo_style custom step v_diff :pre - -NOTE: If you want the quantities calculated by this compute to be -continuous when running from a "restart file"_read_restart.html, then -you should use the same ID for this compute, as in the original run. -This is so that the fix this compute creates to store per-atom -quantities will also have the same ID, and thus be initialized -correctly with time=0 atom velocities from the restart file. - -[Output info:] - -This compute calculates a global vector of length 4, which can be -accessed by indices 1-4 by any command that uses global vector values -from a compute as input. See the "Howto output"_Howto_output.html doc -page for an overview of LAMMPS output options. - -The vector values are "intensive". The vector values will be in -velocity^2 "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute msd"_compute_msd.html - -[Default:] none diff --git a/doc/txt/compute_vcm_chunk.txt b/doc/txt/compute_vcm_chunk.txt deleted file mode 100644 index 7e8ad71208..0000000000 --- a/doc/txt/compute_vcm_chunk.txt +++ /dev/null @@ -1,76 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute vcm/chunk command :h3 - -[Syntax:] - -compute ID group-ID vcm/chunk chunkID :pre - -ID, group-ID are documented in "compute"_compute.html command -vcm/chunk = style name of this compute command -chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul - -[Examples:] - -compute 1 fluid vcm/chunk molchunk :pre - -[Description:] - -Define a computation that calculates the center-of-mass velocity for -multiple chunks of atoms. - -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a single chunk (or no chunk). The ID for this command is specified -as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. - -This compute calculates the x,y,z components of the center-of-mass -velocity for each chunk. This is done by summing mass*velocity for -each atom in the chunk and dividing the sum by the total mass of the -chunk. - -Note that only atoms in the specified group contribute to the -calculation. The "compute chunk/atom"_compute_chunk_atom.html command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. - -The simplest way to output the results of the compute vcm/chunk -calculation to a file is to use the "fix ave/time"_fix_ave_time.html -command, for example: - -compute cc1 all chunk/atom molecule -compute myChunk all vcm/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre - -[Output info:] - -This compute calculates a global array where the number of rows = the -number of chunks {Nchunk} as calculated by the specified "compute -chunk/atom"_compute_chunk_atom.html command. The number of columns = -3 for the x,y,z center-of-mass velocity coordinates of each chunk. -These values can be accessed by any command that uses global array -values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. - -The array values are "intensive". The array values will be in -velocity "units"_units.html. - -[Restrictions:] none - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/compute_voronoi_atom.txt b/doc/txt/compute_voronoi_atom.txt deleted file mode 100644 index 4d7bd56838..0000000000 --- a/doc/txt/compute_voronoi_atom.txt +++ /dev/null @@ -1,226 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute voronoi/atom command :h3 - -[Syntax:] - -compute ID group-ID voronoi/atom keyword arg ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -voronoi/atom = style name of this compute command :l -zero or more keyword/value pairs may be appended :l -keyword = {only_group} or {surface} or {radius} or {edge_histo} or {edge_threshold} -or {face_threshold} or {neighbors} or {peratom} :l - {only_group} = no arg - {occupation} = no arg - {surface} arg = sgroup-ID - sgroup-ID = compute the dividing surface between group-ID and sgroup-ID - this keyword adds a third column to the compute output - {radius} arg = v_r - v_r = radius atom style variable for a poly-disperse Voronoi tessellation - {edge_histo} arg = maxedge - maxedge = maximum number of Voronoi cell edges to be accounted in the histogram - {edge_threshold} arg = minlength - minlength = minimum length for an edge to be counted - {face_threshold} arg = minarea - minarea = minimum area for a face to be counted - {neighbors} value = {yes} or {no} = store list of all neighbors or no - {peratom} value = {yes} or {no} = per-atom quantities accessible or no :pre -:ule - -[Examples:] - -compute 1 all voronoi/atom -compute 2 precipitate voronoi/atom surface matrix -compute 3b precipitate voronoi/atom radius v_r -compute 4 solute voronoi/atom only_group -compute 5 defects voronoi/atom occupation -compute 6 all voronoi/atom neighbors yes :pre - -[Description:] - -Define a computation that calculates the Voronoi tessellation of the -atoms in the simulation box. The tessellation is calculated using all -atoms in the simulation, but non-zero values are only stored for atoms -in the group. - -By default two per-atom quantities are calculated by this compute. -The first is the volume of the Voronoi cell around each atom. Any -point in an atom's Voronoi cell is closer to that atom than any other. -The second is the number of faces of the Voronoi cell. This is -equal to the number of nearest neighbors of the central atom, -plus any exterior faces (see note below). If the {peratom} keyword -is set to "no", the per-atom quantities are still calculated, -but they are not accessible. - -:line - -If the {only_group} keyword is specified the tessellation is performed -only with respect to the atoms contained in the compute group. This is -equivalent to deleting all atoms not contained in the group prior to -evaluating the tessellation. - -If the {surface} keyword is specified a third quantity per atom is -computed: the Voronoi cell surface of the given atom. {surface} takes -a group ID as an argument. If a group other than {all} is specified, -only the Voronoi cell facets facing a neighbor atom from the specified -group are counted towards the surface area. - -In the example above, a precipitate embedded in a matrix, only atoms -at the surface of the precipitate will have non-zero surface area, and -only the outward facing facets of the Voronoi cells are counted (the -hull of the precipitate). The total surface area of the precipitate -can be obtained by running a "reduce sum" compute on c_2\[3\] - -If the {radius} keyword is specified with an atom style variable as -the argument, a poly-disperse Voronoi tessellation is -performed. Examples for radius variables are - -variable r1 atom (type==1)*0.1+(type==2)*0.4 -compute radius all property/atom radius -variable r2 atom c_radius :pre - -Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms -and 0.4 units for type 2 atoms, and v_r2 accesses the radius property -present in atom_style sphere for granular models. - -The {edge_histo} keyword activates the compilation of a histogram of -number of edges on the faces of the Voronoi cells in the compute -group. The argument {maxedge} of the this keyword is the largest number -of edges on a single Voronoi cell face expected to occur in the -sample. This keyword adds the generation of a global vector with -{maxedge}+1 entries. The last entry in the vector contains the number of -faces with more than {maxedge} edges. Since the polygon with the -smallest amount of edges is a triangle, entries 1 and 2 of the vector -will always be zero. - -The {edge_threshold} and {face_threshold} keywords allow the -suppression of edges below a given minimum length and faces below a -given minimum area. Ultra short edges and ultra small faces can occur -as artifacts of the Voronoi tessellation. These keywords will affect -the neighbor count and edge histogram outputs. - -If the {occupation} keyword is specified the tessellation is only -performed for the first invocation of the compute and then stored. -For all following invocations of the compute the number of atoms in -each Voronoi cell in the stored tessellation is counted. In this mode -the compute returns a per-atom array with 2 columns. The first column -is the number of atoms currently in the Voronoi volume defined by this -atom at the time of the first invocation of the compute (note that the -atom may have moved significantly). The second column contains the -total number of atoms sharing the Voronoi cell of the stored -tessellation at the location of the current atom. Numbers in column -one can be any positive integer including zero, while column two -values will always be greater than zero. Column one data can be used -to locate vacancies (the coordinates are given by the atom coordinates -at the time step when the compute was first invoked), while column two -data can be used to identify interstitial atoms. - -If the {neighbors} value is set to yes, then this compute creates a -local array with 3 columns. There is one row for each face of each -Voronoi cell. The 3 columns are the atom ID of the atom that owns the -cell, the atom ID of the atom in the neighboring cell (or zero if the -face is external), and the area of the face. The array can be -accessed by any command that uses local values from a compute as -input. See the "Howto output"_Howto_output.html doc page for an -overview of LAMMPS output options. More specifically, the array can be -accessed by a "dump local"_dump.html command to write a file -containing all the Voronoi neighbors in a system: - -compute 6 all voronoi/atom neighbors yes -dump d2 all local 1 dump.neighbors index c_6\[1\] c_6\[2\] c_6\[3\] :pre - -If the {face_threshold} keyword is used, then only faces -with areas greater than the threshold are stored. - -:line - -The Voronoi calculation is performed by the freely available "Voro++ -package"_voronoi, written by Chris Rycroft at UC Berkeley and LBL, -which must be installed on your system when building LAMMPS for use -with this compute. See instructions on obtaining and installing the -Voro++ software in the src/VORONOI/README file. - -:link(voronoi,http://math.lbl.gov/voro++/) - -NOTE: The calculation of Voronoi volumes is performed by each -processor for the atoms it owns, and includes the effect of ghost -atoms stored by the processor. This assumes that the Voronoi cells of -owned atoms are not affected by atoms beyond the ghost atom cut-off -distance. This is usually a good assumption for liquid and solid -systems, but may lead to underestimation of Voronoi volumes in low -density systems. By default, the set of ghost atoms stored by each -processor is determined by the cutoff used for -"pair_style"_pair_style.html interactions. The cutoff can be set -explicitly via the "comm_modify cutoff"_comm_modify.html command. The -Voronoi cells for atoms adjacent to empty regions will extend into -those regions up to the communication cutoff in x, y, or z. In that -situation, an exterior face is created at the cutoff distance normal -to the x, y, or z direction. For triclinic systems, the exterior face -is parallel to the corresponding reciprocal lattice vector. - -NOTE: The Voro++ package performs its calculation in 3d. This will -still work for a 2d LAMMPS simulation, provided all the atoms have the -same z coordinate. The Voronoi cell of each atom will be a columnar -polyhedron with constant cross-sectional area along the z direction -and two exterior faces at the top and bottom of the simulation box. If -the atoms do not all have the same z coordinate, then the columnar -cells will be accordingly distorted. The cross-sectional area of each -Voronoi cell can be obtained by dividing its volume by the z extent of -the simulation box. Note that you define the z extent of the -simulation box for 2d simulations when using the -"create_box"_create_box.html or "read_data"_read_data.html commands. - -[Output info:] - -By default, this compute calculates a per-atom array with 2 -columns. In regular dynamic tessellation mode the first column is the -Voronoi volume, the second is the neighbor count, as described above -(read above for the output data in case the {occupation} keyword is -specified). These values can be accessed by any command that uses -per-atom values from a compute as input. See the "Howto -output"_Howto_output.html doc page for an overview of LAMMPS output -options. If the {peratom} keyword is set to "no", the per-atom array -is still created, but it is not accessible. - -If the {edge_histo} keyword is used, then this compute generates a -global vector of length {maxedge}+1, containing a histogram of the -number of edges per face. - -If the {neighbors} value is set to yes, then this compute calculates a -local array with 3 columns. There is one row for each face of each -Voronoi cell. - -NOTE: Some LAMMPS commands such as the "compute -reduce"_compute_reduce.html command can accept either a per-atom or -local quantity. If this compute produces both quantities, the command -may access the per-atom quantity, even if you want to access the local -quantity. This effect can be eliminated by using the {peratom} -keyword to turn off the production of the per-atom quantities. For -the default value {yes} both quantities are produced. For the value -{no}, only the local array is produced. - -The Voronoi cell volume will be in distance "units"_units.html cubed. -The Voronoi face area will be in distance "units"_units.html squared. - -[Restrictions:] - -This compute is part of the VORONOI package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -It also requires you have a copy of the Voro++ library built and -installed on your system. See instructions on obtaining and -installing the Voro++ software in the src/VORONOI/README file. - -[Related commands:] - -"dump custom"_dump.html, "dump local"_dump.html - -[Default:] {neighbors} no, {peratom} yes diff --git a/doc/txt/compute_xrd.txt b/doc/txt/compute_xrd.txt deleted file mode 100644 index 41523f25af..0000000000 --- a/doc/txt/compute_xrd.txt +++ /dev/null @@ -1,200 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -compute xrd command :h3 - -[Syntax:] - -compute ID group-ID xrd lambda type1 type2 ... typeN keyword value ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -xrd = style name of this compute command :l -lambda = wavelength of incident radiation (length units) :l -type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) :l - -zero or more keyword/value pairs may be appended :l -keyword = {2Theta} or {c} or {LP} or {manual} or {echo} :l - {2Theta} values = Min2Theta Max2Theta - Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore - (radians or degrees) - {c} values = c1 c2 c3 - c1,c2,c3 = parameters to adjust the spacing of the reciprocal - lattice nodes in the h, k, and l directions respectively - {LP} value = switch to apply Lorentz-polarization factor - 0/1 = off/on - {manual} = flag to use manual spacing of reciprocal lattice points - based on the values of the {c} parameters - {echo} = flag to provide extra output for debugging purposes :pre -:ule - -[Examples:] - -compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo -compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual :pre - -fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1\[1\] c_1\[2\] mode vector file Rad2Theta.xrd -fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2\[1\] c_2\[2\] mode vector file Deg2Theta.xrd :pre - -[Description:] - -Define a computation that calculates x-ray diffraction intensity as described -in "(Coleman)"_#xrd-Coleman on a mesh of reciprocal lattice nodes defined -by the entire simulation domain (or manually) using a simulated radiation -of wavelength lambda. - -The x-ray diffraction intensity, I, at each reciprocal lattice point, k, -is computed from the structure factor, F, using the equations: - -:c,image(Eqs/compute_xrd1.jpg) -:c,image(Eqs/compute_xrd2.jpg) -:c,image(Eqs/compute_xrd3.jpg) -:c,image(Eqs/compute_xrd4.jpg) - -Here, K is the location of the reciprocal lattice node, rj is the -position of each atom, fj are atomic scattering factors, LP is the -Lorentz-polarization factor, and theta is the scattering angle of -diffraction. The Lorentz-polarization factor can be turned off using -the optional {LP} keyword. - -Diffraction intensities are calculated on a three-dimensional mesh of -reciprocal lattice nodes. The mesh spacing is defined either (a) -by the entire simulation domain or (b) manually using selected values as -shown in the 2D diagram below. - -:c,image(JPG/xrd_mesh_small.jpg,JPG/xrd_mesh.jpg) - - -For a mesh defined by the simulation domain, a rectilinear grid is -constructed with spacing {c}*inv(A) along each reciprocal lattice -axis. Where A are the vectors corresponding to the edges of the -simulation cell. If one or two directions has non-periodic boundary -conditions, then the spacing in these directions is defined from the -average of the (inversed) box lengths with periodic boundary conditions. -Meshes defined by the simulation domain must contain at least one periodic -boundary. - -If the {manual} flag is included, the mesh of reciprocal lattice nodes -will defined using the {c} values for the spacing along each -reciprocal lattice axis. Note that manual mapping of the reciprocal -space mesh is good for comparing diffraction results from multiple -simulations; however it can reduce the likelihood that Bragg -reflections will be satisfied unless small spacing parameters (< 0.05 -Angstrom^(-1)) are implemented. Meshes with manual spacing do not -require a periodic boundary. - -The limits of the reciprocal lattice mesh are determined by range of -scattering angles explored. The {2Theta} parameters allows the user -to reduce the scattering angle range to only the region of interest -which reduces the cost of the computation. - -The atomic scattering factors, fj, accounts for the reduction in -diffraction intensity due to Compton scattering. Compute xrd uses -analytical approximations of the atomic scattering factors that vary -for each atom type (type1 type2 ... typeN) and angle of diffraction. -The analytic approximation is computed using the formula -"(Colliex)"_#Colliex: - -:c,image(Eqs/compute_xrd5.jpg) - -Coefficients parameterized by "(Peng)"_#Peng are assigned for each -atom type designating the chemical symbol and charge of each atom -type. Valid chemical symbols for compute xrd are: - - H| He1-| He| Li| Li1+| - Be| Be2+| B| C| Cval| - N| O| O1-| F| F1-| - Ne| Na| Na1+| Mg| Mg2+| - Al| Al3+| Si| Sival| Si4+| - P| S| Cl| Cl1-| Ar| - K| Ca| Ca2+| Sc| Sc3+| - Ti| Ti2+| Ti3+| Ti4+| V| - V2+| V3+| V5+| Cr| Cr2+| - Cr3+| Mn| Mn2+| Mn3+| Mn4+| - Fe| Fe2+| Fe3+| Co| Co2+| - Co| Ni| Ni2+| Ni3+| Cu| - Cu1+| Cu2+| Zn| Zn2+| Ga| - Ga3+| Ge| Ge4+| As| Se| - Br| Br1-| Kr| Rb| Rb1+| - Sr| Sr2+| Y| Y3+| Zr| - Zr4+| Nb| Nb3+| Nb5+| Mo| - Mo3+| Mo5+| Mo6+| Tc| Ru| - Ru3+| Ru4+| Rh| Rh3+| Rh4+| - Pd| Pd2+| Pd4+| Ag| Ag1+| - Ag2+| Cd| Cd2+| In| In3+| - Sn| Sn2+| Sn4+| Sb| Sb3+| - Sb5+| Te| I| I1-| Xe| - Cs| Cs1+| Ba| Ba2+| La| - La3+| Ce| Ce3+| Ce4+| Pr| - Pr3+| Pr4+| Nd| Nd3+| Pm| - Pm3+| Sm| Sm3+| Eu| Eu2+| - Eu3+| Gd| Gd3+| Tb| Tb3+| - Dy| Dy3+| Ho| Ho3+| Er| - Er3+| Tm| Tm3+| Yb| Yb2+| - Yb3+| Lu| Lu3+| Hf| Hf4+| - Ta| Ta5+| W| W6+| Re| - Os| Os4+| Ir| Ir3+| Ir4+| - Pt| Pt2+| Pt4+| Au| Au1+| - Au3+| Hg| Hg1+| Hg2+| Tl| - Tl1+| Tl3+| Pb| Pb2+| Pb4+| - Bi| Bi3+| Bi5+| Po| At| - Rn| Fr| Ra| Ra2+| Ac| - Ac3+| Th| Th4+| Pa| U| - U3+| U4+| U6+| Np| Np3+| - Np4+| Np6+| Pu| Pu3+| Pu4+| - Pu6+| Am| Cm| Bk| Cf :tb(c=5,s=|) - -If the {echo} keyword is specified, compute xrd will provide extra -reporting information to the screen. - -[Output info:] - -This compute calculates a global array. The number of rows in the -array is the number of reciprocal lattice nodes that are explored -which by the mesh. The global array has 2 columns. - -The first column contains the diffraction angle in the units (radians -or degrees) provided with the {2Theta} values. The second column contains -the computed diffraction intensities as described above. - -The array can be accessed by any command that uses global values from -a compute as input. See the "Howto output"_Howto_output.html doc page -for an overview of LAMMPS output options. - -All array values calculated by this compute are "intensive". - -[Restrictions:] - -This compute is part of the USER-DIFFRACTION package. It is only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -The compute_xrd command does not work for triclinic cells. - -[Related commands:] - -"fix ave/histo"_fix_ave_histo.html, -"compute saed"_compute_saed.html - -[Default:] - -The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1, -no manual flag, no echo flag. - -:line - -:link(xrd-Coleman) -[(Coleman)] Coleman, Spearot, Capolungo, MSMSE, 21, 055020 -(2013). - -:link(Colliex) -[(Colliex)] Colliex et al. International Tables for Crystallography -Volume C: Mathematical and Chemical Tables, 249-429 (2004). - -:link(Peng) -[(Peng)] Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76 -(1996). diff --git a/doc/txt/create_bonds.txt b/doc/txt/create_bonds.txt deleted file mode 100644 index 9c073b6c55..0000000000 --- a/doc/txt/create_bonds.txt +++ /dev/null @@ -1,204 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -create_bonds command :h3 - -[Syntax:] - -create_bonds style args ... keyword value ... :pre - -style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l - {many} args = group-ID group2-ID btype rmin rmax - group-ID = ID of first group - group2-ID = ID of second group, bonds will be between atoms in the 2 groups - btype = bond type of created bonds - rmin = minimum distance between pair of atoms to bond together - rmax = maximum distance between pair of atoms to bond together - {single/bond} args = btype batom1 batom2 - btype = bond type of new bond - batom1,batom2 = atom IDs for two atoms in bond - {single/angle} args = atype aatom1 aatom2 aatom3 - atype = angle type of new angle - aatom1,aatom2,aatom3 = atom IDs for three atoms in angle - {single/dihedral} args = dtype datom1 datom2 datom3 datom4 - dtype = dihedral type of new dihedral - datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral - {single/improper} args = itype iatom1 iatom2 iatom3 iatom4 - itype = improper type of new improper - iatom1,iatom2,iatom3,iatom4 = atom IDs for four atoms in improper :pre -zero or more keyword/value pairs may be appended :l -keyword = {special} :l - {special} value = {yes} or {no} :pre -:ule - -[Examples:] - -create_bonds many all all 1 1.0 1.2 -create_bonds many surf solvent 3 2.0 2.4 -create_bonds single/bond 1 1 2 -create_bonds single/angle 5 52 98 107 special no -create_bonds single/dihedral 2 4 19 27 101 -create_bonds single/improper 3 23 26 31 57 :pre - -[Description:] - -Create bonds between pairs of atoms that meet a specified distance -criteria. Or create a single bond, angle, dihedral or improper between 2, 3, -or 4 specified atoms. - -The new bond (angle, dihedral, improper) interactions will then be computed -during a simulation by the bond (angle, dihedral, improper) potential defined by -the "bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html, -"angle_style"_angle_style.html, "angle_coeff"_angle_coeff.html, -"dihedral_style"_dihedral_style.html, -"dihedral_coeff"_dihedral_coeff.html, "improper_style"_improper_style.html, -"improper_coeff"_improper_coeff.html commands. - -The {many} style is useful for adding bonds to a system, e.g. between -nearest neighbors in a lattice of atoms, without having to enumerate -all the bonds in the data file read by the "read_data"_read_data.html -command. - -The {single} styles are useful for adding bonds, angles, dihedrals, impropers -to a system incrementally, then continuing a simulation. - -Note that this command does not auto-create any angle, dihedral or improper -interactions when a bond is added. Nor does it auto-create any bonds -when an angle, dihedral or improper is added. Or auto-create any angles when a -dihedral or improper is added. Thus the flexibility of this command is limited. -It can be used several times to create different types of bond at -different distances. But it cannot typically auto-create all the -bonds or angles or dihedrals or impropers that would normally be defined in a -data file for a complex system of molecules. - -NOTE: If the system has no bonds (angles, dihedrals, impropers) to begin with, -or if more bonds per atom are being added than currently exist, then you -must insure that the number of bond types and the maximum number of -bonds per atom are set to large enough values. And similarly for -angles, dihedrals and impropers. Otherwise an error may occur when too many -bonds (angles, dihedrals, impropers) are added to an atom. If the -"read_data"_read_data.html command is used to define the system, these -parameters can be set via the "bond types" and "extra bond per atom" -fields in the header section of the data file. If the -"create_box"_create_box.html command is used to define the system, -these 2 parameters can be set via its optional "bond/types" and -"extra/bond/per/atom" arguments. And similarly for angles, dihedrals and -impropers. See the doc pages for these 2 commands for details. - -:line - -The {many} style will create bonds between pairs of atoms I,J where I -is in one of the two specified groups, and J is in the other. The two -groups can be the same, e.g. group "all". The created bonds will be -of bond type {btype}, where {btype} must be a value between 1 and the -number of bond types defined. - -For a bond to be created, an I,J pair of atoms must be a distance D -apart such that {rmin} <= D <= {rmax}. - -The following settings must have been made in an input script before -this style is used: - -special_bonds weight for 1-2 interactions must be 0.0 -a "pair_style"_pair_style.html must be defined -no "kspace_style"_kspace_style.html defined -minimum "pair_style"_pair_style.html cutoff + "neighbor"_neighbor.html skin >= {rmax} :ul - -These settings are required so that a neighbor list can be created to -search for nearby atoms. Pairs of atoms that are already bonded -cannot appear in the neighbor list, to avoid creation of duplicate -bonds. The neighbor list for all atom type pairs must also extend to -a distance that encompasses the {rmax} for new bonds to create. - -An additional requirement for this style is that your system must be -ready to perform a simulation. This means, for example, that all -"pair_style"_pair_style.html coefficients be set via the -"pair_coeff"_pair_coeff.html command. A "bond_style"_bond_style.html -command and all bond coefficients must also be set, even if no bonds -exist before this command is invoked. This is because the building of -neighbor list requires initialization and setup of a simulation, -similar to what a "run"_run.html command would require. - -Note that you can change any of these settings after this command -executes, e.g. if you wish to use long-range Coulombic interactions -via the "kspace_style"_kspace_style.html command for your subsequent -simulation. - -:line - -The {single/bond} style creates a single bond of type {btype} between -two atoms with IDs {batom1} and {batom2}. {Btype} must be a value -between 1 and the number of bond types defined. - -The {single/angle} style creates a single angle of type {atype} -between three atoms with IDs {aatom1}, {aatom2}, and {aatom3}. The -ordering of the atoms is the same as in the {Angles} section of a data -file read by the "read_data"_read_data.html command. I.e. the 3 atoms are -ordered linearly within the angle; the central atom is {aatom2}. -{Atype} must be a value between 1 and the number of angle types -defined. - -The {single/dihedral} style creates a single dihedral of type {dtype} -between four atoms with IDs {datom1}, {datom2}, {datom3}, and {datom4}. The -ordering of the atoms is the same as in the {Dihedrals} section of a data file -read by the "read_data"_read_data.html command. I.e. the 4 atoms are ordered -linearly within the dihedral. {dtype} must be a value between 1 and -the number of dihedral types defined. - -The {single/improper} style creates a single improper of type {itype} -between four atoms with IDs {iatom1}, {iatom2}, {iatom3}, and {iatom4}. The -ordering of the atoms is the same as in the {Impropers} section of a data file -read by the "read_data"_read_data.html command. I.e. the 4 atoms are ordered -linearly within the improper. {itype} must be a value between 1 and -the number of improper types defined. - -:line - -The keyword {special} controls whether an internal list of special -bonds is created after one or more bonds, or a single angle, dihedral or -improper is added to the system. - -The default value is {yes}. A value of {no} cannot be used -with the {many} style. - -This is an expensive operation since the bond topology for the system -must be walked to find all 1-2, 1-3, 1-4 interactions to store in an -internal list, which is used when pairwise interactions are weighted; -see the "special_bonds"_special_bonds.html command for details. - -Thus if you are adding a few bonds or a large list of angles all at -the same time, by using this command repeatedly, it is more efficient -to only trigger the internal list to be created once, after the last -bond (or angle, or dihedral, or improper) is added: - -create_bonds single/bond 5 52 98 special no -create_bonds single/bond 5 73 74 special no -... -create_bonds single/bond 5 17 386 special no -create_bonds single/bond 4 112 183 special yes :pre - -Note that you MUST insure the internal list is re-built after the last -bond (angle, dihedral, improper) is added, before performing a simulation. -Otherwise pairwise interactions will not be properly excluded or -weighted. LAMMPS does NOT check that you have done this correctly. - -:line - -[Restrictions:] - -This command cannot be used with molecular systems defined using -molecule template files via the "molecule"_molecule.html and -"atom_style template"_atom_style.html commands. - -[Related commands:] - -"create_atoms"_create_atoms.html, "delete_bonds"_delete_bonds.html - -[Default:] - -The keyword default is special = yes. diff --git a/doc/txt/create_box.txt b/doc/txt/create_box.txt deleted file mode 100644 index cc57c96f93..0000000000 --- a/doc/txt/create_box.txt +++ /dev/null @@ -1,152 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -create_box command :h3 - -[Syntax:] - -create_box N region-ID keyword value ... :pre - -N = # of atom types to use in this simulation :ulb,l -region-ID = ID of region to use as simulation domain :l -zero or more keyword/value pairs may be appended :l -keyword = {bond/types} or {angle/types} or {dihedral/types} or {improper/types} or {extra/bond/per/atom} or {extra/angle/per/atom} or {extra/dihedral/per/atom} or {extra/improper/per/atom} :l - {bond/types} value = # of bond types - {angle/types} value = # of angle types - {dihedral/types} value = # of dihedral types - {improper/types} value = # of improper types - {extra/bond/per/atom} value = # of bonds per atom - {extra/angle/per/atom} value = # of angles per atom - {extra/dihedral/per/atom} value = # of dihedrals per atom - {extra/improper/per/atom} value = # of impropers per atom - {extra/special/per/atom} value = # of special neighbors per atom :pre -:ule - -[Examples:] - -create_box 2 mybox -create_box 2 mybox bond/types 2 extra/bond/per/atom 1 :pre - -[Description:] - -This command creates a simulation box based on the specified region. -Thus a "region"_region.html command must first be used to define a -geometric domain. It also partitions the simulation box into a -regular 3d grid of rectangular bricks, one per processor, based on the -number of processors being used and the settings of the -"processors"_processors.html command. The partitioning can later be -changed by the "balance"_balance.html or "fix -balance"_fix_balance.html commands. - -The argument N is the number of atom types that will be used in the -simulation. - -If the region is not of style {prism}, then LAMMPS encloses the region -(block, sphere, etc) with an axis-aligned orthogonal bounding box -which becomes the simulation domain. - -If the region is of style {prism}, LAMMPS creates a non-orthogonal -simulation domain shaped as a parallelepiped with triclinic symmetry. -As defined by the "region prism"_region.html command, the -parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by 3 -edge vectors starting from the origin given by A = (xhi-xlo,0,0); B = -(xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or -positive or negative values and are called "tilt factors" because they -are the amount of displacement applied to faces of an originally -orthogonal box to transform it into the parallelepiped. - -By default, a {prism} region used with the create_box command must -have tilt factors (xy,xz,yz) that do not skew the box more than half -the distance of the parallel box length. For example, if xlo = 2 and -xhi = 12, then the x box length is 10 and the xy tilt factor must be -between -5 and 5. Similarly, both xz and yz must be between --(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation, -since if the maximum tilt factor is 5 (as in this example), then -configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all -geometrically equivalent. If you wish to define a box with tilt -factors that exceed these limits, you can use the "box tilt"_box.html -command, with a setting of {large}; a setting of {small} is the -default. - -See the "Howto triclinic"_Howto_triclinic.html doc page for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used -triclinic representations. - -When a prism region is used, the simulation domain should normally be -periodic in the dimension that the tilt is applied to, which is given -by the second dimension of the tilt factor (e.g. y for xy tilt). This -is so that pairs of atoms interacting across that boundary will have -one of them shifted by the tilt factor. Periodicity is set by the -"boundary"_boundary.html command. For example, if the xy tilt factor -is non-zero, then the y dimension should be periodic. Similarly, the -z dimension should be periodic if xz or yz is non-zero. LAMMPS does -not require this periodicity, but you may lose atoms if this is not -the case. - -Also note that if your simulation will tilt the box, e.g. via the "fix -deform"_fix_deform.html command, the simulation box must be setup to -be triclinic, even if the tilt factors are initially 0.0. You can -also change an orthogonal box to a triclinic box or vice versa by -using the "change box"_change_box.html command with its {ortho} and -{triclinic} options. - -NOTE: If the system is non-periodic (in a dimension), then you should -not make the lo/hi box dimensions (as defined in your -"region"_region.html command) radically smaller/larger than the extent -of the atoms you eventually plan to create, e.g. via the -"create_atoms"_create_atoms.html command. For example, if your atoms -extend from 0 to 50, you should not specify the box bounds as -10000 -and 10000. This is because as described above, LAMMPS uses the -specified box size to layout the 3d grid of processors. A huge -(mostly empty) box will be sub-optimal for performance when using -"fixed" boundary conditions (see the "boundary"_boundary.html -command). When using "shrink-wrap" boundary conditions (see the -"boundary"_boundary.html command), a huge (mostly empty) box may cause -a parallel simulation to lose atoms the first time that LAMMPS -shrink-wraps the box around the atoms. - -:line - -The optional keywords can be used to create a system that allows for -bond (angle, dihedral, improper) interactions, or for molecules with -special 1-2,1-3,1-4 neighbors to be added later. These optional -keywords serve the same purpose as the analogous keywords that can be -used in a data file which are recognized by the -"read_data"_read_data.html command when it sets up a system. - -Note that if these keywords are not used, then the create_box command -creates an atomic (non-molecular) simulation that does not allow bonds -between pairs of atoms to be defined, or a "bond -potential"_bond_style.html to be specified, or for molecules with -special neighbors to be added to the system by commands such as -"create_atoms mol"_create_atoms.html, "fix deposit"_fix_deposit.html -or "fix pour"_fix_pour.html. - -As an example, see the examples/deposit/in.deposit.molecule script, -which deposits molecules onto a substrate. Initially there are no -molecules in the system, but they are added later by the "fix -deposit"_fix_deposit.html command. The create_box command in the -script uses the bond/types and extra/bond/per/atom keywords to allow -this. If the added molecule contained more than 1 special bond -(allowed by default), an extra/special/per/atom keyword would also -need to be specified. - -:line - -[Restrictions:] - -An "atom_style"_atom_style.html and "region"_region.html must have -been previously defined to use this command. - -[Related commands:] - -"read_data"_read_data.html, "create_atoms"_create_atoms.html, -"region"_region.html - -[Default:] none diff --git a/doc/txt/delete_atoms.txt b/doc/txt/delete_atoms.txt deleted file mode 100644 index a55288e1db..0000000000 --- a/doc/txt/delete_atoms.txt +++ /dev/null @@ -1,152 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -delete_atoms command :h3 - -[Syntax:] - -delete_atoms style args keyword value ... :pre - -style = {group} or {region} or {overlap} or {porosity} :ulb,l - {group} args = group-ID - {region} args = region-ID - {overlap} args = cutoff group1-ID group2-ID - cutoff = delete one atom from pairs of atoms within the cutoff (distance units) - group1-ID = one atom in pair must be in this group - group2-ID = other atom in pair must be in this group - {porosity} args = region-ID fraction seed - region-ID = region within which to perform deletions - fraction = delete this fraction of atoms - seed = random number seed (positive integer) :pre -zero or more keyword/value pairs may be appended :l -keyword = {compress} or {bond} or {mol} :l - {compress} value = {no} or {yes} - {bond} value = {no} or {yes} - {mol} value = {no} or {yes} :pre -:ule - -[Examples:] - -delete_atoms group edge -delete_atoms region sphere compress no -delete_atoms overlap 0.3 all all -delete_atoms overlap 0.5 solvent colloid -delete_atoms porosity cube 0.1 482793 bond yes :pre - -[Description:] - -Delete the specified atoms. This command can be used to carve out -voids from a block of material or to delete created atoms that are too -close to each other (e.g. at a grain boundary). - -For style {group}, all atoms belonging to the group are deleted. - -For style {region}, all atoms in the region volume are deleted. -Additional atoms can be deleted if they are in a molecule for which -one or more atoms were deleted within the region; see the {mol} -keyword discussion below. - -For style {overlap} pairs of atoms whose distance of separation is -within the specified cutoff distance are searched for, and one of the -2 atoms is deleted. Only pairs where one of the two atoms is in the -first group specified and the other atom is in the second group are -considered. The atom that is in the first group is the one that is -deleted. - -Note that it is OK for the two group IDs to be the same (e.g. group -{all}), or for some atoms to be members of both groups. In these -cases, either atom in the pair may be deleted. Also note that if -there are atoms which are members of both groups, the only guarantee -is that at the end of the deletion operation, enough deletions will -have occurred that no atom pairs within the cutoff will remain -(subject to the group restriction). There is no guarantee that the -minimum number of atoms will be deleted, or that the same atoms will -be deleted when running on different numbers of processors. - -For style {porosity} a specified {fraction} of atoms are deleted -within the specified region. For example, if fraction is 0.1, then -10% of the atoms will be deleted. The atoms to delete are chosen -randomly. There is no guarantee that the exact fraction of atoms will -be deleted, or that the same atoms will be deleted when running on -different numbers of processors. - -If the {compress} keyword is set to {yes}, then after atoms are -deleted, then atom IDs are re-assigned so that they run from 1 to the -number of atoms in the system. Note that this is not done for -molecular systems (see the "atom_style"_atom_style.html command), -regardless of the {compress} setting, since it would foul up the bond -connectivity that has already been assigned. However, the -"reset_ids"_reset_ids.html command can be used after this command to -accomplish the same thing. - -Note that the re-assignment of IDs is not really a compression, where -gaps in atom IDs are removed by decrementing atom IDs that are larger. -Instead the IDs for all atoms are erased, and new IDs are assigned so -that the atoms owned by individual processors have consecutive IDs, as -the "create_atoms"_create_atoms.html command explains. - -A molecular system with fixed bonds, angles, dihedrals, or improper -interactions, is one where the topology of the interactions is -typically defined in the data file read by the -"read_data"_read_data.html command, and where the interactions -themselves are defined with the "bond_style"_bond_style.html, -"angle_style"_angle_style.html, etc commands. If you delete atoms -from such a system, you must be careful not to end up with bonded -interactions that are stored by remaining atoms but which include -deleted atoms. This will cause LAMMPS to generate a "missing atoms" -error when the bonded interaction is computed. The {bond} and {mol} -keywords offer two ways to do that. - -It the {bond} keyword is set to {yes} then any bond or angle or -dihedral or improper interaction that includes a deleted atom is also -removed from the lists of such interactions stored by non-deleted -atoms. Note that simply deleting interactions due to dangling bonds -(e.g. at a surface) may result in a inaccurate or invalid model for -the remaining atoms. - -It the {mol} keyword is set to {yes}, then for every atom that is -deleted, all other atoms in the same molecule (with the same molecule -ID) will also be deleted. This is not done for atoms with molecule ID -= 0, since such an ID is assumed to flag isolated atoms that are not -part of molecules. - -NOTE: The molecule deletion operation in invoked after all individual -atoms have been deleted using the rules described above for each -style. This means additional atoms may be deleted that are not in the -group or region, that are not required by the overlap cutoff -criterion, or that will create a higher fraction of porosity than was -requested. - -[Restrictions:] - -The {overlap} styles requires inter-processor communication to acquire -ghost atoms and build a neighbor list. This means that your system -must be ready to perform a simulation before using this command (force -fields setup, atom masses set, etc). Since a neighbor list is used to -find overlapping atom pairs, it also means that you must define a -"pair style"_pair_style.html with the minimum force cutoff distance -between any pair of atoms types (plus the "neighbor"_neighbor.html -skin) >= the specified overlap cutoff. - -If the "special_bonds"_special_bonds.html command is used with a -setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not -appear in the neighbor list, and thus will not be considered for -deletion by the {overlap} styles. You probably don't want to be -deleting one atom in a bonded pair anyway. - -The {bond yes} option cannot be used with molecular systems defined -using molecule template files via the "molecule"_molecule.html and -"atom_style template"_atom_style.html commands. - -[Related commands:] - -"create_atoms"_create_atoms.html, "reset_ids"_reset_ids.html - -[Default:] - -The option defaults are compress = yes, bond = no, mol = no. diff --git a/doc/txt/delete_bonds.txt b/doc/txt/delete_bonds.txt deleted file mode 100644 index 4e33604696..0000000000 --- a/doc/txt/delete_bonds.txt +++ /dev/null @@ -1,154 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -delete_bonds command :h3 - -[Syntax:] - -delete_bonds group-ID style arg keyword ... :pre - -group-ID = group ID :ulb,l -style = {multi} or {atom} or {bond} or {angle} or {dihedral} or - {improper} or {stats} :l - {multi} arg = none - {atom} arg = an atom type or range of types (see below) - {bond} arg = a bond type or range of types (see below) - {angle} arg = an angle type or range of types (see below) - {dihedral} arg = a dihedral type or range of types (see below) - {improper} arg = an improper type or range of types (see below) - {stats} arg = none :pre -zero or more keywords may be appended :l -keyword = {any} or {undo} or {remove} or {special} :l -:ule - -[Examples:] - -delete_bonds frozen multi remove -delete_bonds all atom 4 special -delete_bonds all bond 0*3 special -delete_bonds all stats :pre - -[Description:] - -Turn off (or on) molecular topology interactions, i.e. bonds, angles, -dihedrals, impropers. This command is useful for deleting -interactions that have been previously turned off by bond-breaking -potentials. It is also useful for turning off topology interactions -between frozen or rigid atoms. Pairwise interactions can be turned -off via the "neigh_modify exclude"_neigh_modify.html command. The -"fix shake"_fix_shake.html command also effectively turns off certain -bond and angle interactions. - -For all styles, by default, an interaction is only turned off (or on) -if all the atoms involved are in the specified group. See the {any} -keyword to change the behavior. - -Several of the styles ({atom}, {bond}, {angle}, {dihedral}, -{improper}) take a {type} as an argument. The specified {type} should -be an integer from 0 to N, where N is the number of relevant types -(atom types, bond types, etc). A value of 0 is only relevant for -style {bond}; see details below. In all cases, a wildcard asterisk -can be used in place of or in conjunction with the {type} argument to -specify a range of types. This takes the form "*" or "*n" or "n*" or -"m*n". If N = the number of types, then an asterisk with no numeric -values means all types from 0 to N. A leading asterisk means all -types from 0 to n (inclusive). A trailing asterisk means all types -from n to N (inclusive). A middle asterisk means all types from m to -n (inclusive). Note that it is fine to include a type of 0 for -non-bond styles; it will simply be ignored. - -For style {multi} all bond, angle, dihedral, and improper interactions -of any type, involving atoms in the group, are turned off. - -Style {atom} is the same as style {multi} except that in addition, one -or more of the atoms involved in the bond, angle, dihedral, or -improper interaction must also be of the specified atom type. - -For style {bond}, only bonds are candidates for turn-off, and the bond -must also be of the specified type. Styles {angle}, {dihedral}, and -{improper} are treated similarly. - -For style {bond}, you can set the type to 0 to delete bonds that have -been previously broken by a bond-breaking potential (which sets the -bond type to 0 when a bond is broken); e.g. see the "bond_style -quartic"_bond_style.html command. - -For style {stats} no interactions are turned off (or on); the status -of all interactions in the specified group is simply reported. This -is useful for diagnostic purposes if bonds have been turned off by a -bond-breaking potential during a previous run. - -The default behavior of the delete_bonds command is to turn off -interactions by toggling their type to a negative value, but not to -permanently remove the interaction. E.g. a bond_type of 2 is set to --2. The neighbor list creation routines will not include such an -interaction in their interaction lists. The default is also to not -alter the list of 1-2, 1-3, 1-4 neighbors computed by the -"special_bonds"_special_bonds.html command and used to weight pairwise -force and energy calculations. This means that pairwise computations -will proceed as if the bond (or angle, etc) were still turned on. - -Several keywords can be appended to the argument list to alter the -default behaviors. - -The {any} keyword changes the requirement that all atoms in the bond -(angle, etc) must be in the specified group in order to turn-off the -interaction. Instead, if any of the atoms in the interaction are in -the specified group, it will be turned off (or on if the {undo} -keyword is used). - -The {undo} keyword inverts the delete_bonds command so that the -specified bonds, angles, etc are turned on if they are currently -turned off. This means a negative value is toggled to positive. For -example, for style {angle}, if {type} is specified as 2, then all -angles with current type = -2, are reset to type = 2. Note that the -"fix shake"_fix_shake.html command also sets bond and angle types -negative, so this option should not be used on those interactions. - -The {remove} keyword is invoked at the end of the delete_bonds -operation. It causes turned-off bonds (angles, etc) to be removed -from each atom's data structure and then adjusts the global bond -(angle, etc) counts accordingly. Removal is a permanent change; -removed bonds cannot be turned back on via the {undo} keyword. -Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list. - -The {special} keyword is invoked at the end of the delete_bonds -operation, after (optional) removal. It re-computes the pairwise 1-2, -1-3, 1-4 weighting list. The weighting list computation treats -turned-off bonds the same as turned-on. Thus, turned-off bonds must -be removed if you wish to change the weighting list. - -Note that the choice of {remove} and {special} options affects how -1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that -have been modified by the delete_bonds command. - -[Restrictions:] - -This command requires inter-processor communication to acquire ghost -atoms, to coordinate the deleting of bonds, angles, etc between atoms -shared by multiple processors. This means that your system must be -ready to perform a simulation before using this command (force fields -setup, atom masses set, etc). Just as would be needed to run -dynamics, the force field you define should define a cutoff -(e.g. through a "pair_style"_pair_style.html command) which is long -enough for a processor to acquire the ghost atoms its needs to compute -bond, angle, etc interactions. - -If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4 -weighting list is not re-computed, this can cause a later "fix -shake"_fix_shake.html command to fail due to an atom's bonds being -inconsistent with the weighting list. This should only happen if the -group used in the fix command includes both atoms in the bond, in -which case you probably should be recomputing the weighting list. - -[Related commands:] - -"neigh_modify"_neigh_modify.html exclude, -"special_bonds"_special_bonds.html, "fix shake"_fix_shake.html - -[Default:] none diff --git a/doc/txt/dielectric.txt b/doc/txt/dielectric.txt deleted file mode 100644 index f93be8cc25..0000000000 --- a/doc/txt/dielectric.txt +++ /dev/null @@ -1,39 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dielectric command :h3 - -[Syntax:] - -dielectric value :pre - -value = dielectric constant :ul - -[Examples:] - -dielectric 2.0 :pre - -[Description:] - -Set the dielectric constant for Coulombic interactions (pairwise and -long-range) to this value. The constant is unitless, since it is used -to reduce the strength of the interactions. The value is used in the -denominator of the formulas for Coulombic interactions - e.g. a value -of 4.0 reduces the Coulombic interactions to 25% of their default -strength. See the "pair_style"_pair_style.html command for more -details. - -[Restrictions:] none - -[Related commands:] - -"pair_style"_pair_style.html - -[Default:] - -dielectric 1.0 :pre diff --git a/doc/txt/dihedral_charmm.txt b/doc/txt/dihedral_charmm.txt deleted file mode 100644 index 043188466a..0000000000 --- a/doc/txt/dihedral_charmm.txt +++ /dev/null @@ -1,166 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style charmm command :h3 -dihedral_style charmm/intel command :h3 -dihedral_style charmm/kk command :h3 -dihedral_style charmm/omp command :h3 -dihedral_style charmmfsw command :h3 - -[Syntax:] - -dihedral_style style :pre - -style = {charmm} or {charmmfsw} :ul - -[Examples:] - -dihedral_style charmm -dihedral_style charmmfsw -dihedral_coeff 1 0.2 1 180 1.0 -dihedral_coeff 2 1.8 1 0 1.0 -dihedral_coeff 1 3.1 2 180 0.5 :pre - -[Description:] - -The {charmm} and {charmmfsw} dihedral styles use the potential - -:c,image(Eqs/dihedral_charmm.jpg) - -See "(MacKerell)"_#dihedral-MacKerell for a description of the CHARMM -force field. This dihedral style can also be used for the AMBER force -field (see comment on weighting factors below). See -"(Cornell)"_#dihedral-Cornell for a description of the AMBER force -field. - -NOTE: The newer {charmmfsw} style was released in March 2017. We -recommend it be used instead of the older {charmm} style when running -a simulation with the CHARMM force field, either with long-range -Coulombics or a Coulombic cutoff, via the "pair_style -lj/charmmfsw/coul/long"_pair_charmm.html and "pair_style -lj/charmmfsw/coul/charmmfsh"_pair_charmm.html commands respectively. -Otherwise the older {charmm} style is fine to use. See the discussion -below and more details on the "pair_style charmm"_pair_charmm.html doc -page. - -The following coefficients must be defined for each dihedral type via the -"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) -n (integer >= 0) -d (integer value of degrees) -weighting factor (1.0, 0.5, or 0.0) :ul - -The weighting factor is required to correct for double counting -pairwise non-bonded Lennard-Jones interactions in cyclic systems or -when using the CHARMM dihedral style with non-CHARMM force fields. -With the CHARMM dihedral style, interactions between the 1st and 4th -atoms in a dihedral are skipped during the normal non-bonded force -computation and instead evaluated as part of the dihedral using -special epsilon and sigma values specified with the -"pair_coeff"_pair_charmm.html command of pair styles that contain -"lj/charmm" (e.g. "pair_style lj/charmm/coul/long"_pair_charmm.html) -In 6-membered rings, the same 1-4 interaction would be computed twice -(once for the clockwise 1-4 pair in dihedral 1-2-3-4 and once in the -counterclockwise dihedral 1-6-5-4) and thus the weighting factor has -to be 0.5 in this case. In 4-membered or 5-membered rings, the 1-4 -dihedral also is counted as a 1-2 or 1-3 interaction when going around -the ring in the opposite direction and thus the weighting factor is -0.0, as the 1-2 and 1-3 exclusions take precedence. - -Note that this dihedral weighting factor is unrelated to the scaling -factor specified by the "special bonds"_special_bonds.html command -which applies to all 1-4 interactions in the system. For CHARMM force -fields, the special_bonds 1-4 interaction scaling factor should be set -to 0.0. Since the corresponding 1-4 non-bonded interactions are -computed with the dihedral. This means that if any of the weighting -factors defined as dihedral coefficients (4th coeff above) are -non-zero, then you must use a pair style with "lj/charmm" and set the -special_bonds 1-4 scaling factor to 0.0 (which is the -default). Otherwise 1-4 non-bonded interactions in dihedrals will be -computed twice. - -For simulations using the CHARMM force field with a Coulombic cutoff, -the difference between the {charmm} and {charmmfsw} styles is in the -computation of the 1-4 non-bond interactions, though only if the -distance between the two atoms is within the switching region of the -pairwise potential defined by the corresponding CHARMM pair style, -i.e. within the outer cutoff specified for the pair style. The -{charmmfsw} style should only be used when using the corresponding -"pair_style lj/charmmfsw/coul/charmmfsw"_pair_charmm.html or -"pair_style lj/charmmfsw/coul/long"_pair_charmm.html commands. Use -the {charmm} style with the older "pair_style"_pair_charmm.html -commands that have just "charmm" in their style name. See the -discussion on the "CHARMM pair_style"_pair_charmm.html doc page for -details. - -Note that for AMBER force fields, which use pair styles with "lj/cut", -the special_bonds 1-4 scaling factor should be set to the AMBER -defaults (1/2 and 5/6) and all the dihedral weighting factors (4th -coeff above) must be set to 0.0. In this case, you can use any pair -style you wish, since the dihedral does not need any Lennard-Jones -parameter information and will not compute any 1-4 non-bonded -interactions. Likewise the {charmm} or {charmmfsw} styles are -identical in this case since no 1-4 non-bonded interactions are -computed. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -When using run_style "respa"_run_style.html, these dihedral styles -must be assigned to the same r-RESPA level as {pair} or {outer}. - -When used in combination with CHARMM pair styles, the 1-4 -"special_bonds"_special_bonds.html scaling factors must be set to 0.0. -Otherwise non-bonded contributions for these 1-4 pairs will be -computed multiple times. - -These dihedral styles can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] none - -:line - -:link(dihedral-Cornell) -[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, -Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). - -:link(dihedral-MacKerell) -[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998). diff --git a/doc/txt/dihedral_class2.txt b/doc/txt/dihedral_class2.txt deleted file mode 100644 index 9936f3768d..0000000000 --- a/doc/txt/dihedral_class2.txt +++ /dev/null @@ -1,178 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style class2 command :h3 -dihedral_style class2/omp command :h3 -dihedral_style class2/kk command :h3 - -[Syntax:] - -dihedral_style class2 :pre - -[Examples:] - -dihedral_style class2 -dihedral_coeff 1 100 75 100 70 80 60 -dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 -dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010 -dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 -dihedral_coeff * aat -13.5271 110.2453 105.1270 -dihedral_coeff * bb13 0.0 1.0119 1.1010 :pre - -[Description:] - -The {class2} dihedral style uses the potential - -:c,image(Eqs/dihedral_class2.jpg) - -where Ed is the dihedral term, Embt is a middle-bond-torsion term, -Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat -is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term. - -Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium -bond lengths. - -See "(Sun)"_#dihedral-Sun for a description of the COMPASS class2 force field. - -Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas -must be defined for each dihedral type via the -"dihedral_coeff"_dihedral_coeff.html command as in the example above, -or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands. - -These are the 6 coefficients for the Ed formula: - -K1 (energy) -phi1 (degrees) -K2 (energy) -phi2 (degrees) -K3 (energy) -phi3 (degrees) :ul - -For the Embt formula, each line in a -"dihedral_coeff"_dihedral_coeff.html command in the input script lists -5 coefficients, the first of which is "mbt" to indicate they are -MiddleBondTorsion coefficients. In a data file, these coefficients -should be listed under a "MiddleBondTorsion Coeffs" heading and you -must leave out the "mbt", i.e. only list 4 coefficients after the -dihedral type. - -mbt -A1 (energy/distance) -A2 (energy/distance) -A3 (energy/distance) -r2 (distance) :ul - -For the Eebt formula, each line in a -"dihedral_coeff"_dihedral_coeff.html command in the input script lists -9 coefficients, the first of which is "ebt" to indicate they are -EndBondTorsion coefficients. In a data file, these coefficients -should be listed under a "EndBondTorsion Coeffs" heading and you must -leave out the "ebt", i.e. only list 8 coefficients after the dihedral -type. - -ebt -B1 (energy/distance) -B2 (energy/distance) -B3 (energy/distance) -C1 (energy/distance) -C2 (energy/distance) -C3 (energy/distance) -r1 (distance) -r3 (distance) :ul - -For the Eat formula, each line in a -"dihedral_coeff"_dihedral_coeff.html command in the input script lists -9 coefficients, the first of which is "at" to indicate they are -AngleTorsion coefficients. In a data file, these coefficients should -be listed under a "AngleTorsion Coeffs" heading and you must leave out -the "at", i.e. only list 8 coefficients after the dihedral type. - -at -D1 (energy/radian) -D2 (energy/radian) -D3 (energy/radian) -E1 (energy/radian) -E2 (energy/radian) -E3 (energy/radian) -theta1 (degrees) -theta2 (degrees) :ul - -Theta1 and theta2 are specified in degrees, but LAMMPS converts them -to radians internally; hence the units of D and E are in -energy/radian. - -For the Eaat formula, each line in a -"dihedral_coeff"_dihedral_coeff.html command in the input script lists -4 coefficients, the first of which is "aat" to indicate they are -AngleAngleTorsion coefficients. In a data file, these coefficients -should be listed under a "AngleAngleTorsion Coeffs" heading and you -must leave out the "aat", i.e. only list 3 coefficients after the -dihedral type. - -aat -M (energy/radian^2) -theta1 (degrees) -theta2 (degrees) :ul - -Theta1 and theta2 are specified in degrees, but LAMMPS converts them -to radians internally; hence the units of M are in energy/radian^2. - -For the Ebb13 formula, each line in a -"dihedral_coeff"_dihedral_coeff.html command in the input script lists -4 coefficients, the first of which is "bb13" to indicate they are -BondBond13 coefficients. In a data file, these coefficients should be -listed under a "BondBond13 Coeffs" heading and you must leave out the -"bb13", i.e. only list 3 coefficients after the dihedral type. - -bb13 -N (energy/distance^2) -r1 (distance) -r3 (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This dihedral style can only be used if LAMMPS was built with the -CLASS2 package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] none - -:line - -:link(dihedral-Sun) -[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998). diff --git a/doc/txt/dihedral_coeff.txt b/doc/txt/dihedral_coeff.txt deleted file mode 100644 index 718a73144e..0000000000 --- a/doc/txt/dihedral_coeff.txt +++ /dev/null @@ -1,96 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_coeff command :h3 - -[Syntax:] - -dihedral_coeff N args :pre - -N = dihedral type (see asterisk form below) -args = coefficients for one or more dihedral types :ul - -[Examples:] - -dihedral_coeff 1 80.0 1 3 -dihedral_coeff * 80.0 1 3 0.5 -dihedral_coeff 2* 80.0 1 3 0.5 :pre - -[Description:] - -Specify the dihedral force field coefficients for one or more dihedral types. -The number and meaning of the coefficients depends on the dihedral style. -Dihedral coefficients can also be set in the data file read by the -"read_data"_read_data.html command or in a restart file. - -N can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterisk can be -used to set the coefficients for multiple dihedral types. This takes the -form "*" or "*n" or "n*" or "m*n". If N = the number of dihedral types, -then an asterisk with no numeric values means all types from 1 to N. A -leading asterisk means all types from 1 to n (inclusive). A trailing -asterisk means all types from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). - -Note that using a dihedral_coeff command can override a previous setting -for the same dihedral type. For example, these commands set the coeffs -for all dihedral types, then overwrite the coeffs for just dihedral type 2: - -dihedral_coeff * 80.0 1 3 -dihedral_coeff 2 200.0 1 3 :pre - -A line in a data file that specifies dihedral coefficients uses the exact -same format as the arguments of the dihedral_coeff command in an input -script, except that wild-card asterisks should not be used since -coefficients for all N types must be listed in the file. For example, -under the "Dihedral Coeffs" section of a data file, the line that -corresponds to the 1st example above would be listed as - -1 80.0 1 3 :pre - -The "dihedral_style class2"_dihedral_class2.html is an exception to -this rule, in that an additional argument is used in the input script -to allow specification of the cross-term coefficients. See its doc -page for details. - -NOTE: When comparing the formulas and coefficients for various LAMMPS -dihedral styles with dihedral equations defined by other force fields, -note that some force field implementations divide/multiply the energy -prefactor {K} by the multiple number of torsions that contain the J-K -bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed -dihedral equation applies to each individual dihedral. Thus you need -to define {K} appropriately to account for this difference if -necessary. - -:line - -The list of all dihedral styles defined in LAMMPS is given on the -"dihedral_style"_dihedral_style.html doc page. They are also listed -in more compact form on the "Commands -dihedral"_Commands_bond.html#dihedral doc page. - -On either of those pages, click on the style to display the formula it -computes and its coefficients as specified by the associated -dihedral_coeff command. - -:line - -[Restrictions:] - -This command must come after the simulation box is defined by a -"read_data"_read_data.html, "read_restart"_read_restart.html, or -"create_box"_create_box.html command. - -A dihedral style must be defined before any dihedral coefficients are -set, either in the input script or in a data file. - -[Related commands:] - -"dihedral_style"_dihedral_style.html - -[Default:] none diff --git a/doc/txt/dihedral_cosine_shift_exp.txt b/doc/txt/dihedral_cosine_shift_exp.txt deleted file mode 100644 index e2a46d28d8..0000000000 --- a/doc/txt/dihedral_cosine_shift_exp.txt +++ /dev/null @@ -1,85 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style cosine/shift/exp command :h3 -dihedral_style cosine/shift/exp/omp command :h3 - -[Syntax:] - -dihedral_style cosine/shift/exp :pre - -[Examples:] - -dihedral_style cosine/shift/exp -dihedral_coeff 1 10.0 45.0 2.0 :pre - -[Description:] - -The {cosine/shift/exp} dihedral style uses the potential - -:c,image(Eqs/dihedral_cosine_shift_exp.jpg) - -where Umin, theta, and a are defined for each dihedral type. - -The potential is bounded between \[-Umin:0\] and the minimum is located -at the angle theta0. The a parameter can be both positive or negative -and is used to control the spring constant at the equilibrium. - -The spring constant is given by k=a exp(a) Umin/ \[2 (Exp(a)-1)\]. -For a>3 k/Umin = a/2 to better than 5% relative error. For negative -values of the a parameter, the spring constant is essentially zero, -and anharmonic terms takes over. The potential is furthermore well -behaved in the limit a->0, where it has been implemented to linear -order in a for a < 0.001. - -The following coefficients must be defined for each dihedral type via -the "dihedral_coeff"_dihedral_coeff.html command as in the example -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -umin (energy) -theta (angle) -A (real number) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This dihedral style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html, -"angle_cosine_shift_exp"_angle_cosine_shift_exp.html - -[Default:] none diff --git a/doc/txt/dihedral_fourier.txt b/doc/txt/dihedral_fourier.txt deleted file mode 100644 index 3045f6824b..0000000000 --- a/doc/txt/dihedral_fourier.txt +++ /dev/null @@ -1,77 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style fourier command :h3 -dihedral_style fourier/intel command :h3 -dihedral_style fourier/omp command :h3 - -[Syntax:] - -dihedral_style fourier :pre - -[Examples:] - -dihedral_style fourier -dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0 :pre - -[Description:] - -The {fourier} dihedral style uses the potential: - -:c,image(Eqs/dihedral_fourier.jpg) - -The following coefficients must be defined for each dihedral type via the -"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -m (integer >=1) -K1 (energy) -n1 (integer >= 0) -d1 (degrees) -\[...\] -Km (energy) -nm (integer >= 0) -dm (degrees) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] none - diff --git a/doc/txt/dihedral_harmonic.txt b/doc/txt/dihedral_harmonic.txt deleted file mode 100644 index b4071c863c..0000000000 --- a/doc/txt/dihedral_harmonic.txt +++ /dev/null @@ -1,86 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style harmonic command :h3 -dihedral_style harmonic/intel command :h3 -dihedral_style harmonic/kk command :h3 -dihedral_style harmonic/omp command :h3 - -[Syntax:] - -dihedral_style harmonic :pre - -[Examples:] - -dihedral_style harmonic -dihedral_coeff 1 80.0 1 2 :pre - -[Description:] - -The {harmonic} dihedral style uses the potential - -:c,image(Eqs/dihedral_harmonic.jpg) - -The following coefficients must be defined for each dihedral type via the -"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) -d (+1 or -1) -n (integer >= 0) :ul - -NOTE: Here are important points to take note of when defining LAMMPS -dihedral coefficients for the harmonic style, so that they are -compatible with how harmonic dihedrals are defined by other force -fields: - -The LAMMPS convention is that the trans position = 180 degrees, while -in some force fields trans = 0 degrees. :ulb,l - -Some force fields reverse the sign convention on {d}. :l - -Some force fields let {n} be positive or negative which corresponds to -{d} = 1 or -1 for the harmonic style. :l -:ule - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This dihedral style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] none diff --git a/doc/txt/dihedral_helix.txt b/doc/txt/dihedral_helix.txt deleted file mode 100644 index 3b3607337b..0000000000 --- a/doc/txt/dihedral_helix.txt +++ /dev/null @@ -1,83 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style helix command :h3 -dihedral_style helix/omp command :h3 - -[Syntax:] - -dihedral_style helix :pre - -[Examples:] - -dihedral_style helix -dihedral_coeff 1 80.0 100.0 40.0 :pre - -[Description:] - -The {helix} dihedral style uses the potential - -:c,image(Eqs/dihedral_helix.jpg) - -This coarse-grain dihedral potential is described in "(Guo)"_#Guo. -For dihedral angles in the helical region, the energy function is -represented by a standard potential consisting of three minima, one -corresponding to the trans (t) state and the other to gauche states -(g+ and g-). The paper describes how the A,B,C parameters are chosen -so as to balance secondary (largely driven by local interactions) and -tertiary structure (driven by long-range interactions). - -The following coefficients must be defined for each dihedral type via the -"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -A (energy) -B (energy) -C (energy) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This dihedral style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] none - -:line - -:link(Guo) -[(Guo)] Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996). diff --git a/doc/txt/dihedral_hybrid.txt b/doc/txt/dihedral_hybrid.txt deleted file mode 100644 index a4a2a2808e..0000000000 --- a/doc/txt/dihedral_hybrid.txt +++ /dev/null @@ -1,92 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style hybrid command :h3 - -[Syntax:] - -dihedral_style hybrid style1 style2 ... :pre - -style1,style2 = list of one or more dihedral styles :ul - -[Examples:] - -dihedral_style hybrid harmonic helix -dihedral_coeff 1 harmonic 6.0 1 3 -dihedral_coeff 2* helix 10 10 10 :pre - -[Description:] - -The {hybrid} style enables the use of multiple dihedral styles in one -simulation. An dihedral style is assigned to each dihedral type. For -example, dihedrals in a polymer flow (of dihedral type 1) could be -computed with a {harmonic} potential and dihedrals in the wall -boundary (of dihedral type 2) could be computed with a {helix} -potential. The assignment of dihedral type to style is made via the -"dihedral_coeff"_dihedral_coeff.html command or in the data file. - -In the dihedral_coeff commands, the name of a dihedral style must be -added after the dihedral type, with the remaining coefficients being -those appropriate to that style. In the example above, the 2 -dihedral_coeff commands set dihedrals of dihedral type 1 to be -computed with a {harmonic} potential with coefficients 6.0, 1, 3 for -K, d, n. All other dihedral types (2-N) are computed with a {helix} -potential with coefficients 10, 10, 10 for A, B, C. - -If dihedral coefficients are specified in the data file read via the -"read_data"_read_data.html command, then the same rule applies. -E.g. "harmonic" or "helix", must be added after the dihedral type, for -each line in the "Dihedral Coeffs" section, e.g. - -Dihedral Coeffs :pre - -1 harmonic 6.0 1 3 -2 helix 10 10 10 -... :pre - -If {class2} is one of the dihedral hybrid styles, the same rule holds -for specifying additional AngleTorsion (and EndBondTorsion, etc) -coefficients either via the input script or in the data file. -I.e. {class2} must be added to each line after the dihedral type. For -lines in the AngleTorsion (or EndBondTorsion, etc) section of the data -file for dihedral types that are not {class2}, you must use an -dihedral style of {skip} as a placeholder, e.g. - -AngleTorsion Coeffs :pre - -1 skip -2 class2 1.0 1.0 1.0 3.0 3.0 3.0 30.0 50.0 -... :pre - -Note that it is not necessary to use the dihedral style {skip} in the -input script, since AngleTorsion (or EndBondTorsion, etc) coefficients -need not be specified at all for dihedral types that are not {class2}. - -A dihedral style of {none} with no additional coefficients can be used -in place of a dihedral style, either in a input script dihedral_coeff -command or in the data file, if you desire to turn off interactions -for specific dihedral types. - -:line - -[Restrictions:] - -This dihedral style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -Unlike other dihedral styles, the hybrid dihedral style does not store -dihedral coefficient info for individual sub-styles in a "binary -restart files"_restart.html. Thus when restarting a simulation from a -restart file, you need to re-specify dihedral_coeff commands. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] none diff --git a/doc/txt/dihedral_multi_harmonic.txt b/doc/txt/dihedral_multi_harmonic.txt deleted file mode 100644 index 74f1f6abc6..0000000000 --- a/doc/txt/dihedral_multi_harmonic.txt +++ /dev/null @@ -1,72 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style multi/harmonic command :h3 -dihedral_style multi/harmonic/omp command :h3 - -[Syntax:] - -dihedral_style multi/harmonic :pre - -[Examples:] - -dihedral_style multi/harmonic -dihedral_coeff 1 20 20 20 20 20 :pre - -[Description:] - -The {multi/harmonic} dihedral style uses the potential - -:c,image(Eqs/dihedral_multi_harmonic.jpg) - -The following coefficients must be defined for each dihedral type via the -"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -A1 (energy) -A2 (energy) -A3 (energy) -A4 (energy) -A5 (energy) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This dihedral style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] none diff --git a/doc/txt/dihedral_nharmonic.txt b/doc/txt/dihedral_nharmonic.txt deleted file mode 100644 index 660bbb3f1f..0000000000 --- a/doc/txt/dihedral_nharmonic.txt +++ /dev/null @@ -1,72 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style nharmonic command :h3 -dihedral_style nharmonic/omp command :h3 - -[Syntax:] - -dihedral_style nharmonic :pre - -[Examples:] - -dihedral_style nharmonic -dihedral_coeff * 3 10.0 20.0 30.0 :pre - -[Description:] - -The {nharmonic} dihedral style uses the potential: - -:c,image(Eqs/dihedral_nharmonic.jpg) - -The following coefficients must be defined for each dihedral type via the -"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -n (integer >=1) -A1 (energy) -A2 (energy) -... -An (energy) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] none diff --git a/doc/txt/dihedral_none.txt b/doc/txt/dihedral_none.txt deleted file mode 100644 index 4c1ff2ea5d..0000000000 --- a/doc/txt/dihedral_none.txt +++ /dev/null @@ -1,34 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style none command :h3 - -[Syntax:] - -dihedral_style none :pre - -[Examples:] - -dihedral_style none :pre - -[Description:] - -Using a dihedral style of none means dihedral forces and energies are -not computed, even if quadruplets of dihedral atoms were listed in the -data file read by the "read_data"_read_data.html command. - -See the "dihedral_style zero"_dihedral_zero.html command for a way to -calculate dihedral statistics, but compute no dihedral interactions. - -[Restrictions:] none - -[Related commands:] - -"dihedral_style zero"_dihedral_zero.html - -[Default:] none diff --git a/doc/txt/dihedral_opls.txt b/doc/txt/dihedral_opls.txt deleted file mode 100644 index 7fa5d81a14..0000000000 --- a/doc/txt/dihedral_opls.txt +++ /dev/null @@ -1,85 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style opls command :h3 -dihedral_style opls/intel command :h3 -dihedral_style opls/kk command :h3 -dihedral_style opls/omp command :h3 - -[Syntax:] - -dihedral_style opls :pre - -[Examples:] - -dihedral_style opls -dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT -dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC -dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC :pre - -[Description:] - -The {opls} dihedral style uses the potential - -:c,image(Eqs/dihedral_opls.jpg) - -Note that the usual 1/2 factor is not included in the K values. - -This dihedral potential is used in the OPLS force field and is -described in "(Watkins)"_#Watkins. - -The following coefficients must be defined for each dihedral type via the -"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K1 (energy) -K2 (energy) -K3 (energy) -K4 (energy) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This dihedral style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] none - -:line - -:link(Watkins) -[(Watkins)] Watkins and Jorgensen, J Phys Chem A, 105, 4118-4125 (2001). diff --git a/doc/txt/dihedral_quadratic.txt b/doc/txt/dihedral_quadratic.txt deleted file mode 100644 index dc951e4269..0000000000 --- a/doc/txt/dihedral_quadratic.txt +++ /dev/null @@ -1,74 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style quadratic command :h3 -dihedral_style quadratic/omp command :h3 - -[Syntax:] - -dihedral_style quadratic :pre - -[Examples:] - -dihedral_style quadratic -dihedral_coeff 100.0 80.0 :pre - -[Description:] - -The {quadratic} dihedral style uses the potential: - -:c,image(Eqs/dihedral_quadratic.jpg) - -This dihedral potential can be used to keep a dihedral in a predefined -value (cis=zero, right-hand convention is used). - -The following coefficients must be defined for each dihedral type via -the "dihedral_coeff"_dihedral_coeff.html command as in the example -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -K (energy/radian^2) -phi0 (degrees) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] none - diff --git a/doc/txt/dihedral_spherical.txt b/doc/txt/dihedral_spherical.txt deleted file mode 100644 index 62ba6cf9e5..0000000000 --- a/doc/txt/dihedral_spherical.txt +++ /dev/null @@ -1,89 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style spherical command :h3 - -[Syntax:] - -dihedral_style spherical :pre - -[Examples:] - -dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 -dihedral_coeff 1 3 69.3 1 93.9 1 1 90 0 1 90 0 & - 49.1 0 0.00 0 1 74.4 1 0 0.00 0 & - 25.2 0 0.00 0 0 0.00 0 1 48.1 1 -:pre - -[Description:] - -The {spherical} dihedral style uses the potential: - -:c,image(JPG/dihedral_spherical_angles.jpg) -:c,image(Eqs/dihedral_spherical.jpg) - -For this dihedral style, the energy can be any function that combines the -4-body dihedral-angle (phi) and the two 3-body bond-angles (theta1, theta2). -For this reason, there is usually no need to define 3-body "angle" forces -separately for the atoms participating in these interactions. -It is probably more efficient to incorporate 3-body angle forces into -the dihedral interaction even if it requires adding additional terms to -the expansion (as was done in the second example). A careful choice of -parameters can prevent singularities that occur with traditional -force-fields whenever theta1 or theta2 approach 0 or 180 degrees. - -The last example above corresponds to an interaction with a single energy -minima located near phi=93.9, theta1=74.4, theta2=48.1 degrees, and it remains -numerically stable at all angles (phi, theta1, theta2). In this example, -the coefficients 49.1, and 25.2 can be physically interpreted as the -harmonic spring constants for theta1 and theta2 around their minima. -The coefficient 69.3 is the harmonic spring constant for phi after -division by sin(74.4)*sin(48.1) (the minima positions for theta1 and theta2). - -The following coefficients must be defined for each dihedral type via the -"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in -the Dihedral Coeffs section of a data file read by the -"read_data"_read_data.html command: - -n (integer >= 1) -C1 (energy) -K1 (typically an integer) -a1 (degrees) -u1 (typically 0.0 or 1.0) -L1 (typically an integer) -b1 (degrees, typically 0.0 or 90.0) -v1 (typically 0.0 or 1.0) -M1 (typically an integer) -c1 (degrees, typically 0.0 or 90.0) -w1 (typically 0.0 or 1.0) -\[...\] -Cn (energy) -Kn (typically an integer) -an (degrees) -un (typically 0.0 or 1.0) -Ln (typically an integer) -bn (degrees, typically 0.0 or 90.0) -vn (typically 0.0 or 1.0) -Mn (typically an integer) -cn (degrees, typically 0.0 or 90.0) -wn (typically 0.0 or 1.0) :ul - -:line - -[Restrictions:] - -This dihedral style can only be used if LAMMPS was built with the -USER_MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] none - diff --git a/doc/txt/dihedral_style.txt b/doc/txt/dihedral_style.txt deleted file mode 100644 index 2a5b9baf52..0000000000 --- a/doc/txt/dihedral_style.txt +++ /dev/null @@ -1,131 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style command :h3 - -[Syntax:] - -dihedral_style style :pre - -style = {none} or {hybrid} or {charmm} or {class2} or {harmonic} or {helix} or \ - {multi/harmonic} or {opls} :ul - -[Examples:] - -dihedral_style harmonic -dihedral_style multi/harmonic -dihedral_style hybrid harmonic charmm :pre - -[Description:] - -Set the formula(s) LAMMPS uses to compute dihedral interactions -between quadruplets of atoms, which remain in force for the duration -of the simulation. The list of dihedral quadruplets is read in by a -"read_data"_read_data.html or "read_restart"_read_restart.html command -from a data or restart file. - -Hybrid models where dihedrals are computed using different dihedral -potentials can be setup using the {hybrid} dihedral style. - -The coefficients associated with a dihedral style can be specified in -a data or restart file or via the "dihedral_coeff"_dihedral_coeff.html -command. - -All dihedral potentials store their coefficient data in binary restart -files which means dihedral_style and -"dihedral_coeff"_dihedral_coeff.html commands do not need to be -re-specified in an input script that restarts a simulation. See the -"read_restart"_read_restart.html command for details on how to do -this. The one exception is that dihedral_style {hybrid} only stores -the list of sub-styles in the restart file; dihedral coefficients need -to be re-specified. - -NOTE: When both a dihedral and pair style is defined, the -"special_bonds"_special_bonds.html command often needs to be used to -turn off (or weight) the pairwise interaction that would otherwise -exist between 4 bonded atoms. - -In the formulas listed for each dihedral style, {phi} is the torsional -angle defined by the quadruplet of atoms. This angle has a sign -convention as shown in this diagram: - -:c,image(JPG/dihedral_sign.jpg) - -where the I,J,K,L ordering of the 4 atoms that define the dihedral -is from left to right. - -This sign convention effects several of the dihedral styles listed -below (e.g. charmm, helix) in the sense that the energy formula -depends on the sign of phi, which may be reflected in the value of the -coefficients you specify. - -NOTE: When comparing the formulas and coefficients for various LAMMPS -dihedral styles with dihedral equations defined by other force fields, -note that some force field implementations divide/multiply the energy -prefactor {K} by the multiple number of torsions that contain the J-K -bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed -dihedral equation applies to each individual dihedral. Thus you need -to define {K} appropriately via the -"dihedral_coeff"_dihedral_coeff.html command to account for this -difference if necessary. - -:line - -Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated "dihedral_coeff"_dihedral_coeff.html command. - -Click on the style to display the formula it computes, any additional -arguments specified in the dihedral_style command, and coefficients -specified by the associated "dihedral_coeff"_dihedral_coeff.html -command. - -There are also additional accelerated pair styles included in the -LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the "Commands -dihedral"_Commands_bond.html#dihedral doc page are followed by one or -more of (g,i,k,o,t) to indicate which accelerated styles exist. - -"none"_dihedral_none.html - turn off dihedral interactions -"zero"_dihedral_zero.html - topology but no interactions -"hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul - -"charmm"_dihedral_charmm.html - CHARMM dihedral -"charmmfsw"_dihedral_charmm.html - CHARMM dihedral with force switching -"class2"_dihedral_class2.html - COMPASS (class 2) dihedral -"cosine/shift/exp"_dihedral_cosine_shift_exp.html - dihedral with exponential in spring constant -"fourier"_dihedral_fourier.html - dihedral with multiple cosine terms -"harmonic"_dihedral_harmonic.html - harmonic dihedral -"helix"_dihedral_helix.html - helix dihedral -"multi/harmonic"_dihedral_multi_harmonic.html - dihedral with 5 harmonic terms -"nharmonic"_dihedral_nharmonic.html - same as multi-harmonic with N terms -"opls"_dihedral_opls.html - OPLS dihedral -"quadratic"_dihedral_quadratic.html - dihedral with quadratic term in angle -"spherical"_dihedral_spherical.html - dihedral which includes angle terms to avoid singularities -"table"_dihedral_table.html - tabulated dihedral -"table/cut"_dihedral_table_cut.html - tabulated dihedral with analytic cutoff :ul - -:line - -[Restrictions:] - -Dihedral styles can only be set for atom styles that allow dihedrals -to be defined. - -Most dihedral styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. The doc pages for -individual dihedral potentials tell if it is part of a package. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] - -dihedral_style none diff --git a/doc/txt/dihedral_table.txt b/doc/txt/dihedral_table.txt deleted file mode 100644 index b3cfd37570..0000000000 --- a/doc/txt/dihedral_table.txt +++ /dev/null @@ -1,214 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style table command :h3 -dihedral_style table/omp command :h3 - -[Syntax:] - -dihedral_style table style Ntable :pre - -style = {linear} or {spline} = method of interpolation -Ntable = size of the internal lookup table :ul - -[Examples:] - -dihedral_style table spline 400 -dihedral_style table linear 1000 -dihedral_coeff 1 file.table DIH_TABLE1 -dihedral_coeff 2 file.table DIH_TABLE2 :pre - -[Description:] - -The {table} dihedral style creates interpolation tables of length -{Ntable} from dihedral potential and derivative values listed in a -file(s) as a function of the dihedral angle "phi". The files are read -by the "dihedral_coeff"_dihedral_coeff.html command. - -The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and derivative values at each of -{Ntable} dihedral angles. During a simulation, these tables are used -to interpolate energy and force values on individual atoms as -needed. The interpolation is done in one of 2 styles: {linear} or -{spline}. - -For the {linear} style, the dihedral angle (phi) is used to find 2 -surrounding table values from which an energy or its derivative is -computed by linear interpolation. - -For the {spline} style, cubic spline coefficients are computed and -stored at each of the {Ntable} evenly-spaced values in the -interpolated table. For a given dihedral angle (phi), the appropriate -coefficients are chosen from this list, and a cubic polynomial is used -to compute the energy and the derivative at this angle. - -The following coefficients must be defined for each dihedral type via -the "dihedral_coeff"_dihedral_coeff.html command as in the example -above. - -filename -keyword :ul - -The filename specifies a file containing tabulated energy and -derivative values. The keyword specifies a section of the file. The -format of this file is described below. - -:line - -The format of a tabulated file is as follows (without the -parenthesized comments). It can begin with one or more comment -or blank lines. - -# Table of the potential and its negative derivative :pre - -DIH_TABLE1 (keyword is the first text on line) -N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F) - (blank line) -1 -168.0 -1.40351172223 0.0423346818422 -2 -156.0 -1.70447981034 0.00811786522531 -3 -144.0 -1.62956100432 -0.0184129719987 -... -30 180.0 -0.707106781187 0.0719306095245 :pre - -# Example 2: table of the potential. Forces omitted :pre - -DIH_TABLE2 -N 30 NOF CHECKU testU.dat CHECKF testF.dat :pre - -1 -168.0 -1.40351172223 -2 -156.0 -1.70447981034 -3 -144.0 -1.62956100432 -... -30 180.0 -0.707106781187 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the -"dihedral_coeff"_dihedral_coeff.html command. The next line lists (in -any order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. - -Following a blank line, the next N lines list the tabulated values. On -each line, the 1st value is the index from 1 to N, the 2nd value is -the angle value, the 3rd value is the energy (in energy units), and -the 4th is -dE/d(phi) also in energy units). The 3rd term is the -energy of the 4-atom configuration for the specified angle. The 4th -term (when present) is the negative derivative of the energy with -respect to the angle (in degrees, or radians depending on whether the -user selected DEGREES or RADIANS). Thus the units of the last term -are still energy, not force. The dihedral angle values must increase -from one line to the next. - -Dihedral table splines are cyclic. There is no discontinuity at 180 -degrees (or at any other angle). Although in the examples above, the -angles range from -180 to 180 degrees, in general, the first angle in -the list can have any value (positive, zero, or negative). However -the {range} of angles represented in the table must be {strictly} less -than 360 degrees (2pi radians) to avoid angle overlap. (You may not -supply entries in the table for both 180 and -180, for example.) If -the user's table covers only a narrow range of dihedral angles, -strange numerical behavior can occur in the large remaining gap. - -[Parameters:] - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the N -specified in the "dihedral_style table"_dihedral_style.html command. -Let {Ntable} is the number of table entries requested dihedral_style -command, and let {Nfile} be the parameter following "N" in the -tabulated file ("30" in the sparse example above). What LAMMPS does -is a preliminary interpolation by creating splines using the {Nfile} -tabulated values as nodal points. It uses these to interpolate as -needed to generate energy and derivative values at {Ntable} different -points (which are evenly spaced over a 360 degree range, even if the -angles in the file are not). The resulting tables of length {Ntable} -are then used as described above, when computing energy and force for -individual dihedral angles and their atoms. This means that if you -want the interpolation tables of length {Ntable} to match exactly what -is in the tabulated file (with effectively nopreliminary -interpolation), you should set {Ntable} = {Nfile}. To insure the -nodal points in the user's file are aligned with the interpolated -table entries, the angles in the table should be integer multiples of -360/{Ntable} degrees, or 2*PI/{Ntable} radians (depending on your -choice of angle units). - -The optional "NOF" keyword allows the user to omit the forces -(negative energy derivatives) from the table file (normally located in -the 4th column). In their place, forces will be calculated -automatically by differentiating the potential energy function -indicated by the 3rd column of the table (using either linear or -spline interpolation). - -The optional "DEGREES" keyword allows the user to specify angles in -degrees instead of radians (default). - -The optional "RADIANS" keyword allows the user to specify angles in -radians instead of degrees. (Note: This changes the way the forces -are scaled in the 4th column of the data file.) - -The optional "CHECKU" keyword is followed by a filename. This allows -the user to save all of the {Ntable} different entries in the -interpolated energy table to a file to make sure that the interpolated -function agrees with the user's expectations. (Note: You can -temporarily increase the {Ntable} parameter to a high value for this -purpose. "{Ntable}" is explained above.) - -The optional "CHECKF" keyword is analogous to the "CHECKU" keyword. -It is followed by a filename, and it allows the user to check the -interpolated force table. This option is available even if the user -selected the "NOF" option. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds one -that matches the specified keyword. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart info:] - -This dihedral style writes the settings for the "dihedral_style table" -command to "binary restart files"_restart.html, so a dihedral_style -command does not need to specified in an input script that reads a -restart file. However, the coefficient information is not stored in -the restart file, since it is tabulated in the potential files. Thus, -dihedral_coeff commands do need to be specified in the restart input -script. - -[Restrictions:] - -This dihedral style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html - -[Default:] none diff --git a/doc/txt/dihedral_table_cut.txt b/doc/txt/dihedral_table_cut.txt deleted file mode 100644 index 560f5375a7..0000000000 --- a/doc/txt/dihedral_table_cut.txt +++ /dev/null @@ -1,215 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style table/cut command :h3 - -[Syntax:] - -dihedral_style table/cut style Ntable :pre - -style = {linear} or {spline} = method of interpolation -Ntable = size of the internal lookup table :ul - -[Examples:] - -dihedral_style table/cut spline 400 -dihedral_style table/cut linear 1000 -dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1 -dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2 :pre - -[Description:] - -The {table/cut} dihedral style creates interpolation tables of length -{Ntable} from dihedral potential and derivative values listed in a -file(s) as a function of the dihedral angle "phi". In addition, an -analytic cutoff that is quadratic in the bond-angle (theta) is applied -in order to regularize the dihedral interaction. The dihedral table -files are read by the "dihedral_coeff"_dihedral_coeff.html command. - -The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and derivative values at each of -{Ntable} dihedral angles. During a simulation, these tables are used -to interpolate energy and force values on individual atoms as -needed. The interpolation is done in one of 2 styles: {linear} or -{spline}. - -For the {linear} style, the dihedral angle (phi) is used to find 2 -surrounding table values from which an energy or its derivative is -computed by linear interpolation. - -For the {spline} style, cubic spline coefficients are computed and -stored at each of the {Ntable} evenly-spaced values in the -interpolated table. For a given dihedral angle (phi), the appropriate -coefficients are chosen from this list, and a cubic polynomial is used -to compute the energy and the derivative at this angle. - -The following coefficients must be defined for each dihedral type via -the "dihedral_coeff"_dihedral_coeff.html command as in the example -above. - -style (aat) -cutoff prefactor -cutoff angle1 -cutoff angle2 -filename -keyword :ul - -The cutoff dihedral style uses a tabulated dihedral interaction with a -cutoff function: - -:c,image(Eqs/dihedral_table_cut.jpg) - -The cutoff specifies an prefactor to the cutoff function. While this value -would ordinarily equal 1 there may be situations where the value should change. - -The cutoff angle1 specifies the angle (in degrees) below which the dihedral -interaction is unmodified, i.e. the cutoff function is 1. - -The cutoff function is applied between angle1 and angle2, which is the angle at -which the cutoff function drops to zero. The value of zero effectively "turns -off" the dihedral interaction. - -The filename specifies a file containing tabulated energy and -derivative values. The keyword specifies a section of the file. The -format of this file is described below. - -:line - -The format of a tabulated file is as follows (without the -parenthesized comments). It can begin with one or more comment -or blank lines. - -# Table of the potential and its negative derivative :pre - -DIH_TABLE1 (keyword is the first text on line) -N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F) - (blank line) -1 -168.0 -1.40351172223 0.0423346818422 -2 -156.0 -1.70447981034 0.00811786522531 -3 -144.0 -1.62956100432 -0.0184129719987 -... -30 180.0 -0.707106781187 0.0719306095245 :pre - -# Example 2: table of the potential. Forces omitted :pre - -DIH_TABLE2 -N 30 NOF CHECKU testU.dat CHECKF testF.dat :pre - -1 -168.0 -1.40351172223 -2 -156.0 -1.70447981034 -3 -144.0 -1.62956100432 -... -30 180.0 -0.707106781187 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the -"dihedral_coeff"_dihedral_coeff.html command. The next line lists (in -any order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. - -Following a blank line, the next N lines list the tabulated values. On -each line, the 1st value is the index from 1 to N, the 2nd value is -the angle value, the 3rd value is the energy (in energy units), and -the 4th is -dE/d(phi) also in energy units). The 3rd term is the -energy of the 4-atom configuration for the specified angle. The 4th -term (when present) is the negative derivative of the energy with -respect to the angle (in degrees, or radians depending on whether the -user selected DEGREES or RADIANS). Thus the units of the last term -are still energy, not force. The dihedral angle values must increase -from one line to the next. - -Dihedral table splines are cyclic. There is no discontinuity at 180 -degrees (or at any other angle). Although in the examples above, the -angles range from -180 to 180 degrees, in general, the first angle in -the list can have any value (positive, zero, or negative). However -the {range} of angles represented in the table must be {strictly} less -than 360 degrees (2pi radians) to avoid angle overlap. (You may not -supply entries in the table for both 180 and -180, for example.) If -the user's table covers only a narrow range of dihedral angles, -strange numerical behavior can occur in the large remaining gap. - -[Parameters:] - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the N -specified in the "dihedral_style table"_dihedral_style.html command. -Let {Ntable} is the number of table entries requested dihedral_style -command, and let {Nfile} be the parameter following "N" in the -tabulated file ("30" in the sparse example above). What LAMMPS does -is a preliminary interpolation by creating splines using the {Nfile} -tabulated values as nodal points. It uses these to interpolate as -needed to generate energy and derivative values at {Ntable} different -points (which are evenly spaced over a 360 degree range, even if the -angles in the file are not). The resulting tables of length {Ntable} -are then used as described above, when computing energy and force for -individual dihedral angles and their atoms. This means that if you -want the interpolation tables of length {Ntable} to match exactly what -is in the tabulated file (with effectively nopreliminary -interpolation), you should set {Ntable} = {Nfile}. To insure the -nodal points in the user's file are aligned with the interpolated -table entries, the angles in the table should be integer multiples of -360/{Ntable} degrees, or 2*PI/{Ntable} radians (depending on your -choice of angle units). - -The optional "NOF" keyword allows the user to omit the forces -(negative energy derivatives) from the table file (normally located in -the 4th column). In their place, forces will be calculated -automatically by differentiating the potential energy function -indicated by the 3rd column of the table (using either linear or -spline interpolation). - -The optional "DEGREES" keyword allows the user to specify angles in -degrees instead of radians (default). - -The optional "RADIANS" keyword allows the user to specify angles in -radians instead of degrees. (Note: This changes the way the forces -are scaled in the 4th column of the data file.) - -The optional "CHECKU" keyword is followed by a filename. This allows -the user to save all of the {Ntable} different entries in the -interpolated energy table to a file to make sure that the interpolated -function agrees with the user's expectations. (Note: You can -temporarily increase the {Ntable} parameter to a high value for this -purpose. "{Ntable}" is explained above.) - -The optional "CHECKF" keyword is analogous to the "CHECKU" keyword. -It is followed by a filename, and it allows the user to check the -interpolated force table. This option is available even if the user -selected the "NOF" option. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds one -that matches the specified keyword. - -[Restart info:] - -This dihedral style writes the settings for the "dihedral_style table/cut" -command to "binary restart files"_restart.html, so a dihedral_style -command does not need to specified in an input script that reads a -restart file. However, the coefficient information is not stored in -the restart file, since it is tabulated in the potential files. Thus, -dihedral_coeff commands do need to be specified in the restart input -script. - -[Restrictions:] - -This dihedral style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"dihedral_coeff"_dihedral_coeff.html, "dihedral_style table"_dihedral_table.html - -[Default:] none - -:link(dihedralcut-Salerno) -[(Salerno)] Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018). diff --git a/doc/txt/dihedral_zero.txt b/doc/txt/dihedral_zero.txt deleted file mode 100644 index 0c9995a563..0000000000 --- a/doc/txt/dihedral_zero.txt +++ /dev/null @@ -1,48 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dihedral_style zero command :h3 - -[Syntax:] - -dihedral_style zero {nocoeff} :pre - -[Examples:] - -dihedral_style zero -dihedral_style zero nocoeff -dihedral_coeff * :pre - -[Description:] - -Using a dihedral style of zero means dihedral forces and energies are -not computed, but the geometry of dihedral quadruplets is still -accessible to other commands. - -As an example, the "compute -dihedral/local"_compute_dihedral_local.html command can be used to -compute the theta values for the list of quadruplets of dihedral atoms -listed in the data file read by the "read_data"_read_data.html -command. If no dihedral style is defined, this command cannot be -used. - -The optional {nocoeff} flag allows to read data files with a DihedralCoeff -section for any dihedral style. Similarly, any dihedral_coeff commands -will only be checked for the dihedral type number and the rest ignored. - -Note that the "dihedral_coeff"_dihedral_coeff.html command must be -used for all dihedral types, though no additional values are -specified. - -[Restrictions:] none - -[Related commands:] none - -"dihedral_style none"_dihedral_none.html - -[Default:] none diff --git a/doc/txt/dimension.txt b/doc/txt/dimension.txt deleted file mode 100644 index b7dde76524..0000000000 --- a/doc/txt/dimension.txt +++ /dev/null @@ -1,48 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dimension command :h3 - -[Syntax:] - -dimension N :pre - -N = 2 or 3 :ul - -[Examples:] - -dimension 2 :pre - -[Description:] - -Set the dimensionality of the simulation. By default LAMMPS runs 3d -simulations. To run a 2d simulation, this command should be used -prior to setting up a simulation box via the -"create_box"_create_box.html or "read_data"_read_data.html commands. -Restart files also store this setting. - -See the discussion on the "Howto 2d"_Howto_2d.html doc page for -additional instructions on how to run 2d simulations. - -NOTE: Some models in LAMMPS treat particles as finite-size spheres or -ellipsoids, as opposed to point particles. In 2d, the particles will -still be spheres or ellipsoids, not circular disks or ellipses, -meaning their moment of inertia will be the same as in 3d. - -[Restrictions:] - -This command must be used before the simulation box is defined by a -"read_data"_read_data.html or "create_box"_create_box.html command. - -[Related commands:] - -"fix enforce2d"_fix_enforce2d.html - -[Default:] - -dimension 3 :pre diff --git a/doc/txt/displace_atoms.txt b/doc/txt/displace_atoms.txt deleted file mode 100644 index b0fa2d3bc4..0000000000 --- a/doc/txt/displace_atoms.txt +++ /dev/null @@ -1,139 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -displace_atoms command :h3 - -[Syntax:] - -displace_atoms group-ID style args keyword value ... :pre - -group-ID = ID of group of atoms to displace :ulb,l -style = {move} or {ramp} or {random} or {rotate} :l - {move} args = delx dely delz - delx,dely,delz = distance to displace in each dimension (distance units) - any of delx,dely,delz can be a variable (see below) - {ramp} args = ddim dlo dhi dim clo chi - ddim = {x} or {y} or {z} - dlo,dhi = displacement distance between dlo and dhi (distance units) - dim = {x} or {y} or {z} - clo,chi = lower and upper bound of domain to displace (distance units) - {random} args = dx dy dz seed - dx,dy,dz = random displacement magnitude in each dimension (distance units) - seed = random # seed (positive integer) - {rotate} args = Px Py Pz Rx Ry Rz theta - Px,Py,Pz = origin point of axis of rotation (distance units) - Rx,Ry,Rz = axis of rotation vector - theta = angle of rotation (degrees) :pre - -zero or more keyword/value pairs may be appended :l - keyword = {units} - value = {box} or {lattice} :pre -:ule - -[Examples:] - -displace_atoms top move 0 -5 0 units box -displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5 :pre - -[Description:] - -Displace a group of atoms. This can be used to move atoms a large -distance before beginning a simulation or to randomize atoms initially -on a lattice. For example, in a shear simulation, an initial strain -can be imposed on the system. Or two groups of atoms can be brought -into closer proximity. - -The {move} style displaces the group of atoms by the specified 3d -displacement vector. Any of the 3 quantities defining the vector -components can be specified as an equal-style or atom-style -"variable"_variable.html. If the value is a variable, it should be -specified as v_name, where name is the variable name. In this case, -the variable will be evaluated, and its value(s) used for the -displacement(s). The scale factor implied by the {units} keyword will -also be applied to the variable result. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Atom-style variables can specify the same formulas as -equal-style variables but can also include per-atom values, such as -atom coordinates or per-atom values read from a file. Note that if -the variable references other "compute"_compute.html or "fix"_fix.html -commands, those values must be up-to-date for the current timestep. -See the "Variable Accuracy" section of the "variable"_variable.html -doc page for more details. - -The {ramp} style displaces atoms a variable amount in one dimension -depending on the atom's coordinate in a (possibly) different -dimension. For example, the second example command displaces atoms in -the x-direction an amount between 0.0 and 5.0 distance units. Each -atom's displacement depends on the fractional distance its y -coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside -those bounds will be moved the minimum (0.0) or maximum (5.0) amount. - -The {random} style independently moves each atom in the group by a -random displacement, uniformly sampled from a value between -dx and -+dx in the x dimension, and similarly for y and z. Random numbers are -used in such a way that the displacement of a particular atom is the -same, regardless of how many processors are being used. - -The {rotate} style rotates each atom in the group by the angle {theta} -around a rotation axis {R} = (Rx,Ry,Rz) that goes through a point {P} = -(Px,Py,Pz). The direction of rotation for the atoms around the -rotation axis is consistent with the right-hand rule: if your -right-hand thumb points along {R}, then your fingers wrap around the -axis in the direction of positive theta. - -If the defined "atom_style"_atom_style.html assigns an orientation to -each atom ("atom styles"_atom_style.html ellipsoid, line, tri, body), -then that property is also updated appropriately to correspond to the -atom's rotation. - -Distance units for displacements and the origin point of the {rotate} -style are determined by the setting of {box} or {lattice} for the -{units} keyword. {Box} means distance units as defined by the -"units"_units.html command - e.g. Angstroms for {real} units. -{Lattice} means distance units are in lattice spacings. The -"lattice"_lattice.html command must have been previously used to -define the lattice spacing. - -:line - -NOTE: Care should be taken not to move atoms on top of other atoms. -After the move, atoms are remapped into the periodic simulation box if -needed, and any shrink-wrap boundary conditions (see the -"boundary"_boundary.html command) are enforced which may change the -box size. Other than this effect, this command does not change the -size or shape of the simulation box. See the -"change_box"_change_box.html command if that effect is desired. - -NOTE: Atoms can be moved arbitrarily long distances by this command. -If the simulation box is non-periodic and shrink-wrapped (see the -"boundary"_boundary.html command), this can change its size or shape. -This is not a problem, except that the mapping of processors to the -simulation box is not changed by this command from its initial 3d -configuration; see the "processors"_processors.html command. Thus, if -the box size/shape changes dramatically, the mapping of processors to -the simulation box may not end up as optimal as the initial mapping -attempted to be. - -:line - -[Restrictions:] - -For a 2d simulation, only rotations around the a vector parallel to -the z-axis are allowed. - -[Related commands:] - -"lattice"_lattice.html, "change_box"_change_box.html, -"fix move"_fix_move.html - -[Default:] - -The option defaults are units = lattice. diff --git a/doc/txt/dump.txt b/doc/txt/dump.txt deleted file mode 100644 index 0d08fdf471..0000000000 --- a/doc/txt/dump.txt +++ /dev/null @@ -1,667 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dump command :h3 -"dump vtk"_dump_vtk.html command :h3 -"dump h5md"_dump_h5md.html command :h3 -"dump molfile"_dump_molfile.html command :h3 -"dump netcdf"_dump_netcdf.html command :h3 -"dump image"_dump_image.html command :h3 -"dump movie"_dump_image.html command :h3 -"dump adios"_dump_adios.html command :h3 - -[Syntax:] - -dump ID group-ID style N file args :pre - -ID = user-assigned name for the dump :ulb,l -group-ID = ID of the group of atoms to be dumped :l -style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or -{cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {local/gz} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l -N = dump every this many timesteps :l -file = name of file to write dump info to :l -args = list of arguments for a particular style :l - {atom} args = none - {atom/gz} args = none - {atom/mpiio} args = none - {atom/adios} args = none, discussed on "dump adios"_dump_adios.html doc page - {cfg} args = same as {custom} args, see below - {cfg/gz} args = same as {custom} args, see below - {cfg/mpiio} args = same as {custom} args, see below - {custom}, {custom/gz}, {custom/mpiio} args = see below - {custom/adios} args = same as {custom} args, discussed on "dump adios"_dump_adios.html doc page - {dcd} args = none - {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page - {image} args = discussed on "dump image"_dump_image.html doc page - {local} args = see below - {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page - {movie} args = discussed on "dump image"_dump_image.html doc page - {netcdf} args = discussed on "dump netcdf"_dump_netcdf.html doc page - {netcdf/mpiio} args = discussed on "dump netcdf"_dump_netcdf.html doc page - {vtk} args = same as {custom} args, see below, also "dump vtk"_dump_vtk.html doc page - {xtc} args = none - {xyz} args = none - {xyz/gz} args = none - {xyz/mpiio} args = none :pre - -{custom} or {custom/gz} or {custom/mpiio} or {netcdf} or {netcdf/mpiio} args = list of atom attributes :l - possible attributes = id, mol, proc, procp1, type, element, mass, - x, y, z, xs, ys, zs, xu, yu, zu, - xsu, ysu, zsu, ix, iy, iz, - vx, vy, vz, fx, fy, fz, - q, mux, muy, muz, mu, - radius, diameter, omegax, omegay, omegaz, - angmomx, angmomy, angmomz, tqx, tqy, tqz, - c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre - - id = atom ID - mol = molecule ID - proc = ID of processor that owns atom - procp1 = ID+1 of processor that owns atom - type = atom type - element = name of atom element, as defined by "dump_modify"_dump_modify.html command - mass = atom mass - x,y,z = unscaled atom coordinates - xs,ys,zs = scaled atom coordinates - xu,yu,zu = unwrapped atom coordinates - xsu,ysu,zsu = scaled unwrapped atom coordinates - ix,iy,iz = box image that the atom is in - vx,vy,vz = atom velocities - fx,fy,fz = forces on atoms - q = atom charge - mux,muy,muz = orientation of dipole moment of atom - mu = magnitude of dipole moment of atom - radius,diameter = radius,diameter of spherical particle - omegax,omegay,omegaz = angular velocity of spherical particle - angmomx,angmomy,angmomz = angular momentum of aspherical particle - tqx,tqy,tqz = torque on finite-size particles - c_ID = per-atom vector calculated by a compute with ID - c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) - f_ID = per-atom vector calculated by a fix with ID - f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) - v_name = per-atom vector calculated by an atom-style variable with name - d_name = per-atom floating point vector with name, managed by fix property/atom - i_name = per-atom integer vector with name, managed by fix property/atom :pre - -{local} args = list of local attributes :l - possible attributes = index, c_ID, c_ID\[I\], f_ID, f_ID\[I\] - index = enumeration of local values - c_ID = local vector calculated by a compute with ID - c_ID\[I\] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below) - f_ID = local vector calculated by a fix with ID - f_ID\[I\] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below) :pre - -:ule - -[Examples:] - -dump myDump all atom 100 dump.atom -dump myDump all atom/mpiio 100 dump.atom.mpiio -dump myDump all atom/gz 100 dump.atom.gz -dump 2 subgroup atom 50 dump.run.bin -dump 2 subgroup atom 50 dump.run.mpiio.bin -dump 4a all custom 100 dump.myforce.* id type x y vx fx -dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke -dump 4b flow custom 100 dump.%.myforce id type c_myF\[*\] v_ke -dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz -dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress\[2\] -dump 1 all xtc 1000 file.xtc :pre - -[Description:] - -Dump a snapshot of atom quantities to one or more files every N -timesteps in one of several styles. The {image} and {movie} styles are -the exception: the {image} style renders a JPG, PNG, or PPM image file -of the atom configuration every N timesteps while the {movie} style -combines and compresses them into a movie file; both are discussed in -detail on the "dump image"_dump_image.html doc page. The timesteps on -which dump output is written can also be controlled by a variable. -See the "dump_modify every"_dump_modify.html command. - -Only information for atoms in the specified group is dumped. The -"dump_modify thresh and region and refresh"_dump_modify.html commands -can also alter what atoms are included. Not all styles support -these options; see details on the "dump_modify"_dump_modify.html doc -page. - -As described below, the filename determines the kind of output (text -or binary or gzipped, one big file or one per timestep, one big file -or multiple smaller files). - -NOTE: Because periodic boundary conditions are enforced only on -timesteps when neighbor lists are rebuilt, the coordinates of an atom -written to a dump file may be slightly outside the simulation box. -Re-neighbor timesteps will not typically coincide with the timesteps -dump snapshots are written. See the "dump_modify -pbc"_dump_modify.html command if you with to force coordinates to be -strictly inside the simulation box. - -NOTE: Unless the "dump_modify sort"_dump_modify.html option is -invoked, the lines of atom information written to dump files -(typically one line per atom) will be in an indeterminate order for -each snapshot. This is even true when running on a single processor, -if the "atom_modify sort"_atom_modify.html option is on, which it is -by default. In this case atoms are re-ordered periodically during a -simulation, due to spatial sorting. It is also true when running in -parallel, because data for a single snapshot is collected from -multiple processors, each of which owns a subset of the atoms. - -For the {atom}, {custom}, {cfg}, and {local} styles, sorting is off by -default. For the {dcd}, {xtc}, {xyz}, and {molfile} styles, sorting by -atom ID is on by default. See the "dump_modify"_dump_modify.html doc -page for details. - -The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are identical -in command syntax to the corresponding styles without "gz", however, -they generate compressed files using the zlib library. Thus the filename -suffix ".gz" is mandatory. This is an alternative approach to writing -compressed files via a pipe, as done by the regular dump styles, which -may be required on clusters where the interface to the high-speed network -disallows using the fork() library call (which is needed for a pipe). -For the remainder of this doc page, you should thus consider the {atom} -and {atom/gz} styles (etc) to be inter-changeable, with the exception -of the required filename suffix. - -As explained below, the {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and -{xyz/mpiio} styles are identical in command syntax and in the format -of the dump files they create, to the corresponding styles without -"mpiio", except the single dump file they produce is written in -parallel via the MPI-IO library. For the remainder of this doc page, -you should thus consider the {atom} and {atom/mpiio} styles (etc) to -be inter-changeable. The one exception is how the filename is -specified for the MPI-IO styles, as explained below. - -The precision of values output to text-based dump files can be -controlled by the "dump_modify format"_dump_modify.html command and -its options. - -:line - -The {style} keyword determines what atom quantities are written to the -file and in what format. Settings made via the -"dump_modify"_dump_modify.html command can also alter the format of -individual values and the file itself. - -The {atom}, {local}, and {custom} styles create files in a simple text -format that is self-explanatory when viewing a dump file. Some of the -LAMMPS post-processing tools described on the "Tools"_Tools.html doc -page, including "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, -work with this format, as does the "rerun"_rerun.html command. - -For post-processing purposes the {atom}, {local}, and {custom} text -files are self-describing in the following sense. - -The dimensions of the simulation box are included in each snapshot. -For an orthogonal simulation box this information is formatted as: - -ITEM: BOX BOUNDS xx yy zz -xlo xhi -ylo yhi -zlo zhi :pre - -where xlo,xhi are the maximum extents of the simulation box in the -x-dimension, and similarly for y and z. The "xx yy zz" represent 6 -characters that encode the style of boundary for each of the 6 -simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each of -the 6 characters is either p = periodic, f = fixed, s = shrink wrap, -or m = shrink wrapped with a minimum value. See the -"boundary"_boundary.html command for details. - -For triclinic simulation boxes (non-orthogonal), an orthogonal -bounding box which encloses the triclinic simulation box is output, -along with the 3 tilt factors (xy, xz, yz) of the triclinic box, -formatted as follows: - -ITEM: BOX BOUNDS xy xz yz xx yy zz -xlo_bound xhi_bound xy -ylo_bound yhi_bound xz -zlo_bound zhi_bound yz :pre - -The presence of the text "xy xz yz" in the ITEM line indicates that -the 3 tilt factors will be included on each of the 3 following lines. -This bounding box is convenient for many visualization programs. The -meaning of the 6 character flags for "xx yy zz" is the same as above. - -Note that the first two numbers on each line are now xlo_bound instead -of xlo, etc, since they represent a bounding box. See the "Howto -triclinic"_Howto_triclinic.html doc page for a geometric description -of triclinic boxes, as defined by LAMMPS, simple formulas for how the -6 bounding box extents (xlo_bound,xhi_bound,etc) are calculated from -the triclinic parameters, and how to transform those parameters to and -from other commonly used triclinic representations. - -The "ITEM: ATOMS" line in each snapshot lists column descriptors for -the per-atom lines that follow. For example, the descriptors would be -"id type xs ys zs" for the default {atom} style, and would be the atom -attributes you specify in the dump command for the {custom} style. - -For style {atom}, atom coordinates are written to the file, along with -the atom ID and atom type. By default, atom coords are written in a -scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom -is at a location 1/4 of the distance from xlo to xhi of the box -boundaries. The format can be changed to unscaled coords via the -"dump_modify"_dump_modify.html settings. Image flags can also be -added for each atom via dump_modify. - -Style {custom} allows you to specify a list of atom attributes to be -written to the dump file for each atom. Possible attributes are -listed above and will appear in the order specified. You cannot -specify a quantity that is not defined for a particular simulation - -such as {q} for atom style {bond}, since that atom style doesn't -assign charges. Dumps occur at the very end of a timestep, so atom -attributes will include effects due to fixes that are applied during -the timestep. An explanation of the possible dump custom attributes -is given below. - -For style {local}, local output generated by "computes"_compute.html -and "fixes"_fix.html is used to generate lines of output that is -written to the dump file. This local data is typically calculated by -each processor based on the atoms it owns, but there may be zero or -more entities per atom, e.g. a list of bond distances. An explanation -of the possible dump local attributes is given below. Note that by -using input from the "compute -property/local"_compute_property_local.html command with dump local, -it is possible to generate information on bonds, angles, etc that can -be cut and pasted directly into a data file read by the -"read_data"_read_data.html command. - -Style {cfg} has the same command syntax as style {custom} and writes -extended CFG format files, as used by the -"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualization -package. Since the extended CFG format uses a single snapshot of the -system per file, a wildcard "*" must be included in the filename, as -discussed below. The list of atom attributes for style {cfg} must -begin with either "mass type xs ys zs" or "mass type xsu ysu zsu" -since these quantities are needed to write the CFG files in the -appropriate format (though the "mass" and "type" fields do not appear -explicitly in the file). Any remaining attributes will be stored as -"auxiliary properties" in the CFG files. Note that you will typically -want to use the "dump_modify element"_dump_modify.html command with -CFG-formatted files, to associate element names with atom types, so -that AtomEye can render atoms appropriately. When unwrapped -coordinates {xsu}, {ysu}, and {zsu} are requested, the nominal AtomEye -periodic cell dimensions are expanded by a large factor UNWRAPEXPAND = -10.0, which ensures atoms that are displayed correctly for up to -UNWRAPEXPAND/2 periodic boundary crossings in any direction. Beyond -this, AtomEye will rewrap the unwrapped coordinates. The expansion -causes the atoms to be drawn farther away from the viewer, but it is -easy to zoom the atoms closer, and the interatomic distances are -unaffected. - -The {dcd} style writes DCD files, a standard atomic trajectory format -used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD -files are binary and thus may not be portable to different machines. -The number of atoms per snapshot cannot change with the {dcd} style. -The {unwrap} option of the "dump_modify"_dump_modify.html command -allows DCD coordinates to be written "unwrapped" by the image flags -for each atom. Unwrapped means that if the atom has passed through -a periodic boundary one or more times, the value is printed for what -the coordinate would be if it had not been wrapped back into the -periodic box. Note that these coordinates may thus be far outside -the box size stored with the snapshot. - -The {xtc} style writes XTC files, a compressed trajectory format used -by the GROMACS molecular dynamics package, and described -"here"_http://manual.gromacs.org/current/online/xtc.html. -The precision used in XTC files can be adjusted via the -"dump_modify"_dump_modify.html command. The default value of 1000 -means that coordinates are stored to 1/1000 nanometer accuracy. XTC -files are portable binary files written in the NFS XDR data format, -so that any machine which supports XDR should be able to read them. -The number of atoms per snapshot cannot change with the {xtc} style. -The {unwrap} option of the "dump_modify"_dump_modify.html command allows -XTC coordinates to be written "unwrapped" by the image flags for each -atom. Unwrapped means that if the atom has passed through a periodic -boundary one or more times, the value is printed for what the -coordinate would be if it had not been wrapped back into the periodic -box. Note that these coordinates may thus be far outside the box size -stored with the snapshot. - -The {xyz} style writes XYZ files, which is a simple text-based -coordinate format that many codes can read. Specifically it has -a line with the number of atoms, then a comment line that is -usually ignored followed by one line per atom with the atom type -and the x-, y-, and z-coordinate of that atom. You can use the -"dump_modify element"_dump_modify.html option to change the output -from using the (numerical) atom type to an element name (or some -other label). This will help many visualization programs to guess -bonds and colors. - -Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files -can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a -popular molecular viewing program. - -:line - -Dumps are performed on timesteps that are a multiple of N (including -timestep 0) and on the last timestep of a minimization if the -minimization converges. Note that this means a dump will not be -performed on the initial timestep after the dump command is invoked, -if the current timestep is not a multiple of N. This behavior can be -changed via the "dump_modify first"_dump_modify.html command, which -can also be useful if the dump command is invoked after a minimization -ended on an arbitrary timestep. N can be changed between runs by -using the "dump_modify every"_dump_modify.html command (not allowed -for {dcd} style). The "dump_modify every"_dump_modify.html command -also allows a variable to be used to determine the sequence of -timesteps on which dump files are written. In this mode a dump on the -first timestep of a run will also not be written unless the -"dump_modify first"_dump_modify.html command is used. - -The specified filename determines how the dump file(s) is written. -The default is to write one large text file, which is opened when the -dump command is invoked and closed when an "undump"_undump.html -command is used or when LAMMPS exits. For the {dcd} and {xtc} styles, -this is a single large binary file. - -Dump filenames can contain two wildcard characters. If a "*" -character appears in the filename, then one file per snapshot is -written and the "*" character is replaced with the timestep value. -For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000, -tmp.dump.20000, etc. This option is not available for the {dcd} and -{xtc} styles. Note that the "dump_modify pad"_dump_modify.html -command can be used to insure all timestep numbers are the same length -(e.g. 00010), which can make it easier to read a series of dump files -in order with some post-processing tools. - -If a "%" character appears in the filename, then each of P processors -writes a portion of the dump file, and the "%" character is replaced -with the processor ID from 0 to P-1. For example, tmp.dump.% becomes -tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc. This creates smaller -files and can be a fast mode of output on parallel machines that -support parallel I/O for output. This option is not available for the -{dcd}, {xtc}, and {xyz} styles. - -By default, P = the number of processors meaning one file per -processor, but P can be set to a smaller value via the {nfile} or -{fileper} keywords of the "dump_modify"_dump_modify.html command. -These options can be the most efficient way of writing out dump files -when running on large numbers of processors. - -Note that using the "*" and "%" characters together can produce a -large number of small dump files! - -For the {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and {xyz/mpiio} -styles, a single dump file is written in parallel via the MPI-IO -library, which is part of the MPI standard for versions 2.0 and above. -Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO -package installed, e.g. - -make yes-mpiio # installs the MPIIO package -make mpi # build LAMMPS for your platform :pre - -Second, use a dump filename which contains ".mpiio". Note that it -does not have to end in ".mpiio", just contain those characters. -Unlike MPI-IO restart files, which must be both written and read using -MPI-IO, the dump files produced by these MPI-IO styles are identical -in format to the files produced by their non-MPI-IO style -counterparts. This means you can write a dump file using MPI-IO and -use the "read_dump"_read_dump.html command or perform other -post-processing, just as if the dump file was not written using -MPI-IO. - -Note that MPI-IO dump files are one large file which all processors -write to. You thus cannot use the "%" wildcard character described -above in the filename since that specifies generation of multiple -files. You can use the ".bin" suffix described below in an MPI-IO -dump file; again this file will be written in parallel and have the -same binary format as if it were written without MPI-IO. - -If the filename ends with ".bin", the dump file (or files, if "*" or -"%" is also used) is written in binary format. A binary dump file -will be about the same size as a text version, but will typically -write out much faster. Of course, when post-processing, you will need -to convert it back to text format (see the "binary2txt -tool"_Tools.html#binary) or write your own code to read the binary -file. The format of the binary file can be understood by looking at -the tools/binary2txt.cpp file. This option is only available for the -{atom} and {custom} styles. - -If the filename ends with ".gz", the dump file (or files, if "*" or "%" -is also used) is written in gzipped format. A gzipped dump file will -be about 3x smaller than the text version, but will also take longer -to write. This option is not available for the {dcd} and {xtc} -styles. - -:line - -Note that in the discussion which follows, for styles which can -reference values from a compute or fix, like the {custom}, {cfg}, or -{local} styles, the bracketed index I can be specified using a -wildcard asterisk with the index to effectively specify multiple -values. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -size of the vector (for {mode} = scalar) or the number of columns in -the array (for {mode} = vector), then an asterisk with no numeric -values means all indices from 1 to N. A leading asterisk means all -indices from 1 to n (inclusive). A trailing asterisk means all -indices from n to N (inclusive). A middle asterisk means all indices -from m to n (inclusive). - -Using a wildcard is the same as if the individual columns of the array -had been listed one by one. E.g. these 2 dump commands are -equivalent, since the "compute stress/atom"_compute_stress_atom.html -command creates a per-atom array with 6 columns: - -compute myPress all stress/atom NULL -dump 2 all custom 100 tmp.dump id myPress\[*\] -dump 2 all custom 100 tmp.dump id myPress\[1\] myPress\[2\] myPress\[3\] & - myPress\[4\] myPress\[5\] myPress\[6\] :pre - -:line - -This section explains the local attributes that can be specified as -part of the {local} style. - -The {index} attribute can be used to generate an index number from 1 -to N for each line written into the dump file, where N is the total -number of local datums from all processors, or lines of output that -will appear in the snapshot. Note that because data from different -processors depend on what atoms they currently own, and atoms migrate -between processor, there is no guarantee that the same index will be -used for the same info (e.g. a particular bond) in successive -snapshots. - -The {c_ID} and {c_ID\[I\]} attributes allow local vectors or arrays -calculated by a "compute"_compute.html to be output. The ID in the -attribute should be replaced by the actual ID of the compute that has -been defined previously in the input script. See the -"compute"_compute.html command for details. There are computes for -calculating local information such as indices, types, and energies for -bonds and angles. - -Note that computes which calculate global or per-atom quantities, as -opposed to local quantities, cannot be output in a dump local command. -Instead, global quantities can be output by the "thermo_style -custom"_thermo_style.html command, and per-atom quantities can be -output by the dump custom command. - -If {c_ID} is used as a attribute, then the local vector calculated by -the compute is printed. If {c_ID\[I\]} is used, then I must be in the -range from 1-M, which will print the Ith column of the local array -with M columns calculated by the compute. See the discussion above -for how I can be specified with a wildcard asterisk to effectively -specify multiple values. - -The {f_ID} and {f_ID\[I\]} attributes allow local vectors or arrays -calculated by a "fix"_fix.html to be output. The ID in the attribute -should be replaced by the actual ID of the fix that has been defined -previously in the input script. - -If {f_ID} is used as a attribute, then the local vector calculated by -the fix is printed. If {f_ID\[I\]} is used, then I must be in the -range from 1-M, which will print the Ith column of the local with M -columns calculated by the fix. See the discussion above for how I can -be specified with a wildcard asterisk to effectively specify multiple -values. - -Here is an example of how to dump bond info for a system, including -the distance and energy of each bond: - -compute 1 all property/local batom1 batom2 btype -compute 2 all bond/local dist eng -dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_2\[1\] c_2\[2\] :pre - -:line - -This section explains the atom attributes that can be specified as -part of the {custom} and {cfg} styles. - -The {id}, {mol}, {proc}, {procp1}, {type}, {element}, {mass}, {vx}, -{vy}, {vz}, {fx}, {fy}, {fz}, {q} attributes are self-explanatory. - -{Id} is the atom ID. {Mol} is the molecule ID, included in the data -file for molecular systems. {Proc} is the ID of the processor (0 to -Nprocs-1) that currently owns the atom. {Procp1} is the proc ID+1, -which can be convenient in place of a {type} attribute (1 to Ntypes) -for coloring atoms in a visualization program. {Type} is the atom -type (1 to Ntypes). {Element} is typically the chemical name of an -element, which you must assign to each type via the "dump_modify -element"_dump_modify.html command. More generally, it can be any -string you wish to associated with an atom type. {Mass} is the atom -mass. {Vx}, {vy}, {vz}, {fx}, {fy}, {fz}, and {q} are components of -atom velocity and force and atomic charge. - -There are several options for outputting atom coordinates. The {x}, -{y}, {z} attributes write atom coordinates "unscaled", in the -appropriate distance "units"_units.html (Angstroms, sigma, etc). Use -{xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size, -so that each value is 0.0 to 1.0. If the simulation box is triclinic -(tilted), then all atom coords will still be between 0.0 and 1.0. -I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are -the non-orthogonal vectors of the simulation box edges, as discussed -on the "Howto triclinic"_Howto_triclinic.html doc page. - -Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the -image flags for each atom. Unwrapped means that if the atom has -passed through a periodic boundary one or more times, the value is -printed for what the coordinate would be if it had not been wrapped -back into the periodic box. Note that using {xu}, {yu}, {zu} means -that the coordinate values may be far outside the box bounds printed -with the snapshot. Using {xsu}, {ysu}, {zsu} is similar to using -{xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by -the box size. Atoms that have passed through a periodic boundary will -have the corresponding coordinate increased or decreased by 1.0. - -The image flags can be printed directly using the {ix}, {iy}, {iz} -attributes. For periodic dimensions, they specify which image of the -simulation box the atom is considered to be in. An image of 0 means -it is inside the box as defined. A value of 2 means add 2 box lengths -to get the true value. A value of -1 means subtract 1 box length to -get the true value. LAMMPS updates these flags as atoms cross -periodic boundaries during the simulation. - -The {mux}, {muy}, {muz} attributes are specific to dipolar systems -defined with an atom style of {dipole}. They give the orientation of -the atom's point dipole moment. The {mu} attribute gives the -magnitude of the atom's dipole moment. - -The {radius} and {diameter} attributes are specific to spherical -particles that have a finite size, such as those defined with an atom -style of {sphere}. - -The {omegax}, {omegay}, and {omegaz} attributes are specific to -finite-size spherical particles that have an angular velocity. Only -certain atom styles, such as {sphere} define this quantity. - -The {angmomx}, {angmomy}, and {angmomz} attributes are specific to -finite-size aspherical particles that have an angular momentum. Only -the {ellipsoid} atom style defines this quantity. - -The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that -can sustain a rotational torque due to interactions with other -particles. - -The {c_ID} and {c_ID\[I\]} attributes allow per-atom vectors or arrays -calculated by a "compute"_compute.html to be output. The ID in the -attribute should be replaced by the actual ID of the compute that has -been defined previously in the input script. See the -"compute"_compute.html command for details. There are computes for -calculating the per-atom energy, stress, centro-symmetry parameter, -and coordination number of individual atoms. - -Note that computes which calculate global or local quantities, as -opposed to per-atom quantities, cannot be output in a dump custom -command. Instead, global quantities can be output by the -"thermo_style custom"_thermo_style.html command, and local quantities -can be output by the dump local command. - -If {c_ID} is used as a attribute, then the per-atom vector calculated -by the compute is printed. If {c_ID\[I\]} is used, then I must be in -the range from 1-M, which will print the Ith column of the per-atom -array with M columns calculated by the compute. See the discussion -above for how I can be specified with a wildcard asterisk to -effectively specify multiple values. - -The {f_ID} and {f_ID\[I\]} attributes allow vector or array per-atom -quantities calculated by a "fix"_fix.html to be output. The ID in the -attribute should be replaced by the actual ID of the fix that has been -defined previously in the input script. The "fix -ave/atom"_fix_ave_atom.html command is one that calculates per-atom -quantities. Since it can time-average per-atom quantities produced by -any "compute"_compute.html, "fix"_fix.html, or atom-style -"variable"_variable.html, this allows those time-averaged results to -be written to a dump file. - -If {f_ID} is used as a attribute, then the per-atom vector calculated -by the fix is printed. If {f_ID\[I\]} is used, then I must be in the -range from 1-M, which will print the Ith column of the per-atom array -with M columns calculated by the fix. See the discussion above for -how I can be specified with a wildcard asterisk to effectively specify -multiple values. - -The {v_name} attribute allows per-atom vectors calculated by a -"variable"_variable.html to be output. The name in the attribute -should be replaced by the actual name of the variable that has been -defined previously in the input script. Only an atom-style variable -can be referenced, since it is the only style that generates per-atom -values. Variables of style {atom} can reference individual atom -attributes, per-atom attributes, thermodynamic keywords, or -invoke other computes, fixes, or variables when they are evaluated, so -this is a very general means of creating quantities to output to a -dump file. - -The {d_name} and {i_name} attributes allow to output custom per atom -floating point or integer properties that are managed by -"fix property/atom"_fix_property_atom.html. - -See the "Modify"_Modify.html doc page for information on how to add -new compute and fix styles to LAMMPS to calculate per-atom quantities -which could then be output into dump files. - -:line - -[Restrictions:] - -To write gzipped dump files, you must either compile LAMMPS with the --DLAMMPS_GZIP option or use the styles from the COMPRESS package. -See the "Build settings"_Build_settings.html doc page for details. - -The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are part of -the COMPRESS package. They are only enabled if LAMMPS was built with -that package. See the "Build package"_Build_package.html doc page for -more info. - -The {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and {xyz/mpiio} styles -are part of the MPIIO package. They are only enabled if LAMMPS was -built with that package. See the "Build package"_Build_package.html -doc page for more info. - -The {xtc} style is part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"dump adios"_dump_adios.html "dump h5md"_dump_h5md.html, "dump image"_dump_image.html, -"dump molfile"_dump_molfile.html, "dump_modify"_dump_modify.html, -"undump"_undump.html - -[Default:] - -The defaults for the {image} and {movie} styles are listed on the -"dump image"_dump_image.html doc page. diff --git a/doc/txt/dump_adios.txt b/doc/txt/dump_adios.txt deleted file mode 100644 index e3c919db5a..0000000000 --- a/doc/txt/dump_adios.txt +++ /dev/null @@ -1,73 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dump atoms/adios command :h3 -dump custom/adios command :h3 - -[Syntax:] - -dump ID group-ID atoms/adios N file.bp :pre -dump ID group-ID custom/adios N file.bp args :pre - -ID = user-assigned name for the dump :ulb,l -group-ID = ID of the group of atoms to be imaged :l -adios = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l -N = dump every this many timesteps :l -file.bp = name of file/stream to write to :l -args = same options as in "{dump custom}"_dump.html command :l -:ule - - -[Examples:] - -dump adios1 all atom/adios 100 atoms.bp -dump 4a all custom/adios 100 dump_adios.bp id v_p x y z -dump 2 subgroup custom/adios 100 dump_adios.bp mass type xs ys zs vx vy vz :pre - -[Description:] - -Dump a snapshot of atom coordinates every N timesteps in the -"ADIOS"_adios based "BP" file format, or using different I/O solutions in ADIOS, -to a stream that can be read on-line by another program. -ADIOS-BP files are binary, portable and self-describing. - -:link(adios,https://github.com/ornladios/ADIOS2) - - -[Use from write_dump:] - -It is possible to use these dump styles with the -"write_dump"_write_dump.html command. In this case, the sub-intervals -must not be set at all. The write_dump command can be used to -create a new file at each individual dump. - -dump 4 all atom/adios 100 dump.bp -write_dump all atom/adios singledump.bp :pre - -:line - -[Restrictions:] - -The number of atoms per snapshot CAN change with the adios style. -When using the ADIOS tool 'bpls' to list the content of a .bp file, -bpls will print {__} for the size of the output table indicating that -its size is changing every step. - -The {atom/adios} and {custom/adios} dump styles are part of the USER-ADIOS -package. They are only enabled if LAMMPS was built with that package. -See the "Build package"_Build_package.html doc page for more info. - - -:line - -[Related commands:] - -"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html - -:line - diff --git a/doc/txt/dump_cfg_uef.txt b/doc/txt/dump_cfg_uef.txt deleted file mode 100644 index ca43b0b6ea..0000000000 --- a/doc/txt/dump_cfg_uef.txt +++ /dev/null @@ -1,53 +0,0 @@ - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dump cfg/uef command :h3 - -[Syntax:] - -dump ID group-ID cfg/uef N file mass type xs ys zs args :pre - -ID = user-assigned name for the dump :ulb,l -group-ID = ID of the group of atoms to be dumped :l -N = dump every this many timesteps :l -file = name of file to write dump info to :l -args = same as args for "dump custom"_dump.html :pre - -:ule - -[Examples:] - -dump 1 all cfg/uef 10 dump.*.cfg mass type xs ys zs -dump 2 all cfg/uef 100 dump.*.cfg mass type xs ys zs id c_stress :pre - -[Description:] - -This command is used to dump atomic coordinates in the -reference frame of the applied flow field when -"fix nvt/uef"_fix_nh_uef.html or -"fix npt/uef"_fix_nh_uef.html or is used. Only the atomic -coordinates and frame-invariant scalar quantities -will be in the flow frame. If velocities are selected -as output, for example, they will not be in the same -reference frame as the atomic positions. - -[Restrictions:] - -This fix is part of the USER-UEF package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This command can only be used when "fix nvt/uef"_fix_nh_uef.html -or "fix npt/uef"_fix_nh_uef.html is active. - -[Related commands:] - -"dump"_dump.html, -"fix nvt/uef"_fix_nh_uef.html - -[Default:] none diff --git a/doc/txt/dump_h5md.txt b/doc/txt/dump_h5md.txt deleted file mode 100644 index 6e9e7284df..0000000000 --- a/doc/txt/dump_h5md.txt +++ /dev/null @@ -1,123 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dump h5md command :h3 - -[Syntax:] - -dump ID group-ID h5md N file.h5 args :pre - -ID = user-assigned name for the dump :ulb,l -group-ID = ID of the group of atoms to be imaged :l -h5md = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l -N = dump every this many timesteps :l -file.h5 = name of file to write to :l -args = list of data elements to dump, with their dump "sub-intervals" - position options - image - velocity options - force options - species options - file_from ID: do not open a new file, re-use the already opened file from dump ID - box value = {yes} or {no} - create_group value = {yes} or {no} - author value = quoted string :pre -:ule - -Note that at least one element must be specified and image may only be -present if position is specified first. - -For the elements {position}, {velocity}, {force} and {species}, a -sub-interval may be specified to write the data only every N_element -iterations of the dump (i.e. every N*N_element time steps). This is -specified by this option directly following the element declaration: - -every N_element :pre - -:ule - -[Examples:] - -dump h5md1 all h5md 100 dump_h5md.h5 position image -dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10 -dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe" :pre - -[Description:] - -Dump a snapshot of atom coordinates every N timesteps in the -"HDF5"_HDF5-ws based "H5MD"_h5md file format "(de Buyl)"_#h5md_cpc. -HDF5 files are binary, portable and self-describing. This dump style -will write only one file, on the root node. - -Several dumps may write to the same file, by using file_from and -referring to a previously defined dump. Several groups may also be -stored within the same file by defining several dumps. A dump that -refers (via {file_from}) to an already open dump ID and that concerns -another particle group must specify {create_group yes}. - -:link(h5md,http://nongnu.org/h5md/) - -Each data element is written every N*N_element steps. For {image}, no -sub-interval is needed as it must be present at the same interval as -{position}. {image} must be given after {position} in any case. The -box information (edges in each dimension) is stored at the same -interval than the {position} element, if present. Else it is stored -every N steps. - -NOTE: Because periodic boundary conditions are enforced only on -timesteps when neighbor lists are rebuilt, the coordinates of an atom -written to a dump file may be slightly outside the simulation box. - -[Use from write_dump:] - -It is possible to use this dump style with the -"write_dump"_write_dump.html command. In this case, the sub-intervals -must not be set at all. The write_dump command can be used either to -create a new file or to add current data to an existing dump file by -using the {file_from} keyword. - -Typically, the {species} data is fixed. The following two commands -store the position data every 100 timesteps, with the image data, and -store once the species data in the same file. - -dump h5md1 all h5md 100 dump.h5 position image -write_dump all h5md dump.h5 file_from h5md1 species :pre - -:line - -[Restrictions:] - -The number of atoms per snapshot cannot change with the h5md style. -The position data is stored wrapped (box boundaries not enforced, see -note above). Only orthogonal domains are currently supported. This is -a limitation of the present dump h5md command and not of H5MD itself. - -The {h5md} dump style is part of the USER-H5MD package. It is only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. It also requires -(i) building the ch5md library provided with LAMMPS (See the "Build -package"_Build_package.html doc page for more info.) and (ii) having -the "HDF5"_HDF5-ws library installed (C bindings are sufficient) on -your system. The library ch5md is compiled with the h5cc wrapper -provided by the HDF5 library. - -:link(HDF5-ws,http://www.hdfgroup.org/HDF5/) - -:line - -[Related commands:] - -"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html - -:line - -:link(h5md_cpc) -[(de Buyl)] de Buyl, Colberg and Hofling, H5MD: A structured, -efficient, and portable file format for molecular data, -Comp. Phys. Comm. 185(6), 1546-1553 (2014) - -"\[arXiv:1308.6382\]"_http://arxiv.org/abs/1308.6382/. diff --git a/doc/txt/dump_image.txt b/doc/txt/dump_image.txt deleted file mode 100644 index 2b10e9f230..0000000000 --- a/doc/txt/dump_image.txt +++ /dev/null @@ -1,674 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dump image command :h3 -dump movie command :h3 - -[Syntax:] - -dump ID group-ID style N file color diameter keyword value ... :pre - -ID = user-assigned name for the dump :ulb,l -group-ID = ID of the group of atoms to be imaged :l -style = {image} or {movie} = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l -N = dump every this many timesteps :l -file = name of file to write image to :l -color = atom attribute that determines color of each atom :l -diameter = atom attribute that determines size of each atom :l -zero or more keyword/value pairs may be appended :l -keyword = {atom} or {adiam} or {bond} or {line} or {tri} or {body} or {fix} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {axes} or {subbox} or {shiny} or {ssao} :l - {atom} = yes/no = do or do not draw atoms - {adiam} size = numeric value for atom diameter (distance units) - {bond} values = color width = color and width of bonds - color = {atom} or {type} or {none} - width = number or {atom} or {type} or {none} - number = numeric value for bond width (distance units) - {line} = color width - color = {type} - width = numeric value for line width (distance units) - {tri} = color tflag width - color = {type} - tflag = 1 for just triangle, 2 for just tri edges, 3 for both - width = numeric value for tringle edge width (distance units) - {body} = color bflag1 bflag2 - color = {type} - bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn - {fix} = fixID color fflag1 fflag2 - fixID = ID of fix that generates objects to dray - color = {type} - fflag1,fflag2 = 2 numeric flags to affect how fix objects are drawn - {size} values = width height = size of images - width = width of image in # of pixels - height = height of image in # of pixels - {view} values = theta phi = view of simulation box - theta = view angle from +z axis (degrees) - phi = azimuthal view angle (degrees) - theta or phi can be a variable (see below) - {center} values = flag Cx Cy Cz = center point of image - flag = "s" for static, "d" for dynamic - Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box) - Cx,Cy,Cz can be variables (see below) - {up} values = Ux Uy Uz = direction that is "up" in image - Ux,Uy,Uz = components of up vector - Ux,Uy,Uz can be variables (see below) - {zoom} value = zfactor = size that simulation box appears in image - zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink - zfactor can be a variable (see below) - {persp} value = pfactor = amount of "perspective" in image - pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed) - pfactor can be a variable (see below) - {box} values = yes/no diam = draw outline of simulation box - yes/no = do or do not draw simulation box lines - diam = diameter of box lines as fraction of shortest box length - {axes} values = yes/no length diam = draw xyz axes - yes/no = do or do not draw xyz axes lines next to simulation box - length = length of axes lines as fraction of respective box lengths - diam = diameter of axes lines as fraction of shortest box length - {subbox} values = yes/no diam = draw outline of processor sub-domains - yes/no = do or do not draw sub-domain lines - diam = diameter of sub-domain lines as fraction of shortest box length - {shiny} value = sfactor = shinyness of spheres and cylinders - sfactor = shinyness of spheres and cylinders from 0.0 to 1.0 - {ssao} value = yes/no seed dfactor = SSAO depth shading - yes/no = turn depth shading on/off - seed = random # seed (positive integer) - dfactor = strength of shading from 0.0 to 1.0 :pre -:ule - -[Examples:] - -dump d0 all image 100 dump.*.jpg type type -dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6 -dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720 -dump m0 all movie 1000 movie.mpg type type size 640 480 -dump m1 all movie 1000 movie.avi type type size 640 480 -dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720 :pre - -[Description:] - -Dump a high-quality rendered image of the atom configuration every N -timesteps and save the images either as a sequence of JPEG or PNG or -PPM files, or as a single movie file. The options for this command as -well as the "dump_modify"_dump_modify.html command control what is -included in the image or movie and how it appears. A series of such -images can easily be manually converted into an animated movie of your -simulation or the process can be automated without writing the -intermediate files using the dump movie style; see further details -below. Other dump styles store snapshots of numerical data associated -with atoms in various formats, as discussed on the "dump"_dump.html -doc page. - -Note that a set of images or a movie can be made after a simulation -has been run, using the "rerun"_rerun.html command to read snapshots -from an existing dump file, and using these dump commands in the rerun -script to generate the images/movie. - -Here are two sample images, rendered as 1024x1024 JPEG files. Click -to see the full-size images: - -
- -:image(JPG/dump1_small.jpg,JPG/dump1.jpg) -:image(JPG/dump2_small.jpg,JPG/dump2.jpg) - -
- -Only atoms in the specified group are rendered in the image. The -"dump_modify region and thresh"_dump_modify.html commands can also -alter what atoms are included in the image.\ - -The filename suffix determines whether a JPEG, PNG, or PPM file is -created with the {image} dump style. If the suffix is ".jpg" or -".jpeg", then a JPEG format file is created, if the suffix is ".png", -then a PNG format is created, else a PPM (aka NETPBM) format file is -created. The JPEG and PNG files are binary; PPM has a text mode -header followed by binary data. JPEG images have lossy compression; -PNG has lossless compression; and PPM files are uncompressed but can -be compressed with gzip, if LAMMPS has been compiled with --DLAMMPS_GZIP and a ".gz" suffix is used. - -Similarly, the format of the resulting movie is chosen with the -{movie} dump style. This is handled by the underlying FFmpeg converter -and thus details have to be looked up in the FFmpeg documentation. -Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif -Additional settings of the movie compression like bitrate and -framerate can be set using the "dump_modify"_dump_modify.html command. - -To write out JPEG and PNG format files, you must build LAMMPS with -support for the corresponding JPEG or PNG library. To convert images -into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG -flag. See the "Build settings"_Build_settings.html doc page for -details. - -NOTE: Because periodic boundary conditions are enforced only on -timesteps when neighbor lists are rebuilt, the coordinates of an atom -in the image may be slightly outside the simulation box. - -:line - -Dumps are performed on timesteps that are a multiple of N (including -timestep 0) and on the last timestep of a minimization if the -minimization converges. Note that this means a dump will not be -performed on the initial timestep after the dump command is invoked, -if the current timestep is not a multiple of N. This behavior can be -changed via the "dump_modify first"_dump_modify.html command, which -can be useful if the dump command is invoked after a minimization -ended on an arbitrary timestep. N can be changed between runs by -using the "dump_modify every"_dump_modify.html command. - -Dump {image} filenames must contain a wildcard character "*", so that -one image file per snapshot is written. The "*" character is replaced -with the timestep value. For example, tmp.dump.*.jpg becomes -tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note -that the "dump_modify pad"_dump_modify.html command can be used to -insure all timestep numbers are the same length (e.g. 00010), which -can make it easier to convert a series of images into a movie in the -correct ordering. - -Dump {movie} filenames on the other hand, must not have any wildcard -character since only one file combining all images into a single -movie will be written by the movie encoder. - -:line - -The {color} and {diameter} settings determine the color and size of -atoms rendered in the image. They can be any atom attribute defined -for the "dump custom"_dump.html command, including {type} and -{element}. This includes per-atom quantities calculated by a -"compute"_compute.html, "fix"_fix.html, or "variable"_variable.html, -which are prefixed by "c_", "f_", or "v_" respectively. Note that the -{diameter} setting can be overridden with a numeric value applied to -all atoms by the optional {adiam} keyword. - -If {type} is specified for the {color} setting, then the color of each -atom is determined by its atom type. By default the mapping of types -to colors is as follows: - -type 1 = red -type 2 = green -type 3 = blue -type 4 = yellow -type 5 = aqua -type 6 = cyan :ul - -and repeats itself for types > 6. This mapping can be changed by the -"dump_modify acolor"_dump_modify.html command. - -If {type} is specified for the {diameter} setting then the diameter of -each atom is determined by its atom type. By default all types have -diameter 1.0. This mapping can be changed by the "dump_modify -adiam"_dump_modify.html command. - -If {element} is specified for the {color} and/or {diameter} setting, -then the color and/or diameter of each atom is determined by which -element it is, which in turn is specified by the element-to-type -mapping specified by the "dump_modify element" command. By default -every atom type is C (carbon). Every element has a color and diameter -associated with it, which is the same as the colors and sizes used by -the "AtomEye"_atomeye visualization package. - -:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) - -If other atom attributes are used for the {color} or {diameter} -settings, they are interpreted in the following way. - -If "vx", for example, is used as the {color} setting, then the color -of the atom will depend on the x-component of its velocity. The -association of a per-atom value with a specific color is determined by -a "color map", which can be specified via the -"dump_modify"_dump_modify.html command. The basic idea is that the -atom-attribute will be within a range of values, and every value -within the range is mapped to a specific color. Depending on how the -color map is defined, that mapping can take place via interpolation so -that a value of -3.2 is halfway between "red" and "blue", or -discretely so that the value of -3.2 is "orange". - -If "vx", for example, is used as the {diameter} setting, then the atom -will be rendered using the x-component of its velocity as the -diameter. If the per-atom value <= 0.0, them the atom will not be -drawn. Note that finite-size spherical particles, as defined by -"atom_style sphere"_atom_style.html define a per-particle radius or -diameter, which can be used as the {diameter} setting. - -:line - -The various keywords listed above control how the image is rendered. -As listed below, all of the keywords have defaults, most of which you -will likely not need to change. The "dump modify"_dump_modify.html -also has options specific to the dump image style, particularly for -assigning colors to atoms, bonds, and other image features. - -:line - -The {atom} keyword allow you to turn off the drawing of all atoms, if -the specified value is {no}. Note that this will not turn off the -drawing of particles that are represented as lines, triangles, or -bodies, as discussed below. These particles can be drawn separately -if the {line}, {tri}, or {body} keywords are used. - -The {adiam} keyword allows you to override the {diameter} setting to -set a single numeric {size}. All atoms will be drawn with that -diameter, e.g. 1.5, which is in whatever distance "units"_units.html -the input script defines, e.g. Angstroms. - -:line - -The {bond} keyword allows to you to alter how bonds are drawn. A bond -is only drawn if both atoms in the bond are being drawn due to being -in the specified group and due to other selection criteria -(e.g. region, threshold settings of the -"dump_modify"_dump_modify.html command). By default, bonds are drawn -if they are defined in the input data file as read by the -"read_data"_read_data.html command. Using {none} for both the bond -{color} and {width} value will turn off the drawing of all bonds. - -If {atom} is specified for the bond {color} value, then each bond is -drawn in 2 halves, with the color of each half being the color of the -atom at that end of the bond. - -If {type} is specified for the {color} value, then the color of each -bond is determined by its bond type. By default the mapping of bond -types to colors is as follows: - -type 1 = red -type 2 = green -type 3 = blue -type 4 = yellow -type 5 = aqua -type 6 = cyan :ul - -and repeats itself for bond types > 6. This mapping can be changed by -the "dump_modify bcolor"_dump_modify.html command. - -The bond {width} value can be a numeric value or {atom} or {type} (or -{none} as indicated above). - -If a numeric value is specified, then all bonds will be drawn as -cylinders with that diameter, e.g. 1.0, which is in whatever distance -"units"_units.html the input script defines, e.g. Angstroms. - -If {atom} is specified for the {width} value, then each bond -will be drawn with a width corresponding to the minimum diameter -of the 2 atoms in the bond. - -If {type} is specified for the {width} value then the diameter of each -bond is determined by its bond type. By default all types have -diameter 0.5. This mapping can be changed by the "dump_modify -bdiam"_dump_modify.html command. - -:line - -The {line} keyword can be used when "atom_style line"_atom_style.html -is used to define particles as line segments, and will draw them as -lines. If this keyword is not used, such particles will be drawn as -spheres, the same as if they were regular atoms. The only setting -currently allowed for the {color} value is {type}, which will color -the lines according to the atom type of the particle. By default the -mapping of types to colors is as follows: - -type 1 = red -type 2 = green -type 3 = blue -type 4 = yellow -type 5 = aqua -type 6 = cyan :ul - -and repeats itself for types > 6. There is not yet an option to -change this via the "dump_modify"_dump_modify.html command. - -The line {width} can only be a numeric value, which specifies that all -lines will be drawn as cylinders with that diameter, e.g. 1.0, which -is in whatever distance "units"_units.html the input script defines, -e.g. Angstroms. - -:line - -The {tri} keyword can be used when "atom_style tri"_atom_style.html is -used to define particles as triangles, and will draw them as triangles -or edges (3 lines) or both, depending on the setting for {tflag}. If -edges are drawn, the {width} setting determines the diameters of the -line segments. If this keyword is not used, triangle particles will -be drawn as spheres, the same as if they were regular atoms. The only -setting currently allowed for the {color} value is {type}, which will -color the triangles according to the atom type of the particle. By -default the mapping of types to colors is as follows: - -type 1 = red -type 2 = green -type 3 = blue -type 4 = yellow -type 5 = aqua -type 6 = cyan :ul - -and repeats itself for types > 6. There is not yet an option to -change this via the "dump_modify"_dump_modify.html command. - -:line - -The {body} keyword can be used when "atom_style body"_atom_style.html -is used to define body particles with internal state -(e.g. sub-particles), and will drawn them in a manner specific to the -body style. If this keyword is not used, such particles will be drawn -as spheres, the same as if they were regular atoms. - -The "Howto body"_Howto_body.html doc page describes the body styles -LAMMPS currently supports, and provides more details as to the kind of -body particles they represent and how they are drawn by this dump -image command. For all the body styles, individual atoms can be -either a body particle or a usual point (non-body) particle. Non-body -particles will be drawn the same way they would be as a regular atom. -The {bflag1} and {bflag2} settings are numerical values which are -passed to the body style to affect how the drawing of a body particle -is done. See the "Howto body"_Howto_body.html doc page for a -description of what these parameters mean for each body style. - -The only setting currently allowed for the {color} value is {type}, -which will color the body particles according to the atom type of the -particle. By default the mapping of types to colors is as follows: - -type 1 = red -type 2 = green -type 3 = blue -type 4 = yellow -type 5 = aqua -type 6 = cyan :ul - -and repeats itself for types > 6. There is not yet an option to -change this via the "dump_modify"_dump_modify.html command. - -:line - -The {fix} keyword can be used with a "fix"_fix.html that produces -objects to be drawn. - -The {fflag1} and {fflag2} settings are numerical values which are -passed to the fix to affect how the drawing of its objects is done. -See the individual fix doc page for a description of what these -parameters mean for a particular fix. - -The only setting currently allowed for the {color} value is {type}, -which will color the fix objects according to their type. By default -the mapping of types to colors is as follows: - -type 1 = red -type 2 = green -type 3 = blue -type 4 = yellow -type 5 = aqua -type 6 = cyan :ul - -and repeats itself for types > 6. There is not yet an option to -change this via the "dump_modify"_dump_modify.html command. - -:line - -The {size} keyword sets the width and height of the created images, -i.e. the number of pixels in each direction. - -:line - -The {view}, {center}, {up}, {zoom}, and {persp} values determine how -3d simulation space is mapped to the 2d plane of the image. Basically -they control how the simulation box appears in the image. - -All of the {view}, {center}, {up}, {zoom}, and {persp} values can be -specified as numeric quantities, whose meaning is explained below. -Any of them can also be specified as an "equal-style -variable"_variable.html, by using v_name as the value, where "name" is -the variable name. In this case the variable will be evaluated on the -timestep each image is created to create a new value. If the -equal-style variable is time-dependent, this is a means of changing -the way the simulation box appears from image to image, effectively -doing a pan or fly-by view of your simulation. - -The {view} keyword determines the viewpoint from which the simulation -box is viewed, looking towards the {center} point. The {theta} value -is the vertical angle from the +z axis, and must be an angle from 0 to -180 degrees. The {phi} value is an azimuthal angle around the z axis -and can be positive or negative. A value of 0.0 is a view along the -+x axis, towards the {center} point. If {theta} or {phi} are -specified via variables, then the variable values should be in -degrees. - -The {center} keyword determines the point in simulation space that -will be at the center of the image. {Cx}, {Cy}, and {Cz} are -specified as fractions of the box dimensions, so that (0.5,0.5,0.5) is -the center of the simulation box. These values do not have to be -between 0.0 and 1.0, if you want the simulation box to be offset from -the center of the image. Note, however, that if you choose strange -values for {Cx}, {Cy}, or {Cz} you may get a blank image. Internally, -{Cx}, {Cy}, and {Cz} are converted into a point in simulation space. -If {flag} is set to "s" for static, then this conversion is done once, -at the time the dump command is issued. If {flag} is set to "d" for -dynamic then the conversion is performed every time a new image is -created. If the box size or shape is changing, this will adjust the -center point in simulation space. - -The {up} keyword determines what direction in simulation space will be -"up" in the image. Internally it is stored as a vector that is in the -plane perpendicular to the view vector implied by the {theta} and -{pni} values, and which is also in the plane defined by the view -vector and user-specified up vector. Thus this internal vector is -computed from the user-specified {up} vector as - -up_internal = view cross (up cross view) :pre - -This means the only restriction on the specified {up} vector is that -it cannot be parallel to the {view} vector, implied by the {theta} and -{phi} values. - -The {zoom} keyword scales the size of the simulation box as it appears -in the image. The default {zfactor} value of 1 should display an -image mostly filled by the atoms in the simulation box. A {zfactor} > -1 will make the simulation box larger; a {zfactor} < 1 will make it -smaller. {Zfactor} must be a value > 0.0. - -The {persp} keyword determines how much depth perspective is present -in the image. Depth perspective makes lines that are parallel in -simulation space appear non-parallel in the image. A {pfactor} value -of 0.0 means that parallel lines will meet at infinity (1.0/pfactor), -which is an orthographic rendering with no perspective. A {pfactor} -value between 0.0 and 1.0 will introduce more perspective. A {pfactor} -value > 1 will create a highly skewed image with a large amount of -perspective. - -NOTE: The {persp} keyword is not yet supported as an option. - -:line - -The {box} keyword determines if and how the simulation box boundaries -are rendered as thin cylinders in the image. If {no} is set, then the -box boundaries are not drawn and the {diam} setting is ignored. If -{yes} is set, the 12 edges of the box are drawn, with a diameter that -is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for -2d). The color of the box boundaries can be set with the "dump_modify -boxcolor"_dump_modify.html command. - -The {axes} keyword determines if and how the coordinate axes are -rendered as thin cylinders in the image. If {no} is set, then the -axes are not drawn and the {length} and {diam} settings are ignored. -If {yes} is set, 3 thin cylinders are drawn to represent the x,y,z -axes in colors red,green,blue. The origin of these cylinders will be -offset from the lower left corner of the box by 10%. The {length} -setting determines how long the cylinders will be as a fraction of the -respective box lengths. The {diam} setting determines their thickness -as a fraction of the shortest box length in x,y,z (for 3d) or x,y (for -2d). - -The {subbox} keyword determines if and how processor sub-domain -boundaries are rendered as thin cylinders in the image. If {no} is -set (default), then the sub-domain boundaries are not drawn and the -{diam} setting is ignored. If {yes} is set, the 12 edges of each -processor sub-domain are drawn, with a diameter that is a fraction of -the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color -of the sub-domain boundaries can be set with the "dump_modify -boxcolor"_dump_modify.html command. - -:line - -The {shiny} keyword determines how shiny the objects rendered in the -image will appear. The {sfactor} value must be a value 0.0 <= -{sfactor} <= 1.0, where {sfactor} = 1 is a highly reflective surface -and {sfactor} = 0 is a rough non-shiny surface. - -The {ssao} keyword turns on/off a screen space ambient occlusion -(SSAO) model for depth shading. If {yes} is set, then atoms further -away from the viewer are darkened via a randomized process, which is -perceived as depth. The calculation of this effect can increase the -cost of computing the image by roughly 2x. The strength of the effect -can be scaled by the {dfactor} parameter. If {no} is set, no depth -shading is performed. - -:line - -A series of JPEG, PNG, or PPM images can be converted into a movie -file and then played as a movie using commonly available tools. Using -dump style {movie} automates this step and avoids the intermediate -step of writing (many) image snapshot file. But LAMMPS has to be -compiled with -DLAMMPS_FFMPEG and an FFmpeg executable have to be -installed. - -To manually convert JPEG, PNG or PPM files into an animated GIF or -MPEG or other movie file you can use: - -a) Use the ImageMagick convert program. :ulb,l - -% convert *.jpg foo.gif -% convert -loop 1 *.ppm foo.mpg :pre - -Animated GIF files from ImageMagick are not optimized. You can use -a program like gifsicle to optimize and thus massively shrink them. -MPEG files created by ImageMagick are in MPEG-1 format with a rather -inefficient compression and low quality compared to more modern -compression styles like MPEG-4, H.264, VP8, VP9, H.265 and so on. - -b) Use QuickTime. :l - -Select "Open Image Sequence" under the File menu Load the images into -QuickTime to animate them Select "Export" under the File menu Save the -movie as a QuickTime movie (*.mov) or in another format. QuickTime -can generate very high quality and efficiently compressed movie -files. Some of the supported formats require to buy a license and some -are not readable on all platforms until specific runtime libraries are -installed. - -c) Use FFmpeg :l - -FFmpeg is a command line tool that is available on many platforms and -allows extremely flexible encoding and decoding of movies. - -cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v -cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi :pre - -Front ends for FFmpeg exist for multiple platforms. For more -information see the "FFmpeg homepage"_http://www.ffmpeg.org/ - -:ule - -:line - -Play the movie: - -a) Use your browser to view an animated GIF movie. :ulb,l - -Select "Open File" under the File menu -Load the animated GIF file - -b) Use the freely available mplayer or ffplay tool to view a -movie. Both are available for multiple OSes and support a large -variety of file formats and decoders. :l - -% mplayer foo.mpg -% ffplay bar.avi :pre - -c) Use the "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html -"animate tool"_http://www.sandia.gov/~sjplimp/pizza/doc/animate.html, -which works directly on a series of image files. :l - -a = animate("foo*.jpg") :pre - -d) QuickTime and other Windows- or MacOS-based media players can -obviously play movie files directly. Similarly for corresponding tools -bundled with Linux desktop environments. However, due to licensing -issues with some file formats, the formats may require installing -additional libraries, purchasing a license, or may not be -supported. :l -:ule - -:line - -See the "Modify"_Modify.html doc page for information on how to add -new compute and fix styles to LAMMPS to calculate per-atom quantities -which could then be output into dump files. - -:line - -[Restrictions:] - -To write JPEG images, you must use the -DLAMMPS_JPEG switch when -building LAMMPS and link with a JPEG library. To write PNG images, you -must use the -DLAMMPS_PNG switch when building LAMMPS and link with a -PNG library. - -To write {movie} dumps, you must use the -DLAMMPS_FFMPEG switch when -building LAMMPS and have the FFmpeg executable available on the -machine where LAMMPS is being run. Typically it's name is lowercase, -i.e. ffmpeg. - -See the "Build settings"_Build_settings.html doc page for details. - -Note that since FFmpeg is run as an external program via a pipe, -LAMMPS has limited control over its execution and no knowledge about -errors and warnings printed by it. Those warnings and error messages -will be printed to the screen only. Due to the way image data is -communicated to FFmpeg, it will often print the message - -pipe:: Input/output error :pre - -which can be safely ignored. Other warnings -and errors have to be addressed according to the FFmpeg documentation. -One known issue is that certain movie file formats (e.g. MPEG level 1 -and 2 format streams) have video bandwidth limits that can be crossed -when rendering too large of image sizes. Typical warnings look like -this: - -\[mpeg @ 0x98b5e0\] packet too large, ignoring buffer limits to mux it -\[mpeg @ 0x98b5e0\] buffer underflow st=0 bufi=281407 size=285018 -\[mpeg @ 0x98b5e0\] buffer underflow st=0 bufi=283448 size=285018 :pre - -In this case it is recommended to either reduce the size of the image -or encode in a different format that is also supported by your copy of -FFmpeg, and which does not have this limitation (e.g. .avi, .mkv, -mp4). - - -[Related commands:] - -"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html - -[Default:] - -The defaults for the keywords are as follows: - -adiam = not specified (use diameter setting) -atom = yes -bond = none none (if no bonds in system) -bond = atom 0.5 (if bonds in system) -size = 512 512 -view = 60 30 (for 3d) -view = 0 0 (for 2d) -center = s 0.5 0.5 0.5 -up = 0 0 1 (for 3d) -up = 0 1 0 (for 2d) -zoom = 1.0 -persp = 0.0 -box = yes 0.02 -axes = no 0.0 0.0 -subbox no 0.0 -shiny = 1.0 -ssao = no :ul diff --git a/doc/txt/dump_modify.txt b/doc/txt/dump_modify.txt deleted file mode 100644 index 63a3476d30..0000000000 --- a/doc/txt/dump_modify.txt +++ /dev/null @@ -1,1138 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dump_modify command :h3 - -[Syntax:] - -dump_modify dump-ID keyword values ... :pre - -dump-ID = ID of dump to modify :ulb,l -one or more keyword/value pairs may be appended :l -these keywords apply to various dump styles :l -keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {pbc} or {precision} or {region} or {refresh} or {scale} or {sfactor} or {sort} or {tfactor} or {thermo} or {thresh} or {time} or {units} or {unwrap} :l - {append} arg = {yes} or {no} - {at} arg = N - N = index of frame written upon first dump - {buffer} arg = {yes} or {no} - {delay} arg = Dstep - Dstep = delay output until this timestep - {element} args = E1 E2 ... EN, where N = # of atom types - E1,...,EN = element name, e.g. C or Fe or Ga - {every} arg = N - N = dump every this many timesteps - N can be a variable (see below) - {fileper} arg = Np - Np = write one file for every this many processors - {first} arg = {yes} or {no} - {flush} arg = {yes} or {no} - {format} args = {line} string, {int} string, {float} string, M string, or {none} - string = C-style format string - M = integer from 1 to N, where N = # of per-atom quantities being output - {image} arg = {yes} or {no} - {label} arg = string - string = character string (e.g. BONDS) to use in header of dump local file - {maxfiles} arg = Fmax - Fmax = keep only the most recent {Fmax} snapshots (one snapshot per file) - {nfile} arg = Nf - Nf = write this many files, one from each of Nf processors - {pad} arg = Nchar = # of characters to convert timestep to - {pbc} arg = {yes} or {no} = remap atoms via periodic boundary conditions - {precision} arg = power-of-10 value from 10 to 1000000 - {region} arg = region-ID or "none" - {refresh} arg = c_ID = compute ID that supports a refresh operation - {scale} arg = {yes} or {no} - {sfactor} arg = coordinate scaling factor (> 0.0) - {sort} arg = {off} or {id} or N or -N - off = no sorting of per-atom lines within a snapshot - id = sort per-atom lines by atom ID - N = sort per-atom lines in ascending order by the Nth column - -N = sort per-atom lines in descending order by the Nth column - {tfactor} arg = time scaling factor (> 0.0) - {thermo} arg = {yes} or {no} - {time} arg = {yes} or {no} - {thresh} args = attribute operator value - attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style - operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" - value = numeric value to compare to, or LAST - these 3 args can be replaced by the word "none" to turn off thresholding - {units} arg = {yes} or {no} - {unwrap} arg = {yes} or {no} :pre -these keywords apply only to the {image} and {movie} "styles"_dump_image.html :l -keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or {boxcolor} or {color} or {bitrate} or {framerate} :l - {acolor} args = type color - type = atom type or range of types (see below) - color = name of color or color1/color2/... - {adiam} args = type diam - type = atom type or range of types (see below) - diam = diameter of atoms of that type (distance units) - {amap} args = lo hi style delta N entry1 entry2 ... entryN - lo = number or {min} = lower bound of range of color map - hi = number or {max} = upper bound of range of color map - style = 2 letters = "c" or "d" or "s" plus "a" or "f" - "c" for continuous - "d" for discrete - "s" for sequential - "a" for absolute - "f" for fractional - delta = binsize (only used for style "s", otherwise ignored) - binsize = range is divided into bins of this width - N = # of subsequent entries - entry = value color (for continuous style) - value = number or {min} or {max} = single value within range - color = name of color used for that value - entry = lo hi color (for discrete style) - lo/hi = number or {min} or {max} = lower/upper bound of subset of range - color = name of color used for that subset of values - entry = color (for sequential style) - color = name of color used for a bin of values - {backcolor} arg = color - color = name of color for background - {bcolor} args = type color - type = bond type or range of types (see below) - color = name of color or color1/color2/... - {bdiam} args = type diam - type = bond type or range of types (see below) - diam = diameter of bonds of that type (distance units) - {boxcolor} arg = color - color = name of color for simulation box lines and processor sub-domain lines - {color} args = name R G B - name = name of color - R,G,B = red/green/blue numeric values from 0.0 to 1.0 - {bitrate} arg = rate - rate = target bitrate for movie in kbps - {framerate} arg = fps - fps = frames per second for movie :pre -:ule - -[Examples:] - -dump_modify 1 format line "%d %d %20.15g %g %g" scale yes -dump_modify 1 format float %20.15g scale yes -dump_modify myDump image yes scale no flush yes -dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2 -dump_modify xtcdump precision 10000 sfactor 0.1 -dump_modify 1 every 1000 nfile 20 -dump_modify 1 every v_myVar -dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red :pre - -[Description:] - -Modify the parameters of a previously defined dump command. Not all -parameters are relevant to all dump styles. - -As explained on the "dump"_dump.html doc page, the {atom/mpiio}, -{custom/mpiio}, and {xyz/mpiio} dump styles are identical in command -syntax and in the format of the dump files they create, to the -corresponding styles without "mpiio", except the single dump file they -produce is written in parallel via the MPI-IO library. Thus if a -dump_modify option below is valid for the {atom} style, it is also -valid for the {atom/mpiio} style, and similarly for the other styles -which allow for use of MPI-IO. - -:line - -These keywords apply to various dump styles, including the "dump -image"_dump_image.html and "dump movie"_dump_image.html styles. The -description gives details. - -:line - -The {append} keyword applies to all dump styles except {cfg} and {xtc} -and {dcd}. It also applies only to text output files, not to binary -or gzipped or image/movie files. If specified as {yes}, then dump -snapshots are appended to the end of an existing dump file. If -specified as {no}, then a new dump file will be created which will -overwrite an existing file with the same name. - -:line - -The {at} keyword only applies to the {netcdf} dump style. It can only -be used if the {append yes} keyword is also used. The {N} argument is -the index of which frame to append to. A negative value can be -specified for {N}, which means a frame counted from the end of the -file. The {at} keyword can only be used if the dump_modify command is -before the first command that causes dump snapshots to be output, -e.g. a "run"_run.html or "minimize"_minimize.html command. Once the -dump file has been opened, this keyword has no further effect. - -:line - -The {buffer} keyword applies only to dump styles {atom}, {cfg}, -{custom}, {local}, and {xyz}. It also applies only to text output -files, not to binary or gzipped files. If specified as {yes}, which -is the default, then each processor writes its output into an internal -text buffer, which is then sent to the processor(s) which perform file -writes, and written by those processors(s) as one large chunk of text. -If specified as {no}, each processor sends its per-atom data in binary -format to the processor(s) which perform file wirtes, and those -processor(s) format and write it line by line into the output file. - -The buffering mode is typically faster since each processor does the -relatively expensive task of formatting the output for its own atoms. -However it requires about twice the memory (per processor) for the -extra buffering. - -:line - -The {delay} keyword applies to all dump styles. No snapshots will be -output until the specified {Dstep} timestep or later. Specifying -{Dstep} < 0 is the same as turning off the delay setting. This is a -way to turn off unwanted output early in a simulation, for example, -during an equilibration phase. - -:line - -The {element} keyword applies only to the dump {cfg}, {xyz}, and -{image} styles. It associates element names (e.g. H, C, Fe) with -LAMMPS atom types. See the list of element names at the bottom of -this page. - -In the case of dump {cfg}, this allows the "AtomEye"_atomeye -visualization package to read the dump file and render atoms with the -appropriate size and color. - -In the case of dump {image}, the output images will follow the same -"AtomEye"_atomeye convention. An element name is specified for each -atom type (1 to Ntype) in the simulation. The same element name can -be given to multiple atom types. - -In the case of {xyz} format dumps, there are no restrictions to what -label can be used as an element name. Any white-space separated text -will be accepted. - -:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) - -:line - -The {every} keyword changes the dump frequency originally specified by -the "dump"_dump.html command to a new value. The every keyword can be -specified in one of two ways. It can be a numeric value in which case -it must be > 0. Or it can be an "equal-style variable"_variable.html, -which should be specified as v_name, where name is the variable name. - -In this case, the variable is evaluated at the beginning of a run to -determine the next timestep at which a dump snapshot will be written -out. On that timestep the variable will be evaluated again to -determine the next timestep, etc. Thus the variable should return -timestep values. See the stagger() and logfreq() and stride() math -functions for "equal-style variables"_variable.html, as examples of -useful functions to use in this context. Other similar math functions -could easily be added as options for "equal-style -variables"_variable.html. Also see the next() function, which allows -use of a file-style variable which reads successive values from a -file, each time the variable is evaluated. Used with the {every} -keyword, if the file contains a list of ascending timesteps, you can -output snapshots whenever you wish. - -Note that when using the variable option with the {every} keyword, you -need to use the {first} option if you want an initial snapshot written -to the dump file. The {every} keyword cannot be used with the dump -{dcd} style. - -For example, the following commands will -write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc: - -variable s equal logfreq(10,3,10) -dump 1 all atom 100 tmp.dump -dump_modify 1 every v_s first yes :pre - -The following commands would write snapshots at the timesteps listed -in file tmp.times: - -variable f file tmp.times -variable s equal next(f) -dump 1 all atom 100 tmp.dump -dump_modify 1 every v_s :pre - -NOTE: When using a file-style variable with the {every} keyword, the -file of timesteps must list a first timestep that is beyond the -current timestep (e.g. it cannot be 0). And it must list one or more -timesteps beyond the length of the run you perform. This is because -the dump command will generate an error if the next timestep it reads -from the file is not a value greater than the current timestep. Thus -if you wanted output on steps 0,15,100 of a 100-timestep run, the file -should contain the values 15,100,101 and you should also use the -dump_modify first command. Any final value > 100 could be used in -place of 101. - -:line - -The {first} keyword determines whether a dump snapshot is written on -the very first timestep after the dump command is invoked. This will -always occur if the current timestep is a multiple of N, the frequency -specified in the "dump"_dump.html command, including timestep 0. But -if this is not the case, a dump snapshot will only be written if the -setting of this keyword is {yes}. If it is {no}, which is the -default, then it will not be written. - -:line - -The {flush} keyword determines whether a flush operation is invoked -after a dump snapshot is written to the dump file. A flush insures -the output in that file is current (no buffering by the OS), even if -LAMMPS halts before the simulation completes. Flushes cannot be -performed with dump style {xtc}. - -:line - -The {format} keyword can be used to change the default numeric format -output by the text-based dump styles: {atom}, {custom}, {cfg}, and -{xyz} styles, and their MPIIO variants. Only the {line} or {none} -options can be used with the {atom} and {xyz} styles. - -All the specified format strings are C-style formats, e.g. as used by -the C/C++ printf() command. The {line} keyword takes a single -argument which is the format string for an entire line of output for -each atom (do not include a trailing "\n"), with N fields, which you -must enclose in quotes if it is more than one field. The {int} and -{float} keywords take a single format argument and are applied to all -integer or floating-point quantities output. The setting for {M -string} also takes a single format argument which is used for the Mth -value output in each line, e.g. the 5th column is output in high -precision for "format 5 %20.15g". - -NOTE: When using the {line} keyword for the {cfg} style, the first two -fields (atom ID and type) are not actually written into the CFG file, -however you must include formats for them in the format string. - -The {format} keyword can be used multiple times. The precedence is -that for each value in a line of output, the {M} format (if specified) -is used, else the {int} or {float} setting (if specified) is used, -else the {line} setting (if specified) for that value is used, else -the default setting is used. A setting of {none} clears all previous -settings, reverting all values to their default format. - -NOTE: Atom and molecule IDs are stored internally as 4-byte or 8-byte -signed integers, depending on how LAMMPS was compiled. When -specifying the {format int} option you can use a "%d"-style format -identifier in the format string and LAMMPS will convert this to the -corresponding 8-byte form if it is needed when outputting those -values. However, when specifying the {line} option or {format M -string} option for those values, you should specify a format string -appropriate for an 8-byte signed integer, e.g. one with "%ld", if -LAMMPS was compiled with the -DLAMMPS_BIGBIG option for 8-byte IDs. - -NOTE: Any value written to a text-based dump file that is a per-atom -quantity calculated by a "compute"_compute.html or "fix"_fix.html is -stored internally as a floating-point value. If the value is actually -an integer and you wish it to appear in the text dump file as a -(large) integer, then you need to use an appropriate format. For -example, these commands: - -compute 1 all property/local batom1 batom2 -dump 1 all local 100 tmp.bonds index c_1\[1\] c_1\[2\] -dump_modify 1 format "%d %0.0f %0.0f" :pre - -will output the two atom IDs for atoms in each bond as integers. If -the dump_modify command were omitted, they would appear as -floating-point values, assuming they were large integers (more than 6 -digits). The "index" keyword should use the "%d" format since it is -not generated by a compute or fix, and is stored internally as an -integer. - -:line - -The {fileper} keyword is documented below with the {nfile} keyword. - -:line - -The {image} keyword applies only to the dump {atom} style. If the -image value is {yes}, 3 flags are appended to each atom's coords which -are the absolute box image of the atom in each dimension. For -example, an x image flag of -2 with a normalized coord of 0.5 means -the atom is in the center of the box, but has passed through the box -boundary 2 times and is really 2 box lengths to the left of its -current coordinate. Note that for dump style {custom} these various -values can be printed in the dump file by using the appropriate atom -attributes in the dump command itself. - -:line - -The {label} keyword applies only to the dump {local} style. When -it writes local information, such as bond or angle topology -to a dump file, it will use the specified {label} to format -the header. By default this includes 2 lines: - -ITEM: NUMBER OF ENTRIES -ITEM: ENTRIES ... :pre - -The word "ENTRIES" will be replaced with the string specified, -e.g. BONDS or ANGLES. - -:line - -The {maxfiles} keyword can only be used when a '*' wildcard is -included in the dump file name, i.e. when writing a new file(s) for -each snapshot. The specified {Fmax} is how many snapshots will be -kept. Once this number is reached, the file(s) containing the oldest -snapshot is deleted before a new dump file is written. If the -specified {Fmax} <= 0, then all files are retained. - -This can be useful for debugging, especially if you don't know on what -timestep something bad will happen, e.g. when LAMMPS will exit with an -error. You can dump every timestep, and limit the number of dump -files produced, even if you run for 1000s of steps. - -:line - -The {nfile} or {fileper} keywords can be used in conjunction with the -"%" wildcard character in the specified dump file name, for all dump -styles except the {dcd}, {image}, {movie}, {xtc}, and {xyz} styles -(for which "%" is not allowed). As explained on the "dump"_dump.html -command doc page, the "%" character causes the dump file to be written -in pieces, one piece for each of P processors. By default P = the -number of processors the simulation is running on. The {nfile} or -{fileper} keyword can be used to set P to a smaller value, which can -be more efficient when running on a large number of processors. - -The {nfile} keyword sets P to the specified Nf value. For example, if -Nf = 4, and the simulation is running on 100 processors, 4 files will -be written, by processors 0,25,50,75. Each will collect information -from itself and the next 24 processors and write it to a dump file. - -For the {fileper} keyword, the specified value of Np means write one -file for every Np processors. For example, if Np = 4, every 4th -processor (0,4,8,12,etc) will collect information from itself and the -next 3 processors and write it to a dump file. - -:line - -The {pad} keyword only applies when the dump filename is specified -with a wildcard "*" character which becomes the timestep. If {pad} is -0, which is the default, the timestep is converted into a string of -unpadded length, e.g. 100 or 12000 or 2000000. When {pad} is -specified with {Nchar} > 0, the string is padded with leading zeroes -so they are all the same length = {Nchar}. For example, pad 7 would -yield 0000100, 0012000, 2000000. This can be useful so that -post-processing programs can easily read the files in ascending -timestep order. - -:line - -The {pbc} keyword applies to all the dump styles. As explained on the -"dump"_dump.html doc page, atom coordinates in a dump file may be -slightly outside the simulation box. This is because periodic -boundary conditions are enforced only on timesteps when neighbor lists -are rebuilt, which will not typically coincide with the timesteps dump -snapshots are written. If the setting of this keyword is set to -{yes}, then all atoms will be remapped to the periodic box before the -snapshot is written, then restored to their original position. If it -is set to {no} they will not be. The {no} setting is the default -because it requires no extra computation. - -:line - -The {precision} keyword only applies to the dump {xtc} style. A -specified value of N means that coordinates are stored to 1/N -nanometer accuracy, e.g. for N = 1000, the coordinates are written to -1/1000 nanometer accuracy. - -:line - -The {refresh} keyword only applies to the dump {custom}, {cfg}, -{image}, and {movie} styles. It allows an "incremental" dump file to -be written, by refreshing a compute that is used as a threshold for -determining which atoms are included in a dump snapshot. The -specified {c_ID} gives the ID of the compute. It is prefixed by "c_" -to indicate a compute, which is the only current option. At some -point, other options may be added, e.g. fixes or variables. - -NOTE: This keyword can only be specified once for a dump. Refreshes -of multiple computes cannot yet be performed. - -The definition and motivation of an incremental dump file is as -follows. Instead of outputting all atoms at each snapshot (with some -associated values), you may only wish to output the subset of atoms -with a value that has changed in some way compared to the value the -last time that atom was output. In some scenarios this can result in -a dramatically smaller dump file. If desired, by post-processing the -sequence of snapshots, the values for all atoms at all timesteps can -be inferred. - -A concrete example is a simulation of atom diffusion in a solid, -represented as atoms on a lattice. Diffusive hops are rare. Imagine -that when a hop occurs an atom moves more than a distance {Dhop}. For -any snapshot we only want to output atoms that have hopped since the -last snapshot. This can be accomplished with something the following -commands: - -variable Dhop equal 0.6 -variable check atom "c_dsp\[4\] > v_Dhop" -compute dsp all displace/atom refresh check -dump 1 all custom 20 tmp.dump id type x y z -dump_modify 1 append yes thresh c_dsp\[4\] > $\{Dhop\} refresh c_dsp :pre - -The "compute displace/atom"_compute_displace_atom.html command -calculates the displacement of each atom from its reference position. -The "4" index is the scalar displacement; 1,2,3 are the xyz components -of the displacement. The "dump_modify thresh"_dump_modify.html -command will cause only atoms that have displaced more than 0.6 -Angstroms to be output on a given snapshot (assuming metal units). -However, note that when an atom is output, we also need to update the -reference position for that atom to its new coordinates. So that it -will not be output in every snapshot thereafter. That reference -position is stored by "compute -displace/atom"_compute_displace_atom.html. So the dump_modify -{refresh} option triggers a call to compute displace/atom at the end -of every dump to perform that update. The {refresh check} option -shown as part of the "compute -displace/atom"_compute_displace_atom.html command enables the compute -to respond to the call from the dump command, and update the -appropriate reference positions. This is done be defining an -"atom-style variable"_variable.html, {check} in this example, which -calculates a Boolean value (0 or 1) for each atom, based on the same -criterion used by dump_modify thresh. - -See the "compute displace/atom"_compute_displace_atom.html command for -more details, including an example of how to produce output that -includes an initial snapshot with the reference position of all atoms. - -Note that only computes with a {refresh} option will work with -dump_modify refresh. See individual compute doc pages for details. -Currently, only compute displace/atom supports this option. Others -may be added at some point. If you use a compute that doesn't support -refresh operations, LAMMPS will not complain; dump_modify refresh will -simply do nothing. - -:line - -The {region} keyword only applies to the dump {custom}, {cfg}, -{image}, and {movie} styles. If specified, only atoms in the region -will be written to the dump file or included in the image/movie. Only -one region can be applied as a filter (the last one specified). See -the "region"_region.html command for more details. Note that a region -can be defined as the "inside" or "outside" of a geometric shape, and -it can be the "union" or "intersection" of a series of simpler -regions. - -:line - -The {scale} keyword applies only to the dump {atom} style. A scale -value of {yes} means atom coords are written in normalized units from -0.0 to 1.0 in each box dimension. If the simulation box is triclinic -(tilted), then all atom coords will still be between 0.0 and 1.0. A -value of {no} means they are written in absolute distance units -(e.g. Angstroms or sigma). - -:line - -The {sfactor} and {tfactor} keywords only apply to the dump {xtc} -style. They allow customization of the unit conversion factors used -when writing to XTC files. By default they are initialized for -whatever "units"_units.html style is being used, to write out -coordinates in nanometers and time in picoseconds. I.e. for {real} -units, LAMMPS defines {sfactor} = 0.1 and {tfactor} = 0.001, since the -Angstroms and fmsec used by {real} units are 0.1 nm and 0.001 psec -respectively. If you are using a units system with distance and time -units far from nm and psec, you may wish to write XTC files with -different units, since the compression algorithm used in XTC files is -most effective when the typical magnitude of position data is between -10.0 and 0.1. - -:line - -The {sort} keyword determines whether lines of per-atom output in a -snapshot are sorted or not. A sort value of {off} means they will -typically be written in indeterminate order, either in serial or -parallel. This is the case even in serial if the "atom_modify -sort"_atom_modify.html option is turned on, which it is by default, to -improve performance. A sort value of {id} means sort the output by -atom ID. A sort value of N or -N means sort the output by the value -in the Nth column of per-atom info in either ascending or descending -order. - -The dump {local} style cannot be sorted by atom ID, since there are -typically multiple lines of output per atom. Some dump styles, such -as {dcd} and {xtc}, require sorting by atom ID to format the output -file correctly. If multiple processors are writing the dump file, via -the "%" wildcard in the dump filename, then sorting cannot be -performed. - -NOTE: Unless it is required by the dump style, sorting dump file -output requires extra overhead in terms of CPU and communication cost, -as well as memory, versus unsorted output. - -:line - -The {thermo} keyword only applies the dump {netcdf} style. It -triggers writing of "thermo"_thermo.html information to the dump file -alongside per-atom data. The values included in the dump file are -identical to the values specified by "thermo_style"_thermo_style.html. - -:line - -The {thresh} keyword only applies to the dump {custom}, {cfg}, -{image}, and {movie} styles. Multiple thresholds can be specified. -Specifying {none} turns off all threshold criteria. If thresholds are -specified, only atoms whose attributes meet all the threshold criteria -are written to the dump file or included in the image. The possible -attributes that can be tested for are the same as those that can be -specified in the "dump custom"_dump.html command, with the exception -of the {element} attribute, since it is not a numeric value. Note -that a different attributes can be used than those output by the "dump -custom"_dump.html command. E.g. you can output the coordinates and -stress of atoms whose energy is above some threshold. - -If an atom-style variable is used as the attribute, then it can -produce continuous numeric values or effective Boolean 0/1 values -which may be useful for the comparison operator. Boolean values can -be generated by variable formulas that use comparison or Boolean math -operators or special functions like gmask() and rmask() and grmask(). -See the "variable"_variable.html command doc page for details. - -The specified value must be a simple numeric value or the word LAST. -If LAST is used, it refers to the value of the attribute the last time -the dump command was invoked to produce a snapshot. This is a way to -only dump atoms whose attribute has changed (or not changed). -Three examples follow. - -dump_modify ... thresh ix != LAST :pre - -This will dump atoms which have crossed the periodic x boundary of the -simulation box since the last dump. (Note that atoms that crossed -once and then crossed back between the two dump timesteps would not be -included.) - -region foo sphere 10 20 10 15 -variable inregion atom rmask(foo) -dump_modify ... thresh v_inregion |^ LAST :pre - -This will dump atoms which crossed the boundary of the spherical -region since the last dump. - -variable charge atom "(q > 0.5) || (q < -0.5)" -dump_modify ... thresh v_charge |^ LAST :pre - -This will dump atoms whose charge has changed from an absolute value -less than 1/2 to greater than 1/2 (or vice versa) since the last dump. -E.g. due to reactions and subsequent charge equilibration in a -reactive force field. - -The choice of operators listed above are the usual comparison -operators. The XOR operation (exclusive or) is also included as "|^". -In this context, XOR means that if either the attribute or value is -0.0 and the other is non-zero, then the result is "true" and the -threshold criterion is met. Otherwise it is not met. - -:line - -The {time} keyword only applies to the dump {atom}, {custom}, and -{local} styles (and their COMPRESS package versions {atom/gz}, -{custom/gz} and {local/gz}). If set to {yes}, each frame will will -contain two extra lines before the "ITEM: TIMESTEP" entry: - -ITEM: TIME -\ :pre - -This will output the current elapsed simulation time in current -time units equivalent to the "thermo keyword"_thermo_style.html {time}. -This is to simplify post-processing of trajectories using a variable time -step, e.g. when using "fix dt/reset"_fix_dt_reset.html. -The default setting is {no}. - -:line - -The {units} keyword only applies to the dump {atom}, {custom}, and -{local} styles (and their COMPRESS package versions {atom/gz}, -{custom/gz} and {local/gz}). If set to {yes}, each individual dump -file will contain two extra lines at the very beginning with: - -ITEM: UNITS -\ :pre - -This will output the current selected "units"_units.html style -to the dump file and thus allows visualization and post-processing -tools to determine the choice of units of the data in the dump file. -The default setting is {no}. - -:line - -The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles. -If set to {yes}, coordinates will be written "unwrapped" by the image -flags for each atom. Unwrapped means that if the atom has passed through -a periodic boundary one or more times, the value is printed for what -the coordinate would be if it had not been wrapped back into the -periodic box. Note that these coordinates may thus be far outside the -box size stored with the snapshot. - -:line - -These keywords apply only to the "dump image"_dump_image.html and -"dump movie"_dump_image.html styles. Any keyword that affects an -image, also affects a movie, since the movie is simply a collection of -images. Some of the keywords only affect the "dump -movie"_dump_image.html style. The descriptions give details. - -:line - -The {acolor} keyword can be used with the "dump image"_dump_image.html -command, when its atom color setting is {type}, to set the color that -atoms of each type will be drawn in the image. - -The specified {type} should be an integer from 1 to Ntypes = the -number of atom types. A wildcard asterisk can be used in place of or -in conjunction with the {type} argument to specify a range of atom -types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of atom types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). - -The specified {color} can be a single color which is any of the 140 -pre-defined colors (see below) or a color name defined by the -dump_modify color option. Or it can be two or more colors separated -by a "/" character, e.g. red/green/blue. In the former case, that -color is assigned to all the specified atom types. In the latter -case, the list of colors are assigned in a round-robin fashion to each -of the specified atom types. - -:line - -The {adiam} keyword can be used with the "dump image"_dump_image.html -command, when its atom diameter setting is {type}, to set the size -that atoms of each type will be drawn in the image. The specified -{type} should be an integer from 1 to Ntypes. As with the {acolor} -keyword, a wildcard asterisk can be used as part of the {type} -argument to specify a range of atom types. The specified {diam} is -the size in whatever distance "units"_units.html the input script is -using, e.g. Angstroms. - -:line - -The {amap} keyword can be used with the "dump image"_dump_image.html -command, with its {atom} keyword, when its atom setting is an -atom-attribute, to setup a color map. The color map is used to assign -a specific RGB (red/green/blue) color value to an individual atom when -it is drawn, based on the atom's attribute, which is a numeric value, -e.g. its x-component of velocity if the atom-attribute "vx" was -specified. - -The basic idea of a color map is that the atom-attribute will be -within a range of values, and that range is associated with a series -of colors (e.g. red, blue, green). An atom's specific value (vx = --3.2) can then mapped to the series of colors (e.g. halfway between -red and blue), and a specific color is determined via an interpolation -procedure. - -There are many possible options for the color map, enabled by the -{amap} keyword. Here are the details. - -The {lo} and {hi} settings determine the range of values allowed for -the atom attribute. If numeric values are used for {lo} and/or {hi}, -then values that are lower/higher than that value are set to the -value. I.e. the range is static. If {lo} is specified as {min} or -{hi} as {max} then the range is dynamic, and the lower and/or -upper bound will be calculated each time an image is drawn, based -on the set of atoms being visualized. - -The {style} setting is two letters, such as "ca". The first letter is -either "c" for continuous, "d" for discrete, or "s" for sequential. -The second letter is either "a" for absolute, or "f" for fractional. - -A continuous color map is one in which the color changes continuously -from value to value within the range. A discrete color map is one in -which discrete colors are assigned to sub-ranges of values within the -range. A sequential color map is one in which discrete colors are -assigned to a sequence of sub-ranges of values covering the entire -range. - -An absolute color map is one in which the values to which colors are -assigned are specified explicitly as values within the range. A -fractional color map is one in which the values to which colors are -assigned are specified as a fractional portion of the range. For -example if the range is from -10.0 to 10.0, and the color red is to be -assigned to atoms with a value of 5.0, then for an absolute color map -the number 5.0 would be used. But for a fractional map, the number -0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0. - -The {delta} setting must be specified for all styles, but is only used -for the sequential style; otherwise the value is ignored. It -specifies the bin size to use within the range for assigning -consecutive colors to. For example, if the range is from -10.0 to -10.0 and a {delta} of 1.0 is used, then 20 colors will be assigned to -the range. The first will be from -10.0 <= color1 < -9.0, then 2nd -from -9.0 <= color2 < -8.0, etc. - -The {N} setting is how many entries follow. The format of the entries -depends on whether the color map style is continuous, discrete or -sequential. In all cases the {color} setting can be any of the 140 -pre-defined colors (see below) or a color name defined by the -dump_modify color option. - -For continuous color maps, each entry has a {value} and a {color}. -The {value} is either a number within the range of values or {min} or -{max}. The {value} of the first entry must be {min} and the {value} -of the last entry must be {max}. Any entries in between must have -increasing values. Note that numeric values can be specified either -as absolute numbers or as fractions (0.0 to 1.0) of the range, -depending on the "a" or "f" in the style setting for the color map. - -Here is how the entries are used to determine the color of an -individual atom, given the value X of its atom attribute. X will fall -between 2 of the entry values. The color of the atom is linearly -interpolated (in each of the RGB values) between the 2 colors -associated with those entries. For example, if X = -5.0 and the 2 -surrounding entries are "red" at -10.0 and "blue" at 0.0, then the -atom's color will be halfway between "red" and "blue", which happens -to be "purple". - -For discrete color maps, each entry has a {lo} and {hi} value and a -{color}. The {lo} and {hi} settings are either numbers within the -range of values or {lo} can be {min} or {hi} can be {max}. The {lo} -and {hi} settings of the last entry must be {min} and {max}. Other -entries can have any {lo} and {hi} values and the sub-ranges of -different values can overlap. Note that numeric {lo} and {hi} values -can be specified either as absolute numbers or as fractions (0.0 to -1.0) of the range, depending on the "a" or "f" in the style setting -for the color map. - -Here is how the entries are used to determine the color of an -individual atom, given the value X of its atom attribute. The entries -are scanned from first to last. The first time that {lo} <= X <= -{hi}, X is assigned the color associated with that entry. You can -think of the last entry as assigning a default color (since it will -always be matched by X), and the earlier entries as colors that -override the default. Also note that no interpolation of a color RGB -is done. All atoms will be drawn with one of the colors in the list -of entries. - -For sequential color maps, each entry has only a {color}. Here is how -the entries are used to determine the color of an individual atom, -given the value X of its atom attribute. The range is partitioned -into N bins of width {binsize}. Thus X will fall in a specific bin -from 1 to N, say the Mth bin. If it falls on a boundary between 2 -bins, it is considered to be in the higher of the 2 bins. Each bin is -assigned a color from the E entries. If E < N, then the colors are -repeated. For example if 2 entries with colors red and green are -specified, then the odd numbered bins will be red and the even bins -green. The color of the atom is the color of its bin. Note that the -sequential color map is really a shorthand way of defining a discrete -color map without having to specify where all the bin boundaries are. - -Here is an example of using a sequential color map to color all the -atoms in individual molecules with a different color. See the -examples/pour/in.pour.2d.molecule input script for an example of how -this is used. - -variable colors string & - "red green blue yellow white & - purple pink orange lime gray" -variable mol atom mol%10 -dump 1 all image 250 image.*.jpg v_mol type & - zoom 1.6 adiam 1.5 -dump_modify 1 pad 5 amap 0 10 sa 1 10 $\{colors\} :pre - -In this case, 10 colors are defined, and molecule IDs are -mapped to one of the colors, even if there are 1000s of molecules. - -:line - -The {backcolor} sets the background color of the images. The color -name can be any of the 140 pre-defined colors (see below) or a color -name defined by the dump_modify color option. - -:line - -The {bcolor} keyword can be used with the "dump image"_dump_image.html -command, with its {bond} keyword, when its color setting is {type}, to -set the color that bonds of each type will be drawn in the image. - -The specified {type} should be an integer from 1 to Nbondtypes = the -number of bond types. A wildcard asterisk can be used in place of or -in conjunction with the {type} argument to specify a range of bond -types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of bond types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). - -The specified {color} can be a single color which is any of the 140 -pre-defined colors (see below) or a color name defined by the -dump_modify color option. Or it can be two or more colors separated -by a "/" character, e.g. red/green/blue. In the former case, that -color is assigned to all the specified bond types. In the latter -case, the list of colors are assigned in a round-robin fashion to each -of the specified bond types. - -:line - -The {bdiam} keyword can be used with the "dump image"_dump_image.html -command, with its {bond} keyword, when its diam setting is {type}, to -set the diameter that bonds of each type will be drawn in the image. -The specified {type} should be an integer from 1 to Nbondtypes. As -with the {bcolor} keyword, a wildcard asterisk can be used as part of -the {type} argument to specify a range of bond types. The specified -{diam} is the size in whatever distance "units"_units.html you are -using, e.g. Angstroms. - -:line - -The {bitrate} keyword can be used with the "dump -movie"_dump_image.html command to define the size of the resulting -movie file and its quality via setting how many kbits per second are -to be used for the movie file. Higher bitrates require less -compression and will result in higher quality movies. The quality is -also determined by the compression format and encoder. The default -setting is 2000 kbit/s, which will result in average quality with -older compression formats. - -NOTE: Not all movie file formats supported by dump movie allow the -bitrate to be set. If not, the setting is silently ignored. - -:line - -The {boxcolor} keyword sets the color of the simulation box drawn -around the atoms in each image as well as the color of processor -sub-domain boundaries. See the "dump image box" command for how to -specify that a box be drawn via the {box} keyword, and the sub-domain -boundaries via the {subbox} keyword. The color name can be any of the -140 pre-defined colors (see below) or a color name defined by the -dump_modify color option. - -:line - -The {color} keyword allows definition of a new color name, in addition -to the 140-predefined colors (see below), and associates 3 -red/green/blue RGB values with that color name. The color name can -then be used with any other dump_modify keyword that takes a color -name as a value. The RGB values should each be floating point values -between 0.0 and 1.0 inclusive. - -When a color name is converted to RGB values, the user-defined color -names are searched first, then the 140 pre-defined color names. This -means you can also use the {color} keyword to overwrite one of the -pre-defined color names with new RBG values. - -:line - -The {framerate} keyword can be used with the "dump -movie"_dump_image.html command to define the duration of the resulting -movie file. Movie files written by the dump {movie} command have a -default frame rate of 24 frames per second and the images generated -will be converted at that rate. Thus a sequence of 1000 dump images -will result in a movie of about 42 seconds. To make a movie run -longer you can either generate images more frequently or lower the -frame rate. To speed a movie up, you can do the inverse. Using a -frame rate higher than 24 is not recommended, as it will result in -simply dropping the rendered images. It is more efficient to dump -images less frequently. - -:line - -[Restrictions:] none - -[Related commands:] - -"dump"_dump.html, "dump image"_dump_image.html, "undump"_undump.html - -[Default:] - -The option defaults are - -append = no -buffer = yes for dump styles {atom}, {custom}, {loca}, and {xyz} -element = "C" for every atom type -every = whatever it was set to via the "dump"_dump.html command -fileper = # of processors -first = no -flush = yes -format = %d and %g for each integer or floating point value -image = no -label = ENTRIES -maxfiles = -1 -nfile = 1 -pad = 0 -pbc = no -precision = 1000 -region = none -scale = yes -sort = off for dump styles {atom}, {custom}, {cfg}, and {local} -sort = id for dump styles {dcd}, {xtc}, and {xyz} -thresh = none -units = no -unwrap = no :ul - -acolor = * red/green/blue/yellow/aqua/cyan -adiam = * 1.0 -amap = min max cf 0.0 2 min blue max red -backcolor = black -bcolor = * red/green/blue/yellow/aqua/cyan -bdiam = * 0.5 -bitrate = 2000 -boxcolor = yellow -color = 140 color names are pre-defined as listed below -framerate = 24 :ul - -:line - -These are the standard 109 element names that LAMMPS pre-defines for -use with the "dump image"_dump_image.html and dump_modify commands. - -1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne" -11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca" -21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn" -31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr" -41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn" -51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd" -61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb" -71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg" -81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th" -91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm" -101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt" :ul - -:line - -These are the 140 colors that LAMMPS pre-defines for use with the -"dump image"_dump_image.html and dump_modify commands. Additional -colors can be defined with the dump_modify color command. The 3 -numbers listed for each name are the RGB (red/green/blue) values. -Divide each value by 255 to get the equivalent 0.0 to 1.0 value. - -aliceblue = 240, 248, 255 | -antiquewhite = 250, 235, 215 | -aqua = 0, 255, 255 | -aquamarine = 127, 255, 212 | -azure = 240, 255, 255 | -beige = 245, 245, 220 | -bisque = 255, 228, 196 | -black = 0, 0, 0 | -blanchedalmond = 255, 255, 205 | -blue = 0, 0, 255 | -blueviolet = 138, 43, 226 | -brown = 165, 42, 42 | -burlywood = 222, 184, 135 | -cadetblue = 95, 158, 160 | -chartreuse = 127, 255, 0 | -chocolate = 210, 105, 30 | -coral = 255, 127, 80 | -cornflowerblue = 100, 149, 237 | -cornsilk = 255, 248, 220 | -crimson = 220, 20, 60 | -cyan = 0, 255, 255 | -darkblue = 0, 0, 139 | -darkcyan = 0, 139, 139 | -darkgoldenrod = 184, 134, 11 | -darkgray = 169, 169, 169 | -darkgreen = 0, 100, 0 | -darkkhaki = 189, 183, 107 | -darkmagenta = 139, 0, 139 | -darkolivegreen = 85, 107, 47 | -darkorange = 255, 140, 0 | -darkorchid = 153, 50, 204 | -darkred = 139, 0, 0 | -darksalmon = 233, 150, 122 | -darkseagreen = 143, 188, 143 | -darkslateblue = 72, 61, 139 | -darkslategray = 47, 79, 79 | -darkturquoise = 0, 206, 209 | -darkviolet = 148, 0, 211 | -deeppink = 255, 20, 147 | -deepskyblue = 0, 191, 255 | -dimgray = 105, 105, 105 | -dodgerblue = 30, 144, 255 | -firebrick = 178, 34, 34 | -floralwhite = 255, 250, 240 | -forestgreen = 34, 139, 34 | -fuchsia = 255, 0, 255 | -gainsboro = 220, 220, 220 | -ghostwhite = 248, 248, 255 | -gold = 255, 215, 0 | -goldenrod = 218, 165, 32 | -gray = 128, 128, 128 | -green = 0, 128, 0 | -greenyellow = 173, 255, 47 | -honeydew = 240, 255, 240 | -hotpink = 255, 105, 180 | -indianred = 205, 92, 92 | -indigo = 75, 0, 130 | -ivory = 255, 240, 240 | -khaki = 240, 230, 140 | -lavender = 230, 230, 250 | -lavenderblush = 255, 240, 245 | -lawngreen = 124, 252, 0 | -lemonchiffon = 255, 250, 205 | -lightblue = 173, 216, 230 | -lightcoral = 240, 128, 128 | -lightcyan = 224, 255, 255 | -lightgoldenrodyellow = 250, 250, 210 | -lightgreen = 144, 238, 144 | -lightgrey = 211, 211, 211 | -lightpink = 255, 182, 193 | -lightsalmon = 255, 160, 122 | -lightseagreen = 32, 178, 170 | -lightskyblue = 135, 206, 250 | -lightslategray = 119, 136, 153 | -lightsteelblue = 176, 196, 222 | -lightyellow = 255, 255, 224 | -lime = 0, 255, 0 | -limegreen = 50, 205, 50 | -linen = 250, 240, 230 | -magenta = 255, 0, 255 | -maroon = 128, 0, 0 | -mediumaquamarine = 102, 205, 170 | -mediumblue = 0, 0, 205 | -mediumorchid = 186, 85, 211 | -mediumpurple = 147, 112, 219 | -mediumseagreen = 60, 179, 113 | -mediumslateblue = 123, 104, 238 | -mediumspringgreen = 0, 250, 154 | -mediumturquoise = 72, 209, 204 | -mediumvioletred = 199, 21, 133 | -midnightblue = 25, 25, 112 | -mintcream = 245, 255, 250 | -mistyrose = 255, 228, 225 | -moccasin = 255, 228, 181 | -navajowhite = 255, 222, 173 | -navy = 0, 0, 128 | -oldlace = 253, 245, 230 | -olive = 128, 128, 0 | -olivedrab = 107, 142, 35 | -orange = 255, 165, 0 | -orangered = 255, 69, 0 | -orchid = 218, 112, 214 | -palegoldenrod = 238, 232, 170 | -palegreen = 152, 251, 152 | -paleturquoise = 175, 238, 238 | -palevioletred = 219, 112, 147 | -papayawhip = 255, 239, 213 | -peachpuff = 255, 239, 213 | -peru = 205, 133, 63 | -pink = 255, 192, 203 | -plum = 221, 160, 221 | -powderblue = 176, 224, 230 | -purple = 128, 0, 128 | -red = 255, 0, 0 | -rosybrown = 188, 143, 143 | -royalblue = 65, 105, 225 | -saddlebrown = 139, 69, 19 | -salmon = 250, 128, 114 | -sandybrown = 244, 164, 96 | -seagreen = 46, 139, 87 | -seashell = 255, 245, 238 | -sienna = 160, 82, 45 | -silver = 192, 192, 192 | -skyblue = 135, 206, 235 | -slateblue = 106, 90, 205 | -slategray = 112, 128, 144 | -snow = 255, 250, 250 | -springgreen = 0, 255, 127 | -steelblue = 70, 130, 180 | -tan = 210, 180, 140 | -teal = 0, 128, 128 | -thistle = 216, 191, 216 | -tomato = 253, 99, 71 | -turquoise = 64, 224, 208 | -violet = 238, 130, 238 | -wheat = 245, 222, 179 | -white = 255, 255, 255 | -whitesmoke = 245, 245, 245 | -yellow = 255, 255, 0 | -yellowgreen = 154, 205, 50 :tb(c=5,s=|) diff --git a/doc/txt/dump_molfile.txt b/doc/txt/dump_molfile.txt deleted file mode 100644 index b5f157cf29..0000000000 --- a/doc/txt/dump_molfile.txt +++ /dev/null @@ -1,123 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dump molfile command :h3 - -[Syntax:] - -dump ID group-ID molfile N file format path :pre - -ID = user-assigned name for the dump :ulb,l -group-ID = ID of the group of atoms to be imaged :l -molfile = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l -N = dump every this many timesteps :l -file = name of file to write to :l -format = file format to be used :l -path = file path with plugins (optional) :l -:ule - -[Examples:] - -dump mf1 all molfile 10 melt1.xml hoomd -dump mf2 all molfile 10 melt2-*.pdb pdb . -dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile :pre - -[Description:] - -Dump a snapshot of atom coordinates and selected additional quantities -to one or more files every N timesteps in one of several formats. -Only information for atoms in the specified group is dumped. This -specific dump style uses molfile plugins that are bundled with the -"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and -analysis program. - -Unless the filename contains a * character, the output will be written -to one single file with the specified format. Otherwise there will be -one file per snapshot and the * will be replaced by the time step number -when the snapshot is written. - -NOTE: Because periodic boundary conditions are enforced only on -timesteps when neighbor lists are rebuilt, the coordinates of an atom -written to a dump file may be slightly outside the simulation box. - -The molfile plugin API has a few restrictions that have to be honored -by this dump style: the number of atoms must not change, the atoms -must be sorted, outside of the coordinates no change in atom properties -(like type, mass, charge) will be recorded. - -:line - -The {format} keyword determines what format is used to write out the -dump. For this to work, LAMMPS must be able to find and load a -compatible molfile plugin that supports this format. Settings made via -the "dump_modify"_dump_modify.html command can alter per atom properties -like element names. - -The {path} keyword determines which in directories. This is a "path" -like other search paths, i.e. it can contain multiple directories -separated by a colon (or semi-colon on windows). This keyword is -optional and default to ".", the current directory. - -The {unwrap} option of the "dump_modify"_dump_modify.html command allows -coordinates to be written "unwrapped" by the image flags for each atom. -Unwrapped means that if the atom has passed through a periodic boundary -one or more times, the value is printed for what the coordinate would be -if it had not been wrapped back into the periodic box. Note that these -coordinates may thus be far outside the box size stored with the -snapshot. - -:line - -Dumps are performed on timesteps that are a multiple of N (including -timestep 0) and on the last timestep of a minimization if the -minimization converges. Note that this means a dump will not be -performed on the initial timestep after the dump command is invoked, -if the current timestep is not a multiple of N. This behavior can be -changed via the "dump_modify first"_dump_modify.html command, which can -be useful if the dump command is invoked after a minimization ended on -an arbitrary timestep. N can be changed between runs by using the -"dump_modify every"_dump_modify.html command. The "dump_modify -every"_dump_modify.html command also allows a variable to be used to -determine the sequence of timesteps on which dump files are written. - -:line - -[Restrictions:] - -The {molfile} dump style is part of the USER-MOLFILE package. It is -only enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Molfile plugins provide a consistent programming interface to read and -write file formats commonly used in molecular simulations. The -USER-MOLFILE package only provides the interface code, not the plugins. -These can be obtained from a VMD installation which has to match the -platform that you are using to compile LAMMPS for. By adding plugins -to VMD, support for new file formats can be added to LAMMPS (or VMD -or other programs that use them) without having to re-compile the -application itself. The plugins are installed in the directory: -/plugins//molfile - -NOTE: while the programming interface (API) to the plugins is backward -compatible, the binary interface (ABI) has been changing over time, so -it is necessary to compile this package with the plugin header files -from VMD that match the binary plugins. These header files in the -directory: /plugins/include For convenience, the package ships -with a set of header files that are compatible with VMD 1.9 and 1.9.1 -(June 2012) - -:line - -[Related commands:] - -"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html - -[Default:] - -The default path is ".". All other properties have to be specified. - diff --git a/doc/txt/dump_netcdf.txt b/doc/txt/dump_netcdf.txt deleted file mode 100644 index 52d757eac5..0000000000 --- a/doc/txt/dump_netcdf.txt +++ /dev/null @@ -1,76 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dump netcdf command :h3 -dump netcdf/mpiio command :h3 - -[Syntax:] - -dump ID group-ID netcdf N file args -dump ID group-ID netcdf/mpiio N file args :pre - -ID = user-assigned name for the dump :ulb,l -group-ID = ID of the group of atoms to be imaged :l -{netcdf} or {netcdf/mpiio} = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l -N = dump every this many timesteps :l -file = name of file to write dump info to :l -args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule - -[Examples:] - -dump 1 all netcdf 100 traj.nc type x y z vx vy vz -dump_modify 1 append yes at -1 thermo yes -dump 1 all netcdf/mpiio 1000 traj.nc id type x y z -dump 1 all netcdf 1000 traj.*.nc id type x y z :pre - -[Description:] - -Dump a snapshot of atom coordinates every N timesteps in Amber-style -NetCDF file format. NetCDF files are binary, portable and -self-describing. This dump style will write only one file on the root -node. The dump style {netcdf} uses the "standard NetCDF -library"_netcdf-home. All data is collected on one processor and then -written to the dump file. Dump style {netcdf/mpiio} uses the -"parallel NetCDF library"_pnetcdf-home and MPI-IO to write to the dump -file in parallel; it has better performance on a larger number of -processors. Note that style {netcdf} outputs all atoms sorted by atom -tag while style {netcdf/mpiio} outputs atoms in order of their MPI -rank. - -NetCDF files can be directly visualized via the following tools: - -Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and -all extensions of this dump style. :ule,b - -VMD (http://www.ks.uiuc.edu/Research/vmd/). :l - -AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye -contains a NetCDF reader that is not present in the standard -distribution of AtomEye. :l,ule - -In addition to per-atom data, "thermo"_thermo.html data can be included in the -dump file. The data included in the dump file is identical to the data specified -by "thermo_style"_thermo_style.html. - -:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/) -:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/) - -:line - -[Restrictions:] - -The {netcdf} and {netcdf/mpiio} dump styles are part of the -USER-NETCDF package. They are only enabled if LAMMPS was built with -that package. See the "Build package"_Build_package.html doc page for -more info. - -:line - -[Related commands:] - -"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html diff --git a/doc/txt/dump_vtk.txt b/doc/txt/dump_vtk.txt deleted file mode 100644 index 7eaa59a795..0000000000 --- a/doc/txt/dump_vtk.txt +++ /dev/null @@ -1,179 +0,0 @@ - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dump vtk command :h3 - -[Syntax:] - -dump ID group-ID vtk N file args :pre - -ID = user-assigned name for the dump -group-ID = ID of the group of atoms to be dumped -vtk = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) -N = dump every this many timesteps -file = name of file to write dump info to -args = same as arguments for "dump_style custom"_dump.html :ul - -[Examples:] - -dump dmpvtk all vtk 100 dump*.myforce.vtk id type vx fx -dump dmpvtp flow vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke :pre - -[Description:] - -Dump a snapshot of atom quantities to one or more files every N -timesteps in a format readable by the "VTK visualization -toolkit"_http://www.vtk.org or other visualization tools that use it, -e.g. "ParaView"_http://www.paraview.org. The timesteps on which dump -output is written can also be controlled by a variable; see the -"dump_modify every"_dump_modify.html command for details. - -This dump style is similar to "dump_style custom"_dump.html but uses -the VTK library to write data to VTK simple legacy or XML format -depending on the filename extension specified for the dump file. This -can be either {*.vtk} for the legacy format or {*.vtp} and {*.vtu}, -respectively, for XML format; see the "VTK -homepage"_http://www.vtk.org/VTK/img/file-formats.pdf for a detailed -description of these formats. Since this naming convention conflicts -with the way binary output is usually specified (see below), the -"dump_modify binary"_dump_modify.html command allows setting of a -binary option for this dump style explicitly. - -Only information for atoms in the specified group is dumped. The -"dump_modify thresh and region"_dump_modify.html commands can also -alter what atoms are included; see details below. - -As described below, special characters ("*", "%") in the filename -determine the kind of output. - -IMPORTANT NOTE: Because periodic boundary conditions are enforced only -on timesteps when neighbor lists are rebuilt, the coordinates of an -atom written to a dump file may be slightly outside the simulation -box. - -IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html option -is invoked, the lines of atom information written to dump files will -be in an indeterminate order for each snapshot. This is even true -when running on a single processor, if the "atom_modify -sort"_atom_modify.html option is on, which it is by default. In this -case atoms are re-ordered periodically during a simulation, due to -spatial sorting. It is also true when running in parallel, because -data for a single snapshot is collected from multiple processors, each -of which owns a subset of the atoms. - -For the {vtk} style, sorting is off by default. See the -"dump_modify"_dump_modify.html doc page for details. - -:line - -The dimensions of the simulation box are written to a separate file -for each snapshot (either in legacy VTK or XML format depending on the -format of the main dump file) with the suffix {_boundingBox} appended -to the given dump filename. - -For an orthogonal simulation box this information is saved as a -rectilinear grid (legacy .vtk or .vtr XML format). - -Triclinic simulation boxes (non-orthogonal) are saved as -hexahedrons in either legacy .vtk or .vtu XML format. - -Style {vtk} allows you to specify a list of atom attributes to be -written to the dump file for each atom. The list of possible attributes -is the same as for the "dump_style custom"_dump.html command; see -its doc page for a listing and an explanation of each attribute. - -NOTE: Since position data is required to write VTK files the atom -attributes "x y z" do not have to be specified explicitly; they will -be included in the dump file regardless. Also, in contrast to the -{custom} style, the specified {vtk} attributes are rearranged to -ensure correct ordering of vector components (except for computes and -fixes - these have to be given in the right order) and duplicate -entries are removed. - -The VTK format uses a single snapshot of the system per file, thus -a wildcard "*" must be included in the filename, as discussed below. -Otherwise the dump files will get overwritten with the new snapshot -each time. - -:line - -Dumps are performed on timesteps that are a multiple of N (including -timestep 0) and on the last timestep of a minimization if the -minimization converges. Note that this means a dump will not be -performed on the initial timestep after the dump command is invoked, -if the current timestep is not a multiple of N. This behavior can be -changed via the "dump_modify first"_dump_modify.html command, which -can also be useful if the dump command is invoked after a minimization -ended on an arbitrary timestep. N can be changed between runs by -using the "dump_modify every"_dump_modify.html command. -The "dump_modify every"_dump_modify.html command -also allows a variable to be used to determine the sequence of -timesteps on which dump files are written. In this mode a dump on the -first timestep of a run will also not be written unless the -"dump_modify first"_dump_modify.html command is used. - -Dump filenames can contain two wildcard characters. If a "*" -character appears in the filename, then one file per snapshot is -written and the "*" character is replaced with the timestep value. -For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk, -tmp.dump20000.vtk, etc. Note that the "dump_modify pad"_dump_modify.html -command can be used to insure all timestep numbers are the same length -(e.g. 00010), which can make it easier to read a series of dump files -in order with some post-processing tools. - -If a "%" character appears in the filename, then each of P processors -writes a portion of the dump file, and the "%" character is replaced -with the processor ID from 0 to P-1 preceded by an underscore character. -For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, ... -tmp.dump_P-1.vtp, etc. This creates smaller files and can be a fast -mode of output on parallel machines that support parallel I/O for output. - -By default, P = the number of processors meaning one file per -processor, but P can be set to a smaller value via the {nfile} or -{fileper} keywords of the "dump_modify"_dump_modify.html command. -These options can be the most efficient way of writing out dump files -when running on large numbers of processors. - -For the legacy VTK format "%" is ignored and P = 1, i.e., only -processor 0 does write files. - -Note that using the "*" and "%" characters together can produce a -large number of small dump files! - -If {dump_modify binary} is used, the dump file (or files, if "*" or -"%" is also used) is written in binary format. A binary dump file -will be about the same size as a text version, but will typically -write out much faster. - -:line - -[Restrictions:] - -The {vtk} style does not support writing of gzipped dump files. - -The {vtk} dump style is part of the USER-VTK package. It is only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -To use this dump style, you also must link to the VTK library. See -the info in lib/vtk/README and insure the Makefile.lammps file in that -directory is appropriate for your machine. - -The {vtk} dump style supports neither buffering or custom format -strings. - -[Related commands:] - -"dump"_dump.html, "dump image"_dump_image.html, -"dump_modify"_dump_modify.html, "undump"_undump.html - -[Default:] - -By default, files are written in ASCII format. If the file extension -is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used. - diff --git a/doc/txt/dynamical_matrix.txt b/doc/txt/dynamical_matrix.txt deleted file mode 100644 index 2d9b256694..0000000000 --- a/doc/txt/dynamical_matrix.txt +++ /dev/null @@ -1,70 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -dynamical_matrix command :h3 - -[Syntax:] - -dynamical_matrix group-ID style gamma args keyword value ... :pre - -group-ID = ID of group of atoms to displace :ulb,l -style = {regular} or {eskm} :l -gamma = finite different displacement length (distance units) :l -one or more keyword/arg pairs may be appended :l - keyword = {file} or {binary} - {file} name = name of output file for the dynamical matrix - {binary} arg = {yes} or {no} or {gzip} :pre -:ule - -[Examples:] - -dynamical_matrix 1 regular 0.000001 -dynamical_matrix 1 eskm 0.000001 -dynamical_matrix 3 regular 0.00004 file dynmat.dat -dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes :pre - -[Description:] - -Calculate the dynamical matrix by finite difference of the selected group, - -:c,image(JPG/dynamical_matrix_dynmat.jpg) - -where D is the dynamical matrix and Phi is the force constant matrix defined by - -:c,image(JPG/dynamical_matrix_force_constant.jpg). - -The output for the dynamical matrix is printed three elements at a time. The -three elements are the three beta elements for a respective i/alpha/j combination. -Each line is printed in order of j increasing first, alpha second, and i last. - -If the style eskm is selected, the dynamical matrix will be in units of inverse squared -femtoseconds. These units will then conveniently leave frequencies in THz, where -frequencies, represented as omega, can be calculated from - -:c, image(Eqs/dynamical_matrix_phonons.jpg) - -[Restrictions:] - -The command collects an array of nine times the number of atoms in a group -on every single MPI rank, so the memory requirements can be very significant -for large systems. - -This command is part of the USER-PHONON package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix phonon"_fix_phonon.html - -"compute hma"_compute_hma.html uses an analytic formulation of the hessian -provided by Pair's single_hessian. - -[Default:] - -The default settings are file = "dynmat.dyn", binary = no diff --git a/doc/txt/echo.txt b/doc/txt/echo.txt deleted file mode 100644 index 3436737faa..0000000000 --- a/doc/txt/echo.txt +++ /dev/null @@ -1,38 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -echo command :h3 - -[Syntax:] - -echo style :pre - -style = {none} or {screen} or {log} or {both} :ul - -[Examples:] - -echo both -echo log :pre - -[Description:] - -This command determines whether LAMMPS echoes each input script -command to the screen and/or log file as it is read and processed. If -an input script has errors, it can be useful to look at echoed output -to see the last command processed. - -The "command-line switch"_Run_options.html -echo can be used in place -of this command. - -[Restrictions:] none - -[Related commands:] none - -[Default:] - -echo log :pre diff --git a/doc/txt/fix_adapt.txt b/doc/txt/fix_adapt.txt deleted file mode 100644 index 4f047ec42d..0000000000 --- a/doc/txt/fix_adapt.txt +++ /dev/null @@ -1,309 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix adapt command :h3 - -[Syntax:] - -fix ID group-ID adapt N attribute args ... keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -adapt = style name of this fix command :l -N = adapt simulation settings every this many timesteps :l -one or more attribute/arg pairs may be appended :l -attribute = {pair} or {kspace} or {atom} :l - {pair} args = pstyle pparam I J v_name - pstyle = pair style name, e.g. lj/cut - pparam = parameter to adapt over time - I,J = type pair(s) to set parameter for - v_name = variable with name that calculates value of pparam - {bond} args = bstyle bparam I v_name - bstyle = bond style name, e.g. harmonic - bparam = parameter to adapt over time - I = type bond to set parameter for - v_name = variable with name that calculates value of bparam - {kspace} arg = v_name - v_name = variable with name that calculates scale factor on K-space terms - {atom} args = aparam v_name - aparam = parameter to adapt over time - v_name = variable with name that calculates value of aparam :pre -zero or more keyword/value pairs may be appended :l -keyword = {scale} or {reset} :l - {scale} value = {no} or {yes} - {no} = the variable value is the new setting - {yes} = the variable value multiplies the original setting - {reset} value = {no} or {yes} - {no} = values will remain altered at the end of a run - {yes} = reset altered values to their original values at the end of a run :pre -:ule - -[Examples:] - -fix 1 all adapt 1 pair soft a 1 1 v_prefactor -fix 1 all adapt 1 pair soft a 2* 3 v_prefactor -fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes -fix 1 all adapt 10 atom diameter v_size :pre - -variable ramp_up equal "ramp(0.01,0.5)" -fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up :pre - -[Description:] - -Change or adapt one or more specific simulation attributes or settings -over time as a simulation runs. Pair potential and K-space and atom -attributes which can be varied by this fix are discussed below. Many -other fixes can also be used to time-vary simulation parameters, -e.g. the "fix deform" command will change the simulation box -size/shape and the "fix move" command will change atom positions and -velocities in a prescribed manner. Also note that many commands allow -variables as arguments for specific parameters, if described in that -manner on their doc pages. An equal-style variable can calculate a -time-dependent quantity, so this is another way to vary a simulation -parameter over time. - -If {N} is specified as 0, the specified attributes are only changed -once, before the simulation begins. This is all that is needed if the -associated variables are not time-dependent. If {N} > 0, then changes -are made every {N} steps during the simulation, presumably with a -variable that is time-dependent. - -Depending on the value of the {reset} keyword, attributes changed by -this fix will or will not be reset back to their original values at -the end of a simulation. Even if {reset} is specified as {yes}, a -restart file written during a simulation will contain the modified -settings. - -If the {scale} keyword is set to {no}, then the value the parameter is -set to will be whatever the variable generates. If the {scale} -keyword is set to {yes}, then the value of the altered parameter will -be the initial value of that parameter multiplied by whatever the -variable generates. I.e. the variable is now a "scale factor" applied -in (presumably) a time-varying fashion to the parameter. - -Note that whether scale is {no} or {yes}, internally, the parameters -themselves are actually altered by this fix. Make sure you use the -{reset yes} option if you want the parameters to be restored to their -initial values after the run. - -:line - -The {pair} keyword enables various parameters of potentials defined by -the "pair_style"_pair_style.html command to be changed, if the pair -style supports it. Note that the "pair_style"_pair_style.html and -"pair_coeff"_pair_coeff.html commands must be used in the usual manner -to specify these parameters initially; the fix adapt command simply -overrides the parameters. - -The {pstyle} argument is the name of the pair style. If "pair_style -hybrid or hybrid/overlay"_pair_hybrid.html is used, {pstyle} should be -a sub-style name. If there are multiple sub-styles using the same -pair style, then {pstyle} should be specified as "style:N" where N is -which instance of the pair style you wish to adapt, e.g. the first, -second, etc. For example, {pstyle} could be specified as "soft" or -"lubricate" or "lj/cut:1" or "lj/cut:2". The {pparam} argument is the -name of the parameter to change. This is the current list of pair -styles and parameters that can be varied by this fix. See the doc -pages for individual pair styles and their energy formulas for the -meaning of these parameters: - -"born"_pair_born.html: a,b,c: type pairs: -"born/coul/long, born/coul/msm"_pair_born.html: coulombic_cutoff: type global: -"buck"_pair_buck.html: a,c: type pairs: -"buck/coul/long, buck/coul/msm"_pair_buck.html: coulombic_cutoff: type global: -"buck/mdf"_pair_mdf.html: a,c: type pairs: -"coul/cut"_pair_coul.html: scale: type pairs: -"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs: -"coul/debye"_pair_coul.html: scale: type pairs: -"coul/dsf"_pair_coul.html: coulombic_cutoff: type global: -"coul/long, coul/msm"_pair_coul.html: coulombic_cutoff, scale: type pairs: -"coul/long/soft"_pair_fep_soft.html: scale, lambda, coulombic_cutoff: type pairs: -"eam, eam/alloy, eam/fs"_pair_eam.html: scale: type pairs: -"gauss"_pair_gauss.html: a: type pairs: -"lennard/mdf"_pair_mdf.html: A,B: type pairs: -"lj/class2"_pair_class2.html: epsilon,sigma: type pairs: -"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma,coulombic_cutoff: type pairs: -"lj/cut"_pair_lj.html: epsilon,sigma: type pairs: -"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs: -"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda,coulombic_cutoff: type pairs: -"lj/cut/coul/dsf"_pair_lj.html: cutoff: type global: -"lj/cut/tip4p/cut"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs: -"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: -"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs: -"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs: -"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs: -"lubricate"_pair_lubricate.html: mu: global: -"mie/cut"_pair_mie.html: epsilon,sigma,gamma_repulsive,gamma_attractive: type pairs: -"morse, morse/smooth/linear"_pair_morse.html: D0,R0,alpha: type pairs: -"morse/soft"_pair_morse.html: D0,R0,alpha,lambda: type pairs: -"nm/cut"_pair_nm.html: E0,R0,m,n: type pairs: -"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: E0,R0,m,n,coulombic_cutoff: type pairs: -"reax/c"_pair_reaxc.html: chi, eta, gamma: type global: -"spin/dmi"_pair_spin_dmi.html: coulombic_cutoff: type global: -"spin/exchange"_pair_spin_exchange.html: coulombic_cutoff: type global: -"spin/magelec"_pair_spin_magelec.html: coulombic_cutoff: type global: -"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global: -"table"_pair_table.html: table_cutoff: type pairs: -"ufm"_pair_ufm.html: epsilon,sigma: type pairs: -"soft"_pair_soft.html: a: type pairs: :tb(c=3,s=:) - -NOTE: It is easy to add new pairwise potentials and their parameters -to this list. All it typically takes is adding an extract() method to -the pair_*.cpp file associated with the potential. - -Some parameters are global settings for the pair style, e.g. the -viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html. -Other parameters apply to atom type pairs within the pair style, -e.g. the prefactor "a" for "pair_style soft"_pair_soft.html. - -Note that for many of the potentials, the parameter that can be varied -is effectively a prefactor on the entire energy expression for the -potential, e.g. the lj/cut epsilon. The parameters listed as "scale" -are exactly that, since the energy expression for the -"coul/cut"_pair_coul.html potential (for example) has no labeled -prefactor in its formula. To apply an effective prefactor to some -potentials, multiple parameters need to be altered. For example, the -"Buckingham potential"_pair_buck.html needs both the A and C terms -altered together. To scale the Buckingham potential, you should thus -list the pair style twice, once for A and once for C. - -If a type pair parameter is specified, the {I} and {J} settings should -be specified to indicate which type pairs to apply it to. If a global -parameter is specified, the {I} and {J} settings still need to be -specified, but are ignored. - -Similar to the "pair_coeff command"_pair_coeff.html, I and J can be -specified in one of two ways. Explicit numeric values can be used for -each, as in the 1st example above. I <= J is required. LAMMPS sets -the coefficients for the symmetric J,I interaction to the same values. - -A wild-card asterisk can be used in place of or in conjunction with -the I,J arguments to set the coefficients for multiple pairs of atom -types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of atom types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). Note that only type pairs with I <= J are considered; if -asterisks imply type pairs where J < I, they are ignored. - -IMPROTANT NOTE: If "pair_style hybrid or -hybrid/overlay"_pair_hybrid.html is being used, then the {pstyle} will -be a sub-style name. You must specify I,J arguments that correspond -to type pair values defined (via the "pair_coeff"_pair_coeff.html -command) for that sub-style. - -The {v_name} argument for keyword {pair} is the name of an -"equal-style variable"_variable.html which will be evaluated each time -this fix is invoked to set the parameter to a new value. It should be -specified as v_name, where name is the variable name. Equal-style -variables can specify formulas with various mathematical functions, -and include "thermo_style"_thermo_style.html command keywords for the -simulation box parameters and timestep and elapsed time. Thus it is -easy to specify parameters that change as a function of time or span -consecutive runs in a continuous fashion. For the latter, see the -{start} and {stop} keywords of the "run"_run.html command and the -{elaplong} keyword of "thermo_style custom"_thermo_style.html for -details. - -For example, these commands would change the prefactor coefficient of -the "pair_style soft"_pair_soft.html potential from 10.0 to 30.0 in a -linear fashion over the course of a simulation: - -variable prefactor equal ramp(10,30) -fix 1 all adapt 1 pair soft a * * v_prefactor :pre - -:line - -The {bond} keyword uses the specified variable to change the value of -a bond coefficient over time, very similar to how the {pair} keyword -operates. The only difference is that now a bond coefficient for a -given bond type is adapted. - -A wild-card asterisk can be used in place of or in conjunction with -the bond type argument to set the coefficients for multiple bond types. -This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of -atom types, then an asterisk with no numeric values means all types -from 1 to N. A leading asterisk means all types from 1 to n (inclusive). -A trailing asterisk means all types from n to N (inclusive). A middle -asterisk means all types from m to n (inclusive). - -Currently {bond} does not support bond_style hybrid nor bond_style -hybrid/overlay as bond styles. The only bonds that currently are -working with fix_adapt are - -"gromos"_bond_gromos.html: k, r0: type bonds: -"harmonic"_bond_harmonic.html: k,r0: type bonds :tb(c=3,s=:) - -:line - -The {kspace} keyword used the specified variable as a scale factor on -the energy, forces, virial calculated by whatever K-Space solver is -defined by the "kspace_style"_kspace_style.html command. If the -variable has a value of 1.0, then the solver is unaltered. - -The {kspace} keyword works this way whether the {scale} keyword -is set to {no} or {yes}. - -:line - -The {atom} keyword enables various atom properties to be changed. The -{aparam} argument is the name of the parameter to change. This is the -current list of atom parameters that can be varied by this fix: - -charge = charge on particle -diameter = diameter of particle :ul - -The {v_name} argument of the {atom} keyword is the name of an -"equal-style variable"_variable.html which will be evaluated each time -this fix is invoked to set the parameter to a new value. It should be -specified as v_name, where name is the variable name. See the -discussion above describing the formulas associated with equal-style -variables. The new value is assigned to the corresponding attribute -for all atoms in the fix group. - -NOTE: The {atom} keyword works this way whether the {scale} keyword is -set to {no} or {yes}. I.e. the use of scale yes is not yet supported -by the {atom} keyword. - -If the atom parameter is {diameter} and per-atom density and per-atom -mass are defined for particles (e.g. "atom_style -granular"_atom_style.html), then the mass of each particle is also -changed when the diameter changes (density is assumed to stay -constant). - -For example, these commands would shrink the diameter of all granular -particles in the "center" group from 1.0 to 0.1 in a linear fashion -over the course of a 1000-step simulation: - -variable size equal ramp(1.0,0.1) -fix 1 center adapt 10 atom diameter v_size :pre - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -For "rRESPA time integration"_run_style.html, this fix changes -parameters on the outermost rRESPA level. - -[Restrictions:] none - -[Related commands:] - -"compute ti"_compute_ti.html - -[Default:] - -The option defaults are scale = no, reset = no. diff --git a/doc/txt/fix_adapt_fep.txt b/doc/txt/fix_adapt_fep.txt deleted file mode 100644 index 9a9255db06..0000000000 --- a/doc/txt/fix_adapt_fep.txt +++ /dev/null @@ -1,273 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix adapt/fep command :h3 - -[Syntax:] - -fix ID group-ID adapt/fep N attribute args ... keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -adapt/fep = style name of this fix command :l -N = adapt simulation settings every this many timesteps :l -one or more attribute/arg pairs may be appended :l -attribute = {pair} or {kspace} or {atom} :l - {pair} args = pstyle pparam I J v_name - pstyle = pair style name, e.g. lj/cut - pparam = parameter to adapt over time - I,J = type pair(s) to set parameter for - v_name = variable with name that calculates value of pparam - {kspace} arg = v_name - v_name = variable with name that calculates scale factor on K-space terms - {atom} args = aparam v_name - aparam = parameter to adapt over time - I = type(s) to set parameter for - v_name = variable with name that calculates value of aparam :pre -zero or more keyword/value pairs may be appended :l -keyword = {scale} or {reset} or {after} :l - {scale} value = {no} or {yes} - {no} = the variable value is the new setting - {yes} = the variable value multiplies the original setting - {reset} value = {no} or {yes} - {no} = values will remain altered at the end of a run - {yes} = reset altered values to their original values at the end - of a run - {after} value = {no} or {yes} - {no} = parameters are adapted at timestep N - {yes} = parameters are adapted one timestep after N :pre -:ule - -[Examples:] - -fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor -fix 1 all adapt/fep 1 pair soft a 2* 3 v_prefactor -fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes -fix 1 all adapt/fep 10 atom diameter 1 v_size :pre - -[Description:] - -Change or adapt one or more specific simulation attributes or settings -over time as a simulation runs. - -This is an enhanced version of the "fix adapt"_fix_adapt.html command -with two differences, - -It is possible to modify the charges of chosen atom types only, -instead of scaling all the charges in the system. :ulb,l - -There is a new option {after} for better compatibility with "fix -ave/time". :l -:ule - -This version is suited for free energy calculations using -"compute ti"_compute_ti.html or "compute fep"_compute_fep.html. - -If {N} is specified as 0, the specified attributes are only changed -once, before the simulation begins. This is all that is needed if the -associated variables are not time-dependent. If {N} > 0, then changes -are made every {N} steps during the simulation, presumably with a -variable that is time-dependent. - -Depending on the value of the {reset} keyword, attributes changed by -this fix will or will not be reset back to their original values at -the end of a simulation. Even if {reset} is specified as {yes}, a -restart file written during a simulation will contain the modified -settings. - -If the {scale} keyword is set to {no}, then the value the parameter is -set to will be whatever the variable generates. If the {scale} -keyword is set to {yes}, then the value of the altered parameter will -be the initial value of that parameter multiplied by whatever the -variable generates. I.e. the variable is now a "scale factor" applied -in (presumably) a time-varying fashion to the parameter. Internally, -the parameters themselves are actually altered; make sure you use the -{reset yes} option if you want the parameters to be restored to their -initial values after the run. - -If the {after} keyword is set to {yes}, then the parameters are -changed one timestep after the multiple of N. In this manner, if a fix -such as "fix ave/time" is used to calculate averages at every N -timesteps, all the contributions to the average will be obtained with -the same values of the parameters. - -:line - -The {pair} keyword enables various parameters of potentials defined by -the "pair_style"_pair_style.html command to be changed, if the pair -style supports it. Note that the "pair_style"_pair_style.html and -"pair_coeff"_pair_coeff.html commands must be used in the usual manner -to specify these parameters initially; the fix adapt command simply -overrides the parameters. - -The {pstyle} argument is the name of the pair style. If "pair_style -hybrid or hybrid/overlay"_pair_hybrid.html is used, {pstyle} should be -a sub-style name. For example, {pstyle} could be specified as "soft" -or "lubricate". The {pparam} argument is the name of the parameter to -change. This is the current list of pair styles and parameters that -can be varied by this fix. See the doc pages for individual pair -styles and their energy formulas for the meaning of these parameters: - -"born"_pair_born.html: a,b,c: type pairs: -"buck"_pair_buck.html: a,c: type pairs: -"buck/mdf"_pair_mdf.html: a,c: type pairs: -"coul/cut"_pair_coul.html: scale: type pairs: -"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs: -"coul/long, coul/msm"_pair_coul.html: scale: type pairs: -"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs: -"eam"_pair_eam.html: scale: type pairs: -"gauss"_pair_gauss.html: a: type pairs: -"lennard/mdf"_pair_mdf.html: a,b: type pairs: -"lj/class2"_pair_class2.html: epsilon,sigma: type pairs: -"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs: -"lj/cut"_pair_lj.html: epsilon,sigma: type pairs: -"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: -"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs: -"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: -"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs: -"lj/cut/tip4p/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: -"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs: -"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs: -"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs: -"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs: -"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs: -"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs: -"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs: -"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs: -"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs: -"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:) - -NOTE: It is easy to add new potentials and their parameters to this -list. All it typically takes is adding an extract() method to the -pair_*.cpp file associated with the potential. - -Note that for many of the potentials, the parameter that can be varied -is effectively a prefactor on the entire energy expression for the -potential, e.g. the lj/cut epsilon. The parameters listed as "scale" -are exactly that, since the energy expression for the -"coul/cut"_pair_coul.html potential (for example) has no labeled -prefactor in its formula. To apply an effective prefactor to some -potentials, multiple parameters need to be altered. For example, the -"Buckingham potential"_pair_buck.html needs both the A and C terms -altered together. To scale the Buckingham potential, you should thus -list the pair style twice, once for A and once for C. - -If a type pair parameter is specified, the {I} and {J} settings should -be specified to indicate which type pairs to apply it to. If a global -parameter is specified, the {I} and {J} settings still need to be -specified, but are ignored. - -Similar to the "pair_coeff command"_pair_coeff.html, I and J can be -specified in one of two ways. Explicit numeric values can be used for -each, as in the 1st example above. I <= J is required. LAMMPS sets -the coefficients for the symmetric J,I interaction to the same values. - -A wild-card asterisk can be used in place of or in conjunction with -the I,J arguments to set the coefficients for multiple pairs of atom -types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of atom types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). Note that only type pairs with I <= J are considered; if -asterisks imply type pairs where J < I, they are ignored. - -IMPROTANT NOTE: If "pair_style hybrid or -hybrid/overlay"_pair_hybrid.html is being used, then the {pstyle} will -be a sub-style name. You must specify I,J arguments that correspond -to type pair values defined (via the "pair_coeff"_pair_coeff.html -command) for that sub-style. - -The {v_name} argument for keyword {pair} is the name of an -"equal-style variable"_variable.html which will be evaluated each time -this fix is invoked to set the parameter to a new value. It should be -specified as v_name, where name is the variable name. Equal-style -variables can specify formulas with various mathematical functions, -and include "thermo_style"_thermo_style.html command keywords for the -simulation box parameters and timestep and elapsed time. Thus it is -easy to specify parameters that change as a function of time or span -consecutive runs in a continuous fashion. For the latter, see the -{start} and {stop} keywords of the "run"_run.html command and the -{elaplong} keyword of "thermo_style custom"_thermo_style.html for -details. - -For example, these commands would change the prefactor coefficient of -the "pair_style soft"_pair_soft.html potential from 10.0 to 30.0 in a -linear fashion over the course of a simulation: - -variable prefactor equal ramp(10,30) -fix 1 all adapt 1 pair soft a * * v_prefactor :pre - -:line - -The {kspace} keyword used the specified variable as a scale factor on -the energy, forces, virial calculated by whatever K-Space solver is -defined by the "kspace_style"_kspace_style.html command. If the -variable has a value of 1.0, then the solver is unaltered. - -The {kspace} keyword works this way whether the {scale} keyword -is set to {no} or {yes}. - -:line - -The {atom} keyword enables various atom properties to be changed. The -{aparam} argument is the name of the parameter to change. This is the -current list of atom parameters that can be varied by this fix: - -charge = charge on particle -diameter = diameter of particle :ul - -The {I} argument indicates which atom types are affected. A wild-card -asterisk can be used in place of or in conjunction with the I argument -to set the coefficients for multiple atom types. - -The {v_name} argument of the {atom} keyword is the name of an -"equal-style variable"_variable.html which will be evaluated each time -this fix is invoked to set the parameter to a new value. It should be -specified as v_name, where name is the variable name. See the -discussion above describing the formulas associated with equal-style -variables. The new value is assigned to the corresponding attribute -for all atoms in the fix group. - -If the atom parameter is {diameter} and per-atom density and per-atom -mass are defined for particles (e.g. "atom_style -granular"_atom_style.html), then the mass of each particle is also -changed when the diameter changes (density is assumed to stay -constant). - -For example, these commands would shrink the diameter of all granular -particles in the "center" group from 1.0 to 0.1 in a linear fashion -over the course of a 1000-step simulation: - -variable size equal ramp(1.0,0.1) -fix 1 center adapt 10 atom diameter * v_size :pre - -For "rRESPA time integration"_run_style.html, this fix changes -parameters on the outermost rRESPA level. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"compute fep"_compute_fep.html, "fix adapt"_fix_adapt.html, "compute -ti"_compute_ti.html, "pair_fep_soft"_pair_fep_soft.html - -[Default:] - -The option defaults are scale = no, reset = no, after = no. diff --git a/doc/txt/fix_addforce.txt b/doc/txt/fix_addforce.txt deleted file mode 100644 index 4fdf9a41dd..0000000000 --- a/doc/txt/fix_addforce.txt +++ /dev/null @@ -1,181 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix addforce command :h3 - -[Syntax:] - -fix ID group-ID addforce fx fy fz keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -addforce = style name of this fix command :l -fx,fy,fz = force component values (force units) :l - any of fx,fy,fz can be a variable (see below) :pre -zero or more keyword/value pairs may be appended to args :l -keyword = {every} or {region} or {energy} :l - {every} value = Nevery - Nevery = add force every this many timesteps - {region} value = region-ID - region-ID = ID of region atoms must be in to have added force - {energy} value = v_name - v_name = variable with name that calculates the potential energy of each atom in the added force field :pre -:ule - -[Examples:] - -fix kick flow addforce 1.0 0.0 0.0 -fix kick flow addforce 1.0 0.0 v_oscillate -fix ff boundary addforce 0.0 0.0 v_push energy v_espace :pre - -[Description:] - -Add fx,fy,fz to the corresponding component of force for each atom in -the group. This command can be used to give an additional push to -atoms in a simulation, such as for a simulation of Poiseuille flow in -a channel. - -Any of the 3 quantities defining the force components can be specified -as an equal-style or atom-style "variable"_variable.html, namely {fx}, -{fy}, {fz}. If the value is a variable, it should be specified as -v_name, where name is the variable name. In this case, the variable -will be evaluated each timestep, and its value(s) used to determine -the force component. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent force field. - -Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent force -field with optional time-dependence as well. - -If the {every} keyword is used, the {Nevery} setting determines how -often the forces are applied. The default value is 1, for every -timestep. - -If the {region} keyword is used, the atom must also be in the -specified geometric "region"_region.html in order to have force added -to it. - -:line - -Adding a force to atoms implies a change in their potential energy as -they move due to the applied force field. For dynamics via the "run" -command, this energy can be optionally added to the system's potential -energy for thermodynamic output (see below). For energy minimization -via the "minimize" command, this energy must be added to the system's -potential energy to formulate a self-consistent minimization problem -(see below). - -The {energy} keyword is not allowed if the added force is a constant -vector F = (fx,fy,fz), with all components defined as numeric -constants and not as variables. This is because LAMMPS can compute -the energy for each atom directly as E = -x dot F = -(x*fx + y*fy + -z*fz), so that -Grad(E) = F. - -The {energy} keyword is optional if the added force is defined with -one or more variables, and if you are performing dynamics via the -"run"_run.html command. If the keyword is not used, LAMMPS will set -the energy to 0.0, which is typically fine for dynamics. - -The {energy} keyword is required if the added force is defined with -one or more variables, and you are performing energy minimization via -the "minimize" command. The keyword specifies the name of an -atom-style "variable"_variable.html which is used to compute the -energy of each atom as function of its position. Like variables used -for {fx}, {fy}, {fz}, the energy variable is specified as v_name, -where name is the variable name. - -Note that when the {energy} keyword is used during an energy -minimization, you must insure that the formula defined for the -atom-style "variable"_variable.html is consistent with the force -variable formulas, i.e. that -Grad(E) = F. For example, if the force -were a spring-like F = kx, then the energy formula should be E = --0.5kx^2. If you don't do this correctly, the minimization will not -converge properly. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the potential "energy" inferred by the added force to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. This is a fictitious quantity but is -needed so that the "minimize"_minimize.html command can include the -forces added by this fix in a consistent manner. I.e. there is a -decrease in potential energy when atoms move in the direction of the -added force. - -The "fix_modify"_fix_modify.html {virial} option is supported by this -fix to add the contribution due to the added forces on atoms to the -system's virial as part of "thermodynamic output"_thermo_style.html. -The default is {virial no} - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost -level. - -This fix computes a global scalar and a global 3-vector of forces, -which can be accessed by various "output commands"_Howto_output.html. -The scalar is the potential energy discussed above. The vector is the -total force on the group of atoms before the forces on individual -atoms are changed by the fix. The scalar and vector values calculated -by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. You should not -specify force components with a variable that has time-dependence for -use with a minimizer, since the minimizer increments the timestep as -the iteration count during the minimization. - -NOTE: If you want the fictitious potential energy associated with the -added forces to be included in the total potential energy of the -system (the quantity being minimized), you MUST enable the -"fix_modify"_fix_modify.html {energy} option for this fix. - -[Restrictions:] none - -[Related commands:] - -"fix setforce"_fix_setforce.html, "fix aveforce"_fix_aveforce.html - -[Default:] - -The option default for the every keyword is every = 1. diff --git a/doc/txt/fix_addtorque.txt b/doc/txt/fix_addtorque.txt deleted file mode 100644 index 0963915e7a..0000000000 --- a/doc/txt/fix_addtorque.txt +++ /dev/null @@ -1,98 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix addtorque command :h3 - -[Syntax:] - -fix ID group-ID addtorque Tx Ty Tz :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -addtorque = style name of this fix command :l -Tx,Ty,Tz = torque component values (torque units) :l -any of Tx,Ty,Tz can be a variable (see below) :l -:ule - -[Examples:] - -fix kick bead addtorque 2.0 3.0 5.0 -fix kick bead addtorque 0.0 0.0 v_oscillate :pre - -[Description:] - -Add a set of forces to each atom in -the group such that: - -the components of the total torque applied on the group (around its -center of mass) are Tx,Ty,Tz :ulb,l - -the group would move as a rigid body in the absence of other -forces. :l -:ule - -This command can be used to drive a group of atoms into rotation. - -Any of the 3 quantities defining the torque components can be specified -as an equal-style "variable"_variable.html, namely {Tx}, -{Ty}, {Tz}. If the value is a variable, it should be specified as -v_name, where name is the variable name. In this case, the variable -will be evaluated each timestep, and its value used to determine the -torque component. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent torque. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the potential "energy" inferred by the added forces to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. This is a fictitious quantity but is -needed so that the "minimize"_minimize.html command can include the -forces added by this fix in a consistent manner. I.e. there is a -decrease in potential energy when atoms move in the direction of the -added forces. - -The "fix_modify"_fix_modify.html {respa} option is supported by -this fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its torque. Default is the outermost level. - -This fix computes a global scalar and a global 3-vector, which can be -accessed by various "output commands"_Howto_output.html. The scalar -is the potential energy discussed above. The vector is the total -torque on the group of atoms before the forces on individual atoms are -changed by the fix. The scalar and vector values calculated by this -fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. You should not -specify force components with a variable that has time-dependence for -use with a minimizer, since the minimizer increments the timestep as -the iteration count during the minimization. - -[Restrictions:] - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix addforce"_fix_addforce.html - -[Default:] none diff --git a/doc/txt/fix_append_atoms.txt b/doc/txt/fix_append_atoms.txt deleted file mode 100644 index 860be9c9fa..0000000000 --- a/doc/txt/fix_append_atoms.txt +++ /dev/null @@ -1,112 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix append/atoms command :h3 - -[Syntax:] - -fix ID group-ID append/atoms face ... keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -append/atoms = style name of this fix command :l -face = {zhi} :l -zero or more keyword/value pairs may be appended :l -keyword = {basis} or {size} or {freq} or {temp} or {random} or {units} :l - {basis} values = M itype - M = which basis atom - itype = atom type (1-N) to assign to this basis atom - {size} args = Lz - Lz = z size of lattice region appended in a single event(distance units) - {freq} args = freq - freq = the number of timesteps between append events - {temp} args = target damp seed extent - target = target temperature for the region between zhi-extent and zhi (temperature units) - damp = damping parameter (time units) - seed = random number seed for langevin kicks - extent = extent of thermostatted region (distance units) - {random} args = xmax ymax zmax seed - {xmax}, {ymax}, {zmax} = maximum displacement in particular direction (distance units) - {seed} = random number seed for random displacement - {units} value = {lattice} or {box} - {lattice} = the wall position is defined in lattice units - {box} = the wall position is defined in simulation box units :pre -:ule - -[Examples:] - -fix 1 all append/atoms zhi size 5.0 freq 295 units lattice -fix 4 all append/atoms zhi size 15.0 freq 5 units box -fix A all append/atoms zhi size 1.0 freq 1000 units lattice :pre - -[Description:] - -This fix creates atoms on a lattice, appended on the zhi edge of the -system box. This can be useful when a shock or wave is propagating -from zlo. This allows the system to grow with time to accommodate an -expanding wave. A simulation box must already exist, which is -typically created via the "create_box"_create_box.html command. -Before using this command, a lattice must also be defined using the -"lattice"_lattice.html command. - -This fix will automatically freeze atoms on the zhi edge of the -system, so that overlaps are avoided when new atoms are appended. - -The {basis} keyword specifies an atom type that will be assigned to -specific basis atoms as they are created. See the -"lattice"_lattice.html command for specifics on how basis atoms are -defined for the unit cell of the lattice. By default, all created -atoms are assigned type = 1 unless this keyword specifies differently. - -The {size} keyword defines the size in z of the chunk of material to -be added. - -The {random} keyword will give the atoms random displacements around -their lattice points to simulate some initial temperature. - -The {temp} keyword will cause a region to be thermostatted with a -Langevin thermostat on the zhi boundary. The size of the region is -measured from zhi and is set with the {extent} argument. - -The {units} keyword determines the meaning of the distance units used -to define a wall position, but only when a numeric constant is used. -A {box} value selects standard distance units as defined by the -"units"_units.html command, e.g. Angstroms for units = real or metal. -A {lattice} value means the distance units are in lattice spacings. -The "lattice"_lattice.html command must have been previously used to -define the lattice spacings. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -The boundary on which atoms are added with append/atoms must be -shrink/minimum. The opposite boundary may be any boundary type other -than periodic. - -[Related commands:] - -"fix wall/piston"_fix_wall_piston.html command - -[Default:] - -The keyword defaults are size = 0.0, freq = 0, units = lattice. All -added atoms are of type 1 unless the basis keyword is used. diff --git a/doc/txt/fix_atc.txt b/doc/txt/fix_atc.txt deleted file mode 100644 index 6de917e571..0000000000 --- a/doc/txt/fix_atc.txt +++ /dev/null @@ -1,247 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix atc command :h3 - -[Syntax:] - -fix atc :pre - -fixID = name of fix :l -group = name of group fix is to be applied :l -type = {thermal} or {two_temperature} or {hardy} or {field} :l - {thermal} = thermal coupling with fields: temperature - {two_temperature} = electron-phonon coupling with field: temperature and electron_temperature - {hardy} = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) - {field} = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) :pre -parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l -:ule - -[Examples:] - -fix AtC internal atc thermal Ar_thermal.dat -fix AtC internal atc two_temperature Ar_ttm.mat -fix AtC internal atc hardy -fix AtC internal atc field :pre - -[Description:] - -This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions. - -:c,image(JPG/atc_nanotube.jpg) - -The following coupling example is typical, but non-exhaustive: - # ... commands to create and initialize the MD system :pre - - # initial fix to designate coupling type and group to apply it to - # tag group physics material_file - fix AtC internal atc thermal Ar_thermal.mat :pre - - # create a uniform 12 x 2 x 2 mesh that covers region contain the group - # nx ny nz region periodicity - fix_modify AtC mesh create 12 2 2 mdRegion f p p :pre - - # specify the control method for the type of coupling - # physics control_type - fix_modify AtC thermal control flux :pre - - # specify the initial values for the empirical field "temperature" - # field node_group value - fix_modify AtC initial temperature all 30 :pre - - # create an output stream for nodal fields - # filename output_frequency - fix_modify AtC output atc_fe_output 100 :pre - - run 1000 :pre - -likewise for this post-processing example: - - # ... commands to create and initialize the MD system :pre - - # initial fix to designate post-processing and the group to apply it to - # no material file is allowed nor required - fix AtC internal atc hardy :pre - - # for hardy fix, specific kernel function (function type and range) to # be used as a localization function - fix AtC kernel quartic_sphere 10.0 :pre - - # create a uniform 1 x 1 x 1 mesh that covers region contain the group - # with periodicity this effectively creats a system average - fix_modify AtC mesh create 1 1 1 box p p p :pre - - # change from default lagrangian map to eulerian - # refreshed every 100 steps - fix_modify AtC atom_element_map eulerian 100 :pre - - # start with no field defined - # add mass density, potential energy density, stress and temperature - fix_modify AtC fields add density energy stress temperature :pre - - # create an output stream for nodal fields - # filename output_frequency - fix_modify AtC output nvtFE 100 text :pre - - run 1000 :pre - -the mesh's linear interpolation functions can be used as the localization function -by using the field option: - - fix AtC internal atc field - fix_modify AtC mesh create 1 1 1 box p p p - ... :pre - -Note coupling and post-processing can be combined in the same simulations using separate fixes. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. The "fix_modify"_fix_modify.html options -relevant to this fix are listed below. No global scalar or vector or -per-atom quantities are stored by this fix for access by various -"output commands"_Howto_output.html. No parameter of this fix can be -used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc. In addition, currently: - -the coupling is restricted to thermal physics :ulb,l -the FE computations are done in serial on each processor. :l,ule - -[Related commands:] - -After specifying this fix in your input script, several other "fix_modify"_fix_modify.html commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions. - -fix_modify commands for setup: - -"fix_modify AtC mesh create"_USER/atc/man_mesh_create.html -"fix_modify AtC mesh quadrature"_USER/atc/man_mesh_quadrature.html -"fix_modify AtC mesh read"_USER/atc/man_mesh_read.html -"fix_modify AtC mesh write"_USER/atc/man_mesh_write.html -"fix_modify AtC mesh create_nodeset"_USER/atc/man_mesh_create_nodeset.html -"fix_modify AtC mesh add_to_nodeset"_USER/atc/man_mesh_add_to_nodeset.html -"fix_modify AtC mesh create_faceset box"_USER/atc/man_mesh_create_faceset_box.html -"fix_modify AtC mesh create_faceset plane"_USER/atc/man_mesh_create_faceset_plane.html -"fix_modify AtC mesh create_elementset"_USER/atc/man_mesh_create_elementset.html -"fix_modify AtC mesh delete_elements"_USER/atc/man_mesh_delete_elements.html -"fix_modify AtC mesh nodeset_to_elementset"_USER/atc/man_mesh_nodeset_to_elementset.html -"fix_modify AtC boundary"_USER/atc/man_boundary.html -"fix_modify AtC internal_quadrature"_USER/atc/man_internal_quadrature.html -"fix_modify AtC time_integration (thermal)"_USER/atc/man_thermal_time_integration.html -"fix_modify AtC time_integration (momentum)"_USER/atc/man_momentum_time_integration.html -"fix_modify AtC extrinsic electron_integration"_USER/atc/man_electron_integration.html -"fix_modify AtC internal_element_set"_USER/atc/man_internal_element_set.html -"fix_modify AtC decomposition"_USER/atc/man_decomposition.html :ul - -fix_modify commands for boundary and initial conditions: - -"fix_modify AtC initial"_USER/atc/man_initial.html -"fix_modify AtC fix"_USER/atc/man_fix_nodes.html -"fix_modify AtC unfix"_USER/atc/man_unfix_nodes.html -"fix_modify AtC fix_flux"_USER/atc/man_fix_flux.html -"fix_modify AtC unfix_flux"_USER/atc/man_unfix_flux.html -"fix_modify AtC source"_USER/atc/man_source.html -"fix_modify AtC remove_source"_USER/atc/man_remove_source.html :ul - -fix_modify commands for control and filtering: - -"fix_modify AtC control"_USER/atc/man_control.html -"fix_modify AtC control thermal"_USER/atc/man_control_thermal.html -"fix_modify AtC control thermal correction_max_iterations"_USER/atc/man_control_thermal_correction_max_iterations.html -"fix_modify AtC control momentum"_USER/atc/man_control_momentum.html -"fix_modify AtC control localized_lambda"_USER/atc/man_localized_lambda.html -"fix_modify AtC control lumped_lambda_solve"_USER/atc/man_lumped_lambda_solve.html -"fix_modify AtC control mask_direction"_USER/atc/man_mask_direction.html control -"fix_modify AtC filter"_USER/atc/man_time_filter.html -"fix_modify AtC filter scale"_USER/atc/man_filter_scale.html -"fix_modify AtC filter type"_USER/atc/man_filter_type.html -"fix_modify AtC equilibrium_start"_USER/atc/man_equilibrium_start.html -"fix_modify AtC extrinsic exchange"_USER/atc/man_extrinsic_exchange.html -"fix_modify AtC poisson_solver"_USER/atc/man_poisson_solver.html :ul - -fix_modify commands for output: - -"fix_modify AtC output"_USER/atc/man_output.html -"fix_modify AtC output nodeset"_USER/atc/man_output_nodeset.html -"fix_modify AtC output elementset"_USER/atc/man_output_elementset.html -"fix_modify AtC output boundary_integral"_USER/atc/man_boundary_integral.html -"fix_modify AtC output contour_integral"_USER/atc/man_contour_integral.html -"fix_modify AtC mesh output"_USER/atc/man_mesh_output.html -"fix_modify AtC write_restart"_USER/atc/man_write_restart.html -"fix_modify AtC read_restart"_USER/atc/man_read_restart.html :ul - -fix_modify commands for post-processing: - -"fix_modify AtC kernel"_USER/atc/man_hardy_kernel.html -"fix_modify AtC fields"_USER/atc/man_hardy_fields.html -"fix_modify AtC grdients"_USER/atc/man_hardy_gradients.html -"fix_modify AtC rates"_USER/atc/man_hardy_rates.html -"fix_modify AtC computes"_USER/atc/man_hardy_computes.html -"fix_modify AtC on_the_fly"_USER/atc/man_hardy_on_the_fly.html -"fix_modify AtC pair_interactions/bond_interactions"_USER/atc/man_pair_interactions.html -"fix_modify AtC sample_frequency"_USER/atc/man_sample_frequency.html -"fix_modify AtC set"_USER/atc/man_set.html :ul - -miscellaneous fix_modify commands: - -"fix_modify AtC atom_element_map"_USER/atc/man_atom_element_map.html -"fix_modify AtC atom_weight"_USER/atc/man_atom_weight.html -"fix_modify AtC write_atom_weights"_USER/atc/man_write_atom_weights.html -"fix_modify AtC reset_time"_USER/atc/man_reset_time.html -"fix_modify AtC reset_atomic_reference_positions"_USER/atc/man_reset_atomic_reference_positions.html -"fix_modify AtC fe_md_boundary"_USER/atc/man_fe_md_boundary.html -"fix_modify AtC boundary_faceset"_USER/atc/man_boundary_faceset.html -"fix_modify AtC consistent_fe_initialization"_USER/atc/man_consistent_fe_initialization.html -"fix_modify AtC mass_matrix"_USER/atc/man_mass_matrix.html -"fix_modify AtC material"_USER/atc/man_material.html -"fix_modify AtC atomic_charge"_USER/atc/man_atomic_charge.html -"fix_modify AtC source_integration"_USER/atc/man_source_integration.html -"fix_modify AtC temperature_definition"_USER/atc/man_temperature_definition.html -"fix_modify AtC track_displacement"_USER/atc/man_track_displacement.html -"fix_modify AtC boundary_dynamics"_USER/atc/man_boundary_dynamics.html -"fix_modify AtC add_species"_USER/atc/man_add_species.html -"fix_modify AtC add_molecule"_USER/atc/man_add_molecule.html -"fix_modify AtC remove_species"_USER/atc/man_remove_species.html -"fix_modify AtC remove_molecule"_USER/atc/man_remove_molecule.html :ul - -Note: a set of example input files with the attendant material files are included with this package - -[Default:] -None - -:line - -For detailed exposition of the theory and algorithms please see: - -:link(Wagner) -[(Wagner)] Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. - -:link(Zimmeman2004) -[(Zimmerman2004)] Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319. - -:link(Zimmerman2010) -[(Zimmerman2010)] Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364. - -:link(Templeton2010) -[(Templeton2010)] Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. - -:link(Jones) -[(Jones)] Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940. - -:link(Templeton2011) -[(Templeton2011)] Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736. - -:link(Mandadapu) -[(Mandadapu)] Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115. - -Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation. - diff --git a/doc/txt/fix_atom_swap.txt b/doc/txt/fix_atom_swap.txt deleted file mode 100644 index cb6bc26aa1..0000000000 --- a/doc/txt/fix_atom_swap.txt +++ /dev/null @@ -1,192 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix atom/swap command :h3 - -[Syntax:] - -fix ID group-ID atom/swap N X seed T keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -atom/swap = style name of this fix command :l -N = invoke this fix every N steps :l -X = number of swaps to attempt every N steps :l -seed = random # seed (positive integer) :l -T = scaling temperature of the MC swaps (temperature units) :l -one or more keyword/value pairs may be appended to args :l -keyword = {types} or {mu} or {ke} or {semi-grand} or {region} :l - {types} values = two or more atom types - {mu} values = chemical potential of swap types (energy units) - {ke} value = {no} or {yes} - {no} = no conservation of kinetic energy after atom swaps - {yes} = kinetic energy is conserved after atom swaps - {semi-grand} value = {no} or {yes} - {no} = particle type counts and fractions conserved - {yes} = semi-grand canonical ensemble, particle fractions not conserved - {region} value = region-ID - region-ID = ID of region to use as an exchange/move volume :pre -:ule - -[Examples:] - -fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2 -fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6 -fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0 :pre - -[Description:] - -This fix performs Monte Carlo swaps of atoms of one given atom type -with atoms of the other given atom types. The specified T is used in -the Metropolis criterion dictating swap probabilities. - -Perform X swaps of atoms of one type with atoms of another type -according to a Monte Carlo probability. Swap candidates must be in the -fix group, must be in the region (if specified), and must be of one of -the listed types. Swaps are attempted between candidates that are -chosen randomly with equal probability among the candidate -atoms. Swaps are not attempted between atoms of the same type since -nothing would happen. - -All atoms in the simulation domain can be moved using regular time -integration displacements, e.g. via "fix nvt"_fix_nh.html, resulting -in a hybrid MC+MD simulation. A smaller-than-usual timestep size may -be needed when running such a hybrid simulation, especially if the -swapped atoms are not well equilibrated. - -The {types} keyword is required. At least two atom types must be -specified. - -The {ke} keyword can be set to {no} to turn off kinetic energy -conservation for swaps. The default is {yes}, which means that swapped -atoms have their velocities scaled by the ratio of the masses of the -swapped atom types. This ensures that the kinetic energy of each atom -is the same after the swap as it was before the swap, even though the -atom masses have changed. - -The {semi-grand} keyword can be set to {yes} to switch to the -semi-grand canonical ensemble as discussed in "(Sadigh)"_#Sadigh. This -means that the total number of each particle type does not need to be -conserved. The default is {no}, which means that the only kind of swap -allowed exchanges an atom of one type with an atom of a different -given type. In other words, the relative mole fractions of the swapped -atoms remains constant. Whereas in the semi-grand canonical ensemble, -the composition of the system can change. Note that when using -{semi-grand}, atoms in the fix group whose type is not listed -in the {types} keyword are ineligible for attempted -conversion. An attempt is made to switch -the selected atom (if eligible) to one of the other listed types -with equal probability. Acceptance of each attempt depends upon the Metropolis criterion. - -The {mu} keyword allows users to specify chemical -potentials. This is required and allowed only when using {semi-grand}. -All chemical potentials are absolute, so there is one for -each swap type listed following the {types} keyword. -In semi-grand canonical ensemble simulations the chemical composition -of the system is controlled by the difference in these values. So -shifting all values by a constant amount will have no effect -on the simulation. - -This command may optionally use the {region} keyword to define swap -volume. The specified region must have been previously defined with a -"region"_region.html command. It must be defined with side = {in}. -Swap attempts occur only between atoms that are both within the -specified region. Swaps are not otherwise attempted. - -You should ensure you do not swap atoms belonging to a molecule, or -LAMMPS will soon generate an error when it tries to find those atoms. -LAMMPS will warn you if any of the atoms eligible for swapping have a -non-zero molecule ID, but does not check for this at the time of -swapping. - -If not using {semi-grand} this fix checks to ensure all atoms of the -given types have the same atomic charge. LAMMPS doesn't enforce this -in general, but it is needed for this fix to simplify the -swapping procedure. Successful swaps will swap the atom type and charge -of the swapped atoms. Conversely, when using {semi-grand}, it is assumed that all the atom -types involved in switches have the same charge. Otherwise, charge -would not be conserved. As a consequence, no checks on atomic charges are -performed, and successful switches update the atom type but not the -atom charge. While it is possible to use {semi-grand} with groups of -atoms that have different charges, these charges will not be changed when the -atom types change. - -Since this fix computes total potential energies before and after -proposed swaps, so even complicated potential energy calculations are -OK, including the following: - - long-range electrostatics (kspace) - many body pair styles - hybrid pair styles - eam pair styles - triclinic systems - need to include potential energy contributions from other fixes :ul - -Some fixes have an associated potential energy. Examples of such fixes -include: "efield"_fix_efield.html, "gravity"_fix_gravity.html, -"addforce"_fix_addforce.html, "langevin"_fix_langevin.html, -"restrain"_fix_restrain.html, "temp/berendsen"_fix_temp_berendsen.html, -"temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html. -For that energy to be included in the total potential energy of the -system (the quantity used when performing GCMC moves), -you MUST enable the "fix_modify"_fix_modify.html {energy} option for -that fix. The doc pages for individual "fix"_fix.html commands -specify if this should be done. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the fix to "binary restart -files"_restart.html. This includes information about the random -number generator seed, the next timestep for MC exchanges, the number -of exchange attempts and successes etc. See -the "read_restart"_read_restart.html command for info on how to -re-specify a fix in an input script that reads a restart file, so that -the operation of the fix continues in an uninterrupted fashion. - -NOTE: For this to work correctly, the timestep must [not] be changed -after reading the restart with "reset_timestep"_reset_timestep.html. -The fix will try to detect it and stop with an error. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. - -This fix computes a global vector of length 2, which can be accessed -by various "output commands"_Howto_output.html. The vector values are -the following global cumulative quantities: - -1 = swap attempts -2 = swap successes :ul - -The vector values calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the "Build package"_Build_package.html -doc page for more info. - -[Related commands:] - -"fix nvt"_fix_nh.html, "neighbor"_neighbor.html, -"fix deposit"_fix_deposit.html, "fix evaporate"_fix_evaporate.html, -"delete_atoms"_delete_atoms.html, "fix gcmc"_fix_gcmc.html - -[Default:] - -The option defaults are ke = yes, semi-grand = no, mu = 0.0 for -all atom types. - -:line - -:link(Sadigh) -[(Sadigh)] B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and -L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012). - diff --git a/doc/txt/fix_ave_atom.txt b/doc/txt/fix_ave_atom.txt deleted file mode 100644 index 596f9ee46c..0000000000 --- a/doc/txt/fix_ave_atom.txt +++ /dev/null @@ -1,179 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix ave/atom command :h3 - -[Syntax:] - -fix ID group-ID ave/atom Nevery Nrepeat Nfreq value1 value2 ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -ave/atom = style name of this fix command :l -Nevery = use input values every this many timesteps :l -Nrepeat = # of times to use input values for calculating averages :l -Nfreq = calculate averages every this many timesteps -one or more input values can be listed :l -value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[i\], f_ID, f_ID\[i\], v_name :l - x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) - c_ID = per-atom vector calculated by a compute with ID - c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) - f_ID = per-atom vector calculated by a fix with ID - f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) - v_name = per-atom vector calculated by an atom-style variable with name :pre -:ule - -[Examples:] - -fix 1 all ave/atom 1 100 100 vx vy vz -fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] -fix 1 all ave/atom 10 20 1000 c_my_stress\[*\] :pre - -[Description:] - -Use one or more per-atom vectors as inputs every few timesteps, and -average them atom by atom over longer timescales. The resulting -per-atom averages can be used by other "output -commands"_Howto_output.html such as the "fix -ave/chunk"_fix_ave_chunk.html or "dump custom"_dump.html commands. - -The group specified with the command means only atoms within the group -have their averages computed. Results are set to 0.0 for atoms not in -the group. - -Each input value can be an atom attribute (position, velocity, force -component) or can be the result of a "compute"_compute.html or -"fix"_fix.html or the evaluation of an atom-style -"variable"_variable.html. In the latter cases, the compute, fix, or -variable must produce a per-atom vector, not a global quantity or -local quantity. If you wish to time-average global quantities from a -compute, fix, or variable, then see the "fix -ave/time"_fix_ave_time.html command. - -Each per-atom value of each input vector is averaged independently. - -"Computes"_compute.html that produce per-atom vectors or arrays are -those which have the word {atom} in their style name. See the doc -pages for individual "fixes"_fix.html to determine which ones produce -per-atom vectors or arrays. "Variables"_variable.html of style {atom} -are the only ones that can be used with this fix since they produce -per-atom vectors. - -Note that for values from a compute or fix, the bracketed index I can -be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form "*" or "*n" or "n*" or -"m*n". If N = the size of the vector (for {mode} = scalar) or the -number of columns in the array (for {mode} = vector), then an asterisk -with no numeric values means all indices from 1 to N. A leading -asterisk means all indices from 1 to n (inclusive). A trailing -asterisk means all indices from n to N (inclusive). A middle asterisk -means all indices from m to n (inclusive). - -Using a wildcard is the same as if the individual columns of the array -had been listed one by one. E.g. these 2 fix ave/atom commands are -equivalent, since the "compute stress/atom"_compute_stress_atom.html -command creates a per-atom array with 6 columns: - -compute my_stress all stress/atom NULL -fix 1 all ave/atom 10 20 1000 c_my_stress\[*\] -fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] c_my_stress\[2\] & - c_my_stress\[3\] c_my_stress\[4\] & - c_my_stress\[5\] c_my_stress\[6\] :pre - -:line - -The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what -timesteps the input values will be used in order to contribute to the -average. The final averaged quantities are generated on timesteps -that are a multiple of {Nfreq}. The average is over {Nrepeat} -quantities, computed in the preceding portion of the simulation every -{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and -{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. - -For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. - -:line - -The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are -self-explanatory. Note that other atom attributes can be used as -inputs to this fix by using the "compute -property/atom"_compute_property_atom.html command and then specifying -an input value from that compute. - -NOTE: The x,y,z attributes are values that are re-wrapped inside the -periodic box whenever an atom crosses a periodic boundary. Thus if -you time average an atom that spends half its time on either side of -the periodic box, you will get a value in the middle of the box. If -this is not what you want, consider averaging unwrapped coordinates, -which can be provided by the "compute -property/atom"_compute_property_atom.html command via its xu,yu,zu -attributes. - -If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed term is -appended, the per-atom vector calculated by the compute is used. If a -bracketed term containing an index I is appended, the Ith column of -the per-atom array calculated by the compute is used. Users can also -write code for their own compute styles and "add them to -LAMMPS"_Modify.html. See the discussion above for how I can -be specified with a wildcard asterisk to effectively specify multiple -values. - -If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed term is -appended, the per-atom vector calculated by the fix is used. If a -bracketed term containing an index I is appended, the Ith column of -the per-atom array calculated by the fix is used. Note that some -fixes only produce their values on certain timesteps, which must be -compatible with {Nevery}, else an error will result. Users can also -write code for their own fix styles and "add them to -LAMMPS"_Modify.html. See the discussion above for how I can be -specified with a wildcard asterisk to effectively specify multiple -values. - -If a value begins with "v_", a variable name must follow which has -been previously defined in the input script as an "atom-style -variable"_variable.html Variables of style {atom} can reference -thermodynamic keywords, or invoke other computes, fixes, or variables -when they are evaluated, so this is a very general means of generating -per-atom quantities to time average. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global scalar or vector quantities are -stored by this fix for access by various "output -commands"_Howto_output.html. - -This fix produces a per-atom vector or array which can be accessed by -various "output commands"_Howto_output.html. A vector is produced if -only a single quantity is averaged by this fix. If two or more -quantities are averaged, then an array of values is produced. The -per-atom values can only be accessed on timesteps that are multiples -of {Nfreq} since that is when averaging is performed. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"compute"_compute.html, "fix ave/histo"_fix_ave_histo.html, "fix -ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html, -"variable"_variable.html, - -[Default:] none diff --git a/doc/txt/fix_ave_correlate.txt b/doc/txt/fix_ave_correlate.txt deleted file mode 100644 index 22e8768f1d..0000000000 --- a/doc/txt/fix_ave_correlate.txt +++ /dev/null @@ -1,369 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix ave/correlate command :h3 - -[Syntax:] - -fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -ave/correlate = style name of this fix command :l -Nevery = use input values every this many timesteps :l -Nrepeat = # of correlation time windows to accumulate :l -Nfreq = calculate time window averages every this many timesteps :l -one or more input values can be listed :l -value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l - c_ID = global scalar calculated by a compute with ID - c_ID\[I\] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below) - f_ID = global scalar calculated by a fix with ID - f_ID\[I\] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below) - v_name = global value calculated by an equal-style variable with name - v_name\[I\] = Ith component of a vector-style variable with name :pre - -zero or more keyword/arg pairs may be appended :l -keyword = {type} or {ave} or {start} or {prefactor} or {file} or {overwrite} or {title1} or {title2} or {title3} :l - {type} arg = {auto} or {upper} or {lower} or {auto/upper} or {auto/lower} or {full} - auto = correlate each value with itself - upper = correlate each value with each succeeding value - lower = correlate each value with each preceding value - auto/upper = auto + upper - auto/lower = auto + lower - full = correlate each value with every other value, including itself = auto + upper + lower - {ave} args = {one} or {running} - one = zero the correlation accumulation every Nfreq steps - running = accumulate correlations continuously - {start} args = Nstart - Nstart = start accumulating correlations on this timestep - {prefactor} args = value - value = prefactor to scale all the correlation data by - {file} arg = filename - filename = name of file to output correlation data to - {overwrite} arg = none = overwrite output file with only latest output - {title1} arg = string - string = text to print as 1st line of output file - {title2} arg = string - string = text to print as 2nd line of output file - {title3} arg = string - string = text to print as 3rd line of output file :pre -:ule - -[Examples:] - -fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate -fix 1 all ave/correlate 1 50 10000 & - c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] & - type upper ave running title1 "My correlation data" :pre -fix 1 all ave/correlate 1 50 10000 c_thermo_press\[*\] - -[Description:] - -Use one or more global scalar values as inputs every few timesteps, -calculate time correlations between them at varying time intervals, -and average the correlation data over longer timescales. The -resulting correlation values can be time integrated by -"variables"_variable.html or used by other "output -commands"_Howto_output.html such as "thermo_style -custom"_thermo_style.html, and can also be written to a file. See the -"fix ave/correlate/long"_fix_ave_correlate_long.html command for an -alternate method for computing correlation functions efficiently over -very long time windows. - -The group specified with this command is ignored. However, note that -specified values may represent calculations performed by computes and -fixes which store their own "group" definitions. - -Each listed value can be the result of a "compute"_compute.html or -"fix"_fix.html or the evaluation of an equal-style or vector-style -"variable"_variable.html. In each case, the compute, fix, or variable -must produce a global quantity, not a per-atom or local quantity. If -you wish to spatial- or time-average or histogram per-atom quantities -from a compute, fix, or variable, then see the "fix -ave/chunk"_fix_ave_chunk.html, "fix ave/atom"_fix_ave_atom.html, or -"fix ave/histo"_fix_ave_histo.html commands. If you wish to convert a -per-atom quantity into a single global value, see the "compute -reduce"_compute_reduce.html command. - -The input values must either be all scalars. What kinds of -correlations between input values are calculated is determined by the -{type} keyword as discussed below. - -"Computes"_compute.html that produce global quantities are those which -do not have the word {atom} in their style name. Only a few -"fixes"_fix.html produce global quantities. See the doc pages for -individual fixes for info on which ones produce such values. -"Variables"_variable.html of style {equal} and {vector} are the only -ones that can be used with this fix. Variables of style {atom} cannot -be used, since they produce per-atom values. - -Note that for values from a compute or fix, the bracketed index I can -be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form "*" or "*n" or "n*" or -"m*n". If N = the size of the vector (for {mode} = scalar) or the -number of columns in the array (for {mode} = vector), then an asterisk -with no numeric values means all indices from 1 to N. A leading -asterisk means all indices from 1 to n (inclusive). A trailing -asterisk means all indices from n to N (inclusive). A middle asterisk -means all indices from m to n (inclusive). - -Using a wildcard is the same as if the individual elements of the -vector had been listed one by one. E.g. these 2 fix ave/correlate -commands are equivalent, since the "compute -pressure"_compute_pressure.html command creates a global vector with 6 -values. - -compute myPress all pressure NULL -fix 1 all ave/correlate 1 50 10000 c_myPress\[*\] -fix 1 all ave/correlate 1 50 10000 & - c_myPress\[1\] c_myPress\[2\] c_myPress\[3\] & - c_myPress\[4\] c_myPress\[5\] c_myPress\[6\] :pre - -:line - -The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what -timesteps the input values will be used to calculate correlation data. -The input values are sampled every {Nevery} timesteps. The -correlation data for the preceding samples is computed on timesteps -that are a multiple of {Nfreq}. Consider a set of samples from some -initial time up to an output timestep. The initial time could be the -beginning of the simulation or the last output time; see the {ave} -keyword for options. For the set of samples, the correlation value -Cij is calculated as: - -Cij(delta) = ave(Vi(t)*Vj(t+delta)) :pre - -which is the correlation value between input values Vi and Vj, -separated by time delta. Note that the second value Vj in the pair is -always the one sampled at the later time. The ave() represents an -average over every pair of samples in the set that are separated by -time delta. The maximum delta used is of size ({Nrepeat}-1)*{Nevery}. -Thus the correlation between a pair of input values yields {Nrepeat} -correlation datums: - -Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery) :pre - -For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on -timesteps 0,5,10,15,...,100 will be used to compute the final averages -on timestep 100. Six averages will be computed: Cij(0), Cij(5), -Cij(10), Cij(15), Cij(20), and Cij(25). Cij(10) on timestep 100 will -be the average of 19 samples, namely Vi(0)*Vj(10), Vi(5)*Vj(15), -Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100). - -{Nfreq} must be a multiple of {Nevery}; {Nevery} and {Nrepeat} must be -non-zero. Also, if the {ave} keyword is set to {one} which is the -default, then {Nfreq} >= ({Nrepeat}-1)*{Nevery} is required. - -:line - -If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed term is -appended, the global scalar calculated by the compute is used. If a -bracketed term is appended, the Ith element of the global vector -calculated by the compute is used. See the discussion above for how I -can be specified with a wildcard asterisk to effectively specify -multiple values. - -Note that there is a "compute reduce"_compute_reduce.html command -which can sum per-atom quantities into a global scalar or vector which -can thus be accessed by fix ave/correlate. Or it can be a compute -defined not in your input script, but by "thermodynamic -output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html -or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for -these commands which give the IDs of these computes. Users can also -write code for their own compute styles and "add them to -LAMMPS"_Modify.html. - -If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed term is -appended, the global scalar calculated by the fix is used. If a -bracketed term is appended, the Ith element of the global vector -calculated by the fix is used. See the discussion above for how I can -be specified with a wildcard asterisk to effectively specify multiple -values. - -Note that some fixes only produce their values on certain timesteps, -which must be compatible with {Nevery}, else an error will result. -Users can also write code for their own fix styles and "add them to -LAMMPS"_Modify.html. - -If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. Only equal-style or -vector-style variables can be referenced; the latter requires a -bracketed term to specify the Ith element of the vector calculated by -the variable. See the "variable"_variable.html command for details. -Note that variables of style {equal} or {vector} define a formula -which can reference individual atom properties or thermodynamic -keywords, or they can invoke other computes, fixes, or variables when -they are evaluated, so this is a very general means of specifying -quantities to time correlate. - -:line - -Additional optional keywords also affect the operation of this fix. - -The {type} keyword determines which pairs of input values are -correlated with each other. For N input values Vi, for i = 1 to N, -let the number of pairs = Npair. Note that the second value in the -pair Vi(t)*Vj(t+delta) is always the one sampled at the later time. - -If {type} is set to {auto} then each input value is correlated with -itself. I.e. Cii = Vi*Vi, for i = 1 to N, so Npair = N. :ulb,l - -If {type} is set -to {upper} then each input value is correlated with every succeeding -value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2. :l - -If {type} is set -to {lower} then each input value is correlated with every preceding -value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2. :l - -If {type} is set to {auto/upper} then each input value is correlated -with itself and every succeeding value. I.e. Cij = Vi*Vj, for i >= j, -so Npair = N*(N+1)/2. :l - -If {type} is set to {auto/lower} then each input value is correlated -with itself and every preceding value. I.e. Cij = Vi*Vj, for i <= j, -so Npair = N*(N+1)/2. :l - -If {type} is set to {full} then each input value is correlated with -itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so -Npair = N^2. :l -:ule - -The {ave} keyword determines what happens to the accumulation of -correlation samples every {Nfreq} timesteps. If the {ave} setting is -{one}, then the accumulation is restarted or zeroed every {Nfreq} -timesteps. Thus the outputs on successive {Nfreq} timesteps are -essentially independent of each other. The exception is that the -Cij(0) = Vi(T)*Vj(T) value at a timestep T, where T is a multiple of -{Nfreq}, contributes to the correlation output both at time T and at -time T+Nfreq. - -If the {ave} setting is {running}, then the accumulation is never -zeroed. Thus the output of correlation data at any timestep is the -average over samples accumulated every {Nevery} steps since the fix -was defined. it can only be restarted by deleting the fix via the -"unfix"_unfix.html command, or by re-defining the fix by re-specifying -it. - -The {start} keyword specifies what timestep the accumulation of -correlation samples will begin on. The default is step 0. Setting it -to a larger value can avoid adding non-equilibrated data to the -correlation averages. - -The {prefactor} keyword specifies a constant which will be used as a -multiplier on the correlation data after it is averaged. It is -effectively a scale factor on Vi*Vj, which can be used to account for -the size of the time window or other unit conversions. - -The {file} keyword allows a filename to be specified. Every {Nfreq} -steps, an array of correlation data is written to the file. The -number of rows is {Nrepeat}, as described above. The number of -columns is the Npair+2, also as described above. Thus the file ends -up to be a series of these array sections. - -The {overwrite} keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the {ave running} setting. - -The {title1} and {title2} and {title3} keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the {file} keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified. - -By default, these header lines are as follows: - -# Time-correlated data for fix ID -# TimeStep Number-of-time-windows -# Index TimeDelta Ncount valueI*valueJ valueI*valueJ ... :pre - -In the first line, ID is replaced with the fix-ID. The second line -describes the two values that are printed at the first of each section -of output. In the third line the value pairs are replaced with the -appropriate fields from the fix ave/correlate command. - -:line - -Let Sij = a set of time correlation data for input values I and J, -namely the {Nrepeat} values: - -Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery) :pre - -As explained below, these datums are output as one column of a global -array, which is effectively the correlation matrix. - -The {trap} function defined for "equal-style variables"_variable.html -can be used to perform a time integration of this vector of datums, -using a trapezoidal rule. This is useful for calculating various -quantities which can be derived from time correlation data. If a -normalization factor is needed for the time integration, it can be -included in the variable formula or via the {prefactor} keyword. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global array of values which can be accessed by -various "output commands"_Howto_output.html. The values can only be -accessed on timesteps that are multiples of {Nfreq} since that is when -averaging is performed. The global array has # of rows = {Nrepeat} -and # of columns = Npair+2. The first column has the time delta (in -timesteps) between the pairs of input values used to calculate the -correlation, as described above. The 2nd column has the number of -samples contributing to the correlation average, as described above. -The remaining Npair columns are for I,J pairs of the N input values, -as determined by the {type} keyword, as described above. - -For {type} = {auto}, the Npair = N columns are ordered: C11, C22, ..., -CNN. :ulb,l - -For {type} = {upper}, the Npair = N*(N-1)/2 columns are ordered: C12, -C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N. :l - -For {type} = {lower}, the Npair = N*(N-1)/2 columns are ordered: C21, -C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1. :l - -For {type} = {auto/upper}, the Npair = N*(N+1)/2 columns are ordered: -C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N, -CNN. :l - -For {type} = {auto/lower}, the Npair = N*(N+1)/2 columns are ordered: -C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1, -CNN. :l - -For {type} = {full}, the Npair = N^2 columns are ordered: C11, C12, -..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1, -CNN. :l -:ule - -The array values calculated by this fix are treated as intensive. If -you need to divide them by the number of atoms, you must do this in a -later processing step, e.g. when using them in a -"variable"_variable.html. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix ave/correlate/long"_fix_ave_correlate_long.html, -"compute"_compute.html, "fix ave/time"_fix_ave_time.html, "fix -ave/atom"_fix_ave_atom.html, "fix ave/chunk"_fix_ave_chunk.html, -"fix ave/histo"_fix_ave_histo.html, "variable"_variable.html - -[Default:] none - -The option defaults are ave = one, type = auto, start = 0, no file -output, title 1,2,3 = strings as described above, and prefactor = 1.0. diff --git a/doc/txt/fix_ave_correlate_long.txt b/doc/txt/fix_ave_correlate_long.txt deleted file mode 100644 index d94bf8af7b..0000000000 --- a/doc/txt/fix_ave_correlate_long.txt +++ /dev/null @@ -1,144 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix ave/correlate/long command :h3 - -[Syntax:] - -fix ID group-ID ave/correlate/long Nevery Nfreq value1 value2 ... keyword args ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -ave/correlate/long = style name of this fix command :l -Nevery = use input values every this many timesteps :l -Nfreq = save state of the time correlation functions every this many timesteps :l -one or more input values can be listed :l -value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l - c_ID = global scalar calculated by a compute with ID - c_ID\[I\] = Ith component of global vector calculated by a compute with ID - f_ID = global scalar calculated by a fix with ID - f_ID\[I\] = Ith component of global vector calculated by a fix with ID - v_name = global value calculated by an equal-style variable with name :pre - -zero or more keyword/arg pairs may be appended :l -keyword = {type} or {start} or {file} or {overwrite} or {title1} or {title2} or {ncorr} or {p} or {m} :l - {type} arg = {auto} or {upper} or {lower} or {auto/upper} or {auto/lower} or {full} - auto = correlate each value with itself - upper = correlate each value with each succeeding value - lower = correlate each value with each preceding value - auto/upper = auto + upper - auto/lower = auto + lower - full = correlate each value with every other value, including itself = auto + upper + lower - {start} args = Nstart - Nstart = start accumulating correlations on this timestep - {file} arg = filename - filename = name of file to output correlation data to - {overwrite} arg = none = overwrite output file with only latest output - {title1} arg = string - string = text to print as 1st line of output file - {title2} arg = string - string = text to print as 2nd line of output file - {ncorr} arg = Ncorrelators - Ncorrelators = number of correlators to store - {nlen} args = Nlen - Nlen = length of each correlator - {ncount} args = Ncount - Ncount = number of values over which succesive correlators are averaged :pre -:ule - -[Examples:] - -fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate -fix 1 all ave/correlate/long 1 10000 & - c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] & - type upper title1 "My correlation data" nlen 15 ncount 3 :pre - -[Description:] - -This fix is similar in spirit and syntax to the "fix -ave/correlate"_fix_ave_correlate.html. However, this fix allows the -efficient calculation of time correlation functions on the fly over -extremely long time windows without too much CPU overhead, using a -multiple-tau method "(Ramirez)"_#Ramirez that decreases the resolution -of the stored correlation function with time. - -The group specified with this command is ignored. However, note that -specified values may represent calculations performed by computes and -fixes which store their own "group" definitions. - -Each listed value can be the result of a compute or fix or the -evaluation of an equal-style variable. See the "fix -ave/correlate"_fix_ave_correlate.html doc page for details. - -The {Nevery} and {Nfreq} arguments specify on what timesteps the input -values will be used to calculate correlation data, and the frequency -with which the time correlation functions will be output to a file. -Note that there is no {Nrepeat} argument, unlike the "fix -ave/correlate"_fix_ave_correlate.html command. - -The optional keywords {ncorr}, {nlen}, and {ncount} are unique to this -command and determine the number of correlation points calculated and -the memory and CPU overhead used by this calculation. {Nlen} and -{ncount} determine the amount of averaging done at longer correlation -times. The default values {nlen=16}, {ncount=2} ensure that the -systematic error of the multiple-tau correlator is always below the -level of the statistical error of a typical simulation (which depends -on the ensemble size and the simulation length). - -The maximum correlation time (in time steps) that can be reached is -given by the formula (nlen-1) * ncount^(ncorr-1). Longer correlation -times are discarded and not calculated. With the default values of -the parameters (ncorr=20, nlen=16 and ncount=2), this corresponds to -7864320 time steps. If longer correlation times are needed, the value -of ncorr should be increased. Using nlen=16 and ncount=2, with -ncorr=30, the maximum number of steps that can be correlated is -80530636808. If ncorr=40, correlation times in excess of 8e12 time -steps can be calculated. - -The total memory needed for each correlation pair is roughly -4*ncorr*nlen*8 bytes. With the default values of the parameters, this -corresponds to about 10 KB. - -For the meaning of the additional optional keywords, see the "fix -ave/correlate"_fix_ave_correlate.html doc page. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -Since this fix in intended for the calculation of time correlation -functions over very long MD simulations, the information about this -fix is written automatically to binary restart files, so that the time -correlation calculation can continue in subsequent simulations. None -of the fix_modify options are relevant to this fix. - -No parameter of this fix can be used with the start/stop keywords of -the run command. This fix is not invoked during energy minimization. - -[Restrictions:] - -This compute is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix ave/correlate"_fix_ave_correlate.html - -[Default:] none - -The option defaults for keywords that are also keywords for the "fix -ave/correlate"_fix_ave_correlate.html command are as follows: type = -auto, start = 0, no file output, title 1,2 = strings as described on -the "fix ave/correlate"_fix_ave_correlate.html doc page. - -The option defaults for keywords unique to this command are as -follows: ncorr=20, nlen=16, ncount=2. - -:line - -:link(Ramirez) -[(Ramirez)] J. Ramirez, S.K. Sukumaran, B. Vorselaars and -A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010). diff --git a/doc/txt/fix_ave_histo.txt b/doc/txt/fix_ave_histo.txt deleted file mode 100644 index 0a17813d21..0000000000 --- a/doc/txt/fix_ave_histo.txt +++ /dev/null @@ -1,369 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix ave/histo command :h3 -fix ave/histo/weight command :h3 - -[Syntax:] - -fix ID group-ID style Nevery Nrepeat Nfreq lo hi Nbin value1 value2 ... keyword args ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -style = {ave/histo} or {ave/histo/weight} = style name of this fix command :l -Nevery = use input values every this many timesteps :l -Nrepeat = # of times to use input values for calculating histogram :l -Nfreq = calculate histogram every this many timesteps :l -lo,hi = lo/hi bounds within which to histogram :l -Nbin = # of histogram bins :l -one or more input values can be listed :l -value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l - x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) - c_ID = scalar or vector calculated by a compute with ID - c_ID\[I\] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below) - f_ID = scalar or vector calculated by a fix with ID - f_ID\[I\] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below) - v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name - v_name\[I\] = value calculated by a vector-style variable with name :pre - -zero or more keyword/arg pairs may be appended :l -keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {title1} or {title2} or {title3} :l - {mode} arg = {scalar} or {vector} - scalar = all input values are scalars - vector = all input values are vectors - {kind} arg = {global} or {peratom} or {local} - {file} arg = filename - filename = name of file to output histogram(s) to - {ave} args = {one} or {running} or {window} - one = output a new average value every Nfreq steps - running = output cumulative average of all previous Nfreq steps - window M = output average of M most recent Nfreq steps - {start} args = Nstart - Nstart = start averaging on this timestep - {beyond} arg = {ignore} or {end} or {extra} - ignore = ignore values outside histogram lo/hi bounds - end = count values outside histogram lo/hi bounds in end bins - extra = create 2 extra bins for value outside histogram lo/hi bounds - {overwrite} arg = none = overwrite output file with only latest output - {title1} arg = string - string = text to print as 1st line of output file - {title2} arg = string - string = text to print as 2nd line of output file - {title3} arg = string - string = text to print as 3rd line of output file, only for vector mode :pre -:ule - -[Examples:] - -fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running -fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press\[2\] c_thermo_press\[3\] title1 "My output values" -fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press\[*\] -fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra -fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD\[1\] c_XRD\[2\] :pre - -[Description:] - -Use one or more values as inputs every few timesteps to create a -single histogram. The histogram can then be averaged over longer -timescales. The resulting histogram can be used by other "output -commands"_Howto_output.html, and can also be written to a file. The -fix ave/histo/weight command has identical syntax to fix ave/histo, -except that exactly two values must be specified. See details below. - -The group specified with this command is ignored for global and local -input values. For per-atom input values, only atoms in the group -contribute to the histogram. Note that regardless of the specified -group, specified values may represent calculations performed by -computes and fixes which store their own "group" definition. - -A histogram is simply a count of the number of values that fall within -a histogram bin. {Nbins} are defined, with even spacing between {lo} -and {hi}. Values that fall outside the lo/hi bounds can be treated in -different ways; see the discussion of the {beyond} keyword below. - -Each input value can be an atom attribute (position, velocity, force -component) or can be the result of a "compute"_compute.html or -"fix"_fix.html or the evaluation of an equal-style or vector-style or -atom-style "variable"_variable.html. The set of input values can be -either all global, all per-atom, or all local quantities. Inputs of -different kinds (e.g. global and per-atom) cannot be mixed. Atom -attributes are per-atom vector values. See the doc page for -individual "compute" and "fix" commands to see what kinds of -quantities they generate. See the optional {kind} keyword below for -how to force the fix ave/histo command to disambiguate if necessary. - -Note that the output of this command is a single histogram for all -input values combined together, not one histogram per input value. -See below for details on the format of the output of this fix. - -The input values must either be all scalars or all vectors (or -arrays), depending on the setting of the {mode} keyword. - -If {mode} = scalar, then the input values must be scalars, or vectors -with a bracketed term appended, indicating the Ith value of the vector -is used. - -If {mode} = vector, then the input values must be vectors, or arrays -with a bracketed term appended, indicating the Ith column of the array -is used. - -Note that for values from a compute or fix, the bracketed index I can -be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form "*" or "*n" or "n*" or -"m*n". If N = the size of the vector (for {mode} = scalar) or the -number of columns in the array (for {mode} = vector), then an asterisk -with no numeric values means all indices from 1 to N. A leading -asterisk means all indices from 1 to n (inclusive). A trailing -asterisk means all indices from n to N (inclusive). A middle asterisk -means all indices from m to n (inclusive). - -Using a wildcard is the same as if the individual elements of the -vector or columns of the array had been listed one by one. E.g. these -2 fix ave/histo commands are equivalent, since the "compute -com/chunk"_compute_com_chunk.html command creates a global array with -3 columns: - -compute myCOM all com/chunk -fix 1 all ave/histo 100 1 100 c_myCOM\[*\] file tmp1.com mode vector -fix 2 all ave/histo 100 1 100 c_myCOM\[1\] c_myCOM\[2\] c_myCOM\[3\] file tmp2.com mode vector :pre - -If the fix ave/histo/weight command is used, exactly two values must -be specified. If the values are vectors, they must be the same -length. The first value (a scalar or vector) is what is histogrammed -into bins, in the same manner the fix ave/histo command operates. The -second value (a scalar or vector) is used as a "weight". This means -that instead of each value tallying a "1" to its bin, the -corresponding weight is tallied. E.g. The Nth entry (weight) in the -second vector is tallied to the bin corresponding to the Nth entry in -the first vector. - -:line - -The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what -timesteps the input values will be used in order to contribute to the -histogram. The final histogram is generated on timesteps that are -multiple of {Nfreq}. It is averaged over {Nrepeat} histograms, -computed in the preceding portion of the simulation every {Nevery} -timesteps. {Nfreq} must be a multiple of {Nevery} and {Nevery} must -be non-zero even if {Nrepeat} is 1. Also, the timesteps -contributing to the histogram value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. - -For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values -on timesteps 90,92,94,96,98,100 will be used to compute the final -histogram on timestep 100. Similarly for timesteps -190,192,194,196,198,200 on timestep 200, etc. If Nrepeat=1 and Nfreq -= 100, then no time averaging of the histogram is done; a histogram is -simply generated on timesteps 100,200,etc. - -:line - -The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are -self-explanatory. Note that other atom attributes can be used as -inputs to this fix by using the "compute -property/atom"_compute_property_atom.html command and then specifying -an input value from that compute. - -If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If {mode} = scalar, then if -no bracketed term is appended, the global scalar calculated by the -compute is used. If a bracketed term is appended, the Ith element of -the global vector calculated by the compute is used. If {mode} = -vector, then if no bracketed term is appended, the global or per-atom -or local vector calculated by the compute is used. If a bracketed -term is appended, the Ith column of the global or per-atom or local -array calculated by the compute is used. See the discussion above for -how I can be specified with a wildcard asterisk to effectively specify -multiple values. - -Note that there is a "compute reduce"_compute_reduce.html command -which can sum per-atom quantities into a global scalar or vector which -can thus be accessed by fix ave/histo. Or it can be a compute defined -not in your input script, but by "thermodynamic -output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html -or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for -these commands which give the IDs of these computes. Users can also -write code for their own compute styles and "add them to -LAMMPS"_Modify.html. - -If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If {mode} = scalar, then if -no bracketed term is appended, the global scalar calculated by the fix -is used. If a bracketed term is appended, the Ith element of the -global vector calculated by the fix is used. If {mode} = vector, then -if no bracketed term is appended, the global or per-atom or local -vector calculated by the fix is used. If a bracketed term is -appended, the Ith column of the global or per-atom or local array -calculated by the fix is used. See the discussion above for how I can -be specified with a wildcard asterisk to effectively specify multiple -values. - -Note that some fixes only produce their values on certain timesteps, -which must be compatible with {Nevery}, else an error will result. -Users can also write code for their own fix styles and "add them to -LAMMPS"_Modify.html. - -If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. If {mode} = scalar, then -only equal-style or vector-style variables can be used, which both -produce global values. In this mode, a vector-style variable requires -a bracketed term to specify the Ith element of the vector calculated -by the variable. If {mode} = vector, then only vector-style or -atom-style variables can be used, which produce a global or per-atom -vector respectively. The vector-style variable must be used without a -bracketed term. See the "variable"_variable.html command for details. - -Note that variables of style {equal}, {vector}, and {atom} define a -formula which can reference individual atom properties or -thermodynamic keywords, or they can invoke other computes, fixes, or -variables when they are evaluated, so this is a very general means of -specifying quantities to histogram. - -:line - -Additional optional keywords also affect the operation of this fix. - -If the {mode} keyword is set to {scalar}, then all input values must -be global scalars, or elements of global vectors. If the {mode} -keyword is set to {vector}, then all input values must be global or -per-atom or local vectors, or columns of global or per-atom or local -arrays. - -The {kind} keyword only needs to be set if a compute or fix produces -more than one kind of output (global, per-atom, local). If this is -not the case, then LAMMPS will determine what kind of input is -provided and whether all the input arguments are consistent. If a -compute or fix produces more than one kind of output, the {kind} -keyword should be used to specify which output will be used. The -remaining input arguments must still be consistent. - -The {beyond} keyword determines how input values that fall outside the -{lo} to {hi} bounds are treated. Values such that {lo} <= value <= -{hi} are assigned to one bin. Values on a bin boundary are assigned -to the lower of the 2 bins. If {beyond} is set to {ignore} then -values < {lo} and values > {hi} are ignored, i.e. they are not binned. -If {beyond} is set to {end} then values < {lo} are counted in the -first bin and values > {hi} are counted in the last bin. If {beyond} -is set to {extend} then two extra bins are created, so that there are -Nbins+2 total bins. Values < {lo} are counted in the first bin and -values > {hi} are counted in the last bin (Nbins+2). Values between -{lo} and {hi} (inclusive) are counted in bins 2 through Nbins+1. The -"coordinate" stored and printed for these two extra bins is {lo} and -{hi}. - -The {ave} keyword determines how the histogram produced every {Nfreq} -steps are averaged with histograms produced on previous steps that -were multiples of {Nfreq}, before they are accessed by another output -command or written to a file. - -If the {ave} setting is {one}, then the histograms produced on -timesteps that are multiples of {Nfreq} are independent of each other; -they are output as-is without further averaging. - -If the {ave} setting is {running}, then the histograms produced on -timesteps that are multiples of {Nfreq} are summed and averaged in a -cumulative sense before being output. Each bin value in the histogram -is thus the average of the bin value produced on that timestep with -all preceding values for the same bin. This running average begins -when the fix is defined; it can only be restarted by deleting the fix -via the "unfix"_unfix.html command, or by re-defining the fix by -re-specifying it. - -If the {ave} setting is {window}, then the histograms produced on -timesteps that are multiples of {Nfreq} are summed within a moving -"window" of time, so that the last M histograms are used to produce -the output. E.g. if M = 3 and Nfreq = 1000, then the output on step -10000 will be the combined histogram of the individual histograms on -steps 8000,9000,10000. Outputs on early steps will be sums over less -than M histograms if they are not available. - -The {start} keyword specifies what timestep histogramming will begin -on. The default is step 0. Often input values can be 0.0 at time 0, -so setting {start} to a larger value can avoid including a 0.0 in -a running or windowed histogram. - -The {file} keyword allows a filename to be specified. Every {Nfreq} -steps, one histogram is written to the file. This includes a leading -line that contains the timestep, number of bins, the total count of -values contributing to the histogram, the count of values that were -not histogrammed (see the {beyond} keyword), the minimum value -encountered, and the maximum value encountered. The min/max values -include values that were not histogrammed. Following the leading -line, one line per bin is written into the file. Each line contains -the bin #, the coordinate for the center of the bin (between {lo} and -{hi}), the count of values in the bin, and the normalized count. The -normalized count is the bin count divided by the total count (not -including values not histogrammed), so that the normalized values sum -to 1.0 across all bins. - -The {overwrite} keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the {ave running} setting. - -The {title1} and {title2} and {title3} keywords allow specification of -the strings that will be printed as the first 3 lines of the output -file, assuming the {file} keyword was used. LAMMPS uses default -values for each of these, so they do not need to be specified. - -By default, these header lines are as follows: - -# Histogram for fix ID -# TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value -# Bin Coord Count Count/Total :pre - -In the first line, ID is replaced with the fix-ID. The second line -describes the six values that are printed at the first of each section -of output. The third describes the 4 values printed for each bin in -the histogram. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix produces a global vector and global array which can be -accessed by various "output commands"_Howto_output.html. The values -can only be accessed on timesteps that are multiples of {Nfreq} since -that is when a histogram is generated. The global vector has 4 -values: - -1 = total counts in the histogram -2 = values that were not histogrammed (see {beyond} keyword) -3 = min value of all input values, including ones not histogrammed -4 = max value of all input values, including ones not histogrammed :ul - -The global array has # of rows = Nbins and # of columns = 3. The -first column has the bin coordinate, the 2nd column has the count of -values in that histogram bin, and the 3rd column has the bin count -divided by the total count (not including missing counts), so that the -values in the 3rd column sum to 1.0. - -The vector and array values calculated by this fix are all treated as -intensive. If this is not the case, e.g. due to histogramming -per-atom input values, then you will need to account for that when -interpreting the values produced by this fix. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix -ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html, -"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html, - -[Default:] none - -The option defaults are mode = scalar, kind = figured out from input -arguments, ave = one, start = 0, no file output, beyond = ignore, and -title 1,2,3 = strings as described above. diff --git a/doc/txt/fix_ave_time.txt b/doc/txt/fix_ave_time.txt deleted file mode 100644 index cca881f2f8..0000000000 --- a/doc/txt/fix_ave_time.txt +++ /dev/null @@ -1,348 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix ave/time command :h3 - -[Syntax:] - -fix ID group-ID ave/time Nevery Nrepeat Nfreq value1 value2 ... keyword args ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -ave/time = style name of this fix command :l -Nevery = use input values every this many timesteps :l -Nrepeat = # of times to use input values for calculating averages :l -Nfreq = calculate averages every this many timesteps :l -one or more input values can be listed :l -value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l - c_ID = global scalar or vector calculated by a compute with ID - c_ID\[I\] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below) - f_ID = global scalar or vector calculated by a fix with ID - f_ID\[I\] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below) - v_name = value(s) calculated by an equal-style or vector-style variable with name - v_name\[I\] = value calculated by a vector-style variable with name :pre - -zero or more keyword/arg pairs may be appended :l -keyword = {mode} or {file} or {ave} or {start} or {off} or {overwrite} or {title1} or {title2} or {title3} :l - {mode} arg = {scalar} or {vector} - scalar = all input values are global scalars - vector = all input values are global vectors or global arrays - {ave} args = {one} or {running} or {window M} - one = output a new average value every Nfreq steps - running = output cumulative average of all previous Nfreq steps - window M = output average of M most recent Nfreq steps - {start} args = Nstart - Nstart = start averaging on this timestep - {off} arg = M = do not average this value - M = value # from 1 to Nvalues - {file} arg = filename - filename = name of file to output time averages to - {overwrite} arg = none = overwrite output file with only latest output - {format} arg = string - string = C-style format string - {title1} arg = string - string = text to print as 1st line of output file - {title2} arg = string - string = text to print as 2nd line of output file - {title3} arg = string - string = text to print as 3rd line of output file, only for vector mode :pre -:ule - -[Examples:] - -fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile -fix 1 all ave/time 100 5 1000 c_thermo_press\[2\] ave window 20 & - title1 "My output values" -fix 1 all ave/time 100 5 1000 c_thermo_press\[*\] -fix 1 all ave/time 1 100 1000 f_indent f_indent\[1\] file temp.indent off 1 :pre - -[Description:] - -Use one or more global values as inputs every few timesteps, and -average them over longer timescales. The resulting averages can be -used by other "output commands"_Howto_output.html such as -"thermo_style custom"_thermo_style.html, and can also be written to a -file. Note that if no time averaging is done, this command can be -used as a convenient way to simply output one or more global values to -a file. - -The group specified with this command is ignored. However, note that -specified values may represent calculations performed by computes and -fixes which store their own "group" definitions. - -Each listed value can be the result of a "compute"_compute.html or -"fix"_fix.html or the evaluation of an equal-style or vector-style -"variable"_variable.html. In each case, the compute, fix, or variable -must produce a global quantity, not a per-atom or local quantity. If -you wish to spatial- or time-average or histogram per-atom quantities -from a compute, fix, or variable, then see the "fix -ave/chunk"_fix_ave_chunk.html, "fix ave/atom"_fix_ave_atom.html, -or "fix ave/histo"_fix_ave_histo.html commands. If you wish to sum a -per-atom quantity into a single global quantity, see the "compute -reduce"_compute_reduce.html command. - -"Computes"_compute.html that produce global quantities are those which -do not have the word {atom} in their style name. Only a few -"fixes"_fix.html produce global quantities. See the doc pages for -individual fixes for info on which ones produce such values. -"Variables"_variable.html of style {equal} and {vector} are the only -ones that can be used with this fix. Variables of style {atom} cannot -be used, since they produce per-atom values. - -The input values must either be all scalars or all vectors depending -on the setting of the {mode} keyword. In both cases, the averaging is -performed independently on each input value. I.e. each input scalar -is averaged independently or each element of each input vector is -averaged independently. - -If {mode} = scalar, then the input values must be scalars, or vectors -with a bracketed term appended, indicating the Ith value of the vector -is used. - -If {mode} = vector, then the input values must be vectors, or arrays -with a bracketed term appended, indicating the Ith column of the array -is used. All vectors must be the same length, which is the length of -the vector or number of rows in the array. - -Note that for values from a compute or fix, the bracketed index I can -be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form "*" or "*n" or "n*" or -"m*n". If N = the size of the vector (for {mode} = scalar) or the -number of columns in the array (for {mode} = vector), then an asterisk -with no numeric values means all indices from 1 to N. A leading -asterisk means all indices from 1 to n (inclusive). A trailing -asterisk means all indices from n to N (inclusive). A middle asterisk -means all indices from m to n (inclusive). - -Using a wildcard is the same as if the individual elements of the -vector or columns of the array had been listed one by one. E.g. these -2 fix ave/time commands are equivalent, since the "compute -rdf"_compute_rdf.html command creates, in this case, a global array -with 3 columns, each of length 50: - -compute myRDF all rdf 50 1 2 -fix 1 all ave/time 100 1 100 c_myRDF\[*\] file tmp1.rdf mode vector -fix 2 all ave/time 100 1 100 c_myRDF\[1\] c_myRDF\[2\] c_myRDF\[3\] file tmp2.rdf mode vector :pre - -:line - -The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what -timesteps the input values will be used in order to contribute to the -average. The final averaged quantities are generated on timesteps -that are a multiple of {Nfreq}. The average is over {Nrepeat} -quantities, computed in the preceding portion of the simulation every -{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and -{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. - -For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc. - -:line - -If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If {mode} = scalar, then if -no bracketed term is appended, the global scalar calculated by the -compute is used. If a bracketed term is appended, the Ith element of -the global vector calculated by the compute is used. If {mode} = -vector, then if no bracketed term is appended, the global vector -calculated by the compute is used. If a bracketed term is appended, -the Ith column of the global array calculated by the compute is used. -See the discussion above for how I can be specified with a wildcard -asterisk to effectively specify multiple values. - -Note that there is a "compute reduce"_compute_reduce.html command -which can sum per-atom quantities into a global scalar or vector which -can thus be accessed by fix ave/time. Or it can be a compute defined -not in your input script, but by "thermodynamic -output"_thermo_style.html or other fixes such as "fix -nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See -the doc pages for these commands which give the IDs of these computes. -Users can also write code for their own compute styles and "add them -to LAMMPS"_Modify.html. - -If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If {mode} = scalar, then if -no bracketed term is appended, the global scalar calculated by the fix -is used. If a bracketed term is appended, the Ith element of the -global vector calculated by the fix is used. If {mode} = vector, then -if no bracketed term is appended, the global vector calculated by the -fix is used. If a bracketed term is appended, the Ith column of the -global array calculated by the fix is used. See the discussion above -for how I can be specified with a wildcard asterisk to effectively -specify multiple values. - -Note that some fixes only produce their values on certain timesteps, -which must be compatible with {Nevery}, else an error will result. -Users can also write code for their own fix styles and "add them to -LAMMPS"_Modify.html. - -If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. If {mode} = scalar, then -only equal-style or vector-style variables can be used, which both -produce global values. In this mode, a vector-style variable requires -a bracketed term to specify the Ith element of the vector calculated -by the variable. If {mode} = vector, then only a vector-style -variable can be used, without a bracketed term. See the -"variable"_variable.html command for details. - -Note that variables of style {equal} and {vector} define a formula -which can reference individual atom properties or thermodynamic -keywords, or they can invoke other computes, fixes, or variables when -they are evaluated, so this is a very general means of specifying -quantities to time average. - -:line - -Additional optional keywords also affect the operation of this fix. - -If the {mode} keyword is set to {scalar}, then all input values must -be global scalars, or elements of global vectors. If the {mode} -keyword is set to {vector}, then all input values must be global -vectors, or columns of global arrays. They can also be global arrays, -which are converted into a series of global vectors (one per column), -as explained above. - -The {ave} keyword determines how the values produced every {Nfreq} -steps are averaged with values produced on previous steps that were -multiples of {Nfreq}, before they are accessed by another output -command or written to a file. - -If the {ave} setting is {one}, then the values produced on timesteps -that are multiples of {Nfreq} are independent of each other; they are -output as-is without further averaging. - -If the {ave} setting is {running}, then the values produced on -timesteps that are multiples of {Nfreq} are summed and averaged in a -cumulative sense before being output. Each output value is thus the -average of the value produced on that timestep with all preceding -values. This running average begins when the fix is defined; it can -only be restarted by deleting the fix via the "unfix"_unfix.html -command, or by re-defining the fix by re-specifying it. - -If the {ave} setting is {window}, then the values produced on -timesteps that are multiples of {Nfreq} are summed and averaged within -a moving "window" of time, so that the last M values are used to -produce the output. E.g. if M = 3 and Nfreq = 1000, then the output -on step 10000 will be the average of the individual values on steps -8000,9000,10000. Outputs on early steps will average over less than M -values if they are not available. - -The {start} keyword specifies what timestep averaging will begin on. -The default is step 0. Often input values can be 0.0 at time 0, so -setting {start} to a larger value can avoid including a 0.0 in a -running or windowed average. - -The {off} keyword can be used to flag any of the input values. If a -value is flagged, it will not be time averaged. Instead the most -recent input value will always be stored and output. This is useful -if one of more of the inputs produced by a compute or fix or variable -are effectively constant or are simply current values. E.g. they are -being written to a file with other time-averaged values for purposes -of creating well-formatted output. - -The {file} keyword allows a filename to be specified. Every {Nfreq} -steps, one quantity or vector of quantities is written to the file for -each input value specified in the fix ave/time command. For {mode} = -scalar, this means a single line is written each time output is -performed. Thus the file ends up to be a series of lines, i.e. one -column of numbers for each input value. For {mode} = vector, an array -of numbers is written each time output is performed. The number of -rows is the length of the input vectors, and the number of columns is -the number of values. Thus the file ends up to be a series of these -array sections. - -The {overwrite} keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the {ave running} setting. - -The {format} keyword sets the numeric format of each value when it is -printed to a file via the {file} keyword. Note that all values are -floating point quantities. The default format is %g. You can specify -a higher precision if desired, e.g. %20.16g. - -The {title1} and {title2} and {title3} keywords allow specification of -the strings that will be printed as the first 2 or 3 lines of the -output file, assuming the {file} keyword was used. LAMMPS uses -default values for each of these, so they do not need to be specified. - -By default, these header lines are as follows for {mode} = scalar: - -# Time-averaged data for fix ID -# TimeStep value1 value2 ... :pre - -In the first line, ID is replaced with the fix-ID. In the second line -the values are replaced with the appropriate fields from the fix -ave/time command. There is no third line in the header of the file, -so the {title3} setting is ignored when {mode} = scalar. - -By default, these header lines are as follows for {mode} = vector: - -# Time-averaged data for fix ID -# TimeStep Number-of-rows -# Row value1 value2 ... :pre - -In the first line, ID is replaced with the fix-ID. The second line -describes the two values that are printed at the first of each section -of output. In the third line the values are replaced with the -appropriate fields from the fix ave/time command. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix produces a global scalar or global vector or global array -which can be accessed by various "output commands"_Howto_output.html. -The values can only be accessed on timesteps that are multiples of -{Nfreq} since that is when averaging is performed. - -A scalar is produced if only a single input value is averaged and -{mode} = scalar. A vector is produced if multiple input values are -averaged for {mode} = scalar, or a single input value for {mode} = -vector. In the first case, the length of the vector is the number of -inputs. In the second case, the length of the vector is the same as -the length of the input vector. An array is produced if multiple -input values are averaged and {mode} = vector. The global array has # -of rows = length of the input vectors and # of columns = number of -inputs. - -If the fix produces a scalar or vector, then the scalar and each -element of the vector can be either "intensive" or "extensive", -depending on whether the values contributing to the scalar or vector -element are "intensive" or "extensive". If the fix produces an array, -then all elements in the array must be the same, either "intensive" or -"extensive". If a compute or fix provides the value being time -averaged, then the compute or fix determines whether the value is -intensive or extensive; see the doc page for that compute or fix for -further info. Values produced by a variable are treated as intensive. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix -ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html, -"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html, - -[Default:] - -The option defaults are mode = scalar, ave = one, start = 0, no file -output, format = %g, title 1,2,3 = strings as described above, and no -off settings for any input values. diff --git a/doc/txt/fix_aveforce.txt b/doc/txt/fix_aveforce.txt deleted file mode 100644 index 8c759864c6..0000000000 --- a/doc/txt/fix_aveforce.txt +++ /dev/null @@ -1,118 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix aveforce command :h3 - -[Syntax:] - -fix ID group-ID aveforce fx fy fz keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -aveforce = style name of this fix command :l -fx,fy,fz = force component values (force units) :l - any of fx,fy,fz can be a variable (see below) :pre -zero or more keyword/value pairs may be appended to args :l -keyword = {region} :l - {region} value = region-ID - region-ID = ID of region atoms must be in to have added force :pre -:ule - -[Examples:] - -fix pressdown topwall aveforce 0.0 -1.0 0.0 -fix 2 bottomwall aveforce NULL -1.0 0.0 region top -fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top :pre - -[Description:] - -Apply an additional external force to a group of atoms in such a way -that every atom experiences the same force. This is useful for -pushing on wall or boundary atoms so that the structure of the wall -does not change over time. - -The existing force is averaged for the group of atoms, component by -component. The actual force on each atom is then set to the average -value plus the component specified in this command. This means each -atom in the group receives the same force. - -Any of the fx,fy,fz values can be specified as NULL which means the -force in that dimension is not changed. Note that this is not the -same as specifying a 0.0 value, since that sets all forces to the same -average value without adding in any additional force. - -Any of the 3 quantities defining the force components can be specified -as an equal-style "variable"_variable.html, namely {fx}, {fy}, {fz}. -If the value is a variable, it should be specified as v_name, where -name is the variable name. In this case, the variable will be -evaluated each timestep, and its value used to determine the average -force. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent average force. - -If the {region} keyword is used, the atom must also be in the -specified geometric "region"_region.html in order to have force added -to it. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Howto_output.html. This is the total -force on the group of atoms before the forces on individual atoms are -changed by the fix. The vector values calculated by this fix are -"extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. You should not -specify force components with a variable that has time-dependence for -use with a minimizer, since the minimizer increments the timestep as -the iteration count during the minimization. - -[Restrictions:] none - -[Related commands:] - -"fix setforce"_fix_setforce.html, "fix addforce"_fix_addforce.html - -[Default:] none diff --git a/doc/txt/fix_balance.txt b/doc/txt/fix_balance.txt deleted file mode 100644 index 0f77fd4ecd..0000000000 --- a/doc/txt/fix_balance.txt +++ /dev/null @@ -1,383 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix balance command :h3 - -[Syntax:] - -fix ID group-ID balance Nfreq thresh style args keyword args ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -balance = style name of this fix command :l -Nfreq = perform dynamic load balancing every this many steps :l -thresh = imbalance threshold that must be exceeded to perform a re-balance :l -style = {shift} or {rcb} :l - shift args = dimstr Niter stopthresh - dimstr = sequence of letters containing "x" or "y" or "z", each not more than once - Niter = # of times to iterate within each dimension of dimstr sequence - stopthresh = stop balancing when this imbalance threshold is reached - {rcb} args = none :pre -zero or more keyword/arg pairs may be appended :l -keyword = {weight} or {out} :l - {weight} style args = use weighted particle counts for the balancing - {style} = {group} or {neigh} or {time} or {var} or {store} - {group} args = Ngroup group1 weight1 group2 weight2 ... - Ngroup = number of groups with assigned weights - group1, group2, ... = group IDs - weight1, weight2, ... = corresponding weight factors - {neigh} factor = compute weight based on number of neighbors - factor = scaling factor (> 0) - {time} factor = compute weight based on time spend computing - factor = scaling factor (> 0) - {var} name = take weight from atom-style variable - name = name of the atom-style variable - {store} name = store weight in custom atom property defined by "fix property/atom"_fix_property_atom.html command - name = atom property name (without d_ prefix) - {out} arg = filename - filename = write each processor's sub-domain to a file, at each re-balancing :pre -:ule - -[Examples:] - -fix 2 all balance 1000 1.05 shift x 10 1.05 -fix 2 all balance 100 0.9 shift xy 20 1.1 out tmp.balance -fix 2 all balance 100 0.9 shift xy 20 1.1 weight group 3 substrate 3.0 solvent 1.0 solute 0.8 out tmp.balance -fix 2 all balance 100 1.0 shift x 10 1.1 weight time 0.8 -fix 2 all balance 100 1.0 shift xy 5 1.1 weight var myweight weight neigh 0.6 weight store allweight -fix 2 all balance 1000 1.1 rcb :pre - -[Description:] - -This command adjusts the size and shape of processor sub-domains -within the simulation box, to attempt to balance the number of -particles and thus the computational cost (load) evenly across -processors. The load balancing is "dynamic" in the sense that -re-balancing is performed periodically during the simulation. To -perform "static" balancing, before or between runs, see the -"balance"_balance.html command. - -Load-balancing is typically most useful if the particles in the -simulation box have a spatially-varying density distribution or -where the computational cost varies significantly between different -atoms. E.g. a model of a vapor/liquid interface, or a solid with -an irregular-shaped geometry containing void regions, or -"hybrid pair style simulations"_pair_hybrid.html which combine -pair styles with different computational cost. In these cases, the -LAMMPS default of dividing the simulation box volume into a -regular-spaced grid of 3d bricks, with one equal-volume sub-domain -per processor, may assign numbers of particles per processor in a -way that the computational effort varies significantly. This can -lead to poor performance when the simulation is run in parallel. - -The balancing can be performed with or without per-particle weighting. -With no weighting, the balancing attempts to assign an equal number of -particles to each processor. With weighting, the balancing attempts -to assign an equal aggregate computational weight to each processor, -which typically induces a different number of atoms assigned to each -processor. - -NOTE: The weighting options listed above are documented with the -"balance"_balance.html command in "this section of the balance -command"_balance.html#weighted_balance doc page. That section -describes the various weighting options and gives a few examples of -how they can be used. The weighting options are the same for both the -fix balance and "balance"_balance.html commands. - -Note that the "processors"_processors.html command allows some control -over how the box volume is split across processors. Specifically, for -a Px by Py by Pz grid of processors, it allows choice of Px, Py, and -Pz, subject to the constraint that Px * Py * Pz = P, the total number -of processors. This is sufficient to achieve good load-balance for -some problems on some processor counts. However, all the processor -sub-domains will still have the same shape and same volume. - -On a particular timestep, a load-balancing operation is only performed -if the current "imbalance factor" in particles owned by each processor -exceeds the specified {thresh} parameter. The imbalance factor is -defined as the maximum number of particles (or weight) owned by any -processor, divided by the average number of particles (or weight) per -processor. Thus an imbalance factor of 1.0 is perfect balance. - -As an example, for 10000 particles running on 10 processors, if the -most heavily loaded processor has 1200 particles, then the factor is -1.2, meaning there is a 20% imbalance. Note that re-balances can be -forced even if the current balance is perfect (1.0) be specifying a -{thresh} < 1.0. - -NOTE: This command attempts to minimize the imbalance factor, as -defined above. But depending on the method a perfect balance (1.0) -may not be achieved. For example, "grid" methods (defined below) that -create a logical 3d grid cannot achieve perfect balance for many -irregular distributions of particles. Likewise, if a portion of the -system is a perfect lattice, e.g. the initial system is generated by -the "create_atoms"_create_atoms.html command, then "grid" methods may -be unable to achieve exact balance. This is because entire lattice -planes will be owned or not owned by a single processor. - -NOTE: The imbalance factor is also an estimate of the maximum speed-up -you can hope to achieve by running a perfectly balanced simulation -versus an imbalanced one. In the example above, the 10000 particle -simulation could run up to 20% faster if it were perfectly balanced, -versus when imbalanced. However, computational cost is not strictly -proportional to particle count, and changing the relative size and -shape of processor sub-domains may lead to additional computational -and communication overheads, e.g. in the PPPM solver used via the -"kspace_style"_kspace_style.html command. Thus you should benchmark -the run times of a simulation before and after balancing. - -:line - -The method used to perform a load balance is specified by one of the -listed styles, which are described in detail below. There are 2 kinds -of styles. - -The {shift} style is a "grid" method which produces a logical 3d grid -of processors. It operates by changing the cutting planes (or lines) -between processors in 3d (or 2d), to adjust the volume (area in 2d) -assigned to each processor, as in the following 2d diagram where -processor sub-domains are shown and atoms are colored by the processor -that owns them. The leftmost diagram is the default partitioning of -the simulation box across processors (one sub-box for each of 16 -processors); the middle diagram is after a "grid" method has been -applied. - -:image(JPG/balance_uniform_small.jpg,JPG/balance_uniform.jpg),image(JPG/balance_nonuniform_small.jpg,JPG/balance_nonuniform.jpg),image(JPG/balance_rcb_small.jpg,JPG/balance_rcb.jpg) -:c - -The {rcb} style is a "tiling" method which does not produce a logical -3d grid of processors. Rather it tiles the simulation domain with -rectangular sub-boxes of varying size and shape in an irregular -fashion so as to have equal numbers of particles (or weight) in each -sub-box, as in the rightmost diagram above. - -The "grid" methods can be used with either of the -"comm_style"_comm_style.html command options, {brick} or {tiled}. The -"tiling" methods can only be used with "comm_style -tiled"_comm_style.html. - -When a "grid" method is specified, the current domain partitioning can -be either a logical 3d grid or a tiled partitioning. In the former -case, the current logical 3d grid is used as a starting point and -changes are made to improve the imbalance factor. In the latter case, -the tiled partitioning is discarded and a logical 3d grid is created -with uniform spacing in all dimensions. This is the starting point -for the balancing operation. - -When a "tiling" method is specified, the current domain partitioning -("grid" or "tiled") is ignored, and a new partitioning is computed -from scratch. - -:line - -The {group-ID} is ignored. However the impact of balancing on -different groups of atoms can be affected by using the {group} weight -style as described below. - -The {Nfreq} setting determines how often a re-balance is performed. If -{Nfreq} > 0, then re-balancing will occur every {Nfreq} steps. Each -time a re-balance occurs, a reneighboring is triggered, so {Nfreq} -should not be too small. If {Nfreq} = 0, then re-balancing will be -done every time reneighboring normally occurs, as determined by the -the "neighbor"_neighbor.html and "neigh_modify"_neigh_modify.html -command settings. - -On re-balance steps, re-balancing will only be attempted if the current -imbalance factor, as defined above, exceeds the {thresh} setting. - -:line - -The {shift} style invokes a "grid" method for balancing, as described -above. It changes the positions of cutting planes between processors -in an iterative fashion, seeking to reduce the imbalance factor. - -The {dimstr} argument is a string of characters, each of which must be -an "x" or "y" or "z". Eacn character can appear zero or one time, -since there is no advantage to balancing on a dimension more than -once. You should normally only list dimensions where you expect there -to be a density variation in the particles. - -Balancing proceeds by adjusting the cutting planes in each of the -dimensions listed in {dimstr}, one dimension at a time. For a single -dimension, the balancing operation (described below) is iterated on up -to {Niter} times. After each dimension finishes, the imbalance factor -is re-computed, and the balancing operation halts if the {stopthresh} -criterion is met. - -A re-balance operation in a single dimension is performed using a -density-dependent recursive multisectioning algorithm, where the -position of each cutting plane (line in 2d) in the dimension is -adjusted independently. This is similar to a recursive bisectioning -for a single value, except that the bounds used for each bisectioning -take advantage of information from neighboring cuts if possible, as -well as counts of particles at the bounds on either side of each cuts, -which themselves were cuts in previous iterations. The latter is used -to infer a density of particles near each of the current cuts. At -each iteration, the count of particles on either side of each plane is -tallied. If the counts do not match the target value for the plane, -the position of the cut is adjusted based on the local density. The -low and high bounds are adjusted on each iteration, using new count -information, so that they become closer together over time. Thus as -the recursion progresses, the count of particles on either side of the -plane gets closer to the target value. - -The density-dependent part of this algorithm is often an advantage -when you re-balance a system that is already nearly balanced. It -typically converges more quickly than the geometric bisectioning -algorithm used by the "balance"_balance.html command. However, if can -be a disadvantage if you attempt to re-balance a system that is far -from balanced, and converge more slowly. In this case you probably -want to use the "balance"_balance.html command before starting a run, -so that you begin the run with a balanced system. - -Once the re-balancing is complete and final processor sub-domains -assigned, particles migrate to their new owning processor as part of -the normal reneighboring procedure. - -NOTE: At each re-balance operation, the bisectioning for each cutting -plane (line in 2d) typically starts with low and high bounds separated -by the extent of a processor's sub-domain in one dimension. The size -of this bracketing region shrinks based on the local density, as -described above, which should typically be 1/2 or more every -iteration. Thus if {Niter} is specified as 10, the cutting plane will -typically be positioned to better than 1 part in 1000 accuracy -(relative to the perfect target position). For {Niter} = 20, it will -be accurate to better than 1 part in a million. Thus there is no need -to set {Niter} to a large value. This is especially true if you are -re-balancing often enough that each time you expect only an incremental -adjustment in the cutting planes is necessary. LAMMPS will check if -the threshold accuracy is reached (in a dimension) is less iterations -than {Niter} and exit early. - -:line - -The {rcb} style invokes a "tiled" method for balancing, as described -above. It performs a recursive coordinate bisectioning (RCB) of the -simulation domain. The basic idea is as follows. - -The simulation domain is cut into 2 boxes by an axis-aligned cut in -the longest dimension, leaving one new box on either side of the cut. -All the processors are also partitioned into 2 groups, half assigned -to the box on the lower side of the cut, and half to the box on the -upper side. (If the processor count is odd, one side gets an extra -processor.) The cut is positioned so that the number of atoms in the -lower box is exactly the number that the processors assigned to that -box should own for load balance to be perfect. This also makes load -balance for the upper box perfect. The positioning is done -iteratively, by a bisectioning method. Note that counting atoms on -either side of the cut requires communication between all processors -at each iteration. - -That is the procedure for the first cut. Subsequent cuts are made -recursively, in exactly the same manner. The subset of processors -assigned to each box make a new cut in the longest dimension of that -box, splitting the box, the subset of processors, and the atoms in -the box in two. The recursion continues until every processor is -assigned a sub-box of the entire simulation domain, and owns the atoms -in that sub-box. - -:line - -The {out} keyword writes text to the specified {filename} with the -results of each re-balancing operation. The file contains the bounds -of the sub-domain for each processor after the balancing operation -completes. The format of the file is compatible with the -"Pizza.py"_pizza {mdump} tool which has support for manipulating and -visualizing mesh files. An example is shown here for a balancing by 4 -processors for a 2d problem: - -ITEM: TIMESTEP -0 -ITEM: NUMBER OF NODES -16 -ITEM: BOX BOUNDS -0 10 -0 10 -0 10 -ITEM: NODES -1 1 0 0 0 -2 1 5 0 0 -3 1 5 5 0 -4 1 0 5 0 -5 1 5 0 0 -6 1 10 0 0 -7 1 10 5 0 -8 1 5 5 0 -9 1 0 5 0 -10 1 5 5 0 -11 1 5 10 0 -12 1 10 5 0 -13 1 5 5 0 -14 1 10 5 0 -15 1 10 10 0 -16 1 5 10 0 -ITEM: TIMESTEP -0 -ITEM: NUMBER OF SQUARES -4 -ITEM: SQUARES -1 1 1 2 3 4 -2 1 5 6 7 8 -3 1 9 10 11 12 -4 1 13 14 15 16 :pre - -The coordinates of all the vertices are listed in the NODES section, 5 -per processor. Note that the 4 sub-domains share vertices, so there -will be duplicate nodes in the list. - -The "SQUARES" section lists the node IDs of the 4 vertices in a -rectangle for each processor (1 to 4). - -For a 3d problem, the syntax is similar with 8 vertices listed for -each processor, instead of 4, and "SQUARES" replaced by "CUBES". - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global scalar which is the imbalance factor -after the most recent re-balance and a global vector of length 3 with -additional information about the most recent re-balancing. The 3 -values in the vector are as follows: - -1 = max # of particles per processor -2 = total # iterations performed in last re-balance -3 = imbalance factor right before the last re-balance was performed :ul - -As explained above, the imbalance factor is the ratio of the maximum -number of particles (or total weight) on any processor to the average -number of particles (or total weight) per processor. - -These quantities can be accessed by various "output -commands"_Howto_output.html. The scalar and vector values calculated -by this fix are "intensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -:line - -[Restrictions:] - -For 2d simulations, the {z} style cannot be used. Nor can a "z" -appear in {dimstr} for the {shift} style. - -Balancing through recursive bisectioning ({rcb} style) requires -"comm_style tiled"_comm_style.html - -[Related commands:] - -"group"_group.html, "processors"_processors.html, "balance"_balance.html, -"comm_style"_comm_style.html - -[Default:] none -:link(pizza,http://pizza.sandia.gov) diff --git a/doc/txt/fix_bocs.txt b/doc/txt/fix_bocs.txt deleted file mode 100644 index bb7ac3713c..0000000000 --- a/doc/txt/fix_bocs.txt +++ /dev/null @@ -1,112 +0,0 @@ -<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix bocs command :h3 - -[Syntax:] - -fix ID group-ID bocs keyword values ... :pre - -keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline} - {temp} values = Tstart Tstop Tdamp - {cgiso} values = Pstart Pstop Pdamp - {basis set} - {analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N - {linear_spline} values = input_filename - {cubic_spline} values = input_filename :pre -:ule - -[Examples:] - -fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre - -fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre - -thermo_modify press 1_press :pre - - -[Description:] - -These commands incorporate a pressure correction as described by -Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK -barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna . -The first half of the command mimics a standard fix npt command: - -fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre - -The two differences are replacing {npt} with {bocs}, and replacing -{iso}/{aniso}/{etc} with {cgiso}. -The rest of the command details what form you would like to use for -the pressure correction equation. The choices are: {analytic}, {linear_spline}, -or {cubic_spline}. - -With either spline method, the only argument that needs to follow it -is the name of a file that contains the desired pressure correction -as a function of volume. The file must be formatted so each line has: - -Volume_i, PressureCorrection_i :pre - -Note both the COMMA and the SPACE separating the volume's -value and its corresponding pressure correction. The volumes in the file -must be uniformly spaced. Both the volumes and the pressure corrections -should be provided in the proper units, e.g. if you are using {units real}, -the volumes should all be in cubic angstroms, and the pressure corrections -should all be in atmospheres. Furthermore, the table should start/end at a -volume considerably smaller/larger than you expect your system to sample -during the simulation. If the system ever reaches a volume outside of the -range provided, the simulation will stop. - -With the {analytic} option, the arguments are as follows: - -... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre - -Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you -are using {units real}, {V_avg} should be in cubic angstroms, and the -coefficients should all be in atmospheres * cubic angstroms. - -[Restrictions:] - -As this is computing a (modified) pressure, group-ID should be {all}. - -The pressure correction has only been tested for use with an isotropic -pressure coupling in 3 dimensions. - -By default, LAMMPS will still report the normal value for the pressure -if the pressure is printed via a {thermo} command, or if the pressures -are written to a file every so often. In order to have LAMMPS report the -modified pressure, you must include the {thermo_modify} command given in -the examples. For the last argument in the command, you should put -XXXX_press, where XXXX is the ID given to the fix bocs command (in the -example, the ID of the fix bocs command is 1 ). - -This fix is part of the USER-BOCS package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related:] - -For more details about the pressure correction and the entire BOCS software -package, visit the "BOCS package on GitHub"_bocsgithub and read the release -paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 . - - -:link(bocsgithub,https://github.com/noid-group/BOCS) - -:line - -:link(bocs-Dunn1) -[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015). - -:link(bocs-Martyna) -[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994). - -:link(bocs-Dunn2) -[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018). - - - diff --git a/doc/txt/fix_bond_break.txt b/doc/txt/fix_bond_break.txt deleted file mode 100644 index bde0beae02..0000000000 --- a/doc/txt/fix_bond_break.txt +++ /dev/null @@ -1,145 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix bond/break command :h3 - -[Syntax:] - -fix ID group-ID bond/break Nevery bondtype Rmax keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -bond/break = style name of this fix command :l -Nevery = attempt bond breaking every this many steps :l -bondtype = type of bonds to break :l -Rmax = bond longer than Rmax can break (distance units) :l -zero or more keyword/value pairs may be appended to args :l -keyword = {prob} :l - {prob} values = fraction seed - fraction = break a bond with this probability if otherwise eligible - seed = random number seed (positive integer) :pre -:ule - -[Examples:] - -fix 5 all bond/break 10 2 1.2 -fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829 :pre - -[Description:] - -Break bonds between pairs of atoms as a simulation runs according to -specified criteria. This can be used to model the dissolution of a -polymer network due to stretching of the simulation box or other -deformations. In this context, a bond means an interaction between a -pair of atoms computed by the "bond_style"_bond_style.html command. -Once the bond is broken it will be permanently deleted, as will all -angle, dihedral, and improper interactions that bond is part of. - -This is different than a "pairwise"_pair_style.html bond-order -potential such as Tersoff or AIREBO which infers bonds and many-body -interactions based on the current geometry of a small cluster of atoms -and effectively creates and destroys bonds and higher-order many-body -interactions from timestep to timestep as atoms move. - -A check for possible bond breakage is performed every {Nevery} -timesteps. If two bonded atoms I,J are further than a distance {Rmax} -of each other, if the bond is of type {bondtype}, and if both I and J -are in the specified fix group, then I,J is labeled as a "possible" -bond to break. - -If several bonds involving an atom are stretched, it may have multiple -possible bonds to break. Every atom checks its list of possible bonds -to break and labels the longest such bond as its "sole" bond to break. -After this is done, if atom I is bonded to atom J in its sole bond, -and atom J is bonded to atom I in its sole bond, then the I,J bond is -"eligible" to be broken. - -Note that these rules mean an atom will only be part of at most one -broken bond on a given timestep. It also means that if atom I chooses -atom J as its sole partner, but atom J chooses atom K is its sole -partner (due to Rjk > Rij), then this means atom I will not be part of -a broken bond on this timestep, even if it has other possible bond -partners. - -The {prob} keyword can effect whether an eligible bond is actually -broken. The {fraction} setting must be a value between 0.0 and 1.0. -A uniform random number between 0.0 and 1.0 is generated and the -eligible bond is only broken if the random number < fraction. - -When a bond is broken, data structures within LAMMPS that store bond -topology are updated to reflect the breakage. Likewise, if the bond -is part of a 3-body (angle) or 4-body (dihedral, improper) -interaction, that interaction is removed as well. These changes -typically affect pairwise interactions between atoms that used to be -part of bonds, angles, etc. - -NOTE: One data structure that is not updated when a bond breaks are -the molecule IDs stored by each atom. Even though one molecule -becomes two molecules due to the broken bond, all atoms in both new -molecules retain their original molecule IDs. - -Computationally, each timestep this fix operates, it loops over all -the bonds in the system and computes distances between pairs of bonded -atoms. It also communicates between neighboring processors to -coordinate which bonds are broken. Moreover, if any bonds are broken, -neighbor lists must be immediately updated on the same timestep. This -is to insure that any pairwise interactions that should be turned "on" -due to a bond breaking, because they are no longer excluded by the -presence of the bond and the settings of the -"special_bonds"_special_bonds.html command, will be immediately -recognized. All of these operations increase the cost of a timestep. -Thus you should be cautious about invoking this fix too frequently. - -You can dump out snapshots of the current bond topology via the "dump -local"_dump.html command. - -NOTE: Breaking a bond typically alters the energy of a system. You -should be careful not to choose bond breaking criteria that induce a -dramatic change in energy. For example, if you define a very stiff -harmonic bond and break it when 2 atoms are separated by a distance -far from the equilibrium bond length, then the 2 atoms will be -dramatically released when the bond is broken. More generally, you -may need to thermostat your system to compensate for energy changes -resulting from broken bonds (and angles, dihedrals, impropers). - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes two statistics which it stores in a global vector of -length 2, which can be accessed by various "output -commands"_Howto_output.html. The vector values calculated by this fix -are "intensive". - -These are the 2 quantities: - -(1) # of bonds broken on the most recent breakage timestep -(2) cumulative # of bonds broken :ul - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the "Build package"_Build_package.html -doc page for more info. - -[Related commands:] - -"fix bond/create"_fix_bond_create.html, "fix -bond/react"_fix_bond_react.html, "fix bond/swap"_fix_bond_swap.html, -"dump local"_dump.html, "special_bonds"_special_bonds.html - -[Default:] - -The option defaults are prob = 1.0. diff --git a/doc/txt/fix_bond_create.txt b/doc/txt/fix_bond_create.txt deleted file mode 100644 index e78a283ece..0000000000 --- a/doc/txt/fix_bond_create.txt +++ /dev/null @@ -1,241 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix bond/create command :h3 - -[Syntax:] - -fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -bond/create = style name of this fix command :l -Nevery = attempt bond creation every this many steps :l -itype,jtype = atoms of itype can bond to atoms of jtype :l -Rmin = 2 atoms separated by less than Rmin can bond (distance units) :l -bondtype = type of created bonds :l -zero or more keyword/value pairs may be appended to args :l -keyword = {iparam} or {jparam} or {prob} or {atype} or {dtype} or {itype} :l - {iparam} values = maxbond, newtype - maxbond = max # of bonds of bondtype the itype atom can have - newtype = change the itype atom to this type when maxbonds exist - {jparam} values = maxbond, newtype - maxbond = max # of bonds of bondtype the jtype atom can have - newtype = change the jtype atom to this type when maxbonds exist - {prob} values = fraction seed - fraction = create a bond with this probability if otherwise eligible - seed = random number seed (positive integer) - {atype} value = angletype - angletype = type of created angles - {dtype} value = dihedraltype - dihedraltype = type of created dihedrals - {itype} value = impropertype - impropertype = type of created impropers :pre -:ule - -[Examples:] - -fix 5 all bond/create 10 1 2 0.8 1 -fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 -fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2 :pre - -[Description:] - -Create bonds between pairs of atoms as a simulation runs according to -specified criteria. This can be used to model cross-linking of -polymers, the formation of a percolation network, etc. In this -context, a bond means an interaction between a pair of atoms computed -by the "bond_style"_bond_style.html command. Once the bond is created -it will be permanently in place. Optionally, the creation of a bond -can also create angle, dihedral, and improper interactions that bond -is part of. See the discussion of the {atype}, {dtype}, and {itype} -keywords below. - -This is different than a "pairwise"_pair_style.html bond-order -potential such as Tersoff or AIREBO which infers bonds and many-body -interactions based on the current geometry of a small cluster of atoms -and effectively creates and destroys bonds and higher-order many-body -interactions from timestep to timestep as atoms move. - -A check for possible new bonds is performed every {Nevery} timesteps. -If two atoms I,J are within a distance {Rmin} of each other, if I is -of atom type {itype}, if J is of atom type {jtype}, if both I and J -are in the specified fix group, if a bond does not already exist -between I and J, and if both I and J meet their respective {maxbond} -requirement (explained below), then I,J is labeled as a "possible" -bond pair. - -If several atoms are close to an atom, it may have multiple possible -bond partners. Every atom checks its list of possible bond partners -and labels the closest such partner as its "sole" bond partner. After -this is done, if atom I has atom J as its sole partner, and atom J has -atom I as its sole partner, then the I,J bond is "eligible" to be -formed. - -Note that these rules mean an atom will only be part of at most one -created bond on a given timestep. It also means that if atom I -chooses atom J as its sole partner, but atom J chooses atom K is its -sole partner (due to Rjk < Rij), then this means atom I will not form -a bond on this timestep, even if it has other possible bond partners. - -It is permissible to have {itype} = {jtype}. {Rmin} must be <= the -pairwise cutoff distance between {itype} and {jtype} atoms, as defined -by the "pair_style"_pair_style.html command. - -The {iparam} and {jparam} keywords can be used to limit the bonding -functionality of the participating atoms. Each atom keeps track of -how many bonds of {bondtype} it already has. If atom I of -itype already has {maxbond} bonds (as set by the {iparam} -keyword), then it will not form any more. Likewise for atom J. If -{maxbond} is set to 0, then there is no limit on the number of bonds -that can be formed with that atom. - -The {newtype} value for {iparam} and {jparam} can be used to change -the atom type of atom I or J when it reaches {maxbond} number of bonds -of type {bondtype}. This means it can now interact in a pairwise -fashion with other atoms in a different way by specifying different -"pair_coeff"_pair_coeff.html coefficients. If you do not wish the -atom type to change, simply specify {newtype} as {itype} or {jtype}. - -The {prob} keyword can also effect whether an eligible bond is -actually created. The {fraction} setting must be a value between 0.0 -and 1.0. A uniform random number between 0.0 and 1.0 is generated and -the eligible bond is only created if the random number < fraction. - -Any bond that is created is assigned a bond type of {bondtype} - -When a bond is created, data structures within LAMMPS that store bond -topology are updated to reflect the creation. If the bond is part of -new 3-body (angle) or 4-body (dihedral, improper) interactions, you -can choose to create new angles, dihedrals, impropers as well, using -the {atype}, {dtype}, and {itype} keywords. All of these changes -typically affect pairwise interactions between atoms that are now part -of new bonds, angles, etc. - -NOTE: One data structure that is not updated when a bond breaks are -the molecule IDs stored by each atom. Even though two molecules -become one molecule due to the created bond, all atoms in the new -molecule retain their original molecule IDs. - -If the {atype} keyword is used and if an angle potential is defined -via the "angle_style"_angle_style.html command, then any new 3-body -interactions inferred by the creation of a bond will create new angles -of type {angletype}, with parameters assigned by the corresponding -"angle_coeff"_angle_coeff.html command. Likewise, the {dtype} and -{itype} keywords will create new dihedrals and impropers of type -{dihedraltype} and {impropertype}. - -NOTE: To create a new bond, the internal LAMMPS data structures that -store this information must have space for it. When LAMMPS is -initialized from a data file, the list of bonds is scanned and the -maximum number of bonds per atom is tallied. If some atom will -acquire more bonds than this limit as this fix operates, then the -"extra bond per atom" parameter must be set to allow for it. Ditto -for "extra angle per atom", "extra dihedral per atom", and "extra -improper per atom" if angles, dihedrals, or impropers are being added -when bonds are created. See the "read_data"_read_data.html or -"create_box"_create_box.html command for more details. Note that a -data file with no atoms can be used if you wish to add non-bonded -atoms via the "create atoms"_create_atoms.html command, e.g. for a -percolation simulation. - -NOTE: LAMMPS stores and maintains a data structure with a list of the -1st, 2nd, and 3rd neighbors of each atom (within the bond topology of -the system) for use in weighting pairwise interactions for bonded -atoms. Note that adding a single bond always adds a new 1st neighbor -but may also induce *many* new 2nd and 3rd neighbors, depending on the -molecular topology of your system. The "extra special per atom" -parameter must typically be set to allow for the new maximum total -size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 2 -ways to do this. See the "read_data"_read_data.html or -"create_box"_create_box.html commands for details. - -NOTE: Even if you do not use the {atype}, {dtype}, or {itype} -keywords, the list of topological neighbors is updated for atoms -affected by the new bond. This in turn affects which neighbors are -considered for pairwise interactions, using the weighting rules set by -the "special_bonds"_special_bonds.html command. Consider a new bond -created between atoms I,J. If J has a bonded neighbor K, then K -becomes a 2nd neighbor of I. Even if the {atype} keyword is not used -to create angle I-J-K, the pairwise interaction between I and K will -be potentially turned off or weighted by the 1-3 weighting specified -by the "special_bonds"_special_bonds.html command. This is the case -even if the "angle yes" option was used with that command. The same -is true for 3rd neighbors (1-4 interactions), the {dtype} keyword, and -the "dihedral yes" option used with the -"special_bonds"_special_bonds.html command. - -Note that even if your simulation starts with no bonds, you must -define a "bond_style"_bond_style.html and use the -"bond_coeff"_bond_coeff.html command to specify coefficients for the -{bondtype}. Similarly, if new atom types are specified by the -{iparam} or {jparam} keywords, they must be within the range of atom -types allowed by the simulation and pairwise coefficients must be -specified for the new types. - -Computationally, each timestep this fix operates, it loops over -neighbor lists and computes distances between pairs of atoms in the -list. It also communicates between neighboring processors to -coordinate which bonds are created. Moreover, if any bonds are -created, neighbor lists must be immediately updated on the same -timestep. This is to insure that any pairwise interactions that -should be turned "off" due to a bond creation, because they are now -excluded by the presence of the bond and the settings of the -"special_bonds"_special_bonds.html command, will be immediately -recognized. All of these operations increase the cost of a timestep. -Thus you should be cautious about invoking this fix too frequently. - -You can dump out snapshots of the current bond topology via the "dump -local"_dump.html command. - -NOTE: Creating a bond typically alters the energy of a system. You -should be careful not to choose bond creation criteria that induce a -dramatic change in energy. For example, if you define a very stiff -harmonic bond and create it when 2 atoms are separated by a distance -far from the equilibrium bond length, then the 2 atoms will oscillate -dramatically when the bond is formed. More generally, you may need to -thermostat your system to compensate for energy changes resulting from -created bonds (and angles, dihedrals, impropers). - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes two statistics which it stores in a global vector of -length 2, which can be accessed by various "output -commands"_Howto_output.html. The vector values calculated by this fix -are "intensive". - -These are the 2 quantities: - -(1) # of bonds created on the most recent creation timestep -(2) cumulative # of bonds created :ul - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the "Build package"_Build_package.html -doc page for more info. - -[Related commands:] - -"fix bond/break"_fix_bond_break.html, "fix -bond/react"_fix_bond_react.html, "fix bond/swap"_fix_bond_swap.html, -"dump local"_dump.html, "special_bonds"_special_bonds.html - -[Default:] - -The option defaults are iparam = (0,itype), jparam = (0,jtype), and -prob = 1.0. diff --git a/doc/txt/fix_bond_swap.txt b/doc/txt/fix_bond_swap.txt deleted file mode 100644 index 9a4e7c2b55..0000000000 --- a/doc/txt/fix_bond_swap.txt +++ /dev/null @@ -1,191 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix bond/swap command :h3 - -[Syntax:] - -fix ID group-ID bond/swap Nevery fraction cutoff seed :pre - -ID, group-ID are documented in "fix"_fix.html command -bond/swap = style name of this fix command -Nevery = attempt bond swapping every this many steps -fraction = fraction of group atoms to consider for swapping -cutoff = distance at which swapping will be considered (distance units) -seed = random # seed (positive integer) :ul - -[Examples:] - -fix 1 all bond/swap 50 0.5 1.3 598934 :pre - -[Description:] - -In a simulation of polymer chains, this command attempts to swap bonds -between two different chains, effectively grafting the end of one -chain onto another chain and vice versa. This is done via Monte Carlo -rules using the Boltzmann acceptance criterion. The purpose is to -equilibrate the polymer chain conformations more rapidly than dynamics -alone would do it, by enabling instantaneous large conformational -changes in a dense polymer melt. The polymer chains should thus more -rapidly converge to the proper end-to-end distances and radii of -gyration. It is designed for use with systems of -"FENE"_bond_fene.html or "harmonic"_bond_harmonic.html bead-spring -polymer chains where each polymer is a linear chain of monomers, but -LAMMPS does not enforce this requirement, i.e. any -"bond_style"_bond_style.html can be used. - -A schematic of the kinds of bond swaps that can occur is shown here: - -:c,image(JPG/bondswap.jpg) - -On the left, the red and blue chains have two monomers A1 and B1 close -to each other, which are currently bonded to monomers A2 and B2 -respectively within their own chains. The bond swap operation will -attempt to delete the A1-A2 and B1-B2 bonds and replace them with -A1-B2 and B1-A2 bonds. If the swap is energetically favorable, the -two chains on the right are the result and each polymer chain has -undergone a dramatic conformational change. This reference, -"(Sides)"_#Sides provides more details on how the algorithm works and -its application: - -The bond swapping operation is invoked every {Nevery} timesteps. If -any bond is swapped, a re-build of the neighbor lists is triggered, -since a swap alters the list of which neighbors are considered for -pairwise interaction. At each invocation, each processor considers a -random specified {fraction} of its atoms as potential swapping -monomers for this timestep. Choosing a small {fraction} value can -reduce the likelihood of a reverse swap occurring soon after an -initial swap. - -For each monomer A1, its neighbors are examined to find a possible B1 -monomer. Both A1 and B1 must be in the fix group, their separation -must be less than the specified {cutoff}, and the molecule IDs of A1 -and B1 must be the same (see below). If a suitable partner is found, -the energy change due to swapping the 2 bonds is computed. This -includes changes in pairwise, bond, and angle energies due to the -altered connectivity of the 2 chains. Dihedral and improper -interactions are not allowed to be defined when this fix is used. - -If the energy decreases due to the swap operation, the bond swap is -accepted. If the energy increases it is accepted with probability -exp(-delta/kT) where delta is the increase in energy, k is the -Boltzmann constant, and T is the current temperature of the system. -Whether the swap is accepted or rejected, no other swaps are attempted -by this processor on this timestep. - -The criterion for matching molecule IDs is how bond swaps performed by -this fix conserve chain length. To use this features you must setup -the molecule IDs for your polymer chains in a certain way, typically -in the data file, read by the "read_data"_read_data.html command. -Consider a system of 6-mer chains. You have 2 choices. If the -molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then -swaps will conserve chain length. For a particular monomer there will -be only one other monomer on another chain which is a potential swap -partner. If the molecule IDs for monomers on each chain are set to -1,2,3,3,2,1 then swaps will conserve chain length but swaps will be -able to occur at either end of a chain. Thus for a particular monomer -there will be 2 possible swap partners on another chain. In this -scenario, swaps can also occur within a single chain, i.e. the two -ends of a chain swap with each other. - -NOTE: If your simulation uses molecule IDs in the usual way, where all -monomers on a single chain are assigned the same ID (different for -each chain), then swaps will only occur within the same chain. If you -assign the same molecule ID to all monomers in all chains then -inter-chain swaps will occur, but they will not conserve chain length. -Neither of these scenarios is probably what you want for this fix. - -NOTE: When a bond swap occurs the image flags of monomers in the new -polymer chains can become inconsistent. See the "dump"_dump.html -command for a discussion of image flags. This is not an issue for -running dynamics, but can affect calculation of some diagnostic -quantities or the printing of unwrapped coordinates to a dump file. - -:line - -This fix computes a temperature each time it is invoked for use by the -Boltzmann criterion. To do this, the fix creates its own compute of -style {temp}, as if this command had been issued: - -compute fix-ID_temp all temp :pre - -See the "compute temp"_compute_temp.html command for details. Note -that the ID of the new compute is the fix-ID with underscore + "temp" -appended and the group for the new compute is "all", so that the -temperature of the entire system is used. - -Note that this is NOT the compute used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -"compute_modify"_compute_modify.html command or print this temperature -during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} will have no -effect on this fix. - -:line - -[Restart, fix_modify, thermo output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. Because the state of the random number generator -is not saved in restart files, this means you cannot do "exact" -restarts with this fix, where the simulation continues on the same as -if no restart had taken place. However, in a statistical sense, a -restarted simulation should produce the same behavior. Also note that -each processor generates possible swaps independently of other -processors. Thus if you repeat the same simulation on a different number -of processors, the specific swaps performed will be different. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a "compute"_compute.html you have -defined to this fix which will be used to compute the temperature for -the Boltzmann criterion. - -This fix computes two statistical quantities as a global 2-vector of -output, which can be accessed by various "output -commands"_Howto_output.html. The first component of the vector is the -cumulative number of swaps performed by all processors. The second -component of the vector is the cumulative number of swaps attempted -(whether accepted or rejected). Note that a swap "attempt" only -occurs when swap partners meeting the criteria described above are -found on a particular timestep. The vector values calculated by this -fix are "intensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the "Build package"_Build_package.html -doc page for more info. - -The settings of the "special_bond" command must be 0,1,1 in order to -use this fix, which is typical of bead-spring chains with FENE or -harmonic bonds. This means that pairwise interactions between bonded -atoms are turned off, but are turned on between atoms two or three -hops away along the chain backbone. - -Currently, energy changes in dihedral and improper interactions due to -a bond swap are not considered. Thus a simulation that uses this fix -cannot use a dihedral or improper potential. - -[Related commands:] - -"fix atom/swap"_fix_atom_swap.html - -[Default:] none - -:line - -:link(Sides) -[(Sides)] Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42, -199-208 (2004). diff --git a/doc/txt/fix_box_relax.txt b/doc/txt/fix_box_relax.txt deleted file mode 100644 index d41607e2ed..0000000000 --- a/doc/txt/fix_box_relax.txt +++ /dev/null @@ -1,366 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix box/relax command :h3 - -[Syntax:] - -fix ID group-ID box/relax keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -box/relax = style name of this fix command :l -one or more keyword value pairs may be appended -keyword = {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {nreset} or {vmax} or {dilate} or {scaleyz} or {scalexz} or {scalexy} or {fixedpoint} - {iso} or {aniso} or {tri} value = Ptarget = desired pressure (pressure units) - {x} or {y} or {z} or {xy} or {yz} or {xz} value = Ptarget = desired pressure (pressure units) - {couple} = {none} or {xyz} or {xy} or {yz} or {xz} - {nreset} value = reset reference cell every this many minimizer iterations - {vmax} value = fraction = max allowed volume change in one iteration - {dilate} value = {all} or {partial} - {scaleyz} value = {yes} or {no} = scale yz with lz - {scalexz} value = {yes} or {no} = scale xz with lz - {scalexy} value = {yes} or {no} = scale xy with ly - {fixedpoint} values = x y z - x,y,z = perform relaxation dilation/contraction around this point (distance units) :pre - -:ule - -[Examples:] - -fix 1 all box/relax iso 0.0 vmax 0.001 -fix 2 water box/relax aniso 0.0 dilate partial -fix 2 ice box/relax tri 0.0 couple xy nreset 100 :pre - -[Description:] - -Apply an external pressure or stress tensor to the simulation box -during an "energy minimization"_minimize.html. This allows the box -size and shape to vary during the iterations of the minimizer so that -the final configuration will be both an energy minimum for the -potential energy of the atoms, and the system pressure tensor will be -close to the specified external tensor. Conceptually, specifying a -positive pressure is like squeezing on the simulation box; a negative -pressure typically allows the box to expand. - -:line - -The external pressure tensor is specified using one or more of the -{iso}, {aniso}, {tri}, {x}, {y}, {z}, {xy}, {xz}, {yz}, and {couple} -keywords. These keywords give you the ability to specify all 6 -components of an external stress tensor, and to couple various of -these components together so that the dimensions they represent are -varied together during the minimization. - -Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). -Triclinic (non-orthogonal) simulation boxes have 6 adjustable -dimensions (x,y,z,xy,xz,yz). The "create_box"_create_box.html, "read -data"_read_data.html, and "read_restart"_read_restart.html commands -specify whether the simulation box is orthogonal or non-orthogonal -(triclinic) and explain the meaning of the xy,xz,yz tilt factors. - -The target pressures {Ptarget} for each of the 6 components of the -stress tensor can be specified independently via the {x}, {y}, {z}, -{xy}, {xz}, {yz} keywords, which correspond to the 6 simulation box -dimensions. For example, if the {y} keyword is used, the y-box length -will change during the minimization. If the {xy} keyword is used, the -xy tilt factor will change. A box dimension will not change if that -component is not specified. - -Note that in order to use the {xy}, {xz}, or {yz} keywords, the -simulation box must be triclinic, even if its initial tilt factors are -0.0. - -When the size of the simulation box changes, all atoms are re-scaled -to new positions, unless the keyword {dilate} is specified with a -value of {partial}, in which case only the atoms in the fix group are -re-scaled. This can be useful for leaving the coordinates of atoms in -a solid substrate unchanged and controlling the pressure of a -surrounding fluid. - -The {scaleyz}, {scalexz}, and {scalexy} keywords control whether or -not the corresponding tilt factors are scaled with the associated box -dimensions when relaxing triclinic periodic cells. The default -values {yes} will turn on scaling, which corresponds to adjusting the -linear dimensions of the cell while preserving its shape. Choosing -{no} ensures that the tilt factors are not scaled with the box -dimensions. See below for restrictions and default values in different -situations. In older versions of LAMMPS, scaling of tilt factors was -not performed. The old behavior can be recovered by setting all three -scale keywords to {no}. - -The {fixedpoint} keyword specifies the fixed point for cell relaxation. -By default, it is the center of the box. Whatever point is -chosen will not move during the simulation. For example, if the lower -periodic boundaries pass through (0,0,0), and this point is provided -to {fixedpoint}, then the lower periodic boundaries will remain at -(0,0,0), while the upper periodic boundaries will move twice as -far. In all cases, the particle positions at each iteration are -unaffected by the chosen value, except that all particles are -displaced by the same amount, different on each iteration. - -NOTE: Applying an external pressure to tilt dimensions {xy}, {xz}, {yz} -can sometimes result in arbitrarily large values of the tilt factors, -i.e. a dramatically deformed simulation box. This typically indicates -that there is something badly wrong with how the simulation was -constructed. The two most common sources of this error are applying a -shear stress to a liquid system or specifying an external shear stress -tensor that exceeds the yield stress of the solid. In either case the -minimization may converge to a bogus conformation or not converge at -all. Also note that if the box shape tilts to an extreme shape, -LAMMPS will run less efficiently, due to the large volume of -communication needed to acquire ghost atoms around a processor's -irregular-shaped sub-domain. For extreme values of tilt, LAMMPS may -also lose atoms and generate an error. - -NOTE: Performing a minimization with this fix is not a mathematically -well-defined minimization problem. This is because the objective -function being minimized changes if the box size/shape changes. In -practice this means the minimizer can get "stuck" before you have -reached the desired tolerance. The solution to this is to restart the -minimizer from the new adjusted box size/shape, since that creates a -new objective function valid for the new box size/shape. Repeat as -necessary until the box size/shape has reached its new equilibrium. - -:line - -The {couple} keyword allows two or three of the diagonal components of -the pressure tensor to be "coupled" together. The value specified -with the keyword determines which are coupled. For example, {xz} -means the {Pxx} and {Pzz} components of the stress tensor are coupled. -{Xyz} means all 3 diagonal components are coupled. Coupling means two -things: the instantaneous stress will be computed as an average of the -corresponding diagonal components, and the coupled box dimensions will -be changed together in lockstep, meaning coupled dimensions will be -dilated or contracted by the same percentage every timestep. The -{Ptarget} values for any coupled dimensions must be identical. -{Couple xyz} can be used for a 2d simulation; the {z} dimension is -simply ignored. - -:line - -The {iso}, {aniso}, and {tri} keywords are simply shortcuts that are -equivalent to specifying several other keywords together. - -The keyword {iso} means couple all 3 diagonal components together when -pressure is computed (hydrostatic pressure), and dilate/contract the -dimensions together. Using "iso Ptarget" is the same as specifying -these 4 keywords: - -x Ptarget -y Ptarget -z Ptarget -couple xyz :pre - -The keyword {aniso} means {x}, {y}, and {z} dimensions are controlled -independently using the {Pxx}, {Pyy}, and {Pzz} components of the -stress tensor as the driving forces, and the specified scalar external -pressure. Using "aniso Ptarget" is the same as specifying these 4 -keywords: - -x Ptarget -y Ptarget -z Ptarget -couple none :pre - -The keyword {tri} means {x}, {y}, {z}, {xy}, {xz}, and {yz} dimensions -are controlled independently using their individual stress components -as the driving forces, and the specified scalar pressure as the -external normal stress. Using "tri Ptarget" is the same as specifying -these 7 keywords: - -x Ptarget -y Ptarget -z Ptarget -xy 0.0 -yz 0.0 -xz 0.0 -couple none :pre - -:line - -The {vmax} keyword can be used to limit the fractional change in the -volume of the simulation box that can occur in one iteration of the -minimizer. If the pressure is not settling down during the -minimization this can be because the volume is fluctuating too much. -The specified fraction must be greater than 0.0 and should be << 1.0. -A value of 0.001 means the volume cannot change by more than 1/10 of a -percent in one iteration when {couple xyz} has been specified. For -any other case it means no linear dimension of the simulation box can -change by more than 1/10 of a percent. - -:line - -With this fix, the potential energy used by the minimizer is augmented -by an additional energy provided by the fix. The overall objective -function then is: - -:c,image(Eqs/fix_box_relax1.jpg) - -where {U} is the system potential energy, {P}_t is the desired -hydrostatic pressure, {V} and {V}_0 are the system and reference -volumes, respectively. {E}_{strain} is the strain energy expression -proposed by Parrinello and Rahman "(Parrinello1981)"_#Parrinello1981. -Taking derivatives of {E} w.r.t. the box dimensions, and setting these -to zero, we find that at the minimum of the objective function, the -global system stress tensor [P] will satisfy the relation: - -:c,image(Eqs/fix_box_relax2.jpg) - -where [I] is the identity matrix, [h]_0 is the box dimension tensor of -the reference cell, and [h]_0{d} is the diagonal part of -[h]_0. [S]_{t} is a symmetric stress tensor that is chosen by LAMMPS -so that the upper-triangular components of [P] equal the stress tensor -specified by the user. - -This equation only applies when the box dimensions are equal to those -of the reference dimensions. If this is not the case, then the -converged stress tensor will not equal that specified by the user. We -can resolve this problem by periodically resetting the reference -dimensions. The keyword {nreset} controls how often this is done. If -this keyword is not used, or is given a value of zero, then the -reference dimensions are set to those of the initial simulation domain -and are never changed. A value of {nstep} means that every {nstep} -minimization steps, the reference dimensions are set to those of the -current simulation domain. Note that resetting the reference -dimensions changes the objective function and gradients, which -sometimes causes the minimization to fail. This can be resolved by -changing the value of {nreset}, or simply continuing the minimization -from a restart file. - -NOTE: As normally computed, pressure includes a kinetic- energy or -temperature-dependent component; see the "compute -pressure"_compute_pressure.html command. However, atom velocities are -ignored during a minimization, and the applied pressure(s) specified -with this command are assumed to only be the virial component of the -pressure (the non-kinetic portion). Thus if atoms have a non-zero -temperature and you print the usual thermodynamic pressure, it may not -appear the system is converging to your specified pressure. The -solution for this is to either (a) zero the velocities of all atoms -before performing the minimization, or (b) make sure you are -monitoring the pressure without its kinetic component. The latter can -be done by outputting the pressure from the pressure compute this -command creates (see below) or a pressure compute you define yourself. - -NOTE: Because pressure is often a very sensitive function of volume, -it can be difficult for the minimizer to equilibrate the system the -desired pressure with high precision, particularly for solids. Some -techniques that seem to help are (a) use the "min_modify line -quadratic" option when minimizing with box relaxations, (b) minimize -several times in succession if need be, to drive the pressure closer -to the target pressure, (c) relax the atom positions before relaxing -the box, and (d) relax the box to the target hydrostatic pressure -before relaxing to a target shear stress state. Also note that some -systems (e.g. liquids) will not sustain a non-hydrostatic applied -pressure, which means the minimizer will not converge. - -:line - -This fix computes a temperature and pressure each timestep. The -temperature is used to compute the kinetic contribution to the -pressure, even though this is subsequently ignored by default. To do -this, the fix creates its own computes of style "temp" and "pressure", -as if these commands had been issued: - -compute fix-ID_temp group-ID temp -compute fix-ID_press group-ID pressure fix-ID_temp virial :pre - -See the "compute temp"_compute_temp.html and "compute -pressure"_compute_pressure.html commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is the same -as the fix group. Also note that the pressure compute does not -include a kinetic component. - -Note that these are NOT the computes used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_press}. This means you can change the attributes of this -fix's temperature or pressure via the -"compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} or -{thermo_press} will have no effect on this fix. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {temp} and {press} options are -supported by this fix. You can use them to assign a -"compute"_compute.html you have defined to this fix which will be used -in its temperature and pressure calculation, as described above. Note -that as described above, if you assign a pressure compute to this fix -that includes a kinetic energy component it will affect the -minimization, most likely in an undesirable way. - -NOTE: If both the {temp} and {press} keywords are used in a single -thermo_modify command (or in two separate commands), then the order in -which the keywords are specified is important. Note that a "pressure -compute"_compute_pressure.html defines its own temperature compute as -an argument when it is specified. The {temp} keyword will override -this (for the pressure compute being used by fix box/relax), but only if the -{temp} keyword comes after the {press} keyword. If the {temp} keyword -comes before the {press} keyword, then the new pressure compute -specified by the {press} keyword will be unaffected by the {temp} -setting. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the pressure-volume -energy, plus the strain energy, if it exists, as described above. The -energy values reported at the end of a minimization run under -"Minimization stats" include this energy, and so differ from what -LAMMPS normally reports as potential energy. This fix does not support -the "fix_modify"_fix_modify.html {energy} option, because that would -result in double-counting of the fix energy in the minimization -energy. Instead, the fix energy can be explicitly added to the -potential energy using one of these two variants: - -variable emin equal pe+f_1 :pre - -variable emin equal pe+f_1/atoms :pre - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -This fix is invoked during "energy minimization"_minimize.html, but -not for the purpose of adding a contribution to the energy or forces -being minimized. Instead it alters the simulation box geometry as -described above. - -[Restrictions:] - -Only dimensions that are available can be adjusted by this fix. -Non-periodic dimensions are not available. {z}, {xz}, and {yz}, are -not available for 2D simulations. {xy}, {xz}, and {yz} are only -available if the simulation domain is non-orthogonal. The -"create_box"_create_box.html, "read data"_read_data.html, and -"read_restart"_read_restart.html commands specify whether the -simulation box is orthogonal or non-orthogonal (triclinic) and explain -the meaning of the xy,xz,yz tilt factors. - -The {scaleyz yes} and {scalexz yes} keyword/value pairs can not be used -for 2D simulations. {scaleyz yes}, {scalexz yes}, and {scalexy yes} options -can only be used if the 2nd dimension in the keyword is periodic, -and if the tilt factor is not coupled to the barostat via keywords -{tri}, {yz}, {xz}, and {xy}. - -[Related commands:] - -"fix npt"_fix_nh.html, "minimize"_minimize.html - -[Default:] - -The keyword defaults are dilate = all, vmax = 0.0001, nreset = 0. - -:line - -:link(Parrinello1981) -[(Parrinello1981)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). diff --git a/doc/txt/fix_cmap.txt b/doc/txt/fix_cmap.txt deleted file mode 100644 index aef565e89e..0000000000 --- a/doc/txt/fix_cmap.txt +++ /dev/null @@ -1,144 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix cmap command :h3 - -[Syntax:] - -fix ID group-ID cmap filename :pre - -ID, group-ID are documented in "fix"_fix.html command -cmap = style name of this fix command -filename = force-field file with CMAP coefficients :ul - -[Examples:] - -fix myCMAP all cmap ../potentials/cmap36.data -read_data proteinX.data fix myCMAP crossterm CMAP -fix_modify myCMAP energy yes :pre - -[Description:] - -This command enables CMAP cross-terms to be added to simulations which -use the CHARMM force field. These are relevant for any CHARMM model -of a peptide or protein sequences that is 3 or more amino-acid -residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks2 for details, -including the analytic energy expressions for CMAP interactions. The -CMAP cross-terms add additional potential energy contributions to pairs -of overlapping phi-psi dihedrals of amino-acids, which are important -to properly represent their conformational behavior. - -The examples/cmap directory has a sample input script and data file -for a small peptide, that illustrates use of the fix cmap command. - -As in the example above, this fix should be used before reading a data -file that contains a listing of CMAP interactions. The {filename} -specified should contain the CMAP parameters for a particular version -of the CHARMM force field. Two such files are including in the -lammps/potentials directory: charmm22.cmap and charmm36.cmap. - -The data file read by the "read_data" must contain the topology of all -the CMAP interactions, similar to the topology data for bonds, angles, -dihedrals, etc. Specially it should have a line like this -in its header section: - -N crossterms :pre - -where N is the number of CMAP cross-terms. It should also have a section -in the body of the data file like this with N lines: - -CMAP :pre - - 1 1 8 10 12 18 20 - 2 5 18 20 22 25 27 - \[...\] - N 3 314 315 317 318 330 :pre - -The first column is an index from 1 to N to enumerate the CMAP terms; -it is ignored by LAMMPS. The 2nd column is the "type" of the -interaction; it is an index into the CMAP force field file. The -remaining 5 columns are the atom IDs of the atoms in the two 4-atom -dihedrals that overlap to create the CMAP 5-body interaction. Note -that the "crossterm" and "CMAP" keywords for the header and body -sections match those specified in the read_data command following the -data file name; see the "read_data"_read_data.html doc page for -more details. - -A data file containing CMAP cross-terms can be generated from a PDB -file using the charmm2lammps.pl script in the tools/ch2lmp directory -of the LAMMPS distribution. The script must be invoked with the -optional "-cmap" flag to do this; see the tools/ch2lmp/README file for -more information. - -The potential energy associated with CMAP interactions can be output -as described below. It can also be included in the total potential -energy of the system, as output by the -"thermo_style"_thermo_style.html command, if the "fix_modify -energy"_fix_modify.html command is used, as in the example above. See -the note below about how to include the CMAP energy when performing an -"energy minimization"_minimize.html. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the list of CMAP cross-terms to "binary restart -files"_restart.html. See the "read_restart"_read_restart.html command -for info on how to re-specify a fix in an input script that reads a -restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the potential "energy" of the CMAP interactions system's -potential energy as part of "thermodynamic output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {virial} option is supported by this -fix to add the contribution due to the interaction between atoms to -the system's virial as part of "thermodynamic output"_thermo_style.html. -The default is {virial yes} - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the potential -energy discussed above. The scalar value calculated by this fix is -"extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -NOTE: If you want the potential energy associated with the CMAP terms -forces to be included in the total potential energy of the system (the -quantity being minimized), you MUST enable the -"fix_modify"_fix_modify.html {energy} option for this fix. - -[Restrictions:] - -To function as expected this fix command must be issued {before} a -"read_data"_read_data.html command but {after} a -"read_restart"_read_restart.html command. - -This fix can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"fix_modify"_fix_modify.html, "read_data"_read_data.html - -[Default:] none - -:line - -:link(Buck) -[(Buck)] Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36 -(2006). - -:link(Brooks2) -[(Brooks)] Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009). diff --git a/doc/txt/fix_colvars.txt b/doc/txt/fix_colvars.txt deleted file mode 100644 index 304273d451..0000000000 --- a/doc/txt/fix_colvars.txt +++ /dev/null @@ -1,140 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix colvars command :h3 - -[Syntax:] - -fix ID group-ID colvars configfile keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -colvars = style name of this fix command :l -configfile = the configuration file for the colvars module :l -keyword = {input} or {output} or {seed} or {tstat} :l - {input} arg = colvars.state file name or prefix or NULL (default: NULL) - {output} arg = output filename prefix (default: out) - {seed} arg = seed for random number generator (default: 1966) - {unwrap} arg = {yes} or {no} - use unwrapped coordinates in collective variables (default: yes) - {tstat} arg = fix id of a thermostat or NULL (default: NULL) :pre -:ule - -[Examples:] - -fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide -fix abf all colvars colvars.inp tstat 1 :pre - -[Description:] - -This fix interfaces LAMMPS to the collective variables "Colvars" -library, which allows to calculate potentials of mean force -(PMFs) for any set of colvars, using different sampling methods: -currently implemented are the Adaptive Biasing Force (ABF) method, -metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling -(US) via a flexible harmonic restraint bias. - -This documentation describes only the fix colvars command itself and -LAMMPS specific parts of the code. The full documentation of the -colvars library is available as "this supplementary PDF document"_PDF/colvars-refman-lammps.pdf - -The Colvars library is developed at "https://github.com/colvars/colvars"_https://github.com/colvars/colvars -A detailed discussion of its implementation is in "(Fiorin)"_#Fiorin. - -There are some example scripts for using this package with LAMMPS in the -examples/USER/colvars directory. - -:line - -The only mandatory argument to the fix is the filename to the colvars -input file that contains the input that is independent from the MD -program in which the colvars library has been integrated. - -The {group-ID} entry is ignored. The collective variable module will -always apply to the entire system and there can only be one instance -of the colvars fix at a time. The colvars fix will only communicate -the minimum information necessary and the colvars library supports -multiple, completely independent collective variables, so there is -no restriction to functionality by limiting the number of colvars fixes. - -The {input} keyword allows to specify a state file that would contain -the restart information required in order to continue a calculation from -a prerecorded state. Fix colvars records it state in "binary restart"_restart.html -files, so when using the "read_restart"_read_restart.html command, -this is usually not needed. - -The {output} keyword allows to specify the output prefix. All output -files generated will use this prefix followed by the ".colvars." and -a word like "state" or "traj". - -The {seed} keyword contains the seed for the random number generator -that will be used in the colvars module. - -The {unwrap} keyword controls whether wrapped or unwrapped coordinates -are passed to the colvars library for calculation of the collective -variables and the resulting forces. The default is {yes}, i.e. to use -the image flags to reconstruct the absolute atom positions. -Setting this to {no} will use the current local coordinates that are -wrapped back into the simulation cell at each re-neighboring instead. - -The {tstat} keyword can be either NULL or the label of a thermostatting -fix that thermostats all atoms in the fix colvars group. This will be -used to provide the colvars module with the current thermostat target -temperature. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the current status of the colvars module into -"binary restart files"_restart.html. This is in addition to the text -mode status file that is written by the colvars module itself and the -kind of information in both files is identical. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change from the biasing force added by the fix -to the system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -The {fix_modify configfile } option allows to add settings -from an additional config file to the colvars module. This option can -only be used, after the system has been initialized with a "run"_run.html -command. - -The {fix_modify config } option allows to add settings -from inline strings. Those have to fit on a single line when enclosed -in a pair of double quotes ("), or can span multiple lines when bracketed -by a pair of triple double quotes (""", like python embedded documentation). - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the cumulative -energy change due to this fix. The scalar value calculated by this -fix is "extensive". - -[Restrictions:] - -This fix is part of the USER-COLVARS package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -There can only be one colvars fix active at a time. Since the interface -communicates only the minimum amount of information and colvars module -itself can handle an arbitrary number of collective variables, this is -not a limitation of functionality. - -[Related commands:] - -"fix smd"_fix_smd.html, "fix spring"_fix_spring.html, -"fix plumed"_fix_plumed.html - -[Default:] - -The default options are input = NULL, output = out, seed = 1966, unwrap yes, -and tstat = NULL. - -:line - -:link(Fiorin) -[(Fiorin)] Fiorin, Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594 diff --git a/doc/txt/fix_controller.txt b/doc/txt/fix_controller.txt deleted file mode 100644 index 45eb646b8e..0000000000 --- a/doc/txt/fix_controller.txt +++ /dev/null @@ -1,205 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix controller command :h3 - -[Syntax:] - -fix ID group-ID controller Nevery alpha Kp Ki Kd pvar setpoint cvar :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -controller = style name of this fix command :l -Nevery = invoke controller every this many timesteps :l -alpha = coupling constant for PID equation (see units discussion below) :l -Kp = proportional gain in PID equation (unitless) :l -Ki = integral gain in PID equation (unitless) :l -Kd = derivative gain in PID equation (unitless) :l -pvar = process variable of form c_ID, c_ID\[I\], f_ID, f_ID\[I\], or v_name :l - c_ID = global scalar calculated by a compute with ID - c_ID\[I\] = Ith component of global vector calculated by a compute with ID - f_ID = global scalar calculated by a fix with ID - f_ID\[I\] = Ith component of global vector calculated by a fix with ID - v_name = value calculated by an equal-style variable with name :pre -setpoint = desired value of process variable (same units as process variable) :l -cvar = name of control variable :l -:ule - -[Examples:] - -fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol -fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall -fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol :pre - -[Description:] - -This fix enables control of a LAMMPS simulation using a control loop -feedback mechanism known as a proportional-integral-derivative (PID) -controller. The basic idea is to define a "process variable" which is -a quantity that can be monitored during a running simulation. A -desired target value is chosen for the process variable. A "control -variable" is also defined which is an adjustable attribute of the -running simulation, which the process variable will respond to. The -PID controller continuously adjusts the control variable based on the -difference between the process variable and the target. - -Here are examples of ways in which this fix can be used. The -examples/pid directory contains a script that implements the simple -thermostat. - -Goal | process variable | control variable -Simple thermostat | instantaneous T | thermostat target T -Find melting temperature | average PE per atom | thermostat target T -Control pressure in non-periodic system | force on wall | position of wall -:tb(s=|) - -NOTE: For this fix to work, the control variable must actually induce -a change in a running LAMMPS simulation. Typically this will only -occur if there is some other command (e.g. a thermostat fix) which -uses the control variable as an input parameter. This could be done -directly or indirectly, e.g. the other command uses a variable as -input whose formula uses the control variable. The other command -should alter its behavior dynamically as the variable changes. - -NOTE: If there is a command you think could be used in this fashion, -but does not currently allow a variable as an input parameter, please -notify the LAMMPS developers. It is often not difficult to enable a -command to use a variable as an input parameter. - -The group specified with this command is ignored. However, note that -the process variable may be defined by calculations performed by -computes and fixes which store their own "group" definitions. - -The PID controller is invoked once each {Nevery} timesteps. - -The PID controller is implemented as a discretized version of -the following dynamic equation: - -:c,image(Eqs/fix_controller1.jpg) - -where {c} is the continuous time analog of the control variable, -{e} ={pvar}-{setpoint} is the error in the process variable, and -{alpha}, {Kp}, {Ki}, and {Kd} are constants set by the corresponding -keywords described above. The discretized version of this equation is: - -:c,image(Eqs/fix_controller2.jpg) - -where {tau} = {Nevery} * {timestep} is the time interval between updates, -and the subscripted variables indicate the values of {c} and {e} at -successive updates. - -From the first equation, it is clear that if the three gain values -{Kp}, {Ki}, {Kd} are dimensionless constants, then {alpha} must have -units of \[unit {cvar}\]/\[unit {pvar}\]/\[unit time\] e.g. \[ eV/K/ps -\]. The advantage of this unit scheme is that the value of the -constants should be invariant under a change of either the MD timestep -size or the value of {Nevery}. Similarly, if the LAMMPS "unit -style"_units.html is changed, it should only be necessary to change -the value of {alpha} to reflect this, while leaving {Kp}, {Ki}, and -{Kd} unaltered. - -When choosing the values of the four constants, it is best to first -pick a value and sign for {alpha} that is consistent with the -magnitudes and signs of {pvar} and {cvar}. The magnitude of {Kp} -should then be tested over a large positive range keeping {Ki} = {Kd} =0. -A good value for {Kp} will produce a fast response in {pvar}, without -overshooting the {setpoint}. For many applications, proportional -feedback is sufficient, and so {Ki} = {Kd} =0 can be used. In cases where -there is a substantial lag time in the response of {pvar} to a change -in {cvar}, this can be counteracted by increasing {Kd}. In situations -where {pvar} plateaus without reaching {setpoint}, this can be -counteracted by increasing {Ki}. In the language of Charles Dickens, -{Kp} represents the error of the present, {Ki} the error of the past, -and {Kd} the error yet to come. - -Because this fix updates {cvar}, but does not initialize its value, -the initial value is that assigned by the user in the input script via -the "internal-style variable"_variable.html command. This value is -used (by the other LAMMPS command that used the variable) until this -fix performs its first update of {cvar} after {Nevery} timesteps. On -the first update, the value of the derivative term is set to zero, -because the value of {e_n-1} is not yet defined. - -:line - -The process variable {pvar} can be specified as the output of a -"compute"_compute.html or "fix"_fix.html or the evaluation of a -"variable"_variable.html. In each case, the compute, fix, or variable -must produce a global quantity, not a per-atom or local quantity. - -If {pvar} begins with "c_", a compute ID must follow which has been -previously defined in the input script and which generates a global -scalar or vector. See the individual "compute"_compute.html doc page -for details. If no bracketed integer is appended, the scalar -calculated by the compute is used. If a bracketed integer is -appended, the Ith value of the vector calculated by the compute is -used. Users can also write code for their own compute styles and "add -them to LAMMPS"_Modify.html. - -If {pvar} begins with "f_", a fix ID must follow which has been -previously defined in the input script and which generates a global -scalar or vector. See the individual "fix"_fix.html doc page for -details. Note that some fixes only produce their values on certain -timesteps, which must be compatible with when fix controller -references the values, or else an error results. If no bracketed integer -is appended, the scalar calculated by the fix is used. If a bracketed -integer is appended, the Ith value of the vector calculated by the fix -is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Modify.html. - -If {pvar} begins with "v_", a variable name must follow which has been -previously defined in the input script. Only equal-style variables -can be referenced. See the "variable"_variable.html command for -details. Note that variables of style {equal} define a formula which -can reference individual atom properties or thermodynamic keywords, or -they can invoke other computes, fixes, or variables when they are -evaluated, so this is a very general means of specifying the process -variable. - -The target value {setpoint} for the process variable must be a numeric -value, in whatever units {pvar} is defined for. - -The control variable {cvar} must be the name of an "internal-style -variable"_variable.html previously defined in the input script. Note -that it is not specified with a "v_" prefix, just the name of the -variable. It must be an internal-style variable, because this fix -updates its value directly. Note that other commands can use an -equal-style versus internal-style variable interchangeably. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -Currently, no information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix produces a global vector with 3 values which can be accessed -by various "output commands"_Howto_output.html. The values can be -accessed on any timestep, though they are only updated on timesteps -that are a multiple of {Nevery}. - -The three values are the most recent updates made to the control -variable by each of the 3 terms in the PID equation above. The first -value is the proportional term, the second is the integral term, the -third is the derivative term. - -The units of the vector values will be whatever units the control -variable is in. The vector values calculated by this fix are -"extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix adapt"_fix_adapt.html - -[Default:] none diff --git a/doc/txt/fix_deform.txt b/doc/txt/fix_deform.txt deleted file mode 100644 index 3259f79497..0000000000 --- a/doc/txt/fix_deform.txt +++ /dev/null @@ -1,599 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix deform command :h3 -fix deform/kk command :h3 - -[Syntax:] - -fix ID group-ID deform N parameter args ... keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -deform = style name of this fix command :l -N = perform box deformation every this many timesteps :l -one or more parameter/arg pairs may be appended :l -parameter = {x} or {y} or {z} or {xy} or {xz} or {yz} - {x}, {y}, {z} args = style value(s) - style = {final} or {delta} or {scale} or {vel} or {erate} or {trate} or {volume} or {wiggle} or {variable} - {final} values = lo hi - lo hi = box boundaries at end of run (distance units) - {delta} values = dlo dhi - dlo dhi = change in box boundaries at end of run (distance units) - {scale} values = factor - factor = multiplicative factor for change in box length at end of run - {vel} value = V - V = change box length at this velocity (distance/time units), - effectively an engineering strain rate - {erate} value = R - R = engineering strain rate (1/time units) - {trate} value = R - R = true strain rate (1/time units) - {volume} value = none = adjust this dim to preserve volume of system - {wiggle} values = A Tp - A = amplitude of oscillation (distance units) - Tp = period of oscillation (time units) - {variable} values = v_name1 v_name2 - v_name1 = variable with name1 for box length change as function of time - v_name2 = variable with name2 for change rate as function of time - {xy}, {xz}, {yz} args = style value - style = {final} or {delta} or {vel} or {erate} or {trate} or {wiggle} - {final} value = tilt - tilt = tilt factor at end of run (distance units) - {delta} value = dtilt - dtilt = change in tilt factor at end of run (distance units) - {vel} value = V - V = change tilt factor at this velocity (distance/time units), - effectively an engineering shear strain rate - {erate} value = R - R = engineering shear strain rate (1/time units) - {trate} value = R - R = true shear strain rate (1/time units) - {wiggle} values = A Tp - A = amplitude of oscillation (distance units) - Tp = period of oscillation (time units) - {variable} values = v_name1 v_name2 - v_name1 = variable with name1 for tilt change as function of time - v_name2 = variable with name2 for change rate as function of time :pre - -zero or more keyword/value pairs may be appended :l -keyword = {remap} or {flip} or {units} :l - {remap} value = {x} or {v} or {none} - x = remap coords of atoms in group into deforming box - v = remap velocities of all atoms when they cross periodic boundaries - none = no remapping of x or v - {flip} value = {yes} or {no} - allow or disallow box flips when it becomes highly skewed - {units} value = {lattice} or {box} - lattice = distances are defined in lattice units - box = distances are defined in simulation box units :pre -:ule - -[Examples:] - -fix 1 all deform 1 x final 0.0 9.0 z final 0.0 5.0 units box -fix 1 all deform 1 x trate 0.1 y volume z volume -fix 1 all deform 1 xy erate 0.001 remap v -fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0 :pre - -[Description:] - -Change the volume and/or shape of the simulation box during a dynamics -run. Orthogonal simulation boxes have 3 adjustable parameters -(x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 -adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be -adjusted independently and simultaneously by this command. - -This fix can be used to perform non-equilibrium MD (NEMD) simulations -of a continuously strained system. See the "fix -nvt/sllod"_fix_nvt_sllod.html and "compute -temp/deform"_compute_temp_deform.html commands for more details. Note -that simulation of a continuously extended system (extensional flow) -can be modeled using the "USER-UEF -package"_Packages_details.html#PKG-USER-UEF and its "fix -commands"_fix_nh_uef.html. - -For the {x}, {y}, {z} parameters, the associated dimension cannot be -shrink-wrapped. For the {xy}, {yz}, {xz} parameters, the associated -2nd dimension cannot be shrink-wrapped. Dimensions not varied by this -command can be periodic or non-periodic. Dimensions corresponding to -unspecified parameters can also be controlled by a "fix -npt"_fix_nh.html or "fix nph"_fix_nh.html command. - -The size and shape of the simulation box at the beginning of the -simulation run were either specified by the -"create_box"_create_box.html or "read_data"_read_data.html or -"read_restart"_read_restart.html command used to setup the simulation -initially if it is the first run, or they are the values from the end -of the previous run. The "create_box"_create_box.html, "read -data"_read_data.html, and "read_restart"_read_restart.html commands -specify whether the simulation box is orthogonal or non-orthogonal -(triclinic) and explain the meaning of the xy,xz,yz tilt factors. If -fix deform changes the xy,xz,yz tilt factors, then the simulation box -must be triclinic, even if its initial tilt factors are 0.0. - -As described below, the desired simulation box size and shape at the -end of the run are determined by the parameters of the fix deform -command. Every Nth timestep during the run, the simulation box is -expanded, contracted, or tilted to ramped values between the initial -and final values. - -:line - -For the {x}, {y}, and {z} parameters, this is the meaning of their -styles and values. - -The {final}, {delta}, {scale}, {vel}, and {erate} styles all change -the specified dimension of the box via "constant displacement" which -is effectively a "constant engineering strain rate". This means the -box dimension changes linearly with time from its initial to final -value. - -For style {final}, the final lo and hi box boundaries of a dimension -are specified. The values can be in lattice or box distance units. -See the discussion of the units keyword below. - -For style {delta}, plus or minus changes in the lo/hi box boundaries -of a dimension are specified. The values can be in lattice or box -distance units. See the discussion of the units keyword below. - -For style {scale}, a multiplicative factor to apply to the box length -of a dimension is specified. For example, if the initial box length -is 10, and the factor is 1.1, then the final box length will be 11. A -factor less than 1.0 means compression. - -For style {vel}, a velocity at which the box length changes is -specified in units of distance/time. This is effectively a "constant -engineering strain rate", where rate = V/L0 and L0 is the initial box -length. The distance can be in lattice or box distance units. See -the discussion of the units keyword below. For example, if the -initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then -after 10 psec, the box length will have doubled. After 20 psec, it -will have tripled. - -The {erate} style changes a dimension of the box at a "constant -engineering strain rate". The units of the specified strain rate are -1/time. See the "units"_units.html command for the time units -associated with different choices of simulation units, -e.g. picoseconds for "metal" units). Tensile strain is unitless and -is defined as delta/L0, where L0 is the original box length and delta -is the change relative to the original length. The box length L as a -function of time will change as - -L(t) = L0 (1 + erate*dt) :pre - -where dt is the elapsed time (in time units). Thus if {erate} R is -specified as 0.1 and time units are picoseconds, this means the box -length will increase by 10% of its original length every picosecond. -I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.2, etc. R = --0.01 means the box length will shrink by 1% of its original length -every picosecond. Note that for an "engineering" rate the change is -based on the original box length, so running with R = 1 for 10 -picoseconds expands the box length by a factor of 11 (strain of 10), -which is different that what the {trate} style would induce. - -The {trate} style changes a dimension of the box at a "constant true -strain rate". Note that this is not an "engineering strain rate", as -the other styles are. Rather, for a "true" rate, the rate of change -is constant, which means the box dimension changes non-linearly with -time from its initial to final value. The units of the specified -strain rate are 1/time. See the "units"_units.html command for the -time units associated with different choices of simulation units, -e.g. picoseconds for "metal" units). Tensile strain is unitless and -is defined as delta/L0, where L0 is the original box length and delta -is the change relative to the original length. - -The box length L as a function of time will change as - -L(t) = L0 exp(trate*dt) :pre - -where dt is the elapsed time (in time units). Thus if {trate} R is -specified as ln(1.1) and time units are picoseconds, this means the -box length will increase by 10% of its current (not original) length -every picosecond. I.e. strain after 1 psec = 0.1, strain after 2 psec -= 0.21, etc. R = ln(2) or ln(3) means the box length will double or -triple every picosecond. R = ln(0.99) means the box length will -shrink by 1% of its current length every picosecond. Note that for a -"true" rate the change is continuous and based on the current length, -so running with R = ln(2) for 10 picoseconds does not expand the box -length by a factor of 11 as it would with {erate}, but by a factor of -1024 since the box length will double every picosecond. - -Note that to change the volume (or cross-sectional area) of the -simulation box at a constant rate, you can change multiple dimensions -via {erate} or {trate}. E.g. to double the box volume in a picosecond -picosecond, you could set "x erate M", "y erate M", "z erate M", with -M = pow(2,1/3) - 1 = 0.26, since if each box dimension grows by 26%, -the box volume doubles. Or you could set "x trate M", "y trate M", "z -trate M", with M = ln(1.26) = 0.231, and the box volume would double -every picosecond. - -The {volume} style changes the specified dimension in such a way that -the box volume remains constant while other box dimensions are changed -explicitly via the styles discussed above. For example, "x scale 1.1 -y scale 1.1 z volume" will shrink the z box length as the x,y box -lengths increase, to keep the volume constant (product of x,y,z -lengths). If "x scale 1.1 z volume" is specified and parameter {y} is -unspecified, then the z box length will shrink as x increases to keep -the product of x,z lengths constant. If "x scale 1.1 y volume z -volume" is specified, then both the y,z box lengths will shrink as x -increases to keep the volume constant (product of x,y,z lengths). In -this case, the y,z box lengths shrink so as to keep their relative -aspect ratio constant. - -For solids or liquids, note that when one dimension of the box is -expanded via fix deform (i.e. tensile strain), it may be physically -undesirable to hold the other 2 box lengths constant (unspecified by -fix deform) since that implies a density change. Using the {volume} -style for those 2 dimensions to keep the box volume constant may make -more physical sense, but may also not be correct for materials and -potentials whose Poisson ratio is not 0.5. An alternative is to use -"fix npt aniso"_fix_nh.html with zero applied pressure on those 2 -dimensions, so that they respond to the tensile strain dynamically. - -The {wiggle} style oscillates the specified box length dimension -sinusoidally with the specified amplitude and period. I.e. the box -length L as a function of time is given by - -L(t) = L0 + A sin(2*pi t/Tp) :pre - -where L0 is its initial length. If the amplitude A is a positive -number the box initially expands, then contracts, etc. If A is -negative then the box initially contracts, then expands, etc. The -amplitude can be in lattice or box distance units. See the discussion -of the units keyword below. - -The {variable} style changes the specified box length dimension by -evaluating a variable, which presumably is a function of time. The -variable with {name1} must be an "equal-style variable"_variable.html -and should calculate a change in box length in units of distance. -Note that this distance is in box units, not lattice units; see the -discussion of the {units} keyword below. The formula associated with -variable {name1} can reference the current timestep. Note that it -should return the "change" in box length, not the absolute box length. -This means it should evaluate to 0.0 when invoked on the initial -timestep of the run following the definition of fix deform. It should -evaluate to a value > 0.0 to dilate the box at future times, or a -value < 0.0 to compress the box. - -The variable {name2} must also be an "equal-style -variable"_variable.html and should calculate the rate of box length -change, in units of distance/time, i.e. the time-derivative of the -{name1} variable. This quantity is used internally by LAMMPS to reset -atom velocities when they cross periodic boundaries. It is computed -internally for the other styles, but you must provide it when using an -arbitrary variable. - -Here is an example of using the {variable} style to perform the same -box deformation as the {wiggle} style formula listed above, where we -assume that the current timestep = 0. - -variable A equal 5.0 -variable Tp equal 10.0 -variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)" -variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)" -fix 2 all deform 1 x variable v_displace v_rate remap v :pre - -For the {scale}, {vel}, {erate}, {trate}, {volume}, {wiggle}, and -{variable} styles, the box length is expanded or compressed around its -mid point. - -:line - -For the {xy}, {xz}, and {yz} parameters, this is the meaning of their -styles and values. Note that changing the tilt factors of a triclinic -box does not change its volume. - -The {final}, {delta}, {vel}, and {erate} styles all change the shear -strain at a "constant engineering shear strain rate". This means the -tilt factor changes linearly with time from its initial to final -value. - -For style {final}, the final tilt factor is specified. The value -can be in lattice or box distance units. See the discussion of the -units keyword below. - -For style {delta}, a plus or minus change in the tilt factor is -specified. The value can be in lattice or box distance units. See -the discussion of the units keyword below. - -For style {vel}, a velocity at which the tilt factor changes is -specified in units of distance/time. This is effectively an -"engineering shear strain rate", where rate = V/L0 and L0 is the -initial box length perpendicular to the direction of shear. The -distance can be in lattice or box distance units. See the discussion -of the units keyword below. For example, if the initial tilt factor -is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the -tilt factor will be 15 Angstroms. After 2 psec, it will be 25 -Angstroms. - -The {erate} style changes a tilt factor at a "constant engineering -shear strain rate". The units of the specified shear strain rate are -1/time. See the "units"_units.html command for the time units -associated with different choices of simulation units, -e.g. picoseconds for "metal" units). Shear strain is unitless and is -defined as offset/length, where length is the box length perpendicular -to the shear direction (e.g. y box length for xy deformation) and -offset is the displacement distance in the shear direction (e.g. x -direction for xy deformation) from the unstrained orientation. - -The tilt factor T as a function of time will change as - -T(t) = T0 + L0*erate*dt :pre - -where T0 is the initial tilt factor, L0 is the original length of the -box perpendicular to the shear direction (e.g. y box length for xy -deformation), and dt is the elapsed time (in time units). Thus if -{erate} R is specified as 0.1 and time units are picoseconds, this -means the shear strain will increase by 0.1 every picosecond. I.e. if -the xy shear strain was initially 0.0, then strain after 1 psec = 0.1, -strain after 2 psec = 0.2, etc. Thus the tilt factor would be 0.0 at -time 0, 0.1*ybox at 1 psec, 0.2*ybox at 2 psec, etc, where ybox is the -original y box length. R = 1 or 2 means the tilt factor will increase -by 1 or 2 every picosecond. R = -0.01 means a decrease in shear -strain by 0.01 every picosecond. - -The {trate} style changes a tilt factor at a "constant true shear -strain rate". Note that this is not an "engineering shear strain -rate", as the other styles are. Rather, for a "true" rate, the rate -of change is constant, which means the tilt factor changes -non-linearly with time from its initial to final value. The units of -the specified shear strain rate are 1/time. See the -"units"_units.html command for the time units associated with -different choices of simulation units, e.g. picoseconds for "metal" -units). Shear strain is unitless and is defined as offset/length, -where length is the box length perpendicular to the shear direction -(e.g. y box length for xy deformation) and offset is the displacement -distance in the shear direction (e.g. x direction for xy deformation) -from the unstrained orientation. - -The tilt factor T as a function of time will change as - -T(t) = T0 exp(trate*dt) :pre - -where T0 is the initial tilt factor and dt is the elapsed time (in -time units). Thus if {trate} R is specified as ln(1.1) and time units -are picoseconds, this means the shear strain or tilt factor will -increase by 10% every picosecond. I.e. if the xy shear strain was -initially 0.1, then strain after 1 psec = 0.11, strain after 2 psec = -0.121, etc. R = ln(2) or ln(3) means the tilt factor will double or -triple every picosecond. R = ln(0.99) means the tilt factor will -shrink by 1% every picosecond. Note that the change is continuous, so -running with R = ln(2) for 10 picoseconds does not change the tilt -factor by a factor of 10, but by a factor of 1024 since it doubles -every picosecond. Note that the initial tilt factor must be non-zero -to use the {trate} option. - -Note that shear strain is defined as the tilt factor divided by the -perpendicular box length. The {erate} and {trate} styles control the -tilt factor, but assume the perpendicular box length remains constant. -If this is not the case (e.g. it changes due to another fix deform -parameter), then this effect on the shear strain is ignored. - -The {wiggle} style oscillates the specified tilt factor sinusoidally -with the specified amplitude and period. I.e. the tilt factor T as a -function of time is given by - -T(t) = T0 + A sin(2*pi t/Tp) :pre - -where T0 is its initial value. If the amplitude A is a positive -number the tilt factor initially becomes more positive, then more -negative, etc. If A is negative then the tilt factor initially -becomes more negative, then more positive, etc. The amplitude can be -in lattice or box distance units. See the discussion of the units -keyword below. - -The {variable} style changes the specified tilt factor by evaluating a -variable, which presumably is a function of time. The variable with -{name1} must be an "equal-style variable"_variable.html and should -calculate a change in tilt in units of distance. Note that this -distance is in box units, not lattice units; see the discussion of the -{units} keyword below. The formula associated with variable {name1} -can reference the current timestep. Note that it should return the -"change" in tilt factor, not the absolute tilt factor. This means it -should evaluate to 0.0 when invoked on the initial timestep of the run -following the definition of fix deform. - -The variable {name2} must also be an "equal-style -variable"_variable.html and should calculate the rate of tilt change, -in units of distance/time, i.e. the time-derivative of the {name1} -variable. This quantity is used internally by LAMMPS to reset atom -velocities when they cross periodic boundaries. It is computed -internally for the other styles, but you must provide it when using an -arbitrary variable. - -Here is an example of using the {variable} style to perform the same -box deformation as the {wiggle} style formula listed above, where we -assume that the current timestep = 0. - -variable A equal 5.0 -variable Tp equal 10.0 -variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)" -variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)" -fix 2 all deform 1 xy variable v_displace v_rate remap v :pre - -:line - -All of the tilt styles change the xy, xz, yz tilt factors during a -simulation. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes -are normally bounded by half the distance of the parallel box length. -See the discussion of the {flip} keyword below, to allow this bound to -be exceeded, if desired. - -For example, if xlo = 2 and xhi = 12, then the x box length is 10 and -the xy tilt factor must be between -5 and 5. Similarly, both xz and -yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is -not a limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are all equivalent. - -To obey this constraint and allow for large shear deformations to be -applied via the {xy}, {xz}, or {yz} parameters, the following -algorithm is used. If {prd} is the associated parallel box length (10 -in the example above), then if the tilt factor exceeds the accepted -range of -5 to 5 during the simulation, then the box is flipped to the -other limit (an equivalent box) and the simulation continues. Thus -for this example, if the initial xy tilt factor was 0.0 and "xy final -100.0" was specified, then during the simulation the xy tilt factor -would increase from 0.0 to 5.0, the box would be flipped so that the -tilt factor becomes -5.0, the tilt factor would increase from -5.0 to -5.0, the box would be flipped again, etc. The flip occurs 10 times -and the final tilt factor at the end of the simulation would be 0.0. -During each flip event, atoms are remapped into the new box in the -appropriate manner. - -The one exception to this rule is if the 1st dimension in the tilt -factor (x for xy) is non-periodic. In that case, the limits on the -tilt factor are not enforced, since flipping the box in that dimension -does not change the atom positions due to non-periodicity. In this -mode, if you tilt the system to extreme angles, the simulation will -simply become inefficient due to the highly skewed simulation box. - -:line - -Each time the box size or shape is changed, the {remap} keyword -determines whether atom positions are remapped to the new box. If -{remap} is set to {x} (the default), atoms in the fix group are -remapped; otherwise they are not. Note that their velocities are not -changed, just their positions are altered. If {remap} is set to {v}, -then any atom in the fix group that crosses a periodic boundary will -have a delta added to its velocity equal to the difference in -velocities between the lo and hi boundaries. Note that this velocity -difference can include tilt components, e.g. a delta in the x velocity -when an atom crosses the y periodic boundary. If {remap} is set to -{none}, then neither of these remappings take place. - -Conceptually, setting {remap} to {x} forces the atoms to deform via an -affine transformation that exactly matches the box deformation. This -setting is typically appropriate for solids. Note that though the -atoms are effectively "moving" with the box over time, it is not due -to their having a velocity that tracks the box change, but only due to -the remapping. By contrast, setting {remap} to {v} is typically -appropriate for fluids, where you want the atoms to respond to the -change in box size/shape on their own and acquire a velocity that -matches the box change, so that their motion will naturally track the -box without explicit remapping of their coordinates. - -NOTE: When non-equilibrium MD (NEMD) simulations are performed using -this fix, the option "remap v" should normally be used. This is -because "fix nvt/sllod"_fix_nvt_sllod.html adjusts the atom positions -and velocities to induce a velocity profile that matches the changing -box size/shape. Thus atom coordinates should NOT be remapped by fix -deform, but velocities SHOULD be when atoms cross periodic boundaries, -since that is consistent with maintaining the velocity profile already -created by fix nvt/sllod. LAMMPS will warn you if the {remap} setting -is not consistent with fix nvt/sllod. - -NOTE: For non-equilibrium MD (NEMD) simulations using "remap v" it is -usually desirable that the fluid (or flowing material, e.g. granular -particles) stream with a velocity profile consistent with the -deforming box. As mentioned above, using a thermostat such as "fix -nvt/sllod"_fix_nvt_sllod.html or "fix lavgevin"_fix_langevin.html -(with a bias provided by "compute -temp/deform"_compute_temp_deform.html), will typically accomplish -that. If you do not use a thermostat, then there is no driving force -pushing the atoms to flow in a manner consistent with the deforming -box. E.g. for a shearing system the box deformation velocity may vary -from 0 at the bottom to 10 at the top of the box. But the stream -velocity profile of the atoms may vary from -5 at the bottom to +5 at -the top. You can monitor these effects using the "fix -ave/chunk"_fix_ave_chunk.html, "compute -temp/deform"_compute_temp_deform.html, and "compute -temp/profile"_compute_temp_profile.html commands. One way to induce -atoms to stream consistent with the box deformation is to give them an -initial velocity profile, via the "velocity ramp"_velocity.html -command, that matches the box deformation rate. This also typically -helps the system come to equilibrium more quickly, even if a -thermostat is used. - -NOTE: If a "fix rigid"_fix_rigid.html is defined for rigid bodies, and -{remap} is set to {x}, then the center-of-mass coordinates of rigid -bodies will be remapped to the changing simulation box. This will be -done regardless of whether atoms in the rigid bodies are in the fix -deform group or not. The velocity of the centers of mass are not -remapped even if {remap} is set to {v}, since "fix -nvt/sllod"_fix_nvt_sllod.html does not currently do anything special -for rigid particles. If you wish to perform a NEMD simulation of -rigid particles, you can either thermostat them independently or -include a background fluid and thermostat the fluid via "fix -nvt/sllod"_fix_nvt_sllod.html. - -The {flip} keyword allows the tilt factors for a triclinic box to -exceed half the distance of the parallel box length, as discussed -above. If the {flip} value is set to {yes}, the bound is enforced by -flipping the box when it is exceeded. If the {flip} value is set to -{no}, the tilt will continue to change without flipping. Note that if -you apply large deformations, this means the box shape can tilt -dramatically LAMMPS will run less efficiently, due to the large volume -of communication needed to acquire ghost atoms around a processor's -irregular-shaped sub-domain. For extreme values of tilt, LAMMPS may -also lose atoms and generate an error. - -The {units} keyword determines the meaning of the distance units used -to define various arguments. A {box} value selects standard distance -units as defined by the "units"_units.html command, e.g. Angstroms for -units = real or metal. A {lattice} value means the distance units are -in lattice spacings. The "lattice"_lattice.html command must have -been previously used to define the lattice spacing. Note that the -units choice also affects the {vel} style parameters since it is -defined in terms of distance/time. Also note that the units keyword -does not affect the {variable} style. You should use the {xlat}, -{ylat}, {zlat} keywords of the "thermo_style"_thermo_style.html -command if you want to include lattice spacings in a variable formula. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix will restore the initial box settings from "binary restart -files"_restart.html, which allows the fix to be properly continue -deformation, when using the start/stop options of the "run"_run.html -command. None of the "fix_modify"_fix_modify.html options are -relevant to this fix. No global or per-atom quantities are stored by -this fix for access by various "output commands"_Howto_output.html. - -This fix can perform deformation over multiple runs, using the {start} -and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -You cannot apply x, y, or z deformations to a dimension that is -shrink-wrapped via the "boundary"_boundary.html command. - -You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in -xy) that is shrink-wrapped via the "boundary"_boundary.html command. - -[Related commands:] - -"change_box"_change_box.html - -[Default:] - -The option defaults are remap = x, flip = yes, and units = lattice. diff --git a/doc/txt/fix_dpd_energy.txt b/doc/txt/fix_dpd_energy.txt deleted file mode 100644 index 5e8e295de9..0000000000 --- a/doc/txt/fix_dpd_energy.txt +++ /dev/null @@ -1,106 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix dpd/energy command :h3 -fix dpd/energy/kk command :h3 - -[Syntax:] - -fix ID group-ID dpd/energy :pre - -ID, group-ID are documented in "fix"_fix.html command -dpd/energy = style name of this fix command :ul - -[Examples:] - -fix 1 all dpd/energy :pre - -[Description:] - -Perform constant energy dissipative particle dynamics (DPD-E) -integration. This fix updates the internal energies for particles in -the group at each timestep. It must be used in conjunction with a -deterministic integrator (e.g. "fix nve"_fix_nve.html) that updates -the particle positions and velocities. - -For fix {dpd/energy}, the particle internal temperature is related to -the particle internal energy through a mesoparticle equation of state. -An additional fix must be specified that defines the equation of state -for each particle, e.g. "fix eos/cv"_fix_eos_cv.html. - -This fix must be used with the "pair_style -dpd/fdt/energy"_pair_style.html command. - -Note that numerous variants of DPD can be specified by choosing an -appropriate combination of the integrator and "pair_style -dpd/fdt/energy"_pair_style.html command. DPD under isoenergetic conditions -can be specified by using fix {dpd/energy}, fix {nve} and pair_style -{dpd/fdt/energy}. DPD under isoenthalpic conditions can -be specified by using fix {dpd/energy}, fix {nph} and pair_style -{dpd/fdt/energy}. Examples of each DPD variant are provided in the -examples/USER/dpd directory. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix must be used with an additional fix that specifies time -integration, e.g. "fix nve"_fix_nve.html. - -The fix {dpd/energy} requires the {dpd} "atom_style"_atom_style.html -to be used in order to properly account for the particle internal -energies and temperature. - -The fix {dpd/energy} must be used with an additional fix that specifies the -mesoparticle equation of state for each particle. - -[Related commands:] - -"fix nve"_fix_nve.html "fix eos/cv"_fix_eos_cv.html - -[Default:] none - -:line - -:link(Lisal1) -[(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative -particle dynamics at isothermal, isobaric, isoenergetic, and -isoenthalpic conditions using Shardlow-like splitting algorithms.", -J. Chem. Phys., 135, 204105 (2011). - -:link(Larentzos3) -[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and -W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative -Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research -Laboratory, Aberdeen Proving Ground, MD (2014). diff --git a/doc/txt/fix_dpd_source.txt b/doc/txt/fix_dpd_source.txt deleted file mode 100644 index 691cfe86f1..0000000000 --- a/doc/txt/fix_dpd_source.txt +++ /dev/null @@ -1,101 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix edpd/source command :h3 -fix tdpd/source command :h3 - -[Syntax:] - -fix ID group-ID edpd/source keyword values ... -fix ID group-ID tdpd/source cc_index keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -edpd/source or tdpd/source = style name of this fix command :l -index (only specified for tdpd/source) = index of chemical species (1 to Nspecies) :l -keyword = {sphere} or {cuboid} :l - {sphere} values = cx,cy,cz,radius,source - cx,cy,cz = x,y,z center of spherical domain (distance units) - radius = radius of a spherical domain (distance units) - source = heat source or concentration source (flux units, see below) - {cuboid} values = cx,cy,cz,dLx,dLy,dLz,source - cx,cy,cz = x,y,z lower left corner of a cuboid domain (distance units) - dLx,dLy,dLz = x,y,z side length of a cuboid domain (distance units) - source = heat source or concentration source (flux units, see below) :pre -:ule - -[Examples:] - -fix 1 all edpd/source sphere 0.0 0.0 0.0 5.0 0.01 -fix 1 all edpd/source cuboid 0.0 0.0 0.0 20.0 10.0 10.0 -0.01 -fix 1 all tdpd/source 1 sphere 5.0 0.0 0.0 5.0 0.01 -fix 1 all tdpd/source 2 cuboid 0.0 0.0 0.0 20.0 10.0 10.0 0.01 :pre - -[Description:] - -Fix {edpd/source} adds a heat source as an external heat flux to each -atom in a spherical or cuboid domain, where the {source} is in units -of energy/time. Fix {tdpd/source} adds an external concentration -source of the chemical species specified by {index} as an external -concentration flux for each atom in a spherical or cuboid domain, -where the {source} is in units of mole/volume/time. - -This command can be used to give an additional heat/concentration -source term to atoms in a simulation, such as for a simulation of a -heat conduction with a source term (see Fig.12 in "(Li2014)"_#Li2014b) -or diffusion with a source term (see Fig.1 in "(Li2015)"_#Li2015b), as -an analog of a periodic Poiseuille flow problem. - -If the {sphere} keyword is used, the {cx,cy,cz,radius} defines a -spherical domain to apply the source flux to. - -If the {cuboid} keyword is used, the {cx,cy,cz,dLx,dLy,dLz} defines a -cuboid domain to apply the source flux to. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-MESO package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Fix {edpd/source} must be used with the "pair_style -edpd"_pair_meso.html command. Fix {tdpd/source} must be used with the -"pair_style tdpd"_pair_meso.html command. - -[Related commands:] - -"pair_style edpd"_pair_meso.html, "pair_style tdpd"_pair_meso.html, -"compute edpd/temp/atom"_compute_edpd_temp_atom.html, "compute -tdpd/cc/atom"_compute_tdpd_cc_atom.html - -[Default:] none - -:line - -:link(Li2014b) -[(Li2014)] Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis, -"Energy-conserving dissipative particle dynamics with -temperature-dependent properties", J. Comput. Phys., 265: 113-127 -(2014). DOI: 10.1016/j.jcp.2014.02.003 - -:link(Li2015b) -[(Li2015)] Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis, -"Transport dissipative particle dynamics model for mesoscopic -advection-diffusion-reaction problems", J. Chem. Phys., 143: 014101 -(2015). DOI: 10.1063/1.4923254 diff --git a/doc/txt/fix_drag.txt b/doc/txt/fix_drag.txt deleted file mode 100644 index 92e68d13a4..0000000000 --- a/doc/txt/fix_drag.txt +++ /dev/null @@ -1,65 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix drag command :h3 - -[Syntax:] - -fix ID group-ID drag x y z fmag delta :pre - -ID, group-ID are documented in "fix"_fix.html command -drag = style name of this fix command -x,y,z = coord to drag atoms towards -fmag = magnitude of force to apply to each atom (force units) -delta = cutoff distance inside of which force \ - is not applied (distance units) :ul - -[Examples:] - -fix center small-molecule drag 0.0 10.0 0.0 5.0 2.0 :pre - -[Description:] - -Apply a force to each atom in a group to drag it towards the point -(x,y,z). The magnitude of the force is specified by fmag. If an atom -is closer than a distance delta to the point, then the force is not -applied. - -Any of the x,y,z values can be specified as NULL which means do not -include that dimension in the distance calculation or force -application. - -This command can be used to steer one or more atoms to a new location -in the simulation. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Howto_output.html. This is the total -force on the group of atoms by the drag force. The vector values -calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix spring"_fix_spring.html, "fix spring/self"_fix_spring_self.html, -"fix spring/rg"_fix_spring_rg.html, "fix smd"_fix_smd.html - -[Default:] none diff --git a/doc/txt/fix_drude.txt b/doc/txt/fix_drude.txt deleted file mode 100644 index 80eb79201b..0000000000 --- a/doc/txt/fix_drude.txt +++ /dev/null @@ -1,56 +0,0 @@ - -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix drude command :h3 - -[Syntax:] - -fix ID group-ID drude flag1 flag2 ... flagN :pre - -ID, group-ID are documented in "fix"_fix.html command -drude = style name of this fix command -flag1 flag2 ... flagN = Drude flag for each atom type (1 to N) in the system :ul - -[Examples:] - -fix 1 all drude 1 1 0 1 0 2 2 2 -fix 1 all drude C C N C N D D D :pre - -[Description:] - -Assign each atom type in the system to be one of 3 kinds of atoms -within the Drude polarization model. This fix is designed to be used -with the "thermalized Drude oscillator model"_Howto_drude.html. -Polarizable models in LAMMPS are described on the "Howto -polarizable"_Howto_polarizable.html doc page. - -The three possible types can be designated with an integer (0,1,2) -or capital letter (N,C,D): - -0 or N = non-polarizable atom (not part of Drude model) -1 or C = Drude core -2 or D = Drude electron :ul - -[Restrictions:] - -This fix should be invoked before any other commands that implement -the Drude oscillator model, such as "fix -langevin/drude"_fix_langevin_drude.html, "fix -drude/transform"_fix_drude_transform.html, "compute -temp/drude"_compute_temp_drude.html, "pair_style -thole"_pair_thole.html. - -[Related commands:] - -"fix langevin/drude"_fix_langevin_drude.html, "fix -drude/transform"_fix_drude_transform.html, "compute -temp/drude"_compute_temp_drude.html, "pair_style -thole"_pair_thole.html - -[Default:] None diff --git a/doc/txt/fix_drude_transform.txt b/doc/txt/fix_drude_transform.txt deleted file mode 100644 index a102368b5c..0000000000 --- a/doc/txt/fix_drude_transform.txt +++ /dev/null @@ -1,164 +0,0 @@ - - - -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix drude/transform/direct command :h3 -fix drude/transform/inverse command :h3 - -[Syntax:] - -fix ID group-ID style keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command -style = {drude/transform/direct} or {drude/transform/inverse} :ul - -[Examples:] - -fix 3 all drude/transform/direct -fix 1 all drude/transform/inverse :pre - -[Description:] - -Transform the coordinates of Drude oscillators from real to reduced -and back for thermalizing the Drude oscillators as described in -"(Lamoureux)"_#Lamoureux1 using a Nose-Hoover thermostat. This fix is -designed to be used with the "thermalized Drude oscillator -model"_Howto_drude.html. Polarizable models in LAMMPS are described -on the "Howto polarizable"_Howto_polarizable.html doc page. - -Drude oscillators are a pair of atoms representing a single -polarizable atom. Ideally, the mass of Drude particles would vanish -and their positions would be determined self-consistently by iterative -minimization of the energy, the cores' positions being fixed. It is -however more efficient and it yields comparable results, if the Drude -oscillators (the motion of the Drude particle relative to the core) -are thermalized at a low temperature. In that case, the Drude -particles need a small mass. - -The thermostats act on the reduced degrees of freedom, which are -defined by the following equations. Note that in these equations -upper case denotes atomic or center of mass values and lower case -denotes Drude particle or dipole values. Primes denote the transformed -(reduced) values, while bare letters denote the original values. - -Masses: \begin\{equation\} M' = M + m \end\{equation\} -\begin\{equation\} m' = \frac \{M\, m \} \{M'\} \end\{equation\} -Positions: \begin\{equation\} X' = \frac \{M\, X + m\, x\} \{M'\} -\end\{equation\} \begin\{equation\} x' = x - X \end\{equation\} -Velocities: \begin\{equation\} V' = \frac \{M\, V + m\, v\} \{M'\} -\end\{equation\} \begin\{equation\} v' = v - V \end\{equation\} -Forces: \begin\{equation\} F' = F + f \end\{equation\} -\begin\{equation\} f' = \frac \{ M\, f - m\, F\} \{M'\} -\end\{equation\} - -This transform conserves the total kinetic energy -\begin\{equation\} \frac 1 2 \, (M\, V^2\ + m\, v^2) -= \frac 1 2 \, (M'\, V'^2\ + m'\, v'^2) \end\{equation\} -and the virial defined with absolute positions -\begin\{equation\} X\, F + x\, f = X'\, F' + x'\, f' \end\{equation\} - -:line - -This fix requires each atom know whether it is a Drude particle or -not. You must therefore use the "fix drude"_fix_drude.html command to -specify the Drude status of each atom type. - -NOTE: only the Drude core atoms need to be in the group specified for -this fix. A Drude electron will be transformed together with its core -even if it is not itself in the group. It is safe to include Drude -electrons or non-polarizable atoms in the group. The non-polarizable -atoms will simply not be transformed. - -:line - -This fix does NOT perform time integration. It only transform masses, -coordinates, velocities and forces. Thus you must use separate time -integration fixes, like "fix nve"_fix_nve.html or "fix -npt"_fix_nh.html to actually update the velocities and positions of -atoms. In order to thermalize the reduced degrees of freedom at -different temperatures, two Nose-Hoover thermostats must be defined, -acting on two distinct groups. - -NOTE: The {fix drude/transform/direct} command must appear before any -Nose-Hoover thermostatting fixes. The {fix drude/transform/inverse} -command must appear after any Nose-Hoover thermostatting fixes. - -Example: - -fix fDIRECT all drude/transform/direct -fix fNVT gCORES nvt temp 300.0 300.0 100 -fix fNVT gDRUDES nvt temp 1.0 1.0 100 -fix fINVERSE all drude/transform/inverse -compute TDRUDE all temp/drude -thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE\[1\] c_TDRUDE\[2\] :pre - - -In this example, {gCORES} is the group of the atom cores and {gDRUDES} -is the group of the Drude particles (electrons). The centers of mass -of the Drude oscillators will be thermostatted at 300.0 and the -internal degrees of freedom will be thermostatted at 1.0. The -temperatures of cores and Drude particles, in center-of-mass and -relative coordinates, are calculated using "compute -temp/drude"_compute_temp_drude.html - -In addition, if you want to use a barostat to simulate a system at -constant pressure, only one of the Nose-Hoover fixes must be {npt}, -the other one should be {nvt}. You must add a {compute temp/com} and a -{fix_modify} command so that the temperature of the {npt} fix be just -that of its group (the Drude cores) but the pressure be the overall -pressure {thermo_press}. - -Example: - -compute cTEMP_CORE gCORES temp/com -fix fDIRECT all drude/transform/direct -fix fNPT gCORES npt temp 298.0 298.0 100 iso 1.0 1.0 500 -fix_modify fNPT temp cTEMP_CORE press thermo_press -fix fNVT gDRUDES nvt temp 5.0 5.0 100 -fix fINVERSE all drude/transform/inverse :pre - -In this example, {gCORES} is the group of the atom cores and {gDRUDES} -is the group of the Drude particles. The centers of mass of the Drude -oscillators will be thermostatted at 298.0 and the internal degrees of -freedom will be thermostatted at 5.0. The whole system will be -barostatted at 1.0. - -In order to avoid the flying ice cube problem (irreversible transfer -of linear momentum to the center of mass of the system), you may need -to add a {fix momentum} command: - -fix fMOMENTUM all momentum 100 linear 1 1 1 :pre - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -[Restrictions:] none - -[Related commands:] - -"fix drude"_fix_drude.html, -"fix langevin/drude"_fix_langevin_drude.html, -"compute temp/drude"_compute_temp_drude.html, -"pair_style thole"_pair_thole.html - -[Default:] none - -:line - -:link(Lamoureux1) -[(Lamoureux)] Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003). diff --git a/doc/txt/fix_dt_reset.txt b/doc/txt/fix_dt_reset.txt deleted file mode 100644 index adca2c3072..0000000000 --- a/doc/txt/fix_dt_reset.txt +++ /dev/null @@ -1,103 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix dt/reset command :h3 - -[Syntax:] - -fix ID group-ID dt/reset N Tmin Tmax Xmax keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command -dt/reset = style name of this fix command -N = re-compute dt every N timesteps -Tmin = minimum dt allowed which can be NULL (time units) -Tmax = maximum dt allowed which can be NULL (time units) -Xmax = maximum distance for an atom to move in one timestep (distance units) -zero or more keyword/value pairs may be appended -keyword = {emax} or {units} :ul - {emax} value = Emax - Emax = maximum kinetic energy change for an atom in one timestep (energy units) - {units} value = {lattice} or {box} - lattice = Xmax is defined in lattice units - box = Xmax is defined in simulation box units :pre - -[Examples:] - -fix 5 all dt/reset 10 1.0e-5 0.01 0.1 -fix 5 all dt/reset 10 0.01 2.0 0.2 units box -fix 5 all dt/reset 5 NULL 0.001 0.5 emax 30 units box :pre - -[Description:] - -Reset the timestep size every N steps during a run, so that no atom -moves further than the specified {Xmax} distance, based on current -atom velocities and forces. Optionally an additional criterion is -imposed by the {emax} keyword, so that no atom's kinetic energy -changes by more than the specified {Emax}. - -This can be useful when starting from a configuration with overlapping -atoms, where forces will be large. Or it can be useful when running -an impact simulation where one or more high-energy atoms collide with -a solid, causing a damage cascade. - -This fix overrides the timestep size setting made by the -"timestep"_timestep.html command. The new timestep size {dt} is -computed in the following manner. - -For each atom, the timestep is computed that would cause it to -displace {Xmax} on the next integration step, as a function of its -current velocity and force. Since performing this calculation exactly -would require the solution to a quartic equation, a cheaper estimate -is generated. The estimate is conservative in that the atom's -displacement is guaranteed not to exceed {Xmax}, though it may be -smaller. - -In addition if the {emax} keyword is used, the specified {Emax} value -is enforced as a limit on how much an atom's kinetic energy can -change. If the timestep required is even smaller than for the {Xmax} -displacement, then the smaller timestep is used. - -Given this putative timestep for each atom, the minimum timestep value -across all atoms is computed. Then the {Tmin} and {Tmax} bounds are -applied, if specified. If one (or both) is specified as NULL, it is -not applied. - -When the "run style"_run_style.html is {respa}, this fix resets the -outer loop (largest) timestep, which is the same timestep that the -"timestep"_timestep.html command sets. - -Note that the cumulative simulation time (in time units), which -accounts for changes in the timestep size as a simulation proceeds, -can be accessed by the "thermo_style time"_thermo_style.html keyword. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar stores the last -timestep on which the timestep was reset to a new value. - -The scalar value calculated by this fix is "intensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"timestep"_timestep.html - -[Default:] - -The option defaults are units = lattice, and no emax kinetic energy -limit. diff --git a/doc/txt/fix_efield.txt b/doc/txt/fix_efield.txt deleted file mode 100644 index cecfb6e6a3..0000000000 --- a/doc/txt/fix_efield.txt +++ /dev/null @@ -1,166 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix efield command :h3 - -[Syntax:] - -fix ID group-ID efield ex ey ez keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -efield = style name of this fix command :l -ex,ey,ez = E-field component values (electric field units) :l -any of ex,ey,ez can be a variable (see below) :l -zero or more keyword/value pairs may be appended to args :l -keyword = {region} or {energy} :l - {region} value = region-ID - region-ID = ID of region atoms must be in to have added force - {energy} value = v_name - v_name = variable with name that calculates the potential energy of each atom in the added E-field :pre -:ule - -[Examples:] - -fix kick external-field efield 1.0 0.0 0.0 -fix kick external-field efield 0.0 0.0 v_oscillate :pre - -[Description:] - -Add a force F = qE to each charged atom in the group due to an -external electric field being applied to the system. If the system -contains point-dipoles, also add a torque on the dipoles due to the -external electric field. - -For charges, any of the 3 quantities defining the E-field components -can be specified as an equal-style or atom-style -"variable"_variable.html, namely {ex}, {ey}, {ez}. If the value is a -variable, it should be specified as v_name, where name is the variable -name. In this case, the variable will be evaluated each timestep, and -its value used to determine the E-field component. - -For point-dipoles, equal-style variables can be used, but atom-style -variables are not currently supported, since they imply a spatial -gradient in the electric field which means additional terms with -gradients of the field are required for the force and torque on -dipoles. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent E-field. - -Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent E-field -with optional time-dependence as well. - -If the {region} keyword is used, the atom must also be in the -specified geometric "region"_region.html in order to have force added -to it. - -:line - -Adding a force or torque to atoms implies a change in their potential -energy as they move or rotate due to the applied E-field. - -For dynamics via the "run" command, this energy can be optionally -added to the system's potential energy for thermodynamic output (see -below). For energy minimization via the "minimize" command, this -energy must be added to the system's potential energy to formulate a -self-consistent minimization problem (see below). - -The {energy} keyword is not allowed if the added field is a constant -vector (ex,ey,ez), with all components defined as numeric constants -and not as variables. This is because LAMMPS can compute the energy -for each charged particle directly as E = -x dot qE = -q (x*ex + y*ey -+ z*ez), so that -Grad(E) = F. Similarly for point-dipole particles -the energy can be computed as E = -mu dot E = -(mux*ex + muy*ey + -muz*ez). - -The {energy} keyword is optional if the added force is defined with -one or more variables, and if you are performing dynamics via the -"run"_run.html command. If the keyword is not used, LAMMPS will set -the energy to 0.0, which is typically fine for dynamics. - -The {energy} keyword is required if the added force is defined with -one or more variables, and you are performing energy minimization via -the "minimize" command for charged particles. It is not required for -point-dipoles, but a warning is issued since the minimizer in LAMMPS -does not rotate dipoles, so you should not expect to be able to -minimize the orientation of dipoles in an applied electric field. - -The {energy} keyword specifies the name of an atom-style -"variable"_variable.html which is used to compute the energy of each -atom as function of its position. Like variables used for {ex}, {ey}, -{ez}, the energy variable is specified as v_name, where name is the -variable name. - -Note that when the {energy} keyword is used during an energy -minimization, you must insure that the formula defined for the -atom-style "variable"_variable.html is consistent with the force -variable formulas, i.e. that -Grad(E) = F. For example, if the force -due to the electric field were a spring-like F = kx, then the energy -formula should be E = -0.5kx^2. If you don't do this correctly, the -minimization will not converge properly. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the potential "energy" inferred by the added force due to -the electric field to the system's potential energy as part of -"thermodynamic output"_thermo_style.html. This is a fictitious -quantity but is needed so that the "minimize"_minimize.html command -can include the forces added by this fix in a consistent manner. -I.e. there is a decrease in potential energy when atoms move in the -direction of the added force due to the electric field. - -The "fix_modify"_fix_modify.html {virial} option is supported by this -fix to add the contribution due to the added forces on atoms to the -system's virial as part of "thermodynamic output"_thermo_style.html. -The default is {virial no} - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix adding its forces. Default is the outermost level. - -This fix computes a global scalar and a global 3-vector of forces, -which can be accessed by various "output commands"_Howto_output.html. -The scalar is the potential energy discussed above. The vector is the -total force added to the group of atoms. The scalar and vector values -calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. You should not -specify force components with a variable that has time-dependence for -use with a minimizer, since the minimizer increments the timestep as -the iteration count during the minimization. - -NOTE: If you want the fictitious potential energy associated with the -added forces to be included in the total potential energy of the -system (the quantity being minimized), you MUST enable the -"fix_modify"_fix_modify.html {energy} option for this fix. - -[Restrictions:] - -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix addforce"_fix_addforce.html - -[Default:] none diff --git a/doc/txt/fix_ehex.txt b/doc/txt/fix_ehex.txt deleted file mode 100644 index 79cfce4b01..0000000000 --- a/doc/txt/fix_ehex.txt +++ /dev/null @@ -1,178 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix ehex command :h3 - -[Syntax:] - -fix ID group-ID ehex nevery F keyword value :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -ehex = style name of this fix command :l -nevery = add/subtract heat every this many timesteps :l -F = energy flux into the reservoir (energy/time units) :l -zero or more keyword/value pairs may be appended to args :l -keyword = {region} or {constrain} or {com} or {hex} :l - {region} value = region-ID - region-ID = ID of region (reservoir) atoms must be in for added thermostatting force - {constrain} value = none - apply the constraint algorithm (SHAKE or RATTLE) again at the end of the timestep - {com} value = none - rescale all sites of a constrained cluster of atom if its COM is in the reservoir - {hex} value = none - omit the coordinate correction to recover the HEX algorithm :pre -:ule - -[Examples:] - -# Lennard-Jones, from examples/in.ehex.lj :pre -fix fnve all nve -# specify regions rhot and rcold -... -fix fhot all ehex 1 0.15 region rhot -fix fcold all ehex 1 -0.15 region rcold :pre - -# SPC/E water, from examples/in.ehex.spce -fix fnve all nve -# specify regions rhot and rcold -... -fix fhot all ehex 1 0.075 region rhot constrain com -fix fcold all ehex 1 -0.075 region rcold constrain com -fix frattle all rattle 1e-10 400 0 b 1 a 1 :pre - -[Description:] - -This fix implements the asymmetric version of the enhanced heat -exchange algorithm "(Wirnsberger)"_#Wirnsberger. The eHEX algorithm is -an extension of the heat exchange algorithm "(Ikeshoji)"_#Ikeshoji and -adds an additional coordinate integration to account for higher-order -truncation terms in the operator splitting. The original HEX -algorithm (implemented as "fix heat"_fix_heat.html) is known to -exhibit a slight energy drift limiting the accessible simulation times -to a few nanoseconds. This issue is greatly improved by the new -algorithm decreasing the energy drift by at least a factor of a -hundred (LJ and SPC/E water) with little computational overhead. - -In both algorithms (non-translational) kinetic energy is constantly -swapped between regions (reservoirs) to impose a heat flux onto the -system. The equations of motion are therefore modified if a particle -\(i\) is located inside a reservoir \(\Gamma_k\) where \(k>0\). We -use \(\Gamma_0\) to label those parts of the simulation box which -are not thermostatted.) The input parameter {region-ID} of this fix -corresponds to \(k\). The energy swap is modelled by introducing an -additional thermostatting force to the equations of motion, such that -the time evolution of coordinates and momenta of particle \(i\) -becomes "(Wirnsberger)"_#Wirnsberger - -:c,image(Eqs/fix_ehex_eom.jpg) - -The thermostatting force is given by - -:c,image(Eqs/fix_ehex_f.jpg) - -where \(m_i\) is the mass and \(k(\mathbf r_i)\) maps the particle -position to the respective reservoir. The quantity -\(F_\{\Gamma_\{k(\mathbf r_i)\}\}\) corresponds to the input parameter -{F}, which is the energy flux into the reservoir. Furthermore, -\(K_\{\Gamma_\{k(\mathbf r_i)\}\}\) and \(v_\{\Gamma_\{k(\mathbf r_i)\}\}\) -denote the non-translational kinetic energy and the center of mass -velocity of that reservoir. The thermostatting force does not affect -the center of mass velocities of the individual reservoirs and the -entire simulation box. A derivation of the equations and details on -the numerical implementation with velocity Verlet in LAMMPS can be -found in reference "(Wirnsberger)"#_Wirnsberger. - -NOTE: This fix only integrates the thermostatting force and must be -combined with another integrator, such as "fix nve"_fix_nve.html, to -solve the full equations of motion. - -This fix is different from a thermostat such as "fix nvt"_fix_nh.html -or "fix temp/rescale"_fix_temp_rescale.html in that energy is -added/subtracted continually. Thus if there isn't another mechanism -in place to counterbalance this effect, the entire system will heat or -cool continuously. - -NOTE: If heat is subtracted from the system too aggressively so that -the group's kinetic energy would go to zero, then LAMMPS will halt -with an error message. Increasing the value of {nevery} means that -heat is added/subtracted less frequently but in larger portions. The -resulting temperature profile will therefore be the same. - -This fix will default to "fix_heat"_fix_heat.html (HEX algorithm) if -the keyword {hex} is specified. - -:line - -[Compatibility with SHAKE and RATTLE (rigid molecules)]: - -This fix is compatible with "fix shake"_fix_shake.html and "fix -rattle"_fix_shake.html. If either of these constraining algorithms is -specified in the input script and the keyword {constrain} is set, the -bond distances will be corrected a second time at the end of the -integration step. It is recommended to specify the keyword {com} in -addition to the keyword {constrain}. With this option all sites of a -constrained cluster are rescaled, if its center of mass is located -inside the region. Rescaling all sites of a cluster by the same factor -does not introduce any velocity components along fixed bonds. No -rescaling takes place if the center of mass lies outside the region. - -NOTE: You can only use the keyword {com} along with {constrain}. - -To achieve the highest accuracy it is recommended to use "fix -rattle"_fix_shake.html with the keywords {constrain} and {com} as -shown in the second example. Only if RATTLE is employed, the velocity -constraints will be satisfied. - -NOTE: Even if RATTLE is used and the keywords {com} and {constrain} -are both set, the coordinate constraints will not necessarily be -satisfied up to the target precision. The velocity constraints are -satisfied as long as all sites of a cluster are rescaled (keyword -{com}) and the cluster does not span adjacent reservoirs. The current -implementation of the eHEX algorithm introduces a small error in the -bond distances, which goes to zero with order three in the -timestep. For example, in a simulation of SPC/E water with a timestep -of 2 fs the maximum relative error in the bond distances was found to -be on the order of \(10^\{-7\}\) for relatively large -temperature gradients. A higher precision can be achieved by -decreasing the timestep. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the RIGID package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix heat"_fix_heat.html, "fix -thermal/conductivity"_fix_thermal_conductivity.html, "compute -temp"_compute_temp.html, "compute -temp/region"_compute_temp_region.html - -[Default:] none - -:line - -:link(Ikeshoji) -[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994). - -:link(Wirnsberger) -[(Wirnsberger)] Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, -124104 (2015). diff --git a/doc/txt/fix_electron_stopping.txt b/doc/txt/fix_electron_stopping.txt deleted file mode 100644 index 096629c330..0000000000 --- a/doc/txt/fix_electron_stopping.txt +++ /dev/null @@ -1,165 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix electron/stopping command :h3 - -[Syntax:] - -fix ID group-ID electron/stopping Ecut file keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -electron/stopping = style name of this fix command :l -Ecut = minimum kinetic energy for electronic stopping (energy units) :l -file = name of the file containing the electronic stopping power table :l -zero or more keyword/value pairs may be appended to args :l -keyword = {region} or {minneigh} :l - {region} value = region-ID - region-ID = region, whose atoms will be affected by this fix - {minneigh} value = minneigh - minneigh = minimum number of neighbors an atom to have stopping applied :pre -:ule - -[Examples:] - -fix el all electron/stopping 10.0 elstop-table.txt -fix el all electron/stopping 10.0 elstop-table.txt minneigh 3 -fix el mygroup electron/stopping 1.0 elstop-table.txt region bulk :pre - -[Description:] - -This fix implements inelastic energy loss for fast projectiles in solids. It -applies a friction force to fast moving atoms to slow them down due to -"electronic stopping"_#elstopping (energy lost via electronic collisions per -unit of distance). This fix should be used for simulation of irradiation -damage or ion implantation, where the ions can lose noticeable amounts of -energy from electron excitations. If the electronic stopping power is not -considered, the simulated range of the ions can be severely overestimated -("Nordlund98"_#Nordlund98, "Nordlund95"_#Nordlund95). - -The electronic stopping is implemented by applying a friction force -to each atom as: - -\begin\{equation\} -\vec\{F\}_i = \vec\{F\}^0_i - \frac\{\vec\{v\}_i\}\{\|\vec\{v\}_i\|\} \cdot S_e -\end\{equation\} - -where \(\vec\{F\}_i\) is the resulting total force on the atom. -\(\vec\{F\}^0_i\) is the original force applied to the atom, \(\vec\{v\}_i\) is -its velocity and \(S_e\) is the stopping power of the ion. - -NOTE: In addition to electronic stopping, atomic cascades and irradiation -simulations require the use of an adaptive timestep (see -"fix dt/reset"_fix_dt_reset.html) and the repulsive ZBL potential (see -"ZBL"_pair_zbl.html potential) or similar. Without these settings the -interaction between the ion and the target atoms will be faulty. It is also -common to use in such simulations a thermostat ("fix_nvt"_fix_nh.html) in -the borders of the simulation cell. - -NOTE: This fix removes energy from fast projectiles without depositing it as a -heat to the simulation cell. Such implementation might lead to the unphysical -results when the amount of energy deposited to the electronic system is large, -e.g. simulations of Swift Heavy Ions (energy per nucleon of 100 keV/amu or -higher) or multiple projectiles. You could compensate energy loss by coupling -bulk atoms with some thermostat or control heat transfer between electronic and -atomic subsystems with the two-temperature model ("fix_ttm"_fix_ttm.html). - -At low velocities the electronic stopping is negligible. The electronic -friction is not applied to atoms whose kinetic energy is smaller than {Ecut}, -or smaller than the lowest energy value given in the table in {file}. -Electronic stopping should be applied only when a projectile reaches bulk -material. This fix scans neighbor list and excludes atoms with fewer than -{minneigh} neighbors (by default one). If the pair potential cutoff is large, -minneigh should be increased, though not above the number of nearest neighbors -in bulk material. An alternative is to disable the check for neighbors by -setting {minneigh} to zero and using the {region} keyword. This is necessary -when running simulations of cluster bombardment. - -If the {region} keyword is used, the atom must also be in the specified -geometric "region"_region.html in order to have electronic stopping applied to -it. This is useful if the position of the bulk material is fixed. By default -the electronic stopping is applied everywhere in the simulation cell. - -:line - -The energy ranges and stopping powers are read from the file {file}. -Lines starting with {#} and empty lines are ignored. Otherwise each -line must contain exactly [N+1] numbers, where [N] is the number of atom -types in the simulation. - -The first column is the energy for which the stopping powers on that -line apply. The energies must be sorted from the smallest to the largest. -The other columns are the stopping powers \(S_e\) for each atom type, -in ascending order, in force "units"_units.html. The stopping powers for -intermediate energy values are calculated with linear interpolation between -2 nearest points. - -For example: - -# This is a comment -# atom-1 atom-2 -# eV eV/Ang eV/Ang # units metal - 10 0 0 -250 60 80 -750 100 150 :pre - - -If an atom which would have electronic stopping applied to it has a -kinetic energy higher than the largest energy given in {file}, LAMMPS -will exit with an error message. - -The stopping power depends on the energy of the ion and the target -material. The electronic stopping table can be obtained from -scientific publications, experimental databases or by using -"SRIM"_#SRIM software. Other programs such as "CasP"_#CasP or -"PASS"_#PASS can calculate the energy deposited as a function -of the impact parameter of the ion; these results can be used -to derive the stopping power. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html options are not supported. - -This fix computes a global scalar, which can be accessed by various -"output commands"_Howto_output.html. The scalar is the total energy -loss from electronic stopping applied by this fix since the start of -the latest run. It is considered "intensive". - -The {start/stop} keywords of the "run"_run.html command have no effect -on this fix. - -[Restrictions:] - -This pair style is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build package"_Build_package.html -doc page for more info. - -[Default:] - -The default is no limitation by region, and minneigh = 1. - -:line -:link(elstopping) -[(electronic stopping)] Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29 - -:link(Nordlund98) -[(Nordlund98)] Nordlund, Kai, et al. Physical Review B 57.13 (1998): 7556. - -:link(Nordlund95) -[(Nordlund95)] Nordlund, Kai. Computational materials science 3.4 (1995): 448-456. - -:link(SRIM) -[(SRIM)] SRIM webpage: http://www.srim.org/ - -:link(CasP) -[(CasP)] CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html - -:link(PASS) -[(PASS)] PASS webpage: https://www.sdu.dk/en/DPASS diff --git a/doc/txt/fix_enforce2d.txt b/doc/txt/fix_enforce2d.txt deleted file mode 100644 index 17ac8146fd..0000000000 --- a/doc/txt/fix_enforce2d.txt +++ /dev/null @@ -1,69 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix enforce2d command :h3 -fix enforce2d/kk command :h3 - -[Syntax:] - -fix ID group-ID enforce2d :pre - -ID, group-ID are documented in "fix"_fix.html command -enforce2d = style name of this fix command :ul - -[Examples:] - -fix 5 all enforce2d :pre - -[Description:] - -Zero out the z-dimension velocity and force on each atom in the group. -This is useful when running a 2d simulation to insure that atoms do -not move from their initial z coordinate. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -[Restrictions:] none - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/fix_eos_cv.txt b/doc/txt/fix_eos_cv.txt deleted file mode 100644 index b2ac0eb6b9..0000000000 --- a/doc/txt/fix_eos_cv.txt +++ /dev/null @@ -1,60 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix eos/cv command :h3 - -[Syntax:] - -fix ID group-ID eos/cv cv :pre - -ID, group-ID are documented in "fix"_fix.html command -eos/cv = style name of this fix command -cv = constant-volume heat capacity (energy/temperature units) :ul - -[Examples:] - -fix 1 all eos/cv 0.01 :pre - -[Description:] - -Fix {eos/cv} applies a mesoparticle equation of state to relate the -particle internal energy (u_i) to the particle internal temperature -(dpdTheta_i). The {eos/cv} mesoparticle equation of state requires -the constant-volume heat capacity, and is defined as follows: - -:c,image(Eqs/fix_eos-cv.jpg) - -where Cv is the constant-volume heat capacity, u_cond is the internal -conductive energy, and u_mech is the internal mechanical energy. Note -that alternative definitions of the mesoparticle equation of state are -possible. - -:line - -[Restrictions:] - -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This command also requires use of the "atom_style dpd"_atom_style.html -command. - -[Related commands:] - -"fix shardlow"_fix_shardlow.html, "pair dpd/fdt"_pair_dpd_fdt.html - -[Default:] none - -:line - -:link(Larentzos4) -[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and -W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative -Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research -Laboratory, Aberdeen Proving Ground, MD (2014). diff --git a/doc/txt/fix_eos_table.txt b/doc/txt/fix_eos_table.txt deleted file mode 100644 index 72c8523662..0000000000 --- a/doc/txt/fix_eos_table.txt +++ /dev/null @@ -1,117 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix eos/table command :h3 - -[Syntax:] - -fix ID group-ID eos/table style file N keyword :pre - -ID, group-ID are documented in "fix"_fix.html command -eos/table = style name of this fix command -style = {linear} = method of interpolation -file = filename containing the tabulated equation of state -N = use N values in {linear} tables -keyword = name of table keyword corresponding to table file :ul - -[Examples:] - -fix 1 all eos/table linear eos.table 100000 KEYWORD :pre - -[Description:] - -Fix {eos/table} applies a tabulated mesoparticle equation of state to -relate the particle internal energy (u_i) to the particle internal -temperature (dpdTheta_i). - -Fix {eos/table} creates interpolation tables of length {N} from -internal energy values listed in a file as a function of internal -temperature. - -The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy values at each of {N} internal -temperatures, and vice versa. During a simulation, these tables are -used to interpolate internal energy or temperature values as needed. -The interpolation is done with the {linear} style. - -For the {linear} style, the internal temperature is used to find 2 -surrounding table values from which an internal energy is computed by -linear interpolation, and vice versa. - -The filename specifies a file containing tabulated internal -temperature and internal energy values. The keyword specifies a -section of the file. The format of this file is described below. - -:line - -The format of a tabulated file is as follows (without the -parenthesized comments): - -# EOS TABLE (one or more comment or blank lines) :pre - -KEYWORD (keyword is first text on line) -N 500 (N parameter) - (blank) -1 1.00 0.000 (index, internal temperature, internal energy) -2 1.02 0.001 -... -500 10.0 0.500 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the fix command. - -The next line lists the number of table entries. The parameter "N" is -required and its value is the number of table entries that follow. -Note that this may be different than the {N} specified in the "fix -eos/table"_fix_eos_table.html command. Let Ntable = {N} in the fix -command, and Nfile = "N" in the tabulated file. What LAMMPS does is a -preliminary interpolation by creating splines using the Nfile -tabulated values as nodal points. It uses these to interpolate as -needed to generate energy and temperature values at Ntable different -points. The resulting tables of length Ntable are then used as -described above, when computing energy and temperature relationships. -This means that if you want the interpolation tables of length Ntable -to match exactly what is in the tabulated file (with effectively no -preliminary interpolation), you should set Ntable = Nfile. - -Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -the internal temperature (in temperature units), the 3rd value is the -internal energy (in energy units). - -Note that the internal temperature and internal energy values must -increase from one line to the next. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. - -:line - -[Restrictions:] - -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This command also requires use of the "atom_style dpd"_atom_style.html -command. - -The equation of state must be a monotonically increasing function. - -An error will occur if the internal temperature or internal energies -are not within the table cutoffs. - -[Related commands:] - -"fix shardlow"_fix_shardlow.html, "pair dpd/fdt"_pair_dpd_fdt.html - -[Default:] none diff --git a/doc/txt/fix_eos_table_rx.txt b/doc/txt/fix_eos_table_rx.txt deleted file mode 100644 index 1a2daa0bc6..0000000000 --- a/doc/txt/fix_eos_table_rx.txt +++ /dev/null @@ -1,199 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix eos/table/rx command :h3 -fix eos/table/rx/kk command :h3 - -[Syntax:] - -fix ID group-ID eos/table/rx style file1 N keyword ... :pre - -ID, group-ID are documented in "fix"_fix.html command -eos/table/rx = style name of this fix command -style = {linear} = method of interpolation -file1 = filename containing the tabulated equation of state -N = use N values in {linear} tables -keyword = name of table keyword corresponding to table file -file2 = filename containing the heats of formation of each species (optional) -deltaHf = heat of formation for a single species in energy units (optional) -energyCorr = energy correction in energy units (optional) -tempCorrCoeff = temperature correction coefficient (optional) :ul - -[Examples:] - -fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table -fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5 -fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5 0.025 0.0 :pre - -[Description:] - -Fix {eos/table/rx} applies a tabulated mesoparticle equation -of state to relate the concentration-dependent particle internal -energy (u_i) to the particle internal temperature (dpdTheta_i). - -The concentration-dependent particle internal energy (u_i) is -computed according to the following relation: - -:c,image(Eqs/fix_eos_table_rx.jpg) - -where {m} is the number of species, {c_i,j} is the concentration of -species {j} in particle {i}, {u_j} is the internal energy of species j, -{DeltaH_f,j} is the heat of formation of species {j}, N is the number of -molecules represented by the coarse-grained particle, kb is the -Boltzmann constant, and T is the temperature of the system. Additionally, -it is possible to modify the concentration-dependent particle internal -energy relation by adding an energy correction, temperature-dependent -correction, and/or a molecule-dependent correction. An energy correction can -be specified as a constant (in energy units). A temperature correction can be -specified by multiplying a temperature correction coefficient by the -internal temperature. A molecular correction can be specified by -by multiplying a molecule correction coefficient by the average number of -product gas particles in the coarse-grain particle. - -Fix {eos/table/rx} creates interpolation tables of length {N} from {m} -internal energy values of each species {u_j} listed in a file as a -function of internal temperature. During a simulation, these tables -are used to interpolate internal energy or temperature values as needed. -The interpolation is done with the {linear} style. For the {linear} style, -the internal temperature is used to find 2 surrounding table values from -which an internal energy is computed by linear interpolation. A secant -solver is used to determine the internal temperature from the internal energy. - -The first filename specifies a file containing tabulated internal -temperature and {m} internal energy values for each species {u_j}. -The keyword specifies a section of the file. The format of this -file is described below. - -The second filename specifies a file containing heat of formation -{DeltaH_f,j} for each species. - -In cases where the coarse-grain particle represents a single molecular -species (i.e., no reactions occur and fix {rx} is not present in the input file), -fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} -within a non-reactive DPD simulation. In this case, the heat of formation -filename is replaced with the heat of formation value for the single species. -Additionally, the energy correction and temperature correction coefficients may -also be specified as fix arguments. - -:line - -The format of a tabulated file is as follows (without the -parenthesized comments): - -# EOS TABLE (one or more comment or blank lines) :pre - -KEYWORD (keyword is first text on line) -N 500 h2 no2 n2 ... no (N parameter species1 species2 ... speciesN) - (blank) -1 1.00 0.000 ... 0.0000 (index, internal temperature, internal energy of species 1, ..., internal energy of species m) -2 1.02 0.001 ... 0.0002 -... -500 10.0 0.500 ... 1.0000 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the fix command. - -The next line lists the number of table entries and the species names -that correspond with all the species listed in the reaction equations -through the {fix rx} command. -The parameter "N" is required and its value is the number of table -entries that follow. Let Nfile = "N" in the tabulated file. -What LAMMPS does is a preliminary interpolation by creating splines -using the Nfile tabulated values as nodal points. - -Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -the internal temperature (in temperature units), the 3rd value until -the {m+3} value are the internal energies of the m species (in energy units). - -Note that all internal temperature and internal energy values must -increase from one line to the next. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. - -:line - -The format of a heat of formation file is as follows (without the -parenthesized comments): - -# HEAT OF FORMATION TABLE (one or more comment or blank lines) :pre - (blank) -h2 0.00 (species name, heat of formation) -no2 0.34 -n2 0.00 -... -no 0.93 :pre - -Note that the species can be listed in any order. The tag that is -used as the species name must correspond with the tags used to define -the reactions with the "fix rx"_fix_rx.html command. - -Alternatively, corrections to the EOS can be included by specifying -three additional columns that correspond to the energy correction, -the temperature correction coefficient and molecule correction -coefficient. In this case, the format of the file is as follows: - -# HEAT OF FORMATION TABLE (one or more comment or blank lines) :pre - (blank) -h2 0.00 1.23 0.025 0.0 (species name, heat of formation, energy correction, temperature correction coefficient, molecule correction coefficient) -no2 0.34 0.00 0.000 -1.76 -n2 0.00 0.00 0.000 -1.76 -... -no 0.93 0.00 0.000 -1.76 :pre - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This command also requires use of the "atom_style dpd"_atom_style.html -command. - -The equation of state must be a monotonically increasing function. - -An error will occur if the internal temperature or internal energies -are not within the table cutoffs. - -[Related commands:] - -"fix rx"_fix_rx.html, -"pair dpd/fdt"_pair_dpd_fdt.html - -[Default:] none - -:line diff --git a/doc/txt/fix_evaporate.txt b/doc/txt/fix_evaporate.txt deleted file mode 100644 index 69572b96cf..0000000000 --- a/doc/txt/fix_evaporate.txt +++ /dev/null @@ -1,96 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix evaporate command :h3 - -[Syntax:] - -fix ID group-ID evaporate N M region-ID seed :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -evaporate = style name of this fix command :l -N = delete atoms every this many timesteps :l -M = number of atoms to delete each time :l -region-ID = ID of region within which to perform deletions :l -seed = random number seed to use for choosing atoms to delete :l -zero or more keyword/value pairs may be appended :l -keyword = {molecule} - {molecule} value = {no} or {yes} :pre -:ule - -[Examples:] - -fix 1 solvent evaporate 1000 10 surface 49892 -fix 1 solvent evaporate 1000 10 surface 38277 molecule yes :pre - -[Description:] - -Remove M atoms from the simulation every N steps. This can be used, -for example, to model evaporation of solvent particles or molecules -(i.e. drying) of a system. Every N steps, the number of atoms in the -fix group and within the specified region are counted. M of these are -chosen at random and deleted. If there are less than M eligible -particles, then all of them are deleted. - -If the setting for the {molecule} keyword is {no}, then only single -atoms are deleted. In this case, you should insure you do not delete -only a portion of a molecule (only some of its atoms), or LAMMPS will -soon generate an error when it tries to find those atoms. LAMMPS will -warn you if any of the atoms eligible for deletion have a non-zero -molecule ID, but does not check for this at the time of deletion. - -If the setting for the {molecule} keyword is {yes}, then when an atom -is chosen for deletion, the entire molecule it is part of is deleted. -The count of deleted atoms is incremented by the number of atoms in -the molecule, which may make it exceed {M}. If the molecule ID of the -chosen atom is 0, then it is assumed to not be part of a molecule, and -just the single atom is deleted. - -As an example, if you wish to delete 10 water molecules every {N} -steps, you should set {M} to 30. If only the water's oxygen atoms -were in the fix group, then two hydrogen atoms would be deleted when -an oxygen atom is selected for deletion, whether the hydrogen atoms -are inside the evaporation region or not. - -Note that neighbor lists are re-built on timesteps that atoms are -removed. Thus you should not remove atoms too frequently or you will -incur overhead due to the cost of building neighbor lists. - -NOTE: If you are monitoring the temperature of a system where the atom -count is changing due to evaporation, you typically should use the -"compute_modify dynamic yes"_compute_modify.html command for the -temperature compute you are using. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global scalar, which can be accessed by various -"output commands"_Howto_output.html. The scalar is the cumulative -number of deleted atoms. The scalar value calculated by this fix is -"intensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix deposit"_fix_deposit.html - -[Default:] - -The option defaults are molecule = no. diff --git a/doc/txt/fix_external.txt b/doc/txt/fix_external.txt deleted file mode 100644 index dd7f7914e9..0000000000 --- a/doc/txt/fix_external.txt +++ /dev/null @@ -1,157 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix external command :h3 - -[Syntax:] - -fix ID group-ID external mode args :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -external = style name of this fix command :l -mode = {pf/callback} or {pf/array} :l - {pf/callback} args = Ncall Napply - Ncall = make callback every Ncall steps - Napply = apply callback forces every Napply steps - {pf/array} args = Napply - Napply = apply array forces every Napply steps :pre -:ule - -[Examples:] - -fix 1 all external pf/callback 1 1 -fix 1 all external pf/callback 100 1 -fix 1 all external pf/array 10 :pre - -[Description:] - -This fix allows external programs that are running LAMMPS through its -"library interface"_Howto_library.html to modify certain LAMMPS -properties on specific timesteps, similar to the way other fixes do. -The external driver can be a "C/C++ or Fortran -program"_Howto_library.html or a "Python script"_Python_head.html. - -:line - -If mode is {pf/callback} then the fix will make a callback every -{Ncall} timesteps or minimization iterations to the external program. -The external program computes forces on atoms by setting values in an -array owned by the fix. The fix then adds these forces to each atom -in the group, once every {Napply} steps, similar to the way the "fix -addforce"_fix_addforce.html command works. Note that if {Ncall} > -{Napply}, the force values produced by one callback will persist, and -be used multiple times to update atom forces. - -The callback function "foo" is invoked by the fix as: - -foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal); :pre - -The arguments are as follows: - -ptr = pointer provided by and simply passed back to external driver -timestep = current LAMMPS timestep -nlocal = # of atoms on this processor -ids = list of atom IDs on this processor -x = coordinates of atoms on this processor -fexternal = forces to add to atoms on this processor :ul - -Note that timestep is a "bigint" which is defined in src/lmptype.h, -typically as a 64-bit integer. - -Fexternal are the forces returned by the driver program. - -The fix has a set_callback() method which the external driver can call -to pass a pointer to its foo() function. See the -couple/lammps_quest/lmpqst.cpp file in the LAMMPS distribution for an -example of how this is done. This sample application performs -classical MD using quantum forces computed by a density functional -code "Quest"_quest. - -:link(quest,http://dft.sandia.gov/Quest) - -:line - -If mode is {pf/array} then the fix simply stores force values in an -array. The fix adds these forces to each atom in the group, once -every {Napply} steps, similar to the way the "fix -addforce"_fix_addforce.html command works. - -The name of the public force array provided by the FixExternal -class is - -double **fexternal; :pre - -It is allocated by the FixExternal class as an (N,3) array where N is -the number of atoms owned by a processor. The 3 corresponds to the -fx, fy, fz components of force. - -It is up to the external program to set the values in this array to -the desired quantities, as often as desired. For example, the driver -program might perform an MD run in stages of 1000 timesteps each. In -between calls to the LAMMPS "run"_run.html command, it could retrieve -atom coordinates from LAMMPS, compute forces, set values in fexternal, -etc. - -:line - -To use this fix during energy minimization, the energy corresponding -to the added forces must also be set so as to be consistent with the -added forces. Otherwise the minimization will not converge correctly. - -This can be done from the external driver by calling this public -method of the FixExternal class: - -void set_energy(double eng); :pre - -where eng is the potential energy. Eng is an extensive quantity, -meaning it should be the sum over per-atom energies of all affected -atoms. It should also be provided in "energy units"_units.html -consistent with the simulation. See the details below for how to -insure this energy setting is used appropriately in a minimization. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the potential "energy" set by the external driver to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. This is a fictitious quantity but is -needed so that the "minimize"_minimize.html command can include the -forces added by this fix in a consistent manner. I.e. there is a -decrease in potential energy when atoms move in the direction of the -added force. - -The "fix_modify"_fix_modify.html {virial} option is supported by this -fix to add the contribution due to the interactions computed by the -external program to the system's virial as part of "thermodynamic -output"_thermo_style.html. The default is {virial yes} - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the potential -energy discussed above. The scalar stored by this fix is "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -NOTE: If you want the fictitious potential energy associated with the -added forces to be included in the total potential energy of the -system (the quantity being minimized), you MUST enable the -"fix_modify"_fix_modify.html {energy} option for this fix. - -[Restrictions:] none - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/fix_ffl.txt b/doc/txt/fix_ffl.txt deleted file mode 100644 index a5d3f80a62..0000000000 --- a/doc/txt/fix_ffl.txt +++ /dev/null @@ -1,124 +0,0 @@ - - - -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix ffl command :h3 - -[Syntax:] - -fix ID id-group ffl tau Tstart Tstop seed \[flip-type\] :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -ffl = style name of this fix command :l -tau = thermostat parameter (positive real) :l -Tstart, Tstop = temperature ramp during the run :l -seed = random number seed to use for generating noise (positive integer) :l -one more value may be appended :l - flip-type = determines the flipping type, can be chosen between rescale - no_flip - hard - soft, if no flip type is given, rescale will be chosen by default :pre -:ule - -[Examples:] - -fix 3 boundary ffl 10 300 300 31415 -fix 1 all ffl 100 500 500 9265 soft :pre - -[Description:] - -Apply a Fast-Forward Langevin Equation (FFL) thermostat as described -in "(Hijazi)"_#Hijazi. Contrary to -"fix langevin"_fix_langevin.html, this fix performs both -thermostatting and evolution of the Hamiltonian equations of motion, so it -should not be used together with "fix nve"_fix_nve.html -- at least not -on the same atom groups. - -The time-evolution of a single particle undergoing Langevin dynamics is described -by the equations - -\begin\{equation\} \frac \{dq\}\{dt\} = \frac\{p\}\{m\}, \end\{equation\} - -\begin\{equation\} \frac \{dp\}\{dt\} = -\gamma p + W + F, \end\{equation\} - -where \(F\) is the physical force, \(\gamma\) is the friction coefficient, and \(W\) is a -Gaussian random force. - -The friction coefficient is the inverse of the thermostat parameter : \(\gamma = 1/\tau\), with \(\tau\) the thermostat parameter {tau}. -The thermostat parameter is given in the time units, \(\gamma\) is in inverse time units. - -Equilibrium sampling a temperature T is obtained by specifying the -target value as the {Tstart} and {Tstop} arguments, so that the internal -constants depending on the temperature are computed automatically. - -The random number {seed} must be a positive integer. A Marsaglia random -number generator is used. Each processor uses the input seed to -generate its own unique seed and its own stream of random numbers. -Thus the dynamics of the system will not be identical on two runs on -different numbers of processors. - -The flipping type {flip-type} can be chosen between 4 types described in -"(Hijazi)"_#Hijazi. The flipping operation occurs during the thermostatting -step and it flips the momenta of the atoms. If no_flip is chosen, no flip -will be executed and the integration will be the same as a standard -Langevin thermostat "(Bussi)"_#Bussi3. The other flipping types are : rescale - hard - soft. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -The instantaneous values of the extended variables are written to -"binary restart files"_restart.html. Because the state of the random -number generator is not saved in restart files, this means you cannot -do "exact" restarts with this fix, where the simulation continues on -the same as if no restart had taken place. However, in a statistical -sense, a restarted simulation should produce the same behavior. -Note however that you should use a different seed each time you -restart, otherwise the same sequence of random numbers will be used -each time, which might lead to stochastic synchronization and -subtle artifacts in the sampling. - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Langevin thermostatting to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the cumulative -energy change due to this fix. The scalar value calculated by this -fix is "extensive". - -[Restrictions:] - -In order to perform constant-pressure simulations please use -"fix press/berendsen"_fix_press_berendsen.html, rather than -"fix npt"_fix_nh.html, to avoid duplicate integration of the -equations of motion. - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix -viscous"_fix_viscous.html, "fix nvt"_fix_nh.html, "pair_style -dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html, "fix gle"_fix_gle.html - -:line - -:link(Hijazi) -[(Hijazi)] M. Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018) -:link(Bussi3) -[(Bussi)] G. Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007) - diff --git a/doc/txt/fix_filter_corotate.txt b/doc/txt/fix_filter_corotate.txt deleted file mode 100644 index 4868761d42..0000000000 --- a/doc/txt/fix_filter_corotate.txt +++ /dev/null @@ -1,86 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix filter/corotate command :h3 - -[Syntax:] - -fix ID group-ID filter/corotate keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -one or more constraint/value pairs are appended :l -constraint = {b} or {a} or {t} or {m} :l - {b} values = one or more bond types - {a} values = one or more angle types - {t} values = one or more atom types - {m} value = one or more mass values :pre -:ule - -[Examples:] - -timestep 8 -run_style respa 3 2 8 bond 1 pair 2 kspace 3 -fix cor all filter/corotate m 1.0 :pre - -fix cor all filter/corotate b 4 19 a 3 5 2 :pre - -[Description:] - -This fix implements a corotational filter for a mollified impulse -method. In biomolecular simulations, it allows the usage of larger -timesteps for long-range electrostatic interactions. For details, see -"(Fath)"_#Fath2017. - -When using "run_style respa"_run_style.html for a biomolecular -simulation with high-frequency covalent bonds, the outer time-step is -restricted to below ~ 4fs due to resonance problems. This fix filters -the outer stage of the respa and thus a larger (outer) time-step can -be used. Since in large biomolecular simulations the computation of -the long-range electrostatic contributions poses a major bottleneck, -this can significantly accelerate the simulation. - -The filter computes a cluster decomposition of the molecular structure -following the criteria indicated by the options a, b, t and m. This -process is similar to the approach in "fix shake"_fix_shake.html, -however, the clusters are not kept constrained. Instead, the position -is slightly modified only for the computation of long-range forces. A -good cluster decomposition constitutes in building clusters which -contain the fastest covalent bonds inside clusters. - -If the clusters are chosen suitably, the "run_style -respa"_run_style.html is stable for outer time-steps of at least 8fs. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about these fixes is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to these fixes. No global or per-atom quantities are -stored by these fixes for access by various "output -commands"_Howto_output.html. No parameter of these fixes can be used -with the {start/stop} keywords of the "run"_run.html command. These -fixes are not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Currently, it does not support "molecule templates"_molecule.html. - -[Related commands:] - - -[Default:] none - -:line - -:link(Fath2017) -[(Fath)] Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017). diff --git a/doc/txt/fix_flow_gauss.txt b/doc/txt/fix_flow_gauss.txt deleted file mode 100644 index 46a9477aa2..0000000000 --- a/doc/txt/fix_flow_gauss.txt +++ /dev/null @@ -1,160 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix flow/gauss command :h3 - -[Syntax:] - -fix ID group-ID flow/gauss xflag yflag zflag keyword :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -flow/gauss = style name of this fix command :l -xflag,yflag,zflag = 0 or 1 :l - 0 = do not conserve current in this dimension - 1 = conserve current in this dimension :pre -zero or more keyword/value pairs may be appended :l -keyword = {energy} :l - {energy} value = no or yes - no = do not compute work done by this fix - yes = compute work done by this fix :pre -:ule - -[Examples:] - -fix GD fluid flow/gauss 1 0 0 -fix GD fluid flow/gauss 1 1 1 energy yes :pre - -[Description:] - -This fix implements the Gaussian dynamics (GD) method to simulate a -system at constant mass flux "(Strong)"_#Strong. GD is a -nonequilibrium molecular dynamics simulation method that can be used -to study fluid flows through pores, pipes, and channels. In its -original implementation GD was used to compute the pressure required -to achieve a fixed mass flux through an opening. The flux can be -conserved in any combination of the directions, x, y, or z, using -xflag,yflag,zflag. This fix does not initialize a net flux through a -system, it only conserves the center-of-mass momentum that is present -when the fix is declared in the input script. Use the -"velocity"_velocity.html command to generate an initial center-of-mass -momentum. - -GD applies an external fluctuating gravitational field that acts as a -driving force to keep the system away from equilibrium. To maintain -steady state, a profile-unbiased thermostat must be implemented to -dissipate the heat that is added by the driving force. "Compute -temp/profile"_compute_temp_profile.html can be used to implement a -profile-unbiased thermostat. - -A common use of this fix is to compute a pressure drop across a pipe, -pore, or membrane. The pressure profile can be computed in LAMMPS with -"compute stress/atom"_compute_stress_atom.html and "fix -ave/chunk"_fix_ave_chunk.html, or with the hardy method in "fix -atc"_fix_atc.html. Note that the simple "compute -stress/atom"_compute_stress_atom.html method is only accurate away -from inhomogeneities in the fluid, such as fixed wall atoms. Further, -the computed pressure profile must be corrected for the acceleration -applied by GD before computing a pressure drop or comparing it to -other methods, such as the pump method "(Zhu)"_#Zhu. The pressure -correction is discussed and described in "(Strong)"_#Strong. - -For a complete example including the considerations discussed -above, see the examples/USER/flow_gauss directory. - -NOTE: Only the flux of the atoms in group-ID will be conserved. If the -velocities of the group-ID atoms are coupled to the velocities of -other atoms in the simulation, the flux will not be conserved. For -example, in a simulation with fluid atoms and harmonically constrained -wall atoms, if a single thermostat is applied to group {all}, the -fluid atom velocities will be coupled to the wall atom velocities, and -the flux will not be conserved. This issue can be avoided by -thermostatting the fluid and wall groups separately. - -Adding an acceleration to atoms does work on the system. This added -energy can be optionally subtracted from the potential energy for the -thermodynamic output (see below) to check that the timestep is small -enough to conserve energy. Since the applied acceleration is -fluctuating in time, the work cannot be computed from a potential. As -a result, computing the work is slightly more computationally -expensive than usual, so it is not performed by default. To invoke the -work calculation, use the {energy} keyword. The -"fix_modify"_fix_modify.html {energy} option also invokes the work -calculation, and overrides an {energy no} setting here. If neither -{energy yes} or {fix_modify energy yes} are set, the global scalar -computed by the fix will return zero. - -NOTE: In order to check energy conservation, any other fixes that do -work on the system must have {fix_modify energy yes} set as well. This -includes thermostat fixes and any constraints that hold the positions -of wall atoms fixed, such as "fix spring/self"_fix_spring_self.html. - -If this fix is used in a simulation with the "rRESPA"_run_style.html -integrator, the applied acceleration must be computed and applied at the same -rRESPA level as the interactions between the flowing fluid and the obstacle. -The rRESPA level at which the acceleration is applied can be changed using -the "fix_modify"_fix_modify.html {respa} option discussed below. If the -flowing fluid and the obstacle interact through multiple interactions that are -computed at different rRESPA levels, then there must be a separate flow/gauss -fix for each level. For example, if the flowing fluid and obstacle interact -through pairwise and long-range Coulomb interactions, which are computed at -rRESPA levels 3 and 4, respectively, then there must be two separate -flow/gauss fixes, one that specifies {fix_modify respa 3} and one with -{fix_modify respa 4}. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to subtract the work done from the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows the user to set at which level of the "rRESPA"_run_style.html -integrator the fix computes and adds the external acceleration. Default is the -outermost level. - -This fix computes a global scalar and a global 3-vector of forces, -which can be accessed by various "output commands"_Howto_output.html. -The scalar is the negative of the work done on the system, see above -discussion. The vector is the total force that this fix applied to -the group of atoms on the current timestep. The scalar and vector -values calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -[Restrictions:] none - -[Related commands:] - -"fix addforce"_fix_addforce.html, "compute -temp/profile"_compute_temp_profile.html, "velocity"_velocity.html - -[Default:] - -The option default for the {energy} keyword is energy = no. - -:line - -:link(Strong) -[(Strong)] Strong and Eaves, J. Phys. Chem. B 121, 189 (2017). - -:link(Evans2) -[(Evans)] Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986). - -:link(Zhu) -[(Zhu)] Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002). diff --git a/doc/txt/fix_freeze.txt b/doc/txt/fix_freeze.txt deleted file mode 100644 index 9e085d8b1d..0000000000 --- a/doc/txt/fix_freeze.txt +++ /dev/null @@ -1,88 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix freeze command :h3 -fix freeze/kk command :h3 - -[Syntax:] - -fix ID group-ID freeze :pre - -ID, group-ID are documented in "fix"_fix.html command -freeze = style name of this fix command :ul - -[Examples:] - -fix 2 bottom freeze :pre - -[Description:] - -Zero out the force and torque on a granular particle. This is useful -for preventing certain particles from moving in a simulation. The -"granular pair styles"_pair_gran.html also detect if this fix has been -defined and compute interactions between frozen and non-frozen -particles appropriately, as if the frozen particle has infinite mass. -A similar functionality for normal (point) particles can be obtained -using "fix setforce"_fix_setforce.html. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Howto_output.html. This is the total -force on the group of atoms before the forces on individual atoms are -changed by the fix. The vector values calculated by this fix are -"extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -There can only be a single freeze fix defined. This is because other -the "granular pair styles"_pair_gran.html treat frozen particles -differently and need to be able to reference a single group to which -this fix is applied. - -[Related commands:] - -"atom_style sphere"_atom_style.html, "fix setforce"_fix_setforce.html - -[Default:] none diff --git a/doc/txt/fix_gcmc.txt b/doc/txt/fix_gcmc.txt deleted file mode 100644 index f28cb5771f..0000000000 --- a/doc/txt/fix_gcmc.txt +++ /dev/null @@ -1,465 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix gcmc command :h3 - -[Syntax:] - -fix ID group-ID gcmc N X M type seed T mu displace keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -gcmc = style name of this fix command :l -N = invoke this fix every N steps :l -X = average number of GCMC exchanges to attempt every N steps :l -M = average number of MC moves to attempt every N steps :l -type = atom type for inserted atoms (must be 0 if mol keyword used) :l -seed = random # seed (positive integer) :l -T = temperature of the ideal gas reservoir (temperature units) :l -mu = chemical potential of the ideal gas reservoir (energy units) :l -displace = maximum Monte Carlo translation distance (length units) :l -zero or more keyword/value pairs may be appended to args :l -keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energy}, {charge}, {group}, {grouptype}, {intra_energy}, {tfac_insert}, or {overlap_cutoff} - {mol} value = template-ID - template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command - {mcmoves} values = Patomtrans Pmoltrans Pmolrotate - Patomtrans = proportion of atom translation MC moves - Pmoltrans = proportion of molecule translation MC moves - Pmolrotate = proportion of molecule rotation MC moves - {rigid} value = fix-ID - fix-ID = ID of "fix rigid/small"_fix_rigid.html command - {shake} value = fix-ID - fix-ID = ID of "fix shake"_fix_shake.html command - {region} value = region-ID - region-ID = ID of region where GCMC exchanges and MC moves are allowed - {maxangle} value = maximum molecular rotation angle (degrees) - {pressure} value = pressure of the gas reservoir (pressure units) - {fugacity_coeff} value = fugacity coefficient of the gas reservoir (unitless) - {full_energy} = compute the entire system energy when performing GCMC exchanges and MC moves - {charge} value = charge of inserted atoms (charge units) - {group} value = group-ID - group-ID = group-ID for inserted atoms (string) - {grouptype} values = type group-ID - type = atom type (int) - group-ID = group-ID for inserted atoms (string) - {intra_energy} value = intramolecular energy (energy units) - {tfac_insert} value = scale up/down temperature of inserted atoms (unitless) - {overlap_cutoff} value = maximum pair distance for overlap rejection (distance units) - {max} value = Maximum number of molecules allowed in the system - {min} value = Minimum number of molecules allowed in the system :pre -:ule - -[Examples:] - -fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01 -fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy -fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk :pre - -[Description:] - -This fix performs grand canonical Monte Carlo (GCMC) exchanges of -atoms or molecules with an imaginary ideal gas -reservoir at the specified T and chemical potential (mu) as discussed -in "(Frenkel)"_#Frenkel. It also -attempts Monte Carlo (MC) moves (translations and molecule -rotations) within the simulation cell or -region. If used with the "fix nvt"_fix_nh.html -command, simulations in the grand canonical ensemble (muVT, constant -chemical potential, constant volume, and constant temperature) can be -performed. Specific uses include computing isotherms in microporous -materials, or computing vapor-liquid coexistence curves. - -Every N timesteps the fix attempts both GCMC exchanges -(insertions or deletions) and MC moves of gas atoms or molecules. -On those timesteps, the average number of attempted GCMC exchanges is X, -while the average number of attempted MC moves is M. -For GCMC exchanges of either molecular or atomic gasses, -these exchanges can be either deletions or insertions, -with equal probability. - -The possible choices for MC moves are translation of an atom, -translation of a molecule, and rotation of a molecule. -The relative amounts of each are determined by the optional -{mcmoves} keyword (see below). -The default behavior is as follows. -If the {mol} keyword is used, only molecule translations -and molecule rotations are performed with equal probability. -Conversely, if the {mol} keyword is not used, only atom -translations are performed. -M should typically be -chosen to be approximately equal to the expected number of gas atoms -or molecules of the given type within the simulation cell or region, -which will result in roughly one MC move per atom or molecule -per MC cycle. - -All inserted particles are always added to two groups: the default -group "all" and the fix group specified in the fix command. -In addition, particles are also added to any groups -specified by the {group} and {grouptype} keywords. If inserted -particles are individual atoms, they are assigned the atom type given -by the type argument. If they are molecules, the type argument has no -effect and must be set to zero. Instead, the type of each atom in the -inserted molecule is specified in the file read by the -"molecule"_molecule.html command. - -NOTE: Care should be taken to apply fix gcmc only to -a group that contains only those atoms and molecules -that you wish to manipulate using Monte Carlo. -Hence it is generally not a good idea to specify -the default group "all" in the fix command, although it is allowed. - -This fix cannot be used to perform GCMC insertions of gas atoms or -molecules other than the exchanged type, but GCMC deletions, -and MC translations, and rotations can be performed on any atom/molecule in -the fix group. All atoms in the simulation cell can be moved using -regular time integration translations, e.g. via "fix nvt"_fix_nh.html, -resulting in a hybrid GCMC+MD simulation. A smaller-than-usual -timestep size may be needed when running such a hybrid simulation, -especially if the inserted molecules are not well equilibrated. - -This command may optionally use the {region} keyword to define an -exchange and move volume. The specified region must have been -previously defined with a "region"_region.html command. It must be -defined with side = {in}. Insertion attempts occur only within the -specified region. For non-rectangular regions, random trial points are -generated within the rectangular bounding box until a point is found -that lies inside the region. If no valid point is generated after 1000 -trials, no insertion is performed, but it is counted as an attempted -insertion. Move and deletion attempt candidates are selected from gas -atoms or molecules within the region. If there are no candidates, no -move or deletion is performed, but it is counted as an attempt move or -deletion. If an attempted move places the atom or molecule -center-of-mass outside the specified region, a new attempted move is -generated. This process is repeated until the atom or molecule -center-of-mass is inside the specified region. - -If used with "fix nvt"_fix_nh.html, the temperature of the imaginary -reservoir, T, should be set to be equivalent to the target temperature -used in fix nvt. Otherwise, the imaginary reservoir will not be in -thermal equilibrium with the simulation cell. Also, it is important -that the temperature used by fix nvt be dynamic/dof, which can be -achieved as follows: - -compute mdtemp mdatoms temp -compute_modify mdtemp dynamic/dof yes -fix mdnvt mdatoms nvt temp 300.0 300.0 10.0 -fix_modify mdnvt temp mdtemp :pre - -Note that neighbor lists are re-built every timestep that this fix is -invoked, so you should not set N to be too small. However, periodic -rebuilds are necessary in order to avoid dangerous rebuilds and missed -interactions. Specifically, avoid performing so many MC translations -per timestep that atoms can move beyond the neighbor list skin -distance. See the "neighbor"_neighbor.html command for details. - -When an atom or molecule is to be inserted, its coordinates are chosen -at a random position within the current simulation cell or region, and -new atom velocities are randomly chosen from the specified temperature -distribution given by T. The effective temperature for new atom -velocities can be increased or decreased using the optional keyword -{tfac_insert} (see below). Relative coordinates for atoms in a -molecule are taken from the template molecule provided by the -user. The center of mass of the molecule is placed at the insertion -point. The orientation of the molecule is chosen at random by rotating -about this point. - -Individual atoms are inserted, unless the {mol} keyword is used. It -specifies a {template-ID} previously defined using the -"molecule"_molecule.html command, which reads a file that defines the -molecule. The coordinates, atom types, charges, etc., as well as any -bonding and special neighbor information for the molecule can -be specified in the molecule file. See the "molecule"_molecule.html -command for details. The only settings required to be in this file -are the coordinates and types of atoms in the molecule. - -When not using the {mol} keyword, you should ensure you do not delete -atoms that are bonded to other atoms, or LAMMPS will soon generate an -error when it tries to find bonded neighbors. LAMMPS will warn you if -any of the atoms eligible for deletion have a non-zero molecule ID, -but does not check for this at the time of deletion. - -If you wish to insert molecules using the {mol} keyword that will be -treated as rigid bodies, use the {rigid} keyword, specifying as its -value the ID of a separate "fix rigid/small"_fix_rigid.html command -which also appears in your input script. - -NOTE: If you wish the new rigid molecules (and other rigid molecules) -to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html -or "fix rigid/small/npt"_fix_rigid.html, then you need to use the -"fix_modify dynamic/dof yes" command for the rigid fix. This is to -inform that fix that the molecule count will vary dynamically. - -If you wish to insert molecules via the {mol} keyword, that will have -their bonds or angles constrained via SHAKE, use the {shake} keyword, -specifying as its value the ID of a separate "fix -shake"_fix_shake.html command which also appears in your input script. - -Optionally, users may specify the relative amounts of different MC -moves using the {mcmoves} keyword. The values {Patomtrans}, -{Pmoltrans}, {Pmolrotate} specify the average proportion of -atom translations, molecule translations, and molecule rotations, -respectively. The values must be non-negative integers or real -numbers, with at least one non-zero value. For example, (10,30,0) -would result in 25% of the MC moves being atomic translations, 75% -molecular translations, and no molecular rotations. - -Optionally, users may specify the maximum rotation angle for molecular -rotations using the {maxangle} keyword and specifying the angle in -degrees. Rotations are performed by generating a random point on the -unit sphere and a random rotation angle on the range -\[0,maxangle). The molecule is then rotated by that angle about an -axis passing through the molecule center of mass. The axis is parallel -to the unit vector defined by the point on the unit sphere. The same -procedure is used for randomly rotating molecules when they are -inserted, except that the maximum angle is 360 degrees. - -Note that fix gcmc does not use configurational bias MC or any other -kind of sampling of intramolecular degrees of freedom. Inserted -molecules can have different orientations, but they will all have the -same intramolecular configuration, which was specified in the molecule -command input. - -For atomic gasses, inserted atoms have the specified atom type, but -deleted atoms are any atoms that have been inserted or that already -belong to the fix group. For molecular gasses, exchanged -molecules use the same atom types as in the template molecule supplied -by the user. In both cases, exchanged atoms/molecules are assigned to -two groups: the default group "all" and the fix group -(which can also be "all"). - -The chemical potential is a user-specified input parameter defined -as: - -:c,image(Eqs/fix_gcmc1.jpg) - -The second term mu_ex is the excess chemical potential due to -energetic interactions and is formally zero for the fictitious gas -reservoir but is non-zero for interacting systems. So, while the -chemical potential of the reservoir and the simulation cell are equal, -mu_ex is not, and as a result, the densities of the two are generally -quite different. The first term mu_id is the ideal gas contribution -to the chemical potential. mu_id can be related to the density or -pressure of the fictitious gas reservoir by: - -:c,image(Eqs/fix_gcmc2.jpg) - -where k is Boltzman's constant, -T is the user-specified temperature, rho is the number density, -P is the pressure, and phi is the fugacity coefficient. -The constant Lambda is required for dimensional consistency. -For all unit styles except {lj} it is defined as the thermal -de Broglie wavelength - -:c,image(Eqs/fix_gcmc3.jpg) - -where h is Planck's constant, and m is the mass of the exchanged atom -or molecule. For unit style {lj}, Lambda is simply set to the -unity. Note that prior to March 2017, lambda for unit style {lj} was -calculated using the above formula with h set to the rather specific -value of 0.18292026. Chemical potential under the old definition can -be converted to an equivalent value under the new definition by -subtracting 3kTln(Lambda_old). - -As an alternative to specifying mu directly, the ideal gas reservoir -can be defined by its pressure P using the {pressure} keyword, in -which case the user-specified chemical potential is ignored. The user -may also specify the fugacity coefficient phi using the -{fugacity_coeff} keyword, which defaults to unity. - -The {full_energy} option means that the fix calculates the total -potential energy of the entire simulated system, instead of just -the energy of the part that is changed. The total system -energy before and after the proposed GCMC exchange or MC move -is then used in the -Metropolis criterion to determine whether or not to accept the -proposed change. By default, this option is off, -in which case only -partial energies are computed to determine the energy difference -due to the proposed change. - -The {full_energy} option is needed for systems with complicated -potential energy calculations, including the following: - - long-range electrostatics (kspace) - many-body pair styles - hybrid pair styles - eam pair styles - tail corrections - need to include potential energy contributions from other fixes :ul - -In these cases, LAMMPS will automatically apply the {full_energy} -keyword and issue a warning message. - -When the {mol} keyword is used, the {full_energy} option also includes -the intramolecular energy of inserted and deleted molecules, whereas -this energy is not included when {full_energy} is not used. If this -is not desired, the {intra_energy} keyword can be used to define an -amount of energy that is subtracted from the final energy when a -molecule is inserted, and subtracted from the initial energy when a molecule -is deleted. For molecules that have a non-zero intramolecular energy, -this will ensure roughly the same behavior whether or not the -{full_energy} option is used. - -Inserted atoms and molecules are assigned random velocities based on -the specified temperature T. Because the relative velocity of all -atoms in the molecule is zero, this may result in inserted molecules -that are systematically too cold. In addition, the intramolecular -potential energy of the inserted molecule may cause the kinetic energy -of the molecule to quickly increase or decrease after insertion. The -{tfac_insert} keyword allows the user to counteract these effects by -changing the temperature used to assign velocities to inserted atoms -and molecules by a constant factor. For a particular application, some -experimentation may be required to find a value of {tfac_insert} that -results in inserted molecules that equilibrate quickly to the correct -temperature. - -Some fixes have an associated potential energy. Examples of such fixes -include: "efield"_fix_efield.html, "gravity"_fix_gravity.html, -"addforce"_fix_addforce.html, "langevin"_fix_langevin.html, -"restrain"_fix_restrain.html, -"temp/berendsen"_fix_temp_berendsen.html, -"temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html. -For that energy to be included in the total potential energy of the -system (the quantity used when performing GCMC exchange and MC moves), -you MUST enable -the "fix_modify"_fix_modify.html {energy} option for that fix. The -doc pages for individual "fix"_fix.html commands specify if this -should be done. - -Use the {charge} option to insert atoms with a user-specified point -charge. Note that doing so will cause the system to become -non-neutral. LAMMPS issues a warning when using long-range -electrostatics (kspace) with non-neutral systems. See the "compute -group/group"_compute_group_group.html documentation for more details -about simulating non-neutral systems with kspace on. - -Use of this fix typically will cause the number of atoms to fluctuate, -therefore, you will want to use the -"compute_modify dynamic/dof"_compute_modify.html command to insure that the -current number of atoms is used as a normalizing factor each time -temperature is computed. A simple example of this is: - -compute_modify thermo_temp dynamic yes :pre - -A more complicated example is listed earlier on this page -in the context of NVT dynamics. - -NOTE: If the density of the cell is initially very small or zero, and -increases to a much larger density after a period of equilibration, -then certain quantities that are only calculated once at the start -(kspace parameters) may no longer be accurate. The -solution is to start a new simulation after the equilibrium density -has been reached. - -With some pair_styles, such as "Buckingham"_pair_buck.html, -"Born-Mayer-Huggins"_pair_born.html and "ReaxFF"_pair_reaxc.html, two -atoms placed close to each other may have an arbitrary large, negative -potential energy due to the functional form of the potential. While -these unphysical configurations are inaccessible to typical dynamical -trajectories, they can be generated by Monte Carlo moves. The -{overlap_cutoff} keyword suppresses these moves by effectively -assigning an infinite positive energy to all new configurations that -place any pair of atoms closer than the specified overlap cutoff -distance. - -The {max} and {min} keywords allow for the restriction of the number -of atoms in the simulation. They automatically reject all insertion -or deletion moves that would take the system beyond the set boundaries. -Should the system already be beyond the boundary, only moves that bring -the system closer to the bounds may be accepted. - -The {group} keyword adds all inserted atoms to the -"group"_group.html of the group-ID value. The {grouptype} keyword -adds all inserted atoms of the specified type to the -"group"_group.html of the group-ID value. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the fix to "binary restart -files"_restart.html. This includes information about the random -number generator seed, the next timestep for MC exchanges, the number -of MC step attempts and successes etc. See -the "read_restart"_read_restart.html command for info on how to -re-specify a fix in an input script that reads a restart file, so that -the operation of the fix continues in an uninterrupted fashion. - -NOTE: For this to work correctly, the timestep must [not] be changed -after reading the restart with "reset_timestep"_reset_timestep.html. -The fix will try to detect it and stop with an error. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. - -This fix computes a global vector of length 8, which can be accessed -by various "output commands"_Howto_output.html. The vector values are -the following global cumulative quantities: - -1 = translation attempts -2 = translation successes -3 = insertion attempts -4 = insertion successes -5 = deletion attempts -6 = deletion successes -7 = rotation attempts -8 = rotation successes :ul - -The vector values calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the "Build package"_Build_package.html -doc page for more info. - -Do not set "neigh_modify once yes" or else this fix will never be -called. Reneighboring is required. - -Can be run in parallel, but aspects of the GCMC part will not scale -well in parallel. Only usable for 3D simulations. - -When using fix gcmc in combination with fix shake or fix rigid, -only GCMC exchange moves are supported, so the argument -{M} must be zero. - -Note that very lengthy simulations involving insertions/deletions of -billions of gas molecules may run out of atom or molecule IDs and -trigger an error, so it is better to run multiple shorter-duration -simulations. Likewise, very large molecules have not been tested and -may turn out to be problematic. - -Use of multiple fix gcmc commands in the same input script can be -problematic if using a template molecule. The issue is that the -user-referenced template molecule in the second fix gcmc command may -no longer exist since it might have been deleted by the first fix gcmc -command. An existing template molecule will need to be referenced by -the user for each subsequent fix gcmc command. - -[Related commands:] - -"fix atom/swap"_fix_atom_swap.html, -"fix nvt"_fix_nh.html, "neighbor"_neighbor.html, -"fix deposit"_fix_deposit.html, "fix evaporate"_fix_evaporate.html, -"delete_atoms"_delete_atoms.html - -[Default:] - -The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0, -fugacity_coeff = 1.0, intra_energy = 0.0, tfac_insert = 1.0. -(Patomtrans, Pmoltrans, Pmolrotate) = (1, 0, 0) for mol = no and -(0, 1, 1) for mol = yes. full_energy = no, -except for the situations where full_energy is required, as -listed above. - -:line - -:link(Frenkel) -[(Frenkel)] Frenkel and Smit, Understanding Molecular Simulation, -Academic Press, London, 2002. diff --git a/doc/txt/fix_gld.txt b/doc/txt/fix_gld.txt deleted file mode 100644 index 97c3d0e408..0000000000 --- a/doc/txt/fix_gld.txt +++ /dev/null @@ -1,155 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix gld command :h3 - -[Syntax:] - -fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -gld = style name of this fix command :l -Tstart,Tstop = desired temperature at start/end of run (temperature units) :l -N_k = number of terms in the Prony series representation of the memory kernel :l -seed = random number seed to use for white noise (positive integer) :l -series = {pprony} is presently the only available option :l -c_k = the weight of the kth term in the Prony series (mass per time units) :l -tau_k = the time constant of the kth term in the Prony series (time units) :l -zero or more keyword/value pairs may be appended :l -keyword = {frozen} or {zero} - {frozen} value = {no} or {yes} - {no} = initialize extended variables using values drawn from equilibrium distribution at Tstart - {yes} = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature) - {zero} value = {no} or {yes} - {no} = do not set total random force to zero - {yes} = set total random force to zero :pre -:ule - -[Examples:] - -fix 1 all gld 1.0 1.0 2 82885 pprony 0.5 1.0 1.0 2.0 frozen yes zero yes -fix 3 rouse gld 7.355 7.355 4 48823 pprony 107.1 0.02415 186.0 0.04294 428.6 0.09661 1714 0.38643 :pre - -[Description:] - -Applies Generalized Langevin Dynamics to a group of atoms, as -described in "(Baczewski)"_#Baczewski. This is intended to model the -effect of an implicit solvent with a temporally non-local dissipative -force and a colored Gaussian random force, consistent with the -Fluctuation-Dissipation Theorem. The functional form of the memory -kernel associated with the temporally non-local force is constrained -to be a Prony series. - -NOTE: While this fix bears many similarities to "fix -langevin"_fix_langevin.html, it has one significant -difference. Namely, "fix gld"_fix_gld.html performs time integration, -whereas "fix langevin"_fix_langevin.html does NOT. To this end, the -specification of another fix to perform time integration, such as "fix -nve"_fix_nve.html, is NOT necessary. - -With this fix active, the force on the {j}th atom is given as - -:c,image(Eqs/fix_gld1.jpg) - -Here, the first term is representative of all conservative (pairwise, -bonded, etc) forces external to this fix, the second is the temporally -non-local dissipative force given as a Prony series, and the third is -the colored Gaussian random force. - -The Prony series form of the memory kernel is chosen to enable an -extended variable formalism, with a number of exemplary mathematical -features discussed in "(Baczewski)"_#Baczewski. In particular, 3N_k -extended variables are added to each atom, which effect the action of -the memory kernel without having to explicitly evaluate the integral -over time in the second term of the force. This also has the benefit -of requiring the generation of uncorrelated random forces, rather than -correlated random forces as specified in the third term of the force. - -Presently, the Prony series coefficients are limited to being greater -than or equal to zero, and the time constants are limited to being -greater than zero. To this end, the value of series MUST be set to -{pprony}, for now. Future updates will allow for negative coefficients -and other representations of the memory kernel. It is with these -updates in mind that the series option was included. - -The units of the Prony series coefficients are chosen to be mass per -time to ensure that the numerical integration scheme stably approaches -the Newtonian and Langevin limits. Details of these limits, and the -associated numerical concerns are discussed in -"(Baczewski)"_#Baczewski. - -The desired temperature at each timestep is ramped from {Tstart} to -{Tstop} over the course of the next run. - -The random # {seed} must be a positive integer. A Marsaglia random -number generator is used. Each processor uses the input seed to -generate its own unique seed and its own stream of random -numbers. Thus the dynamics of the system will not be identical on two -runs on different numbers of processors. - -:line - -The keyword/value option pairs are used in the following ways. - -The keyword {frozen} can be used to specify how the extended variables -associated with the GLD memory kernel are initialized. Specifying no -(the default), the initial values are drawn at random from an -equilibrium distribution at {Tstart}, consistent with the -Fluctuation-Dissipation Theorem. Specifying yes, initializes the -extended variables to zero. - -The keyword {zero} can be used to eliminate drift due to the -thermostat. Because the random forces on different atoms are -independent, they do not sum exactly to zero. As a result, this fix -applies a small random force to the entire system, and the -center-of-mass of the system undergoes a slow random walk. If the -keyword {zero} is set to {yes}, the total random force is set exactly -to zero by subtracting off an equal part of it from each atom in the -group. As a result, the center-of-mass of a system with zero initial -momentum will not drift over time. - -:line - -[Restart, run start/stop, minimize info:] - -The instantaneous values of the extended variables are written to -"binary restart files"_restart.html. Because the state of the random -number generator is not saved in restart files, this means you cannot -do "exact" restarts with this fix, where the simulation continues on -the same as if no restart had taken place. However, in a statistical -sense, a restarted simulation should produce the same behavior. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Howto_output.html. - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html, -"pair_style dpd/tstat"_pair_dpd.html - -[Default:] - -The option defaults are frozen = no, zero = no. - -:line - -:link(Baczewski) -[(Baczewski)] A.D. Baczewski and S.D. Bond, J. Chem. Phys. 139, 044107 (2013). diff --git a/doc/txt/fix_gle.txt b/doc/txt/fix_gle.txt deleted file mode 100644 index a8026256b0..0000000000 --- a/doc/txt/fix_gle.txt +++ /dev/null @@ -1,156 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix gle command :h3 - -[Syntax:] - -fix ID id-group gle Ns Tstart Tstop seed Amatrix \[noneq Cmatrix\] \[every stride\] :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -gle = style name of this fix command :l -Ns = number of additional fictitious momenta :l -Tstart, Tstop = temperature ramp during the run :l -Amatrix = file to read the drift matrix A from :l -seed = random number seed to use for generating noise (positive integer) :l -zero or more keyword/value pairs may be appended :l - keyword = {noneq} or {every} - {noneq} Cmatrix = file to read the non-equilibrium covariance matrix from - {every} stride = apply the GLE once every time steps. Reduces the accuracy - of the integration of the GLE, but has *no effect* on the accuracy of equilibrium - sampling. It might change sampling properties when used together with {noneq}. :pre -:ule - -[Examples:] - -fix 3 boundary gle 6 300 300 31415 smart.A -fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C :pre - -[Description:] - -Apply a Generalized Langevin Equation (GLE) thermostat as described -in "(Ceriotti)"_#Ceriotti. The formalism allows one to obtain a number -of different effects ranging from efficient sampling of all -vibrational modes in the system to inexpensive (approximate) -modelling of nuclear quantum effects. Contrary to -"fix langevin"_fix_langevin.html, this fix performs both -thermostatting and evolution of the Hamiltonian equations of motion, so it -should not be used together with "fix nve"_fix_nve.html -- at least not -on the same atom groups. - -Each degree of freedom in the thermostatted group is supplemented -with Ns additional degrees of freedom s, and the equations of motion -become - -dq/dt=p/m -d(p,s)/dt=(F,0) - A(p,s) + B dW/dt :pre - -where F is the physical force, A is the drift matrix (that generalizes -the friction in Langevin dynamics), B is the diffusion term and dW/dt -un-correlated Gaussian random forces. The A matrix couples the physical -(q,p) dynamics with that of the additional degrees of freedom, -and makes it possible to obtain effectively a history-dependent -noise and friction kernel. - -The drift matrix should be given as an external file {Afile}, -as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are -optimal for a given application and the system of choice can be -obtained from "(GLE4MD)"_#GLE4MD. - -Equilibrium sampling a temperature T is obtained by specifying the -target value as the {Tstart} and {Tstop} arguments, so that the diffusion -matrix that gives canonical sampling for a given A is computed automatically. -However, the GLE framework also allow for non-equilibrium sampling, that -can be used for instance to model inexpensively zero-point energy -effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the {noneq} -keyword followed by the name of the file that contains the static covariance -matrix for the non-equilibrium dynamics. Please note, that the covariance -matrix is expected to be given in [temperature units]. - -Since integrating GLE dynamics can be costly when used together with -simple potentials, one can use the {every} optional keyword to -apply the Langevin terms only once every several MD steps, in a -multiple time-step fashion. This should be used with care when doing -non-equilibrium sampling, but should have no effect on equilibrium -averages when using canonical sampling. - -The random number {seed} must be a positive integer. A Marsaglia random -number generator is used. Each processor uses the input seed to -generate its own unique seed and its own stream of random numbers. -Thus the dynamics of the system will not be identical on two runs on -different numbers of processors. - -Note also that the Generalized Langevin Dynamics scheme that is -implemented by the "fix gld"_fix_gld.html scheme is closely related -to the present one. In fact, it should be always possible to cast the -Prony series form of the memory kernel used by GLD into an appropriate -input matrix for "fix gle"_fix_gle.html. While the GLE scheme is more -general, the form used by "fix gld"_fix_gld.html can be more directly -related to the representation of an implicit solvent environment. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -The instantaneous values of the extended variables are written to -"binary restart files"_restart.html. Because the state of the random -number generator is not saved in restart files, this means you cannot -do "exact" restarts with this fix, where the simulation continues on -the same as if no restart had taken place. However, in a statistical -sense, a restarted simulation should produce the same behavior. -Note however that you should use a different seed each time you -restart, otherwise the same sequence of random numbers will be used -each time, which might lead to stochastic synchronization and -subtle artifacts in the sampling. - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Langevin thermostatting to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the cumulative -energy change due to this fix. The scalar value calculated by this -fix is "extensive". - -[Restrictions:] - -The GLE thermostat in its current implementation should not be used -with rigid bodies, SHAKE or RATTLE. It is expected that all the -thermostatted degrees of freedom are fully flexible, and the sampled -ensemble will not be correct otherwise. - -In order to perform constant-pressure simulations please use -"fix press/berendsen"_fix_press_berendsen.html, rather than -"fix npt"_fix_nh.html, to avoid duplicate integration of the -equations of motion. - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix -viscous"_fix_viscous.html, "fix nvt"_fix_nh.html, "pair_style -dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html - -:line - -:link(Ceriotti) -[(Ceriotti)] Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6, -1170-80 (2010) - -:link(GLE4MD) -[(GLE4MD)] "http://gle4md.org/"_http://gle4md.org/ - -:link(Ceriotti2) -[(Ceriotti2)] Ceriotti, Bussi and Parrinello, Phys Rev Lett 103, -030603 (2009) diff --git a/doc/txt/fix_gravity.txt b/doc/txt/fix_gravity.txt deleted file mode 100644 index c529a04d34..0000000000 --- a/doc/txt/fix_gravity.txt +++ /dev/null @@ -1,144 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix gravity command :h3 -fix gravity/omp command :h3 -fix gravity/kk command :h3 - -[Syntax:] - -fix ID group gravity magnitude style args :pre - -ID, group are documented in "fix"_fix.html command :ulb,l -gravity = style name of this fix command :l -magnitude = size of acceleration (force/mass units) :l -magnitude can be a variable (see below) :l -style = {chute} or {spherical} or {gradient} or {vector} :l - {chute} args = angle - angle = angle in +x away from -z or -y axis in 3d/2d (in degrees) - angle can be a variable (see below) - {spherical} args = phi theta - phi = azimuthal angle from +x axis (in degrees) - theta = angle from +z or +y axis in 3d/2d (in degrees) - phi or theta can be a variable (see below) - {vector} args = x y z - x y z = vector direction to apply the acceleration - x or y or z can be a variable (see below) :pre -:ule - -[Examples:] - -fix 1 all gravity 1.0 chute 24.0 -fix 1 all gravity v_increase chute 24.0 -fix 1 all gravity 1.0 spherical 0.0 -180.0 -fix 1 all gravity 10.0 spherical v_phi v_theta -fix 1 all gravity 100.0 vector 1 1 0 :pre - -[Description:] - -Impose an additional acceleration on each particle in the group. This -fix is typically used with granular systems to include a "gravity" -term acting on the macroscopic particles. More generally, it can -represent any kind of driving field, e.g. a pressure gradient inducing -a Poiseuille flow in a fluid. Note that this fix operates differently -than the "fix addforce"_fix_addforce.html command. The addforce fix -adds the same force to each atom, independent of its mass. This -command imparts the same acceleration to each atom (force/mass). - -The {magnitude} of the acceleration is specified in force/mass units. -For granular systems (LJ units) this is typically 1.0. See the -"units"_units.html command for details. - -Style {chute} is typically used for simulations of chute flow where -the specified {angle} is the chute angle, with flow occurring in the +x -direction. For 3d systems, the tilt is away from the z axis; for 2d -systems, the tilt is away from the y axis. - -Style {spherical} allows an arbitrary 3d direction to be specified for -the acceleration vector. {Phi} and {theta} are defined in the usual -spherical coordinates. Thus for acceleration acting in the -z -direction, {theta} would be 180.0 (or -180.0). {Theta} = 90.0 and -{phi} = -90.0 would mean acceleration acts in the -y direction. For -2d systems, {phi} is ignored and {theta} is an angle in the xy plane -where {theta} = 0.0 is the y-axis. - -Style {vector} imposes an acceleration in the vector direction given -by (x,y,z). Only the direction of the vector is important; it's -length is ignored. For 2d systems, the {z} component is ignored. - -Any of the quantities {magnitude}, {angle}, {phi}, {theta}, {x}, {y}, -{z} which define the gravitational magnitude and direction, can be -specified as an equal-style "variable"_variable.html. If the value is -a variable, it should be specified as v_name, where name is the -variable name. In this case, the variable will be evaluated each -timestep, and its value used to determine the quantity. You should -insure that the variable calculates a result in the appropriate units, -e.g. force/mass or degrees. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent gravitational -field. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the gravitational potential energy of the system to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. This scalar is the gravitational -potential energy of the particles in the defined field, namely mass * -(g dot x) for each particles, where x and mass are the particles -position and mass, and g is the gravitational field. The scalar value -calculated by this fix is "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"atom_style sphere"_atom_style.html, "fix addforce"_fix_addforce.html - -[Default:] none diff --git a/doc/txt/fix_grem.txt b/doc/txt/fix_grem.txt deleted file mode 100644 index edf11b337c..0000000000 --- a/doc/txt/fix_grem.txt +++ /dev/null @@ -1,111 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix grem command :h3 - -[Syntax:] - -fix ID group-ID grem lambda eta H0 thermostat-ID :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -grem = style name of this fix command :l -lambda = intercept parameter of linear effective temperature function :l -eta = slope parameter of linear effective temperature function :l -H0 = shift parameter of linear effective temperature function :l -thermostat-ID = ID of Nose-Hoover thermostat or barostat used in simulation :l,ule - -[Examples:] - -fix fxgREM all grem 400 -0.01 -30000 fxnpt -thermo_modify press fxgREM_press :pre - -fix fxgREM all grem 502 -0.15 -80000 fxnvt :pre - -[Description:] - -This fix implements the molecular dynamics version of the generalized -replica exchange method (gREM) originally developed by "(Kim)"_#Kim2010, -which uses non-Boltzmann ensembles to sample over first order phase -transitions. The is done by defining replicas with an enthalpy -dependent effective temperature - -:c,image(Eqs/fix_grem.jpg) - -with {eta} negative and steep enough to only intersect the -characteristic microcanonical temperature (Ts) of the system once, -ensuring a unimodal enthalpy distribution in that replica. {Lambda} is -the intercept and effects the generalized ensemble similar to how -temperature effects a Boltzmann ensemble. {H0} is a reference -enthalpy, and is typically set as the lowest desired sampled enthalpy. -Further explanation can be found in our recent papers -"(Malolepsza)"_#Malolepsza. - -This fix requires a Nose-Hoover thermostat fix reference passed to the -grem as {thermostat-ID}. Two distinct temperatures exist in this -generalized ensemble, the effective temperature defined above, and a -kinetic temperature that controls the velocity distribution of -particles as usual. Either constant volume or constant pressure -algorithms can be used. - -The fix enforces a generalized ensemble in a single replica -only. Typically, this ideology is combined with replica exchange with -replicas differing by {lambda} only for simplicity, but this is not -required. A multi-replica simulation can be run within the LAMMPS -environment using the "temper/grem"_temper_grem.html command. This -utilizes LAMMPS partition mode and requires the number of available -processors be on the order of the number of desired replicas. A -100-replica simulation would require at least 100 processors (1 per -world at minimum). If a many replicas are needed on a small number of -processors, multi-replica runs can be run outside of LAMMPS. An -example of this can be found in examples/USER/misc/grem and has no -limit on the number of replicas per processor. However, this is very -inefficient and error prone and should be avoided if possible. - -In general, defining the generalized ensembles is unique for every -system. When starting a many-replica simulation without any knowledge -of the underlying microcanonical temperature, there are several tricks -we have utilized to optimize the process. Choosing a less-steep {eta} -yields broader distributions, requiring fewer replicas to map the -microcanonical temperature. While this likely struggles from the same -sampling problems gREM was built to avoid, it provides quick insight -to Ts. Initially using an evenly-spaced {lambda} distribution -identifies regions where small changes in enthalpy lead to large -temperature changes. Replicas are easily added where needed. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "thermo_modify"_thermo_modify.html {press} option is supported -by this fix to add the rescaled kinetic pressure as part of -"thermodynamic output"_thermo_style.html. - -[Restrictions:] - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"temper/grem"_temper_grem.html, "fix nvt"_fix_nh.html, "fix -npt"_fix_nh.html, "thermo_modify"_thermo_modify.html - -[Default:] none - -:line - -:link(Kim2010) -[(Kim)] Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010). - -:link(Malolepsza) -[(Malolepsza)] Malolepsza, Secor, Keyes, J Phys Chem B 119 (42), -13379-13384 (2015). diff --git a/doc/txt/fix_halt.txt b/doc/txt/fix_halt.txt deleted file mode 100644 index 8e85dc7ea5..0000000000 --- a/doc/txt/fix_halt.txt +++ /dev/null @@ -1,147 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix halt command :h3 - -[Syntax:] - -fix ID group-ID halt N attribute operator avalue keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -halt = style name of this fix command :l -N = check halt condition every N steps :l -attribute = {bondmax} or {tlimit} or v_name :l - bondmax = length of longest bond in the system - tlimit = elapsed CPU time - v_name = name of "equal-style variable"_variable.html :pre -operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l -avalue = numeric value to compare attribute to :l -zero or more keyword/value pairs may be appended :l -keyword = {error} or {message} :l - {error} value = {hard} or {soft} or {continue} - {message} value = {yes} or {no} :pre -:ule - -[Examples:] - -fix 10 all halt 1 bondmax > 1.5 -fix 10 all print 10 v_myCheck != 0 error soft :pre - -[Description:] - -Check a condition every N steps during a simulation run. N must be >= -1. If the condition is met, exit the run immediately. In this -context a "run" can be dynamics or minimization iterations, as -specified by the "run"_run.html or "minimize"_minimize.html command. - -The specified group-ID is ignored by this fix. - -The specified {attribute} can be one of the options listed above, -namely {bondmax} or {tlimit}, or an "equal-style -variable"_variable.html referenced as {v_name}, where "name" is the -name of a variable that has been defined previously in the input -script. - -The {bondmax} attribute will loop over all bonds in the system, -compute their current lengths, and set {attribute} to the longest bond -distance. - -The {tlimit} attribute queries the elapsed CPU time (in seconds) since -the current run began, and sets {attribute} to that value. This is an -alternative way to limit the length of a simulation run, similar to -the "timer"_timer.html timeout command. There are two differences in -using this method versus the timer command option. The first is that -the clock starts at the beginning of the current run (not when the -timer or fix command is specified), so that any setup time for the run -is not included in the elapsed time. The second is that the timer -invocation and syncing across all processors (via MPI_Allreduce) is -not performed once every {N} steps by this command. Instead it is -performed (typically) only a small number of times and the elapsed -times are used to predict when the end-of-the-run will be. Both of -these attributes can be useful when performing benchmark calculations -for a desired length of time with minimal overhead. For example, if -a run is performing 1000s of timesteps/sec, the overhead for syncing -the timer frequently across a large number of processors may be -non-negligible. - -Equal-style variables evaluate to a numeric value. See the -"variable"_variable.html command for a description. They calculate -formulas which can involve mathematical operations, atom properties, -group properties, thermodynamic properties, global values calculated -by a "compute"_compute.html or "fix"_fix.html, or references to other -"variables"_variable.html. Thus they are a very general means of -computing some attribute of the current system. For example, the -following "bondmax" variable will calculate the same quantity as the -hstyle = bondmax option. - -compute bdist all bond/local dist -compute bmax all reduce max c_bdist -variable bondmax equal c_bmax :pre - -Thus these two versions of a fix halt command will do the same thing: - -fix 10 all halt 1 bondmax > 1.5 -fix 10 all halt 1 v_bondmax > 1.5 :pre - -The version with "bondmax" will just run somewhat faster, due to less -overhead in computing bond lengths and not storing them in a separate -compute. - -The choice of operators listed above are the usual comparison -operators. The XOR operation (exclusive or) is also included as "|^". -In this context, XOR means that if either the attribute or avalue is -0.0 and the other is non-zero, then the result is "true". Otherwise -it is "false". - -The specified {avalue} must be a numeric value. - -:line - -The optional {error} keyword determines how the current run is halted. -If its value is {hard}, then LAMMPS will stop with an error message. - -If its value is {soft}, LAMMPS will exit the current run, but continue -to execute subsequent commands in the input script. However, -additional "run"_run.html or "minimize"_minimize.html commands will be -skipped. For example, this allows a script to output the current -state of the system, e.g. via a "write_dump"_write_dump.html or -"write_restart"_write_restart.html command. - -If its value is {continue}, the behavior is the same as for {soft}, -except subsequent "run"_run.html or "minimize"_minimize.html commands -are executed. This allows your script to remedy the condition that -triggered the halt, if necessary. Note that you may wish use the -"unfix"_unfix.html command on the fix halt ID, so that the same -condition is not immediately triggered in a subsequent run. - -The optional {message} keyword determines whether a message is printed -to the screen and logfile when the halt condition is triggered. If -{message} is set to yes, a one line message with the values that -triggered the halt is printed. If {message} is set to no, no message -is printed; the run simply exits. The latter may be desirable for -post-processing tools that extract thermodynamic information from log -files. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -[Restrictions:] none - -[Related commands:] - -"variable"_variable.html - -[Default:] - -The option defaults are error = hard and message = yes. diff --git a/doc/txt/fix_heat.txt b/doc/txt/fix_heat.txt deleted file mode 100644 index 640b211f99..0000000000 --- a/doc/txt/fix_heat.txt +++ /dev/null @@ -1,128 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix heat command :h3 - -[Syntax:] - -fix ID group-ID heat N eflux :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -heat = style name of this fix command :l -N = add/subtract heat every this many timesteps :l -eflux = rate of heat addition or subtraction (energy/time units) :l -eflux can be a variable (see below) :l -zero or more keyword/value pairs may be appended to args :l -keyword = {region} :l - {region} value = region-ID - region-ID = ID of region atoms must be in to have added force :pre -:ule - -[Examples:] - -fix 3 qin heat 1 1.0 -fix 3 qin heat 10 v_flux -fix 4 qout heat 1 -1.0 region top :pre - -[Description:] - -Add non-translational kinetic energy (heat) to a group of atoms in a -manner that conserves their aggregate momentum. Two of these fixes -can be used to establish a temperature gradient across a simulation -domain by adding heat (energy) to one group of atoms (hot reservoir) -and subtracting heat from another (cold reservoir). E.g. a simulation -sampling from the McDLT ensemble. - -If the {region} keyword is used, the atom must be in both the group -and the specified geometric "region"_region.html in order to have -energy added or subtracted to it. If not specified, then the atoms in -the group are affected wherever they may move to. - -Heat addition/subtraction is performed every N timesteps. The {eflux} -parameter can be specified as a numeric constant or as a variable (see -below). If it is a numeric constant or equal-style variable which -evaluates to a scalar value, then the {eflux} determines the change in -aggregate energy of the entire group of atoms per unit time, e.g. in -eV/psec for "metal units"_units.html. In this case it is an -"extensive" quantity, meaning its magnitude should be scaled with the -number of atoms in the group. Note that since {eflux} has per-time -units (i.e. it is a flux), this means that a larger value of N will -add/subtract a larger amount of energy each time the fix is invoked. - -NOTE: The heat-exchange (HEX) algorithm implemented by this fix is -known to exhibit a pronounced energy drift. An improved algorithm -(eHEX) is available as a "fix ehex"_fix_ehex.html command and might be -preferable if energy conservation is important. - -If {eflux} is specified as an atom-style variable (see below), then -the variable computes one value per atom. In this case, each value is -the energy flux for a single atom, again in units of energy per unit -time. In this case, each value is an "intensive" quantity, which need -not be scaled with the number of atoms in the group. - -As mentioned above, the {eflux} parameter can be specified as an -equal-style or atom_style "variable"_variable.html. If the value is a -variable, it should be specified as v_name, where name is the variable -name. In this case, the variable will be evaluated each timestep, and -its value(s) used to determine the flux. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent flux. - -Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent flux -with optional time-dependence as well. - -NOTE: If heat is subtracted from the system too aggressively so that -the group's kinetic energy would go to zero, or any individual atom's -kinetic energy would go to zero for the case where {eflux} is an -atom-style variable, then LAMMPS will halt with an error message. - -Fix heat is different from a thermostat such as "fix nvt"_fix_nh.html -or "fix temp/rescale"_fix_temp_rescale.html in that energy is -added/subtracted continually. Thus if there isn't another mechanism -in place to counterbalance this effect, the entire system will heat or -cool continuously. You can use multiple heat fixes so that the net -energy change is 0.0 or use "fix viscous"_fix_viscous.html to drain -energy from the system. - -This fix does not change the coordinates of its atoms; it only scales -their velocities. Thus you must still use an integration fix -(e.g. "fix nve"_fix_nve.html) on the affected atoms. This fix should -not normally be used on atoms that have their temperature controlled -by another fix - e.g. "fix nvt"_fix_nh.html or "fix -langevin"_fix_langevin.html fix. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. This scalar is the most recent -value by which velocities were scaled. The scalar value calculated by -this fix is "intensive". If {eflux} is specified as an atom-style -variable, this fix computes the average value by which the velocities -were scaled for all of the atoms that had their velocities scaled. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix ehex"_fix_ehex.html, "compute temp"_compute_temp.html, "compute -temp/region"_compute_temp_region.html - -[Default:] none diff --git a/doc/txt/fix_hyper_global.txt b/doc/txt/fix_hyper_global.txt deleted file mode 100644 index bfe8203b50..0000000000 --- a/doc/txt/fix_hyper_global.txt +++ /dev/null @@ -1,263 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -fix hyper/global command :h3 - -[Syntax:] - -fix ID group-ID hyper/global cutbond qfactor Vmax Tequil :pre - -ID, group-ID are documented in "fix"_fix.html command -hyper/global = style name of this fix command -cutbond = max distance at which a pair of atoms is considered bonded (distance units) -qfactor = max strain at which bias potential goes to 0.0 (unitless) -Vmax = height of bias potential (energy units) -Tequil = equilibration temperature (temperature units) :ul - -[Examples:] - -fix 1 all hyper/global 1.0 0.3 0.8 300.0 :pre - -[Description:] - -This fix is meant to be used with the "hyper"_hyper.html command to -perform a bond-boost global hyperdynamics (GHD) simulation. The role -of this fix is to a select a single pair of atoms in the system at -each timestep to add a global bias potential to, which will alter the -dynamics of the system in a manner that effectively accelerates time. -This is in contrast to the "fix hyper/local"_fix_hyper_local.html -command, which can be user to perform a local hyperdynamics (LHD) -simulation, by adding a local bias potential to multiple pairs of -atoms at each timestep. GHD can time accelerate a small simulation -with up to a few 100 atoms. For larger systems, LHD is needed to -achieve good time acceleration. - -For a system that undergoes rare transition events, where one or more -atoms move over an energy barrier to a new potential energy basin, the -effect of the bias potential is to induce more rapid transitions. -This can lead to a dramatic speed-up in the rate at which events -occurs, without altering their relative frequencies, thus leading to -an overall increase in the elapsed real time of the simulation as -compared to running for the same number of timesteps with normal MD. -See the "hyper"_hyper.html doc page for a more general discussion of -hyperdynamics and citations that explain both GHD and LHD. - -The equations and logic used by this fix and described here to perform -GHD follow the description given in "(Voter2013)"_#Voter2013ghd. The -bond-boost form of a bias potential for HD is due to Miron and -Fichthorn as described in "(Miron)"_#Mironghd. In LAMMPS we use a -simplified version of bond-boost GHD where a single bond in the system -is biased at any one timestep. - -Bonds are defined between each pair of I,J atoms whose R0ij distance -is less than {cutbond}, when the system is in a quenched state -(minimum) energy. Note that these are not "bonds" in a covalent -sense. A bond is simply any pair of atoms that meet the distance -criterion. {Cutbond} is an argument to this fix; it is discussed -below. A bond is only formed if one or both of the I.J atoms are in -the specified group. - -The current strain of bond IJ (when running dynamics) is defined as - -Eij = (Rij - R0ij) / R0ij :pre - -where Rij is the current distance between atoms I,J, and R0ij is the -equilibrium distance in the quenched state. - -The bias energy Vij of any bond IJ is defined as - -Vij = Vmax * (1 - (Eij/q)^2) for abs(Eij) < qfactor - = 0 otherwise :pre - -where the prefactor {Vmax} and the cutoff {qfactor} are arguments to -this fix; they are discussed below. This functional form is an -inverse parabola centered at 0.0 with height Vmax and which goes to -0.0 at +/- qfactor. - -Let Emax = the maximum of abs(Eij) for all IJ bonds in the system on a -given timestep. On that step, Vij is added as a bias potential to -only the single bond with strain Emax, call it Vij(max). Note that -Vij(max) will be 0.0 if Emax >= qfactor on that timestep. Also note -that Vij(max) is added to the normal interatomic potential that is -computed between all atoms in the system at every step. - -The derivative of Vij(max) with respect to the position of each atom -in the Emax bond gives a bias force Fij(max) acting on the bond as - -Fij(max) = - dVij(max)/dEij = 2 Vmax Eij / qfactor^2 for abs(Eij) < qfactor - = 0 otherwise :pre - -which can be decomposed into an equal and opposite force acting on -only the two I,J atoms in the Emax bond. - -The time boost factor for the system is given each timestep I by - -Bi = exp(beta * Vij(max)) :pre - -where beta = 1/kTequil, and {Tequil} is the temperature of the system -and an argument to this fix. Note that Bi >= 1 at every step. - -NOTE: To run a GHD simulation, the input script must also use the "fix -langevin"_fix_langevin.html command to thermostat the atoms at the -same {Tequil} as specified by this fix, so that the system is running -constant-temperature (NVT) dynamics. LAMMPS does not check that this -is done. - -The elapsed time t_hyper for a GHD simulation running for {N} -timesteps is simply - -t_hyper = Sum (i = 1 to N) Bi * dt :pre - -where dt is the timestep size defined by the "timestep"_timestep.html -command. The effective time acceleration due to GHD is thus t_hyper / -N*dt, where N*dt is elapsed time for a normal MD run of N timesteps. - -Note that in GHD, the boost factor varies from timestep to timestep. -Likewise, which bond has Emax strain and thus which pair of atoms the -bias potential is added to, will also vary from timestep to timestep. -This is in contrast to local hyperdynamics (LHD) where the boost -factor is an input parameter; see the "fix -hyper/local"_fix_hyper_local.html doc page for details. - -:line - -Here is additional information on the input parameters for GHD. - -The {cutbond} argument is the cutoff distance for defining bonds -between pairs of nearby atoms. A pair of I,J atoms in their -equilibrium, minimum-energy configuration, which are separated by a -distance Rij < {cutbond}, are flagged as a bonded pair. Setting -{cubond} to be ~25% larger than the nearest-neighbor distance in a -crystalline lattice is a typical choice for solids, so that bonds -exist only between nearest neighbor pairs. - -The {qfactor} argument is the limiting strain at which the bias -potential goes to 0.0. It is dimensionless, so a value of 0.3 means a -bond distance can be up to 30% larger or 30% smaller than the -equilibrium (quenched) R0ij distance and the two atoms in the bond -could still experience a non-zero bias force. - -If {qfactor} is set too large, then transitions from one energy basin -to another are affected because the bias potential is non-zero at the -transition state (e.g. saddle point). If {qfactor} is set too small -than little boost is achieved because the Eij strain of some bond in -the system will (nearly) always exceed {qfactor}. A value of 0.3 for -{qfactor} is typically reasonable. - -The {Vmax} argument is the prefactor on the bias potential. Ideally, -tt should be set to a value slightly less than the smallest barrier -height for an event to occur. Otherwise the applied bias potential -may be large enough (when added to the interatomic potential) to -produce a local energy basin with a maxima in the center. This can -produce artificial energy minima in the same basin that trap an atom. -Or if {Vmax} is even larger, it may induce an atom(s) to rapidly -transition to another energy basin. Both cases are "bad dynamics" -which violate the assumptions of GHD that guarantee an accelerated -time-accurate trajectory of the system. - -Note that if {Vmax} is set too small, the GHD simulation will run -correctly. There will just be fewer events because the hyper time -(t_hyper equation above) will be shorter. - -NOTE: If you have no physical intuition as to the smallest barrier -height in your system, a reasonable strategy to determine the largest -{Vmax} you can use for a GHD model, is to run a sequence of -simulations with smaller and smaller {Vmax} values, until the event -rate does not change (as a function of hyper time). - -The {Tequil} argument is the temperature at which the system is -simulated; see the comment above about the "fix -langevin"_fix_langevin.html thermostatting. It is also part of the -beta term in the exponential factor that determines how much boost is -achieved as a function of the bias potential. - -In general, the lower the value of {Tequil} and the higher the value -of {Vmax}, the more time boost will be achievable by the GHD -algorithm. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy of the bias potential to the system's -potential energy as part of "thermodynamic output"_thermo_style.html. - -This fix computes a global scalar and global vector of length 12, which -can be accessed by various "output commands"_Howto_output.html. The -scalar is the magnitude of the bias potential (energy units) applied on -the current timestep. The vector stores the following quantities: - -1 = boost factor on this step (unitless) -2 = max strain Eij of any bond on this step (absolute value, unitless) -3 = ID of first atom in the max-strain bond -4 = ID of second atom in the max-strain bond -5 = average # of bonds/atom on this step :ul - -6 = fraction of timesteps where the biased bond has bias = 0.0 during this run -7 = fraction of timesteps where the biased bond has negative strain during this run -8 = max drift distance of any atom during this run (distance units) -9 = max bond length during this run (distance units) :ul - -10 = cumulative hyper time since fix was defined (time units) -11 = cumulative count of event timesteps since fix was defined -12 = cumulative count of atoms in events since fix was defined :ul - -The first 5 quantities are for the current timestep. Quantities 6-9 -are for the current hyper run. They are reset each time a new hyper -run is performed. Quantities 19-12 are cumulative across multiple -runs (since the point in the input script the fix was defined). - -For value 8, drift is the distance an atom moves between two quenched -states when the second quench determines an event has occurred. Atoms -involved in an event will typically move the greatest distance since -others typically remain near their original quenched position. - -For value 11, events are checked for by the "hyper"_hyper.html command -once every {Nevent} timesteps. This value is the count of those -timesteps on which one (or more) events was detected. It is NOT the -number of distinct events, since more than one event may occur in the -same {Nevent} time window. - -For value 12, each time the "hyper"_hyper.html command checks for an -event, it invokes a compute to flag zero or more atoms as -participating in one or more events. E.g. atoms that have displaced -more than some distance from the previous quench state. Value 11 is -the cumulative count of the number of atoms participating in any of -the events that were found. - -The scalar and vector values calculated by this fix are all -"intensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This command can only be used if LAMMPS was built with the REPLICA -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"hyper"_hyper.html, "fix hyper/local"_fix_hyper_local.html - -[Default:] None - -:line - -:link(Voter2013ghd) -[(Voter2013)] S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139, -144110 (2013). - -:link(Mironghd) -[(Miron)] R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003). diff --git a/doc/txt/fix_imd.txt b/doc/txt/fix_imd.txt deleted file mode 100644 index 3e7792d51a..0000000000 --- a/doc/txt/fix_imd.txt +++ /dev/null @@ -1,160 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix imd command :h3 - -[Syntax:] - -fix ID group-ID imd trate port keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -imd = style name of this fix command :l -port = port number on which the fix listens for an IMD client :l -keyword = {unwrap} or {fscale} or {trate} :l - {unwrap} arg = {on} or {off} - off = coordinates are wrapped back into the principal unit cell (default) - on = "unwrapped" coordinates using the image flags used - {fscale} arg = factor - factor = floating point number to scale IMD forces (default: 1.0) - {trate} arg = transmission rate of coordinate data sets (default: 1) - {nowait} arg = {on} or {off} - off = LAMMPS waits to be connected to an IMD client before continuing (default) - on = LAMMPS listens for an IMD client, but continues with the run :pre -:ule - -[Examples:] - -fix vmd all imd 5678 -fix comm all imd 8888 trate 5 unwrap on fscale 10.0 :pre - -[Description:] - -This fix implements the "Interactive MD" (IMD) protocol which allows -realtime visualization and manipulation of MD simulations through the -IMD protocol, as initially implemented in VMD and NAMD. Specifically -it allows LAMMPS to connect an IMD client, for example the "VMD -visualization program"_VMD, so that it can monitor the progress of the -simulation and interactively apply forces to selected atoms. - -If LAMMPS is compiled with the pre-processor flag -DLAMMPS_ASYNC_IMD -then fix imd will use POSIX threads to spawn a IMD communication -thread on MPI rank 0 in order to offload data reading and writing -from the main execution thread and potentially lower the inferred -latencies for slow communication links. This feature has only been -tested under linux. - -There are example scripts for using this package with LAMMPS in -examples/USER/imd. Additional examples and a driver for use with the -Novint Falcon game controller as haptic device can be found at: -http://sites.google.com/site/akohlmey/software/vrpn-icms. - -The source code for this fix includes code developed by the -Theoretical and Computational Biophysics Group in the Beckman -Institute for Advanced Science and Technology at the University of -Illinois at Urbana-Champaign. We thank them for providing a software -interface that allows codes like LAMMPS to hook to "VMD"_VMD. - -Upon initialization of the fix, it will open a communication port on -the node with MPI task 0 and wait for an incoming connection. As soon -as an IMD client is connected, the simulation will continue and the -fix will send the current coordinates of the fix's group to the IMD -client at every trate MD step. When using r-RESPA, trate applies to -the steps of the outmost RESPA level. During a run with an active IMD -connection also the IMD client can request to apply forces to selected -atoms of the fix group. - -The port number selected must be an available network port number. On -many machines, port numbers < 1024 are reserved for accounts with -system manager privilege and specific applications. If multiple imd -fixes would be active at the same time, each needs to use a different -port number. - -The {nowait} keyword controls the behavior of the fix when no IMD -client is connected. With the default setting of {off}, LAMMPS will -wait until a connection is made before continuing with the -execution. Setting {nowait} to {on} will have the LAMMPS code be ready -to connect to a client, but continue with the simulation. This can for -example be used to monitor the progress of an ongoing calculation -without the need to be permanently connected or having to download a -trajectory file. - -The {trate} keyword allows to select how often the coordinate data is -sent to the IMD client. It can also be changed on request of the IMD -client through an IMD protocol message. The {unwrap} keyword allows -to send "unwrapped" coordinates to the IMD client that undo the -wrapping back of coordinates into the principle unit cell, as done by -default in LAMMPS. The {fscale} keyword allows to apply a scaling -factor to forces transmitted by the IMD client. The IMD protocols -stipulates that forces are transferred in kcal/mol/angstrom under the -assumption that coordinates are given in angstrom. For LAMMPS runs -with different units or as a measure to tweak the forces generated by -the manipulation of the IMD client, this option allows to make -adjustments. - -To connect VMD to a listening LAMMPS simulation on the same machine -with fix imd enabled, one needs to start VMD and load a coordinate or -topology file that matches the fix group. When the VMD command -prompts appears, one types the command line: - -imd connect localhost 5678 :pre - -This assumes that {fix imd} was started with 5678 as a port -number for the IMD protocol. - -The steps to do interactive manipulation of a running simulation in -VMD are the following: - -In the Mouse menu of the VMD Main window, select "Mouse -> Force -> -Atom". You may alternately select "Residue", or "Fragment" to apply -forces to whole residues or fragments. Your mouse can now be used to -apply forces to your simulation. Click on an atom, residue, or -fragment and drag to apply a force. Click quickly without moving the -mouse to turn the force off. You can also use a variety of 3D position -trackers to apply forces to your simulation. Game controllers or haptic -devices with force-feedback such as the Novint Falcon or Sensable -PHANTOM allow you to feel the resistance due to inertia or interactions -with neighbors that the atoms experience you are trying to move, as if -they were real objects. See the "VMD IMD Homepage"_imdvmd and the -"VRPN-ICMS Homepage"_vrpnicms for more details. - -If IMD control messages are received, a line of text describing the -message and its effect will be printed to the LAMMPS output screen, if -screen output is active. - -:link(VMD,http://www.ks.uiuc.edu/Research/vmd) -:link(imdvmd,http://www.ks.uiuc.edu/Research/vmd/imd/) -:link(vrpnicms,http://sites.google.com/site/akohlmey/software/vrpn-icms) - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global scalar or vector or per-atom -quantities are stored by this fix for access by various "output -commands"_Howto_output.html. No parameter of this fix can be used -with the {start/stop} keywords of the "run"_run.html command. This -fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -When used in combination with VMD, a topology or coordinate file has -to be loaded, which matches (in number and ordering of atoms) the -group the fix is applied to. The fix internally sorts atom IDs by -ascending integer value; in VMD (and thus the IMD protocol) those will -be assigned 0-based consecutive index numbers. - -When using multiple active IMD connections at the same time, each -needs to use a different port number. - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/fix_indent.txt b/doc/txt/fix_indent.txt deleted file mode 100644 index ca93c78c79..0000000000 --- a/doc/txt/fix_indent.txt +++ /dev/null @@ -1,205 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix indent command :h3 - -[Syntax:] - -fix ID group-ID indent K keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -indent = style name of this fix command :l -K = force constant for indenter surface (force/distance^2 units) :l -one or more keyword/value pairs may be appended :l -keyword = {sphere} or {cylinder} or {plane} or {side} or {units} :l - {sphere} args = x y z R - x,y,z = initial position of center of indenter (distance units) - R = sphere radius of indenter (distance units) - any of x,y,z,R can be a variable (see below) - {cylinder} args = dim c1 c2 R - dim = {x} or {y} or {z} = axis of cylinder - c1,c2 = coords of cylinder axis in other 2 dimensions (distance units) - R = cylinder radius of indenter (distance units) - any of c1,c2,R can be a variable (see below) - {plane} args = dim pos side - dim = {x} or {y} or {z} = plane perpendicular to this dimension - pos = position of plane in dimension x, y, or z (distance units) - pos can be a variable (see below) - side = {lo} or {hi} - {side} value = {in} or {out} - {in} = the indenter acts on particles inside the sphere or cylinder - {out} = the indenter acts on particles outside the sphere or cylinder - {units} value = {lattice} or {box} - lattice = the geometry is defined in lattice units - box = the geometry is defined in simulation box units :pre -:ule - -[Examples:] - -fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0 -fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in -fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box :pre - -[Description:] - -Insert an indenter within a simulation box. The indenter repels all -atoms in the group that touch it, so it can be used to push into a -material or as an obstacle in a flow. Or it can be used as a -constraining wall around a simulation; see the discussion of the -{side} keyword below. - -The indenter can either be spherical or cylindrical or planar. You -must set one of those 3 keywords. - -A spherical indenter exerts a force of magnitude - -F(r) = - K (r - R)^2 :pre - -on each atom where {K} is the specified force constant, {r} is the -distance from the atom to the center of the indenter, and {R} is the -radius of the indenter. The force is repulsive and F(r) = 0 for {r} > -{R}. - -A cylindrical indenter exerts the same force, except that {r} is the -distance from the atom to the center axis of the cylinder. The -cylinder extends infinitely along its axis. - -Spherical and cylindrical indenters account for periodic boundaries in -two ways. First, the center point of a spherical indenter (x,y,z) or -axis of a cylindrical indenter (c1,c2) is remapped back into the -simulation box, if the box is periodic in a particular dimension. -This occurs every timestep if the indenter geometry is specified with -a variable (see below), e.g. it is moving over time. Second, the -calculation of distance to the indenter center or axis accounts for -periodic boundaries. Both of these mean that an indenter can -effectively move through and straddle one or more periodic boundaries. - -A planar indenter is really an axis-aligned infinite-extent wall -exerting the same force on atoms in the system, where {R} is the -position of the plane and {r-R} is the distance from the plane. If -the {side} parameter of the plane is specified as {lo} then it will -indent from the lo end of the simulation box, meaning that atoms with -a coordinate less than the plane's current position will be pushed -towards the hi end of the box and atoms with a coordinate higher than -the plane's current position will feel no force. Vice versa if {side} -is specified as {hi}. - -Any of the 4 quantities defining a spherical indenter's geometry can -be specified as an equal-style "variable"_variable.html, namely {x}, -{y}, {z}, or {R}. Similarly, for a cylindrical indenter, any of {c1}, -{c2}, or {R}, can be a variable. For a planar indenter, {pos} can be -a variable. If the value is a variable, it should be specified as -v_name, where name is the variable name. In this case, the variable -will be evaluated each timestep, and its value used to define the -indenter geometry. - -Note that equal-style variables can specify formulas with various -mathematical functions, and include "thermo_style"_thermo_style.html -command keywords for the simulation box parameters and timestep and -elapsed time. Thus it is easy to specify indenter properties that -change as a function of time or span consecutive runs in a continuous -fashion. For the latter, see the {start} and {stop} keywords of the -"run"_run.html command and the {elaplong} keyword of "thermo_style -custom"_thermo_style.html for details. - -For example, if a spherical indenter's x-position is specified as v_x, -then this variable definition will keep it's center at a relative -position in the simulation box, 1/4 of the way from the left edge to -the right edge, even if the box size changes: - -variable x equal "xlo + 0.25*lx" :pre - -Similarly, either of these variable definitions will move the indenter -from an initial position at 2.5 at a constant velocity of 5: - -variable x equal "2.5 + 5*elaplong*dt" -variable x equal vdisplace(2.5,5) :pre - -If a spherical indenter's radius is specified as v_r, then these -variable definitions will grow the size of the indenter at a specified -rate. - -variable r0 equal 0.0 -variable rate equal 1.0 -variable r equal "v_r0 + step*dt*v_rate" :pre - -If the {side} keyword is specified as {out}, which is the default, -then particles outside the indenter are pushed away from its outer -surface, as described above. This only applies to spherical or -cylindrical indenters. If the {side} keyword is specified as {in}, -the action of the indenter is reversed. Particles inside the indenter -are pushed away from its inner surface. In other words, the indenter -is now a containing wall that traps the particles inside it. If the -radius shrinks over time, it will squeeze the particles. - -The {units} keyword determines the meaning of the distance units used -to define the indenter geometry. A {box} value selects standard -distance units as defined by the "units"_units.html command, -e.g. Angstroms for units = real or metal. A {lattice} value means the -distance units are in lattice spacings. The "lattice"_lattice.html -command must have been previously used to define the lattice spacing. -The (x,y,z) coords of the indenter position are scaled by the x,y,z -lattice spacings respectively. The radius of a spherical or -cylindrical indenter is scaled by the x lattice spacing. - -Note that the units keyword only affects indenter geometry parameters -specified directly with numbers, not those specified as variables. In -the latter case, you should use the {xlat}, {ylat}, {zlat} keywords of -the "thermo_style"_thermo_style.html command if you want to include -lattice spacings in a variable formula. - -The force constant {K} is not affected by the {units} keyword. It is -always in force/distance^2 units where force and distance are defined -by the "units"_units.html command. If you wish K to be scaled by the -lattice spacing, you can define K with a variable whose formula -contains {xlat}, {ylat}, {zlat} keywords of the -"thermo_style"_thermo_style.html command, e.g. - -variable k equal 100.0/xlat/xlat -fix 1 all indent $k sphere ... :pre - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy of interaction between atoms and the indenter to -the system's potential energy as part of "thermodynamic -output"_thermo_style.html. The energy of each particle interacting -with the indenter is K/3 (r - R)^3. - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -This fix computes a global scalar energy and a global 3-vector of -forces (on the indenter), which can be accessed by various "output -commands"_Howto_output.html. The scalar and vector values calculated -by this fix are "extensive". - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. Note that if you -define the indenter geometry with a variable using a time-dependent -formula, LAMMPS uses the iteration count in the minimizer as the -timestep. But it is almost certainly a bad idea to have the indenter -change its position or size during a minimization. LAMMPS does not -check if you have done this. - -NOTE: If you want the atom/indenter interaction energy to be included -in the total potential energy of the system (the quantity being -minimized), you must enable the "fix_modify"_fix_modify.html {energy} -option for this fix. - -[Restrictions:] none - -[Related commands:] none - -[Default:] - -The option defaults are side = out and units = lattice. diff --git a/doc/txt/fix_ipi.txt b/doc/txt/fix_ipi.txt deleted file mode 100644 index 64486a9cc7..0000000000 --- a/doc/txt/fix_ipi.txt +++ /dev/null @@ -1,101 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix ipi command :h3 - -[Syntax:] - -fix ID group-ID ipi address port \[unix\] \[reset\] :pre - -ID, group-ID are documented in "fix"_fix.html command -ipi = style name of this fix command -address = internet address (FQDN or IP), or UNIX socket name -port = port number (ignored for UNIX sockets) -optional keyword = {unix}, if present uses a unix socket -optional keyword = {reset}, if present reset electrostatics at each call :ul - -[Examples:] - -fix 1 all ipi my.server.com 12345 -fix 1 all ipi mysocket 666 unix reset - -[Description:] - -This fix enables LAMMPS to be run as a client for the i-PI Python -wrapper "(IPI)"_#ipihome for performing a path integral molecular dynamics -(PIMD) simulation. The philosophy behind i-PI is described in the -following publication "(IPI-CPC)"_#IPICPC. - -A version of the i-PI package, containing only files needed for use -with LAMMPS, is provided in the tools/i-pi directory. See the -tools/i-pi/manual.pdf for an introduction to i-PI. The -examples/USER/i-pi directory contains example scripts for using i-PI -with LAMMPS. - -In brief, the path integral molecular dynamics is performed by the -Python wrapper, while the client (LAMMPS in this case) simply computes -forces and energy for each configuration. The communication between -the two components takes place using sockets, and is reduced to the -bare minimum. All the parameters of the dynamics are specified in the -input of i-PI, and all the parameters of the force field must be -specified as LAMMPS inputs, preceding the {fix ipi} command. - -The server address must be specified by the {address} argument, and -can be either the IP address, the fully-qualified name of the server, -or the name of a UNIX socket for local, faster communication. In the -case of internet sockets, the {port} argument specifies the port -number on which i-PI is listening, while the {unix} optional switch -specifies that the socket is a UNIX socket. - -Note that there is no check of data integrity, or that the atomic -configurations make sense. It is assumed that the species in the i-PI -input are listed in the same order as in the data file of LAMMPS. The -initial configuration is ignored, as it will be substituted with the -coordinates received from i-PI before forces are ever evaluated. - -A note of caution when using potentials that contain long-range -electrostatics, or that contain parameters that depend on box size: -all of these options will be initialized based on the cell size in the -LAMMPS-side initial configuration and kept constant during the run. -This is required to e.g. obtain reproducible and conserved forces. -If the cell varies too wildly, it may be advisable to re-initialize -these interactions at each call. This behavior can be requested by -setting the {reset} switch. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -There is no restart information associated with this fix, since all -the dynamical parameters are dealt with by i-PI. - -[Restrictions:] - -Using this fix on anything other than all atoms requires particular -care, since i-PI will know nothing on atoms that are not those whose -coordinates are transferred. However, one could use this strategy to -define an external potential acting on the atoms that are moved by -i-PI. - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. Because of the -use of UNIX domain sockets, this fix will only work in a UNIX -environment. - -[Related commands:] - -"fix nve"_fix_nve.html - -:line - -:link(IPICPC) -[(IPI-CPC)] Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, -1019-1026 (2014). - -:link(ipihome) -[(IPI)] -"http://epfl-cosmo.github.io/gle4md/index.html?page=ipi"_http://epfl-cosmo.github.io/gle4md/index.html?page=ipi diff --git a/doc/txt/fix_langevin.txt b/doc/txt/fix_langevin.txt deleted file mode 100644 index 49ecf96ff6..0000000000 --- a/doc/txt/fix_langevin.txt +++ /dev/null @@ -1,347 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix langevin command :h3 -fix langevin/kk command :h3 - -[Syntax:] - -fix ID group-ID langevin Tstart Tstop damp seed keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -langevin = style name of this fix command :l -Tstart,Tstop = desired temperature at start/end of run (temperature units) :l -Tstart can be a variable (see below) :l -damp = damping parameter (time units) :l -seed = random number seed to use for white noise (positive integer) :l -zero or more keyword/value pairs may be appended :l -keyword = {angmom} or {omega} or {scale} or {tally} or {zero} :l - {angmom} value = {no} or factor - {no} = do not thermostat rotational degrees of freedom via the angular momentum - factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below - {gjf} value = {no} or {vfull} or {vhalf} - {no} = use standard formulation - {vfull} = use Gronbech-Jensen/Farago formulation - {vhalf} = use 2GJ formulation - {omega} value = {no} or {yes} - {no} = do not thermostat rotational degrees of freedom via the angular velocity - {yes} = do thermostat rotational degrees of freedom via the angular velocity - {scale} values = type ratio - type = atom type (1-N) - ratio = factor by which to scale the damping coefficient - {tally} value = {no} or {yes} - {no} = do not tally the energy added/subtracted to atoms - {yes} = do tally the energy added/subtracted to atoms - {zero} value = {no} or {yes} - {no} = do not set total random force to zero - {yes} = set total random force to zero :pre -:ule - -[Examples:] - -fix 3 boundary langevin 1.0 1.0 1000.0 699483 -fix 1 all langevin 1.0 1.1 100.0 48279 scale 3 1.5 -fix 1 all langevin 1.0 1.1 100.0 48279 angmom 3.333 :pre - -[Description:] - -Apply a Langevin thermostat as described in "(Schneider)"_#Schneider1 -to a group of atoms which models an interaction with a background -implicit solvent. Used with "fix nve"_fix_nve.html, this command -performs Brownian dynamics (BD), since the total force on each atom -will have the form: - -F = Fc + Ff + Fr -Ff = - (m / damp) v -Fr is proportional to sqrt(Kb T m / (dt damp)) :pre - -Fc is the conservative force computed via the usual inter-particle -interactions ("pair_style"_pair_style.html, -"bond_style"_bond_style.html, etc). - -The Ff and Fr terms are added by this fix on a per-particle basis. -See the "pair_style dpd/tstat"_pair_dpd.html command for a -thermostatting option that adds similar terms on a pairwise basis to -pairs of interacting particles. - -Ff is a frictional drag or viscous damping term proportional to the -particle's velocity. The proportionality constant for each atom is -computed as m/damp, where m is the mass of the particle and damp is -the damping factor specified by the user. - -Fr is a force due to solvent atoms at a temperature T randomly bumping -into the particle. As derived from the fluctuation/dissipation -theorem, its magnitude as shown above is proportional to sqrt(Kb T m / -dt damp), where Kb is the Boltzmann constant, T is the desired -temperature, m is the mass of the particle, dt is the timestep size, -and damp is the damping factor. Random numbers are used to randomize -the direction and magnitude of this force as described in -"(Dunweg)"_#Dunweg1, where a uniform random number is used (instead of -a Gaussian random number) for speed. - -Note that unless you use the {omega} or {angmom} keywords, the -thermostat effect of this fix is applied to only the translational -degrees of freedom for the particles, which is an important -consideration for finite-size particles, which have rotational degrees -of freedom, are being thermostatted. The translational degrees of -freedom can also have a bias velocity removed from them before -thermostatting takes place; see the description below. - -NOTE: Unlike the "fix nvt"_fix_nh.html command which performs -Nose/Hoover thermostatting AND time integration, this fix does NOT -perform time integration. It only modifies forces to effect -thermostatting. Thus you must use a separate time integration fix, -like "fix nve"_fix_nve.html to actually update the velocities and -positions of atoms using the modified forces. Likewise, this fix -should not normally be used on atoms that also have their temperature -controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix -temp/rescale"_fix_temp_rescale.html commands. - -See the "Howto thermostat"_Howto_thermostat.html doc page for -a discussion of different ways to compute temperature and perform -thermostatting. - -The desired temperature at each timestep is a ramped value during the -run from {Tstart} to {Tstop}. - -{Tstart} can be specified as an equal-style or atom-style -"variable"_variable.html. In this case, the {Tstop} setting is -ignored. If the value is a variable, it should be specified as -v_name, where name is the variable name. In this case, the variable -will be evaluated each timestep, and its value used to determine the -target temperature. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent temperature. - -Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent -temperature with optional time-dependence as well. - -Like other fixes that perform thermostatting, this fix can be used -with "compute commands"_compute.html that remove a "bias" from the -atom velocities. E.g. removing the center-of-mass velocity from a -group of atoms or removing the x-component of velocity from the -calculation. This is not done by default, but only if the -"fix_modify"_fix_modify.html command is used to assign a temperature -compute to this fix that includes such a bias term. See the doc pages -for individual "compute commands"_compute.html to determine which ones -include a bias. In this case, the thermostat works in the following -manner: bias is removed from each atom, thermostatting is performed on -the remaining thermal degrees of freedom, and the bias is added back -in. - -The {damp} parameter is specified in time units and determines how -rapidly the temperature is relaxed. For example, a value of 100.0 -means to relax the temperature in a timespan of (roughly) 100 time -units (tau or fmsec or psec - see the "units"_units.html command). -The damp factor can be thought of as inversely related to the -viscosity of the solvent. I.e. a small relaxation time implies a -hi-viscosity solvent and vice versa. See the discussion about gamma -and viscosity in the documentation for the "fix -viscous"_fix_viscous.html command for more details. - -The random # {seed} must be a positive integer. A Marsaglia random -number generator is used. Each processor uses the input seed to -generate its own unique seed and its own stream of random numbers. -Thus the dynamics of the system will not be identical on two runs on -different numbers of processors. - -:line - -The keyword/value option pairs are used in the following ways. - -The keyword {angmom} and {omega} keywords enable thermostatting of -rotational degrees of freedom in addition to the usual translational -degrees of freedom. This can only be done for finite-size particles. - -A simulation using atom_style sphere defines an omega for finite-size -spheres. A simulation using atom_style ellipsoid defines a finite -size and shape for aspherical particles and an angular momentum. -The Langevin formulas for thermostatting the rotational degrees of -freedom are the same as those above, where force is replaced by -torque, m is replaced by the moment of inertia I, and v is replaced by -omega (which is derived from the angular momentum in the case of -aspherical particles). - -The rotational temperature of the particles can be monitored by the -"compute temp/sphere"_compute_temp_sphere.html and "compute -temp/asphere"_compute_temp_asphere.html commands with their rotate -options. - -For the {omega} keyword there is also a scale factor of 10.0/3.0 that -is applied as a multiplier on the Ff (damping) term in the equation -above and of sqrt(10.0/3.0) as a multiplier on the Fr term. This does -not affect the thermostatting behavior of the Langevin formalism but -insures that the randomized rotational diffusivity of spherical -particles is correct. - -For the {angmom} keyword a similar scale factor is needed which is -10.0/3.0 for spherical particles, but is anisotropic for aspherical -particles (e.g. ellipsoids). Currently LAMMPS only applies an -isotropic scale factor, and you can choose its magnitude as the -specified value of the {angmom} keyword. If your aspherical particles -are (nearly) spherical than a value of 10.0/3.0 = 3.333 is a good -choice. If they are highly aspherical, a value of 1.0 is as good a -choice as any, since the effects on rotational diffusivity of the -particles will be incorrect regardless. Note that for any reasonable -scale factor, the thermostatting effect of the {angmom} keyword on the -rotational temperature of the aspherical particles should still be -valid. - -The keyword {scale} allows the damp factor to be scaled up or down by -the specified factor for atoms of that type. This can be useful when -different atom types have different sizes or masses. It can be used -multiple times to adjust damp for several atom types. Note that -specifying a ratio of 2 increases the relaxation time which is -equivalent to the solvent's viscosity acting on particles with 1/2 the -diameter. This is the opposite effect of scale factors used by the -"fix viscous"_fix_viscous.html command, since the damp factor in fix -{langevin} is inversely related to the gamma factor in fix {viscous}. -Also note that the damping factor in fix {langevin} includes the -particle mass in Ff, unlike fix {viscous}. Thus the mass and size of -different atom types should be accounted for in the choice of ratio -values. - -The keyword {tally} enables the calculation of the cumulative energy -added/subtracted to the atoms as they are thermostatted. Effectively -it is the energy exchanged between the infinite thermal reservoir and -the particles. As described below, this energy can then be printed -out or added to the potential energy of the system to monitor energy -conservation. - -NOTE: this accumulated energy does NOT include kinetic energy removed -by the {zero} flag. LAMMPS will print a warning when both options are -active. - -The keyword {zero} can be used to eliminate drift due to the -thermostat. Because the random forces on different atoms are -independent, they do not sum exactly to zero. As a result, this fix -applies a small random force to the entire system, and the -center-of-mass of the system undergoes a slow random walk. If the -keyword {zero} is set to {yes}, the total random force is set exactly -to zero by subtracting off an equal part of it from each atom in the -group. As a result, the center-of-mass of a system with zero initial -momentum will not drift over time. - -The keyword {gjf} can be used to run the "Gronbech-Jensen/Farago -"_#Gronbech-Jensen time-discretization of the Langevin model. As -described in the papers cited below, the purpose of this method is to -enable longer timesteps to be used (up to the numerical stability -limit of the integrator), while still producing the correct Boltzmann -distribution of atom positions. - -The current implementation provides the user with the option to output -the velocity in one of two forms: {vfull} or {vhalf}, which replaces -the outdated option {yes}. The {gjf} option {vfull} outputs the on-site -velocity given in "Gronbech-Jensen/Farago"_#Gronbech-Jensen; this velocity -is shown to be systematically lower than the target temperature by a small -amount, which grows quadratically with the timestep. -The {gjf} option {vhalf} outputs the 2GJ half-step velocity given in -"Gronbech Jensen/Gronbech-Jensen"_#2Gronbech-Jensen; for linear systems, -this velocity is shown to not have any statistical errors for any stable time step. -An overview of statistically correct Boltzmann and Maxwell-Boltzmann -sampling of true on-site and true half-step velocities is given in -"Gronbech-Jensen"_#1Gronbech-Jensen. -Regardless of the choice of output velocity, the sampling of the configurational -distribution of atom positions is the same, and linearly consistent with the -target temperature. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. Because the state of the random number generator -is not saved in restart files, this means you cannot do "exact" -restarts with this fix, where the simulation continues on the same as -if no restart had taken place. However, in a statistical sense, a -restarted simulation should produce the same behavior. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a temperature "compute"_compute.html -you have defined to this fix which will be used in its thermostatting -procedure, as described above. For consistency, the group used by -this fix and by the compute should be the same. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Langevin thermostatting to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. Note that use of this option requires -setting the {tally} keyword to {yes}. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the cumulative -energy change due to this fix. The scalar value calculated by this -fix is "extensive". Note that calculation of this quantity requires -setting the {tally} keyword to {yes}. - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -For {gjf} do not choose damp=dt/2. {gjf} is not compatible -with run_style respa. - -[Related commands:] - -"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix -viscous"_fix_viscous.html, "fix nvt"_fix_nh.html, "pair_style -dpd/tstat"_pair_dpd.html - -[Default:] - -The option defaults are angmom = no, omega = no, scale = 1.0 for all -types, tally = no, zero = no, gjf = no. - -:line - -:link(Dunweg1) -[(Dunweg)] Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). - -:link(Schneider1) -[(Schneider)] Schneider and Stoll, Phys Rev B, 17, 1302 (1978). - -:link(Gronbech-Jensen) -[(Gronbech-Jensen)] Gronbech-Jensen and Farago, Mol Phys, 111, 983 -(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, 185, 524 (2014) - -:link(2Gronbech-Jensen) -[(Gronbech-Jensen)] Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511 (2019) - -:link(1Gronbech-Jensen) -[(Gronbech-Jensen)] Gronbech-Jensen, Mol Phys (2019); https://doi.org/10.1080/00268976.2019.1662506 diff --git a/doc/txt/fix_langevin_drude.txt b/doc/txt/fix_langevin_drude.txt deleted file mode 100644 index dae12fb156..0000000000 --- a/doc/txt/fix_langevin_drude.txt +++ /dev/null @@ -1,274 +0,0 @@ - - - -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix langevin/drude command :h3 - -[Syntax:] - -fix ID group-ID langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -langevin/drude = style name of this fix command :l -Tcom = desired temperature of the centers of mass (temperature units) :l -damp_com = damping parameter for the thermostat on centers of mass (time units) :l -seed_com = random number seed to use for white noise of the thermostat on centers of mass (positive integer) :l -Tdrude = desired temperature of the Drude oscillators (temperature units) :l -damp_drude = damping parameter for the thermostat on Drude oscillators (time units) :l -seed_drude = random number seed to use for white noise of the thermostat on Drude oscillators (positive integer) :l -zero or more keyword/value pairs may be appended :l -keyword = {zero} :l - {zero} value = {no} or {yes} - {no} = do not set total random force on centers of mass to zero - {yes} = set total random force on centers of mass to zero :pre -:ule - -[Examples:] - -fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451 -fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes :pre - -[Description:] - -Apply two Langevin thermostats as described in "(Jiang)"_#Jiang1 for -thermalizing the reduced degrees of freedom of Drude oscillators. -This link describes how to use the "thermalized Drude oscillator -model"_Howto_drude.html in LAMMPS and polarizable models in LAMMPS -are discussed on the "Howto polarizable"_Howto_polarizable.html doc -page. - -Drude oscillators are a way to simulate polarizables atoms, by -splitting them into a core and a Drude particle bound by a harmonic -bond. The thermalization works by transforming the particles degrees -of freedom by these equations. In these equations upper case denotes -atomic or center of mass values and lower case denotes Drude particle -or dipole values. Primes denote the transformed (reduced) values, -while bare letters denote the original values. - -Velocities: -\begin\{equation\} V' = \frac \{M\, V + m\, v\} \{M'\} \end\{equation\} -\begin\{equation\} v' = v - V \end\{equation\} -Masses: -\begin\{equation\} M' = M + m \end\{equation\} -\begin\{equation\} m' = \frac \{M\, m \} \{M'\} \end\{equation\} -The Langevin forces are computed as -\begin\{equation\} F' = - \frac \{M'\} \{\mathtt\{damp\_com\}\}\, V' + F_r' \end\{equation\} -\begin\{equation\} f' = - \frac \{m'\} \{\mathtt\{damp\_drude\}\}\, v' + f_r' \end\{equation\} -\(F_r'\) is a random force proportional to -\(\sqrt \{ \frac \{2\, k_B \mathtt\{Tcom\}\, m'\} - \{\mathrm dt\, \mathtt\{damp\_com\} \} - \} \). -\(f_r'\) is a random force proportional to -\(\sqrt \{ \frac \{2\, k_B \mathtt\{Tdrude\}\, m'\} - \{\mathrm dt\, \mathtt\{damp\_drude\} \} - \} \). -Then the real forces acting on the particles are computed from the inverse -transform: -\begin\{equation\} F = \frac M \{M'\}\, F' - f' \end\{equation\} -\begin\{equation\} f = \frac m \{M'\}\, F' + f' \end\{equation\} - -This fix also thermostats non-polarizable atoms in the group at -temperature {Tcom}, as if they had a massless Drude partner. The -Drude particles themselves need not be in the group. The center of -mass and the dipole are thermostatted iff the core atom is in the -group. - -Note that the thermostat effect of this fix is applied to only the -translational degrees of freedom of the particles, which is an -important consideration if finite-size particles, which have -rotational degrees of freedom, are being thermostatted. The -translational degrees of freedom can also have a bias velocity removed -from them before thermostatting takes place; see the description below. - -NOTE: Like the "fix langevin"_fix_langevin.html command, this fix does -NOT perform time integration. It only modifies forces to effect -thermostatting. Thus you must use a separate time integration fix, like -"fix nve"_fix_nve.html or "fix nph"_fix_nh.html to actually update the -velocities and positions of atoms using the modified forces. -Likewise, this fix should not normally be used on atoms that also have -their temperature controlled by another fix - e.g. by "fix -nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html commands. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -:line - -This fix requires each atom know whether it is a Drude particle or -not. You must therefore use the "fix drude"_fix_drude.html command to -specify the Drude status of each atom type. - -NOTE: only the Drude core atoms need to be in the group specified for -this fix. A Drude electron will be transformed together with its cores -even if it is not itself in the group. It is safe to include Drude -electrons or non-polarizable atoms in the group. The non-polarizable -atoms will simply be thermostatted as if they had a massless Drude -partner (electron). - -NOTE: Ghost atoms need to know their velocity for this fix to act -correctly. You must use the "comm_modify"_comm_modify.html command to -enable this, e.g. - -comm_modify vel yes :pre - -:line - -{Tcom} is the target temperature of the centers of mass, which would -be used to thermostat the non-polarizable atoms. {Tdrude} is the -(normally low) target temperature of the core-Drude particle pairs -(dipoles). {Tcom} and {Tdrude} can be specified as an equal-style -"variable"_variable.html. If the value is a variable, it should be -specified as v_name, where name is the variable name. In this case, -the variable will be evaluated each timestep, and its value used to -determine the target temperature. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent temperature. - -Like other fixes that perform thermostatting, this fix can be used with -"compute commands"_compute.html that remove a "bias" from the atom -velocities. E.g. removing the center-of-mass velocity from a group of -atoms. This is not done by default, but only if the -"fix_modify"_fix_modify.html command is used to assign a temperature -compute to this fix that includes such a bias term. See the doc pages -for individual "compute commands"_compute.html to determine which ones -include a bias. In this case, the thermostat works in the following -manner: bias is removed from each atom, thermostatting is performed on -the remaining thermal degrees of freedom, and the bias is added back -in. NOTE: this feature has not been tested. - -Note: The temperature thermostatting the core-Drude particle pairs -should be chosen low enough, so as to mimic as closely as possible the -self-consistent minimization. It must however be high enough, so that -the dipoles can follow the local electric field exerted by the -neighboring atoms. The optimal value probably depends on the -temperature of the centers of mass and on the mass of the Drude -particles. - -{damp_com} is the characteristic time for reaching thermal equilibrium -of the centers of mass. For example, a value of 100.0 means to relax -the temperature of the centers of mass in a timespan of (roughly) 100 -time units (tau or fmsec or psec - see the "units"_units.html -command). {damp_drude} is the characteristic time for reaching -thermal equilibrium of the dipoles. It is typically a few timesteps. - -The number {seed_com} and {seed_drude} are positive integers. They set -the seeds of the Marsaglia random number generators used for -generating the random forces on centers of mass and on the -dipoles. Each processor uses the input seed to generate its own unique -seed and its own stream of random numbers. Thus the dynamics of the -system will not be identical on two runs on different numbers of -processors. - -The keyword {zero} can be used to eliminate drift due to the -thermostat on centers of mass. Because the random forces on different -centers of mass are independent, they do not sum exactly to zero. As -a result, this fix applies a small random force to the entire system, -and the momentum of the total center of mass of the system undergoes a -slow random walk. If the keyword {zero} is set to {yes}, the total -random force on the centers of mass is set exactly to zero by -subtracting off an equal part of it from each center of mass in the -group. As a result, the total center of mass of a system with zero -initial momentum will not drift over time. - -The actual temperatures of cores and Drude particles, in -center-of-mass and relative coordinates, respectively, can be -calculated using the "compute temp/drude"_compute_temp_drude.html -command. - -:line - -Usage example for rigid bodies in the NPT ensemble: - -comm_modify vel yes -fix TEMP all langevin/drude 300. 100. 1256 1. 20. 13977 zero yes -fix NPH ATOMS rigid/nph/small molecule iso 1. 1. 500. -fix NVE DRUDES nve -compute TDRUDE all temp/drude -thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE\[1\] c_TDRUDE\[2\] :pre - -Comments: - -Drude particles should not be in the rigid group, otherwise the Drude -oscillators will be frozen and the system will lose its -polarizability. :ulb,l - -{zero yes} avoids a drift of the center of mass of -the system, but is a bit slower. :l - -Use two different random seeds to avoid unphysical correlations. :l - -Temperature is controlled by the fix {langevin/drude}, so the -time-integration fixes do not thermostat. Don't forget to -time-integrate both cores and Drude particles. :l - -Pressure is time-integrated only once by using {nve} for Drude -particles and {nph} for atoms/cores (or vice versa). Do not use {nph} -for both. :l - -The temperatures of cores and Drude particles are calculated by -"compute temp/drude"_compute_temp_drude.html :l - -Contrary to the alternative thermostatting using Nose-Hoover thermostat -fix {npt} and "fix drude/transform"_fix_drude_transform.html, the -{fix_modify} command is not required here, because the fix {nph} -computes the global pressure even if its group is {ATOMS}. This is -what we want. If we thermostatted {ATOMS} using {npt}, the pressure -should be the global one, but the temperature should be only that of -the cores. That's why the command {fix_modify} should be called in -that case. :l -:ule - - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. Because the state of the random number generator -is not saved in restart files, this means you cannot do "exact" -restarts with this fix, where the simulation continues on the same as -if no restart had taken place. However, in a statistical sense, a -restarted simulation should produce the same behavior. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a temperature "compute"_compute.html -you have defined to this fix which will be used in its thermostatting -procedure, as described above. For consistency, the group used by the -compute should include the group of this fix and the Drude particles. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix langevin"_fix_langevin.html, -"fix drude"_fix_drude.html, -"fix drude/transform"_fix_drude_transform.html, -"compute temp/drude"_compute_temp_drude.html, -"pair_style thole"_pair_thole.html - -[Default:] - -The option defaults are zero = no. - -:line - -:link(Jiang1) -[(Jiang)] Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J -Phys Chem Lett, 2, 87-92 (2011). diff --git a/doc/txt/fix_langevin_eff.txt b/doc/txt/fix_langevin_eff.txt deleted file mode 100644 index e55e40c6c8..0000000000 --- a/doc/txt/fix_langevin_eff.txt +++ /dev/null @@ -1,113 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix langevin/eff command :h3 - -[Syntax:] - -fix ID group-ID langevin/eff Tstart Tstop damp seed keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -langevin/eff = style name of this fix command :l -Tstart,Tstop = desired temperature at start/end of run (temperature units) :l -damp = damping parameter (time units) :l -seed = random number seed to use for white noise (positive integer) :l -zero or more keyword/value pairs may be appended :l -keyword = {scale} or {tally} or {zero} - {scale} values = type ratio - type = atom type (1-N) - ratio = factor by which to scale the damping coefficient - {tally} values = {no} or {yes} - {no} = do not tally the energy added/subtracted to atoms - {yes} = do tally the energy added/subtracted to atoms :pre - {zero} value = {no} or {yes} - {no} = do not set total random force to zero - {yes} = set total random force to zero :pre -:ule - -[Examples:] - -fix 3 boundary langevin/eff 1.0 1.0 10.0 699483 -fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5 :pre - -[Description:] - -Apply a Langevin thermostat as described in "(Schneider)"_#Schneider2 -to a group of nuclei and electrons in the "electron force -field"_pair_eff.html model. Used with "fix nve/eff"_fix_nve_eff.html, -this command performs Brownian dynamics (BD), since the total force on -each atom will have the form: - -F = Fc + Ff + Fr -Ff = - (m / damp) v -Fr is proportional to sqrt(Kb T m / (dt damp)) :pre - -Fc is the conservative force computed via the usual inter-particle -interactions ("pair_style"_pair_style.html). - -The Ff and Fr terms are added by this fix on a per-particle basis. - -The operation of this fix is exactly like that described by the "fix -langevin"_fix_langevin.html command, except that the thermostatting -is also applied to the radial electron velocity for electron -particles. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. Because the state of the random number generator -is not saved in restart files, this means you cannot do "exact" -restarts with this fix, where the simulation continues on the same as -if no restart had taken place. However, in a statistical sense, a -restarted simulation should produce the same behavior. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a temperature "compute"_compute.html -you have defined to this fix which will be used in its thermostatting -procedure, as described above. For consistency, the group used by -this fix and by the compute should be the same. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Langevin thermostatting to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. Note that use of this option requires -setting the {tally} keyword to {yes}. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the cumulative -energy change due to this fix. The scalar value calculated by this -fix is "extensive". Note that calculation of this quantity requires -setting the {tally} keyword to {yes}. - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] none - -This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix langevin"_fix_langevin.html - -[Default:] - -The option defaults are scale = 1.0 for all types and tally = no. - -:line - -:link(Dunweg2) -[(Dunweg)] Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). - -:link(Schneider2) -[(Schneider)] Schneider and Stoll, Phys Rev B, 17, 1302 (1978). diff --git a/doc/txt/fix_langevin_spin.txt b/doc/txt/fix_langevin_spin.txt deleted file mode 100644 index e5dccc5e57..0000000000 --- a/doc/txt/fix_langevin_spin.txt +++ /dev/null @@ -1,102 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix langevin/spin command :h3 - -[Syntax:] - -fix ID group-ID langevin/spin T Tdamp seed :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -langevin/spin = style name of this fix command :l -T = desired temperature of the bath (temperature units, K in metal units) :l -Tdamp = transverse magnetic damping parameter (adim) :l -seed = random number seed to use for white noise (positive integer) :l -:ule - -[Examples:] - -fix 2 all langevin/spin 300.0 0.01 21 :pre - -[Description:] - -Apply a Langevin thermostat as described in "(Mayergoyz)"_#Mayergoyz1 to the -magnetic spins associated to the atoms. -Used with "fix nve/spin"_fix_nve_spin.html, this command performs -Brownian dynamics (BD). -A random torque and a transverse dissipation are applied to each spin i according to -the following stochastic differential equation: - -:c,image(Eqs/fix_langevin_spin_sLLG.jpg) - -with lambda the transverse damping, and eta a random vector. -This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG) -equation. - -The components of eta are drawn from a Gaussian probability law. Their amplitude -is defined as a proportion of the temperature of the external thermostat T (in K -in metal units). - -More details about this implementation are reported in "(Tranchida)"_#Tranchida2. - -Note: due to the form of the sLLG equation, this fix has to be defined just -before the nve/spin fix (and after all other magnetic fixes). -As an example: - -fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0 -fix 2 all langevin/spin 300.0 0.01 21 -fix 3 all nve/spin lattice moving :pre - -is correct, but defining a force/spin command after the langevin/spin command -would give an error message. - -Note: The random # {seed} must be a positive integer. A Marsaglia random -number generator is used. Each processor uses the input seed to -generate its own unique seed and its own stream of random numbers. -Thus the dynamics of the system will not be identical on two runs on -different numbers of processors. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. Because the state of the random number generator -is not saved in restart files, this means you cannot do "exact" -restarts with this fix, where the simulation continues on the same as -if no restart had taken place. However, in a statistical sense, a -restarted simulation should produce the same behavior. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -The {langevin/spin} fix is part of the SPIN package. This style is -only enabled if LAMMPS was built with this package. See the "Build -package"_Build_package.html doc page for more info. - -The numerical integration has to be performed with {fix nve/spin} -when {fix langevin/spin} is enabled. - -This fix has to be the last defined magnetic fix before the time -integration fix (e.g. {fix nve/spin}). - -[Related commands:] - -"fix nve/spin"_fix_nve_spin.html, "fix precession/spin"_fix_precession_spin.html - -[Default:] none - -:line - -:link(Mayergoyz1) -[(Mayergoyz)] I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009) - -:link(Tranchida2) -[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, -Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/txt/fix_latte.txt b/doc/txt/fix_latte.txt deleted file mode 100644 index e6edf6ac8a..0000000000 --- a/doc/txt/fix_latte.txt +++ /dev/null @@ -1,210 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix latte command :h3 - -[Syntax:] - -fix ID group-ID latte peID :pre - -ID, group-ID are documented in "fix"_fix.html command -latte = style name of this fix command -peID = NULL or ID of compute used to calculate per-atom energy :ul - -[Examples:] - -fix dftb all latte NULL :pre - -[Description:] - -This fix style is a wrapper on the self-consistent charge transfer -density functional based tight binding (DFTB) code LATTE. If you -download and build LATTE, it can be called as a library by LAMMPS via -this fix to run dynamics or perform energy minimization using DFTB -forces and energies computed by LATTE. - -LATTE is principally developed and supported by Marc Cawkwell and -co-workers at Los Alamos National Laboratory (LANL). See the full -list of contributors in the src/LATTE/README file. - -To use this fix, the LATTE program needs to be compiled as a library -and linked with LAMMPS. LATTE can be downloaded (or cloned) from -"https://github.com/lanl/LATTE"_https://github.com/lanl/LATTE. -Instructions on how to download and build LATTE on your system can be -found in the lib/latte/README. Note that you can also use the "make -lib-latte" command from the LAMMPS src directory to automate this -process. - -Once LAMMPS is built with the LATTE package, you can run the example -input scripts for molecular dynamics or energy minimization that are -found in examples/latte. - -A step-by-step tutorial can be followed at: "LAMMPS-LATTE -tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS - -The {peID} argument is not yet supported by fix latte, so it must be -specified as NULL. Eventually it will be used to enable LAMMPS to -calculate a Coulomb potential as an alternative to LATTE performing -the calculation. - -:line - -LATTE is a code for performing self-consistent charge transfer -tight-binding (SC-TB) calculations of total energies and the forces -acting on atoms in molecules and solids. This tight-binding method is -becoming more and more popular and widely used in chemistry, -biochemistry, material science, etc. - -The SC-TB formalism is derived from an expansion of the Kohn-Sham -density functional to second order in charge fluctuations about a -reference charge of overlapping atom-centered densities and bond -integrals are parameterized using a Slater-Koster tight-binding -approach. This procedure, which usually is referred to as the DFTB -method has been described in detail by ("Elstner"_#Elstner) and -("Finnis"_#Finnis2) and coworkers. - -The work of the LATTE developers follows that of Elstner closely with -respect to the physical model. However, the development of LATTE is -geared principally toward large-scale, long duration, microcanonical -quantum-based Born-Oppenheimer molecular dynamics (QMD) simulations. -One of the main bottlenecks of an electronic structure calculation is -the solution of the generalized eigenvalue problem which scales with -the cube of the system size O(N^3). - -The Theoretical and Computer sciences divisions at Los Alamos National -Laboratory have accumulated large experience addressing this issue by -calculating the density matrix directly instead of using -diagonalization. We typically use a recursive sparse Fermi-operator -expansion using second-order spectral projection functions -(SP2-algorithm), which was introduced by Niklasson in 2002 -("Niklasson2002"_#Niklasson2002), ("Rubensson"_#Rubensson), -("Mniszewski"_#Mniszewski). When the matrices involved in the -recursive expansion are sufficiently sparse, the calculation of the -density matrix scales linearly as a function of the system size O(N). - -Another important feature is the extended Lagrangian framework for -Born-Oppenheimer molecular dynamics (XL-BOMD) -("Niklasson2008"_#Niklasson2008) ("Niklasson2014"_#Niklasson2014), -("Niklasson2017"_#Niklasson2017) that allows for a drastic reduction -or even a complete removal of the iterative self-consistent field -optimization. Often only a single density matrix calculation per -molecular dynamics time step is required, yet total energy stability -is well maintained. The SP2 and XL-BOMD techniques enables stable -linear scaling MD simulations with a very small computational -overhead. This opens a number of opportunities in many different -areas of chemistry and materials science, as we now can simulate -larger system sizes and longer time scales -("Cawkwell2012"_#Cawkwell2012), ("Negre2016"_#Negre2016). - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the potential energy computed by LATTE to the system's -potential energy as part of "thermodynamic output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {virial} option is supported by this -fix to add the LATTE DFTB contribution to the system's virial as part -of "thermodynamic output"_thermo_style.html. The default is {virial -yes} - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the potential -energy discussed above. The scalar value calculated by this fix is -"extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The DFTB forces computed by LATTE via this fix are imposed during an -energy minimization, invoked by the "minimize"_minimize.html command. - -NOTE: If you want the potential energy associated with the DFTB -forces to be included in the total potential energy of the system (the -quantity being minimized), you MUST enable the -"fix_modify"_fix_modify.html {energy} option for this fix. - -[Restrictions:] - -This fix is part of the LATTE package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -You must use metal units, as set by the "units"_units.html command to -use this fix. - -LATTE does not currently compute per-atom energy or per-atom virial -contributions. So they will not show up as part of the calculations -performed by the "compute pe/atom"_compute_pe_atom.html or "compute -stress/atom"_compute_stress_atom.html commands. - -Currently, LAMMPS must be run in serial or as a single MPI task, to -use this fix. This is typically not a bottleneck, since LATTE will be -doing 99% or more of the work to compute quantum-accurate forces. - -NOTE: NEB calculations can be done using this fix using multiple -replicas and running LAMMPS in parallel. However, each replica must -be run on a single MPI task. For details, see the "neb"_neb.html -command doc page and the "-partition command-line -switch"_Run_options.html - -[Related commands:] none - -[Default:] none - -:line - -:link(Elstner) -[(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, -M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, -7260 (1998). - -:link(Elstner1) -[(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner, -M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, -7260 (1998). - -:link(Finnis2) -[(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van -Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998). - -:link(Mniszewski) -[(Mniszewski)] S. M. Mniszewski, M. J. Cawkwell, M. E. Wall, -J. Mohd-Yusof, N. Bock, T. C. Germann, and A. M. N. Niklasson, -J. Chem. Theory Comput., 11, 4644 (2015). - -:link(Niklasson2002) -[(Niklasson2002)] A. M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002). - -:link(Rubensson) -[(Rubensson)] E. H. Rubensson, A. M. N. Niklasson, SIAM -J. Sci. Comput. 36 (2), 147-170, (2014). - -:link(Niklasson2008) -[(Niklasson2008)] A. M. N. Niklasson, Phys. Rev. Lett., 100, 123004 -(2008). - -:link(Niklasson2014) -[(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys., -141, 164123, (2014). - -:link(Niklasson2017) -[(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017). - -:link(Cawkwell2012) -[(Cawkwell2012)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 -(17), 174308 (2012). - -:link(Negre2016) -[(Negre2016)] C. F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, -N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp., -12, 3063 (2016). diff --git a/doc/txt/fix_lb_fluid.txt b/doc/txt/fix_lb_fluid.txt deleted file mode 100644 index d9012d8cb3..0000000000 --- a/doc/txt/fix_lb_fluid.txt +++ /dev/null @@ -1,370 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix lb/fluid command :h3 - -[Syntax:] - -fix ID group-ID lb/fluid nevery LBtype viscosity density keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -lb/fluid = style name of this fix command :l -nevery = update the lattice-Boltzmann fluid every this many timesteps :l -LBtype = 1 to use the standard finite difference LB integrator, -2 to use the LB integrator of "Ollila et al."_#Ollila :l -viscosity = the fluid viscosity (units of mass/(time*length)). :l -density = the fluid density. :l - -zero or more keyword/value pairs may be appended :l -keyword = {setArea} or {setGamma} or {scaleGamma} or {dx} or {dm} or {a0} or {noise} or {calcforce} or {trilinear} or {D3Q19} or {read_restart} or {write_restart} or {zwall_velocity} or {bodyforce} or {printfluid} :l - {setArea} values = type node_area - type = atom type (1-N) - node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default). - {setGamma} values = gamma - gamma = user set value for the force coupling constant. - {scaleGamma} values = type gammaFactor - type = atom type (1-N) - gammaFactor = factor to scale the {setGamma} gamma value by, for the specified atom type. - {dx} values = dx_LB = the lattice spacing. - {dm} values = dm_LB = the lattice-Boltzmann mass unit. - {a0} values = a_0_real = the square of the speed of sound in the fluid. - {noise} values = Temperature seed - Temperature = fluid temperature. - seed = random number generator seed (positive integer) - {calcforce} values = N forcegroup-ID - N = output the force and torque every N timesteps - forcegroup-ID = ID of the particle group to calculate the force and torque of - {trilinear} values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil). - {D3Q19} values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice). - {read_restart} values = restart file = name of the restart file to use to restart a fluid run. - {write_restart} values = N = write a restart file every N MD timesteps. - {zwall_velocity} values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax). - {bodyforce} values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid. - {printfluid} values = N = print the fluid density and velocity at each grid point every N timesteps. :pre -:ule - -[Examples:] - -fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce sphere1 -fix 1 all lb/fluid 1 1 1.0 0.0009982071 setArea 1 1.144592082 dx 2.0 dm 0.3 trilinear noise 300.0 8979873 :pre - -[Description:] - -Implement a lattice-Boltzmann fluid on a uniform mesh covering the LAMMPS -simulation domain. The MD particles described by {group-ID} apply a velocity -dependent force to the fluid. - -The lattice-Boltzmann algorithm solves for the fluid motion governed by -the Navier Stokes equations, - -:c,image(Eqs/fix_lb_fluid_navierstokes.jpg) - -with, - -:c,image(Eqs/fix_lb_fluid_viscosity.jpg) - -where rho is the fluid density, u is the local fluid velocity, sigma -is the stress tensor, F is a local external force, and eta and Lambda -are the shear and bulk viscosities respectively. Here, we have -implemented - -:c,image(Eqs/fix_lb_fluid_stress.jpg), - -with a_0 set to 1/3 (dx/dt)^2 by default. - -The algorithm involves tracking the time evolution of a set of partial -distribution functions which evolve according to a velocity -discretized version of the Boltzmann equation, - -:c,image(Eqs/fix_lb_fluid_boltzmann.jpg) - -where the first term on the right hand side represents a single time -relaxation towards the equilibrium distribution function, and tau is a -parameter physically related to the viscosity. On a technical note, -we have implemented a 15 velocity model (D3Q15) as default; however, -the user can switch to a 19 velocity model (D3Q19) through the use of -the {D3Q19} keyword. This fix provides the user with the choice of -two algorithms to solve this equation, through the specification of -the keyword {LBtype}. If {LBtype} is set equal to 1, the standard -finite difference LB integrator is used. If {LBtype} is set equal to -2, the algorithm of "Ollila et al."_#Ollila is used. - -Physical variables are then defined in terms of moments of the distribution -functions, - -:c,image(Eqs/fix_lb_fluid_properties.jpg) - -Full details of the lattice-Boltzmann algorithm used can be found in -"Mackay et al."_#fluid-Mackay. - -The fluid is coupled to the MD particles described by {group-ID} -through a velocity dependent force. The contribution to the fluid -force on a given lattice mesh site j due to MD particle alpha is -calculated as: - -:c,image(Eqs/fix_lb_fluid_fluidforce.jpg) - -where v_n is the velocity of the MD particle, u_f is the fluid -velocity interpolated to the particle location, and gamma is the force -coupling constant. Zeta is a weight assigned to the grid point, -obtained by distributing the particle to the nearest lattice sites. -For this, the user has the choice between a trilinear stencil, which -provides a support of 8 lattice sites, or the immersed boundary method -Peskin stencil, which provides a support of 64 lattice sites. While -the Peskin stencil is seen to provide more stable results, the -trilinear stencil may be better suited for simulation of objects close -to walls, due to its smaller support. Therefore, by default, the -Peskin stencil is used; however the user may switch to the trilinear -stencil by specifying the keyword, {trilinear}. - -By default, the force coupling constant, gamma, is calculated according to - -:c,image(Eqs/fix_lb_fluid_gammadefault.jpg). - -Here, m_v is the mass of the MD particle, m_u is a representative -fluid mass at the particle location, and dt_collision is a collision -time, chosen such that tau/dt_collision = 1 (see "Mackay and -Denniston"_#Mackay2 for full details). In order to calculate m_u, the -fluid density is interpolated to the MD particle location, and -multiplied by a volume, node_area*dx_lb, where node_area represents -the portion of the surface area of the composite object associated -with a given MD particle. By default, node_area is set equal to -dx_lb*dx_lb; however specific values for given atom types can be set -using the {setArea} keyword. - -The user also has the option of specifying their own value for the -force coupling constant, for all the MD particles associated with the -fix, through the use of the {setGamma} keyword. This may be useful -when modelling porous particles. See "Mackay et al."_#fluid-Mackay for a -detailed description of the method by which the user can choose an -appropriate gamma value. - -NOTE: while this fix applies the force of the particles on the fluid, -it does not apply the force of the fluid to the particles. When the -force coupling constant is set using the default method, there is only -one option to include this hydrodynamic force on the particles, and -that is through the use of the "lb/viscous"_fix_lb_viscous.html fix. -This fix adds the hydrodynamic force to the total force acting on the -particles, after which any of the built-in LAMMPS integrators can be -used to integrate the particle motion. However, if the user specifies -their own value for the force coupling constant, as mentioned in -"Mackay et al."_#fluid-Mackay, the built-in LAMMPS integrators may prove to -be unstable. Therefore, we have included our own integrators "fix -lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html, and "fix -lb/pc"_fix_lb_pc.html, to solve for the particle motion in these -cases. These integrators should not be used with the -"lb/viscous"_fix_lb_viscous.html fix, as they add hydrodynamic forces -to the particles directly. In addition, they can not be used if the -force coupling constant has been set the default way. - -NOTE: if the force coupling constant is set using the default method, -and the "lb/viscous"_fix_lb_viscous.html fix is NOT used to add the -hydrodynamic force to the total force acting on the particles, this -physically corresponds to a situation in which an infinitely massive -particle is moving through the fluid (since collisions between the -particle and the fluid do not act to change the particle's velocity). -Therefore, the user should set the mass of the particle to be -significantly larger than the mass of the fluid at the particle -location, in order to approximate an infinitely massive particle (see -the dragforce test run for an example). - -:line - -Inside the fix, parameters are scaled by the lattice-Boltzmann -timestep, dt, grid spacing, dx, and mass unit, dm. dt is set equal to -(nevery*dt_MD), where dt_MD is the MD timestep. By default, dm is set -equal to 1.0, and dx is chosen so that tau/(dt) = -(3*eta*dt)/(rho*dx^2) is approximately equal to 1. However, the user -has the option of specifying their own values for dm, and dx, by using -the optional keywords {dm}, and {dx} respectively. - -NOTE: Care must be taken when choosing both a value for dx, and a -simulation domain size. This fix uses the same subdivision of the -simulation domain among processors as the main LAMMPS program. In -order to uniformly cover the simulation domain with lattice sites, the -lengths of the individual LAMMPS sub-domains must all be evenly -divisible by dx. If the simulation domain size is cubic, with equal -lengths in all dimensions, and the default value for dx is used, this -will automatically be satisfied. - -Physical parameters describing the fluid are specified through -{viscosity}, {density}, and {a0}. If the force coupling constant is -set the default way, the surface area associated with the MD particles -is specified using the {setArea} keyword. If the user chooses to -specify a value for the force coupling constant, this is set using the -{setGamma} keyword. These parameters should all be given in terms of -the mass, distance, and time units chosen for the main LAMMPS run, as -they are scaled by the LB timestep, lattice spacing, and mass unit, -inside the fix. - -:line - -The {setArea} keyword allows the user to associate a surface area with -a given atom type. For example if a spherical composite object of -radius R is represented as a spherical shell of N evenly distributed -MD particles, all of the same type, the surface area per particle -associated with that atom type should be set equal to 4*pi*R^2/N. -This keyword should only be used if the force coupling constant, -gamma, is set the default way. - -The {setGamma} keyword allows the user to specify their own value for -the force coupling constant, gamma, instead of using the default -value. - -The {scaleGamma} keyword should be used in conjunction with the -{setGamma} keyword, when the user wishes to specify different gamma -values for different atom types. This keyword allows the user to -scale the {setGamma} gamma value by a factor, gammaFactor, for a given -atom type. - -The {dx} keyword allows the user to specify a value for the LB grid -spacing. - -The {dm} keyword allows the user to specify the LB mass unit. - -If the {a0} keyword is used, the value specified is used for the -square of the speed of sound in the fluid. If this keyword is not -present, the speed of sound squared is set equal to (1/3)*(dx/dt)^2. -Setting a0 > (dx/dt)^2 is not allowed, as this may lead to -instabilities. - -If the {noise} keyword is used, followed by a positive temperature -value, and a positive integer random number seed, a thermal -lattice-Boltzmann algorithm is used. If {LBtype} is set equal to 1 -(i.e. the standard LB integrator is chosen), the thermal LB algorithm -of "Adhikari et al."_#Adhikari is used; however if {LBtype} is set -equal to 2 both the LB integrator, and thermal LB algorithm described -in "Ollila et al."_#Ollila are used. - -If the {calcforce} keyword is used, both the fluid force and torque -acting on the specified particle group are printed to the screen every -N timesteps. - -If the keyword {trilinear} is used, the trilinear stencil is used to -interpolate the particle nodes onto the fluid mesh. By default, the -immersed boundary method, Peskin stencil is used. Both of these -interpolation methods are described in "Mackay et al."_#fluid-Mackay. - -If the keyword {D3Q19} is used, the 19 velocity (D3Q19) lattice is -used by the lattice-Boltzmann algorithm. By default, the 15 velocity -(D3Q15) lattice is used. - -If the keyword {write_restart} is used, followed by a positive -integer, N, a binary restart file is printed every N LB timesteps. -This restart file only contains information about the fluid. -Therefore, a LAMMPS restart file should also be written in order to -print out full details of the simulation. - -NOTE: When a large number of lattice grid points are used, the restart -files may become quite large. - -In order to restart the fluid portion of the simulation, the keyword -{read_restart} is specified, followed by the name of the binary -lb_fluid restart file to be used. - -If the {zwall_velocity} keyword is used y-velocities are assigned to -the lower and upper walls. This keyword requires the presence of -walls in the z-direction. This is set by assigning fixed boundary -conditions in the z-direction. If fixed boundary conditions are -present in the z-direction, and this keyword is not used, the walls -are assumed to be stationary. - -If the {bodyforce} keyword is used, a constant body force is added to -the fluid, defined by it's x, y and z components. - -If the {printfluid} keyword is used, followed by a positive integer, N, -the fluid densities and velocities at each lattice site are printed to the -screen every N timesteps. - -:line - -For further details, as well as descriptions and results of several -test runs, see "Mackay et al."_#fluid-Mackay. Please include a citation to -this paper if the lb_fluid fix is used in work contributing to -published research. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -Due to the large size of the fluid data, this fix writes it's own -binary restart files, if requested, independent of the main LAMMPS -"binary restart files"_restart.html; no information about {lb_fluid} -is written to the main LAMMPS "binary restart files"_restart.html. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Howto_output.html. No parameter -of this fix can be used with the {start/stop} keywords of the -"run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix can only be used with an orthogonal simulation domain. - -Walls have only been implemented in the z-direction. Therefore, the -boundary conditions, as specified via the main LAMMPS boundary command -must be periodic for x and y, and either fixed or periodic for z. -Shrink-wrapped boundary conditions are not permitted with this fix. - -This fix must be used before any of "fix -lb/viscous"_fix_lb_viscous.html, "fix -lb/momentum"_fix_lb_momentum.html, "fix -lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html, and/ or "fix -lb/pc"_fix_lb_pc.html , as the fluid needs to be initialized before -any of these routines try to access its properties. In addition, in -order for the hydrodynamic forces to be added to the particles, this -fix must be used in conjunction with the -"lb/viscous"_fix_lb_viscous.html fix if the force coupling constant is -set by default, or either the "lb/viscous"_fix_lb_viscous.html fix or -one of the "lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html or -"lb/pc"_fix_lb_pc.html integrators, if the user chooses to specify -their own value for the force coupling constant. - -[Related commands:] - -"fix lb/viscous"_fix_lb_viscous.html, "fix -lb/momentum"_fix_lb_momentum.html, "fix -lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html, "fix -lb/pc"_fix_lb_pc.html - -[Default:] - -By default, the force coupling constant is set according to - -:c,image(Eqs/fix_lb_fluid_gammadefault.jpg) - -and an area of dx_lb^2 per node, used to calculate the fluid mass at -the particle node location, is assumed. - -dx is chosen such that tau/(delta t_LB) = -(3 eta dt_LB)/(rho dx_lb^2) is approximately equal to 1. -dm is set equal to 1.0. -a0 is set equal to (1/3)*(dx_lb/dt_lb)^2. -The Peskin stencil is used as the default interpolation method. -The D3Q15 lattice is used for the lattice-Boltzmann algorithm. -If walls are present, they are assumed to be stationary. - -:line - -:link(Ollila) -[(Ollila et al.)] Ollila, S.T.T., Denniston, C., Karttunen, M., and Ala-Nissila, T., Fluctuating lattice-Boltzmann model for complex fluids, J. Chem. Phys. 134 (2011) 064902. - -:link(fluid-Mackay) -[(Mackay et al.)] Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. - -:link(Mackay2) -[(Mackay and Denniston)] Mackay, F. E., and Denniston, C., Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces, J. Comput. Phys. 237 (2013) 289-298. - -:link(Adhikari) -[(Adhikari et al.)] Adhikari, R., Stratford, K., Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479. diff --git a/doc/txt/fix_lb_momentum.txt b/doc/txt/fix_lb_momentum.txt deleted file mode 100644 index 408978f64c..0000000000 --- a/doc/txt/fix_lb_momentum.txt +++ /dev/null @@ -1,73 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix lb/momentum command :h3 - -[Syntax:] - -fix ID group-ID lb/momentum nevery keyword values ... :pre - -ID, group-ID are documented in the "fix"_fix.html command :ulb,l -lb/momentum = style name of this fix command :l -nevery = adjust the momentum every this many timesteps :l -zero or more keyword/value pairs may be appended :l -keyword = {linear} :l - {linear} values = xflag yflag zflag - xflag,yflag,zflag = 0/1 to exclude/include each dimension. :pre -:ule - -[Examples:] - -fix 1 sphere lb/momentum -fix 1 all lb/momentum linear 1 1 0 :pre - -[Description:] - -This fix is based on the "fix momentum"_fix_momentum.html command, and -was created to be used in place of that command, when a -lattice-Boltzmann fluid is present. - -Zero the total linear momentum of the system, including both the atoms -specified by group-ID and the lattice-Boltzmann fluid every nevery -timesteps. This is accomplished by adjusting the particle velocities -and the fluid velocities at each lattice site. - -NOTE: This fix only considers the linear momentum of the system. - -By default, the subtraction is performed for each dimension. This can -be changed by specifying the keyword {linear}, along with a set of -three flags set to 0/1 in order to exclude/ include the corresponding -dimension. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -Can only be used if a lattice-Boltzmann fluid has been created via the -"fix lb/fluid"_fix_lb_fluid.html command, and must come after this -command. - -This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix momentum"_fix_momentum.html, "fix lb/fluid"_fix_lb_fluid.html - -[Default:] - -Zeros the total system linear momentum in each dimension. diff --git a/doc/txt/fix_lb_pc.txt b/doc/txt/fix_lb_pc.txt deleted file mode 100644 index 05b5eb20a2..0000000000 --- a/doc/txt/fix_lb_pc.txt +++ /dev/null @@ -1,62 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix lb/pc command :h3 - -[Syntax:] - -fix ID group-ID lb/pc :pre - -ID, group-ID are documented in the "fix"_fix.html command -lb/pc = style name of this fix command :ul - -[Examples:] - -fix 1 all lb/pc :pre - -[Description:] - -Update the positions and velocities of the individual particles -described by {group-ID}, experiencing velocity-dependent hydrodynamic -forces, using the integration algorithm described in "Mackay et -al."_#Mackay1. This integration algorithm should only be used if a -user-specified value for the force-coupling constant used in "fix -lb/fluid"_fix_lb_fluid.html has been set; do not use this integration -algorithm if the force coupling constant has been set by default. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Can only be used if a lattice-Boltzmann fluid has been created via the -"fix lb/fluid"_fix_lb_fluid.html command, and must come after this -command. - -[Related commands:] - -"fix lb/fluid"_fix_lb_fluid.html "fix -lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html - -[Default:] None. - -:line - -:link(Mackay1) -[(Mackay et al.)] Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. diff --git a/doc/txt/fix_lb_rigid_pc_sphere.txt b/doc/txt/fix_lb_rigid_pc_sphere.txt deleted file mode 100644 index ddaa552ecc..0000000000 --- a/doc/txt/fix_lb_rigid_pc_sphere.txt +++ /dev/null @@ -1,146 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix lb/rigid/pc/sphere command :h3 - -[Syntax:] - -fix ID group-ID lb/rigid/pc/sphere bodystyle args keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -lb/rigid/pc/sphere = style name of this fix command :l -bodystyle = {single} or {molecule} or {group} :l - {single} args = none - {molecule} args = none - {group} args = N groupID1 groupID2 ... - N = # of groups :pre -zero or more keyword/value pairs may be appended :l -keyword = {force} or {torque} or {innerNodes} :l - {force} values = M xflag yflag zflag - M = which rigid body from 1-Nbody (see asterisk form below) - xflag,yflag,zflag = off/on if component of center-of-mass force is active - {torque} values = M xflag yflag zflag - M = which rigid body from 1-Nbody (see asterisk form below) - xflag,yflag,zflag = off/on if component of center-of-mass torque is active - {innerNodes} values = innergroup-ID - innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid :pre -:ule - -[Examples:] - -fix 1 spheres lb/rigid/pc/sphere -fix 1 all lb/rigid/pc/sphere force 1 0 0 innerNodes ForceAtoms :pre - -[Description:] - -This fix is based on the "fix rigid"_fix_rigid.html command, and was -created to be used in place of that fix, to integrate the equations of -motion of spherical rigid bodies when a lattice-Boltzmann fluid is -present with a user-specified value of the force-coupling constant. -The fix uses the integration algorithm described in "Mackay et -al."_#Mackay to update the positions, velocities, and orientations of -a set of spherical rigid bodies experiencing velocity dependent -hydrodynamic forces. The spherical bodies are assumed to rotate as -solid, uniform density spheres, with moments of inertia calculated -using the combined sum of the masses of all the constituent particles -(which are assumed to be point particles). - -:line - -By default, all of the atoms that this fix acts on experience a -hydrodynamic force due to the presence of the lattice-Boltzmann fluid. -However, the {innerNodes} keyword allows the user to specify atoms -belonging to a rigid object which do not interact with the -lattice-Boltzmann fluid (i.e. these atoms do not feel a hydrodynamic -force from the lattice-Boltzmann fluid). This can be used to -distinguish between atoms on the surface of a non-porous object, and -those on the inside. - -This feature can be used, for example, when implementing a hard sphere -interaction between two spherical objects. Instead of interactions -occurring between the particles on the surfaces of the two spheres, it -is desirable simply to place an atom at the center of each sphere, -which does not contribute to the hydrodynamic force, and have these -central atoms interact with one another. - -:line - -Apart from the features described above, this fix is very similar to -the rigid fix (although it includes fewer optional arguments, and -assumes the constituent atoms are point particles); see -"fix rigid"_fix_rigid.html for a complete documentation. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about the {rigid} and {rigid/nve} fixes are written to -"binary restart files"_restart.html. - -Similar to the "fix rigid"_fix_rigid.html command: The rigid fix -computes a global scalar which can be accessed by various "output -commands"_Howto_output.html. The scalar value calculated by these -fixes is "intensive". The scalar is the current temperature of the -collection of rigid bodies. This is averaged over all rigid bodies -and their translational and rotational degrees of freedom. The -translational energy of a rigid body is 1/2 m v^2, where m = total -mass of the body and v = the velocity of its center of mass. The -rotational energy of a rigid body is 1/2 I w^2, where I = the moment -of inertia tensor of the body and w = its angular velocity. Degrees -of freedom constrained by the {force} and {torque} keywords are -removed from this calculation. - -All of these fixes compute a global array of values which can be -accessed by various "output commands"_Howto_output.html. The number -of rows in the array is equal to the number of rigid bodies. The -number of columns is 15. Thus for each rigid body, 15 values are -stored: the xyz coords of the center of mass (COM), the xyz components -of the COM velocity, the xyz components of the force acting on the -COM, the xyz components of the torque acting on the COM, and the xyz -image flags of the COM, which have the same meaning as image flags for -atom positions (see the "dump" command). The force and torque values -in the array are not affected by the {force} and {torque} keywords in -the fix rigid command; they reflect values before any changes are made -by those keywords. - -The ordering of the rigid bodies (by row in the array) is as follows. -For the {single} keyword there is just one rigid body. For the -{molecule} keyword, the bodies are ordered by ascending molecule ID. -For the {group} keyword, the list of group IDs determines the ordering -of bodies. - -The array values calculated by these fixes are "intensive", meaning -they are independent of the number of atoms in the simulation. - -No parameter of these fixes can be used with the {start/stop} keywords -of the "run"_run.html command. These fixes are not invoked during -"energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Can only be used if a lattice-Boltzmann fluid has been created via the -"fix lb/fluid"_fix_lb_fluid.html command, and must come after this -command. Should only be used if the force coupling constant used in -"fix lb/fluid"_fix_lb_fluid.html has been set by the user; this -integration fix cannot be used if the force coupling constant is set -by default. - -[Related commands:] - -"fix lb/fluid"_fix_lb_fluid.html, "fix lb/pc"_fix_lb_pc.html - -[Default:] - -The defaults are force * on on on, and torque * on on on. - -:line - -:link(Mackay) -[(Mackay et al.)] Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. diff --git a/doc/txt/fix_lb_viscous.txt b/doc/txt/fix_lb_viscous.txt deleted file mode 100644 index ba91a2cd54..0000000000 --- a/doc/txt/fix_lb_viscous.txt +++ /dev/null @@ -1,94 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix lb/viscous command :h3 - -[Syntax:] - -fix ID group-ID lb/viscous :pre - -ID, group-ID are documented in "fix"_fix.html command -lb/viscous = style name of this fix command :ul - -[Examples:] - -fix 1 flow lb/viscous - -[Description:] - -This fix is similar to the "fix viscous"_fix_viscous.html command, and -is to be used in place of that command when a lattice-Boltzmann fluid -is present, and the user wishes to integrate the particle motion using -one of the built in LAMMPS integrators. - -This fix adds a force, F = - Gamma*(velocity-fluid_velocity), to each -atom, where Gamma is the force coupling constant described in the "fix -lb/fluid"_fix_lb_fluid.html command (which applies an equal and -opposite force to the fluid). - -NOTE: This fix should only be used in conjunction with one of the -built in LAMMPS integrators; it should not be used with the "fix -lb/pc"_fix_lb_pc.html or "fix -lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html integrators, which -already include the hydrodynamic forces. These latter fixes should -only be used if the force coupling constant has been set by the user -(instead of using the default value); if the default force coupling -value is used, then this fix provides the only method for adding the -hydrodynamic forces to the particles. - -:line - -For further details, as well as descriptions and results of several -test runs, see "Mackay et al."_#Mackay3. Please include a citation to -this paper if this fix is used in work contributing to published -research. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -As described in the "fix viscous"_fix_viscous.html documentation: - -"No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. This fix should only -be used with damped dynamics minimizers that allow for -non-conservative forces. See the "min_style"_min_style.html command -for details." - -[Restrictions:] - -This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Can only be used if a lattice-Boltzmann fluid has been created via the -"fix lb/fluid"_fix_lb_fluid.html command, and must come after this -command. - -This fix should not be used if either the "fix lb/pc"_fix_lb_pc.html -or "fix lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html integrator is -used. - -[Related commands:] - -"fix lb/fluid"_fix_lb_fluid.html, "fix lb/pc"_fix_lb_pc.html, "fix -lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html - -[Default:] none - -:line - -:link(Mackay3) -[(Mackay et al.)] Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. diff --git a/doc/txt/fix_lineforce.txt b/doc/txt/fix_lineforce.txt deleted file mode 100644 index 3114ed6250..0000000000 --- a/doc/txt/fix_lineforce.txt +++ /dev/null @@ -1,51 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix lineforce command :h3 - -[Syntax:] - -fix ID group-ID lineforce x y z :pre - -ID, group-ID are documented in "fix"_fix.html command -lineforce = style name of this fix command -x y z = direction of line as a 3-vector :ul - -[Examples:] - -fix hold boundary lineforce 0.0 1.0 1.0 :pre - -[Description:] - -Adjust the forces on each atom in the group so that only the component -of force along the linear direction specified by the vector (x,y,z) -remains. This is done by subtracting out components of force in the -plane perpendicular to the line. - -If the initial velocity of the atom is 0.0 (or along the line), then -it should continue to move along the line thereafter. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -[Restrictions:] none - -[Related commands:] - -"fix planeforce"_fix_planeforce.html - -[Default:] none diff --git a/doc/txt/fix_manifoldforce.txt b/doc/txt/fix_manifoldforce.txt deleted file mode 100644 index a25b9f0b2e..0000000000 --- a/doc/txt/fix_manifoldforce.txt +++ /dev/null @@ -1,66 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix manifoldforce command :h3 - -[Syntax:] - -fix ID group-ID manifoldforce manifold manifold-args ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -manifold = name of the manifold :l -manifold-args = parameters for the manifold :l - -:ule - -[Examples:] - -fix constrain all manifoldforce sphere 5.0 - -[Description:] - -This fix subtracts each time step from the force the component along -the normal of the specified "manifold"_Howto_manifold.html. This can be -used in combination with "minimize"_minimize.html to remove overlap -between particles while keeping them (roughly) constrained to the -given manifold, e.g. to set up a run with "fix -nve/manifold/rattle"_fix_nve_manifold_rattle.html. I have found that -only {hftn} and {quickmin} with a very small time step perform -adequately though. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is invoked during "energy -minimization"_minimize.html. - -:line - -[Restrictions:] - -This fix is part of the USER-MANIFOLD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Only use this with {min_style hftn} or {min_style quickmin}. If not, -the constraints will not be satisfied very well at all. A warning is -generated if the {min_style} is incompatible but no error. - -:line - -[Related commands:] - -"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html, "fix -nvt/manifold/rattle"_fix_nvt_manifold_rattle.html - diff --git a/doc/txt/fix_meso.txt b/doc/txt/fix_meso.txt deleted file mode 100644 index 8c0ce5a9b7..0000000000 --- a/doc/txt/fix_meso.txt +++ /dev/null @@ -1,52 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix meso command :h3 - -[Syntax:] - -fix ID group-ID meso :pre - -ID, group-ID are documented in "fix"_fix.html command -meso = style name of this fix command :ul - -[Examples:] - -fix 1 all meso :pre - -[Description:] - -Perform time integration to update position, velocity, internal energy -and local density for atoms in the group each timestep. This fix is -needed to time-integrate mesoscopic systems where particles carry -internal variables such as SPH or DPDE. - -See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in -LAMMPS. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix meso/stationary" - -[Default:] none diff --git a/doc/txt/fix_meso_move.txt b/doc/txt/fix_meso_move.txt deleted file mode 100644 index abd6e0cca1..0000000000 --- a/doc/txt/fix_meso_move.txt +++ /dev/null @@ -1,233 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix meso/move command :h3 - -[Syntax:] - -fix ID group-ID meso/move style args keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -meso/move = style name of this fix command :l -style = {linear} or {wiggle} or {rotate} or {variable} :l - {linear} args = Vx Vy Vz - Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL - {wiggle} args = Ax Ay Az period - Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL - period = period of oscillation (time units) - {rotate} args = Px Py Pz Rx Ry Rz period - Px,Py,Pz = origin point of axis of rotation (distance units) - Rx,Ry,Rz = axis of rotation vector - period = period of rotation (time units) - {variable} args = v_dx v_dy v_dz v_vx v_vy v_vz - v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL - v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL :pre - -zero or more keyword/value pairs may be appended :l -keyword = {units} :l - {units} value = {box} or {lattice} :pre -:ule - -[Examples:] - -fix 1 boundary meso/move wiggle 3.0 0.0 0.0 1.0 units box -fix 2 boundary meso/move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0 -fix 2 boundary meso/move variable v_myx v_myy NULL v_VX v_VY NULL :pre - -[Description:] - -Perform updates of position, velocity, internal energy and local -density for mesoscopic particles in the group each timestep using the -specified settings or formulas, without regard to forces on the -particles. This can be useful for boundary, solid bodies or other -particles, whose movement can influence nearby particles. - -The operation of this fix is exactly like that described by the -"fix move"_fix_move.html command, except that particles' density, -internal energy and extrapolated velocity are also updated. - -NOTE: The particles affected by this fix should not be time integrated -by other fixes (e.g. "fix meso"_fix_meso.html, "fix -meso/stationary"_fix_meso_stationary.html), since that will change their -positions and velocities twice. - -NOTE: As particles move due to this fix, they will pass through periodic -boundaries and be remapped to the other side of the simulation box, -just as they would during normal time integration (e.g. via the "fix -meso"_fix_meso.html command). It is up to you to decide whether periodic -boundaries are appropriate with the kind of particle motion you are -prescribing with this fix. - -NOTE: As discussed below, particles are moved relative to their initial -position at the time the fix is specified. These initial coordinates -are stored by the fix in "unwrapped" form, by using the image flags -associated with each particle. See the "dump custom"_dump.html command -for a discussion of "unwrapped" coordinates. See the Atoms section of -the "read_data"_read_data.html command for a discussion of image flags -and how they are set for each particle. You can reset the image flags -(e.g. to 0) before invoking this fix by using the "set image"_set.html -command. - -:line - -The {linear} style moves particles at a constant velocity, so that their -position {X} = (x,y,z) as a function of time is given in vector -notation as - -X(t) = X0 + V * delta :pre - -where {X0} = (x0,y0,z0) is their position at the time the fix is -specified, {V} is the specified velocity vector with components -(Vx,Vy,Vz), and {delta} is the time elapsed since the fix was -specified. This style also sets the velocity of each particle to V = -(Vx,Vy,Vz). If any of the velocity components is specified as NULL, -then the position and velocity of that component is time integrated -the same as the "fix meso"_fix_meso.html command would perform, using -the corresponding force component on the particle. - -Note that the {linear} style is identical to using the {variable} -style with an "equal-style variable"_variable.html that uses the -vdisplace() function. E.g. - -variable V equal 10.0 -variable x equal vdisplace(0.0,$V) -fix 1 boundary move variable v_x NULL NULL v_V NULL NULL :pre - -The {wiggle} style moves particles in an oscillatory fashion, so that -their position {X} = (x,y,z) as a function of time is given in vector -notation as - -X(t) = X0 + A sin(omega*delta) :pre - -where {X0} = (x0,y0,z0) is their position at the time the fix is -specified, {A} is the specified amplitude vector with components -(Ax,Ay,Az), {omega} is 2 PI / {period}, and {delta} is the time -elapsed since the fix was specified. This style also sets the -velocity of each particle to the time derivative of this expression. -If any of the amplitude components is specified as NULL, then the -position and velocity of that component is time integrated the same as -the "fix meso"_fix_meso.html command would perform, using the -corresponding force component on the particle. - -Note that the {wiggle} style is identical to using the {variable} -style with "equal-style variables"_variable.html that use the -swiggle() and cwiggle() functions. E.g. - -variable A equal 10.0 -variable T equal 5.0 -variable omega equal 2.0*PI/$T -variable x equal swiggle(0.0,$A,$T) -variable v equal v_omega*($A-cwiggle(0.0,$A,$T)) -fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre - -The {rotate} style rotates particles around a rotation axis {R} = -(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz). The {period} of -the rotation is also specified. The direction of rotation for the -particles around the rotation axis is consistent with the right-hand -rule: if your right-hand thumb points along {R}, then your fingers wrap -around the axis in the direction of rotation. - -This style also sets the velocity of each particle to (omega cross -Rperp) where omega is its angular velocity around the rotation axis and -Rperp is a perpendicular vector from the rotation axis to the particle. - -The {variable} style allows the position and velocity components of -each particle to be set by formulas specified via the -"variable"_variable.html command. Each of the 6 variables is -specified as an argument to the fix as v_name, where name is the -variable name that is defined elsewhere in the input script. - -Each variable must be of either the {equal} or {atom} style. -{Equal}-style variables compute a single numeric quantity, that can be -a function of the timestep as well as of other simulation values. -{Atom}-style variables compute a numeric quantity for each particle, that -can be a function per-atom quantities, such as the particle's position, as -well as of the timestep and other simulation values. Note that this -fix stores the original coordinates of each particle (see note below) so -that per-atom quantity can be used in an atom-style variable formula. -See the "variable"_variable.html command for details. - -The first 3 variables (v_dx,v_dy,v_dz) specified for the {variable} -style are used to calculate a displacement from the particle's original -position at the time the fix was specified. The second 3 variables -(v_vx,v_vy,v_vz) specified are used to compute a velocity for each -particle. - -Any of the 6 variables can be specified as NULL. If both the -displacement and velocity variables for a particular x,y,z component -are specified as NULL, then the position and velocity of that -component is time integrated the same as the "fix meso"_fix_meso.html -command would perform, using the corresponding force component on the -particle. If only the velocity variable for a component is specified as -NULL, then the displacement variable will be used to set the position -of the particle, and its velocity component will not be changed. If only -the displacement variable for a component is specified as NULL, then -the velocity variable will be used to set the velocity of the particle, -and the position of the particle will be time integrated using that -velocity. - -The {units} keyword determines the meaning of the distance units used -to define the {linear} velocity and {wiggle} amplitude and {rotate} -origin. This setting is ignored for the {variable} style. A {box} -value selects standard units as defined by the "units"_units.html -command, e.g. velocity in Angstroms/fmsec and amplitude and position -in Angstroms for units = real. A {lattice} value means the velocity -units are in lattice spacings per time and the amplitude and position -are in lattice spacings. The "lattice"_lattice.html command must have -been previously used to define the lattice spacing. Each of these 3 -quantities may be dependent on the x,y,z dimension, since the lattice -spacings can be different in x,y,z. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the original coordinates of moving particles to "binary -restart files"_restart.html, as well as the initial timestep, so that -the motion can be continuous in a restarted simulation. See the -"read_restart"_read_restart.html command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. - -NOTE: Because the move positions are a function of the current -timestep and the initial timestep, you cannot reset the timestep to a -different value after reading a restart file, if you expect a fix move -command to work in an uninterrupted fashion. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. - -This fix produces a per-atom array which can be accessed by various -"output commands"_Howto_output.html. The number of columns for each -atom is 3, and the columns store the original unwrapped x,y,z coords -of each particle. The per-atom values can be accessed on any timestep. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-SDPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that atoms store density and internal energy as -defined by the "atom_style meso"_atom_style.html command. - -All particles in the group must be mesoscopic SPH/SDPD particles. - -[Related commands:] - -"fix move"_fix_move.html, "fix meso"_fix_meso.html, -"displace_atoms"_displace_atoms.html - -[Default:] - -The option default is units = lattice. diff --git a/doc/txt/fix_meso_stationary.txt b/doc/txt/fix_meso_stationary.txt deleted file mode 100644 index 1a546efec0..0000000000 --- a/doc/txt/fix_meso_stationary.txt +++ /dev/null @@ -1,53 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix meso/stationary command :h3 - -[Syntax:] - -fix ID group-ID meso/stationary :pre - -ID, group-ID are documented in "fix"_fix.html command -meso = style name of this fix command :ul - -[Examples:] - -fix 1 boundary meso/stationary :pre - -[Description:] - -Perform time integration to update internal energy and local density, -but not position or velocity for atoms in the group each timestep. -This fix is needed for SPH simulations to correctly time-integrate -fixed boundary particles which constrain a fluid to a given region in -space. - -See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in -LAMMPS. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-SPH package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix meso" - -[Default:] none diff --git a/doc/txt/fix_modify.txt b/doc/txt/fix_modify.txt deleted file mode 100644 index f7882c58f7..0000000000 --- a/doc/txt/fix_modify.txt +++ /dev/null @@ -1,157 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix_modify command :h3 - -[Syntax:] - -fix_modify fix-ID keyword value ... :pre - -fix-ID = ID of the fix to modify :ulb,l -one or more keyword/value pairs may be appended :l -keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} or {bodyforces} :l - {temp} value = compute ID that calculates a temperature - {press} value = compute ID that calculates a pressure - {energy} value = {yes} or {no} - {virial} value = {yes} or {no} - {respa} value = {1} to {max respa level} or {0} (for outermost level) - {dynamic/dof} value = {yes} or {no} - yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature - {bodyforces} value = {early} or {late} - early/late = compute rigid-body forces/torques early or late in the timestep :pre -:ule - -[Examples:] - -fix_modify 3 temp myTemp press myPress -fix_modify 1 energy yes -fix_modify tether respa 2 :pre - -[Description:] - -Modify one or more parameters of a previously defined fix. Only -specific fix styles support specific parameters. See the doc pages -for individual fix commands for info on which ones support which -fix_modify parameters. - -The {temp} keyword is used to determine how a fix computes -temperature. The specified compute ID must have been previously -defined by the user via the "compute"_compute.html command and it must -be a style of compute that calculates a temperature. All fixes that -compute temperatures define their own compute by default, as described -in their documentation. Thus this option allows the user to override -the default method for computing T. - -The {press} keyword is used to determine how a fix computes pressure. -The specified compute ID must have been previously defined by the user -via the "compute"_compute.html command and it must be a style of -compute that calculates a pressure. All fixes that compute pressures -define their own compute by default, as described in their -documentation. Thus this option allows the user to override the -default method for computing P. - -The {energy} keyword can be used with fixes that support it. -{energy yes} adds a contribution to the potential energy of the -system. The fix's global and per-atom -energy is included in the calculation performed by the "compute -pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html -commands. See the "thermo_style"_thermo_style.html command for info -on how potential energy is output. For fixes that tally a global -energy, it can be printed by using the keyword f_ID in the -thermo_style custom command, where ID is the fix-ID of the appropriate -fix. - -NOTE: You must also specify the {energy yes} setting for a fix if you -are using it when performing an "energy minimization"_minimize.html -and if you want the energy and forces it produces to be part of the -optimization criteria. - -The {virial} keyword can be used with fixes that support it. -{virial yes} adds a contribution to the virial of the -system. The fix's global and per-atom -virial is included in the calculation performed by the "compute -pressure"_compute_pressure.html or -"compute stress/atom"_compute_stress_atom.html -commands. See the "thermo_style"_thermo_style.html command for info -on how pressure is output. - -NOTE: You must specify the {virial yes} setting for a fix if you -are doing "box relaxation"_fix_box_relax.html and -if you want virial contribution of the fix to be part of the -relaxation criteria, although this seems unlikely. - -NOTE: This option is only supported by fixes that explicitly say -so. For some of these (e.g. the "fix shake"_fix_shake.html command) -the default setting is {virial yes}, for others it is {virial no}. - -For fixes that set or modify forces, it may be possible to select at -which "r-RESPA"_run_style.html level the fix operates via the {respa} -keyword. The RESPA level at which the fix is active can be selected. -This is a number ranging from 1 to the number of levels. If the RESPA -level is larger than the current maximum, the outermost level will be -used, which is also the default setting. This default can be restored -using a value of {0} for the RESPA level. The affected fix has to be -enabled to support this feature; if not, {fix_modify} will report an -error. Active fixes with a custom RESPA level setting are reported -with their specified level at the beginning of a r-RESPA run. - -The {dynamic/dof} keyword determines whether the number of atoms N in -the fix group and their associated degrees of freedom are re-computed -each time a temperature is computed. Only fix styles that calculate -their own internal temperature use this option. Currently this is -only the "fix rigid/nvt/small"_fix_rigid.html and "fix -rigid/npt/small"_fix_rigid.html commands for the purpose of -thermostatting rigid body translation and rotation. By default, N and -their DOF are assumed to be constant. If you are adding atoms or -molecules to the system (see the "fix pour"_fix_pour.html, "fix -deposit"_fix_deposit.html, and "fix gcmc"_fix_gcmc.html commands) or -expect atoms or molecules to be lost (e.g. due to exiting the -simulation box or via "fix evaporate"_fix_evaporate.html), then -this option should be used to insure the temperature is correctly -normalized. - -NOTE: Other thermostatting fixes, such as "fix nvt"_fix_nh.html, do -not use the {dynamic/dof} keyword because they use a temperature -compute to calculate temperature. See the "compute_modify -dynamic/dof"_compute_modify.html command for a similar way to insure -correct temperature normalization for those thermostats. - -The {bodyforces} keyword determines whether the forces and torques -acting on rigid bodies are computed {early} at the post-force stage of -each timestep (right after per-atom forces have been computed and -communicated among processors), or {late} at the final-integrate stage -of each timestep (after any other fixes have finished their post-force -tasks). Only the rigid-body integration fixes use this option, which -includes "fix rigid"_fix_rigid.html and "fix -rigid/small"_fix_rigid.html, and their variants, and also "fix -poems"_fix_poems.html. - -The default is {late}. If there are other fixes that add forces to -individual atoms, then the rigid-body constraints will include these -forces when time-integrating the rigid bodies. If {early} is -specified, then new fixes can be written that use or modify the -per-body force and torque, before time-integration of the rigid bodies -occurs. Note however this has the side effect, that fixes such as -"fix addforce"_fix_addforce.html, "fix setforce"_fix_setforce.html, -"fix spring"_fix_spring.html, which add forces to individual atoms -will have no effect on the motion of the rigid bodies if they are -specified in the input script after the fix rigid command. LAMMPS -will give a warning if that is the case. - -[Restrictions:] none - -[Related commands:] - -"fix"_fix.html, "compute temp"_compute_temp.html, "compute -pressure"_compute_pressure.html, "thermo_style"_thermo_style.html - -[Default:] - -The option defaults are temp = ID defined by fix, press = ID defined -by fix, energy = no, virial = different for each fix style, respa = 0, -bodyforce = late. diff --git a/doc/txt/fix_momentum.txt b/doc/txt/fix_momentum.txt deleted file mode 100644 index aeedad0719..0000000000 --- a/doc/txt/fix_momentum.txt +++ /dev/null @@ -1,97 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix momentum command :h3 -fix momentum/kk command :h3 - -[Syntax:] - -fix ID group-ID momentum N keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -momentum = style name of this fix command :l -N = adjust the momentum every this many timesteps -one or more keyword/value pairs may be appended :l -keyword = {linear} or {angular} or {rescale} :l - {linear} values = xflag yflag zflag - xflag,yflag,zflag = 0/1 to exclude/include each dimension - {angular} values = none :pre - {rescale} values = none :pre -:ule - -[Examples:] - -fix 1 all momentum 1 linear 1 1 0 -fix 1 all momentum 1 linear 1 1 1 rescale -fix 1 all momentum 100 linear 1 1 1 angular :pre - -[Description:] - -Zero the linear and/or angular momentum of the group of atoms every N -timesteps by adjusting the velocities of the atoms. One (or both) of -the {linear} or {angular} keywords must be specified. - -If the {linear} keyword is used, the linear momentum is zeroed by -subtracting the center-of-mass velocity of the group from each atom. -This does not change the relative velocity of any pair of atoms. One -or more dimensions can be excluded from this operation by setting the -corresponding flag to 0. - -If the {angular} keyword is used, the angular momentum is zeroed by -subtracting a rotational component from each atom. - -This command can be used to insure the entire collection of atoms (or -a subset of them) does not drift or rotate during the simulation due -to random perturbations (e.g. "fix langevin"_fix_langevin.html -thermostatting). - -The {rescale} keyword enables conserving the kinetic energy of the group -of atoms by rescaling the velocities after the momentum was removed. - -Note that the "velocity"_velocity.html command can be used to create -initial velocities with zero aggregate linear and/or angular momentum. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix recenter"_fix_recenter.html, "velocity"_velocity.html - -[Default:] none diff --git a/doc/txt/fix_move.txt b/doc/txt/fix_move.txt deleted file mode 100644 index b8ccfbebfe..0000000000 --- a/doc/txt/fix_move.txt +++ /dev/null @@ -1,225 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix move command :h3 - -[Syntax:] - -fix ID group-ID move style args keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -move = style name of this fix command :l -style = {linear} or {wiggle} or {rotate} or {variable} :l - {linear} args = Vx Vy Vz - Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL - {wiggle} args = Ax Ay Az period - Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL - period = period of oscillation (time units) - {rotate} args = Px Py Pz Rx Ry Rz period - Px,Py,Pz = origin point of axis of rotation (distance units) - Rx,Ry,Rz = axis of rotation vector - period = period of rotation (time units) - {variable} args = v_dx v_dy v_dz v_vx v_vy v_vz - v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL - v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL :pre - -zero or more keyword/value pairs may be appended :l -keyword = {units} :l - {units} value = {box} or {lattice} :pre -:ule - -[Examples:] - -fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box -fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0 -fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL :pre - -[Description:] - -Perform updates of position and velocity for atoms in the group each -timestep using the specified settings or formulas, without regard to -forces on the atoms. This can be useful for boundary or other atoms, -whose movement can influence nearby atoms. - -NOTE: The atoms affected by this fix should not normally be time -integrated by other fixes (e.g. "fix nve"_fix_nve.html, "fix -nvt"_fix_nh.html), since that will change their positions and -velocities twice. - -NOTE: As atoms move due to this fix, they will pass through periodic -boundaries and be remapped to the other side of the simulation box, -just as they would during normal time integration (e.g. via the "fix -nve"_fix_nve.html command). It is up to you to decide whether -periodic boundaries are appropriate with the kind of atom motion you -are prescribing with this fix. - -NOTE: As discussed below, atoms are moved relative to their initial -position at the time the fix is specified. These initial coordinates -are stored by the fix in "unwrapped" form, by using the image flags -associated with each atom. See the "dump custom"_dump.html command -for a discussion of "unwrapped" coordinates. See the Atoms section of -the "read_data"_read_data.html command for a discussion of image flags -and how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this fix by using the "set image"_set.html -command. - -:line - -The {linear} style moves atoms at a constant velocity, so that their -position {X} = (x,y,z) as a function of time is given in vector -notation as - -X(t) = X0 + V * delta :pre - -where {X0} = (x0,y0,z0) is their position at the time the fix is -specified, {V} is the specified velocity vector with components -(Vx,Vy,Vz), and {delta} is the time elapsed since the fix was -specified. This style also sets the velocity of each atom to V = -(Vx,Vy,Vz). If any of the velocity components is specified as NULL, -then the position and velocity of that component is time integrated -the same as the "fix nve"_fix_nve.html command would perform, using -the corresponding force component on the atom. - -Note that the {linear} style is identical to using the {variable} -style with an "equal-style variable"_variable.html that uses the -vdisplace() function. E.g. - -variable V equal 10.0 -variable x equal vdisplace(0.0,$V) -fix 1 boundary move variable v_x NULL NULL v_V NULL NULL :pre - -The {wiggle} style moves atoms in an oscillatory fashion, so that -their position {X} = (x,y,z) as a function of time is given in vector -notation as - -X(t) = X0 + A sin(omega*delta) :pre - -where {X0} = (x0,y0,z0) is their position at the time the fix is -specified, {A} is the specified amplitude vector with components -(Ax,Ay,Az), {omega} is 2 PI / {period}, and {delta} is the time -elapsed since the fix was specified. This style also sets the -velocity of each atom to the time derivative of this expression. If -any of the amplitude components is specified as NULL, then the -position and velocity of that component is time integrated the same as -the "fix nve"_fix_nve.html command would perform, using the -corresponding force component on the atom. - -Note that the {wiggle} style is identical to using the {variable} -style with "equal-style variables"_variable.html that use the -swiggle() and cwiggle() functions. E.g. - -variable A equal 10.0 -variable T equal 5.0 -variable omega equal 2.0*PI/$T -variable x equal swiggle(0.0,$A,$T) -variable v equal v_omega*($A-cwiggle(0.0,$A,$T)) -fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre - -The {rotate} style rotates atoms around a rotation axis {R} = -(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz). The {period} of -the rotation is also specified. The direction of rotation for the -atoms around the rotation axis is consistent with the right-hand rule: -if your right-hand thumb points along {R}, then your fingers wrap -around the axis in the direction of rotation. - -This style also sets the velocity of each atom to (omega cross Rperp) -where omega is its angular velocity around the rotation axis and Rperp -is a perpendicular vector from the rotation axis to the atom. If the -defined "atom_style"_atom_style.html assigns an angular velocity or -angular momentum or orientation to each atom ("atom -styles"_atom_style.html sphere, ellipsoid, line, tri, body), then -those properties are also updated appropriately to correspond to the -atom's motion and rotation over time. - -The {variable} style allows the position and velocity components of -each atom to be set by formulas specified via the -"variable"_variable.html command. Each of the 6 variables is -specified as an argument to the fix as v_name, where name is the -variable name that is defined elsewhere in the input script. - -Each variable must be of either the {equal} or {atom} style. -{Equal}-style variables compute a single numeric quantity, that can be -a function of the timestep as well as of other simulation values. -{Atom}-style variables compute a numeric quantity for each atom, that -can be a function per-atom quantities, such as the atom's position, as -well as of the timestep and other simulation values. Note that this -fix stores the original coordinates of each atom (see note below) so -that per-atom quantity can be used in an atom-style variable formula. -See the "variable"_variable.html command for details. - -The first 3 variables (v_dx,v_dy,v_dz) specified for the {variable} -style are used to calculate a displacement from the atom's original -position at the time the fix was specified. The second 3 variables -(v_vx,v_vy,v_vz) specified are used to compute a velocity for each -atom. - -Any of the 6 variables can be specified as NULL. If both the -displacement and velocity variables for a particular x,y,z component -are specified as NULL, then the position and velocity of that -component is time integrated the same as the "fix nve"_fix_nve.html -command would perform, using the corresponding force component on the -atom. If only the velocity variable for a component is specified as -NULL, then the displacement variable will be used to set the position -of the atom, and its velocity component will not be changed. If only -the displacement variable for a component is specified as NULL, then -the velocity variable will be used to set the velocity of the atom, -and the position of the atom will be time integrated using that -velocity. - -The {units} keyword determines the meaning of the distance units used -to define the {linear} velocity and {wiggle} amplitude and {rotate} -origin. This setting is ignored for the {variable} style. A {box} -value selects standard units as defined by the "units"_units.html -command, e.g. velocity in Angstroms/fmsec and amplitude and position -in Angstroms for units = real. A {lattice} value means the velocity -units are in lattice spacings per time and the amplitude and position -are in lattice spacings. The "lattice"_lattice.html command must have -been previously used to define the lattice spacing. Each of these 3 -quantities may be dependent on the x,y,z dimension, since the lattice -spacings can be different in x,y,z. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the original coordinates of moving atoms to "binary -restart files"_restart.html, as well as the initial timestep, so that -the motion can be continuous in a restarted simulation. See the -"read_restart"_read_restart.html command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. - -NOTE: Because the move positions are a function of the current -timestep and the initial timestep, you cannot reset the timestep to a -different value after reading a restart file, if you expect a fix move -command to work in an uninterrupted fashion. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. - -This fix produces a per-atom array which can be accessed by various -"output commands"_Howto_output.html. The number of columns for each -atom is 3, and the columns store the original unwrapped x,y,z coords -of each atom. The per-atom values can be accessed on any timestep. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -For "rRESPA time integration"_run_style.html, this fix adjusts the -position and velocity of atoms on the outermost rRESPA level. - -[Restrictions:] none - -[Related commands:] - -"fix nve"_fix_nve.html, "displace_atoms"_displace_atoms.html - -[Default:] none - -The option default is units = lattice. diff --git a/doc/txt/fix_mscg.txt b/doc/txt/fix_mscg.txt deleted file mode 100644 index 1ad7804127..0000000000 --- a/doc/txt/fix_mscg.txt +++ /dev/null @@ -1,130 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix mscg command :h3 - -[Syntax:] - -fix ID group-ID mscg N keyword args ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -mscg = style name of this fix command :l -N = envoke this fix every this many timesteps :l -zero or more keyword/value pairs may be appended :l -keyword = {range} or {name} or {max} :l - {range} arg = {on} or {off} - {on} = range finding functionality is performed - {off} = force matching functionality is performed - {name} args = name1 ... nameN - name1,...,nameN = string names for each atom type (1-Ntype) - {max} args = maxb maxa maxd - maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom :pre -:ule - -[Examples:] - -fix 1 all mscg 1 -fix 1 all mscg 1 range name A B -fix 1 all mscg 1 max 4 8 20 :pre - -[Description:] - -This fix applies the Multi-Scale Coarse-Graining (MSCG) method to -snapshots from a dump file to generate potentials for coarse-grained -simulations from all-atom simulations, using a force-matching -technique ("Izvekov"_#Izvekov, "Noid"_#Noid). - -It makes use of the MS-CG library, written and maintained by Greg -Voth's group at the University of Chicago, which is freely available -on their "MS-CG GitHub -site"_https://github.com/uchicago-voth/MSCG-release. See instructions -on obtaining and installing the MS-CG library in the src/MSCG/README -file, which must be done before you build LAMMPS with this fix command -and use the command in a LAMMPS input script. - -An example script using this fix is provided the examples/mscg -directory. - -The general workflow for using LAMMPS in conjunction with the MS-CG -library to create a coarse-grained model and run coarse-grained -simulations is as follows: - -Perform all-atom simulations on the system to be coarse grained. -Generate a trajectory mapped to the coarse-grained model. -Create input files for the MS-CG library. -Run the range finder functionality of the MS-CG library. -Run the force matching functionality of the MS-CG library. -Check the results of the force matching. -Run coarse-grained simulations using the new coarse-grained potentials. :ol - -This fix can perform the range finding and force matching steps 4 and -5 of the above workflow when used in conjunction with the -"rerun"_rerun.html command. It does not perform steps 1-3 and 6-7. - -Step 2 can be performed using a Python script (what is the name?) -provided with the MS-CG library which defines the coarse-grained model -and converts a standard LAMMPS dump file for an all-atom simulation -(step 1) into a LAMMPS dump file which has the positions of and forces -on the coarse-grained beads. - -In step 3, an input file named "control.in" is needed by the MS-CG -library which sets parameters for the range finding and force matching -functionalities. See the examples/mscg/control.in file as an example. -And see the documentation provided with the MS-CG library for more -info on this file. - -When this fix is used to perform steps 4 and 5, the MS-CG library also -produces additional output files. The range finder functionality -(step 4) outputs files defining pair and bonded interaction ranges. -The force matching functionality (step 5) outputs tabulated force -files for every interaction in the system. Other diagnostic files can -also be output depending on the parameters in the MS-CG library input -script. Again, see the documentation provided with the MS-CG library -for more info. - -:line - -The {range} keyword specifies which MS-CG library functionality should -be invoked. If {on}, the step 4 range finder functionality is invoked. -{off}, the step 5 force matching functionality is invoked. - -If the {name} keyword is used, string names are defined to associate -with the integer atom types in LAMMPS. {Ntype} names must be -provided, one for each atom type (1-Ntype). - -The {max} keyword specifies the maximum number of bonds, angles, and -dihedrals a bead can have in the coarse-grained model. - -[Restrictions:] - -This fix is part of the MSCG package. It is only enabled if LAMMPS was -built with that package. See the "Build package"_Build_package.html -doc page for more info. - -The MS-CG library uses C++11, which may not be supported by older -compilers. The MS-CG library also has some additional numeric library -dependencies, which are described in its documentation. - -Currently, the MS-CG library is not setup to run in parallel with MPI, -so this fix can only be used in a serial LAMMPS build and run -on a single processor. - -[Related commands:] none - -[Default:] - -The default keyword settings are range off, max 4 12 36. - -:line - -:link(Izvekov) -[(Izvekov)] Izvekov, Voth, J Chem Phys 123, 134105 (2005). - -:link(Noid) -[(Noid)] Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J -Chem Phys 128, 134105 (2008). diff --git a/doc/txt/fix_msst.txt b/doc/txt/fix_msst.txt deleted file mode 100644 index a46e79c5b0..0000000000 --- a/doc/txt/fix_msst.txt +++ /dev/null @@ -1,193 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix msst command :h3 - -[Syntax:] - -fix ID group-ID msst dir shockvel keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -msst = style name of this fix :l -dir = {x} or {y} or {z} :l -shockvel = shock velocity (strictly positive, distance/time units) :l -zero or more keyword value pairs may be appended :l -keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} or {beta} or {dftb} :l - {q} value = cell mass-like parameter (mass^2/distance^4 units) - {mu} value = artificial viscosity (mass/length/time units) - {p0} value = initial pressure in the shock equations (pressure units) - {v0} value = initial simulation cell volume in the shock equations (distance^3 units) - {e0} value = initial total energy (energy units) - {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) - {dftb} value = {yes} or {no} for whether using MSST in conjunction with DFTB+ - {beta} value = scale factor for improved energy conservation :pre -:ule - -[Examples:] - -fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5 -fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4 v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01 -fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5 dftb yes beta 0.5 :pre - -[Description:] - -This command performs the Multi-Scale Shock Technique (MSST) -integration to update positions and velocities each timestep to mimic -a compressive shock wave passing over the system. See "(Reed)"_#Reed -for a detailed description of this method. The MSST varies the cell -volume and temperature in such a way as to restrain the system to the -shock Hugoniot and the Rayleigh line. These restraints correspond to -the macroscopic conservation laws dictated by a shock -front. {shockvel} determines the steady shock velocity that will be -simulated. - -To perform a simulation, choose a value of {q} that provides volume -compression on the timescale of 100 fs to 1 ps. If the volume is not -compressing, either the shock speed is chosen to be below the material -sound speed or {p0} has been chosen inaccurately. Volume compression -at the start can be sped up by using a non-zero value of {tscale}. Use -the smallest value of {tscale} that results in compression. - -Under some special high-symmetry conditions, the pressure (volume) -and/or temperature of the system may oscillate for many cycles even -with an appropriate choice of mass-like parameter {q}. Such -oscillations have physical significance in some cases. The optional -{mu} keyword adds an artificial viscosity that helps break the system -symmetry to equilibrate to the shock Hugoniot and Rayleigh line more -rapidly in such cases. - -The keyword {tscale} is a factor between 0 and 1 that determines what -fraction of thermal kinetic energy is converted to compressive strain -kinetic energy at the start of the simulation. Setting this parameter -to a non-zero value may assist in compression at the start of -simulations where it is slow to occur. - -If keywords {e0}, {p0},or {v0} are not supplied, these quantities will -be calculated on the first step, after the energy specified by -{tscale} is removed. The value of {e0} is not used in the dynamical -equations, but is used in calculating the deviation from the Hugoniot. - -The keyword {beta} is a scaling term that can be added to the MSST -ionic equations of motion to account for drift in the conserved -quantity during long timescale simulations, similar to a Berendsen -thermostat. See "(Reed)"_#Reed and "(Goldman)"_#Goldman2 for more -details. The value of {beta} must be between 0.0 and 1.0 inclusive. -A value of 0.0 means no contribution, a value of 1.0 means a full -contribution. - -Values of shockvel less than a critical value determined by the -material response will not have compressive solutions. This will be -reflected in lack of significant change of the volume in the MSST. - -For all pressure styles, the simulation box stays orthogonal in shape. -Parrinello-Rahman boundary conditions (tilted box) are supported by -LAMMPS, but are not implemented for MSST. - -This fix computes a temperature and pressure and potential energy each -timestep. To do this, the fix creates its own computes of style "temp" -"pressure", and "pe", as if these commands had been issued: - -compute fix-ID_MSST_temp all temp -compute fix-ID_MSST_press all pressure fix-ID_MSST_temp :pre -compute fix-ID_MSST_pe all pe :pre - -See the "compute temp"_compute_temp.html and "compute -pressure"_compute_pressure.html commands for details. Note that the -IDs of the new computes are the fix-ID + "_MSST_temp" or "_MSST_press" -or "_MSST_pe". The group for the new computes is "all". - -:line - -The {dftb} keyword is to allow this fix to be used when LAMMPS is -being driven by DFTB+, a density-functional tight-binding code. If the -keyword {dftb} is used with a value of {yes}, then the MSST equations -are altered to account for the electron entropy contribution to the -Hugonio relations and total energy. See "(Reed2)"_#Reed2 and -"(Goldman)"_#Goldman2 for details on this contribution. In this case, -you must define a "fix external"_fix_external.html command in your -input script, which is used to callback to DFTB+ during the LAMMPS -timestepping. DFTB+ will communicate its info to LAMMPS via that fix. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of all internal variables to "binary restart -files"_restart.html. See the "read_restart"_read_restart.html command -for info on how to re-specify a fix in an input script that reads a -restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -The progress of the MSST can be monitored by printing the global -scalar and global vector quantities computed by the fix. - -The scalar is the cumulative energy change due to the fix. This is -also the energy added to the potential energy by the -"fix_modify"_fix_modify.html {energy} command. With this command, the -thermo keyword {etotal} prints the conserved quantity of the MSST -dynamic equations. This can be used to test if the MD timestep is -sufficiently small for accurate integration of the dynamic -equations. See also "thermo_style"_thermo_style.html command. - -The global vector contains four values in this order: - -\[{dhugoniot}, {drayleigh}, {lagrangian_speed}, {lagrangian_position}\] - -{dhugoniot} is the departure from the Hugoniot (temperature units). -{drayleigh} is the departure from the Rayleigh line (pressure units). -{lagrangian_speed} is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units). -{lagrangian_position} is the computational cell position in the reference frame moving at the shock speed. This is usually a good estimate of distance of the computational cell behind the shock front. :ol - -To print these quantities to the log file with descriptive column -headers, the following LAMMPS commands are suggested: - -fix msst all msst z -fix_modify msst energy yes -variable dhug equal f_msst\[1\] -variable dray equal f_msst\[2\] -variable lgr_vel equal f_msst\[3\] -variable lgr_pos equal f_msst\[4\] -thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst :pre - -These fixes compute a global scalar and a global vector of 4 -quantities, which can be accessed by various "output -commands"_Howto_output.html. The scalar values calculated by this fix -are "extensive"; the vector values are "intensive". - -[Restrictions:] - -This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -All cell dimensions must be periodic. This fix can not be used with a -triclinic cell. The MSST fix has been tested only for the group-ID -all. - -[Related commands:] - -"fix nphug"_fix_nphug.html, "fix deform"_fix_deform.html - -[Default:] - -The keyword defaults are q = 10, mu = 0, tscale = 0.01, dftb = no, -beta = 0.0. Note that p0, v0, and e0 are calculated on the first -timestep. - -:line - -:link(Reed) -[(Reed)] Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 -(2003). - -:link(Reed2) -[(Reed2)] Reed, J. Phys. Chem. C, 116, 2205 (2012). - -:link(Goldman2) -[(Goldman)] Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner, -J. Phys. Chem. C, 117, 7885 (2013). diff --git a/doc/txt/fix_mvv_dpd.txt b/doc/txt/fix_mvv_dpd.txt deleted file mode 100644 index 507f271469..0000000000 --- a/doc/txt/fix_mvv_dpd.txt +++ /dev/null @@ -1,97 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix mvv/dpd command :h3 -fix mvv/edpd command :h3 -fix mvv/tdpd command :h3 - -[Syntax:] - -fix ID group-ID mvv/dpd lambda :pre -fix ID group-ID mvv/edpd lambda :pre -fix ID group-ID mvv/tdpd lambda :pre - -ID, group-ID are documented in "fix"_fix.html command -mvv/dpd, mvv/edpd, mvv/tdpd = style name of this fix command -lambda = (optional) relaxation parameter (unitless) :ul - -[Examples:] - -fix 1 all mvv/dpd -fix 1 all mvv/dpd 0.5 -fix 1 all mvv/edpd -fix 1 all mvv/edpd 0.5 -fix 1 all mvv/tdpd -fix 1 all mvv/tdpd 0.5 :pre - -[Description:] - -Perform time integration using the modified velocity-Verlet (MVV) -algorithm to update position and velocity (fix mvv/dpd), or position, -velocity and temperature (fix mvv/edpd), or position, velocity and -concentration (fix mvv/tdpd) for particles in the group each timestep. - -The modified velocity-Verlet (MVV) algorithm aims to improve the -stability of the time integrator by using an extrapolated version of -the velocity for the force evaluation: - -:c,image(Eqs/fix_mvv_dpd.jpg) - -where the parameter λ depends on the -specific choice of DPD parameters, and needs to be tuned on a -case-by-case basis. Specification of a {lambda} value is optional. -If specified, the setting must be from 0.0 to 1.0. If not specified, -a default value of 0.5 is used, which effectively reproduces the -standard velocity-Verlet (VV) scheme. For more details, see -"Groot"_#Groot2. - -Fix {mvv/dpd} updates the position and velocity of each atom. It can -be used with the "pair_style mdpd"_pair_meso.html command or other -pair styles such as "pair dpd"_pair_dpd.html. - -Fix {mvv/edpd} updates the per-atom temperature, in addition to -position and velocity, and must be used with the "pair_style -edpd"_pair_meso.html command. - -Fix {mvv/tdpd} updates the per-atom chemical concentration, in -addition to position and velocity, and must be used with the -"pair_style tdpd"_pair_meso.html command. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-MESO package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_style mdpd"_pair_meso.html, "pair_style edpd"_pair_meso.html, -"pair_style tdpd"_pair_meso.html - -[Default:] - -The default value for the optional {lambda} parameter is 0.5. - -:line - -:link(Groot2) -[(Groot)] Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI: -10.1063/1.474784 - diff --git a/doc/txt/fix_neb.txt b/doc/txt/fix_neb.txt deleted file mode 100644 index 87292bb5cd..0000000000 --- a/doc/txt/fix_neb.txt +++ /dev/null @@ -1,237 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix neb command :h3 - -[Syntax:] - -fix ID group-ID neb Kspring keyword value :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -neb = style name of this fix command :l -Kspring = spring constant for parallel nudging force (force/distance units or force units, see parallel keyword) :l -zero or more keyword/value pairs may be appended :l -keyword = {parallel} or {perp} or {end} :l - {parallel} value = {neigh} or {ideal} - {neigh} = parallel nudging force based on distance to neighbor replicas (Kspring = force/distance units) - {ideal} = parallel nudging force based on interpolated ideal position (Kspring = force units) - {perp} value = {Kspring2} - {Kspring2} = spring constant for perpendicular nudging force (force/distance units) - {end} values = estyle Kspring3 - {estyle} = {first} or {last} or {last/efirst} or {last/efirst/middle} - {first} = apply force to first replica - {last} = apply force to last replica - {last/efirst} = apply force to last replica and set its target energy to that of first replica - {last/efirst/middle} = same as {last/efirst} plus prevent middle replicas having lower energy than first replica - {Kspring3} = spring constant for target energy term (1/distance units) :pre,ule - -[Examples:] - -fix 1 active neb 10.0 -fix 2 all neb 1.0 perp 1.0 end last -fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0 -fix 1 all neb 1.0 parallel ideal end last/efirst 1 :pre - -[Description:] - -Add nudging forces to atoms in the group for a multi-replica -simulation run via the "neb"_neb.html command to perform a nudged -elastic band (NEB) calculation for finding the transition state. -Hi-level explanations of NEB are given with the "neb"_neb.html command -and on the "Howto replica"_Howto_replica.html doc page. The fix neb -command must be used with the "neb" command and defines how -inter-replica nudging forces are computed. A NEB calculation is -divided in two stages. In the first stage n replicas are relaxed -toward a MEP until convergence. In the second stage, the climbing -image scheme (see "(Henkelman2)"_#Henkelman2) is enabled, so that the -replica having the highest energy relaxes toward the saddle point -(i.e. the point of highest energy along the MEP), and a second -relaxation is performed. - -A key purpose of the nudging forces is to keep the replicas equally -spaced. During the NEB calculation, the 3N-length vector of -interatomic force Fi = -Grad(V) for each replica I is altered. For -all intermediate replicas (i.e. for 1 < I < N, except the climbing -replica) the force vector becomes: - -Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fnudge_perp :pre - -T' is the unit "tangent" vector for replica I and is a function of Ri, -Ri-1, Ri+1, and the potential energy of the 3 replicas; it points -roughly in the direction of (Ri+i - Ri-1); see the -"(Henkelman1)"_#Henkelman1 paper for details. Ri are the atomic -coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its -neighbor replicas. The term (Grad(V) dot T') is used to remove the -component of the gradient parallel to the path which would tend to -distribute the replica unevenly along the path. Fnudge_parallel is an -artificial nudging force which is applied only in the tangent -direction and which maintains the equal spacing between replicas (see -below for more information). Fnudge_perp is an optional artificial -spring which is applied in a direction perpendicular to the tangent -direction and which prevent the paths from forming acute kinks (see -below for more information). - -In the second stage of the NEB calculation, the interatomic force Fi -for the climbing replica (the replica of highest energy after the -first stage) is changed to: - -Fi = -Grad(V) + 2 (Grad(V) dot T') T' :pre - -and the relaxation procedure is continued to a new converged MEP. - -:line - -The keyword {parallel} specifies how the parallel nudging force is -computed. With a value of {neigh}, the parallel nudging force is -computed as in "(Henkelman1)"_#Henkelman1 by connecting each -intermediate replica with the previous and the next image: - -Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre - -Note that in this case the specified {Kspring} is in force/distance -units. - -With a value of {ideal}, the spring force is computed as suggested in -"(WeinanE)"_#WeinanE : - -Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre - -where RD is the "reaction coordinate" see "neb"_neb.html section, and -RDideal is the ideal RD for which all the images are equally spaced. -I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where -I is the replica number). The meanDist is the average distance -between replicas. Note that in this case the specified {Kspring} is -in force units. - -Note that the {ideal} form of nudging can often be more effective at -keeping the replicas equally spaced. - -:line - -The keyword {perp} specifies if and how a perpendicular nudging force -is computed. It adds a spring force perpendicular to the path in -order to prevent the path from becoming too strongly kinked. It can -significantly improve the convergence of the NEB calculation when the -resolution is poor. I.e. when few replicas are used; see -"(Maras)"_#Maras1 for details. - -The perpendicular spring force is given by - -Fnudge_perp = {Kspring2} * F(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre - -where {Kspring2} is the specified value. F(Ri-1 Ri R+1) is a smooth -scalar function of the angle Ri-1 Ri Ri+1. It is equal to 0.0 when -the path is straight and is equal to 1 when the angle Ri-1 Ri Ri+1 is -acute. F(Ri-1 Ri R+1) is defined in "(Jonsson)"_#Jonsson. - -If {Kspring2} is set to 0.0 (the default) then no perpendicular spring -force is added. - -:line - -By default, no additional forces act on the first and last replicas -during the NEB relaxation, so these replicas simply relax toward their -respective local minima. By using the key word {end}, additional -forces can be applied to the first and/or last replicas, to enable -them to relax toward a MEP while constraining their energy E to the -target energy ETarget. - -If ETarget>E, the interatomic force Fi for the specified replica becomes: - -Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)*Kspring3) T', {when} Grad(V) dot T' < 0 -Fi = -Grad(V) + (Grad(V) dot T' + (ETarget- E)*Kspring3) T', {when} Grad(V) dot T' > 0 -:pre - -The "spring" constant on the difference in energies is the specified -{Kspring3} value. - -When {estyle} is specified as {first}, the force is applied to the -first replica. When {estyle} is specified as {last}, the force is -applied to the last replica. Note that the {end} keyword can be used -twice to add forces to both the first and last replicas. - -For both these {estyle} settings, the target energy {ETarget} is set -to the initial energy of the replica (at the start of the NEB -calculation). - -If the {estyle} is specified as {last/efirst} or {last/efirst/middle}, -force is applied to the last replica, but the target energy {ETarget} -is continuously set to the energy of the first replica, as it evolves -during the NEB relaxation. - -The difference between these two {estyle} options is as follows. When -{estyle} is specified as {last/efirst}, no change is made to the -inter-replica force applied to the intermediate replicas (neither -first or last). If the initial path is too far from the MEP, an -intermediate replica may relax "faster" and reach a lower energy than -the last replica. In this case the intermediate replica will be -relaxing toward its own local minima. This behavior can be prevented -by specifying {estyle} as {last/efirst/middle} which will alter the -inter-replica force applied to intermediate replicas by removing the -contribution of the gradient to the inter-replica force. This will -only be done if a particular intermediate replica has a lower energy -than the first replica. This should effectively prevent the -intermediate replicas from over-relaxing. - -After converging a NEB calculation using an {estyle} of -{last/efirst/middle}, you should check that all intermediate replicas -have a larger energy than the first replica. If this is not the case, -the path is probably not a MEP. - -Finally, note that the last replica may never reach the target energy -if it is stuck in a local minima which has a larger energy than the -target energy. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -as invoked by the "minimize"_minimize.html command via the -"neb"_neb.html command. - -[Restrictions:] - -This command can only be used if LAMMPS was built with the REPLICA -package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"neb"_neb.html - -[Default:] - -The option defaults are parallel = neigh, perp = 0.0, ends is not -specified (no inter-replica force on the end replicas). - -:line - -:link(Henkelman1) -[(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000). - -:link(Henkelman2) -[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, -9901-9904 (2000). - -:link(WeinanE) -[(WeinanE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002). - -:link(Jonsson) -[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum -Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti, -and Coker World Scientific, Singapore, 1998, p 385. - -:link(Maras1) -[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, -Comp Phys Comm, 205, 13-21 (2016). diff --git a/doc/txt/fix_neb_spin.txt b/doc/txt/fix_neb_spin.txt deleted file mode 100644 index e62d297270..0000000000 --- a/doc/txt/fix_neb_spin.txt +++ /dev/null @@ -1,76 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix neb/spin command :h3 - -[Syntax:] - -fix ID group-ID neb/spin Kspring :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -neb/spin = style name of this fix command :l -Kspring = spring constant for parallel nudging force -(force/distance units or force units, see parallel keyword) :pre,ule - -[Examples:] - -fix 1 active neb/spin 1.0 - -[Description:] - -Add nudging forces to spins in the group for a multi-replica -simulation run via the "neb/spin"_neb_spin.html command to perform a -geodesic nudged elastic band (GNEB) calculation for finding the -transition state. -Hi-level explanations of GNEB are given with the -"neb/spin"_neb_spin.html command and on the -"Howto replica"_Howto_replica.html doc page. -The fix neb/spin command must be used with the "neb/spin" command and -defines how inter-replica nudging forces are computed. A GNEB -calculation is divided in two stages. In the first stage n replicas -are relaxed toward a MEP until convergence. In the second stage, the -climbing image scheme is enabled, so that the replica having the highest -energy relaxes toward the saddle point (i.e. the point of highest energy -along the MEP), and a second relaxation is performed. - -The nudging forces are calculated as explained in -"(BessarabB)"_#BessarabB). -See this reference for more explanation about their expression. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -as invoked by the "minimize"_minimize.html command via the -"neb/spin"_neb_spin.html command. - -[Restrictions:] - -This command can only be used if LAMMPS was built with the SPIN -package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"neb_spin"_neb_spin.html - -[Default:] - -none - -:line - -:link(BessarabB) -[(BessarabB)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, -335-347 (2015). diff --git a/doc/txt/fix_nh.txt b/doc/txt/fix_nh.txt deleted file mode 100644 index a07d4e7965..0000000000 --- a/doc/txt/fix_nh.txt +++ /dev/null @@ -1,651 +0,0 @@ -<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nvt command :h3 -fix nvt/intel command :h3 -fix nvt/kk command :h3 -fix nvt/omp command :h3 -fix npt command :h3 -fix npt/intel command :h3 -fix npt/kk command :h3 -fix npt/omp command :h3 -fix nph command :h3 -fix nph/kk command :h3 -fix nph/omp command :h3 - -[Syntax:] - -fix ID group-ID style_name keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -style_name = {nvt} or {npt} or {nph} :l -one or more keyword/value pairs may be appended :l -keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate} or {scalexy} or {scaleyz} or {scalexz} or {flip} or {fixedpoint} or {update} - {temp} values = Tstart Tstop Tdamp - Tstart,Tstop = external temperature at start/end of run - Tdamp = temperature damping parameter (time units) - {iso} or {aniso} or {tri} values = Pstart Pstop Pdamp - Pstart,Pstop = scalar external pressure at start/end of run (pressure units) - Pdamp = pressure damping parameter (time units) - {x} or {y} or {z} or {xy} or {yz} or {xz} values = Pstart Pstop Pdamp - Pstart,Pstop = external stress tensor component at start/end of run (pressure units) - Pdamp = stress damping parameter (time units) - {couple} = {none} or {xyz} or {xy} or {yz} or {xz} - {tchain} value = N - N = length of thermostat chain (1 = single thermostat) - {pchain} values = N - N length of thermostat chain on barostat (0 = no thermostat) - {mtk} value = {yes} or {no} = add in MTK adjustment term or not - {tloop} value = M - M = number of sub-cycles to perform on thermostat - {ploop} value = M - M = number of sub-cycles to perform on barostat thermostat - {nreset} value = reset reference cell every this many timesteps - {drag} value = Df - Df = drag factor added to barostat/thermostat (0.0 = no drag) - {dilate} value = dilate-group-ID - dilate-group-ID = only dilate atoms in this group due to barostat volume changes - {scalexy} value = {yes} or {no} = scale xy with ly - {scaleyz} value = {yes} or {no} = scale yz with lz - {scalexz} value = {yes} or {no} = scale xz with lz - {flip} value = {yes} or {no} = allow or disallow box flips when it becomes highly skewed - {fixedpoint} values = x y z - x,y,z = perform barostat dilation/contraction around this point (distance units) - {update} value = {dipole} or {dipole/dlm} - dipole = update dipole orientation (only for sphere variants) - dipole/dlm = use DLM integrator to update dipole orientation (only for sphere variants) :pre -:ule - -[Examples:] - -fix 1 all nvt temp 300.0 300.0 100.0 -fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 -fix 2 jello npt temp 300.0 300.0 100.0 tri 5.0 5.0 1000.0 -fix 2 ice nph x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 :pre - -[Description:] - -These commands perform time integration on Nose-Hoover style -non-Hamiltonian equations of motion which are designed to generate -positions and velocities sampled from the canonical (nvt), -isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This -updates the position and velocity for atoms in the group each -timestep. - -The thermostatting and barostatting is achieved by adding some dynamic -variables which are coupled to the particle velocities -(thermostatting) and simulation domain dimensions (barostatting). In -addition to basic thermostatting and barostatting, these fixes can -also create a chain of thermostats coupled to the particle thermostat, -and another chain of thermostats coupled to the barostat -variables. The barostat can be coupled to the overall box volume, or -to individual dimensions, including the {xy}, {xz} and {yz} tilt -dimensions. The external pressure of the barostat can be specified as -either a scalar pressure (isobaric ensemble) or as components of a -symmetric stress tensor (constant stress ensemble). When used -correctly, the time-averaged temperature and stress tensor of the -particles will match the target values specified by Tstart/Tstop and -Pstart/Pstop. - -The equations of motion used are those of Shinoda et al in -"(Shinoda)"_#nh-Shinoda, which combine the hydrostatic equations of -Martyna, Tobias and Klein in "(Martyna)"_#nh-Martyna with the strain -energy proposed by Parrinello and Rahman in -"(Parrinello)"_#nh-Parrinello. The time integration schemes closely -follow the time-reversible measure-preserving Verlet and rRESPA -integrators derived by Tuckerman et al in "(Tuckerman)"_#nh-Tuckerman. - -:line - -The thermostat parameters for fix styles {nvt} and {npt} is specified -using the {temp} keyword. Other thermostat-related keywords are -{tchain}, {tloop} and {drag}, which are discussed below. - -The thermostat is applied to only the translational degrees of freedom -for the particles. The translational degrees of freedom can also have -a bias velocity removed before thermostatting takes place; see the -description below. The desired temperature at each timestep is a -ramped value during the run from {Tstart} to {Tstop}. The {Tdamp} -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 10.0 means to relax -the temperature in a timespan of (roughly) 10 time units (e.g. tau or -fmsec or psec - see the "units"_units.html command). The atoms in the -fix group are the only ones whose velocities and positions are updated -by the velocity/position update portion of the integration. - -NOTE: A Nose-Hoover thermostat will not work well for arbitrary values -of {Tdamp}. If {Tdamp} is too small, the temperature can fluctuate -wildly; if it is too large, the temperature will take a very long time -to equilibrate. A good choice for many models is a {Tdamp} of around -100 timesteps. Note that this is NOT the same as 100 time units for -most "units"_units.html settings. A simple way to ensure this, is -via using an "immediate variable"_variable.html expression accessing -the thermo property 'dt', which is the length of the time step. Example: - -fix 1 all nvt temp 300.0 300.0 $(100.0*dt) :pre - - -:line - -The barostat parameters for fix styles {npt} and {nph} is specified -using one or more of the {iso}, {aniso}, {tri}, {x}, {y}, {z}, {xy}, -{xz}, {yz}, and {couple} keywords. These keywords give you the -ability to specify all 6 components of an external stress tensor, and -to couple various of these components together so that the dimensions -they represent are varied together during a constant-pressure -simulation. - -Other barostat-related keywords are {pchain}, {mtk}, {ploop}, -{nreset}, {drag}, and {dilate}, which are discussed below. - -Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). -Triclinic (non-orthogonal) simulation boxes have 6 adjustable -dimensions (x,y,z,xy,xz,yz). The "create_box"_create_box.html, "read -data"_read_data.html, and "read_restart"_read_restart.html commands -specify whether the simulation box is orthogonal or non-orthogonal -(triclinic) and explain the meaning of the xy,xz,yz tilt factors. - -The target pressures for each of the 6 components of the stress tensor -can be specified independently via the {x}, {y}, {z}, {xy}, {xz}, {yz} -keywords, which correspond to the 6 simulation box dimensions. For -each component, the external pressure or tensor component at each -timestep is a ramped value during the run from {Pstart} to {Pstop}. -If a target pressure is specified for a component, then the -corresponding box dimension will change during a simulation. For -example, if the {y} keyword is used, the y-box length will change. If -the {xy} keyword is used, the xy tilt factor will change. A box -dimension will not change if that component is not specified, although -you have the option to change that dimension via the "fix -deform"_fix_deform.html command. - -Note that in order to use the {xy}, {xz}, or {yz} keywords, the -simulation box must be triclinic, even if its initial tilt factors are -0.0. - -For all barostat keywords, the {Pdamp} parameter operates like the -{Tdamp} parameter, determining the time scale on which pressure is -relaxed. For example, a value of 10.0 means to relax the pressure in -a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see -the "units"_units.html command). - -NOTE: A Nose-Hoover barostat will not work well for arbitrary values -of {Pdamp}. If {Pdamp} is too small, the pressure and volume can -fluctuate wildly; if it is too large, the pressure will take a very -long time to equilibrate. A good choice for many models is a {Pdamp} -of around 1000 timesteps. However, note that {Pdamp} is specified in -time units, and that timesteps are NOT the same as time units for most -"units"_units.html settings. - -Regardless of what atoms are in the fix group (the only atoms which -are time integrated), a global pressure or stress tensor is computed -for all atoms. Similarly, when the size of the simulation box is -changed, all atoms are re-scaled to new positions, unless the keyword -{dilate} is specified with a {dilate-group-ID} for a group that -represents a subset of the atoms. This can be useful, for example, to -leave the coordinates of atoms in a solid substrate unchanged and -controlling the pressure of a surrounding fluid. This option should -be used with care, since it can be unphysical to dilate some atoms and -not others, because it can introduce large, instantaneous -displacements between a pair of atoms (one dilated, one not) that are -far from the dilation origin. Also note that for atoms not in the fix -group, a separate time integration fix like "fix nve"_fix_nve.html or -"fix nvt"_fix_nh.html can be used on them, independent of whether they -are dilated or not. - -:line - -The {couple} keyword allows two or three of the diagonal components of -the pressure tensor to be "coupled" together. The value specified -with the keyword determines which are coupled. For example, {xz} -means the {Pxx} and {Pzz} components of the stress tensor are coupled. -{Xyz} means all 3 diagonal components are coupled. Coupling means two -things: the instantaneous stress will be computed as an average of the -corresponding diagonal components, and the coupled box dimensions will -be changed together in lockstep, meaning coupled dimensions will be -dilated or contracted by the same percentage every timestep. The -{Pstart}, {Pstop}, {Pdamp} parameters for any coupled dimensions must -be identical. {Couple xyz} can be used for a 2d simulation; the {z} -dimension is simply ignored. - -:line - -The {iso}, {aniso}, and {tri} keywords are simply shortcuts that are -equivalent to specifying several other keywords together. - -The keyword {iso} means couple all 3 diagonal components together when -pressure is computed (hydrostatic pressure), and dilate/contract the -dimensions together. Using "iso Pstart Pstop Pdamp" is the same as -specifying these 4 keywords: - -x Pstart Pstop Pdamp -y Pstart Pstop Pdamp -z Pstart Pstop Pdamp -couple xyz :pre - -The keyword {aniso} means {x}, {y}, and {z} dimensions are controlled -independently using the {Pxx}, {Pyy}, and {Pzz} components of the -stress tensor as the driving forces, and the specified scalar external -pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying -these 4 keywords: - -x Pstart Pstop Pdamp -y Pstart Pstop Pdamp -z Pstart Pstop Pdamp -couple none :pre - -The keyword {tri} means {x}, {y}, {z}, {xy}, {xz}, and {yz} dimensions -are controlled independently using their individual stress components -as the driving forces, and the specified scalar pressure as the -external normal stress. Using "tri Pstart Pstop Pdamp" is the same as -specifying these 7 keywords: - -x Pstart Pstop Pdamp -y Pstart Pstop Pdamp -z Pstart Pstop Pdamp -xy 0.0 0.0 Pdamp -yz 0.0 0.0 Pdamp -xz 0.0 0.0 Pdamp -couple none :pre - -:line - -In some cases (e.g. for solids) the pressure (volume) and/or -temperature of the system can oscillate undesirably when a Nose/Hoover -barostat and thermostat is applied. The optional {drag} keyword will -damp these oscillations, although it alters the Nose/Hoover equations. -A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged. -A non-zero value adds a drag term; the larger the value specified, the -greater the damping effect. Performing a short run and monitoring the -pressure and temperature is the best way to determine if the drag term -is working. Typically a value between 0.2 to 2.0 is sufficient to -damp oscillations after a few periods. Note that use of the drag -keyword will interfere with energy conservation and will also change -the distribution of positions and velocities so that they do not -correspond to the nominal NVT, NPT, or NPH ensembles. - -An alternative way to control initial oscillations is to use chain -thermostats. The keyword {tchain} determines the number of thermostats -in the particle thermostat. A value of 1 corresponds to the original -Nose-Hoover thermostat. The keyword {pchain} specifies the number of -thermostats in the chain thermostatting the barostat degrees of -freedom. A value of 0 corresponds to no thermostatting of the -barostat variables. - -The {mtk} keyword controls whether or not the correction terms due to -Martyna, Tuckerman, and Klein are included in the equations of motion -"(Martyna)"_#nh-Martyna. Specifying {no} reproduces the original -Hoover barostat, whose volume probability distribution function -differs from the true NPT and NPH ensembles by a factor of 1/V. Hence -using {yes} is more correct, but in many cases the difference is -negligible. - -The keyword {tloop} can be used to improve the accuracy of integration -scheme at little extra cost. The initial and final updates of the -thermostat variables are broken up into {tloop} sub-steps, each of -length {dt}/{tloop}. This corresponds to using a first-order -Suzuki-Yoshida scheme "(Tuckerman)"_#nh-Tuckerman. The keyword {ploop} -does the same thing for the barostat thermostat. - -The keyword {nreset} controls how often the reference dimensions used -to define the strain energy are reset. If this keyword is not used, -or is given a value of zero, then the reference dimensions are set to -those of the initial simulation domain and are never changed. If the -simulation domain changes significantly during the simulation, then -the final average pressure tensor will differ significantly from the -specified values of the external stress tensor. A value of {nstep} -means that every {nstep} timesteps, the reference dimensions are set -to those of the current simulation domain. - -The {scaleyz}, {scalexz}, and {scalexy} keywords control whether or -not the corresponding tilt factors are scaled with the associated box -dimensions when barostatting triclinic periodic cells. The default -values {yes} will turn on scaling, which corresponds to adjusting the -linear dimensions of the cell while preserving its shape. Choosing -{no} ensures that the tilt factors are not scaled with the box -dimensions. See below for restrictions and default values in different -situations. In older versions of LAMMPS, scaling of tilt factors was -not performed. The old behavior can be recovered by setting all three -scale keywords to {no}. - -The {flip} keyword allows the tilt factors for a triclinic box to -exceed half the distance of the parallel box length, as discussed -below. If the {flip} value is set to {yes}, the bound is enforced by -flipping the box when it is exceeded. If the {flip} value is set to -{no}, the tilt will continue to change without flipping. Note that if -applied stress induces large deformations (e.g. in a liquid), this -means the box shape can tilt dramatically and LAMMPS will run less -efficiently, due to the large volume of communication needed to -acquire ghost atoms around a processor's irregular-shaped sub-domain. -For extreme values of tilt, LAMMPS may also lose atoms and generate an -error. - -The {fixedpoint} keyword specifies the fixed point for barostat volume -changes. By default, it is the center of the box. Whatever point is -chosen will not move during the simulation. For example, if the lower -periodic boundaries pass through (0,0,0), and this point is provided -to {fixedpoint}, then the lower periodic boundaries will remain at -(0,0,0), while the upper periodic boundaries will move twice as -far. In all cases, the particle trajectories are unaffected by the -chosen value, except for a time-dependent constant translation of -positions. - -If the {update} keyword is used with the {dipole} value, then the -orientation of the dipole moment of each particle is also updated -during the time integration. This option should be used for models -where a dipole moment is assigned to finite-size particles, -e.g. spheroids via use of the "atom_style hybrid sphere -dipole"_atom_style.html command. - -The default dipole orientation integrator can be changed to the -Dullweber-Leimkuhler-McLachlan integration scheme -"(Dullweber)"_#nh-Dullweber when using {update} with the value -{dipole/dlm}. This integrator is symplectic and time-reversible, -giving better energy conservation and allows slightly longer timesteps -at only a small additional computational cost. - -:line - -NOTE: Using a barostat coupled to tilt dimensions {xy}, {xz}, {yz} can -sometimes result in arbitrarily large values of the tilt dimensions, -i.e. a dramatically deformed simulation box. LAMMPS allows the tilt -factors to grow a small amount beyond the normal limit of half the box -length (0.6 times the box length), and then performs a box "flip" to -an equivalent periodic cell. See the discussion of the {flip} keyword -above, to allow this bound to be exceeded, if desired. - -The flip operation is described in more detail in the doc page for -"fix deform"_fix_deform.html. Both the barostat dynamics and the atom -trajectories are unaffected by this operation. However, if a tilt -factor is incremented by a large amount (1.5 times the box length) on -a single timestep, LAMMPS can not accommodate this event and will -terminate the simulation with an error. This error typically indicates -that there is something badly wrong with how the simulation was -constructed, such as specifying values of {Pstart} that are too far -from the current stress value, or specifying a timestep that is too -large. Triclinic barostatting should be used with care. This also is -true for other barostat styles, although they tend to be more -forgiving of insults. In particular, it is important to recognize that -equilibrium liquids can not support a shear stress and that -equilibrium solids can not support shear stresses that exceed the -yield stress. - -One exception to this rule is if the 1st dimension in the tilt factor -(x for xy) is non-periodic. In that case, the limits on the tilt -factor are not enforced, since flipping the box in that dimension does -not change the atom positions due to non-periodicity. In this mode, -if you tilt the system to extreme angles, the simulation will simply -become inefficient due to the highly skewed simulation box. - -NOTE: Unlike the "fix temp/berendsen"_fix_temp_berendsen.html command -which performs thermostatting but NO time integration, these fixes -perform thermostatting/barostatting AND time integration. Thus you -should not use any other time integration fix, such as "fix -nve"_fix_nve.html on atoms to which this fix is applied. Likewise, -fix nvt and fix npt should not normally be used on atoms that also -have their temperature controlled by another fix - e.g. by "fix -langevin"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html -commands. - -See the "Howto thermostat"_Howto_thermostat.html and "Howto -barostat"_Howto_barostat.html doc pages for a discussion of different -ways to compute temperature and perform thermostatting and -barostatting. - -:line - -These fixes compute a temperature and pressure each timestep. To do -this, the thermostat and barostat fixes create their own computes of -style "temp" and "pressure", as if one of these sets of commands had -been issued: - -For fix nvt: -compute fix-ID_temp group-ID temp - -For fix npt and fix nph: -compute fix-ID_temp all temp -compute fix-ID_press all pressure fix-ID_temp :pre - -For fix nvt, the group for the new temperature compute is the same as -the fix group. For fix npt and fix nph, the group for both the new -temperature and pressure compute is "all" since pressure is computed -for the entire system. In the case of fix nph, the temperature -compute is not used for thermostatting, but just for a kinetic-energy -contribution to the pressure. See the "compute -temp"_compute_temp.html and "compute pressure"_compute_pressure.html -commands for details. Note that the IDs of the new computes are the -fix-ID + underscore + "temp" or fix_ID + underscore + "press". - -Note that these are NOT the computes used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_press}. This means you can change the attributes of these -fix's temperature or pressure via the -"compute_modify"_compute_modify.html command. Or you can print this -temperature or pressure during thermodynamic output via the -"thermo_style custom"_thermo_style.html command using the appropriate -compute-ID. It also means that changing attributes of {thermo_temp} -or {thermo_press} will have no effect on this fix. - -Like other fixes that perform thermostatting, fix nvt and fix npt can -be used with "compute commands"_compute.html that calculate a -temperature after removing a "bias" from the atom velocities. -E.g. removing the center-of-mass velocity from a group of atoms or -only calculating temperature on the x-component of velocity or only -calculating temperature for atoms in a geometric region. This is not -done by default, but only if the "fix_modify"_fix_modify.html command -is used to assign a temperature compute to this fix that includes such -a bias term. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. - -:line - -These fixes can be used with either the {verlet} or {respa} -"integrators"_run_style.html. When using one of the barostat fixes -with {respa}, LAMMPS uses an integrator constructed -according to the following factorization of the Liouville propagator -(for two rRESPA levels): - -:c,image(Eqs/fix_nh1.jpg) - -This factorization differs somewhat from that of Tuckerman et al, in -that the barostat is only updated at the outermost rRESPA level, -whereas Tuckerman's factorization requires splitting the pressure into -pieces corresponding to the forces computed at each rRESPA level. In -theory, the latter method will exhibit better numerical stability. In -practice, because Pdamp is normally chosen to be a large multiple of -the outermost rRESPA timestep, the barostat dynamics are not the -limiting factor for numerical stability. Both factorizations are -time-reversible and can be shown to preserve the phase space measure -of the underlying non-Hamiltonian equations of motion. - -NOTE: This implementation has been shown to conserve linear momentum -up to machine precision under NVT dynamics. Under NPT dynamics, -for a system with zero initial total linear momentum, the total -momentum fluctuates close to zero. It may occasionally undergo brief -excursions to non-negligible values, before returning close to zero. -Over long simulations, this has the effect of causing the center-of-mass -to undergo a slow random walk. This can be mitigated by resetting -the momentum at infrequent intervals using the -"fix momentum"_fix_momentum.html command. - -:line - -The fix npt and fix nph commands can be used with rigid bodies or -mixtures of rigid bodies and non-rigid particles (e.g. solvent). But -there are also "fix rigid/npt"_fix_rigid.html and "fix -rigid/nph"_fix_rigid.html commands, which are typically a more natural -choice. See the doc page for those commands for more discussion of -the various ways to do this. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -These fixes writes the state of all the thermostat and barostat -variables to "binary restart files"_restart.html. See the -"read_restart"_read_restart.html command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} and {press} options are -supported by these fixes. You can use them to assign a -"compute"_compute.html you have defined to this fix which will be used -in its thermostatting or barostatting procedure, as described above. -If you do this, note that the kinetic energy derived from the compute -temperature should be consistent with the virial term computed using -all atoms for the pressure. LAMMPS will warn you if you choose to -compute temperature on a subset of atoms. - -NOTE: If both the {temp} and {press} keywords are used in a single -thermo_modify command (or in two separate commands), then the order in -which the keywords are specified is important. Note that a "pressure -compute"_compute_pressure.html defines its own temperature compute as -an argument when it is specified. The {temp} keyword will override -this (for the pressure compute being used by fix npt), but only if the -{temp} keyword comes after the {press} keyword. If the {temp} keyword -comes before the {press} keyword, then the new pressure compute -specified by the {press} keyword will be unaffected by the {temp} -setting. - -The "fix_modify"_fix_modify.html {energy} option is supported by these -fixes to add the energy change induced by Nose/Hoover thermostatting -and barostatting to the system's potential energy as part of -"thermodynamic output"_thermo_style.html. - -These fixes compute a global scalar and a global vector of quantities, -which can be accessed by various "output commands"_Howto_output.html. -The scalar value calculated by these fixes is "extensive"; the vector -values are "intensive". - -The scalar is the cumulative energy change due to the fix. - -The vector stores internal Nose/Hoover thermostat and barostat -variables. The number and meaning of the vector values depends on -which fix is used and the settings for keywords {tchain} and {pchain}, -which specify the number of Nose/Hoover chains for the thermostat and -barostat. If no thermostatting is done, then {tchain} is 0. If no -barostatting is done, then {pchain} is 0. In the following list, -"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in -the barostat. Its value is 0 if no barostat is used, else its value -is 6 if any off-diagonal stress tensor component is barostatted, else -its value is 1 if {couple xyz} is used or {couple xy} for a 2d -simulation, otherwise its value is 3. - -The order of values in the global vector and their meaning is as -follows. The notation means there are tchain values for eta, followed -by tchain for eta_dot, followed by ndof for omega, etc: - -eta\[tchain\] = particle thermostat displacements (unitless) -eta_dot\[tchain\] = particle thermostat velocities (1/time units) -omega\[ndof\] = barostat displacements (unitless) -omega_dot\[ndof\] = barostat velocities (1/time units) -etap\[pchain\] = barostat thermostat displacements (unitless) -etap_dot\[pchain\] = barostat thermostat velocities (1/time units) -PE_eta\[tchain\] = potential energy of each particle thermostat displacement (energy units) -KE_eta_dot\[tchain\] = kinetic energy of each particle thermostat velocity (energy units) -PE_omega\[ndof\] = potential energy of each barostat displacement (energy units) -KE_omega_dot\[ndof\] = kinetic energy of each barostat velocity (energy units) -PE_etap\[pchain\] = potential energy of each barostat thermostat displacement (energy units) -KE_etap_dot\[pchain\] = kinetic energy of each barostat thermostat velocity (energy units) -PE_strain\[1\] = scalar strain energy (energy units) :ul - -These fixes can ramp their external temperature and pressure over -multiple runs, using the {start} and {stop} keywords of the -"run"_run.html command. See the "run"_run.html command for details of -how to do this. - -These fixes are not invoked during "energy -minimization"_minimize.html. - -:line - -[Restrictions:] - -{X}, {y}, {z} cannot be barostatted if the associated dimension is not -periodic. {Xy}, {xz}, and {yz} can only be barostatted if the -simulation domain is triclinic and the 2nd dimension in the keyword -({y} dimension in {xy}) is periodic. {Z}, {xz}, and {yz}, cannot be -barostatted for 2D simulations. The "create_box"_create_box.html, -"read data"_read_data.html, and "read_restart"_read_restart.html -commands specify whether the simulation box is orthogonal or -non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz -tilt factors. - -For the {temp} keyword, the final Tstop cannot be 0.0 since it would -make the external T = 0.0 at some timestep during the simulation which -is not allowed in the Nose/Hoover formulation. - -The {scaleyz yes} and {scalexz yes} keyword/value pairs can not be used -for 2D simulations. {scaleyz yes}, {scalexz yes}, and {scalexy yes} options -can only be used if the 2nd dimension in the keyword is periodic, -and if the tilt factor is not coupled to the barostat via keywords -{tri}, {yz}, {xz}, and {xy}. - -These fixes can be used with dynamic groups as defined by the -"group"_group.html command. Likewise they can be used with groups to -which atoms are added or deleted over time, e.g. a deposition -simulation. However, the conservation properties of the thermostat -and barostat are defined for systems with a static set of atoms. You -may observe odd behavior if the atoms in a group vary dramatically -over time or the atom count becomes very small. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix_modify"_fix_modify.html, -"run_style"_run_style.html - -[Default:] - -The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1, -ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, -flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd -dimension and not coupled to barostat, otherwise no. - -:line - -:link(nh-Martyna) -[(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). - -:link(nh-Parrinello) -[(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). - -:link(nh-Tuckerman) -[(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and -Martyna, J Phys A: Math Gen, 39, 5629 (2006). - -:link(nh-Shinoda) -[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). - -:link(nh-Dullweber) -[(Dullweber)] Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, -5840 (1997). diff --git a/doc/txt/fix_nh_eff.txt b/doc/txt/fix_nh_eff.txt deleted file mode 100644 index d7c0457708..0000000000 --- a/doc/txt/fix_nh_eff.txt +++ /dev/null @@ -1,142 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nvt/eff command :h3 -fix npt/eff command :h3 -fix nph/eff command :h3 - -[Syntax:] - -fix ID group-ID style_name keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -style_name = {nvt/eff} or {npt/eff} or {nph/eff} :l -one or more keyword value pairs may be appended -keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate} - {temp} values = Tstart Tstop Tdamp - Tstart,Tstop = external temperature at start/end of run - Tdamp = temperature damping parameter (time units) - {iso} or {aniso} or {tri} values = Pstart Pstop Pdamp - Pstart,Pstop = scalar external pressure at start/end of run (pressure units) - Pdamp = pressure damping parameter (time units) - {x} or {y} or {z} or {xy} or {yz} or {xz} values = Pstart Pstop Pdamp - Pstart,Pstop = external stress tensor component at start/end of run (pressure units) - Pdamp = stress damping parameter (time units) - {couple} = {none} or {xyz} or {xy} or {yz} or {xz} - {tchain} value = length of thermostat chain (1 = single thermostat) - {pchain} values = length of thermostat chain on barostat (0 = no thermostat) - {mtk} value = {yes} or {no} = add in MTK adjustment term or not - {tloop} value = number of sub-cycles to perform on thermostat - {ploop} value = number of sub-cycles to perform on barostat thermostat - {nreset} value = reset reference cell every this many timesteps - {drag} value = drag factor added to barostat/thermostat (0.0 = no drag) - {dilate} value = {all} or {partial} :pre -:ule - -[Examples:] - -fix 1 all nvt/eff temp 300.0 300.0 0.1 -fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0 -fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0 -fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 :pre - -[Description:] - -These commands perform time integration on Nose-Hoover style -non-Hamiltonian equations of motion for nuclei and electrons in the -group for the "electron force field"_pair_eff.html model. The fixes -are designed to generate positions and velocities sampled from the -canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph) -ensembles. This is achieved by adding some dynamic variables which -are coupled to the particle velocities (thermostatting) and simulation -domain dimensions (barostatting). In addition to basic thermostatting -and barostatting, these fixes can also create a chain of thermostats -coupled to the particle thermostat, and another chain of thermostats -coupled to the barostat variables. The barostat can be coupled to the -overall box volume, or to individual dimensions, including the {xy}, -{xz} and {yz} tilt dimensions. The external pressure of the barostat -can be specified as either a scalar pressure (isobaric ensemble) or as -components of a symmetric stress tensor (constant stress ensemble). -When used correctly, the time-averaged temperature and stress tensor -of the particles will match the target values specified by -Tstart/Tstop and Pstart/Pstop. - -The operation of these fixes is exactly like that described by the -"fix nvt, npt, and nph"_fix_nh.html commands, except that the radius -and radial velocity of electrons are also updated. Likewise the -temperature and pressure calculated by the fix, using the computes it -creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html -doc page), are performed with computes that include the eFF contribution -to the temperature or kinetic energy from the electron radial velocity. - -NOTE: there are two different pressures that can be reported for eFF -when defining the pair_style (see "pair eff/cut"_pair_eff.html to -understand these settings), one (default) that considers electrons do -not contribute radial virial components (i.e. electrons treated as -incompressible 'rigid' spheres) and one that does. The radial -electronic contributions to the virials are only tallied if the -flexible pressure option is set, and this will affect both global and -per-atom quantities. In principle, the true pressure of a system is -somewhere in between the rigid and the flexible eFF pressures, but, -for most cases, the difference between these two pressures will not be -significant over long-term averaged runs (i.e. even though the energy -partitioning changes, the total energy remains similar). - -NOTE: currently, there is no available option for the user to set or -create temperature distributions that include the radial electronic -degrees of freedom with the "velocity"_velocity.html command, so the -the user must allow for these degrees of freedom to equilibrate -(i.e. equi-partitioning of energy) through time integration. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -See the doc page for the "fix nvt, npt, and nph"_fix_nh.html commands -for details. - -[Restrictions:] - -This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Other restriction discussed on the doc page for the "fix nvt, npt, and -nph"_fix_nh.html commands also apply. - -NOTE: The temperature for systems (regions or groups) with only -electrons and no nuclei is 0.0 (i.e. not defined) in the current -temperature calculations, a practical example would be a uniform -electron gas or a very hot plasma, where electrons remain delocalized -from the nuclei. This is because, even though electron virials are -included in the temperature calculation, these are averaged over the -nuclear degrees of freedom only. In such cases a corrective term must -be added to the pressure to get the correct kinetic contribution. - -[Related commands:] - -"fix nvt"_fix_nh.html, "fix nph"_fix_nh.html, "fix npt"_fix_nh.html, -"fix_modify"_fix_modify.html, "run_style"_run_style.html - -[Default:] - -The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = -ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none. - -:line - -:link(Martyna1) -[(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). - -:link(Parrinello) -[(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). - -:link(Tuckerman1) -[(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and -Martyna, J Phys A: Math Gen, 39, 5629 (2006). - -:link(Shinoda2) -[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). diff --git a/doc/txt/fix_nh_uef.txt b/doc/txt/fix_nh_uef.txt deleted file mode 100644 index 4d58ee7c49..0000000000 --- a/doc/txt/fix_nh_uef.txt +++ /dev/null @@ -1,228 +0,0 @@ -<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nvt/uef command :h3 -fix npt/uef command :h3 - -[Syntax:] - -fix ID group-ID style_name erate edot_x edot_y temp Tstart Tstop Tdamp keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -style_name = {nvt/uef} or {npt/uef} :l -{Tstart}, {Tstop}, and {Tdamp} are documented in the "fix npt"_fix_nh.html command :l -{edot_x} and {edot_y} are the strain rates in the x and y directions (1/(time units)) :l -one or more keyword/value pairs may be appended :l -keyword = {ext} or {strain} or {iso} or {x} or {y} or {z} or {tchain} or {pchain} or {tloop} or {ploop} or {mtk} - {ext} value = {x} or {y} or {z} or {xy} or {yz} or {xz} = external dimensions - sets the external dimensions used to calculate the scalar pressure - {strain} values = e_x e_y = initial strain - usually not needed, but may be needed to resume a run with a data file. - {iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, {mtk} keywords - documented by the "fix npt"_fix_nh.html command :pre -:ule - -[Examples:] - -fix uniax_nvt all nvt/uef temp 400 400 100 erate 0.00001 -0.000005 -fix biax_nvt all nvt/uef temp 400 400 100 erate 0.000005 0.000005 -fix uniax_npt all npt/uef temp 400 400 300 iso 1 1 3000 erate 0.00001 -0.000005 ext yz -fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000 :pre - -[Description:] - -This fix can be used to simulate non-equilibrium molecular dynamics -(NEMD) under diagonal flow fields, including uniaxial and bi-axial -flow. Simulations under continuous extensional flow may be carried -out for an indefinite amount of time. It is an implementation of the -boundary conditions from "(Dobson)"_#Dobson, and also uses numerical -lattice reduction as was proposed by "(Hunt)"_#Hunt. The lattice -reduction algorithm is from "(Semaev)"_Semaev. The fix is intended for -simulations of homogeneous flows, and integrates the SLLOD equations -of motion, originally proposed by Hoover and Ladd (see "(Evans and -Morriss)"_#Sllod). Additional detail about this implementation can be -found in "(Nicholson and Rutledge)"_#Nicholson. - -Note that NEMD simulations of a continuously strained system can be -performed using the "fix deform"_fix_deform.html, "fix -nvt/sllod"_fix_nvt_sllod.html, and "compute -temp/deform"_compute_temp_deform.html commands. - -The applied flow field is set by the {eps} keyword. The values -{edot_x} and {edot_y} correspond to the strain rates in the xx and yy -directions. It is implicitly assumed that the flow field is -traceless, and therefore the strain rate in the zz direction is eqal -to -({edot_x} + {edot_y}). - -NOTE: Due to an instability in the SLLOD equations under extension, -"fix momentum"_fix_momentum.html should be used to regularly reset the -linear momentum. - -The boundary conditions require a simulation box that does not have a -consistent alignment relative to the applied flow field. Since LAMMPS -utilizes an upper-triangular simulation box, it is not possible to -express the evolving simulation box in the same coordinate system as -the flow field. This fix keeps track of two coordinate systems: the -flow frame, and the upper triangular LAMMPS frame. The coordinate -systems are related to each other through the QR decomposition, as is -illustrated in the image below. - -:c,image(JPG/uef_frames.jpg) - -During most molecular dynamics operations, the system is represented -in the LAMMPS frame. Only when the positions and velocities are -updated is the system rotated to the flow frame, and it is rotated -back to the LAMMPS frame immediately afterwards. For this reason, all -vector-valued quantities (except for the tensors from -"compute_pressure/uef"_compute_pressure_uef.html and -"compute_temp/uef"_compute_temp_uef.html) will be computed in the -LAMMPS frame. Rotationally invariant scalar quantities like the -temperature and hydrostatic pressure are frame-invariant and will be -computed correctly. Additionally, the system is in the LAMMPS frame -during all of the output steps, and therefore trajectory files made -using the dump command will be in the LAMMPS frame unless the -"dump_cfg/uef"_dump_cfg_uef.html command is used. - -:line - -Temperature control is achieved with the default Nose-Hoover style -thermostat documented in "fix npt"_fix_nh.html. When this fix is -active, only the peculiar velocity of each atom is stored, defined as -the velocity relative to the streaming velocity. This is in contrast -to "fix nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame -velocity, and removes the contribution from the streaming velocity in -order to compute the temperature. - -Pressure control is achieved using the default Nose-Hoover barostat -documented in "fix npt"_fix_nh.html. There are two ways to control the -pressure using this fix. The first method involves using the {ext} -keyword along with the {iso} pressure style. With this method, the -pressure is controlled by scaling the simulation box isotropically to -achieve the average pressure only in the directions specified by -{ext}. For example, if the {ext} value is set to {xy}, the average -pressure (Pxx+Pyy)/2 will be controlled. - -This example command will control the total hydrostatic pressure under -uniaxial tension: - -fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz :pre - -This example command will control the average stress in compression -directions, which would typically correspond to free surfaces under -drawing with uniaxial tension: - -fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy :pre - -The second method for pressure control involves setting the normal -stresses using the {x}, {y} , and/or {z} keywords. When using this -method, the same pressure must be specified via {Pstart} and {Pstop} -for all dimensions controlled. Any choice of pressure conditions that -would cause LAMMPS to compute a deviatoric stress are not permissible -and will result in an error. Additionally, all dimensions with -controlled stress must have the same applied strain rate. The {ext} -keyword must be set to the default value ({xyz}) when using this -method. - -For example, the following commands will work: - -fix f3 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 y 1 1 5 erate -0.5 -0.5 -fix f4 all npt/uef temp 0.7 0.7 0.5 z 1 1 5 erate 0.5 0.5 :pre - -The following commands will not work: - -fix f5 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 1 1 5 erate -0.5 -0.5 -fix f6 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 2 2 5 erate 0.5 0.5 :pre - -:line - -These fix computes a temperature and pressure each timestep. To do -this, it creates its own computes of style "temp/uef" and -"pressure/uef", as if one of these two sets of commands had been -issued: - -compute fix-ID_temp group-ID temp/uef -compute fix-ID_press group-ID pressure/uef fix-ID_temp :pre - -compute fix-ID_temp all temp/uef -compute fix-ID_press all pressure/uef fix-ID_temp :pre - -See the "compute temp/uef"_compute_temp_uef.html and "compute -pressure/uef"_compute_pressure_uef.html commands for details. Note -that the IDs of the new computes are the fix-ID + underscore + "temp" -or fix_ID + underscore + "press". - -[Restart, fix_modify, output, run start/stop, minimize info:] - -The fix writes the state of all the thermostat and barostat variables, -as well as the cumulative strain applied, to "binary restart -files"_restart.html. See the "read_restart"_read_restart.html command -for info on how to re-specify a fix in an input script that reads a -restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -NOTE: It is not necessary to set the {strain} keyword when resuming a -run from a restart file. Only for resuming from data files, which do -not contain the cumulative applied strain, will this keyword be -necessary. - -This fix can be used with the "fix_modify"_fix_modify.html {temp} and -{press} options. The temperature and pressure computes used must be of -type {temp/uef} and {pressure/uef}. - -This fix computes the same global scalar and vector quantities as "fix -npt"_fix_nh.html. - -The fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-UEF package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Due to requirements of the boundary conditions, when the {strain} -keyword is set to zero (or unset), the initial simulation box must be -cubic and have style triclinic. If the box is initially of type ortho, -use "change_box"_change_box.html before invoking the fix. - -NOTE: When resuming from restart files, you may need to use "box tilt -large"_box.html since lammps has internal criteria from lattice -reduction that are not the same as the criteria in the numerical -lattice reduction algorithm. - -[Related commands:] - -"fix nvt"_fix_nh.html, "fix nvt/sllod"_fix_nvt_sllod.html, "compute -temp/uef"_compute_temp_uef.html, "compute -pressure/uef"_compute_pressure_uef.html, "dump -cfg/uef"_dump_cfg_uef.html - -[Default:] - -The default keyword values specific to this fix are exy = xyz, strain -= 0 0. The remaining defaults are the same as for {fix -npt}_fix_nh.html except tchain = 1. The reason for this change is -given in "fix nvt/sllod"_fix_nvt_sllod.html. - -:line - -:link(Dobson) -[(Dobson)] Dobson, J Chem Phys, 141, 184103 (2014). - -:link(Hunt) -[(Hunt)] Hunt, Mol Simul, 42, 347 (2016). - -:link(Semaev) -[(Semaev)] Semaev, Cryptography and Lattices, 181 (2001). - -:link(Sllod) -[(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984). - -:link(Nicholson) -[(Nicholson and Rutledge)] Nicholson and Rutledge, J Chem Phys, 145, -244903 (2016). diff --git a/doc/txt/fix_nph_asphere.txt b/doc/txt/fix_nph_asphere.txt deleted file mode 100644 index 5cabf930e7..0000000000 --- a/doc/txt/fix_nph_asphere.txt +++ /dev/null @@ -1,152 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nph/asphere command :h3 -fix nph/asphere/omp command :h3 - -[Syntax:] - -fix ID group-ID nph/asphere args keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command -nph/asphere = style name of this fix command -additional barostat related keyword/value pairs from the "fix nph"_fix_nh.html command can be appended :ul - -[Examples:] - -fix 1 all nph/asphere iso 0.0 0.0 1000.0 -fix 2 all nph/asphere x 5.0 5.0 1000.0 -fix 2 all nph/asphere x 5.0 5.0 1000.0 drag 0.2 -fix 2 water nph/asphere aniso 0.0 0.0 1000.0 dilate partial :pre - -[Description:] - -Perform constant NPH integration to update position, velocity, -orientation, and angular velocity each timestep for aspherical or -ellipsoidal particles in the group using a Nose/Hoover pressure -barostat. P is pressure; H is enthalpy. This creates a system -trajectory consistent with the isenthalpic ensemble. - -This fix differs from the "fix nph"_fix_nh.html command, which assumes -point particles and only updates their position and velocity. - -Additional parameters affecting the barostat are specified by keywords -and values documented with the "fix nph"_fix_nh.html command. See, -for example, discussion of the {aniso}, and {dilate} keywords. - -The particles in the fix group are the only ones whose velocities and -positions are updated by the velocity/position update portion of the -NPH integration. - -Regardless of what particles are in the fix group, a global pressure is -computed for all particles. Similarly, when the size of the simulation -box is changed, all particles are re-scaled to new positions, unless the -keyword {dilate} is specified with a value of {partial}, in which case -only the particles in the fix group are re-scaled. The latter can be -useful for leaving the coordinates of particles in a solid substrate -unchanged and controlling the pressure of a surrounding fluid. - -:line - -This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp/asphere" and -"pressure", as if these commands had been issued: - -compute fix-ID_temp all temp/asphere -compute fix-ID_press all pressure fix-ID_temp :pre - -See the "compute temp/asphere"_compute_temp_asphere.html and "compute -pressure"_compute_pressure.html commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is "all" -since pressure is computed for the entire system. - -Note that these are NOT the computes used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_press}. This means you can change the attributes of this -fix's temperature or pressure via the -"compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} or -{thermo_press} will have no effect on this fix. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the Nose/Hoover barostat to "binary -restart files"_restart.html. See the "read_restart"_read_restart.html -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} and {press} options are -supported by this fix. You can use them to assign a -"compute"_compute.html you have defined to this fix which will be used -in its thermostatting or barostatting procedure. If you do this, note -that the kinetic energy derived from the compute temperature should be -consistent with the virial term computed using all atoms for the -pressure. LAMMPS will warn you if you choose to compute temperature -on a subset of atoms. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Nose/Hoover barostatting to -the system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes the same global scalar and global vector of -quantities as does the "fix nph"_fix_nh.html command. - -This fix can ramp its target pressure over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the "atom_style ellipsoid"_atom_style.html -command. - -All particles in the group must be finite-size. They cannot be point -particles, but they can be aspherical or spherical as defined by their -shape attribute. - -[Related commands:] - -"fix nph"_fix_nh.html, "fix nve_asphere"_fix_nve_asphere.html, "fix -nvt_asphere"_fix_nvt_asphere.html, "fix -npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html - -[Default:] none diff --git a/doc/txt/fix_nph_body.txt b/doc/txt/fix_nph_body.txt deleted file mode 100644 index e04c240de9..0000000000 --- a/doc/txt/fix_nph_body.txt +++ /dev/null @@ -1,147 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nph/body command :h3 - -[Syntax:] - -fix ID group-ID nph/body args keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command -nph/body = style name of this fix command -additional barostat related keyword/value pairs from the "fix nph"_fix_nh.html command can be appended :ul - -[Examples:] - -fix 1 all nph/body iso 0.0 0.0 1000.0 -fix 2 all nph/body x 5.0 5.0 1000.0 -fix 2 all nph/body x 5.0 5.0 1000.0 drag 0.2 -fix 2 water nph/body aniso 0.0 0.0 1000.0 dilate partial :pre - -[Description:] - -Perform constant NPH integration to update position, velocity, -orientation, and angular velocity each timestep for body -particles in the group using a Nose/Hoover pressure -barostat. P is pressure; H is enthalpy. This creates a system -trajectory consistent with the isenthalpic ensemble. - -This fix differs from the "fix nph"_fix_nh.html command, which assumes -point particles and only updates their position and velocity. - -Additional parameters affecting the barostat are specified by keywords -and values documented with the "fix nph"_fix_nh.html command. See, -for example, discussion of the {aniso}, and {dilate} keywords. - -The particles in the fix group are the only ones whose velocities and -positions are updated by the velocity/position update portion of the -NPH integration. - -Regardless of what particles are in the fix group, a global pressure is -computed for all particles. Similarly, when the size of the simulation -box is changed, all particles are re-scaled to new positions, unless the -keyword {dilate} is specified with a value of {partial}, in which case -only the particles in the fix group are re-scaled. The latter can be -useful for leaving the coordinates of particles in a solid substrate -unchanged and controlling the pressure of a surrounding fluid. - -:line - -This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp/body" and -"pressure", as if these commands had been issued: - -compute fix-ID_temp all temp/body -compute fix-ID_press all pressure fix-ID_temp :pre - -See the "compute temp/body"_compute_temp_body.html and "compute -pressure"_compute_pressure.html commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is "all" -since pressure is computed for the entire system. - -Note that these are NOT the computes used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_press}. This means you can change the attributes of this -fix's temperature or pressure via the -"compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} or -{thermo_press} will have no effect on this fix. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the Nose/Hoover barostat to "binary -restart files"_restart.html. See the "read_restart"_read_restart.html -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} and {press} options are -supported by this fix. You can use them to assign a -"compute"_compute.html you have defined to this fix which will be used -in its thermostatting or barostatting procedure. If you do this, note -that the kinetic energy derived from the compute temperature should be -consistent with the virial term computed using all atoms for the -pressure. LAMMPS will warn you if you choose to compute temperature -on a subset of atoms. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Nose/Hoover barostatting to -the system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes the same global scalar and global vector of -quantities as does the "fix nph"_fix_nh.html command. - -This fix can ramp its target pressure over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the "atom_style body"_atom_style.html -command. - -[Related commands:] - -"fix nph"_fix_nh.html, "fix nve_body"_fix_nve_body.html, "fix -nvt_body"_fix_nvt_body.html, "fix -npt_body"_fix_npt_body.html, "fix_modify"_fix_modify.html - -[Default:] none diff --git a/doc/txt/fix_nph_sphere.txt b/doc/txt/fix_nph_sphere.txt deleted file mode 100644 index f94c057c93..0000000000 --- a/doc/txt/fix_nph_sphere.txt +++ /dev/null @@ -1,159 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nph/sphere command :h3 -fix nph/sphere/omp command :h3 - -[Syntax:] - -fix ID group-ID nph/sphere args keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -nph/sphere = style name of this fix command :l -keyword = {disc} :l - {disc} value = none = treat particles as 2d discs, not spheres :pre -additional barostat related keyword/value pairs from the "fix nph"_fix_nh.html command can be appended :l,ule - -[Examples:] - -fix 1 all nph/sphere iso 0.0 0.0 1000.0 -fix 2 all nph/sphere x 5.0 5.0 1000.0 -fix 2 all nph/sphere x 5.0 5.0 1000.0 disc -fix 2 all nph/sphere x 5.0 5.0 1000.0 drag 0.2 -fix 2 water nph/sphere aniso 0.0 0.0 1000.0 dilate partial :pre - -[Description:] - -Perform constant NPH integration to update position, velocity, and -angular velocity each timestep for finite-size spherical particles in -the group using a Nose/Hoover pressure barostat. P is pressure; H is -enthalpy. This creates a system trajectory consistent with the -isenthalpic ensemble. - -This fix differs from the "fix nph"_fix_nh.html command, which assumes -point particles and only updates their position and velocity. - -If the {disc} keyword is used, then each particle is treated as a 2d -disc (circle) instead of as a sphere. This is only possible for 2d -simulations, as defined by the "dimension"_dimension.html keyword. -The only difference between discs and spheres in this context is their -moment of inertia, as used in the time integration. - -Additional parameters affecting the barostat are specified by keywords -and values documented with the "fix nph"_fix_nh.html command. See, -for example, discussion of the {aniso}, and {dilate} keywords. - -The particles in the fix group are the only ones whose velocities and -positions are updated by the velocity/position update portion of the -NPH integration. - -Regardless of what particles are in the fix group, a global pressure is -computed for all particles. Similarly, when the size of the simulation -box is changed, all particles are re-scaled to new positions, unless the -keyword {dilate} is specified with a value of {partial}, in which case -only the particles in the fix group are re-scaled. The latter can be -useful for leaving the coordinates of particles in a solid substrate -unchanged and controlling the pressure of a surrounding fluid. - -:line - -This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp/sphere" and -"pressure", as if these commands had been issued: - -compute fix-ID_temp all temp/sphere -compute fix-ID_press all pressure fix-ID_temp :pre - -See the "compute temp/sphere"_compute_temp_sphere.html and "compute -pressure"_compute_pressure.html commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is "all" -since pressure is computed for the entire system. - -Note that these are NOT the computes used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_press}. This means you can change the attributes of this -fix's temperature or pressure via the -"compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} or -{thermo_press} will have no effect on this fix. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the Nose/Hoover barostat to "binary -restart files"_restart.html. See the "read_restart"_read_restart.html -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} and {press} options are -supported by this fix. You can use them to assign a -"compute"_compute.html you have defined to this fix which will be used -in its thermostatting or barostatting procedure. If you do this, note -that the kinetic energy derived from the compute temperature should be -consistent with the virial term computed using all atoms for the -pressure. LAMMPS will warn you if you choose to compute temperature -on a subset of atoms. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Nose/Hoover barostatting to -the system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes the same global scalar and global vector of -quantities as does the "fix nph"_fix_nh.html command. - -This fix can ramp its target pressure over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the "atom_style sphere"_atom_style.html -command. - -All particles in the group must be finite-size spheres. They cannot -be point particles. - -Use of the {disc} keyword is only allowed for 2d simulations, as -defined by the "dimension"_dimension.html keyword. - -[Related commands:] - -"fix nph"_fix_nh.html, "fix nve_sphere"_fix_nve_sphere.html, "fix -nvt_sphere"_fix_nvt_sphere.html, "fix npt_sphere"_fix_npt_sphere.html, -"fix_modify"_fix_modify.html - -[Default:] none diff --git a/doc/txt/fix_nphug.txt b/doc/txt/fix_nphug.txt deleted file mode 100644 index 855a4c9ae4..0000000000 --- a/doc/txt/fix_nphug.txt +++ /dev/null @@ -1,228 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nphug command :h3 -fix nphug/omp command :h3 - -[Syntax:] - -fix ID group-ID nphug keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -one or more keyword value pairs may be appended -keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate} or {scaleyz} or {scalexz} or {scalexy} - {temp} values = Value1 Value2 Tdamp - Value1, Value2 = Nose-Hoover target temperatures, ignored by Hugoniostat - Tdamp = temperature damping parameter (time units) - {iso} or {aniso} or {tri} values = Pstart Pstop Pdamp - Pstart,Pstop = scalar external pressures, must be equal (pressure units) - Pdamp = pressure damping parameter (time units) - {x} or {y} or {z} or {xy} or {yz} or {xz} values = Pstart Pstop Pdamp - Pstart,Pstop = external stress tensor components, must be equal (pressure units) - Pdamp = stress damping parameter (time units) - {couple} = {none} or {xyz} or {xy} or {yz} or {xz} - {tchain} value = length of thermostat chain (1 = single thermostat) - {pchain} values = length of thermostat chain on barostat (0 = no thermostat) - {mtk} value = {yes} or {no} = add in MTK adjustment term or not - {tloop} value = number of sub-cycles to perform on thermostat - {ploop} value = number of sub-cycles to perform on barostat thermostat - {nreset} value = reset reference cell every this many timesteps - {drag} value = drag factor added to barostat/thermostat (0.0 = no drag) - {dilate} value = {all} or {partial} - {scaleyz} value = {yes} or {no} = scale yz with lz - {scalexz} value = {yes} or {no} = scale xz with lz - {scalexy} value = {yes} or {no} = scale xy with ly :pre -:ule - -[Examples:] - -fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 -fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0 :pre - -[Description:] - -This command is a variant of the Nose-Hoover -"fix npt"_fix_nh.html fix style. -It performs time integration of the Hugoniostat equations -of motion developed by Ravelo et al. "(Ravelo)"_#Ravelo1. -These equations compress the system to a state with average -axial stress or pressure equal to the specified target value -and that satisfies the Rankine-Hugoniot (RH) -jump conditions for steady shocks. - -The compression can be performed -either -hydrostatically (using keyword {iso}, {aniso}, or {tri}) or uniaxially -(using keywords {x}, {y}, or {z}). In the hydrostatic case, -the cell dimensions change dynamically so that the average axial stress -in all three directions converges towards the specified target value. -In the uniaxial case, the chosen cell dimension changes dynamically -so that the average -axial stress in that direction converges towards the target value. The -other two cell dimensions are kept fixed (zero lateral strain). - -This leads to the following additional restrictions on the keywords: - -One and only one of the following keywords should be used: {iso}, {aniso}, {tri}, {x}, {y}, {z} -The specified initial and final target pressures must be the same. -The keywords {xy}, {xz}, {yz} may not be used. -The only admissible value for the couple keyword is {xyz}, which has the same effect as keyword {iso} -The {temp} keyword must be used to specify the time constant for kinetic energy relaxation, but initial and final target temperature values are ignored. :ul - -Essentially, a Hugoniostat simulation is an NPT simulation in which the -user-specified target temperature is replaced with a time-dependent -target temperature Tt obtained from the following equation: - -:c,image(Eqs/fix_nphug.jpg) - -where T and Tt are the instantaneous and target temperatures, -P and P0 are the instantaneous and reference pressures or axial stresses, -depending on whether hydrostatic or uniaxial compression is being -performed, V and V0 are the instantaneous and reference volumes, -E and E0 are the instantaneous and reference internal energy (potential -plus kinetic), Ndof is the number of degrees of freedom used in the -definition of temperature, and kB is the Boltzmann constant. Delta is the -negative deviation of the instantaneous temperature from the target temperature. -When the system reaches a stable equilibrium, the value of Delta should -fluctuate about zero. - -The values of E0, V0, and P0 are the instantaneous values at the start of -the simulation. These can be overridden using the fix_modify keywords {e0}, -{v0}, and {p0} described below. - -:line - -NOTE: Unlike the "fix temp/berendsen"_fix_temp_berendsen.html command -which performs thermostatting but NO time integration, this fix -performs thermostatting/barostatting AND time integration. Thus you -should not use any other time integration fix, such as "fix -nve"_fix_nve.html on atoms to which this fix is applied. Likewise, -this fix should not be used on atoms that have their temperature -controlled by another fix - e.g. by "fix langevin"_fix_nh.html or "fix -temp/rescale"_fix_temp_rescale.html commands. - -:line - -This fix computes a temperature and pressure at each timestep. To do -this, the fix creates its own computes of style "temp" and "pressure", -as if one of these two sets of commands had been issued: - -compute fix-ID_temp group-ID temp -compute fix-ID_press group-ID pressure fix-ID_temp :pre - -compute fix-ID_temp all temp -compute fix-ID_press all pressure fix-ID_temp :pre - -See the "compute temp"_compute_temp.html and "compute -pressure"_compute_pressure.html commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press". The group for -the new computes is "all" since pressure is computed for the entire -system. - -Note that these are NOT the computes used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_press}. This means you can change the attributes of this -fix's temperature or pressure via the -"compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} or -{thermo_press} will have no effect on this fix. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the values of E0, V0, and P0, as well as the -state of all the thermostat and barostat -variables to "binary restart files"_restart.html. See the -"read_restart"_read_restart.html command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. - -The "fix_modify"_fix_modify.html {e0}, {v0} and {p0} keywords -can be used to define the values of E0, V0, and P0. Note the -the values for {e0} and {v0} are extensive, and so must correspond -to the total energy and volume of the entire system, not energy and -volume per atom. If any of these quantities are not specified, then the -instantaneous value in the system at the start of the simulation is used. - -The "fix_modify"_fix_modify.html {temp} and {press} options are -supported by these fixes. You can use them to assign a -"compute"_compute.html you have defined to this fix which will be used -in its thermostatting or barostatting procedure, as described above. -If you do this, note that the kinetic energy derived from the compute -temperature should be consistent with the virial term computed using -all atoms for the pressure. LAMMPS will warn you if you choose to -compute temperature on a subset of atoms. - -The "fix_modify"_fix_modify.html {energy} option is supported by these -fixes to add the energy change induced by Nose/Hoover thermostatting -and barostatting to the system's potential energy as part of -"thermodynamic output"_thermo_style.html. Either way, this energy is *not* -included in the definition of internal energy E when calculating the value -of Delta in the above equation. - -These fixes compute a global scalar and a global vector of quantities, -which can be accessed by various "output commands"_Howto_output.html. -The scalar value calculated by these fixes is "extensive"; the vector -values are "intensive". - -The scalar is the cumulative energy change due to the fix. - -The vector stores three quantities unique to this fix (Delta, Us, and up), -followed by all the internal Nose/Hoover thermostat and barostat -variables defined for "fix npt"_fix_nh.html. Delta is the deviation -of the temperature from the target temperature, given by the above equation. -Us and up are the shock and particle velocity corresponding to a steady -shock calculated from the RH conditions. They have units of distance/time. - -[Restrictions:] - -This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -All the usual restrictions for "fix npt"_fix_nh.html apply, -plus the additional ones mentioned above. - -[Related commands:] - -"fix msst"_fix_msst.html, "fix npt"_fix_nh.html, "fix_modify"_fix_modify.html - -[Default:] - -The keyword defaults are the same as those for "fix npt"_fix_nh.html - -:line - -:link(Ravelo1) -[(Ravelo)] Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004). diff --git a/doc/txt/fix_npt_asphere.txt b/doc/txt/fix_npt_asphere.txt deleted file mode 100644 index 194f4ff499..0000000000 --- a/doc/txt/fix_npt_asphere.txt +++ /dev/null @@ -1,176 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix npt/asphere command :h3 -fix npt/asphere/omp command :h3 - -[Syntax:] - -fix ID group-ID npt/asphere keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command -npt/asphere = style name of this fix command -additional thermostat and barostat related keyword/value pairs from the "fix npt"_fix_nh.html command can be appended :ul - -[Examples:] - -fix 1 all npt/asphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 -fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 -fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2 -fix 2 water npt/asphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial :pre - -[Description:] - -Perform constant NPT integration to update position, velocity, -orientation, and angular velocity each timestep for aspherical or -ellipsoidal particles in the group using a Nose/Hoover temperature -thermostat and Nose/Hoover pressure barostat. P is pressure; T is -temperature. This creates a system trajectory consistent with the -isothermal-isobaric ensemble. - -This fix differs from the "fix npt"_fix_nh.html command, which -assumes point particles and only updates their position and velocity. - -The thermostat is applied to both the translational and rotational -degrees of freedom for the aspherical particles, assuming a compute is -used which calculates a temperature that includes the rotational -degrees of freedom (see below). The translational degrees of freedom -can also have a bias velocity removed from them before thermostatting -takes place; see the description below. - -Additional parameters affecting the thermostat and barostat are -specified by keywords and values documented with the "fix -npt"_fix_nh.html command. See, for example, discussion of the {temp}, -{iso}, {aniso}, and {dilate} keywords. - -The particles in the fix group are the only ones whose velocities and -positions are updated by the velocity/position update portion of the -NPT integration. - -Regardless of what particles are in the fix group, a global pressure is -computed for all particles. Similarly, when the size of the simulation -box is changed, all particles are re-scaled to new positions, unless the -keyword {dilate} is specified with a value of {partial}, in which case -only the particles in the fix group are re-scaled. The latter can be -useful for leaving the coordinates of particles in a solid substrate -unchanged and controlling the pressure of a surrounding fluid. - -:line - -This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp/asphere" and -"pressure", as if these commands had been issued: - -compute fix-ID_temp all temp/asphere -compute fix-ID_press all pressure fix-ID_temp :pre - -See the "compute temp/asphere"_compute_temp_asphere.html and "compute -pressure"_compute_pressure.html commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is "all" -since pressure is computed for the entire system. - -Note that these are NOT the computes used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_press}. This means you can change the attributes of this -fix's temperature or pressure via the -"compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} or -{thermo_press} will have no effect on this fix. - -Like other fixes that perform thermostatting, this fix can be used -with "compute commands"_compute.html that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the "fix_modify"_fix_modify.html command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the Nose/Hoover thermostat and barostat -to "binary restart files"_restart.html. See the -"read_restart"_read_restart.html command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} and {press} options are -supported by this fix. You can use them to assign a -"compute"_compute.html you have defined to this fix which will be used -in its thermostatting or barostatting procedure. If you do this, note -that the kinetic energy derived from the compute temperature should be -consistent with the virial term computed using all atoms for the -pressure. LAMMPS will warn you if you choose to compute temperature -on a subset of atoms. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting and -barostatting to the system's potential energy as part of -"thermodynamic output"_thermo_style.html. - -This fix computes the same global scalar and global vector of -quantities as does the "fix npt"_fix_nh.html command. - -This fix can ramp its target temperature and pressure over multiple -runs, using the {start} and {stop} keywords of the "run"_run.html -command. See the "run"_run.html command for details of how to do -this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the "atom_style ellipsoid"_atom_style.html -command. - -All particles in the group must be finite-size. They cannot be point -particles, but they can be aspherical or spherical as defined by their -shape attribute. - -[Related commands:] - -"fix npt"_fix_nh.html, "fix nve_asphere"_fix_nve_asphere.html, "fix -nvt_asphere"_fix_nvt_asphere.html, "fix_modify"_fix_modify.html - -[Default:] none diff --git a/doc/txt/fix_npt_body.txt b/doc/txt/fix_npt_body.txt deleted file mode 100644 index 1d608137b6..0000000000 --- a/doc/txt/fix_npt_body.txt +++ /dev/null @@ -1,171 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix npt/body command :h3 - -[Syntax:] - -fix ID group-ID npt/body keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command -npt/body = style name of this fix command -additional thermostat and barostat related keyword/value pairs from the "fix npt"_fix_nh.html command can be appended :ul - -[Examples:] - -fix 1 all npt/body temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 -fix 2 all npt/body temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 -fix 2 all npt/body temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2 -fix 2 water npt/body temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial :pre - -[Description:] - -Perform constant NPT integration to update position, velocity, -orientation, and angular velocity each timestep for body -particles in the group using a Nose/Hoover temperature -thermostat and Nose/Hoover pressure barostat. P is pressure; T is -temperature. This creates a system trajectory consistent with the -isothermal-isobaric ensemble. - -This fix differs from the "fix npt"_fix_nh.html command, which -assumes point particles and only updates their position and velocity. - -The thermostat is applied to both the translational and rotational -degrees of freedom for the body particles, assuming a compute is -used which calculates a temperature that includes the rotational -degrees of freedom (see below). The translational degrees of freedom -can also have a bias velocity removed from them before thermostatting -takes place; see the description below. - -Additional parameters affecting the thermostat and barostat are -specified by keywords and values documented with the "fix -npt"_fix_nh.html command. See, for example, discussion of the {temp}, -{iso}, {aniso}, and {dilate} keywords. - -The particles in the fix group are the only ones whose velocities and -positions are updated by the velocity/position update portion of the -NPT integration. - -Regardless of what particles are in the fix group, a global pressure is -computed for all particles. Similarly, when the size of the simulation -box is changed, all particles are re-scaled to new positions, unless the -keyword {dilate} is specified with a value of {partial}, in which case -only the particles in the fix group are re-scaled. The latter can be -useful for leaving the coordinates of particles in a solid substrate -unchanged and controlling the pressure of a surrounding fluid. - -:line - -This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp/body" and -"pressure", as if these commands had been issued: - -compute fix-ID_temp all temp/body -compute fix-ID_press all pressure fix-ID_temp :pre - -See the "compute temp/body"_compute_temp_body.html and "compute -pressure"_compute_pressure.html commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is "all" -since pressure is computed for the entire system. - -Note that these are NOT the computes used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_press}. This means you can change the attributes of this -fix's temperature or pressure via the -"compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} or -{thermo_press} will have no effect on this fix. - -Like other fixes that perform thermostatting, this fix can be used -with "compute commands"_compute.html that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the "fix_modify"_fix_modify.html command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the Nose/Hoover thermostat and barostat -to "binary restart files"_restart.html. See the -"read_restart"_read_restart.html command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} and {press} options are -supported by this fix. You can use them to assign a -"compute"_compute.html you have defined to this fix which will be used -in its thermostatting or barostatting procedure. If you do this, note -that the kinetic energy derived from the compute temperature should be -consistent with the virial term computed using all atoms for the -pressure. LAMMPS will warn you if you choose to compute temperature -on a subset of atoms. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting and -barostatting to the system's potential energy as part of -"thermodynamic output"_thermo_style.html. - -This fix computes the same global scalar and global vector of -quantities as does the "fix npt"_fix_nh.html command. - -This fix can ramp its target temperature and pressure over multiple -runs, using the {start} and {stop} keywords of the "run"_run.html -command. See the "run"_run.html command for details of how to do -this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the "atom_style body"_atom_style.html -command. - -[Related commands:] - -"fix npt"_fix_nh.html, "fix nve_body"_fix_nve_body.html, "fix -nvt_body"_fix_nvt_body.html, "fix_modify"_fix_modify.html - -[Default:] none diff --git a/doc/txt/fix_npt_sphere.txt b/doc/txt/fix_npt_sphere.txt deleted file mode 100644 index 6ebb68e176..0000000000 --- a/doc/txt/fix_npt_sphere.txt +++ /dev/null @@ -1,185 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix npt/sphere command :h3 -fix npt/sphere/omp command :h3 - -[Syntax:] - -fix ID group-ID npt/sphere keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command -npt/sphere = style name of this fix command -zero or more keyword/value pairs may be appended :l -keyword = {disc} :l - {disc} value = none = treat particles as 2d discs, not spheres :pre -additional thermostat and barostat related keyword/value pairs from the "fix npt"_fix_nh.html command can be appended :l,ule - - -[Examples:] - -fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 -fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 -fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 disc -fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2 -fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial :pre - -[Description:] - -Perform constant NPT integration to update position, velocity, and -angular velocity each timestep for finite-sizex spherical particles in -the group using a Nose/Hoover temperature thermostat and Nose/Hoover -pressure barostat. P is pressure; T is temperature. This creates a -system trajectory consistent with the isothermal-isobaric ensemble. - -This fix differs from the "fix npt"_fix_nh.html command, which -assumes point particles and only updates their position and velocity. - -The thermostat is applied to both the translational and rotational -degrees of freedom for the spherical particles, assuming a compute is -used which calculates a temperature that includes the rotational -degrees of freedom (see below). The translational degrees of freedom -can also have a bias velocity removed from them before thermostatting -takes place; see the description below. - -If the {disc} keyword is used, then each particle is treated as a 2d -disc (circle) instead of as a sphere. This is only possible for 2d -simulations, as defined by the "dimension"_dimension.html keyword. -The only difference between discs and spheres in this context is their -moment of inertia, as used in the time integration. - -Additional parameters affecting the thermostat and barostat are -specified by keywords and values documented with the "fix -npt"_fix_nh.html command. See, for example, discussion of the {temp}, -{iso}, {aniso}, and {dilate} keywords. - -The particles in the fix group are the only ones whose velocities and -positions are updated by the velocity/position update portion of the -NPT integration. - -Regardless of what particles are in the fix group, a global pressure is -computed for all particles. Similarly, when the size of the simulation -box is changed, all particles are re-scaled to new positions, unless the -keyword {dilate} is specified with a value of {partial}, in which case -only the particles in the fix group are re-scaled. The latter can be -useful for leaving the coordinates of particles in a solid substrate -unchanged and controlling the pressure of a surrounding fluid. - -:line - -This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp/sphere" and -"pressure", as if these commands had been issued: - -compute fix-ID_temp all temp/sphere -compute fix-ID_press all pressure fix-ID_temp :pre - -See the "compute temp/sphere"_compute_temp_sphere.html and "compute -pressure"_compute_pressure.html commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is "all" -since pressure is computed for the entire system. - -Note that these are NOT the computes used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_press}. This means you can change the attributes of this -fix's temperature or pressure via the -"compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} or -{thermo_press} will have no effect on this fix. - -Like other fixes that perform thermostatting, this fix can be used -with "compute commands"_compute.html that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the "fix_modify"_fix_modify.html command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the Nose/Hoover thermostat and barostat -to "binary restart files"_restart.html. See the -"read_restart"_read_restart.html command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} and {press} options are -supported by this fix. You can use them to assign a -"compute"_compute.html you have defined to this fix which will be used -in its thermostatting or barostatting procedure. If you do this, note -that the kinetic energy derived from the compute temperature should be -consistent with the virial term computed using all atoms for the -pressure. LAMMPS will warn you if you choose to compute temperature -on a subset of atoms. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting and -barostatting to the system's potential energy as part of -"thermodynamic output"_thermo_style.html. - -This fix computes the same global scalar and global vector of -quantities as does the "fix npt"_fix_nh.html command. - -This fix can ramp its target temperature and pressure over multiple -runs, using the {start} and {stop} keywords of the "run"_run.html -command. See the "run"_run.html command for details of how to do -this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the "atom_style sphere"_atom_style.html -command. - -All particles in the group must be finite-size spheres. They cannot -be point particles. - -Use of the {disc} keyword is only allowed for 2d simulations, as -defined by the "dimension"_dimension.html keyword. - -[Related commands:] - -"fix npt"_fix_nh.html, "fix nve_sphere"_fix_nve_sphere.html, "fix -nvt_sphere"_fix_nvt_sphere.html, "fix -npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html - -[Default:] none diff --git a/doc/txt/fix_nve.txt b/doc/txt/fix_nve.txt deleted file mode 100644 index 2347f957ae..0000000000 --- a/doc/txt/fix_nve.txt +++ /dev/null @@ -1,72 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve command :h3 -fix nve/intel command :h3 -fix nve/kk command :h3 -fix nve/omp command :h3 - -[Syntax:] - -fix ID group-ID nve :pre - -ID, group-ID are documented in "fix"_fix.html command -nve = style name of this fix command :ul - -[Examples:] - -fix 1 all nve :pre - -[Description:] - -Perform constant NVE integration to update position and velocity for -atoms in the group each timestep. V is volume; E is energy. This -creates a system trajectory consistent with the microcanonical -ensemble. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix nvt"_fix_nh.html, "fix npt"_fix_nh.html - -[Default:] none diff --git a/doc/txt/fix_nve_asphere.txt b/doc/txt/fix_nve_asphere.txt deleted file mode 100644 index bd9e4ae873..0000000000 --- a/doc/txt/fix_nve_asphere.txt +++ /dev/null @@ -1,85 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/asphere command :h3 -fix nve/asphere/intel command :h3 - -[Syntax:] - -fix ID group-ID nve/asphere :pre - -ID, group-ID are documented in "fix"_fix.html command -nve/asphere = style name of this fix command :ul - -[Examples:] - -fix 1 all nve/asphere :pre - -[Description:] - -Perform constant NVE integration to update position, velocity, -orientation, and angular velocity for aspherical particles in the -group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. - -This fix differs from the "fix nve"_fix_nve.html command, which -assumes point particles and only updates their position and velocity. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the "atom_style ellipsoid"_atom_style.html -command. - -All particles in the group must be finite-size. They cannot be point -particles, but they can be aspherical or spherical as defined by their -shape attribute. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix nve/sphere"_fix_nve_sphere.html - -[Default:] none diff --git a/doc/txt/fix_nve_asphere_noforce.txt b/doc/txt/fix_nve_asphere_noforce.txt deleted file mode 100644 index c0598e8839..0000000000 --- a/doc/txt/fix_nve_asphere_noforce.txt +++ /dev/null @@ -1,65 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/asphere/noforce command :h3 - -[Syntax:] - -fix ID group-ID nve/asphere/noforce :pre - -ID, group-ID are documented in "fix"_fix.html command -nve/asphere/noforce = style name of this fix command :ul - -[Examples:] - -fix 1 all nve/asphere/noforce - -[Description:] - -Perform updates of position and orientation, but not velocity or -angular momentum for atoms in the group each timestep. In other -words, the force and torque on the atoms is ignored and their velocity -and angular momentum are not updated. The atom velocities and -angular momenta are used to update their positions and orientation. - -This is useful as an implicit time integrator for Fast Lubrication -Dynamics, since the velocity and angular momentum are updated by the -"pair_style lubricuteU"_pair_lubricateU.html command. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the "atom_style ellipsoid"_atom_style.html -command. - -All particles in the group must be finite-size. They cannot be point -particles, but they can be aspherical or spherical as defined by their -shape attribute. - -[Related commands:] - -"fix nve/noforce"_fix_nve_noforce.html, "fix -nve/asphere"_fix_nve_asphere.html - -[Default:] none diff --git a/doc/txt/fix_nve_awpmd.txt b/doc/txt/fix_nve_awpmd.txt deleted file mode 100644 index 11951c2fe1..0000000000 --- a/doc/txt/fix_nve_awpmd.txt +++ /dev/null @@ -1,56 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/awpmd command :h3 - -[Syntax:] - -fix ID group-ID nve/awpmd :pre - -ID, group-ID are documented in "fix"_fix.html command -nve/awpmd = style name of this fix command :ul - -[Examples:] - -fix 1 all nve/awpmd :pre - -[Description:] - -Perform constant NVE integration to update position and velocity for -nuclei and electrons in the group for the "Antisymmetrized Wave Packet -Molecular Dynamics"_pair_awpmd.html model. V is volume; E is energy. -This creates a system trajectory consistent with the microcanonical -ensemble. - -The operation of this fix is exactly like that described by the "fix -nve"_fix_nve.html command, except that the width and width-velocity of -the electron wave functions are also updated. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-AWPMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix nve"_fix_nve.html - -[Default:] none diff --git a/doc/txt/fix_nve_body.txt b/doc/txt/fix_nve_body.txt deleted file mode 100644 index 1a9efb5e13..0000000000 --- a/doc/txt/fix_nve_body.txt +++ /dev/null @@ -1,62 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/body command :h3 - -[Syntax:] - -fix ID group-ID nve/body :pre - -ID, group-ID are documented in "fix"_fix.html command -nve/body = style name of this fix command :ul - -[Examples:] - -fix 1 all nve/body :pre - -[Description:] - -Perform constant NVE integration to update position, velocity, -orientation, and angular velocity for body particles in the group each -timestep. V is volume; E is energy. This creates a system trajectory -consistent with the microcanonical ensemble. See the "Howto -body"_Howto_body.html doc page for more details on using body -particles. - -This fix differs from the "fix nve"_fix_nve.html command, which -assumes point particles and only updates their position and velocity. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the "atom_style body"_atom_style.html -command. - -All particles in the group must be body particles. They cannot be -point particles. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix nve/sphere"_fix_nve_sphere.html, "fix -nve/asphere"_fix_nve_asphere.html - -[Default:] none diff --git a/doc/txt/fix_nve_eff.txt b/doc/txt/fix_nve_eff.txt deleted file mode 100644 index 556b95deba..0000000000 --- a/doc/txt/fix_nve_eff.txt +++ /dev/null @@ -1,54 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/eff command :h3 - -[Syntax:] - -fix ID group-ID nve/eff :pre - -ID, group-ID are documented in "fix"_fix.html command -nve/eff = style name of this fix command :ul - -[Examples:] - -fix 1 all nve/eff :pre - -[Description:] - -Perform constant NVE integration to update position and velocity for -nuclei and electrons in the group for the "electron force -field"_pair_eff.html model. V is volume; E is energy. This creates a -system trajectory consistent with the microcanonical ensemble. - -The operation of this fix is exactly like that described by the "fix -nve"_fix_nve.html command, except that the radius and radial velocity -of electrons are also updated. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix nvt/eff"_fix_nh_eff.html, "fix -npt/eff"_fix_nh_eff.html - -[Default:] none diff --git a/doc/txt/fix_nve_limit.txt b/doc/txt/fix_nve_limit.txt deleted file mode 100644 index 8c8c66a0da..0000000000 --- a/doc/txt/fix_nve_limit.txt +++ /dev/null @@ -1,86 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/limit command :h3 - -[Syntax:] - -fix ID group-ID nve/limit xmax :pre - -ID, group-ID are documented in "fix"_fix.html command -nve = style name of this fix command -xmax = maximum distance an atom can move in one timestep (distance units) :ul - -[Examples:] - -fix 1 all nve/limit 0.1 :pre - -[Description:] - -Perform constant NVE updates of position and velocity for atoms in the -group each timestep. A limit is imposed on the maximum distance an -atom can move in one timestep. This is useful when starting a -simulation with a configuration containing highly overlapped atoms. -Normally this would generate huge forces which would blow atoms out of -the simulation box, causing LAMMPS to stop with an error. - -Using this fix can overcome that problem. Forces on atoms must still -be computable (which typically means 2 atoms must have a separation -distance > 0.0). But large velocities generated by large forces are -reset to a value that corresponds to a displacement of length {xmax} -in a single timestep. {Xmax} is specified in distance units; see the -"units"_units.html command for details. The value of {xmax} should be -consistent with the neighbor skin distance and the frequency of -neighbor list re-building, so that pairwise interactions are not -missed on successive timesteps as atoms move. See the -"neighbor"_neighbor.html and "neigh_modify"_neigh_modify.html commands -for details. - -Note that if a velocity reset occurs the integrator will not conserve -energy. On steps where no velocity resets occur, this integrator is -exactly like the "fix nve"_fix_nve.html command. Since forces are -unaltered, pressures computed by thermodynamic output will still be -very large for overlapped configurations. - -NOTE: You should not use "fix shake"_fix_shake.html in conjunction -with this fix. That is because fix shake applies constraint forces -based on the predicted positions of atoms after the next timestep. -It has no way of knowing the timestep may change due to this fix, -which will cause the constraint forces to be invalid. A better -strategy is to turn off fix shake when performing initial dynamics -that need this fix, then turn fix shake on when doing normal dynamics -with a fixed-size timestep. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the count of how -many updates of atom's velocity/position were limited by the maximum -distance criterion. This should be roughly the number of atoms so -affected, except that updates occur at both the beginning and end of a -timestep in a velocity Verlet timestepping algorithm. This is a -cumulative quantity for the current run, but is re-initialized to zero -each time a run is performed. The scalar value calculated by this fix -is "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix nve"_fix_nve.html, "fix nve/noforce"_fix_nve_noforce.html, -"pair_style soft"_pair_soft.html - -[Default:] none diff --git a/doc/txt/fix_nve_line.txt b/doc/txt/fix_nve_line.txt deleted file mode 100644 index 896e3b810d..0000000000 --- a/doc/txt/fix_nve_line.txt +++ /dev/null @@ -1,57 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/line command :h3 - -[Syntax:] - -fix ID group-ID nve/line :pre - -ID, group-ID are documented in "fix"_fix.html command -nve/line = style name of this fix command :ul - -[Examples:] - -fix 1 all nve/line :pre - -[Description:] - -Perform constant NVE integration to update position, velocity, -orientation, and angular velocity for line segment particles in the -group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. See "Howto -spherical"_Howto_spherical.html doc page for an overview of using line -segment particles. - -This fix differs from the "fix nve"_fix_nve.html command, which -assumes point particles and only updates their position and velocity. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that particles be line segments as defined by the -"atom_style line"_atom_style.html command. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix nve/asphere"_fix_nve_asphere.html - -[Default:] none diff --git a/doc/txt/fix_nve_manifold_rattle.txt b/doc/txt/fix_nve_manifold_rattle.txt deleted file mode 100644 index 5301ea603c..0000000000 --- a/doc/txt/fix_nve_manifold_rattle.txt +++ /dev/null @@ -1,102 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/manifold/rattle command :h3 - -[Syntax:] - -fix ID group-ID nve/manifold/rattle tol maxit manifold manifold-args keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -nve/manifold/rattle = style name of this fix command :l -tol = tolerance to which Newton iteration must converge :l -maxit = maximum number of iterations to perform :l -manifold = name of the manifold :l -manifold-args = parameters for the manifold :l -one or more keyword/value pairs may be appended :l -keyword = {every} - {every} values = N - N = print info about iteration every N steps. N = 0 means no output :pre -:ule - -[Examples:] - -fix 1 all nve/manifold/rattle 1e-4 10 sphere 5.0 -fix step all nve/manifold/rattle 1e-8 100 ellipsoid 2.5 2.5 5.0 every 25 :pre - -[Description:] - -Perform constant NVE integration to update position and velocity for -atoms constrained to a curved surface (manifold) in the group each -timestep. The constraint is handled by RATTLE "(Andersen)"_#Andersen1 -written out for the special case of single-particle constraints as -explained in "(Paquay)"_#Paquay2. V is volume; E is energy. This way, -the dynamics of particles constrained to curved surfaces can be -studied. If combined with "fix langevin"_fix_langevin.html, this -generates Brownian motion of particles constrained to a curved -surface. For a list of currently supported manifolds and their -parameters, see the "Howto manifold"_Howto_manifold.html doc page. - -Note that the particles must initially be close to the manifold in -question. If not, RATTLE will not be able to iterate until the -constraint is satisfied, and an error is generated. For simple -manifolds this can be achieved with {region} and {create_atoms} -commands, but for more complex surfaces it might be more useful to -write a script. - -The manifold args may be equal-style variables, like so: - -variable R equal "ramp(5.0,3.0)" -fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R :pre - -In this case, the manifold parameter will change in time according to -the variable. This is not a problem for the time integrator as long -as the change of the manifold is slow with respect to the dynamics of -the particles. Note that if the manifold has to exert work on the -particles because of these changes, the total energy might not be -conserved. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -:line - -[Restrictions:] - -This fix is part of the USER-MANIFOLD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -:line - -[Related commands:] - -"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix -manifoldforce"_fix_manifoldforce.html - -[Default:] every = 0, tchain = 3 - -:line - -:link(Andersen1) -[(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983). - -:link(Paquay2) -[(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016). -preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/. - - diff --git a/doc/txt/fix_nve_noforce.txt b/doc/txt/fix_nve_noforce.txt deleted file mode 100644 index da8d16bbb7..0000000000 --- a/doc/txt/fix_nve_noforce.txt +++ /dev/null @@ -1,54 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/noforce command :h3 - -[Syntax:] - -fix ID group-ID nve :pre - -ID, group-ID are documented in "fix"_fix.html command -nve/noforce = style name of this fix command :ul - -[Examples:] - -fix 3 wall nve/noforce :pre - -[Description:] - -Perform updates of position, but not velocity for atoms in the group -each timestep. In other words, the force on the atoms is ignored and -their velocity is not updated. The atom velocities are used to update -their positions. - -This can be useful for wall atoms, when you set their velocities, and -want the wall to move (or stay stationary) in a prescribed fashion. - -This can also be accomplished via the "fix setforce"_fix_setforce.html -command, but with fix nve/noforce, the forces on the wall atoms are -unchanged, and can thus be printed by the "dump"_dump.html command or -queried with an equal-style "variable"_variable.html that uses the -fcm() group function to compute the total force on the group of atoms. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix nve"_fix_nve.html - -[Default:] none diff --git a/doc/txt/fix_nve_sphere.txt b/doc/txt/fix_nve_sphere.txt deleted file mode 100644 index 225359dfa7..0000000000 --- a/doc/txt/fix_nve_sphere.txt +++ /dev/null @@ -1,122 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/sphere command :h3 -fix nve/sphere/omp command :h3 -fix nve/sphere/kk command :h3 - -[Syntax:] - -fix ID group-ID nve/sphere :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -nve/sphere = style name of this fix command :l -zero or more keyword/value pairs may be appended :l -keyword = {update} or {disc} :l - {update} value = {dipole} or {dipole/dlm} - dipole = update orientation of dipole moment during integration - dipole/dlm = use DLM integrator to update dipole orientation - {disc} value = none = treat particles as 2d discs, not spheres :pre -:ule - -[Examples:] - -fix 1 all nve/sphere -fix 1 all nve/sphere update dipole -fix 1 all nve/sphere disc -fix 1 all nve/sphere update dipole/dlm :pre - -[Description:] - -Perform constant NVE integration to update position, velocity, and -angular velocity for finite-size spherical particles in the group each -timestep. V is volume; E is energy. This creates a system trajectory -consistent with the microcanonical ensemble. - -This fix differs from the "fix nve"_fix_nve.html command, which -assumes point particles and only updates their position and velocity. - -If the {update} keyword is used with the {dipole} value, then the -orientation of the dipole moment of each particle is also updated -during the time integration. This option should be used for models -where a dipole moment is assigned to finite-size particles, -e.g. spheroids via use of the "atom_style hybrid sphere -dipole"_atom_style.html command. - -The default dipole orientation integrator can be changed to the -Dullweber-Leimkuhler-McLachlan integration scheme -"(Dullweber)"_#nh-Dullweber when using {update} with the value -{dipole/dlm}. This integrator is symplectic and time-reversible, -giving better energy conservation and allows slightly longer timesteps -at only a small additional computational cost. - -If the {disc} keyword is used, then each particle is treated as a 2d -disc (circle) instead of as a sphere. This is only possible for 2d -simulations, as defined by the "dimension"_dimension.html keyword. -The only difference between discs and spheres in this context is their -moment of inertia, as used in the time integration. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the "atom_style sphere"_atom_style.html -command. If the {dipole} keyword is used, then they must also store a -dipole moment as defined by the "atom_style dipole"_atom_style.html -command. - -All particles in the group must be finite-size spheres. They cannot -be point particles. - -Use of the {disc} keyword is only allowed for 2d simulations, as -defined by the "dimension"_dimension.html keyword. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix nve/asphere"_fix_nve_asphere.html - -[Default:] none - -:line - -:link(nve-Dullweber) -[(Dullweber)] Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, -5840 (1997). diff --git a/doc/txt/fix_nve_spin.txt b/doc/txt/fix_nve_spin.txt deleted file mode 100644 index 8e6284639b..0000000000 --- a/doc/txt/fix_nve_spin.txt +++ /dev/null @@ -1,82 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/spin command :h3 - -[Syntax:] - -fix ID group-ID nve/spin keyword values :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -nve/spin = style name of this fix command :l -keyword = {lattice} :l - {lattice} value = {moving} or {frozen} - moving = integrate both spin and atomic degress of freedom - frozen = integrate spins on a fixed lattice :pre -:ule - -[Examples:] - -fix 3 all nve/spin lattice moving -fix 1 all nve/spin lattice frozen :pre - -[Description:] - -Perform a symplectic integration for the spin or spin-lattice system. - -The {lattice} keyword defines if the spins are integrated on a lattice -of fixed atoms (lattice = frozen), or if atoms are moving -(lattice = moving). -The first case corresponds to a spin dynamics calculation, and -the second to a spin-lattice calculation. -By default a spin-lattice integration is performed (lattice = moving). - -The {nve/spin} fix applies a Suzuki-Trotter decomposition to -the equations of motion of the spin lattice system, following the scheme: - -:c,image(Eqs/fix_integration_spin_stdecomposition.jpg) - -according to the implementation reported in "(Omelyan)"_#Omelyan1. - -A sectoring method enables this scheme for parallel calculations. -The implementation of this sectoring algorithm is reported -in "(Tranchida)"_#Tranchida1. - -:line - -[Restrictions:] - -This fix style can only be used if LAMMPS was built with the SPIN -package. See the "Build package"_Build_package.html doc page for more -info. - -To use the spin algorithm, it is necessary to define a map with -the atom_modify command. Typically, by adding the command: - -atom_modify map array :pre - -before you create the simulation box. Note that the keyword "hash" -instead of "array" is also valid. - -[Related commands:] - -"atom_style spin"_atom_style.html, "fix nve"_fix_nve.html - -[Default:] - -The option default is lattice = moving. - -:line - -:link(Omelyan1) -[(Omelyan)] Omelyan, Mryglod, and Folk. Phys. Rev. Lett. -86(5), 898. (2001). - -:link(Tranchida1) -[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, -Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/txt/fix_nve_tri.txt b/doc/txt/fix_nve_tri.txt deleted file mode 100644 index c14907ca02..0000000000 --- a/doc/txt/fix_nve_tri.txt +++ /dev/null @@ -1,57 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/tri command :h3 - -[Syntax:] - -fix ID group-ID nve/tri :pre - -ID, group-ID are documented in "fix"_fix.html command -nve/tri = style name of this fix command :ul - -[Examples:] - -fix 1 all nve/tri :pre - -[Description:] - -Perform constant NVE integration to update position, velocity, -orientation, and angular momentum for triangular particles in the -group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. See the -"Howto spherical"_Howto_spherical.html doc page for an overview of -using triangular particles. - -This fix differs from the "fix nve"_fix_nve.html command, which -assumes point particles and only updates their position and velocity. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that particles be triangles as defined by the -"atom_style tri"_atom_style.html command. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix nve/asphere"_fix_nve_asphere.html - -[Default:] none diff --git a/doc/txt/fix_nvk.txt b/doc/txt/fix_nvk.txt deleted file mode 100644 index 98f63487b7..0000000000 --- a/doc/txt/fix_nvk.txt +++ /dev/null @@ -1,71 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nvk command :h3 - -[Syntax:] - -fix ID group-ID nvk :pre - -ID, group-ID are documented in "fix"_fix.html command -nvk = style name of this fix command :ul - -[Examples:] - -fix 1 all nvk :pre - -[Description:] - -Perform constant kinetic energy integration using the Gaussian -thermostat to update position and velocity for atoms in the group each -timestep. V is volume; K is kinetic energy. This creates a system -trajectory consistent with the isokinetic ensemble. - -The equations of motion used are those of Minary et al in -"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in -"(Zhang)"_#nvk-Zhang. - -The kinetic energy will be held constant at its value given when fix -nvk is initiated. If a different kinetic energy is desired, the -"velocity"_velocity.html command should be used to change the kinetic -energy prior to this fix. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -The Gaussian thermostat only works when it is applied to all atoms in -the simulation box. Therefore, the group must be set to all. - -This fix has not yet been implemented to work with the RESPA integrator. - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] none - -[Default:] none - -:line - -:link(nvk-Minary) -[(Minary)] Minary, Martyna, and Tuckerman, J Chem Phys, 18, 2510 (2003). - -:link(nvk-Zhang) -[(Zhang)] Zhang, J Chem Phys, 106, 6102 (1997). diff --git a/doc/txt/fix_nvt_asphere.txt b/doc/txt/fix_nvt_asphere.txt deleted file mode 100644 index a2187f8495..0000000000 --- a/doc/txt/fix_nvt_asphere.txt +++ /dev/null @@ -1,152 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nvt/asphere command :h3 -fix nvt/asphere/omp command :h3 - -[Syntax:] - -fix ID group-ID nvt/asphere keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command -nvt/asphere = style name of this fix command -additional thermostat related keyword/value pairs from the "fix nvt"_fix_nh.html command can be appended :ul - -[Examples:] - -fix 1 all nvt/asphere temp 300.0 300.0 100.0 -fix 1 all nvt/asphere temp 300.0 300.0 100.0 drag 0.2 :pre - -[Description:] - -Perform constant NVT integration to update position, velocity, -orientation, and angular velocity each timestep for aspherical or -ellipsoidal particles in the group using a Nose/Hoover temperature -thermostat. V is volume; T is temperature. This creates a system -trajectory consistent with the canonical ensemble. - -This fix differs from the "fix nvt"_fix_nh.html command, which -assumes point particles and only updates their position and velocity. - -The thermostat is applied to both the translational and rotational -degrees of freedom for the aspherical particles, assuming a compute is -used which calculates a temperature that includes the rotational -degrees of freedom (see below). The translational degrees of freedom -can also have a bias velocity removed from them before thermostatting -takes place; see the description below. - -Additional parameters affecting the thermostat are specified by -keywords and values documented with the "fix nvt"_fix_nh.html -command. See, for example, discussion of the {temp} and {drag} -keywords. - -This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp/asphere", as if this command -had been issued: - -compute fix-ID_temp group-ID temp/asphere :pre - -See the "compute temp/asphere"_compute_temp_asphere.html command for -details. Note that the ID of the new compute is the fix-ID + -underscore + "temp", and the group for the new compute is the same as -the fix group. - -Note that this is NOT the compute used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -"compute_modify"_compute_modify.html command or print this temperature -during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} will have no -effect on this fix. - -Like other fixes that perform thermostatting, this fix can be used -with "compute commands"_compute.html that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the "fix_modify"_fix_modify.html command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the Nose/Hoover thermostat to "binary -restart files"_restart.html. See the "read_restart"_read_restart.html -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a "compute"_compute.html you have -defined to this fix which will be used in its thermostatting -procedure. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting to -the system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes the same global scalar and global vector of -quantities as does the "fix nvt"_fix_nh.html command. - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the ASPHERE package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the "atom_style ellipsoid"_atom_style.html -command. - -All particles in the group must be finite-size. They cannot be point -particles, but they can be aspherical or spherical as defined by their -shape attribute. - -[Related commands:] - -"fix nvt"_fix_nh.html, "fix nve_asphere"_fix_nve_asphere.html, "fix -npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html - -[Default:] none diff --git a/doc/txt/fix_nvt_body.txt b/doc/txt/fix_nvt_body.txt deleted file mode 100644 index 62c7cfecf8..0000000000 --- a/doc/txt/fix_nvt_body.txt +++ /dev/null @@ -1,147 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nvt/body command :h3 - -[Syntax:] - -fix ID group-ID nvt/body keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command -nvt/body = style name of this fix command -additional thermostat related keyword/value pairs from the "fix nvt"_fix_nh.html command can be appended :ul - -[Examples:] - -fix 1 all nvt/body temp 300.0 300.0 100.0 -fix 1 all nvt/body temp 300.0 300.0 100.0 drag 0.2 :pre - -[Description:] - -Perform constant NVT integration to update position, velocity, -orientation, and angular velocity each timestep for body -particles in the group using a Nose/Hoover temperature -thermostat. V is volume; T is temperature. This creates a system -trajectory consistent with the canonical ensemble. - -This fix differs from the "fix nvt"_fix_nh.html command, which -assumes point particles and only updates their position and velocity. - -The thermostat is applied to both the translational and rotational -degrees of freedom for the body particles, assuming a compute is -used which calculates a temperature that includes the rotational -degrees of freedom (see below). The translational degrees of freedom -can also have a bias velocity removed from them before thermostatting -takes place; see the description below. - -Additional parameters affecting the thermostat are specified by -keywords and values documented with the "fix nvt"_fix_nh.html -command. See, for example, discussion of the {temp} and {drag} -keywords. - -This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp/body", as if this command -had been issued: - -compute fix-ID_temp group-ID temp/body :pre - -See the "compute temp/body"_compute_temp_body.html command for -details. Note that the ID of the new compute is the fix-ID + -underscore + "temp", and the group for the new compute is the same as -the fix group. - -Note that this is NOT the compute used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -"compute_modify"_compute_modify.html command or print this temperature -during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} will have no -effect on this fix. - -Like other fixes that perform thermostatting, this fix can be used -with "compute commands"_compute.html that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the "fix_modify"_fix_modify.html command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the Nose/Hoover thermostat to "binary -restart files"_restart.html. See the "read_restart"_read_restart.html -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a "compute"_compute.html you have -defined to this fix which will be used in its thermostatting -procedure. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting to -the system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes the same global scalar and global vector of -quantities as does the "fix nvt"_fix_nh.html command. - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that atoms store torque and angular momentum and a -quaternion as defined by the "atom_style body"_atom_style.html -command. - -[Related commands:] - -"fix nvt"_fix_nh.html, "fix nve_body"_fix_nve_body.html, "fix -npt_body"_fix_npt_body.html, "fix_modify"_fix_modify.html - -[Default:] none diff --git a/doc/txt/fix_nvt_manifold_rattle.txt b/doc/txt/fix_nvt_manifold_rattle.txt deleted file mode 100644 index 0c4b81aa32..0000000000 --- a/doc/txt/fix_nvt_manifold_rattle.txt +++ /dev/null @@ -1,81 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nvt/manifold/rattle command :h3 - -[Syntax:] - -fix ID group-ID nvt/manifold/rattle tol maxit manifold manifold-args keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -nvt/manifold/rattle = style name of this fix command :l -tol = tolerance to which Newton iteration must converge :l -maxit = maximum number of iterations to perform :l -manifold = name of the manifold :l -manifold-args = parameters for the manifold :l -one or more keyword/value pairs may be appended :l -keyword = {temp} or {tchain} or {every} - {temp} values = Tstart Tstop Tdamp - Tstart, Tstop = external temperature at start/end of run - Tdamp = temperature damping parameter (time units) - {tchain} value = N - N = length of thermostat chain (1 = single thermostat) - {every} value = N - N = print info about iteration every N steps. N = 0 means no output :pre -:ule - -[Examples:] - -fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0 - -[Description:] - -This fix combines the RATTLE-based "(Andersen)"_#Andersen2 time -integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html -"(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the -canonical ensemble of particles constrained to a curved surface -(manifold). This sampling does suffer from discretization bias of -O(dt). For a list of currently supported manifolds and their -parameters, see the "Howto manifold"_Howto_manifold.html doc page. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -:line - -[Restrictions:] - -This fix is part of the USER-MANIFOLD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -:line - -[Related commands:] - -"fix nve/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix -manifoldforce"_fix_manifoldforce.html [Default:] every = 0 - -:line - -:link(Andersen2) -[(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983). - -:link(Paquay3) -[(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016). -preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/. - diff --git a/doc/txt/fix_nvt_sllod.txt b/doc/txt/fix_nvt_sllod.txt deleted file mode 100644 index 7050be58b3..0000000000 --- a/doc/txt/fix_nvt_sllod.txt +++ /dev/null @@ -1,188 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nvt/sllod command :h3 -fix nvt/sllod/intel command :h3 -fix nvt/sllod/omp command :h3 - -[Syntax:] - -fix ID group-ID nvt/sllod keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command -nvt/sllod = style name of this fix command -additional thermostat related keyword/value pairs from the "fix nvt"_fix_nh.html command can be appended :ul - -[Examples:] - -fix 1 all nvt/sllod temp 300.0 300.0 100.0 -fix 1 all nvt/sllod temp 300.0 300.0 100.0 drag 0.2 :pre - -[Description:] - -Perform constant NVT integration to update positions and velocities -each timestep for atoms in the group using a Nose/Hoover temperature -thermostat. V is volume; T is temperature. This creates a system -trajectory consistent with the canonical ensemble. - -This thermostat is used for a simulation box that is changing size -and/or shape, for example in a non-equilibrium MD (NEMD) simulation. -The size/shape change is induced by use of the "fix -deform"_fix_deform.html command, so each point in the simulation box -can be thought of as having a "streaming" velocity. This -position-dependent streaming velocity is subtracted from each atom's -actual velocity to yield a thermal velocity which is used for -temperature computation and thermostatting. For example, if the box -is being sheared in x, relative to y, then points at the bottom of the -box (low y) have a small x velocity, while points at the top of the -box (hi y) have a large x velocity. These velocities do not -contribute to the thermal "temperature" of the atom. - -NOTE: "Fix deform"_fix_deform.html has an option for remapping either -atom coordinates or velocities to the changing simulation box. To use -fix nvt/sllod, fix deform should NOT remap atom positions, because fix -nvt/sllod adjusts the atom positions and velocities to create a -velocity profile that matches the changing box size/shape. Fix deform -SHOULD remap atom velocities when atoms cross periodic boundaries -since that is consistent with maintaining the velocity profile created -by fix nvt/sllod. LAMMPS will give an error if this setting is not -consistent. - -The SLLOD equations of motion, originally proposed by Hoover and Ladd -(see "(Evans and Morriss)"_#Evans3), were proven to be equivalent to -Newton's equations of motion for shear flow by "(Evans and -Morriss)"_#Evans3. They were later shown to generate the desired -velocity gradient and the correct production of work by stresses for -all forms of homogeneous flow by "(Daivis and Todd)"_#Daivis. As -implemented in LAMMPS, they are coupled to a Nose/Hoover chain -thermostat in a velocity Verlet formulation, closely following the -implementation used for the "fix nvt"_fix_nh.html command. - -NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-sllod -discusses use of the SLLOD method and non-equilibrium MD (NEMD) -thermostatting generally, for both simple and complex fluids, -e.g. molecular systems. The latter can be tricky to do correctly. - -Additional parameters affecting the thermostat are specified by -keywords and values documented with the "fix nvt"_fix_nh.html -command. See, for example, discussion of the {temp} and {drag} -keywords. - -This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp/deform", as if this command had -been issued: - -compute fix-ID_temp group-ID temp/deform :pre - -See the "compute temp/deform"_compute_temp_deform.html command for -details. Note that the ID of the new compute is the fix-ID + -underscore + "temp", and the group for the new compute is the same as -the fix group. - -Note that this is NOT the compute used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -"compute_modify"_compute_modify.html command or print this temperature -during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} will have no -effect on this fix. - -Like other fixes that perform thermostatting, this fix can be used -with "compute commands"_compute.html that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the "fix_modify"_fix_modify.html command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the Nose/Hoover thermostat to "binary -restart files"_restart.html. See the "read_restart"_read_restart.html -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a "compute"_compute.html you have -defined to this fix which will be used in its thermostatting -procedure. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting to -the system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes the same global scalar and global vector of -quantities as does the "fix nvt"_fix_nh.html command. - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix works best without Nose-Hoover chain thermostats, i.e. using -tchain = 1. Setting tchain to larger values can result in poor -equilibration. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix nvt"_fix_nh.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html, -"fix_modify"_fix_modify.html, "compute -temp/deform"_compute_temp_deform.html - -[Default:] - -Same as "fix nvt"_fix_nh.html, except tchain = 1. - -:line - -:link(Evans3) -[(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984). - -:link(Daivis) -[(Daivis and Todd)] Daivis and Todd, J Chem Phys, 124, 194103 (2006). - -:link(Daivis-sllod) -[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book), -Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/txt/fix_nvt_sllod_eff.txt b/doc/txt/fix_nvt_sllod_eff.txt deleted file mode 100644 index 5cba15c8cf..0000000000 --- a/doc/txt/fix_nvt_sllod_eff.txt +++ /dev/null @@ -1,94 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nvt/sllod/eff command :h3 - -[Syntax:] - -fix ID group-ID nvt/sllod/eff keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command -nvt/sllod/eff = style name of this fix command -additional thermostat related keyword/value pairs from the "fix nvt/eff"_fix_nh_eff.html command can be appended :ul - -[Examples:] - -fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 -fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2 :pre - -[Description:] - -Perform constant NVT integration to update positions and velocities -each timestep for nuclei and electrons in the group for the "electron -force field"_pair_eff.html model, using a Nose/Hoover temperature -thermostat. V is volume; T is temperature. This creates a system -trajectory consistent with the canonical ensemble. - -The operation of this fix is exactly like that described by the "fix -nvt/sllod"_fix_nvt_sllod.html command, except that the radius and -radial velocity of electrons are also updated and thermostatted. -Likewise the temperature calculated by the fix, using the compute it -creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html doc -page), is performed with a "compute -temp/deform/eff"_compute_temp_deform_eff.html command that includes -the eFF contribution to the temperature from the electron radial -velocity. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the Nose/Hoover thermostat to "binary -restart files"_restart.html. See the "read_restart"_read_restart.html -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a "compute"_compute.html you have -defined to this fix which will be used in its thermostatting -procedure. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting to -the system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes the same global scalar and global vector of -quantities as does the "fix nvt/eff"_fix_nh_eff.html command. - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix works best without Nose-Hoover chain thermostats, i.e. using -tchain = 1. Setting tchain to larger values can result in poor -equilibration. - -[Related commands:] - -"fix nve/eff"_fix_nve_eff.html, "fix nvt/eff"_fix_nh_eff.html, "fix -langevin/eff"_fix_langevin_eff.html, "fix -nvt/sllod"_fix_nvt_sllod.html, "fix_modify"_fix_modify.html, "compute -temp/deform/eff"_compute_temp_deform_eff.html - -[Default:] - -Same as "fix nvt/eff"_fix_nh_eff.html, except tchain = 1. - -:line - -:link(Tuckerman2) -[(Tuckerman)] Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, -106, 5615 (1997). diff --git a/doc/txt/fix_nvt_sphere.txt b/doc/txt/fix_nvt_sphere.txt deleted file mode 100644 index 75222e0de8..0000000000 --- a/doc/txt/fix_nvt_sphere.txt +++ /dev/null @@ -1,161 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nvt/sphere command :h3 -fix nvt/sphere/omp command :h3 - -[Syntax:] - -fix ID group-ID nvt/sphere keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -nvt/sphere = style name of this fix command :l -zero or more keyword/value pairs may be appended :l -keyword = {disc} :l - {disc} value = none = treat particles as 2d discs, not spheres :pre -additional thermostat related keyword/value pairs from the "fix nvt"_fix_nh.html command can be appended :l,ule - -[Examples:] - -fix 1 all nvt/sphere temp 300.0 300.0 100.0 -fix 1 all nvt/sphere temp 300.0 300.0 100.0 disc -fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2 :pre - -[Description:] - -Perform constant NVT integration to update position, velocity, and -angular velocity each timestep for finite-size spherical particles in -the group using a Nose/Hoover temperature thermostat. V is volume; T -is temperature. This creates a system trajectory consistent with the -canonical ensemble. - -This fix differs from the "fix nvt"_fix_nh.html command, which -assumes point particles and only updates their position and velocity. - -The thermostat is applied to both the translational and rotational -degrees of freedom for the spherical particles, assuming a compute is -used which calculates a temperature that includes the rotational -degrees of freedom (see below). The translational degrees of freedom -can also have a bias velocity removed from them before thermostatting -takes place; see the description below. - -If the {disc} keyword is used, then each particle is treated as a 2d -disc (circle) instead of as a sphere. This is only possible for 2d -simulations, as defined by the "dimension"_dimension.html keyword. -The only difference between discs and spheres in this context is their -moment of inertia, as used in the time integration. - -Additional parameters affecting the thermostat are specified by -keywords and values documented with the "fix nvt"_fix_nh.html -command. See, for example, discussion of the {temp} and {drag} -keywords. - -This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp/sphere", as if this command -had been issued: - -compute fix-ID_temp group-ID temp/sphere :pre - -See the "compute temp/sphere"_compute_temp_sphere.html command for -details. Note that the ID of the new compute is the fix-ID + -underscore + "temp", and the group for the new compute is the same as -the fix group. - -Note that this is NOT the compute used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -"compute_modify"_compute_modify.html command or print this temperature -during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} will have no -effect on this fix. - -Like other fixes that perform thermostatting, this fix can be used -with "compute commands"_compute.html that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the "fix_modify"_fix_modify.html command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the state of the Nose/Hoover thermostat to "binary -restart files"_restart.html. See the "read_restart"_read_restart.html -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a "compute"_compute.html you have -defined to this fix which will be used in its thermostatting -procedure. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change induced by Nose/Hoover thermostatting to -the system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes the same global scalar and global vector of -quantities as does the "fix nvt"_fix_nh.html command. - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix requires that atoms store torque and angular velocity (omega) -and a radius as defined by the "atom_style sphere"_atom_style.html -command. - -All particles in the group must be finite-size spheres. They cannot -be point particles. - -Use of the {disc} keyword is only allowed for 2d simulations, as -defined by the "dimension"_dimension.html keyword. - -[Related commands:] - -"fix nvt"_fix_nh.html, "fix nve_sphere"_fix_nve_sphere.html, "fix -nvt_asphere"_fix_nvt_asphere.html, "fix -npt_sphere"_fix_npt_sphere.html, "fix_modify"_fix_modify.html - -[Default:] none diff --git a/doc/txt/fix_oneway.txt b/doc/txt/fix_oneway.txt deleted file mode 100644 index 433ceb50f2..0000000000 --- a/doc/txt/fix_oneway.txt +++ /dev/null @@ -1,60 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix oneway command :h3 - -[Syntax:] - -fix ID group-ID oneway N region-ID direction :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -oneway = style name of this fix command :l -N = apply this fix every this many timesteps :l -region-ID = ID of region where fix is active :l -direction = {x} or {-x} or {y} or {-y} or {z} or {-z} = coordinate and direction of the oneway constraint :l -:ule - -[Examples:] - -fix ions oneway 10 semi -x -fix all oneway 1 left -z -fix all oneway 1 right z :pre - -[Description:] - -Enforce that particles in the group and in a given region can only -move in one direction. This is done by reversing a particle's -velocity component, if it has the wrong sign in the specified -dimension. The effect is that the particle moves in one direction -only. - -This can be used, for example, as a simple model of a semi-permeable -membrane, or as an implementation of Maxwell's demon. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix wall/reflect"_fix_wall_reflect.html command - -[Default:] none - -:line - diff --git a/doc/txt/fix_orient.txt b/doc/txt/fix_orient.txt deleted file mode 100644 index 9d8e4e8628..0000000000 --- a/doc/txt/fix_orient.txt +++ /dev/null @@ -1,201 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix orient/fcc command :h3 -fix orient/bcc command :h3 - -fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1 -fix ID group-ID orient/bcc nstats dir alat dE cutlo cuthi file0 file1 :pre - -ID, group-ID are documented in "fix"_fix.html command -nstats = print stats every this many steps, 0 = never -dir = 0/1 for which crystal is used as reference -alat = fcc/bcc cubic lattice constant (distance units) -dE = energy added to each atom (energy units) -cutlo,cuthi = values between 0.0 and 1.0, cutlo < cuthi -file0,file1 = files that specify orientation of each grain :ul - -[Examples:] - -fix gb all orient/fcc 0 1 4.032008 0.001 0.25 0.75 xi.vec chi.vec -fix gb all orient/bcc 0 1 2.882 0.001 0.25 0.75 ngb.left ngb.right :pre - -[Description:] - -The fix applies an orientation-dependent force to atoms near a planar -grain boundary which can be used to induce grain boundary migration -(in the direction perpendicular to the grain boundary plane). The -motivation and explanation of this force and its application are -described in "(Janssens)"_#Janssens. The adaptation to bcc crystals -is described in "(Wicaksono1)"_#Wicaksono1. The computed force is only -applied to atoms in the fix group. - -The basic idea is that atoms in one grain (on one side of the -boundary) have a potential energy dE added to them. Atoms in the -other grain have 0.0 potential energy added. Atoms near the boundary -(whose neighbor environment is intermediate between the two grain -orientations) have an energy between 0.0 and dE added. This creates -an effective driving force to reduce the potential energy of atoms -near the boundary by pushing them towards one of the grain -orientations. For dir = 1 and dE > 0, the boundary will thus move so -that the grain described by file0 grows and the grain described by -file1 shrinks. Thus this fix is designed for simulations of two-grain -systems, either with one grain boundary and free surfaces parallel to -the boundary, or a system with periodic boundary conditions and two -equal and opposite grain boundaries. In either case, the entire -system can displace during the simulation, and such motion should be -accounted for in measuring the grain boundary velocity. - -The potential energy added to atom I is given by these formulas - -:c,image(Eqs/fix_orient_fcc.jpg) - -which are fully explained in "(Janssens)"_#Janssens. For fcc crystals -this order parameter Xi for atom I in equation (1) is a sum over the -12 nearest neighbors of atom I. For bcc crystals it is the -corresponding sum of the 8 nearest neighbors. Rj is the vector from -atom I to its neighbor J, and RIj is a vector in the reference -(perfect) crystal. That is, if dir = 0/1, then RIj is a vector to an -atom coord from file 0/1. Equation (2) gives the expected value of -the order parameter XiIJ in the other grain. Hi and lo cutoffs are -defined in equations (3) and (4), using the input parameters {cutlo} -and {cuthi} as thresholds to avoid adding grain boundary energy when -the deviation in the order parameter from 0 or 1 is small (e.g. due to -thermal fluctuations in a perfect crystal). The added potential -energy Ui for atom I is given in equation (6) where it is interpolated -between 0 and dE using the two threshold Xi values and the Wi value of -equation (5). - -The derivative of this energy expression gives the force on each atom -which thus depends on the orientation of its neighbors relative to the -2 grain orientations. Only atoms near the grain boundary feel a net -force which tends to drive them to one of the two grain orientations. - -In equation (1), the reference vector used for each neighbor is the -reference vector closest to the actual neighbor position. This means -it is possible two different neighbors will use the same reference -vector. In such cases, the atom in question is far from a perfect -orientation and will likely receive the full dE addition, so the -effect of duplicate reference vector usage is small. - -The {dir} parameter determines which grain wants to grow at the -expense of the other. A value of 0 means the first grain will shrink; -a value of 1 means it will grow. This assumes that {dE} is positive. -The reverse will be true if {dE} is negative. - -The {alat} parameter is the cubic lattice constant for the fcc or bcc -material and is only used to compute a cutoff distance of 1.57 * alat -/ sqrt(2) for finding the 12 or 8 nearest neighbors of each atom -(which should be valid for an fcc or bcc crystal). A longer/shorter -cutoff can be imposed by adjusting {alat}. If a particular atom has -less than 12 or 8 neighbors within the cutoff, the order parameter of -equation (1) is effectively multiplied by 12 or 8 divided by the -actual number of neighbors within the cutoff. - -The {dE} parameter is the maximum amount of additional energy added to -each atom in the grain which wants to shrink. - -The {cutlo} and {cuthi} parameters are used to reduce the force added -to bulk atoms in each grain far away from the boundary. An atom in -the bulk surrounded by neighbors at the ideal grain orientation would -compute an order parameter of 0 or 1 and have no force added. -However, thermal vibrations in the solid will cause the order -parameters to be greater than 0 or less than 1. The cutoff parameters -mask this effect, allowing forces to only be added to atoms with -order-parameters between the cutoff values. - -{File0} and {file1} are filenames for the two grains which each -contain 6 vectors (6 lines with 3 values per line) which specify the -grain orientations. Each vector is a displacement from a central atom -(0,0,0) to a nearest neighbor atom in an fcc lattice at the proper -orientation. The vector lengths should all be identical since an fcc -lattice has a coordination number of 12. Only 6 are listed due to -symmetry, so the list must include one from each pair of -equal-and-opposite neighbors. A pair of orientation files for a -Sigma=5 tilt boundary are shown below. A tutorial that can help for -writing the orientation files is given in "(Wicaksono2)"_#Wicaksono2 - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the potential energy of atom interactions with the grain -boundary driving force to the system's potential energy as part of -"thermodynamic output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by these -fixes. This allows to set at which level of the "r-RESPA"_run_style.html -integrator a fix is adding its forces. Default is the outermost level. - -This fix calculates a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the potential -energy change due to this fix. The scalar value calculated by this -fix is "extensive". - -This fix also calculates a per-atom array which can be accessed by -various "output commands"_Howto_output.html. The array stores the -order parameter Xi and normalized order parameter (0 to 1) for each -atom. The per-atom values can be accessed on any timestep. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix should only be used with fcc or bcc lattices. - -[Related commands:] - -"fix_modify"_fix_modify.html - -[Default:] none - -:line - -:link(Janssens) -[(Janssens)] Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature -Materials, 5, 124-127 (2006). - -:link(Wicaksono1) -[(Wicaksono1)] Wicaksono, Sinclair, Militzer, Computational Materials -Science, 117, 397-405 (2016). - -:link(Wicaksono2) -[(Wicaksono2)] Wicaksono, figshare, -https://dx.doi.org/10.6084/m9.figshare.1488628.v1 (2015). - -:line - -For illustration purposes, here are example files that specify a -Sigma=5 <100> tilt boundary. This is for a lattice constant of 3.5706 -Angs. - -file0: - - 0.798410432046075 1.785300000000000 1.596820864092150 - -0.798410432046075 1.785300000000000 -1.596820864092150 - 2.395231296138225 0.000000000000000 0.798410432046075 - 0.798410432046075 0.000000000000000 -2.395231296138225 - 1.596820864092150 1.785300000000000 -0.798410432046075 - 1.596820864092150 -1.785300000000000 -0.798410432046075 :pre - -file1: - - -0.798410432046075 1.785300000000000 1.596820864092150 - 0.798410432046075 1.785300000000000 -1.596820864092150 - 0.798410432046075 0.000000000000000 2.395231296138225 - 2.395231296138225 0.000000000000000 -0.798410432046075 - 1.596820864092150 1.785300000000000 0.798410432046075 - 1.596820864092150 -1.785300000000000 0.798410432046075 :pre diff --git a/doc/txt/fix_phonon.txt b/doc/txt/fix_phonon.txt deleted file mode 100644 index 73f2f4600b..0000000000 --- a/doc/txt/fix_phonon.txt +++ /dev/null @@ -1,214 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix phonon command :h3 - -[Syntax:] - -fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -phonon = style name of this fix command :l -N = measure the Green's function every this many timesteps :l -Noutput = output the dynamical matrix every this many measurements :l -Nwait = wait this many timesteps before measuring :l -map_file = {file} or {GAMMA} :l - {file} is the file that contains the mapping info between atom ID and the lattice indices. :pre - - {GAMMA} flags to treate the whole simulation box as a unit cell, so that the mapping - info can be generated internally. In this case, dynamical matrix at only the gamma-point - will/can be evaluated. :pre -prefix = prefix for output files :l -one or none keyword/value pairs may be appended :l -keyword = {sysdim} or {nasr} :l - {sysdim} value = d - d = dimension of the system, usually the same as the MD model dimension - {nasr} value = n - n = number of iterations to enforce the acoustic sum rule :pre -:ule - -[Examples:] - -fix 1 all phonon 20 5000 200000 map.in LJ1D sysdim 1 -fix 1 all phonon 20 5000 200000 map.in EAM3D -fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100 :pre - -[Description:] - -Calculate the dynamical matrix from molecular dynamics simulations -based on fluctuation-dissipation theory for a group of atoms. - -Consider a crystal with \(N\) unit cells in three dimensions labeled -\(l = (l_1, l_2, l_3)\) where \(l_i\) are integers. Each unit cell is -defined by three linearly independent vectors \(\mathbf\{a\}_1\), -\(\mathbf\{a\}_2\), \(\mathbf\{a\}_3\) forming a parallelepiped, -containing \(K\) basis atoms labeled \(k\). - -Based on fluctuation-dissipation theory, the force constant -coefficients of the system in reciprocal space are given by -("Campana"_#Campana , "Kong"_#Kong) - -\begin\{equation\} -\mathbf\{\Phi\}_\{k\alpha,k^\prime \beta\}(\mathbf\{q\}) = k_B T \mathbf\{G\}^\{-1\}_\{k\alpha,k^\prime \beta\}(\mathbf\{q\}) -\end\{equation\} - -where \(\mathbf\{G\}\) is the Green's functions coefficients given by - -\begin\{equation\} -\mathbf\{G\}_\{k\alpha,k^\prime \beta\}(\mathbf\{q\}) = \left< \mathbf\{u\}_\{k\alpha\}(\mathbf\{q\}) \bullet \mathbf\{u\}_\{k^\prime \beta\}^*(\mathbf\{q\}) \right> -\end\{equation\} - -where \(\left< \ldots \right>\) denotes the ensemble average, and - -\begin\{equation\} -\mathbf\{u\}_\{k\alpha\}(\mathbf\{q\}) = \sum_l \mathbf\{u\}_\{l k \alpha\} \exp\{(i\mathbf\{qr\}_l)\} -\end\{equation\} - -is the \(\alpha\) component of the atomic displacement for the \(k\) -th atom in the unit cell in reciprocal space at \(\mathbf\{q\}\). In -practice, the Green's functions coefficients can also be measured -according to the following formula, - -\begin\{equation\} -\mathbf\{G\}_\{k\alpha,k^\prime \beta\}(\mathbf\{q\}) = -\left< \mathbf\{R\}_\{k \alpha\}(\mathbf\{q\}) \bullet \mathbf\{R\}^*_\{k^\prime \beta\}(\mathbf\{q\}) \right> -- \left<\mathbf\{R\}\right>_\{k \alpha\}(\mathbf\{q\}) \bullet \left<\mathbf\{R\}\right>^*_\{k^\prime \beta\}(\mathbf\{q\}) -\end\{equation\} - -where \(\mathbf\{R\}\) is the instantaneous positions of atoms, and -\(\left<\mathbf\{R\}\right>\) is the averaged atomic positions. It -gives essentially the same results as the displacement method and is -easier to implement in an MD code. - -Once the force constant matrix is known, the dynamical matrix -\(\mathbf\{D\}\) can then be obtained by - -\begin\{equation\} -\mathbf\{D\}_\{k\alpha, k^\prime\beta\}(\mathbf\{q\}) = -(m_k m_\{k^\prime\})^\{-\frac\{1\}\{2\}\} \mathbf\{\Phi\}_\{k \alpha, k^\prime \beta\}(\mathbf\{q\}) -\end\{equation\} - -whose eigenvalues are exactly the phonon frequencies at \(\mathbf\{q\}\). - -This fix uses positions of atoms in the specified group and calculates -two-point correlations. To achieve this. the positions of the atoms -are examined every {Nevery} steps and are Fourier-transformed into -reciprocal space, where the averaging process and correlation -computation is then done. After every {Noutput} measurements, the -matrix \(\mathbf\{G\}(\mathbf\{q\})\) is calculated and inverted to -obtain the elastic stiffness coefficients. The dynamical matrices are -then constructed and written to {prefix}.bin.timestep files in binary -format and to the file {prefix}.log for each wave-vector -\(\mathbf\{q\}\). - -A detailed description of this method can be found in -("Kong2011"_#Kong2011). - -The {sysdim} keyword is optional. If specified with a value smaller -than the dimensionality of the LAMMPS simulation, its value is used -for the dynamical matrix calculation. For example, using LAMMPS ot -model a 2D or 3D system, the phonon dispersion of a 1D atomic chain -can be computed using {sysdim} = 1. - -The {nasr} keyword is optional. An iterative procedure is employed to -enforce the acoustic sum rule on \(\Phi\) at \(\Gamma\), and the number -provided by keyword {nasr} gives the total number of iterations. For a -system whose unit cell has only one atom, {nasr} = 1 is sufficient; -for other systems, {nasr} = 10 is typically sufficient. - -The {map_file} contains the mapping information between the lattice -indices and the atom IDs, which tells the code which atom sits at -which lattice point; the lattice indices start from 0. An auxiliary -code, "latgen"_http://code.google.com/p/latgen, can be employed to -generate the compatible map file for various crystals. - -In case one simulates a non-periodic system, where the whole simulation -box is treated as a unit cell, one can set {map_file} as {GAMMA}, so -that the mapping info will be generated internally and a file is not -needed. In this case, the dynamical matrix at only the gamma-point -will/can be evaluated. Please keep in mind that fix-phonon is designed -for cyrstals, it will be inefficient and even degrade the performance -of lammps in case the unit cell is too large. - -The calculated dynamical matrix elements are written out in -"energy/distance^2/mass"_units.html units. The coordinates for {q} -points in the log file is in the units of the basis vectors of the -corresponding reciprocal lattice. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to change the temperature compute from thermo_temp -to the one that reflects the true temperature of atoms in the group. - -No global scalar or vector or per-atom quantities are stored by this -fix for access by various "output commands"_Howto_output.html. - -Instead, this fix outputs its initialization information (including -mapping information) and the calculated dynamical matrices to the file -{prefix}.log, with the specified {prefix}. The dynamical matrices are -also written to files {prefix}.bin.timestep in binary format. These -can be read by the post-processing tool in tools/phonon to compute the -phonon density of states and/or phonon dispersion curves. - -No parameter of this fix can be used with the {start/stop} keywords -of the "run"_run.html command. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix assumes a crystalline system with periodical lattice. The -temperature of the system should not exceed the melting temperature to -keep the system in its solid state. - -This fix is part of the USER-PHONON package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires LAMMPS be built with an FFT library. See the "Build -settings"_Build_settings.html doc page for details. - -[Related commands:] - -"compute msd"_compute_msd.html, -"dynamical_matrix"_dynamical_matrix.html - -[Default:] - -The option defaults are sysdim = the same dimension as specified by -the "dimension"_dimension.html command, and nasr = 20. - -:line - -:link(Campana) -[(Campana)] C. Campana and -M. H. Muser, {Practical Green's function approach to the -simulation of elastic semi-infinite solids}, "Phys. Rev. B \[74\], -075420 (2006)"_http://dx.doi.org/10.1103/PhysRevB.74.075420 - -:link(Kong) -[(Kong)] L.T. Kong, G. Bartels, C. Campana, -C. Denniston, and Martin H. Muser, {Implementation of Green's -function molecular dynamics: An extension to LAMMPS}, "Computer -Physics Communications \[180\](6):1004-1010 -(2009)."_http://dx.doi.org/10.1016/j.cpc.2008.12.035 - -L.T. Kong, C. Denniston, and Martin H. Muser, -{An improved version of the Green's function molecular dynamics -method}, "Computer Physics Communications \[182\](2):540-541 -(2011)."_http://dx.doi.org/10.1016/j.cpc.2010.10.006 - -:link(Kong2011) -[(Kong2011)] L.T. Kong, {Phonon dispersion measured directly from -molecular dynamics simulations}, "Computer Physics Communications -\[182\](10):2201-2207, -(2011)."_http://dx.doi.org/10.1016/j.cpc.2011.04.019 diff --git a/doc/txt/fix_pimd.txt b/doc/txt/fix_pimd.txt deleted file mode 100644 index a826244973..0000000000 --- a/doc/txt/fix_pimd.txt +++ /dev/null @@ -1,178 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix pimd command :h3 - -[Syntax:] - -fix ID group-ID pimd keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -pimd = style name of this fix command :l -zero or more keyword/value pairs may be appended :l -keyword = {method} or {fmass} or {sp} or {temp} or {nhc} :l - {method} value = {pimd} or {nmpimd} or {cmd} - {fmass} value = scaling factor on mass - {sp} value = scaling factor on Planck constant - {temp} value = temperature (temperarate units) - {nhc} value = Nc = number of chains in Nose-Hoover thermostat :pre -:ule - -[Examples:] - -fix 1 all pimd method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4 :pre - -[Description:] - -This command performs quantum molecular dynamics simulations based on -the Feynman path integral to include effects of tunneling and -zero-point motion. In this formalism, the isomorphism of a quantum -partition function for the original system to a classical partition -function for a ring-polymer system is exploited, to efficiently sample -configurations from the canonical ensemble "(Feynman)"_#Feynman. -The classical partition function and its components are given -by the following equations: - -:c,image(Eqs/fix_pimd.jpg) - -The interested user is referred to any of the numerous references on -this methodology, but briefly, each quantum particle in a path -integral simulation is represented by a ring-polymer of P quasi-beads, -labeled from 1 to P. During the simulation, each quasi-bead interacts -with beads on the other ring-polymers with the same imaginary time -index (the second term in the effective potential above). The -quasi-beads also interact with the two neighboring quasi-beads through -the spring potential in imaginary-time space (first term in effective -potential). To sample the canonical ensemble, a Nose-Hoover massive -chain thermostat is applied "(Tuckerman)"_#pimd-Tuckerman. With the -massive chain algorithm, a chain of NH thermostats is coupled to each -degree of freedom for each quasi-bead. The keyword {temp} sets the -target temperature for the system and the keyword {nhc} sets the -number {Nc} of thermostats in each chain. For example, for a -simulation of N particles with P beads in each ring-polymer, the total -number of NH thermostats would be 3 x N x P x Nc. - -NOTE: This fix implements a complete velocity-verlet integrator -combined with NH massive chain thermostat, so no other time -integration fix should be used. - -The {method} keyword determines what style of PIMD is performed. A -value of {pimd} is standard PIMD. A value of {nmpimd} is for -normal-mode PIMD. A value of {cmd} is for centroid molecular dynamics -(CMD). The difference between the styles is as follows. - -In standard PIMD, the value used for a bead's fictitious mass is -arbitrary. A common choice is to use Mi = m/P, which results in the -mass of the entire ring-polymer being equal to the real quantum -particle. But it can be difficult to efficiently integrate the -equations of motion for the stiff harmonic interactions in the ring -polymers. - -A useful way to resolve this issue is to integrate the equations of -motion in a normal mode representation, using Normal Mode -Path-Integral Molecular Dynamics (NMPIMD) "(Cao1)"_#Cao1. In NMPIMD, -the NH chains are attached to each normal mode of the ring-polymer and -the fictitious mass of each mode is chosen as Mk = the eigenvalue of -the Kth normal mode for k > 0. The k = 0 mode, referred to as the -zero-frequency mode or centroid, corresponds to overall translation of -the ring-polymer and is assigned the mass of the real particle. - -Motion of the centroid can be effectively uncoupled from the other -normal modes by scaling the fictitious masses to achieve a partial -adiabatic separation. This is called a Centroid Molecular Dynamics -(CMD) approximation "(Cao2)"_#Cao2. The time-evolution (and resulting -dynamics) of the quantum particles can be used to obtain centroid time -correlation functions, which can be further used to obtain the true -quantum correlation function for the original system. The CMD method -also uses normal modes to evolve the system, except only the k > 0 -modes are thermostatted, not the centroid degrees of freedom. - -The keyword {fmass} sets a further scaling factor for the fictitious -masses of beads, which can be used for the Partial Adiabatic CMD -"(Hone)"_#Hone, or to be set as P, which results in the fictitious -masses to be equal to the real particle masses. - -The keyword {sp} is a scaling factor on Planck's constant, which can -be useful for debugging or other purposes. The default value of 1.0 -is appropriate for most situations. - -The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme -as described in "(Calhoun)"_#Calhoun. In LAMMPS this is done by using -"multi-replica feature"_Howto_replica.html in LAMMPS, where each -quasi-particle system is stored and simulated on a separate partition -of processors. The following diagram illustrates this approach. The -original system with 2 ring polymers is shown in red. Since each ring -has 4 quasi-beads (imaginary time slices), there are 4 replicas of the -system, each running on one of the 4 partitions of processors. Each -replica (shown in green) owns one quasi-bead in each ring. - -:c,image(JPG/pimd.jpg) - -To run a PIMD simulation with M quasi-beads in each ring polymer using -N MPI tasks for each partition's domain-decomposition, you would use P -= MxN processors (cores) and run the simulation as follows: - -mpirun -np P lmp_mpi -partition MxN -in script :pre - -Note that in the LAMMPS input script for a multi-partition simulation, -it is often very useful to define a "uloop-style -variable"_variable.html such as - -variable ibead uloop M pad :pre - -where M is the number of quasi-beads (partitions) used in the -calculation. The uloop variable can then be used to manage I/O -related tasks for each of the partitions, e.g. - -dump dcd all dcd 10 system_$\{ibead\}.dcd -restart 1000 system_$\{ibead\}.restart1 system_$\{ibead\}.restart2 -read_restart system_$\{ibead\}.restart2 :pre - -[Restrictions:] - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -A PIMD simulation can be initialized with a single data file read via -the "read_data"_read_data.html command. However, this means all -quasi-beads in a ring polymer will have identical positions and -velocities, resulting in identical trajectories for all quasi-beads. -To avoid this, users can simply initialize velocities with different -random number seeds assigned to each partition, as defined by the -uloop variable, e.g. - -velocity all create 300.0 1234$\{ibead\} rot yes dist gaussian :pre - -[Default:] - -The keyword defaults are method = pimd, fmass = 1.0, sp = 1.0, temp = 300.0, -and nhc = 2. - -:line - -:link(Feynman) -[(Feynman)] R. Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and -Path Integrals, McGraw-Hill, New York (1965). - -:link(pimd-Tuckerman) -[(Tuckerman)] M. Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993). - -:link(Cao1) -[(Cao1)] J. Cao and B. Berne, J Chem Phys, 99, 2902 (1993). - -:link(Cao2) -[(Cao2)] J. Cao and G. Voth, J Chem Phys, 100, 5093 (1994). - -:link(Hone) -[(Hone)] T. Hone, P. Rossky, G. Voth, J Chem Phys, 124, -154103 (2006). - -:link(Calhoun) -[(Calhoun)] A. Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, -415 (1996). diff --git a/doc/txt/fix_planeforce.txt b/doc/txt/fix_planeforce.txt deleted file mode 100644 index ffe1952e31..0000000000 --- a/doc/txt/fix_planeforce.txt +++ /dev/null @@ -1,53 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix planeforce command :h3 - -[Syntax:] - -fix ID group-ID planeforce x y z :pre - -ID, group-ID are documented in "fix"_fix.html command -planeforce = style name of this fix command -x y z = 3-vector that is normal to the plane :ul - -[Examples:] - -fix hold boundary planeforce 1.0 0.0 0.0 :pre - -[Description:] - -Adjust the forces on each atom in the group so that only the -components of force in the plane specified by the normal vector -(x,y,z) remain. This is done by subtracting out the component of -force perpendicular to the plane. - -If the initial velocity of the atom is 0.0 (or in the plane), then it -should continue to move in the plane thereafter. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -[Restrictions:] none - -[Related commands:] - -"fix lineforce"_fix_lineforce.html - -[Default:] none - - diff --git a/doc/txt/fix_plumed.txt b/doc/txt/fix_plumed.txt deleted file mode 100644 index 86807f531d..0000000000 --- a/doc/txt/fix_plumed.txt +++ /dev/null @@ -1,118 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix plumed command :h3 - -[Syntax:] - -fix ID group-ID plumed keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -plumed = style name of this fix command :l -keyword = {plumedfile} or {outfile} :l - {plumedfile} arg = name of PLUMED input file to use (default: NULL) - {outfile} arg = name of file on which to write the PLUMED log (default: NULL) :pre -:ule - -[Examples:] - -fix pl all plumed all plumed plumedfile plumed.dat outfile p.log - -[Description:] - -This fix instructs LAMMPS to call the "PLUMED"_plumedhome library, which -allows one to perform various forms of trajectory analysis on the fly -and to also use methods such as umbrella sampling and metadynamics to -enhance the sampling of phase space. - -The documentation included here only describes the fix plumed command -itself. This command is LAMMPS specific, whereas most of the -functionality implemented in PLUMED will work with a range of MD codes, -and when PLUMED is used as a stand alone code for analysis. The full -"documentation for PLUMED"_plumeddocs is available online and included -in the PLUMED source code. The PLUMED library development is hosted at -"https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2 -A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED. - -There is an example input for using this package with LAMMPS in the -examples/USER/plumed directory. - -:line - -The command to make LAMMPS call PLUMED during a run requires two keyword -value pairs pointing to the PLUMED input file and an output file for the -PLUMED log. The user must specify these arguments every time PLUMED is -to be used. Furthermore, the fix plumed command should appear in the -LAMMPS input file [after] relevant input parameters (e.g. the timestep) -have been set. - -The {group-ID} entry is ignored. LAMMPS will always pass all the atoms -to PLUMED and there can only be one instance of the plumed fix at a -time. The way the plumed fix is implemented ensures that the minimum -amount of information required is communicated. Furthermore, PLUMED -supports multiple, completely independent collective variables, multiple -independent biases and multiple independent forms of analysis. There is -thus really no restriction in functionality by only allowing only one -plumed fix in the LAMMPS input. - -The {plumedfile} keyword allows the user to specify the name of the -PLUMED input file. Instructions as to what should be included in a -plumed input file can be found in the "documentation for -PLUMED"_plumeddocs - -The {outfile} keyword allows the user to specify the name of a file in -which to output the PLUMED log. This log file normally just repeats the -information that is contained in the input file to confirm it was -correctly read and parsed. The names of the files in which the results -are stored from the various analysis options performed by PLUMED will -be specified by the user in the PLUMED input file. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -When performing a restart of a calculation that involves PLUMED you must -include a RESTART command in the PLUMED input file as detailed in the -"PLUMED documentation"_plumeddocs. When the restart command is found in -the PLUMED input PLUMED will append to the files that were generated in -the run that was performed previously. No part of the PLUMED restart -data is included in the LAMMPS restart files. Furthermore, any history -dependent bias potentials that were accumulated in previous calculations -will be read in when the RESTART command is included in the PLUMED -input. - -The "fix_modify"_fix_modify.html {energy} option is not supported by -this fix. - -Nothing is computed by this fix that can be accessed by any of the -"output commands"_Howto_output.html within LAMMPS. All the quantities -of interest can be output by commands that are native to PLUMED, -however. - -[Restrictions:] - -This fix is part of the USER-PLUMED package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -There can only be one plumed fix active at a time. - -[Related commands:] - -"fix smd"_fix_smd.html -"fix colvars"_fix_colvars.html - -[Default:] - -The default options are plumedfile = NULL and outfile = NULL - -:line - -:link(PLUMED) -[(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014) - -:link(plumeddocs,http://www.plumed.org/doc.html) -:link(plumedhome,http://www.plumed.org/) diff --git a/doc/txt/fix_poems.txt b/doc/txt/fix_poems.txt deleted file mode 100644 index 027a15a5ff..0000000000 --- a/doc/txt/fix_poems.txt +++ /dev/null @@ -1,142 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix poems command :h3 - -Syntax: - -fix ID group-ID poems keyword values :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -poems = style name of this fix command :l -keyword = {group} or {file} or {molecule} :l - {group} values = list of group IDs - {molecule} values = none - {file} values = filename :pre -:ule - -[Examples:] - -fix 3 fluid poems group clump1 clump2 clump3 -fix 3 fluid poems file cluster.list :pre - -[Description:] - -Treats one or more sets of atoms as coupled rigid bodies. This means -that each timestep the total force and torque on each rigid body is -computed and the coordinates and velocities of the atoms are updated -so that the collection of bodies move as a coupled set. This can be -useful for treating a large biomolecule as a collection of connected, -coarse-grained particles. - -The coupling, associated motion constraints, and time integration is -performed by the software package "Parallelizable Open source -Efficient Multibody Software (POEMS)"_poems which computes the -constrained rigid-body motion of articulated (jointed) multibody -systems "(Anderson)"_#Anderson. POEMS was written and is distributed -by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee, -and other members of his group at Rensselaer Polytechnic Institute -(RPI). Rudranarayan developed the LAMMPS/POEMS interface. For -copyright information on POEMS and other details, please refer to the -documents in the poems directory distributed with LAMMPS. - -:link(poems,http://www.rpi.edu/~anderk5/lab) - -This fix updates the positions and velocities of the rigid atoms with -a constant-energy time integration, so you should not update the same -atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin). - -Each body must have a non-degenerate inertia tensor, which means if -must contain at least 3 non-collinear atoms. Which atoms are in which -bodies can be defined via several options. - -For option {group}, each of the listed groups is treated as a rigid -body. Note that only atoms that are also in the fix group are -included in each rigid body. - -For option {molecule}, each set of atoms in the group with a different -molecule ID is treated as a rigid body. - -For option {file}, sets of atoms are read from the specified file and -each set is treated as a rigid body. Each line of the file specifies -a rigid body in the following format: - -ID type atom1-ID atom2-ID atom3-ID ... - -ID as an integer from 1 to M (the number of rigid bodies). Type is -any integer; it is not used by the fix poems command. The remaining -arguments are IDs of atoms in the rigid body, each typically from 1 to -N (the number of atoms in the system). Only atoms that are also in -the fix group are included in each rigid body. Blank lines and lines -that begin with '#' are skipped. - -A connection between a pair of rigid bodies is inferred if one atom is -common to both bodies. The POEMS solver treats that atom as a -spherical joint with 3 degrees of freedom. Currently, a collection of -bodies can only be connected by joints as a linear chain. The entire -collection of rigid bodies can represent one or more chains. Other -connection topologies (tree, ring) are not allowed, but will be added -later. Note that if no joints exist, it is more efficient to use the -"fix rigid"_fix_rigid.html command to simulate the system. - -When the poems fix is defined, it will print out statistics on the -total # of clusters, bodies, joints, atoms involved. A cluster in -this context means a set of rigid bodies connected by joints. - -For computational efficiency, you should turn off pairwise and bond -interactions within each rigid body, as they no longer contribute to -the motion. The "neigh_modify exclude" and "delete_bonds" commands -can be used to do this if each rigid body is a group. - -For computational efficiency, you should only define one fix poems -which includes all the desired rigid bodies. LAMMPS will allow -multiple poems fixes to be defined, but it is more expensive. - -The degrees-of-freedom removed by coupled rigid bodies are accounted -for in temperature and pressure computations. Similarly, the rigid -body contribution to the pressure virial is also accounted for. The -latter is only correct if forces within the bodies have been turned -off, and there is only a single fix poems defined. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {bodyforces} option is supported by -this fix style to set whether per-body forces and torques are computed -early or late in a timestep, i.e. at the post-force stage or at the -final-integrate stage, respectively. - -No global or per-atom quantities are stored by this fix for access by -various "output commands"_Howto_output.html. No parameter of this fix -can be used with the {start/stop} keywords of the "run"_run.html -command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the POEMS package. It is only enabled if LAMMPS -was built with that package, which also requires the POEMS library be -built and linked with LAMMPS. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix rigid"_fix_rigid.html, "delete_bonds"_delete_bonds.html, -"neigh_modify"_neigh_modify.html exclude - -[Default:] none - -:line - -:link(Anderson) -[(Anderson)] Anderson, Mukherjee, Critchley, Ziegler, and Lipton -"POEMS: Parallelizable Open-source Efficient Multibody Software ", -Engineering With Computers (2006). ("link to -paper"_http://dx.doi.org/10.1007/s00366-006-0026-x) diff --git a/doc/txt/fix_pour.txt b/doc/txt/fix_pour.txt deleted file mode 100644 index 65f01c00fb..0000000000 --- a/doc/txt/fix_pour.txt +++ /dev/null @@ -1,270 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix pour command :h3 - -[Syntax:] - -fix ID group-ID pour N type seed keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -pour = style name of this fix command :l -N = # of particles to insert :l -type = atom type to assign to inserted particles (offset for molecule insertion) :l -seed = random # seed (positive integer) :l -one or more keyword/value pairs may be appended to args :l -keyword = {region} or {diam} or {vol} or {rate} or {dens} or {vel} or {mol} or {rigid} or {shake} or {ignore} :l - {region} value = region-ID - region-ID = ID of region to use as insertion volume - {diam} values = dstyle args - dstyle = {one} or {range} or {poly} - {one} args = D - D = single diameter for inserted particles (distance units) - {range} args = Dlo Dhi - Dlo,Dhi = range of diameters for inserted particles (distance units) - {poly} args = Npoly D1 P1 D2 P2 ... - Npoly = # of (D,P) pairs - D1,D2,... = diameter for subset of inserted particles (distance units) - P1,P2,... = percentage of inserted particles with this diameter (0-1) - {id} values = idflag - idflag = {max} or {next} = how to choose IDs for inserted particles and molecules - {vol} values = fraction Nattempt - fraction = desired volume fraction for filling insertion volume - Nattempt = max # of insertion attempts per particle - {rate} value = V - V = z velocity (3d) or y velocity (2d) at which - insertion volume moves (velocity units) - {dens} values = Rholo Rhohi - Rholo,Rhohi = range of densities for inserted particles (mass/volume units) - {vel} values (3d) = vxlo vxhi vylo vyhi vz - {vel} values (2d) = vxlo vxhi vy - vxlo,vxhi = range of x velocities for inserted particles (velocity units) - vylo,vyhi = range of y velocities for inserted particles (velocity units) - vz = z velocity (3d) assigned to inserted particles (velocity units) - vy = y velocity (2d) assigned to inserted particles (velocity units) - {mol} value = template-ID - template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command - {molfrac} values = f1 f2 ... fN - f1 to fN = relative probability of creating each of N molecules in template-ID - {rigid} value = fix-ID - fix-ID = ID of "fix rigid/small"_fix_rigid.html command - {shake} value = fix-ID - fix-ID = ID of "fix shake"_fix_shake.html command - {ignore} value = none - skip any line or triangle particles when detecting possible - overlaps with inserted particles :pre -:ule - -[Examples:] - -fix 3 all pour 1000 2 29494 region myblock -fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam range 0.9 1.1 -fix 2 all pour 10000 1 19985583 region disk diam poly 2 0.7 0.4 1.5 0.6 -fix ins all pour 500 1 4767548 vol 0.8 10 region slab mol object rigid myRigid :pre - -[Description:] - -Insert finite-size particles or molecules into the simulation box -every few timesteps within a specified region until N particles or -molecules have been inserted. This is typically used to model the -pouring of granular particles into a container under the influence of -gravity. For the remainder of this doc page, a single inserted atom -or molecule is referred to as a "particle". - -If inserted particles are individual atoms, they are assigned the -specified atom type. If they are molecules, the type of each atom in -the inserted molecule is specified in the file read by the -"molecule"_molecule.html command, and those values are added to the -specified atom type. E.g. if the file specifies atom types 1,2,3, and -those are the atom types you want for inserted molecules, then specify -{type} = 0. If you specify {type} = 2, the in the inserted molecule -will have atom types 3,4,5. - -All atoms in the inserted particle are assigned to two groups: the -default group "all" and the group specified in the fix pour command -(which can also be "all"). - -This command must use the {region} keyword to define an insertion -volume. The specified region must have been previously defined with a -"region"_region.html command. It must be of type {block} or a z-axis -{cylinder} and must be defined with side = {in}. The cylinder style -of region can only be used with 3d simulations. - -Individual atoms are inserted, unless the {mol} keyword is used. It -specifies a {template-ID} previously defined using the -"molecule"_molecule.html command, which reads a file that defines the -molecule. The coordinates, atom types, center-of-mass, moments of -inertia, etc, as well as any bond/angle/etc and special neighbor -information for the molecule can be specified in the molecule file. -See the "molecule"_molecule.html command for details. The only -settings required to be in this file are the coordinates and types of -atoms in the molecule. - -If the molecule template contains more than one molecule, the relative -probability of depositing each molecule can be specified by the -{molfrac} keyword. N relative probabilities, each from 0.0 to 1.0, are -specified, where N is the number of molecules in the template. Each -time a molecule is inserted, a random number is used to sample from -the list of relative probabilities. The N values must sum to 1.0. - -If you wish to insert molecules via the {mol} keyword, that will be -treated as rigid bodies, use the {rigid} keyword, specifying as its -value the ID of a separate "fix rigid/small"_fix_rigid.html -command which also appears in your input script. - -NOTE: If you wish the new rigid molecules (and other rigid molecules) -to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html -or "fix rigid/small/npt"_fix_rigid.html, then you need to use the -"fix_modify dynamic/dof yes" command for the rigid fix. This is to -inform that fix that the molecule count will vary dynamically. - -If you wish to insert molecules via the {mol} keyword, that will have -their bonds or angles constrained via SHAKE, use the {shake} keyword, -specifying as its value the ID of a separate "fix -shake"_fix_shake.html command which also appears in your input script. - -Each timestep particles are inserted, they are placed randomly inside -the insertion volume so as to mimic a stream of poured particles. If -they are molecules they are also oriented randomly. Each atom in the -particle is tested for overlaps with existing particles, including -effects due to periodic boundary conditions if applicable. If an -overlap is detected, another random insertion attempt is made; see the -{vol} keyword discussion below. The larger the volume of the -insertion region, the more particles that can be inserted at any one -timestep. Particles are inserted again after enough time has elapsed -that the previously inserted particles fall out of the insertion -volume under the influence of gravity. Insertions continue every so -many timesteps until the desired # of particles has been inserted. - -NOTE: If you are monitoring the temperature of a system where the -particle count is changing due to adding particles, you typically -should use the "compute_modify dynamic yes"_compute_modify.html -command for the temperature compute you are using. - -:line - -All other keywords are optional with defaults as shown below. - -The {diam} option is only used when inserting atoms and specifies the -diameters of inserted particles. There are 3 styles: {one}, {range}, -or {poly}. For {one}, all particles will have diameter {D}. For -{range}, the diameter of each particle will be chosen randomly and -uniformly between the specified {Dlo} and {Dhi} bounds. For {poly}, a -series of {Npoly} diameters is specified. For each diameter a -percentage value from 0.0 to 1.0 is also specified. The {Npoly} -percentages must sum to 1.0. For the example shown above with "diam 2 -0.7 0.4 1.5 0.6", all inserted particles will have a diameter of 0.7 -or 1.5. 40% of the particles will be small; 60% will be large. - -Note that for molecule insertion, the diameters of individual atoms in -the molecule can be specified in the file read by the -"molecule"_molecule.html command. If not specified, the diameter of -each atom in the molecule has a default diameter of 1.0. - -The {id} option has two settings which are used to determine the atom -or molecule IDs to assign to inserted particles/molecules. In both -cases a check is done of the current system to find the maximum -current atom and molecule ID of any existing particle. Newly inserted -particles and molecules are assigned IDs that increment those max -values. For the {max} setting, which is the default, this check is -done at every insertion step, which allows for particles to leave the -system, and their IDs to potentially be re-used. For the {next} -setting this check is done only once when the fix is specified, which -can be more efficient if you are sure particles will not be added in -some other way. - -The {vol} option specifies what volume fraction of the insertion -volume will be filled with particles. For particles with a size -specified by the {diam range} keyword, they are assumed to all be of -maximum diameter {Dhi} for purposes of computing their contribution to -the volume fraction. - -The higher the volume fraction value, the more particles are inserted -each timestep. Since inserted particles cannot overlap, the maximum -volume fraction should be no higher than about 0.6. Each timestep -particles are inserted, LAMMPS will make up to a total of M tries to -insert the new particles without overlaps, where M = # of inserted -particles * Nattempt. If LAMMPS is unsuccessful at completing all -insertions, it prints a warning. - -The {dens} and {vel} options enable inserted particles to have a range -of densities or xy velocities. The specific values for a particular -inserted particle will be chosen randomly and uniformly between the -specified bounds. Internally, the density value for a particle is -converted to a mass, based on the radius (volume) of the particle. -The {vz} or {vy} value for option {vel} assigns a z-velocity (3d) or -y-velocity (2d) to each inserted particle. - -The {rate} option moves the insertion volume in the z direction (3d) -or y direction (2d). This enables pouring particles from a -successively higher height over time. - -The {ignore} option is useful when running a simulation that used line -segment (2d) or triangle (3d) particles, typically to define -boundaries for spherical granular particles to interact with. See the -"atom_style line or tri"_atom_style.html command for details. Lines -and triangles store their size, and if the size is large it may -overlap (in a spherical sense) with the insertion region, even if the -line/triangle is oriented such that there is no actual overlap. This -can prevent particles from being inserted. The {ignore} keyword -causes the overlap check to skip any line or triangle particles. -Obviously you should only use it if there is in fact no overlap of the -line or triangle particles with the insertion region. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. This means you must be careful when restarting a -pouring simulation, when the restart file was written in the middle of -the pouring operation. Specifically, you should use a new fix pour -command in the input script for the restarted simulation that -continues the operation. You will need to adjust the arguments of the -original fix pour command to do this. - -Also note that because the state of the random number generator is not -saved in restart files, you cannot do "exact" restarts with this fix, -where the simulation continues on the same as if no restart had taken -place. However, in a statistical sense, a restarted simulation should -produce the same behavior if you adjust the fix pour parameters -appropriately. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Howto_output.html. No parameter -of this fix can be used with the {start/stop} keywords of the -"run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -For 3d simulations, a gravity fix in the -z direction must be defined -for use in conjunction with this fix. For 2d simulations, gravity -must be defined in the -y direction. - -The specified insertion region cannot be a "dynamic" region, as -defined by the "region"_region.html command. - -[Related commands:] - -"fix deposit"_fix_deposit.html, "fix gravity"_fix_gravity.html, -"region"_region.html - -[Default:] - -Insertions are performed for individual particles, i.e. no {mol} -setting is defined. If the {mol} keyword is used, the default for -{molfrac} is an equal probabilities for all molecules in the template. -Additional option defaults are diam = one 1.0, dens = 1.0 1.0, vol = -0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0 (for 3d), vel = 0.0 0.0 0.0 -(for 2d), and id = max. diff --git a/doc/txt/fix_press_berendsen.txt b/doc/txt/fix_press_berendsen.txt deleted file mode 100644 index 7f47a29ba3..0000000000 --- a/doc/txt/fix_press_berendsen.txt +++ /dev/null @@ -1,226 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix press/berendsen command :h3 - -[Syntax:] - -fix ID group-ID press/berendsen keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -press/berendsen = style name of this fix command :l -one or more keyword value pairs may be appended -keyword = {iso} or {aniso} or {x} or {y} or {z} or {couple} or {dilate} or {modulus} - {iso} or {aniso} values = Pstart Pstop Pdamp - Pstart,Pstop = scalar external pressure at start/end of run (pressure units) - Pdamp = pressure damping parameter (time units) - {x} or {y} or {z} values = Pstart Pstop Pdamp - Pstart,Pstop = external stress tensor component at start/end of run (pressure units) - Pdamp = stress damping parameter (time units) - {couple} = {none} or {xyz} or {xy} or {yz} or {xz} - {modulus} value = bulk modulus of system (pressure units) - {dilate} value = {all} or {partial} :pre -:ule - -[Examples:] - -fix 1 all press/berendsen iso 0.0 0.0 1000.0 -fix 2 all press/berendsen aniso 0.0 0.0 1000.0 dilate partial :pre - -[Description:] - -Reset the pressure of the system by using a Berendsen barostat -"(Berendsen)"_#Berendsen1, which rescales the system volume and -(optionally) the atoms coordinates within the simulation box every -timestep. - -Regardless of what atoms are in the fix group, a global pressure is -computed for all atoms. Similarly, when the size of the simulation -box is changed, all atoms are re-scaled to new positions, unless the -keyword {dilate} is specified with a value of {partial}, in which case -only the atoms in the fix group are re-scaled. The latter can be -useful for leaving the coordinates of atoms in a solid substrate -unchanged and controlling the pressure of a surrounding fluid. - -NOTE: Unlike the "fix npt"_fix_nh.html or "fix nph"_fix_nh.html -commands which perform Nose/Hoover barostatting AND time integration, -this fix does NOT perform time integration. It only modifies the box -size and atom coordinates to effect barostatting. Thus you must use a -separate time integration fix, like "fix nve"_fix_nve.html or "fix -nvt"_fix_nh.html to actually update the positions and velocities of -atoms. This fix can be used in conjunction with thermostatting fixes -to control the temperature, such as "fix nvt"_fix_nh.html or "fix -langevin"_fix_langevin.html or "fix -temp/berendsen"_fix_temp_berendsen.html. - -See the "Howto baroostat"_Howto_barostat.html doc page for a -discussion of different ways to perform barostatting. - -:line - -The barostat is specified using one or more of the {iso}, {aniso}, -{x}, {y}, {z}, and {couple} keywords. These keywords give you the -ability to specify the 3 diagonal components of an external stress -tensor, and to couple various of these components together so that the -dimensions they represent are varied together during a -constant-pressure simulation. Unlike the "fix npt"_fix_nh.html and -"fix nph"_fix_nh.html commands, this fix cannot be used with triclinic -(non-orthogonal) simulation boxes to control all 6 components of the -general pressure tensor. - -The target pressures for each of the 3 diagonal components of the -stress tensor can be specified independently via the {x}, {y}, {z}, -keywords, which correspond to the 3 simulation box dimensions. For -each component, the external pressure or tensor component at each -timestep is a ramped value during the run from {Pstart} to {Pstop}. -If a target pressure is specified for a component, then the -corresponding box dimension will change during a simulation. For -example, if the {y} keyword is used, the y-box length will change. A -box dimension will not change if that component is not specified, -although you have the option to change that dimension via the "fix -deform"_fix_deform.html command. - -For all barostat keywords, the {Pdamp} parameter determines the time -scale on which pressure is relaxed. For example, a value of 10.0 -means to relax the pressure in a timespan of (roughly) 10 time units -(tau or fmsec or psec - see the "units"_units.html command). - -NOTE: A Berendsen barostat will not work well for arbitrary values of -{Pdamp}. If {Pdamp} is too small, the pressure and volume can -fluctuate wildly; if it is too large, the pressure will take a very -long time to equilibrate. A good choice for many models is a {Pdamp} -of around 1000 timesteps. However, note that {Pdamp} is specified in -time units, and that timesteps are NOT the same as time units for most -"units"_units.html settings. - -NOTE: The relaxation time is actually also a function of the bulk -modulus of the system (inverse of isothermal compressibility). The -bulk modulus has units of pressure and is the amount of pressure that -would need to be applied (isotropically) to reduce the volume of the -system by a factor of 2 (assuming the bulk modulus was a constant, -independent of density, which it's not). The bulk modulus can be set -via the keyword {modulus}. The {Pdamp} parameter is effectively -multiplied by the bulk modulus, so if the pressure is relaxing faster -than expected or desired, increasing the bulk modulus has the same -effect as increasing {Pdamp}. The converse is also true. LAMMPS does -not attempt to guess a correct value of the bulk modulus; it just uses -10.0 as a default value which gives reasonable relaxation for a -Lennard-Jones liquid, but will be way off for other materials and way -too small for solids. Thus you should experiment to find appropriate -values of {Pdamp} and/or the {modulus} when using this fix. - -:line - -The {couple} keyword allows two or three of the diagonal components of -the pressure tensor to be "coupled" together. The value specified -with the keyword determines which are coupled. For example, {xz} -means the {Pxx} and {Pzz} components of the stress tensor are coupled. -{Xyz} means all 3 diagonal components are coupled. Coupling means two -things: the instantaneous stress will be computed as an average of the -corresponding diagonal components, and the coupled box dimensions will -be changed together in lockstep, meaning coupled dimensions will be -dilated or contracted by the same percentage every timestep. The -{Pstart}, {Pstop}, {Pdamp} parameters for any coupled dimensions must -be identical. {Couple xyz} can be used for a 2d simulation; the {z} -dimension is simply ignored. - -:line - -The {iso} and {aniso} keywords are simply shortcuts that are -equivalent to specifying several other keywords together. - -The keyword {iso} means couple all 3 diagonal components together when -pressure is computed (hydrostatic pressure), and dilate/contract the -dimensions together. Using "iso Pstart Pstop Pdamp" is the same as -specifying these 4 keywords: - -x Pstart Pstop Pdamp -y Pstart Pstop Pdamp -z Pstart Pstop Pdamp -couple xyz :pre - -The keyword {aniso} means {x}, {y}, and {z} dimensions are controlled -independently using the {Pxx}, {Pyy}, and {Pzz} components of the -stress tensor as the driving forces, and the specified scalar external -pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying -these 4 keywords: - -x Pstart Pstop Pdamp -y Pstart Pstop Pdamp -z Pstart Pstop Pdamp -couple none :pre - -:line - -This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp" and "pressure", -as if these commands had been issued: - -compute fix-ID_temp group-ID temp -compute fix-ID_press group-ID pressure fix-ID_temp :pre - -See the "compute temp"_compute_temp.html and "compute -pressure"_compute_pressure.html commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press", and the group for the new computes is the same -as the fix group. - -Note that these are NOT the computes used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_press}. This means you can change the attributes of this -fix's temperature or pressure via the -"compute_modify"_compute_modify.html command or print this temperature -or pressure during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} or -{thermo_press} will have no effect on this fix. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {temp} and {press} options are -supported by this fix. You can use them to assign a -"compute"_compute.html you have defined to this fix which will be used -in its temperature and pressure calculations. If you do this, note -that the kinetic energy derived from the compute temperature should be -consistent with the virial term computed using all atoms for the -pressure. LAMMPS will warn you if you choose to compute temperature -on a subset of atoms. - -No global or per-atom quantities are stored by this fix for access by -various "output commands"_Howto_output.html. - -This fix can ramp its target pressure over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -Any dimension being adjusted by this fix must be periodic. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix nph"_fix_nh.html, "fix -npt"_fix_nh.html, "fix temp/berendsen"_fix_temp_berendsen.html, -"fix_modify"_fix_modify.html - -[Default:] - -The keyword defaults are dilate = all, modulus = 10.0 in units of -pressure for whatever "units"_units.html are defined. - -:line - -:link(Berendsen1) - -[(Berendsen)] Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem -Phys, 81, 3684 (1984). diff --git a/doc/txt/fix_print.txt b/doc/txt/fix_print.txt deleted file mode 100644 index cafc180718..0000000000 --- a/doc/txt/fix_print.txt +++ /dev/null @@ -1,105 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix print command :h3 - -[Syntax:] - -fix ID group-ID print N string keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -print = style name of this fix command :l -N = print every N steps; N can be a variable (see below) :l -string = text string to print with optional variable names :l -zero or more keyword/value pairs may be appended :l -keyword = {file} or {append} or {screen} or {title} :l - {file} value = filename - {append} value = filename - {screen} value = {yes} or {no} - {title} value = string - string = text to print as 1st line of output file :pre -:ule - -[Examples:] - -fix extra all print 100 "Coords of marker atom = $x $y $z" -fix extra all print 100 "Coords of marker atom = $x $y $z" file coord.txt :pre - -[Description:] - -Print a text string every N steps during a simulation run. This can -be used for diagnostic purposes or as a debugging tool to monitor some -quantity during a run. The text string must be a single argument, so -it should be enclosed in double quotes if it is more than one word. -If it contains variables it must be enclosed in double quotes to -insure they are not evaluated when the input script line is read, but -will instead be evaluated each time the string is printed. - -Instead of a numeric value, N can be specified as an "equal-style -variable"_variable.html, which should be specified as v_name, where -name is the variable name. In this case, the variable is evaluated at -the beginning of a run to determine the [next] timestep at which the -string will be written out. On that timestep, the variable will be -evaluated again to determine the next timestep, etc. -Thus the variable should return timestep values. See the stagger() -and logfreq() and stride() math functions for "equal-style -variables"_variable.html, as examples of useful functions to use in -this context. For example, the following commands will print output at -timesteps 10,20,30,100,200,300,1000,2000,etc: - -variable s equal logfreq(10,3,10) -fix extra all print v_s "Coords of marker atom = $x $y $z" :pre - -The specified group-ID is ignored by this fix. - -See the "variable"_variable.html command for a description of {equal} -style variables which are the most useful ones to use with the fix -print command, since they are evaluated afresh each timestep that the -fix print line is output. Equal-style variables calculate formulas -involving mathematical operations, atom properties, group properties, -thermodynamic properties, global values calculated by a -"compute"_compute.html or "fix"_fix.html, or references to other -"variables"_variable.html. - -If the {file} or {append} keyword is used, a filename is specified to -which the output generated by this fix will be written. If {file} is -used, then the filename is overwritten if it already exists. If -{append} is used, then the filename is appended to if it already -exists, or created if it does not exist. - -If the {screen} keyword is used, output by this fix to the screen and -logfile can be turned on or off as desired. - -The {title} keyword allow specification of the string that will be -printed as the first line of the output file, assuming the {file} -keyword was used. By default, the title line is as follows: - -# Fix print output for fix ID :pre - -where ID is replaced with the fix-ID. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"variable"_variable.html, "print"_print.html - -[Default:] - -The option defaults are no file output, screen = yes, and title string -as described above. diff --git a/doc/txt/fix_property_atom.txt b/doc/txt/fix_property_atom.txt deleted file mode 100644 index a62f523c5d..0000000000 --- a/doc/txt/fix_property_atom.txt +++ /dev/null @@ -1,290 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix property/atom command :h3 -fix property/atom/kk command :h3 - -[Syntax:] - -fix ID group-ID property/atom vec1 vec2 ... keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -property/atom = style name of this fix command :l -vec1,vec2,... = {mol} or {q} or {rmass} or {i_name} or {d_name} :l - {mol} = molecule IDs - {q} = charge - {rmass} = per-atom mass - {i_name} = new integer vector referenced by name - {d_name} = new floating-point vector referenced by name :pre -zero of more keyword/value pairs may be appended :l -keyword = {ghost} :l - {ghost} value = {no} or {yes} for whether ghost atom info in communicated :pre -:ule - -[Examples:] - -fix 1 all property/atom mol -fix 1 all property/atom i_myflag1 i_myflag2 -fix 1 all property/atom d_sx d_sy d_sz :pre - -[Description:] - -Create one or more additional per-atom vectors to store information -about atoms and to use during a simulation. The specified {group-ID} -is ignored by this fix. - -The atom style used for a simulation defines a set of per-atom -properties, as explained on the "atom_style"_atom_style.html and -"read_data"_read_data.html doc pages. The latter command allows these -properties to be defined for each atom in the system when a data file -is read. This fix will augment the set of properties with new custom -ones. This can be useful in several scenarios. - -If the atom style does not define molecule IDs, per-atom charge, -or per-atom mass, they can be added using the {mol}, {q} or {rmass} -keywords. This can be useful, e.g, to define "molecules" to use as -rigid bodies with the "fix rigid"_fix_rigid.html command, or just to -carry around an extra flag with the atoms (stored as a molecule ID) -that can be used to group atoms without having to use the group -command (which is limited to a total of 32 groups including {all}). - -Another application would be to use the {rmass} flag in order to have -per-atom masses instead of per-type masses, for example this can be -useful to study isotope effects with partial isotope substitution. -Please "see below"_#isotopes for an example of simulating a mixture -of light and heavy water with the TIP4P water potential. - -An alternative to using fix {property/atom} in these ways is to -use an atom style that does define molecule IDs or charge or per-atom -mass (indirectly via diameter and density) or to use a hybrid atom -style that combines two or more atom styles -to provide the union of all atom properties. However, this has two -practical drawbacks: first, it typically necessitates changing the -format of the data file, which can be tedious for large systems; -and second, it may define additional properties that are not needed -such as bond lists, which has some overhead when there are no bonds. - -In the future, we may add additional per-atom properties similar to -{mol}, {q} or {rmass}, which "turn-on" specific properties defined -by some atom styles, so they can be used by atom styles that do not -define them. - -More generally, the {i_name} and {d_name} vectors allow one or more -new custom per-atom properties to be defined. Each name must be -unique and can use alphanumeric or underscore characters. These -vectors can store whatever values you decide are useful in your -simulation. As explained below there are several ways to initialize -and access and output these values, both via input script commands and -in new code that you add to LAMMPS. - -This is effectively a simple way to add per-atom properties to a model -without needing to write code for a new "atom style"_atom_style.html -that defines the properties. Note however that implementing a new -atom style allows new atom properties to be more tightly and -seamlessly integrated with the rest of the code. - -The new atom properties encode values that migrate with atoms to new -processors and are written to restart files. If you want the new -properties to also be defined for ghost atoms, then use the {ghost} -keyword with a value of {yes}. This will invoke extra communication -when ghost atoms are created (at every re-neighboring) to insure the -new properties are also defined for the ghost atoms. - -NOTE: If you use this command with the {mol}, {q} or {rmass} vectors, -then you most likely want to set {ghost} yes, since these properties -are stored with ghost atoms if you use an "atom_style"_atom_style.html -that defines them, and many LAMMPS operations that use molecule IDs or -charge, such as neighbor lists and pair styles, will expect ghost -atoms to have these values. LAMMPS will issue a warning it you define -those vectors but do not set {ghost} yes. - -NOTE: The properties for ghost atoms are not updated every timestep, -but only once every few steps when neighbor lists are re-built. Thus -the {ghost} keyword is suitable for static properties, like molecule -IDs, but not for dynamic properties that change every step. For the -latter, the code you add to LAMMPS to change the properties will also -need to communicate their new values to/from ghost atoms, an operation -that can be invoked from within a "pair style"_pair_style.html or -"fix"_fix.html or "compute"_compute.html that you write. - -NOTE: If this fix is defined [after] the simulation box is created, -a 'run 0' command should be issued to properly initialize the storage -created by this fix. - -:line - -This fix is one of a small number that can be defined in an input -script before the simulation box is created or atoms are defined. -This is so it can be used with the "read_data"_read_data.html command -as described below. - -Per-atom properties that are defined by the "atom -style"_atom_style.html are initialized when atoms are created, e.g. by -the "read_data"_read_data.html or "create_atoms"_create_atoms.html -commands. The per-atom properties defined by this fix are not. So -you need to initialize them explicitly. This can be done by the -"read_data"_read_data.html command, using its {fix} keyword and -passing it the fix-ID of this fix. - -Thus these commands: - -fix prop all property/atom mol d_flag -read_data data.txt fix prop NULL Molecules :pre - -would allow a data file to have a section like this: - -Molecules :pre - -1 4 1.5 -2 4 3.0 -3 10 1.0 -4 10 1.0 -5 10 1.0 -... -N 763 4.5 :pre - -where N is the number of atoms, and the first field on each line is -the atom-ID, followed by a molecule-ID and a floating point value that -will be stored in a new property called "flag". Note that the list of -per-atom properties can be in any order. - -Another way of initializing the new properties is via the -"set"_set.html command. For example, if you wanted molecules -defined for every set of 10 atoms, based on their atom-IDs, -these commands could be used: - -fix prop all property/atom mol -variable cluster atom ((id-1)/10)+1 -set atom * mol v_cluster :pre - -The "atom-style variable"_variable.html will create values for atoms -with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9. When the -"set"_set.html commands assigns them to the molecule ID for each atom, -they will be truncated to an integer value, so atoms 31-40 will all be -assigned a molecule ID of 4. - -Note that "atomfile-style variables"_variable.html can also be used in -place of atom-style variables, which means in this case that the -molecule IDs could be read-in from a separate file and assigned by the -"set"_set.html command. This allows you to initialize new per-atom -properties in a completely general fashion. - -:line - -For new atom properties specified as {i_name} or {d_name}, the -"compute property/atom"_compute_property_atom.html command can access -their values. This means that the values can be output via the "dump -custom"_dump.html command, accessed by fixes like "fix -ave/atom"_fix_ave_atom.html, accessed by other computes like "compute -reduce"_compute_reduce.html, or used in "atom-style -variables"_variable.html. - -For example, these commands will output two new properties to a custom -dump file: - -fix prop all property/atom i_flag1 d_flag2 -compute 1 all property/atom i_flag1 d_flag2 -dump 1 all custom 100 tmp.dump id x y z c_1\[1\] c_1\[2\] :pre - -:line - -If you wish to add new "pair styles"_pair_style.html, -"fixes"_fix.html, or "computes"_compute.html that use the per-atom -properties defined by this fix, see the "Modify atom"_Modify_atom.html -doc page which has details on how the properties can be accessed from -added classes. - -:line - -:link(isotopes) - -Example for using per-atom masses with TIP4P water to -study isotope effects. When setting up simulations with the "TIP4P -pair styles"_Howto_tip4p.html for water, you have to provide exactly -one atom type each to identify the water oxygen and hydrogen -atoms. Since the atom mass is normally tied to the atom type, this -makes it impossible to study multiple isotopes in the same simulation. -With {fix property/atom rmass} however, the per-type masses are -replaced by per-atom masses. Asumming you have a working input deck -for regular TIP4P water, where water oxygen is atom type 1 and water -hydrogen is atom type 2, the following lines of input script convert -this to using per-atom masses: - -fix Isotopes all property/atom rmass ghost yes -set type 1 mass 15.9994 -set type 2 mass 1.008 :pre - -When writing out the system data with the "write_data"_write_data.html -command, there will be a new section named with the fix-ID -(i.e. {Isotopes} in this case). Alternatively, you can take an -existing data file and just add this {Isotopes} section with -one line per atom containing atom-ID and mass. Either way, the -extended data file can be read back with: - -fix Isotopes all property/atom rmass ghost yes -read_data tip4p-isotopes.data fix Isotopes NULL Isotopes :pre - -Please note that the first {Isotopes} refers to the fix-ID -and the second to the name of the section. The following input -script code will now change the first 100 water molecules in this -example to heavy water: - -group hwat id 2:300:3 -group hwat id 3:300:3 -set group hwat mass 2.0141018 :pre - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the per-atom values it stores to "binary restart -files"_restart.html, so that the values can be restored when a -simulation is restarted. See the "read_restart"_read_restart.html -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Howto_output.html. No parameter -of this fix can be used with the {start/stop} keywords of the -"run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"read_data"_read_data.html, "set"_set.html, "compute -property/atom"_compute_property_atom.html - -[Default:] - -The default keyword values are ghost = no. diff --git a/doc/txt/fix_python_invoke.txt b/doc/txt/fix_python_invoke.txt deleted file mode 100644 index 2a0124e6bf..0000000000 --- a/doc/txt/fix_python_invoke.txt +++ /dev/null @@ -1,76 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix python/invoke command :h3 - -[Syntax:] - -fix ID group-ID python/invoke N callback function_name :pre - -ID, group-ID are ignored by this fix :ulb,l -python/invoke = style name of this fix command :l -N = execute every N steps :l -callback = {post_force} or {end_of_step} :l - {post_force} = callback after force computations on atoms every N time steps - {end_of_step} = callback after every N time steps :pre -:ule - -[Examples:] - -python post_force_callback here """ -from lammps import lammps :pre - -def post_force_callback(lammps_ptr, vflag): - lmp = lammps(ptr=lammps_ptr) - # access LAMMPS state using Python interface -""" :pre - -python end_of_step_callback here """ -def end_of_step_callback(lammps_ptr): - lmp = lammps(ptr=lammps_ptr) - # access LAMMPS state using Python interface -""" :pre - -fix pf all python/invoke 50 post_force post_force_callback -fix eos all python/invoke 50 end_of_step end_of_step_callback :pre - -[Description:] - -This fix allows you to call a Python function during a simulation run. -The callback is either executed after forces have been applied to atoms -or at the end of every N time steps. - -Callback functions must be declared in the global scope of the -active Python interpreter. This can either be done by defining it -inline using the python command or by importing functions from other -Python modules. If LAMMPS is driven using the library interface from -Python, functions defined in the driving Python interpreter can also -be executed. - -Each callback is given a pointer object as first argument. This can be -used to initialize an instance of the lammps Python interface, which -gives access to the LAMMPS state from Python. - -IMPORTANT NOTE: While you can access the state of LAMMPS via library functions -from these callbacks, trying to execute input script commands will in the best -case not work or in the worst case result in undefined behavior. - -[Restrictions:] - -This fix is part of the PYTHON package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Building LAMMPS with the PYTHON package will link LAMMPS with the -Python library on your system. Settings to enable this are in the -lib/python/Makefile.lammps file. See the lib/python/README file for -information on those settings. - -[Related commands:] - -"python command"_python.html diff --git a/doc/txt/fix_python_move.txt b/doc/txt/fix_python_move.txt deleted file mode 100644 index c64ee788af..0000000000 --- a/doc/txt/fix_python_move.txt +++ /dev/null @@ -1,102 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix python/move command :h3 - -[Syntax:] - -fix python/move pymodule.CLASS :pre - -pymodule.CLASS = use class [CLASS] in module/file [pymodule] to compute how to move atoms - -[Examples:] - -fix 1 all python/move py_nve.NVE -fix 1 all python/move py_nve.NVE_OPT :pre - -[Description:] - -The {python/move} fix style provides a way to define ways how particles -are moved during an MD run from python script code, that is loaded from -a file into LAMMPS and executed at the various steps where other fixes -can be executed. This python script must contain specific python class -definitions. - -This allows to implement complex position updates and also modified -time integration methods. Due to python being an interpreted language, -however, the performance of this fix can be moderately to significantly -slower than the corresponding C++ code. For specific cases, this -performance penalty can be limited through effective use of NumPy. - -:line - -The python module file has to start with the following code: - -from __future__ import print_function -import lammps -import ctypes -import traceback -import numpy as np -# -class LAMMPSFix(object): - def __init__(self, ptr, group_name="all"): - self.lmp = lammps.lammps(ptr=ptr) - self.group_name = group_name -# -class LAMMPSFixMove(LAMMPSFix): - def __init__(self, ptr, group_name="all"): - super(LAMMPSFixMove, self).__init__(ptr, group_name) -# - def init(self): - pass -# - def initial_integrate(self, vflag): - pass -# - def final_integrate(self): - pass -# - def initial_integrate_respa(self, vflag, ilevel, iloop): - pass -# - def final_integrate_respa(self, ilevel, iloop): - pass -# - def reset_dt(self): - pass :pre - -Any classes implementing new atom motion functionality have to be -derived from the [LAMMPSFixMove] class, overriding the available -methods as needed. - -Examples for how to do this are in the {examples/python} folder. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This pair style is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix python/invoke"_fix_python_invoke.html - -[Default:] none - diff --git a/doc/txt/fix_qbmsst.txt b/doc/txt/fix_qbmsst.txt deleted file mode 100644 index 546d8c0813..0000000000 --- a/doc/txt/fix_qbmsst.txt +++ /dev/null @@ -1,219 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix qbmsst command :h3 - -[Syntax:] - -fix ID group-ID qbmsst dir shockvel keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -qbmsst = style name of this fix :l -dir = {x} or {y} or {z} :l -shockvel = shock velocity (strictly positive, velocity units) :l -zero or more keyword/value pairs may be appended :l -keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} or {damp} or {seed}or {f_max} or {N_f} or {eta} or {beta} or {T_init} :l - - {q} value = cell mass-like parameter (mass^2/distance^4 units) - {mu} value = artificial viscosity (mass/distance/time units) - {p0} value = initial pressure in the shock equations (pressure units) - {v0} value = initial simulation cell volume in the shock equations (distance^3 units) - {e0} value = initial total energy (energy units) - {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) - {damp} value = damping parameter (time units) inverse of friction γ - {seed} value = random number seed (positive integer) - {f_max} value = upper cutoff frequency of the vibration spectrum (1/time units) - {N_f} value = number of frequency bins (positive integer) - {eta} value = coupling constant between the shock system and the quantum thermal bath (positive unitless) - {beta} value = the quantum temperature is updated every beta time steps (positive integer) - {T_init} value = quantum temperature for the initial state (temperature units) :pre -:ule - -[Examples:] - -fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units) -fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units) :pre - -Two example input scripts are given, including shocked alpha quartz -and shocked liquid methane. The input script first equilibrate an -initial state with the quantum thermal bath at the target temperature -and then apply the qbmsst to simulate shock compression with quantum -nuclear correction. The following two figures plot related quantities -for shocked alpha quartz. - -:c,image(JPG/qbmsst_init.jpg) - -Figure 1. Classical temperature Tcl = ∑ -mivi2/3NkB vs. time -for coupling the alpha quartz initial state with the quantum thermal -bath at target quantum temperature Tqm = 300 K. The -NpH ensemble is used for time integration while QTB provides the -colored random force. Tcl converges at the timescale -of {damp} which is set to be 1 ps. - -:c,image(JPG/qbmsst_shock.jpg) - -Figure 2. Quantum temperature and pressure vs. time for simulating -shocked alpha quartz with the QBMSST. The shock propagates along the z -direction. Restart of the QBMSST command is demonstrated in the -example input script. Thermodynamic quantities stay continuous before -and after the restart. - -[Description:] - -This command performs the Quantum-Bath coupled Multi-Scale Shock -Technique (QBMSST) integration. See "(Qi)"_#Qi for a detailed -description of this method. The QBMSST provides description of the -thermodynamics and kinetics of shock processes while incorporating -quantum nuclear effects. The {shockvel} setting determines the steady -shock velocity that will be simulated along direction {dir}. - -Quantum nuclear effects "(fix qtb)"_fix_qtb.html can be crucial -especially when the temperature of the initial state is below the -classical limit or there is a great change in the zero point energies -between the initial and final states. Theoretical post processing -quantum corrections of shock compressed water and methane have been -reported as much as 30% of the temperatures "(Goldman)"_#Goldman1. A -self-consistent method that couples the shock to a quantum thermal -bath described by a colored noise Langevin thermostat has been -developed by Qi et al "(Qi)"_#Qi and applied to shocked methane. The -onset of chemistry is reported to be at a pressure on the shock -Hugoniot that is 40% lower than observed with classical molecular -dynamics. - -It is highly recommended that the system be already in an equilibrium -state with a quantum thermal bath at temperature of {T_init}. The fix -command "fix qtb"_fix_qtb.html at constant temperature {T_init} could -be used before applying this command to introduce self-consistent -quantum nuclear effects into the initial state. - -The parameters {q}, {mu}, {e0}, {p0}, {v0} and {tscale} are described -in the command "fix msst"_fix_msst.html. The values of {e0}, {p0}, or -{v0} will be calculated on the first step if not specified. The -parameter of {damp}, {f_max}, and {N_f} are described in the command -"fix qtb"_fix_qtb.html. - -The fix qbmsst command couples the shock system to a quantum thermal -bath with a rate that is proportional to the change of the total -energy of the shock system, etot - etot0. -Here etot consists of both the system energy and a thermal -term, see "(Qi)"_#Qi, and etot0 = {e0} is the -initial total energy. - -The {eta} (η) parameter is a unitless coupling constant -between the shock system and the quantum thermal bath. A small {eta} -value cannot adjust the quantum temperature fast enough during the -temperature ramping period of shock compression while large {eta} -leads to big temperature oscillation. A value of {eta} between 0.3 and -1 is usually appropriate for simulating most systems under shock -compression. We observe that different values of {eta} lead to almost -the same final thermodynamic state behind the shock, as expected. - -The quantum temperature is updated every {beta} (β) steps -with an integration time interval {beta} times longer than the -simulation time step. In that case, etot is taken as its -average over the past {beta} steps. The temperature of the quantum -thermal bath Tqm changes dynamically according to -the following equation where Δt is the MD time step and -γ is the friction constant which is equal to the inverse -of the {damp} parameter. - -
dTqm/dt = -γη∑βl = -1[etot(t-lΔt)-etot0]/3βNkB -
- -The parameter {T_init} is the initial temperature of the quantum -thermal bath and the system before shock loading. - -For all pressure styles, the simulation box stays orthorhombic in -shape. Parrinello-Rahman boundary conditions (tilted box) are -supported by LAMMPS, but are not implemented for QBMSST. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -Because the state of the random number generator is not written to -"binary restart files"_restart.html, this fix cannot be restarted -"exactly" in an uninterrupted fashion. However, in a statistical -sense, a restarted simulation should produce similar behaviors of the -system as if it is not interrupted. To achieve such a restart, one -should write explicitly the same value for {q}, {mu}, {damp}, {f_max}, -{N_f}, {eta}, and {beta} and set {tscale} = 0 if the system is -compressed during the first run. - -The progress of the QBMSST can be monitored by printing the global -scalar and global vector quantities computed by the fix. The global -vector contains five values in this order: - -\[{dhugoniot}, {drayleigh}, {lagrangian_speed}, {lagrangian_position}, -{quantum_temperature}\] - -{dhugoniot} is the departure from the Hugoniot (temperature units). -{drayleigh} is the departure from the Rayleigh line (pressure units). -{lagrangian_speed} is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units). -{lagrangian_position} is the computational cell position in the reference frame moving at the shock speed. This is the distance of the computational cell behind the shock front. -{quantum_temperature} is the temperature of the quantum thermal bath Tqm. :ol - -To print these quantities to the log file with descriptive column -headers, the following LAMMPS commands are suggested. Here the -"fix_modify"_fix_modify.html energy command is also enabled to allow -the thermo keyword {etotal} to print the quantity etot. See -also the "thermo_style"_thermo_style.html command. - -fix fix_id all msst z -fix_modify fix_id energy yes -variable dhug equal f_fix_id\[1\] -variable dray equal f_fix_id\[2\] -variable lgr_vel equal f_fix_id\[3\] -variable lgr_pos equal f_fix_id\[4\] -variable T_qm equal f_fix_id\[5\] -thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id :pre - -The global scalar under the entry f_fix_id is the quantity of thermo -energy as an extra part of etot. This global scalar and the -vector of 5 quantities can be accessed by various "output -commands"_Howto_output.html. It is worth noting that the temp keyword -under the "thermo_style"_thermo_style.html command print the -instantaneous classical temperature Tcl as described -in the command "fix qtb"_fix_qtb.html. - -:line - -[Restrictions:] - -This fix style is part of the USER-QTB package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -All cell dimensions must be periodic. This fix can not be used with a -triclinic cell. The QBMSST fix has been tested only for the group-ID -all. - -:line - -[Related commands:] - -"fix qtb"_fix_qtb.html, "fix msst"_fix_msst.html - -:line - -[Default:] - -The keyword defaults are q = 10, mu = 0, tscale = 0.01, damp = 1, seed -= 880302, f_max = 200.0, N_f = 100, eta = 1.0, beta = 100, and -T_init=300.0. e0, p0, and v0 are calculated on the first step. - -:line - -:link(Goldman1) -[(Goldman)] Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009) - -:link(Qi) -[(Qi)] Qi and Reed, J. Phys. Chem. A 116, 10451 (2012). diff --git a/doc/txt/fix_qeq.txt b/doc/txt/fix_qeq.txt deleted file mode 100644 index 2e3872de60..0000000000 --- a/doc/txt/fix_qeq.txt +++ /dev/null @@ -1,225 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix qeq/point command :h3 -fix qeq/shielded command :h3 -fix qeq/slater command :h3 -fix qeq/dynamic command :h3 -fix qeq/fire command :h3 - -[Syntax:] - -fix ID group-ID style Nevery cutoff tolerance maxiter qfile keyword ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -style = {qeq/point} or {qeq/shielded} or {qeq/slater} or {qeq/dynamic} or {qeq/fire} :l -Nevery = perform charge equilibration every this many steps :l -cutoff = global cutoff for charge-charge interactions (distance unit) :l -tolerance = precision to which charges will be equilibrated :l -maxiter = maximum iterations to perform charge equilibration :l -qfile = a filename with QEq parameters or {coul/streitz} or {reax/c} :l - -zero or more keyword/value pairs may be appended :l -keyword = {alpha} or {qdamp} or {qstep} :l - {alpha} value = Slater type orbital exponent (qeq/slater only) - {qdamp} value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only) - {qstep} value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only) :pre - -:ule - -[Examples:] - -fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1 -fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2 -fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2 -fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq -fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1 :pre - -[Description:] - -Perform the charge equilibration (QEq) method as described in "(Rappe -and Goddard)"_#Rappe1 and formulated in "(Nakano)"_#Nakano1 (also known -as the matrix inversion method) and in "(Rick and Stuart)"_#Rick1 (also -known as the extended Lagrangian method) based on the -electronegativity equilization principle. - -These fixes can be used with any "pair style"_pair_style.html in -LAMMPS, so long as per-atom charges are defined. The most typical -use-case is in conjunction with a "pair style"_pair_style.html that -performs charge equilibration periodically (e.g. every timestep), such -as the ReaxFF or Streitz-Mintmire potential. -But these fixes can also be used with -potentials that normally assume per-atom charges are fixed, e.g. a -"Buckingham"_pair_buck.html or "LJ/Coulombic"_pair_lj.html potential. - -Because the charge equilibration calculation is effectively -independent of the pair style, these fixes can also be used to perform -a one-time assignment of charges to atoms. For example, you could -define the QEq fix, perform a zero-timestep run via the "run"_run.html -command without any pair style defined which would set per-atom -charges (based on the current atom configuration), then remove the fix -via the "unfix"_unfix.html command before performing further dynamics. - -NOTE: Computing and using charge values different from published -values defined for a fixed-charge potential like Buckingham or CHARMM -or AMBER, can have a strong effect on energies and forces, and -produces a different model than the published versions. - -NOTE: The "fix qeq/comb"_fix_qeq_comb.html command must still be used -to perform charge equilibration with the "COMB -potential"_pair_comb.html. The "fix qeq/reax"_fix_qeq_reax.html -command can be used to perform charge equilibration with the "ReaxFF -force field"_pair_reaxc.html, although fix qeq/shielded yields the -same results as fix qeq/reax if {Nevery}, {cutoff}, and {tolerance} -are the same. Eventually the fix qeq/reax command will be deprecated. - -The QEq method minimizes the electrostatic energy of the system (or -equalizes the derivative of energy with respect to charge of all the -atoms) by adjusting the partial charge on individual atoms based on -interactions with their neighbors within {cutoff}. It requires a few -parameters, in {metal} units, for each atom type which provided in a -file specified by {qfile}. The file has the following format - -1 chi eta gamma zeta qcore -2 chi eta gamma zeta qcore -... -Ntype chi eta gamma zeta qcore :pre - -There have to be parameters given for every atom type. Wildcard entries -are possible using the same syntax as elsewhere in LAMMPS -(i.e., n*m, n*, *m, *). Later entries will overwrite previous ones. -Empty lines or any text following the pound sign (#) are ignored. -Each line starts with the atom type followed by five parameters. -Only a subset of the parameters is used by each QEq style as described -below, thus the others can be set to 0.0 if desired, but all five -entries per line are required. - -{chi} = electronegativity in energy units -{eta} = self-Coulomb potential in energy units -{gamma} = shielded Coulomb constant defined by "ReaxFF force field"_#vanDuin in distance units -{zeta} = Slater type orbital exponent defined by the "Streitz-Mintmire"_#Streitz1 potential in reverse distance units -{qcore} = charge of the nucleus defined by the "Streitz-Mintmire potential"_#Streitz1 potential in charge units :ul - -The {qeq/point} style describes partial charges on atoms as point -charges. Interaction between a pair of charged particles is 1/r, -which is the simplest description of the interaction between charges. -Only the {chi} and {eta} parameters from the {qfile} file are used. -Note that Coulomb catastrophe can occur if repulsion between the pair -of charged particles is too weak. This style solves partial charges -on atoms via the matrix inversion method. A tolerance of 1.0e-6 is -usually a good number. - -The {qeq/shielded} style describes partial charges on atoms also as -point charges, but uses a shielded Coulomb potential to describe the -interaction between a pair of charged particles. Interaction through -the shielded Coulomb is given by equation (13) of the "ReaxFF force -field"_#vanDuin paper. The shielding accounts for charge overlap -between charged particles at small separation. This style is the same -as "fix qeq/reax"_fix_qeq_reax.html, and can be used with "pair_style -reax/c"_pair_reaxc.html. Only the {chi}, {eta}, and {gamma} -parameters from the {qfile} file are used. When using the string -{reax/c} as filename, these parameters are extracted directly from -an active {reax/c} pair style. This style solves partial -charges on atoms via the matrix inversion method. A tolerance of -1.0e-6 is usually a good number. - -The {qeq/slater} style describes partial charges on atoms as spherical -charge densities centered around atoms via the Slater 1{s} orbital, so -that the interaction between a pair of charged particles is the -product of two Slater 1{s} orbitals. The expression for the Slater -1{s} orbital is given under equation (6) of the -"Streitz-Mintmire"_#Streitz1 paper. Only the {chi}, {eta}, {zeta}, and -{qcore} parameters from the {qfile} file are used. When using the string -{coul/streitz} as filename, these parameters are extracted directly from -an active {coul/streitz} pair style. This style solves -partial charges on atoms via the matrix inversion method. A tolerance -of 1.0e-6 is usually a good number. Keyword {alpha} can be used to -change the Slater type orbital exponent. - -The {qeq/dynamic} style describes partial charges on atoms as point -charges that interact through 1/r, but the extended Lagrangian method -is used to solve partial charges on atoms. Only the {chi} and {eta} -parameters from the {qfile} file are used. Note that Coulomb -catastrophe can occur if repulsion between the pair of charged -particles is too weak. A tolerance of 1.0e-3 is usually a good -number. Keyword {qdamp} can be used to change the damping factor, while -keyword {qstep} can be used to change the time step size. - -The "{qeq/fire}"_#Shan style describes the same charge model and charge -solver as the {qeq/dynamic} style, but employs a FIRE minimization -algorithm to solve for equilibrium charges. -Keyword {qdamp} can be used to change the damping factor, while -keyword {qstep} can be used to change the time step size. - -Note that {qeq/point}, {qeq/shielded}, and {qeq/slater} describe -different charge models, whereas the matrix inversion method and the -extended Lagrangian method ({qeq/dynamic} and {qeq/fire}) are -different solvers. - -Note that {qeq/point}, {qeq/dynamic} and {qeq/fire} styles all describe -charges as point charges that interact through 1/r relationship, but -solve partial charges on atoms using different solvers. These three -styles should yield comparable results if -the QEq parameters and {Nevery}, {cutoff}, and {tolerance} are the -same. Style {qeq/point} is typically faster, {qeq/dynamic} scales -better on larger sizes, and {qeq/fire} is faster than {qeq/dynamic}. - -NOTE: To avoid the evaluation of the derivative of charge with respect -to position, which is typically ill-defined, the system should have a -zero net charge. - -NOTE: Developing QEq parameters (chi, eta, gamma, zeta, and qcore) is -non-trivial. Charges on atoms are not guaranteed to equilibrate with -arbitrary choices of these parameters. We do not develop these QEq -parameters. See the examples/qeq directory for some examples. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about these fixes is written to "binary restart -files"_restart.html. No global scalar or vector or per-atom -quantities are stored by these fixes for access by various "output -commands"_Howto_output.html. No parameter of these fixes can be used -with the {start/stop} keywords of the "run"_run.html command. - -Thexe fixes are invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -These fixes are part of the QEQ package. They are only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix qeq/reax"_fix_qeq_reax.html, "fix qeq/comb"_fix_qeq_comb.html - -[Default:] none - -:line - -:link(Rappe1) -[(Rappe and Goddard)] A. K. Rappe and W. A. Goddard III, J Physical -Chemistry, 95, 3358-3363 (1991). - -:link(Nakano1) -[(Nakano)] A. Nakano, Computer Physics Communications, 104, 59-69 (1997). - -:link(Rick1) -[(Rick and Stuart)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chemical Physics -101, 16141 (1994). - -:link(Streitz1) -[(Streitz-Mintmire)] F. H. Streitz, J. W. Mintmire, Physical Review B, 50, -16, 11996 (1994) - -:link(vanDuin) -[(ReaxFF)] A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J -Physical Chemistry, 105, 9396-9049 (2001) - -:link(Shan) -[(QEq/Fire)] T.-R. Shan, A. P. Thompson, S. J. Plimpton, in preparation diff --git a/doc/txt/fix_qeq_comb.txt b/doc/txt/fix_qeq_comb.txt deleted file mode 100644 index 714d03f602..0000000000 --- a/doc/txt/fix_qeq_comb.txt +++ /dev/null @@ -1,131 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix qeq/comb command :h3 -fix qeq/comb/omp command :h3 - -[Syntax:] - -fix ID group-ID qeq/comb Nevery precision keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -qeq/comb = style name of this fix command :l -Nevery = perform charge equilibration every this many steps :l -precision = convergence criterion for charge equilibration :l -zero or more keyword/value pairs may be appended :l -keyword = {file} :l - {file} value = filename - filename = name of file to write QEQ equilibration info to :pre -:ule - -[Examples:] - -fix 1 surface qeq/comb 10 0.0001 :pre - -[Description:] - -Perform charge equilibration (QeQ) in conjunction with the COMB -(Charge-Optimized Many-Body) potential as described in -"(COMB_1)"_#COMB_1 and "(COMB_2)"_#COMB_2. It performs the charge -equilibration portion of the calculation using the so-called QEq -method, whereby the charge on each atom is adjusted to minimize the -energy of the system. This fix can only be used with the COMB -potential; see the "fix qeq/reax"_fix_qeq_reax.html command for a QeQ -calculation that can be used with any potential. - -Only charges on the atoms in the specified group are equilibrated. -The fix relies on the pair style (COMB in this case) to calculate the -per-atom electronegativity (effective force on the charges). An -electronegativity equalization calculation (or QEq) is performed in an -iterative fashion, which in parallel requires communication at each -iteration for processors to exchange charge information about nearby -atoms with each other. See "Rappe_and_Goddard"_#Rappe_and_Goddard and -"Rick_and_Stuart"_#Rick_and_Stuart for details. - -During a run, charge equilibration is performed every {Nevery} time -steps. Charge equilibration is also always enforced on the first step -of each run. The {precision} argument controls the tolerance for the -difference in electronegativity for all atoms during charge -equilibration. {Precision} is a trade-off between the cost of -performing charge equilibration (more iterations) and accuracy. - -If the {file} keyword is used, then information about each -equilibration calculation is written to the specified file. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is performing charge equilibration. Default is -the outermost level. - -This fix produces a per-atom vector which can be accessed by various -"output commands"_Howto_output.html. The vector stores the gradient -of the charge on each atom. The per-atom values be accessed on any -timestep. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -This fix can be invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix command currently only supports "pair style {comb}"_pair_comb.html. - -[Related commands:] - -"pair_style comb"_pair_comb.html - -[Default:] - -No file output is performed. - -:line - -:link(COMB_1) -[(COMB_1)] J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007), - -:link(COMB_2) -[(COMB_2)] T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R. -Phillpot, Phys Rev B, 81, 125328 (2010). - -:link(Rappe_and_Goddard) -[(Rappe_and_Goddard)] A. K. Rappe, W. A. Goddard, J Phys Chem 95, 3358 -(1991). - -:link(Rick_and_Stuart) -[(Rick_and_Stuart)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys -101, 16141 (1994). diff --git a/doc/txt/fix_qeq_reax.txt b/doc/txt/fix_qeq_reax.txt deleted file mode 100644 index b62d46d9de..0000000000 --- a/doc/txt/fix_qeq_reax.txt +++ /dev/null @@ -1,129 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix qeq/reax command :h3 -fix qeq/reax/kk command :h3 -fix qeq/reax/omp command :h3 - -[Syntax:] - -fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params args :pre - -ID, group-ID are documented in "fix"_fix.html command -qeq/reax = style name of this fix command -Nevery = perform QEq every this many steps -cutlo,cuthi = lo and hi cutoff for Taper radius -tolerance = precision to which charges will be equilibrated -params = reax/c or a filename -args = {dual} (optional) :ul - -[Examples:] - -fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c -fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq :pre - -[Description:] - -Perform the charge equilibration (QEq) method as described in "(Rappe -and Goddard)"_#Rappe2 and formulated in "(Nakano)"_#Nakano2. It is -typically used in conjunction with the ReaxFF force field model as -implemented in the "pair_style reax/c"_pair_reaxc.html command, but -it can be used with any potential in LAMMPS, so long as it defines and -uses charges on each atom. The "fix qeq/comb"_fix_qeq_comb.html -command should be used to perform charge equilibration with the "COMB -potential"_pair_comb.html. For more technical details about the -charge equilibration performed by fix qeq/reax, see the -"(Aktulga)"_#qeq-Aktulga paper. - -The QEq method minimizes the electrostatic energy of the system by -adjusting the partial charge on individual atoms based on interactions -with their neighbors. It requires some parameters for each atom type. -If the {params} setting above is the word "reax/c", then these are -extracted from the "pair_style reax/c"_pair_reaxc.html command and -the ReaxFF force field file it reads in. If a file name is specified -for {params}, then the parameters are taken from the specified file -and the file must contain one line for each atom type. The latter -form must be used when performing QeQ with a non-ReaxFF potential. -Each line should be formatted as follows: - -itype chi eta gamma :pre - -where {itype} is the atom type from 1 to Ntypes, {chi} denotes the -electronegativity in eV, {eta} denotes the self-Coulomb -potential in eV, and {gamma} denotes the valence orbital -exponent. Note that these 3 quantities are also in the ReaxFF -potential file, except that eta is defined here as twice the eta value -in the ReaxFF file. Note that unlike the rest of LAMMPS, the units -of this fix are hard-coded to be A, eV, and electronic charge. - -The optional {dual} keyword allows to perform the optimization -of the S and T matrices in parallel. This is only supported for -the {qeq/reax/omp} style. Otherwise they are processed separately. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. No global scalar or vector or per-atom -quantities are stored by this fix for access by various "output -commands"_Howto_output.html. No parameter of this fix can be used -with the {start/stop} keywords of the "run"_run.html command. - -This fix is invoked during "energy minimization"_minimize.html. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This fix is part of the USER-REAXC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix does not correctly handle interactions -involving multiple periodic images of the same atom. Hence, it should not -be used for periodic cell dimensions less than 10 angstroms. - -[Related commands:] - -"pair_style reax/c"_pair_reaxc.html - -[Default:] none - -:line - -:link(Rappe2) - [(Rappe)] Rappe and Goddard III, Journal of Physical Chemistry, 95, -3358-3363 (1991). - -:link(Nakano2) -[(Nakano)] Nakano, Computer Physics Communications, 104, 59-69 (1997). - -:link(qeq-Aktulga) -[(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, -245-259 (2012). diff --git a/doc/txt/fix_qmmm.txt b/doc/txt/fix_qmmm.txt deleted file mode 100644 index c39a58ed86..0000000000 --- a/doc/txt/fix_qmmm.txt +++ /dev/null @@ -1,66 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix qmmm command :h3 - -[Syntax:] - -fix ID group-ID qmmm :pre - -ID, group-ID are documented in "fix"_fix.html command -qmmm = style name of this fix command :ul - -[Examples:] - -fix 1 qmol qmmm - -[Description:] - -This fix provides functionality to enable a quantum -mechanics/molecular mechanics (QM/MM) coupling of LAMMPS to a quantum -mechanical code. The current implementation only supports an ONIOM -style mechanical coupling to the "Quantum ESPRESSO"_espresso plane -wave DFT package. Electrostatic coupling is in preparation and the -interface has been written in a manner that coupling to other QM codes -should be possible without changes to LAMMPS itself. - -:link(espresso,http://www.quantum-espresso.org) - -The interface code for this is in the lib/qmmm directory of the LAMMPS -distribution and is being made available at this early stage of -development in order to encourage contributions for interfaces to -other QM codes. This will allow the LAMMPS side of the implementation -to be adapted if necessary before being finalized. - -Details about how to use this fix are currently documented in the -description of the QM/MM interface code itself in lib/qmmm/README. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global scalar or vector or per-atom -quantities are stored by this fix for access by various "output -commands"_Howto_output.html. No parameter of this fix can be used -with the {start/stop} keywords of the "run"_run.html command. This -fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-QMMM package. It is only enabled if -LAMMPS was built with that package. It also requires building a -library provided with LAMMPS. See the "Build -package"_Build_package.html doc page for more info. - -The fix is only functional when LAMMPS is built as a library and -linked with a compatible QM program and a QM/MM front end into a QM/MM -executable. See the lib/qmmm/README file for details. - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/fix_qtb.txt b/doc/txt/fix_qtb.txt deleted file mode 100644 index c412146604..0000000000 --- a/doc/txt/fix_qtb.txt +++ /dev/null @@ -1,182 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix qtb command :h3 - -[Syntax:] - -fix ID group-ID qtb keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -qtb = style name of this fix :l -zero or more keyword/value pairs may be appended :l -keyword = {temp} or {damp} or {seed} or {f_max} or {N_f} :l - {temp} value = target quantum temperature (temperature units) - {damp} value = damping parameter (time units) inverse of friction &gamma; - {seed} value = random number seed (positive integer) - {f_max} value = upper cutoff frequency of the vibration spectrum (1/time units) - {N_f} value = number of frequency bins (positive integer) :pre -:ule - -[Examples:] - -fix 1 all nve -fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units) -fix 2 all nph iso 1.01325 1.01325 1 -fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units) :pre - -[Description:] - -This command performs the quantum thermal bath scheme proposed by -"(Dammak)"_#Dammak to include self-consistent quantum nuclear effects, -when used in conjunction with the "fix nve"_fix_nve.html or "fix -nph"_fix_nh.html commands. - -Classical molecular dynamics simulation does not include any quantum -nuclear effect. Quantum treatment of the vibrational modes will -introduce zero point energy into the system, alter the energy power -spectrum and bias the heat capacity from the classical limit. Missing -all the quantum nuclear effects, classical MD cannot model systems at -temperatures lower than their classical limits. This effect is -especially important for materials with a large population of hydrogen -atoms and thus higher classical limits. - -The equation of motion implemented by this command follows a Langevin -form: - -
miai = fi -+ Ri - -miγvi.
- -Here mi, ai, fi -, Ri, γ and vi -represent mass, acceleration, force exerted by all other atoms, random -force, frictional coefficient (the inverse of damping parameter damp), -and velocity. The random force Ri is "colored" so -that any vibrational mode with frequency ω will have a -temperature-sensitive energy θ(ω,T) which -resembles the energy expectation for a quantum harmonic oscillator -with the same natural frequency: - -
θ(ω,T) = -ℏω/2 + -ℏω[exp(ℏω/kBT)-1]-1 -
- -To efficiently generate the random forces, we employ the method -of "(Barrat)"_#Barrat, that circumvents the need to generate all -random forces for all times before the simulation. The memory -requirement of this approach is less demanding and independent -of the simulation duration. Since the total random force Rtot -does not necessarily vanish for a finite number of atoms, -Ri is replaced by Ri - Rtot/Ntot -to avoid collective motion of the system. - -The {temp} parameter sets the target quantum temperature. LAMMPS will -still have an output temperature in its thermo style. That is the -instantaneous classical temperature Tcl derived from -the atom velocities at thermal equilibrium. A non-zero -Tcl will be present even when the quantum -temperature approaches zero. This is associated with zero-point energy -at low temperatures. - -
Tcl = ∑ -mivi2/3NkB -
- -The {damp} parameter is specified in time units, and it equals the -inverse of the frictional coefficient γ. γ -should be as small as possible but slightly larger than the timescale -of anharmonic coupling in the system which is about 10 ps to 100 -ps. When γ is too large, it gives an energy spectrum that -differs from the desired Bose-Einstein spectrum. When γ -is too small, the quantum thermal bath coupling to the system will be -less significant than anharmonic effects, reducing to a classical -limit. We find that setting γ between 5 THz and 1 THz -could be appropriate depending on the system. - -The random number {seed} is a positive integer used to initiate a -Marsaglia random number generator. Each processor uses the input seed -to generate its own unique seed and its own stream of random -numbers. Thus the dynamics of the system will not be identical on two -runs on different numbers of processors. - -The {f_max} parameter truncate the noise frequency domain so that -vibrational modes with frequencies higher than {f_max} will not be -modulated. If we denote Δt as the time interval for the -MD integration, {f_max} is always reset by the code to make -α = (int)(2{f_max}Δt)-1 a -positive integer and print out relative information. An appropriate -value for the cutoff frequency {f_max} would be around 2~3 -fD, where fD is the Debye -frequency. - -The {N_f} parameter is the frequency grid size, the number of points -from 0 to {f_max} in the frequency domain that will be -sampled. 3×2 {N_f} per-atom random numbers are required -in the random force generation and there could be as many atoms as in -the whole simulation that can migrate into every individual -processor. A larger {N_f} provides a more accurate sampling of the -spectrum while consumes more memory. With fixed {f_max} and -γ, {N_f} should be big enough to converge the classical -temperature Tcl as a function of target quantum bath -temperature. Memory usage per processor could be from 10 to 100 -Mbytes. - -NOTE: Unlike the "fix nvt"_fix_nh.html command which performs -Nose/Hoover thermostatting AND time integration, this fix does NOT -perform time integration. It only modifies forces to a colored -thermostat. Thus you must use a separate time integration fix, like -"fix nve"_fix_nve.html or "fix nph"_fix_nh.html to actually update the -velocities and positions of atoms (as shown in the -examples). Likewise, this fix should not normally be used with other -fixes or commands that also specify system temperatures , e.g. "fix -nvt"_fix_nh.html and "fix temp/rescale"_fix_temp_rescale.html. - -:line - -[Restart, fix_modify, output, run start/stop, minimizie info:] - -No information about this fix is written to "binary restart -files"_restart.html. Because the state of the random number generator -is not saved in restart files, this means you cannot do "exact" -restarts with this fix. However, in a statistical sense, a restarted -simulation should produce similar behaviors of the system. - -This fix is not invoked during "energy minimization"_minimize.html. - -:line - -[Restrictions:] - -This fix style is part of the USER-QTB package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -:line - -[Related commands:] - -"fix nve"_fix_nve.html, "fix nph"_fix_nh.html, "fix -langevin"_fix_langevin.html, "fix qbmsst"_fix_qbmsst.html - -:line - -[Default:] - -The keyword defaults are temp = 300, damp = 1, seed = 880302, -f_max=200.0 and N_f = 100. - -:line - -:link(Dammak) -[(Dammak)] Dammak, Chalopin, Laroche, Hayoun, and Greffet, Phys Rev -Lett, 103, 190601 (2009). - -:link(Barrat) -[(Barrat)] Barrat and Rodney, J. Stat. Phys, 144, 679 (2011). diff --git a/doc/txt/fix_reaxc_bonds.txt b/doc/txt/fix_reaxc_bonds.txt deleted file mode 100644 index 9cd4ed7610..0000000000 --- a/doc/txt/fix_reaxc_bonds.txt +++ /dev/null @@ -1,107 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix reax/c/bonds command :h3 -fix reax/c/bonds/kk command :h3 - -[Syntax:] - -fix ID group-ID reaxc/bonds Nevery filename :pre - -ID, group-ID are documented in "fix"_fix.html command -reax/bonds = style name of this fix command -Nevery = output interval in timesteps -filename = name of output file :ul - -[Examples:] - -fix 1 all reax/c/bonds 100 bonds.reaxc :pre - -[Description:] - -Write out the bond information computed by the ReaxFF potential specified -by "pair_style reax/c"_pair_reaxc.html in the exact same format as the -original stand-alone ReaxFF code of Adri van Duin. The bond information -is written to {filename} on timesteps that are multiples of {Nevery}, -including timestep 0. For time-averaged chemical species analysis, -please see the "fix reaxc/c/species"_fix_reaxc_species.html command. - -The specified group-ID is ignored by this fix. - -The format of the output file should be reasonably self-explanatory. -The meaning of the column header abbreviations is as follows: - -id = atom id -type = atom type -nb = number of bonds -id_1 = atom id of first bond -id_nb = atom id of Nth bond -mol = molecule id -bo_1 = bond order of first bond -bo_nb = bond order of Nth bond -abo = atom bond order (sum of all bonds) -nlp = number of lone pairs -q = atomic charge :ul - -If the filename ends with ".gz", the output file is written in gzipped -format. A gzipped dump file will be about 3x smaller than the text -version, but will also take longer to write. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in "Speed"_Speed.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See "Speed"_Speed.html of the manual for -more instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -The fix reax/c/bonds command requires that the "pair_style -reax/c"_pair_reaxc.html is invoked. This fix is part of the -USER-REAXC package. It is only enabled if LAMMPS was built with that -package. See the "Build package"_Build_package.html doc page for more -info. - -To write gzipped bond files, you must compile LAMMPS with the --DLAMMPS_GZIP option. - -[Related commands:] - -"pair_style reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html - -[Default:] none diff --git a/doc/txt/fix_reaxc_species.txt b/doc/txt/fix_reaxc_species.txt deleted file mode 100644 index 60fa3a1d70..0000000000 --- a/doc/txt/fix_reaxc_species.txt +++ /dev/null @@ -1,186 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix reax/c/species command :h3 -fix reax/c/species/kk command :h3 - -[Syntax:] - -fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -reax/c/species = style name of this command :l - -Nevery = sample bond-order every this many timesteps :l -Nrepeat = # of bond-order samples used for calculating averages :l -Nfreq = calculate average bond-order every this many timesteps :l -filename = name of output file :l - -zero or more keyword/value pairs may be appended :l -keyword = {cutoff} or {element} or {position} :l - {cutoff} value = I J Cutoff - I, J = atom types - Cutoff = Bond-order cutoff value for this pair of atom types - {element} value = Element1, Element2, ... - {position} value = posfreq filepos - posfreq = write position files every this many timestep - filepos = name of position output file :pre -:ule - -[Examples:] - -fix 1 all reax/c/species 10 10 100 species.out -fix 1 all reax/c/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55 -fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH.pos :pre - -[Description:] - -Write out the chemical species information computed by the ReaxFF -potential specified by "pair_style reax/c"_pair_reaxc.html. -Bond-order values (either averaged or instantaneous, depending on -value of {Nrepeat}) are used to determine chemical bonds. Every -{Nfreq} timesteps, chemical species information is written to -{filename} as a two line output. The first line is a header -containing labels. The second line consists of the following: -timestep, total number of molecules, total number of distinct species, -number of molecules of each species. In this context, "species" means -a unique molecule. The chemical formula of each species is given in -the first line. - -If the filename ends with ".gz", the output file is written in gzipped -format. A gzipped dump file will be about 3x smaller than the text version, -but will also take longer to write. - -Optional keyword {cutoff} can be assigned to change the minimum -bond-order values used in identifying chemical bonds between pairs of -atoms. Bond-order cutoffs should be carefully chosen, as bond-order -cutoffs that are too small may include too many bonds (which will -result in an error), while cutoffs that are too large will result in -fragmented molecules. The default cutoff of 0.3 usually gives good -results. - -The optional keyword {element} can be used to specify the chemical -symbol printed for each LAMMPS atom type. The number of symbols must -match the number of LAMMPS atom types and each symbol must consist of -1 or 2 alphanumeric characters. Normally, these symbols should be -chosen to match the chemical identity of each LAMMPS atom type, as -specified using the "reax/c pair_coeff"_pair_reaxc.html command and -the ReaxFF force field file. - -The optional keyword {position} writes center-of-mass positions of -each identified molecules to file {filepos} every {posfreq} timesteps. -The first line contains information on timestep, total number of -molecules, total number of distinct species, and box dimensions. The -second line is a header containing labels. From the third line -downward, each molecule writes a line of output containing the -following information: molecule ID, number of atoms in this molecule, -chemical formula, total charge, and center-of-mass xyz positions of -this molecule. The xyz positions are in fractional coordinates -relative to the box dimensions. - -For the keyword {position}, the {filepos} is the name of the output -file. It can contain the wildcard character "*". If the "*" -character appears in {filepos}, then one file per snapshot is written -at {posfreq} and the "*" character is replaced with the timestep -value. For example, AuO.pos.* becomes AuO.pos.0, AuO.pos.1000, etc. - -:line - -The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what -timesteps the bond-order values are sampled to get the average bond -order. The species analysis is performed using the average bond-order -on timesteps that are a multiple of {Nfreq}. The average is over -{Nrepeat} bond-order samples, computed in the preceding portion of the -simulation every {Nevery} timesteps. {Nfreq} must be a multiple of -{Nevery} and {Nevery} must be non-zero even if {Nrepeat} is 1. -Also, the timesteps -contributing to the average bond-order cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. - -For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order -values on timesteps 90,92,94,96,98,100 will be used to compute the -average bond-order for the species analysis output on timestep 100. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes both a global vector of length 2 and a per-atom -vector, either of which can be accessed by various "output -commands"_Howto_output.html. The values in the global vector are -"intensive". - -The 2 values in the global vector are as follows: - -1 = total number of molecules -2 = total number of distinct species :ul - -The per-atom vector stores the molecule ID for each atom as identified -by the fix. If an atom is not in a molecule, its ID will be 0. -For atoms in the same molecule, the molecule ID for all of them -will be the same and will be equal to the smallest atom ID of -any atom in the molecule. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in "Speed"_Speed.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See "Speed"_Speed.html of the manual for -more instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -The "fix reax/c/species" currently only works with "pair_style -reax/c"_pair_reaxc.html and it requires that the "pair_style -reax/c"_pair_reaxc.html be invoked. This fix is part of the -USER-REAXC package. It is only enabled if LAMMPS was built with that -package. See the "Build package"_Build_package.html doc page for more -info. - -To write gzipped species files, you must compile LAMMPS with the --DLAMMPS_GZIP option. - -It should be possible to extend it to other reactive pair_styles (such as -"rebo"_pair_airebo.html, "airebo"_pair_airebo.html, -"comb"_pair_comb.html, and "bop"_pair_bop.html), but this has not yet been done. - -[Related commands:] - -"pair_style reax/c"_pair_reaxc.html, "fix reax/c/bonds"_fix_reaxc_bonds.html - -[Default:] - -The default values for bond-order cutoffs are 0.3 for all I-J pairs. The -default element symbols are C, H, O, N. Position files are not written -by default. diff --git a/doc/txt/fix_recenter.txt b/doc/txt/fix_recenter.txt deleted file mode 100644 index 05c93c3e2f..0000000000 --- a/doc/txt/fix_recenter.txt +++ /dev/null @@ -1,126 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix recenter command :h3 - -[Syntax:] - -fix ID group-ID recenter x y z keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -recenter = style name of this fix command :l -x,y,z = constrain center-of-mass to these coords (distance units), \ - any coord can also be NULL or INIT (see below) :l -zero or more keyword/value pairs may be appended :l -keyword = {shift} or {units} :l - {shift} value = group-ID - group-ID = group of atoms whose coords are shifted - {units} value = {box} or {lattice} or {fraction} :pre -:ule - -[Examples:] - -fix 1 all recenter 0.0 0.5 0.0 -fix 1 all recenter INIT INIT NULL -fix 1 all recenter INIT 0.0 0.0 units box :pre - -[Description:] - -Constrain the center-of-mass position of a group of atoms by adjusting -the coordinates of the atoms every timestep. This is simply a small -shift that does not alter the dynamics of the system or change the -relative coordinates of any pair of atoms in the group. This can be -used to insure the entire collection of atoms (or a portion of them) -do not drift during the simulation due to random perturbations -(e.g. "fix langevin"_fix_langevin.html thermostatting). - -Distance units for the x,y,z values are determined by the setting of -the {units} keyword, as discussed below. One or more x,y,z values can -also be specified as NULL, which means exclude that dimension from -this operation. Or it can be specified as INIT which means to -constrain the center-of-mass to its initial value at the beginning of -the run. - -The center-of-mass (COM) is computed for the group specified by the -fix. If the current COM is different than the specified x,y,z, then a -group of atoms has their coordinates shifted by the difference. By -default the shifted group is also the group specified by the fix. A -different group can be shifted by using the {shift} keyword. For -example, the COM could be computed on a protein to keep it in the -center of the simulation box. But the entire system (protein + water) -could be shifted. - -If the {units} keyword is set to {box}, then the distance units of -x,y,z are defined by the "units"_units.html command - e.g. Angstroms -for {real} units. A {lattice} value means the distance units are in -lattice spacings. The "lattice"_lattice.html command must have been -previously used to define the lattice spacing. A {fraction} value -means a fractional distance between the lo/hi box boundaries, e.g. 0.5 -= middle of the box. The default is to use lattice units. - -Note that the "velocity"_velocity.html command can be used to create -velocities with zero aggregate linear and/or angular momentum. - -NOTE: This fix performs its operations at the same point in the -timestep as other time integration fixes, such as "fix -nve"_fix_nve.html, "fix nvt"_fix_nh.html, or "fix npt"_fix_nh.html. -Thus fix recenter should normally be the last such fix specified in -the input script, since the adjustments it makes to atom coordinates -should come after the changes made by time integration. LAMMPS will -warn you if your fixes are not ordered this way. - -NOTE: If you use this fix on a small group of atoms (e.g. a molecule -in solvent) without using the {shift} keyword to adjust the positions -of all atoms in the system, then the results can be unpredictable. -For example, if the molecule is pushed consistently in one direction -by a flowing solvent, its velocity will increase. But its coordinates -will be re-centered, meaning it is moved back towards the force. Thus -over time, the velocity and effective temperature of the molecule -could become very large, though it won't actually be moving due to the -re-centering. If you are thermostatting the entire system, then the -solvent would be cooled to compensate. A better solution for this -simulation scenario is to use the "fix spring"_fix_spring.html command -to tether the molecule in place. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the distance the -group is moved by fix recenter. - -This fix also computes global 3-vector which can be accessed by -various "output commands"_Howto_output.html. The 3 quantities in the -vector are xyz components of displacement applied to the group of -atoms by the fix. - -The scalar and vector values calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix should not be used with an x,y,z setting that causes a large -shift in the system on the 1st timestep, due to the requested COM -being very different from the initial COM. This could cause atoms to -be lost, especially in parallel. Instead, use the -"displace_atoms"_displace_atoms.html command, which can be used to -move atoms a large distance. - -[Related commands:] - -"fix momentum"_fix_momentum.html, "velocity"_velocity.html - -[Default:] - -The option defaults are shift = fix group-ID, and units = lattice. diff --git a/doc/txt/fix_rhok.txt b/doc/txt/fix_rhok.txt deleted file mode 100644 index 7f0a72d1b3..0000000000 --- a/doc/txt/fix_rhok.txt +++ /dev/null @@ -1,56 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix rhok command :h3 - -fix ID group-ID rhok nx ny nz K a :pre - -ID, group-ID are documented in "fix"_fix.html command -nx, ny, nz = k-vector of collective density field -K = spring constant of bias potential -a = anchor point of bias potential :ul - -[Examples:] - -fix bias all rhok 16 0 0 4.0 16.0 -fix 1 all npt temp 0.8 0.8 4.0 z 2.2 2.2 8.0 -# output of 4 values from fix rhok: U_bias rho_k_RE rho_k_IM |rho_k| -thermo_style custom step temp pzz lz f_bias f_bias\[1\] f_bias\[2\] f_bias\[3\] :pre - -[Description:] - -The fix applies a force to atoms given by the potential - -:c,image(Eqs/fix_rhok.jpg) - -as described in "(Pedersen)"_#Pedersen. - -This field, which biases configurations with long-range order, can be -used to study crystal-liquid interfaces and determine melting -temperatures "(Pedersen)"_#Pedersen. - -An example of using the interface pinning method is located in the -{examples/USER/misc/rhok} directory. - -[Restrictions:] - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"thermo_style"_thermo_style.html - -[Default:] none - -:line - -:link(Pedersen) -[(Pedersen)] Pedersen, J. Chem. Phys., 139, 104102 (2013). - diff --git a/doc/txt/fix_rigid.txt b/doc/txt/fix_rigid.txt deleted file mode 100644 index d45705b2b2..0000000000 --- a/doc/txt/fix_rigid.txt +++ /dev/null @@ -1,857 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix rigid command :h3 -fix rigid/omp command :h3 -fix rigid/nve command :h3 -fix rigid/nve/omp command :h3 -fix rigid/nvt command :h3 -fix rigid/nvt/omp command :h3 -fix rigid/npt command :h3 -fix rigid/npt/omp command :h3 -fix rigid/nph command :h3 -fix rigid/nph/omp command :h3 -fix rigid/small command :h3 -fix rigid/small/omp command :h3 -fix rigid/nve/small command :h3 -fix rigid/nvt/small command :h3 -fix rigid/npt/small command :h3 -fix rigid/nph/small command :h3 - -[Syntax:] - -fix ID group-ID style bodystyle args keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {rigid/small} or {rigid/nve/small} or {rigid/nvt/small} or {rigid/npt/small} or {rigid/nph/small} :l -bodystyle = {single} or {molecule} or {group} :l - {single} args = none - {molecule} args = none - {custom} args = {i_propname} or {v_varname} - i_propname = an integer property defined via fix property/atom - v_varname = an atom-style or atomfile-style variable - {group} args = N groupID1 groupID2 ... - N = # of groups - groupID1, groupID2, ... = list of N group IDs :pre - -zero or more keyword/value pairs may be appended :l -keyword = {langevin} or {reinit} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l - {langevin} values = Tstart Tstop Tperiod seed - Tstart,Tstop = desired temperature at start/stop of run (temperature units) - Tdamp = temperature damping parameter (time units) - seed = random number seed to use for white noise (positive integer) - {reinit} = {yes} or {no} - {temp} values = Tstart Tstop Tdamp - Tstart,Tstop = desired temperature at start/stop of run (temperature units) - Tdamp = temperature damping parameter (time units) - {iso} or {aniso} values = Pstart Pstop Pdamp - Pstart,Pstop = scalar external pressure at start/end of run (pressure units) - Pdamp = pressure damping parameter (time units) - {x} or {y} or {z} values = Pstart Pstop Pdamp - Pstart,Pstop = external stress tensor component at start/end of run (pressure units) - Pdamp = stress damping parameter (time units) - {couple} = {none} or {xyz} or {xy} or {yz} or {xz} - {tparam} values = Tchain Titer Torder - Tchain = length of Nose/Hoover thermostat chain - Titer = number of thermostat iterations performed - Torder = 3 or 5 = Yoshida-Suzuki integration parameters - {pchain} values = Pchain - Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat - {dilate} value = dilate-group-ID - dilate-group-ID = only dilate atoms in this group due to barostat volume changes - {force} values = M xflag yflag zflag - M = which rigid body from 1-Nbody (see asterisk form below) - xflag,yflag,zflag = off/on if component of center-of-mass force is active - {torque} values = M xflag yflag zflag - M = which rigid body from 1-Nbody (see asterisk form below) - xflag,yflag,zflag = off/on if component of center-of-mass torque is active - {infile} filename - filename = file with per-body values of mass, center-of-mass, moments of inertia - {mol} value = template-ID - template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command :pre -:ule - -[Examples:] - -fix 1 clump rigid single reinit yes -fix 1 clump rigid/small molecule -fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984 -fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0 reinit no -fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on -fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984 -fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off -fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0 -fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz -fix 1 water rigid/nph molecule iso 0.5 0.5 1.0 -fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 :pre - -variable bodyid atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3) -fix 1 clump rigid custom v_bodyid :pre - -variable bodyid atomfile bodies.txt -fix 1 clump rigid custom v_bodyid :pre - -fix 0 all property/atom i_bodyid -read_restart data.rigid fix 0 NULL Bodies -fix 1 clump rigid/small custom i_bodyid :pre - -[Description:] - -Treat one or more sets of atoms as independent rigid bodies. This -means that each timestep the total force and torque on each rigid body -is computed as the sum of the forces and torques on its constituent -particles. The coordinates, velocities, and orientations of the atoms -in each body are then updated so that the body moves and rotates as a -single entity. This is implemented by creating internal data structures -for each rigid body and performing time integration on these data -structures. Positions, velocities, and orientations of the constituent -particles are regenerated from the rigid body data structures in every -time step. This restricts which operations and fixes can be applied to -rigid bodies. See below for a detailed discussion. - -Examples of large rigid bodies are a colloidal particle, or portions -of a biomolecule such as a protein. - -Example of small rigid bodies are patchy nanoparticles, such as those -modeled in "this paper"_#Zhang1 by Sharon Glotzer's group, clumps of -granular particles, lipid molecules consisting of one or more point -dipoles connected to other spheroids or ellipsoids, irregular -particles built from line segments (2d) or triangles (3d), and -coarse-grain models of nano or colloidal particles consisting of a -small number of constituent particles. Note that the "fix -shake"_fix_shake.html command can also be used to rigidify small -molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats -the constituent atoms as point masses. - -These fixes also update the positions and velocities of the atoms in -each rigid body via time integration, in the NVE, NVT, NPT, or NPH -ensemble, as described below. - -There are two main variants of this fix, fix rigid and fix -rigid/small. The NVE/NVT/NPT/NHT versions belong to one of the two -variants, as their style names indicate. - -NOTE: Not all of the {bodystyle} options and keyword/value options are -available for both the {rigid} and {rigid/small} variants. See -details below. - -The {rigid} styles are typically the best choice for a system with a -small number of large rigid bodies, each of which can extend across -the domain of many processors. It operates by creating a single -global list of rigid bodies, which all processors contribute to. -MPI_Allreduce operations are performed each timestep to sum the -contributions from each processor to the force and torque on all the -bodies. This operation will not scale well in parallel if large -numbers of rigid bodies are simulated. - -The {rigid/small} styles are typically best for a system with a large -number of small rigid bodies. Each body is assigned to the atom -closest to the geometrical center of the body. The fix operates using -local lists of rigid bodies owned by each processor and information is -exchanged and summed via local communication between neighboring -processors when ghost atom info is accumulated. - -NOTE: To use the {rigid/small} styles the ghost atom cutoff must be -large enough to span the distance between the atom that owns the body -and every other atom in the body. This distance value is printed out -when the rigid bodies are defined. If the -"pair_style"_pair_style.html cutoff plus neighbor skin does not span -this distance, then you should use the "comm_modify -cutoff"_comm_modify.html command with a setting epsilon larger than -the distance. - -Which of the two variants is faster for a particular problem is hard -to predict. The best way to decide is to perform a short test run. -Both variants should give identical numerical answers for short runs. -Long runs should give statistically similar results, but round-off -differences may accumulate to produce divergent trajectories. - -NOTE: You should not update the atoms in rigid bodies via other -time-integration fixes (e.g. "fix nve"_fix_nve.html, "fix -nvt"_fix_nh.html, "fix npt"_fix_nh.html, "fix move"_fix_move.html), -or you will have conflicting updates to positions and velocities -resulting in unphysical behavior in most cases. When performing a hybrid -simulation with some atoms in rigid bodies, and some not, a separate -time integration fix like "fix nve"_fix_nve.html or "fix -nvt"_fix_nh.html should be used for the non-rigid particles. - -NOTE: These fixes are overkill if you simply want to hold a collection -of atoms stationary or have them move with a constant velocity. A -simpler way to hold atoms stationary is to not include those atoms in -your time integration fix. E.g. use "fix 1 mobile nve" instead of -"fix 1 all nve", where "mobile" is the group of atoms that you want to -move. You can move atoms with a constant velocity by assigning them -an initial velocity (via the "velocity"_velocity.html command), -setting the force on them to 0.0 (via the "fix -setforce"_fix_setforce.html command), and integrating them as usual -(e.g. via the "fix nve"_fix_nve.html command). - -IMPORTANT NOTE: The aggregate properties of each rigid body are -calculated at the start of a simulation run and are maintained in -internal data structures. The properties include the position and -velocity of the center-of-mass of the body, its moments of inertia, and -its angular momentum. This is done using the properties of the -constituent atoms of the body at that point in time (or see the {infile} -keyword option). Thereafter, changing these properties of individual -atoms in the body will have no effect on a rigid body's dynamics, unless -they effect any computation of per-atom forces or torques. If the -keyword {reinit} is set to {yes} (the default), the rigid body data -structures will be recreated at the beginning of each {run} command; -if the keyword {reinit} is set to {no}, the rigid body data structures -will be built only at the very first {run} command and maintained for -as long as the rigid fix is defined. For example, you might think you -could displace the atoms in a body or add a large velocity to each atom -in a body to make it move in a desired direction before a 2nd run is -performed, using the "set"_set.html or -"displace_atoms"_displace_atoms.html or "velocity"_velocity.html -commands. But these commands will not affect the internal attributes -of the body unless {reinit} is set to {yes}. With {reinit} set to {no} -(or using the {infile} option, which implies {reinit} {no}) the position -and velocity of individual atoms in the body will be reset when time -integration starts again. - -:line - -Each rigid body must have two or more atoms. An atom can belong to at -most one rigid body. Which atoms are in which bodies can be defined -via several options. - -NOTE: With the {rigid/small} styles, which require that {bodystyle} be -specified as {molecule} or {custom}, you can define a system that has -no rigid bodies initially. This is useful when you are using the -{mol} keyword in conjunction with another fix that is adding rigid -bodies on-the-fly as molecules, such as "fix deposit"_fix_deposit.html -or "fix pour"_fix_pour.html. - -For bodystyle {single} the entire fix group of atoms is treated as one -rigid body. This option is only allowed for the {rigid} styles. - -For bodystyle {molecule}, atoms are grouped into rigid bodies by their -respective molecule IDs: each set of atoms in the fix group with the -same molecule ID is treated as a different rigid body. This option is -allowed for both the {rigid} and {rigid/small} styles. Note that -atoms with a molecule ID = 0 will be treated as a single rigid body. -For a system with atomic solvent (typically this is atoms with -molecule ID = 0) surrounding rigid bodies, this may not be what you -want. Thus you should be careful to use a fix group that only -includes atoms you want to be part of rigid bodies. - -Bodystyle {custom} is similar to bodystyle {molecule} except that it -is more flexible in using other per-atom properties to define the sets -of atoms that form rigid bodies. An integer vector defined by the -"fix property/atom"_fix_property_atom.html command can be used. Or an -"atom-style or atomfile-style variable"_variable.html can be used; the -floating-point value produced by the variable is rounded to an -integer. As with bodystyle {molecule}, each set of atoms in the fix -groups with the same integer value is treated as a different rigid -body. Since fix property/atom vectors and atom-style variables -produce values for all atoms, you should be careful to use a fix group -that only includes atoms you want to be part of rigid bodies. - -NOTE: To compute the initial center-of-mass position and other -properties of each rigid body, the image flags for each atom in the -body are used to "unwrap" the atom coordinates. Thus you must insure -that these image flags are consistent so that the unwrapping creates a -valid rigid body (one where the atoms are close together), -particularly if the atoms in a single rigid body straddle a periodic -boundary. This means the input data file or restart file must define -the image flags for each atom consistently or that you have used the -"set"_set.html command to specify them correctly. If a dimension is -non-periodic then the image flag of each atom must be 0 in that -dimension, else an error is generated. - -The {force} and {torque} keywords discussed next are only allowed for -the {rigid} styles. - -By default, each rigid body is acted on by other atoms which induce an -external force and torque on its center of mass, causing it to -translate and rotate. Components of the external center-of-mass force -and torque can be turned off by the {force} and {torque} keywords. -This may be useful if you wish a body to rotate but not translate, or -vice versa, or if you wish it to rotate or translate continuously -unaffected by interactions with other particles. Note that if you -expect a rigid body not to move or rotate by using these keywords, you -must insure its initial center-of-mass translational or angular -velocity is 0.0. Otherwise the initial translational or angular -momentum the body has will persist. - -An xflag, yflag, or zflag set to {off} means turn off the component of -force of torque in that dimension. A setting of {on} means turn on -the component, which is the default. Which rigid body(s) the settings -apply to is determined by the first argument of the {force} and -{torque} keywords. It can be an integer M from 1 to Nbody, where -Nbody is the number of rigid bodies defined. A wild-card asterisk can -be used in place of, or in conjunction with, the M argument to set the -flags for multiple rigid bodies. This takes the form "*" or "*n" or -"n*" or "m*n". If N = the number of rigid bodies, then an asterisk -with no numeric values means all bodies from 1 to N. A leading -asterisk means all bodies from 1 to n (inclusive). A trailing -asterisk means all bodies from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). Note that you can use the -{force} or {torque} keywords as many times as you like. If a -particular rigid body has its component flags set multiple times, the -settings from the final keyword are used. - -NOTE: For computational efficiency, you may wish to turn off pairwise -and bond interactions within each rigid body, as they no longer -contribute to the motion. The "neigh_modify -exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html -commands are used to do this. If the rigid bodies have strongly -overlapping atoms, you may need to turn off these interactions to -avoid numerical problems due to large equal/opposite intra-body forces -swamping the contribution of small inter-body forces. - -For computational efficiency, you should typically define one fix -rigid or fix rigid/small command which includes all the desired rigid -bodies. LAMMPS will allow multiple rigid fixes to be defined, but it -is more expensive. - -:line - -The constituent particles within a rigid body can be point particles -(the default in LAMMPS) or finite-size particles, such as spheres or -ellipsoids or line segments or triangles. See the "atom_style sphere -and ellipsoid and line and tri"_atom_style.html commands for more -details on these kinds of particles. Finite-size particles contribute -differently to the moment of inertia of a rigid body than do point -particles. Finite-size particles can also experience torque (e.g. due -to "frictional granular interactions"_pair_gran.html) and have an -orientation. These contributions are accounted for by these fixes. - -Forces between particles within a body do not contribute to the -external force or torque on the body. Thus for computational -efficiency, you may wish to turn off pairwise and bond interactions -between particles within each rigid body. The "neigh_modify -exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html -commands are used to do this. For finite-size particles this also -means the particles can be highly overlapped when creating the rigid -body. - -:line - -The {rigid}, {rigid/nve}, {rigid/small}, and {rigid/small/nve} styles -perform constant NVE time integration. They are referred to below as -the 4 NVE rigid styles. The only difference is that the {rigid} and -{rigid/small} styles use an integration technique based on Richardson -iterations. The {rigid/nve} and {rigid/small/nve} styles uses the -methods described in the paper by "Miller"_#Miller3, which are thought -to provide better energy conservation than an iterative approach. - -The {rigid/nvt} and {rigid/nvt/small} styles performs constant NVT -integration using a Nose/Hoover thermostat with chains as described -originally in "(Hoover)"_#Hoover and "(Martyna)"_#Martyna2, which -thermostats both the translational and rotational degrees of freedom -of the rigid bodies. They are referred to below as the 2 NVT rigid -styles. The rigid-body algorithm used by {rigid/nvt} is described in -the paper by "Kamberaj"_#Kamberaj. - -The {rigid/npt}, {rigid/nph}, {rigid/npt/small}, and {rigid/nph/small} -styles perform constant NPT or NPH integration using a Nose/Hoover -barostat with chains. They are referred to below as the 4 NPT and NPH -rigid styles. For the NPT case, the same Nose/Hoover thermostat is -also used as with {rigid/nvt} and {rigid/nvt/small}. - -The barostat parameters are specified using one or more of the {iso}, -{aniso}, {x}, {y}, {z} and {couple} keywords. These keywords give you -the ability to specify 3 diagonal components of the external stress -tensor, and to couple these components together so that the dimensions -they represent are varied together during a constant-pressure -simulation. The effects of these keywords are similar to those -defined in "fix npt/nph"_fix_nh.html - -NOTE: Currently the {rigid/npt}, {rigid/nph}, {rigid/npt/small}, and -{rigid/nph/small} styles do not support triclinic (non-orthogonal) -boxes. - -The target pressures for each of the 6 components of the stress tensor -can be specified independently via the {x}, {y}, {z} keywords, which -correspond to the 3 simulation box dimensions. For each component, -the external pressure or tensor component at each timestep is a ramped -value during the run from {Pstart} to {Pstop}. If a target pressure is -specified for a component, then the corresponding box dimension will -change during a simulation. For example, if the {y} keyword is used, -the y-box length will change. A box dimension will not change if that -component is not specified, although you have the option to change -that dimension via the "fix deform"_fix_deform.html command. - -For all barostat keywords, the {Pdamp} parameter operates like the -{Tdamp} parameter, determining the time scale on which pressure is -relaxed. For example, a value of 10.0 means to relax the pressure in -a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see -the "units"_units.html command). - -Regardless of what atoms are in the fix group (the only atoms which -are time integrated), a global pressure or stress tensor is computed -for all atoms. Similarly, when the size of the simulation box is -changed, all atoms are re-scaled to new positions, unless the keyword -{dilate} is specified with a {dilate-group-ID} for a group that -represents a subset of the atoms. This can be useful, for example, to -leave the coordinates of atoms in a solid substrate unchanged and -controlling the pressure of a surrounding fluid. Another example is a -system consisting of rigid bodies and point particles where the -barostat is only coupled with the rigid bodies. This option should be -used with care, since it can be unphysical to dilate some atoms and -not others, because it can introduce large, instantaneous -displacements between a pair of atoms (one dilated, one not) that are -far from the dilation origin. - -The {couple} keyword allows two or three of the diagonal components of -the pressure tensor to be "coupled" together. The value specified -with the keyword determines which are coupled. For example, {xz} -means the {Pxx} and {Pzz} components of the stress tensor are coupled. -{Xyz} means all 3 diagonal components are coupled. Coupling means two -things: the instantaneous stress will be computed as an average of the -corresponding diagonal components, and the coupled box dimensions will -be changed together in lockstep, meaning coupled dimensions will be -dilated or contracted by the same percentage every timestep. The -{Pstart}, {Pstop}, {Pdamp} parameters for any coupled dimensions must -be identical. {Couple xyz} can be used for a 2d simulation; the {z} -dimension is simply ignored. - -The {iso} and {aniso} keywords are simply shortcuts that are -equivalent to specifying several other keywords together. - -The keyword {iso} means couple all 3 diagonal components together when -pressure is computed (hydrostatic pressure), and dilate/contract the -dimensions together. Using "iso Pstart Pstop Pdamp" is the same as -specifying these 4 keywords: - -x Pstart Pstop Pdamp -y Pstart Pstop Pdamp -z Pstart Pstop Pdamp -couple xyz :pre - -The keyword {aniso} means {x}, {y}, and {z} dimensions are controlled -independently using the {Pxx}, {Pyy}, and {Pzz} components of the -stress tensor as the driving forces, and the specified scalar external -pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying -these 4 keywords: - -x Pstart Pstop Pdamp -y Pstart Pstop Pdamp -z Pstart Pstop Pdamp -couple none :pre - -:line - -The keyword/value option pairs are used in the following ways. - -The {reinit} keyword determines, whether the rigid body properties -are re-initialized between run commands. With the option {yes} (the -default) this is done, with the option {no} this is not done. Turning -off the re-initialization can be helpful to protect rigid bodies against -unphysical manipulations between runs or when properties cannot be -easily re-computed (e.g. when read from a file). When using the {infile} -keyword, the {reinit} option is automatically set to {no}. - -The {langevin} and {temp} and {tparam} keywords perform thermostatting -of the rigid bodies, altering both their translational and rotational -degrees of freedom. What is meant by "temperature" of a collection of -rigid bodies and how it can be monitored via the fix output is -discussed below. - -The {langevin} keyword applies a Langevin thermostat to the constant -NVE time integration performed by any of the 4 NVE rigid styles: -{rigid}, {rigid/nve}, {rigid/small}, {rigid/small/nve}. It cannot be -used with the 2 NVT rigid styles: {rigid/nvt}, {rigid/small/nvt}. The -desired temperature at each timestep is a ramped value during the run -from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in time -units and determines how rapidly the temperature is relaxed. For -example, a value of 100.0 means to relax the temperature in a timespan -of (roughly) 100 time units (tau or fmsec or psec - see the -"units"_units.html command). The random # {seed} must be a positive -integer. - -The way that Langevin thermostatting operates is explained on the "fix -langevin"_fix_langevin.html doc page. If you wish to simply viscously -damp the rotational motion without thermostatting, you can set -{Tstart} and {Tstop} to 0.0, which means only the viscous drag term in -the Langevin thermostat will be applied. See the discussion on the -"fix viscous"_fix_viscous.html doc page for details. - -NOTE: When the {langevin} keyword is used with fix rigid versus fix -rigid/small, different dynamics will result for parallel runs. This -is because of the way random numbers are used in the two cases. The -dynamics for the two cases should be statistically similar, but will -not be identical, even for a single timestep. - -The {temp} and {tparam} keywords apply a Nose/Hoover thermostat to the -NVT time integration performed by the 2 NVT rigid styles. They cannot -be used with the 4 NVE rigid styles. The desired temperature at each -timestep is a ramped value during the run from {Tstart} to {Tstop}. -The {Tdamp} parameter is specified in time units and determines how -rapidly the temperature is relaxed. For example, a value of 100.0 -means to relax the temperature in a timespan of (roughly) 100 time -units (tau or fmsec or psec - see the "units"_units.html command). - -Nose/Hoover chains are used in conjunction with this thermostat. The -{tparam} keyword can optionally be used to change the chain settings -used. {Tchain} is the number of thermostats in the Nose Hoover chain. -This value, along with {Tdamp} can be varied to dampen undesirable -oscillations in temperature that can occur in a simulation. As a rule -of thumb, increasing the chain length should lead to smaller -oscillations. The keyword {pchain} specifies the number of -thermostats in the chain thermostatting the barostat degrees of -freedom. - -NOTE: There are alternate ways to thermostat a system of rigid bodies. -You can use "fix langevin"_fix_langevin.html to treat the individual -particles in the rigid bodies as effectively immersed in an implicit -solvent, e.g. a Brownian dynamics model. For hybrid systems with both -rigid bodies and solvent particles, you can thermostat only the -solvent particles that surround one or more rigid bodies by -appropriate choice of groups in the compute and fix commands for -temperature and thermostatting. The solvent interactions with the -rigid bodies should then effectively thermostat the rigid body -temperature as well without use of the Langevin or Nose/Hoover options -associated with the fix rigid commands. - -:line - -The {mol} keyword can only be used with the {rigid/small} styles. It -must be used when other commands, such as "fix -deposit"_fix_deposit.html or "fix pour"_fix_pour.html, add rigid -bodies on-the-fly during a simulation. You specify a {template-ID} -previously defined using the "molecule"_molecule.html command, which -reads a file that defines the molecule. You must use the same -{template-ID} that the other fix which is adding rigid bodies uses. -The coordinates, atom types, atom diameters, center-of-mass, and -moments of inertia can be specified in the molecule file. See the -"molecule"_molecule.html command for details. The only settings -required to be in this file are the coordinates and types of atoms in -the molecule, in which case the molecule command calculates the other -quantities itself. - -Note that these other fixes create new rigid bodies, in addition to -those defined initially by this fix via the {bodystyle} setting. - -Also note that when using the {mol} keyword, extra restart information -about all rigid bodies is written out whenever a restart file is -written out. See the NOTE in the next section for details. - -:line - -The {infile} keyword allows a file of rigid body attributes to be read -in from a file, rather then having LAMMPS compute them. There are 5 -such attributes: the total mass of the rigid body, its center-of-mass -position, its 6 moments of inertia, its center-of-mass velocity, and -the 3 image flags of the center-of-mass position. For rigid bodies -consisting of point particles or non-overlapping finite-size -particles, LAMMPS can compute these values accurately. However, for -rigid bodies consisting of finite-size particles which overlap each -other, LAMMPS will ignore the overlaps when computing these 4 -attributes. The amount of error this induces depends on the amount of -overlap. To avoid this issue, the values can be pre-computed -(e.g. using Monte Carlo integration). - -The format of the file is as follows. Note that the file does not -have to list attributes for every rigid body integrated by fix rigid. -Only bodies which the file specifies will have their computed -attributes overridden. The file can contain initial blank lines or -comment lines starting with "#" which are ignored. The first -non-blank, non-comment line should list N = the number of lines to -follow. The N successive lines contain the following information: - -ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm -ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm -... -IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm :pre - -The rigid body IDs are all positive integers. For the {single} -bodystyle, only an ID of 1 can be used. For the {group} bodystyle, -IDs from 1 to Ng can be used where Ng is the number of specified -groups. For the {molecule} bodystyle, use the molecule ID for the -atoms in a specific rigid body as the rigid body ID. - -The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are -self-explanatory. The center-of-mass should be consistent with what -is calculated for the position of the rigid body with all its atoms -unwrapped by their respective image flags. If this produces a -center-of-mass that is outside the simulation box, LAMMPS wraps it -back into the box. - -The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the -values consistent with the current orientation of the rigid body -around its center of mass. The values are with respect to the -simulation box XYZ axes, not with respect to the principal axes of the -rigid body itself. LAMMPS performs the latter calculation internally. - -The (vxcm,vycm,vzcm) values are the velocity of the center of mass. -The (lx,ly,lz) values are the angular momentum of the body. The -(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you -wish the body to have no initial motion. - -The (ixcm,iycm,izcm) values are the image flags of the center of mass -of the body. For periodic dimensions, they specify which image of the -simulation box the body is considered to be in. An image of 0 means -it is inside the box as defined. A value of 2 means add 2 box lengths -to get the true value. A value of -1 means subtract 1 box length to -get the true value. LAMMPS updates these flags as the rigid bodies -cross periodic boundaries during the simulation. - -NOTE: If you use the {infile} or {mol} keywords and write restart -files during a simulation, then each time a restart file is written, -the fix also write an auxiliary restart file with the name -rfile.rigid, where "rfile" is the name of the restart file, -e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary -file is in the same format described above. Thus it can be used in a -new input script that restarts the run and re-specifies a rigid fix -using an {infile} keyword and the appropriate filename. Note that the -auxiliary file will contain one line for every rigid body, even if the -original file only listed a subset of the rigid bodies. - -:line - -If you use a "temperature compute"_compute.html with a group that -includes particles in rigid bodies, the degrees-of-freedom removed by -each rigid body are accounted for in the temperature (and pressure) -computation, but only if the temperature group includes all the -particles in a particular rigid body. - -A 3d rigid body has 6 degrees of freedom (3 translational, 3 -rotational), except for a collection of point particles lying on a -straight line, which has only 5, e.g a dimer. A 2d rigid body has 3 -degrees of freedom (2 translational, 1 rotational). - -NOTE: You may wish to explicitly subtract additional -degrees-of-freedom if you use the {force} and {torque} keywords to -eliminate certain motions of one or more rigid bodies. LAMMPS does -not do this automatically. - -The rigid body contribution to the pressure of the system (virial) is -also accounted for by this fix. - -:line - -If your simulation is a hybrid model with a mixture of rigid bodies -and non-rigid particles (e.g. solvent) there are several ways these -rigid fixes can be used in tandem with "fix nve"_fix_nve.html, "fix -nvt"_fix_nh.html, "fix npt"_fix_nh.html, and "fix nph"_fix_nh.html. - -If you wish to perform NVE dynamics (no thermostatting or -barostatting), use one of 4 NVE rigid styles to integrate the rigid -bodies, and "fix nve"_fix_nve.html to integrate the non-rigid -particles. - -If you wish to perform NVT dynamics (thermostatting, but no -barostatting), you can use one of the 2 NVT rigid styles for the rigid -bodies, and any thermostatting fix for the non-rigid particles ("fix -nvt"_fix_nh.html, "fix langevin"_fix_langevin.html, "fix -temp/berendsen"_fix_temp_berendsen.html). You can also use one of the -4 NVE rigid styles for the rigid bodies and thermostat them using "fix -langevin"_fix_langevin.html on the group that contains all the -particles in the rigid bodies. The net force added by "fix -langevin"_fix_langevin.html to each rigid body effectively thermostats -its translational center-of-mass motion. Not sure how well it does at -thermostatting its rotational motion. - -If you with to perform NPT or NPH dynamics (barostatting), you cannot -use both "fix npt"_fix_nh.html and the NPT or NPH rigid styles. This -is because there can only be one fix which monitors the global -pressure and changes the simulation box dimensions. So you have 3 -choices: - -Use one of the 4 NPT or NPH styles for the rigid bodies. Use the -{dilate} all option so that it will dilate the positions of the -non-rigid particles as well. Use "fix nvt"_fix_nh.html (or any other -thermostat) for the non-rigid particles. :ulb,l - -Use "fix npt"_fix_nh.html for the group of non-rigid particles. Use -the {dilate} all option so that it will dilate the center-of-mass -positions of the rigid bodies as well. Use one of the 4 NVE or 2 NVT -rigid styles for the rigid bodies. :l - -Use "fix press/berendsen"_fix_press_berendsen.html to compute the -pressure and change the box dimensions. Use one of the 4 NVE or 2 NVT -rigid styles for the rigid bodies. Use "fix nvt"_fix_nh.html (or any -other thermostat) for the non-rigid particles. :l -:ule - -In all case, the rigid bodies and non-rigid particles both contribute -to the global pressure and the box is scaled the same by any of the -barostatting fixes. - -You could even use the 2nd and 3rd options for a non-hybrid simulation -consisting of only rigid bodies, assuming you give "fix -npt"_fix_nh.html an empty group, though it's an odd thing to do. The -barostatting fixes ("fix npt"_fix_nh.html and "fix -press/berensen"_fix_press_berendsen.html) will monitor the pressure -and change the box dimensions, but not time integrate any particles. -The integration of the rigid bodies will be performed by fix -rigid/nvt. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about the 4 NVE rigid styles is written to "binary -restart files"_restart.html. The exception is if the {infile} or -{mol} keyword is used, in which case an auxiliary file is written out -with rigid body information each time a restart file is written, as -explained above for the {infile} keyword. For the 2 NVT rigid styles, -the state of the Nose/Hoover thermostat is written to "binary restart -files"_restart.html. Ditto for the 4 NPT and NPH rigid styles, and -the state of the Nose/Hoover barostat. See the -"read_restart"_read_restart.html command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. - -The "fix_modify"_fix_modify.html {energy} option is supported by the 6 -NVT, NPT, NPH rigid styles to add the energy change induced by the -thermostatting to the system's potential energy as part of -"thermodynamic output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {virial} option is supported by this -fix to add the contribution due to keeping the objects rigid to the -system's virial as part of "thermodynamic output"_thermo_style.html. -The default is {virial yes} - -The "fix_modify"_fix_modify.html {temp} and {press} options are -supported by the 4 NPT and NPH rigid styles to change the computes -used to calculate the instantaneous pressure tensor. Note that the 2 -NVT rigid fixes do not use any external compute to compute -instantaneous temperature. - -The "fix_modify"_fix_modify.html {bodyforces} option is supported by -all rigid styles to set whether per-body forces and torques are -computed early or late in a timestep, i.e. at the post-force stage or -at the final-integrate stage or the timestep, respectively. - -The 2 NVE rigid fixes compute a global scalar which can be accessed by -various "output commands"_Howto_output.html. The scalar value -calculated by these fixes is "intensive". The scalar is the current -temperature of the collection of rigid bodies. This is averaged over -all rigid bodies and their translational and rotational degrees of -freedom. The translational energy of a rigid body is 1/2 m v^2, where -m = total mass of the body and v = the velocity of its center of mass. -The rotational energy of a rigid body is 1/2 I w^2, where I = the -moment of inertia tensor of the body and w = its angular velocity. -Degrees of freedom constrained by the {force} and {torque} keywords -are removed from this calculation, but only for the {rigid} and -{rigid/nve} fixes. - -The 6 NVT, NPT, NPH rigid fixes compute a global scalar which can be -accessed by various "output commands"_Howto_output.html. The scalar -value calculated by these fixes is "extensive". The scalar is the -cumulative energy change due to the thermostatting and barostatting -the fix performs. - -All of the {rigid} styles (not the {rigid/small} styles) compute a -global array of values which can be accessed by various "output -commands"_Howto_output.html. Similar information about the bodies -defined by the {rigid/small} styles can be accessed via the "compute -rigid/local"_compute_rigid_local.html command. - -The number of rows in the array is equal to the number of rigid -bodies. The number of columns is 15. Thus for each rigid body, 15 -values are stored: the xyz coords of the center of mass (COM), the xyz -components of the COM velocity, the xyz components of the force acting -on the COM, the xyz components of the torque acting on the COM, and -the xyz image flags of the COM. - -The center of mass (COM) for each body is similar to unwrapped -coordinates written to a dump file. It will always be inside (or -slightly outside) the simulation box. The image flags have the same -meaning as image flags for atom positions (see the "dump" command). -This means you can calculate the unwrapped COM by applying the image -flags to the COM, the same as when unwrapped coordinates are written -to a dump file. - -The force and torque values in the array are not affected by the -{force} and {torque} keywords in the fix rigid command; they reflect -values before any changes are made by those keywords. - -The ordering of the rigid bodies (by row in the array) is as follows. -For the {single} keyword there is just one rigid body. For the -{molecule} keyword, the bodies are ordered by ascending molecule ID. -For the {group} keyword, the list of group IDs determines the ordering -of bodies. - -The array values calculated by these fixes are "intensive", meaning -they are independent of the number of atoms in the simulation. - -No parameter of these fixes can be used with the {start/stop} keywords -of the "run"_run.html command. These fixes are not invoked during -"energy minimization"_minimize.html. - -:line - -[Restrictions:] - -These fixes are all part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Assigning a temperature via the "velocity create"_velocity.html -command to a system with "rigid bodies"_fix_rigid.html may not have -the desired outcome for two reasons. First, the velocity command can -be invoked before the rigid-body fix is invoked or initialized and the -number of adjusted degrees of freedom (DOFs) is known. Thus it is not -possible to compute the target temperature correctly. Second, the -assigned velocities may be partially canceled when constraints are -first enforced, leading to a different temperature than desired. A -workaround for this is to perform a "run 0"_run.html command, which -insures all DOFs are accounted for properly, and then rescale the -temperature to the desired value before performing a simulation. For -example: - -velocity all create 300.0 12345 -run 0 # temperature may not be 300K -velocity all scale 300.0 # now it should be :pre - -[Related commands:] - -"delete_bonds"_delete_bonds.html, "neigh_modify"_neigh_modify.html -exclude, "fix shake"_fix_shake.html - -[Default:] - -The option defaults are force * on on on and torque * on on on, -meaning all rigid bodies are acted on by center-of-mass force and -torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3, reinit = yes. - -:line - -:link(Hoover) -[(Hoover)] Hoover, Phys Rev A, 31, 1695 (1985). - -:link(Kamberaj) -[(Kamberaj)] Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005). - -:link(Martyna2) -[(Martyna)] Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992); -Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117. - -:link(Miller3) -[(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, -J Chem Phys, 116, 8649 (2002). - -:link(Zhang1) -[(Zhang)] Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004). diff --git a/doc/txt/fix_rigid_meso.txt b/doc/txt/fix_rigid_meso.txt deleted file mode 100644 index a9c68b2c04..0000000000 --- a/doc/txt/fix_rigid_meso.txt +++ /dev/null @@ -1,350 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix rigid/meso command :h3 - -[Syntax:] - -fix ID group-ID rigid/meso bodystyle args keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -rigid/meso = style name of this fix command :l -bodystyle = {single} or {molecule} or {group} :l - {single} args = none - {molecule} args = none - {custom} args = {i_propname} or {v_varname} - i_propname = an integer property defined via fix property/atom - v_varname = an atom-style or atomfile-style variable - {group} args = N groupID1 groupID2 ... - N = # of groups - groupID1, groupID2, ... = list of N group IDs :pre - -zero or more keyword/value pairs may be appended :l -keyword = {reinit} or {force} or {torque} or {infile} :l - {reinit} = {yes} or {no} - {force} values = M xflag yflag zflag - M = which rigid body from 1-Nbody (see asterisk form below) - xflag,yflag,zflag = off/on if component of center-of-mass force is active - {torque} values = M xflag yflag zflag - M = which rigid body from 1-Nbody (see asterisk form below) - xflag,yflag,zflag = off/on if component of center-of-mass torque is active - {infile} filename - filename = file with per-body values of mass, center-of-mass, moments of inertia :pre -:ule - -[Examples:] - -fix 1 ellipsoid rigid/meso single -fix 1 rods rigid/meso molecule -fix 1 spheres rigid/meso single force 1 off off on -fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on -fix 2 spheres rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off :pre - -[Description:] - -Treat one or more sets of mesoscopic SPH/SDPD particles as independent -rigid bodies. This means that each timestep the total force and torque -on each rigid body is computed as the sum of the forces and torques on -its constituent particles. The coordinates and velocities of the -particles in each body are then updated so that the body moves and -rotates as a single entity using the methods described in the paper by -"(Miller)"_#Miller. Density and internal energy of the particles will -also be updated. This is implemented by creating internal data structures -for each rigid body and performing time integration on these data -structures. Positions and velocities of the constituent particles are -regenerated from the rigid body data structures in every time step. This -restricts which operations and fixes can be applied to rigid bodies. See -below for a detailed discussion. - -The operation of this fix is exactly like that described by the -"fix rigid/nve"_fix_rigid.html command, except that particles' density, -internal energy and extrapolated velocity are also updated. - -NOTE: You should not update the particles in rigid bodies via other -time-integration fixes (e.g. "fix meso"_fix_meso.html, -"fix meso/stationary"_fix_meso_stationary.html), or you will have conflicting -updates to positions and velocities resulting in unphysical behavior in most -cases. When performing a hybrid simulation with some atoms in rigid bodies, -and some not, a separate time integration fix like "fix meso"_fix_meso.html -should be used for the non-rigid particles. - -NOTE: These fixes are overkill if you simply want to hold a collection -of particles stationary or have them move with a constant velocity. To -hold particles stationary use "fix -meso/stationary"_fix_meso_stationary.html instead. If you would like to -move particles with a constant velocity use "fix -meso/move"_fix_meso_move.html. - -IMPORTANT NOTE: The aggregate properties of each rigid body are -calculated at the start of a simulation run and are maintained in -internal data structures. The properties include the position and -velocity of the center-of-mass of the body, its moments of inertia, and -its angular momentum. This is done using the properties of the -constituent particles of the body at that point in time (or see the {infile} -keyword option). Thereafter, changing these properties of individual -particles in the body will have no effect on a rigid body's dynamics, unless -they effect any computation of per-particle forces or torques. If the -keyword {reinit} is set to {yes} (the default), the rigid body data -structures will be recreated at the beginning of each {run} command; -if the keyword {reinit} is set to {no}, the rigid body data structures -will be built only at the very first {run} command and maintained for -as long as the rigid fix is defined. For example, you might think you -could displace the particles in a body or add a large velocity to each particle -in a body to make it move in a desired direction before a 2nd run is -performed, using the "set"_set.html or -"displace_atoms"_displace_atoms.html or "velocity"_velocity.html -commands. But these commands will not affect the internal attributes -of the body unless {reinit} is set to {yes}. With {reinit} set to {no} -(or using the {infile} option, which implies {reinit} {no}) the position -and velocity of individual particles in the body will be reset when time -integration starts again. - -:line - -Each rigid body must have two or more particles. A particle can belong -to at most one rigid body. Which particles are in which bodies can be -defined via several options. - -For bodystyle {single} the entire fix group of particles is treated as -one rigid body. - -For bodystyle {molecule}, particles are grouped into rigid bodies by their -respective molecule IDs: each set of particles in the fix group with the -same molecule ID is treated as a different rigid body. Note that particles -with a molecule ID = 0 will be treated as a single rigid body. For a -system with solvent (typically this is particles with molecule ID = 0) -surrounding rigid bodies, this may not be what you want. Thus you -should be careful to use a fix group that only includes particles you -want to be part of rigid bodies. - -Bodystyle {custom} is similar to bodystyle {molecule} except that it -is more flexible in using other per-atom properties to define the sets -of particles that form rigid bodies. An integer vector defined by the -"fix property/atom"_fix_property_atom.html command can be used. Or an -"atom-style or atomfile-style variable"_variable.html can be used; the -floating-point value produced by the variable is rounded to an -integer. As with bodystyle {molecule}, each set of particles in the fix -groups with the same integer value is treated as a different rigid -body. Since fix property/atom vectors and atom-style variables -produce values for all particles, you should be careful to use a fix group -that only includes particles you want to be part of rigid bodies. - -For bodystyle {group}, each of the listed groups is treated as a -separate rigid body. Only particles that are also in the fix group are -included in each rigid body. - -NOTE: To compute the initial center-of-mass position and other -properties of each rigid body, the image flags for each particle in the -body are used to "unwrap" the particle coordinates. Thus you must -insure that these image flags are consistent so that the unwrapping -creates a valid rigid body (one where the particles are close together) -, particularly if the particles in a single rigid body straddle a -periodic boundary. This means the input data file or restart file must -define the image flags for each particle consistently or that you have -used the "set"_set.html command to specify them correctly. If a -dimension is non-periodic then the image flag of each particle must be -0 in that dimension, else an error is generated. - -By default, each rigid body is acted on by other particles which induce -an external force and torque on its center of mass, causing it to -translate and rotate. Components of the external center-of-mass force -and torque can be turned off by the {force} and {torque} keywords. -This may be useful if you wish a body to rotate but not translate, or -vice versa, or if you wish it to rotate or translate continuously -unaffected by interactions with other particles. Note that if you -expect a rigid body not to move or rotate by using these keywords, you -must insure its initial center-of-mass translational or angular -velocity is 0.0. Otherwise the initial translational or angular -momentum, the body has, will persist. - -An xflag, yflag, or zflag set to {off} means turn off the component of -force or torque in that dimension. A setting of {on} means turn on -the component, which is the default. Which rigid body(s) the settings -apply to is determined by the first argument of the {force} and -{torque} keywords. It can be an integer M from 1 to Nbody, where -Nbody is the number of rigid bodies defined. A wild-card asterisk can -be used in place of, or in conjunction with, the M argument to set the -flags for multiple rigid bodies. This takes the form "*" or "*n" or -"n*" or "m*n". If N = the number of rigid bodies, then an asterisk -with no numeric values means all bodies from 1 to N. A leading -asterisk means all bodies from 1 to n (inclusive). A trailing -asterisk means all bodies from n to N (inclusive). A middle asterisk -means all bodies from m to n (inclusive). Note that you can use the -{force} or {torque} keywords as many times as you like. If a -particular rigid body has its component flags set multiple times, the -settings from the final keyword are used. - -For computational efficiency, you should typically define one fix -rigid/meso command which includes all the desired rigid bodies. LAMMPS -will allow multiple rigid/meso fixes to be defined, but it is more -expensive. - -:line - -The keyword/value option pairs are used in the following ways. - -The {reinit} keyword determines, whether the rigid body properties -are re-initialized between run commands. With the option {yes} (the -default) this is done, with the option {no} this is not done. Turning -off the re-initialization can be helpful to protect rigid bodies against -unphysical manipulations between runs or when properties cannot be -easily re-computed (e.g. when read from a file). When using the {infile} -keyword, the {reinit} option is automatically set to {no}. - -:line - -The {infile} keyword allows a file of rigid body attributes to be read -in from a file, rather then having LAMMPS compute them. There are 5 -such attributes: the total mass of the rigid body, its center-of-mass -position, its 6 moments of inertia, its center-of-mass velocity, and -the 3 image flags of the center-of-mass position. For rigid bodies -consisting of point particles or non-overlapping finite-size -particles, LAMMPS can compute these values accurately. However, for -rigid bodies consisting of finite-size particles which overlap each -other, LAMMPS will ignore the overlaps when computing these 4 -attributes. The amount of error this induces depends on the amount of -overlap. To avoid this issue, the values can be pre-computed -(e.g. using Monte Carlo integration). - -The format of the file is as follows. Note that the file does not -have to list attributes for every rigid body integrated by fix rigid. -Only bodies which the file specifies will have their computed -attributes overridden. The file can contain initial blank lines or -comment lines starting with "#" which are ignored. The first -non-blank, non-comment line should list N = the number of lines to -follow. The N successive lines contain the following information: - -ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm -ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm -... -IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm :pre - -The rigid body IDs are all positive integers. For the {single} -bodystyle, only an ID of 1 can be used. For the {group} bodystyle, -IDs from 1 to Ng can be used where Ng is the number of specified -groups. For the {molecule} bodystyle, use the molecule ID for the -atoms in a specific rigid body as the rigid body ID. - -The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are -self-explanatory. The center-of-mass should be consistent with what -is calculated for the position of the rigid body with all its atoms -unwrapped by their respective image flags. If this produces a -center-of-mass that is outside the simulation box, LAMMPS wraps it -back into the box. - -The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the -values consistent with the current orientation of the rigid body -around its center of mass. The values are with respect to the -simulation box XYZ axes, not with respect to the principal axes of the -rigid body itself. LAMMPS performs the latter calculation internally. - -The (vxcm,vycm,vzcm) values are the velocity of the center of mass. -The (lx,ly,lz) values are the angular momentum of the body. The -(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you -wish the body to have no initial motion. - -The (ixcm,iycm,izcm) values are the image flags of the center of mass -of the body. For periodic dimensions, they specify which image of the -simulation box the body is considered to be in. An image of 0 means -it is inside the box as defined. A value of 2 means add 2 box lengths -to get the true value. A value of -1 means subtract 1 box length to -get the true value. LAMMPS updates these flags as the rigid bodies -cross periodic boundaries during the simulation. - -NOTE: If you use the {infile} keyword and write restart -files during a simulation, then each time a restart file is written, -the fix also write an auxiliary restart file with the name -rfile.rigid, where "rfile" is the name of the restart file, -e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary -file is in the same format described above. Thus it can be used in a -new input script that restarts the run and re-specifies a rigid fix -using an {infile} keyword and the appropriate filename. Note that the -auxiliary file will contain one line for every rigid body, even if the -original file only listed a subset of the rigid bodies. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information is written to "binary restart files"_restart.html. -If the {infile} keyword is used, an auxiliary file is written out -with rigid body information each time a restart file is written, as -explained above for the {infile} keyword. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. - -This fix computes a global array of values which can be accessed by -various "output commands"_Howto_output.html. - -The number of rows in the array is equal to the number of rigid -bodies. The number of columns is 28. Thus for each rigid body, 28 -values are stored: the xyz coords of the center of mass (COM), the xyz -components of the COM velocity, the xyz components of the force acting -on the COM, the components of the 4-vector quaternion representing the -orientation of the rigid body, the xyz components of the angular velocity -of the body around its COM, the xyz components of the torque acting on the -COM, the 3 principal components of the moment of inertia, the xyz components -of the angular momentum of the body around its COM, and the xyz image -flags of the COM. - -The center of mass (COM) for each body is similar to unwrapped -coordinates written to a dump file. It will always be inside (or -slightly outside) the simulation box. The image flags have the same -meaning as image flags for particle positions (see the "dump" command). -This means you can calculate the unwrapped COM by applying the image -flags to the COM, the same as when unwrapped coordinates are written -to a dump file. - -The force and torque values in the array are not affected by the -{force} and {torque} keywords in the fix rigid command; they reflect -values before any changes are made by those keywords. - -The ordering of the rigid bodies (by row in the array) is as follows. -For the {single} keyword there is just one rigid body. For the -{molecule} keyword, the bodies are ordered by ascending molecule ID. -For the {group} keyword, the list of group IDs determines the ordering -of bodies. - -The array values calculated by this fix are "intensive", meaning they -are independent of the number of particles in the simulation. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -This fix is not invoked during "energy minimization"_minimize.html. - -:line - -[Restrictions:] - -This fix is part of the USER-SDPD package and also depends on the RIGID -package. It is only enabled if LAMMPS was built with both packages. See -the "Build package"_Build_package.html doc page for more info. - -This fix requires that atoms store density and internal energy as -defined by the "atom_style meso"_atom_style.html command. - -All particles in the group must be mesoscopic SPH/SDPD particles. - -[Related commands:] - -"fix meso/move"_fix_meso_move.html, "fix rigid"_fix_rigid.html, -"neigh_modify exclude"_neigh_modify.html - -[Default:] - -The option defaults are force * on on on and torque * on on on, -meaning all rigid bodies are acted on by center-of-mass force and -torque. Also reinit = yes. - -:line - -:link(Miller) -[(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, -J Chem Phys, 116, 8649 (2002). diff --git a/doc/txt/fix_rx.txt b/doc/txt/fix_rx.txt deleted file mode 100644 index ad42c577aa..0000000000 --- a/doc/txt/fix_rx.txt +++ /dev/null @@ -1,226 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix rx command :h3 -fix rx/kk command :h3 - -[Syntax:] - -fix ID group-ID rx file localTemp matrix solver minSteps ... :pre - -ID, group-ID are documented in "fix"_fix.html command -rx = style name of this fix command -file = filename containing the reaction kinetic equations and Arrhenius parameters -localTemp = {none,lucy} = no local temperature averaging or local temperature defined through Lucy weighting function -matrix = {sparse, dense} format for the stoichiometric matrix -solver = {lammps_rk4,rkf45} = rk4 is an explicit 4th order Runge-Kutta method; rkf45 is an adaptive 4th-order Runge-Kutta-Fehlberg method -minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45) -maxSteps = maximum number of steps for the rkf45 solver (rkf45 only) -relTol = relative tolerance for the rkf45 solver (rkf45 only) -absTol = absolute tolerance for the rkf45 solver (rkf45 only) -diag = Diagnostics frequency for the rkf45 solver (optional, rkf45 only) :ul - -[Examples:] - -fix 1 all rx kinetics.rx none dense lammps_rk4 -fix 1 all rx kinetics.rx none sparse lammps_rk4 1 -fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10 -fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1 :pre - -[Description:] - -Fix {rx} solves the reaction kinetic ODEs for a given reaction set that is -defined within the file associated with this command. - -For a general reaction such that - -:c,image(Eqs/fix_rx_reaction.jpg) - -the reaction rate equation is defined to be of the form - -:c,image(Eqs/fix_rx_reactionRate.jpg) - -In the current implementation, the exponents are defined to be equal -to the stoichiometric coefficients. A given reaction set consisting -of {n} reaction equations will contain a total of {m} species. A set -of {m} ordinary differential equations (ODEs) that describe the change -in concentration of a given species as a function of time are then -constructed based on the {n} reaction rate equations. - -The ODE systems are solved over the full DPD timestep {dt} using either a 4th -order Runge-Kutta {rk4} method with a fixed step-size {h}, specified -by the {lammps_rk4} keyword, or a 4th order Runge-Kutta-Fehlberg (rkf45) method -with an adaptive step-size for {h}. The number of ODE steps per DPD timestep -for the rk4 method is optionally specified immediately after the rk4 -keyword. The ODE step-size is set as {dt/num_steps}. Smaller -step-sizes tend to yield more accurate results but there is not -control on the error. For error control, use the rkf45 ODE solver. - -The rkf45 method adjusts the step-size so that the local truncation error is held -within the specified absolute and relative tolerances. The initial step-size {h0} -can be specified by the user or estimated internally. It is recommended that the user -specify {h0} since this will generally reduced the number of ODE integration steps -required. {h0} is defined as {dt / min_steps} if min_steps >= 1. If min_steps == 0, -{h0} is estimated such that an explicit Euler method would likely produce -an acceptable solution. This is generally overly conservative for the 4th-order -method and users are advised to specify {h0} as some fraction of the DPD timestep. -For small DPD timesteps, only one step may be necessary depending upon the tolerances. -Note that more than min_steps ODE steps may be taken depending upon the ODE stiffness -but no more than max_steps will be taken. If max_steps is reached, an error warning -is printed and the simulation is stopped. - -After each ODE step, the solution error {e} is tested and weighted using the absTol -and relTol values. The error vector is weighted as {e} / (relTol * |{u}| + absTol) -where {u} is the solution vector. If the norm of the error is <= 1, the solution is -accepted, {h} is increased by a proportional amount, and the next ODE step is begun. -Otherwise, {h} is shrunk and the ODE step is repeated. - -Run-time diagnostics are available for the rkf45 ODE solver. The frequency -(in time-steps) that diagnostics are reported is controlled by the last (optional) -12th argument. A negative frequency means that diagnostics are reported once at the -end of each run. A positive value N means that the diagnostics are reported once -per N time-steps. - -The diagnostics report the average # of integrator steps and RHS function evaluations -and run-time per ODE as well as the average/RMS/min/max per process. If the -reporting frequency is 1, the RMS/min/max per ODE are also reported. The per ODE -statistics can be used to adjust the tolerance and min/max step parameters. The -statistics per MPI process can be useful to examine any load imbalance caused by the -adaptive ODE solver. (Some DPD particles can take longer to solve than others. This -can lead to an imbalance across the MPI processes.) - -:line - -The filename specifies a file that contains the entire set of reaction -kinetic equations and corresponding Arrhenius parameters. The format of -this file is described below. - -There is no restriction on the total number or reaction equations that -are specified. The species names are arbitrary string names that are -associated with the species concentrations. Each species in a given -reaction must be preceded by it's stoichiometric coefficient. The -only delimiters that are recognized between the species are either a -{+} or {=} character. The {=} character corresponds to an -irreversible reaction. After specifying the reaction, the reaction -rate constant is determined through the temperature dependent -Arrhenius equation: - -:c,image(Eqs/fix_rx.jpg) - -where {A} is the Arrhenius factor in time units or concentration/time -units, {n} is the unitless exponent of the temperature dependence, and -{E_a} is the activation energy in energy units. The temperature -dependence can be removed by specifying the exponent as zero. - -The internal temperature of the coarse-grained particles can be used -in constructing the reaction rate constants at every DPD timestep by -specifying the keyword {none}. Alternatively, the keyword {lucy} can -be specified to compute a local-average particle internal temperature -for use in the reaction rate constant expressions. The local-average -particle internal temperature is defined as: - -:c,image(Eqs/fix_rx_localTemp.jpg) - -where the Lucy function is expressed as: - -:c,image(Eqs/fix_rx_localTemp2.jpg) - -The self-particle interaction is included in the above equation. - -The stoichiometric coefficients for the reaction mechanism are stored -in either a sparse or dense matrix format. The dense matrix should only be -used for small reaction mechanisms. The sparse matrix should be used when there -are many reactions (e.g., more than 5). This allows the number of reactions and -species to grow while keeping the computational cost tractable. The matrix -format can be specified as using either the {sparse} or {dense} keywords. -If all stoichiometric coefficients for a reaction are small integers (whole -numbers <= 3), a fast exponential function is used. This can save significant -computational time so users are encouraged to use integer coefficients -where possible. - -:line - -The format of a tabulated file is as follows (without the -parenthesized comments): - -# Rxn equations and parameters (one or more comment or blank lines) :pre -1.0 hcn + 1.0 no2 = 1.0 no + 0.5 n2 + 0.5 h2 + 1.0 co 2.49E+01 0.0 1.34 (rxn equation, A, n, Ea) -1.0 hcn + 1.0 no = 1.0 co + 1.0 n2 + 0.5 h2 2.16E+00 0.0 1.52 -... -1.0 no + 1.0 co = 0.5 n2 + 1.0 co2 1.66E+06 0.0 0.69 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. - -Following a blank line, the next N lines list the N reaction -equations. Each species within the reaction equation is specified -through its stoichiometric coefficient and a species tag. Reactant -species are specified on the left-hand side of the equation and -product species are specified on the right-hand side of the equation. -After specifying the reactant and product species, the final three -arguments of each line represent the Arrhenius parameter {A}, the -temperature exponent {n}, and the activation energy {Ea}. - -Note that the species tags that are defined in the reaction equations -are used by the "fix eos/table/rx"_fix_eos_table_rx.html command to -define the thermodynamic properties of each species. Furthermore, the -number of species molecules (i.e., concentration) can be specified -either with the "set"_set.html command using the "d_" prefix or by -reading directly the concentrations from a data file. For the latter -case, the "read_data"_read_data.html command with the fix keyword -should be specified, where the fix-ID will be the "fix rx" ID with a -"_SPECIES" suffix, e.g. - -fix foo all rx reaction.file ... -read_data data.dpd fix foo_SPECIES NULL Species - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This command also requires use of the "atom_style dpd"_atom_style.html -command. - -This command can only be used with a constant energy or constant -enthalpy DPD simulation. - -[Related commands:] - -"fix eos/table/rx"_fix_eos_table_rx.html, -"fix shardlow"_fix_shardlow.html, -"pair dpd/fdt/energy"_pair_dpd_fdt.html - -[Default:] none diff --git a/doc/txt/fix_saed_vtk.txt b/doc/txt/fix_saed_vtk.txt deleted file mode 100644 index 60708cd696..0000000000 --- a/doc/txt/fix_saed_vtk.txt +++ /dev/null @@ -1,190 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix saed/vtk command :h3 - -[Syntax:] - -fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -saed/vtk = style name of this fix command :l -Nevery = use input values every this many timesteps :l -Nrepeat = # of times to use input values for calculating averages :l -Nfreq = calculate averages every this many timesteps :l -c_ID = saed compute ID :l - -keyword = {file} or {ave} or {start} or {file} or {overwrite}:l - {ave} args = {one} or {running} or {window M} - one = output a new average value every Nfreq steps - running = output cumulative average of all previous Nfreq steps - window M = output average of M most recent Nfreq steps - {start} args = Nstart - Nstart = start averaging on this timestep - {file} arg = filename - filename = name of file to output time averages to - {overwrite} arg = none = overwrite output file with only latest output :pre - -:ule - -[Examples:] - -compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 -compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo :pre - -fix 1 all saed/vtk 1 1 1 c_1 file Al2O3_001.saed -fix 2 all saed/vtk 1 1 1 c_2 file Ni_000.saed :pre - -[Description:] - -Time average computed intensities from "compute saed"_compute_saed.html and -write output to a file in the 3rd generation vtk image data format for -visualization directly in parallelized visualization software packages -like ParaView and VisIt. Note that if no time averaging is done, this -command can be used as a convenient way to simply output diffraction -intensities at a single snapshot. - -To produce output in the image data vtk format ghost data is added -outside the {Kmax} range assigned in the compute saed. The ghost data is -assigned a value of -1 and can be removed setting a minimum isovolume -of 0 within the visualization software. SAED images can be created by -visualizing a spherical slice of the data that is centered at -R_Ewald*\[h k l\]/norm(\[h k l\]), where R_Ewald=1/lambda. - -The group specified within this command is ignored. However, note that -specified values may represent calculations performed by saed computes -which store their own "group" definitions. - -Fix saed/vtk is designed to work only with "compute saed"_compute_saed.html -values, e.g. - -compute 3 top saed 0.0251 Al O -fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed :pre - -:line - -The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what -timesteps the input values will be used in order to contribute to the -average. The final averaged quantities are generated on timesteps -that are a multiple of {Nfreq}. The average is over {Nrepeat} -quantities, computed in the preceding portion of the simulation every -{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and -{Nevery} must be non-zero even if {Nrepeat} is 1. -Also, the timesteps -contributing to the average value cannot overlap, -i.e. Nrepeat*Nevery can not exceed Nfreq. - -For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on -timesteps 90,92,94,96,98,100 will be used to compute the final average -on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on -timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time -averaging is done; values are simply generated on timesteps -100,200,etc. - -:line - -The output for fix ave/time/saed is a file written with the 3rd generation -vtk image data formatting. The filename assigned by the {file} keyword is -appended with _N.vtk where N is an index (0,1,2...) to account for multiple -diffraction intensity outputs. - -By default the header contains the following information (with example data): - -# vtk DataFile Version 3.0 c_SAED -Image data set -ASCII -DATASET STRUCTURED_POINTS -DIMENSIONS 337 219 209 -ASPECT_RATIO 0.00507953 0.00785161 0.00821458 -ORIGIN -0.853361 -0.855826 -0.854316 -POINT_DATA 15424827 -SCALARS intensity float -LOOKUP_TABLE default -...data :pre - -In this example, kspace is sampled across a 337 x 219 x 209 point mesh -where the mesh spacing is approximately 0.005, 0.007, and 0.008 -inv(length) units in the k1, k2, and k3 directions, respectively. -The data is shifted by -0.85, -0.85, -0.85 inv(length) units so that -the origin will lie at 0, 0, 0. Here, 15,424,827 kspace points are -sampled in total. - -:line - -Additional optional keywords also affect the operation of this fix. - -The {ave} keyword determines how the values produced every {Nfreq} -steps are averaged with values produced on previous steps that were -multiples of {Nfreq}, before they are accessed by another output -command or written to a file. - -If the {ave} setting is {one}, then the values produced on timesteps -that are multiples of {Nfreq} are independent of each other; they are -output as-is without further averaging. - -If the {ave} setting is {running}, then the values produced on -timesteps that are multiples of {Nfreq} are summed and averaged in a -cumulative sense before being output. Each output value is thus the -average of the value produced on that timestep with all preceding -values. This running average begins when the fix is defined; it can -only be restarted by deleting the fix via the "unfix"_unfix.html -command, or by re-defining the fix by re-specifying it. - -If the {ave} setting is {window}, then the values produced on -timesteps that are multiples of {Nfreq} are summed and averaged within -a moving "window" of time, so that the last M values are used to -produce the output. E.g. if M = 3 and Nfreq = 1000, then the output -on step 10000 will be the average of the individual values on steps -8000,9000,10000. Outputs on early steps will average over less than M -values if they are not available. - -The {start} keyword specifies what timestep averaging will begin on. -The default is step 0. Often input values can be 0.0 at time 0, so -setting {start} to a larger value can avoid including a 0.0 in a -running or windowed average. - -The {file} keyword allows a filename to be specified. Every {Nfreq} -steps, the vector of saed intensity data is written to a new file using -the 3rd generation vtk format. The base of each file is assigned by -the {file} keyword and this string is appended with _N.vtk where N is -an index (0,1,2...) to account for situations with multiple diffraction -intensity outputs. - -The {overwrite} keyword will continuously overwrite the output file -with the latest output, so that it only contains one timestep worth of -output. This option can only be used with the {ave running} setting. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -The attributes for fix_saed_vtk must match the values assigned in the -associated "compute_saed"_compute_saed.html command. - -[Related commands:] - -"compute_saed"_compute_saed.html - -[Default:] - -The option defaults are ave = one, start = 0, no file output. - -:line - -:link(Coleman) -[(Coleman)] Coleman, Spearot, Capolungo, MSMSE, 21, 055020 -(2013). - diff --git a/doc/txt/fix_setforce.txt b/doc/txt/fix_setforce.txt deleted file mode 100644 index 5ee289ec5c..0000000000 --- a/doc/txt/fix_setforce.txt +++ /dev/null @@ -1,144 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix setforce command :h3 -fix setforce/kk command :h3 -fix setforce/spin command :h3 - -[Syntax:] - -fix ID group-ID setforce fx fy fz keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -setforce = style name of this fix command :l -fx,fy,fz = force component values :l -any of fx,fy,fz can be a variable (see below) :l -zero or more keyword/value pairs may be appended to args :l -keyword = {region} :l - {region} value = region-ID - region-ID = ID of region atoms must be in to have added force :pre -:ule - -[Examples:] - -fix freeze indenter setforce 0.0 0.0 0.0 -fix 2 edge setforce NULL 0.0 0.0 -fix 1 edge setforce/spin 0.0 0.0 0.0 -fix 2 edge setforce NULL 0.0 v_oscillate :pre - -[Description:] - -Set each component of force on each atom in the group to the specified -values fx,fy,fz. This erases all previously computed forces on the -atom, though additional fixes could add new forces. This command can -be used to freeze certain atoms in the simulation by zeroing their -force, either for running dynamics or performing an energy -minimization. For dynamics, this assumes their initial velocity is -also zero. - -Any of the fx,fy,fz values can be specified as NULL which means do not -alter the force component in that dimension. - -Any of the 3 quantities defining the force components can be specified -as an equal-style or atom-style "variable"_variable.html, namely {fx}, -{fy}, {fz}. If the value is a variable, it should be specified as -v_name, where name is the variable name. In this case, the variable -will be evaluated each timestep, and its value used to determine the -force component. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent force field. - -Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent force -field with optional time-dependence as well. - -If the {region} keyword is used, the atom must also be in the -specified geometric "region"_region.html in order to have force added -to it. - -:line - -Style {spin} suffix sets the components of the magnetic precession -vectors instead of the mechanical forces. This also erases all -previously computed magnetic precession vectors on the atom, though -additional magnetic fixes could add new forces. - -This command can be used to freeze the magnetic moment of certain -atoms in the simulation by zeroing their precession vector. - -All options defined above remain valid, they just apply to the magnetic -precession vectors instead of the forces. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -The region keyword is also supported by Kokkos, but a Kokkos-enabled -region must be used. See the region "region"_region.html command for -more information. - -These accelerated styles are part of the r Kokkos package. They are -only enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by -this fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is setting the forces to the desired values; on all -other levels, the force is set to 0.0 for the atoms in the fix group, -so that setforce values are not counted multiple times. Default is to -to override forces at the outermost level. - -This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Howto_output.html. This is the total -force on the group of atoms before the forces on individual atoms are -changed by the fix. The vector values calculated by this fix are -"extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command, but you cannot set -forces to any value besides zero when performing a minimization. Use -the "fix addforce"_fix_addforce.html command if you want to apply a -non-zero force to atoms during a minimization. - -[Restrictions:] - -The fix {setforce/spin} only makes sense when LAMMPS was built with the -SPIN package. - -[Related commands:] - -"fix addforce"_fix_addforce.html, "fix aveforce"_fix_aveforce.html - -[Default:] none diff --git a/doc/txt/fix_shake.txt b/doc/txt/fix_shake.txt deleted file mode 100644 index 5c11f96b98..0000000000 --- a/doc/txt/fix_shake.txt +++ /dev/null @@ -1,233 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix shake command :h3 -fix rattle command :h3 - -[Syntax:] - -fix ID group-ID style tol iter N constraint values ... keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -style = shake or rattle = style name of this fix command :l -tol = accuracy tolerance of SHAKE solution :l -iter = max # of iterations in each SHAKE solution :l -N = print SHAKE statistics every this many timesteps (0 = never) :l -one or more constraint/value pairs are appended :l -constraint = {b} or {a} or {t} or {m} :l - {b} values = one or more bond types - {a} values = one or more angle types - {t} values = one or more atom types - {m} value = one or more mass values :pre -zero or more keyword/value pairs may be appended :l -keyword = {mol} :l - {mol} value = template-ID - template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command :pre -:ule - -[Examples:] - -fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2 -fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 -fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol -fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31 -fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol :pre - -[Description:] - -Apply bond and angle constraints to specified bonds and angles in the -simulation by either the SHAKE or RATTLE algorithms. This typically -enables a longer timestep. - -[SHAKE vs RATTLE:] - -The SHAKE algorithm was invented for schemes such as standard Verlet -timestepping, where only the coordinates are integrated and the -velocities are approximated as finite differences to the trajectories -("Ryckaert et al. (1977)"_#Ryckaert). If the velocities are -integrated explicitly, as with velocity Verlet which is what LAMMPS -uses as an integration method, a second set of constraining forces is -required in order to eliminate velocity components along the bonds -("Andersen (1983)"_#Andersen3). - -In order to formulate individual constraints for SHAKE and RATTLE, -focus on a single molecule whose bonds are constrained. Let Ri and Vi -be the position and velocity of atom {i} at time {n}, for -{i} =1,...,{N}, where {N} is the number of sites of our reference -molecule. The distance vector between sites {i} and {j} is given by - -:c,image(Eqs/fix_rattle_rij.jpg) - -The constraints can then be formulated as - -:c,image(Eqs/fix_rattle_constraints.jpg) - -The SHAKE algorithm satisfies the first condition, i.e. the sites at -time {n+1} will have the desired separations Dij immediately after the -coordinates are integrated. If we also enforce the second condition, -the velocity components along the bonds will vanish. RATTLE satisfies -both conditions. As implemented in LAMMPS, fix rattle uses fix shake -for satisfying the coordinate constraints. Therefore the settings and -optional keywords are the same for both fixes, and all the information -below about SHAKE is also relevant for RATTLE. - -[SHAKE:] - -Each timestep the specified bonds and angles are reset to their -equilibrium lengths and angular values via the SHAKE algorithm -("Ryckaert et al. (1977)"_#Ryckaert). This is done by applying an -additional constraint force so that the new positions preserve the -desired atom separations. The equations for the additional force are -solved via an iterative method that typically converges to an accurate -solution in a few iterations. The desired tolerance (e.g. 1.0e-4 = 1 -part in 10000) and maximum # of iterations are specified as arguments. -Setting the N argument will print statistics to the screen and log -file about regarding the lengths of bonds and angles that are being -constrained. Small delta values mean SHAKE is doing a good job. - -In LAMMPS, only small clusters of atoms can be constrained. This is -so the constraint calculation for a cluster can be performed by a -single processor, to enable good parallel performance. A cluster is -defined as a central atom connected to others in the cluster by -constrained bonds. LAMMPS allows for the following kinds of clusters -to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or -one central atom bonded to 2 others and the angle between the 3 atoms -also constrained. This means water molecules or CH2 or CH3 groups may -be constrained, but not all the C-C backbone bonds of a long polymer -chain. - -The {b} constraint lists bond types that will be constrained. The {t} -constraint lists atom types. All bonds connected to an atom of the -specified type will be constrained. The {m} constraint lists atom -masses. All bonds connected to atoms of the specified masses will be -constrained (within a fudge factor of MASSDELTA specified in -fix_shake.cpp). The {a} constraint lists angle types. If both bonds -in the angle are constrained then the angle will also be constrained -if its type is in the list. - -For all constraints, a particular bond is only constrained if both -atoms in the bond are in the group specified with the SHAKE fix. - -The degrees-of-freedom removed by SHAKE bonds and angles are accounted -for in temperature and pressure computations. Similarly, the SHAKE -contribution to the pressure of the system (virial) is also accounted -for. - -NOTE: This command works by using the current forces on atoms to -calculate an additional constraint force which when added will leave -the atoms in positions that satisfy the SHAKE constraints (e.g. bond -length) after the next time integration step. If you define fixes -(e.g. "fix efield"_fix_efield.html) that add additional force to the -atoms after fix shake operates, then this fix will not take them into -account and the time integration will typically not satisfy the SHAKE -constraints. The solution for this is to make sure that fix shake is -defined in your input script after any other fixes which add or change -forces (to atoms that fix shake operates on). - -:line - -The {mol} keyword should be used when other commands, such as "fix -deposit"_fix_deposit.html or "fix pour"_fix_pour.html, add molecules -on-the-fly during a simulation, and you wish to constrain the new -molecules via SHAKE. You specify a {template-ID} previously defined -using the "molecule"_molecule.html command, which reads a file that -defines the molecule. You must use the same {template-ID} that the -command adding molecules uses. The coordinates, atom types, special -bond restrictions, and SHAKE info can be specified in the molecule -file. See the "molecule"_molecule.html command for details. The only -settings required to be in this file (by this command) are the SHAKE -info of atoms in the molecule. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[RATTLE:] - -The velocity constraints lead to a linear system of equations which -can be solved analytically. The implementation of the algorithm in -LAMMPS closely follows ("Andersen (1983)"_#Andersen3). - -NOTE: The fix rattle command modifies forces and velocities and thus -should be defined after all other integration fixes in your input -script. If you define other fixes that modify velocities or forces -after fix rattle operates, then fix rattle will not take them into -account and the overall time integration will typically not satisfy -the RATTLE constraints. You can check whether the constraints work -correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp -to 1 and recompiling LAMMPS. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -The "fix_modify"_fix_modify.html {virial} option is supported by this -fix to add the contribution due to keeping the constraints to the -system's virial as part of "thermodynamic output"_thermo_style.html. -The default is {virial yes} - -No information about these fixes is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to these fixes. No global or per-atom quantities are -stored by these fixes for access by various "output -commands"_Howto_output.html. No parameter of these fixes can be used -with the {start/stop} keywords of the "run"_run.html command. These -fixes are not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -These fixes are part of the RIGID package. They are only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -For computational efficiency, there can only be one shake or rattle -fix defined in a simulation. - -If you use a tolerance that is too large or a max-iteration count that -is too small, the constraints will not be enforced very strongly, -which can lead to poor energy conservation. You can test for this in -your system by running a constant NVE simulation with a particular set -of SHAKE parameters and monitoring the energy versus time. - -SHAKE or RATTLE should not be used to constrain an angle at 180 -degrees (e.g. linear CO2 molecule). This causes numeric difficulties. -You can use "fix rigid or fix rigid/small"_fix_rigid.html instead to -make a linear molecule rigid. - -[Related commands:] none - -[Default:] none - -:line - -:link(Ryckaert) -[(Ryckaert)] J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen, -J of Comp Phys, 23, 327-341 (1977). - -:link(Andersen3) -[(Andersen)] H. Andersen, J of Comp Phys, 52, 24-34 (1983). diff --git a/doc/txt/fix_shardlow.txt b/doc/txt/fix_shardlow.txt deleted file mode 100644 index c1be146fa6..0000000000 --- a/doc/txt/fix_shardlow.txt +++ /dev/null @@ -1,119 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix shardlow command :h3 -fix shardlow/kk command :h3 - -[Syntax:] - -fix ID group-ID shardlow :pre - -ID, group-ID are documented in "fix"_fix.html command -shardlow = style name of this fix command :ul - -[Examples:] - -fix 1 all shardlow :pre - -[Description:] - -Specifies that the Shardlow splitting algorithm (SSA) is to be used to -integrate the DPD equations of motion. The SSA splits the integration -into a stochastic and deterministic integration step. The fix -{shardlow} performs the stochastic integration step and must be used -in conjunction with a deterministic integrator (e.g. "fix -nve"_fix_nve.html or "fix nph"_fix_nh.html). The stochastic -integration of the dissipative and random forces is performed prior to -the deterministic integration of the conservative force. Further -details regarding the method are provided in "(Lisal)"_#Lisal and -"(Larentzos1)"_#Larentzos1sh. - -The fix {shardlow} must be used with the "pair_style -dpd/fdt"_pair_style.html or "pair_style -dpd/fdt/energy"_pair_style.html command to properly initialize the -fluctuation-dissipation theorem parameter(s) sigma (and kappa, if -necessary). - -Note that numerous variants of DPD can be specified by choosing an -appropriate combination of the integrator and "pair_style -dpd/fdt"_pair_style.html command. DPD under isothermal conditions can -be specified by using fix {shardlow}, fix {nve} and pair_style -{dpd/fdt}. DPD under isoenergetic conditions can be specified by -using fix {shardlow}, fix {nve} and pair_style {dpd/fdt/energy}. DPD -under isobaric conditions can be specified by using fix shardlow, fix -{nph} and pair_style {dpd/fdt}. DPD under isoenthalpic conditions can -be specified by using fix shardlow, fix {nph} and pair_style -{dpd/fdt/energy}. Examples of each DPD variant are provided in the -examples/USER/dpd directory. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix is currently limited to orthogonal simulation cell -geometries. - -This fix must be used with an additional fix that specifies time -integration, e.g. "fix nve"_fix_nve.html or "fix nph"_fix_nh.html. - -The Shardlow splitting algorithm requires the sizes of the sub-domain -lengths to be larger than twice the cutoff+skin. Generally, the -domain decomposition is dependent on the number of processors -requested. - -[Related commands:] - -"pair_style dpd/fdt"_pair_dpd_fdt.html, "fix eos/cv"_fix_eos_cv.html - -[Default:] none - -:line - -:link(Lisal) -[(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative -particle dynamics as isothermal, isobaric, isoenergetic, and -isoenthalpic conditions using Shardlow-like splitting algorithms.", -J. Chem. Phys., 135, 204105 (2011). - -:link(Larentzos1sh) -[(Larentzos1)] J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and -W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic -Dissipative Particle Dynamics Using Shardlow-Like Splitting -Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014). - -:link(Larentzos2sh) -[(Larentzos2)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and -W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative -Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research -Laboratory, Aberdeen Proving Ground, MD (2014). diff --git a/doc/txt/fix_smd.txt b/doc/txt/fix_smd.txt deleted file mode 100644 index 907df7ab1f..0000000000 --- a/doc/txt/fix_smd.txt +++ /dev/null @@ -1,157 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix smd command :h3 - -[Syntax:] - -fix ID group-ID smd type values keyword values :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -smd = style name of this fix command :l -mode = {cvel} or {cfor} to select constant velocity or constant force SMD :l - {cvel} values = K vel - K = spring constant (force/distance units) - vel = velocity of pulling (distance/time units) - {cfor} values = force - force = pulling force (force units) :pre -keyword = {tether} or {couple} :l - {tether} values = x y z R0 - x,y,z = point to which spring is tethered - R0 = distance of end of spring from tether point (distance units) - {couple} values = group-ID2 x y z R0 - group-ID2 = 2nd group to couple to fix group with a spring - x,y,z = direction of spring, automatically computed with 'auto' - R0 = distance of end of spring (distance units) :pre -:ule - -[Examples:] - -fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0 -fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0 -fix stretch cterm smd cvel 20.0 0.0001 couple nterm auto auto auto 0.0 -fix pull cterm smd cfor 5.0 tether 25.0 25.0 25.0 0.0 :pre - -[Description:] - -This fix implements several options of steered MD (SMD) as reviewed in -"(Izrailev)"_#Izrailev, which allows to induce conformational changes -in systems and to compute the potential of mean force (PMF) along the -assumed reaction coordinate "(Park)"_#Park based on Jarzynski's -equality "(Jarzynski)"_#Jarzynski. This fix borrows a lot from "fix -spring"_fix_spring.html and "fix setforce"_fix_setforce.html. - -You can apply a moving spring force to a group of atoms ({tether} -style) or between two groups of atoms ({couple} style). The spring -can then be used in either constant velocity ({cvel}) mode or in -constant force ({cfor}) mode to induce transitions in your systems. -When running in {tether} style, you may need some way to fix some -other part of the system (e.g. via "fix -spring/self"_fix_spring_self.html) - -The {tether} style attaches a spring between a point at a distance of -R0 away from a fixed point {x,y,z} and the center of mass of the fix -group of atoms. A restoring force of magnitude K (R - R0) Mi / M is -applied to each atom in the group where {K} is the spring constant, Mi -is the mass of the atom, and M is the total mass of all atoms in the -group. Note that {K} thus represents the total force on the group of -atoms, not a per-atom force. - -In {cvel} mode the distance R is incremented or decremented -monotonously according to the pulling (or pushing) velocity. -In {cfor} mode a constant force is added and the actual distance -in direction of the spring is recorded. - -The {couple} style links two groups of atoms together. The first -group is the fix group; the second is specified by group-ID2. The -groups are coupled together by a spring that is at equilibrium when -the two groups are displaced by a vector in direction {x,y,z} with -respect to each other and at a distance R0 from that displacement. -Note that {x,y,z} only provides a direction and will be internally -normalized. But since it represents the {absolute} displacement of -group-ID2 relative to the fix group, (1,1,0) is a different spring -than (-1,-1,0). For each vector component, the displacement can be -described with the {auto} parameter. In this case the direction is -re-computed in every step, which can be useful for steering a local -process where the whole object undergoes some other change. When the -relative positions and distance between the two groups are not in -equilibrium, the same spring force described above is applied to atoms -in each of the two groups. - -For both the {tether} and {couple} styles, any of the x,y,z values can -be specified as NULL which means do not include that dimension in the -distance calculation or force application. - -For constant velocity pulling ({cvel} mode), the running integral -over the pulling force in direction of the spring is recorded and -can then later be used to compute the potential of mean force (PMF) -by averaging over multiple independent trajectories along the same -pulling path. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -The fix stores the direction of the spring, current pulling target -distance and the running PMF to "binary restart files"_restart.html. -See the "read_restart"_read_restart.html command for info on how to -re-specify a fix in an input script that reads a restart file, so that -the operation of the fix continues in an uninterrupted fashion. - -The "fix_modify"_fix_modify.html {virial} option is supported by this -fix to add the contribution due to the added forces on atoms to the -system's virial as part of "thermodynamic output"_thermo_style.html. -The default is {virial no} - -The "fix_modify"_fix_modify.html {respa} option is supported by -this fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -This fix computes a vector list of 7 quantities, which can be accessed -by various "output commands"_Howto_output.html. The quantities in the -vector are in this order: the x-, y-, and z-component of the pulling -force, the total force in direction of the pull, the equilibrium -distance of the spring, the distance between the two reference points, -and finally the accumulated PMF (the sum of pulling forces times -displacement). - -The force is the total force on the group of atoms by the spring. In -the case of the {couple} style, it is the force on the fix group -(group-ID) or the negative of the force on the 2nd group (group-ID2). -The vector values calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix drag"_fix_drag.html, "fix spring"_fix_spring.html, -"fix spring/self"_fix_spring_self.html, -"fix spring/rg"_fix_spring_rg.html, -"fix colvars"_fix_colvars.html, "fix plumed"_fix_plumed.html - -[Default:] none - -:line - -:link(Izrailev) -[(Izrailev)] Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar, -Wriggers, Schulten. Computational Molecular Dynamics: Challenges, -Methods, Ideas, volume 4 of Lecture Notes in Computational Science and -Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998. - -:link(Park) -[(Park)] Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004) - -:link(Jarzynski) -[(Jarzynski)] Jarzynski, Phys. Rev. Lett. 78, 2690 (1997) diff --git a/doc/txt/fix_smd_adjust_dt.txt b/doc/txt/fix_smd_adjust_dt.txt deleted file mode 100644 index 3535ddfcc2..0000000000 --- a/doc/txt/fix_smd_adjust_dt.txt +++ /dev/null @@ -1,60 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix smd/adjust_dt command :h3 - -[Syntax:] - -fix ID group-ID smd/adjust_dt arg :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -smd/adjust_dt = style name of this fix command :l -arg = {s_fact} :l - {s_fact} = safety factor :pre - -:ule - -[Examples:] - -fix 1 all smd/adjust_dt 0.1 :pre - -[Description:] - -The fix calculates a new stable time increment for use with the SMD -time integrators. - -The stable time increment is based on multiple conditions. For the SPH -pair styles, a CFL criterion (Courant, Friedrichs & Lewy, 1928) is -evaluated, which determines the speed of sound cannot propagate -further than a typical spacing between particles within a single time -step to ensure no information is lost. For the contact pair styles, a -linear analysis of the pair potential determines a stable maximum time -step. - -This fix inquires the minimum stable time increment across all -particles contained in the group for which this fix is defined. An -additional safety factor {s_fact} is applied to the time increment. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach -Dynamics in LAMMPS. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -Currently, no part of USER-SMD supports restarting nor minimization. - -[Restrictions:] - -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"smd/tlsph_dt"_compute_smd_tlsph_dt.html - -[Default:] none diff --git a/doc/txt/fix_smd_integrate_tlsph.txt b/doc/txt/fix_smd_integrate_tlsph.txt deleted file mode 100644 index 029605ff7f..0000000000 --- a/doc/txt/fix_smd_integrate_tlsph.txt +++ /dev/null @@ -1,55 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix smd/integrate_tlsph command :h3 - -[Syntax:] - -fix ID group-ID smd/integrate_tlsph keyword values :pre - -ID, group-ID are documented in "fix"_fix.html command -smd/integrate_tlsph = style name of this fix command -zero or more keyword/value pairs may be appended -keyword = {limit_velocity} :ul - - {limit_velocity} value = max_vel - max_vel = maximum allowed velocity :pre - -[Examples:] - -fix 1 all smd/integrate_tlsph -fix 1 all smd/integrate_tlsph limit_velocity 1000 :pre - -[Description:] - -The fix performs explicit time integration for particles which -interact according with the Total-Lagrangian SPH pair style. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach -Dynamics in LAMMPS. - -The {limit_velocity} keyword will control the velocity, scaling the -norm of the velocity vector to max_vel in case it exceeds this -velocity limit. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -Currently, no part of USER-SMD supports restarting nor -minimization. This fix has no outputs. - -[Restrictions:] - -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html - -[Default:] none diff --git a/doc/txt/fix_smd_integrate_ulsph.txt b/doc/txt/fix_smd_integrate_ulsph.txt deleted file mode 100644 index a99574cc85..0000000000 --- a/doc/txt/fix_smd_integrate_ulsph.txt +++ /dev/null @@ -1,63 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix smd/integrate_ulsph command :h3 - -[Syntax:] - -fix ID group-ID smd/integrate_ulsph keyword :pre - -ID, group-ID are documented in "fix"_fix.html command -smd/integrate_ulsph = style name of this fix command -zero or more keyword/value pairs may be appended -keyword = adjust_radius or limit_velocity :ul - -adjust_radius values = adjust_radius_factor min_nn max_nn - adjust_radius_factor = factor which scale the smooth/kernel radius - min_nn = minimum number of neighbors - max_nn = maximum number of neighbors -limit_velocity values = max_velocity - max_velocity = maximum allowed velocity. - -[Examples:] - -fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50 -fix 1 all smd/integrate_ulsph limit_velocity 1000 :pre - -[Description:] - -The fix performs explicit time integration for particles which -interact with the updated Lagrangian SPH pair style. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach -Dynamics in LAMMPS. - -The {adjust_radius} keyword activates dynamic adjustment of the -per-particle SPH smoothing kernel radius such that the number of -neighbors per particles remains within the interval {min_nn} to -{max_nn}. The parameter {adjust_radius_factor} determines the amount -of adjustment per timestep. Typical values are {adjust_radius_factor} -=1.02, {min_nn} =15, and {max_nn} =20. - -The {limit_velocity} keyword will control the velocity, scaling the norm of -the velocity vector to max_vel in case it exceeds this velocity limit. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -Currently, no part of USER-SMD supports restarting nor -minimization. This fix has no outputs. - -[Restrictions:] - -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/fix_smd_move_triangulated_surface.txt b/doc/txt/fix_smd_move_triangulated_surface.txt deleted file mode 100644 index fca21b78f7..0000000000 --- a/doc/txt/fix_smd_move_triangulated_surface.txt +++ /dev/null @@ -1,79 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix smd/move_tri_surf command :h3 - -[Syntax:] - -fix ID group-ID smd/move_tri_surf keyword :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -smd/move_tri_surf keyword = style name of this fix command :l -keyword = {*LINEAR} or {*WIGGLE} or {*ROTATE} :l - - {*LINEAR} args = Vx Vy Vz - Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL - {*WIGGLE} args = Vx Vy Vz max_travel - vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL - max_travel = wiggle amplitude - {*ROTATE} args = Px Py Pz Rx Ry Rz period - Px,Py,Pz = origin point of axis of rotation (distance units) - Rx,Ry,Rz = axis of rotation vector - period = period of rotation (time units) :pre -:ule - -[Examples:] - -fix 1 tool smd/move_tri_surf *LINEAR 20 20 10 -fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10 -fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1 :pre - -[Description:] - -This fix applies only to rigid surfaces read from .STL files via fix -"smd/wall_surface"_fix_smd_wall_surface.html . It updates position -and velocity for the particles in the group each timestep without -regard to forces on the particles. The rigid surfaces can thus be -moved along simple trajectories during the simulation. - -The {*LINEAR} style moves particles with the specified constant velocity -vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle -to V = (Vx,Vy,Vz). - -The {*WIGGLE} style moves particles in an oscillatory fashion. -Particles are moved along (vx, vy, vz) with constant velocity until a -displacement of max_travel is reached. Then, the velocity vector is -reversed. This process is repeated. - -The {*ROTATE} style rotates particles around a rotation axis R = -(Rx,Ry,Rz) that goes through a point P = (Px,Py,Pz). The period of the -rotation is also specified. This style also sets the velocity of each -particle to (omega cross Rperp) where omega is its angular velocity -around the rotation axis and Rperp is a perpendicular vector from the -rotation axis to the particle. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach -Dynamics in LAMMPS. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -Currently, no part of USER-SMD supports restarting nor -minimization. This fix has no outputs. - -[Restrictions:] - -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"smd/triangle_mesh_vertices"_compute_smd_triangle_vertices.html, -"smd/wall_surface"_fix_smd_wall_surface.html - -[Default:] none diff --git a/doc/txt/fix_smd_setvel.txt b/doc/txt/fix_smd_setvel.txt deleted file mode 100644 index b170eff860..0000000000 --- a/doc/txt/fix_smd_setvel.txt +++ /dev/null @@ -1,84 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix smd/setvel command :h3 - -[Syntax:] - -fix ID group-ID smd/setvel vx vy vz keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -smd/setvel = style name of this fix command :l -vx,vy,vz = velocity component values :l -any of vx,vy,vz can be a variable (see below) :l -zero or more keyword/value pairs may be appended to args :l -keyword = {region} :l - {region} value = region-ID - region-ID = ID of region particles must be in to have their velocities set :pre -:ule - -[Examples:] - -fix top_velocity top_group setvel 1.0 0.0 0.0 :pre - -[Description:] - -Set each component of velocity on each particle in the group to the specified -values vx,vy,vz, regardless of the forces acting on the particle. This command can -be used to impose velocity boundary conditions. - -Any of the vx,vy,vz values can be specified as NULL which means do not -alter the velocity component in that dimension. - -This fix is indented to be used together with a time integration fix. - -Any of the 3 quantities defining the velocity components can be specified -as an equal-style or atom-style "variable"_variable.html, namely {vx}, -{vy}, {vz}. If the value is a variable, it should be specified as -v_name, where name is the variable name. In this case, the variable -will be evaluated each timestep, and its value used to determine the -force component. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent velocity field. - -Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent velocity -field with optional time-dependence as well. - -If the {region} keyword is used, the particle must also be in the -specified geometric "region"_region.html in order to have its velocity set by this command. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -Currently, no part of USER-SMD supports restarting nor minimization -None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Howto_output.html. This is the total -force on the group of atoms. The vector values calculated by this fix -are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -[Restrictions:] - -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/fix_smd_wall_surface.txt b/doc/txt/fix_smd_wall_surface.txt deleted file mode 100644 index 47527363a2..0000000000 --- a/doc/txt/fix_smd_wall_surface.txt +++ /dev/null @@ -1,71 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix smd/wall_surface command :h3 - -[Syntax:] - -fix ID group-ID smd/wall_surface arg type mol-ID :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -smd/wall_surface = style name of this fix command :l -arg = {file} :l - {file} = file name of a triangular mesh in stl format :pre -type = particle type to be given to the new particles created by this fix :l -mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535) :l,ule - -[Examples:] - -fix stl_surf all smd/wall_surface tool.stl 2 65535 :pre - -[Description:] - -This fix creates reads a triangulated surface from a file in .STL -format. For each triangle, a new particle is created which stores the -barycenter of the triangle and the vertex positions. The radius of -the new particle is that of the minimum circle which encompasses the -triangle vertices. - -The triangulated surface can be used as a complex rigid wall via the -"smd/tri_surface"_pair_smd_triangulated_surface.html pair style. It -is possible to move the triangulated surface via the -"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html fix style. - -Immediately after a .STL file has been read, the simulation needs to -be run for 0 timesteps in order to properly register the new particles -in the system. See the "funnel_flow" example in the USER-SMD examples -directory. - -See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach -Dynamics in LAMMPS. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -Currently, no part of USER-SMD supports restarting nor -minimization. This fix has no outputs. - -[Restrictions:] - -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -The molecule ID given to the particles created by this fix have to be -equal to or larger than 65535. - -Within each .STL file, only a single triangulated object must be -present, even though the STL format allows for the possibility of -multiple objects in one file. - -[Related commands:] - -"smd/triangle_mesh_vertices"_compute_smd_triangle_vertices.html, -"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html, -"smd/tri_surface"_pair_smd_triangulated_surface.html - -[Default:] none diff --git a/doc/txt/fix_spring.txt b/doc/txt/fix_spring.txt deleted file mode 100644 index 690fc3e67c..0000000000 --- a/doc/txt/fix_spring.txt +++ /dev/null @@ -1,142 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix spring command :h3 - -[Syntax:] - -fix ID group-ID spring keyword values :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -spring = style name of this fix command :l -keyword = {tether} or {couple} :l - {tether} values = K x y z R0 - K = spring constant (force/distance units) - x,y,z = point to which spring is tethered - R0 = equilibrium distance from tether point (distance units) - {couple} values = group-ID2 K x y z R0 - group-ID2 = 2nd group to couple to fix group with a spring - K = spring constant (force/distance units) - x,y,z = direction of spring - R0 = equilibrium distance of spring (distance units) :pre -:ule - -[Examples:] - -fix pull ligand spring tether 50.0 0.0 0.0 0.0 0.0 -fix pull ligand spring tether 50.0 0.0 0.0 0.0 5.0 -fix pull ligand spring tether 50.0 NULL NULL 2.0 3.0 -fix 5 bilayer1 spring couple bilayer2 100.0 NULL NULL 10.0 0.0 -fix longitudinal pore spring couple ion 100.0 NULL NULL -20.0 0.0 -fix radial pore spring couple ion 100.0 0.0 0.0 NULL 5.0 :pre - -[Description:] - -Apply a spring force to a group of atoms or between two groups of -atoms. This is useful for applying an umbrella force to a small -molecule or lightly tethering a large group of atoms (e.g. all the -solvent or a large molecule) to the center of the simulation box so -that it doesn't wander away over the course of a long simulation. It -can also be used to hold the centers of mass of two groups of atoms at -a given distance or orientation with respect to each other. - -The {tether} style attaches a spring between a fixed point {x,y,z} and -the center of mass of the fix group of atoms. The equilibrium -position of the spring is R0. At each timestep the distance R from -the center of mass of the group of atoms to the tethering point is -computed, taking account of wrap-around in a periodic simulation box. -A restoring force of magnitude K (R - R0) Mi / M is applied to each -atom in the group where {K} is the spring constant, Mi is the mass of -the atom, and M is the total mass of all atoms in the group. Note -that {K} thus represents the spring constant for the total force on -the group of atoms, not for a spring applied to each atom. - -The {couple} style links two groups of atoms together. The first -group is the fix group; the second is specified by group-ID2. The -groups are coupled together by a spring that is at equilibrium when -the two groups are displaced by a vector {x,y,z} with respect to each -other and at a distance R0 from that displacement. Note that {x,y,z} -is the equilibrium displacement of group-ID2 relative to the fix -group. Thus (1,1,0) is a different spring than (-1,-1,0). When the -relative positions and distance between the two groups are not in -equilibrium, the same spring force described above is applied to atoms -in each of the two groups. - -For both the {tether} and {couple} styles, any of the x,y,z values can -be specified as NULL which means do not include that dimension in the -distance calculation or force application. - -The first example above pulls the ligand towards the point (0,0,0). -The second example holds the ligand near the surface of a sphere of -radius 5 around the point (0,0,0). The third example holds the ligand -a distance 3 away from the z=2 plane (on either side). - -The fourth example holds 2 bilayers a distance 10 apart in z. For the -last two examples, imagine a pore (a slab of atoms with a cylindrical -hole cut out) oriented with the pore axis along z, and an ion moving -within the pore. The fifth example holds the ion a distance of -20 -below the z = 0 center plane of the pore (umbrella sampling). The -last example holds the ion a distance 5 away from the pore axis -(assuming the center-of-mass of the pore in x,y is the pore axis). - -NOTE: The center of mass of a group of atoms is calculated in -"unwrapped" coordinates using atom image flags, which means that the -group can straddle a periodic boundary. See the "dump"_dump.html doc -page for a discussion of unwrapped coordinates. It also means that a -spring connecting two groups or a group and the tether point can cross -a periodic boundary and its length be calculated correctly. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy stored in the spring to the system's potential -energy as part of "thermodynamic output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the spring energy -= 0.5 * K * r^2. - -This fix also computes global 4-vector which can be accessed by -various "output commands"_Howto_output.html. The first 3 quantities -in the vector are xyz components of the total force added to the group -of atoms by the spring. In the case of the {couple} style, it is the -force on the fix group (group-ID) or the negative of the force on the -2nd group (group-ID2). The 4th quantity in the vector is the -magnitude of the force added by the spring, as a positive value if -(r-R0) > 0 and a negative value if (r-R0) < 0. This sign convention -can be useful when using the spring force to compute a potential of -mean force (PMF). - -The scalar and vector values calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -NOTE: If you want the spring energy to be included in the total -potential energy of the system (the quantity being minimized), you -MUST enable the "fix_modify"_fix_modify.html {energy} option for this -fix. - -[Restrictions:] none - -[Related commands:] - -"fix drag"_fix_drag.html, "fix spring/self"_fix_spring_self.html, -"fix spring/rg"_fix_spring_rg.html, "fix smd"_fix_smd.html - -[Default:] none diff --git a/doc/txt/fix_spring_chunk.txt b/doc/txt/fix_spring_chunk.txt deleted file mode 100644 index 9d4e8afd09..0000000000 --- a/doc/txt/fix_spring_chunk.txt +++ /dev/null @@ -1,86 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix spring/chunk command :h3 - -[Syntax:] - -fix ID group-ID spring/chunk K chunkID comID :pre - -ID, group-ID are documented in "fix"_fix.html command -spring/chunk = style name of this fix command -K = spring constant for each chunk (force/distance units) -chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command -comID = ID of "compute com/chunk"_compute_com_chunk.html command :ul - -[Examples:] - -fix restrain all spring/chunk 100 chunkID comID :pre - -[Description:] - -Apply a spring force to the center-of-mass (COM) of chunks of atoms as -defined by the "compute chunk/atom"_compute_chunk_atom.html command. -Chunks can be molecules or spatial bins or other groupings of atoms. -This is a way of tethering each chunk to its initial COM coordinates. - -The {chunkID} is the ID of a compute chunk/atom command defined in the -input script. It is used to define the chunks. The {comID} is the ID -of a compute com/chunk command defined in the input script. It is -used to compute the COMs of each chunk. - -At the beginning of the first "run"_run.html or -"minimize"_minimize.html command after this fix is defined, the -initial COM of each chunk is calculated and stored as R0m, where M is -the chunk number. Thereafter, at every timestep (or minimization -iteration), the current COM of each chunk is calculated as Rm. A -restoring force of magnitude K (Rm - R0m) Mi / Mm is applied to each -atom in each chunk where {K} is the specified spring constant, Mi is -the mass of the atom, and Mm is the total mass of all atoms in the -chunk. Note that {K} thus represents the spring constant for the -total force on each chunk of atoms, not for a spring applied to each -atom. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy stored in all the springs to the system's potential -energy as part of "thermodynamic output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the energy of all -the springs, i.e. 0.5 * K * r^2 per-spring. - -The scalar value calculated by this fix is "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -NOTE: If you want the spring energies to be included in the total -potential energy of the system (the quantity being minimized), you -MUST enable the "fix_modify"_fix_modify.html {energy} option for this -fix. - -[Restrictions:] none - -[Related commands:] - -"fix spring"_fix_spring.html, "fix spring/self"_fix_spring_self.html, -"fix spring/rg"_fix_spring_rg.html - -[Default:] none diff --git a/doc/txt/fix_spring_rg.txt b/doc/txt/fix_spring_rg.txt deleted file mode 100644 index b252163958..0000000000 --- a/doc/txt/fix_spring_rg.txt +++ /dev/null @@ -1,70 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix spring/rg command :h3 - -[Syntax:] - -fix ID group-ID spring/rg K RG0 :pre - -ID, group-ID are documented in "fix"_fix.html command -spring/rg = style name of this fix command -K = harmonic force constant (force/distance units) -RG0 = target radius of gyration to constrain to (distance units) :ul - if RG0 = NULL, use the current RG as the target value :pre - -[Examples:] - -fix 1 protein spring/rg 5.0 10.0 -fix 2 micelle spring/rg 5.0 NULL :pre - -[Description:] - -Apply a harmonic restraining force to atoms in the group to affect -their central moment about the center of mass (radius of gyration). -This fix is useful to encourage a protein or polymer to fold/unfold -and also when sampling along the radius of gyration as a reaction -coordinate (i.e. for protein folding). - -The radius of gyration is defined as RG in the first formula. The -energy of the constraint and associated force on each atom is given by -the second and third formulas, when the group is at a different RG -than the target value RG0. - -:c,image(Eqs/fix_spring_rg.jpg) - -The (xi - center-of-mass) term is computed taking into account -periodic boundary conditions, m_i is the mass of the atom, and M is -the mass of the entire group. Note that K is thus a force constant -for the aggregate force on the group of atoms, not a per-atom force. - -If RG0 is specified as NULL, then the RG of the group is computed at -the time the fix is specified, and that value is used as the target. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -[Restrictions:] none - -[Related commands:] - -"fix spring"_fix_spring.html, "fix spring/self"_fix_spring_self.html -"fix drag"_fix_drag.html, "fix smd"_fix_smd.html - -[Default:] none diff --git a/doc/txt/fix_spring_self.txt b/doc/txt/fix_spring_self.txt deleted file mode 100644 index 0ac1d5eecb..0000000000 --- a/doc/txt/fix_spring_self.txt +++ /dev/null @@ -1,83 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix spring/self command :h3 - -[Syntax:] - -fix ID group-ID spring/self K dir :pre - -ID, group-ID are documented in "fix"_fix.html command -spring/self = style name of this fix command -K = spring constant (force/distance units) -dir = xyz, xy, xz, yz, x, y, or z (optional, default: xyz) :ul - -[Examples:] - -fix tether boundary-atoms spring/self 10.0 -fix zrest move spring/self 10.0 z :pre - -[Description:] - -Apply a spring force independently to each atom in the group to tether -it to its initial position. The initial position for each atom is its -location at the time the fix command was issued. At each timestep, -the magnitude of the force on each atom is -Kr, where r is the -displacement of the atom from its current position to its initial -position. The distance r correctly takes into account any crossings -of periodic boundary by the atom since it was in its initial -position. - -With the (optional) dir flag, one can select in which direction the -spring force is applied. By default, the restraint is applied in all -directions, but it can be limited to the xy-, xz-, yz-plane and the -x-, y-, or z-direction, thus restraining the atoms to a line or a -plane, respectively. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the original coordinates of tethered atoms to "binary -restart files"_restart.html, so that the spring effect will be the -same in a restarted simulation. See the -"read_restart"_read_restart.html command for info on how to re-specify -a fix in an input script that reads a restart file, so that the -operation of the fix continues in an uninterrupted fashion. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy stored in the per-atom springs to the system's -potential energy as part of "thermodynamic output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by -this fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is an energy which is -the sum of the spring energy for each atom, where the per-atom energy -is 0.5 * K * r^2. The scalar value calculated by this fix is -"extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -NOTE: If you want the per-atom spring energy to be included in the -total potential energy of the system (the quantity being minimized), -you MUST enable the "fix_modify"_fix_modify.html {energy} option for -this fix. - -[Restrictions:] none - -[Related commands:] - -"fix drag"_fix_drag.html, "fix spring"_fix_spring.html, -"fix smd"_fix_smd.html, "fix spring/rg"_fix_spring_rg.html - -[Default:] none diff --git a/doc/txt/fix_srd.txt b/doc/txt/fix_srd.txt deleted file mode 100644 index 018813c361..0000000000 --- a/doc/txt/fix_srd.txt +++ /dev/null @@ -1,398 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix srd command :h3 - -[Syntax:] - -fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command -srd = style name of this fix command -N = reset SRD particle velocities every this many timesteps -groupbig-ID = ID of group of large particles that SRDs interact with -Tsrd = temperature of SRD particles (temperature units) -hgrid = grid spacing for SRD grouping (distance units) -seed = random # seed (positive integer) :ul - -zero or more keyword/value pairs may be appended :ulb,l -keyword = {lamda} or {collision} or {overlap} or {inside} or {exact} or {radius} or {bounce} or {search} or {cubic} or {shift} or {tstat} or {rescale} :l - {lamda} value = mean free path of SRD particles (distance units) - {collision} value = {noslip} or {slip} = collision model - {overlap} value = {yes} or {no} = whether big particles may overlap - {inside} value = {error} or {warn} or {ignore} = how SRD particles which end up inside a big particle are treated - {exact} value = {yes} or {no} - {radius} value = rfactor = scale collision radius by this factor - {bounce} value = Nbounce = max # of collisions an SRD particle can undergo in one timestep - {search} value = sgrid = grid spacing for collision partner searching (distance units) - {cubic} values = style tolerance - style = {error} or {warn} - tolerance = fractional difference allowed (0 <= tol <= 1) - {shift} values = flag shiftseed - flag = {yes} or {no} or {possible} = SRD bin shifting for better statistics - {yes} = perform bin shifting each time SRD velocities are rescaled - {no} = no shifting - {possible} = shift depending on mean free path and bin size - shiftseed = random # seed (positive integer) - {tstat} value = {yes} or {no} = thermostat SRD particles or not - {rescale} value = {yes} or {no} or {rotate} or {collide} = rescaling of SRD velocities - {yes} = rescale during velocity rotation and collisions - {no} = no rescaling - {rotate} = rescale during velocity rotation, but not collisions - {collide} = rescale during collisions, but not velocity rotation :pre -:ule - -[Examples:] - -fix 1 srd srd 10 big 1.0 0.25 482984 -fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5 :pre - -[Description:] - -Treat a group of particles as stochastic rotation dynamics (SRD) -particles that serve as a background solvent when interacting with big -(colloidal) particles in groupbig-ID. The SRD formalism is described -in "(Hecht)"_#Hecht. The key idea behind using SRD particles as a -cheap coarse-grained solvent is that SRD particles do not interact -with each other, but only with the solute particles, which in LAMMPS -can be spheroids, ellipsoids, or line segments, or triangles, or rigid -bodies containing multiple spheroids or ellipsoids or line segments -or triangles. The collision and rotation properties of the model -imbue the SRD particles with fluid-like properties, including an -effective viscosity. Thus simulations with large solute particles can -be run more quickly, to measure solute properties like diffusivity -and viscosity in a background fluid. The usual LAMMPS fixes for such -simulations, such as "fix deform"_fix_deform.html, "fix -viscosity"_fix_viscosity.html, and "fix nvt/sllod"_fix_nvt_sllod.html, -can be used in conjunction with the SRD model. - -For more details on how the SRD model is implemented in LAMMPS, "this -paper"_#Petersen1 describes the implementation and usage of pure SRD -fluids. "This paper"_#Lechman, which is nearly complete, describes -the implementation and usage of mixture systems (solute particles in -an SRD fluid). See the examples/srd directory for sample input -scripts using SRD particles in both settings. - -This fix does 2 things: - -(1) It advects the SRD particles, performing collisions between SRD -and big particles or walls every timestep, imparting force and torque -to the big particles. Collisions also change the position and -velocity of SRD particles. - -(2) It resets the velocity distribution of SRD particles via random -rotations every N timesteps. - -SRD particles have a mass, temperature, characteristic timestep -dt_SRD, and mean free path between collisions (lamda). The -fundamental equation relating these 4 quantities is - -lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass) :pre - -The mass of SRD particles is set by the "mass"_mass.html command -elsewhere in the input script. The SRD timestep dt_SRD is N times the -step dt defined by the "timestep"_timestep.html command. Big -particles move in the normal way via a time integration "fix"_fix.html -with a short timestep dt. SRD particles advect with a large timestep -dt_SRD >= dt. - -If the {lamda} keyword is not specified, the SRD temperature -{Tsrd} is used in the above formula to compute lamda. If the {lamda} -keyword is specified, then the {Tsrd} setting is ignored and the above -equation is used to compute the SRD temperature. - -The characteristic length scale for the SRD fluid is set by {hgrid} -which is used to bin SRD particles for purposes of resetting their -velocities. Normally hgrid is set to be 1/4 of the big particle -diameter or smaller, to adequately resolve fluid properties around the -big particles. - -Lamda cannot be smaller than 0.6 * hgrid, else an error is generated -(unless the {shift} keyword is used, see below). The velocities of -SRD particles are bounded by Vmax, which is set so that an SRD -particle will not advect further than Dmax = 4*lamda in dt_SRD. This -means that roughly speaking, Dmax should not be larger than a big -particle diameter, else SRDs may pass through big particles without -colliding. A warning is generated if this is the case. - -Collisions between SRD particles and big particles or walls are -modeled as a lightweight SRD point particle hitting a heavy big -particle of given diameter or a wall at a point on its surface and -bouncing off with a new velocity. The collision changes the momentum -of the SRD particle. It imparts a force and torque to the big -particle. It imparts a force to a wall. Static or moving SRD walls -are setup via the "fix wall/srd"_fix_wall_srd.html command. For the -remainder of this doc page, a collision of an SRD particle with a wall -can be viewed as a collision with a big particle of infinite radius -and mass. - -The {collision} keyword sets the style of collisions. The {slip} -style means that the tangential component of the SRD particle momentum -is preserved. Thus a force is imparted to a big particle, but no -torque. The normal component of the new SRD velocity is sampled from -a Gaussian distribution at temperature {Tsrd}. - -For the {noslip} style, both the normal and tangential components of -the new SRD velocity are sampled from a Gaussian distribution at -temperature {Tsrd}. Additionally, a new tangential direction for the -SRD velocity is chosen randomly. This collision style imparts torque -to a big particle. Thus a time integrator "fix"_fix.html that rotates -the big particles appropriately should be used. - -:line - -The {overlap} keyword should be set to {yes} if two (or more) big -particles can ever overlap. This depends on the pair potential -interaction used for big-big interactions, or could be the case if -multiple big particles are held together as rigid bodies via the "fix -rigid"_fix_rigid.html command. If the {overlap} keyword is {no} and -big particles do in fact overlap, then SRD/big collisions can generate -an error if an SRD ends up inside two (or more) big particles at once. -How this error is treated is determined by the {inside} keyword. -Running with {overlap} set to {no} allows for faster collision -checking, so it should only be set to {yes} if needed. - -The {inside} keyword determines how a collision is treated if the -computation determines that the timestep started with the SRD particle -already inside a big particle. If the setting is {error} then this -generates an error message and LAMMPS stops. If the setting is {warn} -then this generates a warning message and the code continues. If the -setting is {ignore} then no message is generated. One of the output -quantities logged by the fix (see below) tallies the number of such -events, so it can be monitored. Note that once an SRD particle is -inside a big particle, it may remain there for several steps until it -drifts outside the big particle. - -The {exact} keyword determines how accurately collisions are computed. -A setting of {yes} computes the time and position of each collision as -SRD and big particles move together. A setting of {no} estimates the -position of each collision based on the end-of-timestep positions of -the SRD and big particle. If {overlap} is set to yes, the setting of -the {exact} keyword is ignored since time-accurate collisions are -needed. - -The {radius} keyword scales the effective size of big particles. If -big particles will overlap as they undergo dynamics, then this keyword -can be used to scale down their effective collision radius by an -amount {rfactor}, so that SRD particle will only collide with one big -particle at a time. For example, in a Lennard-Jones system at a -temperature of 1.0 (in reduced LJ units), the minimum separation -between two big particles is as small as about 0.88 sigma. Thus an -{rfactor} value of 0.85 should prevent dual collisions. - -The {bounce} keyword can be used to limit the maximum number of -collisions an SRD particle undergoes in a single timestep as it -bounces between nearby big particles. Note that if the limit is -reached, the SRD can be left inside a big particle. A setting of 0 is -the same as no limit. - -:line - -There are 2 kinds of bins created and maintained when running an SRD -simulation. The first are "SRD bins" which are used to bin SRD -particles and reset their velocities, as discussed above. The second -are "search bins" which are used to identify SRD/big particle -collisions. - -The {search} keyword can be used to choose a search bin size for -identifying SRD/big particle collisions. The default is to use the -{hgrid} parameter for SRD bins as the search bin size. Choosing a -smaller or large value may be more efficient, depending on the -problem. But, in a statistical sense, it should not change the -simulation results. - -The {cubic} keyword can be used to generate an error or warning when -the bin size chosen by LAMMPS creates SRD bins that are non-cubic or -different than the requested value of {hgrid} by a specified -{tolerance}. Note that using non-cubic SRD bins can lead to -undetermined behavior when rotating the velocities of SRD particles, -hence LAMMPS tries to protect you from this problem. - -LAMMPS attempts to set the SRD bin size to exactly {hgrid}. However, -there must be an integer number of bins in each dimension of the -simulation box. Thus the actual bin size will depend on the size and -shape of the overall simulation box. The actual bin size is printed -as part of the SRD output when a simulation begins. - -If the actual bin size in non-cubic by an amount exceeding the -tolerance, an error or warning is printed, depending on the style of -the {cubic} keyword. Likewise, if the actual bin size differs from -the requested {hgrid} value by an amount exceeding the tolerance, then -an error or warning is printed. The {tolerance} is a fractional -difference. E.g. a tolerance setting of 0.01 on the shape means that -if the ratio of any 2 bin dimensions exceeds (1 +/- tolerance) then an -error or warning is generated. Similarly, if the ratio of any bin -dimension with {hgrid} exceeds (1 +/- tolerance), then an error or -warning is generated. - -NOTE: The fix srd command can be used with simulations the size and/or -shape of the simulation box changes. This can be due to non-periodic -boundary conditions or the use of fixes such as the "fix -deform"_fix_deform.html or "fix wall/srd"_fix_wall_srd.html commands -to impose a shear on an SRD fluid or an interaction with an external -wall. If the box size changes then the size of SRD bins must be -recalculated every reneighboring. This is not necessary if only the -box shape changes. This re-binning is always done so as to fit an -integer number of bins in the current box dimension, whether it be a -fixed, shrink-wrapped, or periodic boundary, as set by the -"boundary"_boundary.html command. If the box size or shape changes, -then the size of the search bins must be recalculated every -reneighboring. Note that changing the SRD bin size may alter the -properties of the SRD fluid, such as its viscosity. - -The {shift} keyword determines whether the coordinates of SRD -particles are randomly shifted when binned for purposes of rotating -their velocities. When no shifting is performed, SRD particles are -binned and the velocity distribution of the set of SRD particles in -each bin is adjusted via a rotation operator. This is a statistically -valid operation if SRD particles move sufficiently far between -successive rotations. This is determined by their mean-free path -lamda. If lamda is less than 0.6 of the SRD bin size, then shifting -is required. A shift means that all of the SRD particles are shifted -by a vector whose coordinates are chosen randomly in the range \[-1/2 -bin size, 1/2 bin size\]. Note that all particles are shifted by the -same vector. The specified random number {shiftseed} is used to -generate these vectors. This operation sufficiently randomizes which -SRD particles are in the same bin, even if lamda is small. - -If the {shift} flag is set to {no}, then no shifting is performed, but -bin data will be communicated if bins overlap processor boundaries. -An error will be generated if lamda < 0.6 of the SRD bin size. If the -{shift} flag is set to {possible}, then shifting is performed only if -lamda < 0.6 of the SRD bin size. A warning is generated to let you -know this is occurring. If the {shift} flag is set to {yes} then -shifting is performed regardless of the magnitude of lamda. Note that -the {shiftseed} is not used if the {shift} flag is set to {no}, but -must still be specified. - -Note that shifting of SRD coordinates requires extra communication, -hence it should not normally be enabled unless required. - -The {tstat} keyword will thermostat the SRD particles to the specified -{Tsrd}. This is done every N timesteps, during the velocity rotation -operation, by rescaling the thermal velocity of particles in each SRD -bin to the desired temperature. If there is a streaming velocity -associated with the system, e.g. due to use of the "fix -deform"_fix_deform.html command to perform a simulation undergoing -shear, then that is also accounted for. The mean velocity of each bin -of SRD particles is set to the position-dependent streaming velocity, -based on the coordinates of the center of the SRD bin. Note that -collisions of SRD particles with big particles or walls has a -thermostatting effect on the colliding particles, so it may not be -necessary to thermostat the SRD particles on a bin by bin basis in -that case. Also note that for streaming simulations, if no -thermostatting is performed (the default), then it may take a long -time for the SRD fluid to come to equilibrium with a velocity profile -that matches the simulation box deformation. - -The {rescale} keyword enables rescaling of an SRD particle's velocity -if it would travel more than 4 mean-free paths in an SRD timestep. If -an SRD particle exceeds this velocity it is possible it will be lost -when migrating to other processors or that collisions with big -particles will be missed, either of which will generate errors. Thus -the safest mode is to run with rescaling enabled. However rescaling -removes kinetic energy from the system (the particle's velocity is -reduced). The latter will not typically be a problem if -thermostatting is enabled via the {tstat} keyword or if SRD collisions -with big particles or walls effectively thermostat the system. If you -wish to turn off rescaling (on is the default), e.g. for a pure SRD -system with no thermostatting so that the temperature does not decline -over time, the {rescale} keyword can be used. The {no} value turns -rescaling off during collisions and the per-bin velocity rotation -operation. The {collide} and {rotate} values turn it on for -one of the operations and off for the other. - -:line - -NOTE: This fix is normally used for simulations with a huge number of -SRD particles relative to the number of big particles, e.g. 100 to 1. -In this scenario, computations that involve only big particles -(neighbor list creation, communication, time integration) can slow -down dramatically due to the large number of background SRD particles. - -Three other input script commands will largely overcome this effect, -speeding up an SRD simulation by a significant amount. These are the -"atom_modify first"_atom_modify.html, "neigh_modify -include"_neigh_modify.html, and "comm_modify group"_comm_modify.html -commands. Each takes a group-ID as an argument, which in this case -should be the group-ID of the big solute particles. - -Additionally, when a "pair_style"_pair_style.html for big/big particle -interactions is specified, the "pair_coeff"_pair_coeff.html command -should be used to turn off big/SRD interactions, e.g. by setting their -epsilon or cutoff length to 0.0. - -The "delete_atoms overlap" command may be useful in setting up an SRD -simulation to insure there are no initial overlaps between big and SRD -particles. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix tabulates several SRD statistics which are stored in a vector -of length 12, which can be accessed by various "output -commands"_Howto_output.html. The vector values calculated by this fix -are "intensive", meaning they do not scale with the size of the -simulation. Technically, the first 8 do scale with the size of the -simulation, but treating them as intensive means they are not scaled -when printed as part of thermodynamic output. - -These are the 12 quantities. All are values for the current timestep, -except for quantity 5 and the last three, each of which are -cumulative quantities since the beginning of the run. - -(1) # of SRD/big collision checks performed -(2) # of SRDs which had a collision -(3) # of SRD/big collisions (including multiple bounces) -(4) # of SRD particles inside a big particle -(5) # of SRD particles whose velocity was rescaled to be < Vmax -(6) # of bins for collision searching -(7) # of bins for SRD velocity rotation -(8) # of bins in which SRD temperature was computed -(9) SRD temperature -(10) # of SRD particles which have undergone max # of bounces -(11) max # of bounces any SRD particle has had in a single step -(12) # of reneighborings due to SRD particles moving too far :ul - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This command can only be used if LAMMPS was built with the SRD -package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"fix wall/srd"_fix_wall_srd.html - -[Default:] - -The option defaults are lamda inferred from Tsrd, collision = noslip, -overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0, -search = hgrid, cubic = error 0.01, shift = no, tstat = no, and -rescale = yes. - -:line - -:link(Hecht) -[(Hecht)] Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005). - -:link(Petersen1) -[(Petersen)] Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J -Chem Phys, 132, 174106 (2010). - -:link(Lechman) -[(Lechman)] Lechman, et al, in preparation (2010). diff --git a/doc/txt/fix_store_force.txt b/doc/txt/fix_store_force.txt deleted file mode 100644 index 33ebc962d5..0000000000 --- a/doc/txt/fix_store_force.txt +++ /dev/null @@ -1,71 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix store/force command :h3 - -[Syntax:] - -fix ID group-ID store/force :pre - -ID, group-ID are documented in "fix"_fix.html command -store/force = style name of this fix command :ul - -[Examples:] - -fix 1 all store/force :pre - -[Description:] - -Store the forces on atoms in the group at the point during each -timestep when the fix is invoked, as described below. This is useful -for storing forces before constraints or other boundary conditions are -computed which modify the forces, so that unmodified forces can be -"written to a dump file"_dump.html or accessed by other "output -commands"_Howto_output.html that use per-atom quantities. - -This fix is invoked at the point in the velocity-Verlet timestepping -immediately after "pair"_pair_style.html, "bond"_bond_style.html, -"angle"_angle_style.html, "dihedral"_dihedral_style.html, -"improper"_improper_style.html, and "long-range"_kspace_style.html -forces have been calculated. It is the point in the timestep when -various fixes that compute constraint forces are calculated and -potentially modify the force on each atom. Examples of such fixes are -"fix shake"_fix_shake.html, "fix wall"_fix_wall.html, and "fix -indent"_fix_indent.html. - -NOTE: The order in which various fixes are applied which operate at -the same point during the timestep, is the same as the order they are -specified in the input script. Thus normally, if you want to store -per-atom forces due to force field interactions, before constraints -are applied, you should list this fix first within that set of fixes, -i.e. before other fixes that apply constraints. However, if you wish -to include certain constraints (e.g. fix shake) in the stored force, -then it could be specified after some fixes and before others. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix produces a per-atom array which can be accessed by various -"output commands"_Howto_output.html. The number of columns for each -atom is 3, and the columns store the x,y,z forces on each atom. The -per-atom values be accessed on any timestep. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix store_state"_fix_store_state.html - -[Default:] none diff --git a/doc/txt/fix_store_state.txt b/doc/txt/fix_store_state.txt deleted file mode 100644 index df05adc5b9..0000000000 --- a/doc/txt/fix_store_state.txt +++ /dev/null @@ -1,127 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix store/state command :h3 - -[Syntax:] - -fix ID group-ID store/state N input1 input2 ... keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -store/state = style name of this fix command :l -N = store atom attributes every N steps, N = 0 for initial store only :l -input = one or more atom attributes :l - possible attributes = id, mol, type, mass, - x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz, - vx, vy, vz, fx, fy, fz, - q, mux, muy, muz, mu, - radius, diameter, omegax, omegay, omegaz, - angmomx, angmomy, angmomz, tqx, tqy, tqz, - c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name, - d_name, i_name :pre - - id = atom ID - mol = molecule ID - type = atom type - mass = atom mass - x,y,z = unscaled atom coordinates - xs,ys,zs = scaled atom coordinates - xu,yu,zu = unwrapped atom coordinates - xsu,ysu,zsu = scaled unwrapped atom coordinates - ix,iy,iz = box image that the atom is in - vx,vy,vz = atom velocities - fx,fy,fz = forces on atoms - q = atom charge - mux,muy,muz = orientation of dipolar atom - mu = magnitued of dipole moment of atom - radius,diameter = radius.diameter of spherical particle - omegax,omegay,omegaz = angular velocity of spherical particle - angmomx,angmomy,angmomz = angular momentum of aspherical particle - tqx,tqy,tqz = torque on finite-size particles - c_ID = per-atom vector calculated by a compute with ID - c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID - f_ID = per-atom vector calculated by a fix with ID - f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID - v_name = per-atom vector calculated by an atom-style variable with name - d_name = per-atom floating point vector name, managed by fix property/atom - i_name = per-atom integer vector name, managed by fix property/atom :pre - -zero or more keyword/value pairs may be appended :l -keyword = {com} :l - {com} value = {yes} or {no} :pre -:ule - -[Examples:] - -fix 1 all store/state 0 x y z -fix 1 all store/state 0 xu yu zu com yes -fix 2 all store/state 1000 vx vy vz :pre - -[Description:] - -Define a fix that stores attributes for each atom in the group at the -time the fix is defined. If {N} is 0, then the values are never -updated, so this is a way of archiving an atom attribute at a given -time for future use in a calculation or output. See the discussion of -"output commands"_Howto_output.html that take fixes as inputs. - -If {N} is not zero, then the attributes will be updated every {N} -steps. - -NOTE: Actually, only atom attributes specified by keywords like {xu} -or {vy} or {radius} are initially stored immediately at the point in -your input script when the fix is defined. Attributes specified by a -compute, fix, or variable are not initially stored until the first run -following the fix definition begins. This is because calculating -those attributes may require quantities that are not defined in -between runs. - -The list of possible attributes is the same as that used by the "dump -custom"_dump.html command, which describes their meaning. - -If the {com} keyword is set to {yes} then the {xu}, {yu}, and {zu} -inputs store the position of each atom relative to the center-of-mass -of the group of atoms, instead of storing the absolute position. - -The requested values are stored in a per-atom vector or array as -discussed below. Zeroes are stored for atoms not in the specified -group. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the per-atom values it stores to "binary restart -files"_restart.html, so that the values can be restored when a -simulation is restarted. See the "read_restart"_read_restart.html -command for info on how to re-specify a fix in an input script that -reads a restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. - -If a single input is specified, this fix produces a per-atom vector. -If multiple inputs are specified, a per-atom array is produced where -the number of columns for each atom is the number of inputs. These -can be accessed by various "output commands"_Howto_output.html. The -per-atom values be accessed on any timestep. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"dump custom"_dump.html, "compute -property/atom"_compute_property_atom.html, -"fix property/atom"_fix_property_atom.html, "variable"_variable.html - -[Default:] - -The option default is com = no. diff --git a/doc/txt/fix_temp_berendsen.txt b/doc/txt/fix_temp_berendsen.txt deleted file mode 100644 index c1f1626782..0000000000 --- a/doc/txt/fix_temp_berendsen.txt +++ /dev/null @@ -1,163 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix temp/berendsen command :h3 - -[Syntax:] - -fix ID group-ID temp/berendsen Tstart Tstop Tdamp :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -temp/berendsen = style name of this fix command :l -Tstart,Tstop = desired temperature at start/end of run :l - Tstart can be a variable (see below) :pre -Tdamp = temperature damping parameter (time units) :l -:ule - -[Examples:] - -fix 1 all temp/berendsen 300.0 300.0 100.0 :pre - -[Description:] - -Reset the temperature of a group of atoms by using a Berendsen -thermostat "(Berendsen)"_#Berendsen2, which rescales their velocities -every timestep. - -The thermostat is applied to only the translational degrees of freedom -for the particles, which is an important consideration for finite-size -particles which have rotational degrees of freedom are being -thermostatted with this fix. The translational degrees of freedom can -also have a bias velocity removed from them before thermostatting -takes place; see the description below. - -The desired temperature at each timestep is a ramped value during the -run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in -time units and determines how rapidly the temperature is relaxed. For -example, a value of 100.0 means to relax the temperature in a timespan -of (roughly) 100 time units (tau or fmsec or psec - see the -"units"_units.html command). - -{Tstart} can be specified as an equal-style "variable"_variable.html. -In this case, the {Tstop} setting is ignored. If the value is a -variable, it should be specified as v_name, where name is the variable -name. In this case, the variable will be evaluated each timestep, and -its value used to determine the target temperature. - -NOTE: This thermostat will generate an error if the current -temperature is zero at the end of a timestep. It cannot rescale a -zero temperature. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent temperature. - -NOTE: Unlike the "fix nvt"_fix_nh.html command which performs -Nose/Hoover thermostatting AND time integration, this fix does NOT -perform time integration. It only modifies velocities to effect -thermostatting. Thus you must use a separate time integration fix, -like "fix nve"_fix_nve.html to actually update the positions of atoms -using the modified velocities. Likewise, this fix should not normally -be used on atoms that also have their temperature controlled by -another fix - e.g. by "fix nvt"_fix_nh.html or "fix -langevin"_fix_langevin.html commands. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp", as if this command had been -issued: - -compute fix-ID_temp group-ID temp :pre - -See the "compute temp"_compute_temp.html command for details. Note -that the ID of the new compute is the fix-ID + underscore + "temp", -and the group for the new compute is the same as the fix group. - -Note that this is NOT the compute used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -"compute_modify"_compute_modify.html command or print this temperature -during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} will have no -effect on this fix. - -Like other fixes that perform thermostatting, this fix can be used -with "compute commands"_compute.html that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the "fix_modify"_fix_modify.html command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a temperature "compute"_compute.html -you have defined to this fix which will be used in its thermostatting -procedure, as described above. For consistency, the group used by -this fix and by the compute should be the same. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change implied by a velocity rescaling to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the cumulative -energy change due to this fix. The scalar value calculated by this -fix is "extensive". - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix can be used with dynamic groups as defined by the -"group"_group.html command. Likewise it can be used with groups to -which atoms are added or deleted over time, e.g. a deposition -simulation. However, the conservation properties of the thermostat -and barostat are defined for systems with a static set of atoms. You -may observe odd behavior if the atoms in a group vary dramatically -over time or the atom count becomes very small. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix nvt"_fix_nh.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html, -"fix_modify"_fix_modify.html, "compute temp"_compute_temp.html, -"fix press/berendsen"_fix_press_berendsen.html - -[Default:] none - -:line - -:link(Berendsen2) - -[(Berendsen)] Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem -Phys, 81, 3684 (1984). diff --git a/doc/txt/fix_temp_csvr.txt b/doc/txt/fix_temp_csvr.txt deleted file mode 100644 index e50f821bfe..0000000000 --- a/doc/txt/fix_temp_csvr.txt +++ /dev/null @@ -1,168 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix temp/csvr command :h3 -fix temp/csld command :h3 - -[Syntax:] - -fix ID group-ID temp/csvr Tstart Tstop Tdamp seed :pre -fix ID group-ID temp/csld Tstart Tstop Tdamp seed :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -temp/csvr or temp/csld = style name of this fix command :l -Tstart,Tstop = desired temperature at start/end of run :l - Tstart can be a variable (see below) :pre -Tdamp = temperature damping parameter (time units) :l -seed = random number seed to use for white noise (positive integer) :l -:ule - -[Examples:] - -fix 1 all temp/csvr 300.0 300.0 100.0 54324 :pre -fix 1 all temp/csld 100.0 300.0 10.0 123321 :pre - -[Description:] - -Adjust the temperature with a canonical sampling thermostat that uses -global velocity rescaling with Hamiltonian dynamics ({temp/csvr}) -"(Bussi1)"_#Bussi1, or Langevin dynamics ({temp/csld}) -"(Bussi2)"_#Bussi2. In the case of {temp/csvr} the thermostat is -similar to the empirical Berendsen thermostat in -"temp/berendsen"_fix_temp_berendsen.html, but chooses the actual -scaling factor from a suitably chosen (gaussian) distribution rather -than having it determined from the time constant directly. In the case -of {temp/csld} the velocities are updated to a linear combination of -the current velocities with a gaussian distribution of velocities at -the desired temperature. Both thermostats are applied every timestep. - -The thermostat is applied to only the translational degrees of freedom -for the particles, which is an important consideration for finite-size -particles which have rotational degrees of freedom are being -thermostatted with these fixes. The translational degrees of freedom -can also have a bias velocity removed from them before thermostatting -takes place; see the description below. - -The desired temperature at each timestep is a ramped value during the -run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in -time units and determines how rapidly the temperature is relaxed. For -example, a value of 100.0 means to relax the temperature in a timespan -of (roughly) 100 time units (tau or fmsec or psec - see the -"units"_units.html command). - -{Tstart} can be specified as an equal-style "variable"_variable.html. -In this case, the {Tstop} setting is ignored. If the value is a -variable, it should be specified as v_name, where name is the variable -name. In this case, the variable will be evaluated each timestep, and -its value used to determine the target temperature. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent temperature. - -NOTE: Unlike the "fix nvt"_fix_nh.html command which performs -Nose/Hoover thermostatting AND time integration, these fixes do NOT -perform time integration. They only modify velocities to effect -thermostatting. Thus you must use a separate time integration fix, -like "fix nve"_fix_nve.html to actually update the positions of atoms -using the modified velocities. Likewise, these fixes should not -normally be used on atoms that also have their temperature controlled -by another fix - e.g. by "fix nvt"_fix_nh.html or "fix -langevin"_fix_langevin.html commands. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -These fixes compute a temperature each timestep. To do this, the fix -creates its own compute of style "temp", as if this command had been -issued: - -compute fix-ID_temp group-ID temp :pre - -See the "compute temp"_compute_temp.html command for details. Note -that the ID of the new compute is the fix-ID + underscore + "temp", -and the group for the new compute is the same as the fix group. - -Note that this is NOT the compute used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -"compute_modify"_compute_modify.html command or print this temperature -during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} will have no -effect on this fix. - -Like other fixes that perform thermostatting, these fixes can be used -with "compute commands"_compute.html that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the "fix_modify"_fix_modify.html command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about these fixes are written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {temp} option is supported by these -fixes. You can use it to assign a temperature "compute"_compute.html -you have defined to these fixes which will be used in its thermostatting -procedure, as described above. For consistency, the group used by -these fixes and by the compute should be the same. - -These fixes can ramp its target temperature over multiple runs, using -the {start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -These fixes are not invoked during "energy minimization"_minimize.html. - -These fixes compute a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the cumulative -energy change due to the fix. The scalar value calculated by this fix -is "extensive". - -[Restrictions:] - -These fixes are not compatible with "fix shake"_fix_shake.html. - -The fix can be used with dynamic groups as defined by the -"group"_group.html command. Likewise it can be used with groups to -which atoms are added or deleted over time, e.g. a deposition -simulation. However, the conservation properties of the thermostat -and barostat are defined for systems with a static set of atoms. You -may observe odd behavior if the atoms in a group vary dramatically -over time or the atom count becomes very small. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix nvt"_fix_nh.html, "fix -temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html, -"fix_modify"_fix_modify.html, "compute temp"_compute_temp.html, -"fix temp/berendsen"_fix_temp_berendsen.html - -[Default:] none - -:line - -:link(Bussi1) -[(Bussi1)] Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007) -:link(Bussi2) -[(Bussi2)] Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007) diff --git a/doc/txt/fix_temp_rescale.txt b/doc/txt/fix_temp_rescale.txt deleted file mode 100644 index 5640317f1c..0000000000 --- a/doc/txt/fix_temp_rescale.txt +++ /dev/null @@ -1,153 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix temp/rescale command :h3 - -[Syntax:] - -fix ID group-ID temp/rescale N Tstart Tstop window fraction :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -temp/rescale = style name of this fix command :l -N = perform rescaling every N steps :l -Tstart,Tstop = desired temperature at start/end of run (temperature units) :l - Tstart can be a variable (see below) :pre -window = only rescale if temperature is outside this window (temperature units) :l -fraction = rescale to target temperature by this fraction :l -:ule - -[Examples:] - -fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5 -fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 -fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 :pre - -[Description:] - -Reset the temperature of a group of atoms by explicitly rescaling -their velocities. - -The rescaling is applied to only the translational degrees of freedom -for the particles, which is an important consideration if finite-size -particles which have rotational degrees of freedom are being -thermostatted with this fix. The translational degrees of freedom can -also have a bias velocity removed from them before thermostatting -takes place; see the description below. - -Rescaling is performed every N timesteps. The target temperature is a -ramped value between the {Tstart} and {Tstop} temperatures at the -beginning and end of the run. - -NOTE: This thermostat will generate an error if the current -temperature is zero at the end of a timestep it is invoked on. It -cannot rescale a zero temperature. - -{Tstart} can be specified as an equal-style "variable"_variable.html. -In this case, the {Tstop} setting is ignored. If the value is a -variable, it should be specified as v_name, where name is the variable -name. In this case, the variable will be evaluated each timestep, and -its value used to determine the target temperature. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent temperature. - -Rescaling is only performed if the difference between the current and -desired temperatures is greater than the {window} value. The amount -of rescaling that is applied is a {fraction} (from 0.0 to 1.0) of the -difference between the actual and desired temperature. E.g. if -{fraction} = 1.0, the temperature is reset to exactly the desired -value. - -NOTE: Unlike the "fix nvt"_fix_nh.html command which performs -Nose/Hoover thermostatting AND time integration, this fix does NOT -perform time integration. It only modifies velocities to effect -thermostatting. Thus you must use a separate time integration fix, -like "fix nve"_fix_nve.html to actually update the positions of atoms -using the modified velocities. Likewise, this fix should not normally -be used on atoms that also have their temperature controlled by -another fix - e.g. by "fix nvt"_fix_nh.html or "fix -langevin"_fix_langevin.html commands. - -See the "Howto thermostat"_Howto_thermostat.html doc page for a -discussion of different ways to compute temperature and perform -thermostatting. - -This fix computes a temperature each timestep. To do this, the fix -creates its own compute of style "temp", as if one of this command had -been issued: - -compute fix-ID_temp group-ID temp :pre - -See the "compute temp"_compute_temp.html for details. Note that the -ID of the new compute is the fix-ID + underscore + "temp", and the -group for the new compute is the same as the fix group. - -Note that this is NOT the compute used by thermodynamic output (see -the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}. -This means you can change the attributes of this fix's temperature -(e.g. its degrees-of-freedom) via the -"compute_modify"_compute_modify.html command or print this temperature -during thermodynamic output via the "thermo_style -custom"_thermo_style.html command using the appropriate compute-ID. -It also means that changing attributes of {thermo_temp} will have no -effect on this fix. - -Like other fixes that perform thermostatting, this fix can be used -with "compute commands"_compute.html that calculate a temperature -after removing a "bias" from the atom velocities. E.g. removing the -center-of-mass velocity from a group of atoms or only calculating -temperature on the x-component of velocity or only calculating -temperature for atoms in a geometric region. This is not done by -default, but only if the "fix_modify"_fix_modify.html command is used -to assign a temperature compute to this fix that includes such a bias -term. See the doc pages for individual "compute -commands"_compute.html to determine which ones include a bias. In -this case, the thermostat works in the following manner: the current -temperature is calculated taking the bias into account, bias is -removed from each atom, thermostatting is performed on the remaining -thermal degrees of freedom, and the bias is added back in. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a temperature "compute"_compute.html -you have defined to this fix which will be used in its thermostatting -procedure, as described above. For consistency, the group used by -this fix and by the compute should be the same. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change implied by a velocity rescaling to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the cumulative -energy change due to this fix. The scalar value calculated by this -fix is "extensive". - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"fix langevin"_fix_langevin.html, "fix nvt"_fix_nh.html, -"fix_modify"_fix_modify.html - -[Default:] none diff --git a/doc/txt/fix_temp_rescale_eff.txt b/doc/txt/fix_temp_rescale_eff.txt deleted file mode 100644 index 83b360df85..0000000000 --- a/doc/txt/fix_temp_rescale_eff.txt +++ /dev/null @@ -1,76 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix temp/rescale/eff command :h3 - -[Syntax:] - -fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction :pre - -ID, group-ID are documented in "fix"_fix.html command -temp/rescale/eff = style name of this fix command -N = perform rescaling every N steps -Tstart,Tstop = desired temperature at start/end of run (temperature units) -window = only rescale if temperature is outside this window (temperature units) -fraction = rescale to target temperature by this fraction :ul - -[Examples:] - -fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0 :pre - -[Description:] - -Reset the temperature of a group of nuclei and electrons in the -"electron force field"_pair_eff.html model by explicitly rescaling -their velocities. - -The operation of this fix is exactly like that described by the "fix -temp/rescale"_fix_temp_rescale.html command, except that the rescaling -is also applied to the radial electron velocity for electron -particles. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {temp} option is supported by this -fix. You can use it to assign a temperature "compute"_compute.html -you have defined to this fix which will be used in its thermostatting -procedure, as described above. For consistency, the group used by -this fix and by the compute should be the same. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy change implied by a velocity rescaling to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the cumulative -energy change due to this fix. The scalar value calculated by this -fix is "extensive". - -This fix can ramp its target temperature over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the USER-EFF package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix langevin/eff"_fix_langevin_eff.html, "fix -nvt/eff"_fix_nh_eff.html, "fix_modify"_fix_modify.html, -"fix temp rescale"_fix_temp_rescale.html, - -[Default:] none diff --git a/doc/txt/fix_tfmc.txt b/doc/txt/fix_tfmc.txt deleted file mode 100644 index e14663bebd..0000000000 --- a/doc/txt/fix_tfmc.txt +++ /dev/null @@ -1,152 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix tfmc command :h3 - -[Syntax:] - -fix ID group-ID tfmc Delta Temp seed keyword value :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -tfmc = style name of this fix command :l -Delta = maximal displacement length (distance units) :l -Temp = imposed temperature of the system :l -seed = random number seed (positive integer) :l -zero or more keyword/arg pairs may be appended :l -keyword = {com} or {rot} :l - {com} args = xflag yflag zflag - xflag,yflag,zflag = 0/1 to exclude/include each dimension - {rot} args = none :pre -:ule - -[Examples:] - -fix 1 all tfmc 0.1 1000.0 159345 -fix 1 all tfmc 0.05 600.0 658943 com 1 1 0 -fix 1 all tfmc 0.1 750.0 387068 com 1 1 1 rot :pre - -[Description:] - -Perform uniform-acceptance force-bias Monte Carlo (fbMC) simulations, -using the time-stamped force-bias Monte Carlo (tfMC) algorithm -described in "(Mees)"_#Mees and "(Bal)"_#Bal. - -One successful use case of force-bias Monte Carlo methods is that they -can be used to extend the time scale of atomistic simulations, in -particular when long time scale relaxation effects must be considered; -some interesting examples are given in the review by "(Neyts)"_#Neyts. -An example of a typical use case would be the modelling of chemical -vapor deposition (CVD) processes on a surface, in which impacts by -gas-phase species can be performed using MD, but subsequent relaxation -of the surface is too slow to be done using MD only. Using tfMC can -allow for a much faster relaxation of the surface, so that higher -fluxes can be used, effectively extending the time scale of the -simulation. (Such an alternating simulation approach could be set up -using a "loop"_jump.html.) - -The initial version of tfMC algorithm in "(Mees)"_#Mees contained an -estimation of the effective time scale of such a simulation, but it -was later shown that the speed-up one can gain from a tfMC simulation -is system- and process-dependent, ranging from none to several orders -of magnitude. In general, solid-state processes such as -(re)crystallization or growth can be accelerated by up to two or three -orders of magnitude, whereas diffusion in the liquid phase is not -accelerated at all. The observed pseudodynamics when using the tfMC -method is not the actual dynamics one would obtain using MD, but the -relative importance of processes can match the actual relative -dynamics of the system quite well, provided {Delta} is chosen with -care. Thus, the system's equilibrium is reached faster than in MD, -along a path that is generally roughly similar to a typical MD -simulation (but not necessarily so). See "(Bal)"_#Bal for details. - -Each step, all atoms in the selected group are displaced using the -stochastic tfMC algorithm, which is designed to sample the canonical -(NVT) ensemble at the temperature {Temp}. Although tfMC is a Monte -Carlo algorithm and thus strictly speaking does not perform time -integration, it is similar in the sense that it uses the forces on all -atoms in order to update their positions. Therefore, it is implemented -as a time integration fix, and no other fixes of this type (such as -"fix nve"_fix_nve.html) should be used at the same time. Because -velocities do not play a role in this kind of Monte Carlo simulations, -instantaneous temperatures as calculated by "temperature -computes"_compute_temp.html or "thermodynamic -output"_thermo_style.html have no meaning: the only relevant -temperature is the sampling temperature {Temp}. Similarly, performing -tfMC simulations does not require setting a "timestep"_timestep.html -and the "simulated time"_thermo_style.html as calculated by LAMMPS is -meaningless. - -The critical parameter determining the success of a tfMC simulation is -{Delta}, the maximal displacement length of the lightest element in -the system: the larger it is, the longer the effective time scale of -the simulation will be (there is an approximately quadratic -dependence). However, {Delta} must also be chosen sufficiently small -in order to comply with detailed balance; in general values between 5 -and 10 % of the nearest neighbor distance are found to be a good -choice. For a more extensive discussion with specific examples, please -refer to "(Bal)"_#Bal, which also describes how the code calculates -element-specific maximal displacements from {Delta}, based on the -fourth root of their mass. - -Because of the uncorrelated movements of the atoms, the center-of-mass -of the fix group will not necessarily be stationary, just like its -orientation. When the {com} keyword is used, all atom positions will -be shifted (after every tfMC iteration) in order to fix the position -of the center-of-mass along the included directions, by setting the -corresponding flag to 1. The {rot} keyword does the same for the -rotational component of the tfMC displacements after every iteration. - -NOTE: the {com} and {rot} keywords should not be used if an external -force is acting on the specified fix group, along the included -directions. This can be either a true external force (e.g. through -"fix wall"_fix_wall.html) or forces due to the interaction with atoms -not included in the fix group. This is because in such cases, -translations or rotations of the fix group could be induced by these -external forces, and removing them will lead to a violation of -detailed balance. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the MC package. It is only enabled if LAMMPS was -built with that package. See the "Build package"_Build_package.html -doc page for more info. - -This fix is not compatible with "fix shake"_fix_shake.html. - -[Related commands:] - -"fix gcmc"_fix_gcmc.html, "fix nvt"_fix_nh.html - -[Default:] - -The option default is com = 0 0 0 - -:line - -:link(Bal) -[(Bal)] K. M Bal and E. C. Neyts, J. Chem. Phys. 141, 204104 (2014). - -:link(Mees) -[(Mees)] M. J. Mees, G. Pourtois, E. C. Neyts, B. J. Thijsse, and -A. Stesmans, Phys. Rev. B 85, 134301 (2012). - -:link(Neyts) -[(Neyts)] E. C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320 -(2013). diff --git a/doc/txt/fix_thermal_conductivity.txt b/doc/txt/fix_thermal_conductivity.txt deleted file mode 100644 index 2ab32b25f0..0000000000 --- a/doc/txt/fix_thermal_conductivity.txt +++ /dev/null @@ -1,163 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix thermal/conductivity command :h3 - -[Syntax:] - -fix ID group-ID thermal/conductivity N edim Nbin keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -thermal/conductivity = style name of this fix command :l -N = perform kinetic energy exchange every N steps :l -edim = {x} or {y} or {z} = direction of kinetic energy transfer :l -Nbin = # of layers in edim direction (must be even number) :l - -zero or more keyword/value pairs may be appended :l -keyword = {swap} :l - {swap} value = Nswap = number of swaps to perform every N steps :pre -:ule - -[Examples:] - -fix 1 all thermal/conductivity 100 z 20 -fix 1 all thermal/conductivity 50 z 20 swap 2 :pre - -[Description:] - -Use the Muller-Plathe algorithm described in "this -paper"_#Muller-Plathe1 to exchange kinetic energy between two particles -in different regions of the simulation box every N steps. This -induces a temperature gradient in the system. As described below this -enables the thermal conductivity of a material to be calculated. This -algorithm is sometimes called a reverse non-equilibrium MD (reverse -NEMD) approach to computing thermal conductivity. This is because the -usual NEMD approach is to impose a temperature gradient on the system -and measure the response as the resulting heat flux. In the -Muller-Plathe method, the heat flux is imposed, and the temperature -gradient is the system's response. - -See the "compute heat/flux"_compute_heat_flux.html command for details -on how to compute thermal conductivity in an alternate way, via the -Green-Kubo formalism. - -The simulation box is divided into {Nbin} layers in the {edim} -direction, where the layer 1 is at the low end of that dimension and -the layer {Nbin} is at the high end. Every N steps, Nswap pairs of -atoms are chosen in the following manner. Only atoms in the fix group -are considered. The hottest Nswap atoms in layer 1 are selected. -Similarly, the coldest Nswap atoms in the "middle" layer (see below) -are selected. The two sets of Nswap atoms are paired up and their -velocities are exchanged. This effectively swaps their kinetic -energies, assuming their masses are the same. If the masses are -different, an exchange of velocities relative to center of mass motion -of the 2 atoms is performed, to conserve kinetic energy. Over time, -this induces a temperature gradient in the system which can be -measured using commands such as the following, which writes the -temperature profile (assuming z = edim) to the file tmp.profile: - -compute ke all ke/atom -variable temp atom c_ke/1.5 -compute layers all chunk/atom bin/1d z lower 0.05 units reduced -fix 3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile :pre - -Note that by default, Nswap = 1, though this can be changed by the -optional {swap} keyword. Setting this parameter appropriately, in -conjunction with the swap rate N, allows the heat flux to be adjusted -across a wide range of values, and the kinetic energy to be exchanged -in large chunks or more smoothly. - -The "middle" layer for velocity swapping is defined as the {Nbin}/2 + -1 layer. Thus if {Nbin} = 20, the two swapping layers are 1 and 11. -This should lead to a symmetric temperature profile since the two -layers are separated by the same distance in both directions in a -periodic sense. This is why {Nbin} is restricted to being an even -number. - -As described below, the total kinetic energy transferred by these -swaps is computed by the fix and can be output. Dividing this -quantity by time and the cross-sectional area of the simulation box -yields a heat flux. The ratio of heat flux to the slope of the -temperature profile is proportional to the thermal conductivity of the -fluid, in appropriate units. See the "Muller-Plathe -paper"_#Muller-Plathe1 for details. - -NOTE: If your system is periodic in the direction of the heat flux, -then the flux is going in 2 directions. This means the effective heat -flux in one direction is reduced by a factor of 2. You will see this -in the equations for thermal conductivity (kappa) in the Muller-Plathe -paper. LAMMPS is simply tallying kinetic energy which does not -account for whether or not your system is periodic; you must use the -value appropriately to yield a kappa for your system. - -NOTE: After equilibration, if the temperature gradient you observe is -not linear, then you are likely swapping energy too frequently and are -not in a regime of linear response. In this case you cannot -accurately infer a thermal conductivity and should try increasing the -Nevery parameter. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the cumulative -kinetic energy transferred between the bottom and middle of the -simulation box (in the {edim} direction) is stored as a scalar -quantity by this fix. This quantity is zeroed when the fix is defined -and accumulates thereafter, once every N steps. The units of the -quantity are energy; see the "units"_units.html command for details. -The scalar value calculated by this fix is "intensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Swaps conserve both momentum and kinetic energy, even if the masses of -the swapped atoms are not equal. Thus you should not need to -thermostat the system. If you do use a thermostat, you may want to -apply it only to the non-swapped dimensions (other than {vdim}). - -LAMMPS does not check, but you should not use this fix to swap the -kinetic energy of atoms that are in constrained molecules, e.g. via -"fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is -because application of the constraints will alter the amount of -transferred momentum. You should, however, be able to use flexible -molecules. See the "Zhang paper"_#Zhang2 for a discussion and results -of this idea. - -When running a simulation with large, massive particles or molecules -in a background solvent, you may want to only exchange kinetic energy -between solvent particles. - -[Related commands:] - -"fix ehex"_fix_ehex.html, "fix heat"_fix_heat.html, "fix -ave/chunk"_fix_ave_chunk.html, "fix viscosity"_fix_viscosity.html, -"compute heat/flux"_compute_heat_flux.html - -[Default:] - -The option defaults are swap = 1. - -:line - -:link(Muller-Plathe1) -[(Muller-Plathe)] Muller-Plathe, J Chem Phys, 106, 6082 (1997). - -:link(Zhang2) -[(Zhang)] Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B, -109, 15060-15067 (2005). diff --git a/doc/txt/fix_ti_spring.txt b/doc/txt/fix_ti_spring.txt deleted file mode 100644 index d212579510..0000000000 --- a/doc/txt/fix_ti_spring.txt +++ /dev/null @@ -1,163 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix ti/spring command :h3 - -[Syntax:] - -fix ID group-ID ti/spring k t_s t_eq keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -ti/spring = style name of this fix command :l -k = spring constant (force/distance units) :l -t_eq = number of steps for the equilibration procedure :l -t_s = number of steps for the switching procedure :l -zero or more keyword/value pairs may be appended to args :l -keyword = {function} :l - {function} value = function-ID - function-ID = ID of the switching function (1 or 2) :pre -:ule - -[Example:] - -fix 1 all ti/spring 50.0 2000 1000 function 2 :pre - -[Description:] - -This fix allows you to compute the free energy of crystalline solids -by performing a nonequilibrium thermodynamic integration between the -solid of interest and an Einstein crystal. A detailed explanation of -how to use this command and choose its parameters for optimal -performance and accuracy is given in the paper by -"Freitas"_#Freitas1. The paper also presents a short summary of the -theory of nonequilibrium thermodynamic integration. - -The thermodynamic integration procedure is performed by rescaling the -force on each atom. Given an atomic configuration the force (F) on -each atom is given by - -:c,image(Eqs/fix_ti_spring_force.jpg) - -where F_solid is the force that acts on an atom due to an interatomic -potential ({e.g.} EAM potential), F_harm is the force due to the -Einstein crystal harmonic spring, and lambda is the coupling parameter -of the thermodynamic integration. An Einstein crystal is a solid where -each atom is attached to its equilibrium position by a harmonic spring -with spring constant {k}. With this fix a spring force is applied -independently to each atom in the group defined by the fix to tether -it to its initial position. The initial position of each atom is its -position at the time the fix command was issued. - -The fix acts as follows: during the first {t_eq} steps after the fix -is defined the value of lambda is zero. This is the period to -equilibrate the system in the lambda = 0 state. After this the value -of lambda changes dynamically during the simulation from 0 to 1 -according to the function defined using the keyword {function} -(described below), this switching from lambda from 0 to 1 is done in -{t_s} steps. Then comes the second equilibration period of {t_eq} to -equilibrate the system in the lambda = 1 state. After that, the -switching back to the lambda = 0 state is made using {t_s} timesteps -and following the same switching function. After this period the value -of lambda is kept equal to zero and the fix has no other effect on the -dynamics of the system. - -The processes described above is known as nonequilibrium thermodynamic -integration and is has been shown ("Freitas"_#Freitas1) to present a -much superior efficiency when compared to standard equilibrium -methods. The reason why the switching it is made in both directions -(potential to Einstein crystal and back) is to eliminate the -dissipated heat due to the nonequilibrium process. Further details -about nonequilibrium thermodynamic integration and its implementation -in LAMMPS is available in "Freitas"_#Freitas1. - -The {function} keyword allows the use of two different lambda -paths. Option {1} results in a constant rate of change of lambda with -time: - -:c,image(Eqs/fix_ti_spring_function_1.jpg) - -where tau is the scaled time variable {t/t_s}. The option {2} performs -the lambda switching at a rate defined by the following switching -function - -:c,image(Eqs/fix_ti_spring_function_2.jpg) - -This function has zero slope as lambda approaches its extreme values -(0 and 1), according to "de Koning"_#deKoning96 this results in -smaller fluctuations on the integral to be computed on the -thermodynamic integration. The use of option {2} is recommended since -it results in better accuracy and less dissipation without any -increase in computational resources cost. - -NOTE: As described in "Freitas"_#Freitas1, it is important to keep the -center-of-mass fixed during the thermodynamic integration. A nonzero -total velocity will result in divergences during the integration due -to the fact that the atoms are 'attached' to their equilibrium -positions by the Einstein crystal. Check the option {zero} of "fix -langevin"_fix_langevin.html and "velocity"_velocity.html. The use of -the Nose-Hoover thermostat ("fix nvt"_fix_nh.html) is {NOT} -recommended due to its well documented issues with the canonical -sampling of harmonic degrees of freedom (notice that the {chain} -option will {NOT} solve this problem). The Langevin thermostat ("fix -langevin"_fix_langevin.html) correctly thermostats the system and we -advise its usage with ti/spring command. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the original coordinates of tethered atoms to "binary -restart files"_restart.html, so that the spring effect will be the -same in a restarted simulation. See the "read -restart"_read_restart.html command for info on how to re-specify a fix -in an input script that reads a restart file, so that the operation of -the fix continues in an uninterrupted fashion. - -The "fix modify"_fix_modify.html {energy} option is supported by this -fix to add the energy stored in the per-atom springs to the system's -potential energy as part of "thermodynamic output"_thermo_style.html. - -This fix computes a global scalar and a global vector quantities which -can be accessed by various "output commands"_Howto_output.html. The -scalar is an energy which is the sum of the spring energy for each -atom, where the per-atom energy is 0.5 * k * r^2. The vector has 2 -positions, the first one is the coupling parameter lambda and the -second one is the time derivative of lambda. The scalar and vector -values calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -NOTE: If you want the per-atom spring energy to be included in the -total potential energy of the system (the quantity being minimized), -you MUST enable the "fix modify"_fix_modify.html {energy} option for -this fix. - -[Related commands:] - -"fix spring"_fix_spring.html, "fix adapt"_fix_adapt.html - -[Restrictions:] - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Default:] - -The keyword default is function = 1. - -:line - -:link(Freitas1) -[(Freitas)] Freitas, Asta, and de Koning, Computational Materials -Science, 112, 333 (2016). - -:link(deKoning96) -[(de Koning)] de Koning and Antonelli, Phys Rev E, 53, 465 (1996). diff --git a/doc/txt/fix_tmd.txt b/doc/txt/fix_tmd.txt deleted file mode 100644 index 73e95ba9fe..0000000000 --- a/doc/txt/fix_tmd.txt +++ /dev/null @@ -1,130 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix tmd command :h3 - -[Syntax:] - -fix ID group-ID tmd rho_final file1 N file2 :pre - -ID, group-ID are documented in "fix"_fix.html command -tmd = style name of this fix command -rho_final = desired value of rho at the end of the run (distance units) -file1 = filename to read target structure from -N = dump TMD statistics every this many timesteps, 0 = no dump -file2 = filename to write TMD statistics to (only needed if N > 0) :ul - -[Examples:] - -fix 1 all nve -fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file :pre - -[Description:] - -Perform targeted molecular dynamics (TMD) on a group of atoms. A -holonomic constraint is used to force the atoms to move towards (or -away from) the target configuration. The parameter "rho" is -monotonically decreased (or increased) from its initial value to -rho_final at the end of the run. - -Rho has distance units and is a measure of the root-mean-squared -distance (RMSD) between the current configuration of the atoms in the -group and the target coordinates listed in file1. Thus a value of -rho_final = 0.0 means move the atoms all the way to the final -structure during the course of the run. - -The target file1 can be ASCII text or a gzipped text file (detected by -a .gz suffix). The format of the target file1 is as follows: - -0.0 25.0 xlo xhi -0.0 25.0 ylo yhi -0.0 25.0 zlo zhi -125 24.97311 1.69005 23.46956 0 0 -1 -126 1.94691 2.79640 1.92799 1 0 0 -127 0.15906 3.46099 0.79121 1 0 0 -... :pre - -The first 3 lines may or may not be needed, depending on the format of -the atoms to follow. If image flags are included with the atoms, the -1st 3 lo/hi lines must appear in the file. If image flags are not -included, the 1st 3 lines should not appear. The 3 lines contain the -simulation box dimensions for the atom coordinates, in the same format -as in a LAMMPS data file (see the "read_data"_read_data.html command). - -The remaining lines each contain an atom ID and its target x,y,z -coordinates. The atom lines (all or none of them) can optionally be -followed by 3 integer values: nx,ny,nz. For periodic dimensions, they -specify which image of the box the atom is considered to be in, i.e. a -value of N (positive or negative) means add N times the box length to -the coordinate to get the true value. - -The atom lines can be listed in any order, but every atom in the group -must be listed in the file. Atoms not in the fix group may also be -listed; they will be ignored. - -TMD statistics are written to file2 every N timesteps, unless N is -specified as 0, which means no statistics. - -The atoms in the fix tmd group should be integrated (via a fix nve, -nvt, npt) along with other atoms in the system. - -Restarts can be used with a fix tmd command. For example, imagine a -10000 timestep run with a rho_initial = 11 and a rho_final = 1. If a -restart file was written after 2000 time steps, then the configuration -in the file would have a rho value of 9. A new 8000 time step run -could be performed with the same rho_final = 1 to complete the -conformational change at the same transition rate. Note that for -restarted runs, the name of the TMD statistics file should be changed -to prevent it being overwritten. - -For more information about TMD, see "(Schlitter1)"_#Schlitter1 and -"(Schlitter2)"_#Schlitter2. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. - -This fix can ramp its rho parameter over multiple runs, using the -{start} and {stop} keywords of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] - -All TMD fixes must be listed in the input script after all integrator -fixes (nve, nvt, npt) are applied. This ensures that atoms are moved -before their positions are corrected to comply with the constraint. - -Atoms that have a TMD fix applied should not be part of a group to -which a SHAKE fix is applied. This is because LAMMPS assumes there -are not multiple competing holonomic constraints applied to the same -atoms. - -To read gzipped target files, you must compile LAMMPS with the --DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html -doc page for details. - -[Related commands:] none - -[Default:] none - -:line - -:link(Schlitter1) -[(Schlitter1)] Schlitter, Swegat, Mulders, "Distance-type reaction -coordinates for modelling activated processes", J Molecular Modeling, -7, 171-177 (2001). - -:link(Schlitter2) -[(Schlitter2)] Schlitter and Klahn, "The free energy of a reaction -coordinate at multiple constraints: a concise formulation", Molecular -Physics, 101, 3439-3443 (2003). diff --git a/doc/txt/fix_ttm.txt b/doc/txt/fix_ttm.txt deleted file mode 100644 index 85407f2466..0000000000 --- a/doc/txt/fix_ttm.txt +++ /dev/null @@ -1,330 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix ttm command :h3 -fix ttm/mod command :h3 - -[Syntax:] - -fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile -fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -style = {ttm} or {ttm_mod} :l -seed = random number seed to use for white noise (positive integer) :l -remaining arguments for fix ttm: :l - C_e = electronic specific heat (energy/(electron*temperature) units) - rho_e = electronic density (electrons/volume units) - kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units) - gamma_p = friction coefficient due to electron-ion interactions (mass/time units) - gamma_s = friction coefficient due to electronic stopping (mass/time units) - v_0 = electronic stopping critical velocity (velocity units) - Nx = number of thermal solve grid points in the x-direction (positive integer) - Ny = number of thermal solve grid points in the y-direction (positive integer) - Nz = number of thermal solve grid points in the z-direction (positive integer) - T_infile = filename to read initial electronic temperature from - N = dump TTM temperatures every this many timesteps, 0 = no dump - T_outfile = filename to write TTM temperatures to (only needed if N > 0) :pre -remaining arguments for fix ttm/mod: :l - init_file = file with the parameters to TTM - Nx = number of thermal solve grid points in the x-direction (positive integer) - Ny = number of thermal solve grid points in the y-direction (positive integer) - Nz = number of thermal solve grid points in the z-direction (positive integer) - T_infile = filename to read initial electronic temperature from - N = dump TTM temperatures every this many timesteps, 0 = no dump - T_outfile = filename to write TTM temperatures to (only needed if N > 0) :pre -:ule - -[Examples:] - -fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out -fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out -fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out :pre - -[Description:] - -Use a two-temperature model (TTM) to represent heat transfer through -and between electronic and atomic subsystems. LAMMPS models the -atomic subsystem as usual with a molecular dynamics model and the -classical force field specified by the user, but the electronic -subsystem is modeled as a continuum, or a background "gas", on a -regular grid. Energy can be transferred spatially within the grid -representing the electrons. Energy can also be transferred between -the electronic and the atomic subsystems. The algorithm underlying -this fix was derived by D. M. Duffy and A. M. Rutherford and is -discussed in two J Physics: Condensed Matter papers: "(Duffy)"_#Duffy -and "(Rutherford)"_#Rutherford. They used this algorithm in cascade -simulations where a primary knock-on atom (PKA) was initialized with a -high velocity to simulate a radiation event. - -The description in this sub-section applies to both fix ttm and fix -ttm/mod. Fix ttm/mod adds options to account for external heat -sources (e.g. at a surface) and for specifying parameters that allow -the electronic heat capacity to depend strongly on electronic -temperature. It is more expensive computationally than fix ttm -because it treats the thermal diffusion equation as non-linear. More -details on fix ttm/mod are given below. - -Heat transfer between the electronic and atomic subsystems is carried -out via an inhomogeneous Langevin thermostat. This thermostat differs -from the regular Langevin thermostat ("fix -langevin"_fix_langevin.html) in three important ways. First, the -Langevin thermostat is applied uniformly to all atoms in the -user-specified group for a single target temperature, whereas the TTM -fix applies Langevin thermostatting locally to atoms within the -volumes represented by the user-specified grid points with a target -temperature specific to that grid point. Second, the Langevin -thermostat couples the temperature of the atoms to an infinite heat -reservoir, whereas the heat reservoir for fix TTM is finite and -represents the local electrons. Third, the TTM fix allows users to -specify not just one friction coefficient, but rather two independent -friction coefficients: one for the electron-ion interactions -({gamma_p}), and one for electron stopping ({gamma_s}). - -When the friction coefficient due to electron stopping, {gamma_s}, is -non-zero, electron stopping effects are included for atoms moving -faster than the electron stopping critical velocity, {v_0}. For -further details about this algorithm, see "(Duffy)"_#Duffy and -"(Rutherford)"_#Rutherford. - -Energy transport within the electronic subsystem is solved according -to the heat diffusion equation with added source terms for heat -transfer between the subsystems: - -:c,image(Eqs/fix_ttm.jpg) - -where C_e is the specific heat, rho_e is the density, kappa_e is the -thermal conductivity, T is temperature, the "e" and "a" subscripts -represent electronic and atomic subsystems respectively, g_p is the -coupling constant for the electron-ion interaction, and g_s is the -electron stopping coupling parameter. C_e, rho_e, and kappa_e are -specified as parameters to the fix. The other quantities are derived. -The form of the heat diffusion equation used here is almost the same -as that in equation 6 of "(Duffy)"_#Duffy, with the exception that the -electronic density is explicitly represented, rather than being part -of the specific heat parameter. - -Currently, fix ttm assumes that none of the user-supplied parameters -will vary with temperature. Note that "(Duffy)"_#Duffy used a tanh() -functional form for the temperature dependence of the electronic -specific heat, but ignored temperature dependencies of any of the -other parameters. See more discussion below for fix ttm/mod. - -These fixes require use of periodic boundary conditions and a 3D -simulation. Periodic boundary conditions are also used in the heat -equation solve for the electronic subsystem. This varies from the -approach of "(Rutherford)"_#Rutherford where the atomic subsystem was -embedded within a larger continuum representation of the electronic -subsystem. - -The initial electronic temperature input file, {T_infile}, is a text -file LAMMPS reads in with no header and with four numeric columns -(ix,iy,iz,Temp) and with a number of rows equal to the number of -user-specified grid points (Nx by Ny by Nz). The ix,iy,iz are node -indices from 0 to nxnodes-1, etc. For example, the initial electronic -temperatures on a 1 by 2 by 3 grid could be specified in a {T_infile} -as follows: - -0 0 0 1.0 -0 0 1 1.0 -0 0 2 1.0 -0 1 0 2.0 -0 1 1 2.0 -0 1 2 2.0 :pre - -where the electronic temperatures along the y=0 plane have been set to -1.0, and the electronic temperatures along the y=1 plane have been set -to 2.0. The order of lines in this file is no important. If all the -nodal values are not specified, LAMMPS will generate an error. - -The temperature output file, {T_oufile}, is created and written by -this fix. Temperatures for both the electronic and atomic subsystems -at every node and every N timesteps are output. If N is specified as -zero, no output is generated, and no output filename is needed. The -format of the output is as follows. One long line is written every -output timestep. The timestep itself is given in the first column. -The next Nx*Ny*Nz columns contain the temperatures for the atomic -subsystem, and the final Nx*Ny*Nz columns contain the temperatures for -the electronic subsystem. The ordering of the Nx*Ny*Nz columns is -with the z index varying fastest, y the next fastest, and x the -slowest. - -These fixes do not change the coordinates of their atoms; they only -scales their velocities. Thus a time integration fix (e.g. "fix -nve"_fix_nve.html) should still be used to time integrate the affected -atoms. The fixes should not normally be used on atoms that have their -temperature controlled by another fix - e.g. "fix nvt"_fix_nh.html or -"fix langevin"_fix_langevin.html. - -NOTE: The current implementations of these fixes create a copy of the -electron grid that overlays the entire simulation domain, for each -processor. Values on the grid are summed across all processors. Thus -you should insure that this grid is not too large, else your -simulation could incur high memory and communication costs. - -:line - -[Additional details for fix ttm/mod] - -Fix ttm/mod uses the heat diffusion equation with possible external -heat sources (e.g. laser heating in ablation simulations): - -:c,image(Eqs/fix_ttm_mod.jpg) - -where theta is the Heaviside step function, I_0 is the (absorbed) -laser pulse intensity for ablation simulations, l_skin is the depth -of skin-layer, and all other designations have the same meaning as in -the former equation. The duration of the pulse is set by the parameter -{tau} in the {init_file}. - -Fix ttm/mod also allows users to specify the dependencies of C_e and -kappa_e on the electronic temperature. The specific heat is expressed -as - -:c,image(Eqs/fix_ttm_ce.jpg) - -where {X} = T_e/1000, and the thermal conductivity is defined as -kappa_e = D_e*rho_e*C_e, where D_e is the thermal diffusion -coefficient. - -Electronic pressure effects are included in the TTM model to account -for the blast force acting on ions because of electronic pressure -gradient (see "(Chen)"_Chen, "(Norman)"_#Norman). The total force -acting on an ion is: - -:c,image(Eqs/fix_ttm_blast.jpg) - -where F_langevin is a force from Langevin thermostat simulating -electron-phonon coupling, and nabla P_e/n_ion is the electron blast -force. - -The electronic pressure is taken to be P_e = B*rho_e*C_e*T_e - -The current fix ttm/mod implementation allows TTM simulations with a -vacuum. The vacuum region is defined as the grid cells with zero -electronic temperature. The numerical scheme does not allow energy -exchange with such cells. Since the material can expand to previously -unoccupied region in some simulations, the vacuum border can be -allowed to move. It is controlled by the {surface_movement} parameter -in the {init_file}. If it is set to 1, then "vacuum" cells can be -changed to "electron-filled" cells with the temperature {T_e_min} if -atoms move into them (currently only implemented for the case of -1-dimensional motion of flat surface normal to the X axis). The -initial borders of vacuum can be set in the {init_file} via {lsurface} -and {rsurface} parameters. In this case, electronic pressure gradient -is calculated as - -:c,image(Eqs/fix_ttm_blast1.jpg) - -where lambda is the electron mean free path (see "(Norman)"_#Norman, -"(Pisarev)"_#Pisarev) - -The fix ttm/mod parameter file {init_file} has the following syntax/ -Every line with the odd number is considered as a comment and -ignored. The lines with the even numbers are treated as follows: - -a_0, energy/(temperature*electron) units -a_1, energy/(temperature^2*electron) units -a_2, energy/(temperature^3*electron) units -a_3, energy/(temperature^4*electron) units -a_4, energy/(temperature^5*electron) units -C_0, energy/(temperature*electron) units -A, 1/temperature units -rho_e, electrons/volume units -D_e, length^2/time units -gamma_p, mass/time units -gamma_s, mass/time units -v_0, length/time units -I_0, energy/(time*length^2) units -lsurface, electron grid units (positive integer) -rsurface, electron grid units (positive integer) -l_skin, length units -tau, time units -B, dimensionless -lambda, length units -n_ion, ions/volume units -surface_movement: 0 to disable tracking of surface motion, 1 to enable -T_e_min, temperature units :pre - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -These fixes write the state of the electronic subsystem and the energy -exchange between the subsystems to "binary restart -files"_restart.html. See the "read_restart"_read_restart.html command -for info on how to re-specify a fix in an input script that reads a -restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -Because the state of the random number generator is not saved in the -restart files, this means you cannot do "exact" restarts with this -fix, where the simulation continues on the same as if no restart had -taken place. However, in a statistical sense, a restarted simulation -should produce the same behavior. - -None of the "fix_modify"_fix_modify.html options are relevant to these -fixes. - -Both fixes compute 2 output quantities stored in a vector of length 2, -which can be accessed by various "output commands"_Howto_output.html. -The first quantity is the total energy of the electronic -subsystem. The second quantity is the energy transferred from the -electronic to the atomic subsystem on that timestep. Note that the -velocity verlet integrator applies the fix ttm forces to the atomic -subsystem as two half-step velocity updates: one on the current -timestep and one on the subsequent timestep. Consequently, the change -in the atomic subsystem energy is lagged by half a timestep relative -to the change in the electronic subsystem energy. As a result of this, -users may notice slight fluctuations in the sum of the atomic and -electronic subsystem energies reported at the end of the timestep. - -The vector values calculated are "extensive". - -No parameter of the fixes can be used with the {start/stop} keywords -of the "run"_run.html command. The fixes are not invoked during -"energy minimization"_minimize.html. - -[Restrictions:] - -Fix {ttm} is part of the MISC package. It is only enabled if LAMMPS -was built with that package. Fix {ttm/mod} is part of the USER-MISC -package. It is only enabled if LAMMPS was built with that package. -See the "Build package"_Build_package.html doc page for more info. - -These fixes can only be used for 3d simulations and orthogonal -simulation boxes. You must also use periodic -"boundary"_boundary.html conditions. - -[Related commands:] - -"fix langevin"_fix_langevin.html, "fix dt/reset"_fix_dt_reset.html - -[Default:] none - -:line - -:link(Duffy) -[(Duffy)] D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19, -016207-016218 (2007). - -:link(Rutherford) -[(Rutherford)] A M Rutherford and D M Duffy, J. Phys.: -Condens. Matter, 19, 496201-496210 (2007). - -:link(Chen) -[(Chen)] J Chen, D Tzou and J Beraun, Int. J. Heat -Mass Transfer, 49, 307-316 (2006). - -:link(Norman) -[(Norman)] G E Norman, S V Starikov, V V Stegailov et al., Contrib. -Plasma Phys., 53, 129-139 (2013). - -:link(Pisarev) -[(Pisarev)] V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26, -475401 (2014). diff --git a/doc/txt/fix_tune_kspace.txt b/doc/txt/fix_tune_kspace.txt deleted file mode 100644 index f5173b4cae..0000000000 --- a/doc/txt/fix_tune_kspace.txt +++ /dev/null @@ -1,103 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix tune/kspace command :h3 - -[Syntax:] - -fix ID group-ID tune/kspace N :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -tune/kspace = style name of this fix command :l -N = invoke this fix every N steps :l -:ule - -[Examples:] - -fix 2 all tune/kspace 100 :pre - -[Description:] - -This fix tests each kspace style (Ewald, PPPM, and MSM), and -automatically selects the fastest style to use for the remainder -of the run. If the fastest style is Ewald or PPPM, the fix also -adjusts the Coulombic cutoff towards optimal speed. Future versions -of this fix will automatically select other kspace parameters -to use for maximum simulation speed. The kspace parameters may -include the style, cutoff, grid points in each direction, order, -Ewald parameter, MSM parallelization cut-point, MPI tasks to use, etc. - -The rationale for this fix is to provide the user with -as-fast-as-possible simulations that include long-range electrostatics -(kspace) while meeting the user-prescribed accuracy requirement. A -simple heuristic could never capture the optimal combination of -parameters for every possible run-time scenario. But by performing -short tests of various kspace parameter sets, this fix allows -parameters to be tailored specifically to the user's machine, MPI -ranks, use of threading or accelerators, the simulated system, and the -simulation details. In addition, it is possible that parameters could -be evolved with the simulation on-the-fly, which is useful for systems -that are dynamically evolving (e.g. changes in box size/shape or -number of particles). - -When this fix is invoked, LAMMPS will perform short timed tests of -various parameter sets to determine the optimal parameters. Tests are -performed on-the-fly, with a new test initialized every N steps. N should -be chosen large enough so that adequate CPU time lapses between tests, -thereby providing statistically significant timings. But N should not be -chosen to be so large that an unfortunate parameter set test takes an -inordinate amount of wall time to complete. An N of 100 for most problems -seems reasonable. Once an optimal parameter set is found, that set is -used for the remainder of the run. - -This fix uses heuristics to guide it's selection of parameter sets to test, -but the actual timed results will be used to decide which set to use in the -simulation. - -It is not necessary to discard trajectories produced using sub-optimal -parameter sets, or a mix of various parameter sets, since the user-prescribed -accuracy will have been maintained throughout. However, some users may prefer -to use this fix only to discover the optimal parameter set for a given setup -that can then be used on subsequent production runs. - -This fix starts with kspace parameters that are set by the user with the -"kspace_style"_kspace_style.html and "kspace_modify"_kspace_modify.html -commands. The prescribed accuracy will be maintained by this fix throughout -the simulation. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the KSPACE package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Do not set "neigh_modify once yes" or else this fix will never be -called. Reneighboring is required. - -This fix is not compatible with a hybrid pair style, long-range dispersion, -TIP4P water support, or long-range point dipole support. - -[Related commands:] - -"kspace_style"_kspace_style.html, "boundary"_boundary.html -"kspace_modify"_kspace_modify.html, "pair_style -lj/cut/coul/long"_pair_lj.html, "pair_style -lj/charmm/coul/long"_pair_charmm.html, "pair_style -lj/long"_pair_lj_long.html, "pair_style -lj/long/coul/long"_pair_lj_long.html, -"pair_style buck/coul/long"_pair_buck.html - -[Default:] - diff --git a/doc/txt/fix_vector.txt b/doc/txt/fix_vector.txt deleted file mode 100644 index e1bfbe5738..0000000000 --- a/doc/txt/fix_vector.txt +++ /dev/null @@ -1,162 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix vector command :h3 - -[Syntax:] - -fix ID group-ID vector Nevery value1 value2 ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -vector = style name of this fix command :l -Nevery = use input values every this many timesteps :l -one or more input values can be listed :l -value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l - c_ID = global scalar calculated by a compute with ID - c_ID\[I\] = Ith component of global vector calculated by a compute with ID - f_ID = global scalar calculated by a fix with ID - f_ID\[I\] = Ith component of global vector calculated by a fix with ID - v_name = value calculated by an equal-style variable with name - v_name\[I\] = Ith component of vector-style variable with name :pre -:ule - -[Examples:] - -fix 1 all vector 100 c_myTemp -fix 1 all vector 5 c_myTemp v_integral :pre - -[Description:] - -Use one or more global values as inputs every few timesteps, and -simply store them. For a single specified value, the values are -stored as a global vector of growing length. For multiple specified -values, they are stored as rows in a global array, whose number of -rows is growing. The resulting vector or array can be used by other -"output commands"_Howto_output.html. - -One way to to use this command is to accumulate a vector that is -time-integrated using the "variable trap()"_variable.html function. -For example the velocity auto-correlation function (VACF) can be -time-integrated, to yield a diffusion coefficient, as follows: - -compute 2 all vacf -fix 5 all vector 1 c_2\[4\] -variable diff equal dt*trap(f_5) -thermo_style custom step v_diff :pre - -The group specified with this command is ignored. However, note that -specified values may represent calculations performed by computes and -fixes which store their own "group" definitions. - -Each listed value can be the result of a "compute"_compute.html or -"fix"_fix.html or the evaluation of an equal-style or vector-style -"variable"_variable.html. In each case, the compute, fix, or variable -must produce a global quantity, not a per-atom or local quantity. And -the global quantity must be a scalar, not a vector or array. - -"Computes"_compute.html that produce global quantities are those which -do not have the word {atom} in their style name. Only a few -"fixes"_fix.html produce global quantities. See the doc pages for -individual fixes for info on which ones produce such values. -"Variables"_variable.html of style {equal} or {vector} are the only -ones that can be used with this fix. Variables of style {atom} cannot -be used, since they produce per-atom values. - -The {Nevery} argument specifies on what timesteps the input values -will be used in order to be stored. Only timesteps that are a -multiple of {Nevery}, including timestep 0, will contribute values. - -Note that if you perform multiple runs, using the "pre no" option of -the "run"_run.html command to avoid initialization on subsequent runs, -then you need to use the {stop} keyword with the first "run"_run.html -command with a timestep value that encompasses all the runs. This is -so that the vector or array stored by this fix can be allocated to a -sufficient size. - -:line - -If a value begins with "c_", a compute ID must follow which has been -previously defined in the input script. If no bracketed term is -appended, the global scalar calculated by the compute is used. If a -bracketed term is appended, the Ith element of the global vector -calculated by the compute is used. - -Note that there is a "compute reduce"_compute_reduce.html command -which can sum per-atom quantities into a global scalar or vector which -can thus be accessed by fix vector. Or it can be a compute defined -not in your input script, but by "thermodynamic -output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html -or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for -these commands which give the IDs of these computes. Users can also -write code for their own compute styles and "add them to -LAMMPS"_Modify.html. - -If a value begins with "f_", a fix ID must follow which has been -previously defined in the input script. If no bracketed term is -appended, the global scalar calculated by the fix is used. If a -bracketed term is appended, the Ith element of the global vector -calculated by the fix is used. - -Note that some fixes only produce their values on certain timesteps, -which must be compatible with {Nevery}, else an error will result. -Users can also write code for their own fix styles and "add them to -LAMMPS"_Modify.html. - -If a value begins with "v_", a variable name must follow which has -been previously defined in the input script. An equal-style or -vector-style variable can be referenced; the latter requires a -bracketed term to specify the Ith element of the vector calculated by -the variable. See the "variable"_variable.html command for details. -Note that variables of style {equal} and {vector} define a formula -which can reference individual atom properties or thermodynamic -keywords, or they can invoke other computes, fixes, or variables when -they are evaluated, so this is a very general means of specifying -quantities to be stored by fix vector. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix produces a global vector or global array which can be -accessed by various "output commands"_Howto_output.html. The values -can only be accessed on timesteps that are multiples of {Nevery}. - -A vector is produced if only a single input value is specified. -An array is produced if multiple input values are specified. -The length of the vector or the number of rows in the array grows -by 1 every {Nevery} timesteps. - -If the fix produces a vector, then the entire vector will be either -"intensive" or "extensive", depending on whether the values stored in -the vector are "intensive" or "extensive". If the fix produces an -array, then all elements in the array must be the same, either -"intensive" or "extensive". If a compute or fix provides the value -stored, then the compute or fix determines whether the value is -intensive or extensive; see the doc page for that compute or fix for -further info. Values produced by a variable are treated as intensive. - -This fix can allocate storage for stored values accumulated over -multiple runs, using the {start} and {stop} keywords of the -"run"_run.html command. See the "run"_run.html command for details of -how to do this. If using the "run pre no"_run.html command option, -this is required to allow the fix to allocate sufficient storage for -stored values. - -This fix is not invoked during "energy minimization"_minimize.html. - -[Restrictions:] none - -[Related commands:] - -"compute"_compute.html, "variable"_variable.html - -[Default:] none diff --git a/doc/txt/fix_viscosity.txt b/doc/txt/fix_viscosity.txt deleted file mode 100644 index d86b13d055..0000000000 --- a/doc/txt/fix_viscosity.txt +++ /dev/null @@ -1,168 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix viscosity command :h3 - -[Syntax:] - -fix ID group-ID viscosity N vdim pdim Nbin keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -viscosity = style name of this fix command :l -N = perform momentum exchange every N steps :l -vdim = {x} or {y} or {z} = which momentum component to exchange :l -pdim = {x} or {y} or {z} = direction of momentum transfer :l -Nbin = # of layers in pdim direction (must be even number) :l - -zero or more keyword/value pairs may be appended :l -keyword = {swap} or {target} :l - {swap} value = Nswap = number of swaps to perform every N steps - {vtarget} value = V or INF = target velocity of swap partners (velocity units) :pre -:ule - -[Examples:] - -fix 1 all viscosity 100 x z 20 -fix 1 all viscosity 50 x z 20 swap 2 vtarget 1.5 :pre - -[Description:] - -Use the Muller-Plathe algorithm described in "this -paper"_#Muller-Plathe2 to exchange momenta between two particles in -different regions of the simulation box every N steps. This induces a -shear velocity profile in the system. As described below this enables -a viscosity of the fluid to be calculated. This algorithm is -sometimes called a reverse non-equilibrium MD (reverse NEMD) approach -to computing viscosity. This is because the usual NEMD approach is to -impose a shear velocity profile on the system and measure the response -via an off-diagonal component of the stress tensor, which is -proportional to the momentum flux. In the Muller-Plathe method, the -momentum flux is imposed, and the shear velocity profile is the -system's response. - -The simulation box is divided into {Nbin} layers in the {pdim} -direction, where the layer 1 is at the low end of that dimension and -the layer {Nbin} is at the high end. Every N steps, Nswap pairs of -atoms are chosen in the following manner. Only atoms in the fix group -are considered. Nswap atoms in layer 1 with positive velocity -components in the {vdim} direction closest to the target value {V} are -selected. Similarly, Nswap atoms in the "middle" layer (see below) with -negative velocity components in the {vdim} direction closest to the -negative of the target value {V} are selected. The two sets of Nswap -atoms are paired up and their {vdim} momenta components are swapped -within each pair. This resets their velocities, typically in opposite -directions. Over time, this induces a shear velocity profile in the -system which can be measured using commands such as the following, -which writes the profile to the file tmp.profile: - -compute layers all chunk/atom bin/1d z lower 0.05 units reduced -fix f1 all ave/chunk 100 10 1000 layers vx file tmp.profile :pre - -Note that by default, Nswap = 1 and vtarget = INF, though this can be -changed by the optional {swap} and {vtarget} keywords. When vtarget = -INF, one or more atoms with the most positive and negative velocity -components are selected. Setting these parameters appropriately, in -conjunction with the swap rate N, allows the momentum flux rate to be -adjusted across a wide range of values, and the momenta to be -exchanged in large chunks or more smoothly. - -The "middle" layer for momenta swapping is defined as the {Nbin}/2 + 1 -layer. Thus if {Nbin} = 20, the two swapping layers are 1 and 11. -This should lead to a symmetric velocity profile since the two layers -are separated by the same distance in both directions in a periodic -sense. This is why {Nbin} is restricted to being an even number. - -As described below, the total momentum transferred by these velocity -swaps is computed by the fix and can be output. Dividing this -quantity by time and the cross-sectional area of the simulation box -yields a momentum flux. The ratio of momentum flux to the slope of -the shear velocity profile is proportional to the viscosity of the -fluid, in appropriate units. See the "Muller-Plathe -paper"_#Muller-Plathe2 for details. - -NOTE: If your system is periodic in the direction of the momentum -flux, then the flux is going in 2 directions. This means the -effective momentum flux in one direction is reduced by a factor of 2. -You will see this in the equations for viscosity in the Muller-Plathe -paper. LAMMPS is simply tallying momentum which does not account for -whether or not your system is periodic; you must use the value -appropriately to yield a viscosity for your system. - -NOTE: After equilibration, if the velocity profile you observe is not -linear, then you are likely swapping momentum too frequently and are -not in a regime of linear response. In this case you cannot -accurately infer a viscosity and should try increasing the Nevery -parameter. - -An alternative method for calculating a viscosity is to run a NEMD -simulation, as described on the "Howto nemd"_Howto_nemd.html doc page. -NEMD simulations deform the simulation box via the "fix -deform"_fix_deform.html command. Thus they cannot be run on a charged -system using a "PPPM solver"_kspace_style.html since PPPM does not -currently support non-orthogonal boxes. Using fix viscosity keeps the -box orthogonal; thus it does not suffer from this limitation. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global scalar which can be accessed by various -"output commands"_Howto_output.html. The scalar is the cumulative -momentum transferred between the bottom and middle of the simulation -box (in the {pdim} direction) is stored as a scalar quantity by this -fix. This quantity is zeroed when the fix is defined and accumulates -thereafter, once every N steps. The units of the quantity are -momentum = mass*velocity. The scalar value calculated by this fix is -"intensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Swaps conserve both momentum and kinetic energy, even if the masses of -the swapped atoms are not equal. Thus you should not need to -thermostat the system. If you do use a thermostat, you may want to -apply it only to the non-swapped dimensions (other than {vdim}). - -LAMMPS does not check, but you should not use this fix to swap -velocities of atoms that are in constrained molecules, e.g. via "fix -shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because -application of the constraints will alter the amount of transferred -momentum. You should, however, be able to use flexible molecules. -See the "Maginn paper"_#Maginn for an example of using this algorithm -in a computation of alcohol molecule properties. - -When running a simulation with large, massive particles or molecules -in a background solvent, you may want to only exchange momenta between -solvent particles. - -[Related commands:] - -"fix ave/chunk"_fix_ave_chunk.html, "fix -thermal/conductivity"_fix_thermal_conductivity.html - -[Default:] - -The option defaults are swap = 1 and vtarget = INF. - -:line - -:link(Muller-Plathe2) -[(Muller-Plathe)] Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999). - -:link(Maginn) -[(Maginn)] Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, -260, 218-231 (2007). diff --git a/doc/txt/fix_viscous.txt b/doc/txt/fix_viscous.txt deleted file mode 100644 index c5a3ede0b2..0000000000 --- a/doc/txt/fix_viscous.txt +++ /dev/null @@ -1,105 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix viscous command :h3 - -[Syntax:] - -fix ID group-ID viscous gamma keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -viscous = style name of this fix command :l -gamma = damping coefficient (force/velocity units) :l -zero or more keyword/value pairs may be appended :l -keyword = {scale} - {scale} values = type ratio - type = atom type (1-N) - ratio = factor to scale the damping coefficient by :pre -:ule - -[Examples:] - -fix 1 flow viscous 0.1 -fix 1 damp viscous 0.5 scale 3 2.5 :pre - -[Description:] - -Add a viscous damping force to atoms in the group that is proportional -to the velocity of the atom. The added force can be thought of as a -frictional interaction with implicit solvent, i.e. the no-slip Stokes -drag on a spherical particle. In granular simulations this can be -useful for draining the kinetic energy from the system in a controlled -fashion. If used without additional thermostatting (to add kinetic -energy to the system), it has the effect of slowly (or rapidly) -freezing the system; hence it can also be used as a simple energy -minimization technique. - -The damping force F is given by F = - gamma * velocity. The larger -the coefficient, the faster the kinetic energy is reduced. If the -optional keyword {scale} is used, gamma can scaled up or down by the -specified factor for atoms of that type. It can be used multiple -times to adjust gamma for several atom types. - -NOTE: You should specify gamma in force/velocity units. This is not -the same as mass/time units, at least for some of the LAMMPS -"units"_units.html options like "real" or "metal" that are not -self-consistent. - -In a Brownian dynamics context, gamma = Kb T / D, where Kb = -Boltzmann's constant, T = temperature, and D = particle diffusion -coefficient. D can be written as Kb T / (3 pi eta d), where eta = -dynamic viscosity of the frictional fluid and d = diameter of -particle. This means gamma = 3 pi eta d, and thus is proportional to -the viscosity of the fluid and the particle diameter. - -In the current implementation, rather than have the user specify a -viscosity, gamma is specified directly in force/velocity units. If -needed, gamma can be adjusted for atoms of different sizes -(i.e. sigma) by using the {scale} keyword. - -Note that Brownian dynamics models also typically include a randomized -force term to thermostat the system at a chosen temperature. The "fix -langevin"_fix_langevin.html command does this. It has the same -viscous damping term as fix viscous and adds a random force to each -atom. The random force term is proportional to the sqrt of the chosen -thermostatting temperature. Thus if you use fix langevin with a -target T = 0, its random force term is zero, and you are essentially -performing the same operation as fix viscous. Also note that the -gamma of fix viscous is related to the damping parameter of "fix -langevin"_fix_langevin.html, however the former is specified in units -of force/velocity and the latter in units of time, so that it can more -easily be used as a thermostat. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is modifying forces. Default is the outermost level. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. This fix should only -be used with damped dynamics minimizers that allow for -non-conservative forces. See the "min_style"_min_style.html command -for details. - -[Restrictions:] none - -[Related commands:] - -"fix langevin"_fix_langevin.html - -[Default:] none diff --git a/doc/txt/fix_wall.txt b/doc/txt/fix_wall.txt deleted file mode 100644 index 7868bacf04..0000000000 --- a/doc/txt/fix_wall.txt +++ /dev/null @@ -1,352 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix wall/lj93 command :h3 -fix wall/lj93/kk command :h3 -fix wall/lj126 command :h3 -fix wall/lj1043 command :h3 -fix wall/colloid command :h3 -fix wall/harmonic command :h3 -fix wall/morse command :h3 - -[Syntax:] - -fix ID group-ID style face args ... keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -style = {wall/lj93} or {wall/lj126} or {wall/lj1043} or {wall/colloid} or {wall/harmonic} or {wall/morse} :l -one or more face/arg pairs may be appended :l -face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l - args for styles {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} :l - args = coord epsilon sigma cutoff - coord = position of wall = EDGE or constant or variable - EDGE = current lo or hi edge of simulation box - constant = number like 0.0 or -30.0 (distance units) - variable = "equal-style variable"_variable.html like v_x or v_wiggle - epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) - epsilon can be a variable (see below) - sigma = size factor for wall-particle interaction (distance units) - sigma can be a variable (see below) - cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre - args for style {morse} :l - args = coord D_0 alpha r_0 cutoff - coord = position of wall = EDGE or constant or variable - EDGE = current lo or hi edge of simulation box - constant = number like 0.0 or -30.0 (distance units) - variable = "equal-style variable"_variable.html like v_x or v_wiggle - D_0 = depth of the potential (energy units) - D_0 can be a variable (see below) - alpha = width factor for wall-particle interaction (1/distance units) - alpha can be a variable (see below) - r_0 = distance of the potential minimum from the face of region (distance units) - r_0 can be a variable (see below) - cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre -zero or more keyword/value pairs may be appended :l -keyword = {units} or {fld} :l - {units} value = {lattice} or {box} - {lattice} = the wall position is defined in lattice units - {box} = the wall position is defined in simulation box units - {fld} value = {yes} or {no} - {yes} = invoke the wall constraint to be compatible with implicit FLD - {no} = invoke the wall constraint in the normal way - {pbc} value = {yes} or {no} - {yes} = allow periodic boundary in a wall dimension - {no} = require non-perioidic boundaries in any wall dimension :pre -:ule - -[Examples:] - -fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box -fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5 -fix wallhi all wall/morse xhi EDGE 1.0 1.0 1.0 2.5 units box -fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5 -fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 :pre - -[Description:] - -Bound the simulation domain on one or more of its faces with a flat -wall that interacts with the atoms in the group by generating a force -on the atom in a direction perpendicular to the wall. The energy of -wall-particle interactions depends on the style. - -For style {wall/lj93}, the energy E is given by the 9/3 potential: - -:c,image(Eqs/fix_wall_lj93.jpg) - -For style {wall/lj126}, the energy E is given by the 12/6 potential: - -:c,image(Eqs/pair_lj.jpg) - -For style {wall/lj1043}, the energy E is given by the 10/4/3 potential: - -:c,image(Eqs/fix_wall_lj1043.jpg) - -For style {wall/colloid}, the energy E is given by an integrated form -of the "pair_style colloid"_pair_colloid.html potential: - -:c,image(Eqs/fix_wall_colloid.jpg) - -For style {wall/harmonic}, the energy E is given by a harmonic spring -potential: - -:c,image(Eqs/fix_wall_harmonic.jpg) - -For style {wall/morse}, the energy E is given by a Morse potential: - -:c,image(Eqs/pair_morse.jpg) - -In all cases, {r} is the distance from the particle to the wall at -position {coord}, and Rc is the {cutoff} distance at which the -particle and wall no longer interact. The energy of the wall -potential is shifted so that the wall-particle interaction energy is -0.0 at the cutoff distance. - -Up to 6 walls or faces can be specified in a single command: {xlo}, -{xhi}, {ylo}, {yhi}, {zlo}, {zhi}. A {lo} face interacts with -particles near the lower side of the simulation box in that dimension. -A {hi} face interacts with particles near the upper side of the -simulation box in that dimension. - -The position of each wall can be specified in one of 3 ways: as the -EDGE of the simulation box, as a constant value, or as a variable. If -EDGE is used, then the corresponding boundary of the current -simulation box is used. If a numeric constant is specified then the -wall is placed at that position in the appropriate dimension (x, y, or -z). In both the EDGE and constant cases, the wall will never move. -If the wall position is a variable, it should be specified as v_name, -where name is an "equal-style variable"_variable.html name. In this -case the variable is evaluated each timestep and the result becomes -the current position of the reflecting wall. Equal-style variables -can specify formulas with various mathematical functions, and include -"thermo_style"_thermo_style.html command keywords for the simulation -box parameters and timestep and elapsed time. Thus it is easy to -specify a time-dependent wall position. See examples below. - -For the {wall/lj93} and {wall/lj126} and {wall/lj1043} styles, -{epsilon} and {sigma} are the usual Lennard-Jones parameters, which -determine the strength and size of the particle as it interacts with -the wall. Epsilon has energy units. Note that this {epsilon} and -{sigma} may be different than any {epsilon} or {sigma} values defined -for a pair style that computes particle-particle interactions. - -The {wall/lj93} interaction is derived by integrating over a 3d -half-lattice of Lennard-Jones 12/6 particles. The {wall/lj126} -interaction is effectively a harder, more repulsive wall interaction. -The {wall/lj1043} interaction is yet a different form of wall -interaction, described in Magda et al in "(Magda)"_#Magda. - -For the {wall/colloid} style, {R} is the radius of the colloid -particle, {D} is the distance from the surface of the colloid particle -to the wall (r-R), and {sigma} is the size of a constituent LJ -particle inside the colloid particle and wall. Note that the cutoff -distance Rc in this case is the distance from the colloid particle -center to the wall. The prefactor {epsilon} can be thought of as an -effective Hamaker constant with energy units for the strength of the -colloid-wall interaction. More specifically, the {epsilon} pre-factor -= 4 * pi^2 * rho_wall * rho_colloid * epsilon * sigma^6, where epsilon -and sigma are the LJ parameters for the constituent LJ -particles. Rho_wall and rho_colloid are the number density of the -constituent particles, in the wall and colloid respectively, in units -of 1/volume. - -The {wall/colloid} interaction is derived by integrating over -constituent LJ particles of size {sigma} within the colloid particle -and a 3d half-lattice of Lennard-Jones 12/6 particles of size {sigma} -in the wall. As mentioned in the preceding paragraph, the density of -particles in the wall and colloid can be different, as specified by -the {epsilon} pre-factor. - -For the {wall/harmonic} style, {epsilon} is effectively the spring -constant K, and has units (energy/distance^2). The input parameter -{sigma} is ignored. The minimum energy position of the harmonic -spring is at the {cutoff}. This is a repulsive-only spring since the -interaction is truncated at the {cutoff} - -For the {wall/morse} style, the three parameters are in this order: -{D_0} the depth of the potential, {alpha} the width parameter, and -{r_0} the location of the minimum. {D_0} has energy units, {alpha} -inverse distance units, and {r_0} distance units. - -For any wall, the {epsilon} and/or {sigma} and/or {alpha} parameter can -be specified -as an "equal-style variable"_variable.html, in which case it should be -specified as v_name, where name is the variable name. As with a -variable wall position, the variable is evaluated each timestep and -the result becomes the current epsilon or sigma of the wall. -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent wall interaction. - -NOTE: For all of the styles, you must insure that r is always > 0 for -all particles in the group, or LAMMPS will generate an error. This -means you cannot start your simulation with particles at the wall -position {coord} (r = 0) or with particles on the wrong side of the -wall (r < 0). For the {wall/lj93} and {wall/lj126} styles, the energy -of the wall/particle interaction (and hence the force on the particle) -blows up as r -> 0. The {wall/colloid} style is even more -restrictive, since the energy blows up as D = r-R -> 0. This means -the finite-size particles of radius R must be a distance larger than R -from the wall position {coord}. The {harmonic} style is a softer -potential and does not blow up as r -> 0, but you must use a large -enough {epsilon} that particles always reamin on the correct side of -the wall (r > 0). - -The {units} keyword determines the meaning of the distance units used -to define a wall position, but only when a numeric constant or -variable is used. It is not relevant when EDGE is used to specify a -face position. In the variable case, the variable is assumed to -produce a value compatible with the {units} setting you specify. - -A {box} value selects standard distance units as defined by the -"units"_units.html command, e.g. Angstroms for units = real or metal. -A {lattice} value means the distance units are in lattice spacings. -The "lattice"_lattice.html command must have been previously used to -define the lattice spacings. - -The {fld} keyword can be used with a {yes} setting to invoke the wall -constraint before pairwise interactions are computed. This allows an -implicit FLD model using "pair_style lubricateU"_pair_lubricateU.html -to include the wall force in its calculations. If the setting is -{no}, wall forces are imposed after pairwise interactions, in the -usual manner. - -The {pbc} keyword can be used with a {yes} setting to allow walls to -be specified in a periodic dimension. See the -"boundary"_boundary.html command for options on simulation box -boundaries. The default for {pbc} is {no}, which means the system -must be non-periodic when using a wall. But you may wish to use a -periodic box. E.g. to allow some particles to interact with the wall -via the fix group-ID, and others to pass through it and wrap around a -periodic box. In this case you should insure that the wall if -sufficiently far enough away from the box boundary. If you do not, -then particles may interact with both the wall and with periodic -images on the other side of the box, which is probably not what you -want. - -:line - -Here are examples of variable definitions that move the wall position -in a time-dependent fashion using equal-style -"variables"_variable.html. The wall interaction parameters (epsilon, -sigma) could be varied with additional variable definitions. - -variable ramp equal ramp(0,10) -fix 1 all wall xlo v_ramp 1.0 1.0 2.5 :pre - -variable linear equal vdisplace(0,20) -fix 1 all wall xlo v_linear 1.0 1.0 2.5 :pre - -variable wiggle equal swiggle(0.0,5.0,3.0) -fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 :pre - -variable wiggle equal cwiggle(0.0,5.0,3.0) -fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 :pre - -The ramp(lo,hi) function adjusts the wall position linearly from lo to -hi over the course of a run. The vdisplace(c0,velocity) function does -something similar using the equation position = c0 + velocity*delta, -where delta is the elapsed time. - -The swiggle(c0,A,period) function causes the wall position to -oscillate sinusoidally according to this equation, where omega = 2 PI -/ period: - -position = c0 + A sin(omega*delta) :pre - -The cwiggle(c0,A,period) function causes the wall position to -oscillate sinusoidally according to this equation, which will have an -initial wall velocity of 0.0, and thus may impose a gentler -perturbation on the particles: - -position = c0 + A (1 - cos(omega*delta)) :pre - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy of interaction between atoms and each wall to -the system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {virial} option is supported by this -fix to add the contribution due to the interaction between -atoms and each wall to the system's virial as part of "thermodynamic -output"_thermo_style.html. The default is {virial no} - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -This fix computes a global scalar energy and a global vector of -forces, which can be accessed by various "output -commands"_Howto_output.html. Note that the scalar energy is the sum -of interactions with all defined walls. If you want the energy on a -per-wall basis, you need to use multiple fix wall commands. The -length of the vector is equal to the number of walls defined by the -fix. Each vector value is the normal force on a specific wall. Note -that an outward force on a wall will be a negative value for {lo} -walls and a positive value for {hi} walls. The scalar and vector -values calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -NOTE: If you want the atom/wall interaction energy to be included in -the total potential energy of the system (the quantity being -minimized), you MUST enable the "fix_modify"_fix_modify.html {energy} -option for this fix. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] none - -[Related commands:] - -"fix wall/reflect"_fix_wall_reflect.html, -"fix wall/gran"_fix_wall_gran.html, -"fix wall/region"_fix_wall_region.html - -[Default:] - -The option defaults units = lattice, fld = no, and pbc = no. - -:line - -:link(Magda) -[(Magda)] Magda, Tirrell, Davis, J Chem Phys, 83, 1888-1901 (1985); -erratum in JCP 84, 2901 (1986). diff --git a/doc/txt/fix_wall_body_polygon.txt b/doc/txt/fix_wall_body_polygon.txt deleted file mode 100644 index 45cbb2841d..0000000000 --- a/doc/txt/fix_wall_body_polygon.txt +++ /dev/null @@ -1,104 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix wall/body/polygon command :h3 - -[Syntax:] - -fix ID group-ID wall/body/polygon k_n c_n c_t wallstyle args keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -wall/body/polygon = style name of this fix command :l -k_n = normal repulsion strength (force/distance or pressure units) :l -c_n = normal damping coefficient (force/distance or pressure units) :l -c_t = tangential damping coefficient (force/distance or pressure units) :l -wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l -args = list of arguments for a particular style :l - {xplane} or {yplane} args = lo hi - lo,hi = position of lower and upper plane (distance units), either can be NULL) - {zcylinder} args = radius - radius = cylinder radius (distance units) :pre -zero or more keyword/value pairs may be appended to args :l -keyword = {wiggle} :l - {wiggle} values = dim amplitude period - dim = {x} or {y} or {z} - amplitude = size of oscillation (distance units) - period = time of oscillation (time units) :pre -:ule - -[Examples:] - -fix 1 all wall/body/polygon 1000.0 20.0 5.0 xplane -10.0 10.0 - -[Description:] - -This fix is for use with 2d models of body particles of style -{rounded/polygon}. It bounds the simulation domain with wall(s). All -particles in the group interact with the wall when they are close -enough to touch it. The nature of the interaction between the wall -and the polygon particles is the same as that between the polygon -particles themselves, which is similar to a Hookean potential. See -the "Howto body"_Howto_body.html doc page for more details on using -body particles. - -The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as -those specified with the "pair_style -body/rounded/polygon"_pair_body_rounded_polygon.html command. - -The {wallstyle} can be planar or cylindrical. The 2 planar options -specify a pair of walls in a dimension. Wall positions are given by -{lo} and {hi}. Either of the values can be specified as NULL if a -single wall is desired. For a {zcylinder} wallstyle, the cylinder's -axis is at x = y = 0.0, and the radius of the cylinder is specified. - -Optionally, the wall can be moving, if the {wiggle} keyword is -appended. - -For the {wiggle} keyword, the wall oscillates sinusoidally, similar to -the oscillations of particles which can be specified by the "fix -move"_fix_move.html command. This is useful in packing simulations of -particles. The arguments to the {wiggle} keyword specify a dimension -for the motion, as well as it's {amplitude} and {period}. Note that -if the dimension is in the plane of the wall, this is effectively a -shearing motion. If the dimension is perpendicular to the wall, it is -more of a shaking motion. A {zcylinder} wall can only be wiggled in -the z dimension. - -Each timestep, the position of a wiggled wall in the appropriate {dim} -is set according to this equation: - -position = coord + A - A cos (omega * delta) :pre - -where {coord} is the specified initial position of the wall, {A} is -the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time -elapsed since the fix was specified. The velocity of the wall is set -to the derivative of this expression. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Howto_output.html. No parameter -of this fix can be used with the {start/stop} keywords of the -"run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Any dimension (xy) that has a wall must be non-periodic. - -[Related commands:] - -"atom_style body"_atom_style.html, "pair_style -body/rounded/polygon"_pair_body_rounded_polygon.html - -[Default:] none diff --git a/doc/txt/fix_wall_body_polyhedron.txt b/doc/txt/fix_wall_body_polyhedron.txt deleted file mode 100644 index 231ab1f0fe..0000000000 --- a/doc/txt/fix_wall_body_polyhedron.txt +++ /dev/null @@ -1,103 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix wall/body/polyhedron command :h3 - -[Syntax:] - -fix ID group-ID wall/body/polyhedron k_n c_n c_t wallstyle args keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -wall/body/polyhedron = style name of this fix command :l -k_n = normal repulsion strength (force/distance units or pressure units - see discussion below) :l -c_n = normal damping coefficient (force/distance units or pressure units - see discussion below) :l -c_t = tangential damping coefficient (force/distance units or pressure units - see discussion below) :l -wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l -args = list of arguments for a particular style :l - {xplane} or {yplane} args = lo hi - lo,hi = position of lower and upper plane (distance units), either can be NULL) - {zcylinder} args = radius - radius = cylinder radius (distance units) :pre -zero or more keyword/value pairs may be appended to args :l -keyword = {wiggle} :l - {wiggle} values = dim amplitude period - dim = {x} or {y} or {z} - amplitude = size of oscillation (distance units) - period = time of oscillation (time units) :pre -:ule - -[Examples:] - -fix 1 all wall/body/polyhedron 1000.0 20.0 5.0 xplane -10.0 10.0 - -[Description:] - -This fix is for use with 3d models of body particles of style -{rounded/polyhedron}. It bounds the simulation domain with wall(s). -All particles in the group interact with the wall when they are close -enough to touch it. The nature of the interaction between the wall -and the polygon particles is the same as that between the polygon -particles themselves, which is similar to a Hookean potential. See -the "Howto body"_Howto_body.html doc page for more details on using -body particles. - -The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as -those specified with the "pair_style -body/rounded/polyhedron"_pair_body_rounded_polyhedron.html command. - -The {wallstyle} can be planar or cylindrical. The 3 planar options -specify a pair of walls in a dimension. Wall positions are given by -{lo} and {hi}. Either of the values can be specified as NULL if a -single wall is desired. For a {zcylinder} wallstyle, the cylinder's -axis is at x = y = 0.0, and the radius of the cylinder is specified. - -Optionally, the wall can be moving, if the {wiggle} keyword is appended. - -For the {wiggle} keyword, the wall oscillates sinusoidally, similar to -the oscillations of particles which can be specified by the "fix -move"_fix_move.html command. This is useful in packing simulations of -particles. The arguments to the {wiggle} keyword specify a dimension -for the motion, as well as it's {amplitude} and {period}. Note that -if the dimension is in the plane of the wall, this is effectively a -shearing motion. If the dimension is perpendicular to the wall, it is -more of a shaking motion. A {zcylinder} wall can only be wiggled in -the z dimension. - -Each timestep, the position of a wiggled wall in the appropriate {dim} -is set according to this equation: - -position = coord + A - A cos (omega * delta) :pre - -where {coord} is the specified initial position of the wall, {A} is -the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time -elapsed since the fix was specified. The velocity of the wall is set -to the derivative of this expression. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Howto_output.html. No parameter -of this fix can be used with the {start/stop} keywords of the -"run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Any dimension (xyz) that has a wall must be non-periodic. - -[Related commands:] - -"atom_style body"_atom_style.html, "pair_style -body/rounded/polyhedron"_pair_body_rounded_polyhedron.html - -[Default:] none diff --git a/doc/txt/fix_wall_ees.txt b/doc/txt/fix_wall_ees.txt deleted file mode 100644 index 4cc91f5222..0000000000 --- a/doc/txt/fix_wall_ees.txt +++ /dev/null @@ -1,118 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix wall/ees command :h3 -fix wall/region/ees command :h3 - -[Syntax:] - -fix ID group-ID style args :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -style = {wall/ees} or {wall/region/ees} :l - args for style {wall/ees}: one or more {face parameters} groups may be appended - face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} - parameters = coord epsilon sigma cutoff - coord = position of wall = EDGE or constant or variable - EDGE = current lo or hi edge of simulation box - constant = number like 0.0 or -30.0 (distance units) - variable = "equal-style variable"_variable.html like v_x or v_wiggle - epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) - epsilon can be a variable (see below) - sigma = size factor for wall-particle interaction (distance units) - sigma can be a variable (see below) - cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre - - args for style {wall/region/ees}: {region-ID} {epsilon} {sigma} {cutoff} - region-ID = region whose boundary will act as wall - epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) - sigma = size factor for wall-particle interaction (distance units) - cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre - :ule - -[Examples:] - -fix wallhi all wall/ees xlo -1.0 1.0 1.0 2.5 units box -fix wallhi all wall/ees xhi EDGE 1.0 1.0 2.5 -fix wallhi all wall/ees v_wiggle 23.2 1.0 1.0 2.5 -fix zwalls all wall/ees zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 :pre - -fix ees_cube all wall/region/ees myCube 1.0 1.0 2.5 :pre - - -[Description:] - -Fix {wall/ees} bounds the simulation domain on one or more of its -faces with a flat wall that interacts with the ellipsoidal atoms in the -group by generating a force on the atom in a direction perpendicular to -the wall and a torque parallel with the wall. The energy of -wall-particle interactions E is given by: - -:c,image(Eqs/fix_wall_ees.jpg) - -Introduced by Babadi and Ejtehadi in "(Babadi)"_#BabadiEjtehadi. Here, -{r} is the distance from the particle to the wall at position {coord}, -and Rc is the {cutoff} distance at which the particle and wall no -longer interact. Also, sigma_n is the distance between center of -ellipsoid and the nearest point of its surface to the wall. The energy -of the wall is: - -:c,image(JPG/fix_wall_ees_image.jpg) - -Details of using this command and specifications are the same as -fix/wall command. You can also find an example in USER/ees/ under -examples/ directory. - -The prefactor {epsilon} can be thought of as an -effective Hamaker constant with energy units for the strength of the -ellipsoid-wall interaction. More specifically, the {epsilon} pre-factor -= 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon -* sigma_a * sigma_b * sigma_c, where epsilon is the LJ parameters for -the constituent LJ particles and sigma_a, sigma_b, and sigma_c are radii -of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number -density of the constituent particles, in the wall and ellipsoid -respectively, in units of 1/volume. - -NOTE: You must insure that r is always bigger than sigma_n for -all particles in the group, or LAMMPS will generate an error. This -means you cannot start your simulation with particles touching the wall -position {coord} (r = sigma_n) or with particles penetrating the wall -(0 =< r < sigma_n) or with particles on the wrong side of the -wall (r < 0). - - -Fix {wall/region/ees} treats the surface of the geometric region defined -by the {region-ID} as a bounding wall which interacts with nearby -ellipsoidal particles according to the EES potential introduced above. - -Other details of this command are the same as for the "fix -wall/region"_fix_wall_region.html command. One may also find an example -of using this fix in the examples/USER/misc/ees/ directory. - -[Restrictions:] - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This fix requires that atoms be ellipsoids as defined by the -"atom_style ellipsoid"_atom_style.html command. - -[Related commands:] - -"fix wall"_fix_wall.html, -"pair resquared"_pair_resquared.html - -[Default:] - -none - -:line - -:link(BabadiEjtehadi) -[(Babadi)] Babadi and Ejtehadi, EPL, 77 (2007) 23002. diff --git a/doc/txt/fix_wall_gran.txt b/doc/txt/fix_wall_gran.txt deleted file mode 100644 index 4b3ff15cc9..0000000000 --- a/doc/txt/fix_wall_gran.txt +++ /dev/null @@ -1,186 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix wall/gran command :h3 - -[Syntax:] - -fix ID group-ID wall/gran fstyle fstyle_params wallstyle args keyword values ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -wall/gran = style name of this fix command :l -fstyle = style of force interactions between particles and wall :l - possible choices: hooke, hooke/history, hertz/history, granular :pre -fstyle_params = parameters associated with force interaction style :l - For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: - Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) - Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) - gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) - gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) - xmu = static yield criterion (unitless value between 0.0 and 1.0e4) - dampflag = 0 or 1 if tangential damping force is excluded or included :pre - For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre -wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l -args = list of arguments for a particular style :l - {xplane} or {yplane} or {zplane} args = lo hi - lo,hi = position of lower and upper plane (distance units), either can be NULL) - {zcylinder} args = radius - radius = cylinder radius (distance units) :pre -zero or more keyword/value pairs may be appended to args :l -keyword = {wiggle} or {shear} :l - {wiggle} values = dim amplitude period - dim = {x} or {y} or {z} - amplitude = size of oscillation (distance units) - period = time of oscillation (time units) - {shear} values = dim vshear - dim = {x} or {y} or {z} - vshear = magnitude of shear velocity (velocity units) :pre -:ule - -[Examples:] - -fix 1 all wall/gran hooke 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 -fix 1 all wall/gran hooke/history 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL -fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 -fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox -fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone -fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre - -[Description:] - -Bound the simulation domain of a granular system with a frictional -wall. All particles in the group interact with the wall when they are -close enough to touch it. - -The nature of the wall/particle interactions are determined by the -{fstyle} setting. It can be any of the styles defined by the -"pair_style gran/*"_pair_gran.html or the more general "pair_style -granular"_pair_granular.html" commands. Currently the options are -{hooke}, {hooke/history}, or {hertz/history} for the former, and -{granular} with all the possible options of the associated -{pair_coeff} command for the latter. The equation for the force -between the wall and particles touching it is the same as the -corresponding equation on the "pair_style gran/*"_pair_gran.html and -"pair_style_granular"_pair_granular.html doc pages, in the limit of -one of the two particles going to infinite radius and mass (flat -wall). Specifically, delta = radius - r = overlap of particle with -wall, m_eff = mass of particle, and the effective radius of contact = -RiRj/Ri+Rj is set to the radius of the particle. - -The parameters {Kn}, {Kt}, {gamma_n}, {gamma_t}, {xmu} and {dampflag} -have the same meaning and units as those specified with the -"pair_style gran/*"_pair_gran.html commands. This means a NULL can be -used for either {Kt} or {gamma_t} as described on that page. If a -NULL is used for {Kt}, then a default value is used where {Kt} = 2/7 -{Kn}. If a NULL is used for {gamma_t}, then a default value is used -where {gamma_t} = 1/2 {gamma_n}. - -All the model choices for cohesion, tangential friction, rolling -friction and twisting friction supported by the "pair_style -granular"_pair_granular.html through its {pair_coeff} command are also -supported for walls. These are discussed in greater detail on the doc -page for "pair_style granular"_pair_granular.html. - -Note that you can choose a different force styles and/or different -values for the wall/particle coefficients than for particle/particle -interactions. E.g. if you wish to model the wall as a different -material. - -NOTE: As discussed on the doc page for "pair_style -gran/*"_pair_gran.html, versions of LAMMPS before 9Jan09 used a -different equation for Hertzian interactions. This means Hertizian -wall/particle interactions have also changed. They now include a -sqrt(radius) term which was not present before. Also the previous -versions used Kn and Kt from the pairwise interaction and hardwired -dampflag to 1, rather than letting them be specified directly. This -means you can set the values of the wall/particle coefficients -appropriately in the current code to reproduce the results of a -previous Hertzian monodisperse calculation. For example, for the -common case of a monodisperse system with particles of diameter 1, Kn, -Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were -previously. - -The effective mass {m_eff} in the formulas listed on the "pair_style -granular"_pair_gran.html doc page is the mass of the particle for -particle/wall interactions (mass of wall is infinite). If the -particle is part of a rigid body, its mass is replaced by the mass of -the rigid body in those formulas. This is determined by searching for -a "fix rigid"_fix_rigid.html command (or its variants). - -The {wallstyle} can be planar or cylindrical. The 3 planar options -specify a pair of walls in a dimension. Wall positions are given by -{lo} and {hi}. Either of the values can be specified as NULL if a -single wall is desired. For a {zcylinder} wallstyle, the cylinder's -axis is at x = y = 0.0, and the radius of the cylinder is specified. - -Optionally, the wall can be moving, if the {wiggle} or {shear} -keywords are appended. Both keywords cannot be used together. - -For the {wiggle} keyword, the wall oscillates sinusoidally, similar to -the oscillations of particles which can be specified by the "fix -move"_fix_move.html command. This is useful in packing simulations of -granular particles. The arguments to the {wiggle} keyword specify a -dimension for the motion, as well as it's {amplitude} and {period}. -Note that if the dimension is in the plane of the wall, this is -effectively a shearing motion. If the dimension is perpendicular to -the wall, it is more of a shaking motion. A {zcylinder} wall can only -be wiggled in the z dimension. - -Each timestep, the position of a wiggled wall in the appropriate {dim} -is set according to this equation: - -position = coord + A - A cos (omega * delta) :pre - -where {coord} is the specified initial position of the wall, {A} is -the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time -elapsed since the fix was specified. The velocity of the wall is set -to the derivative of this expression. - -For the {shear} keyword, the wall moves continuously in the specified -dimension with velocity {vshear}. The dimension must be tangential to -walls with a planar {wallstyle}, e.g. in the {y} or {z} directions for -an {xplane} wall. For {zcylinder} walls, a dimension of {z} means the -cylinder is moving in the z-direction along it's axis. A dimension of -{x} or {y} means the cylinder is spinning around the z-axis, either in -the clockwise direction for {vshear} > 0 or counter-clockwise for -{vshear} < 0. In this case, {vshear} is the tangential velocity of -the wall at whatever {radius} has been defined. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -This fix writes the shear friction state of atoms interacting with the -wall to "binary restart files"_restart.html, so that a simulation can -continue correctly if granular potentials with shear "history" effects -are being used. See the "read_restart"_read_restart.html command for -info on how to re-specify a fix in an input script that reads a -restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Howto_output.html. No parameter -of this fix can be used with the {start/stop} keywords of the -"run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Any dimension (xyz) that has a granular wall must be non-periodic. - -[Related commands:] - -"fix move"_fix_move.html, -"fix wall/gran/region"_fix_wall_gran_region.html, -"pair_style gran/*"_pair_gran.html -"pair_style granular"_pair_granular.html - -[Default:] none diff --git a/doc/txt/fix_wall_gran_region.txt b/doc/txt/fix_wall_gran_region.txt deleted file mode 100644 index 50dad364e0..0000000000 --- a/doc/txt/fix_wall_gran_region.txt +++ /dev/null @@ -1,220 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix wall/gran/region command :h3 - -[Syntax:] - -fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -wall/region = style name of this fix command :l -fstyle = style of force interactions between particles and wall :l - possible choices: hooke, hooke/history, hertz/history, granular :pre -fstyle_params = parameters associated with force interaction style :l - For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: - Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) - Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) - gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) - gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) - xmu = static yield criterion (unitless value between 0.0 and 1.0e4) - dampflag = 0 or 1 if tangential damping force is excluded or included :pre - For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre -wallstyle = region (see "fix wall/gran"_fix_wall_gran.html for options for other kinds of walls) :l -region-ID = region whose boundary will act as wall :l,ule - -[Examples:] - -fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone -fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox -fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone -fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre - -[Description:] - -Treat the surface of the geometric region defined by the {region-ID} -as a bounding frictional wall which interacts with nearby finite-size -granular particles when they are close enough to touch the wall. See -the "fix wall/region"_fix_wall_region.html and "fix -wall/gran"_fix_wall_gran.html commands for related kinds of walls for -non-granular particles and simpler wall geometries, respectively. - -Here are snapshots of example models using this command. -Corresponding input scripts can be found in examples/granregion. -Click on the images to see a bigger picture. Movies of these -simulations are "here on the Movies -page"_http://lammps.sandia.gov/movies.html#granregion of the LAMMPS -web site. - -:image(JPG/gran_funnel_small.jpg,JPG/gran_funnel.png) -:image(JPG/gran_mixer_small.jpg,JPG/gran_mixer.png) - -:line - -The distance between a particle and the region boundary is the -distance to the nearest point on the region surface. The force the -wall exerts on the particle is along the direction between that point -and the particle center, which is the direction normal to the surface -at that point. Note that if the region surface is comprised of -multiple "faces", then each face can exert a force on the particle if -it is close enough. E.g. for "region_style block"_region.html, a -particle in the interior, near a corner of the block, could feel wall -forces from 1, 2, or 3 faces of the block. - -Regions are defined using the "region"_region.html command. Note that -the region volume can be interior or exterior to the bounding surface, -which will determine in which direction the surface interacts with -particles, i.e. the direction of the surface normal. The exception to -this is if one or more {open} options are specified for the region -command, in which case particles interact with both the interior and -exterior surfaces of regions. - -Regions can either be primitive shapes (block, sphere, cylinder, etc) -or combinations of primitive shapes specified via the {union} or -{intersect} region styles. These latter styles can be used to -construct particle containers with complex shapes. - -Regions can also move dynamically via the "region"_region.html command -keywords (move) and {rotate}, or change their shape by use of variables -as inputs to the "region"_region.html command. If such a region is used -with this fix, then the region surface will move in time in the -corresponding manner. - -NOTE: As discussed on the "region"_region.html command doc page, -regions in LAMMPS do not get wrapped across periodic boundaries. It -is up to you to ensure that the region location with respect to -periodic or non-periodic boundaries is specified appropriately via the -"region"_region.html and "boundary"_boundary.html commands when using -a region as a wall that bounds particle motion. - -NOTE: For primitive regions with sharp corners and/or edges (e.g. a -block or cylinder), wall/particle forces are computed accurately for -both interior and exterior regions. For {union} and {intersect} -regions, additional sharp corners and edges may be present due to the -intersection of the surfaces of 2 or more primitive volumes. These -corners and edges can be of two types: concave or convex. Concave -points/edges are like the corners of a cube as seen by particles in -the interior of a cube. Wall/particle forces around these features -are computed correctly. Convex points/edges are like the corners of a -cube as seen by particles exterior to the cube, i.e. the points jut -into the volume where particles are present. LAMMPS does NOT compute -the location of these convex points directly, and hence wall/particle -forces in the cutoff volume around these points suffer from -inaccuracies. The basic problem is that the outward normal of the -surface is not continuous at these points. This can cause particles -to feel no force (they don't "see" the wall) when in one location, -then move a distance epsilon, and suddenly feel a large force because -they now "see" the wall. In a worst-case scenario, this can blow -particles out of the simulation box. Thus, as a general rule you -should not use the fix wall/gran/region command with {union} or -{interesect} regions that have convex points or edges resulting from -the union/intersection (convex points/edges in the union/intersection -due to a single sub-region are still OK). - -NOTE: Similarly, you should not define {union} or {intersert} regions -for use with this command that share an overlapping common face that -is part of the overall outer boundary (interior boundary is OK), even -if the face is smooth. E.g. two regions of style block in a {union} -region, where the two blocks overlap on one or more of their faces. -This is because LAMMPS discards points that are part of multiple -sub-regions when calculating wall/particle interactions, to avoid -double-counting the interaction. Having two coincident faces could -cause the face to become invisible to the particles. The solution is -to make the two faces differ by epsilon in their position. - -The nature of the wall/particle interactions are determined by the -{fstyle} setting. It can be any of the styles defined by the -"pair_style gran/*"_pair_gran.html or the more general "pair_style -granular"_pair_granular.html" commands. Currently the options are -{hooke}, {hooke/history}, or {hertz/history} for the former, and -{granular} with all the possible options of the associated -{pair_coeff} command for the latter. The equation for the force -between the wall and particles touching it is the same as the -corresponding equation on the "pair_style gran/*"_pair_gran.html and -"pair_style_granular"_pair_granular.html doc pages, but the effective -radius is calculated using the radius of the particle and the radius -of curvature of the wall at the contact point. - -Specifically, delta = radius - r = overlap of particle with wall, -m_eff = mass of particle, and RiRj/Ri+Rj is the effective radius, with -Rj replaced by the radius of curvature of the wall at the contact -point. The radius of curvature can be negative for a concave wall -section, e.g. the interior of cylinder. For a flat wall, delta = -radius - r = overlap of particle with wall, m_eff = mass of particle, -and the effective radius of contact is just the radius of the -particle. - -The parameters {Kn}, {Kt}, {gamma_n}, {gamma_t}, {xmu} and {dampflag} -have the same meaning and units as those specified with the -"pair_style gran/*"_pair_gran.html commands. This means a NULL can be -used for either {Kt} or {gamma_t} as described on that page. If a -NULL is used for {Kt}, then a default value is used where {Kt} = 2/7 -{Kn}. If a NULL is used for {gamma_t}, then a default value is used -where {gamma_t} = 1/2 {gamma_n}. - -All the model choices for cohesion, tangential friction, rolling -friction and twisting friction supported by the "pair_style -granular"_pair_granular.html through its {pair_coeff} command are also -supported for walls. These are discussed in greater detail on the doc -page for "pair_style granular"_pair_granular.html. - -Note that you can choose a different force styles and/or different -values for the 6 wall/particle coefficients than for particle/particle -interactions. E.g. if you wish to model the wall as a different -material. - -[Restart, fix_modify, output, run start/stop, minimize info:] - -Similar to "fix wall/gran"_fix_wall_gran.html command, this fix writes -the shear friction state of atoms interacting with the wall to "binary -restart files"_restart.html, so that a simulation can continue -correctly if granular potentials with shear "history" effects are -being used. This fix also includes info about a moving region in the -restart file. See the "read_restart"_read_restart.html command for -info on how to re-specify a fix in an input script that reads a -restart file, so that the operation of the fix continues in an -uninterrupted fashion. - -NOTE: Information about region definitions is NOT included in restart -files, as discussed on the "read_restart"_read_restart.html doc page. -So you must re-define your region and if it is a moving region, define -its motion attributes in a way that is consistent with the simulation -that wrote the restart file. In particular, if you want to change the -region motion attributes (e.g. its velocity), then you should ensure -the position/orientation of the region at the initial restart timestep -is the same as it was on the timestep the restart file was written. -If this is not possible, you may need to ignore info in the restart -file by defining a new fix wall/gran/region command in your restart -script, e.g. with a different fix ID. Or if you want to keep the -shear history info but discard the region motion information, you can -use the same fix ID for fix wall/gran/region, but assign it a region -with a different region ID. - -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Howto_output.html. No parameter -of this fix can be used with the {start/stop} keywords of the -"run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix is part of the GRANULAR package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix_move"_fix_move.html, -"fix wall/gran"_fix_wall_gran.html, -"fix wall/region"_fix_wall_region.html, -"pair_style granular"_pair_gran.html, -"region"_region.html - -[Default:] none - diff --git a/doc/txt/fix_wall_piston.txt b/doc/txt/fix_wall_piston.txt deleted file mode 100644 index 475517ed66..0000000000 --- a/doc/txt/fix_wall_piston.txt +++ /dev/null @@ -1,120 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix wall/piston command :h3 - -[Syntax:] - -fix ID group-ID wall/piston face ... keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -wall/piston = style name of this fix command :l -face = {zlo} :l -zero or more keyword/value pairs may be appended :l -keyword = {pos} or {vel} or {ramp} or {units} :l - {pos} args = z - z = z coordinate at which the piston begins (distance units) - {vel} args = vz - vz = final velocity of the piston (velocity units) - {ramp} = use a linear velocity ramp from 0 to vz - {temp} args = target damp seed extent - target = target velocity for region immediately ahead of the piston - damp = damping parameter (time units) - seed = random number seed for langevin kicks - extent = extent of thermostatted region (distance units) - {units} value = {lattice} or {box} - {lattice} = the wall position is defined in lattice units - {box} = the wall position is defined in simulation box units :pre -:ule - -[Examples:] - -fix xwalls all wall/piston zlo -fix walls all wall/piston zlo pos 1.0 vel 10.0 units box -fix top all wall/piston zlo vel 10.0 ramp :pre - -[Description:] - -Bound the simulation with a moving wall which reflect particles in the -specified group and drive the system with an effective infinite-mass -piston capable of driving shock waves. - -A momentum mirror technique is used, which means that if an atom (or -the wall) moves such that an atom is outside the wall on a timestep by -a distance delta (e.g. due to "fix nve"_fix_nve.html), then it is put -back inside the face by the same delta, and the velocity relative to -the moving wall is flipped in z. For instance, a stationary particle -hit with a piston wall with velocity vz, will end the timestep with a -velocity of 2*vz. - -Currently the {face} keyword can only be {zlo}. This creates a piston -moving in the positive z direction. Particles with z coordinate less -than the wall position are reflected to a z coordinate greater than -the wall position. If the piston velocity is vpz and the particle -velocity before reflection is vzi, the particle velocity after -reflection is -vzi + 2*vpz. - -The initial position of the wall can be specified by the {pos} keyword. - -The final velocity of the wall can be specified by the {vel} keyword - -The {ramp} keyword will cause the wall/piston to adjust the velocity -linearly from zero velocity to {vel} over the course of the run. If -the {ramp} keyword is omitted then the wall/piston moves at a constant -velocity defined by {vel}. - -The {temp} keyword will cause the region immediately in front of the -wall/piston to be thermostatted with a Langevin thermostat. This -region moves with the piston. The damping and kicking are measured in -the reference frame of the piston. So, a temperature of zero would -mean all particles were moving at exactly the speed of the -wall/piston. - -The {units} keyword determines the meaning of the distance units used -to define a wall position, but only when a numeric constant is used. - -A {box} value selects standard distance units as defined by the -"units"_units.html command, e.g. Angstroms for units = real or metal. -A {lattice} value means the distance units are in lattice spacings. -The "lattice"_lattice.html command must have been previously used to -define the lattice spacings. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output commands"_Howto_output.html. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -This fix style is part of the SHOCK package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -The face that has the wall/piston must be boundary type 's' -(shrink-wrapped). The opposing face can be -any boundary type other than periodic. - -A wall/piston should not be used with rigid bodies such as those -defined by a "fix rigid" command. This is because the wall/piston -displaces atoms directly rather than exerting a force on them. - -[Related commands:] - -"fix wall/reflect"_fix_wall.html command, "fix -append/atoms"_fix_append_atoms.html command - -[Default:] - -The keyword defaults are pos = 0, vel = 0, units = lattice. diff --git a/doc/txt/fix_wall_region.txt b/doc/txt/fix_wall_region.txt deleted file mode 100644 index 702ca8e694..0000000000 --- a/doc/txt/fix_wall_region.txt +++ /dev/null @@ -1,202 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix wall/region command :h3 - -[Syntax:] - -fix ID group-ID wall/region region-ID style args ... cutoff :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -wall/region = style name of this fix command :l -region-ID = region whose boundary will act as wall :l -style = {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} or {morse} :l -args for styles {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} = :l - epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) - sigma = size factor for wall-particle interaction (distance units) :pre -args for style {morse} = :l - D_0 = depth of the potential (energy units) - alpha = width parameter (1/distance units) - r_0 = distance of the potential minimum from wall position (distance units) :pre -cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :l -:ule - -[Examples:] - -fix wall all wall/region mySphere lj93 1.0 1.0 2.5 -fix wall all wall/region mySphere harmonic 1.0 0.0 2.5 -fix wall all wall/region box_top morse 1.0 1.0 1.5 3.0 :pre - -[Description:] - -Treat the surface of the geometric region defined by the {region-ID} -as a bounding wall which interacts with nearby particles according to -the specified style. - -The distance between a particle and the surface is the distance to the -nearest point on the surface and the force the wall exerts on the -particle is along the direction between that point and the particle, -which is the direction normal to the surface at that point. Note that -if the region surface is comprised of multiple "faces", then each face -can exert a force on the particle if it is close enough. E.g. for -"region_style block"_region.html, a particle in the interior, near a -corner of the block, could feel wall forces from 1, 2, or 3 faces of -the block. - -Regions are defined using the "region"_region.html command. Note that -the region volume can be interior or exterior to the bounding surface, -which will determine in which direction the surface interacts with -particles, i.e. the direction of the surface normal. The surface of -the region only exerts forces on particles "inside" the region; if a -particle is "outside" the region it will generate an error, because it -has moved through the wall. - -Regions can either be primitive shapes (block, sphere, cylinder, etc) -or combinations of primitive shapes specified via the {union} or -{intersect} region styles. These latter styles can be used to -construct particle containers with complex shapes. Regions can also -change over time via the "region"_region.html command keywords (move) -and {rotate}. If such a region is used with this fix, then the of -region surface will move over time in the corresponding manner. - -NOTE: As discussed on the "region"_region.html command doc page, -regions in LAMMPS do not get wrapped across periodic boundaries. It -is up to you to insure that periodic or non-periodic boundaries are -specified appropriately via the "boundary"_boundary.html command when -using a region as a wall that bounds particle motion. This also means -that if you embed a region in your simulation box and want it to -repulse particles from its surface (using the "side out" option in the -"region"_region.html command), that its repulsive force will not be -felt across a periodic boundary. - -NOTE: For primitive regions with sharp corners and/or edges (e.g. a -block or cylinder), wall/particle forces are computed accurately for -both interior and exterior regions. For {union} and {intersect} -regions, additional sharp corners and edges may be present due to the -intersection of the surfaces of 2 or more primitive volumes. These -corners and edges can be of two types: concave or convex. Concave -points/edges are like the corners of a cube as seen by particles in -the interior of a cube. Wall/particle forces around these features -are computed correctly. Convex points/edges are like the corners of a -cube as seen by particles exterior to the cube, i.e. the points jut -into the volume where particles are present. LAMMPS does NOT compute -the location of these convex points directly, and hence wall/particle -forces in the cutoff volume around these points suffer from -inaccuracies. The basic problem is that the outward normal of the -surface is not continuous at these points. This can cause particles -to feel no force (they don't "see" the wall) when in one location, -then move a distance epsilon, and suddenly feel a large force because -they now "see" the wall. In a worst-case scenario, this can blow -particles out of the simulation box. Thus, as a general rule you -should not use the fix wall/gran/region command with {union} or -{interesect} regions that have convex points or edges resulting from -the union/intersection (convex points/edges in the union/intersection -due to a single sub-region are still OK). - -NOTE: Similarly, you should not define {union} or {intersert} regions -for use with this command that share an overlapping common face that -is part of the overall outer boundary (interior boundary is OK), even -if the face is smooth. E.g. two regions of style block in a {union} -region, where the two blocks overlap on one or more of their faces. -This is because LAMMPS discards points that are part of multiple -sub-regions when calculating wall/particle interactions, to avoid -double-counting the interaction. Having two coincident faces could -cause the face to become invisible to the particles. The solution is -to make the two faces differ by epsilon in their position. - -The energy of wall-particle interactions depends on the specified -style. - -For style {lj93}, the energy E is given by the 9/3 potential: - -:c,image(Eqs/fix_wall_lj93.jpg) - -For style {lj126}, the energy E is given by the 12/6 potential: - -:c,image(Eqs/pair_lj.jpg) - -For style {wall/lj1043}, the energy E is given by the 10/4/3 potential: - -:c,image(Eqs/fix_wall_lj1043.jpg) - -For style {colloid}, the energy E is given by an integrated form of -the "pair_style colloid"_pair_colloid.html potential: - -:c,image(Eqs/fix_wall_colloid.jpg) - -For style {wall/harmonic}, the energy E is given by a harmonic spring -potential (the distance parameter is ignored): - -:c,image(Eqs/fix_wall_harmonic.jpg) - -For style {wall/morse}, the energy E is given by the Morse potential: - -:c,image(Eqs/pair_morse.jpg) - -Unlike other styles, this requires three parameters ({D_0}, {alpha}, {r_0} -in this order) instead of two like for the other wall styles. - -In all cases, {r} is the distance from the particle to the region -surface, and Rc is the {cutoff} distance at which the particle and -surface no longer interact. The cutoff is always the last argument. -The energy of the wall potential is shifted so that the wall-particle -interaction energy is 0.0 at the cutoff distance. - -For a full description of these wall styles, see fix_style -"wall"_fix_wall.html - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the energy of interaction between atoms and the wall to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {virial} option is supported by this -fix to add the contribution due to the interaction between -atoms and each wall to the system's virial as part of "thermodynamic -output"_thermo_style.html. The default is {virial no} - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -This fix computes a global scalar energy and a global 3-length vector -of forces, which can be accessed by various "output -commands"_Howto_output.html. The scalar energy is the sum of energy -interactions for all particles interacting with the wall represented -by the region surface. The 3 vector quantities are the x,y,z -components of the total force acting on the wall due to the particles. -The scalar and vector values calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -The forces due to this fix are imposed during an energy minimization, -invoked by the "minimize"_minimize.html command. - -NOTE: If you want the atom/wall interaction energy to be included in -the total potential energy of the system (the quantity being -minimized), you MUST enable the "fix_modify"_fix_modify.html {energy} -option for this fix. - -[Restrictions:] none - -[Related commands:] - -"fix wall/lj93"_fix_wall.html, -"fix wall/lj126"_fix_wall.html, -"fix wall/lj1043"_fix_wall.html, -"fix wall/colloid"_fix_wall.html, -"fix wall/harmonic"_fix_wall.html, -"fix wall/gran"_fix_wall_gran.html - -[Default:] none diff --git a/doc/txt/fix_wall_srd.txt b/doc/txt/fix_wall_srd.txt deleted file mode 100644 index 3a50c45ab7..0000000000 --- a/doc/txt/fix_wall_srd.txt +++ /dev/null @@ -1,190 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix wall/srd command :h3 - -[Syntax:] - -fix ID group-ID wall/srd face arg ... keyword value ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -wall/srd = style name of this fix command :l -one or more face/arg pairs may be appended :l -face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l - {xlo},{ylo},{zlo} arg = EDGE or constant or variable - EDGE = current lo edge of simulation box - constant = number like 0.0 or -30.0 (distance units) - variable = "equal-style variable"_variable.html like v_x or v_wiggle - {xhi},{yhi},{zhi} arg = EDGE or constant or variable - EDGE = current hi edge of simulation box - constant = number like 50.0 or 100.3 (distance units) - variable = "equal-style variable"_variable.html like v_x or v_wiggle :pre -zero or more keyword/value pairs may be appended :l -keyword = {units} :l - {units} value = {lattice} or {box} - {lattice} = the wall position is defined in lattice units - {box} = the wall position is defined in simulation box units :pre -:ule - -[Examples:] - -fix xwalls all wall/srd xlo EDGE xhi EDGE -fix walls all wall/srd xlo 0.0 ylo 10.0 units box -fix top all wall/srd zhi v_pressdown :pre - -[Description:] - -Bound the simulation with one or more walls which interact with -stochastic reaction dynamics (SRD) particles as slip (smooth) or -no-slip (rough) flat surfaces. The wall interaction is actually -invoked via the "fix srd"_fix_srd.html command, only on the group of -SRD particles it defines, so the group setting for the fix wall/srd -command is ignored. - -A particle/wall collision occurs if an SRD particle moves outside the -wall on a timestep. This alters the position and velocity of the SRD -particle and imparts a force to the wall. - -The {collision} and {Tsrd} settings specified via the "fix -srd"_fix_srd.html command affect the SRD/wall collisions. A {slip} -setting for the {collision} keyword means that the tangential -component of the SRD particle momentum is preserved. Thus only a -normal force is imparted to the wall. The normal component of the new -SRD velocity is sampled from a Gaussian distribution at temperature -{Tsrd}. - -For a {noslip} setting of the {collision} keyword, both the normal and -tangential components of the new SRD velocity are sampled from a -Gaussian distribution at temperature {Tsrd}. Additionally, a new -tangential direction for the SRD velocity is chosen randomly. This -collision style imparts both a normal and tangential force to the -wall. - -Up to 6 walls or faces can be specified in a single command: {xlo}, -{xhi}, {ylo}, {yhi}, {zlo}, {zhi}. A {lo} face reflects particles -that move to a coordinate less than the wall position, back in the -{hi} direction. A {hi} face reflects particles that move to a -coordinate higher than the wall position, back in the {lo} direction. - -The position of each wall can be specified in one of 3 ways: as the -EDGE of the simulation box, as a constant value, or as a variable. If -EDGE is used, then the corresponding boundary of the current -simulation box is used. If a numeric constant is specified then the -wall is placed at that position in the appropriate dimension (x, y, or -z). In both the EDGE and constant cases, the wall will never move. -If the wall position is a variable, it should be specified as v_name, -where name is an "equal-style variable"_variable.html name. In this -case the variable is evaluated each timestep and the result becomes -the current position of the reflecting wall. Equal-style variables -can specify formulas with various mathematical functions, and include -"thermo_style"_thermo_style.html command keywords for the simulation -box parameters and timestep and elapsed time. Thus it is easy to -specify a time-dependent wall position. - -NOTE: Because the trajectory of the SRD particle is tracked as it -collides with the wall, you must insure that r = distance of the -particle from the wall, is always > 0 for SRD particles, or LAMMPS -will generate an error. This means you cannot start your simulation -with SRD particles at the wall position {coord} (r = 0) or with -particles on the wrong side of the wall (r < 0). - -NOTE: If you have 2 or more walls that come together at an edge or -corner (e.g. walls in the x and y dimensions), then be sure to set the -{overlap} keyword to {yes} in the "fix srd"_fix_srd.html command, -since the walls effectively overlap when SRD particles collide with -them. LAMMPS will issue a warning if you do not do this. - -NOTE: The walls of this fix only interact with SRD particles, as -defined by the "fix srd"_fix_srd.html command. If you are simulating -a mixture containing other kinds of particles, then you should -typically use "another wall command"_fix_wall.html to act on the other -particles. Since SRD particles will be colliding both with the walls -and the other particles, it is important to insure that the other -particle's finite extent does not overlap an SRD wall. If you do not -do this, you may generate errors when SRD particles end up "inside" -another particle or a wall at the beginning of a collision step. - -The {units} keyword determines the meaning of the distance units used -to define a wall position, but only when a numeric constant is used. -It is not relevant when EDGE or a variable is used to specify a face -position. - -A {box} value selects standard distance units as defined by the -"units"_units.html command, e.g. Angstroms for units = real or metal. -A {lattice} value means the distance units are in lattice spacings. -The "lattice"_lattice.html command must have been previously used to -define the lattice spacings. - -:line - -Here are examples of variable definitions that move the wall position -in a time-dependent fashion using equal-style -"variables"_variable.html. - - -variable ramp equal ramp(0,10) -fix 1 all wall/srd xlo v_ramp :pre - -variable linear equal vdisplace(0,20) -fix 1 all wall/srd xlo v_linear :pre - -variable wiggle equal swiggle(0.0,5.0,3.0) -fix 1 all wall/srd xlo v_wiggle :pre - -variable wiggle equal cwiggle(0.0,5.0,3.0) -fix 1 all wall/srd xlo v_wiggle :pre - -The ramp(lo,hi) function adjusts the wall position linearly from lo to -hi over the course of a run. The displace(c0,velocity) function does -something similar using the equation position = c0 + velocity*delta, -where delta is the elapsed time. - -The swiggle(c0,A,period) function causes the wall position to -oscillate sinusoidally according to this equation, where omega = 2 PI -/ period: - -position = c0 + A sin(omega*delta) :pre - -The cwiggle(c0,A,period) function causes the wall position to -oscillate sinusoidally according to this equation, which will have an -initial wall velocity of 0.0, and thus may impose a gentler -perturbation on the particles: - -position = c0 + A (1 - cos(omega*delta)) :pre - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. - -This fix computes a global array of values which can be accessed by -various "output commands"_Howto_output.html. The number of rows in -the array is equal to the number of walls defined by the fix. The -number of columns is 3, for the x,y,z components of force on each -wall. - -Note that an outward normal force on a wall will be a negative value -for {lo} walls and a positive value for {hi} walls. The array values -calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. - -[Restrictions:] - -Any dimension (xyz) that has an SRD wall must be non-periodic. - -[Related commands:] - -"fix srd"_fix_srd.html - -[Default:] none diff --git a/doc/txt/group.txt b/doc/txt/group.txt deleted file mode 100644 index 256c4ed7f5..0000000000 --- a/doc/txt/group.txt +++ /dev/null @@ -1,294 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -group command :h3 - -[Syntax:] - -group ID style args :pre - -ID = user-defined name of the group :ulb,l -style = {delete} or {clear} or {empty} or {region} or \ - {type} or {id} or {molecule} or {variable} or \ - {include} or {subtract} or {union} or {intersect} or \ - {dynamic} or {static} :l - {delete} = no args - {clear} = no args - {empty} = no args - {region} args = region-ID - {type} or {id} or {molecule} - args = list of one or more atom types, atom IDs, or molecule IDs - any entry in list can be a sequence formatted as A:B or A:B:C where - A = starting index, B = ending index, - C = increment between indices, 1 if not specified - args = logical value - logical = "<" or "<=" or ">" or ">=" or "==" or "!=" - value = an atom type or atom ID or molecule ID (depending on {style}) - args = logical value1 value2 - logical = "<>" - value1,value2 = atom types or atom IDs or molecule IDs (depending on {style}) - {variable} args = variable-name - {include} args = molecule - molecule = add atoms to group with same molecule ID as atoms already in group - {subtract} args = two or more group IDs - {union} args = one or more group IDs - {intersect} args = two or more group IDs - {dynamic} args = parent-ID keyword value ... - one or more keyword/value pairs may be appended - keyword = {region} or {var} or {every} - {region} value = region-ID - {var} value = name of variable - {property} value = name of per-atom property - {every} value = N = update group every this many timesteps - {static} = no args :pre -:ule - -[Examples:] - -group edge region regstrip -group water type 3 4 -group sub id 10 25 50 -group sub id 10 25 50 500:1000 -group sub id 100:10000:10 -group sub id <= 150 -group polyA molecule <> 50 250 -group hienergy variable eng -group hienergy include molecule -group boundary subtract all a2 a3 -group boundary union lower upper -group boundary intersect upper flow -group boundary delete -group mine dynamic all region myRegion every 100 :pre - - -[Description:] - -Identify a collection of atoms as belonging to a group. The group ID -can then be used in other commands such as "fix"_fix.html, -"compute"_compute.html, "dump"_dump.html, or "velocity"_velocity.html -to act on those atoms together. - -If the group ID already exists, the group command adds the specified -atoms to the group. - -NOTE: By default groups are static, meaning the atoms are permanently -assigned to the group. For example, if the {region} style is used to -assign atoms to a group, the atoms will remain in the group even if -they later move out of the region. As explained below, the {dynamic} -style can be used to make a group dynamic so that a periodic -determination is made as to which atoms are in the group. Since many -LAMMPS commands operate on groups of atoms, you should think carefully -about whether making a group dynamic makes sense for your model. - -A group with the ID {all} is predefined. All atoms belong to this -group. This group cannot be deleted, or made dynamic. - -The {delete} style removes the named group and un-assigns all atoms -that were assigned to that group. Since there is a restriction (see -below) that no more than 32 groups can be defined at any time, the -{delete} style allows you to remove groups that are no longer needed, -so that more can be specified. You cannot delete a group if it has -been used to define a current "fix"_fix.html or "compute"_compute.html -or "dump"_dump.html. - -The {clear} style un-assigns all atoms that were assigned to that -group. This may be dangerous to do during a simulation run, -e.g. using the "run every"_run.html command if a fix or compute or -other operation expects the atoms in the group to remain constant, but -LAMMPS does not check for this. - -The {empty} style creates an empty group, which is useful for commands -like "fix gcmc"_fix_gcmc.html or with complex scripts that add atoms -to a group. - -The {region} style puts all atoms in the region volume into the group. -Note that this is a static one-time assignment. The atoms remain -assigned (or not assigned) to the group even in they later move out of -the region volume. - -The {type}, {id}, and {molecule} styles put all atoms with the -specified atom types, atom IDs, or molecule IDs into the group. These -3 styles can use arguments specified in one of two formats. - -The first format is a list of values (types or IDs). For example, the -2nd command in the examples above puts all atoms of type 3 or 4 into -the group named {water}. Each entry in the list can be a -colon-separated sequence A:B or A:B:C, as in two of the examples -above. A "sequence" generates a sequence of values (types or IDs), -with an optional increment. The first example with 500:1000 has the -default increment of 1 and would add all atom IDs from 500 to 1000 -(inclusive) to the group sub, along with 10,25,50 since they also -appear in the list of values. The second example with 100:10000:10 -uses an increment of 10 and would thus would add atoms IDs -100,110,120, ... 9990,10000 to the group sub. - -The second format is a {logical} followed by one or two values (type -or ID). The 7 valid logicals are listed above. All the logicals -except <> take a single argument. The 3rd example above adds all -atoms with IDs from 1 to 150 to the group named {sub}. The logical <> -means "between" and takes 2 arguments. The 4th example above adds all -atoms belonging to molecules with IDs from 50 to 250 (inclusive) to -the group named polyA. - -The {variable} style evaluates a variable to determine which atoms to -add to the group. It must be an "atom-style variable"_variable.html -previously defined in the input script. If the variable evaluates -to a non-zero value for a particular atom, then that atom is added -to the specified group. - -Atom-style variables can specify formulas that include thermodynamic -quantities, per-atom values such as atom coordinates, or per-atom -quantities calculated by computes, fixes, or other variables. They -can also include Boolean logic where 2 numeric values are compared to -yield a 1 or 0 (effectively a true or false). Thus using the -{variable} style, is a general way to flag specific atoms to include -or exclude from a group. - -For example, these lines define a variable "eatom" that calculates the -potential energy of each atom and includes it in the group if its -potential energy is above the threshold value -3.0. - -compute 1 all pe/atom -compute 2 all reduce sum c_1 -thermo_style custom step temp pe c_2 -run 0 :pre - -variable eatom atom "c_1 > -3.0" -group hienergy variable eatom :pre - -Note that these lines - -compute 2 all reduce sum c_1 -thermo_style custom step temp pe c_2 -run 0 :pre - -are necessary to insure that the "eatom" variable is current when the -group command invokes it. Because the eatom variable computes the -per-atom energy via the pe/atom compute, it will only be current if a -run has been performed which evaluated pairwise energies, and the -pe/atom compute was actually invoked during the run. Printing the -thermodynamic info for compute 2 insures that this is the case, since -it sums the pe/atom compute values (in the reduce compute) to output -them to the screen. See the "Variable Accuracy" section of the -"variable"_variable.html doc page for more details on insuring that -variables are current when they are evaluated between runs. - -The {include} style with its arg {molecule} adds atoms to a group that -have the same molecule ID as atoms already in the group. The molecule -ID = 0 is ignored in this operation, since it is assumed to flag -isolated atoms that are not part of molecules. An example of where -this operation is useful is if the {region} style has been used -previously to add atoms to a group that are within a geometric region. -If molecules straddle the region boundary, then atoms outside the -region that are part of molecules with atoms inside the region will -not be in the group. Using the group command a 2nd time with {include -molecule} will add those atoms that are outside the region to the -group. - -NOTE: The {include molecule} operation is relatively expensive in a -parallel sense. This is because it requires communication of relevant -molecule IDs between all the processors and each processor to loop -over its atoms once per processor, to compare its atoms to the list of -molecule IDs from every other processor. Hence it scales as N, rather -than N/P as most of the group operations do, where N is the number of -atoms, and P is the number of processors. - -The {subtract} style takes a list of two or more existing group names -as arguments. All atoms that belong to the 1st group, but not to any -of the other groups are added to the specified group. - -The {union} style takes a list of one or more existing group names as -arguments. All atoms that belong to any of the listed groups are -added to the specified group. - -The {intersect} style takes a list of two or more existing group names -as arguments. Atoms that belong to every one of the listed groups are -added to the specified group. - -:line - -The {dynamic} style flags an existing or new group as dynamic. This -means atoms will be (re)assigned to the group periodically as a -simulation runs. This is in contrast to static groups where atoms are -permanently assigned to the group. The way the assignment occurs is -as follows. Only atoms in the group specified as the parent group via -the parent-ID are assigned to the dynamic group before the following -conditions are applied. If the {region} keyword is used, atoms not in -the specified region are removed from the dynamic group. If the {var} -keyword is used, the variable name must be an atom-style or -atomfile-style variable. The variable is evaluated and atoms whose -per-atom values are 0.0, are removed from the dynamic group. If the {property} -keyword is used, the per-atom property name must be a previously defined -per-atom property. The per-atom property is evaluated and atoms whose -values are 0.0 are removed from the dynamic group. - -The assignment of atoms to a dynamic group is done at the beginning of -each run and on every timestep that is a multiple of {N}, which is the -argument for the {every} keyword (N = 1 is the default). For an -energy minimization, via the "minimize"_minimize.html command, an -assignment is made at the beginning of the minimization, but not -during the iterations of the minimizer. - -The point in the timestep at which atoms are assigned to a dynamic -group is after the initial stage of velocity Verlet time integration -has been performed, and before neighbor lists or forces are computed. -This is the point in the timestep where atom positions have just -changed due to the time integration, so the region criterion should be -accurate, if applied. - -NOTE: If the {region} keyword is used to determine what atoms are in -the dynamic group, atoms can move outside of the simulation box -between reneighboring events. Thus if you want to include all atoms -on the left side of the simulation box, you probably want to set the -left boundary of the region to be outside the simulation box by some -reasonable amount (e.g. up to the cutoff of the potential), else they -may be excluded from the dynamic region. - -Here is an example of using a dynamic group to shrink the set of atoms -being integrated by using a spherical region with a variable radius -(shrinking from 18 to 5 over the course of the run). This could be -used to model a quench of the system, freezing atoms outside the -shrinking sphere, then converting the remaining atoms to a static -group and running further. - -variable nsteps equal 5000 -variable rad equal 18-(step/v_nsteps)*(18-5) -region ss sphere 20 20 0 v_rad -group mobile dynamic all region ss -fix 1 mobile nve -run $\{nsteps\} -group mobile static -run $\{nsteps\} :pre - -NOTE: All fixes and computes take a group ID as an argument, but they -do not all allow for use of a dynamic group. If you get an error -message that this is not allowed, but feel that it should be for the -fix or compute in question, then please post your reasoning to the -LAMMPS mail list and we can change it. - -The {static} style removes the setting for a dynamic group, converting -it to a static group (the default). The atoms in the static group are -those currently in the dynamic group. - -:line - -[Restrictions:] - -There can be no more than 32 groups defined at one time, including -"all". - -The parent group of a dynamic group cannot itself be a dynamic group. - -[Related commands:] - -"dump"_dump.html, "fix"_fix.html, "region"_region.html, -"velocity"_velocity.html - -[Default:] - -All atoms belong to the "all" group. diff --git a/doc/txt/group2ndx.txt b/doc/txt/group2ndx.txt deleted file mode 100644 index ed9bcb003a..0000000000 --- a/doc/txt/group2ndx.txt +++ /dev/null @@ -1,64 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -group2ndx command :h3 -ndx2group command :h3 - -[Syntax:] - -group2ndx file group-ID ... -ndx2group file group-ID ... :pre - -file = name of index file to write out or read in :ulb,l -zero or more group IDs may be appended :l -:ule - -[Examples:] - -group2ndx allindex.ndx -group2ndx someindex.ndx upper lower mobile -ndx2group someindex.ndx -ndx2group someindex.ndx mobile :pre - -[Description:] - -Write or read a Gromacs style index file in text format that associates -atom IDs with the corresponding group definitions. This index file can be -used with in combination with Gromacs analysis tools or to import group -definitions into the "fix colvars"_fix_colvars.html input file. It can -also be used to save and restore group definitions for static groups. - -The {group2ndx} command will write group definitions to an index file. -Without specifying any group IDs, all groups will be written to the index -file. When specifying group IDs, only those groups will be written to the -index file. In order to follow the Gromacs conventions, the group {all} -will be renamed to {System} in the index file. - -The {ndx2group} command will create of update group definitions from those -stored in an index file. Without specifying any group IDs, all groups except -{System} will be read from the index file and the corresponding groups -recreated. If a group of the same name already exists, it will be completely -reset. When specifying group IDs, those groups, if present, will be read -from the index file and restored. - -:line - -[Restrictions:] - -This command requires that atoms have atom IDs, since this is the -information that is written to the index file. - -These commands are part of the USER-COLVARS package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"group"_group.html, "dump"_dump.html, "fix colvars"_fix_colvars.html - -[Default:] none diff --git a/doc/txt/hyper.txt b/doc/txt/hyper.txt deleted file mode 100644 index b0428a7a3e..0000000000 --- a/doc/txt/hyper.txt +++ /dev/null @@ -1,192 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -hyper command :h3 - -[Syntax:] - -hyper N Nevent fix-ID compute-ID keyword values ... :pre - -N = # of timesteps to run :ulb,l -Nevent = check for events every this many steps :l -fix-ID = ID of a fix that applies a global or local bias potential, can be NULL :l -compute-ID = ID of a compute that identifies when an event has occurred :l -zero or more keyword/value pairs may be appended :l -keyword = {min} or {dump} or {rebond} :l - {min} values = etol ftol maxiter maxeval - etol = stopping tolerance for energy, used in quenching - ftol = stopping tolerance for force, used in quenching - maxiter = max iterations of minimize, used in quenching - maxeval = max number of force/energy evaluations, used in quenching - {dump} value = dump-ID - dump-ID = ID of dump to trigger whenever an event takes place - {rebond} value = Nrebond - Nrebond = frequency at which to reset bonds, even if no event has occurred - :pre -:ule - -[Examples:] - -compute event all event/displace 1.0 -fix HG mobile hyper/global 3.0 0.3 0.4 800.0 -hyper 5000 100 HG event min 1.0e-6 1.0e-6 100 100 dump 1 dump 5 :pre - -[Description:] - -Run a bond-boost hyperdynamics (HD) simulation where time is -accelerated by application of a bias potential to one or more pairs of -nearby atoms in the system. This command can be used to run both -global and local hyperdynamics. In global HD a single bond within the -system is biased on each timestep. In local HD multiple bonds -(separated by a sufficient distance) can be biased simultaneously at -each timestep. In the bond-boost hyperdynamics context, a "bond" is -not a covalent bond between a pair of atoms in a molecule. Rather it -is simply a pair of nearby atoms as discussed below. - -Both global and local HD are described in "(Voter2013)"_#Voter2013 by -Art Voter and collaborators. Similar to parallel replica dynamics -(PRD), global and local HD are methods for performing accelerated -dynamics that are suitable for infrequent-event systems that obey -first-order kinetics. A good overview of accelerated dynamics methods -for such systems in given in "(Voter2002)"_#Voter2002hd from the same -group. To quote from the review paper: "The dynamical evolution is -characterized by vibrational excursions within a potential basin, -punctuated by occasional transitions between basins." The transition -probability is characterized by p(t) = k*exp(-kt) where k is the rate -constant. Running multiple replicas gives an effective enhancement in -the timescale spanned by the multiple simulations, while waiting for -an event to occur. - -Both HD and PRD produce a time-accurate trajectory that effectively -extends the timescale over which a system can be simulated, but they -do it differently. HD uses a single replica of the system and -accelerates time by biasing the interaction potential in a manner such -that each timestep is effectively longer. PRD creates Nr replicas of -the system and runs dynamics on each independently with a normal -unbiased potential until an event occurs in one of the replicas. The -time between events is reduced by a factor of Nr replicas. For both -methods, per CPU second, more physical time elapses and more events -occur. See the "prd"_prd.html doc page for more info about PRD. - -An HD run has several stages, which are repeated each time an event -occurs, as explained below. The logic for an HD run is as follows: - -quench -create initial list of bonds :pre - -while (time remains): - run dynamics for Nevent steps - quench - check for an event - if event occurred: reset list of bonds - restore pre-quench state :pre - -The list of bonds is the list of atom pairs of atoms that are within a -short cutoff distance of each other after the system energy is -minimized (quenched). This list is created and reset by a "fix -hyper/global"_fix_hyper_global.html or "fix -hyper/local"_fix_hyper_local.html command specified as {fix-ID}. At -every dynamics timestep, the same fix selects one of more bonds to -apply a bias potential to. - -NOTE: The style of fix associated with the specified {fix-ID} -determines whether you are running the global versus local -hyperdynamics algorithm. - -Dynamics (with the bias potential) is run continuously, stopping every -{Nevent} steps to check if a transition event has occurred. The -specified {N} for total steps must be a multiple of {Nevent}. check -is performed by quenching the system and comparing the resulting atom -coordinates to the coordinates from the previous basin. - -A quench is an energy minimization and is performed by whichever -algorithm has been defined by the "min_style"_min_style.html command. -Minimization parameters may be set via the -"min_modify"_min_modify.html command and by the {min} keyword of the -hyper command. The latter are the settings that would be used with -the "minimize"_minimize.html command. Note that typically, you do not -need to perform a highly-converged minimization to detect a transition -event, though you may need to in order to prevent a set of atoms in -the system from relaxing to a saddle point. - -The event check is performed by a compute with the specified -{compute-ID}. Currently there is only one compute that works with the -hyper command, which is the "compute -event/displace"_compute_event_displace.html command. Other -event-checking computes may be added. "Compute -event/displace"_compute_event_displace.html checks whether any atom in -the compute group has moved further than a specified threshold -distance. If so, an event has occurred. - -If this happens, the list of bonds is reset, since some bond pairs -are likely now too far apart, and new pairs are likely close enough -to be considered a bond. The pre-quenched state of the -system (coordinates and velocities) is restored, and dynamics continue. - -At the end of the hyper run, a variety of statistics are output to the -screen and logfile. These include info relevant to both global and -local hyperdynamics, such as the number of events and the elapsed -hyper time (accelerated time), And it includes info specific to one or -the other, depending on which style of fix was specified by {fix-ID}. - -:line - -The optional keywords operate as follows. - -As explained above, the {min} keyword can be used to specify -parameters for the quench. Their meaning is the same -as for the "minimize"_minimize.html command - -The {dump} keyword can be used to trigger a specific dump command with -the specified {dump-ID} to output a snapshot each time an event is -detected. It can be specified multiple times with different {dump-ID} -values, as in the example above. These snapshots will be for the -quenched state of the system on a timestep that is a multiple of -{Nevent}, i.e. a timestep after the event has occurred. Note that any -dump command in the input script will also output snapshots at -whatever timestep interval it defines via its {N} argument; see the -"dump"_dump.html command for details. This means if you only want a -particular dump to output snapshots when events are detected, you -should specify its {N} as a value larger than the length of the -hyperdynamics run. - -As in the code logic above, the bond list is normally only reset when -an event occurs. The {rebond} keyword will force a reset of the bond -list every {Nrebond} steps, even if an event has not occurred. -{Nrebond} must be a multiple of {Nevent}. This can be useful to check -if more frequent resets alter event statistics, perhaps because the -parameters chosen for defining what is a bond and what is an event are -producing bad dynamics in the presence of the bias potential. - -:line - -[Restrictions:] - -This command can only be used if LAMMPS was built with the REPLICA -package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"fix hyper/global"_fix_hyper_global.html, "fix -hyper/local"_fix_hyper_local.html, "compute -event/displace"_compute_event_displace.html, "prd"_prd.html - -[Default:] - -The option defaults are min = 0.1 0.1 40 50 and time = steps. - -:line - -:link(Voter2013) -[(Voter2013)] S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139, -144110 (2013). - -:link(Voter2002hd) -[(Voter2002)] Voter, Montalenti, Germann, Annual Review of Materials -Research 32, 321 (2002). diff --git a/doc/txt/if.txt b/doc/txt/if.txt deleted file mode 100644 index ceec8f55db..0000000000 --- a/doc/txt/if.txt +++ /dev/null @@ -1,191 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -if command :h3 - -[Syntax:] - -if boolean then t1 t2 ... elif boolean f1 f2 ... elif boolean f1 f2 ... else e1 e2 ... :pre - -boolean = a Boolean expression evaluated as TRUE or FALSE (see below) -then = required word -t1,t2,...,tN = one or more LAMMPS commands to execute if condition is met, each enclosed in quotes -elif = optional word, can appear multiple times -f1,f2,...,fN = one or more LAMMPS commands to execute if elif condition is met, each enclosed in quotes (optional arguments) -else = optional argument -e1,e2,...,eN = one or more LAMMPS commands to execute if no condition is met, each enclosed in quotes (optional arguments) :ul - -[Examples:] - -if "$\{steps\} > 1000" then quit -if "$\{myString\} == a10" then quit -if "$x <= $y" then "print X is smaller = $x" else "print Y is smaller = $y" -if "($\{eng\} > 0.0) || ($n < 1000)" then & - "timestep 0.005" & -elif $n<10000 & - "timestep 0.01" & -else & - "timestep 0.02" & - "print 'Max step reached'" -if "$\{eng\} > $\{eng_previous\}" then "jump file1" else "jump file2" :pre - -[Description:] - -This command provides an if-then-else capability within an input -script. A Boolean expression is evaluated and the result is TRUE or -FALSE. Note that as in the examples above, the expression can contain -variables, as defined by the "variable"_variable.html command, which -will be evaluated as part of the expression. Thus a user-defined -formula that reflects the current state of the simulation can be used -to issue one or more new commands. - -If the result of the Boolean expression is TRUE, then one or more -commands (t1, t2, ..., tN) are executed. If it is FALSE, then Boolean -expressions associated with successive elif keywords are evaluated -until one is found to be true, in which case its commands (f1, f2, -..., fN) are executed. If no Boolean expression is TRUE, then the -commands associated with the else keyword, namely (e1, e2, ..., eN), -are executed. The elif and else keywords and their associated -commands are optional. If they aren't specified and the initial -Boolean expression is FALSE, then no commands are executed. - -The syntax for Boolean expressions is described below. - -Each command (t1, f1, e1, etc) can be any valid LAMMPS input script -command. If the command is more than one word, it must enclosed in -quotes, so it will be treated as a single argument, as in the examples -above. - -NOTE: If a command itself requires a quoted argument (e.g. a -"print"_print.html command), then double and single quotes can be used -and nested in the usual manner, as in the examples above and below. -The "Commands parse"_Commands_parse.html doc page has more details on -using quotes in arguments. Only one of level of nesting is allowed, -but that should be sufficient for most use cases. - -Note that by using the line continuation character "&", the if command -can be spread across many lines, though it is still a single command: - -if "$a < $b" then & - "print 'Minimum value = $a'" & - "run 1000" & -else & - 'print "Minimum value = $b"' & - "minimize 0.001 0.001 1000 10000" :pre - -Note that if one of the commands to execute is "quit"_quit.html, as in -the first example above, then executing the command will cause LAMMPS -to halt. - -Note that by jumping to a label in the same input script, the if -command can be used to break out of a loop. See the "variable -delete"_variable.html command for info on how to delete the associated -loop variable, so that it can be re-used later in the input script. - -Here is an example of a loop which checks every 1000 steps if the -system temperature has reached a certain value, and if so, breaks out -of the loop to finish the run. Note that any variable could be -checked, so long as it is current on the timestep when the run -completes. As explained on the "variable"_variable.html doc page, -this can be insured by including the variable in thermodynamic output. - -variable myTemp equal temp -label loop -variable a loop 1000 -run 1000 -if "$\{myTemp\} < 300.0" then "jump SELF break" -next a -jump SELF loop -label break -print "ALL DONE" :pre - -Here is an example of a double loop which uses the if and -"jump"_jump.html commands to break out of the inner loop when a -condition is met, then continues iterating through the outer loop. - -label loopa -variable a loop 5 - label loopb - variable b loop 5 - print "A,B = $a,$b" - run 10000 - if "$b > 2" then "jump SELF break" - next b - jump in.script loopb -label break -variable b delete -next a -jump SELF loopa :pre - -:line - -The Boolean expressions for the if and elif keywords have a C-like -syntax. Note that each expression is a single argument within the if -command. Thus if you want to include spaces in the expression for -clarity, you must enclose the entire expression in quotes. - -An expression is built out of numbers (which start with a digit or -period or minus sign) or strings (which start with a letter and can -contain alphanumeric characters or underscores): - -0.2, 100, 1.0e20, -15.4, etc -InP, myString, a123, ab_23_cd, etc :pre - -and Boolean operators: - -A == B, A != B, A < B, A <= B, A > B, A >= B, A && B, A || B, A |^ B, !A :pre - -Each A and B is a number or string or a variable reference like $a or -$\{abc\}, or A or B can be another Boolean expression. - -If a variable is used it can produce a number when evaluated, like an -"equal-style variable"_variable.html. Or it can produce a string, -like an "index-style variable"_variable.html. For an individual -Boolean operator, A and B must both be numbers or must both be -strings. You cannot compare a number to a string. - -Expressions are evaluated left to right and have the usual C-style -precedence: the unary logical NOT operator "!" has the highest -precedence, the 4 relational operators "<", "<=", ">", and ">=" are -next; the two remaining relational operators "==" and "!=" are next; -then the logical AND operator "&&"; and finally the logical OR -operator "||" and logical XOR (exclusive or) operator "|^" have the -lowest precedence. Parenthesis can be used to group one or more -portions of an expression and/or enforce a different order of -evaluation than what would occur with the default precedence. - -When the 6 relational operators (first 6 in list above) compare 2 -numbers, they return either a 1.0 or 0.0 depending on whether the -relationship between A and B is TRUE or FALSE. When the 6 relational -operators compare 2 strings, they also return a 1.0 or 0.0 for TRUE or -FALSE, but the comparison is done by the C function strcmp(). - -When the 3 logical operators (last 3 in list above) compare 2 numbers, -they also return either a 1.0 or 0.0 depending on whether the -relationship between A and B is TRUE or FALSE (or just A). The -logical AND operator will return 1.0 if both its arguments are -non-zero, else it returns 0.0. The logical OR operator will return -1.0 if either of its arguments is non-zero, else it returns 0.0. The -logical XOR operator will return 1.0 if one of its arguments is zero -and the other non-zero, else it returns 0.0. The logical NOT operator -returns 1.0 if its argument is 0.0, else it returns 0.0. The 3 -logical operators can only be used to operate on numbers, not on -strings. - -The overall Boolean expression produces a TRUE result if the result is -non-zero. If the result is zero, the expression result is FALSE. - -:line - -[Restrictions:] none - -[Related commands:] - -"variable"_variable.html, "print"_print.html - -[Default:] none diff --git a/doc/txt/improper_class2.txt b/doc/txt/improper_class2.txt deleted file mode 100644 index 704944920e..0000000000 --- a/doc/txt/improper_class2.txt +++ /dev/null @@ -1,124 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style class2 command :h3 -improper_style class2/omp command :h3 -improper_style class2/kk command :h3 - -[Syntax:] - -improper_style class2 :pre - -[Examples:] - -improper_style class2 -improper_coeff 1 100.0 0 -improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06 :pre - -[Description:] - -The {class2} improper style uses the potential - -:c,image(Eqs/improper_class2.jpg) - -where Ei is the improper term and Eaa is an angle-angle term. The 3 X -terms in Ei are an average over 3 out-of-plane angles. - -The 4 atoms in an improper quadruplet (listed in the data file read by -the "read_data"_read_data.html command) are ordered I,J,K,L. X_IJKL -refers to the angle between the plane of I,J,K and the plane of J,K,L, -and the bond JK lies in both planes. Similarly for X_KJLI and X_LJIK. -Note that atom J appears in the common bonds (JI, JK, JL) of all 3 X -terms. Thus J (the 2nd atom in the quadruplet) is the atom of -symmetry in the 3 X angles. - -The subscripts on the various theta's refer to different combinations -of 3 atoms (I,J,K,L) used to form a particular angle. E.g. Theta_IJL -is the angle formed by atoms I,J,L with J in the middle. Theta1, -theta2, theta3 are the equilibrium positions of those angles. Again, -atom J (the 2nd atom in the quadruplet) is the atom of symmetry in the -theta angles, since it is always the center atom. - -Since atom J is the atom of symmetry, normally the bonds J-I, J-K, J-L -would exist for an improper to be defined between the 4 atoms, but -this is not required. - -See "(Sun)"_#improper-Sun for a description of the COMPASS class2 force field. - -Coefficients for the Ei and Eaa formulas must be defined for each -improper type via the "improper_coeff"_improper_coeff.html command as -in the example above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands. - -These are the 2 coefficients for the Ei formula: - -K (energy/radian^2) -X0 (degrees) :ul - -X0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. - -For the Eaa formula, each line in a -"improper_coeff"_improper_coeff.html command in the input script lists -7 coefficients, the first of which is "aa" to indicate they are -AngleAngle coefficients. In a data file, these coefficients should be -listed under a "AngleAngle Coeffs" heading and you must leave out the -"aa", i.e. only list 6 coefficients after the improper type. - -aa -M1 (energy/distance) -M2 (energy/distance) -M3 (energy/distance) -theta1 (degrees) -theta2 (degrees) -theta3 (degrees) :ul - -The theta values are specified in degrees, but LAMMPS converts them to -radians internally; hence the units of M are in energy/radian^2. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This improper style can only be used if LAMMPS was built with the -CLASS2 package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -[Default:] none - -:line - -:link(improper-Sun) -[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998). diff --git a/doc/txt/improper_coeff.txt b/doc/txt/improper_coeff.txt deleted file mode 100644 index 1d2083d7ad..0000000000 --- a/doc/txt/improper_coeff.txt +++ /dev/null @@ -1,89 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_coeff command :h3 - -[Syntax:] - -improper_coeff N args :pre - -N = improper type (see asterisk form below) -args = coefficients for one or more improper types :ul - -[Examples:] - -improper_coeff 1 300.0 0.0 -improper_coeff * 80.2 -1 2 -improper_coeff *4 80.2 -1 2 :pre - -[Description:] - -Specify the improper force field coefficients for one or more improper -types. The number and meaning of the coefficients depends on the -improper style. Improper coefficients can also be set in the data -file read by the "read_data"_read_data.html command or in a restart -file. - -N can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterisk can be -used to set the coefficients for multiple improper types. This takes -the form "*" or "*n" or "n*" or "m*n". If N = the number of improper -types, then an asterisk with no numeric values means all types from 1 -to N. A leading asterisk means all types from 1 to n (inclusive). A -trailing asterisk means all types from n to N (inclusive). A middle -asterisk means all types from m to n (inclusive). - -Note that using an improper_coeff command can override a previous -setting for the same improper type. For example, these commands set -the coeffs for all improper types, then overwrite the coeffs for just -improper type 2: - -improper_coeff * 300.0 0.0 -improper_coeff 2 50.0 0.0 :pre - -A line in a data file that specifies improper coefficients uses the -exact same format as the arguments of the improper_coeff command in an -input script, except that wild-card asterisks should not be used since -coefficients for all N types must be listed in the file. For example, -under the "Improper Coeffs" section of a data file, the line that -corresponds to the 1st example above would be listed as - -1 300.0 0.0 :pre - -The "improper_style class2"_improper_class2.html is an exception to -this rule, in that an additional argument is used in the input script -to allow specification of the cross-term coefficients. See its doc -page for details. - -:line - -The list of all improper styles defined in LAMMPS is given on the -"improper_style"_improper_style.html doc page. They are also listed -in more compact form on the "Commands -improper"_Commands_bond.html#improper doc page. - -On either of those pages, click on the style to display the formula it -computes and its coefficients as specified by the associated -improper_coeff command. - -:line - -[Restrictions:] - -This command must come after the simulation box is defined by a -"read_data"_read_data.html, "read_restart"_read_restart.html, or -"create_box"_create_box.html command. - -An improper style must be defined before any improper coefficients are -set, either in the input script or in a data file. - -[Related commands:] - -"improper_style"_improper_style.html - -[Default:] none diff --git a/doc/txt/improper_cossq.txt b/doc/txt/improper_cossq.txt deleted file mode 100644 index 8bd02afb84..0000000000 --- a/doc/txt/improper_cossq.txt +++ /dev/null @@ -1,85 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style cossq command :h3 -improper_style cossq/omp command :h3 - -[Syntax:] - -improper_style cossq :pre - -[Examples:] - -improper_style cossq -improper_coeff 1 4.0 0.0 :pre - -[Description:] - -The {cossq} improper style uses the potential - -:c,image(Eqs/improper_cossq.jpg) - -where x is the improper angle, x0 is its equilibrium value, and K is a -prefactor. - -If the 4 atoms in an improper quadruplet (listed in the data file read -by the "read_data"_read_data.html command) are ordered I,J,K,L then X -is the angle between the plane of I,J,K and the plane of J,K,L. -Alternatively, you can think of atoms J,K,L as being in a plane, and -atom I above the plane, and X as a measure of how far out-of-plane I -is with respect to the other 3 atoms. - -Note that defining 4 atoms to interact in this way, does not mean that -bonds necessarily exist between I-J, J-K, or K-L, as they would in a -linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an -improper to be defined between the 4 atoms. - -The following coefficients must be defined for each improper type via -the "improper_coeff"_improper_coeff.html command as in the example -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -K (energy) -X0 (degrees) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -[Default:] none diff --git a/doc/txt/improper_cvff.txt b/doc/txt/improper_cvff.txt deleted file mode 100644 index d57fddc512..0000000000 --- a/doc/txt/improper_cvff.txt +++ /dev/null @@ -1,86 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style cvff command :h3 -improper_style cvff/intel command :h3 -improper_style cvff/omp command :h3 - -[Syntax:] - -improper_style cvff :pre - -[Examples:] - -improper_style cvff -improper_coeff 1 80.0 -1 4 :pre - -[Description:] - -The {cvff} improper style uses the potential - -:c,image(Eqs/improper_cvff.jpg) - -where phi is the improper dihedral angle. - -If the 4 atoms in an improper quadruplet (listed in the data file read -by the "read_data"_read_data.html command) are ordered I,J,K,L then -the improper dihedral angle is between the plane of I,J,K and the -plane of J,K,L. Note that because this is effectively a dihedral -angle, the formula for this improper style is the same as for -"dihedral_style harmonic"_dihedral_harmonic.html. - -Note that defining 4 atoms to interact in this way, does not mean that -bonds necessarily exist between I-J, J-K, or K-L, as they would in a -linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an -improper to be defined between the 4 atoms. - -The following coefficients must be defined for each improper type via -the "improper_coeff"_improper_coeff.html command as in the example -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -K (energy) -d (+1 or -1) -n (0,1,2,3,4,6) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This improper style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -[Default:] none diff --git a/doc/txt/improper_distance.txt b/doc/txt/improper_distance.txt deleted file mode 100644 index bfd92f57ec..0000000000 --- a/doc/txt/improper_distance.txt +++ /dev/null @@ -1,58 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style distance command :h3 - -[Syntax:] - -improper_style distance - -[Examples:] - -improper_style distance -improper_coeff 1 80.0 100.0 :pre - -[Description:] - -The {distance} improper style uses the potential - -:c,image(Eqs/improper_dist-1.jpg) - -where d is the distance between the central atom and the plane formed -by the other three atoms. If the 4 atoms in an improper quadruplet -(listed in the data file read by the "read_data"_read_data.html -command) are ordered I,J,K,L then the I-atom is assumed to be the -central atom. - -:c,image(JPG/improper_distance.jpg) - -Note that defining 4 atoms to interact in this way, does not mean that -bonds necessarily exist between I-J, J-K, or K-L, as they would in a -linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an -improper to be defined between the 4 atoms. - -The following coefficients must be defined for each improper type via -the improper_coeff command as in the example above, or in the data -file or restart files read by the read_data or read_restart commands: - -K_2 (energy/distance^2) -K_4 (energy/distance^4) :ul - -:line - -[Restrictions:] - -This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -[Default:] none diff --git a/doc/txt/improper_distharm.txt b/doc/txt/improper_distharm.txt deleted file mode 100644 index 52815e76aa..0000000000 --- a/doc/txt/improper_distharm.txt +++ /dev/null @@ -1,53 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style distharm command :h3 - -[Syntax:] - -improper_style distharm - -[Examples:] - -improper_style distharm -improper_coeff 1 25.0 0.5 :pre - -[Description:] - -The {distharm} improper style uses the potential - -:c,image(Eqs/improper_distharm.jpg) - -where d is the oriented distance between the central atom and the plane formed -by the other three atoms. If the 4 atoms in an improper quadruplet -(listed in the data file read by the "read_data"_read_data.html -command) are ordered I,J,K,L then the L-atom is assumed to be the -central atom. Note that this is different from the convention used -in the improper_style distance. The distance d is oriented and can take -on negative values. This may lead to unwanted behavior if d0 is not equal to zero. - -The following coefficients must be defined for each improper type via -the improper_coeff command as in the example above, or in the data -file or restart files read by the read_data or read_restart commands: - -K (energy/distance^2) -d0 (distance) :ul - -:line - -[Restrictions:] - -This improper style can only be used if LAMMPS was built with the -USER-YAFF package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -[Default:] none diff --git a/doc/txt/improper_fourier.txt b/doc/txt/improper_fourier.txt deleted file mode 100644 index f4f59ed636..0000000000 --- a/doc/txt/improper_fourier.txt +++ /dev/null @@ -1,81 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style fourier command :h3 -improper_style fourier/omp command :h3 - -[Syntax:] - -improper_style fourier :pre - -[Examples:] - -improper_style fourier -improper_coeff 1 100.0 0.0 1.0 0.5 1 :pre - -[Description:] - -The {fourier} improper style uses the following potential: - -:c,image(Eqs/improper_fourier.jpg) - -where K is the force constant, C0, C1, C2 are dimensionless coefficients, -and omega is the angle between the IL axis and the IJK plane: - -:c,image(JPG/umbrella.jpg) - -If all parameter (see below) is not zero, the all the three possible angles will taken in account. - -The following coefficients must be defined for each improper type via -the "improper_coeff"_improper_coeff.html command as in the example -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -K (energy) -C0 (unitless) -C1 (unitless) -C2 (unitless) -all (0 or 1, optional) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -[Default:] none - diff --git a/doc/txt/improper_harmonic.txt b/doc/txt/improper_harmonic.txt deleted file mode 100644 index 1e9e7172f9..0000000000 --- a/doc/txt/improper_harmonic.txt +++ /dev/null @@ -1,90 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style harmonic command :h3 -improper_style harmonic/intel command :h3 -improper_style harmonic/kk command :h3 -improper_style harmonic/omp command :h3 - -[Syntax:] - -improper_style harmonic :pre - -[Examples:] - -improper_style harmonic -improper_coeff 1 100.0 0 :pre - -[Description:] - -The {harmonic} improper style uses the potential - -:c,image(Eqs/improper_harmonic.jpg) - -where X is the improper angle, X0 is its equilibrium value, and K is a -prefactor. Note that the usual 1/2 factor is included in K. - -If the 4 atoms in an improper quadruplet (listed in the data file read -by the "read_data"_read_data.html command) are ordered I,J,K,L then X -is the angle between the plane of I,J,K and the plane of J,K,L. -Alternatively, you can think of atoms J,K,L as being in a plane, and -atom I above the plane, and X as a measure of how far out-of-plane I -is with respect to the other 3 atoms. - -Note that defining 4 atoms to interact in this way, does not mean that -bonds necessarily exist between I-J, J-K, or K-L, as they would in a -linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an -improper to be defined between the 4 atoms. - -The following coefficients must be defined for each improper type via -the "improper_coeff"_improper_coeff.html command as in the example -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -K (energy/radian^2) -X0 (degrees) :ul - -X0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This improper style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -[Default:] none diff --git a/doc/txt/improper_hybrid.txt b/doc/txt/improper_hybrid.txt deleted file mode 100644 index 929eec43e1..0000000000 --- a/doc/txt/improper_hybrid.txt +++ /dev/null @@ -1,70 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style hybrid command :h3 - -[Syntax:] - -improper_style hybrid style1 style2 ... :pre - -style1,style2 = list of one or more improper styles :ul - -[Examples:] - -improper_style hybrid harmonic helix -improper_coeff 1 harmonic 120.0 30 -improper_coeff 2 cvff 20.0 -1 2 :pre - -[Description:] - -The {hybrid} style enables the use of multiple improper styles in one -simulation. An improper style is assigned to each improper type. For -example, impropers in a polymer flow (of improper type 1) could be -computed with a {harmonic} potential and impropers in the wall -boundary (of improper type 2) could be computed with a {cvff} -potential. The assignment of improper type to style is made via the -"improper_coeff"_improper_coeff.html command or in the data file. - -In the improper_coeff command, the first coefficient sets the improper -style and the remaining coefficients are those appropriate to that -style. In the example above, the 2 improper_coeff commands would set -impropers of improper type 1 to be computed with a {harmonic} -potential with coefficients 120.0, 30 for K, X0. Improper type 2 -would be computed with a {cvff} potential with coefficients 20.0, -1, -2 for K, d, n. - -If the improper {class2} potential is one of the hybrid styles, it -requires additional AngleAngle coefficients be specified in the data -file. These lines must also have an additional "class2" argument -added after the improper type. For improper types which are assigned -to other hybrid styles, use the style name (e.g. "harmonic") -appropriate to that style. The AngleAngle coeffs for that improper -type will then be ignored. - -An improper style of {none} can be specified as the 2nd argument to -the improper_coeff command, if you desire to turn off certain improper -types. - -:line - -[Restrictions:] - -This improper style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -Unlike other improper styles, the hybrid improper style does not store -improper coefficient info for individual sub-styles in a "binary -restart files"_restart.html. Thus when restarting a simulation from a -restart file, you need to re-specify improper_coeff commands. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -[Default:] none diff --git a/doc/txt/improper_inversion_harmonic.txt b/doc/txt/improper_inversion_harmonic.txt deleted file mode 100644 index bf114daeb0..0000000000 --- a/doc/txt/improper_inversion_harmonic.txt +++ /dev/null @@ -1,65 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style inversion/harmonic command :h3 - -[Syntax:] - -improper_style inversion/harmonic :pre - -[Examples:] - -improper_style inversion/harmonic -improper_coeff 1 18.776340 0.000000 :pre - -[Description:] - -The {inversion/harmonic} improper style follows the Wilson-Decius -out-of-plane angle definition and uses an harmonic potential: - -:c,image(Eqs/improper_inversion_harmonic.jpg) - -where K is the force constant and omega is the angle evaluated for -all three axis-plane combinations centered around the atom I. For -the IL axis and the IJK plane omega looks as follows: - -:c,image(JPG/umbrella.jpg) - -Note that the {inversion/harmonic} angle term evaluation differs to -the "improper_umbrella"_improper_umbrella.html due to the cyclic -evaluation of all possible angles omega. - -The following coefficients must be defined for each improper type via -the "improper_coeff"_improper_coeff.html command as in the example -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -K (energy) -omega0 (degrees) :ul - -If omega0 = 0 the potential term has a minimum for the planar -structure. Otherwise it has two minima at +/- omega0, with a barrier -in between. - -:line - -[Restrictions:] - -This improper style can only be used if LAMMPS was built with the -USER-MOFFF package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -[Default:] none - -:line - diff --git a/doc/txt/improper_none.txt b/doc/txt/improper_none.txt deleted file mode 100644 index 78a7489837..0000000000 --- a/doc/txt/improper_none.txt +++ /dev/null @@ -1,34 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style none command :h3 - -[Syntax:] - -improper_style none :pre - -[Examples:] - -improper_style none :pre - -[Description:] - -Using an improper style of none means improper forces and energies are -not computed, even if quadruplets of improper atoms were listed in the -data file read by the "read_data"_read_data.html command. - -See the "improper_style zero"_improper_zero.html command for a way to -calculate improper statistics, but compute no improper interactions. - -[Restrictions:] none - -[Related commands:] - -"improper_style zero"_improper_zero.html - -[Default:] none diff --git a/doc/txt/improper_ring.txt b/doc/txt/improper_ring.txt deleted file mode 100644 index 8a2ee29e17..0000000000 --- a/doc/txt/improper_ring.txt +++ /dev/null @@ -1,92 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style ring command :h3 -improper_style ring/omp command :h3 - -[Syntax:] - -improper_style ring :pre - -[Examples:] - -improper_style ring -improper_coeff 1 8000 70.5 :pre - -[Description:] - -The {ring} improper style uses the potential - -:c,image(Eqs/improper_ring.jpg) - -where K is a prefactor, theta is the angle formed by the atoms -specified by (i,j,k,l) indices and theta0 its equilibrium value. - -If the 4 atoms in an improper quadruplet (listed in the data file read -by the "read_data"_read_data.html command) are ordered i,j,k,l then -theta_{ijl} is the angle between atoms i,j and l, theta_{ijk} is the -angle between atoms i,j and k, theta_{kjl} is the angle between atoms -j,k, and l. - -The "ring" improper style implements the improper potential introduced -by Destree et al., in Equation (9) of "(Destree)"_#Destree. This -potential does not affect small amplitude vibrations but is used in an -ad-hoc way to prevent the onset of accidentally large amplitude -fluctuations leading to the occurrence of a planar conformation of the -three bonds i-j, j-k and j-l, an intermediate conformation toward the -chiral inversion of a methine carbon. In the "Impropers" section of -data file four atoms: i, j, k and l are specified with i,j and l lying -on the backbone of the chain and k specifying the chirality of j. - -The following coefficients must be defined for each improper type via -the "improper_coeff"_improper_coeff.html command as in the example -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -K (energy) -theta0 (degrees) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -:link(Destree) -[(Destree)] M. Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert, -J Chem Phys, 112, 9632 (2000). - diff --git a/doc/txt/improper_sqdistharm.txt b/doc/txt/improper_sqdistharm.txt deleted file mode 100644 index 7473fd8c5d..0000000000 --- a/doc/txt/improper_sqdistharm.txt +++ /dev/null @@ -1,54 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style sqdistharm command :h3 - -[Syntax:] - -improper_style sqdistharm - -[Examples:] - -improper_style sqdistharm -improper_coeff 1 50.0 0.1 :pre - -[Description:] - -The {sqdistharm} improper style uses the potential - -:c,image(Eqs/improper_sqdistharm.jpg) - -where d is the distance between the central atom and the plane formed -by the other three atoms. If the 4 atoms in an improper quadruplet -(listed in the data file read by the "read_data"_read_data.html -command) are ordered I,J,K,L then the L-atom is assumed to be the -central atom. Note that this is different from the convention used -in the improper_style distance. - -The following coefficients must be defined for each improper type via -the improper_coeff command as in the example above, or in the data -file or restart files read by the read_data or read_restart commands: - -K (energy/distance^4) -d0^2 (distance^2) :ul - -Note that d0^2 (in units distance^2) has be provided and not d0. - -:line - -[Restrictions:] - -This improper style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -[Default:] none diff --git a/doc/txt/improper_style.txt b/doc/txt/improper_style.txt deleted file mode 100644 index cd72da4d07..0000000000 --- a/doc/txt/improper_style.txt +++ /dev/null @@ -1,107 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style command :h3 - -[Syntax:] - -improper_style style :pre - -style = {none} or {hybrid} or {class2} or {cvff} or {harmonic} :ul - -[Examples:] - -improper_style harmonic -improper_style cvff -improper_style hybrid cvff harmonic :pre - -[Description:] - -Set the formula(s) LAMMPS uses to compute improper interactions -between quadruplets of atoms, which remain in force for the duration -of the simulation. The list of improper quadruplets is read in by a -"read_data"_read_data.html or "read_restart"_read_restart.html command -from a data or restart file. Note that the ordering of the 4 atoms in -an improper quadruplet determines the definition of the improper -angle used in the formula for each style. See the doc pages of -individual styles for details. - -Hybrid models where impropers are computed using different improper -potentials can be setup using the {hybrid} improper style. - -The coefficients associated with an improper style can be specified in -a data or restart file or via the "improper_coeff"_improper_coeff.html -command. - -All improper potentials store their coefficient data in binary restart -files which means improper_style and -"improper_coeff"_improper_coeff.html commands do not need to be -re-specified in an input script that restarts a simulation. See the -"read_restart"_read_restart.html command for details on how to do -this. The one exception is that improper_style {hybrid} only stores -the list of sub-styles in the restart file; improper coefficients need -to be re-specified. - -NOTE: When both an improper and pair style is defined, the -"special_bonds"_special_bonds.html command often needs to be used to -turn off (or weight) the pairwise interaction that would otherwise -exist between a group of 4 bonded atoms. - -:line - -Here is an alphabetic list of improper styles defined in LAMMPS. -Click on the style to display the formula it computes and coefficients -specified by the associated "improper_coeff"_improper_coeff.html -command. - -Click on the style to display the formula it computes, any additional -arguments specified in the improper_style command, and coefficients -specified by the associated "improper_coeff"_improper_coeff.html -command. - -There are also additional accelerated pair styles included in the -LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the "Commands -improper"_Commands_bond.html#improper doc page are followed by one or -more of (g,i,k,o,t) to indicate which accelerated styles exist. - -"none"_improper_none.html - turn off improper interactions -"zero"_improper_zero.html - topology but no interactions -"hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul - -"class2"_improper_class2.html - COMPASS (class 2) improper -"cossq"_improper_cossq.html - improper with a cosine squared term -"cvff"_improper_cvff.html - CVFF improper -"distance"_improper_distance.html - improper based on distance between atom planes -"distharm"_improper_distharm.html - improper that is harmonic in the out-of-plane distance -"fourier"_improper_fourier.html - improper with multiple cosine terms -"harmonic"_improper_harmonic.html - harmonic improper -"inversion/harmonic"_improper_inversion_harmonic.html - harmonic improper with Wilson-Decius out-of-plane definition -"ring"_improper_ring.html - improper which prevents planar conformations -"umbrella"_improper_umbrella.html - DREIDING improper :ul -"sqdistharm"_improper_sqdistharm.html - improper that is harmonic in the square of the out-of-plane distance - -:line - -[Restrictions:] - -Improper styles can only be set for atom_style choices that allow -impropers to be defined. - -Most improper styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. The doc pages for -individual improper potentials tell if it is part of a package. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -[Default:] - -improper_style none :pre diff --git a/doc/txt/improper_umbrella.txt b/doc/txt/improper_umbrella.txt deleted file mode 100644 index 9fe6ac07e1..0000000000 --- a/doc/txt/improper_umbrella.txt +++ /dev/null @@ -1,89 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style umbrella command :h3 -improper_style umbrella/omp command :h3 - -[Syntax:] - -improper_style umbrella :pre - -[Examples:] - -improper_style umbrella -improper_coeff 1 100.0 180.0 :pre - -[Description:] - -The {umbrella} improper style uses the following potential, which is -commonly referred to as a classic inversion and used in the -"DREIDING"_Howto_bioFF.html force field: - -:c,image(Eqs/improper_umbrella.jpg) - -where K is the force constant and omega is the angle between the IL -axis and the IJK plane: - -:c,image(JPG/umbrella.jpg) - -If omega0 = 0 the potential term has a minimum for the planar -structure. Otherwise it has two minima at +/- omega0, with a barrier -in between. - -See "(Mayo)"_#umbrella-Mayo for a description of the DREIDING force field. - -The following coefficients must be defined for each improper type via -the "improper_coeff"_improper_coeff.html command as in the example -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -K (energy) -omega0 (degrees) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This improper style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"improper_coeff"_improper_coeff.html - -[Default:] none - -:line - -:link(umbrella-Mayo) -[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990), diff --git a/doc/txt/improper_zero.txt b/doc/txt/improper_zero.txt deleted file mode 100644 index f3f3485b57..0000000000 --- a/doc/txt/improper_zero.txt +++ /dev/null @@ -1,48 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -improper_style zero command :h3 - -[Syntax:] - -improper_style zero {nocoeff} :pre - -[Examples:] - -improper_style zero -improper_style zero nocoeff -improper_coeff * :pre - -[Description:] - -Using an improper style of zero means improper forces and energies are -not computed, but the geometry of improper quadruplets is still -accessible to other commands. - -As an example, the "compute -improper/local"_compute_improper_local.html command can be used to -compute the chi values for the list of quadruplets of improper atoms -listed in the data file read by the "read_data"_read_data.html -command. If no improper style is defined, this command cannot be -used. - -The optional {nocoeff} flag allows to read data files with a ImproperCoeff -section for any improper style. Similarly, any improper_coeff commands -will only be checked for the improper type number and the rest ignored. - -Note that the "improper_coeff"_improper_coeff.html command must be -used for all improper types, though no additional values are -specified. - -[Restrictions:] none - -[Related commands:] none - -"improper_style none"_improper_none.html - -[Default:] none diff --git a/doc/txt/include.txt b/doc/txt/include.txt deleted file mode 100644 index c114056313..0000000000 --- a/doc/txt/include.txt +++ /dev/null @@ -1,40 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -include command :h3 - -[Syntax:] - -include file :pre - -file = filename of new input script to switch to :ul - -[Examples:] - -include newfile -include in.run2 :pre - -[Description:] - -This command opens a new input script file and begins reading LAMMPS -commands from that file. When the new file is finished, the original -file is returned to. Include files can be nested as deeply as -desired. If input script A includes script B, and B includes A, then -LAMMPS could run for a long time. - -If the filename is a variable (see the "variable"_variable.html -command), different processor partitions can run different input -scripts. - -[Restrictions:] none - -[Related commands:] - -"variable"_variable.html, "jump"_jump.html - -[Default:] none diff --git a/doc/txt/info.txt b/doc/txt/info.txt deleted file mode 100644 index 99211de4fb..0000000000 --- a/doc/txt/info.txt +++ /dev/null @@ -1,122 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -info command :h3 - -[Syntax:] - -info args :pre - -args = one or more of the following keywords: {out}, {all}, {system}, {memory}, {communication}, {computes}, {dumps}, {fixes}, {groups}, {regions}, {variables}, {coeffs}, {styles}, {time}, or {configuration} - {out} values = {screen}, {log}, {append} filename, {overwrite} filename - {styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {pair}, {region} :ul - -[Examples:] - -info system -info groups computes variables -info all out log -info all out append info.txt -info styles all -info styles atom :pre - -[Description:] - -Print out information about the current internal state of the running -LAMMPS process. This can be helpful when debugging or validating -complex input scripts. Several output categories are available and -one or more output category may be requested. - -The {out} flag controls where the output is sent. It can only be sent -to one target. By default this is the screen, if it is active. The -{log} argument selects the log file instead. With the {append} and -{overwrite} option, followed by a filename, the output is written -to that file, which is either appended to or overwritten, respectively. - -The {all} flag activates printing all categories listed below. - -The {configuration} category prints some information about the -LAMMPS version as well as architecture and OS it is run on. - -The {memory} category prints some information about the current -memory allocation of MPI rank 0 (this the amount of dynamically -allocated memory reported by LAMMPS classes). Where supported, -also some OS specific information about the size of the reserved -memory pool size (this is where malloc() and the new operator -request memory from) and the maximum resident set size is reported -(this is the maximum amount of physical memory occupied so far). - -The {system} category prints a general system overview listing. This -includes the unit style, atom style, number of atoms, bonds, angles, -dihedrals, and impropers and the number of the respective types, box -dimensions and properties, force computing styles and more. - -The {communication} category prints a variety of information about -communication and parallelization: the MPI library version level, -the number of MPI ranks and OpenMP threads, the communication style -and layout, the processor grid dimensions, ghost atom communication -mode, cutoff, and related settings. - -The {computes} category prints a list of all currently defined -computes, their IDs and styles and groups they operate on. - -The {dumps} category prints a list of all currently active dumps, -their IDs, styles, filenames, groups, and dump frequencies. - -The {fixes} category prints a list of all currently defined fixes, -their IDs and styles and groups they operate on. - -The {groups} category prints a list of all currently defined groups. - -The {regions} category prints a list of all currently defined regions, -their IDs and styles and whether "inside" or "outside" atoms are -selected. - -The {variables} category prints a list of all currently defined -variables, their names, styles, definition and last computed value, if -available. - -The {coeffs} category prints a list for each defined force style -(pair, bond, angle, dihedral, improper) indicating which of the -corresponding coefficients have been set. This can be very helpful -to debug error messages like "All pair coeffs are not set". - -The {styles} category prints the list of styles available in the -current LAMMPS binary. It supports one of the following options -to control which category of styles is printed out: - -all -angle -atom -bond -compute -command -dump -dihedral -fix -improper -integrate -kspace -minimize -pair -region :ul - -The {time} category prints the accumulated CPU and wall time for the -process that writes output (usually MPI rank 0). - -[Restrictions:] none - -[Related commands:] - -"print"_print.html - -[Default:] - -The {out} option has the default {screen}. - -The {styles} option has the default {all}. diff --git a/doc/txt/jump.txt b/doc/txt/jump.txt deleted file mode 100644 index 5bda178515..0000000000 --- a/doc/txt/jump.txt +++ /dev/null @@ -1,129 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -jump command :h3 - -[Syntax:] - -jump file label :pre - -file = filename of new input script to switch to -label = optional label within file to jump to :ul - -[Examples:] - -jump newfile -jump in.run2 runloop -jump SELF runloop :pre - -[Description:] - -This command closes the current input script file, opens the file with -the specified name, and begins reading LAMMPS commands from that file. -Unlike the "include"_include.html command, the original file is not -returned to, although by using multiple jump commands it is possible -to chain from file to file or back to the original file. - -If the word "SELF" is used for the filename, then the current input -script is re-opened and read again. - -NOTE: The SELF option is not guaranteed to work when the current input -script is being read through stdin (standard input), e.g. - -lmp_g++ < in.script :pre - -since the SELF option invokes the C-library rewind() call, which may -not be supported for stdin on some systems or by some MPI -implementations. This can be worked around by using the "-in -command-line switch"_Run_options.html, e.g. - -lmp_g++ -in in.script :pre - -or by using the "-var command-line switch"_Run_options.html to pass -the script name as a variable to the input script. In the latter -case, a "variable"_variable.html called "fname" could be used in place -of SELF, e.g. - -lmp_g++ -var fname in.script < in.script :pre - -The 2nd argument to the jump command is optional. If specified, it is -treated as a label and the new file is scanned (without executing -commands) until the label is found, and commands are executed from -that point forward. This can be used to loop over a portion of the -input script, as in this example. These commands perform 10 runs, -each of 10000 steps, and create 10 dump files named file.1, file.2, -etc. The "next"_next.html command is used to exit the loop after 10 -iterations. When the "a" variable has been incremented for the tenth -time, it will cause the next jump command to be skipped. - -variable a loop 10 -label loop -dump 1 all atom 100 file.$a -run 10000 -undump 1 -next a -jump in.lj loop :pre - -If the jump {file} argument is a variable, the jump command can be -used to cause different processor partitions to run different input -scripts. In this example, LAMMPS is run on 40 processors, with 4 -partitions of 10 procs each. An in.file containing the example -variable and jump command will cause each partition to run a different -simulation. - -mpirun -np 40 lmp_ibm -partition 4x10 -in in.file :pre - -variable f world script.1 script.2 script.3 script.4 -jump $f :pre - -Here is an example of a loop which checks every 1000 steps if the -system temperature has reached a certain value, and if so, breaks out -of the loop to finish the run. Note that any variable could be -checked, so long as it is current on the timestep when the run -completes. As explained on the "variable"_variable.html doc page, -this can be insured by including the variable in thermodynamic output. - -variable myTemp equal temp -label loop -variable a loop 1000 -run 1000 -if "$\{myTemp\} < 300.0" then "jump SELF break" -next a -jump SELF loop -label break -print "ALL DONE" :pre - -Here is an example of a double loop which uses the if and -"jump"_jump.html commands to break out of the inner loop when a -condition is met, then continues iterating through the outer loop. - -label loopa -variable a loop 5 - label loopb - variable b loop 5 - print "A,B = $a,$b" - run 10000 - if "$b > 2" then "jump SELF break" - next b - jump in.script loopb -label break -variable b delete -next a -jump SELF loopa :pre - -[Restrictions:] - -If you jump to a file and it does not contain the specified label, -LAMMPS will come to the end of the file and exit. - -[Related commands:] - -"variable"_variable.html, "include"_include.html, "label"_label.html, -"next"_next.html - -[Default:] none diff --git a/doc/txt/kim_commands.txt b/doc/txt/kim_commands.txt deleted file mode 100644 index e50950eae7..0000000000 --- a/doc/txt/kim_commands.txt +++ /dev/null @@ -1,780 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -kim_init command :h3 -kim_interactions command :h3 -kim_query command :h3 -kim_param command :h3 - -[Syntax:] - -kim_init model user_units unitarg -kim_interactions typeargs -kim_query variable formatarg query_function queryargs -kim_param get param_name index_range variables formatarg -kim_param set param_name index_range values -:pre - -:link(formatarg_options) -model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM) :ulb,l -user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script :l -unitarg = {unit_conversion_mode} (optional) :l -typeargs = atom type to species mapping (one entry per atom type) or {fixed_types} for models with a preset fixed mapping :l -variable(s) = single name or list of names of (string style) LAMMPS variable(s) where a query result or parameter get result is stored. Variables that do not exist will be created by the command. :l -formatarg = {list, split, or explicit} (optional): :l -{list} = returns a single string with a list of space separated values - (e.g. "1.0 2.0 3.0"), which is placed in a LAMMPS variable as - defined by the {variable} argument. \[default for {kim_query}\] -{split} = returns the values separately in new variables with names based - on the prefix specified in {variable} and a number appended to - indicate which element in the list of values is in the variable. -{explicit} = returns the values separately in one more more variable names - provided as arguments that preceed {formatarg}. \[default for {kim_param}\] :pre -query_function = name of the OpenKIM web API query function to be used :l -queryargs = a series of {keyword=value} pairs that represent the web query; supported keywords depend on the query function :l -param_name = name of a KIM portable model parameter :l -index_range = KIM portable model parameter index range (an integer for a single element, or pair of integers separated by a colon for a range of elements) :l -values = new value(s) to replace the current value(s) of a KIM portable model parameter :l,ule - - -[Examples:] - -kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal -kim_interactions Si -kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real -kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode -kim_interactions C H O -kim_init Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolventsPolymers__SM_039297821658_000 real -kim_interactions fixed_types -kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] -kim_param get gamma 1 varGamma -kim_param set gamma 1 3.0 -:pre - -[Description:] - -The set of {kim_commands} provide a high-level wrapper around the -"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org -repository of interatomic models (IMs) (potentials and force fields), -so that they can be used by LAMMPS scripts. These commands do not implement -any computations directly, but rather generate LAMMPS input commands based -on the information retrieved from the OpenKIM repository to initialize and -activate OpenKIM IMs and query their predictions for use in the LAMMPS script. -All LAMMPS input commands generated and executed by {kim_commands} are -echoed to the LAMMPS log file. - -Benefits of Using OpenKIM IMs :h4 - -Employing OpenKIM IMs provides LAMMPS users with multiple benefits: - -Reliability :h5 - -All content archived in OpenKIM is reviewed by the "KIM Editor"_https://openkim.org/governance/ for quality. -IMs in OpenKIM are archived with full provenance control. Each is associated with a maintainer responsible for the integrity of the content. All changes are tracked and recorded. -IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/doc/evaluation/kim-tests/ that compute a host of material properties, and "KIM Verification Checks"_https://openkim.org/doc/evaluation/kim-verification-checks/ that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM's page accessible through the "OpenKIM browse interface"_https://openkim.org/browse. :ul - -Reproducibility :h5 - -Each IM in OpenKIM is issued a unique identifier ("KIM ID"_https://openkim.org/doc/schema/kim-ids/), which includes a version number (last three digits). Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID. -OpenKIM is a member organization of "DataCite"_https://datacite.org/ and issues digital object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility. :ul - -Convenience :h5 - -IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the {kim_init} command documented on this page. -The {kim_query} web query tool provides the ability to use the predictions of IMs for supported material properties (computed via "KIM Tests"_https://openkim.org/doc/evaluation/kim-tests/) as part of a LAMMPS input script setup and analysis. -Support is provided for unit conversion between the "unit style"_units.html used in the LAMMPS input script and the units required by the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units. :ul - -:link(IM_types) -Types of IMs in OpenKIM :h4 - -There are two types of IMs archived in OpenKIM: - -:link(PM_type) -The first type is called a {KIM Portable Model} (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see "complete list of supported codes"_https://openkim.org/projects-using-kim/). -The second type is called a {KIM Simulator Model} (SM). A KIM SM is an IM that is implemented natively within a simulation code ({simulator}) that supports the KIM API Simulator Model Interface (SMI); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol - -With these two IM types, OpenKIM can archive and test almost all IMs that -can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see -the "upload instructions"_https://openkim.org/doc/repository/adding-content/.) - -OpenKIM IMs are uniquely identified by a -"KIM ID"_https://openkim.org/doc/schema/kim-ids/. -The extended KIM ID consists of -a human-readable prefix identifying the type of IM, authors, publication year, -and supported species, separated by two underscores from the KIM ID itself, -which begins with an IM code -({MO} for a KIM Portable Model, and {SM} for a KIM Simulator Model) -followed by a unique 12-digit code and a 3-digit version identifier. -By convention SM prefixes begin with {Sim_} to readily identify them. - -SW_StillingerWeber_1985_Si__MO_405512056662_005 -Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 :pre - -Each OpenKIM IM has a dedicated "Model Page" on "OpenKIM"_https://openkim.org -providing all the information on the IM including a title, description, -authorship and citation information, test and verification check results, -visualizations of results, a wiki with documentation and user comments, and -access to raw files, and other information. -The URL for the Model Page is constructed from the -"extended KIM ID"_https://openkim.org/doc/schema/kim-ids/ of the IM: - -https://openkim.org/id/extended_KIM_ID -:pre - -For example, for the Stillinger--Weber potential -listed above the Model Page is located at: - -"https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005 -:pre - -See the "current list of KIM PMs and SMs archived in OpenKIM"_https://openkim.org/browse/models/by-species. -This list is sorted by species and can be filtered to display only -IMs for certain species combinations. - -See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to -learn how to install a pre-build binary of the OpenKIM Repository of Models. - -NOTE: It is also possible to locally install IMs not archived in OpenKIM, -in which case their names do not have to conform to the KIM ID format. - -Using OpenKIM IMs with LAMMPS :h4 - -Two commands are employed when using OpenKIM IMs, one to select the -IM and perform necessary initialization ({kim_init}), and the second -to set up the IM for use by executing any necessary LAMMPS commands -({kim_interactions}). Both are required. - -See the {examples/kim} directory for example input scripts that use KIM PMs -and KIM SMs. - -OpenKIM IM Initialization ({kim_init}) :h5 - -The {kim_init} mode command must be issued [before] -the simulation box is created (normally at the top of the file). -This command sets the OpenKIM IM that will be used and may issue -additional commands changing LAMMPS default settings that are required -for using the selected IM (such as "units"_units.html or -"atom_style"_atom_style.html). If needed, those settings can be overridden, -however, typically a script containing a {kim_init} command -would not include {units} and {atom_style} commands. - -The required arguments of {kim_init} are the {model} name of the -IM to be used in the simulation (for an IM archived in OpenKIM this is -its "extended KIM ID"_https://openkim.org/doc/schema/kim-ids/, and -the {user_units}, which are the LAMMPS "units style"_units.html used -in the input script. (Any dimensioned numerical values in the input -script and values read in from files are expected to be in the -{user_units} system.) - -The selected IM can be either a "KIM PM or a KIM SM"_#IM_types. -For a KIM SM, the {kim_init} command verifies that the SM is designed -to work with LAMMPS (and not another simulation code). -In addition, the LAMMPS version used for defining -the SM and the LAMMPS version being currently run are -printed to help diagnose any incompatible changes to input script or -command syntax between the two LAMMPS versions. - -Based on the selected model {kim_init} may modify the -"atom_style"_atom_style.html. -Some SMs have requirements for this setting. If this is the case, then -{atom_style} will be set to the required style. Otherwise, the value is left -unchanged (which in the absence of an {atom_style} command in the input script -is the "default atom_style value"_atom_style.html). - -Regarding units, the {kim_init} command behaves in different ways depending -on whether or not {unit conversion mode} is activated as indicated by the -optional {unitarg} argument. -If unit conversion mode is [not] active, then {user_units} must -either match the required units of the IM or the IM must be able -to adjust its units to match. (The latter is only possible with some KIM PMs; -SMs can never adjust their units.) If a match is possible, the LAMMPS -"units"_units.html command is called to set the units to -{user_units}. If the match fails, the simulation is terminated with -an error. - -Here is an example of a LAMMPS script to compute the cohesive energy -of a face-centered cubic (fcc) lattice for the Ercolessi and Adams (1994) -potential for Al: - -kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal -boundary p p p -lattice fcc 4.032 -region simbox block 0 1 0 1 0 1 units lattice -create_box 1 simbox -create_atoms 1 box -mass 1 26.981539 -kim_interactions Al -run 0 -variable Ec equal (pe/count(all))/$\{_u_energy\} -print "Cohesive Energy = $\{EcJ\} eV" -:pre - -The above script will end with an error in the {kim_init} line if the -IM is changed to another potential for Al that does not work with {metal} -units. To address this {kim_init} offers the {unit_conversion_mode} -as shown below. -If unit conversion mode {is} active, then {kim_init} calls the LAMMPS -"units"_units.html command to set the units to the IM's required or -preferred units. Conversion factors between the IM's units and the {user_units} -are defined for all "physical quantities"_units.html (mass, distance, etc.). -(Note that converting to or from the "lj" unit style is not supported.) -These factors are stored as "internal style variables"_variable.html with -the following standard names: - -_u_mass -_u_distance -_u_time -_u_energy -_u_velocity -_u_force -_u_torque -_u_temperature -_u_pressure -_u_viscosity -_u_charge -_u_dipole -_u_efield -_u_density :pre - -If desired, the input script can be designed to work with these conversion -factors so that the script will work without change with any OpenKIM IM. -(This approach is used in the -"OpenKIM Testing Framework"_https://openkim.org/doc/evaluation/kim-tests/.) -For example, the script given above for the cohesive energy of fcc Al -can be rewritten to work with any IM regardless of units. The following -script constructs an fcc lattice with a lattice parameter defined in -meters, computes the total energy, and prints the cohesive energy in -Joules regardless of the units of the IM. - -kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode -boundary p p p -lattice fcc 4.032e-10*$\{_u_distance\} -region simbox block 0 1 0 1 0 1 units lattice -create_box 1 simbox -create_atoms 1 box -mass 1 4.480134e-26*$\{_u_mass\} -kim_interactions Al -run 0 -variable Ec_in_J equal (pe/count(all))/$\{_u_energy\} -print "Cohesive Energy = $\{Ec_in_J\} J" :pre - -Note the multiplication by $\{_u_distance\} and $\{_u_mass\} to convert -from SI units (specified in the {kim_init} command) to whatever units the -IM uses (metal in this case), and the division by $\{_u_energy\} -to convert from the IM's energy units to SI units (Joule). This script -will work correctly for any IM for Al (KIM PM or SM) selected by the -{kim_init} command. - -Care must be taken to apply unit conversion to dimensional variables read in -from a file. For example, if a configuration of atoms is read in from a -dump file using the "read_dump"_read_dump.html command, the following can -be done to convert the box and all atomic positions to the correct units: - -variable xyfinal equal xy*$\{_u_distance\} -variable xzfinal equal xz*$\{_u_distance\} -variable yzfinal equal yz*$\{_u_distance\} -change_box all x scale $\{_u_distance\} & - y scale $\{_u_distance\} & - z scale $\{_u_distance\} & - xy final $\{xyfinal\} & - xz final $\{xzfinal\} & - yz final $\{yzfinal\} & - remap :pre - -NOTE: Unit conversion will only work if the conversion factors are placed in -all appropriate places in the input script. It is up to the user to do this -correctly. - -OpenKIM IM Execution ({kim_interactions}) :h5 - -The second and final step in using an OpenKIM IM is to execute the -{kim_interactions} command. This command must be preceded by a {kim_init} -command and a command that defines the number of atom types {N} (such as -"create_box"_create_box.html). -The {kim_interactions} command has one argument {typeargs}. This argument -contains either a list of {N} chemical species, which defines a mapping between -atom types in LAMMPS to the available species in the OpenKIM IM, or the -keyword {fixed_types} for models that have a preset fixed mapping (i.e. -the mapping between LAMMPS atom types and chemical species is defined by -the model and cannot be changed). In the latter case, the user must consult -the model documentation to see how many atom types there are and how they -map to the chemical species. - -For example, consider an OpenKIM IM that supports Si and C species. -If the LAMMPS simulation has four atom types, where the first three are Si, -and the fourth is C, the following {kim_interactions} command would be used: - -kim_interactions Si Si Si C -:pre - -Alternatively, for a model with a fixed mapping the command would be: - -kim_interactions fixed_types -:pre - -The {kim_interactions} command performs all the necessary steps to set up -the OpenKIM IM selected in the {kim_init} command. The specific actions depend -on whether the IM is a KIM PM or a KIM SM. For a KIM PM, -a "pair_style kim"_pair_kim.html command is executed followed by -the appropriate {pair_coeff} command. For example, for the -Ercolessi and Adams (1994) KIM PM for Al set by the following commands: - -kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal -... -... box specification lines skipped -... -kim_interactions Al :pre - -the {kim_interactions} command executes the following LAMMPS input commands: - -pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 -pair_coeff * * Al :pre - -For a KIM SM, the generated input commands may be more complex -and require that LAMMPS is built with the required packages included -for the type of potential being used. The set of commands to be executed -is defined in the SM specification file, which is part of the SM package. -For example, for the Strachan et al. (2003) ReaxFF SM -set by the following commands: - -kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real -... -... box specification lines skipped -... -kim_interactions C H N O :pre - -the {kim_interactions} command executes the following LAMMPS input commands: - -pair_style reax/c lmp_control safezone 2.0 mincap 100 -pair_coeff * * ffield.reax.rdx C H N O -fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq :pre - -Note that the files {lmp_control}, {ffield.reax.rdx} and {param.qeq} -are specific to the Strachan et al. (2003) ReaxFF parameterization -and are archived as part of the SM package in OpenKIM. -Note also that parameters like cutoff radii and charge tolerances, -which have an effect on IM predictions, are also included in the -SM definition ensuring reproducibility. - -NOTE: When using {kim_init} and {kim_interactions} to select -and set up an OpenKIM IM, other LAMMPS commands -for the same functions (such as pair_style, pair_coeff, bond_style, -bond_coeff, fixes related to charge equilibration, etc.) should normally -not appear in the input script. - -Using OpenKIM Web Queries in LAMMPS ({kim_query}) :h5 - -The {kim_query} command performs a web query to retrieve the predictions -of an IM set by {kim_init} for material properties archived in -"OpenKIM"_https://openkim.org. - -NOTE: The {kim_query} command must be preceded by a {kim_init} command. - -The syntax for the {kim_query} command is as follows: - -kim_query variable formatarg query_function queryargs -:pre - -The result of the query is stored in one or more -"string style variables"_variable.html as determined by the -optional {formatarg} argument "documented above"_#formatarg_options. -For the "list" setting of {formatarg} (or if {formatarg} is not -specified), the result is returned as a space-separated list of -values in {variable}. -The {formatarg} keyword "split" separates the result values into -individual variables of the form {prefix_I}, where {prefix} is set to the -{kim_query} {variable} argument and {I} ranges from 1 to the number of -returned values. The number and order of the returned values is determined -by the type of query performed. (Note that the "explicit" setting of -{formatarg} is not supported by {kim_query}.) - -NOTE: {kim_query} only supports queries that return a single result or -an array of values. More complex queries that return a JSON structure -are not currently supported. An attempt to use {kim_query} in such -cases will generate an error. - -The second required argument {query_function} is the name of the -query function to be called (e.g. {get_lattice_constant_cubic}). -All following "arguments"_Commands_parse.html are parameters handed over to -the web query in the format {keyword=value}, where {value} is always -an array of one or more comma-separated items in brackets. -The list of supported keywords and the type and format of their values -depend on the query function used. The current list of query functions -is available on the OpenKIM webpage at -"https://openkim.org/doc/usage/kim-query"_https://openkim.org/doc/usage/kim-query. - -NOTE: All query functions require the {model} keyword, which identifies -the IM whose predictions are being queried. This keyword is automatically -generated by {kim_query} based on the IM set in {kim_init} and must not -be specified as an argument to {kim_query}. - -NOTE: Each {query_function} is associated with a default method (implemented -as a "KIM Test"_https://openkim.org/doc/evaluation/kim-tests/) -used to compute this property. In cases where there are multiple -methods in OpenKIM for computing a property, a {method} keyword can -be provided to select the method of choice. See the -"query documentation"_https://openkim.org/doc/repository/kim-query -to see which methods are available for a given {query function}. - -{kim_query} Usage Examples and Further Clarifications :h5 - -The data obtained by {kim_query} commands can be used as part of the setup -or analysis phases of LAMMPS simulations. Some examples are given below. - -[Define an equilibrium fcc crystal] - -kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal -boundary p p p -kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] -lattice fcc $\{a0\} -... :pre - -The {kim_query} command retrieves from "OpenKIM"_https://openkim.org -the equilibrium lattice constant predicted by the Ercolessi and Adams (1994) -potential for the fcc structure and places it in -variable {a0}. This variable is then used on the next line to set up the -crystal. By using {kim_query}, the user is saved the trouble and possible -error of tracking this value down, or of having to perform an energy -minimization to find the equilibrium lattice constant. - -Note that in {unit_conversion_mode} the results obtained from a -{kim_query} would need to be converted to the appropriate units system. -For example, in the above script, the lattice command would need to be -changed to: "lattice fcc $\{a0\}*$\{_u_distance\}". - -[Define an equilibrium hcp crystal] - -kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal -boundary p p p -kim_query latconst split get_lattice_constant_hexagonal crystal=\["hcp"\] species=\["Zr"\] units=\["angstrom"\] -variable a0 equal latconst_1 -variable c0 equal latconst_2 -variable c_to_a equal $\{c0\}/$\{a0\} -lattice custom $\{a0\} a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 $\{c_to_a\} & - basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 -... :pre - -In this case the {kim_query} returns two arguments (since the hexagonal -close packed (hcp) structure has two independent lattice constants). -The {formatarg} keyword "split" places the two values into -the variables {latconst_1} and {latconst_2}. (These variables are -created if they do not already exist.) For convenience the variables -{a0} and {c0} are created in order to make the remainder of the -input script more readable. - -[Define a crystal at finite temperature accounting for thermal expansion] - -kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal -boundary p p p -kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] -kim_query alpha get_linear_thermal_expansion_coefficient_cubic crystal=\["fcc"\] species=\["Al"\] units=\["1/K"\] temperature=\[293.15\] temperature_units=\["K"\] -variable DeltaT equal 300 -lattice fcc $\{a0\}*$\{alpha\}*$\{DeltaT\} -... :pre - -As in the previous example, the equilibrium lattice constant is obtained -for the Ercolessi and Adams (1994) potential. However, in this case the -crystal is scaled to the appropriate lattice constant at room temperature -(293.15 K) by using the linear thermal expansion constant predicted by the -potential. - -NOTE: When passing numerical values as arguments (as in the case -of the temperature in the above example) it is also possible to pass a -tolerance indicating how close to the value is considered a match. -If no tolerance is passed a default value is used. If multiple results -are returned (indicating that the tolerance is too large), {kim_query} -will return an error. See the -"query documentation"_https://openkim.org/doc/repository/kim-query -to see which numerical arguments and tolerances are available for a -given {query function}. - -[Compute defect formation energy] - -kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal -... -... Build fcc crystal containing some defect and compute the total energy -... which is stored in the variable {Etot} -... -kim_query Ec get_cohesive_energy_cubic crystal=\["fcc"\] species=\["Al"\] units=\["eV"\] -variable Eform equal $\{Etot\} - count(all)*$\{Ec\} -... :pre - -The defect formation energy {Eform} is computed by subtracting from {Etot} the -ideal fcc cohesive energy of the atoms in the system obtained from -"OpenKIM"_https://openkim.org for the Ercolessi and Adams (1994) potential. - -NOTE: {kim_query} commands return results archived in -"OpenKIM"_https://openkim.org. These results are obtained -using programs for computing material properties -(KIM Tests and KIM Test Drivers) that were contributed to OpenKIM. -In order to give credit to Test developers, the number of times results -from these programs are queried is tracked. No other information about -the nature of the query or its source is recorded. - -Accessing KIM Model Parameters from LAMMPS ({kim_param}) :h5 - -All IMs are functional forms containing a set of -parameters. The values of these parameters are typically -selected to best reproduce a training set of quantum mechanical -calculations or available experimental data. For example, a -Lennard-Jones potential intended to model argon might have the values of -its two parameters, epsilon and sigma, fit to the -dimer dissociation energy or thermodynamic properties at a critical point -of the phase diagram. - -Normally a user employing an IM should not modify its parameters since, -as noted above, these are selected to reproduce material properties. -However, there are cases where accessing and modifying IM parameters -is desired, such as for assessing uncertainty, fitting an IM, -or working with an ensemble of IMs. As explained "above"_#IM_types, -IMs archived in OpenKIM are either Portable Models (PMs) or -Simulator Models (SMs). KIM PMs are complete independent implementations -of an IM, whereas KIM SMs are wrappers to an IM implemented within LAMMPS. -Two different mechanisms are provided for accessing IM parameters in these -two cases: - -For a KIM PM, the {kim_param} command can be used to {get} and {set} the values of the PM's parameters as explained below. -For a KIM SM, the user should consult the documentation page for the specific IM and follow instructions there for how to modify its parameters (if possible). :ul - -The {kim_param get} and {kim_param set} commands provide an interface -to access and change the parameters of a KIM PM that "publishes" its -parameters and makes them publicly available (see the -"KIM API documentation"_https://kim-api.readthedocs.io/en/devel/features.html -for details). - -NOTE: The {kim_param get/set} commands must be preceded by {kim_init}. -The {kim_param set} command must additionally be preceded by a -{kim_interactions} command (or alternatively by a {pair_style kim} -and {pair_coeff} commands). The {kim_param set} command may be used wherever a {pair_coeff} command may occur. - -The syntax for the {kim_param} command is as follows: - -kim_param get param_name index_range variable formatarg -kim_param set param_name index_range values -:pre - -Here, {param_name} is the name of a KIM PM parameter (which is published -by the PM and available for access). The specific string used to identify -a parameter is defined by the PM. For example, for the -"Stillinger--Weber (SW) potential in OpenKIM"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005, -the parameter names are {A, B, p, q, sigma, gamma, cutoff, lambda, costheta0}. - -NOTE: The list of all the parameters that a PM exposes for access/mutation are -automatically written to the lammps log file when {kim_init} is called. - -Each published parameter of a KIM PM takes the form of an array of -numerical values. The array can contain one element for a single-valued -parameter, or a set of values. For example, the -"multispecies SW potential for the Zn-Cd-Hg-S-Se-Te system"_https://openkim.org/id/SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 -has the same parameter names as the -"single-species SW potential"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005, -but each parameter array contains 21 entries that correspond to the parameter -values used for each pairwise combination of the model's six supported species -(this model does not have parameters specific to individual ternary -combinations of its supported species). - -The {index_range} argument may either be an integer referring to -a specific element within the array associated with the parameter -specified by {param_name}, or a pair of integers separated by a colon -that refer to a slice of this array. In both cases, one-based indexing is -used to refer to the entries of the array. - -The result of a {get} operation for a specific {index_range} is stored in -one or more "LAMMPS string style variables"_variable.html as determined -by the optional {formatarg} argument "documented above."_#formatarg_options -If not specified, the default for {formatarg} is "explicit" for the -{kim_param} command. - -For the case where the result is an array with multiple values -(i.e. {index_range} contains a range), the optional "split" or "explicit" -{formatarg} keywords can be used to separate the results into multiple -variables; see the examples below. -Multiple parameters can be retrieved with a single call to {kim_param get} -by repeating the argument list following {get}. - -For a {set} operation, the {values} argument contains the new value(s) -for the element(s) of the parameter specified by {index_range}. For the case -where multiple values are being set, {values} contains a set of values -separated by spaces. Multiple parameters can be set with a single call to -{kim_param set} by repeating the argument list following {set}. - -{kim_param} Usage Examples and Further Clarifications :h5 - -Examples of getting and setting KIM PM parameters with further -clarifications are provided below. - -[Getting a scalar parameter] - -kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal -... -kim_param get A 1 VARA -:pre - -In this case, the value of the SW {A} parameter is retrieved and placed -in the LAMMPS variable {VARA}. The variable {VARA} can be used -in the remainder of the input script in the same manner as any other -LAMMPS variable. - -[Getting multiple scalar parameters with a single call] - -kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal -... -kim_param get A 1 VARA B 1 VARB -:pre - -This retrieves the {A} and {B} parameters of the SW potential and stores -them in the LAMMPS variables {VARA} and {VARB}. - -[Getting a range of values from a parameter] - -There are several options when getting a range of values from a parameter -determined by the {formatarg} argument. - -kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal -... -kim_param get lambda 7:9 LAM_TeTe LAM_TeZn LAM_TeSe -:pre - -In this case, {formatarg} is not specified and therefore the default -"explicit" mode is used. (The behavior would be the same if the word -{explicit} were added after {LAM_TeSe}.) Elements 7, 8 and 9 of parameter -lambda retrieved by the {get} operation are placed in the LAMMPS variables -{LAM_TeTe}, {LAM_TeZn} and {LAM_TeSe}, respectively. - -NOTE: In the above example, elements 7--9 of the lambda parameter correspond -to Te-Te, Te-Zm and Te-Se interactions. This can be determined by visiting -the "model page for the specified potential"_https://openkim.org/id/SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 -and looking at its parameter file linked to at the bottom of the page -(file with .param ending) and consulting the README documentation -provided with the driver for the PM being used. A link to the driver -is provided at the top of the model page. - -kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal -... -kim_param get lambda 15:17 LAMS list -variable LAM_VALUE index $\{LAMS\} -label loop_on_lambda -... -... do something with current value of lambda -... -next LAM_VALUE -jump SELF loop_on_lambda -:pre - -In this case, the "list" mode of {formatarg} is used. -The result of the {get} operation is stored in the LAMMPS variable -{LAMS} as a string containing the three retrieved values separated -by spaces, e.g "1.0 2.0 3.0". This can be used in LAMMPS with an -{index} variable to access the values one at a time within a loop -as shown in the example. At each iteration of the loop {LAM_VALUE} -contains the current value of lambda. - -kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal -... -kim_param get lambda 15:17 LAM split -:pre - -In this case, the "split" mode of {formatarg} is used. -The three values retrieved by the {get} operation are stored in -the three LAMMPS variables {LAM_15}, {LAM_16} and {LAM_17}. -The provided name "LAM" is used as prefix and the location in -the lambda array is appended to create the variable names. - -[Setting a scalar parameter] - -kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal -... -kim_interactions Si -kim_param set gamma 1 2.6 -:pre - -Here, the SW potential's gamma parameter is set to 2.6. Note that the {get} -and {set} commands work together, so that a {get} following a {set} -operation will return the new value that was set. For example: - -... -kim_interactions Si -kim_param get gamma 1 ORIG_GAMMA -kim_param set gamma 1 2.6 -kim_param get gamma 1 NEW_GAMMA -... -print "original gamma = $\{ORIG_GAMMA\}, new gamma = $\{NEW_GAMMA\}" -:pre - -Here, {ORIG_GAMMA} will contain the original gamma value for the SW -potential, while {NEW_GAMMA} will contain the value 2.6. - -[Setting multiple scalar parameters with a single call] - -kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal -... -kim_interactions Cd Te -variable VARG equal 2.6 -variable VARS equal 2.0951 -kim_param set gamma 1 $\{VARG\} sigma 3 $\{VARS\} -:pre - -In this case, the first element of the {gamma} parameter and -third element of the {sigma} parameter are set to 2.6 and 2.0951, -respectively. This example also shows how LAMMPS variables can -be used when setting parameters. - -[Setting a range of values of a parameter] - -kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal -... -kim_interactions Cd Te Zn Se Hg S -kim_param set sigma 2:6 2.35214 2.23869 2.04516 2.43269 1.80415 -:pre - -In this case, elements 2 through 6 of the parameter {sigma} -are set to the values 2.35214, 2.23869, 2.04516, 2.43269 and 1.80415 in -order. - -Citation of OpenKIM IMs :h4 - -When publishing results obtained using OpenKIM IMs researchers are requested -to cite the OpenKIM project "(Tadmor)"_#kim-mainpaper, KIM API -"(Elliott)"_#kim-api, and the specific IM codes used in the simulations, -in addition to the relevant scientific references for the IM. -The citation format for an IM is displayed on its page on -"OpenKIM"_https://openkim.org along with the corresponding BibTex file, -and is automatically added to the LAMMPS {log.cite} file. - -Citing the IM software (KIM infrastructure and specific PM or SM codes) -used in the simulation gives credit to the researchers who developed them -and enables open source efforts like OpenKIM to function. - - -[Restrictions:] - -The set of {kim_commands} is part of the KIM package. It is only enabled if -LAMMPS is built with that package. A requirement for the KIM package, -is the KIM API library that must be downloaded from the -"OpenKIM website"_https://openkim.org/kim-api/ and installed before -LAMMPS is compiled. When installing LAMMPS from binary, the kim-api package -is a dependency that is automatically downloaded and installed. See the KIM -section of the "Packages details"_Packages_details.html for details. - -Furthermore, when using {kim_commands} to run KIM SMs, any packages required -by the native potential being used or other commands or fixes that it invokes -must be installed. - -[Related commands:] - -"pair_style kim"_pair_kim.html - -:line - -:link(kim-mainpaper) -[(Tadmor)] Tadmor, Elliott, Sethna, Miller and Becker, JOM, 63, 17 (2011). -doi: "https://doi.org/10.1007/s11837-011-0102-6"_https://doi.org/10.1007/s11837-011-0102-6 - -:link(kim-api) -[(Elliott)] Elliott, Tadmor and Bernstein, "https://openkim.org/kim-api"_https://openkim.org/kim-api (2011) -doi: "https://doi.org/10.25950/FF8F563A"_https://doi.org/10.25950/FF8F563A diff --git a/doc/txt/kspace_modify.txt b/doc/txt/kspace_modify.txt deleted file mode 100644 index c5a2ce1b69..0000000000 --- a/doc/txt/kspace_modify.txt +++ /dev/null @@ -1,474 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -kspace_modify command :h3 - -[Syntax:] - -kspace_modify keyword value ... :pre - -one or more keyword/value pairs may be listed :ulb,l -keyword = {collective} or {compute} or {cutoff/adjust} or {diff} or {disp/auto} or {fftbench} or {force/disp/kspace} or {force/disp/real} or {force} or {gewald/disp} or {gewald} or {kmax/ewald} or {mesh} or {minorder} or {mix/disp} or {order/disp} or {order} or {overlap} or {scafacos} or {slab} or {splittol} :l - {collective} value = {yes} or {no} - {compute} value = {yes} or {no} - {cutoff/adjust} value = {yes} or {no} - {diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode - {disp/auto} value = yes or no - {fftbench} value = {yes} or {no} - {force/disp/real} value = accuracy (force units) - {force/disp/kspace} value = accuracy (force units) - {force} value = accuracy (force units) - {gewald} value = rinv (1/distance units) - rinv = G-ewald parameter for Coulombics - {gewald/disp} value = rinv (1/distance units) - rinv = G-ewald parameter for dispersion - {kmax/ewald} value = kx ky kz - kx,ky,kz = number of Ewald sum kspace vectors in each dimension - {mesh} value = x y z - x,y,z = grid size in each dimension for long-range Coulombics - {mesh/disp} value = x y z - x,y,z = grid size in each dimension for 1/r^6 dispersion - {minorder} value = M - M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication - {mix/disp} value = {pair} or {geom} or {none} - {order} value = N - N = extent of Gaussian for PPPM or MSM mapping of charge to grid - {order/disp} value = N - N = extent of Gaussian for PPPM mapping of dispersion term to grid - {overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor - {pressure/scalar} value = {yes} or {no} - {scafacos} values = option value1 value2 ... - option = {tolerance} - value = {energy} or {energy_rel} or {field} or {field_rel} or {potential} or {potential_rel} - option = {fmm_tuning} - value = {0} or {1} - {slab} value = volfactor or {nozforce} - volfactor = ratio of the total extended volume used in the - 2d approximation compared with the volume of the simulation domain - {nozforce} turns off kspace forces in the z direction - {splittol} value = tol - tol = relative size of two eigenvalues (see discussion below) :pre -:ule - -[Examples:] - -kspace_modify mesh 24 24 30 order 6 -kspace_modify slab 3.0 -kspace_modify scafacos tolerance energy :pre - -[Description:] - -Set parameters used by the kspace solvers defined by the -"kspace_style"_kspace_style.html command. Not all parameters are -relevant to all kspace styles. - -:line - -The {collective} keyword applies only to PPPM. It is set to {no} by -default, except on IBM BlueGene machines. If this option is set to -{yes}, LAMMPS will use MPI collective operations to remap data for -3d-FFT operations instead of the default point-to-point communication. -This is faster on IBM BlueGene machines, and may also be faster on -other machines if they have an efficient implementation of MPI -collective operations and adequate hardware. - -:line - -The {compute} keyword allows Kspace computations to be turned off, -even though a "kspace_style"_kspace_style.html is defined. This is -not useful for running a real simulation, but can be useful for -debugging purposes or for computing only partial forces that do not -include the Kspace contribution. You can also do this by simply not -defining a "kspace_style"_kspace_style.html, but a Kspace-compatible -"pair_style"_pair_style.html requires a kspace style to be defined. -This keyword gives you that option. - -:line - -The {cutoff/adjust} keyword applies only to MSM. If this option is -turned on, the Coulombic cutoff will be automatically adjusted at the -beginning of the run to give the desired estimated error. Other -cutoffs such as LJ will not be affected. If the grid is not set using -the {mesh} command, this command will also attempt to use the optimal -grid that minimizes cost using an estimate given by -"(Hardy)"_#Hardy1. Note that this cost estimate is not exact, somewhat -experimental, and still may not yield the optimal parameters. - -:line - -The {diff} keyword specifies the differentiation scheme used by the -PPPM method to compute forces on particles given electrostatic -potentials on the PPPM mesh. The {ik} approach is the default for -PPPM and is the original formulation used in "(Hockney)"_#Hockney1. It -performs differentiation in Kspace, and uses 3 FFTs to transfer each -component of the computed fields back to real space for total of 4 -FFTs per timestep. - -The analytic differentiation {ad} approach uses only 1 FFT to transfer -information back to real space for a total of 2 FFTs per timestep. It -then performs analytic differentiation on the single quantity to -generate the 3 components of the electric field at each grid point. -This is sometimes referred to as "smoothed" PPPM. This approach -requires a somewhat larger PPPM mesh to achieve the same accuracy as -the {ik} method. Currently, only the {ik} method (default) can be -used for a triclinic simulation cell with PPPM. The {ad} method is -always used for MSM. - -NOTE: Currently, not all PPPM styles support the {ad} option. Support -for those PPPM variants will be added later. - -:line - -The {disp/auto} option controls whether the pppm/disp is allowed to -generate PPPM parameters automatically. If set to {no}, parameters have -to be specified using the {gewald/disp}, {mesh/disp}, -{force/disp/real} or {force/disp/kspace} keywords, or -the code will stop with an error message. When this option is set to -{yes}, the error message will not appear and the simulation will start. -For a typical application, using the automatic parameter generation -will provide simulations that are either inaccurate or slow. Using this -option is thus not recommended. For guidelines on how to obtain good -parameters, see the "How-To"_Howto_dispersion.html discussion. - -:line - -The {fftbench} keyword applies only to PPPM. It is off by default. If -this option is turned on, LAMMPS will perform a short FFT benchmark -computation and report its timings, and will thus finish a some seconds -later than it would if this option were off. - -:line - -The {force/disp/real} and {force/disp/kspace} keywords set the force -accuracy for the real and space computations for the dispersion part -of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder1, optimal -performance and accuracy in the results is obtained when these values -are different. - -:line - -The {force} keyword overrides the relative accuracy parameter set by -the "kspace_style"_kspace_style.html command with an absolute -accuracy. The accuracy determines the RMS error in per-atom forces -calculated by the long-range solver and is thus specified in force -units. A negative value for the accuracy setting means to use the -relative accuracy parameter. The accuracy setting is used in -conjunction with the pairwise cutoff to determine the number of -K-space vectors for style {ewald}, the FFT grid size for style -{pppm}, or the real space grid size for style {msm}. - -:line - -The {gewald} keyword sets the value of the Ewald or PPPM G-ewald -parameter for charge as {rinv} in reciprocal distance units. Without -this setting, LAMMPS chooses the parameter automatically as a function -of cutoff, precision, grid spacing, etc. This means it can vary from -one simulation to the next which may not be desirable for matching a -KSpace solver to a pre-tabulated pairwise potential. This setting can -also be useful if Ewald or PPPM fails to choose a good grid spacing -and G-ewald parameter automatically. If the value is set to 0.0, -LAMMPS will choose the G-ewald parameter automatically. MSM does not -use the {gewald} parameter. - -:line - -The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald -parameter for dispersion as {rinv} in reciprocal distance units. It -has the same meaning as the {gewald} setting for Coulombics. - -:line - -The {kmax/ewald} keyword sets the number of kspace vectors in each -dimension for kspace style {ewald}. The three values must be positive -integers, or else (0,0,0), which unsets the option. When this option -is not set, the Ewald sum scheme chooses its own kspace vectors, -consistent with the user-specified accuracy and pairwise cutoff. In -any case, if kspace style {ewald} is invoked, the values used are -printed to the screen and the log file at the start of the run. - -:line - -The {mesh} keyword sets the grid size for kspace style {pppm} or -{msm}. In the case of PPPM, this is the FFT mesh, and each dimension -must be factorizable into powers of 2, 3, and 5. In the case of MSM, -this is the finest scale real-space mesh, and each dimension must be -factorizable into powers of 2. When this option is not set, the PPPM -or MSM solver chooses its own grid size, consistent with the -user-specified accuracy and pairwise cutoff. Values for x,y,z of -0,0,0 unset the option. - -:line - -The {mesh/disp} keyword sets the grid size for kspace style -{pppm/disp}. This is the FFT mesh for long-range dispersion and ach -dimension must be factorizable into powers of 2, 3, and 5. When this -option is not set, the PPPM solver chooses its own grid size, -consistent with the user-specified accuracy and pairwise cutoff. -Values for x,y,z of 0,0,0 unset the option. - -:line - -The {minorder} keyword allows LAMMPS to reduce the {order} setting if -necessary to keep the communication of ghost grid point limited to -exchanges between nearest-neighbor processors. See the discussion of -the {overlap} keyword for details. If the {overlap} keyword is set to -{yes}, which is the default, this is never needed. If it set to {no} -and overlap occurs, then LAMMPS will reduce the order setting, one -step at a time, until the ghost grid overlap only extends to nearest -neighbor processors. The {minorder} keyword limits how small the -{order} setting can become. The minimum allowed value for PPPM is 2, -which is the default. If {minorder} is set to the same value as -{order} then no reduction is allowed, and LAMMPS will generate an -error if the grid communication is non-nearest-neighbor and {overlap} -is set to {no}. The {minorder} keyword is not currently supported in -MSM. - -:line - -The {mix/disp} keyword selects the mixing rule for the dispersion -coefficients. With {pair}, the dispersion coefficients of unlike -types are computed as indicated with "pair_modify"_pair_modify.html. -With {geom}, geometric mixing is enforced on the dispersion -coefficients in the kspace coefficients. When using the arithmetic -mixing rule, this will speed-up the simulations but introduces some -error in the force computations, as shown in "(Wennberg)"_#Wennberg. -With {none}, it is assumed that no mixing rule is -applicable. Splitting of the dispersion coefficients will be performed -as described in "(Isele-Holder)"_#Isele-Holder1. - -This splitting can be influenced with the {splittol} keywords. Only -the eigenvalues that are larger than tol compared to the largest -eigenvalues are included. Using this keywords the original matrix of -dispersion coefficients is approximated. This leads to faster -computations, but the accuracy in the reciprocal space computations of -the dispersion part is decreased. - -:line - -The {order} keyword determines how many grid spacings an atom's charge -extends when it is mapped to the grid in kspace style {pppm} or {msm}. -The default for this parameter is 5 for PPPM and 8 for MSM, which -means each charge spans 5 or 8 grid cells in each dimension, -respectively. For the LAMMPS implementation of MSM, the order can -range from 4 to 10 and must be even. For PPPM, the minimum allowed -setting is 2 and the maximum allowed setting is 7. The larger the -value of this parameter, the smaller that LAMMPS will set the grid -size, to achieve the requested accuracy. Conversely, the smaller the -order value, the larger the grid size will be. Note that there is an -inherent trade-off involved: a small grid will lower the cost of FFTs -or MSM direct sum, but a larger order parameter will increase the cost -of interpolating charge/fields to/from the grid. - -The PPPM order parameter may be reset by LAMMPS when it sets up the -FFT grid if the implied grid stencil extends beyond the grid cells -owned by neighboring processors. Typically this will only occur when -small problems are run on large numbers of processors. A warning will -be generated indicating the order parameter is being reduced to allow -LAMMPS to run the problem. Automatic adjustment of the order parameter -is not supported in MSM. - -:line - -The {order/disp} keyword determines how many grid spacings an atom's -dispersion term extends when it is mapped to the grid in kspace style -{pppm/disp}. It has the same meaning as the {order} setting for -Coulombics. - -:line - -The {overlap} keyword can be used in conjunction with the {minorder} -keyword with the PPPM styles to adjust the amount of communication -that occurs when values on the FFT grid are exchanged between -processors. This communication is distinct from the communication -inherent in the parallel FFTs themselves, and is required because -processors interpolate charge and field values using grid point values -owned by neighboring processors (i.e. ghost point communication). If -the {overlap} keyword is set to {yes} then this communication is -allowed to extend beyond nearest-neighbor processors, e.g. when using -lots of processors on a small problem. If it is set to {no} then the -communication will be limited to nearest-neighbor processors and the -{order} setting will be reduced if necessary, as explained by the -{minorder} keyword discussion. The {overlap} keyword is always set to -{yes} in MSM. - -:line - -The {pressure/scalar} keyword applies only to MSM. If this option is -turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will -be computed, which can be used, for example, to run an isotropic barostat. -Computing the full pressure tensor with MSM is expensive, and this option -provides a faster alternative. The scalar pressure is computed using a -relationship between the Coulombic energy and pressure "(Hummer)"_#Hummer -instead of using the virial equation. This option cannot be used to access -individual components of the pressure tensor, to compute per-atom virial, -or with suffix kspace/pair styles of MSM, like OMP or GPU. - -:line - -The {scafacos} keyword is used for settings that are passed to the -ScaFaCoS library when using "kspace_style scafacos"_kspace_style.html. - -The {tolerance} option affects how the {accuracy} specified with the -"kspace_style"_kspace_style.html command is interpreted by ScaFaCoS. -The following values may be used: - -energy = absolute accuracy in total Coulombic energy -energy_rel = relative accuracy in total Coulombic energy -potential = absolute accuracy in total Coulombic potential -potential_rel = relative accuracy in total Coulombic potential -field = absolute accuracy in electric field -field_rel = relative accuracy in electric field :ul - -The values with suffix _rel indicate the tolerance is a relative -tolerance; the other values impose an absolute tolerance on the given -quantity. Absolute tolerance in this case means, that for a given -quantity q and a given absolute tolerance of t_a the result should -be between q-t_a and q+t_a. For a relative tolerance t_r the relative -error should not be greater than t_r, i.e. abs(1 - (result/q)) < t_r. -As a consequence of this, the tolerance type should be checked, when -performing computations with a high absolute field / energy. E.g. -if the total energy in the system is 1000000.0 an absolute tolerance -of 1e-3 would mean that the result has to be between 999999.999 and -1000000.001, which would be equivalent to a relative tolerance of -1e-9. - -The energy and energy_rel values, set a tolerance based on the total -Coulombic energy of the system. The potential and potential_rel set a -tolerance based on the per-atom Coulombic energy. The field and -field_rel tolerance types set a tolerance based on the electric field -values computed by ScaFaCoS. Since per-atom forces are derived from -the per-atom electric field, this effectively sets a tolerance on the -forces, similar to other LAMMPS KSpace styles, as explained on the -"kspace_style"_kspace_style.html doc page. - -Note that not all ScaFaCoS solvers support all tolerance types. -These are the allowed values for each method: - -fmm = energy and energy_rel -p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic) -p3m = field -ewald = field -direct = has no tolerance tuning :ul - -If the tolerance type is not changed, the default values for the -tolerance type are the first values in the above list, e.g. energy -is the default tolerance type for the fmm solver. - -The {fmm_tuning} option is only relevant when using the FMM method. -It activates (value=1) or deactivates (value=0) an internal tuning -mechanism for the FMM solver. The tuning operation runs sequentially -and can be very time-consuming. Usually it is not needed for systems -with a homogeneous charge distribution. The default for this option is -therefore {0}. The FMM internal tuning is performed once, when the -solver is set up. - -:line - -The {slab} keyword allows an Ewald or PPPM solver to be used for a -systems that are periodic in x,y but non-periodic in z - a -"boundary"_boundary.html setting of "boundary p p f". This is done by -treating the system as if it were periodic in z, but inserting empty -volume between atom slabs and removing dipole inter-slab interactions -so that slab-slab interactions are effectively turned off. The -volfactor value sets the ratio of the extended dimension in z divided -by the actual dimension in z. The recommended value is 3.0. A larger -value is inefficient; a smaller value introduces unwanted slab-slab -interactions. The use of fixed boundaries in z means that the user -must prevent particle migration beyond the initial z-bounds, typically -by providing a wall-style fix. The methodology behind the {slab} -option is explained in the paper by "(Yeh)"_#Yeh. The {slab} option -is also extended to non-neutral systems "(Ballenegger)"_#Ballenegger. - -An alternative slab option can be invoked with the {nozforce} keyword -in lieu of the volfactor. This turns off all kspace forces in the z -direction. The {nozforce} option is not supported by MSM. For MSM, -any combination of periodic, non-periodic, or shrink-wrapped -boundaries can be set using "boundary"_boundary.html (the slab -approximation in not needed). The {slab} keyword is not currently -supported by Ewald or PPPM when using a triclinic simulation cell. The -slab correction has also been extended to point dipole interactions -"(Klapp)"_#Klapp in "kspace_style"_kspace_style.html {ewald/disp}, -{ewald/dipole}, and {pppm/dipole}. - -NOTE: If you wish to apply an electric field in the Z-direction, in -conjunction with the {slab} keyword, you should do it by adding -explicit charged particles to the +/- Z surfaces. If you do it via -the "fix efield"_fix_efield.html command, it will not give the correct -dielectric constant due to the Yeh/Berkowitz "(Yeh)"_#Yeh correction -not being compatible with how "fix efield"_fix_efield.html works. - -:line - -The {force/disp/real} and {force/disp/kspace} keywords set the force -accuracy for the real and space computations for the dispersion part -of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder1, optimal -performance and accuracy in the results is obtained when these values -are different. - -The {disp/auto} option controls whether the pppm/disp is allowed to -generate PPPM parameters automatically. If set to {no}, parameters -have to be specified using the {gewald/disp}, {mesh/disp}, -{force/disp/real} or {force/disp/kspace} keywords, or the code will -stop with an error message. When this option is set to {yes}, the -error message will not appear and the simulation will start. For a -typical application, using the automatic parameter generation will -provide simulations that are either inaccurate or slow. Using this -option is thus not recommended. For guidelines on how to obtain good -parameters, see the "Howto dispersion"_Howto_dispersion.html doc page. - -:line - -[Restrictions:] none - -[Related commands:] - -"kspace_style"_kspace_style.html, "boundary"_boundary.html - -[Default:] - -The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp = -5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0, -gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust = -yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = -ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace -= -1.0, split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, -order = order/disp = 7. For scafacos settings, the scafacos tolerance -option depends on the method chosen, as documented above. The -scafacos fmm_tuning default = 0. - -:line - -:link(Hockney1) -[(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles, -Adam Hilger, NY (1989). - -:link(Yeh) -[(Yeh)] Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999). - -:link(Ballenegger) -[(Ballenegger)] Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107 -(2009). - -:link(Klapp) -[(Klapp)] Klapp, Schoen, J Chem Phys, 117, 8050 (2002). - -:link(Hardy1) -[(Hardy)] David Hardy thesis: Multilevel Summation for the Fast -Evaluation of Forces for the Simulation of Biomolecules, University of -Illinois at Urbana-Champaign, (2006). - -:link(Hummer) -[(Hummer)] Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998) - -:link(Isele-Holder1) -[(Isele-Holder)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J -Chem Theory Comput, 9, 5412 (2013). - -:link(Wennberg) -[(Wennberg)] Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, -9, 3527 (2013). diff --git a/doc/txt/label.txt b/doc/txt/label.txt deleted file mode 100644 index adab44188c..0000000000 --- a/doc/txt/label.txt +++ /dev/null @@ -1,36 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -label command :h3 - -[Syntax:] - -label ID :pre - -ID = string used as label name :ul - -[Examples:] - -label xyz -label loop :pre - -[Description:] - -Label this line of the input script with the chosen ID. Unless a jump -command was used previously, this does nothing. But if a -"jump"_jump.html command was used with a label argument to begin -invoking this script file, then all command lines in the script prior -to this line will be ignored. I.e. execution of the script will begin -at this line. This is useful for looping over a section of the input -script as discussed in the "jump"_jump.html command. - -[Restrictions:] none - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/lammps.book b/doc/txt/lammps.book deleted file mode 100644 index 9daa990b89..0000000000 --- a/doc/txt/lammps.book +++ /dev/null @@ -1,849 +0,0 @@ -#HTMLDOC 1.8.28 --t pdf14 -f "Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow -Manual.html -Intro.html -Intro_overview.html -Manual_version.html -Intro_features.html -Intro_nonfeatures.html -Intro_opensource.html -Intro_authors.html -Intro_website.html -Install.html -Install_linux.html -Install_mac.html -Install_windows.html -Install_tarball.html -Install_git.html -Install_svn.html -Install_patch.html -Build.html -Build_cmake.html -Build_make.html -Build_link.html -Build_basics.html -Build_settings.html -Build_package.html -Build_extras.html -Build_windows.html -Build_development.html -Run_head.html -Run_basics.html -Run_options.html -Run_output.html -Run_windows.html -Commands.html -Commands_input.html -Commands_parse.html -Commands_structure.html -Commands_category.html -Commands_all.html -Commands_fix.html -Commands_compute.html -Commands_pair.html -Commands_bond.html -Commands_kspace.html -Commands_removed.html -Packages.html -Packages_standard.html -Packages_user.html -Packages_details.html -Speed.html -Speed_bench.html -Speed_measure.html -Speed_tips.html -Speed_packages.html -Speed_gpu.html -Speed_intel.html -Speed_kokkos.html -Speed_omp.html -Speed_opt.html -Speed_compare.html -Howto.html -Howto_github.html -Howto_pylammps.html -Howto_bash.html -Howto_restart.html -Howto_viz.html -Howto_multiple.html -Howto_replica.html -Howto_library.html -Howto_couple.html -Howto_client_server.html -Howto_output.html -Howto_chunk.html -Howto_2d.html -Howto_triclinic.html -Howto_walls.html -Howto_nemd.html -Howto_granular.html -Howto_spherical.html -Howto_dispersion.html -Howto_temperature.html -Howto_thermostat.html -Howto_barostat.html -Howto_elastic.html -Howto_kappa.html -Howto_viscosity.html -Howto_diffusion.html -Howto_bioFF.html -Howto_tip3p.html -Howto_tip4p.html -Howto_spc.html -Howto_body.html -Howto_polarizable.html -Howto_coreshell.html -Howto_drude.html -Howto_drude2.html -Howto_manifold.html -Howto_spins.html -Examples.html -Tools.html -Modify.html -Modify_overview.html -Modify_contribute.html -Modify_atom.html -Modify_pair.html -Modify_bond.html -Modify_compute.html -Modify_fix.html -Modify_command.html -Modify_dump.html -Modify_kspace.html -Modify_min.html -Modify_region.html -Modify_body.html -Modify_thermo.html -Modify_variable.html -Python_head.html -Python_overview.html -Python_run.html -Python_shlib.html -Python_install.html -Python_mpi.html -Python_test.html -Python_library.html -Python_pylammps.html -Python_examples.html -Python_call.html -Errors.html -Errors_common.html -Errors_bugs.html -Errors_messages.html -Errors_warnings.html -Manual_build.html - 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- -lammps_commands_compute.html -compute.html -compute_modify.html -compute_ackland_atom.html -compute_adf.html -compute_angle.html -compute_angle_local.html -compute_angmom_chunk.html -compute_basal_atom.html -compute_body_local.html -compute_bond.html -compute_bond_local.html -compute_centro_atom.html -compute_chunk_atom.html -compute_chunk_spread_atom.html -compute_cluster_atom.html -compute_cna_atom.html -compute_cnp_atom.html -compute_com.html -compute_com_chunk.html -compute_contact_atom.html -compute_coord_atom.html -compute_damage_atom.html -compute_dihedral.html -compute_dihedral_local.html -compute_dilatation_atom.html -compute_dipole_chunk.html -compute_displace_atom.html -compute_dpd.html -compute_dpd_atom.html -compute_edpd_temp_atom.html -compute_entropy_atom.html -compute_erotate_asphere.html -compute_erotate_rigid.html -compute_erotate_sphere.html -compute_erotate_sphere_atom.html -compute_event_displace.html -compute_fep.html -compute_global_atom.html -compute_group_group.html -compute_gyration.html -compute_gyration_chunk.html -compute_gyration_shape.html -compute_gyration_shape_chunk.html -compute_heat_flux.html -compute_hexorder_atom.html -compute_hma.html -compute_improper.html -compute_improper_local.html -compute_inertia_chunk.html -compute_ke.html -compute_ke_atom.html -compute_ke_atom_eff.html -compute_ke_eff.html -compute_ke_rigid.html -compute_meso_e_atom.html -compute_meso_rho_atom.html -compute_meso_t_atom.html -compute_momentum.html -compute_msd.html -compute_msd_chunk.html -compute_msd_nongauss.html -compute_omega_chunk.html -compute_orientorder_atom.html -compute_pair.html -compute_pair_local.html -compute_pe.html -compute_pe_atom.html -compute_plasticity_atom.html -compute_pressure.html -compute_pressure_cylinder.html -compute_pressure_uef.html -compute_property_atom.html -compute_property_chunk.html -compute_property_local.html -compute_ptm_atom.html -compute_rdf.html -compute_reduce.html -compute_reduce_chunk.html -compute_rigid_local.html -compute_saed.html -compute_slice.html -compute_smd_contact_radius.html -compute_smd_damage.html -compute_smd_hourglass_error.html -compute_smd_internal_energy.html -compute_smd_plastic_strain.html -compute_smd_plastic_strain_rate.html -compute_smd_rho.html -compute_smd_tlsph_defgrad.html -compute_smd_tlsph_dt.html -compute_smd_tlsph_num_neighs.html -compute_smd_tlsph_shape.html -compute_smd_tlsph_strain.html -compute_smd_tlsph_strain_rate.html -compute_smd_tlsph_stress.html -compute_smd_triangle_vertices.html -compute_smd_ulsph_num_neighs.html -compute_smd_ulsph_strain.html -compute_smd_ulsph_strain_rate.html -compute_smd_ulsph_stress.html -compute_smd_vol.html -compute_sna_atom.html -compute_spin.html -compute_stress_atom.html -compute_stress_mop.html -compute_tally.html -compute_tdpd_cc_atom.html -compute_temp.html -compute_temp_asphere.html -compute_temp_body.html -compute_temp_chunk.html -compute_temp_com.html -compute_temp_cs.html -compute_temp_deform.html -compute_temp_deform_eff.html -compute_temp_drude.html -compute_temp_eff.html -compute_temp_partial.html -compute_temp_profile.html -compute_temp_ramp.html -compute_temp_region.html -compute_temp_region_eff.html -compute_temp_rotate.html -compute_temp_sphere.html -compute_temp_uef.html -compute_ti.html -compute_torque_chunk.html -compute_vacf.html -compute_vcm_chunk.html -compute_voronoi_atom.html -compute_xrd.html - -lammps_commands_pair.html -pair_style.html -pair_coeff.html -pair_modify.html -pair_write.html -pair_adp.html -pair_agni.html -pair_airebo.html -pair_atm.html -pair_awpmd.html -pair_beck.html -pair_body_nparticle.html -pair_body_rounded_polygon.html -pair_body_rounded_polyhedron.html -pair_bop.html -pair_born.html -pair_brownian.html -pair_buck.html -pair_buck_long.html -pair_buck6d_coul_gauss.html -pair_charmm.html -pair_class2.html -pair_colloid.html -pair_comb.html -pair_cosine_squared.html -pair_coul.html -pair_coul_diel.html -pair_coul_shield.html -pair_cs.html -pair_dipole.html -pair_dpd.html -pair_dpd_fdt.html -pair_dsmc.html -pair_e3b.html -pair_drip.html -pair_eam.html -pair_edip.html -pair_eff.html -pair_eim.html -pair_exp6_rx.html -pair_extep.html -pair_gauss.html -pair_gayberne.html -pair_gran.html -pair_granular.html -pair_gromacs.html -pair_gw.html -pair_ilp_graphene_hbn.html -pair_hbond_dreiding.html -pair_hybrid.html -pair_kim.html -pair_kolmogorov_crespi_full.html -pair_kolmogorov_crespi_z.html -pair_lcbop.html -pair_lebedeva_z.html -pair_line_lj.html -pair_list.html -pair_lj.html -pair_lj96.html -pair_lj_cubic.html -pair_lj_expand.html -pair_lj_long.html -pair_lj_smooth.html -pair_lj_smooth_linear.html -pair_fep_soft.html -pair_lj_switch3_coulgauss.html -pair_local_density.html -pair_lubricate.html -pair_lubricateU.html -pair_mdf.html -pair_meamc.html -pair_meam_spline.html -pair_meam_sw_spline.html -pair_meso.html -pair_mgpt.html -pair_mie.html -pair_mm3_switch3_coulgauss.html -pair_momb.html -pair_morse.html -pair_multi_lucy.html -pair_multi_lucy_rx.html -pair_nb3b_harmonic.html -pair_nm.html -pair_none.html -pair_oxdna.html -pair_oxdna2.html -pair_peri.html -pair_polymorphic.html -pair_python.html -pair_quip.html -pair_reaxc.html -pair_resquared.html -pair_sdk.html -pair_sdpd_taitwater_isothermal.html -pair_smd_hertz.html -pair_smd_tlsph.html -pair_smd_triangulated_surface.html -pair_smd_ulsph.html -pair_smtbq.html -pair_snap.html -pair_soft.html -pair_sph_heatconduction.html -pair_sph_idealgas.html -pair_sph_lj.html -pair_sph_rhosum.html -pair_sph_taitwater.html -pair_sph_taitwater_morris.html -pair_spin_dipole.html -pair_spin_dmi.html -pair_spin_exchange.html -pair_spin_magelec.html -pair_spin_neel.html -pair_srp.html -pair_sw.html -pair_table.html -pair_table_rx.html -pair_tersoff.html -pair_tersoff_mod.html -pair_tersoff_zbl.html -pair_thole.html -pair_tri_lj.html -pair_ufm.html -pair_vashishta.html -pair_yukawa.html -pair_yukawa_colloid.html -pair_zbl.html -pair_zero.html - -lammps_commands_bond.html -bond_style.html -bond_coeff.html -bond_write.html -bond_class2.html -bond_fene.html -bond_fene_expand.html -bond_gromos.html -bond_harmonic.html -bond_harmonic_shift.html -bond_harmonic_shift_cut.html -bond_hybrid.html -bond_morse.html -bond_mm3.html -bond_none.html -bond_nonlinear.html -bond_oxdna.html -bond_quartic.html -bond_table.html -bond_zero.html - -lammps_commands_angle.html -angle_style.html -angle_coeff.html -angle_charmm.html -angle_class2.html -angle_cosine.html -angle_cosine_buck6d.html -angle_cosine_delta.html -angle_cosine_periodic.html -angle_cosine_shift.html -angle_cosine_shift_exp.html -angle_cosine_squared.html -angle_cross.html -angle_dipole.html -angle_fourier.html -angle_fourier_simple.html -angle_harmonic.html -angle_hybrid.html -angle_mm3.html -angle_none.html -angle_quartic.html -angle_sdk.html -angle_table.html -angle_zero.html - -lammps_commands_dihedral.html -dihedral_style.html -dihedral_coeff.html -dihedral_charmm.html -dihedral_class2.html -dihedral_cosine_shift_exp.html -dihedral_fourier.html -dihedral_harmonic.html -dihedral_helix.html -dihedral_hybrid.html -dihedral_multi_harmonic.html -dihedral_nharmonic.html -dihedral_none.html -dihedral_opls.html -dihedral_quadratic.html -dihedral_spherical.html -dihedral_table.html -dihedral_table_cut.html -dihedral_zero.html - -lammps_commands_improper.html -improper_style.html -improper_coeff.html -improper_class2.html -improper_cossq.html -improper_cvff.html -improper_distance.html -improper_distharm.html -improper_fourier.html -improper_harmonic.html -improper_hybrid.html -improper_inversion_harmonic.html -improper_none.html -improper_ring.html -improper_umbrella.html -improper_sqdistharm.html -improper_zero.html - -lammps_commands_kspace.html -kspace_style.html -kspace_modify.html - -lammps_commands_atc.html -fix_atc.html -USER/atc/man_add_molecule.html -USER/atc/man_add_species.html -USER/atc/man_atom_element_map.html -USER/atc/man_atom_weight.html -USER/atc/man_atomic_charge.html -USER/atc/man_boundary.html -USER/atc/man_boundary_dynamics.html -USER/atc/man_boundary_faceset.html -USER/atc/man_boundary_integral.html -USER/atc/man_consistent_fe_initialization.html -USER/atc/man_contour_integral.html -USER/atc/man_control.html -USER/atc/man_control_momentum.html -USER/atc/man_control_thermal.html -USER/atc/man_control_thermal_correction_max_iterations.html -USER/atc/man_decomposition.html -USER/atc/man_electron_integration.html -USER/atc/man_equilibrium_start.html -USER/atc/man_extrinsic_exchange.html -USER/atc/man_fe_md_boundary.html -USER/atc/man_fem_mesh.html -USER/atc/man_filter_scale.html -USER/atc/man_filter_type.html -USER/atc/man_fix_atc.html -USER/atc/man_fix_flux.html -USER/atc/man_fix_nodes.html -USER/atc/man_hardy_computes.html -USER/atc/man_hardy_fields.html -USER/atc/man_hardy_gradients.html -USER/atc/man_hardy_kernel.html -USER/atc/man_hardy_on_the_fly.html -USER/atc/man_hardy_rates.html -USER/atc/man_initial.html -USER/atc/man_internal_atom_integrate.html -USER/atc/man_internal_element_set.html -USER/atc/man_internal_quadrature.html -USER/atc/man_kernel_function.html -USER/atc/man_localized_lambda.html -USER/atc/man_lumped_lambda_solve.html -USER/atc/man_mask_direction.html -USER/atc/man_mass_matrix.html -USER/atc/man_material.html -USER/atc/man_mesh_add_to_nodeset.html -USER/atc/man_mesh_create.html -USER/atc/man_mesh_create_elementset.html -USER/atc/man_mesh_create_faceset_box.html -USER/atc/man_mesh_create_faceset_plane.html -USER/atc/man_mesh_create_nodeset.html -USER/atc/man_mesh_delete_elements.html -USER/atc/man_mesh_nodeset_to_elementset.html -USER/atc/man_mesh_output.html -USER/atc/man_mesh_quadrature.html -USER/atc/man_mesh_read.html -USER/atc/man_mesh_write.html -USER/atc/man_momentum_time_integration.html -USER/atc/man_output.html -USER/atc/man_output_elementset.html -USER/atc/man_output_nodeset.html -USER/atc/man_pair_interactions.html -USER/atc/man_poisson_solver.html -USER/atc/man_read_restart.html -USER/atc/man_remove_molecule.html -USER/atc/man_remove_source.html -USER/atc/man_remove_species.html -USER/atc/man_reset_atomic_reference_positions.html -USER/atc/man_reset_time.html -USER/atc/man_sample_frequency.html -USER/atc/man_set.html -USER/atc/man_source.html -USER/atc/man_source_integration.html -USER/atc/man_temperature_definition.html -USER/atc/man_thermal_time_integration.html -USER/atc/man_time_filter.html -USER/atc/man_track_displacement.html -USER/atc/man_unfix_flux.html -USER/atc/man_unfix_nodes.html -USER/atc/man_write_atom_weights.html -USER/atc/man_write_restart.html diff --git a/doc/txt/lammps_commands.txt b/doc/txt/lammps_commands.txt deleted file mode 100644 index 97ca099447..0000000000 --- a/doc/txt/lammps_commands.txt +++ /dev/null @@ -1,12 +0,0 @@ - -LAMMPS Commands :h1 - -The following pages contain the detailed documentation of all -LAMMPS commands included in this version of LAMMPS. Generic -commands are listed first (in alphabetical order) followed by -command categories like compute styles or pair styles and so on. - -The documentation for the USER-ATC package fix_modify commands -follow at the very end of this manual. - -General Commands :h2 diff --git a/doc/txt/lammps_commands_angle.txt b/doc/txt/lammps_commands_angle.txt deleted file mode 100644 index 24a3136a3a..0000000000 --- a/doc/txt/lammps_commands_angle.txt +++ /dev/null @@ -1,2 +0,0 @@ - -Angle Style Commands :h2 diff --git a/doc/txt/lammps_commands_atc.txt b/doc/txt/lammps_commands_atc.txt deleted file mode 100644 index 6cf2bb8239..0000000000 --- a/doc/txt/lammps_commands_atc.txt +++ /dev/null @@ -1,2 +0,0 @@ - -AtC Commands :h2 diff --git a/doc/txt/lammps_commands_bond.txt b/doc/txt/lammps_commands_bond.txt deleted file mode 100644 index 5f6af7fee9..0000000000 --- a/doc/txt/lammps_commands_bond.txt +++ /dev/null @@ -1,2 +0,0 @@ - -Bond Style Commands :h2 diff --git a/doc/txt/lammps_commands_compute.txt b/doc/txt/lammps_commands_compute.txt deleted file mode 100644 index cf233abccf..0000000000 --- a/doc/txt/lammps_commands_compute.txt +++ /dev/null @@ -1,2 +0,0 @@ - -Compute Commands :h2 diff --git a/doc/txt/lammps_commands_dihedral.txt b/doc/txt/lammps_commands_dihedral.txt deleted file mode 100644 index c93a1eb0cd..0000000000 --- a/doc/txt/lammps_commands_dihedral.txt +++ /dev/null @@ -1,2 +0,0 @@ - -Dihedral Style Commands :h2 diff --git a/doc/txt/lammps_commands_fix.txt b/doc/txt/lammps_commands_fix.txt deleted file mode 100644 index 32345196e3..0000000000 --- a/doc/txt/lammps_commands_fix.txt +++ /dev/null @@ -1,2 +0,0 @@ - -Fix Commands :h2 diff --git a/doc/txt/lammps_commands_improper.txt b/doc/txt/lammps_commands_improper.txt deleted file mode 100644 index fd580cebd5..0000000000 --- a/doc/txt/lammps_commands_improper.txt +++ /dev/null @@ -1,2 +0,0 @@ - -Improper Style Commands :h2 diff --git a/doc/txt/lammps_commands_kspace.txt b/doc/txt/lammps_commands_kspace.txt deleted file mode 100644 index a187b55d37..0000000000 --- a/doc/txt/lammps_commands_kspace.txt +++ /dev/null @@ -1,2 +0,0 @@ - -Kspace Style Commands :h2 diff --git a/doc/txt/lammps_commands_pair.txt b/doc/txt/lammps_commands_pair.txt deleted file mode 100644 index ee2789a215..0000000000 --- a/doc/txt/lammps_commands_pair.txt +++ /dev/null @@ -1,2 +0,0 @@ - -Pair Style Commands :h2 diff --git a/doc/txt/lattice.txt b/doc/txt/lattice.txt deleted file mode 100644 index 3b50dc044b..0000000000 --- a/doc/txt/lattice.txt +++ /dev/null @@ -1,293 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -lattice command :h3 - -[Syntax:] - -lattice style scale keyword values ... :pre - -style = {none} or {sc} or {bcc} or {fcc} or {hcp} or {diamond} or \ - {sq} or {sq2} or {hex} or {custom} :ulb,l -scale = scale factor between lattice and simulation box :l - scale = reduced density rho* (for LJ units) - scale = lattice constant in distance units (for all other units) :pre -zero or more keyword/value pairs may be appended :l -keyword = {origin} or {orient} or {spacing} or {a1} or {a2} or {a3} or {basis} :l - {origin} values = x y z - x,y,z = fractions of a unit cell (0 <= x,y,z < 1) - {orient} values = dim i j k - dim = {x} or {y} or {z} - i,j,k = integer lattice directions - {spacing} values = dx dy dz - dx,dy,dz = lattice spacings in the x,y,z box directions - {a1},{a2},{a3} values = x y z - x,y,z = primitive vector components that define unit cell - {basis} values = x y z - x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1) :pre -:ule - -[Examples:] - -lattice fcc 3.52 -lattice hex 0.85 -lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0 -lattice custom 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 & - basis 0.0 0.0 0.0 basis 0.5 0.5 0.5 -lattice none 2.0 :pre - -[Description:] - -Define a lattice for use by other commands. In LAMMPS, a lattice is -simply a set of points in space, determined by a unit cell with basis -atoms, that is replicated infinitely in all dimensions. The arguments -of the lattice command can be used to define a wide variety of -crystallographic lattices. - -A lattice is used by LAMMPS in two ways. First, the -"create_atoms"_create_atoms.html command creates atoms on the lattice -points inside the simulation box. Note that the -"create_atoms"_create_atoms.html command allows different atom types -to be assigned to different basis atoms of the lattice. Second, the -lattice spacing in the x,y,z dimensions implied by the lattice, can be -used by other commands as distance units -(e.g. "create_box"_create_box.html, "region"_region.html and -"velocity"_velocity.html), which are often convenient to use when the -underlying problem geometry is atoms on a lattice. - -The lattice style must be consistent with the dimension of the -simulation - see the "dimension"_dimension.html command. Styles {sc} -or {bcc} or {fcc} or {hcp} or {diamond} are for 3d problems. Styles -{sq} or {sq2} or {hex} are for 2d problems. Style {custom} can be -used for either 2d or 3d problems. - -A lattice consists of a unit cell, a set of basis atoms within that -cell, and a set of transformation parameters (scale, origin, orient) -that map the unit cell into the simulation box. The vectors a1,a2,a3 -are the edge vectors of the unit cell. This is the nomenclature for -"primitive" vectors in solid-state crystallography, but in LAMMPS the -unit cell they determine does not have to be a "primitive cell" of -minimum volume. - -Note that the lattice command can be used multiple times in an input -script. Each time it is invoked, the lattice attributes are -re-defined and are used for all subsequent commands (that use lattice -attributes). For example, a sequence of lattice, -"region"_region.html, and "create_atoms"_create_atoms.html commands -can be repeated multiple times to build a poly-crystalline model with -different geometric regions populated with atoms in different lattice -orientations. - -:line - -A lattice of style {none} does not define a unit cell and basis set, -so it cannot be used with the "create_atoms"_create_atoms.html -command. However it does define a lattice spacing via the specified -scale parameter. As explained above the lattice spacings in x,y,z can -be used by other commands as distance units. No additional -keyword/value pairs can be specified for the {none} style. By -default, a "lattice none 1.0" is defined, which means the lattice -spacing is the same as one distance unit, as defined by the -"units"_units.html command. - -Lattices of style {sc}, {fcc}, {bcc}, and {diamond} are 3d lattices -that define a cubic unit cell with edge length = 1.0. This means a1 = -1 0 0, a2 = 0 1 0, and a3 = 0 0 1. Style {hcp} has a1 = 1 0 0, a2 = 0 -sqrt(3) 0, and a3 = 0 0 sqrt(8/3). The placement of the basis atoms -within the unit cell are described in any solid-state physics text. A -{sc} lattice has 1 basis atom at the lower-left-bottom corner of the -cube. A {bcc} lattice has 2 basis atoms, one at the corner and one at -the center of the cube. A {fcc} lattice has 4 basis atoms, one at the -corner and 3 at the cube face centers. A {hcp} lattice has 4 basis -atoms, two in the z = 0 plane and 2 in the z = 0.5 plane. A {diamond} -lattice has 8 basis atoms. - -Lattices of style {sq} and {sq2} are 2d lattices that define a square -unit cell with edge length = 1.0. This means a1 = 1 0 0 and a2 = 0 1 -0. A {sq} lattice has 1 basis atom at the lower-left corner of the -square. A {sq2} lattice has 2 basis atoms, one at the corner and one -at the center of the square. A {hex} style is also a 2d lattice, but -the unit cell is rectangular, with a1 = 1 0 0 and a2 = 0 sqrt(3) 0. -It has 2 basis atoms, one at the corner and one at the center of the -rectangle. - -A lattice of style {custom} allows you to specify a1, a2, a3, and a -list of basis atoms to put in the unit cell. By default, a1 and a2 -and a3 are 3 orthogonal unit vectors (edges of a unit cube). But you -can specify them to be of any length and non-orthogonal to each other, -so that they describe a tilted parallelepiped. Via the {basis} -keyword you add atoms, one at a time, to the unit cell. Its arguments -are fractional coordinates (0.0 <= x,y,z < 1.0). The position vector -x of a basis atom within the unit cell is thus a linear combination of -the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3, -where bx,by,bz are the 3 values specified for the {basis} keyword. - -:line - -This sub-section discusses the arguments that determine how the -idealized unit cell is transformed into a lattice of points within the -simulation box. - -The {scale} argument determines how the size of the unit cell will be -scaled when mapping it into the simulation box. I.e. it determines a -multiplicative factor to apply to the unit cell, to convert it to a -lattice of the desired size and distance units in the simulation box. -The meaning of the {scale} argument depends on the "units"_units.html -being used in your simulation. - -For all unit styles except {lj}, the scale argument is specified in -the distance units defined by the unit style. For example, in {real} -or {metal} units, if the unit cell is a unit cube with edge length -1.0, specifying scale = 3.52 would create a cubic lattice with a -spacing of 3.52 Angstroms. In {cgs} units, the spacing would be 3.52 -cm. - -For unit style {lj}, the scale argument is the Lennard-Jones reduced -density, typically written as rho*. LAMMPS converts this value into -the multiplicative factor via the formula "factor^dim = rho/rho*", -where rho = N/V with V = the volume of the lattice unit cell and N = -the number of basis atoms in the unit cell (described below), and dim -= 2 or 3 for the dimensionality of the simulation. Effectively, this -means that if LJ particles of size sigma = 1.0 are used in the -simulation, the lattice of particles will be at the desired reduced -density. - -The {origin} option specifies how the unit cell will be shifted or -translated when mapping it into the simulation box. The x,y,z values -are fractional values (0.0 <= x,y,z < 1.0) meaning shift the lattice -by a fraction of the lattice spacing in each dimension. The meaning -of "lattice spacing" is discussed below. - -The {orient} option specifies how the unit cell will be rotated when -mapping it into the simulation box. The {dim} argument is one of the -3 coordinate axes in the simulation box. The other 3 arguments are -the crystallographic direction in the lattice that you want to orient -along that axis, specified as integers. E.g. "orient x 2 1 0" means -the x-axis in the simulation box will be the \[210\] lattice -direction, and similarly for y and z. The 3 lattice directions you -specify do not have to be unit vectors, but they must be mutually -orthogonal and obey the right-hand rule, i.e. (X cross Y) points in -the Z direction. - -NOTE: The preceding paragraph describing lattice directions is only -valid for orthogonal cubic unit cells (or square in 2d). If you are -using a {hcp} or {hex} lattice or the more general lattice style -{custom} with non-orthogonal a1,a2,a3 vectors, then you should think -of the 3 {orient} vectors as creating a 3x3 rotation matrix which is -applied to a1,a2,a3 to rotate the original unit cell to a new -orientation in the simulation box. - -:line - -Several LAMMPS commands have the option to use distance units that are -inferred from "lattice spacings" in the x,y,z box directions. -E.g. the "region"_region.html command can create a block of size -10x20x20, where 10 means 10 lattice spacings in the x direction. - -NOTE: Though they are called lattice spacings, all the commands that -have a "units lattice" option, simply use the 3 values as scale -factors on the distance units defined by the "units"_units.html -command. Thus if you do not like the lattice spacings computed by -LAMMPS (e.g. for a non-orthogonal or rotated unit cell), you can -define the 3 values to be whatever you wish, via the {spacing} option. - -If the {spacing} option is not specified, the lattice spacings are -computed by LAMMPS in the following way. A unit cell of the lattice -is mapped into the simulation box (scaled and rotated), so that it now -has (perhaps) a modified size and orientation. The lattice spacing in -X is defined as the difference between the min/max extent of the x -coordinates of the 8 corner points of the modified unit cell (4 in -2d). Similarly, the Y and Z lattice spacings are defined as the -difference in the min/max of the y and z coordinates. - -Note that if the unit cell is orthogonal with axis-aligned edges (no -rotation via the {orient} keyword), then the lattice spacings in each -dimension are simply the scale factor (described above) multiplied by -the length of a1,a2,a3. Thus a {hex} style lattice with a scale -factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and -3*sqrt(3.0) in y. - -NOTE: For non-orthogonal unit cells and/or when a rotation is applied -via the {orient} keyword, then the lattice spacings computed by LAMMPS -are typically less intuitive. In particular, in these cases, there is -no guarantee that a particular lattice spacing is an integer multiple -of the periodicity of the lattice in that direction. Thus, if you -create an orthogonal periodic simulation box whose size in a dimension -is a multiple of the lattice spacing, and then fill it with atoms via -the "create_atoms"_create_atoms.html command, you will NOT necessarily -create a periodic system. I.e. atoms may overlap incorrectly at the -faces of the simulation box. - -The {spacing} option sets the 3 lattice spacings directly. All must -be non-zero (use 1.0 for dz in a 2d simulation). The specified values -are multiplied by the multiplicative factor described above that is -associated with the scale factor. Thus a spacing of 1.0 means one -unit cell edge length independent of the scale factor. As mentioned -above, this option can be useful if the spacings LAMMPS computes are -inconvenient to use in subsequent commands, which can be the case for -non-orthogonal or rotated lattices. - -Note that whenever the lattice command is used, the values of the -lattice spacings LAMMPS calculates are printed out. Thus their effect -in commands that use the spacings should be decipherable. - -:line - -Example commands for generating a Wurtzite crystal (courtesy -of Aidan Thompson), with its 8 atom unit cell. - -variable a equal 4.340330 -variable b equal $a*sqrt(3.0) -variable c equal $a*sqrt(8.0/3.0) :pre - -variable 1_3 equal 1.0/3.0 -variable 2_3 equal 2.0/3.0 -variable 1_6 equal 1.0/6.0 -variable 5_6 equal 5.0/6.0 -variable 1_12 equal 1.0/12.0 -variable 5_12 equal 5.0/12.0 :pre - -lattice custom 1.0 & - a1 $a 0.0 0.0 & - a2 0.0 $b 0.0 & - a3 0.0 0.0 $c & - basis 0.0 0.0 0.0 & - basis 0.5 0.5 0.0 & - basis $\{1_3\} 0.0 0.5 & - basis $\{5_6\} 0.5 0.5 & - basis 0.0 0.0 0.625 & - basis 0.5 0.5 0.625 & - basis $\{1_3\} 0.0 0.125 & - basis $\{5_6\} 0.5 0.125 :pre - -region myreg block 0 1 0 1 0 1 -create_box 2 myreg -create_atoms 1 box & - basis 5 2 & - basis 6 2 & - basis 7 2 & - basis 8 2 :pre - -:line - -[Restrictions:] - -The {a1,a2,a3,basis} keywords can only be used with style {custom}. - -[Related commands:] - -"dimension"_dimension.html, "create_atoms"_create_atoms.html, -"region"_region.html - -[Default:] - -lattice none 1.0 :pre - -For other lattice styles, the option defaults are origin = 0.0 0.0 -0.0, orient = x 1 0 0, orient = y 0 1 0, orient = z 0 0 1, a1 = 1 0 0, -a2 = 0 1 0, and a3 = 0 0 1. diff --git a/doc/txt/log.txt b/doc/txt/log.txt deleted file mode 100644 index d526158a3c..0000000000 --- a/doc/txt/log.txt +++ /dev/null @@ -1,45 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -log command :h3 - -[Syntax:] - -log file keyword :pre - -file = name of new logfile -keyword = {append} if output should be appended to logfile (optional) :ul - -[Examples:] - -log log.equil -log log.equil append :pre - -[Description:] - -This command closes the current LAMMPS log file, opens a new file with -the specified name, and begins logging information to it. If the -specified file name is {none}, then no new log file is opened. If the -optional keyword {append} is specified, then output will be appended -to an existing log file, instead of overwriting it. - -If multiple processor partitions are being used, the file name should -be a variable, so that different processors do not attempt to write to -the same log file. - -The file "log.lammps" is the default log file for a LAMMPS run. The -name of the initial log file can also be set by the "-log command-line -switch"_Run_options.html. - -[Restrictions:] none - -[Related commands:] none - -[Default:] - -The default LAMMPS log file is named log.lammps diff --git a/doc/txt/mass.txt b/doc/txt/mass.txt deleted file mode 100644 index c693963044..0000000000 --- a/doc/txt/mass.txt +++ /dev/null @@ -1,84 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -mass command :h3 - -[Syntax:] - -mass I value :pre - -I = atom type (see asterisk form below) -value = mass :ul - -[Examples:] - -mass 1 1.0 -mass * 62.5 -mass 2* 62.5 :pre - -[Description:] - -Set the mass for all atoms of one or more atom types. Per-type mass -values can also be set in the "read_data"_read_data.html data file -using the "Masses" keyword. See the "units"_units.html command for -what mass units to use. - -The I index can be specified in one of two ways. An explicit numeric -value can be used, as in the 1st example above. Or a wild-card -asterisk can be used to set the mass for multiple atom types. This -takes the form "*" or "*n" or "n*" or "m*n". If N = the number of -atom types, then an asterisk with no numeric values means all types -from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). - -A line in a "data file"_read_data.html that follows the "Masses" -keyword specifies mass using the same format as the arguments of the -mass command in an input script, except that no wild-card asterisk can -be used. For example, under the "Masses" section of a data file, the -line that corresponds to the 1st example above would be listed as - -1 1.0 :pre - -Note that the mass command can only be used if the "atom -style"_atom_style.html requires per-type atom mass to be set. -Currently, all but the {sphere} and {ellipsoid} and {peri} styles do. -They require mass to be set for individual particles, not types. -Per-atom masses are defined in the data file read by the -"read_data"_read_data.html command, or set to default values by the -"create_atoms"_create_atoms.html command. Per-atom masses can also be -set to new values by the "set mass"_set.html or "set density"_set.html -commands. - -Also note that "pair_style eam"_pair_eam.html and "pair_style -bop"_pair_bop.html commands define the masses of atom types in their -respective potential files, in which case the mass command is normally -not used. - -If you define a "hybrid atom style"_atom_style.html which includes one -(or more) sub-styles which require per-type mass and one (or more) -sub-styles which require per-atom mass, then you must define both. -However, in this case the per-type mass will be ignored; only the -per-atom mass will be used by LAMMPS. - -[Restrictions:] - -This command must come after the simulation box is defined by a -"read_data"_read_data.html, "read_restart"_read_restart.html, or -"create_box"_create_box.html command. - -All masses must be defined before a simulation is run. They must also -all be defined before a "velocity"_velocity.html or "fix -shake"_fix_shake.html command is used. - -The mass assigned to any type or atom must be > 0.0. - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/min_modify.txt b/doc/txt/min_modify.txt deleted file mode 100644 index c23ca67852..0000000000 --- a/doc/txt/min_modify.txt +++ /dev/null @@ -1,135 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -min_modify command :h3 - -[Syntax:] - -min_modify keyword values ... :pre - -one or more keyword/value pairs may be listed :ulb,l -keyword = {dmax} or {line} or {norm} or {alpha_damp} or {discrete_factor} - {dmax} value = max - max = maximum distance for line search to move (distance units) - {line} value = {backtrack} or {quadratic} or {forcezero} or {spin_cubic} or {spin_none} - backtrack,quadratic,forcezero,spin_cubic,spin_none = style of linesearch to use - {norm} value = {two} or {max} - two = Euclidean two-norm (length of 3N vector) - inf = max force component across all 3-vectors - max = max force norm across all 3-vectors - {alpha_damp} value = damping - damping = fictitious Gilbert damping for spin minimization (adim) - {discrete_factor} value = factor - factor = discretization factor for adaptive spin timestep (adim) :pre -:ule - -[Examples:] - -min_modify dmax 0.2 :pre - -[Description:] - -This command sets parameters that affect the energy minimization -algorithms selected by the "min_style"_min_style.html command. The -various settings may affect the convergence rate and overall number of -force evaluations required by a minimization, so users can experiment -with these parameters to tune their minimizations. - -The {cg} and {sd} minimization styles have an outer iteration and an -inner iteration which is steps along a one-dimensional line search in -a particular search direction. The {dmax} parameter is how far any -atom can move in a single line search in any dimension (x, y, or z). -For the {quickmin} and {fire} minimization styles, the {dmax} setting -is how far any atom can move in a single iteration (timestep). Thus a -value of 0.1 in real "units"_units.html means no atom will move -further than 0.1 Angstroms in a single outer iteration. This prevents -highly overlapped atoms from being moved long distances (e.g. through -another atom) due to large forces. - -The choice of line search algorithm for the {cg} and {sd} minimization -styles can be selected via the {line} keyword. -The default {quadratic} line search algorithm starts out using -the robust backtracking method described below. However, once -the system gets close to a local -minimum and the linesearch steps get small, so that the energy -is approximately quadratic in the step length, it uses the -estimated location of zero gradient as the linesearch step, -provided the energy change is downhill. -This becomes more efficient than backtracking -for highly-converged relaxations. The {forcezero} -line search algorithm is similar to {quadratic}. -It may be more efficient than {quadratic} on some systems. - -The backtracking search is robust and should always find a local energy -minimum. However, it will "converge" when it can no longer reduce the -energy of the system. Individual atom forces may still be larger than -desired at this point, because the energy change is measured as the -difference of two large values (energy before and energy after) and -that difference may be smaller than machine epsilon even if atoms -could move in the gradient direction to reduce forces further. - -The choice of a norm can be modified for the min styles {cg}, {sd}, -{quickmin}, {fire}, {spin}, {spin/cg} and {spin/lbfgs} using -the {norm} keyword. -The default {two} norm computes the 2-norm (Euclidean length) of the -global force vector: - -:c,image(Eqs/norm_two.jpg) - -The {max} norm computes the length of the 3-vector force -for each atom (2-norm), and takes the maximum value of those across -all atoms - -:c,image(Eqs/norm_max.jpg) - -The {inf} norm takes the maximum component across the forces of -all atoms in the system: - -:c,image(Eqs/norm_inf.jpg) - -For the min styles {spin}, {spin/cg} and {spin/lbfgs}, the force -norm is replaced by the spin-torque norm. - -Keywords {alpha_damp} and {discrete_factor} only make sense when -a "min_spin"_min_spin.html command is declared. -Keyword {alpha_damp} defines an analog of a magnetic Gilbert -damping. It defines a relaxation rate toward an equilibrium for -a given magnetic system. -Keyword {discrete_factor} defines a discretization factor for the -adaptive timestep used in the {spin} minimization. -See "min_spin"_min_spin.html for more information about those -quantities. - -The choice of a line search algorithm for the {spin/cg} and -{spin/lbfgs} styles can be specified via the {line} keyword. -The {spin_cubic} and {spin_none} only make sense when one of those -two minimization styles is declared. -The {spin_cubic} performs the line search based on a cubic interpolation -of the energy along the search direction. The {spin_none} keyword -deactivates the line search procedure. -The {spin_none} is a default value for {line} keyword for both {spin/lbfgs} -and {spin/cg}. Convergence of {spin/lbfgs} can be more robust if -{spin_cubic} line search is used. - -[Restrictions:] - -For magnetic GNEB calculations, only {spin_none} value for {line} keyword can be used -when styles {spin/cg} and {spin/lbfgs} are employed. -See "neb/spin"_neb_spin.html for more explanation. - -[Related commands:] - -"min_style"_min_style.html, "minimize"_minimize.html - -[Default:] - -The option defaults are dmax = 0.1, line = quadratic and norm = two. - -For the {spin}, {spin/cg} and {spin/lbfgs} styles, the -option defaults are alpha_damp = 1.0, discrete_factor = 10.0, -line = spin_none, and norm = euclidean. diff --git a/doc/txt/min_spin.txt b/doc/txt/min_spin.txt deleted file mode 100644 index 89766891c8..0000000000 --- a/doc/txt/min_spin.txt +++ /dev/null @@ -1,104 +0,0 @@ -"LAMMPS WWW Page"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) -:line - -min_style spin command :h3 -min_style spin/cg command :h3 -min_style spin/lbfgs command :h3 - -[Syntax:] - -min_style spin -min_style spin/cg -min_style spin/lbfgs :pre - -[Examples:] - -min_style spin/lbfgs -min_modify line spin_cubic discrete_factor 10.0 :pre - -[Description:] - -Apply a minimization algorithm to use when a "minimize"_minimize.html -command is performed. - -Style {spin} defines a damped spin dynamics with an adaptive -timestep, according to: - -:c,image(Eqs/min_spin_damping.jpg) - -with lambda a damping coefficient (similar to a Gilbert -damping). -Lambda can be defined by setting the {alpha_damp} keyword with the -"min_modify"_min_modify.html command. - -The minimization procedure solves this equation using an -adaptive timestep. The value of this timestep is defined -by the largest precession frequency that has to be solved in the -system: - -:c,image(Eqs/min_spin_timestep.jpg) - -with {|omega|_{max}} the norm of the largest precession frequency -in the system (across all processes, and across all replicas if a -spin/neb calculation is performed). - -Kappa defines a discretization factor {discrete_factor} for the -definition of this timestep. -{discrete_factor} can be defined with the "min_modify"_min_modify.html -command. - -Style {spin/cg} defines an orthogonal spin optimization -(OSO) combined to a conjugate gradient (CG) algorithm. -The "min_modify"_min_modify.html command can be used to -couple the {spin/cg} to a line search procedure, and to modify the -discretization factor {discrete_factor}. -By default, style {spin/cg} does not employ the line search procedure -and uses the adaptive time-step technique in the same way as style {spin}. - -Style {spin/lbfgs} defines an orthogonal spin optimization -(OSO) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno -(L-BFGS) algorithm. -By default, style {spin/lbfgs} does not employ line search procedure. -If the line search procedure is not used then the discrete factor defines -the maximum root mean squared rotation angle of spins by equation {pi/(5*Kappa)}. -The default value for Kappa is 10. -The {spin_cubic} line search can improve the convergence of the -{spin/lbfgs} algorithm. - -The "min_modify"_min_modify.html command can be used to -activate the line search procedure, and to modify the -discretization factor {discrete_factor}. - -For more information about styles {spin/cg} and {spin/lbfgs}, -see their implementation reported in "(Ivanov)"_#Ivanov1. - -NOTE: All the {spin} styles replace the force tolerance by a torque -tolerance. See "minimize"_minimize.html for more explanation. - -NOTE: The {spin/cg} and {spin/lbfgs} styles can be used -for magnetic NEB calculations only if the line search procedure -is deactivated. See "neb/spin"_neb_spin.html for more explanation. - -[Restrictions:] - -This minimization procedure is only applied to spin degrees of -freedom for a frozen lattice configuration. - -[Related commands:] - -"min_style"_min_style.html, "minimize"_minimize.html, -"min_modify"_min_modify.html - -[Default:] - -The option defaults are {alpha_damp} = 1.0, {discrete_factor} = -10.0, {line} = spin_none and {norm} = euclidean. - -:line - -:link(Ivanov1) -[(Ivanov)] Ivanov, Uzdin, Jonsson. arXiv preprint arXiv:1904.02669, (2019). diff --git a/doc/txt/min_style.txt b/doc/txt/min_style.txt deleted file mode 100644 index 8816d62ffa..0000000000 --- a/doc/txt/min_style.txt +++ /dev/null @@ -1,140 +0,0 @@ -"LAMMPS WWW Page"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) -:line - -min_style command :h3 - -[Syntax:] - -min_style style :pre - -style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} or {spin/cg} or {spin/lbfgs} :ul - -[Examples:] - -min_style cg -min_style spin -min_style fire :pre - -[Description:] - -Choose a minimization algorithm to use when a "minimize"_minimize.html -command is performed. - -Style {cg} is the Polak-Ribiere version of the conjugate gradient (CG) -algorithm. At each iteration the force gradient is combined with the -previous iteration information to compute a new search direction -perpendicular (conjugate) to the previous search direction. The PR -variant affects how the direction is chosen and how the CG method is -restarted when it ceases to make progress. The PR variant is thought -to be the most effective CG choice for most problems. - -Style {hftn} is a Hessian-free truncated Newton algorithm. At each -iteration a quadratic model of the energy potential is solved by a -conjugate gradient inner iteration. The Hessian (second derivatives) -of the energy is not formed directly, but approximated in each -conjugate search direction by a finite difference directional -derivative. When close to an energy minimum, the algorithm behaves -like a Newton method and exhibits a quadratic convergence rate to high -accuracy. In most cases the behavior of {hftn} is similar to {cg}, -but it offers an alternative if {cg} seems to perform poorly. This -style is not affected by the "min_modify"_min_modify.html command. - -Style {sd} is a steepest descent algorithm. At each iteration, the -search direction is set to the downhill direction corresponding to the -force vector (negative gradient of energy). Typically, steepest -descent will not converge as quickly as CG, but may be more robust in -some situations. - -Style {quickmin} is a damped dynamics method described in -"(Sheppard)"_#Sheppard, where the damping parameter is related to the -projection of the velocity vector along the current force vector for -each atom. The velocity of each atom is initialized to 0.0 by this -style, at the beginning of a minimization. - -Style {fire} is a damped dynamics method described in -"(Bitzek)"_#Bitzek, which is similar to {quickmin} but adds a variable -timestep and alters the projection operation to maintain components of -the velocity non-parallel to the current force vector. The velocity -of each atom is initialized to 0.0 by this style, at the beginning of -a minimization. - -Style {spin} is a damped spin dynamics with an adaptive -timestep. - -Style {spin/cg} uses an orthogonal spin optimization (OSO) -combined to a conjugate gradient (CG) approach to minimize spin -configurations. - -Style {spin/lbfgs} uses an orthogonal spin optimization (OSO) -combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno -(LBFGS) approach to minimize spin configurations. - -See the "min/spin"_min_spin.html doc page for more information -about the {spin}, {spin/cg} and {spin/lbfgs} styles. - -Either the {quickmin} and {fire} styles are useful in the context of -nudged elastic band (NEB) calculations via the "neb"_neb.html command. - -Either the {spin}, {spin/cg} and {spin/lbfgs} styles are useful -in the context of magnetic geodesic nudged elastic band (GNEB) calculations -via the "neb/spin"_neb_spin.html command. - -NOTE: The damped dynamic minimizers use whatever timestep you have -defined via the "timestep"_timestep.html command. Often they will -converge more quickly if you use a timestep about 10x larger than you -would normally use for dynamics simulations. - -NOTE: The {quickmin}, {fire}, {hftn}, and {cg/kk} styles do not yet -support the use of the "fix box/relax"_fix_box_relax.html command or -minimizations involving the electron radius in "eFF"_pair_eff.html -models. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] none - -[Related commands:] - -"min_modify"_min_modify.html, "minimize"_minimize.html, "neb"_neb.html - -[Default:] - -min_style cg :pre - -:line - -:link(Sheppard) -[(Sheppard)] Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 -(2008). See ref 1 in this paper for original reference to Qmin in -Jonsson, Mills, Jacobsen. - -:link(Bitzek) -[(Bitzek)] Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, -97, 170201 (2006). - diff --git a/doc/txt/minimize.txt b/doc/txt/minimize.txt deleted file mode 100644 index da203c7d2d..0000000000 --- a/doc/txt/minimize.txt +++ /dev/null @@ -1,315 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -minimize command :h3 -minimize/kk command :h3 - -[Syntax:] - -minimize etol ftol maxiter maxeval :pre - -etol = stopping tolerance for energy (unitless) -ftol = stopping tolerance for force (force units) -maxiter = max iterations of minimizer -maxeval = max number of force/energy evaluations :ul - -[Examples:] - -minimize 1.0e-4 1.0e-6 100 1000 -minimize 0.0 1.0e-8 1000 100000 :pre - -[Description:] - -Perform an energy minimization of the system, by iteratively adjusting -atom coordinates. Iterations are terminated when one of the stopping -criteria is satisfied. At that point the configuration will hopefully -be in local potential energy minimum. More precisely, the -configuration should approximate a critical point for the objective -function (see below), which may or may not be a local minimum. - -The minimization algorithm used is set by the -"min_style"_min_style.html command. Other options are set by the -"min_modify"_min_modify.html command. Minimize commands can be -interspersed with "run"_run.html commands to alternate between -relaxation and dynamics. The minimizers bound the distance atoms move -in one iteration, so that you can relax systems with highly overlapped -atoms (large energies and forces) by pushing the atoms off of each -other. - -Alternate means of relaxing a system are to run dynamics with a small -or "limited timestep"_fix_nve_limit.html. Or dynamics can be run -using "fix viscous"_fix_viscous.html to impose a damping force that -slowly drains all kinetic energy from the system. The "pair_style -soft"_pair_soft.html potential can be used to un-overlap atoms while -running dynamics. - -Note that you can minimize some atoms in the system while holding the -coordinates of other atoms fixed by applying "fix -setforce"_fix_setforce.html to the other atoms. See a fuller -discussion of using fixes while minimizing below. - -The "minimization styles"_min_style.html {cg}, {sd}, and {hftn} -involves an outer iteration loop which sets the search direction along -which atom coordinates are changed. An inner iteration is then -performed using a line search algorithm. The line search typically -evaluates forces and energies several times to set new coordinates. -Currently, a backtracking algorithm is used which may not be optimal -in terms of the number of force evaluations performed, but appears to -be more robust than previous line searches we've tried. The -backtracking method is described in Nocedal and Wright's Numerical -Optimization (Procedure 3.1 on p 41). - -The "minimization styles"_min_style.html {quickmin} and {fire} perform -damped dynamics using an Euler integration step. Thus they require a -"timestep"_timestep.html be defined. - -NOTE: The damped dynamic minimizers use whatever timestep you have -defined via the "timestep"_timestep.html command. Often they will -converge more quickly if you use a timestep about 10x larger than you -would normally use for dynamics simulations. - -:line - -In all cases, the objective function being minimized is the total -potential energy of the system as a function of the N atom -coordinates: - -:c,image(Eqs/min_energy.jpg) - -where the first term is the sum of all non-bonded "pairwise -interactions"_pair_style.html including "long-range Coulombic -interactions"_kspace_style.html, the 2nd through 5th terms are -"bond"_bond_style.html, "angle"_angle_style.html, -"dihedral"_dihedral_style.html, and "improper"_improper_style.html -interactions respectively, and the last term is energy due to -"fixes"_fix.html which can act as constraints or apply force to atoms, -such as through interaction with a wall. See the discussion below about -how fix commands affect minimization. - -The starting point for the minimization is the current configuration -of the atoms. - -:line - -The minimization procedure stops if any of several criteria are met: - -the change in energy between outer iterations is less than {etol} -the 2-norm (length) of the global force vector is less than the {ftol} -the line search fails because the step distance backtracks to 0.0 -the number of outer iterations or timesteps exceeds {maxiter} -the number of total force evaluations exceeds {maxeval} :ul - -NOTE: the "minimization style"_min_style.html {spin}, -{spin/cg}, and {spin/lbfgs} replace -the force tolerance {ftol} by a torque tolerance. -The minimization procedure stops if the 2-norm (length) of the torque vector on atom -(defined as the cross product between the -atomic spin and its precession vectors omega) is less than {ftol}, -or if any of the other criteria are met. Torque have the same units as the energy. - -NOTE: You can also use the "fix halt"_fix_halt.html command to specify -a general criterion for exiting a minimization, that is a calculation -performed on the state of the current system, as defined by an -"equal-style variable"_variable.html. - -For the first criterion, the specified energy tolerance {etol} is -unitless; it is met when the energy change between successive -iterations divided by the energy magnitude is less than or equal to -the tolerance. For example, a setting of 1.0e-4 for {etol} means an -energy tolerance of one part in 10^4. For the damped dynamics -minimizers this check is not performed for a few steps after -velocities are reset to 0, otherwise the minimizer would prematurely -converge. - -For the second criterion, the specified force tolerance {ftol} is in -force units, since it is the length of the global force vector for all -atoms, e.g. a vector of size 3N for N atoms. Since many of the -components will be near zero after minimization, you can think of -{ftol} as an upper bound on the final force on any component of any -atom. For example, a setting of 1.0e-4 for {ftol} means no x, y, or z -component of force on any atom will be larger than 1.0e-4 (in force -units) after minimization. - -Either or both of the {etol} and {ftol} values can be set to 0.0, in -which case some other criterion will terminate the minimization. - -During a minimization, the outer iteration count is treated as a -timestep. Output is triggered by this timestep, e.g. thermodynamic -output or dump and restart files. - -Using the "thermo_style custom"_thermo_style.html command with the -{fmax} or {fnorm} keywords can be useful for monitoring the progress -of the minimization. Note that these outputs will be calculated only -from forces on the atoms, and will not include any extra degrees of -freedom, such as from the "fix box/relax"_fix_box_relax.html command. - -Following minimization, a statistical summary is printed that lists -which convergence criterion caused the minimizer to stop, as well as -information about the energy, force, final line search, and -iteration counts. An example is as follows: - -Minimization stats: - Stopping criterion = max iterations - Energy initial, next-to-last, final = - -0.626828169302 -2.82642039062 -2.82643549739 - Force two-norm initial, final = 2052.1 91.9642 - Force max component initial, final = 346.048 9.78056 - Final line search alpha, max atom move = 2.23899e-06 2.18986e-05 - Iterations, force evaluations = 2000 12724 :pre - -The 3 energy values are for before and after the minimization and on -the next-to-last iteration. This is what the {etol} parameter checks. - -The two-norm force values are the length of the global force vector -before and after minimization. This is what the {ftol} parameter -checks. - -The max-component force values are the absolute value of the largest -component (x,y,z) in the global force vector, i.e. the infinity-norm -of the force vector. - -The alpha parameter for the line-search, when multiplied by the max -force component (on the last iteration), gives the max distance any -atom moved during the last iteration. Alpha will be 0.0 if the line -search could not reduce the energy. Even if alpha is non-zero, if the -"max atom move" distance is tiny compared to typical atom coordinates, -then it is possible the last iteration effectively caused no atom -movement and thus the evaluated energy did not change and the -minimizer terminated. Said another way, even with non-zero forces, -it's possible the effect of those forces is to move atoms a distance -less than machine precision, so that the energy cannot be further -reduced. - -The iterations and force evaluation values are what is checked by the -{maxiter} and {maxeval} parameters. - -:line - -NOTE: There are several force fields in LAMMPS which have -discontinuities or other approximations which may prevent you from -performing an energy minimization to high tolerances. For example, -you should use a "pair style"_pair_style.html that goes to 0.0 at the -cutoff distance when performing minimization (even if you later change -it when running dynamics). If you do not do this, the total energy of -the system will have discontinuities when the relative distance -between any pair of atoms changes from cutoff+epsilon to -cutoff-epsilon and the minimizer may behave poorly. Some of the -many-body potentials use splines and other internal cutoffs that -inherently have this problem. The "long-range Coulombic -styles"_kspace_style.html (PPPM, Ewald) are approximate to within the -user-specified tolerance, which means their energy and forces may not -agree to a higher precision than the Kspace-specified tolerance. In -all these cases, the minimizer may give up and stop before finding a -minimum to the specified energy or force tolerance. - -Note that a cutoff Lennard-Jones potential (and others) can be shifted -so that its energy is 0.0 at the cutoff via the -"pair_modify"_pair_modify.html command. See the doc pages for -individual "pair styles"_pair_style.html for details. Note that -Coulombic potentials always have a cutoff, unless versions with a -long-range component are used (e.g. "pair_style -lj/cut/coul/long"_pair_lj.html). The CHARMM potentials go to 0.0 at -the cutoff (e.g. "pair_style lj/charmm/coul/charmm"_pair_charmm.html), -as do the GROMACS potentials (e.g. "pair_style -lj/gromacs"_pair_gromacs.html). - -If a soft potential ("pair_style soft"_pair_soft.html) is used the -Astop value is used for the prefactor (no time dependence). - -The "fix box/relax"_fix_box_relax.html command can be used to apply an -external pressure to the simulation box and allow it to shrink/expand -during the minimization. - -Only a few other fixes (typically those that add forces) are invoked -during minimization. See the doc pages for individual "fix"_fix.html -commands to see which ones are relevant. Current examples of fixes -that can be used include: - -"fix addforce"_fix_addforce.html -"fix addtorque"_fix_addtorque.html -"fix efield"_fix_efield.html -"fix enforce2d"_fix_enforce2d.html -"fix indent"_fix_indent.html -"fix lineforce"_fix_lineforce.html -"fix planeforce"_fix_planeforce.html -"fix setforce"_fix_setforce.html -"fix spring"_fix_spring.html -"fix spring/self"_fix_spring_self.html -"fix viscous"_fix_viscous.html -"fix wall"_fix_wall.html -"fix wall/region"_fix_wall_region.html :ul - -NOTE: Some fixes which are invoked during minimization have an -associated potential energy. For that energy to be included in the -total potential energy of the system (the quantity being minimized), -you MUST enable the "fix_modify"_fix_modify.html {energy} option for -that fix. The doc pages for individual "fix"_fix.html commands -specify if this should be done. - -NOTE: The minimizers in LAMMPS do not allow for bonds (or angles, etc) -to be held fixed while atom coordinates are being relaxed, e.g. via -"fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html. See more -info in the Restrictions section below. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -Features that are not yet implemented are listed here, in case someone -knows how they could be coded: - -It is an error to use "fix shake"_fix_shake.html with minimization -because it turns off bonds that should be included in the potential -energy of the system. The effect of a fix shake can be approximated -during a minimization by using stiff spring constants for the bonds -and/or angles that would normally be constrained by the SHAKE -algorithm. - -"Fix rigid"_fix_rigid.html is also not supported by minimization. It -is not an error to have it defined, but the energy minimization will -not keep the defined body(s) rigid during the minimization. Note that -if bonds, angles, etc internal to a rigid body have been turned off -(e.g. via "neigh_modify exclude"_neigh_modify.html), they will not -contribute to the potential energy which is probably not what is -desired. - -Pair potentials that produce torque on a particle (e.g. "granular -potentials"_pair_gran.html or the "GayBerne -potential"_pair_gayberne.html for ellipsoidal particles) are not -relaxed by a minimization. More specifically, radial relaxations are -induced, but no rotations are induced by a minimization, so such a -system will not fully relax. - -[Related commands:] - -"min_modify"_min_modify.html, "min_style"_min_style.html, -"run_style"_run_style.html - -[Default:] none diff --git a/doc/txt/molecule.txt b/doc/txt/molecule.txt deleted file mode 100644 index e8b6bd8a7e..0000000000 --- a/doc/txt/molecule.txt +++ /dev/null @@ -1,471 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -molecule command :h3 - -[Syntax:] - -molecule ID file1 keyword values ... file2 keyword values ... fileN ... :pre - -ID = user-assigned name for the molecule template :ulb,l -file1,file2,... = names of files containing molecule descriptions :l -zero or more keyword/value pairs may be appended after each file :l -keyword = {offset} or {toff} or {boff} or {aoff} or {doff} or {ioff} or {scale} :l - {offset} values = Toff Boff Aoff Doff Ioff - Toff = offset to add to atom types - Boff = offset to add to bond types - Aoff = offset to add to angle types - Doff = offset to add to dihedral types - Ioff = offset to add to improper types - {toff} value = Toff - Toff = offset to add to atom types - {boff} value = Boff - Boff = offset to add to bond types - {aoff} value = Aoff - Aoff = offset to add to angle types - {doff} value = Doff - Doff = offset to add to dihedral types - {ioff} value = Ioff - Ioff = offset to add to improper types - {scale} value = sfactor - sfactor = scale factor to apply to the size and mass of the molecule :pre -:ule - -[Examples:] - -molecule 1 mymol.txt -molecule 1 co2.txt h2o.txt -molecule CO2 co2.txt boff 3 aoff 2 -molecule 1 mymol.txt offset 6 9 18 23 14 -molecule objects file.1 scale 1.5 file.1 scale 2.0 file.2 scale 1.3 :pre - - -[Description:] - -Define a molecule template that can be used as part of other LAMMPS -commands, typically to define a collection of particles as a bonded -molecule or a rigid body. Commands that currently use molecule -templates include: - -"fix deposit"_fix_deposit.html -"fix pour"_fix_pour.html -"fix rigid/small"_fix_rigid.html -"fix shake"_fix_shake.html -"fix gcmc"_fix_gcmc.html -"create_atoms"_create_atoms.html -"atom_style template"_atom_style.html :ul - -The ID of a molecule template can only contain alphanumeric characters -and underscores. - -A single template can contain multiple molecules, listed one per file. -Some of the commands listed above currently use only the first -molecule in the template, and will issue a warning if the template -contains multiple molecules. The "atom_style -template"_atom_style.html command allows multiple-molecule templates -to define a system with more than one templated molecule. - -Each filename can be followed by optional keywords which are applied -only to the molecule in the file as used in this template. This is to -make it easy to use the same molecule file in different molecule -templates or in different simulations. You can specify the same file -multiple times with different optional keywords. - -The {offset}, {toff}, {aoff}, {doff}, {ioff} keywords add the -specified offset values to the atom types, bond types, angle types, -dihedral types, and/or improper types as they are read from the -molecule file. E.g. if {toff} = 2, and the file uses atom types -1,2,3, then each created molecule will have atom types 3,4,5. For the -{offset} keyword, all five offset values must be specified, but -individual values will be ignored if the molecule template does not -use that attribute (e.g. no bonds). - -The {scale} keyword scales the size of the molecule. This can be -useful for modeling polydisperse granular rigid bodies. The scale -factor is applied to each of these properties in the molecule file, if -they are defined: the individual particle coordinates (Coords -section), the individual mass of each particle (Masses section), the -individual diameters of each particle (Diameters section), the total -mass of the molecule (header keyword = mass), the center-of-mass of -the molecule (header keyword = com), and the moments of inertia of the -molecule (header keyword = inertia). - -NOTE: The molecule command can be used to define molecules with bonds, -angles, dihedrals, impropers, or special bond lists of neighbors -within a molecular topology, so that you can later add the molecules -to your simulation, via one or more of the commands listed above. -Since this topology-related information requires that suitable storage -is reserved when LAMMPS creates the simulation box (e.g. when using -the "create_box"_create_box.html command or the -"read_data"_read_data.html command) suitable space has to be reserved -so you do not overflow those pre-allocated data structures when adding -molecules later. Both the "create_box"_create_box.html command and -the "read_data"_read_data.html command have "extra" options which -insure space is allocated for storing topology info for molecules that -are added later. - -The format of an individual molecule file is similar but -(not identical) to the data file read by the "read_data"_read_data.html -commands, and is as follows. - -A molecule file has a header and a body. The header appears first. -The first line of the header is always skipped; it typically contains -a description of the file. Then lines are read one at a time. Lines -can have a trailing comment starting with '#' that is ignored. If the -line is blank (only white-space after comment is deleted), it is -skipped. If the line contains a header keyword, the corresponding -value(s) is read from the line. If it doesn't contain a header -keyword, the line begins the body of the file. - -The body of the file contains zero or more sections. The first line -of a section has only a keyword. The next line is skipped. The -remaining lines of the section contain values. The number of lines -depends on the section keyword as described below. Zero or more blank -lines can be used between sections. Sections can appear in any order, -with a few exceptions as noted below. - -These are the recognized header keywords. Header lines can come in -any order. The numeric value(s) are read from the beginning of the -line. The keyword should appear at the end of the line. All these -settings have default values, as explained below. A line need only -appear if the value(s) are different than the default. - -N {atoms} = # of atoms N in molecule, default = 0 -Nb {bonds} = # of bonds Nb in molecule, default = 0 -Na {angles} = # of angles Na in molecule, default = 0 -Nd {dihedrals} = # of dihedrals Nd in molecule, default = 0 -Ni {impropers} = # of impropers Ni in molecule, default = 0 -Mtotal {mass} = total mass of molecule -Xc Yc Zc {com} = coordinates of center-of-mass of molecule -Ixx Iyy Izz Ixy Ixz Iyz {inertia} = 6 components of inertia tensor of molecule :ul - -For {mass}, {com}, and {inertia}, the default is for LAMMPS to -calculate this quantity itself if needed, assuming the molecules -consists of a set of point particles or finite-size particles (with a -non-zero diameter) that do not overlap. If finite-size particles in -the molecule do overlap, LAMMPS will not account for the overlap -effects when calculating any of these 3 quantities, so you should -pre-compute them yourself and list the values in the file. - -The mass and center-of-mass coordinates (Xc,Yc,Zc) are -self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) -should be the values consistent with the current orientation of the -rigid body around its center of mass. The values are with respect to -the simulation box XYZ axes, not with respect to the principal axes of -the rigid body itself. LAMMPS performs the latter calculation -internally. - -These are the allowed section keywords for the body of the file. - -{Coords, Types, Charges, Diameters, Masses} = atom-property sections -{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections -{Special Bond Counts, Special Bonds} = special neighbor info -{Shake Flags, Shake Atoms, Shake Bond Types} = SHAKE info :ul - -If a Bonds section is specified then the Special Bond Counts and -Special Bonds sections can also be used, if desired, to explicitly -list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see -details below). This is optional since if these sections are not -included, LAMMPS will auto-generate this information. Note that -LAMMPS uses this info to properly exclude or weight bonded pairwise -interactions between bonded atoms. See the -"special_bonds"_special_bonds.html command for more details. One -reason to list the special bond info explicitly is for the -"thermalized Drude oscillator model"_Howto_drude.html which treats the -bonds between nuclear cores and Drude electrons in a different manner. - -NOTE: Whether a section is required depends on how the molecule -template is used by other LAMMPS commands. For example, to add a -molecule via the "fix deposit"_fix_deposit.html command, the Coords -and Types sections are required. To add a rigid body via the "fix -pour"_fix_pour.html command, the Bonds (Angles, etc) sections are not -required, since the molecule will be treated as a rigid body. Some -sections are optional. For example, the "fix pour"_fix_pour.html -command can be used to add "molecules" which are clusters of -finite-size granular particles. If the Diameters section is not -specified, each particle in the molecule will have a default diameter -of 1.0. See the doc pages for LAMMPS commands that use molecule -templates for more details. - -Each section is listed below in alphabetic order. The format of each -section is described including the number of lines it must contain and -rules (if any) for whether it can appear in the data file. In each -case the ID is ignored; it is simply included for readability, and -should be a number from 1 to Nlines for the section, indicating which -atom (or bond, etc) the entry applies to. The lines are assumed to be -listed in order from 1 to Nlines, but LAMMPS does not check for this. - -:line - -{Coords} section: - -one line per atom -line syntax: ID x y z -x,y,z = coordinate of atom :ul - -:line - -{Types} section: - -one line per atom -line syntax: ID type -type = atom type of atom :ul - -:line - -{Charges} section: - -one line per atom -line syntax: ID q -q = charge on atom :ul - -This section is only allowed for "atom styles"_atom_style.html that -support charge. If this section is not included, the default charge -on each atom in the molecule is 0.0. - -:line - -{Diameters} section: - -one line per atom -line syntax: ID diam -diam = diameter of atom :ul - -This section is only allowed for "atom styles"_atom_style.html that -support finite-size spherical particles, e.g. atom_style sphere. If -not listed, the default diameter of each atom in the molecule is 1.0. - -:line - -{Masses} section: - -one line per atom -line syntax: ID mass -mass = mass of atom :ul - -This section is only allowed for "atom styles"_atom_style.html that -support per-atom mass, as opposed to per-type mass. See the -"mass"_mass.html command for details. If this section is not -included, the default mass for each atom is derived from its volume -(see Diameters section) and a default density of 1.0, in -"units"_units.html of mass/volume. - -:line - -{Bonds} section: - -one line per bond -line syntax: ID type atom1 atom2 -type = bond type (1-Nbondtype) -atom1,atom2 = IDs of atoms in bond :ul - -The IDs for the two atoms in each bond should be values -from 1 to Natoms, where Natoms = # of atoms in the molecule. - -:line - -{Angles} section: - -one line per angle -line syntax: ID type atom1 atom2 atom3 -type = angle type (1-Nangletype) -atom1,atom2,atom3 = IDs of atoms in angle :ul - -The IDs for the three atoms in each angle should be values from 1 to -Natoms, where Natoms = # of atoms in the molecule. The 3 atoms are -ordered linearly within the angle. Thus the central atom (around -which the angle is computed) is the atom2 in the list. - -:line - -{Dihedrals} section: - -one line per dihedral -line syntax: ID type atom1 atom2 atom3 atom4 -type = dihedral type (1-Ndihedraltype) -atom1,atom2,atom3,atom4 = IDs of atoms in dihedral :ul - -The IDs for the four atoms in each dihedral should be values from 1 to -Natoms, where Natoms = # of atoms in the molecule. The 4 atoms are -ordered linearly within the dihedral. - -:line - -{Impropers} section: - -one line per improper -line syntax: ID type atom1 atom2 atom3 atom4 -type = improper type (1-Nimpropertype) -atom1,atom2,atom3,atom4 = IDs of atoms in improper :ul - -The IDs for the four atoms in each improper should be values from 1 to -Natoms, where Natoms = # of atoms in the molecule. The ordering of -the 4 atoms determines the definition of the improper angle used in -the formula for the defined "improper style"_improper_style.html. See -the doc pages for individual styles for details. - -:line - -{Special Bond Counts} section: - -one line per atom -line syntax: ID N1 N2 N3 -N1 = # of 1-2 bonds -N2 = # of 1-3 bonds -N3 = # of 1-4 bonds :ul - -N1, N2, N3 are the number of 1-2, 1-3, 1-4 neighbors respectively of -this atom within the topology of the molecule. See the -"special_bonds"_special_bonds.html doc page for more discussion of -1-2, 1-3, 1-4 neighbors. If this section appears, the Special Bonds -section must also appear. - -As explained above, LAMMPS will auto-generate this information if this -section is not specified. If specified, this section will -override what would be auto-generated. - -:line - -{Special Bonds} section: - -one line per atom -line syntax: ID a b c d ... -a,b,c,d,... = IDs of atoms in N1+N2+N3 special bonds :ul - -A, b, c, d, etc are the IDs of the n1+n2+n3 atoms that are 1-2, 1-3, -1-4 neighbors of this atom. The IDs should be values from 1 to -Natoms, where Natoms = # of atoms in the molecule. The first N1 -values should be the 1-2 neighbors, the next N2 should be the 1-3 -neighbors, the last N3 should be the 1-4 neighbors. No atom ID should -appear more than once. See the "special_bonds"_special_bonds.html doc -page for more discussion of 1-2, 1-3, 1-4 neighbors. If this section -appears, the Special Bond Counts section must also appear. - -As explained above, LAMMPS will auto-generate this information if this -section is not specified. If specified, this section will override -what would be auto-generated. - -:line - -{Shake Flags} section: - -one line per atom -line syntax: ID flag -flag = 0,1,2,3,4 :ul - -This section is only needed when molecules created using the template -will be constrained by SHAKE via the "fix shake" command. The other -two Shake sections must also appear in the file, following this one. - -The meaning of the flag for each atom is as follows. See the "fix -shake"_fix_shake.html doc page for a further description of SHAKE -clusters. - -0 = not part of a SHAKE cluster -1 = part of a SHAKE angle cluster (two bonds and the angle they form) -2 = part of a 2-atom SHAKE cluster with a single bond -3 = part of a 3-atom SHAKE cluster with two bonds -4 = part of a 4-atom SHAKE cluster with three bonds :ul - -:line - -{Shake Atoms} section: - -one line per atom -line syntax: ID a b c d -a,b,c,d = IDs of atoms in cluster :ul - -This section is only needed when molecules created using the template -will be constrained by SHAKE via the "fix shake" command. The other -two Shake sections must also appear in the file. - -The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms -in the SHAKE cluster that this atom belongs to. The number of values -that must appear is determined by the shake flag for the atom (see the -Shake Flags section above). All atoms in a particular cluster should -list their a,b,c,d values identically. - -If flag = 0, no a,b,c,d values are listed on the line, just the -(ignored) ID. - -If flag = 1, a,b,c are listed, where a = ID of central atom in the -angle, and b,c the other two atoms in the angle. - -If flag = 2, a,b are listed, where a = ID of atom in bond with the -lowest ID, and b = ID of atom in bond with the highest ID. - -If flag = 3, a,b,c are listed, where a = ID of central atom, -and b,c = IDs of other two atoms bonded to the central atom. - -If flag = 4, a,b,c,d are listed, where a = ID of central atom, -and b,c,d = IDs of other three atoms bonded to the central atom. - -See the "fix shake"_fix_shake.html doc page for a further description -of SHAKE clusters. - -:line - -{Shake Bond Types} section: - -one line per atom -line syntax: ID a b c -a,b,c = bond types (or angle type) of bonds (or angle) in cluster :ul - -This section is only needed when molecules created using the template -will be constrained by SHAKE via the "fix shake" command. The other -two Shake sections must also appear in the file. - -The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds -in the SHAKE cluster that this atom belongs to. The number of values -that must appear is determined by the shake flag for the atom (see the -Shake Flags section above). All atoms in a particular cluster should -list their a,b,c values identically. - -If flag = 0, no a,b,c values are listed on the line, just the -(ignored) ID. - -If flag = 1, a,b,c are listed, where a = bondtype of the bond between -the central atom and the first non-central atom (value b in the Shake -Atoms section), b = bondtype of the bond between the central atom and -the 2nd non-central atom (value c in the Shake Atoms section), and c = -the angle type (1 to Nangletypes) of the angle between the 3 atoms. - -If flag = 2, only a is listed, where a = bondtype of the bond between -the 2 atoms in the cluster. - -If flag = 3, a,b are listed, where a = bondtype of the bond between -the central atom and the first non-central atom (value b in the Shake -Atoms section), and b = bondtype of the bond between the central atom -and the 2nd non-central atom (value c in the Shake Atoms section). - -If flag = 4, a,b,c are listed, where a = bondtype of the bond between -the central atom and the first non-central atom (value b in the Shake -Atoms section), b = bondtype of the bond between the central atom and -the 2nd non-central atom (value c in the Shake Atoms section), and c = -bondtype of the bond between the central atom and the 3rd non-central -atom (value d in the Shake Atoms section). - -See the "fix shake"_fix_shake.html doc page for a further description -of SHAKE clusters. - -:line - -[Restrictions:] - -This command must come after the simulation box is define by a -"read_data"_read_data.html, "read_restart"_read_restart.html, or -"create_box"_create_box.html command. - -[Related commands:] - -"fix deposit"_fix_deposit.html, "fix pour"_fix_pour.html, -"fix gcmc"_fix_gcmc.html - -[Default:] - -The default keywords values are offset 0 0 0 0 0 and scale = 1.0. diff --git a/doc/txt/neb.txt b/doc/txt/neb.txt deleted file mode 100644 index fbe06d3d3d..0000000000 --- a/doc/txt/neb.txt +++ /dev/null @@ -1,426 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -neb command :h3 - -[Syntax:] - -neb etol ftol N1 N2 Nevery file-style arg keyword :pre - -etol = stopping tolerance for energy (energy units) :ulb,l -ftol = stopping tolerance for force (force units) :l -N1 = max # of iterations (timesteps) to run initial NEB :l -N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l -Nevery = print replica energies and reaction coordinates every this many timesteps :l -file-style = {final} or {each} or {none} :l - {final} arg = filename - filename = file with initial coords for final replica - coords for intermediate replicas are linearly interpolated - between first and last replica - {each} arg = filename - filename = unique filename for each replica (except first) - with its initial coords - {none} arg = no argument all replicas assumed to already have - their initial coords :pre -keyword = {verbose} -:ule - -[Examples:] - -neb 0.1 0.0 1000 500 50 final coords.final -neb 0.0 0.001 1000 500 50 each coords.initial.$i -neb 0.0 0.001 1000 500 50 none verbose :pre - -[Description:] - -Perform a nudged elastic band (NEB) calculation using multiple -replicas of a system. Two or more replicas must be used; the first -and last are the end points of the transition path. - -NEB is a method for finding both the atomic configurations and height -of the energy barrier associated with a transition state, e.g. for an -atom to perform a diffusive hop from one energy basin to another in a -coordinated fashion with its neighbors. The implementation in LAMMPS -follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA, -"(HenkelmanB)"_#HenkelmanB, "(Nakano)"_#Nakano3 and "(Maras)"_#Maras2. - -Each replica runs on a partition of one or more processors. Processor -partitions are defined at run-time using the "-partition command-line -switch"_Run_options.html. Note that if you have MPI installed, you -can run a multi-replica simulation with more replicas (partitions) -than you have physical processors, e.g you can run a 10-replica -simulation on just one or two processors. You will simply not get the -performance speed-up you would see with one or more physical -processors per replica. See the "Howto replica"_Howto_replica.html -doc page for further discussion. - -NOTE: As explained below, a NEB calculation performs a damped dynamics -minimization across all the replicas. The minimizer uses whatever -timestep you have defined in your input script, via the -"timestep"_timestep.html command. Often NEB will converge more -quickly if you use a timestep about 10x larger than you would normally -use for dynamics simulations. - -When a NEB calculation is performed, it is assumed that each replica -is running the same system, though LAMMPS does not check for this. -I.e. the simulation domain, the number of atoms, the interaction -potentials, and the starting configuration when the neb command is -issued should be the same for every replica. - -In a NEB calculation each replica is connected to other replicas by -inter-replica nudging forces. These forces are imposed by the "fix -neb"_fix_neb.html command, which must be used in conjunction with the -neb command. The group used to define the fix neb command defines the -NEB atoms which are the only ones that inter-replica springs are -applied to. If the group does not include all atoms, then non-NEB -atoms have no inter-replica springs and the forces they feel and their -motion is computed in the usual way due only to other atoms within -their replica. Conceptually, the non-NEB atoms provide a background -force field for the NEB atoms. They can be allowed to move during the -NEB minimization procedure (which will typically induce different -coordinates for non-NEB atoms in different replicas), or held fixed -using other LAMMPS commands such as "fix setforce"_fix_setforce.html. -Note that the "partition"_partition.html command can be used to invoke -a command on a subset of the replicas, e.g. if you wish to hold NEB or -non-NEB atoms fixed in only the end-point replicas. - -The initial atomic configuration for each of the replicas can be -specified in different manners via the {file-style} setting, as -discussed below. Only atoms whose initial coordinates should differ -from the current configuration need be specified. - -Conceptually, the initial and final configurations for the first -replica should be states on either side of an energy barrier. - -As explained below, the initial configurations of intermediate -replicas can be atomic coordinates interpolated in a linear fashion -between the first and last replicas. This is often adequate for -simple transitions. For more complex transitions, it may lead to slow -convergence or even bad results if the minimum energy path (MEP, see -below) of states over the barrier cannot be correctly converged to -from such an initial path. In this case, you will want to generate -initial states for the intermediate replicas that are geometrically -closer to the MEP and read them in. - -:line - -For a {file-style} setting of {final}, a filename is specified which -contains atomic coordinates for zero or more atoms, in the format -described below. For each atom that appears in the file, the new -coordinates are assigned to that atom in the final replica. Each -intermediate replica also assigns a new position to that atom in an -interpolated manner. This is done by using the current position of -the atom as the starting point and the read-in position as the final -point. The distance between them is calculated, and the new position -is assigned to be a fraction of the distance. E.g. if there are 10 -replicas, the 2nd replica will assign a position that is 10% of the -distance along a line between the starting and final point, and the -9th replica will assign a position that is 90% of the distance along -the line. Note that for this procedure to produce consistent -coordinates across all the replicas, the current coordinates need to -be the same in all replicas. LAMMPS does not check for this, but -invalid initial configurations will likely result if it is not the -case. - -NOTE: The "distance" between the starting and final point is -calculated in a minimum-image sense for a periodic simulation box. -This means that if the two positions are on opposite sides of a box -(periodic in that dimension), the distance between them will be small, -because the periodic image of one of the atoms is close to the other. -Similarly, even if the assigned position resulting from the -interpolation is outside the periodic box, the atom will be wrapped -back into the box when the NEB calculation begins. - -For a {file-style} setting of {each}, a filename is specified which is -assumed to be unique to each replica. This can be done by using a -variable in the filename, e.g. - -variable i equal part -neb 0.0 0.001 1000 500 50 each coords.initial.$i :pre - -which in this case will substitute the partition ID (0 to N-1) for the -variable I, which is also effectively the replica ID. See the -"variable"_variable.html command for other options, such as using -world-, universe-, or uloop-style variables. - -Each replica (except the first replica) will read its file, formatted -as described below, and for any atom that appears in the file, assign -the specified coordinates to its atom. The various files do not need -to contain the same set of atoms. - -For a {file-style} setting of {none}, no filename is specified. Each -replica is assumed to already be in its initial configuration at the -time the neb command is issued. This allows each replica to define -its own configuration by reading a replica-specific data or restart or -dump file, via the "read_data"_read_data.html, -"read_restart"_read_restart.html, or "read_dump"_read_dump.html -commands. The replica-specific names of these files can be specified -as in the discussion above for the {each} file-style. Also see the -section below for how a NEB calculation can produce restart files, so -that a long calculation can be restarted if needed. - -NOTE: None of the {file-style} settings change the initial -configuration of any atom in the first replica. The first replica -must thus be in the correct initial configuration at the time the neb -command is issued. - -:line - -A NEB calculation proceeds in two stages, each of which is a -minimization procedure, performed via damped dynamics. To enable -this, you must first define a damped dynamics -"min_style"_min_style.html, such as {quickmin} or {fire}. The {cg}, -{sd}, and {hftn} styles cannot be used, since they perform iterative -line searches in their inner loop, which cannot be easily synchronized -across multiple replicas. - -The minimizer tolerances for energy and force are set by {etol} and -{ftol}, the same as for the "minimize"_minimize.html command. - -A non-zero {etol} means that the NEB calculation will terminate if the -energy criterion is met by every replica. The energies being compared -to {etol} do not include any contribution from the inter-replica -nudging forces, since these are non-conservative. A non-zero {ftol} -means that the NEB calculation will terminate if the force criterion -is met by every replica. The forces being compared to {ftol} include -the inter-replica nudging forces. - -The maximum number of iterations in each stage is set by {N1} and -{N2}. These are effectively timestep counts since each iteration of -damped dynamics is like a single timestep in a dynamics -"run"_run.html. During both stages, the potential energy of each -replica and its normalized distance along the reaction path (reaction -coordinate RD) will be printed to the screen and log file every -{Nevery} timesteps. The RD is 0 and 1 for the first and last replica. -For intermediate replicas, it is the cumulative distance (normalized -by the total cumulative distance) between adjacent replicas, where -"distance" is defined as the length of the 3N-vector of differences in -atomic coordinates, where N is the number of NEB atoms involved in the -transition. These outputs allow you to monitor NEB's progress in -finding a good energy barrier. {N1} and {N2} must both be multiples -of {Nevery}. - -In the first stage of NEB, the set of replicas should converge toward -a minimum energy path (MEP) of conformational states that transition -over a barrier. The MEP for a transition is defined as a sequence of -3N-dimensional states, each of which has a potential energy gradient -parallel to the MEP itself. The configuration of highest energy along -a MEP corresponds to a saddle point. The replica states will also be -roughly equally spaced along the MEP due to the inter-replica nudging -force added by the "fix neb"_fix_neb.html command. - -In the second stage of NEB, the replica with the highest energy is -selected and the inter-replica forces on it are converted to a force -that drives its atom coordinates to the top or saddle point of the -barrier, via the barrier-climbing calculation described in -"(HenkelmanB)"_#HenkelmanB. As before, the other replicas rearrange -themselves along the MEP so as to be roughly equally spaced. - -When both stages are complete, if the NEB calculation was successful, -the configurations of the replicas should be along (close to) the MEP -and the replica with the highest energy should be an atomic -configuration at (close to) the saddle point of the transition. The -potential energies for the set of replicas represents the energy -profile of the transition along the MEP. - -:line - -A few other settings in your input script are required or advised to -perform a NEB calculation. See the NOTE about the choice of timestep -at the beginning of this doc page. - -An atom map must be defined which it is not by default for "atom_style -atomic"_atom_style.html problems. The "atom_modify -map"_atom_modify.html command can be used to do this. - -The minimizers in LAMMPS operate on all atoms in your system, even -non-NEB atoms, as defined above. To prevent non-NEB atoms from moving -during the minimization, you should use the "fix -setforce"_fix_setforce.html command to set the force on each of those -atoms to 0.0. This is not required, and may not even be desired in -some cases, but if those atoms move too far (e.g. because the initial -state of your system was not well-minimized), it can cause problems -for the NEB procedure. - -The damped dynamics "minimizers"_min_style.html, such as {quickmin} -and {fire}), adjust the position and velocity of the atoms via an -Euler integration step. Thus you must define an appropriate -"timestep"_timestep.html to use with NEB. As mentioned above, NEB -will often converge more quickly if you use a timestep about 10x -larger than you would normally use for dynamics simulations. - -:line - -Each file read by the neb command containing atomic coordinates used -to initialize one or more replicas must be formatted as follows. - -The file can be ASCII text or a gzipped text file (detected by a .gz -suffix). The file can contain initial blank lines or comment lines -starting with "#" which are ignored. The first non-blank, non-comment -line should list N = the number of lines to follow. The N successive -lines contain the following information: - -ID1 x1 y1 z1 -ID2 x2 y2 z2 -... -IDN xN yN zN :pre - -The fields are the atom ID, followed by the x,y,z coordinates. The -lines can be listed in any order. Additional trailing information on -the line is OK, such as a comment. - -Note that for a typical NEB calculation you do not need to specify -initial coordinates for very many atoms to produce differing starting -and final replicas whose intermediate replicas will converge to the -energy barrier. Typically only new coordinates for atoms -geometrically near the barrier need be specified. - -Also note there is no requirement that the atoms in the file -correspond to the NEB atoms in the group defined by the "fix -neb"_fix_neb.html command. Not every NEB atom need be in the file, -and non-NEB atoms can be listed in the file. - -:line - -Four kinds of output can be generated during a NEB calculation: energy -barrier statistics, thermodynamic output by each replica, dump files, -and restart files. - -When running with multiple partitions (each of which is a replica in -this case), the print-out to the screen and master log.lammps file -contains a line of output, printed once every {Nevery} timesteps. It -contains the timestep, the maximum force per replica, the maximum -force per atom (in any replica), potential gradients in the initial, -final, and climbing replicas, the forward and backward energy -barriers, the total reaction coordinate (RDT), and the normalized -reaction coordinate and potential energy of each replica. - -The "maximum force per replica" is the two-norm of the 3N-length force -vector for the atoms in each replica, maximized across replicas, which -is what the {ftol} setting is checking against. In this case, N is -all the atoms in each replica. The "maximum force per atom" is the -maximum force component of any atom in any replica. The potential -gradients are the two-norm of the 3N-length force vector solely due to -the interaction potential i.e. without adding in inter-replica -forces. - -The "reaction coordinate" (RD) for each replica is the two-norm of the -3N-length vector of distances between its atoms and the preceding -replica's atoms, added to the RD of the preceding replica. The RD of -the first replica RD1 = 0.0; the RD of the final replica RDN = RDT, -the total reaction coordinate. The normalized RDs are divided by RDT, -so that they form a monotonically increasing sequence from zero to -one. When computing RD, N only includes the atoms being operated on by -the fix neb command. - -The forward (reverse) energy barrier is the potential energy of the -highest replica minus the energy of the first (last) replica. - -Supplementary information for all replicas can be printed out to the -screen and master log.lammps file by adding the verbose keyword. This -information include the following. The "path angle" (pathangle) for -the replica i which is the angle between the 3N-length vectors (Ri-1 - -Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica -i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are -aligned. "angletangrad" is the angle between the 3N-length tangent -vector and the 3N-length force vector at image i. The tangent vector -is calculated as in "(HenkelmanA)"_#HenkelmanA for all intermediate -replicas and at R2 - R1 and RM - RM-1 for the first and last replica, -respectively. "anglegrad" is the angle between the 3N-length energy -gradient vector of replica i and that of replica i+1. It is not -defined for the final replica and reads nan. gradV is the norm of the -energy gradient of image i. ReplicaForce is the two-norm of the -3N-length force vector (including nudging forces) for replica i. -MaxAtomForce is the maximum force component of any atom in replica i. - -When a NEB calculation does not converge properly, the supplementary -information can help understanding what is going wrong. For instance -when the path angle becomes acute, the definition of tangent used in -the NEB calculation is questionable and the NEB cannot may diverge -"(Maras)"_#Maras2. - - -When running on multiple partitions, LAMMPS produces additional log -files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a -NEB calculation, these contain the thermodynamic output for each -replica. - -If "dump"_dump.html commands in the input script define a filename -that includes a {universe} or {uloop} style "variable"_variable.html, -then one dump file (per dump command) will be created for each -replica. At the end of the NEB calculation, the final snapshot in -each file will contain the sequence of snapshots that transition the -system over the energy barrier. Earlier snapshots will show the -convergence of the replicas to the MEP. - -Likewise, "restart"_restart.html filenames can be specified with a -{universe} or {uloop} style "variable"_variable.html, to generate -restart files for each replica. These may be useful if the NEB -calculation fails to converge properly to the MEP, and you wish to -restart the calculation from an intermediate point with altered -parameters. - -There are 2 Python scripts provided in the tools/python directory, -neb_combine.py and neb_final.py, which are useful in analyzing output -from a NEB calculation. Assume a NEB simulation with M replicas, and -the NEB atoms labeled with a specific atom type. - -The neb_combine.py script extracts atom coords for the NEB atoms from -all M dump files and creates a single dump file where each snapshot -contains the NEB atoms from all the replicas and one copy of non-NEB -atoms from the first replica (presumed to be identical in other -replicas). This can be visualized/animated to see how the NEB atoms -relax as the NEB calculation proceeds. - -The neb_final.py script extracts the final snapshot from each of the M -dump files to create a single dump file with M snapshots. This can be -visualized to watch the system make its transition over the energy -barrier. - -To illustrate, here are images from the final snapshot produced by the -neb_combine.py script run on the dump files produced by the two -example input scripts in examples/neb. Click on them to see a larger -image. - -:image(JPG/hop1_small.jpg,JPG/hop1.jpg) -:image(JPG/hop2_small.jpg,JPG/hop2.jpg) - -:line - -[Restrictions:] - -This command can only be used if LAMMPS was built with the REPLICA -package. See the "Build package"_Build_package.html doc -page for more info. - -:line - -[Related commands:] - -"prd"_prd.html, "temper"_temper.html, "fix langevin"_fix_langevin.html, -"fix viscous"_fix_viscous.html - -[Default:] - -none - -:line - -:link(HenkelmanA) -[(HenkelmanA)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000). - -:link(HenkelmanB) -[(HenkelmanB)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, -9901-9904 (2000). - -:link(Nakano3) -[(Nakano)] Nakano, Comp Phys Comm, 178, 280-289 (2008). - -:link(Maras2) -[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, -Comp Phys Comm, 205, 13-21 (2016) diff --git a/doc/txt/neb_spin.txt b/doc/txt/neb_spin.txt deleted file mode 100644 index 217606289f..0000000000 --- a/doc/txt/neb_spin.txt +++ /dev/null @@ -1,379 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -neb/spin command :h3 - -[Syntax:] - -neb/spin etol ttol N1 N2 Nevery file-style arg keyword :pre - -etol = stopping tolerance for energy (energy units) :ulb,l -ttol = stopping tolerance for torque ( units) :l -N1 = max # of iterations (timesteps) to run initial NEB :l -N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l -Nevery = print replica energies and reaction coordinates every this many timesteps :l -file-style = {final} or {each} or {none} :l - {final} arg = filename - filename = file with initial coords for final replica - coords for intermediate replicas are linearly interpolated - between first and last replica - {each} arg = filename - filename = unique filename for each replica (except first) - with its initial coords - {none} arg = no argument all replicas assumed to already have - their initial coords :pre -keyword = {verbose} -:ule - -[Examples:] - -neb/spin 0.1 0.0 1000 500 50 final coords.final -neb/spin 0.0 0.001 1000 500 50 each coords.initial.$i -neb/spin 0.0 0.001 1000 500 50 none verbose :pre - -[Description:] - -Perform a geodesic nudged elastic band (GNEB) calculation using multiple -replicas of a system. Two or more replicas must be used; the first -and last are the end points of the transition path. - -GNEB is a method for finding both the spin configurations and height -of the energy barrier associated with a transition state, e.g. -spins to perform a collective rotation from one energy basin to -another. -The implementation in LAMMPS follows the discussion in the -following paper: "(BessarabA)"_#BessarabA. - -Each replica runs on a partition of one or more processors. Processor -partitions are defined at run-time using the "-partition command-line -switch"_Run_options.html. Note that if you have MPI installed, you -can run a multi-replica simulation with more replicas (partitions) -than you have physical processors, e.g you can run a 10-replica -simulation on just one or two processors. You will simply not get the -performance speed-up you would see with one or more physical -processors per replica. See the "Howto replica"_Howto_replica.html -doc page for further discussion. - -NOTE: As explained below, a GNEB calculation performs a -minimization across all the replicas. One of the "spin"_min_spin.html -style minimizers has to be defined in your input script. - -When a GNEB calculation is performed, it is assumed that each replica -is running the same system, though LAMMPS does not check for this. -I.e. the simulation domain, the number of magnetic atoms, the -interaction potentials, and the starting configuration when the neb -command is issued should be the same for every replica. - -In a GNEB calculation each replica is connected to other replicas by -inter-replica nudging forces. These forces are imposed by the "fix -neb/spin"_fix_neb_spin.html command, which must be used in conjunction -with the neb command. -The group used to define the fix neb/spin command defines the -GNEB magnetic atoms which are the only ones that inter-replica springs -are applied to. -If the group does not include all magnetic atoms, then non-GNEB -magnetic atoms have no inter-replica springs and the torques they feel -and their precession motion is computed in the usual way due only -to other magnetic atoms within their replica. -Conceptually, the non-GNEB atoms provide a background force field for -the GNEB atoms. -Their magnetic spins can be allowed to evolve during the GNEB -minimization procedure. - -The initial spin configuration for each of the replicas can be -specified in different manners via the {file-style} setting, as -discussed below. Only atomic spins whose initial coordinates should -differ from the current configuration need to be specified. - -Conceptually, the initial and final configurations for the first -replica should be states on either side of an energy barrier. - -As explained below, the initial configurations of intermediate -replicas can be spin coordinates interpolated in a linear fashion -between the first and last replicas. This is often adequate for -simple transitions. For more complex transitions, it may lead to slow -convergence or even bad results if the minimum energy path (MEP, see -below) of states over the barrier cannot be correctly converged to -from such an initial path. In this case, you will want to generate -initial states for the intermediate replicas that are geometrically -closer to the MEP and read them in. - -:line - -For a {file-style} setting of {final}, a filename is specified which -contains atomic and spin coordinates for zero or more atoms, in the -format described below. -For each atom that appears in the file, the new coordinates are -assigned to that atom in the final replica. Each intermediate replica -also assigns a new spin to that atom in an interpolated manner. -This is done by using the current direction of the spin at the starting -point and the read-in direction as the final point. -The "angular distance" between them is calculated, and the new direction -is assigned to be a fraction of the angular distance. - -NOTE: The "angular distance" between the starting and final point is -evaluated in the geodesic sense, as described in -"(BessarabA)"_#BessarabA. - -NOTE: The angular interpolation between the starting and final point -is achieved using Rodrigues formula: - -:c,image(Eqs/neb_spin_rodrigues_formula.jpg) - -where m_i^I is the initial spin configuration for the spin i, -omega_i^nu is a rotation angle defined as: - -:c,image(Eqs/neb_spin_angle.jpg) - -with nu the image number, Q the total number of images, and -omega_i the total rotation between the initial and final spins. -k_i defines a rotation axis such as: - -:c,image(Eqs/neb_spin_k.jpg) - -if the initial and final spins are not aligned. -If the initial and final spins are aligned, then their cross -product is null, and the expression above does not apply. -If they point toward the same direction, the intermediate images -conserve the same orientation. -If the initial and final spins are aligned, but point toward -opposite directions, an arbitrary rotation vector belonging to -the plane perpendicular to initial and final spins is chosen. -In this case, a warning message is displayed. - -For a {file-style} setting of {each}, a filename is specified which is -assumed to be unique to each replica. -See the "neb"_neb.html documentation page for more information about this -option. - -For a {file-style} setting of {none}, no filename is specified. Each -replica is assumed to already be in its initial configuration at the -time the neb command is issued. This allows each replica to define -its own configuration by reading a replica-specific data or restart or -dump file, via the "read_data"_read_data.html, -"read_restart"_read_restart.html, or "read_dump"_read_dump.html -commands. The replica-specific names of these files can be specified -as in the discussion above for the {each} file-style. Also see the -section below for how a NEB calculation can produce restart files, so -that a long calculation can be restarted if needed. - -NOTE: None of the {file-style} settings change the initial -configuration of any atom in the first replica. The first replica -must thus be in the correct initial configuration at the time the neb -command is issued. - -:line - -A NEB calculation proceeds in two stages, each of which is a -minimization procedure. To enable -this, you must first define a -"min_style"_min_style.html, using either the {spin}, -{spin/cg}, or {spin/lbfgs} style (see -"min_spin"_min_spin.html for more information). -The other styles cannot be used, since they relax the lattice -degrees of freedom instead of the spins. - -The minimizer tolerances for energy and force are set by {etol} and -{ttol}, the same as for the "minimize"_minimize.html command. - -A non-zero {etol} means that the GNEB calculation will terminate if the -energy criterion is met by every replica. The energies being compared -to {etol} do not include any contribution from the inter-replica -nudging forces, since these are non-conservative. A non-zero {ttol} -means that the GNEB calculation will terminate if the torque criterion -is met by every replica. The torques being compared to {ttol} include -the inter-replica nudging forces. - -The maximum number of iterations in each stage is set by {N1} and -{N2}. These are effectively timestep counts since each iteration of -damped dynamics is like a single timestep in a dynamics -"run"_run.html. During both stages, the potential energy of each -replica and its normalized distance along the reaction path (reaction -coordinate RD) will be printed to the screen and log file every -{Nevery} timesteps. The RD is 0 and 1 for the first and last replica. -For intermediate replicas, it is the cumulative angular distance -(normalized by the total cumulative angular distance) between adjacent -replicas, where "distance" is defined as the length of the 3N-vector of -the geodesic distances in spin coordinates, with N the number of -GNEB spins involved (see equation (13) in "(BessarabA)"_#BessarabA). -These outputs allow you to monitor NEB's progress in -finding a good energy barrier. {N1} and {N2} must both be multiples -of {Nevery}. - -In the first stage of GNEB, the set of replicas should converge toward -a minimum energy path (MEP) of conformational states that transition -over a barrier. The MEP for a transition is defined as a sequence of -3N-dimensional spin states, each of which has a potential energy -gradient parallel to the MEP itself. -The configuration of highest energy along a MEP corresponds to a saddle -point. The replica states will also be roughly equally spaced along -the MEP due to the inter-replica nudging force added by the -"fix neb"_fix_neb.html command. - -In the second stage of GNEB, the replica with the highest energy is -selected and the inter-replica forces on it are converted to a force -that drives its spin coordinates to the top or saddle point of the -barrier, via the barrier-climbing calculation described in -"(BessarabA)"_#BessarabA. As before, the other replicas rearrange -themselves along the MEP so as to be roughly equally spaced. - -When both stages are complete, if the GNEB calculation was successful, -the configurations of the replicas should be along (close to) the MEP -and the replica with the highest energy should be a spin -configuration at (close to) the saddle point of the transition. The -potential energies for the set of replicas represents the energy -profile of the transition along the MEP. - -:line - -An atom map must be defined which it is not by default for "atom_style -atomic"_atom_style.html problems. The "atom_modify -map"_atom_modify.html command can be used to do this. - -An initial value can be defined for the timestep. Although, the {spin} -minimization algorithm is an adaptive timestep methodology, so that -this timestep is likely to evolve during the calculation. - -The minimizers in LAMMPS operate on all spins in your system, even -non-GNEB atoms, as defined above. - -:line - -Each file read by the neb/spin command containing spin coordinates used -to initialize one or more replicas must be formatted as follows. - -The file can be ASCII text or a gzipped text file (detected by a .gz -suffix). The file can contain initial blank lines or comment lines -starting with "#" which are ignored. The first non-blank, non-comment -line should list N = the number of lines to follow. The N successive -lines contain the following information: - -ID1 g1 x1 y1 z1 sx1 sy1 sz1 -ID2 g2 x2 y2 z2 sx2 sy2 sz2 -... -IDN gN yN zN sxN syN szN :pre - -The fields are the atom ID, the norm of the associated magnetic spin, -followed by the {x,y,z} coordinates and the {sx,sy,sz} spin coordinates. -The lines can be listed in any order. Additional trailing information on -the line is OK, such as a comment. - -Note that for a typical GNEB calculation you do not need to specify -initial spin coordinates for very many atoms to produce differing starting -and final replicas whose intermediate replicas will converge to the -energy barrier. Typically only new spin coordinates for atoms -geometrically near the barrier need be specified. - -Also note there is no requirement that the atoms in the file -correspond to the GNEB atoms in the group defined by the "fix -neb"_fix_neb.html command. Not every GNEB atom need be in the file, -and non-GNEB atoms can be listed in the file. - -:line - -Four kinds of output can be generated during a GNEB calculation: energy -barrier statistics, thermodynamic output by each replica, dump files, -and restart files. - -When running with multiple partitions (each of which is a replica in -this case), the print-out to the screen and master log.lammps file -contains a line of output, printed once every {Nevery} timesteps. It -contains the timestep, the maximum torque per replica, the maximum -torque per atom (in any replica), potential gradients in the initial, -final, and climbing replicas, the forward and backward energy -barriers, the total reaction coordinate (RDT), and the normalized -reaction coordinate and potential energy of each replica. - -The "maximum torque per replica" is the two-norm of the -3N-length vector given by the cross product of a spin by its -precession vector omega, in each replica, maximized across replicas, -which is what the {ttol} setting is checking against. In this case, N is -all the atoms in each replica. The "maximum torque per atom" is the -maximum torque component of any atom in any replica. The potential -gradients are the two-norm of the 3N-length magnetic precession vector -solely due to the interaction potential i.e. without adding in -inter-replica forces, and projected along the path tangent (as detailed -in Appendix D of "(BessarabA)"_#BessarabA). - -The "reaction coordinate" (RD) for each replica is the two-norm of the -3N-length vector of geodesic distances between its spins and the preceding -replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), added to -the RD of the preceding replica. The RD of the first replica RD1 = 0.0; -the RD of the final replica RDN = RDT, the total reaction coordinate. -The normalized RDs are divided by RDT, so that they form a monotonically -increasing sequence from zero to one. When computing RD, N only includes -the spins being operated on by the fix neb/spin command. - -The forward (reverse) energy barrier is the potential energy of the -highest replica minus the energy of the first (last) replica. - -Supplementary information for all replicas can be printed out to the -screen and master log.lammps file by adding the verbose keyword. This -information include the following. -The "GradVidottan" are the projections of the potential gradient for -the replica i on its tangent vector (as detailed in Appendix D of -"(BessarabA)"_#BessarabA). -The "DNi" are the non normalized geodesic distances (see equation (13) -of "(BessarabA)"_#BessarabA), between a replica i and the next replica -i+1. For the last replica, this distance is not defined and a "NAN" -value is the corresponding output. - -When a NEB calculation does not converge properly, the supplementary -information can help understanding what is going wrong. - -When running on multiple partitions, LAMMPS produces additional log -files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a -GNEB calculation, these contain the thermodynamic output for each -replica. - -If "dump"_dump.html commands in the input script define a filename -that includes a {universe} or {uloop} style "variable"_variable.html, -then one dump file (per dump command) will be created for each -replica. At the end of the GNEB calculation, the final snapshot in -each file will contain the sequence of snapshots that transition the -system over the energy barrier. Earlier snapshots will show the -convergence of the replicas to the MEP. - -Likewise, "restart"_restart.html filenames can be specified with a -{universe} or {uloop} style "variable"_variable.html, to generate -restart files for each replica. These may be useful if the GNEB -calculation fails to converge properly to the MEP, and you wish to -restart the calculation from an intermediate point with altered -parameters. - -A c file script in provided in the tool/spin/interpolate_gneb -directory, that interpolates the MEP given the information provided -by the verbose output option (as detailed in Appendix D of -"(BessarabA)"_#BessarabA). - -:line - -[Restrictions:] - -This command can only be used if LAMMPS was built with the SPIN -package. See the "Build package"_Build_package.html doc -page for more info. - -For magnetic GNEB calculations, only {spin_none} value for {line} keyword can be used -when styles {spin/cg} and {spin/lbfgs} are employed. - -:line - -[Related commands:] - -"min/spin"_min_spin.html, "fix neb/spin"_fix_neb_spin.html - -[Default:] - -none - -:line - -:link(BessarabA) -[(BessarabA)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, -335-347 (2015). diff --git a/doc/txt/neigh_modify.txt b/doc/txt/neigh_modify.txt deleted file mode 100644 index c97cb53e43..0000000000 --- a/doc/txt/neigh_modify.txt +++ /dev/null @@ -1,218 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -neigh_modify command :h3 - -[Syntax:] - -neigh_modify keyword values ... :pre - -one or more keyword/value pairs may be listed :ulb,l -keyword = {delay} or {every} or {check} or {once} or {cluster} or {include} or {exclude} or {page} or {one} or {binsize} - {delay} value = N - N = delay building until this many steps since last build - {every} value = M - M = build neighbor list every this many steps - {check} value = {yes} or {no} - {yes} = only build if some atom has moved half the skin distance or more - {no} = always build on 1st step that {every} and {delay} are satisfied - {once} - {yes} = only build neighbor list once at start of run and never rebuild - {no} = rebuild neighbor list according to other settings - {cluster} - {yes} = check bond,angle,etc neighbor list for nearby clusters - {no} = do not check bond,angle,etc neighbor list for nearby clusters - {include} value = group-ID - group-ID = only build pair neighbor lists for atoms in this group - {exclude} values: - type M N - M,N = exclude if one atom in pair is type M, other is type N - group group1-ID group2-ID - group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd - molecule/intra group-ID - group-ID = exclude if both atoms are in the same molecule and in group - molecule/inter group-ID - group-ID = exclude if both atoms are in different molecules and in group - none - delete all exclude settings - {page} value = N - N = number of pairs stored in a single neighbor page - {one} value = N - N = max number of neighbors of one atom - {binsize} value = size - size = bin size for neighbor list construction (distance units) :pre -:ule - -[Examples:] - -neigh_modify every 2 delay 10 check yes page 100000 -neigh_modify exclude type 2 3 -neigh_modify exclude group frozen frozen check no -neigh_modify exclude group residue1 chain3 -neigh_modify exclude molecule/intra rigid :pre - -[Description:] - -This command sets parameters that affect the building and use of -pairwise neighbor lists. Depending on what pair interactions and -other commands are defined, a simulation may require one or more -neighbor lists. - -The {every}, {delay}, {check}, and {once} options affect how often -lists are built as a simulation runs. The {delay} setting means never -build new lists until at least N steps after the previous build. The -{every} setting means build lists every M steps (after the delay has -passed). If the {check} setting is {no}, the lists are built on the -first step that satisfies the {delay} and {every} settings. If the -{check} setting is {yes}, then the {every} and {delay} settings -determine when a build may possibly be performed, but an actual build -only occurs if some atom has moved more than half the skin distance -(specified in the "neighbor"_neighbor.html command) since the last -build. - -If the {once} setting is yes, then the neighbor list is only built -once at the beginning of each run, and never rebuilt, except on steps -when a restart file is written, or steps when a fix forces a rebuild -to occur (e.g. fixes that create or delete atoms, such as "fix -deposit"_fix_deposit.html or "fix evaporate"_fix_evaporate.html). -This setting should only be made if you are certain atoms will not -move far enough that the neighbor list should be rebuilt, e.g. running -a simulation of a cold crystal. Note that it is not that expensive to -check if neighbor lists should be rebuilt. - -When the rRESPA integrator is used (see the "run_style"_run_style.html -command), the {every} and {delay} parameters refer to the longest -(outermost) timestep. - -The {cluster} option does a sanity test every time neighbor lists are -built for bond, angle, dihedral, and improper interactions, to check -that each set of 2, 3, or 4 atoms is a cluster of nearby atoms. It -does this by computing the distance between pairs of atoms in the -interaction and insuring they are not further apart than half the -periodic box length. If they are, an error is generated, since the -interaction would be computed between far-away atoms instead of their -nearby periodic images. The only way this should happen is if the -pairwise cutoff is so short that atoms that are part of the same -interaction are not communicated as ghost atoms. This is an unusual -model (e.g. no pair interactions at all) and the problem can be fixed -by use of the "comm_modify cutoff"_comm_modify.html command. Note -that to save time, the default {cluster} setting is {no}, so that this -check is not performed. - -The {include} option limits the building of pairwise neighbor lists to -atoms in the specified group. This can be useful for models where a -large portion of the simulation is particles that do not interact with -other particles or with each other via pairwise interactions. The -group specified with this option must also be specified via the -"atom_modify first"_atom_modify.html command. Note that specifying -"all" as the group-ID effectively turns off the {include} option. - -The {exclude} option turns off pairwise interactions between certain -pairs of atoms, by not including them in the neighbor list. These are -sample scenarios where this is useful: - -In crack simulations, pairwise interactions can be shut off between 2 -slabs of atoms to effectively create a crack. :ulb,l - -When a large collection of atoms is treated as frozen, interactions -between those atoms can be turned off to save needless -computation. E.g. Using the "fix setforce"_fix_setforce.html command -to freeze a wall or portion of a bio-molecule. :l - -When one or more rigid bodies are specified, interactions within each -body can be turned off to save needless computation. See the "fix -rigid"_fix_rigid.html command for more details. :l -:ule - -The {exclude type} option turns off the pairwise interaction if one -atom is of type M and the other of type N. M can equal N. The -{exclude group} option turns off the interaction if one atom is in the -first group and the other is the second. Group1-ID can equal -group2-ID. The {exclude molecule/intra} option turns off the -interaction if both atoms are in the specified group and in the same -molecule, as determined by their molecule ID. The {exclude -molecule/inter} turns off the interaction between pairs of atoms that -have different molecule IDs and are both in the specified group. - -Each of the exclude options can be specified multiple times. The -{exclude type} option is the most efficient option to use; it requires -only a single check, no matter how many times it has been specified. -The other exclude options are more expensive if specified multiple -times; they require one check for each time they have been specified. - -Note that the exclude options only affect pairwise interactions; see -the "delete_bonds"_delete_bonds.html command for information on -turning off bond interactions. - -NOTE: Excluding pairwise interactions will not work correctly when -also using a long-range solver via the -"kspace_style"_kspace_style.html command. LAMMPS will give a warning -to this effect. This is because the short-range pairwise interaction -needs to subtract off a term from the total energy for pairs whose -short-range interaction is excluded, to compensate for how the -long-range solver treats the interaction. This is done correctly for -pairwise interactions that are excluded (or weighted) via the -"special_bonds"_special_bonds.html command. But it is not done for -interactions that are excluded via these neigh_modify exclude options. - -The {page} and {one} options affect how memory is allocated for the -neighbor lists. For most simulations the default settings for these -options are fine, but if a very large problem is being run or a very -long cutoff is being used, these parameters can be tuned. The indices -of neighboring atoms are stored in "pages", which are allocated one -after another as they fill up. The size of each page is set by the -{page} value. A new page is allocated when the next atom's neighbors -could potentially overflow the list. This threshold is set by the -{one} value which tells LAMMPS the maximum number of neighbor's one -atom can have. - -NOTE: LAMMPS can crash without an error message if the number of -neighbors for a single particle is larger than the {page} setting, -which means it is much, much larger than the {one} setting. This is -because LAMMPS doesn't error check these limits for every pairwise -interaction (too costly), but only after all the particle's neighbors -have been found. This problem usually means something is very wrong -with the way you've setup your problem (particle spacing, cutoff -length, neighbor skin distance, etc). If you really expect that many -neighbors per particle, then boost the {one} and {page} settings -accordingly. - -The {binsize} option allows you to specify what size of bins will be -used in neighbor list construction to sort and find neighboring atoms. -By default, for "neighbor style bin"_neighbor.html, LAMMPS uses bins -that are 1/2 the size of the maximum pair cutoff. For "neighbor style -multi"_neighbor.html, the bins are 1/2 the size of the minimum pair -cutoff. Typically these are good values for minimizing the time for -neighbor list construction. This setting overrides the default. -If you make it too big, there is little overhead due to -looping over bins, but more atoms are checked. If you make it too -small, the optimal number of atoms is checked, but bin overhead goes -up. If you set the binsize to 0.0, LAMMPS will use the default -binsize of 1/2 the cutoff. - -[Restrictions:] - -If the "delay" setting is non-zero, then it must be a multiple of the -"every" setting. - -The molecule/intra and molecule/inter exclude options can only be used -with atom styles that define molecule IDs. - -The value of the {page} setting must be at least 10x larger than the -{one} setting. This insures neighbor pages are not mostly empty -space. - -[Related commands:] - -"neighbor"_neighbor.html, "delete_bonds"_delete_bonds.html - -[Default:] - -The option defaults are delay = 10, every = 1, check = yes, once = no, -cluster = no, include = all (same as no include option defined), -exclude = none, page = 100000, one = 2000, and binsize = 0.0. diff --git a/doc/txt/neighbor.txt b/doc/txt/neighbor.txt deleted file mode 100644 index 4a60f957d4..0000000000 --- a/doc/txt/neighbor.txt +++ /dev/null @@ -1,83 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -neighbor command :h3 - -[Syntax:] - -neighbor skin style :pre - -skin = extra distance beyond force cutoff (distance units) -style = {bin} or {nsq} or {multi} :ul - -[Examples:] - -neighbor 0.3 bin -neighbor 2.0 nsq :pre - -[Description:] - -This command sets parameters that affect the building of pairwise -neighbor lists. All atom pairs within a neighbor cutoff distance -equal to the their force cutoff plus the {skin} distance are stored in -the list. Typically, the larger the skin distance, the less often -neighbor lists need to be built, but more pairs must be checked for -possible force interactions every timestep. The default value for -{skin} depends on the choice of units for the simulation; see the -default values below. - -The {skin} distance is also used to determine how often atoms migrate -to new processors if the {check} option of the -"neigh_modify"_neigh_modify.html command is set to {yes}. Atoms are -migrated (communicated) to new processors on the same timestep that -neighbor lists are re-built. - -The {style} value selects what algorithm is used to build the list. -The {bin} style creates the list by binning which is an operation that -scales linearly with N/P, the number of atoms per processor where N = -total number of atoms and P = number of processors. It is almost -always faster than the {nsq} style which scales as (N/P)^2. For -unsolvated small molecules in a non-periodic box, the {nsq} choice can -sometimes be faster. Either style should give the same answers. - -The {multi} style is a modified binning algorithm that is useful for -systems with a wide range of cutoff distances, e.g. due to different -size particles. For the {bin} style, the bin size is set to 1/2 of -the largest cutoff distance between any pair of atom types and a -single set of bins is defined to search over for all atom types. This -can be inefficient if one pair of types has a very long cutoff, but -other type pairs have a much shorter cutoff. For style {multi} the -bin size is set to 1/2 of the shortest cutoff distance and multiple -sets of bins are defined to search over for different atom types. -This imposes some extra setup overhead, but the searches themselves -may be much faster for the short-cutoff cases. See the "comm_modify -mode multi"_comm_modify.html command for a communication option -that may also be beneficial for simulations of this kind. - -The "neigh_modify"_neigh_modify.html command has additional options -that control how often neighbor lists are built and which pairs are -stored in the list. - -When a run is finished, counts of the number of neighbors stored in -the pairwise list and the number of times neighbor lists were built -are printed to the screen and log file. See the "Run -output"_Run_output.html doc page for details. - -[Restrictions:] none - -[Related commands:] - -"neigh_modify"_neigh_modify.html, "units"_units.html, -"comm_modify"_comm_modify.html - -[Default:] - -0.3 bin for units = lj, skin = 0.3 sigma -2.0 bin for units = real or metal, skin = 2.0 Angstroms -0.001 bin for units = si, skin = 0.001 meters = 1.0 mm -0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm :all(b) diff --git a/doc/txt/newton.txt b/doc/txt/newton.txt deleted file mode 100644 index fd7b536920..0000000000 --- a/doc/txt/newton.txt +++ /dev/null @@ -1,62 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -newton command :h3 - -[Syntax:] - -newton flag -newton flag1 flag2 :pre - -flag = {on} or {off} for both pairwise and bonded interactions -flag1 = {on} or {off} for pairwise interactions -flag2 = {on} or {off} for bonded interactions :ul - -[Examples:] - -newton off -newton on off :pre - -[Description:] - -This command turns Newton's 3rd law {on} or {off} for pairwise and -bonded interactions. For most problems, setting Newton's 3rd law to -{on} means a modest savings in computation at the cost of two times -more communication. Whether this is faster depends on problem size, -force cutoff lengths, a machine's compute/communication ratio, and how -many processors are being used. - -Setting the pairwise newton flag to {off} means that if two -interacting atoms are on different processors, both processors compute -their interaction and the resulting force information is not -communicated. Similarly, for bonded interactions, newton {off} means -that if a bond, angle, dihedral, or improper interaction contains -atoms on 2 or more processors, the interaction is computed by each -processor. - -LAMMPS should produce the same answers for any newton flag settings, -except for round-off issues. - -With "run_style"_run_style.html {respa} and only bonded interactions -(bond, angle, etc) computed in the innermost timestep, it may be -faster to turn newton {off} for bonded interactions, to avoid extra -communication in the innermost loop. - -[Restrictions:] - -The newton bond setting cannot be changed after the simulation box is -defined by a "read_data"_read_data.html or -"create_box"_create_box.html command. - -[Related commands:] - -"run_style"_run_style.html respa - -[Default:] - -newton on :pre diff --git a/doc/txt/next.txt b/doc/txt/next.txt deleted file mode 100644 index 3f43b1b752..0000000000 --- a/doc/txt/next.txt +++ /dev/null @@ -1,142 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -next command :h3 - -[Syntax:] - -next variables :pre - -variables = one or more variable names :ul - -[Examples:] - -next x -next a t x myTemp :pre - -[Description:] - -This command is used with variables defined by the -"variable"_variable.html command. It assigns the next value to the -variable from the list of values defined for that variable by the -"variable"_variable.html command. Thus when that variable is -subsequently substituted for in an input script command, the new value -is used. - -See the "variable"_variable.html command for info on how to define and -use different kinds of variables in LAMMPS input scripts. If a -variable name is a single lower-case character from "a" to "z", it can -be used in an input script command as $a or $z. If it is multiple -letters, it can be used as $\{myTemp\}. - -If multiple variables are used as arguments to the {next} command, -then all must be of the same variable style: {index}, {loop}, {file}, -{universe}, or {uloop}. An exception is that {universe}- and -{uloop}-style variables can be mixed in the same {next} command. - -All the variables specified with the next command are incremented by -one value from their respective list of values. A {file}-style -variable reads the next line from its associated file. An -{atomfile}-style variable reads the next set of lines (one per atom) -from its associated file. {String-} or {atom}- or {equal}- or -{world}-style variables cannot be used with the next command, -since they only store a single value. - -When any of the variables in the next command has no more values, a -flag is set that causes the input script to skip the next -"jump"_jump.html command encountered. This enables a loop containing -a next command to exit. As explained in the "variable"_variable.html -command, the variable that has exhausted its values is also deleted. -This allows it to be used and re-defined later in the input script. -{File}-style and {atomfile}-style variables are exhausted when the -end-of-file is reached. - -When the next command is used with {index}- or {loop}-style variables, -the next value is assigned to the variable for all processors. When -the next command is used with {file}-style variables, the next line is -read from its file and the string assigned to the variable. When the -next command is used with {atomfile}-style variables, the next set of -per-atom values is read from its file and assigned to the variable. - -When the next command is used with {universe}- or {uloop}-style -variables, all {universe}- or {uloop}-style variables must be listed -in the next command. This is because of the manner in which the -incrementing is done, using a single lock file for all variables. The -next value (for each variable) is assigned to whichever processor -partition executes the command first. All processors in the partition -are assigned the same value(s). Running LAMMPS on multiple partitions -of processors via the "-partition command-line -switch"_Run_options.html. {Universe}- and {uloop}-style variables are -incremented using the files "tmp.lammps.variable" and -"tmp.lammps.variable.lock" which you will see in your directory during -and after such a LAMMPS run. - -Here is an example of running a series of simulations using the next -command with an {index}-style variable. If this input script is named -in.polymer, 8 simulations would be run using data files from -directories run1 through run8. - -variable d index run1 run2 run3 run4 run5 run6 run7 run8 -shell cd $d -read_data data.polymer -run 10000 -shell cd .. -clear -next d -jump in.polymer :pre - -If the variable "d" were of style {universe}, and the same in.polymer -input script were run on 3 partitions of processors, then the first 3 -simulations would begin, one on each set of processors. Whichever -partition finished first, it would assign variable "d" the 4th value -and run another simulation, and so forth until all 8 simulations were -finished. - -Jump and next commands can also be nested to enable multi-level loops. -For example, this script will run 15 simulations in a double loop. - -variable i loop 3 - variable j loop 5 - clear - ... - read_data data.polymer.$i$j - print Running simulation $i.$j - run 10000 - next j - jump in.script -next i -jump in.script :pre - -Here is an example of a double loop which uses the "if"_if.html and -"jump"_jump.html commands to break out of the inner loop when a -condition is met, then continues iterating through the outer loop. - -label loopa -variable a loop 5 - label loopb - variable b loop 5 - print "A,B = $a,$b" - run 10000 - if $b > 2 then "jump in.script break" - next b - jump in.script loopb -label break -variable b delete :pre -next a -jump in.script loopa :pre - -[Restrictions:] - -As described above. - -[Related commands:] - -"jump"_jump.html, "include"_include.html, "shell"_shell.html, -"variable"_variable.html, - -[Default:] none diff --git a/doc/txt/pair_adp.txt b/doc/txt/pair_adp.txt deleted file mode 100644 index de6717a6c3..0000000000 --- a/doc/txt/pair_adp.txt +++ /dev/null @@ -1,186 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style adp command :h3 -pair_style adp/omp command :h3 - -[Syntax:] - -pair_style adp :pre - -[Examples:] - -pair_style adp -pair_coeff * * Ta.adp Ta -pair_coeff * * ../potentials/AlCu.adp Al Al Cu :pre - -[Description:] - -Style {adp} computes pairwise interactions for metals and metal alloys -using the angular dependent potential (ADP) of "(Mishin)"_#Mishin, -which is a generalization of the "embedded atom method (EAM) -potential"_pair_eam.html. The LAMMPS implementation is discussed in -"(Singh)"_#Singh. The total energy Ei of an atom I is given by - -:c,image(Eqs/pair_adp.jpg) - -where F is the embedding energy which is a function of the atomic -electron density rho, phi is a pair potential interaction, alpha and -beta are the element types of atoms I and J, and s and t = 1,2,3 and -refer to the cartesian coordinates. The mu and lambda terms represent -the dipole and quadruple distortions of the local atomic environment -which extend the original EAM framework by introducing angular forces. - -Note that unlike for other potentials, cutoffs for ADP potentials are -not set in the pair_style or pair_coeff command; they are specified in -the ADP potential files themselves. Likewise, the ADP potential files -list atomic masses; thus you do not need to use the "mass"_mass.html -command to specify them. - -[ADP potentials are available from:] - -The NIST WWW site at http://www.ctcms.nist.gov/potentials. -Note that ADP potentials obtained from NIST must be converted -into the extended DYNAMO {setfl} format discussed below. -:l - -The OpenKIM Project at https://openkim.org/browse/models/by-type provides -ADP potentials that can be used directly in LAMMPS with the "kim_commands -interface"_kim_commands.html. -:l - -:line - -Only a single pair_coeff command is used with the {adp} style which -specifies an extended DYNAMO {setfl} file, which contains information -for M elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of extended {setfl} elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways to -specify the path for the potential file. - -As an example, the potentials/AlCu.adp file, included in the -potentials directory of the LAMMPS distribution, is an extended {setfl} -file which has tabulated ADP values for w elements and their alloy -interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types -and you want the 1st 3 to be Al, and the 4th to be Cu, you would use -the following pair_coeff command: - -pair_coeff * * AlCu.adp Al Al Al Cu :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Al arguments map LAMMPS atom types 1,2,3 to the Al -element in the extended {setfl} file. The final Cu argument maps -LAMMPS atom type 4 to the Al element in the extended {setfl} file. -Note that there is no requirement that your simulation use all the -elements specified by the extended {setfl} file. - -If a mapping value is specified as NULL, the mapping is not performed. -This can be used when an {adp} potential is used as part of the -{hybrid} pair style. The NULL values are placeholders for atom types -that will be used with other potentials. - -{Adp} files in the {potentials} directory of the LAMMPS distribution -have an ".adp" suffix. A DYNAMO {setfl} file extended for ADP is -formatted as follows. Basically it is the standard {setfl} format -with additional tabulated functions u and w added to the file after -the tabulated pair potentials. See the "pair_eam"_pair_eam.html -command for further details on the {setfl} format. - -lines 1,2,3 = comments (ignored) -line 4: Nelements Element1 Element2 ... ElementN -line 5: Nrho, drho, Nr, dr, cutoff :ul - -Following the 5 header lines are Nelements sections, one for each -element, each with the following format: - -line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC) -embedding function F(rho) (Nrho values) -density function rho(r) (Nr values) :ul - -Following the Nelements sections, Nr values for each pair potential -phi(r) array are listed for all i,j element pairs in the same format -as other arrays. Since these interactions are symmetric (i,j = j,i) -only phi arrays with i >= j are listed, in the following order: i,j = -(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements, -Nelements). The tabulated values for each phi function are listed as -r*phi (in units of eV-Angstroms), since they are for atom pairs, the -same as for "other EAM files"_pair_eam.html. - -After the phi(r) arrays, each of the u(r) arrays are listed in the -same order with the same assumptions of symmetry. Directly following -the u(r), the w(r) arrays are listed. Note that phi(r) is the only -array tabulated with a scaling by r. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, no special mixing rules are needed, since -the ADP potential files specify alloy interactions explicitly. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in tabulated potential files. -Thus, you need to re-specify the pair_style and pair_coeff commands in -an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_eam"_pair_eam.html - -[Default:] none - -:line - -:link(Mishin) -[(Mishin)] Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029 -(2005). - -:link(Singh) -[(Singh)] Singh and Warner, Acta Mater, 58, 5797-5805 (2010), diff --git a/doc/txt/pair_agni.txt b/doc/txt/pair_agni.txt deleted file mode 100644 index aae9c161ca..0000000000 --- a/doc/txt/pair_agni.txt +++ /dev/null @@ -1,132 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style agni command :h3 -pair_style agni/omp command :h3 - -[Syntax:] - -pair_style agni :pre - -[Examples:] -pair_style agni -pair_coeff * * Al.agni Al - -[Description:] - -Style {agni} style computes the many-body vectorial force components for -an atom as - -:c,image(Eqs/pair_agni.jpg) - -{u} labels the individual components, i.e. x, y or z, and {V} is the -corresponding atomic fingerprint. {d} is the Euclidean distance between -any two atomic fingerprints. A total of N_t reference atomic -environments are considered to construct the force field file. {alpha_t} -and {l} are the weight coefficients and length scale parameter of the -non-linear regression model. - -The method implements the recently proposed machine learning access to -atomic forces as discussed extensively in the following publications - -"(Botu1)"_#Botu2015adaptive and "(Botu2)"_#Botu2015learning. The premise -of the method is to map the atomic environment numerically into a -fingerprint, and use machine learning methods to create a mapping to the -vectorial atomic forces. - -Only a single pair_coeff command is used with the {agni} style which -specifies an AGNI potential file containing the parameters of the -force field for the needed elements. These are mapped to LAMMPS atom -types by specifying N additional arguments after the filename in the -pair_coeff command, where N is the number of LAMMPS atom types: - -filename -N element names = mapping of AGNI elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the force field file. - -An AGNI force field is fully specified by the filename which contains the -parameters of the force field, i.e., the reference training environments -used to construct the machine learning force field. Example force field -and input files are provided in the examples/USER/misc/agni directory. - -:line - -Styles with {omp} suffix is functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed on the "Speed -packages"_Speed_packages.html doc page. The accelerated style takes -the same arguments and should produce the same results, except for -round-off and precision issues. - -The accelerated style is part of the USER-OMP. They are only enabled -if LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated style explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -Currently, only elemental systems are implemented. Also, the method -only provides access to the forces and not energies or stresses. -The lack of potential energy data makes this pair style incompatible with -several of the "minimizer algorthms"_min_style.html like {cg} or {sd}. -It should work with damped dynamics based minimizers like {fire} or -{quickmin}. However, one can access the energy via thermodynamic -integration of the forces as discussed in -"(Botu3)"_#Botu2016construct. This pair style is part of the -USER-MISC package. It is only enabled if LAMMPS was built with that -package. See the "Build package"_Build_package.html doc page for more -info. - -The AGNI force field files provided with LAMMPS (see the -potentials directory) are parameterized for metal "units"_units.html. -You can use the AGNI potential with any LAMMPS units, but you would need -to create your own AGNI potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Botu2015adaptive) -[(Botu1)] V. Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015). - -:link(Botu2015learning) -[(Botu2)] V. Botu and R. Ramprasad, Phys. Rev. B, 92(9), 094306 (2015). - -:link(Botu2016construct) -[(Botu3)] V. Botu, R. Batra, J. Chapman and R. Ramprasad, https://arxiv.org/abs/1610.02098 (2016). diff --git a/doc/txt/pair_airebo.txt b/doc/txt/pair_airebo.txt deleted file mode 100644 index 4956ba7575..0000000000 --- a/doc/txt/pair_airebo.txt +++ /dev/null @@ -1,246 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style airebo command :h3 -pair_style airebo/intel command :h3 -pair_style airebo/omp command :h3 -pair_style airebo/morse command :h3 -pair_style airebo/morse/intel command :h3 -pair_style airebo/morse/omp command :h3 -pair_style rebo command :h3 -pair_style rebo/intel command :h3 -pair_style rebo/omp command :h3 - -[Syntax:] - -pair_style style cutoff LJ_flag TORSION_flag cutoff_min :pre - -style = {airebo} or {airebo/morse} or {rebo} -cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only) -LJ_flag = 0/1 to turn off/on the LJ or Morse term (AIREBO and AIREBO-M only, optional) -TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO and AIREBO-M only, optional) -cutoff_min = Start of the transition region of cutoff (sigma scale factor) (AIREBO and AIREBO-M only, optional) :ul - -[Examples:] - -pair_style airebo 3.0 -pair_style airebo 2.5 1 0 -pair_coeff * * ../potentials/CH.airebo H C :pre - -pair_style airebo/morse 3.0 -pair_coeff * * ../potentials/CH.airebo-m H C :pre - -pair_style rebo -pair_coeff * * ../potentials/CH.rebo H C :pre - -[Description:] - -The {airebo} pair style computes the Adaptive Intermolecular Reactive -Empirical Bond Order (AIREBO) Potential of "(Stuart)"_#Stuart for a -system of carbon and/or hydrogen atoms. Note that this is the initial -formulation of AIREBO from 2000, not the later formulation. - -The {airebo/morse} pair style computes the AIREBO-M potential, which -is equivalent to AIREBO, but replaces the LJ term with a Morse potential. -The Morse potentials are parameterized by high-quality quantum chemistry -(MP2) calculations and do not diverge as quickly as particle density -increases. This allows AIREBO-M to retain accuracy to much higher pressures -than AIREBO (up to 40 GPa for Polyethylene). Details for this potential -and its parameterization are given in "(O'Conner)"_#OConnor. - -The {rebo} pair style computes the Reactive Empirical Bond Order (REBO) -Potential of "(Brenner)"_#Brenner. Note that this is the so-called -2nd generation REBO from 2002, not the original REBO from 1990. -As discussed below, 2nd generation REBO is closely related to the -initial AIREBO; it is just a subset of the potential energy terms -with a few slightly different parameters - -The AIREBO potential consists of three terms: - -:c,image(Eqs/pair_airebo.jpg) - -By default, all three terms are included. For the {airebo} style, if -the first two optional flag arguments to the pair_style command are -included, the LJ and torsional terms can be turned off. Note that -both or neither of the flags must be included. If both of the LJ an -torsional terms are turned off, it becomes the 2nd-generation REBO -potential, with a small caveat on the spline fitting procedure -mentioned below. This can be specified directly as pair_style {rebo} -with no additional arguments. - -The detailed formulas for this potential are given in -"(Stuart)"_#Stuart; here we provide only a brief description. - -The E_REBO term has the same functional form as the hydrocarbon REBO -potential developed in "(Brenner)"_#Brenner. The coefficients for -E_REBO in AIREBO are essentially the same as Brenner's potential, but -a few fitted spline values are slightly different. For most cases the -E_REBO term in AIREBO will produce the same energies, forces and -statistical averages as the original REBO potential from which it was -derived. The E_REBO term in the AIREBO potential gives the model its -reactive capabilities and only describes short-ranged C-C, C-H and H-H -interactions (r < 2 Angstroms). These interactions have strong -coordination-dependence through a bond order parameter, which adjusts -the attraction between the I,J atoms based on the position of other -nearby atoms and thus has 3- and 4-body dependence. - -The E_LJ term adds longer-ranged interactions (2 < r < cutoff) using a -form similar to the standard "Lennard Jones potential"_pair_lj.html. -The E_LJ term in AIREBO contains a series of switching functions so -that the short-ranged LJ repulsion (1/r^12) does not interfere with -the energetics captured by the E_REBO term. The extent of the E_LJ -interactions is determined by the {cutoff} argument to the pair_style -command which is a scale factor. For each type pair (C-C, C-H, H-H) -the cutoff is obtained by multiplying the scale factor by the sigma -value defined in the potential file for that type pair. In the -standard AIREBO potential, sigma_CC = 3.4 Angstroms, so with a scale -factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff -would be 10.2 Angstroms. - -By default, the longer-ranged interaction is smoothly switched off -between 2.16 and 3.0 sigma. By specifying {cutoff_min} in addition -to {cutoff}, the switching can be configured to take place between -{cutoff_min} and {cutoff}. {cutoff_min} can only be specified if all -optional arguments are given. - -The E_TORSION term is an explicit 4-body potential that describes -various dihedral angle preferences in hydrocarbon configurations. - -:line - -Only a single pair_coeff command is used with the {airebo}, {airebo} -or {rebo} style which specifies an AIREBO, REBO, or AIREBO-M potential -file with parameters for C and H. Note that as of LAMMPS version -15 May 2019 the {rebo} style in LAMMPS uses its own potential -file (CH.rebo). These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of AIREBO elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -As an example, if your LAMMPS simulation has 4 atom types and you want -the 1st 3 to be C, and the 4th to be H, you would use the following -pair_coeff command: - -pair_coeff * * CH.airebo C C C H :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three C arguments map LAMMPS atom types 1,2,3 to the C -element in the AIREBO file. The final H argument maps LAMMPS atom -type 4 to the H element in the SW file. If a mapping value is -specified as NULL, the mapping is not performed. This can be used -when a {airebo} potential is used as part of the {hybrid} pair style. -The NULL values are placeholders for atom types that will be used with -other potentials. - -The parameters/coefficients for the AIREBO potentials are listed in -the CH.airebo file to agree with the original "(Stuart)"_#Stuart -paper. Thus the parameters are specific to this potential and the way -it was fit, so modifying the file should be done cautiously. - -Similarly the parameters/coefficients for the AIREBO-M potentials are -listed in the CH.airebo-m file to agree with the "(O'Connor)"_#OConnor -paper. Thus the parameters are specific to this potential and the way -it was fit, so modifying the file should be done cautiously. The -AIREBO-M Morse potentials were parameterized using a cutoff of -3.0 (sigma). Modifying this cutoff may impact simulation accuracy. - -This pair style tallies a breakdown of the total AIREBO potential -energy into sub-categories, which can be accessed via the "compute -pair"_compute_pair.html command as a vector of values of length 3. -The 3 values correspond to the following sub-categories: - -{E_REBO} = REBO energy -{E_LJ} = Lennard-Jones energy -{E_TORSION} = Torsion energy :ol - -To print these quantities to the log file (with descriptive column -headings) the following commands could be included in an input script: - -compute 0 all pair airebo -variable REBO equal c_0\[1\] -variable LJ equal c_0\[2\] -variable TORSION equal c_0\[3\] -thermo_style custom step temp epair v_REBO v_LJ v_TORSION :pre - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -These pair styles do not support the "pair_modify"_pair_modify.html -mix, shift, table, and tail options. - -These pair styles do not write their information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -These pair styles can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. They do not support the -{inner}, {middle}, {outer} keywords. - -[Restrictions:] - -These pair styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -These pair potentials require the "newton"_newton.html setting to be -"on" for pair interactions. - -The CH.airebo and CH.airebo-m potential files provided with LAMMPS -(see the potentials directory) are parameterized for metal "units"_units.html. -You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units, -but you would need to create your own AIREBO or AIREBO-M potential file -with coefficients listed in the appropriate units, if your simulation -doesn't use "metal" units. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Stuart) -[(Stuart)] Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486 -(2000). - -:link(Brenner) -[(Brenner)] Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J -Physics: Condensed Matter, 14, 783-802 (2002). - -:link(OConnor) -[(O'Connor)] O'Connor et al., J. Chem. Phys. 142, 024903 (2015). diff --git a/doc/txt/pair_atm.txt b/doc/txt/pair_atm.txt deleted file mode 100644 index adbc6b6f3b..0000000000 --- a/doc/txt/pair_atm.txt +++ /dev/null @@ -1,164 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style atm command :h3 - -[Syntax:] - -pair_style atm cutoff cutoff_triple :pre - -cutoff = cutoff for each pair in 3-body interaction (distance units) -cutoff_triple = additional cutoff applied to product of 3 pairwise distances (distance units) :ul - -[Examples:] - -pair_style atm 4.5 2.5 -pair_coeff * * * 0.072 :pre - -pair_style hybrid/overlay lj/cut 6.5 atm 4.5 2.5 -pair_coeff * * lj/cut 1.0 1.0 -pair_coeff 1 1 atm 1 0.064 -pair_coeff 1 1 atm 2 0.080 -pair_coeff 1 2 atm 2 0.100 -pair_coeff 2 2 atm 2 0.125 :pre - -[Description:] - -The {atm} style computes a 3-body "Axilrod-Teller-Muto"_#Axilrod -potential for the energy E of a system of atoms as - -:c,image(Eqs/pair_atm.jpg) - -where nu is the three-body interaction strength. The distances -between pairs of atoms r12, r23, r31 and the angles gamma1, gamma2, -gamma3 are as shown in this diagram: - -:c,image(JPG/pair_atm_dia.jpg) - -Note that for the interaction between a triplet of atoms I,J,K, there -is no "central" atom. The interaction is symmetric with respect to -permutation of the three atoms. Thus the nu value is -the same for all those permutations of the atom types of I,J,K -and needs to be specified only once, as discussed below. - -The {atm} potential is typically used in combination with a two-body -potential using the "pair_style hybrid/overlay"_pair_hybrid.html -command as in the example above. - -The potential for a triplet of atom is calculated only if all 3 -distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff. -In addition, the product of the 3 distances r12*r23*r31 < -cutoff_triple^3 is required, which excludes from calculation the -triplets with small contribution to the interaction. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the restart files read by the -"read_restart"_read_restart.html commands: - -K = atom type of the third atom (1 to Ntypes) -nu = prefactor (energy/distance^9 units) :ul - -K can be specified in one of two ways. An explicit numeric value can -be used, as in the 2nd example above. J <= K is required. LAMMPS -sets the coefficients for the other 5 symmetric interactions to the -same values. E.g. if I = 1, J = 2, K = 3, then these 6 values are set -to the specified nu: nu123, nu132, nu213, nu231, nu312, nu321. This -enforces the symmetry discussed above. - -A wildcard asterisk can be used for K to set the coefficients for -multiple triplets of atom types. This takes the form "*" or "*n" or -"n*" or "m*n". If N = the number of atom types, then an asterisk with -no numeric values means all types from 1 to N. A leading asterisk -means all types from 1 to n (inclusive). A trailing asterisk means -all types from n to N (inclusive). A middle asterisk means all types -from m to n (inclusive). Note that only type triplets with J <= K are -considered; if asterisks imply type triplets where K < J, they are -ignored. - -Note that a pair_coeff command can override a previous setting for the -same I,J,K triplet. For example, these commands set nu for all I,J.K -triplets, then overwrite nu for just the I,J,K = 2,3,4 triplet: - -pair_coeff * * * 0.25 -pair_coeff 2 3 4 0.1 :pre - -Note that for a simulation with a single atom type, only a single -entry is required, e.g. - -pair_coeff 1 1 1 0.25 :pre - -For a simulation with two atom types, four pair_coeff commands will -specify all possible nu values: - -pair_coeff 1 1 1 nu1 -pair_coeff 1 1 2 nu2 -pair_coeff 1 2 2 nu3 -pair_coeff 2 2 2 nu4 :pre - -For a simulation with three atom types, ten pair_coeff commands will -specify all possible nu values: - -pair_coeff 1 1 1 nu1 -pair_coeff 1 1 2 nu2 -pair_coeff 1 1 3 nu3 -pair_coeff 1 2 2 nu4 -pair_coeff 1 2 3 nu5 -pair_coeff 1 3 3 nu6 -pair_coeff 2 2 2 nu7 -pair_coeff 2 2 3 nu8 -pair_coeff 2 3 3 nu9 -pair_coeff 3 3 3 nu10 :pre - -By default the nu value for all triplets is set to 0.0. Thus it is -not required to provide pair_coeff commands that enumerate triplet -interactions for all K types. If some I,J,K combination is not -specified, then there will be no 3-body ATM interactions for that -combination and all its permutations. However, as with all pair -styles, it is required to specify a pair_coeff command for all I,J -combinations, else an error will result. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair styles do not support the "pair_modify"_pair_modify.html -mix, shift, table, and tail options. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -However, if the {atm} potential is used in combination with other -potentials using the "pair_style hybrid/overlay"_pair_hybrid.html -command then pair_coeff commands need to be re-specified -in the restart input script. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Axilrod) -[(Axilrod)] -Axilrod and Teller, J Chem Phys, 11, 299 (1943); -Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943). diff --git a/doc/txt/pair_awpmd.txt b/doc/txt/pair_awpmd.txt deleted file mode 100644 index 4401f5b706..0000000000 --- a/doc/txt/pair_awpmd.txt +++ /dev/null @@ -1,123 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style awpmd/cut command :h3 - -[Syntax:] - -pair_style awpmd/cut Rc keyword value ... :pre - -Rc = global cutoff, -1 means cutoff of half the shortest box length :ulb,l -zero or more keyword/value pairs may be appended :l -keyword = {hartree} or {dproduct} or {uhf} or {free} or {pbc} or {fix} or {harm} or {ermscale} or {flex_press} :l - {hartree} value = none - {dproduct} value = none - {uhf} value = none - {free} value = none - {pbc} value = Plen - Plen = periodic width of electron = -1 or positive value (distance units) - {fix} value = Flen - Flen = fixed width of electron = -1 or positive value (distance units) - {harm} value = width - width = harmonic width constraint - {ermscale} value = factor - factor = scaling between electron mass and width variable mass - {flex_press} value = none :pre -:ule - - -[Examples:] - -pair_style awpmd/cut -1 -pair_style awpmd/cut 40.0 uhf free -pair_coeff * * -pair_coeff 2 2 20.0 :pre - -[Description:] - -This pair style contains an implementation of the Antisymmetrized Wave -Packet Molecular Dynamics (AWPMD) method. Need citation here. Need -basic formulas here. Could be links to other documents. - -Rc is the cutoff. - -The pair_style command allows for several optional keywords -to be specified. - -The {hartree}, {dproduct}, and {uhf} keywords specify the form of the -initial trial wave function for the system. If the {hartree} keyword -is used, then a Hartree multielectron trial wave function is used. If -the {dproduct} keyword is used, then a trial function which is a -product of two determinants for each spin type is used. If the {uhf} -keyword is used, then an unrestricted Hartree-Fock trial wave function -is used. - -The {free}, {pbc}, and {fix} keywords specify a width constraint on -the electron wave packets. If the {free} keyword is specified, then there is no -constraint. If the {pbc} keyword is used and {Plen} is specified as --1, then the maximum width is half the shortest box length. If {Plen} -is a positive value, then the value is the maximum width. If the -{fix} keyword is used and {Flen} is specified as -1, then electrons -have a constant width that is read from the data file. If {Flen} is a -positive value, then the constant width for all electrons is set to -{Flen}. - -The {harm} keyword allow oscillations in the width of the -electron wave packets. More details are needed. - -The {ermscale} keyword specifies a unitless scaling factor -between the electron masses and the width variable mass. More -details needed. - -If the {flex_press} keyword is used, then a contribution from the -electrons is added to the total virial and pressure of the system. - -This potential is designed to be used with "atom_style -wavepacket"_atom_style.html definitions, in order to handle the -description of systems with interacting nuclei and explicit electrons. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -cutoff (distance units) :ul - -For {awpmd/cut}, the cutoff coefficient is optional. If it is not -used (as in some of the examples above), the default global value -specified in the pair_style command is used. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -The "pair_modify"_pair_modify.html mix, shift, table, and tail options -are not relevant for this pair style. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] - -These are the defaults for the pair_style keywords: {hartree} for the -initial wave function, {free} for the wave packet width. - diff --git a/doc/txt/pair_beck.txt b/doc/txt/pair_beck.txt deleted file mode 100644 index af60041ff9..0000000000 --- a/doc/txt/pair_beck.txt +++ /dev/null @@ -1,108 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style beck command :h3 -pair_style beck/gpu command :h3 -pair_style beck/omp command :h3 - -[Syntax:] - -pair_style beck Rc :pre - -Rc = cutoff for interactions (distance units) :ul - -[Examples:] - -pair_style beck 8.0 -pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 -pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0 :pre - -[Description:] - -Style {beck} computes interactions based on the potential by -"(Beck)"_#Beck, originally designed for simulation of Helium. It -includes truncation at a cutoff distance Rc. - -:c,image(Eqs/pair_beck.jpg) - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands. - -A (energy units) -B (energy-distance^6 units) -a (distance units) -alpha (1/distance units) -beta (1/distance^6 units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global cutoff -Rc is used. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, coefficients must be specified. -No default mixing rules are used. - -This pair style does not support the "pair_modify"_pair_modify.html shift -option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Beck) -[(Beck)] Beck, Molecular Physics, 14, 311 (1968). diff --git a/doc/txt/pair_body_nparticle.txt b/doc/txt/pair_body_nparticle.txt deleted file mode 100644 index 7d841119ca..0000000000 --- a/doc/txt/pair_body_nparticle.txt +++ /dev/null @@ -1,117 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style body/nparticle command :h3 - -[Syntax:] - -pair_style body/nparticle cutoff :pre - -cutoff = global cutoff for interactions (distance units) - -[Examples:] - -pair_style body/nparticle 3.0 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.0 1.5 2.5 :pre - -[Description:] - -Style {body/nparticle} is for use with body particles and calculates -pairwise body/body interactions as well as interactions between body -and point-particles. See the "Howto body"_Howto_body.html doc page -for more details on using body particles. - -This pair style is designed for use with the "nparticle" body style, -which is specified as an argument to the "atom-style body" command. -See the "Howto body"_Howto_body.html doc page for more details about -the body styles LAMMPS supports. The "nparticle" style treats a body -particle as a rigid body composed of N sub-particles. - -The coordinates of a body particle are its center-of-mass (COM). If -the COMs of a pair of body particles are within the cutoff (global or -type-specific, as specified above), then all interactions between -pairs of sub-particles in the two body particles are computed. -E.g. if the first body particle has 3 sub-particles, and the second -has 10, then 30 interactions are computed and summed to yield the -total force and torque on each body particle. - -NOTE: In the example just described, all 30 interactions are computed -even if the distance between a particular pair of sub-particles is -greater than the cutoff. Likewise, no interaction between two body -particles is computed if the two COMs are further apart than the -cutoff, even if the distance between some pairs of their sub-particles -is within the cutoff. Thus care should be used in defining the cutoff -distances for body particles, depending on their shape and size. - -Similar rules apply for a body particle interacting with a point -particle. The distance between the two particles is calculated using -the COM of the body particle and the position of the point particle. -If the distance is within the cutoff and the body particle has N -sub-particles, then N interactions with the point particle are -computed and summed. If the distance is not within the cutoff, no -interactions between the body and point particle are computed. - -The interaction between two sub-particles, or a sub-particle and point -particle, or between two point particles is computed as a Lennard-Jones -interaction, using the standard formula - -:c,image(Eqs/pair_lj.jpg) - -where Rc is the cutoff. As explained above, an interaction involving -one or two body sub-particles may be computed even for r > Rc. - -For style {body}, the following coefficients must be defined for each -pair of atoms types via the "pair_coeff"_pair_coeff.html command as in -the examples above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -epsilon (energy units) -sigma (distance units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global cutoff -is used. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of this pair style can be mixed. The -default mix value is {geometric}. See the "pair_modify" command for -details. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This style is part of the BODY package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Defining particles to be bodies so they participate in body/body or -body/particle interactions requires the use of the "atom_style -body"_atom_style.html command. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "fix rigid"_fix_rigid.html - -[Default:] none diff --git a/doc/txt/pair_body_rounded_polygon.txt b/doc/txt/pair_body_rounded_polygon.txt deleted file mode 100644 index fc07d8fadd..0000000000 --- a/doc/txt/pair_body_rounded_polygon.txt +++ /dev/null @@ -1,133 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style body/rounded/polygon command :h3 - -[Syntax:] - -pair_style body/rounded/polygon c_n c_t mu delta_ua cutoff :pre - -c_n = normal damping coefficient -c_t = tangential damping coefficient -mu = normal friction coefficient during gross sliding -delta_ua = multiple contact scaling factor -cutoff = global separation cutoff for interactions (distance units), see below for definition :pre - -[Examples:] - -pair_style body/rounded/polygon 20.0 5.0 0.0 1.0 0.5 -pair_coeff * * 100.0 1.0 -pair_coeff 1 1 100.0 1.0 :pre - -[Description:] - -Style {body/rounded/polygon} is for use with 2d models of body -particles of style {rounded/polygon}. It calculates pairwise -body/body interactions which can include body particles modeled as -1-vertex circular disks with a specified diameter. See the "Howto -body"_Howto_body.html doc page for more details on using body -rounded/polygon particles. - -This pairwise interaction between rounded polygons is described in -"Fraige"_#pair-Fraige, where a polygon does not have sharp corners, -but is rounded at its vertices by circles centered on each vertex with -a specified diameter. The edges of the polygon are defined between -pairs of adjacent vertices. The circle diameter for each polygon is -specified in the data file read by the "read data"_read_data.html -command. This is a 2d discrete element model (DEM) which allows for -multiple contact points. - -Note that when two particles interact, the effective surface of each -polygon particle is displaced outward from each of its vertices and -edges by half its circle diameter (as in the diagram below of a gray -and yellow square particle). The interaction forces and energies -between two particles are defined with respect to the separation of -their respective rounded surfaces, not by the separation of the -vertices and edges themselves. - -This means that the specified cutoff in the pair_style command is the -cutoff distance, r_c, for the surface separation, \delta_n (see figure -below). This is the distance at which two particles no longer -interact. If r_c is specified as 0.0, then it is a contact-only -interaction. I.e. the two particles must overlap in order to exert a -repulsive force on each other. If r_c > 0.0, then the force between -two particles will be attractive for surface separations from 0 to -r_c, and repulsive once the particles overlap. - -Note that unlike for other pair styles, the specified cutoff is not -the distance between the centers of two particles at which they stop -interacting. This center-to-center distance depends on the shape and -size of the two particles and their relative orientation. LAMMPS -takes that into account when computing the surface separation distance -and applying the r_c cutoff. - -The forces between vertex-vertex, vertex-edge, and edge-edge overlaps -are given by: - -:c,image(Eqs/pair_body_rounded.jpg) - -:c,image(JPG/pair_body_rounded.jpg) - -Note that F_n and F_t are functions of the surface separation \delta_n -= d - (R_i + R_j). In this model, when (R_i + R_j) < d < (R_i + R_j) -+ r_c, that is, 0 < \delta_n < r_c, the cohesive region of the two -surfaces overlap and the two surfaces are attractive to each other. - -In "Fraige"_#pair-Fraige, the tangential friction force between two -particles that are in contact is modeled differently prior to gross -sliding (i.e. static friction) and during gross-sliding (kinetic -friction). The latter takes place when the tangential deformation -exceeds the Coulomb frictional limit. In the current implementation, -however, we do not take into account frictional history, i.e. we do -not keep track of how many time steps the two particles have been in -contact nor calculate the tangential deformation. Instead, we assume -that gross sliding takes place as soon as two particles are in -contact. - -The following coefficients must be defined for each pair of atom types -via the "pair_coeff"_pair_coeff.html command as in the examples above, -or in the data file read by the "read_data"_read_data.html command: - -k_n (energy/distance^2 units) -k_na (energy/distance^2 units) :ul - -Effectively, k_n and k_na are the slopes of the red lines in the plot -above for force versus surface separation, for \delta_n < 0 and 0 < -\delta_n < r_c respectively. - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support the "pair_modify"_pair_modify.html -mix, shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -[Restrictions:] - -These pair styles are part of the BODY package. They are only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair style requires the "newton"_newton.html setting to be "on" -for pair interactions. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:link(pair-Fraige) -[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, -Particuology, 6, 455 (2008). diff --git a/doc/txt/pair_body_rounded_polyhedron.txt b/doc/txt/pair_body_rounded_polyhedron.txt deleted file mode 100644 index e650e5138a..0000000000 --- a/doc/txt/pair_body_rounded_polyhedron.txt +++ /dev/null @@ -1,129 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style body/rounded/polyhedron command :h3 - -[Syntax:] - -pair_style body/rounded/polyhedron c_n c_t mu delta_ua cutoff :pre - -c_n = normal damping coefficient -c_t = tangential damping coefficient -mu = normal friction coefficient during gross sliding -delta_ua = multiple contact scaling factor -cutoff = global separation cutoff for interactions (distance units), see below for definition :pre - -[Examples:] - -pair_style body/rounded/polyhedron 20.0 5.0 0.0 1.0 0.5 -pair_coeff * * 100.0 1.0 -pair_coeff 1 1 100.0 1.0 :pre - -[Description:] - -Style {body/rounded/polygon} is for use with 3d models of body -particles of style {rounded/polyhedron}. It calculates pairwise -body/body interactions which can include body particles modeled as -1-vertex spheres with a specified diameter. See the "Howto -body"_Howto_body.html doc page for more details on using body -rounded/polyhedron particles. - -This pairwise interaction between the rounded polyhedra is described -in "Wang"_#pair-Wang, where a polyhedron does not have sharp corners -and edges, but is rounded at its vertices and edges by spheres -centered on each vertex with a specified diameter. The edges if the -polyhedron are defined between pairs of adjacent vertices. Its faces -are defined by a loop of edges. The sphere diameter for each polygon -is specified in the data file read by the "read data"_read_data.html -command. This is a discrete element model (DEM) which allows for -multiple contact points. - -Note that when two particles interact, the effective surface of each -polyhedron particle is displaced outward from each of its vertices, -edges, and faces by half its sphere diameter. The interaction forces -and energies between two particles are defined with respect to the -separation of their respective rounded surfaces, not by the separation -of the vertices, edges, and faces themselves. - -This means that the specified cutoff in the pair_style command is the -cutoff distance, r_c, for the surface separation, \delta_n (see figure -below). This is the distance at which two particles no longer -interact. If r_c is specified as 0.0, then it is a contact-only -interaction. I.e. the two particles must overlap in order to exert a -repulsive force on each other. If r_c > 0.0, then the force between -two particles will be attractive for surface separations from 0 to -r_c, and repulsive once the particles overlap. - -Note that unlike for other pair styles, the specified cutoff is not -the distance between the centers of two particles at which they stop -interacting. This center-to-center distance depends on the shape and -size of the two particles and their relative orientation. LAMMPS -takes that into account when computing the surface separation distance -and applying the r_c cutoff. - -The forces between vertex-vertex, vertex-edge, vertex-face, edge-edge, -and edge-face overlaps are given by: - -:c,image(Eqs/pair_body_rounded.jpg) - -:c,image(JPG/pair_body_rounded.jpg) - -In "Wang"_#pair-Wang, the tangential friction force between two -particles that are in contact is modeled differently prior to gross -sliding (i.e. static friction) and during gross-sliding (kinetic -friction). The latter takes place when the tangential deformation -exceeds the Coulomb frictional limit. In the current implementation, -however, we do not take into account frictional history, i.e. we do -not keep track of how many time steps the two particles have been in -contact nor calculate the tangential deformation. Instead, we assume -that gross sliding takes place as soon as two particles are in -contact. - -The following coefficients must be defined for each pair of atom types -via the "pair_coeff"_pair_coeff.html command as in the examples above, -or in the data file read by the "read_data"_read_data.html command: - -k_n (energy/distance^2 units) -k_na (energy/distance^2 units) :ul - -Effectively, k_n and k_na are the slopes of the red lines in the plot -above for force versus surface separation, for \delta_n < 0 and 0 < -\delta_n < r_c respectively. - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support the "pair_modify"_pair_modify.html -mix, shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -[Restrictions:] - -These pair styles are part of the BODY package. They are only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair style requires the "newton"_newton.html setting to be "on" -for pair interactions. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:link(pair-Wang) -[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular -Matter, 13, 1 (2011). - diff --git a/doc/txt/pair_bop.txt b/doc/txt/pair_bop.txt deleted file mode 100644 index ef6fff2963..0000000000 --- a/doc/txt/pair_bop.txt +++ /dev/null @@ -1,428 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style bop command :h3 - -[Syntax:] - -pair_style bop keyword ... :pre - -zero or more keywords may be appended :l -keyword = {save} :l - save = pre-compute and save some values :pre -:ule - -[Examples:] - -pair_style bop -pair_coeff * * ../potentials/CdTe_bop Cd Te -pair_style bop save -pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te -comm_modify cutoff 14.70 :pre - -[Description:] - -The {bop} pair style computes Bond-Order Potentials (BOP) based on -quantum mechanical theory incorporating both sigma and pi bonding. -By analytically deriving the BOP from quantum mechanical theory its -transferability to different phases can approach that of quantum -mechanical methods. This potential is similar to the original BOP -developed by Pettifor ("Pettifor_1"_#Pettifor_1, -"Pettifor_2"_#Pettifor_2, "Pettifor_3"_#Pettifor_3) and later updated -by Murdick, Zhou, and Ward ("Murdick"_#Murdick, "Ward"_#Ward). -Currently, BOP potential files for these systems are provided with -LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A system with -only a subset of these elements, including a single element (e.g. C or -Cu or Al or Ga or Zn or CdZn), can also be modeled by using the -appropriate alloy file and assigning all atom types to the -single element or subset of elements via the pair_coeff command, as -discussed below. - -The BOP potential consists of three terms: - -:c,image(Eqs/pair_bop.jpg) - -where phi_ij(r_ij) is a short-range two-body function representing the -repulsion between a pair of ion cores, beta_(sigma,ij)(r_ij) and -beta_(sigma,ij)(r_ij) are respectively sigma and pi bond integrals, -THETA_(sigma,ij) and THETA_(pi,ij) are sigma and pi bond-orders, and -U_prom is the promotion energy for sp-valent systems. - -The detailed formulas for this potential are given in Ward -("Ward"_#Ward); here we provide only a brief description. - -The repulsive energy phi_ij(r_ij) and the bond integrals -beta_(sigma,ij)(r_ij) and beta_(phi,ij)(r_ij) are functions of the -interatomic distance r_ij between atom i and j. Each of these -potentials has a smooth cutoff at a radius of r_(cut,ij). These -smooth cutoffs ensure stable behavior at situations with high sampling -near the cutoff such as melts and surfaces. - -The bond-orders can be viewed as environment-dependent local variables -that are ij bond specific. The maximum value of the sigma bond-order -(THETA_sigma) is 1, while that of the pi bond-order (THETA_pi) is 2, -attributing to a maximum value of the total bond-order -(THETA_sigma+THETA_pi) of 3. The sigma and pi bond-orders reflect the -ubiquitous single-, double-, and triple- bond behavior of -chemistry. Their analytical expressions can be derived from tight- -binding theory by recursively expanding an inter-site Green's function -as a continued fraction. To accurately represent the bonding with a -computationally efficient potential formulation suitable for MD -simulations, the derived BOP only takes (and retains) the first two -levels of the recursive representations for both the sigma and the pi -bond-orders. Bond-order terms can be understood in terms of molecular -orbital hopping paths based upon the Cyrot-Lackmann theorem -("Pettifor_1"_#Pettifor_1). The sigma bond-order with a half-full -valence shell is used to interpolate the bond-order expression that -incorporated explicit valance band filling. This pi bond-order -expression also contains also contains a three-member ring term that -allows implementation of an asymmetric density of states, which helps -to either stabilize or destabilize close-packed structures. The pi -bond-order includes hopping paths of length 4. This enables the -incorporation of dihedral angles effects. - -NOTE: Note that unlike for other potentials, cutoffs for BOP -potentials are not set in the pair_style or pair_coeff command; they -are specified in the BOP potential files themselves. Likewise, the -BOP potential files list atomic masses; thus you do not need to use -the "mass"_mass.html command to specify them. Note that for BOP -potentials with hydrogen, you will likely want to set the mass of H -atoms to be 10x or 20x larger to avoid having to use a tiny timestep. -You can do this by using the "mass"_mass.html command after using the -"pair_coeff"_pair_coeff.html command to read the BOP potential -file. - -One option can be specified as a keyword with the pair_style command. - -The {save} keyword gives you the option to calculate in advance and -store a set of distances, angles, and derivatives of angles. The -default is to not do this, but to calculate them on-the-fly each time -they are needed. The former may be faster, but takes more memory. -The latter requires less memory, but may be slower. It is best to -test this option to optimize the speed of BOP for your particular -system configuration. - -:line - -Only a single pair_coeff command is used with the {bop} style which -specifies a BOP potential file, with parameters for all needed -elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of BOP elements to atom types :ul - -As an example, imagine the CdTe.bop file has BOP values for Cd -and Te. If your LAMMPS simulation has 4 atoms types and you want the -1st 3 to be Cd, and the 4th to be Te, you would use the following -pair_coeff command: - -pair_coeff * * CdTe Cd Cd Cd Te :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Cd arguments map LAMMPS atom types 1,2,3 to the Cd -element in the BOP file. The final Te argument maps LAMMPS atom type -4 to the Te element in the BOP file. - -BOP files in the {potentials} directory of the LAMMPS distribution -have a ".bop" suffix. The potentials are in tabulated form containing -pre-tabulated pair functions for phi_ij(r_ij), beta_(sigma,ij)(r_ij), -and beta_pi,ij)(r_ij). - -The parameters/coefficients format for the different kinds of BOP -files are given below with variables matching the formulation of Ward -("Ward"_#Ward) and Zhou ("Zhou"_#Zhou1). Each header line containing a -":" is preceded by a blank line. - - -:line - -[No angular table file format]: - -The parameters/coefficients format for the BOP potentials input file -containing pre-tabulated functions of g is given below with variables -matching the formulation of Ward ("Ward"_#Ward). This format also -assumes the angular functions have the formulation of ("Ward"_#Ward). - -Line 1: # elements N :ul - -The first line is followed by N lines containing the atomic -number, mass, and element symbol of each element. - -Following the definition of the elements several global variables for -the tabulated functions are given. - -Line 1: nr, nBOt (nr is the number of divisions the radius is broken -into for function tables and MUST be a factor of 5; nBOt is the number -of divisions for the tabulated values of THETA_(S,ij) :ulb,l -Line 2: delta_1-delta_7 (if all are not used in the particular :l -formulation, set unused values to 0.0) :l -:ule - -Following this N lines for e_1-e_N containing p_pi. - -Line 3: p_pi (for e_1) -Line 4: p_pi (for e_2 and continues to e_N) :ul - -The next section contains several pair constants for the number of -interaction types e_i-e_j, with i=1->N, j=i->N - -Line 1: r_cut (for e_1-e_1 interactions) :ulb,l -Line 2: c_sigma, a_sigma, c_pi, a_pi :l -Line 3: delta_sigma, delta_pi :l -Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of -the previous section but is interaction type dependent) :l -:ule - -The next section contains a line for each three body interaction type -e_j-e_i-e_k with i=0->N, j=0->N, k=j->N - -Line 1: g_(sigma0), g_(sigma1), g_(sigma2) (These are coefficients for -g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. "Ward"_#Ward -contains the full expressions for the constants as functions of -b_(sigma,ijk), p_(sigma,ijk), u_(sigma,ijk)) :ulb,l -Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2) :l -:ule - -The next section contains a block for each interaction type for the -phi_ij(r_ij). Each block has nr entries with 5 entries per line. - -Line 1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5) (for the e_1-e_1 -interaction type) :ulb,l -Line 2: phi(r6), phi(r7), phi(r8), phi(r9), phi(r10) (this continues -until nr) :l -... :l -Line nr/5_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the -e_1-e_1 interaction type) :l -:ule - -The next section contains a block for each interaction type for the -beta_(sigma,ij)(r_ij). Each block has nr entries with 5 entries per -line. - -Line 1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), beta_sigma(r4), -beta_sigma(r5) (for the e_1-e_1 interaction type) :ulb,l -Line 2: beta_sigma(r6), beta_sigma(r7), beta_sigma(r8), beta_sigma(r9), -beta_sigma(r10) (this continues until nr) :l -... :l -Line nr/5+1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), -beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type) :l -:ule - -The next section contains a block for each interaction type for -beta_(pi,ij)(r_ij). Each block has nr entries with 5 entries per line. - -Line 1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), beta_pi(r5) -(for the e_1-e_1 interaction type) :ulb,l -Line 2: beta_pi(r6), beta_pi(r7), beta_pi(r8), beta_pi(r9), -beta_pi(r10) (this continues until nr) :l -... :l -Line nr/5+1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), -beta_pi(r5) (for the e_1-e_2 interaction type) :l -:ule - -The next section contains a block for each interaction type for the -THETA_(S,ij)((THETA_(sigma,ij))^(1/2), f_(sigma,ij)). Each block has -nBOt entries with 5 entries per line. - -Line 1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3), -THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) :ulb,l -Line 2: THETA_(S,ij)(r6), THETA_(S,ij)(r7), THETA_(S,ij)(r8), -THETA_(S,ij)(r9), THETA_(S,ij)(r10) (this continues until nBOt) :l -... :l -Line nBOt/5+1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3), -THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) :l -:ule - -The next section contains a block of N lines for e_1-e_N - -Line 1: delta^mu (for e_1) -Line 2: delta^mu (for e_2 and repeats to e_N) :ul - -The last section contains more constants for e_i-e_j interactions with -i=0->N, j=i->N - -Line 1: (A_ij)^(mu*nu) (for e1-e1) -Line 2: (A_ij)^(mu*nu) (for e1-e2 and repeats as above) :ul - -:line - -[Angular spline table file format]: - -The parameters/coefficients format for the BOP potentials input file -containing pre-tabulated functions of g is given below with variables -matching the formulation of Ward ("Ward"_#Ward). This format also -assumes the angular functions have the formulation of ("Zhou"_#Zhou1). - -Line 1: # elements N :ul - -The first line is followed by N lines containing the atomic -number, mass, and element symbol of each element. - -Following the definition of the elements several global variables for -the tabulated functions are given. - -Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken -into for function tables and MUST be a factor of 5; ntheta is the power of the -power of the spline used to fit the angular function; nBOt is the number -of divisions for the tabulated values of THETA_(S,ij) :ulb,l -Line 2: delta_1-delta_7 (if all are not used in the particular :l -formulation, set unused values to 0.0) :l -:ule - -Following this N lines for e_1-e_N containing p_pi. - -Line 3: p_pi (for e_1) -Line 4: p_pi (for e_2 and continues to e_N) :ul - -The next section contains several pair constants for the number of -interaction types e_i-e_j, with i=1->N, j=i->N - -Line 1: r_cut (for e_1-e_1 interactions) :ulb,l -Line 2: c_sigma, a_sigma, c_pi, a_pi :l -Line 3: delta_sigma, delta_pi :l -Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of -the previous section but is interaction type dependent) :l -:ule - -The next section contains a line for each three body interaction type -e_j-e_i-e_k with i=0->N, j=0->N, k=j->N - -Line 1: g0, g1, g2... (These are coefficients for the angular spline -of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. The -function can contain up to 10 term thus 10 constants. The first line -can contain up to five constants. If the spline has more than five -terms the second line will contain the remaining constants The -following lines will then contain the constants for the remaining g0, -g1, g2... (for e_1-e_1-e_2) and the other three body -interactions :l -:ule - -The rest of the table has the same structure as the previous section -(see above). - -:line - -[Angular no-spline table file format]: - -The parameters/coefficients format for the BOP potentials input file -containing pre-tabulated functions of g is given below with variables -matching the formulation of Ward ("Ward"_#Ward). This format also -assumes the angular functions have the formulation of ("Zhou"_#Zhou1). - -Line 1: # elements N :ul - -The first two lines are followed by N lines containing the atomic -number, mass, and element symbol of each element. - -Following the definition of the elements several global variables for -the tabulated functions are given. - -Line 1: nr, ntheta, nBOt (nr is the number of divisions the radius is broken -into for function tables and MUST be a factor of 5; ntheta is the number of -divisions for the tabulated values of the g angular function; nBOt is the number -of divisions for the tabulated values of THETA_(S,ij) :ulb,l -Line 2: delta_1-delta_7 (if all are not used in the particular :l -formulation, set unused values to 0.0) :l -:ule - -Following this N lines for e_1-e_N containing p_pi. - -Line 3: p_pi (for e_1) -Line 4: p_pi (for e_2 and continues to e_N) :ul - -The next section contains several pair constants for the number of -interaction types e_i-e_j, with i=1->N, j=i->N - -Line 1: r_cut (for e_1-e_1 interactions) :ulb,l -Line 2: c_sigma, a_sigma, c_pi, a_pi :l -Line 3: delta_sigma, delta_pi :l -Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of -the previous section but is interaction type dependent) :l -:ule - -The next section contains a line for each three body interaction type -e_j-e_i-e_k with i=0->N, j=0->N, k=j->N - -Line 1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5) (for the e_1-e_1-e_1 -interaction type) :ulb,l -Line 2: g(theta6), g(theta7), g(theta8), g(theta9), g(theta10) (this continues -until ntheta) :l -... :l -Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the -e_1-e_1-e_2 interaction type) :l -:ule - -The rest of the table has the same structure as the previous section (see above). - -:line - -[Mixing, shift, table tail correction, restart]: - -This pair style does not support the "pair_modify"_pair_modify.html -mix, shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -These pair styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -These pair potentials require the "newtion"_newton.html setting to be -"on" for pair interactions. - -The CdTe.bop and GaAs.bop potential files provided with LAMMPS (see the -potentials directory) are parameterized for metal "units"_units.html. -You can use the BOP potential with any LAMMPS units, but you would need -to create your own BOP potential file with coefficients listed in the -appropriate units if your simulation does not use "metal" units. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] - -non-tabulated potential file, a_0 is non-zero. - -:line - -:link(Pettifor_1) -[(Pettifor_1)] D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487 -(1999). - -:link(Pettifor_2) -[(Pettifor_2)] D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84, -4124 (2000). - -:link(Pettifor_3) -[(Pettifor_3)] D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 -(2002). - -:link(Murdick) -[(Murdick)] D.A. Murdick, X.W. Zhou, H.N.G. Wadley, D. Nguyen-Manh, R. -Drautz, and D.G. Pettifor, Phys. Rev. B, 73, 45206 (2006). - -:link(Ward) -[(Ward)] D.K. Ward, X.W. Zhou, B.M. Wong, F.P. Doty, and J.A. -Zimmerman, Phys. Rev. B, 85,115206 (2012). - -:link(Zhou1) -[(Zhou)] X.W. Zhou, D.K. Ward, M. Foster (TBP). diff --git a/doc/txt/pair_born.txt b/doc/txt/pair_born.txt deleted file mode 100644 index d12cea79a6..0000000000 --- a/doc/txt/pair_born.txt +++ /dev/null @@ -1,194 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style born command :h3 -pair_style born/omp command :h3 -pair_style born/gpu command :h3 -pair_style born/coul/long command :h3 -pair_style born/coul/long/gpu command :h3 -pair_style born/coul/long/omp command :h3 -pair_style born/coul/msm command :h3 -pair_style born/coul/msm/omp command :h3 -pair_style born/coul/wolf command :h3 -pair_style born/coul/wolf/gpu command :h3 -pair_style born/coul/wolf/omp command :h3 -pair_style born/coul/dsf command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {born} or {born/coul/long} or {born/coul/msm} or {born/coul/wolf} -args = list of arguments for a particular style :ul - {born} args = cutoff - cutoff = global cutoff for non-Coulombic interactions (distance units) - {born/coul/long} args = cutoff (cutoff2) - cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {born/coul/msm} args = cutoff (cutoff2) - cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {born/coul/wolf} args = alpha cutoff (cutoff2) - alpha = damping parameter (inverse distance units) - cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {born/coul/dsf} args = alpha cutoff (cutoff2) - alpha = damping parameter (inverse distance units) - cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (distance units) :pre - -[Examples:] - -pair_style born 10.0 -pair_coeff * * 6.08 0.317 2.340 24.18 11.51 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre - -pair_style born/coul/long 10.0 -pair_style born/coul/long 10.0 8. -pair_coeff * * 6.08 0.317 2.340 24.18 11.51 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre - -pair_style born/coul/msm 10.0 -pair_style born/coul/msm 10.0 8.0 -pair_coeff * * 6.08 0.317 2.340 24.18 11.51 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre - -pair_style born/coul/wolf 0.25 10.0 -pair_style born/coul/wolf 0.25 10.0 9.0 -pair_coeff * * 6.08 0.317 2.340 24.18 11.51 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre - -pair_style born/coul/dsf 0.1 10.0 12.0 -pair_coeff * * 0.0 1.00 0.00 0.00 0.00 -pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre - -[Description:] - -The {born} style computes the Born-Mayer-Huggins or Tosi/Fumi -potential described in "(Fumi and Tosi)"_#FumiTosi, given by - -:c,image(Eqs/pair_born.jpg) - -where sigma is an interaction-dependent length parameter, rho is an -ionic-pair dependent length parameter, and Rc is the cutoff. - -The styles with {coul/long} or {coul/msm} add a Coulombic term as -described for the "lj/cut"_pair_lj.html pair styles. An additional -damping factor is applied to the Coulombic term so it can be used in -conjunction with the "kspace_style"_kspace_style.html command and its -{ewald} or {pppm} of {msm} option. The Coulombic cutoff specified for -this style means that pairwise interactions within this distance are -computed directly; interactions outside that distance are computed in -reciprocal space. - -If one cutoff is specified for the {born/coul/long} and -{born/coul/msm} style, it is used for both the A,C,D and Coulombic -terms. If two cutoffs are specified, the first is used as the cutoff -for the A,C,D terms, and the second is the cutoff for the Coulombic -term. - -The {born/coul/wolf} style adds a Coulombic term as described for the -Wolf potential in the "coul/wolf"_pair_coul.html pair style. - -The {born/coul/dsf} style computes the Coulomb contribution with the -damped shifted force model as in the "coul/dsf"_pair_coul.html style. - -Note that these potentials are related to the "Buckingham -potential"_pair_buck.html. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -A (energy units) -rho (distance units) -sigma (distance units) -C (energy units * distance units^6) -D (energy units * distance units^8) -cutoff (distance units) :ul - -The second coefficient, rho, must be greater than zero. - -The last coefficient is optional. If not specified, the global A,C,D -cutoff specified in the pair_style command is used. - -For {born/coul/long}, {born/coul/wolf} and {born/coul/dsf} no -Coulombic cutoff can be specified for an individual I,J type pair. -All type pairs use the same global Coulombic cutoff specified in the -pair_style command. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -These pair styles do not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -These styles support the "pair_modify"_pair_modify.html shift option -for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair -interaction. - -The {born/coul/long} pair style supports the -"pair_modify"_pair_modify.html table option to tabulate the -short-range portion of the long-range Coulombic interaction. - -These styles support the pair_modify tail option for adding long-range -tail corrections to energy and pressure. - -Thess styles writes thei information to binary "restart"_restart.html -files, so pair_style and pair_coeff commands do not need to be -specified in an input script that reads a restart file. - -These styles can only be used via the {pair} keyword of the "run_style -respa"_run_style.html command. They do not support the {inner}, -{middle}, {outer} keywords. - -:line - -[Restrictions:] - -The {born/coul/long} style is part of the KSPACE package. It is only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style buck"_pair_buck.html - -[Default:] none - -:line - -:link(FumiTosi) -Fumi and Tosi, J Phys Chem Solids, 25, 31 (1964), -Fumi and Tosi, J Phys Chem Solids, 25, 45 (1964). diff --git a/doc/txt/pair_brownian.txt b/doc/txt/pair_brownian.txt deleted file mode 100644 index 52720daa23..0000000000 --- a/doc/txt/pair_brownian.txt +++ /dev/null @@ -1,143 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style brownian command :h3 -pair_style brownian/omp command :h3 -pair_style brownian/poly command :h3 -pair_style brownian/poly/omp command :h3 - -[Syntax:] - -pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF :pre - -style = {brownian} or {brownian/poly} -mu = dynamic viscosity (dynamic viscosity units) -flaglog = 0/1 log terms in the lubrication approximation on/off -flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects -cutinner = inner cutoff distance (distance units) -cutoff = outer cutoff for interactions (distance units) -t_target = target temp of the system (temperature units) -seed = seed for the random number generator (positive integer) -flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions -flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms :ul - -[Examples:] - -pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1) -pair_coeff 1 1 2.05 2.8 -pair_coeff * * :pre - -[Description:] - -Styles {brownian} and {brownian/poly} compute Brownian forces and -torques on finite-size spherical particles. The former requires -monodisperse spherical particles; the latter allows for polydisperse -spherical particles. - -These pair styles are designed to be used with either the "pair_style -lubricate"_pair_lubricate.html or "pair_style -lubricateU"_pair_lubricateU.html commands to provide thermostatting -when dissipative lubrication forces are acting. Thus the parameters -{mu}, {flaglog}, {flagfld}, {cutinner}, and {cutoff} should be -specified consistent with the settings in the lubrication pair styles. -For details, refer to either of the lubrication pair styles. - -The {t_target} setting is used to specify the target temperature of -the system. The random number {seed} is used to generate random -numbers for the thermostatting procedure. - -The {flagHI} and {flagVF} settings are optional. Neither should be -used, or both must be defined. - -:line - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -cutinner (distance units) -cutoff (distance units) :ul - -The two coefficients are optional. If neither is specified, the two -cutoffs specified in the pair_style command are used. Otherwise both -must be specified. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in "this section"_Speed.html of -the manual. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See "this section"_Speed.html of the manual for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the two cutoff distances for this -pair style can be mixed. The default mix value is {geometric}. See -the "pair_modify" command for details. - -This pair style does not support the "pair_modify"_pair_modify.html -shift option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -These styles are part of the COLLOID package. They are only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Only spherical monodisperse particles are allowed for pair_style -brownian. - -Only spherical particles are allowed for pair_style brownian/poly. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style -lubricate"_pair_lubricate.html, "pair_style -lubricateU"_pair_lubricateU.html - -[Default:] - -The default settings for the optional args are flagHI = 1 and flagVF = -1. - diff --git a/doc/txt/pair_buck.txt b/doc/txt/pair_buck.txt deleted file mode 100644 index ec83e6b339..0000000000 --- a/doc/txt/pair_buck.txt +++ /dev/null @@ -1,191 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style buck command :h3 -pair_style buck/gpu command :h3 -pair_style buck/intel command :h3 -pair_style buck/kk command :h3 -pair_style buck/omp command :h3 -pair_style buck/coul/cut command :h3 -pair_style buck/coul/cut/gpu command :h3 -pair_style buck/coul/cut/intel command :h3 -pair_style buck/coul/cut/kk command :h3 -pair_style buck/coul/cut/omp command :h3 -pair_style buck/coul/long command :h3 -pair_style buck/coul/long/gpu command :h3 -pair_style buck/coul/long/intel command :h3 -pair_style buck/coul/long/kk command :h3 -pair_style buck/coul/long/omp command :h3 -pair_style buck/coul/msm command :h3 -pair_style buck/coul/msm/omp command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/msm} -args = list of arguments for a particular style :ul - {buck} args = cutoff - cutoff = global cutoff for Buckingham interactions (distance units) - {buck/coul/cut} args = cutoff (cutoff2) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {buck/coul/long} args = cutoff (cutoff2) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {buck/coul/msm} args = cutoff (cutoff2) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre - -[Examples:] - -pair_style buck 2.5 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff * * 100.0 1.5 200.0 3.0 :pre - -pair_style buck/coul/cut 10.0 -pair_style buck/coul/cut 10.0 8.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 :pre - -pair_style buck/coul/long 10.0 -pair_style buck/coul/long 10.0 8.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre - -pair_style buck/coul/msm 10.0 -pair_style buck/coul/msm 10.0 8.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre - -[Description:] - -The {buck} style computes a Buckingham potential (exp/6 instead of -Lennard-Jones 12/6) given by - -:c,image(Eqs/pair_buck.jpg) - -where rho is an ionic-pair dependent length parameter, and Rc is the -cutoff on both terms. - -The styles with {coul/cut} or {coul/long} or {coul/msm} add a -Coulombic term as described for the "lj/cut"_pair_lj.html pair styles. -For {buck/coul/long} and {buc/coul/msm}, an additional damping factor -is applied to the Coulombic term so it can be used in conjunction with -the "kspace_style"_kspace_style.html command and its {ewald} or {pppm} -or {msm} option. The Coulombic cutoff specified for this style means -that pairwise interactions within this distance are computed directly; -interactions outside that distance are computed in reciprocal space. - -If one cutoff is specified for the {born/coul/cut} and -{born/coul/long} and {born/coul/msm} styles, it is used for both the -A,C and Coulombic terms. If two cutoffs are specified, the first is -used as the cutoff for the A,C terms, and the second is the cutoff for -the Coulombic term. - -Note that these potentials are related to the "Born-Mayer-Huggins -potential"_pair_born.html. - -NOTE: For all these pair styles, the terms with A and C are always -cutoff. The additional Coulombic term can be cutoff or long-range (no -cutoff) depending on whether the style name includes coul/cut or -coul/long or coul/msm. If you wish the C/r^6 term to be long-range -(no cutoff), then see the "pair_style -buck/long/coul/long"_pair_buck_long.html command. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -A (energy units) -rho (distance units) -C (energy-distance^6 units) -cutoff (distance units) -cutoff2 (distance units) :ul - -The second coefficient, rho, must be greater than zero. -The coefficients A, rho, and C can be written as analytical expressions -of epsilon and sigma, in analogy to the Lennard-Jones potential -"(Khrapak)"_#Khrapak. - -The latter 2 coefficients are optional. If not specified, the global -A,C and Coulombic cutoffs are used. If only one cutoff is specified, -it is used as the cutoff for both A,C and Coulombic interactions for -this type pair. If both coefficients are specified, they are used as -the A,C and Coulombic cutoffs for this type pair. You cannot specify -2 cutoffs for style {buck}, since it has no Coulombic terms. -For {buck/coul/long} only the LJ cutoff can be specified since a -Coulombic cutoff cannot be specified for an individual I,J type pair. -All type pairs use the same global Coulombic cutoff specified in the -pair_style command. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -These pair styles do not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -These styles support the "pair_modify"_pair_modify.html shift option -for the energy of the exp() and 1/r^6 portion of the pair interaction. - -The {buck/coul/long} pair style supports the -"pair_modify"_pair_modify.html table option to tabulate the -short-range portion of the long-range Coulombic interaction. - -These styles support the pair_modify tail option for adding long-range -tail corrections to energy and pressure for the A,C terms in the -pair interaction. - -These styles write their information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -These styles can only be used via the {pair} keyword of the "run_style -respa"_run_style.html command. They do not support the {inner}, -{middle}, {outer} keywords. - -[Restrictions:] - -The {buck/coul/long} style is part of the KSPACE package. They are -only enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style born"_pair_born.html - -[Default:] none - -:link(Khrapak) -[(Khrapak)] Khrapak, Chaudhuri, and Morfill, J Chem Phys, 134, 054120 (2011). diff --git a/doc/txt/pair_buck6d_coul_gauss.txt b/doc/txt/pair_buck6d_coul_gauss.txt deleted file mode 100644 index 1f013e91ef..0000000000 --- a/doc/txt/pair_buck6d_coul_gauss.txt +++ /dev/null @@ -1,138 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style buck6d/coul/gauss/dsf command :h3 -pair_style buck6d/coul/gauss/long command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {buck6d/coul/gauss/dsf} or {buck6d/coul/gauss/long} -args = list of arguments for a particular style :ul - {buck6d/coul/gauss/dsf} args = smooth cutoff (cutoff2) - smooth = smoothing onset within Buckingham cutoff (ratio) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {buck6d/coul/gauss/long} args = smooth smooth2 cutoff (cutoff2) - smooth = smoothing onset within Buckingham cutoff (ratio) - smooth2 = smoothing onset within Coulombic cutoff (ratio) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre - -[Examples:] - -pair_style buck6d/coul/gauss/dsf 0.9000 12.0000 -pair_coeff 1 1 1030. 3.061 457.179 4.521 0.608 :pre - -pair_style buck6d/coul/gauss/long 0.9000 1.0000 12.0000 -pair_coeff 1 1 1030. 3.061 457.179 4.521 0.608 :pre - -[Description:] - -The {buck6d/coul/gauss} styles evaluate vdW and Coulomb -interactions following the MOF-FF force field after -"(Schmid)"_#Schmid. The vdW term of the {buck6d} styles -computes a dispersion damped Buckingham potential: - -:c,image(Eqs/pair_buck6d.jpg) - -where A and C are a force constant, kappa is an ionic-pair dependent -reciprocal length parameter, D is a dispersion correction parameter, -and the cutoff Rc truncates the interaction distance. -The first term in the potential corresponds to the Buckingham -repulsion term and the second term to the dispersion attraction with -a damping correction analog to the Grimme correction used in DFT. -The latter corrects for artifacts occurring at short distances which -become an issue for soft vdW potentials. - -The {buck6d} styles include a smoothing function which is invoked -according to the global smoothing parameter within the specified -cutoff. Hereby a parameter of i.e. 0.9 invokes the smoothing -within 90% of the cutoff. No smoothing is applied at a value -of 1.0. For the {gauss/dsf} style this smoothing is only applicable -for the dispersion damped Buckingham potential. For the {gauss/long} -styles the smoothing function can also be invoked for the real -space coulomb interactions which enforce continuous energies and -forces at the cutoff. - -Both styles {buck6d/coul/gauss/dsf} and {buck6d/coul/gauss/long} -evaluate a Coulomb potential using spherical Gaussian type charge -distributions which effectively dampen electrostatic interactions -for high charges at close distances. The electrostatic potential -is thus evaluated as: - -:c,image(Eqs/pair_coul_gauss.jpg) - -where C is an energy-conversion constant, Qi and Qj are the -charges on the 2 atoms, epsilon is the dielectric constant which -can be set by the "dielectric"_dielectric.html command, alpha is -ion pair dependent damping parameter and erf() is the error-function. -The cutoff Rc truncates the interaction distance. - -The style {buck6d/coul/gauss/dsf} computes the Coulomb interaction -via the damped shifted force model described in "(Fennell)"_#Fennell -approximating an Ewald sum similar to the "pair coul/dsf"_pair_coul.html -styles. In {buck6d/coul/gauss/long} an additional damping factor is -applied to the Coulombic term so it can be used in conjunction with the -"kspace_style"_kspace_style.html command and its {ewald} or {pppm} -options. The Coulombic cutoff in this case separates the real and -reciprocal space evaluation of the Ewald sum. - -If one cutoff is specified it is used for both the vdW and Coulomb -terms. If two cutoffs are specified, the first is used as the cutoff -for the vdW terms, and the second is the cutoff for the Coulombic term. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -A (energy units) -rho (distance^-1 units) -C (energy-distance^6 units) -D (distance^14 units) -alpha (distance^-1 units) -cutoff (distance units) :ul - -The second coefficient, rho, must be greater than zero. The latter -coefficient is optional. If not specified, the global vdW cutoff -is used. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -These pair styles do not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -These styles do not support the "pair_modify"_pair_modify.html shift -option for the energy. Instead the smoothing function should be applied -by setting the global smoothing parameter to a value < 1.0. - -These styles write their information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -[Restrictions:] - -These styles are part of the USER-MOFFF package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:link(Schmid) -[(Schmid)] S. Bureekaew, S. Amirjalayer, M. Tafipolsky, C. Spickermann, T.K. Roy and R. Schmid, Phys. Status Solidi B, 6, 1128 (2013). -:link(Fennell) -[(Fennell)] C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006). diff --git a/doc/txt/pair_buck_long.txt b/doc/txt/pair_buck_long.txt deleted file mode 100644 index ff27f6b005..0000000000 --- a/doc/txt/pair_buck_long.txt +++ /dev/null @@ -1,169 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style buck/long/coul/long command :h3 -pair_style buck/long/coul/long/omp command :h3 - -[Syntax:] - -pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2) :pre - -flag_buck = {long} or {cut} :ulb,l - {long} = use Kspace long-range summation for the dispersion term 1/r^6 - {cut} = use a cutoff :pre -flag_coul = {long} or {off} :l - {long} = use Kspace long-range summation for the Coulombic term 1/r - {off} = omit the Coulombic term :pre -cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units) :l -cutoff2 = global cutoff for Coulombic (optional) (distance units) :l -:ule - -[Examples:] - -pair_style buck/long/coul/long cut off 2.5 -pair_style buck/long/coul/long cut long 2.5 4.0 -pair_style buck/long/coul/long long long 4.0 -pair_coeff * * 1 1 -pair_coeff 1 1 1 3 4 :pre - -[Description:] - -The {buck/long/coul/long} style computes a Buckingham potential (exp/6 -instead of Lennard-Jones 12/6) and Coulombic potential, given by - -:c,image(Eqs/pair_buck.jpg) - -:c,image(Eqs/pair_coulomb.jpg) - -Rc is the cutoff. If one cutoff is specified in the pair_style -command, it is used for both the Buckingham and Coulombic terms. If -two cutoffs are specified, they are used as cutoffs for the Buckingham -and Coulombic terms respectively. - -The purpose of this pair style is to capture long-range interactions -resulting from both attractive 1/r^6 Buckingham and Coulombic 1/r -interactions. This is done by use of the {flag_buck} and {flag_coul} -settings. The "Ismail"_#Ismail paper has more details on when it is -appropriate to include long-range 1/r^6 interactions, using this -potential. - -If {flag_buck} is set to {long}, no cutoff is used on the Buckingham -1/r^6 dispersion term. The long-range portion can be calculated by -using the "kspace_style ewald/disp or pppm/disp"_kspace_style.html -commands. The specified Buckingham cutoff then determines which -portion of the Buckingham interactions are computed directly by the -pair potential versus which part is computed in reciprocal space via -the Kspace style. If {flag_buck} is set to {cut}, the Buckingham -interactions are simply cutoff, as with "pair_style -buck"_pair_buck.html. - -If {flag_coul} is set to {long}, no cutoff is used on the Coulombic -interactions. The long-range portion can calculated by using any of -several "kspace_style"_kspace_style.html command options such as -{pppm} or {ewald}. Note that if {flag_buck} is also set to long, then -the {ewald/disp} or {pppm/disp} Kspace style needs to be used to -perform the long-range calculations for both the Buckingham and -Coulombic interactions. If {flag_coul} is set to {off}, Coulombic -interactions are not computed. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -A (energy units) -rho (distance units) -C (energy-distance^6 units) -cutoff (distance units) -cutoff2 (distance units) :ul - -The second coefficient, rho, must be greater than zero. - -The latter 2 coefficients are optional. If not specified, the global -Buckingham and Coulombic cutoffs specified in the pair_style command -are used. If only one cutoff is specified, it is used as the cutoff -for both Buckingham and Coulombic interactions for this type pair. If -both coefficients are specified, they are used as the Buckingham and -Coulombic cutoffs for this type pair. Note that if you are using -{flag_buck} set to {long}, you cannot specify a Buckingham cutoff for -an atom type pair, since only one global Buckingham cutoff is allowed. -Similarly, if you are using {flag_coul} set to {long}, you cannot -specify a Coulombic cutoff for an atom type pair, since only one -global Coulombic cutoff is allowed. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair styles does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -This pair style supports the "pair_modify"_pair_modify.html shift -option for the energy of the exp() and 1/r^6 portion of the pair -interaction, assuming {flag_buck} is {cut}. - -This pair style does not support the "pair_modify"_pair_modify.html -shift option for the energy of the Buckingham portion of the pair -interaction. - -This pair style supports the "pair_modify"_pair_modify.html table and -table/disp options since they can tabulate the short-range portion of -the long-range Coulombic and dispersion interactions. - -This pair style write its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style supports the use of the {inner}, {middle}, and {outer} -keywords of the "run_style respa"_run_style.html command, meaning the -pairwise forces can be partitioned by distance at different levels of -the rRESPA hierarchy. See the "run_style"_run_style.html command for -details. - -:line - -[Restrictions:] - -This style is part of the KSPACE package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Ismail) -[(Ismail)] Ismail, Tsige, In 't Veld, Grest, Molecular Physics -(accepted) (2007). diff --git a/doc/txt/pair_charmm.txt b/doc/txt/pair_charmm.txt deleted file mode 100644 index f5344b752f..0000000000 --- a/doc/txt/pair_charmm.txt +++ /dev/null @@ -1,271 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj/charmm/coul/charmm command :h3 -pair_style lj/charmm/coul/charmm/intel command :h3 -pair_style lj/charmm/coul/charmm/kk command :h3 -pair_style lj/charmm/coul/charmm/omp command :h3 -pair_style lj/charmm/coul/charmm/implicit command :h3 -pair_style lj/charmm/coul/charmm/implicit/kk command :h3 -pair_style lj/charmm/coul/charmm/implicit/omp command :h3 -pair_style lj/charmm/coul/long command :h3 -pair_style lj/charmm/coul/long/gpu command :h3 -pair_style lj/charmm/coul/long/intel command :h3 -pair_style lj/charmm/coul/long/kk command :h3 -pair_style lj/charmm/coul/long/opt command :h3 -pair_style lj/charmm/coul/long/omp command :h3 -pair_style lj/charmm/coul/msm command :h3 -pair_style lj/charmm/coul/msm/omp command :h3 -pair_style lj/charmmfsw/coul/charmmfsh command :h3 -pair_style lj/charmmfsw/coul/long command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/msm} or {lj/charmmfsw/coul/charmmfsh} or {lj/charmmfsw/coul/long} -args = list of arguments for a particular style :ul - {lj/charmm/coul/charmm} args = inner outer (inner2) (outer2) - inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args) - inner2, outer2 = global switching cutoffs for Coulombic (optional) - {lj/charmm/coul/charmm/implicit} args = inner outer (inner2) (outer2) - inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args) - inner2, outer2 = global switching cutoffs for Coulombic (optional) - {lj/charmm/coul/long} args = inner outer (cutoff) - inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args) - cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) - {lj/charmm/coul/msm} args = inner outer (cutoff) - inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args) - cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) - {lj/charmmfsw/coul/charmmfsh} args = inner outer (cutoff) - inner, outer = global cutoffs for LJ (and Coulombic if only 2 args) - cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) - {lj/charmmfsw/coul/long} args = inner outer (cutoff) - inner, outer = global cutoffs for LJ (and Coulombic if only 2 args) - cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) :pre - -[Examples:] - -pair_style lj/charmm/coul/charmm 8.0 10.0 -pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0 -pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0 -pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0 9.0 -pair_coeff * * 100.0 2.0 -pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre - -pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 -pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0 -pair_coeff * * 100.0 2.0 -pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre - -pair_style lj/charmm/coul/long 8.0 10.0 -pair_style lj/charmm/coul/long 8.0 10.0 9.0 -pair_style lj/charmmfsw/coul/long 8.0 10.0 -pair_style lj/charmmfsw/coul/long 8.0 10.0 9.0 -pair_coeff * * 100.0 2.0 -pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre - -pair_style lj/charmm/coul/msm 8.0 10.0 -pair_style lj/charmm/coul/msm 8.0 10.0 9.0 -pair_coeff * * 100.0 2.0 -pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre - -[Description:] - -These pair styles compute Lennard Jones (LJ) and Coulombic -interactions with additional switching or shifting functions that ramp -the energy and/or force smoothly to zero between an inner and outer -cutoff. They are implementations of the widely used CHARMM force -field used in the "CHARMM"_http://www.scripps.edu/brooks MD code (and -others). See "(MacKerell)"_#pair-MacKerell for a description of the -CHARMM force field. - -The styles with {charmm} (not {charmmfsw} or {charmmfsh}) in their -name are the older, original LAMMPS implementations. They compute the -LJ and Coulombic interactions with an energy switching function (esw, -shown in the formula below as S(r)), which ramps the energy smoothly -to zero between the inner and outer cutoff. This can cause -irregularities in pair-wise forces (due to the discontinuous 2nd -derivative of energy at the boundaries of the switching region), which -in some cases can result in detectable artifacts in an MD simulation. - -The newer styles with {charmmfsw} or {charmmfsh} in their name replace -the energy switching with force switching (fsw) and force shifting -(fsh) functions, for LJ and Coulombic interactions respectively. -These follow the formulas and description given in -"(Steinbach)"_#Steinbach and "(Brooks)"_#Brooks1 to minimize these -artifacts. - -NOTE: The newer {charmmfsw} or {charmmfsh} styles were released in -March 2017. We recommend they be used instead of the older {charmm} -styles. This includes the newer "dihedral_style -charmmfsw"_dihedral_charmm.html command. Eventually code from the new -styles will propagate into the related pair styles (e.g. implicit, -accelerator, free energy variants). - -NOTE: The newest CHARMM pair styles reset the Coulombic energy -conversion factor used internally in the code, from the LAMMPS value -to the CHARMM value, as if it were effectively a parameter of the -force field. This is because the CHARMM code uses a slightly -different value for the this conversion factor in "real -units"_units.html (Kcal/mole), namely CHARMM = 332.0716, LAMMPS = -332.06371. This is to enable more precise agreement by LAMMPS with -the CHARMM force field energies and forces, when using one of these -two CHARMM pair styles. - -:c,image(Eqs/pair_charmm.jpg) - -where S(r) is the energy switching function mentioned above for the -{charmm} styles. See the "(Steinbach)"_#Steinbach paper for the -functional forms of the force switching and force shifting functions -used in the {charmmfsw} and {charmmfsh} styles. - -When using the {lj/charmm/coul/charmm styles}, both the LJ and -Coulombic terms require an inner and outer cutoff. They can be the -same for both formulas or different depending on whether 2 or 4 -arguments are used in the pair_style command. For the -{lj/charmmfsw/coul/charmmfsh} style, the LJ term requires both an -inner and outer cutoff, while the Coulombic term requires only one -cutoff. If the Coulombic cutoff is not specified (2 instead of 3 -arguments), the LJ outer cutoff is used for the Coulombic cutoff. In -all cases where an inner and outer cutoff are specified, the inner -cutoff distance must be less than the outer cutoff. It is typical to -make the difference between the inner and outer cutoffs about 2.0 -Angstroms. - -Style {lj/charmm/coul/charmm/implicit} computes the same formulas as -style {lj/charmm/coul/charmm} except that an additional 1/r term is -included in the Coulombic formula. The Coulombic energy thus varies -as 1/r^2. This is effectively a distance-dependent dielectric term -which is a simple model for an implicit solvent with additional -screening. It is designed for use in a simulation of an unsolvated -biomolecule (no explicit water molecules). - -Styles {lj/charmm/coul/long} and {lj/charmm/coul/msm} compute the same -formulas as style {lj/charmm/coul/charmm} and style -{lj/charmmfsw/coul/long} computes the same formulas as style -{lj/charmmfsw/coul/charmmfsh}, except that an additional damping -factor is applied to the Coulombic term, so it can be used in -conjunction with the "kspace_style"_kspace_style.html command and its -{ewald} or {pppm} or {msm} option. Only one Coulombic cutoff is -specified for these styles; if only 2 arguments are used in the -pair_style command, then the outer LJ cutoff is used as the single -Coulombic cutoff. The Coulombic cutoff specified for these styles -means that pairwise interactions within this distance are computed -directly; interactions outside that distance are computed in -reciprocal space. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) -epsilon_14 (energy units) -sigma_14 (distance units) :ul - -Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum at 2^(1/6) -sigma. - -The latter 2 coefficients are optional. If they are specified, they -are used in the LJ formula between 2 atoms of these types which are -also first and fourth atoms in any dihedral. No cutoffs are specified -because the CHARMM force field does not allow varying cutoffs for -individual atom pairs; all pairs use the global cutoff(s) specified in -the pair_style command. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14, -and sigma_14 coefficients for all of the lj/charmm pair styles can be -mixed. The default mix value is {arithmetic} to coincide with the -usual settings for the CHARMM force field. See the "pair_modify" -command for details. - -None of the {lj/charmm} or {lj/charmmfsw} pair styles support the -"pair_modify"_pair_modify.html shift option, since the Lennard-Jones -portion of the pair interaction is smoothed to 0.0 at the cutoff. - -The {lj/charmm/coul/long} and {lj/charmmfsw/coul/long} styles support -the "pair_modify"_pair_modify.html table option since they can -tabulate the short-range portion of the long-range Coulombic -interaction. - -None of the {lj/charmm} or {lj/charmmfsw} pair styles support the -"pair_modify"_pair_modify.html tail option for adding long-range tail -corrections to energy and pressure, since the Lennard-Jones portion of -the pair interaction is smoothed to 0.0 at the cutoff. - -All of the {lj/charmm} and {lj/charmmfsw} pair styles write their -information to "binary restart files"_restart.html, so pair_style and -pair_coeff commands do not need to be specified in an input script -that reads a restart file. - -The {lj/charmm/coul/long} and {lj/charmmfsw/coul/long} pair styles -support the use of the {inner}, {middle}, and {outer} keywords of the -"run_style respa"_run_style.html command, meaning the pairwise forces -can be partitioned by distance at different levels of the rRESPA -hierarchy. The other styles only support the {pair} keyword of -run_style respa. See the "run_style"_run_style.html command for -details. - -:line - -[Restrictions:] - -All the styles with {coul/charmm} or {coul/charmmfsh} styles are part -of the MOLECULE package. All the styles with {coul/long} style are -part of the KSPACE package. They are only enabled if LAMMPS was built -with those packages. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Brooks1) -[(Brooks)] Brooks, et al, J Comput Chem, 30, 1545 (2009). - -:link(pair-MacKerell) -[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). - -:link(Steinbach) -[(Steinbach)] Steinbach, Brooks, J Comput Chem, 15, 667 (1994). - diff --git a/doc/txt/pair_class2.txt b/doc/txt/pair_class2.txt deleted file mode 100644 index 9e25560071..0000000000 --- a/doc/txt/pair_class2.txt +++ /dev/null @@ -1,180 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj/class2 command :h3 -pair_style lj/class2/gpu command :h3 -pair_style lj/class2/kk command :h3 -pair_style lj/class2/omp command :h3 -pair_style lj/class2/coul/cut command :h3 -pair_style lj/class2/coul/cut/kk command :h3 -pair_style lj/class2/coul/cut/omp command :h3 -pair_style lj/class2/coul/long command :h3 -pair_style lj/class2/coul/long/gpu command :h3 -pair_style lj/class2/coul/long/kk command :h3 -pair_style lj/class2/coul/long/omp command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {lj/class2} or {lj/class2/coul/cut} or {lj/class2/coul/long} -args = list of arguments for a particular style :ul - {lj/class2} args = cutoff - cutoff = global cutoff for class 2 interactions (distance units) - {lj/class2/coul/cut} args = cutoff (cutoff2) - cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {lj/class2/coul/long} args = cutoff (cutoff2) - cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre - -[Examples:] - -pair_style lj/class2 10.0 -pair_coeff * * 100.0 2.5 -pair_coeff 1 2* 100.0 2.5 9.0 :pre - -pair_style lj/class2/coul/cut 10.0 -pair_style lj/class2/coul/cut 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 -pair_coeff 1 1 100.0 3.5 9.0 9.0 :pre - -pair_style lj/class2/coul/long 10.0 -pair_style lj/class2/coul/long 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 :pre - -[Description:] - -The {lj/class2} styles compute a 6/9 Lennard-Jones potential given by - -:c,image(Eqs/pair_class2.jpg) - -Rc is the cutoff. - -The {lj/class2/coul/cut} and {lj/class2/coul/long} styles add a -Coulombic term as described for the "lj/cut"_pair_lj.html pair styles. - -See "(Sun)"_#pair-Sun for a description of the COMPASS class2 force field. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) -cutoff1 (distance units) -cutoff2 (distance units) :ul - -The latter 2 coefficients are optional. If not specified, the global -class 2 and Coulombic cutoffs are used. If only one cutoff is -specified, it is used as the cutoff for both class 2 and Coulombic -interactions for this type pair. If both coefficients are specified, -they are used as the class 2 and Coulombic cutoffs for this type pair. -You cannot specify 2 cutoffs for style {lj/class2}, since it has no -Coulombic terms. - -For {lj/class2/coul/long} only the class 2 cutoff can be specified -since a Coulombic cutoff cannot be specified for an individual I,J -type pair. All type pairs use the same global Coulombic cutoff -specified in the pair_style command. - -:line - -If the pair_coeff command is not used to define coefficients for a -particular I != J type pair, the mixing rule for epsilon and sigma for -all class2 potentials is to use the {sixthpower} formulas documented -by the "pair_modify"_pair_modify.html command. The "pair_modify -mix"_pair_modify.html setting is thus ignored for class2 potentials -for epsilon and sigma. However it is still followed for mixing the -cutoff distance. - -:line - -A version of these styles with a soft core, {lj/cut/soft}, suitable for use in -free energy calculations, is part of the USER-FEP package and is documented with -the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is -only available if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/class2 pair styles can be mixed. -Epsilon and sigma are always mixed with the value {sixthpower}. The -cutoff distance is mixed by whatever option is set by the pair_modify -command (default = geometric). See the "pair_modify" command for -details. - -All of the lj/class2 pair styles support the -"pair_modify"_pair_modify.html shift option for the energy of the -Lennard-Jones portion of the pair interaction. - -The {lj/class2/coul/long} pair style does not support the -"pair_modify"_pair_modify.html table option since a tabulation -capability has not yet been added to this potential. - -All of the lj/class2 pair styles support the -"pair_modify"_pair_modify.html tail option for adding a long-range -tail correction to the energy and pressure of the Lennard-Jones -portion of the pair interaction. - -All of the lj/class2 pair styles write their information to "binary -restart files"_restart.html, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. - -Only the {lj/class2} and {lj/class2/coul/long} pair styles support the use of the -{inner}, {middle}, and {outer} keywords of the "run_style -respa"_run_style.html command, meaning the pairwise forces can be -partitioned by distance at different levels of the rRESPA hierarchy. -The other styles only support the {pair} keyword of run_style respa. -See the "run_style"_run_style.html command for details. - -[Restrictions:] - -These styles are part of the CLASS2 package. They are only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_fep_soft"_pair_fep_soft.html - -[Default:] none - -:line - -:link(pair-Sun) -[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998). diff --git a/doc/txt/pair_coeff.txt b/doc/txt/pair_coeff.txt deleted file mode 100644 index a1bbf94e83..0000000000 --- a/doc/txt/pair_coeff.txt +++ /dev/null @@ -1,134 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_coeff command :h3 - -[Syntax:] - -pair_coeff I J args :pre - -I,J = atom types (see asterisk form below) -args = coefficients for one or more pairs of atom types :ul - -[Examples:] - -pair_coeff 1 2 1.0 1.0 2.5 -pair_coeff 2 * 1.0 1.0 -pair_coeff 3* 1*2 1.0 1.0 2.5 -pair_coeff * * 1.0 1.0 -pair_coeff * * nialhjea 1 1 2 -pair_coeff * 3 morse.table ENTRY1 -pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid) :pre - -[Description:] - -Specify the pairwise force field coefficients for one or more pairs of -atom types. The number and meaning of the coefficients depends on the -pair style. Pair coefficients can also be set in the data file read -by the "read_data"_read_data.html command or in a restart file. - -I and J can be specified in one of two ways. Explicit numeric values -can be used for each, as in the 1st example above. I <= J is -required. LAMMPS sets the coefficients for the symmetric J,I -interaction to the same values. - -A wildcard asterisk can be used in place of or in conjunction with the -I,J arguments to set the coefficients for multiple pairs of atom -types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the -number of atom types, then an asterisk with no numeric values means all -types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). Note that only type pairs with I <= J are considered; if -asterisks imply type pairs where J < I, they are ignored. - -Note that a pair_coeff command can override a previous setting for the -same I,J pair. For example, these commands set the coeffs for all I,J -pairs, then overwrite the coeffs for just the I,J = 2,3 pair: - -pair_coeff * * 1.0 1.0 2.5 -pair_coeff 2 3 2.0 1.0 1.12 :pre - -A line in a data file that specifies pair coefficients uses the exact -same format as the arguments of the pair_coeff command in an input -script, with the exception of the I,J type arguments. In each line of -the "Pair Coeffs" section of a data file, only a single type I is -specified, which sets the coefficients for type I interacting with -type I. This is because the section has exactly N lines, where N = -the number of atom types. For this reason, the wild-card asterisk -should also not be used as part of the I argument. Thus in a data -file, the line corresponding to the 1st example above would be listed -as - -2 1.0 1.0 2.5 :pre - -For many potentials, if coefficients for type pairs with I != J are -not set explicitly by a pair_coeff command, the values are inferred -from the I,I and J,J settings by mixing rules; see the -"pair_modify"_pair_modify.html command for a discussion. Details on -this option as it pertains to individual potentials are described on -the doc page for the potential. - -Many pair styles, typically for many-body potentials, use tabulated -potential files as input, when specifying the pair_coeff command. -Potential files provided with LAMMPS are in the potentials directory -of the distribution. For some potentials, such as EAM, other archives -of suitable files can be found on the Web. They can be used with -LAMMPS so long as they are in the format LAMMPS expects, as discussed -on the individual doc pages. - -When a pair_coeff command using a potential file is specified, LAMMPS -looks for the potential file in 2 places. First it looks in the -location specified. E.g. if the file is specified as "niu3.eam", it -is looked for in the current working directory. If it is specified as -"../potentials/niu3.eam", then it is looked for in the potentials -directory, assuming it is a sister directory of the current working -directory. If the file is not found, it is then looked for in the -directory specified by the LAMMPS_POTENTIALS environment variable. -Thus if this is set to the potentials directory in the LAMMPS distribution, -then you can use those files from anywhere on your system, without -copying them into your working directory. Environment variables are -set in different ways for different shells. Here are example settings -for - -csh, tcsh: - -% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials :pre - -bash: - -% export LAMMPS_POTENTIALS=/path/to/lammps/potentials :pre - -Windows: - -% set LAMMPS_POTENTIALS="C:\\Path to LAMMPS\\Potentials" :pre - -:line - -The alphabetic list of pair styles defined in LAMMPS is given on the -"pair_style"_pair_style.html doc page. They are also listed in more -compact form on the "Commands pair"_Commands_pair.html doc page. - -Click on the style to display the formula it computes and its -coefficients as specified by the associated pair_coeff command. - -:line - -[Restrictions:] - -This command must come after the simulation box is defined by a -"read_data"_read_data.html, "read_restart"_read_restart.html, or -"create_box"_create_box.html command. - -[Related commands:] - -"pair_style"_pair_style.html, "pair_modify"_pair_modify.html, -"read_data"_read_data.html, "read_restart"_read_restart.html, -"pair_write"_pair_write.html - -[Default:] none diff --git a/doc/txt/pair_colloid.txt b/doc/txt/pair_colloid.txt deleted file mode 100644 index e8a44e1cba..0000000000 --- a/doc/txt/pair_colloid.txt +++ /dev/null @@ -1,204 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style colloid command :h3 -pair_style colloid/gpu command :h3 -pair_style colloid/omp command :h3 - -[Syntax:] - -pair_style colloid cutoff :pre - -cutoff = global cutoff for colloidal interactions (distance units) :ul - -[Examples:] - -pair_style colloid 10.0 -pair_coeff * * 25 1.0 10.0 10.0 -pair_coeff 1 1 144 1.0 0.0 0.0 3.0 -pair_coeff 1 2 75.398 1.0 0.0 10.0 9.0 -pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0 :pre - -[Description:] - -Style {colloid} computes pairwise interactions between large colloidal -particles and small solvent particles using 3 formulas. A colloidal -particle has a size > sigma; a solvent particle is the usual -Lennard-Jones particle of size sigma. - -The colloid-colloid interaction energy is given by - -:c,image(Eqs/pair_colloid_cc.jpg) - -where A_cc is the Hamaker constant, a1 and a2 are the radii of the two -colloidal particles, and Rc is the cutoff. This equation results from -describing each colloidal particle as an integrated collection of -Lennard-Jones particles of size sigma and is derived in -"(Everaers)"_#Everaers1. - -The colloid-solvent interaction energy is given by - -:c,image(Eqs/pair_colloid_cs.jpg) - -where A_cs is the Hamaker constant, a is the radius of the colloidal -particle, and Rc is the cutoff. This formula is derived from the -colloid-colloid interaction, letting one of the particle sizes go to -zero. - -The solvent-solvent interaction energy is given by the usual -Lennard-Jones formula - -:c,image(Eqs/pair_colloid_ss.jpg) - -with A_ss set appropriately, which results from letting both particle -sizes go to zero. - -When used in combination with "pair_style -yukawa/colloid"_pair_colloid.html, the two terms become the so-called -DLVO potential, which combines electrostatic repulsion and van der -Waals attraction. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -A (energy units) -sigma (distance units) -d1 (distance units) -d2 (distance units) -cutoff (distance units) :ul - -A is the Hamaker energy prefactor and should typically be set as -follows: - -A_cc = colloid/colloid = 4 pi^2 = 39.5 -A_cs = colloid/solvent = sqrt(A_cc*A_ss) -A_ss = solvent/solvent = 144 (assuming epsilon = 1, so that 144/36 = 4) :ul - -Sigma is the size of the solvent particle or the constituent particles -integrated over in the colloidal particle and should typically be set -as follows: - -Sigma_cc = colloid/colloid = 1.0 -Sigma_cs = colloid/solvent = arithmetic mixing between colloid sigma and solvent sigma -Sigma_ss = solvent/solvent = 1.0 or whatever size the solvent particle is :ul - -Thus typically Sigma_cs = 1.0, unless the solvent particle's size != -1.0. - -D1 and d2 are particle diameters, so that d1 = 2*a1 and d2 = 2*a2 in -the formulas above. Both d1 and d2 must be values >= 0. If d1 > 0 -and d2 > 0, then the pair interacts via the colloid-colloid formula -above. If d1 = 0 and d2 = 0, then the pair interacts via the -solvent-solvent formula. I.e. a d value of 0 is a Lennard-Jones -particle of size sigma. If either d1 = 0 or d2 = 0 and the other is -larger, then the pair interacts via the colloid-solvent formula. - -Note that the diameter of a particular particle type may appear in -multiple pair_coeff commands, as it interacts with other particle -types. You should insure the particle diameter is specified -consistently each time it appears. - -The last coefficient is optional. If not specified, the global cutoff -specified in the pair_style command is used. However, you typically -want different cutoffs for interactions between different particle -sizes. E.g. if colloidal particles of diameter 10 are used with -solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5 -would correspond to a colloid-colloid cutoff of 25. A good -rule-of-thumb is to use a colloid-solvent cutoff that is half the big -diameter + 4 times the small diameter. I.e. 9 = 5 + 4 for the -colloid-solvent cutoff in this case. - -NOTE: When using pair_style colloid for a mixture with 2 (or more) -widely different particles sizes (e.g. sigma=10 colloids in a -background sigma=1 LJ fluid), you will likely want to use these -commands for efficiency: "neighbor multi"_neighbor.html and -"comm_modify multi"_comm_modify.html. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the A, sigma, d1, and d2 -coefficients and cutoff distance for this pair style can be mixed. A -is an energy value mixed like a LJ epsilon. D1 and d2 are distance -values and are mixed like sigma. The default mix value is -{geometric}. See the "pair_modify" command for details. - -This pair style supports the "pair_modify"_pair_modify.html shift -option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This style is part of the COLLOID package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Normally, this pair style should be used with finite-size particles -which have a diameter, e.g. see the "atom_style -sphere"_atom_style.html command. However, this is not a requirement, -since the only definition of particle size is via the pair_coeff -parameters for each type. In other words, the physical radius of the -particle is ignored. Thus you should insure that the d1,d2 parameters -you specify are consistent with the physical size of the particles of -that type. - -Per-particle polydispersity is not yet supported by this pair style; -only per-type polydispersity is enabled via the pair_coeff parameters. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Everaers1) -[(Everaers)] Everaers, Ejtehadi, Phys Rev E, 67, 041710 (2003). diff --git a/doc/txt/pair_comb.txt b/doc/txt/pair_comb.txt deleted file mode 100644 index 45ce3a3b76..0000000000 --- a/doc/txt/pair_comb.txt +++ /dev/null @@ -1,191 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style comb command :h3 -pair_style comb/omp command :h3 -pair_style comb3 command :h3 - -[Syntax:] - -pair_style comb -pair_style comb3 keyword :pre - -keyword = {polar} - {polar} value = {polar_on} or {polar_off} = whether or not to include atomic polarization :pre -:ule - -[Examples:] - -pair_style comb -pair_coeff * * ../potentials/ffield.comb Si -pair_coeff * * ../potentials/ffield.comb Hf Si O :pre -pair_style comb3 polar_off -pair_coeff * * ../potentials/ffield.comb3 O Cu N C O :pre - -[Description:] - -Style {comb} computes the second-generation variable charge COMB -(Charge-Optimized Many-Body) potential. Style {comb3} computes the -third-generation COMB potential. These COMB potentials are described -in "(COMB)"_#COMB and "(COMB3)"_#COMB3. Briefly, the total energy -{ET} of a system of atoms is given by - -:c,image(Eqs/pair_comb1.jpg) - -where {Eiself} is the self-energy of atom {i} -(including atomic ionization energies and electron affinities), -{Eijshort} is the bond-order potential between -atoms {i} and {j}, -{EijCoul} is the Coulomb interactions, -{Epolar} is the polarization term for organic systems -(style {comb3} only), -{EvdW} is the van der Waals energy (style {comb3} only), -{Ebarr} is a charge barrier function, and -{Ecorr} are angular correction terms. - -The COMB potentials (styles {comb} and {comb3}) are variable charge -potentials. The equilibrium charge on each atom is calculated by the -electronegativity equalization (QEq) method. See "Rick"_#Rick2 for -further details. This is implemented by the "fix -qeq/comb"_fix_qeq_comb.html command, which should normally be -specified in the input script when running a model with the COMB -potential. The "fix qeq/comb"_fix_qeq_comb.html command has options -that determine how often charge equilibration is performed, its -convergence criterion, and which atoms are included in the -calculation. - -Only a single pair_coeff command is used with the {comb} and {comb3} -styles which specifies the COMB potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the potential file in the pair_coeff -command, where N is the number of LAMMPS atom types. - -For example, if your LAMMPS simulation of a Si/SiO2/ -HfO2 interface has 4 atom types, and you want the 1st and -last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would -use the following pair_coeff command: - -pair_coeff * * ../potentials/ffield.comb Si Hf O Si :pre - -The first two arguments must be * * so as to span all LAMMPS atom -types. The first and last Si arguments map LAMMPS atom types 1 and 4 -to the Si element in the {ffield.comb} file. The second Hf argument -maps LAMMPS atom type 2 to the Hf element, and the third O argument -maps LAMMPS atom type 3 to the O element in the potential file. If a -mapping value is specified as NULL, the mapping is not performed. -This can be used when a {comb} potential is used as part of the -{hybrid} pair style. The NULL values are placeholders for atom types -that will be used with other potentials. - -For style {comb}, the provided potential file {ffield.comb} contains -all currently-available 2nd generation COMB parameterizations: for Si, -Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style -{comb3}, the potential file {ffield.comb3} contains all -currently-available 3rd generation COMB parameterizations: O, Cu, N, C, -H, Ti, Zn and Zr. The status of the optimization of the compounds, for -example Cu2O, TiN and hydrocarbons, are given in the -following table: - -:c,image(Eqs/pair_comb2.jpg) - -For style {comb3}, in addition to ffield.comb3, a special parameter -file, {lib.comb3}, that is exclusively used for C/O/H systems, will be -automatically loaded if carbon atom is detected in LAMMPS input -structure. This file must be in your working directory or in the -directory pointed to by the environment variable LAMMPS_POTENTIALS, as -described on the "pair_coeff"_pair_coeff.html command doc page. - -Keyword {polar} indicates whether the force field includes -the atomic polarization. Since the equilibration of the polarization -has not yet been implemented, it can only set polar_off at present. - -NOTE: You can not use potential file {ffield.comb} with style {comb3}, -nor file {ffield.comb3} with style {comb}. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above from values in the potential file. - -These pair styles does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -These pair styles do not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style, pair_coeff, and "fix -qeq/comb"_fix_qeq_comb.html commands in an input script that reads a -restart file. - -These pair styles can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -These pair styles are part of the MANYBODY package. It is only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -These pair styles requires the "newton"_newton.html setting to be "on" -for pair interactions. - -The COMB potentials in the {ffield.comb} and {ffield.comb3} files provided -with LAMMPS (see the potentials directory) are parameterized for metal -"units"_units.html. You can use the COMB potential with any LAMMPS -units, but you would need to create your own COMB potential file with -coefficients listed in the appropriate units if your simulation -doesn't use "metal" units. - -[Related commands:] - -"pair_style"_pair_style.html, "pair_coeff"_pair_coeff.html, -"fix qeq/comb"_fix_qeq_comb.html - -[Default:] none - -:line - -:link(COMB) -[(COMB)] T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and -S. R. Phillpot, Phys. Rev. B 81, 125328 (2010) - -:link(COMB3) -[(COMB3)] T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek, -Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74, -255-279 (2013). - -:link(Rick2) -[(Rick)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 -(1994). diff --git a/doc/txt/pair_cosine_squared.txt b/doc/txt/pair_cosine_squared.txt deleted file mode 100644 index f60e33f70d..0000000000 --- a/doc/txt/pair_cosine_squared.txt +++ /dev/null @@ -1,108 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style cosine/squared command :h3 - -[Syntax:] - -pair_style cosine/squared cutoff :pre - -cutoff = global cutoff for cosine-squared interactions (distance units) :ul - -pair_coeff i j eps sigma -pair_coeff i j eps sigma cutoff -pair_coeff i j eps sigma wca -pair_coeff i j eps sigma cutoff wca :pre - -i,j = a particle type -eps = interaction strength, i.e. the depth of the potential minimum (energy units) -sigma = distance of the potential minimum from 0 -cutoff = the cutoff distance for this pair type, if different from global (distance units) -wca = if specified a Weeks-Chandler-Andersen potential (with eps strength and minimum at sigma) is added, otherwise not :ul - -[Examples:] - -pair_style cosine/squared 3.0 -pair_coeff * * 1.0 1.3 -pair_coeff 1 3 1.0 1.3 2.0 -pair_coeff 1 3 1.0 1.3 wca -pair_coeff 1 3 1.0 1.3 2.0 wca :pre - -[Description:] - -Style {cosine/squared} computes a potential of the form - -:c,image(Eqs/pair_cosine_squared.jpg) - -between two point particles, where (sigma, -epsilon) is the location of -the (rightmost) minimum of the potential, as explained in the syntax -section above. - -This potential was first used in (Cooke)_#CKD for a coarse-grained lipid -membrane model. It is generally very useful as a non-specific -interaction potential because it is fully adjustable in depth and width -while joining the minimum at (sigma, -epsilon) and zero at (cutoff, 0) -smoothly, requiring no shifting and causing no related artifacts, tail -energy calculations etc. This evidently requires {cutoff} to be larger -than {sigma}. - -If the {wca} option is used then a Weeks-Chandler-Andersen potential -(Weeks)_#WCA is added to the above specified cosine-squared potential, -specifically the following: - -:c,image(Eqs/pair_cosine_squared_wca.jpg) - -In this case, and this case only, the {sigma} parameter can be equal to -{cutoff} (sigma = cutoff) which will result in ONLY the WCA potential -being used (and print a warning), so the minimum will be attained at -(sigma, 0). This is a convenience feature that enables a purely -repulsive potential to be used without a need to define an additional -pair style and use the hybrid styles. - -The energy and force of this pair style for parameters epsilon = 1.0, -sigma = 1.0, cutoff = 2.5, with and without the WCA potential, are shown -in the graphs below: - -:c,image(JPG/pair_cosine_squared_graphs.jpg) - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -Mixing is not supported for this style. - -The {shift}, {table} and {tail} options are not relevant for this style. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -These pair styles can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. They do not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -The {cosine/squared} style is part of the "USER-MISC" package. It is only -enabled if LAMMPS is build with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, -"pair_style lj/cut"_pair_lj.html - -[Default:] none - -:link(CKD) -[(Cooke)] "Cooke, Kremer and Deserno, Phys. Rev. E, 72, 011506 (2005)" - -:link(WCA) -[(Weeks)] "Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)" diff --git a/doc/txt/pair_coul.txt b/doc/txt/pair_coul.txt deleted file mode 100644 index 06838a97e6..0000000000 --- a/doc/txt/pair_coul.txt +++ /dev/null @@ -1,334 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style coul/cut command :h3 -pair_style coul/cut/gpu command :h3 -pair_style coul/cut/kk command :h3 -pair_style coul/cut/omp command :h3 -pair_style coul/debye command :h3 -pair_style coul/debye/gpu command :h3 -pair_style coul/debye/kk command :h3 -pair_style coul/debye/omp command :h3 -pair_style coul/dsf command :h3 -pair_style coul/dsf/gpu command :h3 -pair_style coul/dsf/kk command :h3 -pair_style coul/dsf/omp command :h3 -pair_style coul/long command :h3 -pair_style coul/long/omp command :h3 -pair_style coul/long/gpu command :h3 -pair_style coul/long/kk command :h3 -pair_style coul/msm command :h3 -pair_style coul/msm/omp command :h3 -pair_style coul/streitz command :h3 -pair_style coul/wolf command :h3 -pair_style coul/wolf/kk command :h3 -pair_style coul/wolf/omp command :h3 -pair_style tip4p/cut command :h3 -pair_style tip4p/long command :h3 -pair_style tip4p/cut/omp command :h3 -pair_style tip4p/long/omp command :h3 - -[Syntax:] - -pair_style coul/cut cutoff -pair_style coul/debye kappa cutoff -pair_style coul/dsf alpha cutoff -pair_style coul/long cutoff -pair_style coul/long/gpu cutoff -pair_style coul/wolf alpha cutoff -pair_style coul/streitz cutoff keyword alpha -pair_style tip4p/cut otype htype btype atype qdist cutoff -pair_style tip4p/long otype htype btype atype qdist cutoff :pre - -cutoff = global cutoff for Coulombic interactions -kappa = Debye length (inverse distance units) -alpha = damping parameter (inverse distance units) :ul - -[Examples:] - -pair_style coul/cut 2.5 -pair_coeff * * -pair_coeff 2 2 3.5 :pre - -pair_style coul/debye 1.4 3.0 -pair_coeff * * -pair_coeff 2 2 3.5 :pre - -pair_style coul/dsf 0.05 10.0 -pair_coeff * * :pre - -pair_style coul/long 10.0 -pair_coeff * * :pre - -pair_style coul/msm 10.0 -pair_coeff * * :pre - -pair_style coul/wolf 0.2 9.0 -pair_coeff * * :pre - -pair_style coul/streitz 12.0 ewald -pair_style coul/streitz 12.0 wolf 0.30 -pair_coeff * * AlO.streitz Al O :pre - -pair_style tip4p/cut 1 2 7 8 0.15 12.0 -pair_coeff * * :pre - -pair_style tip4p/long 1 2 7 8 0.15 10.0 -pair_coeff * * :pre - -[Description:] - -The {coul/cut} style computes the standard Coulombic interaction -potential given by - -:c,image(Eqs/pair_coulomb.jpg) - -where C is an energy-conversion constant, Qi and Qj are the charges on -the 2 atoms, and epsilon is the dielectric constant which can be set -by the "dielectric"_dielectric.html command. The cutoff Rc truncates -the interaction distance. - -:line - -Style {coul/debye} adds an additional exp() damping factor to the -Coulombic term, given by - -:c,image(Eqs/pair_debye.jpg) - -where kappa is the Debye length. This potential is another way to -mimic the screening effect of a polar solvent. - -:line - -Style {coul/dsf} computes Coulombic interactions via the damped -shifted force model described in "Fennell"_#Fennell1, given by: - -:c,image(Eqs/pair_coul_dsf.jpg) - -where {alpha} is the damping parameter and erfc() is the -complementary error-function. The potential corrects issues in the -Wolf model (described below) to provide consistent forces and energies -(the Wolf potential is not differentiable at the cutoff) and smooth -decay to zero. - -:line - -Style {coul/wolf} computes Coulombic interactions via the Wolf -summation method, described in "Wolf"_#Wolf1, given by: - -:c,image(Eqs/pair_coul_wolf.jpg) - -where {alpha} is the damping parameter, and erc() and erfc() are -error-function and complementary error-function terms. This potential -is essentially a short-range, spherically-truncated, -charge-neutralized, shifted, pairwise {1/r} summation. With a -manipulation of adding and subtracting a self term (for i = j) to the -first and second term on the right-hand-side, respectively, and a -small enough {alpha} damping parameter, the second term shrinks and -the potential becomes a rapidly-converging real-space summation. With -a long enough cutoff and small enough alpha parameter, the energy and -forces calculated by the Wolf summation method approach those of the -Ewald sum. So it is a means of getting effective long-range -interactions with a short-range potential. - -:line - -Style {coul/streitz} is the Coulomb pair interaction defined as part -of the Streitz-Mintmire potential, as described in "this -paper"_#Streitz2, in which charge distribution about an atom is modeled -as a Slater 1{s} orbital. More details can be found in the referenced -paper. To fully reproduce the published Streitz-Mintmire potential, -which is a variable charge potential, style {coul/streitz} must be -used with "pair_style eam/alloy"_pair_eam.html (or some other -short-range potential that has been parameterized appropriately) via -the "pair_style hybrid/overlay"_pair_hybrid.html command. Likewise, -charge equilibration must be performed via the "fix -qeq/slater"_fix_qeq.html command. For example: - -pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy -pair_coeff * * coul/streitz AlO.streitz Al O -pair_coeff * * eam/alloy AlO.eam.alloy Al O -fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz :pre - -The keyword {wolf} in the coul/streitz command denotes computing -Coulombic interactions via Wolf summation. An additional damping -parameter is required for the Wolf summation, as described for the -coul/wolf potential above. Alternatively, Coulombic interactions can -be computed via an Ewald summation. For example: - -pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy -kspace_style ewald 1e-6 :pre - -Keyword {ewald} does not need a damping parameter, but a -"kspace_style"_kspace_style.html must be defined, which can be style -{ewald} or {pppm}. The Ewald method was used in Streitz and -Mintmire's original paper, but a Wolf summation offers a speed-up in -some cases. - -For the fix qeq/slater command, the {qfile} can be a filename that -contains QEq parameters as discussed on the "fix qeq"_fix_qeq.html -command doc page. Alternatively {qfile} can be replaced by -"coul/streitz", in which case the fix will extract QEq parameters from -the coul/streitz pair style itself. - -See the examples/strietz directory for an example input script that -uses the Streitz-Mintmire potential. The potentials directory has the -AlO.eam.alloy and AlO.streitz potential files used by the example. - -Note that the Streiz-Mintmire potential is generally used for oxides, -but there is no conceptual problem with extending it to nitrides and -carbides (such as SiC, TiN). Pair coul/strietz used by itself or with -any other pair style such as EAM, MEAM, Tersoff, or LJ in -hybrid/overlay mode. To do this, you would need to provide a -Streitz-Mintmire parameterization for the material being modeled. - -:line - -Styles {coul/long} and {coul/msm} compute the same Coulombic -interactions as style {coul/cut} except that an additional damping -factor is applied so it can be used in conjunction with the -"kspace_style"_kspace_style.html command and its {ewald} or {pppm} -option. The Coulombic cutoff specified for this style means that -pairwise interactions within this distance are computed directly; -interactions outside that distance are computed in reciprocal space. - -Styles {tip4p/cut} and {tip4p/long} implement the Coulomb part of -the TIP4P water model of "(Jorgensen)"_#Jorgensen3, which introduces -a massless site located a short distance away from the oxygen atom -along the bisector of the HOH angle. The atomic types of the oxygen and -hydrogen atoms, the bond and angle types for OH and HOH interactions, -and the distance to the massless charge site are specified as -pair_style arguments. Style {tip4p/cut} uses a global cutoff for -Coulomb interactions; style {tip4p/long} is for use with a long-range -Coulombic solver (Ewald or PPPM). - -NOTE: For each TIP4P water molecule in your system, the atom IDs for -the O and 2 H atoms must be consecutive, with the O atom first. This -is to enable LAMMPS to "find" the 2 H atoms associated with each O -atom. For example, if the atom ID of an O atom in a TIP4P water -molecule is 500, then its 2 H atoms must have IDs 501 and 502. - -See the "Howto tip4p"_Howto_tip4p.html doc page for more information -on how to use the TIP4P pair styles and lists of parameters to set. -Note that the neighbor list cutoff for Coulomb interactions is -effectively extended by a distance 2*qdist when using the TIP4P pair -style, to account for the offset distance of the fictitious charges on -O atoms in water molecules. Thus it is typically best in an -efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2*qdist, to -shrink the size of the neighbor list. This leads to slightly larger -cost for the long-range calculation, so you can test the trade-off for -your model. - -:line - -Note that these potentials are designed to be combined with other pair -potentials via the "pair_style hybrid/overlay"_pair_hybrid.html -command. This is because they have no repulsive core. Hence if they -are used by themselves, there will be no repulsion to keep two -oppositely charged particles from moving arbitrarily close to each -other. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -cutoff (distance units) :ul - -For {coul/cut} and {coul/debye}, the cutoff coefficient is optional. -If it is not used (as in some of the examples above), the default -global value specified in the pair_style command is used. - -For {coul/long} and {coul/msm} no cutoff can be specified for an -individual I,J type pair via the pair_coeff command. All type pairs -use the same global Coulombic cutoff specified in the pair_style -command. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the cutoff distance for the -{coul/cut} style can be mixed. The default mix value is {geometric}. -See the "pair_modify" command for details. - -The "pair_modify"_pair_modify.html shift option is not relevant -for these pair styles. - -The {coul/long} style supports the "pair_modify"_pair_modify.html -table option for tabulation of the short-range portion of the -long-range Coulombic interaction. - -These pair styles do not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -These pair styles write their information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -The {coul/long}, {coul/msm} and {tip4p/long} styles are part of the -KSPACE package. They are only enabled if LAMMPS was built with that -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style, -hybrid/overlay"_pair_hybrid.html, "kspace_style"_kspace_style.html - -[Default:] none - -:line - -:link(Wolf1) -[(Wolf)] D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem -Phys, 110, 8254 (1999). - -:link(Fennell1) -[(Fennell)] C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, -234104 (2006). - -:link(Streitz2) -[(Streitz)] F. H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003 -(1994). - -:link(Jorgensen3) -[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem -Phys, 79, 926 (1983). diff --git a/doc/txt/pair_coul_diel.txt b/doc/txt/pair_coul_diel.txt deleted file mode 100644 index 7708287db9..0000000000 --- a/doc/txt/pair_coul_diel.txt +++ /dev/null @@ -1,113 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style coul/diel command :h3 -pair_style coul/diel/omp command :h3 - -[Syntax:] - -pair_style coul/diel cutoff :pre - -cutoff = global cutoff (distance units) - -[Examples:] - -pair_style coul/diel 3.5 -pair_coeff 1 4 78. 1.375 0.112 :pre - - -[Description:] - -Style {coul/diel} computes a Coulomb correction for implicit solvent -ion interactions in which the dielectric permittivity is distance dependent. -The dielectric permittivity epsilon_D(r) connects to limiting regimes: -One limit is defined by a small dielectric permittivity (close to vacuum) -at or close to contact separation between the ions. At larger separations -the dielectric permittivity reaches a bulk value used in the regular Coulomb -interaction coul/long or coul/cut. -The transition is modeled by a hyperbolic function which is incorporated -in the Coulomb correction term for small ion separations as follows - -:c,image(Eqs/pair_coul_diel.jpg) - -where r_me is the inflection point of epsilon_D(r) and sigma_e is a slope -defining length scale. C is the same Coulomb conversion factor as in the -pair_styles coul/cut, coul/long, and coul/debye. In this way the Coulomb -interaction between ions is corrected at small distances r. The lower -limit of epsilon_D(r->0)=5.2 due to dielectric saturation "(Stiles)"_#Stiles -while the Coulomb interaction reaches its bulk limit by setting -epsilon_D(r->\infty)=epsilon, the bulk value of the solvent which is 78 -for water at 298K. - -Examples of the use of this type of Coulomb interaction include implicit -solvent simulations of salt ions -"(Lenart)"_#Lenart1 and of ionic surfactants "(Jusufi)"_#Jusufi1. -Note that this potential is only reasonable for implicit solvent simulations -and in combination with coul/cut or coul/long. It is also usually combined -with gauss/cut, see "(Lenart)"_#Lenart1 or "(Jusufi)"_#Jusufi1. - -The following coefficients must be defined for each pair of atom -types via the "pair_coeff"_pair_coeff.html command as in the example -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -epsilon (no units) -r_me (distance units) -sigma_e (distance units) :ul - -The global cutoff (r_c) specified in the pair_style command is used. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support parameter mixing. Coefficients must -be given explicitly for each type of particle pairs. - -This pair style supports the "pair_modify"_pair_modify.html shift -option for the energy of the Gauss-potential portion of the pair -interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -[Restrictions:] - -This style is part of the "USER-MISC" package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html -"pair_style gauss/cut"_pair_gauss.html - -[Default:] none - -:line - -:link(Stiles) -[(Stiles)] Stiles , Hubbard, and Kayser, J Chem Phys, 77, -6189 (1982). - -:link(Lenart1) -[(Lenart)] Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, -044509 (2007). - -:link(Jusufi1) -[(Jusufi)] Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, -13783 (2008). diff --git a/doc/txt/pair_coul_shield.txt b/doc/txt/pair_coul_shield.txt deleted file mode 100644 index 8152a1a12e..0000000000 --- a/doc/txt/pair_coul_shield.txt +++ /dev/null @@ -1,93 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style coul/shield command :h3 - -[Syntax:] - -pair_style coul/shield cutoff tap_flag :pre - -cutoff = global cutoff (distance units) -tap_flag = 0/1 to turn off/on the taper function :ul - -[Examples:] - -pair_style coul/shield 16.0 1 -pair_coeff 1 2 0.70 :pre - - -[Description:] - -Style {coul/shield} computes a Coulomb interaction for boron and -nitrogen atoms located in different layers of hexagonal boron -nitride. This potential is designed be used in combination with -the pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - -NOTE: This potential is intended for electrostatic interactions between -two different layers of hexagonal boron nitride. Therefore, to avoid -interaction within the same layers, each layer should have a separate -molecule id and is recommended to use the "full" atom style, so that -charge and molecule ID information is included. - -:c,image(Eqs/pair_coul_shield.jpg) - -Where Tap(r_ij) is the taper function which provides a continuous cutoff -(up to third derivative) for inter-atomic separations larger than r_c -"(Leven1)"_#Leven3, "(Leven2)"_#Leven4 and "(Maaravi)"_#Maaravi1. -Here {lambda} is the shielding parameter that -eliminates the short-range singularity of the classical mono-polar -electrostatic interaction expression "(Maaravi)"_#Maaravi1. - -The shielding parameter {lambda} (1/distance units) must be defined for -each pair of atom types via the "pair_coeff"_pair_coeff.html command as -in the example above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html commands: - -The global cutoff (r_c) specified in the pair_style command is used. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support parameter mixing. Coefficients must -be given explicitly for each type of particle pairs. - -The "pair_modify"_pair_modify.html {table} option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -{tail} option for adding long-range tail corrections to energy and -pressure. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -[Restrictions:] - -This style is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html -"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - -[Default:] tap_flag = 1 - -:line - -:link(Leven3) -[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014). - -:link(Leven4) -[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016). - -:link(Maaravi1) -[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017). diff --git a/doc/txt/pair_cs.txt b/doc/txt/pair_cs.txt deleted file mode 100644 index 5fce65d6f7..0000000000 --- a/doc/txt/pair_cs.txt +++ /dev/null @@ -1,175 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style born/coul/dsf/cs command :h3 -pair_style born/coul/long/cs command :h3 -pair_style born/coul/long/cs/gpu command :h3 -pair_style born/coul/wolf/cs command :h3 -pair_style born/coul/wolf/cs/gpu command :h3 -pair_style buck/coul/long/cs command :h3 -pair_style coul/long/cs command :h3 -pair_style coul/long/cs/gpu command :h3 -pair_style coul/wolf/cs command :h3 -pair_style lj/cut/coul/long/cs command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {born/coul/dsf/cs} or {born/coul/long/cs} or {born/coul/wolf/cs} or {buck/coul/long/cs} or {coul/long/cs} or {coul/wolf/cs} or {lj/cut/coul/long/cs} -args = list of arguments for a particular style :ul - {born/coul/dsf/cs} args = alpha cutoff (cutoff2) - alpha = damping parameter (inverse distance units) - cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (distance units) - {born/coul/long/cs} args = cutoff (cutoff2) - cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {born/coul/wolf/cs} args = alpha cutoff (cutoff2) - alpha = damping parameter (inverse distance units) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {buck/coul/long/cs} args = cutoff (cutoff2) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {coul/long} args = cutoff - cutoff = global cutoff for Coulombic (distance units) - {coul/wolf} args = alpha cutoff - alpha = damping parameter (inverse distance units) - cutoff = global cutoff for Coulombic (distance units) - {lj/cut/coul/long/cs} args = cutoff (cutoff2) - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre - -[Examples:] - -pair_style born/coul/dsf/cs 0.1 10.0 12.0 -pair_coeff * * 0.0 1.00 0.00 0.00 0.00 -pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre - -pair_style born/coul/long/cs 10.0 8.0 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre - -pair_style born/coul/wolf/cs 0.25 10.0 12.0 -pair_coeff * * 0.0 1.00 0.00 0.00 0.00 -pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre - -pair_style buck/coul/long/cs 10.0 -pair_style buck/coul/long/cs 10.0 8.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre - -pair_style coul/long/cs 10.0 -pair_coeff * * :pre - -pair_style coul/wolf/cs 0.2 9.0 -pair_coeff * * :pre - -pair_style lj/cut/coul/long/cs 10.0 -pair_style lj/cut/coul/long/cs 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 :pre - -[Description:] - -These pair styles are designed to be used with the adiabatic -core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham2. See -the "Howto coreshell"_Howto_coreshell.html doc page for an overview of -the model as implemented in LAMMPS. - -All the styles are identical to the corresponding pair style without -the "/cs" in the name: - -"pair_style born/coul/dsf"_pair_born.html -"pair_style born/coul/long"_pair_born.html -"pair_style born/coul/wolf"_pair_born.html -"pair_style buck/coul/long"_pair_buck.html -"pair_style coul/long"_pair_coul.html -"pair_style coul/wolf"_pair_coul.html -"pair_style lj/cut/coul/long"_pair_lj.html :ul - -except that they correctly treat the special case where the distance -between two charged core and shell atoms in the same core/shell pair -approach r = 0.0. - -Styles with a "/long" in the name are used with a long-range solver -for Coulombic interactions via the "kspace_style"_kspace_style.html -command. They require special treatment of the short-range Coulombic -interactions within the cor/shell model. - -Specifically, the short-range Coulomb interaction between a core and -its shell should be turned off using the -"special_bonds"_special_bonds.html command by setting the 1-2 weight -to 0.0, which works because the core and shell atoms are bonded to -each other. This induces a long-range correction approximation which -fails at small distances (~< 10e-8). Therefore, the Coulomb term which -is used to calculate the correction factor is extended by a minimal -distance (r_min = 1.0-6) when the interaction between a core/shell -pair is treated, as follows - -:c,image(Eqs/pair_cs.jpg) - -where C is an energy-conversion constant, Qi and Qj are the charges on -the core and shell, epsilon is the dielectric constant and r_min is the -minimal distance. - -For styles that are not used with a long-range solver, i.e. those with -"/dsf" or "/wolf" in the name, the only correction is the addition of -a minimal distance to avoid the possible r = 0.0 case for a core/shell -pair. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -See the corresponding doc pages for pair styles without the "cs" -suffix to see how mixing, shifting, tabulation, tail correction, -restarting, and rRESPA are handled by theses pair styles. - -:line - -[Restrictions:] - -These pair styles are part of the CORESHELL package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style born"_pair_born.html, -"pair_style buck"_pair_buck.html - -[Default:] none - -:line - -:link(MitchellFinchham2) -[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter, -5, 1031-1038 (1993). diff --git a/doc/txt/pair_dipole.txt b/doc/txt/pair_dipole.txt deleted file mode 100644 index c695601061..0000000000 --- a/doc/txt/pair_dipole.txt +++ /dev/null @@ -1,275 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj/cut/dipole/cut command :h3 -pair_style lj/cut/dipole/cut/gpu command :h3 -pair_style lj/cut/dipole/cut/omp command :h3 -pair_style lj/sf/dipole/sf command :h3 -pair_style lj/sf/dipole/sf/gpu command :h3 -pair_style lj/sf/dipole/sf/omp command :h3 -pair_style lj/cut/dipole/long command :h3 -pair_style lj/cut/dipole/long/gpu command :h3 -pair_style lj/long/dipole/long command :h3 - -[Syntax:] - -pair_style lj/cut/dipole/cut cutoff (cutoff2) -pair_style lj/sf/dipole/sf cutoff (cutoff2) -pair_style lj/cut/dipole/long cutoff (cutoff2) -pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2) :pre - -cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units) :ulb,l -cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units) :l -flag_lj = {long} or {cut} or {off} :l - {long} = use long-range damping on dispersion 1/r^6 term - {cut} = use a cutoff on dispersion 1/r^6 term - {off} = omit disperion 1/r^6 term entirely :pre -flag_coul = {long} or {off} :l - {long} = use long-range damping on Coulombic 1/r and point-dipole terms - {off} = omit Coulombic and point-dipole terms entirely :pre -:ule - -[Examples:] - -pair_style lj/cut/dipole/cut 10.0 -pair_coeff * * 1.0 1.0 -pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre - -pair_style lj/sf/dipole/sf 9.0 -pair_coeff * * 1.0 1.0 -pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5 -pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre - -pair_style lj/cut/dipole/long 10.0 -pair_coeff * * 1.0 1.0 -pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre - -pair_style lj/long/dipole/long long long 3.5 10.0 -pair_coeff * * 1.0 1.0 -pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre - -[Description:] - -Style {lj/cut/dipole/cut} computes interactions between pairs of particles -that each have a charge and/or a point dipole moment. In addition to -the usual Lennard-Jones interaction between the particles (Elj) the -charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole (Epp) -interactions are computed by these formulas for the energy (E), force -(F), and torque (T) between particles I and J. - -:c,image(Eqs/pair_dipole.jpg) - -where qi and qj are the charges on the two particles, pi and pj are -the dipole moment vectors of the two particles, r is their separation -distance, and the vector r = Ri - Rj is the separation vector between -the two particles. Note that Eqq and Fqq are simply Coulombic energy -and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the -torques do not act symmetrically. These formulas are discussed in -"(Allen)"_#Allen2 and in "(Toukmaji)"_#Toukmaji2. - -Also note, that in the code, all of these terms (except Elj) have a -C/epsilon prefactor, the same as the Coulombic term in the LJ + -Coulombic pair styles discussed "here"_pair_lj.html. C is an -energy-conversion constant and epsilon is the dielectric constant -which can be set by the "dielectric"_dielectric.html command. The -same is true of the equations that follow for other dipole pair -styles. - -Style {lj/sf/dipole/sf} computes "shifted-force" interactions between -pairs of particles that each have a charge and/or a point dipole -moment. In general, a shifted-force potential is a (slightly) modified -potential containing extra terms that make both the energy and its -derivative go to zero at the cutoff distance; this removes -(cutoff-related) problems in energy conservation and any numerical -instability in the equations of motion "(Allen)"_#Allen2. Shifted-force -interactions for the Lennard-Jones (E_LJ), charge-charge (Eqq), -charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp) -potentials are computed by these formulas for the energy (E), force -(F), and torque (T) between particles I and J: - -:c,image(Eqs/pair_dipole_sf.jpg) -:c,image(Eqs/pair_dipole_sf2.jpg) - -where epsilon and sigma are the standard LJ parameters, r_c is the -cutoff, qi and qj are the charges on the two particles, pi and pj are -the dipole moment vectors of the two particles, r is their separation -distance, and the vector r = Ri - Rj is the separation vector between -the two particles. Note that Eqq and Fqq are simply Coulombic energy -and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the -torques do not act symmetrically. The shifted-force formula for the -Lennard-Jones potential is reported in "(Stoddard)"_#Stoddard. The -original (non-shifted) formulas for the electrostatic potentials, -forces and torques can be found in "(Price)"_#Price2. The shifted-force -electrostatic potentials have been obtained by applying equation 5.13 -of "(Allen)"_#Allen2. The formulas for the corresponding forces and -torques have been obtained by applying the 'chain rule' as in appendix -C.3 of "(Allen)"_#Allen2. - -If one cutoff is specified in the pair_style command, it is used for -both the LJ and Coulombic (q,p) terms. If two cutoffs are specified, -they are used as cutoffs for the LJ and Coulombic (q,p) terms -respectively. This pair style also supports an optional {scale} keyword -as part of a pair_coeff statement, where the interactions can be -scaled according to this factor. This scale factor is also made available -for use with fix adapt. - -Style {lj/cut/dipole/long} computes long-range point-dipole -interactions as discussed in "(Toukmaji)"_#Toukmaji2. Dipole-dipole, -dipole-charge, and charge-charge interactions are all supported, along -with the standard 12/6 Lennard-Jones interactions, which are computed -with a cutoff. A "kspace_style"_kspace_style.html must be defined to -use this pair style. Currently, only "kspace_style -ewald/disp"_kspace_style.html support long-range point-dipole -interactions. - -Style {lj/long/dipole/long} also computes point-dipole interactions as -discussed in "(Toukmaji)"_#Toukmaji2. Long-range dipole-dipole, -dipole-charge, and charge-charge interactions are all supported, along -with the standard 12/6 Lennard-Jones interactions. LJ interactions -can be cutoff or long-ranged. - -For style {lj/long/dipole/long}, if {flag_lj} is set to {long}, no -cutoff is used on the LJ 1/r^6 dispersion term. The long-range -portion is calculated by using the "kspace_style -ewald_disp"_kspace_style.html command. The specified LJ cutoff then -determines which portion of the LJ interactions are computed directly -by the pair potential versus which part is computed in reciprocal -space via the Kspace style. If {flag_lj} is set to {cut}, the LJ -interactions are simply cutoff, as with "pair_style -lj/cut"_pair_lj.html. If {flag_lj} is set to {off}, LJ interactions -are not computed at all. - -If {flag_coul} is set to {long}, no cutoff is used on the Coulombic or -dipole interactions. The long-range portion is calculated by using -{ewald_disp} of the "kspace_style"_kspace_style.html command. If -{flag_coul} is set to {off}, Coulombic and dipole interactions are not -computed at all. - -Atoms with dipole moments should be integrated using the "fix -nve/sphere update dipole"_fix_nve_sphere.html or the "fix -nvt/sphere update dipole"_fix_nvt_sphere.html command to rotate the -dipole moments. The {omega} option on the "fix -langevin"_fix_langevin.html command can be used to thermostat the -rotational motion. The "compute temp/sphere"_compute_temp_sphere.html -command can be used to monitor the temperature, since it includes -rotational degrees of freedom. The "atom_style -hybrid dipole sphere"_atom_style.html command should be used since -it defines the point dipoles and their rotational state. -The magnitude and orientation of the dipole moment for each particle -can be defined by the "set"_set.html command or in the "Atoms" section -of the data file read in by the "read_data"_read_data.html command. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) -cutoff1 (distance units) -cutoff2 (distance units) :ul - -The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both LJ -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distances for this pair style can be mixed. The default -mix value is {geometric}. See the "pair_modify" command for details. - -For atom type pairs I,J and I != J, the A, sigma, d1, and d2 -coefficients and cutoff distance for this pair style can be mixed. A -is an energy value mixed like a LJ epsilon. D1 and d2 are distance -values and are mixed like sigma. The default mix value is -{geometric}. See the "pair_modify" command for details. - -This pair style does not support the "pair_modify"_pair_modify.html -shift option for the energy of the Lennard-Jones portion of the pair -interaction; such energy goes to zero at the cutoff by construction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -[Restrictions:] - -The {lj/cut/dipole/cut}, {lj/cut/dipole/long}, and -{lj/long/dipole/long} styles are part of the DIPOLE package. They are -only enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -The {lj/sf/dipole/sf} style is part of the USER-MISC package. It is -only enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Using dipole pair styles with {electron} "units"_units.html is not -currently supported. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "set"_set.html, "read_data"_read_data.html, -"fix nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html - -[Default:] none - -:line - -:link(Allen2) -[(Allen)] Allen and Tildesley, Computer Simulation of Liquids, -Clarendon Press, Oxford, 1987. - -:link(Toukmaji2) -[(Toukmaji)] Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113, -10913 (2000). - -:link(Stoddard) -[(Stoddard)] Stoddard and Ford, Phys Rev A, 8, 1504 (1973). - -:link(Price2) -[(Price)] Price, Stone and Alderton, Mol Phys, 52, 987 (1984). diff --git a/doc/txt/pair_dpd.txt b/doc/txt/pair_dpd.txt deleted file mode 100644 index db6fc174d4..0000000000 --- a/doc/txt/pair_dpd.txt +++ /dev/null @@ -1,209 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style dpd command :h3 -pair_style dpd/gpu command :h3 -pair_style dpd/intel command :h3 -pair_style dpd/omp command :h3 -pair_style dpd/tstat command :h3 -pair_style dpd/tstat/gpu command :h3 -pair_style dpd/tstat/omp command :h3 - -[Syntax:] - -pair_style dpd T cutoff seed -pair_style dpd/tstat Tstart Tstop cutoff seed :pre - -T = temperature (temperature units) -Tstart,Tstop = desired temperature at start/end of run (temperature units) -cutoff = global cutoff for DPD interactions (distance units) -seed = random # seed (positive integer) :ul - -[Examples:] - -pair_style dpd 1.0 2.5 34387 -pair_coeff * * 3.0 1.0 -pair_coeff 1 1 3.0 1.0 1.0 :pre - -pair_style dpd/tstat 1.0 1.0 2.5 34387 -pair_coeff * * 1.0 -pair_coeff 1 1 1.0 1.0 :pre - -[Description:] - -Style {dpd} computes a force field for dissipative particle dynamics -(DPD) following the exposition in "(Groot)"_#Groot1. - -Style {dpd/tstat} invokes a DPD thermostat on pairwise interactions, -which is equivalent to the non-conservative portion of the DPD force -field. This pair-wise thermostat can be used in conjunction with any -"pair style"_pair_style.html, and in leiu of per-particle thermostats -like "fix langevin"_fix_langevin.html or ensemble thermostats like -Nose Hoover as implemented by "fix nvt"_fix_nh.html. To use -{dpd/tstat} as a thermostat for another pair style, use the "pair_style -hybrid/overlay"_pair_hybrid.html command to compute both the desired -pair interaction and the thermostat for each pair of particles. - -For style {dpd}, the force on atom I due to atom J is given as a sum -of 3 terms - -:c,image(Eqs/pair_dpd.jpg) - -where Fc is a conservative force, Fd is a dissipative force, and Fr is -a random force. Rij is a unit vector in the direction Ri - Rj, Vij is -the vector difference in velocities of the two atoms = Vi - Vj, alpha -is a Gaussian random number with zero mean and unit variance, dt is -the timestep size, and w(r) is a weighting factor that varies between -0 and 1. Rc is the cutoff. Sigma is set equal to sqrt(2 Kb T gamma), -where Kb is the Boltzmann constant and T is the temperature parameter -in the pair_style command. - -For style {dpd/tstat}, the force on atom I due to atom J is the same -as the above equation, except that the conservative Fc term is -dropped. Also, during the run, T is set each timestep to a ramped -value from Tstart to Tstop. - -For style {dpd}, the pairwise energy associated with style {dpd} is -only due to the conservative force term Fc, and is shifted to be zero -at the cutoff distance Rc. The pairwise virial is calculated using -all 3 terms. For style {dpd/tstat} there is no pairwise energy, but -the last two terms of the formula make a contribution to the virial. - -For style {dpd}, the following coefficients must be defined for each -pair of atoms types via the "pair_coeff"_pair_coeff.html command as in -the examples above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -A (force units) -gamma (force/velocity units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global DPD -cutoff is used. Note that sigma is set equal to sqrt(2 T gamma), -where T is the temperature set by the "pair_style"_pair_style.html -command so it does not need to be specified. - -For style {dpd/tstat}, the coefficients defined for each pair of -atoms types via the "pair_coeff"_pair_coeff.html command is the same, -except that A is not included. - -The GPU-accelerated versions of these styles are implemented based on -the work of "(Afshar)"_#Afshar and "(Phillips)"_#Phillips. - -NOTE: If you are modeling DPD polymer chains, you may want to use the -"pair_style srp"_pair_srp.html command in conjunction with these pair -styles. It is a soft segmental repulsive potential (SRP) that can -prevent DPD polymer chains from crossing each other. - -NOTE: The virial calculation for pressure when using this pair style -includes all the components of force listed above, including the -random force. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -These pair styles do not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -These pair styles do not support the "pair_modify"_pair_modify.html -shift option for the energy of the pair interaction. Note that as -discussed above, the energy due to the conservative Fc term is already -shifted to be 0.0 at the cutoff distance Rc. - -The "pair_modify"_pair_modify.html table option is not relevant -for these pair styles. - -These pair style do not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -These pair styles writes their information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. Note -that the user-specified random number seed is stored in the restart -file, so when a simulation is restarted, each processor will -re-initialize its random number generator the same way it did -initially. This means the random forces will be random, but will not -be the same as they would have been if the original simulation had -continued past the restart time. - -These pair styles can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. They do not support the -{inner}, {middle}, {outer} keywords. - -The {dpd/tstat} style can ramp its target temperature over multiple -runs, using the {start} and {stop} keywords of the "run"_run.html -command. See the "run"_run.html command for details of how to do -this. - -:line - -[Restrictions:] - -The default frequency for rebuilding neighbor lists is every 10 steps -(see the "neigh_modify"_neigh_modify.html command). This may be too -infrequent for style {dpd} simulations since particles move rapidly -and can overlap by large amounts. If this setting yields a non-zero -number of "dangerous" reneighborings (printed at the end of a -simulation), you should experiment with forcing reneighboring more -often and see if system energies/trajectories change. - -These pair styles requires you to use the "comm_modify vel -yes"_comm_modify.html command so that velocities are stored by ghost -atoms. - -These pair styles will not restart exactly when using the -"read_restart"_read_restart.html command, though they should provide -statistically similar results. This is because the forces they -compute depend on atom velocities. See the -"read_restart"_read_restart.html command for more details. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "fix nvt"_fix_nh.html, "fix -langevin"_fix_langevin.html, "pair_style srp"_pair_srp.html - -[Default:] none - -:line - -:link(Groot1) -[(Groot)] Groot and Warren, J Chem Phys, 107, 4423-35 (1997). - -:link(Afshar) -[(Afshar)] Afshar, F. Schmid, A. Pishevar, S. Worley, Comput Phys -Comm, 184, 1119-1128 (2013). - -:link(Phillips) -[(Phillips)] C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput -Phys Comm, 230, 7191-7201 (2011). - diff --git a/doc/txt/pair_dpd_fdt.txt b/doc/txt/pair_dpd_fdt.txt deleted file mode 100644 index 52605aef39..0000000000 --- a/doc/txt/pair_dpd_fdt.txt +++ /dev/null @@ -1,177 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style dpd/fdt command :h3 -pair_style dpd/fdt/energy command :h3 -pair_style dpd/fdt/energy/kk command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {dpd/fdt} or {dpd/fdt/energy} -args = list of arguments for a particular style :ul - {dpd/fdt} args = T cutoff seed - T = temperature (temperature units) - cutoff = global cutoff for DPD interactions (distance units) - seed = random # seed (positive integer) - {dpd/fdt/energy} args = cutoff seed - cutoff = global cutoff for DPD interactions (distance units) - seed = random # seed (positive integer) :pre - -[Examples:] - -pair_style dpd/fdt 300.0 2.5 34387 -pair_coeff * * 3.0 1.0 2.5 :pre - -pair_style dpd/fdt/energy 2.5 34387 -pair_coeff * * 3.0 1.0 0.1 2.5 :pre - -[Description:] - -Styles {dpd/fdt} and {dpd/fdt/energy} compute the force for dissipative -particle dynamics (DPD) simulations. The {dpd/fdt} style is used to -perform DPD simulations under isothermal and isobaric conditions, -while the {dpd/fdt/energy} style is used to perform DPD simulations -under isoenergetic and isoenthalpic conditions (see "(Lisal)"_#Lisal3). -For DPD simulations in general, the force on atom I due to atom J is -given as a sum of 3 terms - -:c,image(Eqs/pair_dpd.jpg) - -where Fc is a conservative force, Fd is a dissipative force, and Fr is -a random force. Rij is a unit vector in the direction Ri - Rj, Vij is -the vector difference in velocities of the two atoms = Vi - Vj, alpha -is a Gaussian random number with zero mean and unit variance, dt is -the timestep size, and w(r) is a weighting factor that varies between -0 and 1. Rc is the cutoff. The weighting factor, omega_ij, varies -between 0 and 1, and is chosen to have the following functional form: - -:c,image(Eqs/pair_dpd_omega.jpg) - -Note that alternative definitions of the weighting function exist, but -would have to be implemented as a separate pair style command. - -For style {dpd/fdt}, the fluctuation-dissipation theorem defines gamma -to be set equal to sigma*sigma/(2 T), where T is the set point -temperature specified as a pair style parameter in the above examples. -The following coefficients must be defined for each pair of atoms types -via the "pair_coeff"_pair_coeff.html command as in the examples above, -or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html commands: - -A (force units) -sigma (force*time^(1/2) units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global DPD -cutoff is used. - -Style {dpd/fdt/energy} is used to perform DPD simulations -under isoenergetic and isoenthalpic conditions. The fluctuation-dissipation -theorem defines gamma to be set equal to sigma*sigma/(2 dpdTheta), where -dpdTheta is the average internal temperature for the pair. The particle -internal temperature is related to the particle internal energy through -a mesoparticle equation of state (see "fix eos"_fix.html). The -differential internal conductive and mechanical energies are computed -within style {dpd/fdt/energy} as: - -:c,image(Eqs/pair_dpd_energy.jpg) - -where - -:c,image(Eqs/pair_dpd_energy_terms.jpg) - -Zeta_ij^q is a second Gaussian random number with zero mean and unit -variance that is used to compute the internal conductive energy. The -fluctuation-dissipation theorem defines alpha*alpha to be set -equal to 2*kB*kappa, where kappa is the mesoparticle thermal -conductivity parameter. The following coefficients must be defined for -each pair of atoms types via the "pair_coeff"_pair_coeff.html -command as in the examples above, or in the data file or restart files -read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -A (force units) -sigma (force*time^(1/2) units) -kappa (energy*temperature/time units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global DPD -cutoff is used. - -The pairwise energy associated with styles {dpd/fdt} and -{dpd/fdt/energy} is only due to the conservative force term Fc, and is -shifted to be zero at the cutoff distance Rc. The pairwise virial is -calculated using only the conservative term. - -The forces computed through the {dpd/fdt} and {dpd/fdt/energy} styles -can be integrated with the velocity-Verlet integration scheme or the -Shardlow splitting integration scheme described by "(Lisal)"_#Lisal3. -In the cases when these pair styles are combined with the -"fix shardlow"_fix_shardlow.html, these pair styles differ from the -other dpd styles in that the dissipative and random forces are split -from the force calculation and are not computed within the pair style. -Thus, only the conservative force is computed by the pair style, -while the stochastic integration of the dissipative and random forces -are handled through the Shardlow splitting algorithm approach. The -Shardlow splitting algorithm is advantageous, especially when -performing DPD under isoenergetic conditions, as it allows -significantly larger timesteps to be taken. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -These commands are part of the USER-DPD package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the -"comm_modify vel yes"_comm_modify.html option so that velocities are -stored by ghost atoms. - -Pair style {dpd/fdt/energy} requires "atom_style dpd"_atom_style.html -to be used in order to properly account for the particle internal -energies and temperatures. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "fix shardlow"_fix_shardlow.html - -[Default:] none - -:line - -:link(Lisal3) -[(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative -particle dynamics at isothermal, isobaric, isoenergetic, and -isoenthalpic conditions using Shardlow-like splitting algorithms.", -J. Chem. Phys., 135, 204105 (2011). diff --git a/doc/txt/pair_drip.txt b/doc/txt/pair_drip.txt deleted file mode 100644 index 84c92b04e4..0000000000 --- a/doc/txt/pair_drip.txt +++ /dev/null @@ -1,141 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style drip command :h3 - -[Syntax:] - -pair_style hybrid/overlay drip \[styles ...\] :pre - -styles = other styles to be overlayed with drip (optional) :ul - -[Examples:] - -pair_style hybrid/overlay drip -pair_coeff * * none -pair_coeff * * drip C.drip C :pre - -pair_style hybrid/overlay drip rebo -pair_coeff * * drip C.drip C -pair_coeff * * rebo CH.airebo C :pre - -pair_style hybrid/overlay drip rebo -pair_coeff * * drip C.drip C NULL -pair_coeff * * rebo CH.airebo C H :pre - - -[Description:] - -Style {drip} computes the interlayer interactions of layered materials using -the dihedral-angle-corrected registry-dependent (DRIP) potential as described -in "(Wen)"_#Wen2018, which is based on the "(Kolmogorov)"_#Kolmogorov2005 -potential and provides an improved prediction for forces. -The total potential energy of a system is - -:c,image(Eqs/pair_drip.jpg) - -where the {r^-6} term models the attractive London dispersion, -the exponential term is designed to capture the registry effect due to -overlapping {pi} bonds, and {fc} is a cutoff function. - - -This potential (DRIP) only provides the interlayer interactions between -graphene layers. So, to perform a realistic simulation, it should be used in -combination with an intralayer potential such as "REBO"_pair_airebo.html and -"Tersoff"_pair_tersoff.html. -To keep the intralayer interactions unaffected, we should avoid applying DRIP -to contribute energy to intralayer interactions. This can be achieved by -assigning different molecular IDs to atoms in different layers, and DRIP is -implemented such that only atoms with different molecular ID can interact with -each other. For this purpose, "atom style"_atom_style.html "molecular" or -"full" has to be used. - -On the other way around, "REBO"_pair_airebo.html ("Tersoff"_pair_tersoff.html -or any other potential used to provide the intralayer interactions) should not -interfere with the interlayer interactions described by DRIP. This is typically -automatically achieved using the commands provided in the {Examples} section -above, since the cutoff distance for carbon-carbon interaction in the intralayer -potentials (e.g. 2 Angstrom for "REBO"_pair_airebo.html) is much smaller than -the equilibrium layer distance of graphene layers (about 3.4 Angstrom). -If you want, you can enforce this by assigning different atom types to atoms in -different layers, and apply an intralayer potential to one atom type. -See "pair_hybrid"_pair_hybrid.html for details. - -:line - -The "pair_coeff"_pair_coeff.html command for DRIP takes {4+N} arguments, where -{N} is the number of LAMMPS atom types. The fist three arguments must be fixed -to be {* * drip}, the fourth argument is the path to the DRIP parameter file, -and the remaining N arguments specifying the mapping between element in the -parameter file and atom types. For example, if your LAMMPS simulation has 3 atom -types and you want all of them to be C, you would use the following pair_coeff -command: - -pair_coeff * * drip C.drip C C C :pre - -If a mapping value is specified as NULL, the mapping is not performed. This -could be useful when DRIP is used to model part of the system where other -element exists. Suppose you have a hydrocarbon system, with C of atom type 1 -and H of atom type 2, you can use the following command to inform DRIP not to -model H atoms: - -pair_style hybrid/overlay drip rebo -pair_coeff * * drip C.drip C NULL -pair_coeff * * rebo CH.airebo C H :pre - -NOTE: The potential parameters developed in "(Wen)"_#Wen2018 are provided with -LAMMPS (see the "potentials" directory). Besides those in "Wen"_#Wen2018, an -additional parameter "normal_cutoff", specific to the LAMMPS implementation, is -used to find the three nearest neighbors of an atom to construct the normal. - - -:line - -[Mixing, shift, table, tail correction, and restart info]: - -This pair style does not support the pair_modify mix, shift, table, -and tail options. - -This pair style does not write their information to binary restart files, since -it is stored in potential files. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. - -[Restrictions:] - -This pair style is part of the USER-MISC package. It is only enabled if LAMMPS -was built with that package. See the "Build package"_Build_package.html doc -page for more info. - -This pair potential requires the "newton"_newton.html setting to be "on" for -pair interactions. - - -The {C.drip} parameter file provided with LAMMPS (see the "potentials" -directory) is parameterized for metal "units"_units.html. You can use the DRIP -potential with any LAMMPS units, but you would need to create your own custom -parameter file with coefficients listed in the appropriate units, if your -simulation doesn't use "metal" units. - - -[Related commands:] - -"pair_style lebedeva_z"_pair_lebedeva_z.html, -"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, -"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html, -"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html. - - -:line - -:link(Wen2018) -[(Wen)] M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, -98, 235404 (2018) - -:link(Kolmogorov2005) -[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) - diff --git a/doc/txt/pair_dsmc.txt b/doc/txt/pair_dsmc.txt deleted file mode 100644 index 8b1ceab858..0000000000 --- a/doc/txt/pair_dsmc.txt +++ /dev/null @@ -1,148 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style dsmc command :h3 - -[Syntax:] - -pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample :pre - -max_cell_size = global maximum cell size for DSMC interactions (distance units) -seed = random # seed (positive integer) -weighting = macroparticle weighting -Tref = reference temperature (temperature units) -Nrecompute = re-compute v*sigma_max every this many timesteps (timesteps) -Nsample = sample this many times in recomputing v*sigma_max :ul - -[Examples:] - -pair_style dsmc 2.5 34387 10 1.0 100 20 -pair_coeff * * 1.0 -pair_coeff 1 1 1.0 :pre - -[Description:] - -Style {dsmc} computes collisions between pairs of particles for a -direct simulation Monte Carlo (DSMC) model following the exposition in -"(Bird)"_#Bird. Each collision resets the velocities of the two -particles involved. The number of pairwise collisions for each pair -or particle types and the length scale within which they occur are -determined by the parameters of the pair_style and pair_coeff -commands. - -Stochastic collisions are performed using the variable hard sphere -(VHS) approach, with the user-defined {max_cell_size} value used as -the maximum DSMC cell size, and reference cross-sections for -collisions given using the pair_coeff command. - -There is no pairwise energy or virial contributions associated with -this pair style. - -The following coefficient must be defined for each pair of atoms types -via the "pair_coeff"_pair_coeff.html command as in the examples above, -or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -sigma (area units, i.e. distance-squared) :ul - -The global DSMC {max_cell_size} determines the maximum cell length -used in the DSMC calculation. A structured mesh is overlayed on the -simulation box such that an integer number of cells are created in -each direction for each processor's sub-domain. Cell lengths are -adjusted up to the user-specified maximum cell size. - -:line - -To perform a DSMC simulation with LAMMPS, several additional options -should be set in your input script, though LAMMPS does not check for -these settings. - -Since this pair style does not compute particle forces, you should use -the "fix nve/noforce" time integration fix for the DSMC particles, -e.g. - -fix 1 all nve/noforce :pre - -This pair style assumes that all particles will communicated to -neighboring processors every timestep as they move. This makes it -possible to perform all collisions between pairs of particles that are -on the same processor. To ensure this occurs, you should use -these commands: - -neighbor 0.0 bin -neigh_modify every 1 delay 0 check no -atom_modify sort 0 0.0 -communicate single cutoff 0.0 :pre - -These commands ensure that LAMMPS communicates particles to -neighboring processors every timestep and that no ghost atoms are -created. The output statistics for a simulation run should indicate -there are no ghost particles or neighbors. - -In order to get correct DSMC collision statistics, users should -specify a Gaussian velocity distribution when populating the -simulation domain. Note that the default velocity distribution is -uniform, which will not give good DSMC collision rates. Specify -"dist gaussian" when using the "velocity"_velocity.html command -as in the following: - -velocity all create 594.6 87287 loop geom dist gaussian :pre - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -This pair style does not support the "pair_modify"_pair_modify.html -shift option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. Note -that the user-specified random number seed is stored in the restart -file, so when a simulation is restarted, each processor will -re-initialize its random number generator the same way it did -initially. This means the random forces will be random, but will not -be the same as they would have been if the original simulation had -continued past the restart time. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This style is part of the MC package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "fix nve/noforce"_fix_nve_noforce.html, -"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html, -"comm_modify"_comm_modify.html - -[Default:] none - -:line - -:link(Bird) -[(Bird)] G. A. Bird, "Molecular Gas Dynamics and the Direct Simulation -of Gas Flows" (1994). diff --git a/doc/txt/pair_e3b.txt b/doc/txt/pair_e3b.txt deleted file mode 100644 index 832b4719c3..0000000000 --- a/doc/txt/pair_e3b.txt +++ /dev/null @@ -1,140 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style e3b command :h3 - -[Syntax:] - -pair_style e3b Otype :pre -Otype = atom type for oxygen :l - -pair_coeff * * keyword :pre -one or more keyword/value pairs must be appended. :l -keyword = {preset} or {Ea} or {Eb} or {Ec} or {E2} or {K3} or {K2} or {Rs} or {Rc3} or {Rc2} or {bondL} or {neigh} :l -If the {preset} keyword is given, no others are needed. -Otherwise, all are mandatory except for {neigh}. -The {neigh} keyword is always optional. :l - {preset} arg = {2011} or {2015} = which set of predefined parameters to use - 2011 = use the potential parameters from "(Tainter 2011)"_#Tainter2011 - 2015 = use the potential parameters from "(Tainter 2015)"_#Tainter2015 - {Ea} arg = three-body energy for type A hydrogen bonding interactions (energy units) - {Eb} arg = three-body energy for type B hydrogen bonding interactions (energy units) - {Ec} arg = three-body energy for type C hydrogen bonding interactions (energy units) - {E2} arg = two-body energy correction (energy units) - {K3} arg = three-body exponential constant (inverse distance units) - {K2} arg = two-body exponential constant (inverse distance units) - {Rc3} arg = three-body cutoff (distance units) - {Rc2} arg = two-body cutoff (distance units) - {Rs} arg = three-body switching function cutoff (distance units) - {bondL} arg = intramolecular OH bond length (distance units) - {neigh} arg = approximate integer number of molecules within Rc3 of an oxygen atom :pre - -[Examples:] - -pair_style e3b 1 -pair_coeff * * Ea 35.85 Eb -240.2 Ec 449.3 E2 108269.9 K3 1.907 K2 4.872 Rc3 5.2 Rc2 5.2 Rs 5.0 bondL 0.9572 :pre - -pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5 -pair_coeff * * e3b preset 2011 :pre - -[Description:] - -The {e3b} style computes an \"explicit three-body\" (E3B) potential for water "(Kumar 2008)"_#Kumar. - -:c,image(Eqs/e3b.jpg) - -This potential was developed as a water model that includes the three-body cooperativity of hydrogen bonding explicitly. -To use it in this way, it must be applied in conjunction with a conventional two-body water model, through {pair_style hybrid/overlay}. -The three body interactions are split into three types: A, B, and C. -Type A corresponds to anti-cooperative double hydrogen bond donor interactions. -Type B corresponds to the cooperative interaction of molecules that both donate and accept a hydrogen bond. -Type C corresponds to anti-cooperative double hydrogen bond acceptor interactions. -The three-body interactions are smoothly cutoff by the switching function s(r) between Rs and Rc3. -The two-body interactions are designed to correct for the effective many-body interactions implicitly included in the conventional two-body potential. -The two-body interactions are cut off sharply at Rc2, because K3 is typically significantly smaller than K2. -See "(Kumar 2008)"_#Kumar for more details. - -Only a single {pair_coeff} command is used with the {e3b} style. -The 1st two arguments must be * *. -The oxygen atom type for the pair style is passed as the only argument to the {pair_style} command, not in the {pair_coeff} command. -The hydrogen atom type is inferred by the ordering of the atoms. - -NOTE: Every atom of type Otype must be part of a water molecule. -Each water molecule must have consecutive IDs with the oxygen first. -This pair style does not test that this criteria is met. - -The {pair_coeff} command must have at least one keyword/value pair, as described above. -The {preset} keyword sets the potential parameters to the values used in "(Tainter 2011)"_#Tainter2011 or "(Tainter 2015)"_#Tainter2015. -To use the water models defined in those references, the {e3b} style should always be used in conjunction with an {lj/cut/tip4p/long} style through {pair_style hybrid/overlay}, as demonstrated in the second example above. -The {preset 2011} option should be used with the "TIP4P water model"_Howto_tip4p.html. -The {preset 2015} option should be used with the "TIP4P/2005 water model"_Howto_tip4p.html. -If the {preset} keyword is used, no other keyword is needed. -Changes to the preset parameters can be made by specifying the {preset} keyword followed by the specific parameter to change, like {Ea}. -Note that the other keywords must come after {preset} in the pair_style command. -The {e3b} style can also be used to implement any three-body potential of the same form by specifying all the keywords except {neigh}: {Ea}, {Eb}, {Ec}, {E2}, {K3}, {K2}, {Rc3}, {Rc2}, {Rs}, and {bondL}. -The keyword {bondL} specifies the intramolecular OH bond length of the water model being used. -This is needed to include H atoms that are within the cutoff even when the attached oxygen atom is not. - -This pair style allocates arrays sized according to the number of pairwise interactions within Rc3. -To do this it needs an estimate for the number of water molecules within Rc3 of an oxygen atom. -This estimate defaults to 10 and can be changed using the {neigh} keyword, which takes an integer as an argument. -If the neigh setting is too small, the simulation will fail with the error "neigh is too small". -If the neigh setting is too large, the pair style will use more memory than necessary. - -This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the "compute pair"_compute_pair.html command as a vector of values of length 4. -The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term. - -See the examples/USER/e3b directory for a complete example script. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style is incompatible with "respa"_run_style.html. - -:line - -[Restrictions:] - -This pair style is part of the USER-MISC package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair style requires the "newton"_newton.html setting to be "on" -for pair interactions. - -This pair style requires a fixed number of atoms in the simulation, so it is incompatible with fixes like "fix deposit"_fix_deposit.html. -If the number of atoms changes between runs, this pair style must be re-initialized by calling the {pair_style} and {pair_coeffs} commands. -This is not a fundamental limitation of the pair style, but the code currently does not support a variable number of atoms. - -The {preset} keyword currently only works with real, metal, si, and cgs "units"_units.html. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "compute pair"_compute_pair.html - -[Default:] - -The option default for the {neigh} keyword is 10. - -:line - -:link(Kumar) -[(Kumar)] Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008) -:link(Tainter2011) -[(Tainter 2011)] Tainter, Pieniazek, Lin, and Skinner, J. Chem. Phys., 134, 184501 (2011) -:link(Tainter2015) -[(Tainter 2015)] Tainter, Shi, and Skinner, 11, 2268 (2015) diff --git a/doc/txt/pair_eam.txt b/doc/txt/pair_eam.txt deleted file mode 100644 index ed1378b6fd..0000000000 --- a/doc/txt/pair_eam.txt +++ /dev/null @@ -1,450 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style eam command :h3 -pair_style eam/gpu command :h3 -pair_style eam/intel command :h3 -pair_style eam/kk command :h3 -pair_style eam/omp command :h3 -pair_style eam/opt command :h3 -pair_style eam/alloy command :h3 -pair_style eam/alloy/gpu command :h3 -pair_style eam/alloy/intel command :h3 -pair_style eam/alloy/kk command :h3 -pair_style eam/alloy/omp command :h3 -pair_style eam/alloy/opt command :h3 -pair_style eam/cd command :h3 -pair_style eam/cd/omp command :h3 -pair_style eam/cd/old command :h3 -pair_style eam/cd/old/omp command :h3 -pair_style eam/fs command :h3 -pair_style eam/fs/gpu command :h3 -pair_style eam/fs/intel command :h3 -pair_style eam/fs/kk command :h3 -pair_style eam/fs/omp command :h3 -pair_style eam/fs/opt command :h3 - -[Syntax:] - -pair_style style :pre - -style = {eam} or {eam/alloy} or {eam/cd} or {eam/cd/old} or {eam/fs} :ul - -[Examples:] - -pair_style eam -pair_coeff * * cuu3 -pair_coeff 1*3 1*3 niu3.eam :pre - -pair_style eam/alloy -pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni :pre - -pair_style eam/cd -pair_coeff * * ../potentials/FeCr.cdeam Fe Cr :pre - -pair_style eam/fs -pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni :pre - -[Description:] - -Style {eam} computes pairwise interactions for metals and metal alloys -using embedded-atom method (EAM) potentials "(Daw)"_#Daw. The total -energy Ei of an atom I is given by - -:c,image(Eqs/pair_eam.jpg) - -where F is the embedding energy which is a function of the atomic -electron density rho, phi is a pair potential interaction, and alpha -and beta are the element types of atoms I and J. The multi-body -nature of the EAM potential is a result of the embedding energy term. -Both summations in the formula are over all neighbors J of atom I -within the cutoff distance. - -The cutoff distance and the tabulated values of the functionals F, -rho, and phi are listed in one or more files which are specified by -the "pair_coeff"_pair_coeff.html command. These are ASCII text files -in a DYNAMO-style format which is described below. DYNAMO was the -original serial EAM MD code, written by the EAM originators. Several -DYNAMO potential files for different metals are included in the -"potentials" directory of the LAMMPS distribution. All of these files -are parameterized in terms of LAMMPS "metal units"_units.html. - -NOTE: The {eam} style reads single-element EAM potentials in the -DYNAMO {funcfl} format. Either single element or alloy systems can be -modeled using multiple {funcfl} files and style {eam}. For the alloy -case LAMMPS mixes the single-element potentials to produce alloy -potentials, the same way that DYNAMO does. Alternatively, a single -DYNAMO {setfl} file or Finnis/Sinclair EAM file can be used by LAMMPS -to model alloy systems by invoking the {eam/alloy} or {eam/cd} or -{eam/fs} styles as described below. These files require no mixing -since they specify alloy interactions explicitly. - -NOTE: Note that unlike for other potentials, cutoffs for EAM -potentials are not set in the pair_style or pair_coeff command; they -are specified in the EAM potential files themselves. Likewise, the -EAM potential files list atomic masses; thus you do not need to use -the "mass"_mass.html command to specify them. - -There are several WWW sites that distribute and document EAM -potentials stored in DYNAMO or other formats: - -http://www.ctcms.nist.gov/potentials -http://cst-www.nrl.navy.mil/ccm6/ap -http://enpub.fulton.asu.edu/cms/potentials/main/main.htm :pre - -These potentials should be usable with LAMMPS, though the alternate -formats would need to be converted to the DYNAMO format used by LAMMPS -and described on this page. The NIST site is maintained by Chandler -Becker (cbecker at nist.gov) who is good resource for info on -interatomic potentials and file formats. - -:line - -For style {eam}, potential values are read from a file that is in the -DYNAMO single-element {funcfl} format. If the DYNAMO file was created -by a Fortran program, it cannot have "D" values in it for exponents. -C only recognizes "e" or "E" for scientific notation. - -Note that unlike for other potentials, cutoffs for EAM potentials are -not set in the pair_style or pair_coeff command; they are specified in -the EAM potential files themselves. - -For style {eam} a potential file must be assigned to each I,I pair of -atom types by using one or more pair_coeff commands, each with a -single argument: - -filename :ul - -Thus the following command - -pair_coeff *2 1*2 cuu3.eam :pre - -will read the cuu3 potential file and use the tabulated Cu values for -F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs -1,2 and 2,1 are ignored). See the "pair_coeff"_pair_coeff.html doc -page for alternate ways to specify the path for the potential file. -In effect, this makes atom types 1 and 2 in LAMMPS be Cu atoms. -Different single-element files can be assigned to different atom types -to model an alloy system. The mixing to create alloy potentials for -type pairs with I != J is done automatically the same way that the -serial DYNAMO code originally did it; you do not need to specify -coefficients for these type pairs. - -{Funcfl} files in the {potentials} directory of the LAMMPS -distribution have an ".eam" suffix. A DYNAMO single-element {funcfl} -file is formatted as follows: - -line 1: comment (ignored) -line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC) -line 3: Nrho, drho, Nr, dr, cutoff :ul - -On line 2, all values but the mass are ignored by LAMMPS. The mass is -in mass "units"_units.html, e.g. mass number or grams/mole for metal -units. The cubic lattice constant is in Angstroms. On line 3, Nrho -and Nr are the number of tabulated values in the subsequent arrays, -drho and dr are the spacing in density and distance space for the -values in those arrays, and the specified cutoff becomes the pairwise -cutoff used by LAMMPS for the potential. The units of dr are -Angstroms; I'm not sure of the units for drho - some measure of -electron density. - -Following the three header lines are three arrays of tabulated values: - -embedding function F(rho) (Nrho values) -effective charge function Z(r) (Nr values) -density function rho(r) (Nr values) :ul - -The values for each array can be listed as multiple values per line, -so long as each array starts on a new line. For example, the -individual Z(r) values are for r = 0,dr,2*dr, ... (Nr-1)*dr. - -The units for the embedding function F are eV. The units for the -density function rho are the same as for drho (see above, electron -density). The units for the effective charge Z are "atomic charge" or -sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used -by LAMMPS to compute the pair potential term in the EAM energy -expression as r*phi, in units of eV-Angstroms, via the formula - -r*phi = 27.2 * 0.529 * Zi * Zj :pre - -where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms. - -:line - -Style {eam/alloy} computes pairwise interactions using the same -formula as style {eam}. However the associated -"pair_coeff"_pair_coeff.html command reads a DYNAMO {setfl} file -instead of a {funcfl} file. {Setfl} files can be used to model a -single-element or alloy system. In the alloy case, as explained -above, {setfl} files contain explicit tabulated values for alloy -interactions. Thus they allow more generality than {funcfl} files for -modeling alloys. - -For style {eam/alloy}, potential values are read from a file that is -in the DYNAMO multi-element {setfl} format, except that element names -(Ni, Cu, etc) are added to one of the lines in the file. If the -DYNAMO file was created by a Fortran program, it cannot have "D" -values in it for exponents. C only recognizes "e" or "E" for -scientific notation. - -Only a single pair_coeff command is used with the {eam/alloy} style -which specifies a DYNAMO {setfl} file, which contains information for -M elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of {setfl} elements to atom types :ul - -As an example, the potentials/NiAlH_jea.eam.alloy file is a {setfl} -file which has tabulated EAM values for 3 elements and their alloy -interactions: Ni, Al, and H. See the "pair_coeff"_pair_coeff.html doc -page for alternate ways to specify the path for the potential file. -If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to -be Ni, and the 4th to be Al, you would use the following pair_coeff -command: - -pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni -element in the {setfl} file. The final Al argument maps LAMMPS atom -type 4 to the Al element in the {setfl} file. Note that there is no -requirement that your simulation use all the elements specified by the -{setfl} file. - -If a mapping value is specified as NULL, the mapping is not performed. -This can be used when an {eam/alloy} potential is used as part of the -{hybrid} pair style. The NULL values are placeholders for atom types -that will be used with other potentials. - -{Setfl} files in the {potentials} directory of the LAMMPS distribution -have an ".eam.alloy" suffix. A DYNAMO multi-element {setfl} file is -formatted as follows: - -lines 1,2,3 = comments (ignored) -line 4: Nelements Element1 Element2 ... ElementN -line 5: Nrho, drho, Nr, dr, cutoff :ul - -In a DYNAMO {setfl} file, line 4 only lists Nelements = the # of -elements in the {setfl} file. For LAMMPS, the element name (Ni, Cu, -etc) of each element must be added to the line, in the order the -elements appear in the file. - -The meaning and units of the values in line 5 is the same as for the -{funcfl} file described above. Note that the cutoff (in Angstroms) is -a global value, valid for all pairwise interactions for all element -pairings. - -Following the 5 header lines are Nelements sections, one for each -element, each with the following format: - -line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC) -embedding function F(rho) (Nrho values) -density function rho(r) (Nr values) :ul - -As with the {funcfl} files, only the mass (in mass "units"_units.html, -e.g. mass number or grams/mole for metal units) is used by LAMMPS from -the 1st line. The cubic lattice constant is in Angstroms. The F and -rho arrays are unique to a single element and have the same format and -units as in a {funcfl} file. - -Following the Nelements sections, Nr values for each pair potential -phi(r) array are listed for all i,j element pairs in the same format -as other arrays. Since these interactions are symmetric (i,j = j,i) -only phi arrays with i >= j are listed, in the following order: i,j = -(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements, -Nelements). Unlike the effective charge array Z(r) in {funcfl} files, -the tabulated values for each phi function are listed in {setfl} files -directly as r*phi (in units of eV-Angstroms), since they are for atom -pairs. - -:line - -Style {eam/cd} is similar to the {eam/alloy} style, except that it -computes alloy pairwise interactions using the concentration-dependent -embedded-atom method (CD-EAM). This model can reproduce the enthalpy -of mixing of alloys over the full composition range, as described in -"(Stukowski)"_#Stukowski. Style {eam/cd/old} is an older, slightly -different and slower two-site formulation of the model "(Caro)"_#Caro. - -The pair_coeff command is specified the same as for the {eam/alloy} -style. However the DYNAMO {setfl} file must has two -lines added to it, at the end of the file: - -line 1: Comment line (ignored) -line 2: N Coefficient0 Coefficient1 ... CoefficientN :ul - -The last line begins with the degree {N} of the polynomial function -{h(x)} that modifies the cross interaction between A and B elements. -Then {N+1} coefficients for the terms of the polynomial are then -listed. - -Modified EAM {setfl} files used with the {eam/cd} style must contain -exactly two elements, i.e. in the current implementation the {eam/cd} -style only supports binary alloys. The first and second elements in -the input EAM file are always taken as the {A} and {B} species. - -{CD-EAM} files in the {potentials} directory of the LAMMPS -distribution have a ".cdeam" suffix. - -:line - -Style {eam/fs} computes pairwise interactions for metals and metal -alloys using a generalized form of EAM potentials due to Finnis and -Sinclair "(Finnis)"_#Finnis1. The total energy Ei of an atom I is -given by - -:c,image(Eqs/pair_eam_fs.jpg) - -This has the same form as the EAM formula above, except that rho is -now a functional specific to the atomic types of both atoms I and J, -so that different elements can contribute differently to the total -electron density at an atomic site depending on the identity of the -element at that atomic site. - -The associated "pair_coeff"_pair_coeff.html command for style {eam/fs} -reads a DYNAMO {setfl} file that has been extended to include -additional rho_alpha_beta arrays of tabulated values. A discussion of -how FS EAM differs from conventional EAM alloy potentials is given in -"(Ackland1)"_#Ackland1. An example of such a potential is the same -author's Fe-P FS potential "(Ackland2)"_#Ackland2. Note that while FS -potentials always specify the embedding energy with a square root -dependence on the total density, the implementation in LAMMPS does not -require that; the user can tabulate any functional form desired in the -FS potential files. - -For style {eam/fs}, the form of the pair_coeff command is exactly the -same as for style {eam/alloy}, e.g. - -pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al :pre - -where there are N additional arguments after the filename, where N is -the number of LAMMPS atom types. See the "pair_coeff"_pair_coeff.html -doc page for alternate ways to specify the path for the potential -file. The N values determine the mapping of LAMMPS atom types to EAM -elements in the file, as described above for style {eam/alloy}. As -with {eam/alloy}, if a mapping value is NULL, the mapping is not -performed. This can be used when an {eam/fs} potential is used as -part of the {hybrid} pair style. The NULL values are used as -placeholders for atom types that will be used with other potentials. - -FS EAM files include more information than the DYNAMO {setfl} format -files read by {eam/alloy}, in that i,j density functionals for all -pairs of elements are included as needed by the Finnis/Sinclair -formulation of the EAM. - -FS EAM files in the {potentials} directory of the LAMMPS distribution -have an ".eam.fs" suffix. They are formatted as follows: - -lines 1,2,3 = comments (ignored) -line 4: Nelements Element1 Element2 ... ElementN -line 5: Nrho, drho, Nr, dr, cutoff :ul - -The 5-line header section is identical to an EAM {setfl} file. - -Following the header are Nelements sections, one for each element I, -each with the following format: - -line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC) -embedding function F(rho) (Nrho values) -density function rho(r) for element I at element 1 (Nr values) -density function rho(r) for element I at element 2 -... -density function rho(r) for element I at element Nelement :ul - -The units of these quantities in line 1 are the same as for {setfl} -files. Note that the rho(r) arrays in Finnis/Sinclair can be -asymmetric (i,j != j,i) so there are Nelements^2 of them listed in the -file. - -Following the Nelements sections, Nr values for each pair potential -phi(r) array are listed in the same manner (r*phi, units of -eV-Angstroms) as in EAM {setfl} files. Note that in Finnis/Sinclair, -the phi(r) arrays are still symmetric, so only phi arrays for i >= j -are listed. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above with the individual styles. You never need to specify -a pair_coeff command with I != J arguments for the eam styles. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -The eam pair styles do not write their information to "binary restart -files"_restart.html, since it is stored in tabulated potential files. -Thus, you need to re-specify the pair_style and pair_coeff commands in -an input script that reads a restart file. - -The eam pair styles can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. They do not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -All of these styles are part of the MANYBODY package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Ackland1) -[(Ackland1)] Ackland, Condensed Matter (2005). - -:link(Ackland2) -[(Ackland2)] Ackland, Mendelev, Srolovitz, Han and Barashev, Journal -of Physics: Condensed Matter, 16, S2629 (2004). - -:link(Daw) -[(Daw)] Daw, Baskes, Phys Rev Lett, 50, 1285 (1983). -Daw, Baskes, Phys Rev B, 29, 6443 (1984). - -:link(Finnis1) -[(Finnis)] Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984). - -:link(Stukowski) -[(Stukowski)] Stukowski, Sadigh, Erhart, Caro; Modeling Simulation -Materials Science & Engineering, 7, 075005 (2009). - -:link(Caro) -[(Caro)] A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005) diff --git a/doc/txt/pair_edip.txt b/doc/txt/pair_edip.txt deleted file mode 100644 index 09eb6ee63a..0000000000 --- a/doc/txt/pair_edip.txt +++ /dev/null @@ -1,172 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style edip command :h3 -pair_style edip/omp command :h3 -pair_style edip/multi command :h3 - -[Syntax:] - -pair_style style :pre - -style = {edip} or {edip/multi} :ul - -[Examples:] - -pair_style edip -pair_coeff * * Si.edip Si - -[Description:] - -The {edip} and {edip/multi} styles compute a 3-body "EDIP"_#EDIP -potential which is popular for modeling silicon materials where -it can have advantages over other models such as the -"Stillinger-Weber"_pair_sw.html or "Tersoff"_pair_tersoff.html -potentials. The {edip} style has been programmed for single element -potentials, while {edip/multi} supports multi-element EDIP runs. - -In EDIP, the energy E of a system of atoms is - -:c,image(Eqs/pair_edip.jpg) - -where phi2 is a two-body term and phi3 is a three-body term. The -summations in the formula are over all neighbors J and K of atom I -within a cutoff distance = a. -Both terms depend on the local environment of atom I through its -effective coordination number defined by Z, which is unity for a -cutoff distance < c and gently goes to 0 at distance = a. - -Only a single pair_coeff command is used with the {edip} style which -specifies a EDIP potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of EDIP elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -As an example, imagine a file Si.edip has EDIP values for Si. - -EDIP files in the {potentials} directory of the LAMMPS -distribution have a ".edip" suffix. Lines that are not blank or -comments (starting with #) define parameters for a triplet of -elements. The parameters in a single entry correspond to the two-body -and three-body coefficients in the formula above: - -element 1 (the center atom in a 3-body interaction) -element 2 -element 3 -A (energy units) -B (distance units) -cutoffA (distance units) -cutoffC (distance units) -alpha -beta -eta -gamma (distance units) -lambda (energy units) -mu -tho -sigma (distance units) -Q0 -u1 -u2 -u3 -u4 :ul - -The A, B, beta, sigma parameters are used only for two-body interactions. -The eta, gamma, lambda, mu, Q0 and all u1 to u4 parameters are used only -for three-body interactions. The alpha and cutoffC parameters are used -for the coordination environment function only. - -The EDIP potential file must contain entries for all the -elements listed in the pair_coeff command. It can also contain -entries for additional elements not being used in a particular -simulation; LAMMPS ignores those entries. - -For a single-element simulation, only a single entry is required -(e.g. SiSiSi). For a two-element simulation, the file must contain 8 -entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that -specify EDIP parameters for all permutations of the two elements -interacting in three-body configurations. Thus for 3 elements, 27 -entries would be required, etc. - -At the moment, only a single element parameterization is -implemented. However, the author is not aware of other -multi-element EDIP parameterization. If you know any and -you are interest in that, please contact the author of -the EDIP package. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -This pair style requires the "newton"_newton.html setting to be "on" -for pair interactions. - -The EDIP potential files provided with LAMMPS (see the potentials directory) -are parameterized for metal "units"_units.html. -You can use the EDIP potential with any LAMMPS units, but you would need -to create your own EDIP potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(EDIP) -[(EDIP)] J F Justo et al, Phys Rev B 58, 2539 (1998). diff --git a/doc/txt/pair_eff.txt b/doc/txt/pair_eff.txt deleted file mode 100644 index 1df94ebecc..0000000000 --- a/doc/txt/pair_eff.txt +++ /dev/null @@ -1,313 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style eff/cut command :h3 - -[Syntax:] - -pair_style eff/cut cutoff keyword args ... :pre - -cutoff = global cutoff for Coulombic interactions :ulb,l -zero or more keyword/value pairs may be appended :l -keyword = {limit/eradius} or {pressure/evirials} or {ecp} - {limit/eradius} args = none - {pressure/evirials} args = none - {ecp} args = type element type element ... - type = LAMMPS atom type (1 to Ntypes) - element = element symbol (e.g. H, Si) :pre -:ule - -[Examples:] - -pair_style eff/cut 39.7 -pair_style eff/cut 40.0 limit/eradius -pair_style eff/cut 40.0 limit/eradius pressure/evirials -pair_style eff/cut 40.0 ecp 1 Si 3 C -pair_coeff * * -pair_coeff 2 2 20.0 -pair_coeff 1 s 0.320852 2.283269 0.814857 -pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621 :pre - -[Description:] - -This pair style contains a LAMMPS implementation of the electron Force -Field (eFF) potential currently under development at Caltech, as -described in "(Jaramillo-Botero)"_#Jaramillo-Botero. The eFF for Z<6 -was first introduced by "(Su)"_#Su in 2007. It has been extended to -higher Zs by using effective core potentials (ECPs) that now cover up -to 2nd and 3rd row p-block elements of the periodic table. - -eFF can be viewed as an approximation to QM wave packet dynamics and -Fermionic molecular dynamics, combining the ability of electronic -structure methods to describe atomic structure, bonding, and chemistry -in materials, and of plasma methods to describe nonequilibrium -dynamics of large systems with a large number of highly excited -electrons. Yet, eFF relies on a simplification of the electronic -wave function in which electrons are described as floating Gaussian -wave packets whose position and size respond to the various dynamic -forces between interacting classical nuclear particles and spherical -Gaussian electron wave packets. The wave function is taken to be a -Hartree product of the wave packets. To compensate for the lack of -explicit antisymmetry in the resulting wave function, a spin-dependent -Pauli potential is included in the Hamiltonian. Substituting this -wave function into the time-dependent Schrodinger equation produces -equations of motion that correspond - to second order - to classical -Hamiltonian relations between electron position and size, and their -conjugate momenta. The N-electron wave function is described as a -product of one-electron Gaussian functions, whose size is a dynamical -variable and whose position is not constrained to a nuclear -center. This form allows for straightforward propagation of the -wave function, with time, using a simple formulation from which the -equations of motion are then integrated with conventional MD -algorithms. In addition to this spin-dependent Pauli repulsion -potential term between Gaussians, eFF includes the electron kinetic -energy from the Gaussians. These two terms are based on -first-principles quantum mechanics. On the other hand, nuclei are -described as point charges, which interact with other nuclei and -electrons through standard electrostatic potential forms. - -The full Hamiltonian (shown below), contains then a standard -description for electrostatic interactions between a set of -delocalized point and Gaussian charges which include, nuclei-nuclei -(NN), electron-electron (ee), and nuclei-electron (Ne). Thus, eFF is a -mixed QM-classical mechanics method rather than a conventional force -field method (in which electron motions are averaged out into ground -state nuclear motions, i.e a single electronic state, and particle -interactions are described via empirically parameterized interatomic -potential functions). This makes eFF uniquely suited to simulate -materials over a wide range of temperatures and pressures where -electronically excited and ionized states of matter can occur and -coexist. Furthermore, the interactions between particles -nuclei and -electrons- reduce to the sum of a set of effective pairwise potentials -in the eFF formulation. The {eff/cut} style computes the pairwise -Coulomb interactions between nuclei and electrons (E_NN,E_Ne,E_ee), -and the quantum-derived Pauli (E_PR) and Kinetic energy interactions -potentials between electrons (E_KE) for a total energy expression -given as, - -:c,image(Eqs/eff_energy_expression.jpg) - -The individual terms are defined as follows: - -:c,image(Eqs/eff_KE.jpg) - -:c,image(Eqs/eff_NN.jpg) - -:c,image(Eqs/eff_Ne.jpg) - -:c,image(Eqs/eff_ee.jpg) - -:c,image(Eqs/eff_Pauli.jpg) - -where, s_i correspond to the electron sizes, the sigmas i's to the -fixed spins of the electrons, Z_i to the charges on the nuclei, R_ij -to the distances between the nuclei or the nuclei and electrons, and -r_ij to the distances between electrons. For additional details see -"(Jaramillo-Botero)"_#Jaramillo-Botero. - -The overall electrostatics energy is given in Hartree units of energy -by default and can be modified by an energy-conversion constant, -according to the units chosen (see "electron_units"_units.html). The -cutoff Rc, given in Bohrs (by default), truncates the interaction -distance. The recommended cutoff for this pair style should follow -the minimum image criterion, i.e. half of the minimum unit cell -length. - -Style {eff/long} (not yet available) computes the same interactions as -style {eff/cut} except that an additional damping factor is applied so -it can be used in conjunction with the -"kspace_style"_kspace_style.html command and its {ewald} or {pppm} -option. The Coulombic cutoff specified for this style means that -pairwise interactions within this distance are computed directly; -interactions outside that distance are computed in reciprocal space. - -This potential is designed to be used with "atom_style -electron"_atom_style.html definitions, in order to handle the -description of systems with interacting nuclei and explicit electrons. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -cutoff (distance units) :ul - -For {eff/cut}, the cutoff coefficient is optional. If it is not used -(as in some of the examples above), the default global value specified -in the pair_style command is used. - -For {eff/long} (not yet available) no cutoff will be specified for an -individual I,J type pair via the "pair_coeff"_pair_coeff.html command. -All type pairs use the same global cutoff specified in the pair_style -command. - -:line - -The {limit/eradius} and {pressure/evirials} keywords are optional. -Neither or both must be specified. If not specified they are unset. - -The {limit/eradius} keyword is used to restrain electron size from -becoming excessively diffuse at very high temperatures were the -Gaussian wave packet representation breaks down, and from expanding as -free particles to infinite size. If unset, electron radius is free to -increase without bounds. If set, a restraining harmonic potential of -the form E = 1/2k_ss^2 for s > L_box/2, where k_s = 1 Hartrees/Bohr^2, -is applied on the electron radius. - -The {pressure/evirials} keyword is used to control between two types -of pressure computation: if unset, the computed pressure does not -include the electronic radial virials contributions to the total -pressure (scalar or tensor). If set, the computed pressure will -include the electronic radial virial contributions to the total -pressure (scalar and tensor). - -The {ecp} keyword is used to associate an ECP representation for a -particular atom type. The ECP captures the orbital overlap between a -core pseudo particle and valence electrons within the Pauli repulsion. -A list of type:element-symbol pairs may be provided for all ECP -representations, after the "ecp" keyword. - -NOTE: Default ECP parameters are provided for C, N, O, Al, and Si. -Users can modify these using the pair_coeff command as exemplified -above. For this, the User must distinguish between two different -functional forms supported, one that captures the orbital overlap -assuming the s-type core interacts with an s-like valence electron -(s-s) and another that assumes the interaction is s-p. For systems -that exhibit significant p-character (e.g. C, N, O) the s-p form is -recommended. The "s" ECP form requires 3 parameters and the "p" 5 -parameters. - -NOTE: there are two different pressures that can be reported for eFF -when defining this pair_style, one (default) that considers electrons -do not contribute radial virial components (i.e. electrons treated as -incompressible 'rigid' spheres) and one that does. The radial -electronic contributions to the virials are only tallied if the -flexible pressure option is set, and this will affect both global and -per-atom quantities. In principle, the true pressure of a system is -somewhere in between the rigid and the flexible eFF pressures, but, -for most cases, the difference between these two pressures will not be -significant over long-term averaged runs (i.e. even though the energy -partitioning changes, the total energy remains similar). - -:line - -NOTE: This implementation of eFF gives a reasonably accurate description -for systems containing nuclei from Z = 1-6 in "all electron" -representations. For systems with increasingly non-spherical -electrons, Users should use the ECP representations. ECPs are now -supported and validated for most of the 2nd and 3rd row elements of -the p-block. Predefined parameters are provided for C, N, O, Al, and -Si. The ECP captures the orbital overlap between the core and valence -electrons (i.e. Pauli repulsion) with one of the functional forms: - -:c,image(Eqs/eff_ECP1.jpg) -:c,image(Eqs/eff_ECP2.jpg) - -Where the 1st form correspond to core interactions with s-type valence -electrons and the 2nd to core interactions with p-type valence -electrons. - -The current version adds full support for models with fixed-core and -ECP definitions. to enable larger timesteps (i.e. by avoiding the -high frequency vibrational modes -translational and radial- of the 2 s -electrons), and in the ECP case to reduce the increased orbital -complexity in higher Z elements (up to Z<18). A fixed-core should be -defined with a mass that includes the corresponding nuclear mass plus -the 2 s electrons in atomic mass units (2x5.4857990943e-4), and a -radius equivalent to that of minimized 1s electrons (see examples -under /examples/USER/eff/fixed-core). An pseudo-core should be -described with a mass that includes the corresponding nuclear mass, -plus all the core electrons (i.e no outer shell electrons), and a -radius equivalent to that of a corresponding minimized full-electron -system. The charge for a pseudo-core atom should be given by the -number of outer shell electrons. - -In general, eFF excels at computing the properties of materials in -extreme conditions and tracing the system dynamics over multi-picosecond -timescales; this is particularly relevant where electron excitations -can change significantly the nature of bonding in the system. It can -capture with surprising accuracy the behavior of such systems because -it describes consistently and in an unbiased manner many different -kinds of bonds, including covalent, ionic, multicenter, ionic, and -plasma, and how they interconvert and/or change when they become -excited. eFF also excels in computing the relative thermochemistry of -isodemic reactions and conformational changes, where the bonds of the -reactants are of the same type as the bonds of the products. eFF -assumes that kinetic energy differences dominate the overall exchange -energy, which is true when the electrons present are nearly spherical -and nodeless and valid for covalent compounds such as dense hydrogen, -hydrocarbons, and diamond; alkali metals (e.g. lithium), alkali earth -metals (e.g. beryllium) and semimetals such as boron; and various -compounds containing ionic and/or multicenter bonds, such as boron -dihydride. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the cutoff distance for the -{eff/cut} style can be mixed. The default mix value is {geometric}. -See the "pair_modify" command for details. - -The "pair_modify"_pair_modify.html shift option is not relevant for -these pair styles. - -The {eff/long} (not yet available) style supports the -"pair_modify"_pair_modify.html table option for tabulation of the -short-range portion of the long-range Coulombic interaction. - -These pair styles do not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -These pair styles write their information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -These pair styles can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. They do not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -These pair styles will only be enabled if LAMMPS is built with the -USER-EFF package. It will only be enabled if LAMMPS was built with -that package. See the "Build package"_Build_package.html doc page for -more info. - -These pair styles require that particles store electron attributes -such as radius, radial velocity, and radial force, as defined by the -"atom_style"_atom_style.html. The {electron} atom style does all of -this. - -Thes pair styles require you to use the "comm_modify vel -yes"_comm_modify.html command so that velocities are stored by ghost -atoms. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] - -If not specified, limit_eradius = 0 and pressure_with_evirials = 0. - -:line - -:link(Su) -[(Su)] Su and Goddard, Excited Electron Dynamics Modeling of Warm -Dense Matter, Phys Rev Lett, 99:185003 (2007). - -:link(Jaramillo-Botero) -[(Jaramillo-Botero)] Jaramillo-Botero, Su, Qi, Goddard, Large-scale, -Long-term Non-adiabatic Electron Molecular Dynamics for Describing -Material Properties and Phenomena in Extreme Environments, J Comp -Chem, 32, 497-512 (2011). diff --git a/doc/txt/pair_eim.txt b/doc/txt/pair_eim.txt deleted file mode 100644 index 5f9dcd4c5c..0000000000 --- a/doc/txt/pair_eim.txt +++ /dev/null @@ -1,173 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style eim command :h3 -pair_style eim/omp command :h3 - -[Syntax:] - -pair_style style :pre - -style = {eim} :ul - -[Examples:] - -pair_style eim -pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl -pair_coeff * * Na Cl ffield.eim Na Na Na Cl -pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na :pre - -[Description:] - -Style {eim} computes pairwise interactions for ionic compounds -using embedded-ion method (EIM) potentials "(Zhou)"_#Zhou2. The -energy of the system E is given by - -:c,image(Eqs/pair_eim1.jpg) - -The first term is a double pairwise sum over the J neighbors of all I -atoms, where phi_ij is a pair potential. The second term sums over -the embedding energy E_i of atom I, which is a function of its charge -q_i and the electrical potential sigma_i at its location. E_i, q_i, -and sigma_i are calculated as - -:c,image(Eqs/pair_eim2.jpg) - -where eta_ji is a pairwise function describing electron flow from atom -I to atom J, and psi_ij is another pairwise function. The multi-body -nature of the EIM potential is a result of the embedding energy term. -A complete list of all the pair functions used in EIM is summarized -below - -:c,image(Eqs/pair_eim3.jpg) - -Here E_b, r_e, r_(c,phi), alpha, beta, A_(psi), zeta, r_(s,psi), -r_(c,psi), A_(eta), r_(s,eta), r_(c,eta), chi, and pair function type -p are parameters, with subscripts ij indicating the two species of -atoms in the atomic pair. - -NOTE: Even though the EIM potential is treating atoms as charged ions, -you should not use a LAMMPS "atom_style"_atom_style.html that stores a -charge on each atom and thus requires you to assign a charge to each -atom, e.g. the {charge} or {full} atom styles. This is because the -EIM potential infers the charge on an atom from the equation above for -q_i; you do not assign charges explicitly. - -:line - -All the EIM parameters are listed in a potential file which is -specified by the "pair_coeff"_pair_coeff.html command. This is an -ASCII text file in a format described below. The "ffield.eim" file -included in the "potentials" directory of the LAMMPS distribution -currently includes nine elements Li, Na, K, Rb, Cs, F, Cl, Br, and I. -A system with any combination of these elements can be modeled. This -file is parameterized in terms of LAMMPS "metal units"_units.html. - -Note that unlike other potentials, cutoffs for EIM potentials are not -set in the pair_style or pair_coeff command; they are specified in the -EIM potential file itself. Likewise, the EIM potential file lists -atomic masses; thus you do not need to use the "mass"_mass.html -command to specify them. - -Only a single pair_coeff command is used with the {eim} style which -specifies an EIM potential file and the element(s) to extract -information for. The EIM elements are mapped to LAMMPS atom types by -specifying N additional arguments after the filename in the pair_coeff -command, where N is the number of LAMMPS atom types: - -Elem1, Elem2, ... -EIM potential file -N element names = mapping of EIM elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -As an example like one of those above, suppose you want to model a -system with Na and Cl atoms. If your LAMMPS simulation has 4 atoms -types and you want the 1st 3 to be Na, and the 4th to be Cl, you would -use the following pair_coeff command: - -pair_coeff * * Na Cl ffield.eim Na Na Na Cl :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The filename is the EIM potential file. The Na and Cl arguments -(before the file name) are the two elements for which info will be -extracted from the potential file. The first three trailing Na -arguments map LAMMPS atom types 1,2,3 to the EIM Na element. The -final Cl argument maps LAMMPS atom type 4 to the EIM Cl element. - -If a mapping value is specified as NULL, the mapping is not performed. -This can be used when an {eim} potential is used as part of the -{hybrid} pair style. The NULL values are placeholders for atom types -that will be used with other potentials. - -The ffield.eim file in the {potentials} directory of the LAMMPS -distribution is formatted as follows: - -Lines starting with # are comments and are ignored by LAMMPS. Lines -starting with "global:" include three global values. The first value -divides the cations from anions, i.e., any elements with -electronegativity above this value are viewed as anions, and any -elements with electronegativity below this value are viewed as -cations. The second and third values are related to the cutoff -function - i.e. the 0.510204, 1.64498, and 0.010204 shown in the above -equation can be derived from these values. - -Lines starting with "element:" are formatted as follows: name of -element, atomic number, atomic mass, electronic negativity, atomic -radius (LAMMPS ignores it), ionic radius (LAMMPS ignores it), cohesive -energy (LAMMPS ignores it), and q0 (must be 0). - -Lines starting with "pair:" are entered as: element 1, element 2, -r_(c,phi), r_(c,phi) (redundant for historical reasons), E_b, r_e, -alpha, beta, r_(c,eta), A_(eta), r_(s,eta), r_(c,psi), A_(psi), zeta, -r_(s,psi), and p. - -The lines in the file can be in any order; LAMMPS extracts the info it -needs. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This style is part of the MANYBODY package. It is only enabled if -LAMMPS was built with that package. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Zhou2) -[(Zhou)] Zhou, submitted for publication (2010). Please contact -Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov. diff --git a/doc/txt/pair_exp6_rx.txt b/doc/txt/pair_exp6_rx.txt deleted file mode 100644 index 790674644d..0000000000 --- a/doc/txt/pair_exp6_rx.txt +++ /dev/null @@ -1,185 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style exp6/rx command :h3 -pair_style exp6/rx/kk command :h3 - -[Syntax:] - -pair_style exp6/rx cutoff ... :pre - -cutoff = global cutoff for DPD interactions (distance units) -weighting = fractional or molecular (optional) :ul - -[Examples:] - -pair_style exp6/rx 10.0 -pair_style exp6/rx 10.0 fractional -pair_style exp6/rx 10.0 molecular -pair_coeff * * exp6.params h2o h2o exponent 1.0 1.0 10.0 -pair_coeff * * exp6.params h2o 1fluid exponent 1.0 1.0 10.0 -pair_coeff * * exp6.params 1fluid 1fluid exponent 1.0 1.0 10.0 -pair_coeff * * exp6.params 1fluid 1fluid none 10.0 -pair_coeff * * exp6.params 1fluid 1fluid polynomial filename 10.0 :pre - -[Description:] - -Style {exp6/rx} is used in reaction DPD simulations, where the -coarse-grained (CG) particles are composed of {m} species whose -reaction rate kinetics are determined from a set of {n} reaction rate -equations through the "fix rx"_fix_rx.html command. The species of -one CG particle can interact with a species in a neighboring CG -particle through a site-site interaction potential model. The -{exp6/rx} style computes an exponential-6 potential given by - -:c,image(Eqs/pair_exp6_rx.jpg) - -where the {epsilon} parameter determines the depth of the potential -minimum located at {Rm}, and {alpha} determines the softness of the repulsion. - -The coefficients must be defined for each species in a given particle -type via the "pair_coeff"_pair_coeff.html command as in the examples -above, where the first argument is the filename that includes the -exponential-6 parameters for each species. The file includes the -species tag followed by the {alpha}, {epsilon} and {Rm} -parameters. The format of the file is described below. - -The second and third arguments specify the site-site interaction -potential between two species contained within two different -particles. The species tags must either correspond to the species -defined in the reaction kinetics files specified with the "fix -rx"_fix_rx.html command or they must correspond to the tag "1fluid", -signifying interaction with a product species mixture determined -through a one-fluid approximation. The interaction potential is -weighted by the geometric average of either the mole fraction concentrations -or the number of molecules associated with the interacting coarse-grained -particles (see the {fractional} or {molecular} weighting pair style options). -The coarse-grained potential is stored before and after the -reaction kinetics solver is applied, where the difference is defined -to be the internal chemical energy (uChem). - -The fourth argument specifies the type of scaling that will be used -to scale the EXP-6 parameters as reactions occur. Currently, there -are three scaling options: {exponent}, {polynomial} and {none}. - -Exponent scaling requires two additional arguments for scaling -the {Rm} and {epsilon} parameters, respectively. The scaling factor -is computed by phi^exponent, where phi is the number of molecules -represented by the coarse-grain particle and exponent is specified -as a pair coefficient argument for {Rm} and {epsilon}, respectively. -The {Rm} and {epsilon} parameters are multiplied by the scaling -factor to give the scaled interaction parameters for the CG particle. - -Polynomial scaling requires a filename to be specified as a pair -coeff argument. The file contains the coefficients to a fifth order -polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend -upon phi (the number of molecules represented by the CG particle). -The format of a polynomial file is provided below. - -The {none} option to the scaling does not have any additional pair coeff -arguments. This is equivalent to specifying the {exponent} option with -{Rm} and {epsilon} exponents of 0.0 and 0.0, respectively. - -The final argument specifies the interaction cutoff (optional). - -:line - -The format of a tabulated file is as follows (without the -parenthesized comments): - -# exponential-6 parameters for various species (one or more comment or blank lines) :pre -h2o exp6 11.00 0.02 3.50 (species, exp6, alpha, Rm, epsilon) -no2 exp6 13.60 0.01 3.70 -... -co2 exp6 13.00 0.03 3.20 :pre - -The format of the polynomial scaling file as follows (without the -parenthesized comments): - -# POLYNOMIAL FILE (one or more comment or blank lines) :pre -# General Functional Form: -# A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F -# -# Parameter A B C D E F - (blank) -alpha 0.0000 0.00000 0.00008 0.04955 -0.73804 13.63201 -epsilon 0.0000 0.00478 -0.06283 0.24486 -0.33737 2.60097 -rm 0.0001 -0.00118 -0.00253 0.05812 -0.00509 1.50106 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. - -Following a blank line, the next N lines list the species and their -corresponding parameters. The first argument is the species tag, the -second argument is the exp6 tag, the 3rd argument is the {alpha} -parameter (energy units), the 4th argument is the {epsilon} parameter -(energy-distance^6 units), and the 5th argument is the {Rm} parameter -(distance units). If a species tag of "1fluid" is listed as a pair -coefficient, a one-fluid approximation is specified where a -concentration-dependent combination of the parameters is computed -through the following equations: - -:c,image(Eqs/pair_exp6_rx_oneFluid.jpg) - -where - -:c,image(Eqs/pair_exp6_rx_oneFluid2.jpg) - -and xa and xb are the mole fractions of a and b, respectively, which -comprise the gas mixture. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -This style does not support the "pair_modify"_pair_modify.html shift option -for the energy of the exp() and 1/r^6 portion of the pair interaction. - -This style does not support the pair_modify tail option for adding long-range -tail corrections to energy and pressure for the A,C terms in the -pair interaction. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] fractional weighting diff --git a/doc/txt/pair_extep.txt b/doc/txt/pair_extep.txt deleted file mode 100644 index 5d69df69e9..0000000000 --- a/doc/txt/pair_extep.txt +++ /dev/null @@ -1,40 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style extep command :h3 - -[Syntax:] - -pair_style extep :pre - -[Examples:] - -pair_style extep -pair_coeff * * BN.extep B N :pre - -[Description:] - -Style {extep} computes the Extended Tersoff Potential (ExTeP) -interactions as described in "(Los2017)"_#Los2017. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_tersoff" pair_tersoff.html - -[Default:] none - -:line - -:link(Los2017) -[(Los2017)] J. H. Los et al. "Extended Tersoff potential for boron nitride: -Energetics and elastic properties of pristine and defective h-BN", -Phys. Rev. B 96 (184108), 2017. diff --git a/doc/txt/pair_fep_soft.txt b/doc/txt/pair_fep_soft.txt deleted file mode 100644 index 0cf2519c73..0000000000 --- a/doc/txt/pair_fep_soft.txt +++ /dev/null @@ -1,360 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj/cut/soft command :h3 -pair_style lj/cut/soft/omp command :h3 -pair_style lj/cut/coul/cut/soft command :h3 -pair_style lj/cut/coul/cut/soft/omp command :h3 -pair_style lj/cut/coul/long/soft command :h3 -pair_style lj/cut/coul/long/soft/omp command :h3 -pair_style lj/cut/tip4p/long/soft command :h3 -pair_style lj/cut/tip4p/long/soft/omp command :h3 -pair_style lj/charmm/coul/long/soft command :h3 -pair_style lj/charmm/coul/long/soft/omp command :h3 -pair_style lj/class2/soft command :h3 -pair_style lj/class2/coul/cut/soft command :h3 -pair_style lj/class2/coul/long/soft command :h3 - pair_style coul/cut/soft command :h3 -pair_style coul/cut/soft/omp command :h3 -pair_style coul/long/soft command :h3 -pair_style coul/long/soft/omp command :h3 -pair_style tip4p/long/soft command :h3 -pair_style tip4p/long/soft/omp command :h3 -pair_style morse/soft command :h3 -[Syntax:] - -pair_style style args :pre - -style = {lj/cut/soft} or {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} or {lj/cut/tip4p/long/soft} or {lj/charmm/coul/long/soft} or {lj/class2/soft} or {lj/class2/coul/cut/soft} or {lj/class2/coul/long/soft} or {coul/cut/soft} or {coul/long/soft} or {tip4p/long/soft} or {morse/soft} -args = list of arguments for a particular style :ul - {lj/cut/soft} args = n alpha_lj cutoff - n, alpha_LJ = parameters of soft-core potential - cutoff = global cutoff for Lennard-Jones interactions (distance units) - {lj/cut/coul/cut/soft} args = n alpha_LJ alpha_C cutoff (cutoff2) - n, alpha_LJ, alpha_C = parameters of soft-core potential - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {lj/cut/coul/long/soft} args = n alpha_LJ alpha_C cutoff - n, alpha_LJ, alpha_C = parameters of the soft-core potential - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {lj/cut/tip4p/long/soft} args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2) - otype,htype = atom types for TIP4P O and H - btype,atype = bond and angle types for TIP4P waters - qdist = distance from O atom to massless charge (distance units) - n, alpha_LJ, alpha_C = parameters of the soft-core potential - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {lj/charmm/coul/long/soft} args = n alpha_LJ alpha_C inner outer (cutoff) - n, alpha_LJ, alpha_C = parameters of the soft-core potential - inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args) - cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args) - {lj/class2/soft} args = n alpha_lj cutoff - n, alpha_LJ = parameters of soft-core potential - cutoff = global cutoff for Lennard-Jones interactions (distance units) - {lj/class2/coul/cut/soft} args = n alpha_LJ alpha_C cutoff (cutoff2) - n, alpha_LJ, alpha_C = parameters of soft-core potential - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {lj/class2/coul/long/soft} args = n alpha_LJ alpha_C cutoff (cutoff2) - n, alpha_LJ, alpha_C = parameters of soft-core potential - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {coul/cut/soft} args = n alpha_C cutoff - n, alpha_C = parameters of the soft-core potential - cutoff = global cutoff for Coulomb interactions (distance units) - {coul/long/soft} args = n alpha_C cutoff - n, alpha_C = parameters of the soft-core potential - cutoff = global cutoff for Coulomb interactions (distance units) - {tip4p/long/soft} args = otype htype btype atype qdist n alpha_C cutoff - otype,htype = atom types for TIP4P O and H - btype,atype = bond and angle types for TIP4P waters - qdist = distance from O atom to massless charge (distance units) - n, alpha_C = parameters of the soft-core potential - cutoff = global cutoff for Coulomb interactions (distance units) - {morse/soft} args = n lf cutoff - n = soft-core parameter - lf = transformation range is lf < lambda < 1 - cutoff = global cutoff for Morse interactions (distance units) -:pre - -[Examples:] - -pair_style lj/cut/soft 2.0 0.5 9.5 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 1.0 9.5 :pre - -pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 -pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 0.5 10.0 -pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5 :pre - -pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 -pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 0.0 10.0 -pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 :pre - -pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 -pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5 -pair_coeff * * 0.155 3.1536 1.0 -pair_coeff 1 1 0.155 3.1536 1.0 9.5 :pre - -pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 -pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1 :pre - -pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5 -pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5 9.5 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 0.0 10.0 -pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 :pre - -pair_style coul/long/soft 1.0 10.0 9.5 -pair_coeff * * 1.0 -pair_coeff 1 1 1.0 9.5 :pre - -pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 -pair_coeff * * 1.0 -pair_coeff 1 1 1.0 9.5 :pre - -pair_style morse/soft 4 0.9 10.0 -pair_coeff * * 100.0 2.0 1.5 1.0 -pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 :pre - -[Description:] - -These pair styles have a soft repulsive core, tunable by a parameter lambda, -in order to avoid singularities during free energy calculations when sites are -created or annihilated "(Beutler)"_#Beutler. When lambda tends to 0 the pair -interaction vanishes with a soft repulsive core. When lambda tends to 1, the pair -interaction approaches the normal, non-soft potential. These pair styles -are suited for "alchemical" free energy calculations using the "fix -adapt/fep"_fix_adapt_fep.html and "compute fep"_compute_fep.html commands. - -The {lj/cut/soft} style and related sub-styles compute the 12-6 Lennard-Jones -and Coulomb potentials modified by a soft core, with the functional form - -:c,image(Eqs/pair_lj_soft.jpg) - -The {lj/class2/soft} style is a 9-6 potential with the exponent of the -denominator of the first term in brackets taking the value 1.5 instead of 2 -(other details differ, see the form of the potential in -"pair_class2"_pair_class2.html). - -Coulomb interactions can also be damped with a soft core at short distance, - -:c,image(Eqs/pair_coul_soft.jpg) - -In the Coulomb part C is an energy-conversion constant, q_i and q_j -are the charges on the 2 atoms, and epsilon is the dielectric constant -which can be set by the "dielectric"_dielectric.html command. - -The coefficient lambda is an activation parameter. When lambda = 1 the pair -potential is identical to a Lennard-Jones term or a Coulomb term or a -combination of both. When lambda = 0 the interactions are deactivated. The -transition between these two extrema is smoothed by a soft repulsive core in -order to avoid singularities in potential energy and forces when sites are -created or annihilated and can overlap "(Beutler)"_#Beutler. - -The parameters n, alpha_LJ and alpha_C are set in the -"pair_style"_pair_style.html command, before the cutoffs. Usual choices for the -exponent are n = 2 or n = 1. For the remaining coefficients alpha_LJ = 0.5 and -alpha_C = 10 Angstrom^2 are appropriate choices. Plots of the 12/6 LJ and -Coulomb terms are shown below, for lambda ranging from 1 to 0 every 0.1. - -:image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg) -:c - -For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles, as well -as for the equivalent {class2} versions, the following coefficients must be -defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html -command as in the examples above, or in the data file or restart files read by -the "read_data"_read_data.html or "read_restart"_read_restart.html commands, or -by mixing as described below: - -epsilon (energy units) -sigma (distance units) -lambda (activation parameter, between 0 and 1) -cutoff1 (distance units) -cutoff2 (distance units) :ul - -The latter two coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both LJ -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. You cannot specify 2 cutoffs for style {lj/cut/soft}, -since it has no Coulombic terms. For the {coul/cut/soft} and -{coul/long/soft} only lambda and the optional cutoff2 are to be -specified. - -Style {lj/cut/tip4p/long/soft} implements a soft-core version of the TIP4P water -model. The usage of the TIP4P pair style is documented in the -"pair_lj"_pair_lj.html styles. In the soft version the parameters n, alpha_LJ -and alpha_C are set in the "pair_style"_pair_style.html command, after the -specific parameters of the TIP4P water model and before the cutoffs. The -activation parameter lambda is supplied as an argument of the -"pair_coeff"_pair_coeff.html command, after epsilon and sigma and before the -optional cutoffs. - -Style {lj/charmm/coul/long/soft} implements a soft-core version of the modified -12-6 LJ potential used in CHARMM and documented in the -"pair_lj_charmm"_pair_charmm.html style. In the soft version the parameters n, -alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before -the global cutoffs. The activation parameter lambda is introduced as an argument -of the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and -before the optional eps14 and sigma14. - -Style {lj/class2/soft} implements a soft-core version of the 9-6 potential in -"pair_class2"_pair_class2.html. In the soft version the parameters n, alpha_LJ -and alpha_C are set in the "pair_style"_pair_style.html command, before the -global cutoffs. The activation parameter lambda is introduced as an argument of -the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and before -the optional cutoffs. - -The {coul/cut/soft}, {coul/long/soft} and {tip4p/long/soft} sub-styles -are designed to be combined with other pair potentials via the -"pair_style hybrid/overlay"_pair_hybrid.html command. This is because -they have no repulsive core. Hence, if used by themselves, there will -be no repulsion to keep two oppositely charged particles from -overlapping each other. In this case, if lambda = 1, a singularity may -occur. These sub-styles are suitable to represent charges embedded in -the Lennard-Jones radius of another site (for example hydrogen atoms -in several water models). - -NOTE: When using the soft-core Coulomb potentials with long-range -solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.) in a free -energy calculation in which sites holding electrostatic charges are -being created or annihilated (using "fix adapt/fep"_fix_adapt_fep.html -and "compute fep"_compute_fep.html) it is important to adapt both the -lambda activation parameter (from 0 to 1, or the reverse) and the -value of the charge (from 0 to its final value, or the reverse). This -ensures that long-range electrostatic terms (kspace) are correct. It -is not necessary to use soft-core Coulomb potentials if the van der -Waals site is present during the free-energy route, thus avoiding -overlap of the charges. Examples are provided in the LAMMPS source -directory tree, under examples/USER/fep. - -NOTE: To avoid division by zero do not set sigma = 0 in the {lj/cut/soft} and -related styles; use the lambda parameter instead to activate/deactivate -interactions, or use epsilon = 0 and sigma = 1. Alternatively, when sites do not -interact though the Lennard-Jones term the {coul/long/soft} or similar sub-style -can be used via the "pair_style hybrid/overlay"_pair_hybrid.html command. - -:line - -The {morse/soft} variant modifies the "pair_morse"_pair_morse.html style at -short range to have a soft core. The functional form differs from that of the -{lj/soft} styles, and is instead given by: - -:c,image(Eqs/pair_morse_soft.jpg) - -The {morse/soft} style requires the following pair coefficients: - -D0 (energy units) -alpha (1/distance units) -r0 (distance units) -lambda (unitless, between 0.0 and 1.0) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global morse cutoff is -used. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, tail correction, restart info]: - -The different versions of the {lj/cut/soft} pair styles support mixing. For atom -type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff -distance for these pair style can be mixed. The default mix value is -{geometric} for 12-6 styles. - -The mixing rule for epsilon and sigma for {lj/class2/soft} 9-6 potentials is to use the -{sixthpower} formulas. The "pair_modify mix"_pair_modify.html setting is thus -ignored for class2 potentials for epsilon and sigma. However it is still -followed for mixing the cutoff distance. See the "pair_modify"_pair_modify.html -command for details. - -The {morse/soft} pair style does not support mixing. Thus, coefficients for all -LJ pairs must be specified explicitly. - -All of the pair styles with soft core support the "pair_modify"_pair_modify.html -shift option for the energy of the Lennard-Jones portion of the pair -interaction. - -The different versions of the {lj/cut/soft} pair styles support the -"pair_modify"_pair_modify.html tail option for adding a long-range tail -correction to the energy and pressure for the Lennard-Jones portion of the pair -interaction. - -NOTE: The analytical form of the tail corrections for energy and pressure used -in the {lj/cut/soft} potentials are approximate, being identical to that of the -corresponding non-soft potentials scaled by a factor lambda^n. The errors due to -this approximation should be negligible. For example, for a cutoff of 2.5 sigma -this approximation leads to maximum relative errors in tail corrections of the -order of 1e-4 for energy and virial (alpha_LJ = 0.5, n = 2). The error vanishes -when lambda approaches 0 or 1. Note that these are the errors affecting the -long-range tail (itself a correction to the interaction energy) which includes -other approximations, namely that the system is homogeneous (local density equal -the average density) beyond the cutoff. - -The {morse/soft} pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and pressure. - -All of these pair styles write information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need to be -specified in an input script that reads a restart file. - -:line - -[Restrictions:] - -The pair styles with soft core are only enabled if LAMMPS was built with the -USER-FEP package. The {long} versions also require the KSPACE package to be -installed. The soft {tip4p} versions also require the MOLECULE package to be -installed. These styles are only enabled if LAMMPS was built with those -packages. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "fix adapt"_fix_adapt.html, -"fix adapt/fep"_fix_adapt_fep.html, "compute fep"_compute_fep.html - -[Default:] none - -:line - -:link(Beutler) -[(Beutler)] Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem -Phys Lett, 222, 529 (1994). diff --git a/doc/txt/pair_gauss.txt b/doc/txt/pair_gauss.txt deleted file mode 100644 index ef924b1ef0..0000000000 --- a/doc/txt/pair_gauss.txt +++ /dev/null @@ -1,187 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style gauss command :h3 -pair_style gauss/gpu command :h3 -pair_style gauss/omp command :h3 -pair_style gauss/cut command :h3 -pair_style gauss/cut/omp command :h3 - -[Syntax:] - -pair_style gauss cutoff -pair_style gauss/cut cutoff :pre - -cutoff = global cutoff for Gauss interactions (distance units) :ul - -[Examples:] - -pair_style gauss 12.0 -pair_coeff * * 1.0 0.9 -pair_coeff 1 4 1.0 0.9 10.0 :pre - -pair_style gauss/cut 3.5 -pair_coeff 1 4 0.2805 1.45 0.112 :pre - - -[Description:] - -Style {gauss} computes a tethering potential of the form - -:c,image(Eqs/pair_gauss.jpg) - -between an atom and its corresponding tether site which will typically -be a frozen atom in the simulation. Rc is the cutoff. - -The following coefficients must be defined for each pair of atom types -via the "pair_coeff"_pair_coeff.html command as in the examples above, -or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -A (energy units) -B (1/distance^2 units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global cutoff -is used. - -Style {gauss/cut} computes a generalized Gaussian interaction potential -between pairs of particles: - -:c,image(Eqs/pair_gauss_cut.jpg) - -where H determines together with the standard deviation sigma_h the -peak height of the Gaussian function, and r_mh the peak position. -Examples of the use of the Gaussian potentials include implicit -solvent simulations of salt ions "(Lenart)"_#Lenart2 and of surfactants -"(Jusufi)"_#Jusufi2. In these instances the Gaussian potential mimics -the hydration barrier between a pair of particles. The hydration -barrier is located at r_mh and has a width of sigma_h. The prefactor -determines the height of the potential barrier. - -The following coefficients must be defined for each pair of atom types -via the "pair_coeff"_pair_coeff.html command as in the example above, -or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -H (energy * distance units) -r_mh (distance units) -sigma_h (distance units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global cutoff -is used. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the A, B, H, sigma_h, r_mh -parameters, and the cutoff distance for these pair styles can be mixed: -A (energy units) -sqrt(1/B) (distance units, see below) -H (energy units) -sigma_h (distance units) -r_mh (distance units) -cutoff (distance units):ul - -The default mix value is {geometric}. -Only {arithmetic} and {geometric} mix values are supported. -See the "pair_modify" command for details. - -The A and H parameters are mixed using the same rules normally -used to mix the "epsilon" parameter in a Lennard Jones interaction. -The sigma_h, r_mh, and the cutoff distance are mixed using the same -rules used to mix the "sigma" parameter in a Lennard Jones interaction. -The B parameter is converted to a distance (sigma), before mixing -(using sigma=B^-0.5), and converted back to a coefficient -afterwards (using B=sigma^2). -Negative A values are converted to positive A values (using abs(A)) -before mixing, and converted back after mixing -(by multiplying by min(sign(Ai),sign(Aj))). -This way, if either particle is repulsive (if Ai<0 or Aj<0), -then the default interaction between both particles will be repulsive. - -The {gauss} style does not support the "pair_modify"_pair_modify.html -shift option. There is no effect due to the Gaussian well beyond the -cutoff; hence reasonable cutoffs need to be specified. - -The {gauss/cut} style supports the "pair_modify"_pair_modify.html shift -option for the energy of the Gauss-potential portion of the pair -interaction. - -The "pair_modify"_pair_modify.html table and tail options are not -relevant for these pair styles. - -These pair styles write their information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -These pair styles can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. They do not support the -{inner}, {middle}, {outer} keywords. - -The {gauss} pair style tallies an "occupancy" count of how many Gaussian-well -sites have an atom within the distance at which the force is a maximum -= sqrt(0.5/b). This quantity can be accessed via the "compute -pair"_compute_pair.html command as a vector of values of length 1. - -To print this quantity to the log file (with a descriptive column -heading) the following commands could be included in an input script: - -compute gauss all pair gauss -variable occ equal c_gauss\[1\] -thermo_style custom step temp epair v_occ :pre - -:line - -[Restrictions:] - -The {gauss/cut} style is part of the "user-misc" package. It is only -enabled if LAMMPS is build with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, -"pair_style coul/diel"_pair_coul_diel.html - -[Default:] none - -:link(Lenart2) -[(Lenart)] Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, -044509 (2007). - -:link(Jusufi2) -[(Jusufi)] Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, -13783 (2008). - diff --git a/doc/txt/pair_gayberne.txt b/doc/txt/pair_gayberne.txt deleted file mode 100644 index 426352dc4c..0000000000 --- a/doc/txt/pair_gayberne.txt +++ /dev/null @@ -1,230 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style gayberne command :h3 -pair_style gayberne/gpu command :h3 -pair_style gayberne/intel command :h3 -pair_style gayberne/omp command :h3 - -[Syntax:] - -pair_style gayberne gamma upsilon mu cutoff :pre - -gamma = shift for potential minimum (typically 1) -upsilon = exponent for eta orientation-dependent energy function -mu = exponent for chi orientation-dependent energy function -cutoff = global cutoff for interactions (distance units) :ul - -[Examples:] - -pair_style gayberne 1.0 1.0 1.0 10.0 -pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 :pre - -[Description:] - -The {gayberne} styles compute a Gay-Berne anisotropic LJ interaction -"(Berardi)"_#Berardi between pairs of ellipsoidal particles or an -ellipsoidal and spherical particle via the formulas - -:c,image(Eqs/pair_gayberne.jpg) - -where A1 and A2 are the transformation matrices from the simulation -box frame to the body frame and r12 is the center to center vector -between the particles. Ur controls the shifted distance dependent -interaction based on the distance of closest approach of the two -particles (h12) and the user-specified shift parameter gamma. When -both particles are spherical, the formula reduces to the usual -Lennard-Jones interaction (see details below for when Gay-Berne treats -a particle as "spherical"). - -For large uniform molecules it has been shown that the energy -parameters are approximately representable in terms of local contact -curvatures "(Everaers)"_#Everaers2: - -:c,image(Eqs/pair_gayberne2.jpg) - -The variable names utilized as potential parameters are for the most -part taken from "(Everaers)"_#Everaers2 in order to be consistent with -the "RE-squared pair potential"_pair_resquared.html. Details on the -upsilon and mu parameters are given -"here"_PDF/pair_resquared_extra.pdf. - -More details of the Gay-Berne formulation are given in the references -listed below and in "this supplementary -document"_PDF/pair_gayberne_extra.pdf. - -Use of this pair style requires the NVE, NVT, or NPT fixes with the -{asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in -order to integrate particle rotation. Additionally, "atom_style -ellipsoid"_atom_style.html should be used since it defines the -rotational state and the size and shape of each ellipsoidal particle. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon = well depth (energy units) -sigma = minimum effective particle radii (distance units) -epsilon_i_a = relative well depth of type I for side-to-side interactions -epsilon_i_b = relative well depth of type I for face-to-face interactions -epsilon_i_c = relative well depth of type I for end-to-end interactions -epsilon_j_a = relative well depth of type J for side-to-side interactions -epsilon_j_b = relative well depth of type J for face-to-face interactions -epsilon_j_c = relative well depth of type J for end-to-end interactions -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global -cutoff specified in the pair_style command is used. - -It is typical with the Gay-Berne potential to define {sigma} as the -minimum of the 3 shape diameters of the particles involved in an I,I -interaction, though this is not required. Note that this is a -different meaning for {sigma} than the "pair_style -resquared"_pair_resquared.html potential uses. - -The epsilon_i and epsilon_j coefficients are actually defined for atom -types, not for pairs of atom types. Thus, in a series of pair_coeff -commands, they only need to be specified once for each atom type. - -Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are -non-zero, the three values are assigned to atom type I. If all the -epsilon_i values are zero, they are ignored. If any of epsilon_j_a, -epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned -to atom type J. If all three epsilon_j values are zero, they are -ignored. Thus the typical way to define the epsilon_i and epsilon_j -coefficients is to list their values in "pair_coeff I J" commands when -I = J, but set them to 0.0 when I != J. If you do list them when I != -J, you should insure they are consistent with their values in other -pair_coeff commands, since only the last setting will be in effect. - -Note that if this potential is being used as a sub-style of -"pair_style hybrid"_pair_hybrid.html, and there is no "pair_coeff I I" -setting made for Gay-Berne for a particular type I (because I-I -interactions are computed by another hybrid pair potential), then you -still need to insure the epsilon a,b,c coefficients are assigned to -that type. e.g. in a "pair_coeff I J" command. - -NOTE: If the epsilon a = b = c for an atom type, and if the shape of -the particle itself is spherical, meaning its 3 shape parameters are -all the same, then the particle is treated as an LJ sphere by the -Gay-Berne potential. This is significant because if two LJ spheres -interact, then the simple Lennard-Jones formula is used to compute -their interaction energy/force using the specified epsilon and sigma -as the standard LJ parameters. This is much cheaper to compute than -the full Gay-Berne formula. To treat the particle as a LJ sphere with -sigma = D, you should normally set epsilon a = b = c = 1.0, set the -pair_coeff sigma = D, and also set the 3 shape parameters for the -particle to D. The one exception is that if the 3 shape parameters -are set to 0.0, which is a valid way in LAMMPS to specify a point -particle, then the Gay-Berne potential will treat that as shape -parameters of 1.0 (i.e. a LJ particle with sigma = 1), since it -requires finite-size particles. In this case you should still set the -pair_coeff sigma to 1.0 as well. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for this pair style can be mixed. The default mix -value is {geometric}. See the "pair_modify" command for details. - -This pair styles supports the "pair_modify"_pair_modify.html shift -option for the energy of the Lennard-Jones portion of the pair -interaction, but only for sphere-sphere interactions. There is no -shifting performed for ellipsoidal interactions due to the anisotropic -dependence of the interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -The {gayberne} style is part of the ASPHERE package. It is only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -These pair style require that atoms store torque and a quaternion to -represent their orientation, as defined by the -"atom_style"_atom_style.html. It also require they store a per-type -"shape"_set.html. The particles cannot store a per-particle -diameter. - -This pair style requires that atoms be ellipsoids as defined by the -"atom_style ellipsoid"_atom_style.html command. - -Particles acted on by the potential can be finite-size aspherical or -spherical particles, or point particles. Spherical particles have all -3 of their shape parameters equal to each other. Point particles have -all 3 of their shape parameters equal to 0.0. - -The Gay-Berne potential does not become isotropic as r increases -"(Everaers)"_#Everaers2. The distance-of-closest-approach -approximation used by LAMMPS becomes less accurate when high-aspect -ratio ellipsoids are used. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "fix nve/asphere"_fix_nve_asphere.html, -"compute temp/asphere"_compute_temp_asphere.html, "pair_style -resquared"_pair_resquared.html - -[Default:] none - -:line - -:link(Everaers2) -[(Everaers)] Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003). - -:link(Berardi) -[(Berardi)] Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998). -Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008). - -:link(Perram) -[(Perram)] Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996). - -:link(Allen3) -[(Allen)] Allen and Germano, Mol Phys 104, 3225-3235 (2006). diff --git a/doc/txt/pair_gran.txt b/doc/txt/pair_gran.txt deleted file mode 100644 index f747d15ec4..0000000000 --- a/doc/txt/pair_gran.txt +++ /dev/null @@ -1,271 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style gran/hooke command :h3 -pair_style gran/hooke/omp command :h3 -pair_style gran/hooke/history command :h3 -pair_style gran/hooke/history/omp command :h3 -pair_style gran/hooke/history/kk command :h3 -pair_style gran/hertz/history command :h3 -pair_style gran/hertz/history/omp command :h3 - -[Syntax:] - -pair_style style Kn Kt gamma_n gamma_t xmu dampflag :pre - -style = {gran/hooke} or {gran/hooke/history} or {gran/hertz/history} :ulb,l -Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l -Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l -gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l -gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l -xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l -dampflag = 0 or 1 if tangential damping force is excluded or included :l -:ule - -NOTE: Versions of LAMMPS before 9Jan09 had different style names for -granular force fields. This is to emphasize the fact that the -Hertzian equation has changed to model polydispersity more accurately. -A side effect of the change is that the Kn, Kt, gamma_n, and gamma_t -coefficients in the pair_style command must be specified with -different values in order to reproduce calculations made with earlier -versions of LAMMPS, even for monodisperse systems. See the NOTE below -for details. - -[Examples:] - -pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1 -pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0 :pre - -[Description:] - -The {gran} styles use the following formulas for the frictional force -between two granular particles, as described in -"(Brilliantov)"_#Brilliantov, "(Silbert)"_#Silbert, and -"(Zhang)"_#Zhang3, when the distance r between two particles of radii -Ri and Rj is less than their contact distance d = Ri + Rj. There is -no force between the particles when r > d. - -The two Hookean styles use this formula: - -:c,image(Eqs/pair_gran_hooke.jpg) - -The Hertzian style uses this formula: - -:c,image(Eqs/pair_gran_hertz.jpg) - -In both equations the first parenthesized term is the normal force -between the two particles and the second parenthesized term is the -tangential force. The normal force has 2 terms, a contact force and a -damping force. The tangential force also has 2 terms: a shear force -and a damping force. The shear force is a "history" effect that -accounts for the tangential displacement between the particles for the -duration of the time they are in contact. This term is included in -pair styles {hooke/history} and {hertz/history}, but is not included -in pair style {hooke}. The tangential damping force term is included -in all three pair styles if {dampflag} is set to 1; it is not included -if {dampflag} is set to 0. - -The other quantities in the equations are as follows: - -delta = d - r = overlap distance of 2 particles -Kn = elastic constant for normal contact -Kt = elastic constant for tangential contact -gamma_n = viscoelastic damping constant for normal contact -gamma_t = viscoelastic damping constant for tangential contact -m_eff = Mi Mj / (Mi + Mj) = effective mass of 2 particles of mass Mi and Mj -Delta St = tangential displacement vector between 2 particles \ - which is truncated to satisfy a frictional yield criterion -n_ij = unit vector along the line connecting the centers of the 2 particles -Vn = normal component of the relative velocity of the 2 particles -Vt = tangential component of the relative velocity of the 2 particles :ul - -The Kn, Kt, gamma_n, and gamma_t coefficients are specified as -parameters to the pair_style command. If a NULL is used for Kt, then -a default value is used where Kt = 2/7 Kn. If a NULL is used for -gamma_t, then a default value is used where gamma_t = 1/2 gamma_n. - -The interpretation and units for these 4 coefficients are different in -the Hookean versus Hertzian equations. - -The Hookean model is one where the normal push-back force for two -overlapping particles is a linear function of the overlap distance. -Thus the specified Kn is in units of (force/distance). Note that this -push-back force is independent of absolute particle size (in the -monodisperse case) and of the relative sizes of the two particles (in -the polydisperse case). This model also applies to the other terms in -the force equation so that the specified gamma_n is in units of -(1/time), Kt is in units of (force/distance), and gamma_t is in units -of (1/time). - -The Hertzian model is one where the normal push-back force for two -overlapping particles is proportional to the area of overlap of the -two particles, and is thus a non-linear function of overlap distance. -Thus Kn has units of force per area and is thus specified in units of -(pressure). The effects of absolute particle size (monodispersity) -and relative size (polydispersity) are captured in the radii-dependent -pre-factors. When these pre-factors are carried through to the other -terms in the force equation it means that the specified gamma_n is in -units of (1/(time*distance)), Kt is in units of (pressure), and -gamma_t is in units of (1/(time*distance)). - -Note that in the Hookean case, Kn can be thought of as a linear spring -constant with units of force/distance. In the Hertzian case, Kn is -like a non-linear spring constant with units of force/area or -pressure, and as shown in the "(Zhang)"_#Zhang3 paper, Kn = 4G / -(3(1-nu)) where nu = the Poisson ratio, G = shear modulus = E / -(2(1+nu)), and E = Young's modulus. Similarly, Kt = 4G / (2-nu). -(NOTE: in an earlier version of the manual, we incorrectly stated that -Kt = 8G / (2-nu).) - -Thus in the Hertzian case Kn and Kt can be set to values that -corresponds to properties of the material being modeled. This is also -true in the Hookean case, except that a spring constant must be chosen -that is appropriate for the absolute size of particles in the model. -Since relative particle sizes are not accounted for, the Hookean -styles may not be a suitable model for polydisperse systems. - -NOTE: In versions of LAMMPS before 9Jan09, the equation for Hertzian -interactions did not include the sqrt(RiRj/Ri+Rj) term and thus was -not as accurate for polydisperse systems. For monodisperse systems, -sqrt(RiRj/Ri+Rj) is a constant factor that effectively scales all 4 -coefficients: Kn, Kt, gamma_n, gamma_t. Thus you can set the values -of these 4 coefficients appropriately in the current code to reproduce -the results of a previous Hertzian monodisperse calculation. For -example, for the common case of a monodisperse system with particles -of diameter 1, all 4 of these coefficients should now be set 2x larger -than they were previously. - -Xmu is also specified in the pair_style command and is the upper limit -of the tangential force through the Coulomb criterion Ft = xmu*Fn, -where Ft and Fn are the total tangential and normal force components -in the formulas above. Thus in the Hookean case, the tangential force -between 2 particles grows according to a tangential spring and -dash-pot model until Ft/Fn = xmu and is then held at Ft = Fn*xmu until -the particles lose contact. In the Hertzian case, a similar analogy -holds, though the spring is no longer linear. - -NOTE: Normally, xmu should be specified as a fractional value between -0.0 and 1.0, however LAMMPS allows large values (up to 1.0e4) to allow -for modeling of systems which can sustain very large tangential -forces. - -The effective mass {m_eff} is given by the formula above for two -isolated particles. If either particle is part of a rigid body, its -mass is replaced by the mass of the rigid body in the formula above. -This is determined by searching for a "fix rigid"_fix_rigid.html -command (or its variants). - -For granular styles there are no additional coefficients to set for -each pair of atom types via the "pair_coeff"_pair_coeff.html command. -All settings are global and are made via the pair_style command. -However you must still use the "pair_coeff"_pair_coeff.html for all -pairs of granular atom types. For example the command - -pair_coeff * * :pre - -should be used if all atoms in the simulation interact via a granular -potential (i.e. one of the pair styles above is used). If a granular -potential is used as a sub-style of "pair_style -hybrid"_pair_hybrid.html, then specific atom types can be used in the -pair_coeff command to determine which atoms interact via a granular -potential. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -The "pair_modify"_pair_modify.html mix, shift, table, and tail options -are not relevant for granular pair styles. - -These pair styles write their information to "binary restart -files"_restart.html, so a pair_style command does not need to be -specified in an input script that reads a restart file. - -These pair styles can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. They do not support the -{inner}, {middle}, {outer} keywords. - -The single() function of these pair styles returns 0.0 for the energy -of a pairwise interaction, since energy is not conserved in these -dissipative potentials. It also returns only the normal component of -the pairwise interaction force. However, the single() function also -calculates 10 extra pairwise quantities. The first 3 are the -components of the tangential force between particles I and J, acting -on particle I. The 4th is the magnitude of this tangential force. -The next 3 (5-7) are the components of the relative velocity in the -normal direction (along the line joining the 2 sphere centers). The -last 3 (8-10) the components of the relative velocity in the -tangential direction. - -These extra quantities can be accessed by the "compute -pair/local"_compute_pair_local.html command, as {p1}, {p2}, ..., -{p10}. - -:line - -[Restrictions:] - -All the granular pair styles are part of the GRANULAR package. It is -only enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -These pair styles require that atoms store torque and angular velocity -(omega) as defined by the "atom_style"_atom_style.html. They also -require a per-particle radius is stored. The {sphere} atom style does -all of this. - -This pair style requires you to use the "comm_modify vel -yes"_comm_modify.html command so that velocities are stored by ghost -atoms. - -These pair styles will not restart exactly when using the -"read_restart"_read_restart.html command, though they should provide -statistically similar results. This is because the forces they -compute depend on atom velocities. See the -"read_restart"_read_restart.html command for more details. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Brilliantov) -[(Brilliantov)] Brilliantov, Spahn, Hertzsch, Poschel, Phys Rev E, 53, -p 5382-5392 (1996). - -:link(Silbert) -[(Silbert)] Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev -E, 64, p 051302 (2001). - -:link(Zhang3) -[(Zhang)] Zhang and Makse, Phys Rev E, 72, p 011301 (2005). diff --git a/doc/txt/pair_gromacs.txt b/doc/txt/pair_gromacs.txt deleted file mode 100644 index e50a21588c..0000000000 --- a/doc/txt/pair_gromacs.txt +++ /dev/null @@ -1,156 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj/gromacs command :h3 -pair_style lj/gromacs/gpu command :h3 -pair_style lj/gromacs/kk command :h3 -pair_style lj/gromacs/omp command :h3 -pair_style lj/gromacs/coul/gromacs command :h3 -pair_style lj/gromacs/coul/gromacs/kk command :h3 -pair_style lj/gromacs/coul/gromacs/omp command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {lj/gromacs} or {lj/gromacs/coul/gromacs} -args = list of arguments for a particular style :ul - {lj/gromacs} args = inner outer - inner, outer = global switching cutoffs for Lennard Jones - {lj/gromacs/coul/gromacs} args = inner outer (inner2) (outer2) - inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args) - inner2, outer2 = global switching cutoffs for Coulombic (optional) :pre - -[Examples:] - -pair_style lj/gromacs 9.0 12.0 -pair_coeff * * 100.0 2.0 -pair_coeff 2 2 100.0 2.0 8.0 10.0 :pre - -pair_style lj/gromacs/coul/gromacs 9.0 12.0 -pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0 -pair_coeff * * 100.0 2.0 :pre - -[Description:] - -The {lj/gromacs} styles compute shifted LJ and Coulombic interactions -with an additional switching function S(r) that ramps the energy and force -smoothly to zero between an inner and outer cutoff. It is a commonly -used potential in the "GROMACS"_http://www.gromacs.org MD code and for -the coarse-grained models of "(Marrink)"_#Marrink. - -:c,image(Eqs/pair_gromacs.jpg) - -r1 is the inner cutoff; rc is the outer cutoff. The coefficients A, B, -and C are computed by LAMMPS to perform the shifting and smoothing. -The function -S(r) is actually applied once to each term of the LJ formula and once -to the Coulombic formula, so there are 2 or 3 sets of A,B,C coefficients -depending on which pair_style is used. The boundary conditions -applied to the smoothing function are as follows: S'(r1) = S''(r1) = 0, -S(rc) = -E(rc), S'(rc) = -E'(rc), and S''(rc) = -E''(rc), -where E(r) is the corresponding term -in the LJ or Coulombic potential energy function. -Single and double primes denote first and second -derivatives with respect to r, respectively. - -The inner and outer cutoff for the LJ and Coulombic terms can be the -same or different depending on whether 2 or 4 arguments are used in -the pair_style command. The inner LJ cutoff must be > 0, but the -inner Coulombic cutoff can be >= 0. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) -inner (distance units) -outer (distance units) :ul - -Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum at 2^(1/6) -sigma. - -The last 2 coefficients are optional inner and outer cutoffs for style -{lj/gromacs}. If not specified, the global {inner} and {outer} values -are used. - -The last 2 coefficients cannot be used with style -{lj/gromacs/coul/gromacs} because this force field does not allow -varying cutoffs for individual atom pairs; all pairs use the global -cutoff(s) specified in the pair_style command. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/cut pair styles can be mixed. -The default mix value is {geometric}. See the "pair_modify" command -for details. - -None of the GROMACS pair styles support the -"pair_modify"_pair_modify.html shift option, since the Lennard-Jones -portion of the pair interaction is already smoothed to 0.0 at the -cutoff. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -None of the GROMACS pair styles support the -"pair_modify"_pair_modify.html tail option for adding long-range tail -corrections to energy and pressure, since there are no corrections for -a potential that goes to 0.0 at the cutoff. - -All of the GROMACS pair styles write their information to "binary -restart files"_restart.html, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. - -All of the GROMACS pair styles can only be used via the {pair} -keyword of the "run_style respa"_run_style.html command. They do not -support the {inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Marrink) -[(Marrink)] Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004). diff --git a/doc/txt/pair_gw.txt b/doc/txt/pair_gw.txt deleted file mode 100644 index ff85955dc0..0000000000 --- a/doc/txt/pair_gw.txt +++ /dev/null @@ -1,121 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style gw command :h3 -pair_style gw/zbl command :h3 - -[Syntax:] - -pair_style style :pre - -style = {gw} or {gw/zbl} :ul - -[Examples:] - -pair_style gw -pair_coeff * * SiC.gw Si C C - -pair_style gw/zbl -pair_coeff * * SiC.gw.zbl C Si :pre - -[Description:] - -The {gw} style computes a 3-body "Gao-Weber"_#Gao potential; -similarly {gw/zbl} combines this potential with a modified -repulsive ZBL core function in a similar fashion as implemented -in the "tersoff/zbl"_pair_tersoff_zbl.html pair style. - -Unfortunately the author of this contributed code has not been -able to submit a suitable documentation explaining the details -of the potentials. The LAMMPS developers thus have finally decided -to release the code anyway with only the technical explanations. -For details of the model and the parameters, please refer to the -linked publication. - -Only a single pair_coeff command is used with the {gw} and {gw/zbl} -styles which specifies a Gao-Weber potential file with parameters -for all needed elements. These are mapped to LAMMPS atom types by -specifying N additional arguments after the filename in the pair_coeff -command, where N is the number of LAMMPS atom types: - -filename -N element names = mapping of GW elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -As an example, imagine a file SiC.gw has Gao-Weber values for Si and C. -If your LAMMPS simulation has 4 atoms types and you want the first 3 to -be Si, and the 4th to be C, you would use the following pair_coeff command: - -pair_coeff * * SiC.gw Si Si Si C :pre - -The first 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to the Si -element in the GW file. The final C argument maps LAMMPS atom type 4 -to the C element in the GW file. If a mapping value is specified as -NULL, the mapping is not performed. This can be used when a {gw} -potential is used as part of the {hybrid} pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. - -Gao-Weber files in the {potentials} directory of the LAMMPS -distribution have a ".gw" suffix. Gao-Weber with ZBL files -have a ".gz.zbl" suffix. The structure of the potential files -is similar to other many-body potentials supported by LAMMPS. -You have to refer to the comments in the files and the literature -to learn more details. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above from values in the potential file. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the MANYBODY package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair style requires the "newton"_newton.html setting to be "on" -for pair interactions. - -The Gao-Weber potential files provided with LAMMPS (see the -potentials directory) are parameterized for metal "units"_units.html. -You can use the GW potential with any LAMMPS units, but you would need -to create your own GW potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Gao) -[(Gao)] Gao and Weber, Nuclear Instruments and Methods in Physics -Research B 191 (2012) 504. diff --git a/doc/txt/pair_hbond_dreiding.txt b/doc/txt/pair_hbond_dreiding.txt deleted file mode 100644 index ec470f601f..0000000000 --- a/doc/txt/pair_hbond_dreiding.txt +++ /dev/null @@ -1,242 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style hbond/dreiding/lj command :h3 -pair_style hbond/dreiding/lj/omp command :h3 -pair_style hbond/dreiding/morse command :h3 -pair_style hbond/dreiding/morse/omp command :h3 - -[Syntax:] - -pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof :pre - -style = {hbond/dreiding/lj} or {hbond/dreiding/morse} -n = cosine angle periodicity -inner_distance_cutoff = global inner cutoff for Donor-Acceptor interactions (distance units) -outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units) -angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor -interactions (degrees) :ul - -[Examples:] - -pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90 -pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0 :pre - -pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90 -pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90 :pre - -[Description:] - -The {hbond/dreiding} styles compute the Acceptor-Hydrogen-Donor (AHD) -3-body hydrogen bond interaction for the "DREIDING"_Howto_bioFF.html -force field, given by: - -:c,image(Eqs/pair_hbond_dreiding.jpg) - -where Rin is the inner spline distance cutoff, Rout is the outer -distance cutoff, theta_c is the angle cutoff, and n is the cosine -periodicity. - -Here, {r} is the radial distance between the donor (D) and acceptor -(A) atoms and {theta} is the bond angle between the acceptor, the -hydrogen (H) and the donor atoms: - -:c,image(JPG/dreiding_hbond.jpg) - -These 3-body interactions can be defined for pairs of acceptor and -donor atoms, based on atom types. For each donor/acceptor atom pair, -the 3rd atom in the interaction is a hydrogen permanently bonded to -the donor atom, e.g. in a bond list read in from a data file via the -"read_data"_read_data.html command. The atom types of possible -hydrogen atoms for each donor/acceptor type pair are specified by the -"pair_coeff"_pair_coeff.html command (see below). - -Style {hbond/dreiding/lj} is the original DREIDING potential of -"(Mayo)"_#pair-Mayo. It uses a LJ 12/10 functional for the Donor-Acceptor -interactions. To match the results in the original paper, use n = 4. - -Style {hbond/dreiding/morse} is an improved version using a Morse -potential for the Donor-Acceptor interactions. "(Liu)"_#Liu showed -that the Morse form gives improved results for Dendrimer simulations, -when n = 2. - -See the "Howto bioFF"_Howto_bioFF.html doc page for more information -on the DREIDING force field. - -NOTE: Because the Dreiding hydrogen bond potential is only one portion -of an overall force field which typically includes other pairwise -interactions, it is common to use it as a sub-style in a "pair_style -hybrid/overlay"_pair_hybrid.html command, where another pair style -provides the repulsive core interaction between pairs of atoms, e.g. a -1/r^12 Lennard-Jones repulsion. - -NOTE: When using the hbond/dreiding pair styles with "pair_style -hybrid/overlay"_pair_hybrid.html, you should explicitly define pair -interactions between the donor atom and acceptor atoms, (as well as -between these atoms and ALL other atoms in your system). Whenever -"pair_style hybrid/overlay"_pair_hybrid.html is used, ordinary mixing -rules are not applied to atoms like the donor and acceptor atoms -because they are typically referenced in multiple pair styles. -Neglecting to do this can cause difficult-to-detect physics problems. - -NOTE: In the original Dreiding force field paper 1-4 non-bonded -interactions ARE allowed. If this is desired for your model, use the -special_bonds command (e.g. "special_bonds lj 0.0 0.0 1.0") to turn -these interactions on. - -:line - -The following coefficients must be defined for pairs of eligible -donor/acceptor types via the "pair_coeff"_pair_coeff.html command as -in the examples above. - -NOTE: Unlike other pair styles and their associated -"pair_coeff"_pair_coeff.html commands, you do not need to specify -pair_coeff settings for all possible I,J type pairs. Only I,J type -pairs for atoms which act as joint donors/acceptors need to be -specified; all other type pairs are assumed to be inactive. - -NOTE: A "pair_coeff"_pair_coeff.html command can be specified multiple -times for the same donor/acceptor type pair. This enables multiple -hydrogen types to be assigned to the same donor/acceptor type pair. -For other pair_styles, if the pair_coeff command is re-used for the -same I.J type pair, the settings for that type pair are overwritten. -For the hydrogen bond potentials this is not the case; the settings -are cumulative. This means the only way to turn off a previous -setting, is to re-use the pair_style command and start over. - -For the {hbond/dreiding/lj} style the list of coefficients is as -follows: - -K = hydrogen atom type = 1 to Ntypes -donor flag = {i} or {j} -epsilon (energy units) -sigma (distance units) -n = exponent in formula above -distance cutoff Rin (distance units) -distance cutoff Rout (distance units) -angle cutoff (degrees) :ul - -For the {hbond/dreiding/morse} style the list of coefficients is as -follows: - -K = hydrogen atom type = 1 to Ntypes -donor flag = {i} or {j} -D0 (energy units) -alpha (1/distance units) -r0 (distance units) -n = exponent in formula above -distance cutoff Rin (distance units) -distance cutoff Rout (distance units) -angle cutoff (degrees) :ul - -A single hydrogen atom type K can be specified, or a wild-card asterisk -can be used in place of or in conjunction with the K arguments to -select multiple types as hydrogen atoms. This takes the form -"*" or "*n" or "n*" or "m*n". See the "pair_coeff"_pair_coeff.html -command doc page for details. - -If the donor flag is {i}, then the atom of type I in the pair_coeff -command is treated as the donor, and J is the acceptor. If the donor -flag is {j}, then the atom of type J in the pair_coeff command is -treated as the donor and I is the donor. This option is required -because the "pair_coeff"_pair_coeff.html command requires that I <= J. - -Epsilon and sigma are settings for the hydrogen bond potential based -on a Lennard-Jones functional form. Note that sigma is defined as the -zero-crossing distance for the potential, not as the energy minimum at -2^(1/6) sigma. - -D0 and alpha and r0 are settings for the hydrogen bond potential based -on a Morse functional form. - -The last 3 coefficients for both styles are optional. If not -specified, the global n, distance cutoff, and angle cutoff specified -in the pair_style command are used. If you wish to only override the -2nd or 3rd optional parameter, you must also specify the preceding -optional parameters. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -These pair styles do not support mixing. You must explicitly identify -each donor/acceptor type pair. - -These styles do not support the "pair_modify"_pair_modify.html shift -option for the energy of the interactions. - -The "pair_modify"_pair_modify.html table option is not relevant for -these pair styles. - -These pair styles do not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -These pair styles do not write their information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands need to be -re-specified in an input script that reads a restart file. - -These pair styles can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. They do not support the -{inner}, {middle}, {outer} keywords. - -These pair styles tally a count of how many hydrogen bonding -interactions they calculate each timestep and the hbond energy. These -quantities can be accessed via the "compute pair"_compute_pair.html -command as a vector of values of length 2. - -To print these quantities to the log file (with a descriptive column -heading) the following commands could be included in an input script: - -compute hb all pair hbond/dreiding/lj -variable n_hbond equal c_hb\[1\] #number hbonds -variable E_hbond equal c_hb\[2\] #hbond energy -thermo_style custom step temp epair v_E_hbond :pre - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(pair-Mayo) -[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). - -:link(Liu) -[(Liu)] Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8) -2798 (2009) diff --git a/doc/txt/pair_hybrid.txt b/doc/txt/pair_hybrid.txt deleted file mode 100644 index 4467ac1d51..0000000000 --- a/doc/txt/pair_hybrid.txt +++ /dev/null @@ -1,383 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style hybrid command :h3 -pair_style hybrid/kk command :h3 -pair_style hybrid/overlay command :h3 -pair_style hybrid/overlay/kk command :h3 - -[Syntax:] - -pair_style hybrid style1 args style2 args ... -pair_style hybrid/overlay style1 args style2 args ... :pre - -style1,style2 = list of one or more pair styles and their arguments :ul - -[Examples:] - -pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0 -pair_coeff 1*2 1*2 eam niu3 -pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0 -pair_coeff 1*2 3 lj/cut 0.5 1.2 :pre - -pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0 -pair_coeff * * lj/cut 1.0 1.0 -pair_coeff * * coul/long :pre - -[Description:] - -The {hybrid} and {hybrid/overlay} styles enable the use of multiple -pair styles in one simulation. With the {hybrid} style, exactly one -pair style is assigned to each pair of atom types. With the -{hybrid/overlay} style, one or more pair styles can be assigned to -each pair of atom types. The assignment of pair styles to type pairs -is made via the "pair_coeff"_pair_coeff.html command. - -Here are two examples of hybrid simulations. The {hybrid} style could -be used for a simulation of a metal droplet on a LJ surface. The -metal atoms interact with each other via an {eam} potential, the -surface atoms interact with each other via a {lj/cut} potential, and -the metal/surface interaction is also computed via a {lj/cut} -potential. The {hybrid/overlay} style could be used as in the 2nd -example above, where multiple potentials are superposed in an additive -fashion to compute the interaction between atoms. In this example, -using {lj/cut} and {coul/long} together gives the same result as if -the {lj/cut/coul/long} potential were used by itself. In this case, -it would be more efficient to use the single combined potential, but -in general any combination of pair potentials can be used together in -to produce an interaction that is not encoded in any single pair_style -file, e.g. adding Coulombic forces between granular particles. - -All pair styles that will be used are listed as "sub-styles" following -the {hybrid} or {hybrid/overlay} keyword, in any order. Each -sub-style's name is followed by its usual arguments, as illustrated in -the example above. See the doc pages of individual pair styles for a -listing and explanation of the appropriate arguments. - -Note that an individual pair style can be used multiple times as a -sub-style. For efficiency this should only be done if your model -requires it. E.g. if you have different regions of Si and C atoms and -wish to use a Tersoff potential for pure Si for one set of atoms, and -a Tersoff potential for pure C for the other set (presumably with some -3rd potential for Si-C interactions), then the sub-style {tersoff} -could be listed twice. But if you just want to use a Lennard-Jones or -other pairwise potential for several different atom type pairs in your -model, then you should just list the sub-style once and use the -pair_coeff command to assign parameters for the different type pairs. - -NOTE: There is one exception to this option to list an individual -pair style multiple times: GPU-enabled pair styles in the GPU package. -This is because the GPU package currently assumes that only one -instance of a pair style is being used. - -In the pair_coeff commands, the name of a pair style must be added -after the I,J type specification, with the remaining coefficients -being those appropriate to that style. If the pair style is used -multiple times in the pair_style command, then an additional numeric -argument must also be specified which is a number from 1 to M where M -is the number of times the sub-style was listed in the pair style -command. The extra number indicates which instance of the sub-style -these coefficients apply to. - -For example, consider a simulation with 3 atom types: types 1 and 2 -are Ni atoms, type 3 are LJ atoms with charges. The following -commands would set up a hybrid simulation: - -pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0 -pair_coeff * * eam/alloy nialhjea Ni Ni NULL -pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0 -pair_coeff 1*2 3 lj/cut 0.8 1.3 :pre - -As an example of using the same pair style multiple times, consider a -simulation with 2 atom types. Type 1 is Si, type 2 is C. The -following commands would model the Si atoms with Tersoff, the C atoms -with Tersoff, and the cross-interactions with Lennard-Jones: - -pair_style hybrid lj/cut 2.5 tersoff tersoff -pair_coeff * * tersoff 1 Si.tersoff Si NULL -pair_coeff * * tersoff 2 C.tersoff NULL C -pair_coeff 1 2 lj/cut 1.0 1.5 :pre - -If pair coefficients are specified in the data file read via the -"read_data"_read_data.html command, then the same rule applies. -E.g. "eam/alloy" or "lj/cut" must be added after the atom type, for -each line in the "Pair Coeffs" section, e.g. - -Pair Coeffs :pre - -1 lj/cut/coul/cut 1.0 1.0 -... :pre - -Note that the pair_coeff command for some potentials such as -"pair_style eam/alloy"_pair_eam.html includes a mapping specification -of elements to all atom types, which in the hybrid case, can include -atom types not assigned to the {eam/alloy} potential. The NULL -keyword is used by many such potentials (eam/alloy, Tersoff, AIREBO, -etc), to denote an atom type that will be assigned to a different -sub-style. - -For the {hybrid} style, each atom type pair I,J is assigned to exactly -one sub-style. Just as with a simulation using a single pair style, -if you specify the same atom type pair in a second pair_coeff command, -the previous assignment will be overwritten. - -For the {hybrid/overlay} style, each atom type pair I,J can be -assigned to one or more sub-styles. If you specify the same atom type -pair in a second pair_coeff command with a new sub-style, then the -second sub-style is added to the list of potentials that will be -calculated for two interacting atoms of those types. If you specify -the same atom type pair in a second pair_coeff command with a -sub-style that has already been defined for that pair of atoms, then -the new pair coefficients simply override the previous ones, as in the -normal usage of the pair_coeff command. E.g. these two sets of -commands are the same: - -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 -pair_coeff 2 2 1.5 0.8 :pre - -pair_style hybrid/overlay lj/cut 2.5 -pair_coeff * * lj/cut 1.0 1.0 -pair_coeff 2 2 lj/cut 1.5 0.8 :pre - -Coefficients must be defined for each pair of atoms types via the -"pair_coeff"_pair_coeff.html command as described above, or in the -data file or restart files read by the "read_data"_read_data.html or -"read_restart"_read_restart.html commands, or by mixing as described -below. - -For both the {hybrid} and {hybrid/overlay} styles, every atom type -pair I,J (where I <= J) must be assigned to at least one sub-style via -the "pair_coeff"_pair_coeff.html command as in the examples above, or -in the data file read by the "read_data"_read_data.html, or by mixing -as described below. - -If you want there to be no interactions between a particular pair of -atom types, you have 3 choices. You can assign the type pair to some -sub-style and use the "neigh_modify exclude type"_neigh_modify.html -command. You can assign it to some sub-style and set the coefficients -so that there is effectively no interaction (e.g. epsilon = 0.0 in a -LJ potential). Or, for {hybrid} and {hybrid/overlay} simulations, you -can use this form of the pair_coeff command in your input script: - -pair_coeff 2 3 none :pre - -or this form in the "Pair Coeffs" section of the data file: - -3 none :pre - -If an assignment to {none} is made in a simulation with the -{hybrid/overlay} pair style, it wipes out all previous assignments of -that atom type pair to sub-styles. - -Note that you may need to use an "atom_style"_atom_style.html hybrid -command in your input script, if atoms in the simulation will need -attributes from several atom styles, due to using multiple pair -potentials. - -:line - -Different force fields (e.g. CHARMM vs AMBER) may have different rules -for applying weightings that change the strength of pairwise -interactions between pairs of atoms that are also 1-2, 1-3, and 1-4 -neighbors in the molecular bond topology, as normally set by the -"special_bonds"_special_bonds.html command. Different weights can be -assigned to different pair hybrid sub-styles via the "pair_modify -special"_pair_modify.html command. This allows multiple force fields -to be used in a model of a hybrid system, however, there is no consistent -approach to determine parameters automatically for the interactions -between the two force fields, this is only recommended when particles -described by the different force fields do not mix. - -Here is an example for mixing CHARMM and AMBER: The global {amber} -setting sets the 1-4 interactions to non-zero scaling factors and -then overrides them with 0.0 only for CHARMM: - -special_bonds amber -pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0 -pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0 :pre - -The this input achieves the same effect: - -special_bonds 0.0 0.0 0.1 -pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0 -pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5 -pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333 -pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0 :pre - -Here is an example for mixing Tersoff with OPLS/AA based on -a data file that defines bonds for all atoms where for the -Tersoff part of the system the force constants for the bonded -interactions have been set to 0. Note the global settings are -effectively {lj/coul 0.0 0.0 0.5} as required for OPLS/AA: - -special_bonds lj/coul 1e-20 1e-20 0.5 -pair_hybrid tersoff lj/cut/coul/long 12.0 -pair_modify pair tersoff special lj/coul 1.0 1.0 1.0 :pre - -For use with the various "compute */tally"_compute_tally.html -computes, the "pair_modify compute/tally"_pair_modify.html -command can be used to selectively turn off processing of -the compute tally styles, for example, if those pair styles -(e.g. many-body styles) do not support this feature. - -See the "pair_modify"_pair_modify.html doc page for details on -the specific syntax, requirements and restrictions. - -:line - -The potential energy contribution to the overall system due to an -individual sub-style can be accessed and output via the "compute -pair"_compute_pair.html command. - -:line - -NOTE: Several of the potentials defined via the pair_style command in -LAMMPS are really many-body potentials, such as Tersoff, AIREBO, MEAM, -ReaxFF, etc. The way to think about using these potentials in a -hybrid setting is as follows. - -A subset of atom types is assigned to the many-body potential with a -single "pair_coeff"_pair_coeff.html command, using "* *" to include -all types and the NULL keywords described above to exclude specific -types not assigned to that potential. If types 1,3,4 were assigned in -that way (but not type 2), this means that all many-body interactions -between all atoms of types 1,3,4 will be computed by that potential. -Pair_style hybrid allows interactions between type pairs 2-2, 1-2, -2-3, 2-4 to be specified for computation by other pair styles. You -could even add a second interaction for 1-1 to be computed by another -pair style, assuming pair_style hybrid/overlay is used. - -But you should not, as a general rule, attempt to exclude the -many-body interactions for some subset of the type pairs within the -set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That -is not conceptually well-defined for many-body interactions, since the -potential will typically calculate energies and foces for small groups -of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to -find the additional atoms in the group. It is typically non-physical -to think of excluding an interaction between a particular pair of -atoms when the potential computes 3-body or 4-body interactions. - -However, you can still use the pair_coeff none setting or the -"neigh_modify exclude"_neigh_modify.html command to exclude certain -type pairs from the neighbor list that will be passed to a many-body -sub-style. This will alter the calculations made by a many-body -potential, since it builds its list of 3-body, 4-body, etc -interactions from the pair list. You will need to think carefully as -to whether it produces a physically meaningful result for your model. - -For example, imagine you have two atom types in your model, type 1 for -atoms in one surface, and type 2 for atoms in the other, and you wish -to use a Tersoff potential to compute interactions within each -surface, but not between surfaces. Then either of these two command -sequences would implement that model: - -pair_style hybrid tersoff -pair_coeff * * tersoff SiC.tersoff C C -pair_coeff 1 2 none :pre - -pair_style tersoff -pair_coeff * * SiC.tersoff C C -neigh_modify exclude type 1 2 :pre - -Either way, only neighbor lists with 1-1 or 2-2 interactions would be -passed to the Tersoff potential, which means it would compute no -3-body interactions containing both type 1 and 2 atoms. - -Here is another example, using hybrid/overlay, to use 2 many-body -potentials together, in an overlapping manner. Imagine you have CNT -(C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C -interactions, and AIREBO for C/C interactions. Si atoms are type 1; C -atoms are type 2. Something like this will work: - -pair_style hybrid/overlay tersoff airebo 3.0 -pair_coeff * * tersoff SiC.tersoff.custom Si C -pair_coeff * * airebo CH.airebo NULL C :pre - -Note that to prevent the Tersoff potential from computing C/C -interactions, you would need to modify the SiC.tersoff file to turn -off C/C interaction, i.e. by setting the appropriate coefficients to -0.0. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. - -Since the {hybrid} and {hybrid/overlay} styles delegate computation to -the individual sub-styles, the suffix versions of the {hybrid} and -{hybrid/overlay} styles are used to propagate the corresponding suffix -to all sub-styles, if those versions exist. Otherwise the -non-accelerated version will be used. - -The individual accelerated sub-styles are part of the GPU, USER-OMP -and OPT packages, respectively. They are only enabled if LAMMPS was -built with those packages. See the "Build package"_Build_package.html -doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -Any pair potential settings made via the -"pair_modify"_pair_modify.html command are passed along to all -sub-styles of the hybrid potential. - -For atom type pairs I,J and I != J, if the sub-style assigned to I,I -and J,J is the same, and if the sub-style allows for mixing, then the -coefficients for I,J can be mixed. This means you do not have to -specify a pair_coeff command for I,J since the I,J type pair will be -assigned automatically to the sub-style defined for both I,I and J,J -and its coefficients generated by the mixing rule used by that -sub-style. For the {hybrid/overlay} style, there is an additional -requirement that both the I,I and J,J pairs are assigned to a single -sub-style. See the "pair_modify" command for details of mixing rules. -See the See the doc page for the sub-style to see if allows for -mixing. - -The hybrid pair styles supports the "pair_modify"_pair_modify.html -shift, table, and tail options for an I,J pair interaction, if the -associated sub-style supports it. - -For the hybrid pair styles, the list of sub-styles and their -respective settings are written to "binary restart -files"_restart.html, so a "pair_style"_pair_style.html command does -not need to specified in an input script that reads a restart file. -However, the coefficient information is not stored in the restart -file. Thus, pair_coeff commands need to be re-specified in the -restart input script. - -These pair styles support the use of the {inner}, {middle}, and -{outer} keywords of the "run_style respa"_run_style.html command, if -their sub-styles do. - -[Restrictions:] - -When using a long-range Coulombic solver (via the -"kspace_style"_kspace_style.html command) with a hybrid pair_style, -one or more sub-styles will be of the "long" variety, -e.g. {lj/cut/coul/long} or {buck/coul/long}. You must insure that the -short-range Coulombic cutoff used by each of these long pair styles is -the same or else LAMMPS will generate an error. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none diff --git a/doc/txt/pair_kim.txt b/doc/txt/pair_kim.txt deleted file mode 100644 index 41593675ba..0000000000 --- a/doc/txt/pair_kim.txt +++ /dev/null @@ -1,112 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style kim command :h3 - -[Syntax:] - -pair_style kim model :pre - -model = name of a KIM model (the KIM ID for models archived in OpenKIM) - -[Examples:] - -pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005 -pair_coeff * * Si :pre - -[Description:] - -This pair style is a wrapper on the "Open Knowledgebase of Interatomic -Models (OpenKIM)"_https://openkim.org repository of interatomic -potentials to enable their use in LAMMPS scripts. - -The preferred interface for using interatomic models archived in -OpenKIM is the "kim_commands interface"_kim_commands.html. That -interface supports both "KIM Portable Models" (PMs) that conform to the -KIM API Portable Model Interface (PMI) and can be used by any -simulation code that conforms to the KIM API/PMI, and -"KIM Simulator Models" that are natively implemented within a single -simulation code (like LAMMPS) and can only be used with it. -The {pair_style kim} command is limited to KIM PMs. It is -used by the "kim_commands interface"_kim_commands.html as needed. - -NOTE: Since {pair_style kim} is called by {kim_interactions} as needed, -is not recommended to be directly used in input scripts. - -:line - -The argument {model} is the name of the KIM PM. -For potentials archived in OpenKIM -this is the extended KIM ID (see "kim_commands"_kim_commands.html -for details). LAMMPS can invoke any KIM PM, however there can -be incompatibilities (for example due to unit matching issues). -In the event of an incompatibility, the code will terminate with -an error message. Check both the LAMMPS and KIM log files for details. - -Only a single {pair_coeff} command is used with the {kim} style, which -specifies the mapping of LAMMPS atom types to the species supported by -the KIM PM. This is done by specifying {N} additional arguments -after the * * in the {pair_coeff} command, where {N} is the number of -LAMMPS atom types: - -N element names = mapping of KIM elements to atom types :ul - -For example, consider a KIM PM that supports Si and C species. -If the LAMMPS simulation has four atom types, where the first three are Si, -and the fourth is C, the following {pair_coeff} command would be used: - -pair_coeff * * Si Si Si C :pre - -The first two arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1, 2, and 3 to Si as -defined within KIM PM. The final C argument maps LAMMPS atom type 4 to C. - -:line - -In addition to the usual LAMMPS error messages, the KIM library itself -may generate errors, which should be printed to the screen. In this -case it is also useful to check the {kim.log} file for additional error -information. The file {kim.log} should be generated in the same -directory where LAMMPS is running. - -To download, build, and install the KIM library on your system, see -the {lib/kim/README} file. Once you have done this and built LAMMPS -with the KIM package installed you can run the example input scripts -in {examples/kim}. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support the "pair_modify"_pair_modify.html -mix, shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since KIM stores the potential parameters. -Thus, you need to re-specify the pair_style and pair_coeff commands in -an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the KIM package. See details on -restrictions in "kim_commands"_kim_commands.html. - -This current version of pair_style kim is compatible with the -kim-api package version 2.0.0 and higher. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "kim_commands"_kim_commands.html - -[Default:] none diff --git a/doc/txt/pair_kolmogorov_crespi_z.txt b/doc/txt/pair_kolmogorov_crespi_z.txt deleted file mode 100644 index d45b5bd2e9..0000000000 --- a/doc/txt/pair_kolmogorov_crespi_z.txt +++ /dev/null @@ -1,76 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style kolmogorov/crespi/z command :h3 - -[Syntax:] - -pair_style \[hybrid/overlay ...\] kolmogorov/crespi/z cutoff :pre - -[Examples:] - -pair_style hybrid/overlay kolmogorov/crespi/z 20.0 -pair_coeff * * none -pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre - -pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 -pair_coeff * * rebo CH.rebo C C -pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre - -[Description:] - -The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction -potential as described in "(Kolmogorov)"_#KC05. An important simplification is made, -which is to take all normals along the z-axis. - -:c,image(Eqs/pair_kolmogorov_crespi_z.jpg) - -It is important to have a sufficiently large cutoff to ensure smooth forces. -Energies are shifted so that they go continuously to zero at the cutoff assuming -that the exponential part of {Vij} (first term) decays sufficiently fast. -This shift is achieved by the last term in the equation for {Vij} above. - -This potential is intended for interactions between two layers of graphene. -Therefore, to avoid interaction between layers in multi-layered materials, -each layer should have a separate atom type and interactions should only -be computed between atom types of neighboring layers. - -The parameter file (e.g. CC.KC), is intended for use with metal -"units"_units.html, with energies in meV. An additional parameter, {S}, -is available to facilitate scaling of energies in accordance with -"(vanWijk)"_#vanWijk. - -This potential must be used in combination with hybrid/overlay. -Other interactions can be set to zero using pair_style {none}. - -[Restrictions:] - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, -"pair_none"_pair_none.html, -"pair_style hybrid/overlay"_pair_hybrid.html, -"pair_style drip"_pair_drip.html, -"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html. -"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html, -"pair_style lebedeva/z"_pair_lebedeva_z.html - -[Default:] none - -:line - -:link(KC05) -[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) - -:link(vanWijk) -[(vanWijk)] M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, -Physical Review Letters, 113, 135504 (2014) diff --git a/doc/txt/pair_lcbop.txt b/doc/txt/pair_lcbop.txt deleted file mode 100644 index 21c809bf6a..0000000000 --- a/doc/txt/pair_lcbop.txt +++ /dev/null @@ -1,97 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lcbop command :h3 - -[Syntax:] - -pair_style lcbop :pre - -[Examples:] - -pair_style lcbop -pair_coeff * * ../potentials/C.lcbop C :pre - -[Description:] - -The {lcbop} pair style computes the long-range bond-order potential -for carbon (LCBOP) of "(Los and Fasolino)"_#Los. See section II in -that paper for the analytic equations associated with the potential. - -Only a single pair_coeff command is used with the {lcbop} style which -specifies an LCBOP potential file with parameters for specific -elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of LCBOP elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -As an example, if your LAMMPS simulation has 4 atom types and you want -the 1st 3 to be C you would use the following pair_coeff command: - -pair_coeff * * C.lcbop C C C NULL :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first C argument maps LAMMPS atom type 1 to the C element in the -LCBOP file. If a mapping value is specified as NULL, the mapping is -not performed. This can be used when a {lcbop} potential is used as -part of the {hybrid} pair style. The NULL values are placeholders for -atom types that will be used with other potentials. - -The parameters/coefficients for the LCBOP potential as applied to C -are listed in the C.lcbop file to agree with the original "(Los and -Fasolino)"_#Los paper. Thus the parameters are specific to this -potential and the way it was fit, so modifying the file should be done -carefully. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support the "pair_modify"_pair_modify.html -mix, shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -[Restrictions:] - -This pair styles is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair potential requires the "newton"_newton.html setting to be -"on" for pair interactions. - -The C.lcbop potential file provided with LAMMPS (see the potentials -directory) is parameterized for metal "units"_units.html. You can use -the LCBOP potential with any LAMMPS units, but you would need to -create your own LCBOP potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. - -[Related commands:] - -"pair_airebo"_pair_airebo.html, "pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Los) -[(Los and Fasolino)] J. H. Los and A. Fasolino, Phys. Rev. B 68, 024107 -(2003). diff --git a/doc/txt/pair_lebedeva_z.txt b/doc/txt/pair_lebedeva_z.txt deleted file mode 100644 index ad6c4c12f4..0000000000 --- a/doc/txt/pair_lebedeva_z.txt +++ /dev/null @@ -1,67 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lebedeva/z command :h3 - -[Syntax:] - -pair_style \[hybrid/overlay ...\] lebedeva/z cutoff :pre - -[Examples:] - -pair_style hybrid/overlay lebedeva/z 20.0 -pair_coeff * * none -pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre - -pair_style hybrid/overlay rebo lebedeva/z 14.0 -pair_coeff * * rebo CH.rebo C C -pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre - -[Description:] - -The {lebedeva/z} style computes the Lebedeva interaction -potential as described in "(Lebedeva et al.)"_#Leb01. An important simplification is made, -which is to take all normals along the z-axis. - -:c,image(Eqs/pair_lebedeva.png) - -It is important to have a sufficiently large cutoff to ensure smooth forces. -Energies are shifted so that they go continuously to zero at the cutoff assuming -that the exponential part of {Vij} (first term) decays sufficiently fast. -This shift is achieved by the last term in the equation for {Vij} above. - -The parameter file (e.g. CC.Lebedeva), is intended for use with metal -"units"_units.html, with energies in meV. An additional parameter, {S}, -is available to facilitate scaling of energies. - -This potential must be used in combination with hybrid/overlay. -Other interactions can be set to zero using pair_style {none}. - -[Restrictions:] - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, -"pair_style none"_pair_none.html, -"pair_style hybrid/overlay"_pair_hybrid.html, -"pair_style drip"_pair_drip.html, -"pair_style ilp/graphene/hbd"_pair_ilp_graphene_hbn.html, -"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, -"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html. - -[Default:] none - -:line - -:link(Leb01) -[(Lebedeva et al.)] I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011) - diff --git a/doc/txt/pair_line_lj.txt b/doc/txt/pair_line_lj.txt deleted file mode 100644 index ca5ececa56..0000000000 --- a/doc/txt/pair_line_lj.txt +++ /dev/null @@ -1,144 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style line/lj command :h3 - -[Syntax:] - -pair_style line/lj cutoff :pre - -cutoff = global cutoff for interactions (distance units) - -[Examples:] - -pair_style line/lj 3.0 -pair_coeff * * 1.0 1.0 1.0 0.8 1.12 -pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0 -pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5 :pre - -[Description:] - -Style {line/lj} treats particles which are line segments as a set of -small spherical particles that tile the line segment length as -explained below. Interactions between two line segments, each with N1 -and N2 spherical particles, are calculated as the pairwise sum of -N1*N2 Lennard-Jones interactions. Interactions between a line segment -with N spherical particles and a point particle are treated as the -pairwise sum of N Lennard-Jones interactions. See the "pair_style -lj/cut"_pair_lj.html doc page for the definition of Lennard-Jones -interactions. - -The set of non-overlapping spherical sub-particles that represent a -line segment are generated in the following manner. Their size is a -function of the line segment length and the specified sub-particle -size for that particle type. If a line segment has a length L and is -of type I, then the number of spheres N that represent the segment is -calculated as N = L/sizeI, rounded up to an integer value. Thus if L -is not evenly divisible by sizeI, N is incremented to include one -extra sphere. The centers of the spheres are spaced equally along the -line segment. Imagine N+1 equally-space points, which include the 2 -end points of the segment. The sphere centers are halfway between -each pair of points. - -The LJ interaction between 2 spheres on different line segments (or a -sphere on a line segment and a point particles) is computed with -sub-particle epsilon, sigma, and cutoff values that are set by the -pair_coeff command, as described below. If the distance between the 2 -spheres is greater than the sub-particle cutoff, there is no -interaction. This means that some pairs of sub-particles on 2 line -segments may interact, but others may not. - -For purposes of creating the neighbor list for pairs of interacting -line segments or lines/point particles, a regular particle-particle -cutoff is used, as defined by the {cutoff} setting above in the -pair_style command or overridden with an optional argument in the -pair_coeff command for a type pair as discussed below. The distance -between the centers of 2 line segments, or the center of a line -segment and a point particle, must be less than this distance (plus -the neighbor skin; see the "neighbor"_neighbor.html command), for -the pair of particles to be included in the neighbor list. - -NOTE: This means that a too-short value for the {cutoff} setting can -exclude a pair of particles from the neighbor list even if pairs of -their sub-particle spheres would interact, based on the sub-particle -cutoff specified in the pair_coeff command. E.g. sub-particles at the -ends of the line segments that are close to each other. Which may not -be what you want, since it means the ends of 2 line segments could -pass through each other. It is up to you to specify a {cutoff} -setting that is consistent with the length of the line segments you -are using and the sub-particle cutoff settings. - -For style {line/lj}, the following coefficients must be defined for -each pair of atom types via the "pair_coeff"_pair_coeff.html command -as in the examples above, or in the data file or restart files read by -the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -sizeI (distance units) -sizeJ (distance units) -epsilon (energy units) -sigma (distance units) -subcutoff (distance units) -cutoff (distance units) :ul - -The {sizeI} and {sizeJ} coefficients are the sub-particle sizes for -line particles of type I and type J. They are used to define the N -sub-particles per segment as described above. These coefficients are -actually stored on a per-type basis. Thus if there are multiple -pair_coeff commands that involve type I, as either the first or -second atom type, you should use consistent values for sizeI or sizeJ -in all of them. If you do not do this, the last value specified for -sizeI will apply to all segments of type I. If typeI or typeJ refers -to point particles, the corresponding sizeI or sizeJ is ignored; it -can be set to 0.0. - -The {epsilon}, {sigma}, and {subcutoff} coefficients are used to -compute an LJ interactions between a pair of sub-particles on 2 line -segments (of type I and J), or between a sub particle/point particle -pair. As discussed above, the {subcutoff} and {cutoff} params are -different. The latter is only used for building the neighbor list -when the distance between centers of two line segments or one segment -and a point particle is calculated. - -The {cutoff} coefficient is optional. If not specified, the global -cutoff is used. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, coefficients must be specified. -No default mixing rules are used. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This style is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Defining particles to be line segments so they participate in -line/line or line/particle interactions requires the use the -"atom_style line"_atom_style.html command. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style tri/lj"_pair_tri_lj.html - -[Default:] none diff --git a/doc/txt/pair_lj96.txt b/doc/txt/pair_lj96.txt deleted file mode 100644 index 19369adc66..0000000000 --- a/doc/txt/pair_lj96.txt +++ /dev/null @@ -1,106 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj96/cut command :h3 -pair_style lj96/cut/gpu command :h3 -pair_style lj96/cut/omp command :h3 - -[Syntax:] - -pair_style lj96/cut cutoff :pre - -cutoff = global cutoff for lj96/cut interactions (distance units) :ul - -[Examples:] - -pair_style lj96/cut 2.5 -pair_coeff * * 1.0 1.0 4.0 -pair_coeff 1 1 1.0 1.0 :pre - -[Description:] - -The {lj96/cut} style compute a 9/6 Lennard-Jones potential, instead -of the standard 12/6 potential, given by - -:c,image(Eqs/pair_lj96.jpg) - -Rc is the cutoff. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global LJ -cutoff specified in the pair_style command is used. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/cut pair styles can be mixed. -The default mix value is {geometric}. See the "pair_modify" command -for details. - -This pair style supports the "pair_modify"_pair_modify.html shift -option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style supports the "pair_modify"_pair_modify.html tail -option for adding a long-range tail correction to the energy and -pressure of the pair interaction. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style supports the use of the {inner}, {middle}, and {outer} -keywords of the "run_style respa"_run_style.html command, meaning the -pairwise forces can be partitioned by distance at different levels of -the rRESPA hierarchy. See the "run_style"_run_style.html command for -details. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none diff --git a/doc/txt/pair_lj_cubic.txt b/doc/txt/pair_lj_cubic.txt deleted file mode 100644 index 0a56672d28..0000000000 --- a/doc/txt/pair_lj_cubic.txt +++ /dev/null @@ -1,128 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj/cubic command :h3 -pair_style lj/cubic/gpu command :h3 -pair_style lj/cubic/omp command :h3 - -[Syntax:] - -pair_style lj/cubic :pre - -[Examples:] - -pair_style lj/cubic -pair_coeff * * 1.0 0.8908987 :pre - -[Description:] - -The {lj/cubic} style computes a truncated LJ interaction potential -whose energy and force are continuous everywhere. Inside the -inflection point the interaction is identical to the standard 12/6 -"Lennard-Jones"_pair_lj.html potential. The LJ function outside the -inflection point is replaced with a cubic function of distance. The -energy, force, and second derivative are continuous at the inflection -point. The cubic coefficient A3 is chosen so that both energy and -force go to zero at the cutoff distance. Outside the cutoff distance -the energy and force are zero. - -:c,image(Eqs/pair_lj_cubic.jpg) - -The location of the inflection point rs is defined -by the LJ diameter, rs/sigma = (26/7)^1/6. The cutoff distance -is defined by rc/rs = 67/48 or rc/sigma = 1.737.... -The analytic expression for the -the cubic coefficient -A3*rmin^3/epsilon = 27.93... is given in the paper by -Holian and Ravelo "(Holian)"_#Holian. - -This potential is commonly used to study the shock mechanics of FCC -solids, as in Ravelo et al. "(Ravelo)"_#Ravelo2. - -The following coefficients must be defined for each pair of atom types -via the "pair_coeff"_pair_coeff.html command as in the example above, -or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) :ul - -Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum, which is -located at rmin = 2^(1/6)*sigma. In the above example, sigma = -0.8908987, so rmin = 1. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/cut pair styles can be mixed. -The default mix value is {geometric}. See the "pair_modify" command -for details. - -The lj/cubic pair style does not support the -"pair_modify"_pair_modify.html shift option, -since pair interaction is already smoothed to 0.0 at the -cutoff. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -The lj/cubic pair style does not support the -"pair_modify"_pair_modify.html tail option for adding long-range tail -corrections to energy and pressure, since there are no corrections for -a potential that goes to 0.0 at the cutoff. - -The lj/cubic pair style writes its information to "binary -restart files"_restart.html, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. - -The lj/cubic pair style can only be used via the {pair} -keyword of the "run_style respa"_run_style.html command. It does not -support the {inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Holian) -[(Holian)] Holian and Ravelo, Phys Rev B, 51, 11275 (1995). -:link(Ravelo2) -[(Ravelo)] Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004). diff --git a/doc/txt/pair_lj_expand.txt b/doc/txt/pair_lj_expand.txt deleted file mode 100644 index 178ba8d1a8..0000000000 --- a/doc/txt/pair_lj_expand.txt +++ /dev/null @@ -1,124 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj/expand command :h3 -pair_style lj/expand/gpu command :h3 -pair_style lj/expand/kk command :h3 -pair_style lj/expand/omp command :h3 -pair_style lj/expand/coul/long command :h3 -pair_style lj/expand/coul/long/gpu command :h3 - -[Syntax:] - -pair_style lj/expand cutoff :pre - -cutoff = global cutoff for lj/expand interactions (distance units) :ul - -[Examples:] - -pair_style lj/expand 2.5 -pair_coeff * * 1.0 1.0 0.5 -pair_coeff 1 1 1.0 1.0 -0.2 2.0 :pre - -pair_style lj/expand/coul/long 2.5 -pair_style lj/expand/coul/long 2.5 4.0 -pair_coeff * * 1.0 1.0 0.5 -pair_coeff 1 1 1.0 1.0 -0.2 3.0 :pre - -[Description:] - -Style {lj/expand} computes a LJ interaction with a distance shifted by -delta which can be useful when particles are of different sizes, since -it is different that using different sigma values in a standard LJ -formula: - -:c,image(Eqs/pair_lj_expand.jpg) - -Rc is the cutoff which does not include the delta distance. I.e. the -actual force cutoff is the sum of cutoff + delta. - -For all of the {lj/expand} pair styles, the following coefficients must -be defined for each pair of atoms types via the -"pair_coeff"_pair_coeff.html command as in the examples above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands, or by mixing as -described below: - -epsilon (energy units) -sigma (distance units) -delta (distance units) -cutoff (distance units) :ul - -The delta values can be positive or negative. The last coefficient is -optional. If not specified, the global LJ cutoff is used. - -For {lj/expand/coul/long} only the LJ cutoff can be specified since a -Coulombic cutoff cannot be specified for an individual I,J type pair. -All type pairs use the same global Coulombic cutoff specified in the -pair_style command. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon, sigma, and shift -coefficients and cutoff distance for this pair style can be mixed. -Shift is always mixed via an {arithmetic} rule. The other -coefficients are mixed according to the pair_modify mix value. The -default mix value is {geometric}. See the "pair_modify" command for -details. - -This pair style supports the "pair_modify"_pair_modify.html shift -option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style supports the "pair_modify"_pair_modify.html tail -option for adding a long-range tail correction to the energy and -pressure of the pair interaction. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none diff --git a/doc/txt/pair_lj_long.txt b/doc/txt/pair_lj_long.txt deleted file mode 100644 index e371030a76..0000000000 --- a/doc/txt/pair_lj_long.txt +++ /dev/null @@ -1,237 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj/long/coul/long command :h3 -pair_style lj/long/coul/long/intel command :h3 -pair_style lj/long/coul/long/omp command :h3 -pair_style lj/long/coul/long/opt command :h3 -pair_style lj/long/tip4p/long command :h3 -pair_style lj/long/tip4p/long/omp command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {lj/long/coul/long} or {lj/long/tip4p/long} -args = list of arguments for a particular style :ul - {lj/long/coul/long} args = flag_lj flag_coul cutoff (cutoff2) - flag_lj = {long} or {cut} or {off} - {long} = use Kspace long-range summation for dispersion 1/r^6 term - {cut} = use a cutoff on dispersion 1/r^6 term - {off} = omit disperion 1/r^6 term entirely - flag_coul = {long} or {off} - {long} = use Kspace long-range summation for Coulombic 1/r term - {off} = omit Coulombic term - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {lj/long/tip4p/long} args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2) - flag_lj = {long} or {cut} - {long} = use Kspace long-range summation for dispersion 1/r^6 term - {cut} = use a cutoff - flag_coul = {long} or {off} - {long} = use Kspace long-range summation for Coulombic 1/r term - {off} = omit Coulombic term - otype,htype = atom types for TIP4P O and H - btype,atype = bond and angle types for TIP4P waters - qdist = distance from O atom to massless charge (distance units) - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre - -[Examples:] - -pair_style lj/long/coul/long cut off 2.5 -pair_style lj/long/coul/long cut long 2.5 4.0 -pair_style lj/long/coul/long long long 2.5 4.0 -pair_coeff * * 1 1 -pair_coeff 1 1 1 3 4 :pre - -pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 -pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 :pre - -[Description:] - -Style {lj/long/coul/long} computes the standard 12/6 Lennard-Jones and -Coulombic potentials, given by - -:c,image(Eqs/pair_lj.jpg) - -:c,image(Eqs/pair_coulomb.jpg) - -where C is an energy-conversion constant, Qi and Qj are the charges on -the 2 atoms, epsilon is the dielectric constant which can be set by -the "dielectric"_dielectric.html command, and Rc is the cutoff. If -one cutoff is specified in the pair_style command, it is used for both -the LJ and Coulombic terms. If two cutoffs are specified, they are -used as cutoffs for the LJ and Coulombic terms respectively. - -The purpose of this pair style is to capture long-range interactions -resulting from both attractive 1/r^6 Lennard-Jones and Coulombic 1/r -interactions. This is done by use of the {flag_lj} and {flag_coul} -settings. The "In 't Veld"_#Veld2 paper has more details on when it is -appropriate to include long-range 1/r^6 interactions, using this -potential. - -Style {lj/long/tip4p/long} implements the TIP4P water model of -"(Jorgensen)"_#Jorgensen4, which introduces a massless site located a -short distance away from the oxygen atom along the bisector of the HOH -angle. The atomic types of the oxygen and hydrogen atoms, the bond -and angle types for OH and HOH interactions, and the distance to the -massless charge site are specified as pair_style arguments. - -NOTE: For each TIP4P water molecule in your system, the atom IDs for -the O and 2 H atoms must be consecutive, with the O atom first. This -is to enable LAMMPS to "find" the 2 H atoms associated with each O -atom. For example, if the atom ID of an O atom in a TIP4P water -molecule is 500, then its 2 H atoms must have IDs 501 and 502. - -See the "Howto tip4p"_Howto_tip4p.html doc page for more -information on how to use the TIP4P pair style. Note that the -neighbor list cutoff for Coulomb interactions is effectively extended -by a distance 2*qdist when using the TIP4P pair style, to account for -the offset distance of the fictitious charges on O atoms in water -molecules. Thus it is typically best in an efficiency sense to use a -LJ cutoff >= Coulombic cutoff + 2*qdist, to shrink the size of the -neighbor list. This leads to slightly larger cost for the long-range -calculation, so you can test the trade-off for your model. - -If {flag_lj} is set to {long}, no cutoff is used on the LJ 1/r^6 -dispersion term. The long-range portion can be calculated by using -the "kspace_style ewald/disp or pppm/disp"_kspace_style.html commands. -The specified LJ cutoff then determines which portion of the LJ -interactions are computed directly by the pair potential versus which -part is computed in reciprocal space via the Kspace style. If -{flag_lj} is set to {cut}, the LJ interactions are simply cutoff, as -with "pair_style lj/cut"_pair_lj.html. - -If {flag_coul} is set to {long}, no cutoff is used on the Coulombic -interactions. The long-range portion can calculated by using any of -several "kspace_style"_kspace_style.html command options such as -{pppm} or {ewald}. Note that if {flag_lj} is also set to long, then -the {ewald/disp} or {pppm/disp} Kspace style needs to be used to -perform the long-range calculations for both the LJ and Coulombic -interactions. If {flag_coul} is set to {off}, Coulombic interactions -are not computed. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) -cutoff1 (distance units) -cutoff2 (distance units) :ul - -Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum at 2^(1/6) -sigma. - -The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both LJ -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. - -Note that if you are using {flag_lj} set to {long}, you -cannot specify a LJ cutoff for an atom type pair, since only one -global LJ cutoff is allowed. Similarly, if you are using {flag_coul} -set to {long}, you cannot specify a Coulombic cutoff for an atom type -pair, since only one global Coulombic cutoff is allowed. - -For {lj/long/tip4p/long} only the LJ cutoff can be specified -since a Coulombic cutoff cannot be specified for an individual I,J -type pair. All type pairs use the same global Coulombic cutoff -specified in the pair_style command. - -:line - -A version of these styles with a soft core, {lj/cut/soft}, suitable for use in -free energy calculations, is part of the USER-FEP package and is documented with -the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is -only available if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/long pair styles can be mixed. -The default mix value is {geometric}. See the "pair_modify" command -for details. - -These pair styles support the "pair_modify"_pair_modify.html shift -option for the energy of the Lennard-Jones portion of the pair -interaction, assuming {flag_lj} is {cut}. - -These pair styles support the "pair_modify"_pair_modify.html table and -table/disp options since they can tabulate the short-range portion of -the long-range Coulombic and dispersion interactions. - -Thes pair styles do not support the "pair_modify"_pair_modify.html -tail option for adding a long-range tail correction to the -Lennard-Jones portion of the energy and pressure. - -These pair styles write their information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -The pair lj/long/coul/long styles support the use of the {inner}, -{middle}, and {outer} keywords of the "run_style respa"_run_style.html -command, meaning the pairwise forces can be partitioned by distance at -different levels of the rRESPA hierarchy. See the -"run_style"_run_style.html command for details. - -:line - -[Restrictions:] - -These styles are part of the KSPACE package. They are only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Veld2) -[(In 't Veld)] In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007). - -:link(Jorgensen4) -[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem -Phys, 79, 926 (1983). diff --git a/doc/txt/pair_lj_smooth.txt b/doc/txt/pair_lj_smooth.txt deleted file mode 100644 index d320cb83ff..0000000000 --- a/doc/txt/pair_lj_smooth.txt +++ /dev/null @@ -1,121 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj/smooth command :h3 -pair_style lj/smooth/omp command :h3 - -[Syntax:] - -pair_style lj/smooth Rin Rc :pre - -Rin = inner cutoff beyond which force smoothing will be applied (distance units) -Rc = outer cutoff for lj/smooth interactions (distance units) :ul - -[Examples:] - -pair_style lj/smooth 8.0 10.0 -pair_coeff * * 10.0 1.5 -pair_coeff 1 1 20.0 1.3 7.0 9.0 :pre - -[Description:] - -Style {lj/smooth} computes a LJ interaction with a force smoothing -applied between the inner and outer cutoff. - -:c,image(Eqs/pair_lj_smooth.jpg) - -The polynomial coefficients C1, C2, C3, C4 are computed by LAMMPS to -cause the force to vary smoothly from the inner cutoff Rin to the -outer cutoff Rc. - -At the inner cutoff the force and its 1st derivative -will match the non-smoothed LJ formula. At the outer cutoff the force -and its 1st derivative will be 0.0. The inner cutoff cannot be 0.0. - -NOTE: this force smoothing causes the energy to be discontinuous both -in its values and 1st derivative. This can lead to poor energy -conservation and may require the use of a thermostat. Plot the energy -and force resulting from this formula via the -"pair_write"_pair_write.html command to see the effect. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) -inner (distance units) -outer (distance units) :ul - -The last 2 coefficients are optional inner and outer cutoffs. If not -specified, the global values for Rin and Rc are used. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon, sigma, Rin -coefficients and the cutoff distance for this pair style can be mixed. -Rin is a cutoff value and is mixed like the cutoff. The other -coefficients are mixed according to the pair_modify mix option. The -default mix value is {geometric}. See the "pair_modify" command for -details. - -This pair style supports the "pair_modify"_pair_modify.html shift -option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure, since the energy of the pair interaction is smoothed to 0.0 -at the cutoff. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair -lj/smooth/linear"_pair_lj_smooth_linear.html - -[Default:] none diff --git a/doc/txt/pair_lj_smooth_linear.txt b/doc/txt/pair_lj_smooth_linear.txt deleted file mode 100644 index 9c509515c0..0000000000 --- a/doc/txt/pair_lj_smooth_linear.txt +++ /dev/null @@ -1,110 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj/smooth/linear command :h3 -pair_style lj/smooth/linear/omp command :h3 - -[Syntax:] - -pair_style lj/smooth/linear cutoff :pre - -cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul - -[Examples:] - -pair_style lj/smooth/linear 2.5 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 0.3 3.0 9.0 :pre - -[Description:] - -Style {lj/smooth/linear} computes a truncated and force-shifted LJ -interaction (aka Shifted Force Lennard-Jones) that combines the -standard 12/6 Lennard-Jones function and subtracts a linear term based -on the cutoff distance, so that both, the potential and the force, go -continuously to zero at the cutoff Rc "(Toxvaerd)"_#Toxvaerd: - -:c,image(Eqs/pair_lj_smooth_linear.jpg) - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global -LJ cutoff specified in the pair_style command is used. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance can be mixed. The default mix value is geometric. -See the "pair_modify" command for details. - -This pair style does not support the "pair_modify"_pair_modify.html -shift option for the energy of the pair interaction, since it goes -to 0.0 at the cutoff by construction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure, since the energy of the pair interaction is smoothed to 0.0 -at the cutoff. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair lj/smooth"_pair_lj_smooth.html - -[Default:] none - -:line - -:link(Toxvaerd) -[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011). diff --git a/doc/txt/pair_local_density.txt b/doc/txt/pair_local_density.txt deleted file mode 100644 index 4def63c5fc..0000000000 --- a/doc/txt/pair_local_density.txt +++ /dev/null @@ -1,207 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style local/density command :h3 - -[Syntax:] - -pair_style style arg :pre - -style = {local/density} -arg = name of file containing tabulated values of local density and the potential :ul - -[Examples:] - -pair_style local/density benzene_water.localdensity.table :pre - -pair_style hybrid/overlay table spline 500 local/density -pair_coeff * * local/density benzene_water.localdensity.table :pre - -[Description:] - -The local density (LD) potential is a mean-field manybody potential, and, in some -sense,a generalization of embedded atom models (EAM). The name "local density -potential" arises from the fact that it assigns an energy to an atom depending -on the number of neighboring atoms of given type around it within a predefined -spherical volume (i.e., within a cutoff). The bottom-up coarse-graining (CG) -literature suggests that such potentials can be widely useful in capturing -effective multibody forces in a computationally efficient manner so as to -improve the quality of CG models of implicit solvation"(Sanyal1)"_#Sanyal1 and -phase-segregation in liquid mixtures"(Sanyal2)"_#Sanyal2, and provide guidelines -to determine the extent of manybody correlations present in a CG -model."(Rosenberger)"_#Rosenberger The LD potential in LAMMPS is primarily -intended to be used as a corrective potential over traditional pair potentials -in bottom-up CG models, i.e., as a hybrid pair style with -other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.). -Because the LD potential is not a pair potential per se, it is implemented -simply as a single auxiliary file with all specifications that will be read -upon initialization. - -NOTE: Thus when used as the only interaction in the system, there is no -corresponding pair_coeff command and when used with other pair styles using the -hybrid/overlay option, the corresponding pair_coeff command must be supplied -* * as placeholders for the atom types. - -:line - -[System with a single CG atom type:] - -A system of a single atom type (e.g., LJ argon) with a single local density (LD) -potential would have an energy given by: - -:c,image(Eqs/pair_local_density_energy.jpg) - -where rho_i is the LD at atom i and F(rho) is similar in spirit to the -embedding function used in EAM potentials. The LD at atom i is given by the sum - -:c,image(Eqs/pair_local_density_ld.jpg) - -where phi is an indicator function that is one at r=0 and zero beyond a cutoff -distance R2. The choice of the functional form of phi is somewhat arbitrary, -but the following piecewise cubic function has proven sufficiently general: -"(Sanyal1)"_#Sanyal1, "(Sanyal2)"_#Sanyal2 "(Rosenberger)"_#Rosenberger - -:c,image(Eqs/pair_local_density_indicator_func.jpg) - -The constants {c} are chosen so that the indicator function smoothly -interpolates between 1 and 0 between the distances R1 and R2, which are -called the inner and outer cutoffs, respectively. Thus phi satisfies -phi(R1) = 1, phi(R2) = dphi/dr @ (r=R1) = dphi/dr @ (r=R2) = 0. The embedding -function F(rho) may or may not have a closed-form expression. To maintain -generality, it is practically represented with a spline-interpolated table -over a predetermined range of rho. Outside of that range it simply adopts zero -values at the endpoints. - -It can be shown that the total force between two atoms due to the LD potential -takes the form of a pair force, which motivates its designation as a LAMMPS -pair style. Please see "(Sanyal1)"_#Sanyal1 for details of the derivation. - -:line - -[Systems with arbitrary numbers of atom types:] - -The potential is easily generalized to systems involving multiple atom types: - -:c,image(Eqs/pair_local_density_energy_multi.jpg) - -with the LD expressed as - -:c,image(Eqs/pair_local_density_ld_multi.jpg) - -where alpha gives the type of atom i, beta the type of atom j, and the -coefficients a and b filter for atom types as specified by the user. a is -called the central atom filter as it determines to which atoms the -potential applies; a_alpha = 1 if the LD potential applies to atom type alpha -else zero. On the other hand, b is called the neighbor atom filter because it -specifies which atom types to use in the calculation of the LD; b_beta = 1 if -atom type beta contributes to the LD and zero otherwise. - -NOTE: Note that the potentials need not be symmetric with respect to atom types, -which is the reason for two distinct sets of coefficients a and b. An atom type -may contribute to the LD but not the potential, or to the potential but not the -LD. Such decisions are made by the user and should (ideally) be motivated on -physical grounds for the problem at hand. - -:line - -[General form for implementation in LAMMPS:] - -Of course, a system with many atom types may have many different possible LD -potentials, each with their own atom type filters, cutoffs, and embedding -functions. The most general form of this potential as implemented in the -pair_style local/density is: - -:c,image(Eqs/pair_local_density_energy_implement.jpg) - -where, k is an index that spans the (arbitrary) number of applied LD potentials -N_LD. Each LD is calculated as before with: - -:c,image(Eqs/pair_local_density_ld_implement.jpg) - -The superscript on the indicator function phi simply indicates that it is -associated with specific values of the cutoff distances R1(k) and R2(k). In -summary, there may be N_LD distinct LD potentials. With each potential type (k), -one must specify: - -the inner and outer cutoffs as R1 and R2 -the central type filter a(k), where k = 1,2,...N_LD -the neighbor type filter b(k), where k = 1,2,...N_LD -the LD potential function F(k)(rho), typically as a table that is later spline-interpolated :ul - -:line - -[Tabulated input file format:] - -Line 1: comment or blank (ignored) -Line 2: comment or blank (ignored) -Line 3: N_LD N_rho (# of LD potentials and # of tabulated values, single space separated) -Line 4: blank (ignored) -Line 5: R1(k) R2(k) (lower and upper cutoffs, single space separated) -Line 6: central-types (central atom types, single space separated) -Line 7: neighbor-types (neighbor atom types single space separated) -Line 8: rho_min rho_max drho (min, max and diff. in tabulated rho values, single space separated) -Line 9: F(k)(rho_min + 0.drho) -Line 10: F(k)(rho_min + 1.drho) -Line 11: F(k)(rho_min + 2.drho) -... -Line 9+N_rho: F(k)(rho_min + N_rho . drho) -Line 10+N_rho: blank (ignored) :pre - -Block 2 :pre - -Block 3 :pre - -Block N_LD :pre - -Lines 5 to 9+N_rho constitute the first block. Thus the input file is separated -(by blank lines) into N_LD blocks each representing a separate LD potential and -each specifying its own upper and lower cutoffs, central and neighbor atoms, -and potential. In general, blank lines anywhere are ignored. - -:line - -[Mixing, shift, table, tail correction, restart, info]: -This pair style does not support automatic mixing. For atom type pairs alpha, -beta and alpha != beta, even if LD potentials of type (alpha, alpha) and -(beta, beta) are provided, you will need to explicitly provide LD potential -types (alpha, beta) and (beta, alpha) if need be (Here, the notation (alpha, -beta) means that alpha is the central atom to which the LD potential is applied -and beta is the neighbor atom which contributes to the LD potential on alpha). - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -The local/density pair style does not write its information to "binary restart -files"_restart.html, since it is stored in tabulated potential files. -Thus, you need to re-specify the pair_style and pair_coeff commands in -an input script that reads a restart file. - -:line - -[Restrictions:] - -The local/density pair style is a part of the USER-MISC package. It is only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - - -:link(Sanyal1) -[(Sanyal1)] Sanyal and Shell, Journal of Chemical Physics, 2016, 145 (3), 034109. -:link(Sanyal2) -[(Sanyal2)] Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693. - -:link(Rosenberger) -[(Rosenberger)] Rosenberger, Sanyal, Shell and van der Vegt, Journal of Chemical Physics, 2019, 151 (4), 044111. diff --git a/doc/txt/pair_lubricate.txt b/doc/txt/pair_lubricate.txt deleted file mode 100644 index 83a67d0300..0000000000 --- a/doc/txt/pair_lubricate.txt +++ /dev/null @@ -1,228 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lubricate command :h3 -pair_style lubricate/omp command :h3 -pair_style lubricate/poly command :h3 -pair_style lubricate/poly/omp command :h3 - -[Syntax:] - -pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF :pre - -style = {lubricate} or {lubricate/poly} -mu = dynamic viscosity (dynamic viscosity units) -flaglog = 0/1 to exclude/include log terms in the lubrication approximation -flagfld = 0/1 to exclude/include Fast Lubrication Dynamics (FLD) effects -cutinner = inner cutoff distance (distance units) -cutoff = outer cutoff for interactions (distance units) -flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions -flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms :ul - -[Examples:] (all assume radius = 1) - -pair_style lubricate 1.5 1 1 2.01 2.5 -pair_coeff 1 1 2.05 2.8 -pair_coeff * * :pre - -pair_style lubricate 1.5 1 1 2.01 2.5 -pair_coeff * * -variable mu equal ramp(1,2) -fix 1 all adapt 1 pair lubricate mu * * v_mu :pre - -[Description:] - -Styles {lubricate} and {lubricate/poly} compute hydrodynamic -interactions between mono-disperse finite-size spherical particles in -a pairwise fashion. The interactions have 2 components. The first is -Ball-Melrose lubrication terms via the formulas in "(Ball and -Melrose)"_#Ball1 - -:c,image(Eqs/pair_lubricate.jpg) - -which represents the dissipation W between two nearby particles due to -their relative velocities in the presence of a background solvent with -viscosity {mu}. Note that this is dynamic viscosity which has units of -mass/distance/time, not kinematic viscosity. - -The Asq (squeeze) term is the strongest and is included if {flagHI} is -set to 1 (default). It scales as 1/gap where gap is the separation -between the surfaces of the 2 particles. The Ash (shear) and Apu -(pump) terms are only included if {flaglog} is set to 1. They are the -next strongest interactions, and the only other singular interaction, -and scale as log(gap). Note that {flaglog} = 1 and {flagHI} = 0 is -invalid, and will result in a warning message, after which {flagHI} will -be set to 1. The Atw (twist) term is currently not included. It is -typically a very small contribution to the lubrication forces. - -The {flagHI} and {flagVF} settings are optional. Neither should be -used, or both must be defined. - -{Cutinner} sets the minimum center-to-center separation that will be -used in calculations irrespective of the actual separation. {Cutoff} -is the maximum center-to-center separation at which an interaction is -computed. Using a {cutoff} less than 3 radii is recommended if -{flaglog} is set to 1. - -The other component is due to the Fast Lubrication Dynamics (FLD) -approximation, described in "(Kumar)"_#Kumar1, which can be -represented by the following equation - -:c,image(Eqs/fld.jpg) - -where U represents the velocities and angular velocities of the -particles, U^{infty} represents the velocity and the angular velocity -of the undisturbed fluid, and E^{infty} represents the rate of strain -tensor of the undisturbed fluid with viscosity {mu}. Again, note that -this is dynamic viscosity which has units of mass/distance/time, not -kinematic viscosity. Volume fraction corrections to R_FU are included -as long as {flagVF} is set to 1 (default). - -NOTE: When using the FLD terms, these pair styles are designed to be -used with explicit time integration and a correspondingly small -timestep. Thus either "fix nve/sphere"_fix_nve_sphere.html or "fix -nve/asphere"_fix_nve_asphere.html should be used for time integration. -To perform implicit FLD, see the "pair_style -lubricateU"_pair_lubricateU.html command. - -Style {lubricate} requires monodisperse spherical particles; style -{lubricate/poly} allows for polydisperse spherical particles. - -The viscosity {mu} can be varied in a time-dependent manner over the -course of a simulation, in which case in which case the pair_style -setting for {mu} will be overridden. See the "fix adapt"_fix_adapt.html -command for details. - -If the suspension is sheared via the "fix deform"_fix_deform.html -command then the pair style uses the shear rate to adjust the -hydrodynamic interactions accordingly. Volume changes due to fix -deform are accounted for when computing the volume fraction -corrections to R_FU. - -When computing the volume fraction corrections to R_FU, the presence -of walls (whether moving or stationary) will affect the volume -fraction available to colloidal particles. This is currently accounted -for with the following types of walls: "wall/lj93"_fix_wall.html, -"wall/lj126"_fix_wall.html, "wall/colloid"_fix_wall.html, and -"wall/harmonic"_fix_wall.html. For these wall styles, the correct -volume fraction will be used when walls do not coincide with the box -boundary, as well as when walls move and thereby cause a change in the -volume fraction. Other wall styles will still work, but they will -result in the volume fraction being computed based on the box -boundaries. - -Since lubrication forces are dissipative, it is usually desirable to -thermostat the system at a constant temperature. If Brownian motion -(at a constant temperature) is desired, it can be set using the -"pair_style brownian"_pair_brownian.html command. These pair styles -and the brownian style should use consistent parameters for {mu}, -{flaglog}, {flagfld}, {cutinner}, {cutoff}, {flagHI} and {flagVF}. - -:line - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -cutinner (distance units) -cutoff (distance units) :ul - -The two coefficients are optional. If neither is specified, the two -cutoffs specified in the pair_style command are used. Otherwise both -must be specified. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in "this section"_Speed.html of -the manual. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See "this section"_Speed.html of the manual for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the two cutoff distances for this -pair style can be mixed. The default mix value is {geometric}. See -the "pair_modify" command for details. - -This pair style does not support the "pair_modify"_pair_modify.html -shift option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -These styles are part of the COLLOID package. They are only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Only spherical monodisperse particles are allowed for pair_style -lubricate. - -Only spherical particles are allowed for pair_style lubricate/poly. - -These pair styles will not restart exactly when using the -"read_restart"_read_restart.html command, though they should provide -statistically similar results. This is because the forces they -compute depend on atom velocities. See the -"read_restart"_read_restart.html command for more details. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style -lubricateU"_pair_lubricateU.html - -[Default:] - -The default settings for the optional args are flagHI = 1 and flagVF = -1. - -:line - -:link(Ball1) -[(Ball)] Ball and Melrose, Physica A, 247, 444-472 (1997). - -:link(Kumar1) -[(Kumar)] Kumar and Higdon, Phys Rev E, 82, 051401 (2010). See also -his thesis for more details: A. Kumar, "Microscale Dynamics in -Suspensions of Non-spherical Particles", Thesis, University of -Illinois Urbana-Champaign, -(2010). ("https://www.ideals.illinois.edu/handle/2142/16032"_https://www.ideals.illinois.edu/handle/2142/16032) diff --git a/doc/txt/pair_lubricateU.txt b/doc/txt/pair_lubricateU.txt deleted file mode 100644 index bfc7c36013..0000000000 --- a/doc/txt/pair_lubricateU.txt +++ /dev/null @@ -1,218 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lubricateU command :h3 -pair_style lubricateU/poly command :h3 - -[Syntax:] - -pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF :pre - -style = {lubricateU} or {lubricateU/poly} -mu = dynamic viscosity (dynamic viscosity units) -flaglog = 0/1 to exclude/include log terms in the lubrication approximation -cutinner = inner cut off distance (distance units) -cutoff = outer cutoff for interactions (distance units) -gdot = shear rate (1/time units) -flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions -flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms :ul - -[Examples:] (all assume radius = 1) - -pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1 -pair_coeff 1 1 2.05 2.8 -pair_coeff * * :pre - -[Description:] - -Styles {lubricateU} and {lubricateU/poly} compute velocities and -angular velocities for finite-size spherical particles such that the -hydrodynamic interaction balances the force and torque due to all -other types of interactions. - -The interactions have 2 components. The first is -Ball-Melrose lubrication terms via the formulas in "(Ball and -Melrose)"_#Ball2 - -:c,image(Eqs/pair_lubricate.jpg) - -which represents the dissipation W between two nearby particles due to -their relative velocities in the presence of a background solvent with -viscosity {mu}. Note that this is dynamic viscosity which has units of -mass/distance/time, not kinematic viscosity. - -The Asq (squeeze) term is the strongest and is included as long as -{flagHI} is set to 1 (default). It scales as 1/gap where gap is the -separation between the surfaces of the 2 particles. The Ash (shear) -and Apu (pump) terms are only included if {flaglog} is set to 1. They -are the next strongest interactions, and the only other singular -interaction, and scale as log(gap). Note that {flaglog} = 1 and -{flagHI} = 0 is invalid, and will result in a warning message, after -which {flagHI} will be set to 1. The Atw (twist) term is currently not -included. It is typically a very small contribution to the lubrication -forces. - -The {flagHI} and {flagVF} settings are optional. Neither should be -used, or both must be defined. - -{Cutinner} sets the minimum center-to-center separation that will be -used in calculations irrespective of the actual separation. {Cutoff} -is the maximum center-to-center separation at which an interaction is -computed. Using a {cutoff} less than 3 radii is recommended if -{flaglog} is set to 1. - -The other component is due to the Fast Lubrication Dynamics (FLD) -approximation, described in "(Kumar)"_#Kumar2. The equation being -solved to balance the forces and torques is - -:c,image(Eqs/fld2.jpg) - -where U represents the velocities and angular velocities of the -particles, U^{infty} represents the velocities and the angular -velocities of the undisturbed fluid, and E^{infty} represents the rate -of strain tensor of the undisturbed fluid flow with viscosity -{mu}. Again, note that this is dynamic viscosity which has units of -mass/distance/time, not kinematic viscosity. Volume fraction -corrections to R_FU are included if {flagVF} is set to 1 (default). - -F{rest} represents the forces and torques due to all other types of -interactions, e.g. Brownian, electrostatic etc. Note that this -algorithm neglects the inertial terms, thereby removing the -restriction of resolving the small interial time scale, which may not -be of interest for colloidal particles. This pair style solves for -the velocity such that the hydrodynamic force balances all other types -of forces, thereby resulting in a net zero force (zero inertia limit). -When defining this pair style, it must be defined last so that when -this style is invoked all other types of forces have already been -computed. For the same reason, it won't work if additional non-pair -styles are defined (such as bond or Kspace forces) as they are -calculated in LAMMPS after the pairwise interactions have been -computed. - -NOTE: When using these styles, the these pair styles are designed to -be used with implicit time integration and a correspondingly larger -timestep. Thus either "fix nve/noforce"_fix_nve_noforce.html should -be used for spherical particles defined via "atom_style -sphere"_atom_style.html or "fix -nve/asphere/noforce"_fix_nve_asphere_noforce.html should be used for -spherical particles defined via "atom_style -ellipsoid"_atom_style.html. This is because the velocity and angular -momentum of each particle is set by the pair style, and should not be -reset by the time integration fix. - -Style {lubricateU} requires monodisperse spherical particles; style -{lubricateU/poly} allows for polydisperse spherical particles. - -If the suspension is sheared via the "fix deform"_fix_deform.html -command then the pair style uses the shear rate to adjust the -hydrodynamic interactions accordingly. Volume changes due to fix -deform are accounted for when computing the volume fraction -corrections to R_FU. - -When computing the volume fraction corrections to R_FU, the presence -of walls (whether moving or stationary) will affect the volume -fraction available to colloidal particles. This is currently accounted -for with the following types of walls: "wall/lj93"_fix_wall.html, -"wall/lj126"_fix_wall.html, "wall/colloid"_fix_wall.html, and -"wall/harmonic"_fix_wall.html. For these wall styles, the correct -volume fraction will be used when walls do not coincide with the box -boundary, as well as when walls move and thereby cause a change in the -volume fraction. To use these wall styles with pair_style {lubricateU} -or {lubricateU/poly}, the {fld yes} option must be specified in the -fix wall command. - -Since lubrication forces are dissipative, it is usually desirable to -thermostat the system at a constant temperature. If Brownian motion -(at a constant temperature) is desired, it can be set using the -"pair_style brownian"_pair_brownian.html command. These pair styles -and the brownian style should use consistent parameters for {mu}, -{flaglog}, {flagfld}, {cutinner}, {cutoff}, {flagHI} and {flagVF}. - -:line - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -cutinner (distance units) -cutoff (distance units) :ul - -The two coefficients are optional. If neither is specified, the two -cutoffs specified in the pair_style command are used. Otherwise both -must be specified. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the two cutoff distances for this -pair style can be mixed. The default mix value is {geometric}. See -the "pair_modify" command for details. - -This pair style does not support the "pair_modify"_pair_modify.html -shift option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -These styles are part of the COLLOID package. They are only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Currently, these pair styles assume that all other types of -forces/torques on the particles have been already been computed when -it is invoked. This requires this style to be defined as the last of -the pair styles, and that no fixes apply additional constraint forces. -One exception is the "fix wall/colloid"_fix_wall.html commands, which -has an "fld" option to apply their wall forces correctly. - -Only spherical monodisperse particles are allowed for pair_style -lubricateU. - -Only spherical particles are allowed for pair_style lubricateU/poly. - -For sheared suspensions, it is assumed that the shearing is done in -the xy plane, with x being the velocity direction and y being the -velocity-gradient direction. In this case, one must use "fix -deform"_fix_deform.html with the same rate of shear (erate). - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style -lubricate"_pair_lubricate.html - -[Default:] - -The default settings for the optional args are flagHI = 1 and flagVF = -1. - -:line - -:link(Ball2) -[(Ball)] Ball and Melrose, Physica A, 247, 444-472 (1997). - -:link(Kumar2) -[(Kumar)] Kumar and Higdon, Phys Rev E, 82, 051401 (2010). diff --git a/doc/txt/pair_mdf.txt b/doc/txt/pair_mdf.txt deleted file mode 100644 index 44c9e7f67d..0000000000 --- a/doc/txt/pair_mdf.txt +++ /dev/null @@ -1,157 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj/mdf command :h3 -pair_style buck/mdf command :h3 -pair_style lennard/mdf command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {lj/mdf} or {buck/mdf} or {lennard/mdf} :ulb,l -args = list of arguments for a particular style :l - {lj/mdf} args = cutoff1 cutoff2 - cutoff1 = inner cutoff for the start of the tapering function - cutoff1 = out cutoff for the end of the tapering function - {buck/mdf} args = cutoff1 cutoff2 - cutoff1 = inner cutoff for the start of the tapering function - cutoff1 = out cutoff for the end of the tapering function - {lennard/mdf} args = cutoff1 cutoff2 - cutoff1 = inner cutoff for the start of the tapering function - cutoff1 = out cutoff for the end of the tapering function :pre -:ule - -[Examples:] - -pair_style lj/mdf 2.5 3.0 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.1 2.8 3.0 3.2 :pre - -pair_style buck 2.5 3.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff * * 100.0 1.5 200.0 3.0 3.5 :pre - -pair_style lennard/mdf 2.5 3.0 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1021760.3664 2120.317338 3.0 3.2 :pre - -[Description:] - -The {lj/mdf}, {buck/mdf} and {lennard/mdf} compute the standard 12-6 -Lennard-Jones and Buckingham potential with the addition of a taper -function that ramps the energy and force smoothly to zero between an -inner and outer cutoff. - -:c,image(Eqs/pair_mdf-1.jpg) - -The tapering, {f(r)}, is done by using the Mei, Davenport, Fernando -function "(Mei)"_#Mei. - -:c,image(Eqs/pair_mdf-2.jpg) - -where - -:c,image(Eqs/pair_mdf-3.jpg) - -Here {r_m} is the inner cutoff radius and {r_cut} is the outer cutoff -radius. - -:line - -For the {lj/mdf} pair_style, the potential energy, {E(r)}, is the -standard 12-6 Lennard-Jones written in the epsilon/sigma form: - -:c,image(Eqs/pair_mdf-4.jpg) - -Either the first two or all of the following coefficients must be -defined for each pair of atoms types via the pair_coeff command as -in the examples above, or in the data file read by the -"read_data"_read_data.html. The two cutoffs default to the global -values and epsilon and sigma can also be determined by mixing as -described below: - -epsilon (energy units) -sigma (distance units) -r_m (distance units) -r_{cut} (distance units) :ul - -:line - -For the {buck/mdf} pair_style, the potential energy, {E(r)}, is the -standard Buckingham potential with three required coefficients. -The two cutoffs can be omitted and default to the corresponding -global values: - -:c,image(Eqs/pair_mdf-5.jpg) - -A (energy units) -\rho (distance units) -C (energy-distance^6 units) -r_m (distance units) -r_{cut} (distance units) :ul - -:line - -For the {lennard/mdf} pair_style, the potential energy, {E(r)}, is the -standard 12-6 Lennard-Jones written in the A/B form: - -:c,image(Eqs/pair_mdf-6.jpg) - -The following coefficients must be defined for each pair of atoms -types via the pair_coeff command as in the examples above, or in the -data file read by the read_data commands, or by mixing as described below. -The two cutoffs default to their global values and must be either both -given or both left out: - -A (energy-distance^12 units) -B (energy-distance^6 units) -r_m (distance units) -r_{cut} (distance units) :ul - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distances for the lj/mdf pair style can be mixed. -The default mix value is {geometric}. See the "pair_modify" command -for details. The other two pair styles buck/mdf and lennard/mdf do not -support mixing, so all I,J pairs of coefficients must be specified -explicitly. - -None of the lj/mdf, buck/mdf, or lennard/mdf pair styles supports -the "pair_modify"_pair_modify.html shift option or long-range -tail corrections to pressure and energy. - -These styles write their information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -These styles can only be used via the {pair} keyword of the "run_style -respa"_run_style.html command. They do not support the {inner}, -{middle}, {outer} keywords. - -:line - -[Restrictions:] - -These pair styles can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Mei) -[(Mei)] Mei, Davenport, Fernando, Phys Rev B, 43 4653 (1991) diff --git a/doc/txt/pair_meam_spline.txt b/doc/txt/pair_meam_spline.txt deleted file mode 100644 index 7a185b4d55..0000000000 --- a/doc/txt/pair_meam_spline.txt +++ /dev/null @@ -1,167 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style meam/spline command :h3 -pair_style meam/spline/omp command :h3 - -[Syntax:] - -pair_style meam/spline :pre - -[Examples:] - -pair_style meam/spline -pair_coeff * * Ti.meam.spline Ti -pair_coeff * * Ti.meam.spline Ti Ti Ti :pre - -[Description:] - -The {meam/spline} style computes pairwise interactions for metals -using a variant of modified embedded-atom method (MEAM) potentials -"(Lenosky)"_#Lenosky1. For a single species ("old-style") MEAM, -the total energy E is given by - -:c,image(Eqs/pair_meam_spline.jpg) - -where rho_i is the density at atom I, theta_jik is the angle between -atoms J, I, and K centered on atom I. The five functions Phi, U, rho, -f, and g are represented by cubic splines. - -The {meam/spline} style also supports a new style multicomponent -modified embedded-atom method (MEAM) potential "(Zhang)"_#Zhang4, where -the total energy E is given by - -:c,image(Eqs/pair_meam_spline_multicomponent.jpg) - -where the five functions Phi, U, rho, f, and g depend on the chemistry -of the atoms in the interaction. In particular, if there are N different -chemistries, there are N different U, rho, and f functions, while there -are N(N+1)/2 different Phi and g functions. The new style multicomponent -MEAM potential files are indicated by the second line in the file starts -with "meam/spline" followed by the number of elements and the name of each -element. - -The cutoffs and the coefficients for these spline functions are listed -in a parameter file which is specified by the -"pair_coeff"_pair_coeff.html command. Parameter files for different -elements are included in the "potentials" directory of the LAMMPS -distribution and have a ".meam.spline" file suffix. All of these -files are parameterized in terms of LAMMPS "metal units"_units.html. - -Note that unlike for other potentials, cutoffs for spline-based MEAM -potentials are not set in the pair_style or pair_coeff command; they -are specified in the potential files themselves. - -Unlike the EAM pair style, which retrieves the atomic mass from the -potential file, the spline-based MEAM potentials do not include mass -information; thus you need to use the "mass"_mass.html command to -specify it. - -Only a single pair_coeff command is used with the {meam/spline} style -which specifies a potential file with parameters for all needed -elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of spline-based MEAM elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -As an example, imagine the Ti.meam.spline file has values for Ti (old style). If -your LAMMPS simulation has 3 atoms types and they are all to be -treated with this potentials, you would use the following pair_coeff -command: - -pair_coeff * * Ti.meam.spline Ti Ti Ti :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element -in the potential file. If a mapping value is specified as NULL, the -mapping is not performed. This can be used when a {meam/spline} -potential is used as part of the {hybrid} pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. The old-style potential maps any non-NULL species named -on the command line to that single type. - -An example with a two component spline (new style) is TiO.meam.spline, where -the command - -pair_coeff * * TiO.meam.spline Ti O :pre - -will map the 1st atom type to Ti and the second atom type to O. Note -in this case that the species names need to match exactly with the -names of the elements in the TiO.meam.spline file; otherwise an -error will be raised. This behavior is different than the old style -MEAM files. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -The {meam/spline} pair style does not write its information to "binary -restart files"_restart.html, since it is stored in an external -potential parameter file. Thus, you need to re-specify the pair_style -and pair_coeff commands in an input script that reads a restart file. - -The {meam/spline} pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. They do not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style requires the "newton"_newton.html setting to be "on" -for pair interactions. - -This pair style is only enabled if LAMMPS was built with the USER-MISC -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html - -[Default:] none - -:line - -:link(Lenosky1) -[(Lenosky)] Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, -Kress, Modelling Simulation Materials Science Engineering, 8, 825 -(2000). - -:link(Zhang4) -[(Zhang)] Zhang and Trinkle, Computational Materials Science, 124, 204-210 (2016). diff --git a/doc/txt/pair_meam_sw_spline.txt b/doc/txt/pair_meam_sw_spline.txt deleted file mode 100644 index a9ad3484d3..0000000000 --- a/doc/txt/pair_meam_sw_spline.txt +++ /dev/null @@ -1,139 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style meam/sw/spline command :h3 - -[Syntax:] - -pair_style meam/sw/spline :pre - -[Examples:] - -pair_style meam/sw/spline -pair_coeff * * Ti.meam.sw.spline Ti -pair_coeff * * Ti.meam.sw.spline Ti Ti Ti :pre - -[Description:] - -The {meam/sw/spline} style computes pairwise interactions for metals -using a variant of modified embedded-atom method (MEAM) potentials -"(Lenosky)"_#Lenosky2 with an additional Stillinger-Weber (SW) term -"(Stillinger)"_#Stillinger1 in the energy. This form of the potential -was first proposed by Nicklas, Fellinger, and Park -"(Nicklas)"_#Nicklas. We refer to it as MEAM+SW. The total energy E -is given by - -:c,image(Eqs/pair_meam_sw_spline.jpg) - -where rho_I is the density at atom I, theta_JIK is the angle between -atoms J, I, and K centered on atom I. The seven functions -Phi, F, G, U, rho, f, and g are represented by cubic splines. - -The cutoffs and the coefficients for these spline functions are listed -in a parameter file which is specified by the -"pair_coeff"_pair_coeff.html command. Parameter files for different -elements are included in the "potentials" directory of the LAMMPS -distribution and have a ".meam.sw.spline" file suffix. All of these -files are parameterized in terms of LAMMPS "metal units"_units.html. - -Note that unlike for other potentials, cutoffs for spline-based -MEAM+SW potentials are not set in the pair_style or pair_coeff -command; they are specified in the potential files themselves. - -Unlike the EAM pair style, which retrieves the atomic mass from the -potential file, the spline-based MEAM+SW potentials do not include -mass information; thus you need to use the "mass"_mass.html command to -specify it. - -Only a single pair_coeff command is used with the meam/sw/spline style -which specifies a potential file with parameters for all needed -elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of spline-based MEAM+SW elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -As an example, imagine the Ti.meam.sw.spline file has values for Ti. -If your LAMMPS simulation has 3 atoms types and they are all to be -treated with this potential, you would use the following pair_coeff -command: - -pair_coeff * * Ti.meam.sw.spline Ti Ti Ti - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element -in the potential file. If a mapping value is specified as NULL, the -mapping is not performed. This can be used when a {meam/sw/spline} -potential is used as part of the hybrid pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. - -NOTE: The {meam/sw/spline} style currently supports only -single-element MEAM+SW potentials. It may be extended for alloy -systems in the future. - -Example input scripts that use this pair style are provided -in the examples/USER/misc/meam_sw_spline directory. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -The pair style does not support multiple element types or mixing. -It has been designed for pure elements only. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -The {meam/sw/spline} pair style does not write its information to -"binary restart files"_restart.html, since it is stored in an external -potential parameter file. Thus, you need to re-specify the pair_style -and pair_coeff commands in an input script that reads a restart file. - -The {meam/sw/spline} pair style can only be used via the {pair} -keyword of the "run_style respa"_run_style.html command. They do not -support the {inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style requires the "newton"_newton.html setting to be "on" -for pair interactions. - -This pair style is only enabled if LAMMPS was built with the USER-MISC -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html, -"pair_style meam/spline"_pair_meam_spline.html - -[Default:] none - -:line - -:link(Lenosky2) -[(Lenosky)] Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, -Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000). - -:link(Stillinger1) -[(Stillinger)] Stillinger, Weber, Phys. Rev. B 31, 5262 (1985). - -:link(Nicklas) -[(Nicklas)] -The spline-based MEAM+SW format was first devised and used to develop -potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger, -and Hyoungki Park at The Ohio State University. - - diff --git a/doc/txt/pair_meso.txt b/doc/txt/pair_meso.txt deleted file mode 100644 index 54186a0e75..0000000000 --- a/doc/txt/pair_meso.txt +++ /dev/null @@ -1,277 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style edpd command :h3 -pair_style mdpd command :h3 -pair_style mdpd/rhosum command :h3 -pair_style tdpd command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {edpd} or {mdpd} or {mdpd/rhosum} or {tdpd} :ulb,l -args = list of arguments for a particular style :l - {edpd} args = cutoff seed - cutoff = global cutoff for eDPD interactions (distance units) - seed = random # seed (integer) (if <= 0, eDPD will use current time as the seed) - {mdpd} args = T cutoff seed - T = temperature (temperature units) - cutoff = global cutoff for mDPD interactions (distance units) - seed = random # seed (integer) (if <= 0, mDPD will use current time as the seed) - {mdpd/rhosum} args = - {tdpd} args = T cutoff seed - T = temperature (temperature units) - cutoff = global cutoff for tDPD interactions (distance units) - seed = random # seed (integer) (if <= 0, tDPD will use current time as the seed) :pre -:ule - -[Examples:] - -pair_style edpd 1.58 9872598 -pair_coeff * * 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 -pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 -pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00 :pre - -pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 65689 -pair_coeff 1 1 mdpd/rhosum 0.75 -pair_coeff 1 1 mdpd -40.0 25.0 18.0 1.0 0.75 :pre - -pair_style tdpd 1.0 1.58 935662 -pair_coeff * * 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 -pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 :pre - -[Description:] - -The {edpd} style computes the pairwise interactions and heat fluxes -for eDPD particles following the formulations in -"(Li2014_JCP)"_#Li2014_JCP and "Li2015_CC"_#Li2015_CC. The time -evolution of an eDPD particle is governed by the conservation of -momentum and energy given by - -:c,image(Eqs/pair_edpd_gov.jpg) - -where the three components of Fi -including the conservative force FijC, dissipative force FijD and random force FijR are expressed as - -:c,image(Eqs/pair_edpd_force.jpg) - -in which the exponent of the weighting function s can be defined as a temperature-dependent -variable. The heat flux between particles accounting for the -collisional heat flux qC, viscous -heat flux qV, and random heat flux -qR are given by - -:c,image(Eqs/pair_edpd_heat.jpg) - -where the mesoscopic heat friction κ is given by - -:c,image(Eqs/pair_edpd_kappa.jpg) - -with υ being the kinematic -viscosity. For more details, see Eq.(15) in "(Li2014_JCP)"_#Li2014_JCP. - -The following coefficients must be defined in eDPD system for each -pair of atom types via the "pair_coeff"_pair_coeff.html command as in -the examples above. - -A (force units) -gamma (force/velocity units) -power_f (positive real) -cutoff (distance units) -kappa (thermal conductivity units) -power_T (positive real) -cutoff_T (distance units) -optional keyword = power or kappa :ul - -The keyword {power} or {kappa} is optional. Both "power" and "kappa" -require 4 parameters c1, c2, -c4, c4 showing the temperature dependence -of the exponent
s(T) = -power_f*(1+c1*(T-1)+c2*(T-1)2 -+c3*(T-1)3+c4*(T-1)4)
-and of the mesoscopic heat friction
-sT(T) = -kappa*(1+c1*(T-1)+c2*(T-1)2 -+c3*(T-1)3+c4*(T-1)4)
-If the keyword {power} or {kappa} is not specified, the eDPD system -will use constant power_f and kappa, which is independent to -temperature changes. - -:line - -The {mdpd/rhosum} style computes the local particle mass density rho -for mDPD particles by kernel function interpolation. - -The following coefficients must be defined for each pair of atom types -via the "pair_coeff"_pair_coeff.html command as in the examples above. - -cutoff (distance units) :ul - -:line - -The {mdpd} style computes the many-body interactions between mDPD -particles following the formulations in -"(Li2013_POF)"_#Li2013_POF. The dissipative and random forces are in -the form same as the classical DPD, but the conservative force is -local density dependent, which are given by - -:c,image(Eqs/pair_mdpd_force.jpg) - -where the first term in FC with a -negative coefficient A < 0 stands for an attractive force within an -interaction range rc, and the second -term with B > 0 is the density-dependent repulsive force within an -interaction range rd. - -The following coefficients must be defined for each pair of atom types via the -"pair_coeff"_pair_coeff.html command as in the examples above. - -A (force units) -B (force units) -gamma (force/velocity units) -cutoff_c (distance units) -cutoff_d (distance units) :ul - -:line - -The {tdpd} style computes the pairwise interactions and chemical -concentration fluxes for tDPD particles following the formulations in -"(Li2015_JCP)"_#Li2015_JCP. The time evolution of a tDPD particle is -governed by the conservation of momentum and concentration given by - -:c,image(Eqs/pair_tdpd_gov.jpg) - -where the three components of Fi -including the conservative force FijC, dissipative force FijD and random force FijR are expressed as - -:c,image(Eqs/pair_tdpd_force.jpg) - -The concentration flux between two tDPD particles includes the Fickian -flux QijD and random flux -QijR, which are given by - -:c,image(Eqs/pair_tdpd_flux.jpg) - -where the parameters kappa and epsilon determine the strength of the -Fickian and random fluxes. ms -is the mass of a single solute molecule. In general, ms is much smaller than the mass of -a tDPD particle m. For more details, see -"(Li2015_JCP)"_#Li2015_JCP. - -The following coefficients must be defined for each pair of atom types via the -"pair_coeff"_pair_coeff.html command as in the examples above. - -A (force units) -gamma (force/velocity units) -power_f (positive real) -cutoff (distance units) -cutoff_CC (distance units) -kappa_i (diffusivity units) -epsilon_i (diffusivity units) -power_cc_i (positive real) :ul - -The last 3 values must be repeated Nspecies times, so that values for -each of the Nspecies chemical species are specified, as indicated by -the "I" suffix. In the first pair_coeff example above for pair_style -tdpd, Nspecies = 1. In the second example, Nspecies = 2, so 3 -additional coeffs are specified (for species 2). - -:line - -[Example scripts] - -There are example scripts for using all these pair styles in -examples/USER/meso. The example for an eDPD simulation models heat -conduction with source terms analog of periodic Poiseuille flow -problem. The setup follows Fig.12 in "(Li2014_JCP)"_#Li2014_JCP. The -output of the short eDPD simulation (about 2 minutes on a single core) -gives a temperature and density profiles as - -:c,image(JPG/examples_edpd.jpg) - -The example for a mDPD simulation models the oscillations of a liquid -droplet started from a liquid film. The mDPD parameters are adopted -from "(Li2013_POF)"_#Li2013_POF. The short mDPD run (about 2 minutes -on a single core) generates a particle trajectory which can -be visualized as follows. - -:c,image(JPG/examples_mdpd_first.jpg,JPG/examples_mdpd.gif) -:c,image(JPG/examples_mdpd_last.jpg) - -The first image is the initial state of the simulation. If you -click it a GIF movie should play in your browser. The second image -is the final state of the simulation. - -The example for a tDPD simulation computes the effective diffusion -coefficient of a tDPD system using a method analogous to the periodic -Poiseuille flow. The tDPD system is specified with two chemical -species, and the setup follows Fig.1 in -"(Li2015_JCP)"_#Li2015_JCP. The output of the short tDPD simulation -(about one and a half minutes on a single core) gives the -concentration profiles of the two chemical species as - -:c,image(JPG/examples_tdpd.jpg) - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -The styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} do not support -mixing. Thus, coefficients for all I,J pairs must be specified explicitly. - -The styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} do not support -the "pair_modify"_pair_modify.html shift, table, and tail options. - -The styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} do not write -information to "binary restart files"_restart.html. Thus, you need -to re-specify the pair_style and pair_coeff commands in an input script -that reads a restart file. - -[Restrictions:] - -The pair styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} are part of -the USER-MESO package. It is only enabled if LAMMPS was built with -that package. See the "Build package"_Build_package.html doc page for -more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "fix mvv/dpd"_fix_mvv_dpd.html, -"fix mvv/edpd"_fix_mvv_dpd.html, "fix mvv/tdpd"_fix_mvv_dpd.html, -"fix edpd/source"_fix_dpd_source.html, "fix tdpd/source"_fix_dpd_source.html, -"compute edpd/temp/atom"_compute_edpd_temp_atom.html, -"compute tdpd/cc/atom"_compute_tdpd_cc_atom.html - -[Default:] none - -:line - -:link(Li2014_JCP) -[(Li2014_JCP)] Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, -265: 113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003. - -:link(Li2015_CC) -[(Li2015_CC)] Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 -(2015). DOI: 10.1039/C5CC01684C. - -:link(Li2013_POF) -[(Li2013_POF)] Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). -DOI: 10.1063/1.4812366. - -:link(Li2015_JCP) -[(Li2015_JCP)] Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, -143: 014101 (2015). DOI: 10.1063/1.4923254. diff --git a/doc/txt/pair_mgpt.txt b/doc/txt/pair_mgpt.txt deleted file mode 100644 index bd55d529b8..0000000000 --- a/doc/txt/pair_mgpt.txt +++ /dev/null @@ -1,219 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style mgpt command :h3 - -[Syntax:] - -pair_style mgpt :pre - -[Examples:] - -pair_style mgpt -pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega -cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin -cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin -pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double -pair_coeff * * parmin potin Omega volpress yes nbody 12 :pre - -[Description:] - -Within DFT quantum mechanics, generalized pseudopotential theory (GPT) -("Moriarty1"_#Moriarty1) provides a first-principles approach to -multi-ion interatomic potentials in d-band transition metals, with a -volume-dependent, real-space total-energy functional for the N-ion -elemental bulk material in the form - -:c,image(Eqs/pair_mgpt.jpg) - -where the prime on each summation sign indicates the exclusion of all -self-interaction terms from the summation. The leading volume term -E_vol as well as the two-ion central-force pair potential v_2 and the -three- and four-ion angular-force potentials, v_3 and v_4, depend -explicitly on the atomic volume Omega, but are structure independent -and transferable to all bulk ion configurations, either ordered or -disordered, and with of without the presence of point and line -defects. The simplified model GPT or MGPT ("Moriarty2"_#Moriarty2, -"Moriarty3"_#Moriarty3), which retains the form of E_tot and permits -more efficient large-scale atomistic simulations, derives from the GPT -through a series of systematic approximations applied to E_vol and the -potentials v_n that are valid for mid-period transition metals with -nearly half-filled d bands. - -Both analytic ("Moriarty2"_#Moriarty2) and matrix -("Moriarty3"_#Moriarty3) representations of MGPT have been developed. -In the more general matrix representation, which can also be applied -to f-band actinide metals and permits both canonical and non-canonical -d/f bands, the multi-ion potentials are evaluated on the fly during a -simulation through d- or f-state matrix multiplication, and the forces -that move the ions are determined analytically. Fast matrix-MGPT -algorithms have been developed independently by Glosli -("Glosli"_#Glosli, "Moriarty3"_#Moriarty3) and by Oppelstrup -("Oppelstrup"_#Oppelstrup) - -The {mgpt} pair style calculates forces, energies, and the total -energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm. -Input potential and control data are entered through the -"pair_coeff"_pair_coeff.html command. Each material treated requires -input parmin and potin potential files, as shown in the above -examples, as well as specification by the user of the initial atomic -volume Omega through pair_coeff. At the beginning of a time step in -any simulation, the total volume of the simulation cell V should -always be equal to Omega*N, where N is the number of metal ions -present, taking into account the presence of any vacancies and/or -interstitials in the case of a solid. In a constant-volume -simulation, which is the normal mode of operation for the {mgpt} pair -style, Omega, V and N all remain constant throughout the simulation -and thus are equal to their initial values. In a constant-stress -simulation, the cell volume V will change (slowly) as the simulation -proceeds. After each time step, the atomic volume should be updated -by the code as Omega = V/N. In addition, the volume term E_vol and -the potentials v_2, v_3 and v_4 have to be removed at the end of the -time step, and then respecified at the new value of Omega. In all -simulations, Omega must remain within the defined volume range for -E_vol and the potentials for the given material. - -The default option volpress yes in the "pair_coeff"_pair_coeff.html -command includes all volume derivatives of E_tot required to calculate -the stress tensor and pressure correctly. The option volpress no -disregards the pressure contribution resulting from the volume term -E_vol, and can be used for testing and analysis purposes. The -additional optional variable nbody controls the specific terms in -E_tot that are calculated. The default option and the normal option -for mid-period transition and actinide metals is nbody 1234 for which -all four terms in E_tot are retained. The option nbody 12, for -example, retains only the volume term and the two-ion pair potential -term and can be used for GPT series-end transition metals that can be -well described without v_3 and v_4. The nbody option can also be used -to test or analyze the contribution of any of the four terms in E_tot -to a given calculated property. - -The {mgpt} pair style makes extensive use of matrix algebra and -includes optimized kernels for the BlueGene/Q architecture and the -Intel/AMD (x86) architectures. When compiled with the appropriate -compiler and compiler switches (-msse3 on x86, and using the IBM XL -compiler on BG/Q), these optimized routines are used automatically. -For BG/Q machines, building with the default Makefile for that -architecture (e.g., "make bgq") should enable the optimized algebra -routines. For x-86 machines, there is a provided Makefile.mgptfast -which enables the fast algebra routines, i.e. build LAMMPS with "make -mgptfast". The user will be informed in the output files of the -matrix kernels in use. To further improve speed, on x86 the option -precision single can be added to the "pair_coeff"_pair_coeff.html -command line, which improves speed (up to a factor of two) at the cost -of doing matrix calculations with 7 digit precision instead of the -default 16. For consistency the default option can be specified -explicitly by the option precision double. - -All remaining potential and control data are contained with the parmin -and potin files, including cutoffs, atomic mass, and other basic MGPT -variables. Specific MGPT potential data for the transition metals -tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials), -and vanadium (V6.1 potentials) are contained in the LAMMPS potentials -directory. The stored files are, respectively, Ta4.mgpt.parmin, -Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin, -Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and -V6.1.mgpt.potin . Useful corresponding informational "README" files -on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the -potentials directory. These latter files indicate the volume mesh and -range for each potential and give appropriate references for the -potentials. It is expected that MGPT potentials for additional -materials will be added over time. - -Useful example MGPT scripts are given in the examples/USER/mgpt -directory. These scripts show the necessary steps to perform -constant-volume calculations and simulations. It is strongly -recommended that the user work through and understand these examples -before proceeding to more complex simulations. - -NOTE: For good performance, LAMMPS should be built with the compiler -flags "-O3 -msse3 -funroll-loops" when including this pair style. The -src/MAKE/OPTIONS/Makefile.mgptfast is an example machine Makefile with -these options included as part of a standard MPI build. Note that it -as provided, it will build with whatever low-level compiler (g++, icc, -etc) is the default for your MPI installation. - -:line - -[Mixing, shift, table tail correction, restart]: - -This pair style does not support the "pair_modify"_pair_modify.html -mix, shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -needs to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the USER-MGPT package and is only enabled -if LAMMPS is built with that package. See the "Build -package"_Build_package.html doc page for more info. - -The MGPT potentials require the "newtion"_newton.html setting to be -"on" for pair style interactions. - -The stored parmin and potin potential files provided with LAMMPS in -the "potentials" directory are written in Rydberg atomic units, with -energies in Rydbergs and distances in Bohr radii. The {mgpt} pair -style converts Rydbergs to Hartrees to make the potential files -compatible with LAMMPS electron "units"_units.html. - -The form of E_tot used in the {mgpt} pair style is only appropriate -for elemental bulk solids and liquids. This includes solids with -point and extended defects such as vacancies, interstitials, grain -boundaries and dislocations. Alloys and free surfaces, however, -require significant modifications, which are not included in the -{mgpt} pair style. Likewise, the {hybrid} pair style is not allowed, -where MGPT would be used for some atoms but not for others. - -Electron-thermal effects are not included in the standard MGPT -potentials provided in the "potentials" directory, where the -potentials have been constructed at zero electron temperature. -Physically, electron-thermal effects may be important in 3d (e.g., V) -and 4d (e.g., Mo) transition metals at high temperatures near melt and -above. It is expected that temperature-dependent MGPT potentials for -such cases will be added over time. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] - -The options defaults for the "pair_coeff"_pair_coeff.html command are -volpress yes, nbody 1234, and precision double. - -:line - -:link(Moriarty1) -[(Moriarty1)] Moriarty, Physical Review B, 38, 3199 (1988). - -:link(Moriarty2) -[(Moriarty2)] Moriarty, Physical Review B, 42, 1609 (1990). -Moriarty, Physical Review B 49, 12431 (1994). - -:link(Moriarty3) -[(Moriarty3)] Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang, -Journal of Materials Research, 21, 563 (2006). - -:link(Glosli) -[(Glosli)] Glosli, unpublished, 2005. -Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference -Series, 46, 254 (2006). - -:link(Oppelstrup) -[(Oppelstrup)] Oppelstrup, unpublished, 2015. -Oppelstrup and Moriarty, to be published. diff --git a/doc/txt/pair_mie.txt b/doc/txt/pair_mie.txt deleted file mode 100644 index 818e37272b..0000000000 --- a/doc/txt/pair_mie.txt +++ /dev/null @@ -1,101 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style mie/cut command :h3 -pair_style mie/cut/gpu command :h3 - -[Syntax:] - -pair_style mie/cut cutoff :pre - -cutoff = global cutoff for mie/cut interactions (distance units) :ul - -[Examples:] - -pair_style mie/cut 10.0 -pair_coeff 1 1 0.72 3.40 23.00 6.66 -pair_coeff 2 2 0.30 3.55 12.65 6.00 -pair_coeff 1 2 0.46 3.32 16.90 6.31 :pre - -[Description:] - -The {mie/cut} style computes the Mie potential, given by - -:c,image(Eqs/pair_mie.jpg) - -Rc is the cutoff and C is a function that depends on the repulsive and -attractive exponents, given by: - -:c,image(Eqs/pair_mie2.jpg) - -Note that for 12/6 exponents, C is equal to 4 and the formula is the -same as the standard Lennard-Jones potential. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) -gammaR -gammaA -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global -cutoff specified in the pair_style command is used. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the mie/cut pair styles can be mixed. -If not explicitly defined, both the repulsive and attractive gamma -exponents for different atoms will be calculated following the same -mixing rule defined for distances. The default mix value is -{geometric}. See the "pair_modify" command for details. - -This pair style supports the "pair_modify"_pair_modify.html shift -option for the energy of the pair interaction. - -This pair style supports the "pair_modify"_pair_modify.html tail -option for adding a long-range tail correction to the energy and -pressure of the pair interaction. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style supports the use of the {inner}, {middle}, and {outer} -keywords of the "run_style respa"_run_style.html command, meaning the -pairwise forces can be partitioned by distance at different levels of -the rRESPA hierarchy. See the "run_style"_run_style.html command for -details. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Mie) -[(Mie)] G. Mie, Ann Phys, 316, 657 (1903). - -:link(Avendano) -[(Avendano)] C. Avendano, T. Lafitte, A. Galindo, C. S. Adjiman, -G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011). - - diff --git a/doc/txt/pair_momb.txt b/doc/txt/pair_momb.txt deleted file mode 100644 index f1989f56f4..0000000000 --- a/doc/txt/pair_momb.txt +++ /dev/null @@ -1,71 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style momb command :h3 - -[Syntax:] - -pair_style momb cutoff s6 d :pre - -cutoff = global cutoff (distance units) -s6 = global scaling factor of the exchange-correlation functional used (unitless) -d = damping scaling factor of Grimme's method (unitless) :ul - -[Examples:] - -pair_style momb 12.0 0.75 20.0 -pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5 :pre - -pair_coeff 1 2 momb 0.0 1.0 1.0 10.2847 2.361 :pre - -[Description:] - -Style {momb} computes pairwise van der Waals (vdW) and short-range -interactions using the Morse potential and "(Grimme)"_#Grimme method -implemented in the Many-Body Metal-Organic (MOMB) force field -described comprehensively in "(Fichthorn)"_#Fichthorn and -"(Zhou)"_#Zhou4. Grimme's method is widely used to correct for -dispersion in density functional theory calculations. - -:c,image(Eqs/pair_momb.jpg) - -For the {momb} pair style, the following coefficients must be defined -for each pair of atoms types via the "pair_coeff"_pair_coeff.html -command as in the examples above, or in the data file or restart files -read by the "read_data"_read_data.html as described below: - -D0 (energy units) -alpha (1/distance units) -r0 (distance units) -C6 (energy*distance^6 units) -Rr (distance units, typically sum of atomic vdW radii) :ul - -:line - -[Restrictions:] - -This style is part of the USER-MISC package. It is only enabled if -LAMMPS is built with that package. See the "Build -package"_Build_package.html doc page on for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style morse"_pair_morse.html - -[Default:] none - -:line - -:link(Grimme) -[(Grimme)] Grimme, J Comput Chem, 27(15), 1787-1799 (2006). - -:link(Fichthorn) -[(Fichthorn)] Fichthorn, Balankura, Qi, CrystEngComm, 18(29), 5410-5417 (2016). - -:link(Zhou4) -[(Zhou)] Zhou, Saidi, Fichthorn, J Phys Chem C, 118(6), 3366-3374 (2014). diff --git a/doc/txt/pair_morse.txt b/doc/txt/pair_morse.txt deleted file mode 100644 index 7faa6ab785..0000000000 --- a/doc/txt/pair_morse.txt +++ /dev/null @@ -1,136 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style morse command :h3 -pair_style morse/gpu command :h3 -pair_style morse/omp command :h3 -pair_style morse/opt command :h3 -pair_style morse/smooth/linear command :h3 -pair_style morse/smooth/linear/omp command :h3 -pair_style morse/kk command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {morse} or {morse/smooth/linear} or {morse/soft} -args = list of arguments for a particular style :ul - {morse} args = cutoff - cutoff = global cutoff for Morse interactions (distance units) - {morse/smooth/linear} args = cutoff - cutoff = global cutoff for Morse interactions (distance units) -:pre - -[Examples:] - -pair_style morse 2.5 -pair_style morse/smooth/linear 2.5 -pair_coeff * * 100.0 2.0 1.5 -pair_coeff 1 1 100.0 2.0 1.5 3.0 :pre - -[Description:] - -Style {morse} computes pairwise interactions with the formula - -:c,image(Eqs/pair_morse.jpg) - -Rc is the cutoff. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -D0 (energy units) -alpha (1/distance units) -r0 (distance units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global morse -cutoff is used. - -:line - -The {morse/smooth/linear} variant is similar to the lj/smooth/linear -variant in that it adds to the potential a shift and a linear term -so that both, potential energy and force, go to zero at the cut-off: - -:c,image(Eqs/pair_morse_smooth_linear.jpg) - -The syntax of the pair_style and pair_coeff commands are the same for -the {morse} and {morse/smooth/linear} styles. - -:line - -A version of the {morse} style with a soft core, {morse/soft}, suitable for use in -free energy calculations, is part of the USER-FEP package and is documented with -the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is only -available if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -None of these pair styles support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -All of these pair styles support the "pair_modify"_pair_modify.html -shift option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table options is not relevant for -the Morse pair styles. - -None of these pair styles support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -All of these pair styles write their information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -These pair styles can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. They do not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -The {morse/smooth/linear} pair style is only enabled if LAMMPS was -built with the USER-MISC package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_fep_soft"_pair_fep_soft.html - -[Default:] none diff --git a/doc/txt/pair_multi_lucy.txt b/doc/txt/pair_multi_lucy.txt deleted file mode 100644 index 0b3a430417..0000000000 --- a/doc/txt/pair_multi_lucy.txt +++ /dev/null @@ -1,199 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style multi/lucy command :h3 - -[Syntax:] - -pair_style multi/lucy style N keyword ... :pre - -style = {lookup} or {linear} = method of interpolation -N = use N values in {lookup}, {linear} tables :ul - -[Examples:] - -pair_style multi/lucy linear 1000 -pair_coeff * * multibody.table ENTRY1 7.0 :pre - -[Description:] - -Style {multi/lucy} computes a density-dependent force following from -the many-body form described in "(Moore)"_#Moore1 and -"(Warren)"_#Warren1 as - -:c,image(Eqs/pair_multi_lucy.jpg) - -which consists of a density-dependent function, A(rho), and a -radial-dependent weight function, omegaDD(rij). The radial-dependent -weight function, omegaDD(rij), is taken as the Lucy function: - -:c,image(Eqs/pair_multi_lucy2.jpg) - -The density-dependent energy for a given particle is given by: - -:c,image(Eqs/pair_multi_lucy_energy.jpg) - -See the supporting information of "(Brennan)"_#Brennan1 or the -publication by "(Moore)"_#Moore1 for more details on the functional -form. - -An interpolation table is used to evaluate the density-dependent -energy (Integral(A(rho)drho) and force (A(rho)). Note that the -pre-factor to the energy is computed after the interpolation, thus the -Integral(A(rho)drho will have units of energy / length^4. - -The interpolation table is created as a pre-computation by fitting -cubic splines to the file values and interpolating the -density-dependent energy and force at each of {N} densities. During a -simulation, the tables are used to interpolate the density-dependent -energy and force as needed for each pair of particles separated by a -distance {R}. The interpolation is done in one of 2 styles: {lookup} -and {linear}. - -For the {lookup} style, the density is used to find the nearest table -entry, which is the density-dependent energy and force. - -For the {linear} style, the density is used to find the 2 surrounding -table values from which the density-dependent energy and force are -computed by linear interpolation. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above. - -filename -keyword -cutoff (distance units) :ul - -The filename specifies a file containing the tabulated -density-dependent energy and force. The keyword specifies a section -of the file. The cutoff is an optional coefficient. If not -specified, the outer cutoff in the table itself (see below) will be -used to build an interpolation table that extend to the largest -tabulated distance. If specified, only file values up to the cutoff -are used to create the interpolation table. The format of this file -is described below. - -:line - -The format of a tabulated file is a series of one or more sections, -defined as follows (without the parenthesized comments): - -# Density-dependent function (one or more comment or blank lines) :pre - -DD-FUNCTION (keyword is first text on line) -N 500 R 1.0 10.0 (N, R, RSQ parameters) - (blank) -1 1.0 25.5 102.34 (index, density, energy/r^4, force) -2 1.02 23.4 98.5 -... -500 10.0 0.001 0.003 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the pair_coeff -command. The next line lists (in any order) one or more parameters -for the table. Each parameter is a keyword followed by one or more -numeric values. - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the {N} -specified in the "pair_style multi/lucy"_pair_multi_lucy.html command. -Let Ntable = {N} in the pair_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate the density-dependent energy and force at -Ntable different points. The resulting tables of length Ntable are -then used as described above, when computing the density-dependent -energy and force. This means that if you want the interpolation -tables of length Ntable to match exactly what is in the tabulated file -(with effectively no preliminary interpolation), you should set Ntable -= Nfile, and use the "RSQ" parameter. This is because the internal -table abscissa is always RSQ (separation distance squared), for -efficient lookup. - -All other parameters are optional. If "R" or "RSQ" does -not appear, then the distances in each line of the table are used -as-is to perform spline interpolation. In this case, the table values -can be spaced in {density} uniformly or however you wish to position table -values in regions of large gradients. - -If used, the parameters "R" or "RSQ" are followed by 2 values {rlo} -and {rhi}. If specified, the density associated with each density-dependent -energy and force value is computed from these 2 values (at high accuracy), rather -than using the (low-accuracy) value listed in each line of the table. -The density values in the table file are ignored in this case. -For "R", distances uniformly spaced between {rlo} and {rhi} are -computed; for "RSQ", squared distances uniformly spaced between -{rlo*rlo} and {rhi*rhi} are computed. - -NOTE: If you use "R" or "RSQ", the tabulated distance values in the -file are effectively ignored, and replaced by new values as described -in the previous paragraph. If the density value in the table is not -very close to the new value (i.e. round-off difference), then you will -be assigning density-dependent energy and force values to a different density, -which is probably not what you want. LAMMPS will warn if this is occurring. - -Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -r (in density units), the 3rd value is the density-dependent function value -(in energy units / length^4), and the 4th is the force (in force units). The -density values must increase from one line to the next. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -The "pair_modify"_pair_modify.html shift, table, and tail options are -not relevant for this pair style. - -This pair style writes the settings for the "pair_style multi/lucy" command -to "binary restart files"_restart.html, so a pair_style command does -not need to specified in an input script that reads a restart file. -However, the coefficient information is not stored in the restart -file, since it is tabulated in the potential files. Thus, pair_coeff -commands do need to be specified in the restart input script. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Warren1) -[(Warren)] Warren, Phys Rev E, 68, 066702 (2003). - -:link(Brennan1) -[(Brennan)] Brennan, J Chem Phys Lett, 5, 2144-2149 (2014). - -:link(Moore1) -[(Moore)] Moore, J Chem Phys, 144, 104501 (2016). - diff --git a/doc/txt/pair_multi_lucy_rx.txt b/doc/txt/pair_multi_lucy_rx.txt deleted file mode 100644 index 819a15b624..0000000000 --- a/doc/txt/pair_multi_lucy_rx.txt +++ /dev/null @@ -1,248 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style multi/lucy/rx command :h3 -pair_style multi/lucy/rx/kk command :h3 - -[Syntax:] - -pair_style multi/lucy/rx style N keyword ... :pre - -style = {lookup} or {linear} = method of interpolation -N = use N values in {lookup}, {linear} tables -weighting = fractional or molecular (optional) :ul - -[Examples:] - -pair_style multi/lucy/rx linear 1000 -pair_style multi/lucy/rx linear 1000 fractional -pair_style multi/lucy/rx linear 1000 molecular -pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0 -pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 :pre - -[Description:] - -Style {multi/lucy/rx} is used in reaction DPD simulations, where the -coarse-grained (CG) particles are composed of {m} species whose -reaction rate kinetics are determined from a set of {n} reaction rate -equations through the "fix rx"_fix_rx.html command. The species of -one CG particle can interact with a species in a neighboring CG -particle through a site-site interaction potential model. Style -{multi/lucy/rx} computes the site-site density-dependent force -following from the many-body form described in "(Moore)"_#Moore2 and -"(Warren)"_#Warren2 as - -:c,image(Eqs/pair_multi_lucy.jpg) - -which consists of a density-dependent function, A(rho), and a -radial-dependent weight function, omegaDD(rij). The radial-dependent -weight function, omegaDD(rij), is taken as the Lucy function: - -:c,image(Eqs/pair_multi_lucy2.jpg) - -The density-dependent energy for a given particle is given by: - -:c,image(Eqs/pair_multi_lucy_energy.jpg) - -See the supporting information of "(Brennan)"_#Brennan2 or the -publication by "(Moore)"_#Moore2 for more details on the functional -form. - -An interpolation table is used to evaluate the density-dependent -energy (Integral(A(rho)drho) and force (A(rho)). Note that the -pre-factor to the energy is computed after the interpolation, thus the -Integral(A(rho)drho will have units of energy / length^4. - -The interpolation table is created as a pre-computation by fitting -cubic splines to the file values and interpolating the -density-dependent energy and force at each of {N} densities. During a -simulation, the tables are used to interpolate the density-dependent -energy and force as needed for each pair of particles separated by a -distance {R}. The interpolation is done in one of 2 styles: {lookup} -and {linear}. - -For the {lookup} style, the density is used to find the nearest table -entry, which is the density-dependent energy and force. - -For the {linear} style, the density is used to find the 2 surrounding -table values from which the density-dependent energy and force are -computed by linear interpolation. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above. - -filename -keyword -species1 -species2 -cutoff (distance units) :ul - -The filename specifies a file containing the tabulated -density-dependent energy and force. The keyword specifies a section -of the file. The cutoff is an optional coefficient. If not -specified, the outer cutoff in the table itself (see below) will be -used to build an interpolation table that extend to the largest -tabulated distance. If specified, only file values up to the cutoff -are used to create the interpolation table. The format of this file -is described below. - -The species tags define the site-site interaction potential between -two species contained within two different particles. The species -tags must either correspond to the species defined in the reaction -kinetics files specified with the "fix rx"_fix_rx.html command or they -must correspond to the tag "1fluid", signifying interaction with a -product species mixture determined through a one-fluid approximation. -The interaction potential is weighted by the geometric average of -either the mole fraction concentrations or the number of molecules -associated with the interacting coarse-grained particles (see the -{fractional} or {molecular} weighting pair style options). The coarse-grained potential is -stored before and after the reaction kinetics solver is applied, where -the difference is defined to be the internal chemical energy (uChem). - -:line - -The format of a tabulated file is a series of one or more sections, -defined as follows (without the parenthesized comments): - -# Density-dependent function (one or more comment or blank lines) :pre - -DD-FUNCTION (keyword is first text on line) -N 500 R 1.0 10.0 (N, R, RSQ parameters) - (blank) -1 1.0 25.5 102.34 (index, density, energy/r^4, force) -2 1.02 23.4 98.5 -... -500 10.0 0.001 0.003 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the pair_coeff -command. The next line lists (in any order) one or more parameters -for the table. Each parameter is a keyword followed by one or more -numeric values. - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the {N} -specified in the "pair_style multi/lucy/rx"_pair_multi_lucy_rx.html -command. Let Ntable = {N} in the pair_style command, and Nfile = "N" -in the tabulated file. What LAMMPS does is a preliminary -interpolation by creating splines using the Nfile tabulated values as -nodal points. It uses these to interpolate the density-dependent -energy and force at Ntable different points. The resulting tables of -length Ntable are then used as described above, when computing the -density-dependent energy and force. This means that if you want the -interpolation tables of length Ntable to match exactly what is in the -tabulated file (with effectively no preliminary interpolation), you -should set Ntable = Nfile, and use the "RSQ" parameter. This is -because the internal table abscissa is always RSQ (separation distance -squared), for efficient lookup. - -All other parameters are optional. If "R" or "RSQ" does not appear, -then the distances in each line of the table are used as-is to perform -spline interpolation. In this case, the table values can be spaced in -{density} uniformly or however you wish to position table values in -regions of large gradients. - -If used, the parameters "R" or "RSQ" are followed by 2 values {rlo} -and {rhi}. If specified, the density associated with each -density-dependent energy and force value is computed from these 2 -values (at high accuracy), rather than using the (low-accuracy) value -listed in each line of the table. The density values in the table -file are ignored in this case. For "R", distances uniformly spaced -between {rlo} and {rhi} are computed; for "RSQ", squared distances -uniformly spaced between {rlo*rlo} and {rhi*rhi} are computed. - -NOTE: If you use "R" or "RSQ", the tabulated distance values in the -file are effectively ignored, and replaced by new values as described -in the previous paragraph. If the density value in the table is not -very close to the new value (i.e. round-off difference), then you will -be assigning density-dependent energy and force values to a different -density, which is probably not what you want. LAMMPS will warn if -this is occurring. - -Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -r (in density units), the 3rd value is the density-dependent function -value (in energy units / length^4), and the 4th is the force (in force -units). The density values must increase from one line to the next. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -The "pair_modify"_pair_modify.html shift, table, and tail options are -not relevant for this pair style. - -This pair style writes the settings for the "pair_style multi/lucy/rx" command -to "binary restart files"_restart.html, so a pair_style command does -not need to specified in an input script that reads a restart file. -However, the coefficient information is not stored in the restart -file, since it is tabulated in the potential files. Thus, pair_coeff -commands do need to be specified in the restart input script. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] fractional weighting - -:line - -:link(Warren2) -[(Warren)] Warren, Phys Rev E, 68, 066702 (2003). - -:link(Brennan2) -[(Brennan)] Brennan, J Chem Phys Lett, 5, 2144-2149 (2014). - -:link(Moore2) -[(Moore)] Moore, J Chem Phys, 144, 104501 (2016). - diff --git a/doc/txt/pair_nb3b_harmonic.txt b/doc/txt/pair_nb3b_harmonic.txt deleted file mode 100644 index 3a6d1026ed..0000000000 --- a/doc/txt/pair_nb3b_harmonic.txt +++ /dev/null @@ -1,101 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style nb3b/harmonic command :h3 - -[Syntax:] - -pair_style nb3b/harmonic :pre - -[Examples:] - -pair_style nb3b/harmonic -pair_coeff * * MgOH.nb3bharmonic Mg O H :pre - -[Description:] - -This pair style computes a non-bonded 3-body harmonic potential for the -energy E of a system of atoms as - -:c,image(Eqs/pair_nb3b_harmonic.jpg) - -where {theta_0} is the equilibrium value of the angle and {K} is a -prefactor. Note that the usual 1/2 factor is included in {K}. The form -of the potential is identical to that used in angle_style {harmonic}, -but in this case, the atoms do not need to be explicitly bonded. - -Only a single pair_coeff command is used with this style which -specifies a potential file with parameters for specified elements. -These are mapped to LAMMPS atom types by specifying N additional -arguments after the filename in the pair_coeff command, where N is the -number of LAMMPS atom types: - -filename -N element names = mapping of elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -As an example, imagine a file SiC.nb3b.harmonic has potential values -for Si and C. If your LAMMPS simulation has 4 atoms types and you -want the 1st 3 to be Si, and the 4th to be C, you would use the -following pair_coeff command: - -pair_coeff * * SiC.nb3b.harmonic Si Si Si C :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to the Si -element in the potential file. The final C argument maps LAMMPS atom -type 4 to the C element in the potential file. If a mapping value is -specified as NULL, the mapping is not performed. This can be used -when the potential is used as part of the {hybrid} pair style. The -NULL values are placeholders for atom types that will be used with -other potentials. An example of a pair_coeff command for use with the -{hybrid} pair style is: - -pair_coeff * * nb3b/harmonic MgOH.nb3b.harmonic Mg O H - -Three-body non-bonded harmonic files in the {potentials} directory of -the LAMMPS distribution have a ".nb3b.harmonic" suffix. Lines that -are not blank or comments (starting with #) define parameters for a -triplet of elements. - -Each entry has six arguments. The first three are atom types as -referenced in the LAMMPS input file. The first argument specifies the -central atom. The fourth argument indicates the {K} parameter. The -fifth argument indicates {theta_0}. The sixth argument indicates a -separation cutoff in Angstroms. - -For a given entry, if the second and third arguments are identical, -then the entry is for a cutoff for the distance between types 1 and 2 -(values for {K} and {theta_0} are irrelevant in this case). - -For a given entry, if the first three arguments are all different, -then the entry is for the {K} and {theta_0} parameters (the cutoff in -this case is irrelevant). - -It is required that the potential file contains entries for {all} -permutations of the elements listed in the pair_coeff command. -If certain combinations are not parameterized the corresponding -parameters should be set to zero. The potential file can also -contain entries for additional elements which are not used in -a particular simulation; LAMMPS ignores those entries. - -:line - -[Restrictions:] - -This pair style can only be used if LAMMPS was built with the MANYBODY -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none diff --git a/doc/txt/pair_nm.txt b/doc/txt/pair_nm.txt deleted file mode 100644 index a42dfa3c98..0000000000 --- a/doc/txt/pair_nm.txt +++ /dev/null @@ -1,168 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style nm/cut command :h3 -pair_style nm/cut/coul/cut command :h3 -pair_style nm/cut/coul/long command :h3 -pair_style nm/cut/omp command :h3 -pair_style nm/cut/coul/cut/omp command :h3 -pair_style nm/cut/coul/long/omp command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {nm/cut} or {nm/cut/coul/cut} or {nm/cut/coul/long} :ulb,l -args = list of arguments for a particular style :l - {nm/cut} args = cutoff - cutoff = global cutoff for Pair interactions (distance units) - {nm/cut/coul/cut} args = cutoff (cutoff2) - cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {nm/cut/coul/long} args = cutoff (cutoff2) - cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre -:ule - -[Examples:] - -pair_style nm/cut 12.0 -pair_coeff * * 0.01 5.4 8.0 7.0 -pair_coeff 1 1 0.01 4.4 7.0 6.0 :pre - -pair_style nm/cut/coul/cut 12.0 15.0 -pair_coeff * * 0.01 5.4 8.0 7.0 -pair_coeff 1 1 0.01 4.4 7.0 6.0 :pre - -pair_style nm/cut/coul/long 12.0 15.0 -pair_coeff * * 0.01 5.4 8.0 7.0 -pair_coeff 1 1 0.01 4.4 7.0 6.0 :pre - -[Description:] - -Style {nm} computes site-site interactions based on the N-M potential -by "Clarke"_#Clarke, mainly used for ionic liquids. A site can -represent a single atom or a united-atom site. The energy of an -interaction has the following form: - -:c,image(Eqs/pair_nm.jpg) - -Rc is the cutoff. - -Style {nm/cut/coul/cut} adds a Coulombic pairwise interaction given by - -:c,image(Eqs/pair_coulomb.jpg) - -where C is an energy-conversion constant, Qi and Qj are the charges on -the 2 atoms, and epsilon is the dielectric constant which can be set -by the "dielectric"_dielectric.html command. If one cutoff is -specified in the pair_style command, it is used for both the NM and -Coulombic terms. If two cutoffs are specified, they are used as -cutoffs for the NM and Coulombic terms respectively. - -Styles {nm/cut/coul/long} compute the same -Coulombic interactions as style {nm/cut/coul/cut} except that an -additional damping factor is applied to the Coulombic term so it can -be used in conjunction with the "kspace_style"_kspace_style.html -command and its {ewald} or {pppm} option. The Coulombic cutoff -specified for this style means that pairwise interactions within this -distance are computed directly; interactions outside that distance are -computed in reciprocal space. - -For all of the {nm} pair styles, the following coefficients must -be defined for each pair of atoms types -via the "pair_coeff"_pair_coeff.html command as in the -examples above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands. - -E0 (energy units) -r0 (distance units) -n (unitless) -m (unitless) -cutoff1 (distance units) -cutoff2 (distance units) :ul - -The latter 2 coefficients are optional. If not specified, the global -NM and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both NM -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the NM and Coulombic cutoffs for this -type pair. You cannot specify 2 cutoffs for style {nm}, since it -has no Coulombic terms. - -For {nm/cut/coul/long} only the NM cutoff can be specified since a -Coulombic cutoff cannot be specified for an individual I,J type pair. -All type pairs use the same global Coulombic cutoff specified in the -pair_style command. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -These pair styles do not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -All of the {nm} pair styles supports the -"pair_modify"_pair_modify.html shift option for the energy of the pair -interaction. - -The {nm/cut/coul/long} pair styles support the -"pair_modify"_pair_modify.html table option since they can tabulate -the short-range portion of the long-range Coulombic interaction. - -All of the {nm} pair styles support the "pair_modify"_pair_modify.html -tail option for adding a long-range tail correction to the energy and -pressure for the NM portion of the pair interaction. - -All of the {nm} pair styles write their information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -All of the {nm} pair styles can only be used via the {pair} keyword of -the "run_style respa"_run_style.html command. They do not support the -{inner}, {middle}, {outer} keywords. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restrictions:] - -These pair styles are part of the MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Clarke) -[(Clarke)] Clarke and Smith, J Chem Phys, 84, 2290 (1986). diff --git a/doc/txt/pair_none.txt b/doc/txt/pair_none.txt deleted file mode 100644 index 960dc05d97..0000000000 --- a/doc/txt/pair_none.txt +++ /dev/null @@ -1,46 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style none command :h3 - -[Syntax:] - -pair_style none :pre - -[Examples:] - -pair_style none :pre - -[Description:] - -Using a pair style of none means pair forces and energies are not -computed. - -With this choice, the force cutoff is 0.0, which means that only atoms -within the neighbor skin distance (see the "neighbor"_neighbor.html -command) are communicated between processors. You must insure the -skin distance is large enough to acquire atoms needed for computing -bonds, angles, etc. - -A pair style of {none} will also prevent pairwise neighbor lists from -being built. However if the "neighbor"_neighbor.html style is {bin}, -data structures for binning are still allocated. If the neighbor skin -distance is small, then these data structures can consume a large -amount of memory. So you should either set the neighbor style to -{nsq} or set the skin distance to a larger value. - -See the "pair_style zero"_pair_zero.html for a way to trigger the -building of a neighbor lists, but compute no pairwise interactions. - -[Restrictions:] none - -[Related commands:] - -"pair_style zero"_pair_zero.html - -[Default:] none diff --git a/doc/txt/pair_peri.txt b/doc/txt/pair_peri.txt deleted file mode 100644 index 5c5a41ca6c..0000000000 --- a/doc/txt/pair_peri.txt +++ /dev/null @@ -1,215 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style peri/pmb command :h3 -pair_style peri/pmb/omp command :h3 -pair_style peri/lps command :h3 -pair_style peri/lps/omp command :h3 -pair_style peri/ves command :h3 -pair_style peri/eps command :h3 - -[Syntax:] - -pair_style style :pre - -style = {peri/pmb} or {peri/lps} or {peri/ves} or {peri/eps} :ul - -[Examples:] - -pair_style peri/pmb -pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 :pre - -pair_style peri/lps -pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 :pre - -pair_style peri/ves -pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001 :pre - -pair_style peri/eps -pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43 :pre - -[Description:] - -The peridynamic pair styles implement material models that can be used -at the mesoscopic and macroscopic scales. See "this -document"_PDF/PDLammps_overview.pdf for an overview of LAMMPS commands -for Peridynamics modeling. - -Style {peri/pmb} implements the Peridynamic bond-based prototype -microelastic brittle (PMB) model. - -Style {peri/lps} implements the Peridynamic state-based linear -peridynamic solid (LPS) model. - -Style {peri/ves} implements the Peridynamic state-based linear -peridynamic viscoelastic solid (VES) model. - -Style {peri/eps} implements the Peridynamic state-based elastic-plastic -solid (EPS) model. - -The canonical papers on Peridynamics are "(Silling 2000)"_#Silling2000 -and "(Silling 2007)"_#Silling2007. The implementation of Peridynamics -in LAMMPS is described in "(Parks)"_#Parks. Also see the "PDLAMMPS -user guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for -more details about its implementation. - -The peridynamic VES and EPS models in PDLAMMPS were implemented by -R. Rahman and J. T. Foster at University of Texas at San Antonio. The -original VES formulation is described in "(Mitchell2011)" and the -original EPS formulation is in "(Mitchell2011a)". Additional PDF docs -that describe the VES and EPS implementations are include in the -LAMMPS distribution in "doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf and -"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf. For questions -regarding the VES and EPS models in LAMMPS you can contact R. Rahman -(rezwanur.rahman at utsa.edu). - -The following coefficients must be defined for each pair of atom types -via the "pair_coeff"_pair_coeff.html command as in the examples above, -or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below. - -For the {peri/pmb} style: - -c (energy/distance/volume^2 units) -horizon (distance units) -s00 (unitless) -alpha (unitless) :ul - -C is the effectively a spring constant for Peridynamic bonds, the -horizon is a cutoff distance for truncating interactions, and s00 and -alpha are used as a bond breaking criteria. The units of c are such -that c/distance = stiffness/volume^2, where stiffness is -energy/distance^2 and volume is distance^3. See the users guide for -more details. - -For the {peri/lps} style: - -K (force/area units) -G (force/area units) -horizon (distance units) -s00 (unitless) -alpha (unitless) :ul - -K is the bulk modulus and G is the shear modulus. The horizon is a -cutoff distance for truncating interactions, and s00 and alpha are -used as a bond breaking criteria. See the users guide for more -details. - -For the {peri/ves} style: - -K (force/area units) -G (force/area units) -horizon (distance units) -s00 (unitless) -alpha (unitless) -m_lambdai (unitless) -m_taubi (unitless) :ul - -K is the bulk modulus and G is the shear modulus. The horizon is a -cutoff distance for truncating interactions, and s00 and alpha are -used as a bond breaking criteria. m_lambdai and m_taubi are the -viscoelastic relaxation parameter and time constant, -respectively. m_lambdai varies within zero to one. For very small -values of m_lambdai the viscoelastic model responds very similar to a -linear elastic model. For details please see the description in -"(Mtchell2011)". - -For the {peri/eps} style: - -K (force/area units) -G (force/area units) -horizon (distance units) -s00 (unitless) -alpha (unitless) -m_yield_stress (force/area units) :ul - -K is the bulk modulus and G is the shear modulus. The horizon is a -cutoff distance and s00 and alpha are used as a bond breaking -criteria. m_yield_stress is the yield stress of the material. For -details please see the description in "(Mtchell2011a)". - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -These pair styles do not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -These pair styles do not support the "pair_modify"_pair_modify.html -shift option. - -The "pair_modify"_pair_modify.html table and tail options are not -relevant for these pair styles. - -These pair styles write their information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -These pair styles can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. They do not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -All of these styles are part of the PERI package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Parks) -[(Parks)] Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), -777-783 (2008). - -:link(Silling2000) -[(Silling 2000)] Silling, J Mech Phys Solids, 48, 175-209 (2000). - -:link(Silling2007) -[(Silling 2007)] Silling, Epton, Weckner, Xu, Askari, J Elasticity, -88, 151-184 (2007). - -:link(Mitchell2011) -[(Mitchell2011)] Mitchell. A non-local, ordinary-state-based -viscoelasticity model for peridynamics. Sandia National Lab Report, -8064:1-28 (2011). - -:link(Mitchell2011a) -[(Mitchell2011a)] Mitchell. A Nonlocal, Ordinary, State-Based -Plasticity Model for Peridynamics. Sandia National Lab Report, -3166:1-34 (2011). diff --git a/doc/txt/pair_polymorphic.txt b/doc/txt/pair_polymorphic.txt deleted file mode 100644 index d9e73d8492..0000000000 --- a/doc/txt/pair_polymorphic.txt +++ /dev/null @@ -1,229 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style polymorphic command :h3 - -[Syntax:] - -pair_style polymorphic :pre - -style = {polymorphic} - -[Examples:] - -pair_style polymorphic -pair_coeff * * TlBr_msw.polymorphic Tl Br -pair_coeff * * AlCu_eam.polymorphic Al Cu -pair_coeff * * GaN_tersoff.polymorphic Ga N -pair_coeff * * GaN_sw.polymorphic GaN :pre - -[Description:] - -The {polymorphic} pair style computes a 3-body free-form potential -("Zhou"_#Zhou3) for the energy E of a system of atoms as - -:c,image(Eqs/polymorphic1.jpg) -:c,image(Eqs/polymorphic2.jpg) -:c,image(Eqs/polymorphic3.jpg) - -where I, J, K represent species of atoms i, j, and k, i_1, ..., i_N -represents a list of i's neighbors, delta_ij is a Direc constant -(i.e., delta_ij = 1 when i = j, and delta_ij = 0 otherwise), eta_ij is -similar constant that can be set either to eta_ij = delta_ij or eta_ij -= 1 - delta_ij depending on the potential type, U_IJ(r_ij), -V_IJ(r_ij), W_IK(r_ik) are pair functions, G_JIK(cos(theta)) is an -angular function, P_IK(delta r_jik) is a function of atomic spacing -differential delta r_jik = r_ij - xi_IJ*r_ik with xi_IJ being a -pair-dependent parameter, and F_IJ(X_ij) is a function of the local -environment variable X_ij. This generic potential is fully defined -once the constants eta_ij and xi_IJ, and the six functions U_IJ(r_ij), -V_IJ(r_ij), W_IK(r_ik), G_JIK(cos(theta)), P_IK(delta r_jik), and -F_IJ(X_ij) are given. Note that these six functions are all one -dimensional, and hence can be provided in an analytic or tabular -form. This allows users to design different potentials solely based on -a manipulation of these functions. For instance, the potential reduces -to Stillinger-Weber potential ("SW"_#SW) if we set - -:c,image(Eqs/polymorphic4.jpg) - -The potential reduces to Tersoff types of potential -("Tersoff"_#Tersoff or "Albe"_#poly-Albe) if we set - -:c,image(Eqs/polymorphic5.jpg) -:c,image(Eqs/polymorphic6.jpg) - -The potential reduces to Rockett-Tersoff ("Wang"_#Wang3) type if we set - -:c,image(Eqs/polymorphic7.jpg) -:c,image(Eqs/polymorphic6.jpg) -:c,image(Eqs/polymorphic8.jpg) - -The potential becomes embedded atom method ("Daw"_#poly-Daw) if we set - -:c,image(Eqs/polymorphic9.jpg) - -In the embedded atom method case, phi_IJ(r_ij) is the pair energy, -F_I(X) is the embedding energy, X is the local electron density, and -f_K(r) is the atomic electron density function. - -If the tabulated functions are created using the parameters of sw, -tersoff, and eam potentials, the polymorphic pair style will produce -the same global properties (energies and stresses) and the same forces -as the sw, tersoff, and eam pair styles. The polymorphic pair style -also produces the same atom properties (energies and stresses) as the -corresponding tersoff and eam pair styles. However, due to a different -partition of global properties to atom properties, the polymorphic -pair style will produce different atom properties (energies and -stresses) as the sw pair style. This does not mean that polymorphic -pair style is different from the sw pair style in this case. It just -means that the definitions of the atom energies and atom stresses are -different. - -Only a single pair_coeff command is used with the polymorphic style -which specifies an potential file for all needed elements. These are -mapped to LAMMPS atom types by specifying N additional arguments after -the filename in the pair_coeff command, where N is the number of -LAMMPS atom types: - -filename -N element names = mapping of Tersoff elements to atom types :ul - -See the pair_coeff doc page for alternate ways to specify the path for -the potential file. Several files for polymorphic potentials are -included in the potentials dir of the LAMMPS distribution. They have a -"poly" suffix. - -As an example, imagine the SiC_tersoff.polymorphic file has tabulated -functions for Si-C tersoff potential. If your LAMMPS simulation has 4 -atoms types and you want the 1st 3 to be Si, and the 4th to be C, you -would use the following pair_coeff command: - -pair_coeff * * SiC_tersoff.polymorphic Si Si Si C :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom -types. The first three Si arguments map LAMMPS atom types 1,2,3 to the -Si element in the polymorphic file. The final C argument maps LAMMPS -atom type 4 to the C element in the polymorphic file. If a mapping -value is specified as NULL, the mapping is not performed. This can be -used when an polymorphic potential is used as part of the hybrid pair -style. The NULL values are placeholders for atom types that will be -used with other potentials. - -Potential files in the potentials directory of the LAMMPS distribution -have a ".poly" suffix. At the beginning of the files, an unlimited -number of lines starting with '#' are used to describe the potential -and are ignored by LAMMPS. The next line lists two numbers: - -ntypes eta :pre - -Here ntypes represent total number of species defined in the potential -file, and eta = 0 or 1. The number ntypes must equal the total number -of different species defined in the pair_coeff command. When eta = 1, -eta_ij defined in the potential functions above is set to 1 - -delta_ij, otherwise eta_ij is set to delta_ij. The next ntypes lines -each lists two numbers and a character string representing atomic -number, atomic mass, and name of the species of the ntypes elements: - -atomic_number atomic-mass element (1) -atomic_number atomic-mass element (2) -... -atomic_number atomic-mass element (ntypes) :pre - -The next ntypes*(ntypes+1)/2 lines contain two numbers: - -cut xi (1) -cut xi (2) -... -cut xi (ntypes*(ntypes+1)/2) :pre - -Here cut means the cutoff distance of the pair functions, xi is the -same as defined in the potential functions above. The -ntypes*(ntypes+1)/2 lines are related to the pairs according to the -sequence of first ii (self) pairs, i = 1, 2, ..., ntypes, and then -then ij (cross) pairs, i = 1, 2, ..., ntypes-1, and j = i+1, i+2, ..., -ntypes (i.e., the sequence of the ij pairs follows 11, 22, ..., 12, -13, 14, ..., 23, 24, ...). - -The final blocks of the potential file are the U, V, W, P, G, and F -functions are listed sequentially. First, U functions are given for -each of the ntypes*(ntypes+1)/2 pairs according to the sequence -described above. For each of the pairs, nr values are listed. Next, -similar arrays are given for V, W, and P functions. Then G functions -are given for all the ntypes*ntypes*ntypes ijk triplets in a natural -sequence i from 1 to ntypes, j from 1 to ntypes, and k from 1 to -ntypes (i.e., ijk = 111, 112, 113, ..., 121, 122, 123 ..., 211, 212, -...). Each of the ijk functions contains ng values. Finally, the F -functions are listed for all ntypes*(ntypes+1)/2 pairs, each -containing nx values. Either analytic or tabulated functions can be -specified. Currently, constant, exponential, sine and cosine analytic -functions are available which are specified with: constant c1 , where -f(x) = c1 exponential c1 c2 , where f(x) = c1 exp(c2*x) sine c1 c2 , -where f(x) = c1 sin(c2*x) cos c1 c2 , where f(x) = c1 cos(c2*x) -Tabulated functions are specified by spline n x1 x2, where n=number of -point, (x1,x2)=range and then followed by n values evaluated uniformly -over these argument ranges. The valid argument ranges of the -functions are between 0 <= r <= cut for the U(r), V(r), W(r) -functions, -cutmax <= delta_r <= cutmax for the P(delta_r) functions, --1 <= costheta <= 1 for the G(costheta) functions, and 0 <= X <= maxX -for the F(X) functions. - -[Mixing, shift, table tail correction, restart]: - -This pair styles does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write their information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -:line - -[Restrictions:] - -If using create_atoms command, atomic masses must be defined in the -input script. If using read_data, atomic masses must be defined in the -atomic structure data file. - -This pair style is part of the MANYBODY package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair potential requires the "newtion"_newton.html setting to be -"on" for pair interactions. - -The potential files provided with LAMMPS (see the potentials -directory) are parameterized for metal "units"_units.html. You can use -any LAMMPS units, but you would need to create your own potential -files. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -:line - -:link(Zhou3) -[(Zhou)] X. W. Zhou, M. E. Foster, R. E. Jones, P. Yang, H. Fan, and -F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015). - -:link(SW) -[(SW)] F. H. Stillinger-Weber, and T. A. Weber, Phys. Rev. B, 31, 5262 (1985). - -:link(Tersoff) -[(Tersoff)] J. Tersoff, Phys. Rev. B, 39, 5566 (1989). - -:link(poly-Albe) -[(Albe)] K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, -66, 035205 (2002). - -:link(Wang3) -[(Wang)] J. Wang, and A. Rockett, Phys. Rev. B, 43, 12571 (1991). - -:link(poly-Daw) -[(Daw)] M. S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984). diff --git a/doc/txt/pair_python.txt b/doc/txt/pair_python.txt deleted file mode 100644 index e8baf14d2e..0000000000 --- a/doc/txt/pair_python.txt +++ /dev/null @@ -1,217 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style python command :h3 - -[Syntax:] - -pair_style python cutoff :pre - -cutoff = global cutoff for interactions in python potential classes - -[Examples:] - -pair_style python 2.5 -pair_coeff * * py_pot.LJCutMelt lj :pre - -pair_style hybrid/overlay coul/long 12.0 python 12.0 -pair_coeff * * coul/long -pair_coeff * * python py_pot.LJCutSPCE OW NULL :pre - -[Description:] - -The {python} pair style provides a way to define pairwise additive -potential functions as python script code that is loaded into LAMMPS -from a python file which must contain specific python class definitions. -This allows to rapidly evaluate different potential functions without -having to modify and re-compile LAMMPS. Due to python being an -interpreted language, however, the performance of this pair style is -going to be significantly slower (often between 20x and 100x) than -corresponding compiled code. This penalty can be significantly reduced -through generating tabulations from the python code through the -"pair_write"_pair_write.html command, which is supported by this style. - -Only a single pair_coeff command is used with the {python} pair style -which specifies a python class inside a python module or file that -LAMMPS will look up in the current directory, the folder pointed to by -the LAMMPS_POTENTIALS environment variable or somewhere in your python -path. A single python module can hold multiple python pair class -definitions. The class definitions itself have to follow specific -rules that are explained below. - -Atom types in the python class are specified through symbolic -constants, typically strings. These are mapped to LAMMPS atom types by -specifying N additional arguments after the class name in the -pair_coeff command, where N must be the number of currently defined -atom types: - -As an example, imagine a file {py_pot.py} has a python potential class -names {LJCutMelt} with parameters and potential functions for a two -Lennard-Jones atom types labeled as 'LJ1' and 'LJ2'. In your LAMMPS -input and you would have defined 3 atom types, out of which the first -two are supposed to be using the 'LJ1' parameters and the third the -'LJ2' parameters, then you would use the following pair_coeff command: - -pair_coeff * * py_pot.LJCutMelt LJ1 LJ1 LJ2 :pre - -The first two arguments [must] be * * so as to span all LAMMPS atom -types. The first two LJ1 arguments map LAMMPS atom types 1 and 2 to -the LJ1 atom type in the LJCutMelt class of the py_pot.py file. The -final LJ2 argument maps LAMMPS atom type 3 to the LJ2 atom type the -python file. If a mapping value is specified as NULL, the mapping is -not performed, any pair interaction with this atom type will be -skipped. This can be used when a {python} potential is used as part of -the {hybrid} or {hybrid/overlay} pair style. The NULL values are then -placeholders for atom types that will be used with other potentials. - -:line - -The python potential file has to start with the following code: - -from __future__ import print_function -# -class LAMMPSPairPotential(object): - def __init__(self): - self.pmap=dict() - self.units='lj' - def map_coeff(self,name,ltype): - self.pmap\[ltype\]=name - def check_units(self,units): - if (units != self.units): - raise Exception("Conflicting units: %s vs. %s" % (self.units,units)) -:pre - -Any classes with definitions of specific potentials have to be derived -from this class and should be initialize in a similar fashion to the -example given below. - -NOTE: The class constructor has to set up a data structure containing -the potential parameters supported by this class. It should also -define a variable {self.units} containing a string matching one of the -options of LAMMPS' "units"_units.html command, which is used to -verify, that the potential definition in the python class and in the -LAMMPS input match. - -Here is an example for a single type Lennard-Jones potential class -{LJCutMelt} in reduced units, which defines an atom type {lj} for -which the parameters epsilon and sigma are both 1.0: - -class LJCutMelt(LAMMPSPairPotential): - def __init__(self): - super(LJCutMelt,self).__init__() - # set coeffs: 48*eps*sig**12, 24*eps*sig**6, - # 4*eps*sig**12, 4*eps*sig**6 - self.units = 'lj' - self.coeff = \{'lj' : \{'lj' : (48.0,24.0,4.0,4.0)\}\} -:pre - -The class also has to provide two methods for the computation of the -potential energy and forces, which have be named {compute_force}, -and {compute_energy}, which both take 3 numerical arguments: - - rsq = the square of the distance between a pair of atoms (float) :l - itype = the (numerical) type of the first atom :l - jtype = the (numerical) type of the second atom :ul - -This functions need to compute the force and the energy, respectively, -and use the result as return value. The functions need to use the -{pmap} dictionary to convert the LAMMPS atom type number to the symbolic -value of the internal potential parameter data structure. Following -the {LJCutMelt} example, here are the two functions: - - def compute_force(self,rsq,itype,jtype): - coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\] - r2inv = 1.0/rsq - r6inv = r2inv*r2inv*r2inv - lj1 = coeff\[0\] - lj2 = coeff\[1\] - return (r6inv * (lj1*r6inv - lj2))*r2inv :pre - - def compute_energy(self,rsq,itype,jtype): - coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\] - r2inv = 1.0/rsq - r6inv = r2inv*r2inv*r2inv - lj3 = coeff\[2\] - lj4 = coeff\[3\] - return (r6inv * (lj3*r6inv - lj4)) :pre - -NOTE: for consistency with the C++ pair styles in LAMMPS, the -{compute_force} function follows the conventions of the Pair::single() -methods and does not return the full force, but the force scaled by -the distance between the two atoms, so this value only needs to be -multiplied by delta x, delta y, and delta z to conveniently obtain the -three components of the force vector between these two atoms. - -:line - -NOTE: The evaluation of scripted python code will slow down the -computation pair-wise interactions quite significantly. However, this -can be largely worked around through using the python pair style not -for the actual simulation, but to generate tabulated potentials on the -fly using the "pair_write"_pair_write.html command. Please see below -for an example LAMMPS input of how to build a table file: - -pair_style python 2.5 -pair_coeff * * py_pot.LJCutMelt lj -shell rm -f melt.table -pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj :pre - -Note that it is strongly recommended to try to [delete] the potential -table file before generating it. Since the {pair_write} command will -always [append] to a table file, while pair style table will use the -[first match]. Thus when changing the potential function in the python -class, the table pair style will still read the old variant unless the -table file is first deleted. - -After switching the pair style to {table}, the potential tables need -to be assigned to the LAMMPS atom types like this: - -pair_style table linear 2000 -pair_coeff 1 1 melt.table lj :pre - -This can also be done for more complex systems. Please see the -{examples/python} folders for a few more examples. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -Mixing of potential parameters has to be handled inside the provided -python module. The python pair style simply assumes that force and -energy computation can be correctly performed for all pairs of atom -types as they are mapped to the atom type labels inside the python -potential class. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the PYTHON package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_write"_pair_write.html, -"pair style table"_pair_table.html - -[Default:] none - - diff --git a/doc/txt/pair_quip.txt b/doc/txt/pair_quip.txt deleted file mode 100644 index e6b01b8853..0000000000 --- a/doc/txt/pair_quip.txt +++ /dev/null @@ -1,108 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style quip command :h3 - -[Syntax:] - -pair_style quip :pre - -[Examples:] - -pair_style quip -pair_coeff * * gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14 -pair_coeff * * sw_example.xml "IP SW" 14 :pre - -[Description:] - -Style {quip} provides an interface for calling potential routines from -the QUIP package. QUIP is built separately, and then linked to -LAMMPS. The most recent version of the QUIP package can be downloaded -from GitHub: -"https://github.com/libAtoms/QUIP"_https://github.com/libAtoms/QUIP. The -interface is chiefly intended to be used to run Gaussian Approximation -Potentials (GAP), which are described in the following publications: -"(Bartok et al)"_#Bartok_2010 and "(PhD thesis of -Bartok)"_#Bartok_PhD. - -Only a single pair_coeff command is used with the {quip} style that -specifies a QUIP potential file containing the parameters of the -potential for all needed elements in XML format. This is followed by a -QUIP initialization string. Finally, the QUIP elements are mapped to -LAMMPS atom types by specifying N atomic numbers, where N is the -number of LAMMPS atom types: - -QUIP filename -QUIP initialization string -N atomic numbers = mapping of QUIP elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -A QUIP potential is fully specified by the filename which contains the -parameters of the potential in XML format, the initialization string, -and the map of atomic numbers. - -GAP potentials can be obtained from the Data repository section of -"http://www.libatoms.org"_http://www.libatoms.org, where the -appropriate initialization strings are also advised. The list of -atomic numbers must be matched to the LAMMPS atom types specified in -the LAMMPS data file or elsewhere. - -Two examples input scripts are provided in the examples/USER/quip -directory. - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support the "pair_modify"_pair_modify.html -mix, shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -[Restrictions:] - -This pair style is part of the USER-QUIP package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -QUIP potentials are parameterized in electron-volts and Angstroms and -therefore should be used with LAMMPS metal "units"_units.html. - -QUIP potentials are generally not designed to work with the scaling -factors set by the "special_bonds"_special_bonds.html command. The -recommended setting in molecular systems is to include all -interactions, i.e. to use {special_bonds lj/coul 1.0 1.0 1.0}. Scaling -factors > 0.0 will be ignored and treated as 1.0. The only exception -to this rule is if you know that your QUIP potential needs to exclude -bonded, 1-3, or 1-4 interactions and does not already do this exclusion -within QUIP. Then a factor 0.0 needs to be used which will remove such -pairs from the neighbor list. This needs to be very carefully tested, -because it may remove pairs from the neighbor list that are still -required. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -:line - -:link(Bartok_2010) - -[(Bartok_2010)] AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical -Review Letters 104, 136403 (2010). - -:link(Bartok_PhD) -[(Bartok_PhD)] A Bartok-Partay, PhD Thesis, University of Cambridge, -(2010). diff --git a/doc/txt/pair_reaxc.txt b/doc/txt/pair_reaxc.txt deleted file mode 100644 index 37482beacf..0000000000 --- a/doc/txt/pair_reaxc.txt +++ /dev/null @@ -1,357 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style reax/c command :h3 -pair_style reax/c/kk command :h3 -pair_style reax/c/omp command :h3 - -[Syntax:] - -pair_style reax/c cfile keyword value :pre - -cfile = NULL or name of a control file :ulb,l -zero or more keyword/value pairs may be appended :l -keyword = {checkqeq} or {lgvdw} or {safezone} or {mincap} - {checkqeq} value = {yes} or {no} = whether or not to require qeq/reax fix - {enobonds} value = {yes} or {no} = whether or not to tally energy of atoms with no bonds - {lgvdw} value = {yes} or {no} = whether or not to use a low gradient vdW correction - {safezone} = factor used for array allocation - {mincap} = minimum size for array allocation :pre -:ule - -[Examples:] - -pair_style reax/c NULL -pair_style reax/c controlfile checkqeq no -pair_style reax/c NULL lgvdw yes -pair_style reax/c NULL safezone 1.6 mincap 100 -pair_coeff * * ffield.reax C H O N :pre - -[Description:] - -Style {reax/c} computes the ReaxFF potential of van Duin, Goddard and -co-workers. ReaxFF uses distance-dependent bond-order functions to -represent the contributions of chemical bonding to the potential -energy. There is more than one version of ReaxFF. The version -implemented in LAMMPS uses the functional forms documented in the -supplemental information of the following paper: "(Chenoweth et al., -2008)"_#Chenoweth_20082. The version integrated into LAMMPS matches -the most up-to-date version of ReaxFF as of summer 2010. For more -technical details about the pair reax/c implementation of ReaxFF, see -the "(Aktulga)"_#Aktulga paper. The {reax/c} style was initially -implemented as a stand-alone C code and is now integrated into LAMMPS -as a package. - -The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that -is derived from the {reax/c} style. The Kokkos version can run on GPUs -and can also use OpenMP multithreading. For more information about the -Kokkos package, see "Packages details"_Packages_details.html and -"Speed kokkos"_Speed_kokkos.html doc pages. One important -consideration when using the {reax/c/kk} style is the choice of either -half or full neighbor lists. This setting can be changed using the -Kokkos "package"_package.html command. - -The {reax/c} style differs from the (obsolete) "pair_style reax" -command in the implementation details. The {reax} style was a -Fortran library, linked to LAMMPS. The {reax} style has been removed -from LAMMPS after the 12 December 2018 version. - -LAMMPS provides several different versions of ffield.reax in its -potentials dir, each called potentials/ffield.reax.label. These are -documented in potentials/README.reax. The default ffield.reax -contains parameterizations for the following elements: C, H, O, N. - -The format of these files is identical to that used originally by van -Duin. We have tested the accuracy of {pair_style reax/c} potential -against the original ReaxFF code for the systems mentioned above. You -can use other ffield files for specific chemical systems that may be -available elsewhere (but note that their accuracy may not have been -tested). - -NOTE: We do not distribute a wide variety of ReaxFF force field files -with LAMMPS. Adri van Duin's group at PSU is the central repository -for this kind of data as they are continuously deriving and updating -parameterizations for different classes of materials. You can submit -a contact request at the Materials Computation Center (MCC) website -"https://www.mri.psu.edu/materials-computation-center/connect-mcc"_https://www.mri.psu.edu/materials-computation-center/connect-mcc, -describing the material(s) you are interested in modeling with ReaxFF. -They can tell you what is currently available or what it would take to -create a suitable ReaxFF parameterization. - -The {cfile} setting can be specified as NULL, in which case default -settings are used. A control file can be specified which defines -values of control variables. Some control variables are -global parameters for the ReaxFF potential. Others define certain -performance and output settings. -Each line in the control file specifies the value for -a control variable. The format of the control file is described -below. - -NOTE: The LAMMPS default values for the ReaxFF global parameters -correspond to those used by Adri van Duin's stand-alone serial -code. If these are changed by setting control variables in the control -file, the results from LAMMPS and the serial code will not agree. - -Examples using {pair_style reax/c} are provided in the examples/reax -sub-directory. - -Use of this pair style requires that a charge be defined for every -atom. See the "atom_style"_atom_style.html and -"read_data"_read_data.html commands for details on how to specify -charges. - -The ReaxFF parameter files provided were created using a charge -equilibration (QEq) model for handling the electrostatic interactions. -Therefore, by default, LAMMPS requires that the "fix -qeq/reax"_fix_qeq_reax.html command be used with {pair_style reax/c} -when simulating a ReaxFF model, to equilibrate charge each timestep. -Using the keyword {checkqeq} with the value {no} -turns off the check for {fix qeq/reax}, -allowing a simulation to be run without charge equilibration. -In this case, the static charges you -assign to each atom will be used for computing the electrostatic -interactions in the system. -See the "fix qeq/reax"_fix_qeq_reax.html command for details. - -Using the optional keyword {lgvdw} with the value {yes} turns on the -low-gradient correction of the ReaxFF/C for long-range London -Dispersion, as described in the "(Liu)"_#Liu_2011 paper. Force field -file {ffield.reax.lg} is designed for this correction, and is trained -for several energetic materials (see "Liu"). When using lg-correction, -recommended value for parameter {thb} is 0.01, which can be set in the -control file. Note: Force field files are different for the original -or lg corrected pair styles, using wrong ffield file generates an -error message. - -Using the optional keyword {enobonds} with the value {yes}, the energy -of atoms with no bonds (i.e. isolated atoms) is included in the total -potential energy and the per-atom energy of that atom. If the value -{no} is specified then the energy of atoms with no bonds is set to -zero. The latter behavior is usual not desired, as it causes -discontinuities in the potential energy when the bonding of an atom -drops to zero. - -Optional keywords {safezone} and {mincap} are used for allocating -reax/c arrays. Increasing these values can avoid memory problems, -such as segmentation faults and bondchk failed errors, that could -occur under certain conditions. These keywords aren't used by the -Kokkos version, which instead uses a more robust memory allocation -scheme that checks if the sizes of the arrays have been exceeded and -automatically allocates more memory. - -The thermo variable {evdwl} stores the sum of all the ReaxFF potential -energy contributions, with the exception of the Coulombic and charge -equilibration contributions which are stored in the thermo variable -{ecoul}. The output of these quantities is controlled by the -"thermo"_thermo.html command. - -This pair style tallies a breakdown of the total ReaxFF potential -energy into sub-categories, which can be accessed via the "compute -pair"_compute_pair.html command as a vector of values of length 14. -The 14 values correspond to the following sub-categories (the variable -names in italics match those used in the original FORTRAN ReaxFF -code): - -{eb} = bond energy -{ea} = atom energy -{elp} = lone-pair energy -{emol} = molecule energy (always 0.0) -{ev} = valence angle energy -{epen} = double-bond valence angle penalty -{ecoa} = valence angle conjugation energy -{ehb} = hydrogen bond energy -{et} = torsion energy -{eco} = conjugation energy -{ew} = van der Waals energy -{ep} = Coulomb energy -{efi} = electric field energy (always 0.0) -{eqeq} = charge equilibration energy :ol - -To print these quantities to the log file (with descriptive column -headings) the following commands could be included in an input script: - -compute reax all pair reax/c -variable eb equal c_reax\[1\] -variable ea equal c_reax\[2\] -\[...\] -variable eqeq equal c_reax\[14\] -thermo_style custom step temp epair v_eb v_ea \[...\] v_eqeq :pre - -Only a single pair_coeff command is used with the {reax/c} style which -specifies a ReaxFF potential file with parameters for all needed -elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N indices = ReaxFF elements :ul - -The filename is the ReaxFF potential file. - -In the ReaxFF potential file, near the top, after the general -parameters, is the atomic parameters section that contains element -names, each with a couple dozen numeric parameters. If there are M -elements specified in the {ffield} file, think of these as numbered 1 -to M. Each of the N indices you specify for the N atom types of LAMMPS -atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will -be mapped to whatever element you specify as the first index value, -etc. If a mapping value is specified as NULL, the mapping is not -performed. This can be used when the {reax/c} style is used as part -of the {hybrid} pair style. The NULL values are placeholders for atom -types that will be used with other potentials. - -As an example, say your LAMMPS simulation has 4 atom types and the -elements are ordered as C, H, O, N in the {ffield} file. If you want -the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be -H, you would use the following pair_coeff command: - -pair_coeff * * ffield.reax C C N H :pre - -:line - -The format of a line in the control file is as follows: - -variable_name value :pre - -and it may be followed by an "!" character and a trailing comment. - -If the value of a control variable is not specified, then default -values are used. What follows is the list of variables along with a -brief description of their use and default values. - -simulation_name: Output files produced by {pair_style reax/c} carry -this name + extensions specific to their contents. Partial energies -are reported with a ".pot" extension, while the trajectory file has -".trj" extension. - -tabulate_long_range: To improve performance, long range interactions -can optionally be tabulated (0 means no tabulation). Value of this -variable denotes the size of the long range interaction table. The -range from 0 to long range cutoff (defined in the {ffield} file) is -divided into {tabulate_long_range} points. Then at the start of -simulation, we fill in the entries of the long range interaction table -by computing the energies and forces resulting from van der Waals and -Coulomb interactions between every possible atom type pairs present in -the input system. During the simulation we consult to the long range -interaction table to estimate the energy and forces between a pair of -atoms. Linear interpolation is used for estimation. (default value = -0) - -energy_update_freq: Denotes the frequency (in number of steps) of -writes into the partial energies file. (default value = 0) - -nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms) -regarding the bonded interactions. (default value = 5.0) - -hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen -bond interactions.(default value = 7.5. A value of 0.0 turns off -hydrogen bonds) - -bond_graph_cutoff: is the threshold used in determining what is a -physical bond, what is not. Bonds and angles reported in the -trajectory file rely on this cutoff. (default value = 0.3) - -thb_cutoff: cutoff value for the strength of bonds to be considered in -three body interactions. (default value = 0.001) - -thb_cutoff_sq: cutoff value for the strength of bond order products -to be considered in three body interactions. (default value = 0.00001) - -write_freq: Frequency of writes into the trajectory file. (default -value = 0) - -traj_title: Title of the trajectory - not the name of the trajectory -file. - -atom_info: 1 means print only atomic positions + charge (default = 0) - -atom_forces: 1 adds net forces to atom lines in the trajectory file -(default = 0) - -atom_velocities: 1 adds atomic velocities to atoms line (default = 0) - -bond_info: 1 prints bonds in the trajectory file (default = 0) - -angle_info: 1 prints angles in the trajectory file (default = 0) - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support the "pair_modify"_pair_modify.html -mix, shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This pair style is part of the USER-REAXC package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -The ReaxFF potential files provided with LAMMPS in the potentials -directory are parameterized for real "units"_units.html. You can use -the ReaxFF potential with any LAMMPS units, but you would need to -create your own potential file with coefficients listed in the -appropriate units if your simulation doesn't use "real" units. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "fix qeq/reax"_fix_qeq_reax.html, "fix -reax/c/bonds"_fix_reaxc_bonds.html, "fix -reax/c/species"_fix_reaxc_species.html - -[Default:] - -The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no, -safezone = 1.2, mincap = 50. - -:line - -:link(Chenoweth_20082) -[(Chenoweth_2008)] Chenoweth, van Duin and Goddard, -Journal of Physical Chemistry A, 112, 1040-1053 (2008). - -:link(Aktulga) -(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, -245-259 (2012). - -:link(Liu_2011) -[(Liu)] L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal -of Physical Chemistry A, 115, 11016-11022 (2011). diff --git a/doc/txt/pair_resquared.txt b/doc/txt/pair_resquared.txt deleted file mode 100644 index 5e760be495..0000000000 --- a/doc/txt/pair_resquared.txt +++ /dev/null @@ -1,234 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style resquared command :h3 -pair_style resquared/gpu command :h3 -pair_style resquared/omp command :h3 - -[Syntax:] - -pair_style resquared cutoff :pre - -cutoff = global cutoff for interactions (distance units) :ul - -[Examples:] - -pair_style resquared 10.0 -pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 :pre - -[Description:] - -Style {resquared} computes the RE-squared anisotropic interaction -"(Everaers)"_#Everaers3, "(Babadi)"_#Babadi between pairs of -ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal -interactions, the potential considers the ellipsoid as being comprised -of small spheres of size sigma. LJ particles are a single sphere of -size sigma. The distinction is made to allow the pair style to make -efficient calculations of ellipsoid/solvent interactions. - -Details for the equations used are given in the references below and -in "this supplementary document"_PDF/pair_resquared_extra.pdf. - -Use of this pair style requires the NVE, NVT, or NPT fixes with the -{asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in -order to integrate particle rotation. Additionally, "atom_style -ellipsoid"_atom_style.html should be used since it defines the -rotational state and the size and shape of each ellipsoidal particle. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -A12 = Energy Prefactor/Hamaker constant (energy units) -sigma = atomic interaction diameter (distance units) -epsilon_i_a = relative well depth of type I for side-to-side interactions -epsilon_i_b = relative well depth of type I for face-to-face interactions -epsilon_i_c = relative well depth of type I for end-to-end interactions -epsilon_j_a = relative well depth of type J for side-to-side interactions -epsilon_j_b = relative well depth of type J for face-to-face interactions -epsilon_j_c = relative well depth of type J for end-to-end interactions -cutoff (distance units) :ul - -The parameters used depend on the type of the interacting particles, -i.e. ellipsoids or LJ spheres. The type of a particle is determined -by the diameters specified for its 3 shape parameters. If all 3 shape -parameters = 0.0, then the particle is treated as an LJ sphere. The -epsilon_i_* or epsilon_j_* parameters are ignored for LJ spheres. If -the 3 shape parameters are > 0.0, then the particle is treated as an -ellipsoid (even if the 3 parameters are equal to each other). - -A12 specifies the energy prefactor which depends on the types of the -two interacting particles. - -For ellipsoid/ellipsoid interactions, the interaction is computed by -the formulas in the supplementary document referenced above. A12 is -the Hamaker constant as described in "(Everaers)"_#Everaers3. In LJ -units: - -:c,image(Eqs/pair_resquared.jpg) - -where rho gives the number density of the spherical particles -composing the ellipsoids and epsilon_LJ determines the interaction -strength of the spherical particles. - -For ellipsoid/LJ sphere interactions, the interaction is also computed -by the formulas in the supplementary document referenced above. A12 -has a modified form (see "here"_PDF/pair_resquared_extra.pdf for -details): - -:c,image(Eqs/pair_resquared2.jpg) - -For ellipsoid/LJ sphere interactions, a correction to the distance- -of-closest approach equation has been implemented to reduce the error -from two particles of disparate sizes; see "this supplementary -document"_PDF/pair_resquared_extra.pdf. - -For LJ sphere/LJ sphere interactions, the interaction is computed -using the standard Lennard-Jones formula, which is much cheaper to -compute than the ellipsoidal formulas. A12 is used as epsilon in the -standard LJ formula: - -:c,image(Eqs/pair_resquared3.jpg) - -and the specified {sigma} is used as the sigma in the standard LJ -formula. - -When one of both of the interacting particles are ellipsoids, then -{sigma} specifies the diameter of the continuous distribution of -constituent particles within each ellipsoid used to model the -RE-squared potential. Note that this is a different meaning for -{sigma} than the "pair_style gayberne"_pair_gayberne.html potential -uses. - -The epsilon_i and epsilon_j coefficients are defined for atom types, -not for pairs of atom types. Thus, in a series of pair_coeff -commands, they only need to be specified once for each atom type. - -Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are -non-zero, the three values are assigned to atom type I. If all the -epsilon_i values are zero, they are ignored. If any of epsilon_j_a, -epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned -to atom type J. If all three epsilon_i values are zero, they are -ignored. Thus the typical way to define the epsilon_i and epsilon_j -coefficients is to list their values in "pair_coeff I J" commands when -I = J, but set them to 0.0 when I != J. If you do list them when I != -J, you should insure they are consistent with their values in other -pair_coeff commands. - -Note that if this potential is being used as a sub-style of -"pair_style hybrid"_pair_hybrid.html, and there is no "pair_coeff I I" -setting made for RE-squared for a particular type I (because I-I -interactions are computed by another hybrid pair potential), then you -still need to insure the epsilon a,b,c coefficients are assigned to -that type in a "pair_coeff I J" command. - -For large uniform molecules it has been shown that the epsilon_*_* -energy parameters are approximately representable in terms of local -contact curvatures "(Everaers)"_#Everaers3: - -:c,image(Eqs/pair_resquared4.jpg) - -where a, b, and c give the particle diameters. - -The last coefficient is optional. If not specified, the global cutoff -specified in the pair_style command is used. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance can be mixed, but only for sphere pairs. The -default mix value is {geometric}. See the "pair_modify" command for -details. Other type pairs cannot be mixed, due to the different -meanings of the energy prefactors used to calculate the interactions -and the implicit dependence of the ellipsoid-sphere interaction on the -equation for the Hamaker constant presented here. Mixing of sigma and -epsilon followed by calculation of the energy prefactors using the -equations above is recommended. - -This pair styles supports the "pair_modify"_pair_modify.html shift -option for the energy of the Lennard-Jones portion of the pair -interaction, but only for sphere-sphere interactions. There is no -shifting performed for ellipsoidal interactions due to the anisotropic -dependence of the interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords of the "run_style -command"_run_style.html. - -:line - -[Restrictions:] - -This style is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair style requires that atoms be ellipsoids as defined by the -"atom_style ellipsoid"_atom_style.html command. - -Particles acted on by the potential can be finite-size aspherical or -spherical particles, or point particles. Spherical particles have all -3 of their shape parameters equal to each other. Point particles have -all 3 of their shape parameters equal to 0.0. - -The distance-of-closest-approach approximation used by LAMMPS becomes -less accurate when high-aspect ratio ellipsoids are used. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "fix nve/asphere"_fix_nve_asphere.html, -"compute temp/asphere"_compute_temp_asphere.html, "pair_style -gayberne"_pair_gayberne.html - -[Default:] none - -:line - -:link(Everaers3) -[(Everaers)] Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003). - -:link(Babadi) -[(Berardi)] Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006). diff --git a/doc/txt/pair_sdk.txt b/doc/txt/pair_sdk.txt deleted file mode 100644 index 7c596ed1d8..0000000000 --- a/doc/txt/pair_sdk.txt +++ /dev/null @@ -1,161 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style lj/sdk command :h3 -pair_style lj/sdk/gpu command :h3 -pair_style lj/sdk/kk command :h3 -pair_style lj/sdk/omp command :h3 -pair_style lj/sdk/coul/long command :h3 -pair_style lj/sdk/coul/long/gpu command :h3 -pair_style lj/sdk/coul/long/omp command :h3 -pair_style lj/sdk/coul/msm command :h3 -pair_style lj/sdk/coul/msm/omp command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {lj/sdk} or {lj/sdk/coul/long} -args = list of arguments for a particular style :ul - {lj/sdk} args = cutoff - cutoff = global cutoff for Lennard Jones interactions (distance units) - {lj/sdk/coul/long} args = cutoff (cutoff2) - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre - -[Examples:] - -pair_style lj/sdk 2.5 -pair_coeff 1 1 lj12_6 1 1.1 2.8 :pre - -pair_style lj/sdk/coul/long 10.0 -pair_style lj/sdk/coul/long 10.0 12.0 -pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre - -pair_style lj/sdk/coul/msm 10.0 -pair_style lj/sdk/coul/msm 10.0 12.0 -pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre - -[Description:] - -The {lj/sdk} styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential, -given by - -:c,image(Eqs/pair_cmm.jpg) - -as required for the SDK Coarse-grained MD parameterization discussed in -"(Shinoda)"_#Shinoda3 and "(DeVane)"_#DeVane. Rc is the cutoff. - -Style {lj/sdk/coul/long} computes the adds Coulombic interactions -with an additional damping factor applied so it can be used in -conjunction with the "kspace_style"_kspace_style.html command and -its {ewald} or {pppm} or {pppm/cg} option. The Coulombic cutoff -specified for this style means that pairwise interactions within -this distance are computed directly; interactions outside that -distance are computed in reciprocal space. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -cg_type (lj9_6, lj12_4, or lj12_6) -epsilon (energy units) -sigma (distance units) -cutoff1 (distance units) :ul - -Note that sigma is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum. The prefactors -are chosen so that the potential minimum is at -epsilon. - -The latter 2 coefficients are optional. If not specified, the global -LJ and Coulombic cutoffs specified in the pair_style command are used. -If only one cutoff is specified, it is used as the cutoff for both LJ -and Coulombic interactions for this type pair. If both coefficients -are specified, they are used as the LJ and Coulombic cutoffs for this -type pair. - -For {lj/sdk/coul/long} and {lj/sdk/coul/msm} only the LJ cutoff can be -specified since a Coulombic cutoff cannot be specified for an -individual I,J type pair. All type pairs use the same global -Coulombic cutoff specified in the pair_style command. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp} or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP, and OPT packages respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, and rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/sdk pair styles {cannot} be mixed, -since different pairs may have different exponents. So all parameters -for all pairs have to be specified explicitly through the "pair_coeff" -command. Defining then in a data file is also not supported, due to -limitations of that file format. - -All of the lj/sdk pair styles support the -"pair_modify"_pair_modify.html shift option for the energy of the -Lennard-Jones portion of the pair interaction. - -The {lj/sdk/coul/long} pair styles support the -"pair_modify"_pair_modify.html table option since they can tabulate -the short-range portion of the long-range Coulombic interaction. - -All of the lj/sdk pair styles write their information to "binary -restart files"_restart.html, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. - -The lj/sdk and lj/cut/coul/long pair styles do not support -the use of the {inner}, {middle}, and {outer} keywords of the "run_style -respa"_run_style.html command. - -:line - -[Restrictions:] - -All of the lj/sdk pair styles are part of the USER-CGSDK package. The -{lj/sdk/coul/long} style also requires the KSPACE package to be built -(which is enabled by default). They are only enabled if LAMMPS was -built with that package. See the "Build package"_Build_package.html -doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "angle_style sdk"_angle_sdk.html - -[Default:] none - -:line - -:link(Shinoda3) -[(Shinoda)] Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007). - -:link(DeVane) -[(DeVane)] Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008). - diff --git a/doc/txt/pair_sdpd_taitwater_isothermal.txt b/doc/txt/pair_sdpd_taitwater_isothermal.txt deleted file mode 100644 index fba97e1bc2..0000000000 --- a/doc/txt/pair_sdpd_taitwater_isothermal.txt +++ /dev/null @@ -1,108 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style sdpd/taitwater/isothermal command :h3 - -[Syntax:] - -pair_style sdpd/taitwater/isothermal temperature viscosity seed -:pre - -temperature = temperature of the fluid (temperature units) -viscosity = dynamic viscosity of the fluid (mass*distance/time units) -seed = random number generator seed (positive integer, optional) :ul - -[Examples:] - -pair_style sdpd/taitwater/isothermal 300. 1. 28681 -pair_coeff * * 1000.0 1430.0 2.4 :pre - -[Description:] - -The sdpd/taitwater/isothermal style computes forces between mesoscopic -particles according to the Smoothed Dissipative Particle Dynamics model -described in this paper by "(Espanol and Revenga)"_#Espanol_Revenga under -the following assumptions: - -:olb -The temperature is constant and uniform. :l -The shear viscosity is constant and uniform. :l -The volume viscosity is negligible before the shear viscosity. :l -The Boltzmann constant is negligible before the heat capacity of a -single mesoscopic particle of fluid. :ole,l - -The third assumption is true for water in nearly incompressible flows. -The fourth holds true for water for any reasonable size one can -imagine for a mesoscopic particle. - -The pressure forces between particles will be computed according to -Tait's equation of state: - -:c,image(Eqs/pair_sph_tait.jpg) - -where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the -reference density and c_0 the reference speed of sound. - -The laminar viscosity and the random forces will be computed according -to formulas described in "(Espanol and Revenga)"_#Espanol_Revenga. - -IMPORTANT NOTE: Similar to "brownian"_pair_brownian.html and -"dpd"_pair_dpd.html styles, the "newton"_newton.html setting for -pairwise interactions needs to be on when running LAMMPS in parallel -if you want to ensure linear momentum conservation. Otherwise random -forces generated for pairs straddling processor boundary will not be -equal and opposite. - -NOTE: The actual random seed used will be a mix of what you specify -and other parameters like the MPI ranks. This is to ensure that -different MPI tasks have distinct seeds. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above. - -rho0 reference density (mass/volume units) -c0 reference soundspeed (distance/time units) -h kernel function cutoff (distance units) :ul - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -This style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This style does not write information to "binary restart -files"_restart.html. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. - -This style can only be used via the {pair} keyword of the "run_style -respa"_run_style.html command. It does not support the {inner}, -{middle}, {outer} keywords. - -[Restrictions:] - -This pair style is part of the USER-SDPD package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair coeff"_pair_coeff.html, "pair sph/rhosum"_pair_sph_rhosum.html - -[Default:] - -The default seed is 0 (before mixing). - -:line - -:link(Espanol_Revenga) -[(Espanol and Revenga)] Espanol, Revenga, Physical Review E, 67, 026705 (2003). diff --git a/doc/txt/pair_smd_hertz.txt b/doc/txt/pair_smd_hertz.txt deleted file mode 100644 index 2581c84dc9..0000000000 --- a/doc/txt/pair_smd_hertz.txt +++ /dev/null @@ -1,60 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style smd/hertz command :h3 - -[Syntax:] - -pair_style smd/hertz scale_factor :pre - -[Examples:] - -pair_style smd/hertz 1.0 -pair_coeff 1 1 - -[Description:] - -The {smd/hertz} style calculates contact forces between SPH particles -belonging to different physical bodies. - -The contact forces are calculated using a Hertz potential, which -evaluates the overlap between two particles (whose spatial extents are -defined via its contact radius). The effect is that a particles -cannot penetrate into each other. The parameter -has units of pressure and should equal roughly one half of the Young's -modulus (or bulk modulus in the case of fluids) of the material model -associated with the SPH particles. - -The parameter {scale_factor} can be used to scale the particles' -contact radii. This can be useful to control how close particles can -approach each other. Usually, {scale_factor} =1.0. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -No mixing is performed automatically. Currently, no part of USER-SMD -supports restarting nor minimization. rRESPA does not apply to this -pair style. - -:line - -[Restrictions:] - -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - diff --git a/doc/txt/pair_smd_tlsph.txt b/doc/txt/pair_smd_tlsph.txt deleted file mode 100644 index 13ffbbabc1..0000000000 --- a/doc/txt/pair_smd_tlsph.txt +++ /dev/null @@ -1,73 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style smd/tlsph command :h3 - -[Syntax:] - -pair_style smd/tlsph args :pre - -[Examples:] - -pair_style smd/tlsph - -[Description:] - -The {smd/tlsph} style computes particle interactions according to -continuum mechanics constitutive laws and a Total-Lagrangian -Smooth-Particle Hydrodynamics algorithm. - -This pair style is invoked with the following command: - -pair_style smd/tlsph -pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp & - *END :pre - -Here, {i} and {j} denote the {LAMMPS} particle types for which this -pair style is defined. Note that {i} and {j} must be equal, i.e., no -{tlsph} cross interactions between different particle types are -allowed. In contrast to the usual {LAMMPS} {pair coeff} definitions, -which are given solely a number of floats and integers, the {tlsph} -{pair coeff} definition is organized using keywords. These keywords -mark the beginning of different sets of parameters for particle -properties, material constitutive models, and damage models. The {pair -coeff} line must be terminated with the {*END} keyword. The use the -line continuation operator {&} is recommended. A typical invocation of -the {tlsph} for a solid body would consist of an equation of state for -computing the pressure (the diagonal components of the stress tensor), -and a material model to compute shear stresses (the off-diagonal -components of the stress tensor). Damage and failure models can also -be added. - -Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a -complete listing of the possible keywords and material models. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -No mixing is performed automatically. Currently, no part of USER-SMD -supports restarting nor minimization. rRESPA does not apply to this -pair style. - -:line - -[Restrictions:] - -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - diff --git a/doc/txt/pair_smd_triangulated_surface.txt b/doc/txt/pair_smd_triangulated_surface.txt deleted file mode 100644 index 9eb5e311b8..0000000000 --- a/doc/txt/pair_smd_triangulated_surface.txt +++ /dev/null @@ -1,61 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style smd/tri_surface command :h3 - -[Syntax:] - -pair_style smd/tri_surface scale_factor :pre - -[Examples:] - -pair_style smd/tri_surface 1.0 -pair_coeff 1 1 - -[Description:] - -The {smd/tri_surface} style calculates contact forces between SPH -particles and a rigid wall boundary defined via the -"smd/wall_surface"_fix_smd_wall_surface.html fix. - -The contact forces are calculated using a Hertz potential, which -evaluates the overlap between a particle (whose spatial extents are -defined via its contact radius) and the triangle. The effect is that -a particle cannot penetrate into the triangular surface. The -parameter has units of pressure and should equal -roughly one half of the Young's modulus (or bulk modulus in the case -of fluids) of the material model associated with the SPH particle - -The parameter {scale_factor} can be used to scale the particles' -contact radii. This can be useful to control how close particles can -approach the triangulated surface. Usually, {scale_factor} =1.0. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -No mixing is performed automatically. -Currently, no part of USER-SMD supports restarting nor minimization. -rRESPA does not apply to this pair style. - -:line - -[Restrictions:] - -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - diff --git a/doc/txt/pair_smd_ulsph.txt b/doc/txt/pair_smd_ulsph.txt deleted file mode 100644 index 39e9c76841..0000000000 --- a/doc/txt/pair_smd_ulsph.txt +++ /dev/null @@ -1,81 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style smd/ulsph command :h3 - -[Syntax:] - -pair_style smd/ulsph args :pre - -these keywords must be given :ul -keyword = {*DENSITY_SUMMATION} or {*DENSITY_CONTINUITY} and {*VELOCITY_GRADIENT} or {*NO_VELOCITY_GRADIENT} and {*GRADIENT_CORRECTION} or {*NO_GRADIENT_CORRECTION} :pre - -[Examples:] - -pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION :pre - -[Description:] - -The {smd/ulsph} style computes particle interactions according to -continuum mechanics constitutive laws and an updated Lagrangian -Smooth-Particle Hydrodynamics algorithm. - -This pair style is invoked similar to the following command: - -pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION -pair_coeff i j *COMMON rho0 c0 Q1 Cp hg & - *END :pre - -Here, {i} and {j} denote the {LAMMPS} particle types for which this -pair style is defined. Note that {i} and {j} can be different, i.e., -{ulsph} cross interactions between different particle types are -allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have -to precede a cross interaction. In contrast to the usual {LAMMPS} -{pair coeff} definitions, which are given solely a number of floats -and integers, the {ulsph} {pair coeff} definition is organized using -keywords. These keywords mark the beginning of different sets of -parameters for particle properties, material constitutive models, and -damage models. The {pair coeff} line must be terminated with the -{*END} keyword. The use the line continuation operator {&} is -recommended. A typical invocation of the {ulsph} for a solid body -would consist of an equation of state for computing the pressure (the -diagonal components of the stress tensor), and a material model to -compute shear stresses (the off-diagonal components of the stress -tensor). - -Note that the use of *GRADIENT_CORRECTION can lead to severe numerical -instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION -is recommended. - -Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a -complete listing of the possible keywords and material models. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -No mixing is performed automatically. Currently, no part of USER-SMD -supports restarting nor minimization. rRESPA does not apply to this -pair style. - -:line - -[Restrictions:] - -This fix is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - diff --git a/doc/txt/pair_smtbq.txt b/doc/txt/pair_smtbq.txt deleted file mode 100644 index 41e124a94f..0000000000 --- a/doc/txt/pair_smtbq.txt +++ /dev/null @@ -1,261 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style smtbq command :h3 - -[Syntax:] - -pair_style smtbq :pre - -[Examples:] - -pair_style smtbq -pair_coeff * * ffield.smtbq.Al2O3 O Al :pre - -[Description:] - -This pair style computes a variable charge SMTB-Q (Second-Moment -tight-Binding QEq) potential as described in "SMTB-Q_1"_#SMTB-Q_1 and -"SMTB-Q_2"_#SMTB-Q_2. Briefly, the energy of metallic-oxygen systems -is given by three contributions: - -:c,image(Eqs/pair_smtbq1.jpg) - -where {Etot} is the total potential energy of the system, -{EES} is the electrostatic part of the total energy, -{EOO} is the interaction between oxygen atoms and -{EMO} is a short-range interaction between metal and oxygen -atoms. This interactions depend on interatomic distance -{rij} and/or the charge {Qi} of atoms -{i}. Cut-off function enables smooth convergence to zero interaction. - -The parameters appearing in the upper expressions are set in the -ffield.SMTBQ.Syst file where Syst corresponds to the selected system -(e.g. field.SMTBQ.Al2O3). Examples for TiO2, -Al2O3 are provided. A single pair_coeff command -is used with the SMTBQ styles which provides the path to the potential -file with parameters for needed elements. These are mapped to LAMMPS -atom types by specifying additional arguments after the potential -filename in the pair_coeff command. Note that atom type 1 must always -correspond to oxygen atoms. As an example, to simulate a TiO2 system, -atom type 1 has to be oxygen and atom type 2 Ti. The following -pair_coeff command should then be used: - -pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti :pre - -The electrostatic part of the energy consists of two components : -self-energy of atom {i} in the form of a second order charge dependent -polynomial and a long-range Coulombic electrostatic interaction. The -latter uses the wolf summation method described in "Wolf"_#Wolf2, -spherically truncated at a longer cutoff, {Rcoul}. The -charge of each ion is modeled by an orbital Slater which depends on -the principal quantum number ({n}) of the outer orbital shared by the -ion. - -Interaction between oxygen, {EOO}, consists of two parts, -an attractive and a repulsive part. The attractive part is effective -only at short range (< r2OO). The attractive -contribution was optimized to study surfaces reconstruction -(e.g. "SMTB-Q_2"_#SMTB-Q_2 in TiO2) and is not necessary -for oxide bulk modeling. The repulsive part is the Pauli interaction -between the electron clouds of oxygen. The Pauli repulsion and the -coulombic electrostatic interaction have same cut off value. In the -ffield.SMTBQ.Syst, the keyword {'buck'} allows to consider only the -repulsive O-O interactions. The keyword {'buckPlusAttr'} allows to -consider the repulsive and the attractive O-O interactions. - -The short-range interaction between metal-oxygen, {EMO} is -based on the second moment approximation of the density of states with -a N-body potential for the band energy term, -{Eicov}, and a Born-Mayer type repulsive terms -as indicated by the keyword {'second_moment'} in the -ffield.SMTBQ.Syst. The energy band term is given by: - -:c,image(Eqs/pair_smtbq2.jpg) - -where {ηi} is the stoichiometry of atom {i}, -{δQi} is the charge delocalization of atom {i}, -compared to its formal charge -{QFi}. n0, the number of hybridized -orbitals, is calculated with to the atomic orbitals shared -{di} and the stoichiometry -{ηi}. {rc1} and {rc2} are the two -cutoff radius around the fourth neighbors in the cutoff function. - -In the formalism used here, {ξ0} is the energy -parameter. {ξ0} is in tight-binding approximation the -hopping integral between the hybridized orbitals of the cation and the -anion. In the literature we find many ways to write the hopping -integral depending on whether one takes the point of view of the anion -or cation. These are equivalent vision. The correspondence between the -two visions is explained in appendix A of the article in the -SrTiO3 "SMTB-Q_3"_#SMTB-Q_3 (parameter {β} shown in -this article is in fact the {βO}). To summarize the -relationship between the hopping integral {ξ0} and the -others, we have in an oxide CnOm the following -relationship: - -:c,image(Eqs/pair_smtbq3.jpg) - -Thus parameter μ, indicated above, is given by : μ = (√n -+ √m) ⁄ 2 - -The potential offers the possibility to consider the polarizability of -the electron clouds of oxygen by changing the slater radius of the -charge density around the oxygen atoms through the parameters {rBB, rB and -rS} in the ffield.SMTBQ.Syst. This change in radius is performed -according to the method developed by E. Maras -"SMTB-Q_2"_#SMTB-Q_2. This method needs to determine the number of -nearest neighbors around the oxygen. This calculation is based on -first ({r1n}) and second ({r2n}) distances -neighbors. - -The SMTB-Q potential is a variable charge potential. The equilibrium -charge on each atom is calculated by the electronegativity -equalization (QEq) method. See "Rick"_#Rick3 for further detail. One -can adjust the frequency, the maximum number of iterative loop and the -convergence of the equilibrium charge calculation. To obtain the -energy conservation in NVE thermodynamic ensemble, we recommend to use -a convergence parameter in the interval 10-5 - -10-6 eV. - -The ffield.SMTBQ.Syst files are provided for few systems. They consist -of nine parts and the lines beginning with '#' are comments (note that -the number of comment lines matter). The first sections are on the -potential parameters and others are on the simulation options and -might be modified. Keywords are character type and must be enclosed in -quotation marks (''). - -1) Number of different element in the oxide: - -Nelem= 2 or 3 -Divided line :ul - -2) Atomic parameters - -For the anion (oxygen) : - -Name of element (char) and stoichiometry in oxide -Formal charge and mass of element -Principal quantum number of outer orbital ({n}), electronegativity ({χ0i}) and hardness ({J0i}) - Ionic radius parameters : max coordination number ({coordBB} = 6 by default), bulk coordination number {(coordB)}, surface coordination number {(coordS)} and {rBB, rB and rS} the slater radius for each coordination number. (note : If you don't want to change the slater radius, use three identical radius values) -Number of orbital shared by the element in the oxide ({di}) -Divided line :ul - -For each cations (metal): - -Name of element (char) and stoichiometry in oxide -Formal charge and mass of element -Number of electron in outer orbital {(ne)}, electronegativity ({χ0i}), hardness ({J0i}) and {rSalter} the slater radius for the cation. -Number of orbitals shared by the elements in the oxide ({di}) -Divided line :ul - -3) Potential parameters: - -Keyword for element1, element2 and interaction potential ('second_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2. If the potential is 'second_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively. -Potential parameter: 

 If type of potential is 'second_moment' : {A (eV)}, {p}, {ξ0} (eV) and {q} 
 {rc1} (Å), {rc2} (Å) and {r0} (Å) 
 If type of potential is 'buck' : {C} (eV) and {ρ} (Å) 
 If type of potential is 'buckPlusAttr' : {C} (eV) and {ρ} (Å) 
 {D} (eV), {B} (Å-1), {r1OO} (Å) and {r2OO} (Å)
-Divided line :ul - -4) Tables parameters: - -Cutoff radius for the Coulomb interaction ({Rcoul}) -Starting radius ({rmin} = 1,18845 Å) and increments ({dr} = 0,001 Å) for creating the potential table. -Divided line :ul - -5) Rick model parameter: - -{Nevery} : parameter to set the frequency ({1/Nevery}) of the charge resolution. The charges are evaluated each {Nevery} time steps. -Max number of iterative loop ({loopmax}) and precision criterion ({prec}) in eV of the charge resolution -Divided line :ul - -6) Coordination parameter: - -First ({r1n}) and second ({r2n}) neighbor distances in Å -Divided line :ul - -7) Charge initialization mode: - -Keyword ({QInitMode}) and initial oxygen charge ({Qinit}). If keyword = 'true', all oxygen charges are initially set equal to {Qinit}. The charges on the cations are initially set in order to respect the neutrality of the box. If keyword = 'false', all atom charges are initially set equal to 0 if you use "create_atom"#create_atom command or the charge specified in the file structure using "read_data"_read_data.html command. -Divided line :ul - -8) Mode for the electronegativity equalization (Qeq) : - -Keyword mode: 
 
 QEqAll  (one QEq group) |   no parameters 
 QEqAllParallel (several QEq groups) |   no parameters 
 Surface |   zlim   (QEq only for z>zlim)
-Parameter if necessary -Divided line :ul - -9) Verbose : - -If you want the code to work in verbose mode or not : 'true' or 'false' -If you want to print or not in file 'Energy_component.txt' the three main contributions to the energy of the system according to the description presented above : 'true' or 'false' and {NEnergy}. This option writes in file every {NEnergy} time step. If the value is 'false' then {NEnergy} = 0. The file take into account the possibility to have several QEq group {g} then it writes: time step, number of atoms in group {g}, electrostatic part of energy, {EES}, the interaction between oxygen, {EOO}, and short range metal-oxygen interaction, {EMO}. -If you want to print in file 'Electroneg_component.txt' the electronegativity component ({∂Etot ⁄∂Qi}) or not: 'true' or 'false' and {NElectroneg}.This option writes in file every {NElectroneg} time step. If the value is 'false' then {NElectroneg} = 0. The file consist in atom number {i}, atom type (1 for oxygen and # higher than 1 for metal), atom position: {x}, {y} and {z}, atomic charge of atom {i}, electrostatic part of atom {i} electronegativity, covalent part of atom {i} electronegativity, the hopping integral of atom {i} {(Zβ2)i} and box electronegativity. :ul - -NOTE: This last option slows down the calculation dramatically. Use -only with a single processor simulation. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info:] - -This pair style does not support the "pair_modify"_pair_modify.html -mix, shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -needs to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restriction:] - -This pair style is part of the USER-SMTBQ package and is only enabled -if LAMMPS is built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This potential requires using atom type 1 for oxygen and atom type -higher than 1 for metal atoms. - -This pair style requires the "newton"_newton.html setting to be "on" -for pair interactions. - -The SMTB-Q potential files provided with LAMMPS (see the potentials -directory) are parameterized for metal "units"_units.html. - -:line - -[Citing this work:] - -Please cite related publication: N. Salles, O. Politano, E. Amzallag -and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189 - -:line - -:link(SMTB-Q_1) -[(SMTB-Q_1)] N. Salles, O. Politano, E. Amzallag, R. Tetot, -Comput. Mater. Sci. 111 (2016) 181-189 - -:link(SMTB-Q_2) -[(SMTB-Q_2)] E. Maras, N. Salles, R. Tetot, T. Ala-Nissila, -H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399 - -:link(SMTB-Q_3) -[(SMTB-Q_3)] R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface -Science 616, 19-8722 28 (2013) - -:link(Wolf2) -[(Wolf)] D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem -Phys, 110, 8254 (1999). - -:link(Rick3) -[(Rick)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 -(1994). diff --git a/doc/txt/pair_snap.txt b/doc/txt/pair_snap.txt deleted file mode 100644 index 37d1a1ed18..0000000000 --- a/doc/txt/pair_snap.txt +++ /dev/null @@ -1,217 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style snap command :h3 -pair_style snap/kk command :h3 - -[Syntax:] - -pair_style snap :pre - -[Examples:] - -pair_style snap -pair_coeff * * InP.snapcoeff InP.snapparam In In P P :pre - -[Description:] - -Pair style {snap} computes interactions using the spectral -neighbor analysis potential (SNAP) "(Thompson)"_#Thompson20142. -Like the GAP framework of Bartok et al. "(Bartok2010)"_#Bartok20102, -"(Bartok2013)"_#Bartok2013 which uses bispectrum components -to characterize the local neighborhood of each atom -in a very general way. The mathematical definition of the -bispectrum calculation used by SNAP is identical -to that used by "compute sna/atom"_compute_sna_atom.html. -In SNAP, the total energy is decomposed into a sum over -atom energies. The energy of atom {i} is -expressed as a weighted sum over bispectrum components. - -:c,image(Eqs/pair_snap.jpg) - -where {B_k^i} is the {k}-th bispectrum component of atom {i}, -and {beta_k^alpha_i} is the corresponding linear coefficient -that depends on {alpha_i}, the SNAP element of atom {i}. The -number of bispectrum components used and their definitions -depend on the value of {twojmax} -defined in the SNAP parameter file described below. -The bispectrum calculation is described in more detail -in "compute sna/atom"_compute_sna_atom.html. - -Note that unlike for other potentials, cutoffs for SNAP potentials are -not set in the pair_style or pair_coeff command; they are specified in -the SNAP potential files themselves. - -Only a single pair_coeff command is used with the {snap} style which -specifies a SNAP coefficient file followed by a SNAP parameter file -and then N additional arguments specifying the mapping of SNAP -elements to LAMMPS atom types, where N is the number of -LAMMPS atom types: - -SNAP coefficient file -SNAP parameter file -N element names = mapping of SNAP elements to atom types :ul - -As an example, if a LAMMPS indium phosphide simulation has 4 atoms -types, with the first two being indium and the 3rd and 4th being -phophorous, the pair_coeff command would look like this: - -pair_coeff * * snap InP.snapcoeff InP.snapparam In In P P :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The two filenames are for the coefficient and parameter files, respectively. -The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the -SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types -3 and 4 to the SNAP 'P' element. - -If a SNAP mapping value is -specified as NULL, the mapping is not performed. -This can be used when a {snap} potential is used as part of the -{hybrid} pair style. The NULL values are placeholders for atom types -that will be used with other potentials. - -The name of the SNAP coefficient file usually ends in the -".snapcoeff" extension. It may contain coefficients -for many SNAP elements. The only requirement is that it -contain at least those element names appearing in the -LAMMPS mapping list. -The name of the SNAP parameter file usually ends in the ".snapparam" -extension. It contains a small number -of parameters that define the overall form of the SNAP potential. -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for these files. - -Quite commonly, -SNAP potentials are combined with one or more other LAMMPS pair styles -using the {hybrid/overlay} pair style. As an example, the SNAP -tantalum potential provided in the LAMMPS potentials directory -combines the {snap} and {zbl} pair styles. It is invoked -by the following commands: - - variable zblcutinner equal 4 - variable zblcutouter equal 4.8 - variable zblz equal 73 - pair_style hybrid/overlay & - zbl $\{zblcutinner\} $\{zblcutouter\} snap - pair_coeff * * zbl 0.0 - pair_coeff 1 1 zbl $\{zblz\} - pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta :pre - -It is convenient to keep these commands in a separate file that can -be inserted in any LAMMPS input script using the "include"_include.html -command. - -The top of the SNAP coefficient file can contain any number of blank and comment lines (start with #), but follows a strict -format after that. The first non-blank non-comment -line must contain two integers: - -nelem = Number of elements -ncoeff = Number of coefficients :ul - -This is followed by one block for each of the {nelem} elements. -The first line of each block contains three entries: - -Element symbol (text string) -R = Element radius (distance units) -w = Element weight (dimensionless) :ul - -This line is followed by {ncoeff} coefficients, one per line. - -The SNAP parameter file can contain blank and comment lines (start -with #) anywhere. Each non-blank non-comment line must contain one -keyword/value pair. The required keywords are {rcutfac} and -{twojmax}. Optional keywords are {rfac0}, {rmin0}, -{switchflag}, and {bzeroflag}. - -The default values for these keywords are - -{rfac0} = 0.99363 -{rmin0} = 0.0 -{switchflag} = 0 -{bzeroflag} = 1 -{quadraticflag} = 1 :ul - -Detailed definitions for all the keywords are given on the "compute -sna/atom"_compute_sna_atom.html doc page. -If {quadraticflag} is set to 1, then the SNAP energy expression includes the quadratic term, -0.5*B^t.alpha.B, where alpha is a symmetric {K} by {K} matrix. -The SNAP element file should contain {K}({K}+1)/2 additional coefficients -for each element, the upper-triangular elements of alpha. - -NOTE: The previously used {diagonalstyle} keyword was removed in 2019, -since all known SNAP potentials use the default value of 3. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS with -user-specifiable parameters as described above. You never need to -specify a pair_coeff command with I != J arguments for this style. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This style is part of the SNAP package. It is only enabled if LAMMPS -was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"compute sna/atom"_compute_sna_atom.html, -"compute snad/atom"_compute_sna_atom.html, -"compute snav/atom"_compute_sna_atom.html - -[Default:] none - -:line - -:link(Thompson20142) -[(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316 (2015). - -:link(Bartok20102) -[(Bartok2010)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010). - -:link(Bartok2013) -[(Bartok2013)] Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013). diff --git a/doc/txt/pair_soft.txt b/doc/txt/pair_soft.txt deleted file mode 100644 index ca0266f34a..0000000000 --- a/doc/txt/pair_soft.txt +++ /dev/null @@ -1,135 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style soft command :h3 -pair_style soft/gpu command :h3 -pair_style soft/omp command :h3 - -[Syntax:] - -pair_style soft cutoff :pre - -cutoff = global cutoff for soft interactions (distance units) :ul - -[Examples:] - -pair_style soft 1.0 -pair_coeff * * 10.0 -pair_coeff 1 1 10.0 3.0 :pre - -pair_style soft 1.0 -pair_coeff * * 0.0 -variable prefactor equal ramp(0,30) -fix 1 all adapt 1 pair soft a * * v_prefactor :pre - -[Description:] - -Style {soft} computes pairwise interactions with the formula - -:c,image(Eqs/pair_soft.jpg) - -It is useful for pushing apart overlapping atoms, since it does not -blow up as r goes to 0. A is a pre-factor that can be made to vary in -time from the start to the end of the run (see discussion below), -e.g. to start with a very soft potential and slowly harden the -interactions over time. Rc is the cutoff. See the "fix -nve/limit"_fix_nve_limit.html command for another way to push apart -overlapping atoms. - -The following coefficients must be defined for each pair of atom types -via the "pair_coeff"_pair_coeff.html command as in the examples above, -or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -A (energy units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global soft -cutoff is used. - -NOTE: The syntax for "pair_coeff"_pair_coeff.html with a single A -coeff is different in the current version of LAMMPS than in older -versions which took two values, Astart and Astop, to ramp between -them. This functionality is now available in a more general form -through the "fix adapt"_fix_adapt.html command, as explained below. -Note that if you use an old input script and specify Astart and Astop -without a cutoff, then LAMMPS will interpret that as A and a cutoff, -which is probably not what you want. - -The "fix adapt"_fix_adapt.html command can be used to vary A for one -or more pair types over the course of a simulation, in which case -pair_coeff settings for A must still be specified, but will be -overridden. For example these commands will vary the prefactor A for -all pairwise interactions from 0.0 at the beginning to 30.0 at the end -of a run: - -variable prefactor equal ramp(0,30) -fix 1 all adapt 1 pair soft a * * v_prefactor :pre - -Note that a formula defined by an "equal-style variable"_variable.html -can use the current timestep, elapsed time in the current run, elapsed -time since the beginning of a series of runs, as well as access other -variables. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the A coefficient and cutoff -distance for this pair style can be mixed. A is always mixed via a -{geometric} rule. The cutoff is mixed according to the pair_modify -mix value. The default mix value is {geometric}. See the -"pair_modify" command for details. - -This pair style does not support the "pair_modify"_pair_modify.html -shift option, since the pair interaction goes to 0.0 at the cutoff. - -The "pair_modify"_pair_modify.html table and tail options are not -relevant for this pair style. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "fix nve/limit"_fix_nve_limit.html, "fix -adapt"_fix_adapt.html - -[Default:] none diff --git a/doc/txt/pair_sph_heatconduction.txt b/doc/txt/pair_sph_heatconduction.txt deleted file mode 100644 index 78a9cf2b63..0000000000 --- a/doc/txt/pair_sph_heatconduction.txt +++ /dev/null @@ -1,63 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style sph/heatconduction command :h3 - -[Syntax:] - -pair_style sph/heatconduction :pre - -[Examples:] - -pair_style sph/heatconduction -pair_coeff * * 1.0 2.4 :pre - -[Description:] - -The sph/heatconduction style computes heat transport between SPH particles. -The transport model is the diffusion equation for the internal energy. - -See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in -LAMMPS. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above. - -D diffusion coefficient (length^2/time units) -h kernel function cutoff (distance units) :ul - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -This style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This style does not write information to "binary restart -files"_restart.html. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. - -This style can only be used via the {pair} keyword of the "run_style -respa"_run_style.html command. It does not support the {inner}, -{middle}, {outer} keywords. - -[Restrictions:] - -This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, pair_sph/rhosum - -[Default:] none diff --git a/doc/txt/pair_sph_idealgas.txt b/doc/txt/pair_sph_idealgas.txt deleted file mode 100644 index 59513e7a73..0000000000 --- a/doc/txt/pair_sph_idealgas.txt +++ /dev/null @@ -1,77 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style sph/idealgas command :h3 - -[Syntax:] - -pair_style sph/idealgas :pre - -[Examples:] - -pair_style sph/idealgas -pair_coeff * * 1.0 2.4 :pre - -[Description:] - -The sph/idealgas style computes pressure forces between particles -according to the ideal gas equation of state: - -:c,image(Eqs/pair_sph_ideal.jpg) - -where gamma = 1.4 is the heat capacity ratio, rho is the local -density, and e is the internal energy per unit mass. This pair style -also computes Monaghan's artificial viscosity to prevent particles -from interpenetrating "(Monaghan)"_#ideal-Monoghan. - -See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in -LAMMPS. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above. - -nu artificial viscosity (no units) -h kernel function cutoff (distance units) :ul - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -This style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This style does not write information to "binary restart -files"_restart.html. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. - -This style can only be used via the {pair} keyword of the "run_style -respa"_run_style.html command. It does not support the {inner}, -{middle}, {outer} keywords. - -[Restrictions:] - -This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, pair_sph/rhosum - -[Default:] none - -:line - -:link(ideal-Monoghan) -[(Monaghan)] Monaghan and Gingold, Journal of Computational Physics, -52, 374-389 (1983). - diff --git a/doc/txt/pair_sph_lj.txt b/doc/txt/pair_sph_lj.txt deleted file mode 100644 index 43e77f1aae..0000000000 --- a/doc/txt/pair_sph_lj.txt +++ /dev/null @@ -1,79 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style sph/lj command :h3 - -[Syntax:] - -pair_style sph/lj :pre - -[Examples:] - -pair_style sph/lj -pair_coeff * * 1.0 2.4 :pre - -[Description:] - -The sph/lj style computes pressure forces between particles according -to the Lennard-Jones equation of state, which is computed according to -Ree's 1980 polynomial fit "(Ree)"_#Ree. The Lennard-Jones parameters -epsilon and sigma are set to unity. This pair style also computes -Monaghan's artificial viscosity to prevent particles from -interpenetrating "(Monaghan)"_#Monoghan. - -See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in -LAMMPS. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above. - -nu artificial viscosity (no units) -h kernel function cutoff (distance units) :ul - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -This style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This style does not write information to "binary restart -files"_restart.html. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. - -This style can only be used via the {pair} keyword of the "run_style -respa"_run_style.html command. It does not support the {inner}, -{middle}, {outer} keywords. - -[Restrictions:] - -As noted above, the Lennard-Jones parameters epsilon and sigma are set -to unity. - -This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, pair_sph/rhosum - -[Default:] none - -:line - -:link(Ree) -[(Ree)] Ree, Journal of Chemical Physics, 73, 5401 (1980). - -:link(Monoghan) -[(Monaghan)] Monaghan and Gingold, Journal of Computational Physics, -52, 374-389 (1983). diff --git a/doc/txt/pair_sph_rhosum.txt b/doc/txt/pair_sph_rhosum.txt deleted file mode 100644 index 9069176f29..0000000000 --- a/doc/txt/pair_sph_rhosum.txt +++ /dev/null @@ -1,64 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style sph/rhosum command :h3 - -[Syntax:] - -pair_style sph/rhosum Nstep :pre - -Nstep = timestep interval :ul - -[Examples:] - -pair_style sph/rhosum 10 -pair_coeff * * 2.4 :pre - -[Description:] - -The sph/rhosum style computes the local particle mass density rho for -SPH particles by kernel function interpolation, every Nstep timesteps. - -See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in -LAMMPS. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above. - -h (distance units) :ul - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -This style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This style does not write information to "binary restart -files"_restart.html. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. - -This style can only be used via the {pair} keyword of the "run_style -respa"_run_style.html command. It does not support the {inner}, -{middle}, {outer} keywords. - -[Restrictions:] - -This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, pair_sph/taitwater - -[Default:] none diff --git a/doc/txt/pair_sph_taitwater.txt b/doc/txt/pair_sph_taitwater.txt deleted file mode 100644 index dcb9e39603..0000000000 --- a/doc/txt/pair_sph_taitwater.txt +++ /dev/null @@ -1,79 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style sph/taitwater command :h3 - -[Syntax:] - -pair_style sph/taitwater :pre - -[Examples:] - -pair_style sph/taitwater -pair_coeff * * 1000.0 1430.0 1.0 2.4 :pre - -[Description:] - -The sph/taitwater style computes pressure forces between SPH particles -according to Tait's equation of state: - -:c,image(Eqs/pair_sph_tait.jpg) - -where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the -reference density and c_0 the reference speed of sound. - -This pair style also computes Monaghan's artificial viscosity to -prevent particles from interpenetrating "(Monaghan)"_#Monaghan. - -See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in -LAMMPS. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above. - -rho0 reference density (mass/volume units) -c0 reference soundspeed (distance/time units) -nu artificial viscosity (no units) -h kernel function cutoff (distance units) :ul - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -This style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This style does not write information to "binary restart -files"_restart.html. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. - -This style can only be used via the {pair} keyword of the "run_style -respa"_run_style.html command. It does not support the {inner}, -{middle}, {outer} keywords. - -[Restrictions:] - -This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, pair_sph/rhosum - -[Default:] none - -:line - -:link(Monaghan) -[(Monaghan)] Monaghan and Gingold, Journal of Computational Physics, -52, 374-389 (1983). diff --git a/doc/txt/pair_sph_taitwater_morris.txt b/doc/txt/pair_sph_taitwater_morris.txt deleted file mode 100644 index b88707d1af..0000000000 --- a/doc/txt/pair_sph_taitwater_morris.txt +++ /dev/null @@ -1,79 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style sph/taitwater/morris command :h3 - -[Syntax:] - -pair_style sph/taitwater/morris :pre - -[Examples:] - -pair_style sph/taitwater/morris -pair_coeff * * 1000.0 1430.0 1.0 2.4 :pre - -[Description:] - -The sph/taitwater/morris style computes pressure forces between SPH -particles according to Tait's equation of state: - -:c,image(Eqs/pair_sph_tait.jpg) - -where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the -reference density and c_0 the reference speed of sound. - -This pair style also computes laminar viscosity "(Morris)"_#Morris. - -See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in -LAMMPS. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above. - -rho0 reference density (mass/volume units) -c0 reference soundspeed (distance/time units) -nu dynamic viscosity (mass*distance/time units) -h kernel function cutoff (distance units) :ul - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -This style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This style does not write information to "binary restart -files"_restart.html. Thus, you need to re-specify the pair_style and -pair_coeff commands in an input script that reads a restart file. - -This style can only be used via the {pair} keyword of the "run_style -respa"_run_style.html command. It does not support the {inner}, -{middle}, {outer} keywords. - -[Restrictions:] - -This pair style is part of the USER-SPH package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, pair_sph/rhosum - -[Default:] none - -:line - -:link(Morris) -[(Morris)] Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997). - - diff --git a/doc/txt/pair_spin_dipole.txt b/doc/txt/pair_spin_dipole.txt deleted file mode 100644 index 36bcd25d5e..0000000000 --- a/doc/txt/pair_spin_dipole.txt +++ /dev/null @@ -1,82 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style spin/dipole/cut command :h3 -pair_style spin/dipole/long command :h3 - -[Syntax:] - -pair_style spin/dipole/cut cutoff -pair_style spin/dipole/long cutoff :pre - -cutoff = global cutoff for magnetic dipole energy and forces -(optional) (distance units) :ulb,l -:ule - -[Examples:] - -pair_style spin/dipole/cut 10.0 -pair_coeff * * 10.0 -pair_coeff 2 3 8.0 :pre - -pair_style spin/dipole/long 9.0 -pair_coeff * * 10.0 -pair_coeff 2 3 6.0 :pre - -[Description:] - -Style {spin/dipole/cut} computes a short-range dipole-dipole -interaction between pairs of magnetic particles that each -have a magnetic spin. -The magnetic dipole-dipole interactions are computed by the -following formulas for the magnetic energy, magnetic precession -vector omega and mechanical force between particles I and J. - -:c,image(Eqs/pair_spin_dipole.jpg) - -where si and sj are the spin on two magnetic particles, -r is their separation distance, and the vector e = (Ri - Rj)/|Ri - Rj| -is the direction vector between the two particles. - -Style {spin/dipole/long} computes long-range magnetic dipole-dipole -interaction. -A "kspace_style"_kspace_style.html must be defined to -use this pair style. Currently, "kspace_style -ewald/dipole/spin"_kspace_style.html and "kspace_style -pppm/dipole/spin"_kspace_style.html support long-range magnetic -dipole-dipole interactions. - -:line - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -[Restrictions:] - -The {spin/dipole/cut} and {spin/dipole/long} styles are part of -the SPIN package. They are only enabled if LAMMPS was built with that -package. See the "Build package"_Build_package.html doc page for more -info. - -Using dipole/spin pair styles with {electron} "units"_units.html is not -currently supported. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "kspace_style"_kspace_style.html -"fix nve/spin"_fix_nve_spin.html - -[Default:] none diff --git a/doc/txt/pair_spin_dmi.txt b/doc/txt/pair_spin_dmi.txt deleted file mode 100644 index cca20d1136..0000000000 --- a/doc/txt/pair_spin_dmi.txt +++ /dev/null @@ -1,91 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style spin/dmi command :h3 - -[Syntax:] - -pair_style spin/dmi cutoff :pre - -cutoff = global cutoff pair (distance in metal units) :ulb,l - -:ule - -[Examples:] - -pair_style spin/dmi 4.0 -pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0 -pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre - -[Description:] - -Style {spin/dmi} computes the Dzyaloshinskii-Moriya (DM) interaction -between pairs of magnetic spins. -According to the expression reported in "(Rohart)"_#Rohart, one has -the following DM energy: - -:c,image(Eqs/pair_spin_dmi_interaction.jpg) - -where si and sj are two neighboring magnetic spins of two particles, -eij = (ri - rj)/|ri-rj| is the unit vector between sites i and j, -and D is the DM vector defining the intensity (in eV) and the direction -of the interaction. - -In "(Rohart)"_#Rohart, D is defined as the direction normal to the film oriented -from the high spin-orbit layer to the magnetic ultra-thin film. - -The application of a spin-lattice Poisson bracket to this energy (as described -in "(Tranchida)"_#Tranchida5) allows to derive a magnetic torque omega, and a -mechanical force F (for spin-lattice calculations only) for each magnetic -particle i: - -:c,image(Eqs/pair_spin_dmi_forces.jpg) - -More details about the derivation of these torques/forces are reported in -"(Tranchida)"_#Tranchida5. - -For the {spin/dmi} pair style, the following coefficients must be defined for -each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in -the examples above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html commands, and -set in the following order: - -rc (distance units) -|D| (energy units) -Dx, Dy, Dz (direction of D) :ul - -Note that rc is the radius cutoff of the considered DM interaction, |D| is -the norm of the DM vector (in eV), and Dx, Dy and Dz define its direction. - -None of those coefficients is optional. If not specified, the {spin/dmi} -pair style cannot be used. - -:line - -[Restrictions:] - -All the {pair/spin} styles are part of the SPIN package. These styles -are only enabled if LAMMPS was built with this package, and if the -atom_style "spin" was declared. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, -"pair_eam"_pair_eam.html, - -[Default:] none - -:line - -:link(Rohart) -[(Rohart)] Rohart and Thiaville, -Physical Review B, 88(18), 184422. (2013). -:link(Tranchida5) -[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, -Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/txt/pair_spin_magelec.txt b/doc/txt/pair_spin_magelec.txt deleted file mode 100644 index 206da4bb51..0000000000 --- a/doc/txt/pair_spin_magelec.txt +++ /dev/null @@ -1,73 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style spin/magelec command :h3 - -[Syntax:] - -pair_style spin/magelec cutoff :pre - -cutoff = global cutoff pair (distance in metal units) :ulb,l - -:ule - -[Examples:] - -pair_style spin/magelec 4.5 -pair_coeff * * magelec 4.5 0.00109 1.0 1.0 1.0 :pre - -[Description:] - -Style {spin/me} computes a magneto-electric interaction between -pairs of magnetic spins. According to the derivation reported in -"(Katsura)"_#Katsura1, this interaction is defined as: - -:c,image(Eqs/pair_spin_me_interaction.jpg) - -where si and sj are neighboring magnetic spins of two particles, -eij = (ri - rj)/|ri-rj| is the normalized separation vector between the -two particles, and E is an electric polarization vector. -The norm and direction of E are giving the intensity and the -direction of a screened dielectric atomic polarization (in eV). - -From this magneto-electric interaction, each spin i will be submitted -to a magnetic torque omega, and its associated atom can be submitted to a -force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html), -such as: - -:c,image(Eqs/pair_spin_me_forces.jpg) - -with h the Planck constant (in metal units). - -More details about the derivation of these torques/forces are reported in -"(Tranchida)"_#Tranchida4. - -:line - -[Restrictions:] - -All the {pair/spin} styles are part of the SPIN package. These styles -are only enabled if LAMMPS was built with this package, and if the -atom_style "spin" was declared. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, -"pair_spin_exchange"_pair_spin_exchange.html, "pair_eam"_pair_eam.html, - -[Default:] none - -:line - -:link(Katsura1) -[(Katsura)] H. Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005) - -:link(Tranchida4) -[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson, -Journal of Computational Physics, 372, 406-425, (2018). diff --git a/doc/txt/pair_srp.txt b/doc/txt/pair_srp.txt deleted file mode 100644 index e784ac3d17..0000000000 --- a/doc/txt/pair_srp.txt +++ /dev/null @@ -1,168 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style srp command :h3 - -[Syntax:] - -pair_style srp cutoff btype dist keyword value ... - -cutoff = global cutoff for SRP interactions (distance units) :ulb,l -btype = bond type to apply SRP interactions to (can be wildcard, see below) :l -distance = {min} or {mid} :l -zero or more keyword/value pairs may be appended :l -keyword = {exclude} :l - {bptype} value = atom type for bond particles - {exclude} value = {yes} or {no} :pre -:ule - -[Examples:] - -pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes -pair_coeff 1 1 dpd 60.0 4.5 1.0 -pair_coeff 1 2 none -pair_coeff 2 2 srp 100.0 0.8 :pre - -pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes -pair_coeff 1 1 dpd 60.0 50 1.0 -pair_coeff 1 2 none -pair_coeff 2 2 srp 40.0 :pre - -pair_style hybrid srp 0.8 2 mid -pair_coeff 1 1 none -pair_coeff 1 2 none -pair_coeff 2 2 srp 100.0 0.8 :pre - -[Description:] - -Style {srp} computes a soft segmental repulsive potential (SRP) that -acts between pairs of bonds. This potential is useful for preventing -bonds from passing through one another when a soft non-bonded -potential acts between beads in, for example, DPD polymer chains. An -example input script that uses this command is provided in -examples/USER/srp. - -Bonds of specified type {btype} interact with one another through a -bond-pairwise potential, such that the force on bond {i} due to bond -{j} is as follows - -:c,image(Eqs/pair_srp1.jpg) - -where {r} and {rij} are the distance and unit vector between the two -bonds. Note that {btype} can be specified as an asterisk "*", which -case the interaction is applied to all bond types. The {mid} option -computes {r} and {rij} from the midpoint distance between bonds. The -{min} option computes {r} and {rij} from the minimum distance between -bonds. The force acting on a bond is mapped onto the two bond atoms -according to the lever rule, - -:c,image(Eqs/pair_srp2.jpg) - -where {L} is the normalized distance from the atom to the point of -closest approach of bond {i} and {j}. The {mid} option takes {L} as -0.5 for each interaction as described in "(Sirk)"_#Sirk2. - -The following coefficients must be defined via the -"pair_coeff"_pair_coeff.html command as in the examples above, or in -the data file or restart file read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -{C} (force units) -{rc} (distance units) :ul - -The last coefficient is optional. If not specified, the global cutoff -is used. - -NOTE: Pair style srp considers each bond of type {btype} to be a -fictitious "particle" of type {bptype}, where {bptype} is either the -largest atom type in the system, or the type set by the {bptype} flag. -Any actual existing particles with this atom type will be deleted at -the beginning of a run. This means you must specify the number of -types in your system accordingly; usually to be one larger than what -would normally be the case, e.g. via the "create_box"_create_box.html -or by changing the header in your "data file"_read_data.html. The -fictitious "bond particles" are inserted at the beginning of the run, -and serve as placeholders that define the position of the bonds. This -allows neighbor lists to be constructed and pairwise interactions to -be computed in almost the same way as is done for actual particles. -Because bonds interact only with other bonds, "pair_style -hybrid"_pair_hybrid.html should be used to turn off interactions -between atom type {bptype} and all other types of atoms. An error -will be flagged if "pair_style hybrid"_pair_hybrid.html is not used. - -The optional {exclude} keyword determines if forces are computed -between first neighbor (directly connected) bonds. For a setting of -{no}, first neighbor forces are computed; for {yes} they are not -computed. A setting of {no} cannot be used with the {min} option for -distance calculation because the minimum distance between directly -connected bonds is zero. - -Pair style {srp} turns off normalization of thermodynamic properties -by particle number, as if the command "thermo_modify norm -no"_thermo_modify.html had been issued. - -The pairwise energy associated with style {srp} is shifted to be zero -at the cutoff distance {rc}. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair styles does not support mixing. - -This pair style does not support the "pair_modify"_pair_modify.html -shift option for the energy of the pair interaction. Note that as -discussed above, the energy term is already shifted to be 0.0 at the -cutoff distance {rc}. - -The "pair_modify"_pair_modify.html table option is not relevant for -this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes global and per-atom information to "binary -restart files"_restart.html. Pair srp should be used with "pair_style -hybrid"_pair_hybrid.html, thus the pair_coeff commands need to be -specified in the input script when reading a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the USER-MISC package. It is only enabled -if LAMMPS was built with that package. See the Making LAMMPS section -for more info. - -This pair style must be used with "pair_style -hybrid"_pair_hybrid.html. - -This pair style requires the "newton"_newton.html command to be {on} -for non-bonded interactions. - -This pair style is not compatible with "rigid body integrators"_fix_rigid.html - -[Related commands:] - -"pair_style hybrid"_pair_hybrid.html, "pair_coeff"_pair_coeff.html, -"pair dpd"_pair_dpd.html - -[Default:] - -The default keyword value is exclude = yes. - -:line - -:link(Sirk2) -[(Sirk)] Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J -Chem Phys, 136 (13) 134903, 2012. diff --git a/doc/txt/pair_sw.txt b/doc/txt/pair_sw.txt deleted file mode 100644 index 33c3892c62..0000000000 --- a/doc/txt/pair_sw.txt +++ /dev/null @@ -1,215 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style sw command :h3 -pair_style sw/gpu command :h3 -pair_style sw/intel command :h3 -pair_style sw/kk command :h3 -pair_style sw/omp command :h3 - -[Syntax:] - -pair_style sw :pre - -[Examples:] - -pair_style sw -pair_coeff * * si.sw Si -pair_coeff * * GaN.sw Ga N Ga :pre - -[Description:] - -The {sw} style computes a 3-body "Stillinger-Weber"_#Stillinger2 -potential for the energy E of a system of atoms as - -:c,image(Eqs/pair_sw.jpg) - -where phi2 is a two-body term and phi3 is a three-body term. The -summations in the formula are over all neighbors J and K of atom I -within a cutoff distance = a*sigma. - -Only a single pair_coeff command is used with the {sw} style which -specifies a Stillinger-Weber potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of SW elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -As an example, imagine a file SiC.sw has Stillinger-Weber values for -Si and C. If your LAMMPS simulation has 4 atoms types and you want -the 1st 3 to be Si, and the 4th to be C, you would use the following -pair_coeff command: - -pair_coeff * * SiC.sw Si Si Si C :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to the Si -element in the SW file. The final C argument maps LAMMPS atom type 4 -to the C element in the SW file. If a mapping value is specified as -NULL, the mapping is not performed. This can be used when a {sw} -potential is used as part of the {hybrid} pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. - -Stillinger-Weber files in the {potentials} directory of the LAMMPS -distribution have a ".sw" suffix. Lines that are not blank or -comments (starting with #) define parameters for a triplet of -elements. The parameters in a single entry correspond to the two-body -and three-body coefficients in the formula above: - -element 1 (the center atom in a 3-body interaction) -element 2 -element 3 -epsilon (energy units) -sigma (distance units) -a -lambda -gamma -costheta0 -A -B -p -q -tol :ul - -The A, B, p, and q parameters are used only for two-body -interactions. The lambda and costheta0 parameters are used only for -three-body interactions. The epsilon, sigma and a parameters are used -for both two-body and three-body interactions. gamma is used only in the -three-body interactions, but is defined for pairs of atoms. -The non-annotated parameters are unitless. - -LAMMPS introduces an additional performance-optimization parameter tol -that is used for both two-body and three-body interactions. In the -Stillinger-Weber potential, the interaction energies become negligibly -small at atomic separations substantially less than the theoretical -cutoff distances. LAMMPS therefore defines a virtual cutoff distance -based on a user defined tolerance tol. The use of the virtual cutoff -distance in constructing atom neighbor lists can significantly reduce -the neighbor list sizes and therefore the computational cost. LAMMPS -provides a {tol} value for each of the three-body entries so that they -can be separately controlled. If tol = 0.0, then the standard -Stillinger-Weber cutoff is used. - -The Stillinger-Weber potential file must contain entries for all the -elements listed in the pair_coeff command. It can also contain -entries for additional elements not being used in a particular -simulation; LAMMPS ignores those entries. - -For a single-element simulation, only a single entry is required -(e.g. SiSiSi). For a two-element simulation, the file must contain 8 -entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that -specify SW parameters for all permutations of the two elements -interacting in three-body configurations. Thus for 3 elements, 27 -entries would be required, etc. - -As annotated above, the first element in the entry is the center atom -in a three-body interaction. Thus an entry for SiCC means a Si atom -with 2 C atoms as neighbors. The parameter values used for the -two-body interaction come from the entry where the 2nd and 3rd -elements are the same. Thus the two-body parameters for Si -interacting with C, comes from the SiCC entry. The three-body -parameters can in principle be specific to the three elements of the -configuration. In the literature, however, the three-body parameters -are usually defined by simple formulas involving two sets of pair-wise -parameters, corresponding to the ij and ik pairs, where i is the -center atom. The user must ensure that the correct combining rule is -used to calculate the values of the three-body parameters for -alloys. Note also that the function phi3 contains two exponential -screening factors with parameter values from the ij pair and ik -pairs. So phi3 for a C atom bonded to a Si atom and a second C atom -will depend on the three-body parameters for the CSiC entry, and also -on the two-body parameters for the CCC and CSiSi entries. Since the -order of the two neighbors is arbitrary, the three-body parameters for -entries CSiC and CCSi should be the same. Similarly, the two-body -parameters for entries SiCC and CSiSi should also be the same. The -parameters used only for two-body interactions (A, B, p, and q) in -entries whose 2nd and 3rd element are different (e.g. SiCSi) are not -used for anything and can be set to 0.0 if desired. -This is also true for the parameters in phi3 that are -taken from the ij and ik pairs (sigma, a, gamma) - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -When using the USER-INTEL package with this style, there is an -additional 5 to 10 percent performance improvement when the -Stillinger-Weber parameters p and q are set to 4 and 0 respectively. -These parameters are common for modeling silicon and water. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above from values in the potential file. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair style requires the "newton"_newton.html setting to be "on" -for pair interactions. - -The Stillinger-Weber potential files provided with LAMMPS (see the -potentials directory) are parameterized for metal "units"_units.html. -You can use the SW potential with any LAMMPS units, but you would need -to create your own SW potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Stillinger2) -[(Stillinger)] Stillinger and Weber, Phys Rev B, 31, 5262 (1985). diff --git a/doc/txt/pair_table.txt b/doc/txt/pair_table.txt deleted file mode 100644 index 22c63a1f32..0000000000 --- a/doc/txt/pair_table.txt +++ /dev/null @@ -1,271 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style table command :h3 -pair_style table/gpu command :h3 -pair_style table/kk command :h3 -pair_style table/omp command :h3 - -[Syntax:] - -pair_style table style N keyword ... :pre - -style = {lookup} or {linear} or {spline} or {bitmap} = method of interpolation -N = use N values in {lookup}, {linear}, {spline} tables -N = use 2^N values in {bitmap} tables -zero or more keywords may be appended -keyword = {ewald} or {pppm} or {msm} or {dispersion} or {tip4p} :ul - -[Examples:] - -pair_style table linear 1000 -pair_style table linear 1000 pppm -pair_style table bitmap 12 -pair_coeff * 3 morse.table ENTRY1 -pair_coeff * 3 morse.table ENTRY1 7.0 :pre - -[Description:] - -Style {table} creates interpolation tables from potential energy and -force values listed in a file(s) as a function of distance. When -performing dynamics or minimization, the interpolation tables are used -to evaluate energy and forces for pairwise interactions between -particles, similar to how analytic formulas are used for other pair -styles. - -The interpolation tables are created as a pre-computation by fitting -cubic splines to the file values and interpolating energy and force -values at each of {N} distances. During a simulation, the tables are -used to interpolate energy and force values as needed for each pair of -particles separated by a distance {R}. The interpolation is done in -one of 4 styles: {lookup}, {linear}, {spline}, or {bitmap}. - -For the {lookup} style, the distance {R} is used to find the nearest -table entry, which is the energy or force. - -For the {linear} style, the distance {R} is used to find the 2 -surrounding table values from which an energy or force is computed by -linear interpolation. - -For the {spline} style, a cubic spline coefficients are computed and -stored for each of the {N} values in the table, one set of splines for -energy, another for force. Note that these splines are different than -the ones used to pre-compute the {N} values. Those splines were fit -to the {Nfile} values in the tabulated file, where often {Nfile} < -{N}. The distance {R} is used to find the appropriate set of spline -coefficients which are used to evaluate a cubic polynomial which -computes the energy or force. - -For the {bitmap} style, the specified {N} is used to create -interpolation tables that are 2^N in length. The distance {R} is used -to index into the table via a fast bit-mapping technique due to -"(Wolff)"_#Wolff2, and a linear interpolation is performed between -adjacent table values. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above. - -filename -keyword -cutoff (distance units) :ul - -The filename specifies a file containing tabulated energy and force -values. The keyword specifies a section of the file. The cutoff is -an optional coefficient. If not specified, the outer cutoff in the -table itself (see below) will be used to build an interpolation table -that extend to the largest tabulated distance. If specified, only -file values up to the cutoff are used to create the interpolation -table. The format of this file is described below. - -If your tabulated potential(s) are designed to be used as the -short-range part of one of the long-range solvers specified by the -"kspace_style"_kspace_style.html command, then you must use one or -more of the optional keywords listed above for the pair_style command. -These are {ewald} or {pppm} or {msm} or {dispersion} or {tip4p}. This -is so LAMMPS can insure the short-range potential and long-range -solver are compatible with each other, as it does for other -short-range pair styles, such as "pair_style -lj/cut/coul/long"_pair_lj.html. Note that it is up to you to insure -the tabulated values for each pair of atom types has the correct -functional form to be compatible with the matching long-range solver. - -:line - -Here are some guidelines for using the pair_style table command to -best effect: - -Vary the number of table points; you may need to use more than you think -to get good resolution. :ulb,l - -Always use the "pair_write"_pair_write.html command to produce a plot -of what the final interpolated potential looks like. This can show up -interpolation "features" you may not like. :l - -Start with the linear style; it's the style least likely to have problems. :l - -Use {N} in the pair_style command equal to the "N" in the tabulation -file, and use the "RSQ" or "BITMAP" parameter, so additional interpolation -is not needed. See discussion below. :l - -Make sure that your tabulated forces and tabulated energies are -consistent (dE/dr = -F) over the entire range of r values. LAMMPS -will warn if this is not the case. :l - -Use as large an inner cutoff as possible. This avoids fitting splines -to very steep parts of the potential. :l -:ule - -:line - -The format of a tabulated file is a series of one or more sections, -defined as follows (without the parenthesized comments): - -# Morse potential for Fe (one or more comment or blank lines) :pre - -MORSE_FE (keyword is first text on line) -N 500 R 1.0 10.0 (N, R, RSQ, BITMAP, FPRIME parameters) - (blank) -1 1.0 25.5 102.34 (index, r, energy, force) -2 1.02 23.4 98.5 -... -500 10.0 0.001 0.003 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the pair_coeff -command. The next line lists (in any order) one or more parameters -for the table. Each parameter is a keyword followed by one or more -numeric values. - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the {N} -specified in the "pair_style table"_pair_style.html command. Let -Ntable = {N} in the pair_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate energy and force values at Ntable different -points. The resulting tables of length Ntable are then used as -described above, when computing energy and force for individual pair -distances. This means that if you want the interpolation tables of -length Ntable to match exactly what is in the tabulated file (with -effectively no preliminary interpolation), you should set Ntable = -Nfile, and use the "RSQ" or "BITMAP" parameter. This is because the -internal table abscissa is always RSQ (separation distance squared), -for efficient lookup. - -All other parameters are optional. If "R" or "RSQ" or "BITMAP" does -not appear, then the distances in each line of the table are used -as-is to perform spline interpolation. In this case, the table values -can be spaced in {r} uniformly or however you wish to position table -values in regions of large gradients. - -If used, the parameters "R" or "RSQ" are followed by 2 values {rlo} -and {rhi}. If specified, the distance associated with each energy and -force value is computed from these 2 values (at high accuracy), rather -than using the (low-accuracy) value listed in each line of the table. -The distance values in the table file are ignored in this case. -For "R", distances uniformly spaced between {rlo} and {rhi} are -computed; for "RSQ", squared distances uniformly spaced between -{rlo*rlo} and {rhi*rhi} are computed. - -NOTE: If you use "R" or "RSQ", the tabulated distance values in the -file are effectively ignored, and replaced by new values as described -in the previous paragraph. If the distance value in the table is not -very close to the new value (i.e. round-off difference), then you will -be assigning energy/force values to a different distance, which is -probably not what you want. LAMMPS will warn if this is occurring. - -If used, the parameter "BITMAP" is also followed by 2 values {rlo} and -{rhi}. These values, along with the "N" value determine the ordering -of the N lines that follow and what distance is associated with each. -This ordering is complex, so it is not documented here, since this -file is typically produced by the "pair_write"_pair_write.html command -with its {bitmap} option. When the table is in BITMAP format, the "N" -parameter in the file must be equal to 2^M where M is the value -specified in the pair_style command. Also, a cutoff parameter cannot -be used as an optional 3rd argument in the pair_coeff command; the -entire table extent as specified in the file must be used. - -If used, the parameter "FPRIME" is followed by 2 values {fplo} and -{fphi} which are the derivative of the force at the innermost and -outermost distances listed in the table. These values are needed by -the spline construction routines. If not specified by the "FPRIME" -parameter, they are estimated (less accurately) by the first 2 and -last 2 force values in the table. This parameter is not used by -BITMAP tables. - -Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -r (in distance units), the 3rd value is the energy (in energy units), -and the 4th is the force (in force units). The r values must increase -from one line to the next (unless the BITMAP parameter is specified). - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -The "pair_modify"_pair_modify.html shift, table, and tail options are -not relevant for this pair style. - -This pair style writes the settings for the "pair_style table" command -to "binary restart files"_restart.html, so a pair_style command does -not need to specified in an input script that reads a restart file. -However, the coefficient information is not stored in the restart -file, since it is tabulated in the potential files. Thus, pair_coeff -commands do need to be specified in the restart input script. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_write"_pair_write.html - -[Default:] none - -:line - -:link(Wolff2) -[(Wolff)] Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). diff --git a/doc/txt/pair_table_rx.txt b/doc/txt/pair_table_rx.txt deleted file mode 100644 index 9b9a6abff8..0000000000 --- a/doc/txt/pair_table_rx.txt +++ /dev/null @@ -1,264 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style table/rx command :h3 -pair_style table/rx/kk command :h3 - -[Syntax:] - -pair_style table style N ... :pre - -style = {lookup} or {linear} or {spline} or {bitmap} = method of interpolation -N = use N values in {lookup}, {linear}, {spline} tables -weighting = fractional or molecular (optional) :ul - -[Examples:] - -pair_style table/rx linear 1000 -pair_style table/rx linear 1000 fractional -pair_style table/rx linear 1000 molecular -pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0 -pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0 -pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0 :pre - -[Description:] - -Style {table/rx} is used in reaction DPD simulations,where the -coarse-grained (CG) particles are composed of {m} species whose -reaction rate kinetics are determined from a set of {n} reaction rate -equations through the "fix rx"_fix_rx.html command. The species of -one CG particle can interact with a species in a neighboring CG -particle through a site-site interaction potential model. Style -{table/rx} creates interpolation tables of length {N} from pair -potential and force values listed in a file(s) as a function of -distance. The files are read by the "pair_coeff"_pair_coeff.html -command. - -The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and force values at each of {N} -distances. During a simulation, these tables are used to interpolate -energy and force values as needed. The interpolation is done in one -of 4 styles: {lookup}, {linear}, {spline}, or {bitmap}. - -For the {lookup} style, the distance between 2 atoms is used to find -the nearest table entry, which is the energy or force. - -For the {linear} style, the pair distance is used to find 2 -surrounding table values from which an energy or force is computed by -linear interpolation. - -For the {spline} style, a cubic spline coefficients are computed and -stored at each of the {N} values in the table. The pair distance is -used to find the appropriate set of coefficients which are used to -evaluate a cubic polynomial which computes the energy or force. - -For the {bitmap} style, the N means to create interpolation tables -that are 2^N in length. The pair distance is used to index into the -table via a fast bit-mapping technique "(Wolff)"_#Wolff and a linear -interpolation is performed between adjacent table values. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above. - -filename -keyword -species1 -species2 -cutoff (distance units) :ul - -The filename specifies a file containing tabulated energy and force -values. The keyword specifies a section of the file. The cutoff is -an optional coefficient. If not specified, the outer cutoff in the -table itself (see below) will be used to build an interpolation table -that extend to the largest tabulated distance. If specified, only -file values up to the cutoff are used to create the interpolation -table. The format of this file is described below. - -The species tags define the site-site interaction potential between -two species contained within two different particles. The species -tags must either correspond to the species defined in the reaction -kinetics files specified with the "fix rx"_fix_rx.html command or they -must correspond to the tag "1fluid", signifying interaction with a -product species mixture determined through a one-fluid approximation. -The interaction potential is weighted by the geometric average of -either the mole fraction concentrations or the number of molecules -associated with the interacting coarse-grained particles (see the -{fractional} or {molecular} weighting pair style options). The coarse-grained potential is -stored before and after the reaction kinetics solver is applied, where -the difference is defined to be the internal chemical energy (uChem). - -:line - -Here are some guidelines for using the pair_style table/rx command to -best effect: - -Vary the number of table points; you may need to use more than you think -to get good resolution. :ulb,l - -Always use the "pair_write"_pair_write.html command to produce a plot -of what the final interpolated potential looks like. This can show up -interpolation "features" you may not like. :l - -Start with the linear style; it's the style least likely to have problems. :l - -Use {N} in the pair_style command equal to the "N" in the tabulation -file, and use the "RSQ" or "BITMAP" parameter, so additional interpolation -is not needed. See discussion below. :l - -Make sure that your tabulated forces and tabulated energies are consistent -(dE/dr = -F) along the entire range of r values. :l - -Use as large an inner cutoff as possible. This avoids fitting splines -to very steep parts of the potential. :l -:ule - -:line - -The format of a tabulated file is a series of one or more sections, -defined as follows (without the parenthesized comments): - -# Morse potential for Fe (one or more comment or blank lines) :pre - -MORSE_FE (keyword is first text on line) -N 500 R 1.0 10.0 (N, R, RSQ, BITMAP, FPRIME parameters) - (blank) -1 1.0 25.5 102.34 (index, r, energy, force) -2 1.02 23.4 98.5 -... -500 10.0 0.001 0.003 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the pair_coeff -command. The next line lists (in any order) one or more parameters -for the table. Each parameter is a keyword followed by one or more -numeric values. - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the {N} -specified in the "pair_style table/rx"_pair_style.html command. Let -Ntable = {N} in the pair_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate as needed to generate energy and force -values at Ntable different points. The resulting tables of length -Ntable are then used as described above, when computing energy and -force for individual pair distances. This means that if you want the -interpolation tables of length Ntable to match exactly what is in the -tabulated file (with effectively no preliminary interpolation), you -should set Ntable = Nfile, and use the "RSQ" or "BITMAP" parameter. -The internal table abscissa is RSQ (separation distance squared). - -All other parameters are optional. If "R" or "RSQ" or "BITMAP" does -not appear, then the distances in each line of the table are used -as-is to perform spline interpolation. In this case, the table values -can be spaced in {r} uniformly or however you wish to position table -values in regions of large gradients. - -If used, the parameters "R" or "RSQ" are followed by 2 values {rlo} -and {rhi}. If specified, the distance associated with each energy and -force value is computed from these 2 values (at high accuracy), rather -than using the (low-accuracy) value listed in each line of the table. -The distance values in the table file are ignored in this case. -For "R", distances uniformly spaced between {rlo} and {rhi} are -computed; for "RSQ", squared distances uniformly spaced between -{rlo*rlo} and {rhi*rhi} are computed. - -If used, the parameter "BITMAP" is also followed by 2 values {rlo} and -{rhi}. These values, along with the "N" value determine the ordering -of the N lines that follow and what distance is associated with each. -This ordering is complex, so it is not documented here, since this -file is typically produced by the "pair_write"_pair_write.html command -with its {bitmap} option. When the table is in BITMAP format, the "N" -parameter in the file must be equal to 2^M where M is the value -specified in the pair_style command. Also, a cutoff parameter cannot -be used as an optional 3rd argument in the pair_coeff command; the -entire table extent as specified in the file must be used. - -If used, the parameter "FPRIME" is followed by 2 values {fplo} and -{fphi} which are the derivative of the force at the innermost and -outermost distances listed in the table. These values are needed by -the spline construction routines. If not specified by the "FPRIME" -parameter, they are estimated (less accurately) by the first 2 and -last 2 force values in the table. This parameter is not used by -BITMAP tables. - -Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -r (in distance units), the 3rd value is the energy (in energy units), -and the 4th is the force (in force units). The r values must increase -from one line to the next (unless the BITMAP parameter is specified). - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -The "pair_modify"_pair_modify.html shift, table, and tail options are -not relevant for this pair style. - -This pair style writes the settings for the "pair_style table/rx" command -to "binary restart files"_restart.html, so a pair_style command does -not need to specified in an input script that reads a restart file. -However, the coefficient information is not stored in the restart -file, since it is tabulated in the potential files. Thus, pair_coeff -commands do need to be specified in the restart input script. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This command is part of the USER-DPD package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] fractional weighting - -:line - -:link(Wolff) -[(Wolff)] Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). diff --git a/doc/txt/pair_tersoff.txt b/doc/txt/pair_tersoff.txt deleted file mode 100644 index 4b7bb0d93d..0000000000 --- a/doc/txt/pair_tersoff.txt +++ /dev/null @@ -1,252 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style tersoff command :h3 -pair_style tersoff/table command :h3 -pair_style tersoff/gpu command :h3 -pair_style tersoff/intel command :h3 -pair_style tersoff/kk command :h3 -pair_style tersoff/omp command :h3 -pair_style tersoff/table/omp command :h3 - -[Syntax:] - -pair_style style :pre - -style = {tersoff} or {tersoff/table} or {tersoff/gpu} or {tersoff/omp} or {tersoff/table/omp} :ul - -[Examples:] - -pair_style tersoff -pair_coeff * * Si.tersoff Si -pair_coeff * * SiC.tersoff Si C Si :pre - -pair_style tersoff/table -pair_coeff * * SiCGe.tersoff Si(D) :pre - -[Description:] - -The {tersoff} style computes a 3-body Tersoff potential -"(Tersoff_1)"_#Tersoff_11 for the energy E of a system of atoms as - -:c,image(Eqs/pair_tersoff_1.jpg) - -where f_R is a two-body term and f_A includes three-body interactions. -The summations in the formula are over all neighbors J and K of atom I -within a cutoff distance = R + D. - -The {tersoff/table} style uses tabulated forms for the two-body, -environment and angular functions. Linear interpolation is performed -between adjacent table entries. The table length is chosen to be -accurate within 10^-6 with respect to the {tersoff} style energy. -The {tersoff/table} should give better performance in terms of speed. - -Only a single pair_coeff command is used with the {tersoff} style -which specifies a Tersoff potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of Tersoff elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -As an example, imagine the SiC.tersoff file has Tersoff values for Si -and C. If your LAMMPS simulation has 4 atoms types and you want the -1st 3 to be Si, and the 4th to be C, you would use the following -pair_coeff command: - -pair_coeff * * SiC.tersoff Si Si Si C :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to the Si -element in the Tersoff file. The final C argument maps LAMMPS atom -type 4 to the C element in the Tersoff file. If a mapping value is -specified as NULL, the mapping is not performed. This can be used -when a {tersoff} potential is used as part of the {hybrid} pair style. -The NULL values are placeholders for atom types that will be used with -other potentials. - -Tersoff files in the {potentials} directory of the LAMMPS distribution -have a ".tersoff" suffix. Lines that are not blank or comments -(starting with #) define parameters for a triplet of elements. The -parameters in a single entry correspond to coefficients in the formula -above: - -element 1 (the center atom in a 3-body interaction) -element 2 (the atom bonded to the center atom) -element 3 (the atom influencing the 1-2 bond in a bond-order sense) -m -gamma -lambda3 (1/distance units) -c -d -costheta0 (can be a value < -1 or > 1) -n -beta -lambda2 (1/distance units) -B (energy units) -R (distance units) -D (distance units) -lambda1 (1/distance units) -A (energy units) :ul - -The n, beta, lambda2, B, lambda1, and A parameters are only used for -two-body interactions. The m, gamma, lambda3, c, d, and costheta0 -parameters are only used for three-body interactions. The R and D -parameters are used for both two-body and three-body interactions. The -non-annotated parameters are unitless. The value of m must be 3 or 1. - -The Tersoff potential file must contain entries for all the elements -listed in the pair_coeff command. It can also contain entries for -additional elements not being used in a particular simulation; LAMMPS -ignores those entries. - -For a single-element simulation, only a single entry is required -(e.g. SiSiSi). For a two-element simulation, the file must contain 8 -entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that -specify Tersoff parameters for all permutations of the two elements -interacting in three-body configurations. Thus for 3 elements, 27 -entries would be required, etc. - -As annotated above, the first element in the entry is the center atom -in a three-body interaction and it is bonded to the 2nd atom and the -bond is influenced by the 3rd atom. Thus an entry for SiCC means Si -bonded to a C with another C atom influencing the bond. Thus -three-body parameters for SiCSi and SiSiC entries will not, in -general, be the same. The parameters used for the two-body -interaction come from the entry where the 2nd element is repeated. -Thus the two-body parameters for Si interacting with C, comes from the -SiCC entry. - -The parameters used for a particular -three-body interaction come from the entry with the corresponding -three elements. The parameters used only for two-body interactions -(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd -element are different (e.g. SiCSi) are not used for anything and can -be set to 0.0 if desired. - -Note that the twobody parameters in entries such as SiCC and CSiSi -are often the same, due to the common use of symmetric mixing rules, -but this is not always the case. For example, the beta and n parameters in -Tersoff_2 "(Tersoff_2)"_#Tersoff_21 are not symmetric. - -We chose the above form so as to enable users to define all commonly -used variants of the Tersoff potential. In particular, our form -reduces to the original Tersoff form when m = 3 and gamma = 1, while -it reduces to the form of "Albe et al."_#Albe when beta = 1 and m = 1. -Note that in the current Tersoff implementation in LAMMPS, m must be -specified as either 3 or 1. Tersoff used a slightly different but -equivalent form for alloys, which we will refer to as Tersoff_2 -potential "(Tersoff_2)"_#Tersoff_21. The {tersoff/table} style implements -Tersoff_2 parameterization only. - -LAMMPS parameter values for Tersoff_2 can be obtained as follows: -gamma_ijk = omega_ik, lambda3 = 0 and the value of -m has no effect. The parameters for species i and j can be calculated -using the Tersoff_2 mixing rules: - -:c,image(Eqs/pair_tersoff_2.jpg) - -Tersoff_2 parameters R and S must be converted to the LAMMPS -parameters R and D (R is different in both forms), using the following -relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the -Tersoff_2 parameters. - -In the potentials directory, the file SiCGe.tersoff provides the -LAMMPS parameters for Tersoff's various versions of Si, as well as his -alloy parameters for Si, C, and Ge. This file can be used for pure Si, -(three different versions), pure C, pure Ge, binary SiC, and binary -SiGe. LAMMPS will generate an error if this file is used with any -combination involving C and Ge, since there are no entries for the GeC -interactions (Tersoff did not publish parameters for this -cross-interaction.) Tersoff files are also provided for the SiC alloy -(SiC.tersoff) and the GaN (GaN.tersoff) alloys. - -Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou -for helping clarify how Tersoff parameters for alloys have been -defined in various papers. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above from values in the potential file. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair style requires the "newton"_newton.html setting to be "on" -for pair interactions. - -The Tersoff potential files provided with LAMMPS (see the potentials -directory) are parameterized for metal "units"_units.html. You can -use the Tersoff potential with any LAMMPS units, but you would need to -create your own Tersoff potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Tersoff_11) -[(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988). - -:link(Albe) -[(Albe)] J. Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: -Condens. Matter, 15, 5649(2003). - -:link(Tersoff_21) -[(Tersoff_2)] J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248) diff --git a/doc/txt/pair_tersoff_mod.txt b/doc/txt/pair_tersoff_mod.txt deleted file mode 100644 index 2df23045a3..0000000000 --- a/doc/txt/pair_tersoff_mod.txt +++ /dev/null @@ -1,206 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style tersoff/mod command :h3 -pair_style tersoff/mod/c command :h3 -pair_style tersoff/mod/gpu command :h3 -pair_style tersoff/mod/kk command :h3 -pair_style tersoff/mod/omp command :h3 -pair_style tersoff/mod/c/omp command :h3 - -[Syntax:] - -pair_style tersoff/mod :pre - -pair_style tersoff/mod/c :pre - -[Examples:] - -pair_style tersoff/mod -pair_coeff * * Si.tersoff.mod Si Si :pre - -pair_style tersoff/mod/c -pair_coeff * * Si.tersoff.modc Si Si :pre - -[Description:] - -The {tersoff/mod} and {tersoff/mod/c} styles computes a bond-order type -interatomic potential "(Kumagai)"_#Kumagai based on a 3-body Tersoff -potential "(Tersoff_1)"_#Tersoff_12, "(Tersoff_2)"_#Tersoff_22 with -modified cutoff function and angular-dependent term, giving the energy -E of a system of atoms as - -:c,image(Eqs/pair_tersoff_mod.jpg) - -where f_R is a two-body term and f_A includes three-body interactions. -The summations in the formula are over all neighbors J and K of atom I -within a cutoff distance = R + D. -The {tersoff/mod/c} style differs from {tersoff/mod} only in the -formulation of the V_ij term, where it contains an additional c0 term. - -:c,image(Eqs/pair_tersoff_mod_c.jpg) - -The modified cutoff function f_C proposed by "(Murty)"_#Murty and -having a continuous second-order differential is employed. The -angular-dependent term g(theta) was modified to increase the -flexibility of the potential. - -The {tersoff/mod} potential is fitted to both the elastic constants -and melting point by employing the modified Tersoff potential function -form in which the angular-dependent term is improved. The model -performs extremely well in describing the crystalline, liquid, and -amorphous phases "(Schelling)"_#Schelling. - -Only a single pair_coeff command is used with the {tersoff/mod} style -which specifies a Tersoff/MOD potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of Tersoff/MOD elements to atom types :ul - -As an example, imagine the Si.tersoff_mod file has Tersoff values for Si. -If your LAMMPS simulation has 3 Si atoms types, you would use the following -pair_coeff command: - -pair_coeff * * Si.tersoff_mod Si Si Si :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The three Si arguments map LAMMPS atom types 1,2,3 to the Si element -in the Tersoff/MOD file. If a mapping value is specified as NULL, the -mapping is not performed. This can be used when a {tersoff/mod} -potential is used as part of the {hybrid} pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. - -Tersoff/MOD file in the {potentials} directory of the LAMMPS -distribution have a ".tersoff.mod" suffix. Potential files for the -{tersoff/mod/c} style have the suffix ".tersoff.modc". Lines that are -not blank or comments (starting with #) define parameters for a triplet -of elements. The parameters in a single entry correspond to -coefficients in the formulae above: - -element 1 (the center atom in a 3-body interaction) -element 2 (the atom bonded to the center atom) -element 3 (the atom influencing the 1-2 bond in a bond-order sense) -beta -alpha -h -eta -beta_ters = 1 (dummy parameter) -lambda2 (1/distance units) -B (energy units) -R (distance units) -D (distance units) -lambda1 (1/distance units) -A (energy units) -n -c1 -c2 -c3 -c4 -c5 -c0 (energy units, tersoff/mod/c only):ul - -The n, eta, lambda2, B, lambda1, and A parameters are only used for -two-body interactions. The beta, alpha, c1, c2, c3, c4, c5, h -parameters are only used for three-body interactions. The R and D -parameters are used for both two-body and three-body interactions. -The c0 term applies to {tersoff/mod/c} only. The non-annotated -parameters are unitless. - -The Tersoff/MOD potential file must contain entries for all the elements -listed in the pair_coeff command. It can also contain entries for -additional elements not being used in a particular simulation; LAMMPS -ignores those entries. - -For a single-element simulation, only a single entry is required -(e.g. SiSiSi). As annotated above, the first element in the entry is -the center atom in a three-body interaction and it is bonded to the -2nd atom and the bond is influenced by the 3rd atom. Thus an entry -for SiSiSi means Si bonded to a Si with another Si atom influencing the bond. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair style requires the "newton"_newton.html setting to be "on" -for pair interactions. - -The Tersoff/MOD potential files provided with LAMMPS (see the potentials -directory) are parameterized for metal "units"_units.html. You can -use the Tersoff/MOD potential with any LAMMPS units, but you would need to -create your own Tersoff/MOD potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Kumagai) -[(Kumagai)] T. Kumagai, S. Izumi, S. Hara, S. Sakai, -Comp. Mat. Science, 39, 457 (2007). - -:link(Tersoff_12) -[(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988). - -:link(Tersoff_22) -[(Tersoff_2)] J. Tersoff, Phys Rev B, 38, 9902 (1988). - -:link(Murty) -[(Murty)] M.V.R. Murty, H.A. Atwater, Phys Rev B, 51, 4889 (1995). - -:link(Schelling) -[(Schelling)] Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008). diff --git a/doc/txt/pair_tersoff_zbl.txt b/doc/txt/pair_tersoff_zbl.txt deleted file mode 100644 index 5f03ffd94e..0000000000 --- a/doc/txt/pair_tersoff_zbl.txt +++ /dev/null @@ -1,267 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style tersoff/zbl command :h3 -pair_style tersoff/zbl/gpu command :h3 -pair_style tersoff/zbl/kk command :h3 -pair_style tersoff/zbl/omp command :h3 - -[Syntax:] - -pair_style tersoff/zbl :pre - -[Examples:] - -pair_style tersoff/zbl -pair_coeff * * SiC.tersoff.zbl Si C Si :pre - -[Description:] - -The {tersoff/zbl} style computes a 3-body Tersoff potential -"(Tersoff_1)"_#zbl-Tersoff_1 with a close-separation pairwise modification -based on a Coulomb potential and the Ziegler-Biersack-Littmark -universal screening function "(ZBL)"_#zbl-ZBL, giving the energy E of a -system of atoms as - -:c,image(Eqs/pair_tersoff_zbl.jpg) - -The f_F term is a fermi-like function used to smoothly connect the ZBL -repulsive potential with the Tersoff potential. There are 2 -parameters used to adjust it: A_F and r_C. A_F controls how "sharp" -the transition is between the two, and r_C is essentially the cutoff -for the ZBL potential. - -For the ZBL portion, there are two terms. The first is the Coulomb -repulsive term, with Z1, Z2 as the number of protons in each nucleus, -e as the electron charge (1 for metal and real units) and epsilon0 as -the permittivity of vacuum. The second part is the ZBL universal -screening function, with a0 being the Bohr radius (typically 0.529 -Angstroms), and the remainder of the coefficients provided by the -original paper. This screening function should be applicable to most -systems. However, it is only accurate for small separations -(i.e. less than 1 Angstrom). - -For the Tersoff portion, f_R is a two-body term and f_A includes -three-body interactions. The summations in the formula are over all -neighbors J and K of atom I within a cutoff distance = R + D. - -Only a single pair_coeff command is used with the {tersoff/zbl} style -which specifies a Tersoff/ZBL potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of Tersoff/ZBL elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values -for Si and C. If your LAMMPS simulation has 4 atoms types and you -want the 1st 3 to be Si, and the 4th to be C, you would use the -following pair_coeff command: - -pair_coeff * * SiC.tersoff Si Si Si C :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to the Si -element in the Tersoff/ZBL file. The final C argument maps LAMMPS -atom type 4 to the C element in the Tersoff/ZBL file. If a mapping -value is specified as NULL, the mapping is not performed. This can be -used when a {tersoff/zbl} potential is used as part of the {hybrid} -pair style. The NULL values are placeholders for atom types that will -be used with other potentials. - -Tersoff/ZBL files in the {potentials} directory of the LAMMPS -distribution have a ".tersoff.zbl" suffix. Lines that are not blank -or comments (starting with #) define parameters for a triplet of -elements. The parameters in a single entry correspond to coefficients -in the formula above: - -element 1 (the center atom in a 3-body interaction) -element 2 (the atom bonded to the center atom) -element 3 (the atom influencing the 1-2 bond in a bond-order sense) -m -gamma -lambda3 (1/distance units) -c -d -costheta0 (can be a value < -1 or > 1) -n -beta -lambda2 (1/distance units) -B (energy units) -R (distance units) -D (distance units) -lambda1 (1/distance units) -A (energy units) -Z_i -Z_j -ZBLcut (distance units) -ZBLexpscale (1/distance units) :ul - -The n, beta, lambda2, B, lambda1, and A parameters are only used for -two-body interactions. The m, gamma, lambda3, c, d, and costheta0 -parameters are only used for three-body interactions. The R and D -parameters are used for both two-body and three-body interactions. The -Z_i,Z_j, ZBLcut, ZBLexpscale parameters are used in the ZBL repulsive -portion of the potential and in the Fermi-like function. The -non-annotated parameters are unitless. The value of m must be 3 or 1. - -The Tersoff/ZBL potential file must contain entries for all the -elements listed in the pair_coeff command. It can also contain -entries for additional elements not being used in a particular -simulation; LAMMPS ignores those entries. - -For a single-element simulation, only a single entry is required -(e.g. SiSiSi). For a two-element simulation, the file must contain 8 -entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that -specify Tersoff parameters for all permutations of the two elements -interacting in three-body configurations. Thus for 3 elements, 27 -entries would be required, etc. - -As annotated above, the first element in the entry is the center atom -in a three-body interaction and it is bonded to the 2nd atom and the -bond is influenced by the 3rd atom. Thus an entry for SiCC means Si -bonded to a C with another C atom influencing the bond. Thus -three-body parameters for SiCSi and SiSiC entries will not, in -general, be the same. The parameters used for the two-body -interaction come from the entry where the 2nd element is repeated. -Thus the two-body parameters for Si interacting with C, comes from the -SiCC entry. - -The parameters used for a particular -three-body interaction come from the entry with the corresponding -three elements. The parameters used only for two-body interactions -(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd -element are different (e.g. SiCSi) are not used for anything and can -be set to 0.0 if desired. - -Note that the twobody parameters in entries such as SiCC and CSiSi -are often the same, due to the common use of symmetric mixing rules, -but this is not always the case. For example, the beta and n parameters in -Tersoff_2 "(Tersoff_2)"_#zbl-Tersoff_2 are not symmetric. - -We chose the above form so as to enable users to define all commonly -used variants of the Tersoff portion of the potential. In particular, -our form reduces to the original Tersoff form when m = 3 and gamma = -1, while it reduces to the form of "Albe et al."_#zbl-Albe when beta = 1 -and m = 1. Note that in the current Tersoff implementation in LAMMPS, -m must be specified as either 3 or 1. Tersoff used a slightly -different but equivalent form for alloys, which we will refer to as -Tersoff_2 potential "(Tersoff_2)"_#zbl-Tersoff_2. - -LAMMPS parameter values for Tersoff_2 can be obtained as follows: -gamma = omega_ijk, lambda3 = 0 and the value of -m has no effect. The parameters for species i and j can be calculated -using the Tersoff_2 mixing rules: - -:c,image(Eqs/pair_tersoff_2.jpg) - -Tersoff_2 parameters R and S must be converted to the LAMMPS -parameters R and D (R is different in both forms), using the following -relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the -Tersoff_2 parameters. - -In the potentials directory, the file SiCGe.tersoff provides the -LAMMPS parameters for Tersoff's various versions of Si, as well as his -alloy parameters for Si, C, and Ge. This file can be used for pure Si, -(three different versions), pure C, pure Ge, binary SiC, and binary -SiGe. LAMMPS will generate an error if this file is used with any -combination involving C and Ge, since there are no entries for the GeC -interactions (Tersoff did not publish parameters for this -cross-interaction.) Tersoff files are also provided for the SiC alloy -(SiC.tersoff) and the GaN (GaN.tersoff) alloys. - -Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou -for helping clarify how Tersoff parameters for alloys have been -defined in various papers. Also thanks to Ram Devanathan for -providing the base ZBL implementation. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above from values in the potential file. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair style requires the "newton"_newton.html setting to be "on" -for pair interactions. - -The Tersoff/ZBL potential files provided with LAMMPS (see the -potentials directory) are parameterized for metal "units"_units.html. -You can use the Tersoff potential with any LAMMPS units, but you would -need to create your own Tersoff potential file with coefficients -listed in the appropriate units if your simulation doesn't use "metal" -units. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(zbl-Tersoff_1) -[(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988). - -:link(zbl-ZBL) -[(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges -of Ions in Matter' Vol 1, 1985, Pergamon Press. - -:link(zbl-Albe) -[(Albe)] J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.: -Condens. Matter, 15, 5649(2003). - -:link(zbl-Tersoff_2) -[(Tersoff_2)] J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248) diff --git a/doc/txt/pair_thole.txt b/doc/txt/pair_thole.txt deleted file mode 100644 index c7a304ca41..0000000000 --- a/doc/txt/pair_thole.txt +++ /dev/null @@ -1,192 +0,0 @@ - - - -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style thole command :h3 -pair_style lj/cut/thole/long command :h3 -pair_style lj/cut/thole/long/omp command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {thole} or {lj/cut/thole/long} or {lj/cut/thole/long/omp} -args = list of arguments for a particular style :ul - {thole} args = damp cutoff - damp = global damping parameter - cutoff = global cutoff (distance units) - {lj/cut/thole/long} or {lj/cut/thole/long/omp} args = damp cutoff (cutoff2) - damp = global damping parameter - cutoff = global cutoff for LJ (and Thole if only 1 arg) (distance units) - cutoff2 = global cutoff for Thole (optional) (distance units) :pre - -[Examples:] - -pair_style hybrid/overlay ... thole 2.6 12.0 -pair_coeff 1 1 thole 1.0 -pair_coeff 1 2 thole 1.0 2.6 10.0 -pair_coeff * 2 thole 1.0 2.6 :pre - -pair_style lj/cut/thole/long 2.6 12.0 :pre - -[Description:] - -The {thole} pair styles are meant to be used with force fields that -include explicit polarization through Drude dipoles. This link -describes how to use the "thermalized Drude oscillator -model"_Howto_drude.html in LAMMPS and polarizable models in LAMMPS are -discussed on the "Howto polarizable"_Howto_polarizable.html doc page. - -The {thole} pair style should be used as a sub-style within in the -"pair_hybrid/overlay"_pair_hybrid.html command, in conjunction with a -main pair style including Coulomb interactions, i.e. any pair style -containing {coul/cut} or {coul/long} in its style name. - -The {lj/cut/thole/long} pair style is equivalent to, but more convenient that -the frequent combination {hybrid/overlay lj/cut/coul/long cutoff thole damp -cutoff2}. It is not only a shorthand for this pair_style combination, but -it also allows for mixing pair coefficients instead of listing them all. -The {lj/cut/thole/long} pair style is also a bit faster because it avoids an -overlay and can benefit from OMP acceleration. Moreover, it uses a more -precise approximation of the direct Coulomb interaction at short range similar -to "coul/long/cs"_pair_cs.html, which stabilizes the temperature of -Drude particles. - -The {thole} pair styles compute the Coulomb interaction damped at -short distances by a function - -\begin\{equation\} T_\{ij\}(r_\{ij\}) = 1 - \left( 1 + -\frac\{s_\{ij\} r_\{ij\} \}\{2\} \right) -\exp \left( - s_\{ij\} r_\{ij\} \right) \end\{equation\} - -This function results from an adaptation to point charges -"(Noskov)"_#Noskov1 of the dipole screening scheme originally proposed -by "Thole"_#Thole1. The scaling coefficient \(s_\{ij\} \) is determined -by the polarizability of the atoms, \( \alpha_i \), and by a Thole -damping parameter \( a \). This Thole damping parameter usually takes -a value of 2.6, but in certain force fields the value can depend upon -the atom types. The mixing rule for Thole damping parameters is the -arithmetic average, and for polarizabilities the geometric average -between the atom-specific values. - -\begin\{equation\} s_\{ij\} = \frac\{ a_\{ij\} \}\{ -(\alpha_\{ij\})^\{1/3\} \} = \frac\{ (a_i + a_j)/2 \}\{ -\[(\alpha_i\alpha_j)^\{1/2\}\]^\{1/3\} \} \end\{equation\} - -The damping function is only applied to the interactions between the -point charges representing the induced dipoles on polarizable sites, -that is, charges on Drude particles, \( q_\{D,i\} \), and opposite -charges, \( -q_\{D,i\} \), located on the respective core particles -(to which each Drude particle is bonded). Therefore, Thole screening -is not applied to the full charge of the core particle \( q_i \), but -only to the \( -q_\{D,i\} \) part of it. - -The interactions between core charges are subject to the weighting -factors set by the "special_bonds"_special_bonds.html command. The -interactions between Drude particles and core charges or -non-polarizable atoms are also subject to these weighting factors. The -Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from -their respective cores. - -For pair_style {thole}, the following coefficients must be defined for -each pair of atoms types via the "pair_coeff"_pair_coeff.html command -as in the example above. - -alpha (distance units^3) -damp -cutoff (distance units) :ul - -The last two coefficients are optional. If not specified the global -Thole damping parameter or global cutoff specified in the pair_style -command are used. In order to specify a cutoff (third argument) a damp -parameter (second argument) must also be specified. - -For pair style {lj/cut/thole/long}, the following coefficients must be -defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html -command. - -epsilon (energy units) -sigma (length units) -alpha (distance units^3) -damps -LJ cutoff (distance units) :ul - -The last two coefficients are optional and default to the global values from -the {pair_style} command line. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Mixing]: - -The {thole} pair style does not support mixing. Thus, coefficients -for all I,J pairs must be specified explicitly. - -The {lj/cut/thole/long} pair style does support mixing. Mixed coefficients -are defined using - -\begin\{equation\} \alpha_\{ij\} = \sqrt\{\alpha_i\alpha_j\}\end\{equation\} -\begin\{equation\} a_\{ij\} = \frac 1 2 (a_i + a_j)\end\{equation\} - -[Restrictions:] - -These pair styles are part of the USER-DRUDE package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair_style should currently not be used with the "charmm dihedral -style"_dihedral_charmm.html if the latter has non-zero 1-4 weighting -factors. This is because the {thole} pair style does not know which -pairs are 1-4 partners of which dihedrals. - -The {lj/cut/thole/long} pair style should be used with a "Kspace solver"_kspace_style.html -like PPPM or Ewald, which is only enabled if LAMMPS was built with the kspace -package. - -[Related commands:] - -"fix drude"_fix_drude.html, "fix -langevin/drude"_fix_langevin_drude.html, "fix -drude/transform"_fix_drude_transform.html, "compute -temp/drude"_compute_temp_drude.html -"pair_style lj/cut/coul/long"_pair_lj.html - -[Default:] none - -:line - -:link(Noskov1) -[(Noskov)] Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005). - -:link(Thole1) -[(Thole)] Chem Phys, 59, 341 (1981). diff --git a/doc/txt/pair_tri_lj.txt b/doc/txt/pair_tri_lj.txt deleted file mode 100644 index 75108c0743..0000000000 --- a/doc/txt/pair_tri_lj.txt +++ /dev/null @@ -1,115 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style tri/lj command :h3 - -[Syntax:] - -pair_style tri/lj cutoff :pre - -cutoff = global cutoff for interactions (distance units) - -[Examples:] - -pair_style tri/lj 3.0 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.0 1.5 2.5 :pre - -[Description:] - -Style {tri/lj} treats particles which are triangles as a set of small -spherical particles that tile the triangle surface as explained below. -Interactions between two triangles, each with N1 and N2 spherical -particles, are calculated as the pairwise sum of N1*N2 Lennard-Jones -interactions. Interactions between a triangle with N spherical -particles and a point particle are treated as the pairwise sum of N -Lennard-Jones interactions. See the "pair_style lj/cut"_pair_lj.html -doc page for the definition of Lennard-Jones interactions. - -The cutoff distance for an interaction between 2 triangles, or between -a triangle and a point particle, is calculated from the position of -the triangle (its centroid), not between pairs of individual spheres -comprising the triangle. Thus an interaction is either calculated in -its entirety or not at all. - -The set of non-overlapping spherical particles that represent a -triangle, for purposes of this pair style, are generated in the -following manner. Assume the triangle is of type I, and sigma_II has -been specified. We want a set of spheres with centers in the plane of -the triangle, none of them larger in diameter than sigma_II, which -completely cover the triangle's area, but with minimal overlap and a -minimal total number of spheres. This is done in a recursive manner. -Place a sphere at the centroid of the original triangle. Calculate -what diameter it must have to just cover all 3 corner points of the -triangle. If that diameter is equal to or smaller than sigma_II, then -include a sphere of the calculated diameter in the set of covering -spheres. It the diameter is larger than sigma_II, then split the -triangle into 2 triangles by bisecting its longest side. Repeat the -process on each sub-triangle, recursing as far as needed to generate a -set of covering spheres. When finished, the original criteria are -met, and the set of covering spheres should be near minimal in number -and overlap, at least for input triangles with a reasonable -aspect-ratio. - -The LJ interaction between 2 spheres on different triangles of types -I,J is computed with an arithmetic mixing of the sigma values of the 2 -spheres and using the specified epsilon value for I,J atom types. -Note that because the sigma values for triangles spheres is computed -using only sigma_II values, specific to the triangles's type, this -means that any specified sigma_IJ values (for I != J) are effectively -ignored. - -For style {tri/lj}, the following coefficients must be defined for -each pair of atoms types via the "pair_coeff"_pair_coeff.html command -as in the examples above, or in the data file or restart files read by -the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -epsilon (energy units) -sigma (distance units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global cutoff -is used. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of this pair style can be mixed. The -default mix value is {geometric}. See the "pair_modify" command for -details. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This style is part of the ASPHERE package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -Defining particles to be triangles so they participate in tri/tri or -tri/particle interactions requires the use the "atom_style -tri"_atom_style.html command. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style line/lj"_pair_line_lj.html - -[Default:] none diff --git a/doc/txt/pair_ufm.txt b/doc/txt/pair_ufm.txt deleted file mode 100644 index f0efcfbf19..0000000000 --- a/doc/txt/pair_ufm.txt +++ /dev/null @@ -1,134 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style ufm command :h3 -pair_style ufm/gpu command :h3 -pair_style ufm/omp command :h3 -pair_style ufm/opt command :h3 - -[Syntax:] - -pair_style ufm cutoff :pre - -cutoff = global cutoff for {ufm} interactions (distance units) :ul - -[Examples:] - -pair_style ufm 4.0 -pair_coeff 1 1 100.0 1.0 2.5 -pair_coeff * * 100.0 1.0 :pre - - -pair_style ufm 4.0 -pair_coeff * * 10.0 1.0 -variable prefactor equal ramp(10,100) -fix 1 all adapt 1 pair ufm epsilon * * v_prefactor :pre - -[Description:] - -Style {ufm} computes pairwise interactions using the Uhlenbeck-Ford model (UFM) potential "(Paula Leite2016)"_#PL2 which is given by - -:c,image(Eqs/pair_ufm.jpg) - -where rc is the cutoff, sigma is a distance-scale and epsilon is an energy-scale, i.e., a product of Boltzmann constant kB, temperature T and the Uhlenbeck-Ford p-parameter which is responsible -to control the softness of the interactions "(Paula Leite2017)"_#PL1. -This model is useful as a reference system for fluid-phase free-energy calculations "(Paula Leite2016)"_#PL2. - -The following coefficients must be defined for each pair of atom types -via the "pair_coeff"_pair_coeff.html command as in the examples above, -or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global {ufm} -cutoff is used. - - -The "fix adapt"_fix_adapt.html command can be used to vary epsilon and sigma for this pair style over the course of a simulation, in which case -pair_coeff settings for epsilon and sigma must still be specified, but will be -overridden. For example these commands will vary the prefactor epsilon for -all pairwise interactions from 10.0 at the beginning to 100.0 at the end -of a run: - -variable prefactor equal ramp(10,100) -fix 1 all adapt 1 pair ufm epsilon * * v_prefactor :pre - -NOTE: The thermodynamic integration procedure can be performed with this potential using "fix adapt"_fix_adapt.html. This command will rescale the force on each atom by varying a scale variable, which always starts with value 1.0. The syntax is the same described above, however, changing epsilon to scale. A detailed explanation of how to use this command and perform nonequilibrium thermodynamic integration in LAMMPS is given in the paper by "(Freitas)"_#Freitas2. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the A coefficient and cutoff -distance for this pair style can be mixed. A is always mixed via a -{geometric} rule. The cutoff is mixed according to the pair_modify -mix value. The default mix value is {geometric}. See the -"pair_modify" command for details. - -This pair style support the "pair_modify"_pair_modify.html shift option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table and tail are not relevant for this -pair style. - -This pair style does not support the "pair_modify"_pair_modify.html tail option for adding long-range tail corrections to energy and pressure. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "fix adapt"_fix_adapt.html - -[Default:] none - - -:link(PL1) -[(Paula Leite2017)] Paula Leite, Santos-Florez, and de Koning, Phys Rev E, 96, -32115 (2017). - -:link(PL2) -[(Paula Leite2016)] Paula Leite , Freitas, Azevedo, and de Koning, J Chem Phys, 126, -044509 (2016). - -:link(Freitas2) -[(Freitas)] Freitas, Asta, and de Koning, Computational Materials Science, 112, 333 (2016). diff --git a/doc/txt/pair_vashishta.txt b/doc/txt/pair_vashishta.txt deleted file mode 100644 index 7ffb16cc83..0000000000 --- a/doc/txt/pair_vashishta.txt +++ /dev/null @@ -1,246 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style vashishta command :h3 -pair_style vashishta/gpu command :h3 -pair_style vashishta/omp command :h3 -pair_style vashishta/kk command :h3 -pair_style vashishta/table command :h3 -pair_style vashishta/table/omp command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {vashishta} or {vashishta/table} or {vashishta/omp} or {vashishta/table/omp} -args = list of arguments for a particular style :ul - {vashishta} or {vashishta/omp} args = none - {vashishta/table} or {vashishta/table/omp} args = Ntable cutinner - Ntable = # of tabulation points - cutinner = tablulate from cutinner to cutoff :pre - -[Examples:] - -pair_style vashishta -pair_coeff * * SiC.vashishta Si C :pre - -pair_style vashishta/table 100000 0.2 -pair_coeff * * SiC.vashishta Si C :pre - -[Description:] - -The {vashishta} and {vashishta/table} styles compute the combined -2-body and 3-body family of potentials developed in the group of Priya -Vashishta and collaborators. By combining repulsive, screened -Coulombic, screened charge-dipole, and dispersion interactions with a -bond-angle energy based on the Stillinger-Weber potential, this -potential has been used to describe a variety of inorganic compounds, -including SiO2 "Vashishta1990"_#Vashishta1990, SiC -"Vashishta2007"_#Vashishta2007, and InP "Branicio2009"_#Branicio2009. - -The potential for the energy U of a system of atoms is - -:c,image(Eqs/pair_vashishta.jpg) - -where we follow the notation used in "Branicio2009"_#Branicio2009. -U2 is a two-body term and U3 is a three-body term. The -summation over two-body terms is over all neighbors J within -a cutoff distance = {rc}. The twobody terms are shifted and -tilted by a linear function so that the energy and force are -both zero at {rc}. The summation over three-body terms -is over all neighbors J and K within a cut-off distance = {r0}, -where the exponential screening function becomes zero. - -The {vashishta} style computes these formulas analytically. The -{vashishta/table} style tabulates the analytic values for {Ntable} -points from cutinner to the cutoff of the potential. The points are -equally spaced in R^2 space from cutinner^2 to cutoff^2. For the -two-body term in the above equation, a linear interpolation for each -pairwise distance between adjacent points in the table. In practice -the tabulated version can run 3-5x faster than the analytic version -with moderate to little loss of accuracy for Ntable values -between 10000 and 1000000. It is not recommended to use less than -5000 tabulation points. - -Only a single pair_coeff command is used with either style which -specifies a Vashishta potential file with parameters for all needed -elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N element names = mapping of Vashishta elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential file. - -As an example, imagine a file SiC.vashishta has parameters for -Si and C. If your LAMMPS simulation has 4 atoms types and you want -the 1st 3 to be Si, and the 4th to be C, you would use the following -pair_coeff command: - -pair_coeff * * SiC.vashishta Si Si Si C :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to the Si -element in the file. The final C argument maps LAMMPS atom type 4 -to the C element in the file. If a mapping value is specified as -NULL, the mapping is not performed. This can be used when a {vashishta} -potential is used as part of the {hybrid} pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. - -Vashishta files in the {potentials} directory of the LAMMPS -distribution have a ".vashishta" suffix. Lines that are not blank or -comments (starting with #) define parameters for a triplet of -elements. The parameters in a single entry correspond to the two-body -and three-body coefficients in the formulae above: - -element 1 (the center atom in a 3-body interaction) -element 2 -element 3 -H (energy units) -eta -Zi (electron charge units) -Zj (electron charge units) -lambda1 (distance units) -D (energy units) -lambda4 (distance units) -W (energy units) -rc (distance units) -B (energy units) -gamma -r0 (distance units) -C -costheta0 :ul - -The non-annotated parameters are unitless. The Vashishta potential -file must contain entries for all the elements listed in the -pair_coeff command. It can also contain entries for additional -elements not being used in a particular simulation; LAMMPS ignores -those entries. For a single-element simulation, only a single entry -is required (e.g. SiSiSi). For a two-element simulation, the file -must contain 8 entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, -CCSi, CCC), that specify parameters for all permutations of the two -elements interacting in three-body configurations. Thus for 3 -elements, 27 entries would be required, etc. - -Depending on the particular version of the Vashishta potential, the -values of these parameters may be keyed to the identities of zero, -one, two, or three elements. In order to make the input file format -unambiguous, general, and simple to code, LAMMPS uses a slightly -confusing method for specifying parameters. All parameters are -divided into two classes: two-body and three-body. Two-body and -three-body parameters are handled differently, as described below. -The two-body parameters are H, eta, lambda1, D, lambda4, W, rc, gamma, -and r0. They appear in the above formulae with two subscripts. The -parameters Zi and Zj are also classified as two-body parameters, even -though they only have 1 subscript. The three-body parameters are B, -C, costheta0. They appear in the above formulae with three -subscripts. Two-body and three-body parameters are handled -differently, as described below. - -The first element in each entry is the center atom in a three-body -interaction, while the second and third elements are two neighbor -atoms. Three-body parameters for a central atom I and two neighbors J -and K are taken from the IJK entry. Note that even though three-body -parameters do not depend on the order of J and K, LAMMPS stores -three-body parameters for both IJK and IKJ. The user must ensure that -these values are equal. Two-body parameters for an atom I interacting -with atom J are taken from the IJJ entry, where the 2nd and 3rd -elements are the same. Thus the two-body parameters for Si interacting -with C come from the SiCC entry. Note that even though two-body -parameters (except possibly gamma and r0 in U3) do not depend on the -order of the two elements, LAMMPS will get the Si-C value from the -SiCC entry and the C-Si value from the CSiSi entry. The user must -ensure that these values are equal. Two-body parameters appearing in -entries where the 2nd and 3rd elements are different are stored but -never used. It is good practice to enter zero for these values. Note -that the three-body function U3 above contains the two-body parameters -gamma and r0. So U3 for a central C atom bonded to an Si atom and a -second C atom will take three-body parameters from the CSiC entry, but -two-body parameters from the CCC and CSiSi entries. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above from values in the potential file. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -These pair style are part of the MANYBODY package. They is only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -These pair styles requires the "newton"_newton.html setting to be "on" -for pair interactions. - -The Vashishta potential files provided with LAMMPS (see the potentials -directory) are parameterized for metal "units"_units.html. You can -use the Vashishta potential with any LAMMPS units, but you would need -to create your own potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Vashishta1990) -[(Vashishta1990)] P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B -41, 12197 (1990). - -:link(Vashishta2007) -[(Vashishta2007)] P. Vashishta, R. K. Kalia, A. Nakano, -J. P. Rino. J. Appl. Phys. 101, 103515 (2007). - -:link(Branicio2009) -[(Branicio2009)] Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed -Matter 21 (2009) 095002 diff --git a/doc/txt/pair_write.txt b/doc/txt/pair_write.txt deleted file mode 100644 index 48ad76e76e..0000000000 --- a/doc/txt/pair_write.txt +++ /dev/null @@ -1,79 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_write command :h3 - -[Syntax:] - -pair_write itype jtype N style inner outer file keyword Qi Qj :pre - -itype,jtype = 2 atom types -N = # of values -style = {r} or {rsq} or {bitmap} -inner,outer = inner and outer cutoff (distance units) -file = name of file to write values to -keyword = section name in file for this set of tabulated values -Qi,Qj = 2 atom charges (charge units) (optional) :ul - -[Examples:] - -pair_write 1 3 500 r 1.0 10.0 table.txt LJ -pair_write 1 1 1000 rsq 2.0 8.0 table.txt Yukawa_1_1 -0.5 0.5 :pre - -[Description:] - -Write energy and force values to a file as a function of distance for -the currently defined pair potential. This is useful for plotting the -potential function or otherwise debugging its values. If the file -already exists, the table of values is appended to the end of the file -to allow multiple tables of energy and force to be included in one -file. - -The energy and force values are computed at distances from inner to -outer for 2 interacting atoms of type itype and jtype, using the -appropriate "pair_coeff"_pair_coeff.html coefficients. If the style -is {r}, then N distances are used, evenly spaced in r; if the style is -{rsq}, N distances are used, evenly spaced in r^2. - -For example, for N = 7, style = {r}, inner = 1.0, and outer = 4.0, -values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0. - -If the style is {bitmap}, then 2^N values are written to the file in a -format and order consistent with how they are read in by the -"pair_coeff"_pair_coeff.html command for pair style {table}. For -reasonable accuracy in a bitmapped table, choose N >= 12, an {inner} -value that is smaller than the distance of closest approach of 2 -atoms, and an {outer} value <= cutoff of the potential. - -If the pair potential is computed between charged atoms, the charges -of the pair of interacting atoms can optionally be specified. If not -specified, values of Qi = Qj = 1.0 are used. - -The file is written in the format used as input for the -"pair_style"_pair_style.html {table} option with {keyword} as the -section name. Each line written to the file lists an index number -(1-N), a distance (in distance units), an energy (in energy units), -and a force (in force units). - -[Restrictions:] - -All force field coefficients for pair and other kinds of interactions -must be set before this command can be invoked. - -Due to how the pairwise force is computed, an inner value > 0.0 must -be specified even if the potential has a finite value at r = 0.0. - -For EAM potentials, the pair_write command only tabulates the -pairwise portion of the potential, not the embedding portion. - -[Related commands:] - -"pair_style table"_pair_table.html, -"pair_style"_pair_style.html, "pair_coeff"_pair_coeff.html - -[Default:] none diff --git a/doc/txt/pair_yukawa.txt b/doc/txt/pair_yukawa.txt deleted file mode 100644 index 154fd3e836..0000000000 --- a/doc/txt/pair_yukawa.txt +++ /dev/null @@ -1,104 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style yukawa command :h3 -pair_style yukawa/gpu command :h3 -pair_style yukawa/omp command :h3 -pair_style yukawa/kk command :h3 - -[Syntax:] - -pair_style yukawa kappa cutoff :pre - -kappa = screening length (inverse distance units) -cutoff = global cutoff for Yukawa interactions (distance units) :ul - -[Examples:] - -pair_style yukawa 2.0 2.5 -pair_coeff 1 1 100.0 2.3 -pair_coeff * * 100.0 :pre - -[Description:] - -Style {yukawa} computes pairwise interactions with the formula - -:c,image(Eqs/pair_yukawa.jpg) - -Rc is the cutoff. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -A (energy*distance units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global yukawa -cutoff is used. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the A coefficient and cutoff -distance for this pair style can be mixed. A is an energy value mixed -like a LJ epsilon. The default mix value is {geometric}. See the -"pair_modify" command for details. - -This pair style supports the "pair_modify"_pair_modify.html shift -option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none diff --git a/doc/txt/pair_yukawa_colloid.txt b/doc/txt/pair_yukawa_colloid.txt deleted file mode 100644 index b36c4c235c..0000000000 --- a/doc/txt/pair_yukawa_colloid.txt +++ /dev/null @@ -1,154 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style yukawa/colloid command :h3 -pair_style yukawa/colloid/gpu command :h3 -pair_style yukawa/colloid/omp command :h3 - -[Syntax:] - -pair_style yukawa/colloid kappa cutoff :pre - -kappa = screening length (inverse distance units) -cutoff = global cutoff for colloidal Yukawa interactions (distance units) :ul - -[Examples:] - -pair_style yukawa/colloid 2.0 2.5 -pair_coeff 1 1 100.0 2.3 -pair_coeff * * 100.0 :pre - -[Description:] - -Style {yukawa/colloid} computes pairwise interactions with the formula - -:c,image(Eqs/pair_yukawa_colloid.jpg) - -where Ri and Rj are the radii of the two particles and Rc is the -cutoff. - -In contrast to "pair_style yukawa"_pair_yukawa.html, this functional -form arises from the Coulombic interaction between two colloid -particles, screened due to the presence of an electrolyte, see the -book by "Safran"_#Safran for a derivation in the context of DLVO -theory. "Pair_style yukawa"_pair_yukawa.html is a screened Coulombic -potential between two point-charges and uses no such approximation. - -This potential applies to nearby particle pairs for which the Derjagin -approximation holds, meaning h << Ri + Rj, where h is the -surface-to-surface separation of the two particles. - -When used in combination with "pair_style colloid"_pair_colloid.html, -the two terms become the so-called DLVO potential, which combines -electrostatic repulsion and van der Waals attraction. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -A (energy/distance units) -cutoff (distance units) :ul - -The prefactor A is determined from the relationship between surface -charge and surface potential due to the presence of electrolyte. Note -that the A for this potential style has different units than the A -used in "pair_style yukawa"_pair_yukawa.html. For low surface -potentials, i.e. less than about 25 mV, A can be written as: - -A = 2 * PI * R*eps*eps0 * kappa * psi^2 :pre - -where - -R = colloid radius (distance units) -eps0 = permittivity of free space (charge^2/energy/distance units) -eps = relative permittivity of fluid medium (dimensionless) -kappa = inverse screening length (1/distance units) -psi = surface potential (energy/charge units) :ul - -The last coefficient is optional. If not specified, the global -yukawa/colloid cutoff is used. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the A coefficient and cutoff -distance for this pair style can be mixed. A is an energy value mixed -like a LJ epsilon. The default mix value is {geometric}. See the -"pair_modify" command for details. - -This pair style supports the "pair_modify"_pair_modify.html shift -option for the energy of the pair interaction. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This style is part of the COLLOID package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -This pair style requires that atoms be finite-size spheres with a -diameter, as defined by the "atom_style sphere"_atom_style.html -command. - -Per-particle polydispersity is not yet supported by this pair style; -per-type polydispersity is allowed. This means all particles of the -same type must have the same diameter. Each type can have a different -diameter. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Safran) -[(Safran)] Safran, Statistical Thermodynamics of Surfaces, Interfaces, -And Membranes, Westview Press, ISBN: 978-0813340791 (2003). diff --git a/doc/txt/pair_zbl.txt b/doc/txt/pair_zbl.txt deleted file mode 100644 index 4c8dfb5455..0000000000 --- a/doc/txt/pair_zbl.txt +++ /dev/null @@ -1,139 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style zbl command :h3 -pair_style zbl/gpu command :h3 -pair_style zbl/kk command :h3 -pair_style zbl/omp command :h3 - -[Syntax:] - -pair_style zbl inner outer :pre - -inner = distance where switching function begins -outer = global cutoff for ZBL interaction :ul - -[Examples:] - -pair_style zbl 3.0 4.0 -pair_coeff * * 73.0 73.0 -pair_coeff 1 1 14.0 14.0 :pre - -[Description:] - -Style {zbl} computes the Ziegler-Biersack-Littmark (ZBL) screened nuclear -repulsion for describing high-energy collisions between atoms. -"(Ziegler)"_#Ziegler. It includes an additional switching function -that ramps the energy, force, and curvature smoothly to zero -between an inner and outer cutoff. The potential -energy due to a pair of atoms at a distance r_ij is given by: - -:c,image(Eqs/pair_zbl.jpg) - -where e is the electron charge, epsilon_0 is the electrical -permittivity of vacuum, and Z_i and Z_j are the nuclear charges of the -two atoms. The switching function S(r) is identical to that used by -"pair_style lj/gromacs"_pair_gromacs.html. Here, the inner and outer -cutoff are the same for all pairs of atom types. - -The following coefficients must be defined for each pair of atom types -via the "pair_coeff"_pair_coeff.html command as in the examples above, -or in the LAMMPS data file. - -Z_i (atomic number for first atom type, e.g. 13.0 for aluminum) :ul -Z_j (ditto for second atom type) :ul - -The values of Z_i and Z_j are normally equal to the atomic -numbers of the two atom types. Thus, the user may optionally -specify only the coefficients for each I==I pair, and rely -on the obvious mixing rule for cross interactions (see below). -Note that when I==I it is required that Z_i == Z_j. When used -with "hybrid/overlay"_pair_hybrid.html and pairs are assigned -to more than one sub-style, the mixing rule is not used and -each pair of types interacting with the ZBL sub-style must -be included in a pair_coeff command. - -NOTE: The numerical values of the exponential decay constants in the -screening function depend on the unit of distance. In the above -equation they are given for units of angstroms. LAMMPS will -automatically convert these values to the distance unit of the -specified LAMMPS "units"_units.html setting. The values of Z should -always be given as multiples of a proton's charge, e.g. 29.0 for -copper. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the Z_i and Z_j coefficients -can be mixed by taking Z_i and Z_j from the values specified for -I == I and J == J cases. When used -with "hybrid/overlay"_pair_hybrid.html and pairs are assigned -to more than one sub-style, the mixing rule is not used and -each pair of types interacting with the ZBL sub-style -must be included in a pair_coeff command. -The "pair_modify"_pair_modify.html mix option has no effect on -the mixing behavior - -The ZBL pair style does not support the "pair_modify"_pair_modify.html -shift option, since the ZBL interaction is already smoothed to 0.0 at -the cutoff. - -The "pair_modify"_pair_modify.html table option is not relevant for -this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure, since there are no corrections for a potential that goes to -0.0 at the cutoff. - -This pair style does not write information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands must be -specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Ziegler) -[(Ziegler)] J.F. Ziegler, J. P. Biersack and U. Littmark, "The -Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985. diff --git a/doc/txt/pair_zero.txt b/doc/txt/pair_zero.txt deleted file mode 100644 index def28b6856..0000000000 --- a/doc/txt/pair_zero.txt +++ /dev/null @@ -1,86 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style zero command :h3 - -[Syntax:] - -pair_style zero cutoff {nocoeff} :pre - -zero = style name of this pair style -cutoff = global cutoff (distance units) -nocoeff = ignore all pair_coeff parameters (optional) :ul - -[Examples:] - -pair_style zero 10.0 -pair_style zero 5.0 nocoeff -pair_coeff * * -pair_coeff 1 2*4 3.0 :pre - -[Description:] - -Define a global or per-type cutoff length for the purpose of -building a neighbor list and acquiring ghost atoms, but do -not compute any pairwise forces or energies. - -This can be useful for fixes or computes which require a neighbor list -to enumerate pairs of atoms within some cutoff distance, but when -pairwise forces are not otherwise needed. Examples are the "fix -bond/create"_fix_bond_create.html, "compute rdf"_compute_rdf.html, -"compute voronoi/atom"_compute_voronoi_atom.html commands. - -Note that the "comm_modify cutoff"_comm_modify.html command can be -used to insure communication of ghost atoms even when a pair style is -not defined, but it will not trigger neighbor list generation. - -The optional {nocoeff} flag allows to read data files with a PairCoeff -section for any pair style. Similarly, any pair_coeff commands -will only be checked for the atom type numbers and the rest ignored. -In this case, only the global cutoff will be used. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -cutoff (distance units) :ul - -This coefficient is optional. If not specified, the global cutoff -specified in the pair_style command is used. If the pair_style has -been specified with the optional {nocoeff} flag, then a cutoff -pair coefficient is ignored. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -The cutoff distance for this pair style can be mixed. The default mix -value is {geometric}. See the "pair_modify" command for details. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style supports the use of the {inner}, {middle}, -and {outer} keywords of the "run_style respa"_run_style.html command. - -:line - -[Restrictions:] none - -[Related commands:] - -"pair_style none"_pair_none.html - -[Default:] none - diff --git a/doc/txt/partition.txt b/doc/txt/partition.txt deleted file mode 100644 index 86673c226b..0000000000 --- a/doc/txt/partition.txt +++ /dev/null @@ -1,72 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -partition command :h3 - -[Syntax:] - -partition style N command ... :pre - -style = {yes} or {no} -N = partition number (see asterisk form below) -command = any LAMMPS command :ul - -[Examples:] - -partition yes 1 processors 4 10 6 -partition no 5 print "Active partition" -partition yes *5 fix all nve -partition yes 6* fix all nvt temp 1.0 1.0 0.1 :pre - -[Description:] - -This command invokes the specified command on a subset of the -partitions of processors you have defined via the "-partition -command-line switch"_Run_options.html. - -Normally, every input script command in your script is invoked by -every partition. This behavior can be modified by defining world- or -universe-style "variables"_variable.html that have different values -for each partition. This mechanism can be used to cause your script -to jump to different input script files on different partitions, if -such a variable is used in a "jump"_jump.html command. - -The "partition" command is another mechanism for having as input -script operate differently on different partitions. It is basically a -prefix on any LAMMPS command. The command will only be invoked on -the partition(s) specified by the {style} and {N} arguments. - -If the {style} is {yes}, the command will be invoked on any partition -which matches the {N} argument. If the {style} is {no} the command -will be invoked on all the partitions which do not match the Np -argument. - -Partitions are numbered from 1 to Np, where Np is the number of -partitions specified by the "-partition command-line -switch"_Run_options.html. - -{N} can be specified in one of two ways. An explicit numeric value -can be used, as in the 1st example above. Or a wild-card asterisk can -be used to span a range of partition numbers. This takes the form "*" -or "*n" or "n*" or "m*n". An asterisk with no numeric values means -all partitions from 1 to Np. A leading asterisk means all partitions -from 1 to n (inclusive). A trailing asterisk means all partitions -from n to Np (inclusive). A middle asterisk means all partitions from -m to n (inclusive). - -This command can be useful for the "run_style verlet/split" command -which imposed requirements on how the "processors"_processors.html -command lays out a 3d grid of processors in each of 2 partitions. - -[Restrictions:] none - -[Related commands:] - -"run_style verlet/split"_run_style.html - -[Default:] none diff --git a/doc/txt/prd.txt b/doc/txt/prd.txt deleted file mode 100644 index e1d6fc1b4e..0000000000 --- a/doc/txt/prd.txt +++ /dev/null @@ -1,337 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -prd command :h3 - -[Syntax:] - -prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ... :pre - -N = # of timesteps to run (not including dephasing/quenching) :ulb,l -t_event = timestep interval between event checks :l -n_dephase = number of velocity randomizations to perform in each dephase run :l -t_dephase = number of timesteps to run dynamics after each velocity randomization during dephase :l -t_correlate = number of timesteps within which 2 consecutive events are considered to be correlated :l -compute-ID = ID of the compute used for event detection :l -random_seed = random # seed (positive integer) :l -zero or more keyword/value pairs may be appended :l -keyword = {min} or {temp} or {vel} :l - {min} values = etol ftol maxiter maxeval - etol = stopping tolerance for energy, used in quenching - ftol = stopping tolerance for force, used in quenching - maxiter = max iterations of minimize, used in quenching - maxeval = max number of force/energy evaluations, used in quenching - {temp} value = Tdephase - Tdephase = target temperature for velocity randomization, used in dephasing - {vel} values = loop dist - loop = {all} or {local} or {geom}, used in dephasing - dist = {uniform} or {gaussian}, used in dephasing - {time} value = {steps} or {clock} - {steps} = simulation runs for N timesteps on each replica (default) - {clock} = simulation runs for N timesteps across all replicas :pre -:ule - -[Examples:] - -prd 5000 100 10 10 100 1 54982 -prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200 :pre - -[Description:] - -Run a parallel replica dynamics (PRD) simulation using multiple -replicas of a system. One or more replicas can be used. The total -number of steps {N} to run can be interpreted in one of two ways; see -discussion of the {time} keyword below. - -PRD is described in "(Voter1998)"_#Voter1998 by Art Voter. Similar to -global or local hyperdynamics (HD), PRD is a method for performing -accelerated dynamics that is suitable for infrequent-event systems -that obey first-order kinetics. A good overview of accelerated -dynamics methods for such systems in given in this review paper -"(Voter2002)"_#Voter2002prd from Art's group. To quote from the -paper: "The dynamical evolution is characterized by vibrational -excursions within a potential basin, punctuated by occasional -transitions between basins." The transition probability is -characterized by p(t) = k*exp(-kt) where k is the rate constant. -Running multiple replicas gives an effective enhancement in the -timescale spanned by the multiple simulations, while waiting for an -event to occur. - -Both PRD and HD produce a time-accurate trajectory that effectively -extends the timescale over which a system can be simulated, but they -do it differently. PRD creates Nr replicas of the system and runs -dynamics on each independently with a normal unbiased potential until -an event occurs in one of the replicas. The time between events is -reduced by a factor of Nr replicas. HD uses a single replica of the -system and accelerates time by biasing the interaction potential in a -manner such that each timestep is effectively longer. For both -methods, per CPU second, more physical time elapses and more events -occur. See the "hyper"_hyper.html doc page for more info about HD. - -In PRD, each replica runs on a partition of one or more processors. -Processor partitions are defined at run-time using the "-partition -command-line switch"_Run_options.html. Note that if you have MPI -installed, you can run a multi-replica simulation with more replicas -(partitions) than you have physical processors, e.g you can run a -10-replica simulation on one or two processors. However for PRD, this -makes little sense, since running a replica on virtual instead of -physical processors,offers no effective parallel speed-up in searching -for infrequent events. See the "Howto replica"_Howto_replica.html doc -page for further discussion. - -When a PRD simulation is performed, it is assumed that each replica is -running the same model, though LAMMPS does not check for this. -I.e. the simulation domain, the number of atoms, the interaction -potentials, etc should be the same for every replica. - -A PRD run has several stages, which are repeated each time an "event" -occurs in one of the replicas, as explained below. The logic for a -PRD run is as follows: - -while (time remains): - dephase for n_dephase*t_dephase steps - until (event occurs on some replica): - run dynamics for t_event steps - quench - check for uncorrelated event on any replica - until (no correlated event occurs): - run dynamics for t_correlate steps - quench - check for correlated event on this replica - event replica shares state with all replicas :pre - -Before this loop begins, the state of the system on replica 0 is -shared with all replicas, so that all replicas begin from the same -initial state. The first potential energy basin is identified by -quenching (an energy minimization, see below) the initial state and -storing the resulting coordinates for reference. - -In the first stage, dephasing is performed by each replica -independently to eliminate correlations between replicas. This is -done by choosing a random set of velocities, based on the -{random_seed} that is specified, and running {t_dephase} timesteps of -dynamics. This is repeated {n_dephase} times. At each of the -{n_dephase} stages, if an event occurs during the {t_dephase} steps of -dynamics for a particular replica, the replica repeats the stage until -no event occurs. - -If the {temp} keyword is not specified, the target temperature for -velocity randomization for each replica is the current temperature of -that replica. Otherwise, it is the specified {Tdephase} temperature. -The style of velocity randomization is controlled using the keyword -{vel} with arguments that have the same meaning as their counterparts -in the "velocity"_velocity.html command. - -In the second stage, each replica runs dynamics continuously, stopping -every {t_event} steps to check if a transition event has occurred. -This check is performed by quenching the system and comparing the -resulting atom coordinates to the coordinates from the previous basin. -The first time through the PRD loop, the "previous basin" is the set -of quenched coordinates from the initial state of the system. - -A quench is an energy minimization and is performed by whichever -algorithm has been defined by the "min_style"_min_style.html command. -Minimization parameters may be set via the -"min_modify"_min_modify.html command and by the {min} keyword of the -PRD command. The latter are the settings that would be used with the -"minimize"_minimize.html command. Note that typically, you do not -need to perform a highly-converged minimization to detect a transition -event, though you may need to in order to prevent a set of atoms in -the system from relaxing to a saddle point. - -The event check is performed by a compute with the specified -{compute-ID}. Currently there is only one compute that works with the -PRD command, which is the "compute -event/displace"_compute_event_displace.html command. Other -event-checking computes may be added. "Compute -event/displace"_compute_event_displace.html checks whether any atom in -the compute group has moved further than a specified threshold -distance. If so, an "event" has occurred. - -In the third stage, the replica on which the event occurred (event -replica) continues to run dynamics to search for correlated events. -This is done by running dynamics for {t_correlate} steps, quenching -every {t_event} steps, and checking if another event has occurred. - -The first time no correlated event occurs, the final state of the -event replica is shared with all replicas, the new basin reference -coordinates are updated with the quenched state, and the outer loop -begins again. While the replica event is searching for correlated -events, all the other replicas also run dynamics and event checking -with the same schedule, but the final states are always overwritten by -the state of the event replica. - -The outer loop of the pseudo-code above continues until {N} steps of -dynamics have been performed. Note that {N} only includes the -dynamics of stages 2 and 3, not the steps taken during dephasing or -the minimization iterations of quenching. The specified {N} is -interpreted in one of two ways, depending on the {time} keyword. If -the {time} value is {steps}, which is the default, then each replica -runs for {N} timesteps. If the {time} value is {clock}, then the -simulation runs until {N} aggregate timesteps across all replicas have -elapsed. This aggregate time is the "clock" time defined below, which -typically advances nearly M times faster than the timestepping on a -single replica, where M is the number of replicas. - -:line - -Four kinds of output can be generated during a PRD run: event -statistics, thermodynamic output by each replica, dump files, and -restart files. - -When running with multiple partitions (each of which is a replica in -this case), the print-out to the screen and master log.lammps file is -limited to event statistics. Note that if a PRD run is performed on -only a single replica then the event statistics will be intermixed -with the usual thermodynamic output discussed below. - -The quantities printed each time an event occurs are the timestep, CPU -time, clock, event number, a correlation flag, the number of -coincident events, and the replica number of the chosen event. - -The timestep is the usual LAMMPS timestep, except that time does not -advance during dephasing or quenches, but only during dynamics. Note -that are two kinds of dynamics in the PRD loop listed above that -contribute to this timestepping. The first is when all replicas are -performing independent dynamics, waiting for an event to occur. The -second is when correlated events are being searched for, but only one -replica is running dynamics. - -The CPU time is the total elapsed time on each processor, since the -start of the PRD run. - -The clock is the same as the timestep except that it advances by M -steps per timestep during the first kind of dynamics when the M -replicas are running independently. The clock advances by only 1 step -per timestep during the second kind of dynamics, when only a single -replica is checking for a correlated event. Thus "clock" time -represents the aggregate time (in steps) that has effectively elapsed -during a PRD simulation on M replicas. If most of the PRD run is -spent in the second stage of the loop above, searching for infrequent -events, then the clock will advance nearly M times faster than it -would if a single replica was running. Note the clock time between -successive events should be drawn from p(t). - -The event number is a counter that increments with each event, whether -it is uncorrelated or correlated. - -The correlation flag will be 0 when an uncorrelated event occurs -during the second stage of the loop listed above, i.e. when all -replicas are running independently. The correlation flag will be 1 -when a correlated event occurs during the third stage of the loop -listed above, i.e. when only one replica is running dynamics. - -When more than one replica detects an event at the end of the same -event check (every {t_event} steps) during the second stage, then -one of them is chosen at random. The number of coincident events is -the number of replicas that detected an event. Normally, this value -should be 1. If it is often greater than 1, then either the number of -replicas is too large, or {t_event} is too large. - -The replica number is the ID of the replica (from 0 to M-1) in which -the event occurred. - -:line - -When running on multiple partitions, LAMMPS produces additional log -files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For -the PRD command, these contain the thermodynamic output for each -replica. You will see short runs and minimizations corresponding to -the dynamics and quench operations of the loop listed above. The -timestep will be reset appropriately depending on whether the -operation advances time or not. - -After the PRD command completes, timing statistics for the PRD run are -printed in each replica's log file, giving a breakdown of how much CPU -time was spent in each stage (dephasing, dynamics, quenching, etc). - -:line - -Any "dump files"_dump.html defined in the input script, will be -written to during a PRD run at timesteps corresponding to both -uncorrelated and correlated events. This means the requested dump -frequency in the "dump"_dump.html command is ignored. There will be -one dump file (per dump command) created for all partitions. - -The atom coordinates of the dump snapshot are those of the minimum -energy configuration resulting from quenching following a transition -event. The timesteps written into the dump files correspond to the -timestep at which the event occurred and NOT the clock. A dump -snapshot corresponding to the initial minimum state used for event -detection is written to the dump file at the beginning of each PRD -run. - -:line - -If the "restart"_restart.html command is used, a single restart file -for all the partitions is generated, which allows a PRD run to be -continued by a new input script in the usual manner. - -The restart file is generated at the end of the loop listed above. If -no correlated events are found, this means it contains a snapshot of -the system at time T + {t_correlate}, where T is the time at which the -uncorrelated event occurred. If correlated events were found, then it -contains a snapshot of the system at time T + {t_correlate}, where T -is the time of the last correlated event. - -The restart frequency specified in the "restart"_restart.html command -is interpreted differently when performing a PRD run. It does not -mean the timestep interval between restart files. Instead it means an -event interval for uncorrelated events. Thus a frequency of 1 means -write a restart file every time an uncorrelated event occurs. A -frequency of 10 means write a restart file every 10th uncorrelated -event. - -When an input script reads a restart file from a previous PRD run, the -new script can be run on a different number of replicas or processors. -However, it is assumed that {t_correlate} in the new PRD command is -the same as it was previously. If not, the calculation of the "clock" -value for the first event in the new run will be slightly off. - -:line - -[Restrictions:] - -This command can only be used if LAMMPS was built with the REPLICA -package. See the "Build package"_Build_package.html doc -page for more info. - -The {N} and {t_correlate} settings must be integer multiples of -{t_event}. - -Runs restarted from restart file written during a PRD run will not -produce identical results due to changes in the random numbers used -for dephasing. - -This command cannot be used when any fixes are defined that keep track -of elapsed time to perform time-dependent operations. Examples -include the "ave" fixes such as "fix ave/chunk"_fix_ave_chunk.html. -Also "fix dt/reset"_fix_dt_reset.html and "fix -deposit"_fix_deposit.html. - -[Related commands:] - -"compute event/displace"_compute_event_displace.html, -"min_modify"_min_modify.html, "min_style"_min_style.html, -"run_style"_run_style.html, "minimize"_minimize.html, -"velocity"_velocity.html, "temper"_temper.html, "neb"_neb.html, -"tad"_tad.html, "hyper"_hyper.html - -[Default:] - -The option defaults are min = 0.1 0.1 40 50, no temp setting, vel = -geom gaussian, and time = steps. - -:line - -:link(Voter1998) -[(Voter1998)] Voter, Phys Rev B, 57, 13985 (1998). - -:link(Voter2002prd) -[(Voter2002)] Voter, Montalenti, Germann, Annual Review of Materials -Research 32, 321 (2002). diff --git a/doc/txt/print.txt b/doc/txt/print.txt deleted file mode 100644 index 476d4104fa..0000000000 --- a/doc/txt/print.txt +++ /dev/null @@ -1,84 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -print command :h3 - -[Syntax:] - -print string keyword value :pre - -string = text string to print, which may contain variables :ulb,l -zero or more keyword/value pairs may be appended :l -keyword = {file} or {append} or {screen} or {universe} :l - {file} value = filename - {append} value = filename - {screen} value = {yes} or {no} - {universe} value = {yes} or {no} :pre -:ule - -[Examples:] - -print "Done with equilibration" file info.dat -print Vol=$v append info.dat screen no -print "The system volume is now $v" -print 'The system volume is now $v' -print "NEB calculation 1 complete" screen no universe yes -print """ -System volume = $v -System temperature = $t -""" :pre - -[Description:] - -Print a text string to the screen and logfile. The text string must -be a single argument, so if it is one line but more than one word, it -should be enclosed in single or double quotes. To generate multiple -lines of output, the string can be enclosed in triple quotes, as in -the last example above. If the text string contains variables, they -will be evaluated and their current values printed. - -If the {file} or {append} keyword is used, a filename is specified to -which the output will be written. If {file} is used, then the -filename is overwritten if it already exists. If {append} is used, -then the filename is appended to if it already exists, or created if -it does not exist. - -If the {screen} keyword is used, output to the screen and logfile can -be turned on or off as desired. - -If the {universe} keyword is used, output to the global screen and -logfile can be turned on or off as desired. In multi-partition -calculations, the {screen} option and the corresponding output only -apply to the screen and logfile of the individual partition. - -If you want the print command to be executed multiple times (with -changing variable values), there are 3 options. First, consider using -the "fix print"_fix_print.html command, which will print a string -periodically during a simulation. Second, the print command can be -used as an argument to the {every} option of the "run"_run.html -command. Third, the print command could appear in a section of the -input script that is looped over (see the "jump"_jump.html and -"next"_next.html commands). - -See the "variable"_variable.html command for a description of {equal} -style variables which are typically the most useful ones to use with -the print command. Equal-style variables can calculate formulas -involving mathematical operations, atom properties, group properties, -thermodynamic properties, global values calculated by a -"compute"_compute.html or "fix"_fix.html, or references to other -"variables"_variable.html. - -[Restrictions:] none - -[Related commands:] - -"fix print"_fix_print.html, "variable"_variable.html - -[Default:] - -The option defaults are no file output, screen = yes, and universe = no. diff --git a/doc/txt/processors.txt b/doc/txt/processors.txt deleted file mode 100644 index b9bd927f96..0000000000 --- a/doc/txt/processors.txt +++ /dev/null @@ -1,341 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -processors command :h3 - -[Syntax:] - -processors Px Py Pz keyword args ... :pre - -Px,Py,Pz = # of processors in each dimension of 3d grid overlaying the simulation domain :ulb,l -zero or more keyword/arg pairs may be appended :l -keyword = {grid} or {map} or {part} or {file} :l - {grid} arg = gstyle params ... - gstyle = {onelevel} or {twolevel} or {numa} or {custom} - onelevel params = none - twolevel params = Nc Cx Cy Cz - Nc = number of cores per node - Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node - numa params = none - custom params = infile - infile = file containing grid layout - {map} arg = {cart} or {cart/reorder} or {xyz} or {xzy} or {yxz} or {yzx} or {zxy} or {zyx} - cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0 - cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1 - xyz,xzy,yxz,yzx,zxy,zyx = map processors to 3d grid in IJK ordering - {numa} arg = none - {part} args = Psend Precv cstyle - Psend = partition # (1 to Np) which will send its processor layout - Precv = partition # (1 to Np) which will recv the processor layout - cstyle = {multiple} - {multiple} = Psend grid will be multiple of Precv grid in each dimension - {file} arg = outfile - outfile = name of file to write 3d grid of processors to :pre -:ule - -[Examples:] - -processors * * 5 -processors 2 4 4 -processors * * 8 map xyz -processors * * * grid numa -processors * * * grid twolevel 4 * * 1 -processors 4 8 16 grid custom myfile -processors * * * part 1 2 multiple :pre - -[Description:] - -Specify how processors are mapped as a regular 3d grid to the global -simulation box. The mapping involves 2 steps. First if there are P -processors it means choosing a factorization P = Px by Py by Pz so -that there are Px processors in the x dimension, and similarly for the -y and z dimensions. Second, the P processors are mapped to the -regular 3d grid. The arguments to this command control each of these -2 steps. - -The Px, Py, Pz parameters affect the factorization. Any of the 3 -parameters can be specified with an asterisk "*", which means LAMMPS -will choose the number of processors in that dimension of the grid. -It will do this based on the size and shape of the global simulation -box so as to minimize the surface-to-volume ratio of each processor's -sub-domain. - -Choosing explicit values for Px or Py or Pz can be used to override -the default manner in which LAMMPS will create the regular 3d grid of -processors, if it is known to be sub-optimal for a particular problem. -E.g. a problem where the extent of atoms will change dramatically in a -particular dimension over the course of the simulation. - -The product of Px, Py, Pz must equal P, the total # of processors -LAMMPS is running on. For a "2d simulation"_dimension.html, Pz must -equal 1. - -Note that if you run on a prime number of processors P, then a grid -such as 1 x P x 1 will be required, which may incur extra -communication costs due to the high surface area of each processor's -sub-domain. - -Also note that if multiple partitions are being used then P is the -number of processors in this partition; see the "-partition -command-line switch"_Run_options.html doc page for details. Also note -that you can prefix the processors command with the -"partition"_partition.html command to easily specify different -Px,Py,Pz values for different partitions. - -You can use the "partition"_partition.html command to specify -different processor grids for different partitions, e.g. - -partition yes 1 processors 4 4 4 -partition yes 2 processors 2 3 2 :pre - -NOTE: This command only affects the initial regular 3d grid created -when the simulation box is first specified via a -"create_box"_create_box.html or "read_data"_read_data.html or -"read_restart"_read_restart.html command. Or if the simulation box is -re-created via the "replicate"_replicate.html command. The same -regular grid is initially created, regardless of which -"comm_style"_comm_style.html command is in effect. - -If load-balancing is never invoked via the "balance"_balance.html or -"fix balance"_fix_balance.html commands, then the initial regular grid -will persist for all simulations. If balancing is performed, some of -the methods invoked by those commands retain the logical topology of -the initial 3d grid, and the mapping of processors to the grid -specified by the processors command. However the grid spacings in -different dimensions may change, so that processors own sub-domains of -different sizes. If the "comm_style tiled"_comm_style.html command is -used, methods invoked by the balancing commands may discard the 3d -grid of processors and tile the simulation domain with sub-domains of -different sizes and shapes which no longer have a logical 3d -connectivity. If that occurs, all the information specified by the -processors command is ignored. - -:line - -The {grid} keyword affects the factorization of P into Px,Py,Pz and it -can also affect how the P processor IDs are mapped to the 3d grid of -processors. - -The {onelevel} style creates a 3d grid that is compatible with the -Px,Py,Pz settings, and which minimizes the surface-to-volume ratio of -each processor's sub-domain, as described above. The mapping of -processors to the grid is determined by the {map} keyword setting. - -The {twolevel} style can be used on machines with multicore nodes to -minimize off-node communication. It insures that contiguous -sub-sections of the 3d grid are assigned to all the cores of a node. -For example if {Nc} is 4, then 2x2x1 or 2x1x2 or 1x2x2 sub-sections of -the 3d grid will correspond to the cores of each node. This affects -both the factorization and mapping steps. - -The {Cx}, {Cy}, {Cz} settings are similar to the {Px}, {Py}, {Pz} -settings, only their product should equal {Nc}. Any of the 3 -parameters can be specified with an asterisk "*", which means LAMMPS -will choose the number of cores in that dimension of the node's -sub-grid. As with Px,Py,Pz, it will do this based on the size and -shape of the global simulation box so as to minimize the -surface-to-volume ratio of each processor's sub-domain. - -NOTE: For the {twolevel} style to work correctly, it assumes the MPI -ranks of processors LAMMPS is running on are ordered by core and then -by node. E.g. if you are running on 2 quad-core nodes, for a total of -8 processors, then it assumes processors 0,1,2,3 are on node 1, and -processors 4,5,6,7 are on node 2. This is the default rank ordering -for most MPI implementations, but some MPIs provide options for this -ordering, e.g. via environment variable settings. - -The {numa} style operates similar to the {twolevel} keyword except -that it auto-detects which cores are running on which nodes. -Currently, it does this in only 2 levels, but it may be extended in -the future to account for socket topology and other non-uniform memory -access (NUMA) costs. It also uses a different algorithm than the -{twolevel} keyword for doing the two-level factorization of the -simulation box into a 3d processor grid to minimize off-node -communication, and it does its own MPI-based mapping of nodes and -cores to the regular 3d grid. Thus it may produce a different layout -of the processors than the {twolevel} options. - -The {numa} style will give an error if the number of MPI processes is -not divisible by the number of cores used per node, or any of the Px -or Py of Pz values is greater than 1. - -NOTE: Unlike the {twolevel} style, the {numa} style does not require -any particular ordering of MPI ranks i norder to work correctly. This -is because it auto-detects which processes are running on which nodes. - -The {custom} style uses the file {infile} to define both the 3d -factorization and the mapping of processors to the grid. - -The file should have the following format. Any number of initial -blank or comment lines (starting with a "#" character) can be present. -The first non-blank, non-comment line should have -3 values: - -Px Py Py :pre - -These must be compatible with the total number of processors -and the Px, Py, Pz settings of the processors command. - -This line should be immediately followed by -P = Px*Py*Pz lines of the form: - -ID I J K :pre - -where ID is a processor ID (from 0 to P-1) and I,J,K are the -processors location in the 3d grid. I must be a number from 1 to Px -(inclusive) and similarly for J and K. The P lines can be listed in -any order, but no processor ID should appear more than once. - -:line - -The {map} keyword affects how the P processor IDs (from 0 to P-1) are -mapped to the 3d grid of processors. It is only used by the -{onelevel} and {twolevel} grid settings. - -The {cart} style uses the family of MPI Cartesian functions to perform -the mapping, namely MPI_Cart_create(), MPI_Cart_get(), -MPI_Cart_shift(), and MPI_Cart_rank(). It invokes the -MPI_Cart_create() function with its reorder flag = 0, so that MPI is -not free to reorder the processors. - -The {cart/reorder} style does the same thing as the {cart} style -except it sets the reorder flag to 1, so that MPI can reorder -processors if it desires. - -The {xyz}, {xzy}, {yxz}, {yzx}, {zxy}, and {zyx} styles are all -similar. If the style is IJK, then it maps the P processors to the -grid so that the processor ID in the I direction varies fastest, the -processor ID in the J direction varies next fastest, and the processor -ID in the K direction varies slowest. For example, if you select -style {xyz} and you have a 2x2x2 grid of 8 processors, the assignments -of the 8 octants of the simulation domain will be: - -proc 0 = lo x, lo y, lo z octant -proc 1 = hi x, lo y, lo z octant -proc 2 = lo x, hi y, lo z octant -proc 3 = hi x, hi y, lo z octant -proc 4 = lo x, lo y, hi z octant -proc 5 = hi x, lo y, hi z octant -proc 6 = lo x, hi y, hi z octant -proc 7 = hi x, hi y, hi z octant :pre - -Note that, in principle, an MPI implementation on a particular machine -should be aware of both the machine's network topology and the -specific subset of processors and nodes that were assigned to your -simulation. Thus its MPI_Cart calls can optimize the assignment of -MPI processes to the 3d grid to minimize communication costs. In -practice, however, few if any MPI implementations actually do this. -So it is likely that the {cart} and {cart/reorder} styles simply give -the same result as one of the IJK styles. - -Also note, that for the {twolevel} grid style, the {map} setting is -used to first map the nodes to the 3d grid, then again to the cores -within each node. For the latter step, the {cart} and {cart/reorder} -styles are not supported, so an {xyz} style is used in their place. - -:line - -The {part} keyword affects the factorization of P into Px,Py,Pz. - -It can be useful when running in multi-partition mode, e.g. with the -"run_style verlet/split"_run_style.html command. It specifies a -dependency between a sending partition {Psend} and a receiving -partition {Precv} which is enforced when each is setting up their own -mapping of their processors to the simulation box. Each of {Psend} -and {Precv} must be integers from 1 to Np, where Np is the number of -partitions you have defined via the "-partition command-line -switch"_Run_options.html. - -A "dependency" means that the sending partition will create its -regular 3d grid as Px by Py by Pz and after it has done this, it will -send the Px,Py,Pz values to the receiving partition. The receiving -partition will wait to receive these values before creating its own -regular 3d grid and will use the sender's Px,Py,Pz values as a -constraint. The nature of the constraint is determined by the -{cstyle} argument. - -For a {cstyle} of {multiple}, each dimension of the sender's processor -grid is required to be an integer multiple of the corresponding -dimension in the receiver's processor grid. This is a requirement of -the "run_style verlet/split"_run_style.html command. - -For example, assume the sending partition creates a 4x6x10 grid = 240 -processor grid. If the receiving partition is running on 80 -processors, it could create a 4x2x10 grid, but it will not create a -2x4x10 grid, since in the y-dimension, 6 is not an integer multiple of -4. - -NOTE: If you use the "partition"_partition.html command to invoke -different "processors" commands on different partitions, and you also -use the {part} keyword, then you must insure that both the sending and -receiving partitions invoke the "processors" command that connects the -2 partitions via the {part} keyword. LAMMPS cannot easily check for -this, but your simulation will likely hang in its setup phase if this -error has been made. - -:line - -The {file} keyword writes the mapping of the factorization of P -processors and their mapping to the 3d grid to the specified file -{outfile}. This is useful to check that you assigned physical -processors in the manner you desired, which can be tricky to figure -out, especially when running on multiple partitions or on, a multicore -machine or when the processor ranks were reordered by use of the -"-reorder command-line switch"_Run_options.html or due to use of -MPI-specific launch options such as a config file. - -If you have multiple partitions you should insure that each one writes -to a different file, e.g. using a "world-style variable"_variable.html -for the filename. The file has a self-explanatory header, followed by -one-line per processor in this format: - -world-ID universe-ID original-ID: I J K: name - -The IDs are the processor's rank in this simulation (the world), the -universe (of multiple simulations), and the original MPI communicator -used to instantiate LAMMPS, respectively. The world and universe IDs -will only be different if you are running on more than one partition; -see the "-partition command-line switch"_Run_options.html. The -universe and original IDs will only be different if you used the -"-reorder command-line switch"_Run_options.html to reorder the -processors differently than their rank in the original communicator -LAMMPS was instantiated with. - -I,J,K are the indices of the processor in the regular 3d grid, each -from 1 to Nd, where Nd is the number of processors in that dimension -of the grid. - -The {name} is what is returned by a call to MPI_Get_processor_name() -and should represent an identifier relevant to the physical processors -in your machine. Note that depending on the MPI implementation, -multiple cores can have the same {name}. - -:line - -[Restrictions:] - -This command cannot be used after the simulation box is defined by a -"read_data"_read_data.html or "create_box"_create_box.html command. -It can be used before a restart file is read to change the 3d -processor grid from what is specified in the restart file. - -The {grid numa} keyword only currently works with the {map cart} -option. - -The {part} keyword (for the receiving partition) only works with the -{grid onelevel} or {grid twolevel} options. - -[Related commands:] - -"partition"_partition.html, "-reorder command-line -switch"_Run_options.html - -[Default:] - -The option defaults are Px Py Pz = * * *, grid = onelevel, and map = -cart. diff --git a/doc/txt/quit.txt b/doc/txt/quit.txt deleted file mode 100644 index 802df97711..0000000000 --- a/doc/txt/quit.txt +++ /dev/null @@ -1,46 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -quit command :h3 - -[Syntax:] - -quit status :pre - -status = numerical exit status (optional) - -[Examples:] - -quit -if "$n > 10000" then "quit 1" :pre - -[Description:] - -This command causes LAMMPS to exit, after shutting down all output -cleanly. - -It can be used as a debug statement in an input script, to terminate -the script at some intermediate point. - -It can also be used as an invoked command inside the "then" or "else" -portion of an "if"_if.html command. - -The optional status argument is an integer which signals the return -status to a program calling LAMMPS. A return status of 0 usually -indicates success. A status != 0 is failure, where the specified -value can be used to distinguish the kind of error, e.g. where in the -input script the quit was invoked. If not specified, a status of 0 is -returned. - -[Restrictions:] none - -[Related commands:] - -"if"_if.html - -[Default:] none diff --git a/doc/txt/read_data.txt b/doc/txt/read_data.txt deleted file mode 100644 index 5fb91ba797..0000000000 --- a/doc/txt/read_data.txt +++ /dev/null @@ -1,1169 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -read_data command :h3 - -[Syntax:] - -read_data file keyword args ... :pre - -file = name of data file to read in :ulb,l -zero or more keyword/arg pairs may be appended :l -keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {extra/bond/per/atom} or {extra/angle/per/atom} or {extra/dihedral/per/atom} or {extra/improper/per/atom} or {group} or {nocoeff} or {fix} :l - {add} arg = {append} or {IDoffset} or {IDoffset MOLoffset} or {merge} - append = add new atoms with atom IDs appended to current IDs - IDoffset = add new atoms with atom IDs having IDoffset added - MOLoffset = add new atoms with molecule IDs having MOLoffset added (only when molecule IDs are enabled) - merge = add new atoms with their atom IDs (and molecule IDs) unchanged - {offset} args = toff boff aoff doff ioff - toff = offset to add to atom types - boff = offset to add to bond types - aoff = offset to add to angle types - doff = offset to add to dihedral types - ioff = offset to add to improper types - {shift} args = Sx Sy Sz - Sx,Sy,Sz = distance to shift atoms when adding to system (distance units) - {extra/atom/types} arg = # of extra atom types - {extra/bond/types} arg = # of extra bond types - {extra/angle/types} arg = # of extra angle types - {extra/dihedral/types} arg = # of extra dihedral types - {extra/improper/types} arg = # of extra improper types - {extra/bond/per/atom} arg = leave space for this many new bonds per atom - {extra/angle/per/atom} arg = leave space for this many new angles per atom - {extra/dihedral/per/atom} arg = leave space for this many new dihedrals per atom - {extra/improper/per/atom} arg = leave space for this many new impropers per atom - {extra/special/per/atom} arg = leave space for extra 1-2,1-3,1-4 interactions per atom - {group} args = groupID - groupID = add atoms in data file to this group - {nocoeff} = ignore force field parameters - {fix} args = fix-ID header-string section-string - fix-ID = ID of fix to process header lines and sections of data file - header-string = header lines containing this string will be passed to fix - section-string = section names with this string will be passed to fix :pre -:ule - -[Examples:] - -read_data data.lj -read_data ../run7/data.polymer.gz -read_data data.protein fix mycmap crossterm CMAP -read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0 -read_data data.water add merge 1 group solvent :pre - -[Description:] - -Read in a data file containing information LAMMPS needs to run a -simulation. The file can be ASCII text or a gzipped text file -(detected by a .gz suffix). This is one of 3 ways to specify initial -atom coordinates; see the "read_restart"_read_restart.html and -"create_atoms"_create_atoms.html commands for alternative methods. -Also see the explanation of the "-restart command-line -switch"_Run_options.html which can convert a restart file to a data -file. - -This command can be used multiple times to add new atoms and their -properties to an existing system by using the {add}, {offset}, and -{shift} keywords. See more details below, which includes the use case -for the {extra} keywords. - -The {group} keyword adds all the atoms in the data file to the -specified group-ID. The group will be created if it does not already -exist. This is useful if you are reading multiple data files and wish -to put sets of atoms into different groups so they can be operated on -later. E.g. a group of added atoms can be moved to new positions via -the "displace_atoms"_displace_atoms.html command. Note that atoms -read from the data file are also always added to the "all" group. The -"group"_group.html command discusses atom groups, as used in LAMMPS. - -The {nocoeff} keyword tells read_data to ignore force field parameters. -The various Coeff sections are still read and have to have the correct -number of lines, but they are not applied. This also allows to read a -data file without having any pair, bond, angle, dihedral or improper -styles defined, or to read a data file for a different force field. - -The use of the {fix} keyword is discussed below. - -:line - -[Reading multiple data files] - -The read_data command can be used multiple times with the same or -different data files to build up a complex system from components -contained in individual data files. For example one data file could -contain fluid in a confined domain; a second could contain wall atoms, -and the second file could be read a third time to create a wall on the -other side of the fluid. The third set of atoms could be rotated to -an opposing direction using the "displace_atoms"_displace_atoms.html -command, after the third read_data command is used. - -The {add}, {offset}, {shift}, {extra}, and {group} keywords are -useful in this context. - -If a simulation box does not yet exist, the {add} keyword -cannot be used; the read_data command is being used for the first -time. If a simulation box does exist, due to using the -"create_box"_create_box.html command, or a previous read_data command, -then the {add} keyword must be used. - -NOTE: The simulation box size (xlo to xhi, ylo to yhi, zlo to zhi) in -the new data file will be merged with the existing simulation box to -create a large enough box in each dimension to contain both the -existing and new atoms. Each box dimension never shrinks due to this -merge operation, it only stays the same or grows. Care must be used if -you are growing the existing simulation box in a periodic dimension. -If there are existing atoms with bonds that straddle that periodic -boundary, then the atoms may become far apart if the box size grows. -This will separate the atoms in the bond, which can lead to "lost" -bond atoms or bad dynamics. - -The three choices for the {add} argument affect how the atom IDs and -molecule IDs of atoms in the data file are treated. If {append} is -specified, atoms in the data file are added to the current system, -with their atom IDs reset so that an atom-ID = M in the data file -becomes atom-ID = N+M, where N is the largest atom ID in the current -system. This rule is applied to all occurrences of atom IDs in the -data file, e.g. in the Velocity or Bonds section. This is also done -for molecule IDs, if the atom style does support molecule IDs or -they are enabled via fix property/atom. If {IDoffset} is specified, -then {IDoffset} is a numeric value is given, e.g. 1000, so that an -atom-ID = M in the data file becomes atom-ID = 1000+M. For systems -with enabled molecule IDs, another numerical argument {MOLoffset} -is required representing the equivalent offset for molecule IDs. -If {merge} is specified, the data file atoms -are added to the current system without changing their IDs. They are -assumed to merge (without duplication) with the currently defined -atoms. It is up to you to insure there are no multiply defined atom -IDs, as LAMMPS only performs an incomplete check that this is the case -by insuring the resulting max atom-ID >= the number of atoms. For -molecule IDs, there is no check done at all. - -The {offset} and {shift} keywords can only be used if the {add} -keyword is also specified. - -The {offset} keyword adds the specified offset values to the atom -types, bond types, angle types, dihedral types, and improper types as -they are read from the data file. E.g. if {toff} = 2, and the file -uses atom types 1,2,3, then the added atoms will have atom types -3,4,5. These offsets apply to all occurrences of types in the data -file, e.g. for the Atoms or Masses or Pair Coeffs or Bond Coeffs -sections. This makes it easy to use atoms and molecules and their -attributes from a data file in different simulations, where you want -their types (atom, bond, angle, etc) to be different depending on what -other types already exist. All five offset values must be specified, -but individual values will be ignored if the data file does not use -that attribute (e.g. no bonds). - -The {shift} keyword can be used to specify an (Sx, Sy, Sz) -displacement applied to the coordinates of each atom. Sz must be 0.0 -for a 2d simulation. This is a mechanism for adding structured -collections of atoms at different locations within the simulation box, -to build up a complex geometry. It is up to you to insure atoms do -not end up overlapping unphysically which would lead to bad dynamics. -Note that the "displace_atoms"_displace_atoms.html command can be used -to move a subset of atoms after they have been read from a data file. -Likewise, the "delete_atoms"_delete_atoms.html command can be used to -remove overlapping atoms. Note that the shift values (Sx, Sy, Sz) are -also added to the simulation box information (xlo, xhi, ylo, yhi, zlo, -zhi) in the data file to shift its boundaries. E.g. xlo_new = xlo + -Sx, xhi_new = xhi + Sx. - -The {extra} keywords can only be used the first time the read_data -command is used. They are useful if you intend to add new atom, bond, -angle, etc types later with additional read_data commands. This is -because the maximum number of allowed atom, bond, angle, etc types is -set by LAMMPS when the system is first initialized. If you do not use -the {extra} keywords, then the number of these types will be limited -to what appears in the first data file you read. For example, if the -first data file is a solid substrate of Si, it will likely specify a -single atom type. If you read a second data file with a different -material (water molecules) that sit on top of the substrate, you will -want to use different atom types for those atoms. You can only do -this if you set the {extra/atom/types} keyword to a sufficiently large -value when reading the substrate data file. Note that use of the -{extra} keywords also allows each data file to contain sections like -Masses or Pair Coeffs or Bond Coeffs which are sized appropriately for -the number of types in that data file. If the {offset} keyword is -used appropriately when each data file is read, the values in those -sections will be stored correctly in the larger data structures -allocated by the use of the {extra} keywords. E.g. the substrate file -can list mass and pair coefficients for type 1 silicon atoms. The -water file can list mass and pair coefficients for type 1 and type 2 -hydrogen and oxygen atoms. Use of the {extra} and {offset} keywords -will store those mass and pair coefficient values appropriately in -data structures that allow for 3 atom types (Si, H, O). Of course, -you would still need to specify coefficients for H/Si and O/Si -interactions in your input script to have a complete pairwise -interaction model. - -An alternative to using the {extra} keywords with the read_data -command, is to use the "create_box"_create_box.html command to -initialize the simulation box and all the various type limits you need -via its {extra} keywords. Then use the read_data command one or more -times to populate the system with atoms, bonds, angles, etc, using the -{offset} keyword if desired to alter types used in the various data -files you read. - -:line - -[Format of a data file] - -The structure of the data file is important, though many settings and -sections are optional or can come in any order. See the examples -directory for sample data files for different problems. - -A data file has a header and a body. The header appears first. The -first line of the header is always skipped; it typically contains a -description of the file. Then lines are read one at a time. Lines -can have a trailing comment starting with '#' that is ignored. If the -line is blank (only white-space after comment is deleted), it is -skipped. If the line contains a header keyword, the corresponding -value(s) is read from the line. If it doesn't contain a header -keyword, the line begins the body of the file. - -The body of the file contains zero or more sections. The first line -of a section has only a keyword. This line can have a trailing -comment starting with '#' that is either ignored or can be used to -check for a style match, as described below. The next line is -skipped. The remaining lines of the section contain values. The -number of lines depends on the section keyword as described below. -Zero or more blank lines can be used between sections. Sections can -appear in any order, with a few exceptions as noted below. - -The keyword {fix} can be used one or more times. Each usage specifies -a fix that will be used to process a specific portion of the data -file. Any header line containing {header-string} and any section with -a name containing {section-string} will be passed to the specified -fix. See the "fix property/atom"_fix_property_atom.html command for -an example of a fix that operates in this manner. The doc page for -the fix defines the syntax of the header line(s) and section(s) that -it reads from the data file. Note that the {header-string} can be -specified as NULL, in which case no header lines are passed to the -fix. This means that it can infer the length of its Section from -standard header settings, such as the number of atoms. - -The formatting of individual lines in the data file (indentation, -spacing between words and numbers) is not important except that header -and section keywords (e.g. atoms, xlo xhi, Masses, Bond Coeffs) must -be capitalized as shown and can't have extra white-space between their -words - e.g. two spaces or a tab between the 2 words in "xlo xhi" or -the 2 words in "Bond Coeffs", is not valid. - -:line - -[Format of the header of a data file] - -These are the recognized header keywords. Header lines can come in -any order. The value(s) are read from the beginning of the line. -Thus the keyword {atoms} should be in a line like "1000 atoms"; the -keyword {ylo yhi} should be in a line like "-10.0 10.0 ylo yhi"; the -keyword {xy xz yz} should be in a line like "0.0 5.0 6.0 xy xz yz". -All these settings have a default value of 0, except the lo/hi box -size defaults are -0.5 and 0.5. A line need only appear if the value -is different than the default. - -{atoms} = # of atoms in system -{bonds} = # of bonds in system -{angles} = # of angles in system -{dihedrals} = # of dihedrals in system -{impropers} = # of impropers in system -{atom types} = # of atom types in system -{bond types} = # of bond types in system -{angle types} = # of angle types in system -{dihedral types} = # of dihedral types in system -{improper types} = # of improper types in system -{extra bond per atom} = leave space for this many new bonds per atom (deprecated, use extra/bond/per/atom keyword) -{extra angle per atom} = leave space for this many new angles per atom (deprecated, use extra/angle/per/atom keyword) -{extra dihedral per atom} = leave space for this many new dihedrals per atom (deprecated, use extra/dihedral/per/atom keyword) -{extra improper per atom} = leave space for this many new impropers per atom (deprecated, use extra/improper/per/atom keyword) -{extra special per atom} = leave space for this many new special bonds per atom (deprecated, use extra/special/per/atom keyword) -{ellipsoids} = # of ellipsoids in system -{lines} = # of line segments in system -{triangles} = # of triangles in system -{bodies} = # of bodies in system -{xlo xhi} = simulation box boundaries in x dimension -{ylo yhi} = simulation box boundaries in y dimension -{zlo zhi} = simulation box boundaries in z dimension -{xy xz yz} = simulation box tilt factors for triclinic system :ul - -The initial simulation box size is determined by the lo/hi settings. -In any dimension, the system may be periodic or non-periodic; see the -"boundary"_boundary.html command. When the simulation box is created -it is also partitioned into a regular 3d grid of rectangular bricks, -one per processor, based on the number of processors being used and -the settings of the "processors"_processors.html command. The -partitioning can later be changed by the "balance"_balance.html or -"fix balance"_fix_balance.html commands. - -If the {xy xz yz} line does not appear, LAMMPS will set up an -axis-aligned (orthogonal) simulation box. If the line does appear, -LAMMPS creates a non-orthogonal simulation domain shaped as a -parallelepiped with triclinic symmetry. The parallelepiped has its -"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting -from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C = -(xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or positive or negative values -and are called "tilt factors" because they are the amount of -displacement applied to faces of an originally orthogonal box to -transform it into the parallelepiped. - -By default, the tilt factors (xy,xz,yz) can not skew the box more than -half the distance of the corresponding parallel box length. For -example, if xlo = 2 and xhi = 12, then the x box length is 10 and the -xy tilt factor must be between -5 and 5. Similarly, both xz and yz -must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not -a limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are all geometrically equivalent. If you wish to define a box -with tilt factors that exceed these limits, you can use the "box -tilt"_box.html command, with a setting of {large}; a setting of -{small} is the default. - -See the "Howto triclinic"_Howto_triclinic.html doc page for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used -triclinic representations. - -When a triclinic system is used, the simulation domain should normally -be periodic in the dimension that the tilt is applied to, which is -given by the second dimension of the tilt factor (e.g. y for xy tilt). -This is so that pairs of atoms interacting across that boundary will -have one of them shifted by the tilt factor. Periodicity is set by -the "boundary"_boundary.html command. For example, if the xy tilt -factor is non-zero, then the y dimension should be periodic. -Similarly, the z dimension should be periodic if xz or yz is non-zero. -LAMMPS does not require this periodicity, but you may lose atoms if -this is not the case. - -Also note that if your simulation will tilt the box, e.g. via the "fix -deform"_fix_deform.html command, the simulation box must be setup to -be triclinic, even if the tilt factors are initially 0.0. You can -also change an orthogonal box to a triclinic box or vice versa by -using the "change box"_change_box.html command with its {ortho} and -{triclinic} options. - -For 2d simulations, the {zlo zhi} values should be set to bound the z -coords for atoms that appear in the file; the default of -0.5 0.5 is -valid if all z coords are 0.0. For 2d triclinic simulations, the xz -and yz tilt factors must be 0.0. - -If the system is periodic (in a dimension), then atom coordinates can -be outside the bounds (in that dimension); they will be remapped (in a -periodic sense) back inside the box. Note that if the {add} option is -being used to add atoms to a simulation box that already exists, this -periodic remapping will be performed using simulation box bounds that -are the union of the existing box and the box boundaries in the new -data file. - -NOTE: If the system is non-periodic (in a dimension), then all atoms -in the data file must have coordinates (in that dimension) that are -"greater than or equal to" the lo value and "less than or equal to" -the hi value. If the non-periodic dimension is of style "fixed" (see -the "boundary"_boundary.html command), then the atom coords must be -strictly "less than" the hi value, due to the way LAMMPS assign atoms -to processors. Note that you should not make the lo/hi values -radically smaller/larger than the extent of the atoms. For example, -if your atoms extend from 0 to 50, you should not specify the box -bounds as -10000 and 10000. This is because LAMMPS uses the specified -box size to layout the 3d grid of processors. A huge (mostly empty) -box will be sub-optimal for performance when using "fixed" boundary -conditions (see the "boundary"_boundary.html command). When using -"shrink-wrap" boundary conditions (see the "boundary"_boundary.html -command), a huge (mostly empty) box may cause a parallel simulation to -lose atoms when LAMMPS shrink-wraps the box around the atoms. The -read_data command will generate an error in this case. - -The "extra bond per atom" setting (angle, dihedral, improper) is only -needed if new bonds (angles, dihedrals, impropers) will be added to -the system when a simulation runs, e.g. by using the "fix -bond/create"_fix_bond_create.html command. Using this header flag -is deprecated; please use the {extra/bond/per/atom} keyword (and -correspondingly for angles, dihedrals and impropers) in the read_data -command instead. Either will pre-allocate space in LAMMPS data -structures for storing the new bonds (angles, dihedrals, impropers). - -The "extra special per atom" setting is typically only needed if new -bonds/angles/etc will be added to the system, e.g. by using the "fix -bond/create"_fix_bond_create.html command. Or if entire new molecules -will be added to the system, e.g. by using the -"fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands, -which will have more special 1-2,1-3,1-4 neighbors than any other -molecules defined in the data file. Using this header flag is -deprecated; please use the {extra/special/per/atom} keyword instead. -Using this setting will pre-allocate space in the LAMMPS data -structures for storing these neighbors. See the -"special_bonds"_special_bonds.html and "molecule"_molecule.html doc -pages for more discussion of 1-2,1-3,1-4 neighbors. - -NOTE: All of the "extra" settings are only applied in the first data -file read and when no simulation box has yet been created; as soon as -the simulation box is created (and read_data implies that), these -settings are {locked} and cannot be changed anymore. Please see the -description of the {add} keyword above for reading multiple data files. -If they appear in later data files, they are ignored. - -The "ellipsoids" and "lines" and "triangles" and "bodies" settings are -only used with "atom_style ellipsoid or line or tri or -body"_atom_style.html and specify how many of the atoms are -finite-size ellipsoids or lines or triangles or bodies; the remainder -are point particles. See the discussion of ellipsoidflag and the -{Ellipsoids} section below. See the discussion of lineflag and the -{Lines} section below. See the discussion of triangleflag and the -{Triangles} section below. See the discussion of bodyflag and the -{Bodies} section below. - -NOTE: For "atom_style template"_atom_style.html, the molecular -topology (bonds,angles,etc) is contained in the molecule templates -read-in by the "molecule"_molecule.html command. This means you -cannot set the {bonds}, {angles}, etc header keywords in the data -file, nor can you define {Bonds}, {Angles}, etc sections as discussed -below. You can set the {bond types}, {angle types}, etc header -keywords, though it is not necessary. If specified, they must match -the maximum values defined in any of the template molecules. - -:line - -[Format of the body of a data file] - -These are the section keywords for the body of the file. - -{Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies} = atom-property sections -{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections -{Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \ - Improper Coeffs} = force field sections -{BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, \ - EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, \ - BondBond13 Coeffs, AngleAngle Coeffs} = class 2 force field sections :ul - -These keywords will check an appended comment for a match with the -currently defined style: - -{Atoms, Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs} :ul - -For example, these lines: - -Atoms # sphere -Pair Coeffs # lj/cut :pre - -will check if the currently-defined "atom_style"_atom_style.html is -{sphere}, and the current "pair_style"_pair_style.html is {lj/cut}. -If not, LAMMPS will issue a warning to indicate that the data file -section likely does not contain the correct number or type of -parameters expected for the currently-defined style. - -Each section is listed below in alphabetic order. The format of each -section is described including the number of lines it must contain and -rules (if any) for where it can appear in the data file. - -Any individual line in the various sections can have a trailing -comment starting with "#" for annotation purposes. E.g. in the -Atoms section: - -10 1 17 -1.0 10.0 5.0 6.0 # salt ion :pre - -:line - -{Angle Coeffs} section: - -one line per angle type :ulb,l -line syntax: ID coeffs :l - ID = angle type (1-N) - coeffs = list of coeffs :pre -example: :l - 6 70 108.5 0 0 :pre -:ule - -The number and meaning of the coefficients are specific to the defined -angle style. See the "angle_style"_angle_style.html and -"angle_coeff"_angle_coeff.html commands for details. Coefficients can -also be set via the "angle_coeff"_angle_coeff.html command in the -input script. - -:line - -{AngleAngle Coeffs} section: - -one line per improper type :ulb,l -line syntax: ID coeffs :l - ID = improper type (1-N) - coeffs = list of coeffs (see "improper_coeff"_improper_coeff.html) :pre -:ule - -:line - -{AngleAngleTorsion Coeffs} section: - -one line per dihedral type :ulb,l -line syntax: ID coeffs :l - ID = dihedral type (1-N) - coeffs = list of coeffs (see "dihedral_coeff"_dihedral_coeff.html) :pre -:ule - -:line - -{Angles} section: - -one line per angle :ulb,l -line syntax: ID type atom1 atom2 atom3 :l - ID = number of angle (1-Nangles) - type = angle type (1-Nangletype) - atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle :pre -example: :b - 2 2 17 29 430 :pre -:ule - -The 3 atoms are ordered linearly within the angle. Thus the central -atom (around which the angle is computed) is the atom2 in the list. -E.g. H,O,H for a water molecule. The {Angles} section must appear -after the {Atoms} section. All values in this section must be -integers (1, not 1.0). - -:line - -{AngleTorsion Coeffs} section: - -one line per dihedral type :ulb,l -line syntax: ID coeffs :l - ID = dihedral type (1-N) - coeffs = list of coeffs (see "dihedral_coeff"_dihedral_coeff.html) :pre -:ule - -:line - -{Atoms} section: - -one line per atom -line syntax: depends on atom style :ul - -An {Atoms} section must appear in the data file if natoms > 0 in the -header section. The atoms can be listed in any order. These are the -line formats for each "atom style"_atom_style.html in LAMMPS. As -discussed below, each line can optionally have 3 flags (nx,ny,nz) -appended to it, which indicate which image of a periodic simulation -box the atom is in. These may be important to include for some kinds -of analysis. - -angle: atom-ID molecule-ID atom-type x y z -atomic: atom-ID atom-type x y z -body: atom-ID atom-type bodyflag mass x y z -bond: atom-ID molecule-ID atom-type x y z -charge: atom-ID atom-type q x y z -dipole: atom-ID atom-type q x y z mux muy muz -dpd: atom-ID atom-type theta x y z -edpd: atom-ID atom-type edpd_temp edpd_cv x y z -mdpd: atom-ID atom-type rho x y z -tdpd: atom-ID atom-type x y z cc1 cc2 ... ccNspecies -electron: atom-ID atom-type q spin eradius x y z -ellipsoid: atom-ID atom-type ellipsoidflag density x y z -full: atom-ID molecule-ID atom-type q x y z -line: atom-ID molecule-ID atom-type lineflag density x y z -meso: atom-ID atom-type rho e cv x y z -molecular: atom-ID molecule-ID atom-type x y z -peri: atom-ID atom-type volume density x y z -smd: atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z -sphere: atom-ID atom-type diameter density x y z -spin: atom-ID atom-type sp x y z spx spy spz -template: atom-ID molecule-ID template-index template-atom atom-type x y z -tri: atom-ID molecule-ID atom-type triangleflag density x y z -wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z -hybrid: atom-ID atom-type x y z sub-style1 sub-style2 ... :tb(s=:) - -The per-atom values have these meanings and units, listed alphabetically: - -atom-ID = integer ID of atom -atom-type = type of atom (1-Ntype) -bodyflag = 1 for body particles, 0 for point particles -cc = chemical concentration for tDPD particles for each species (mole/volume units) -contact-radius = ??? (distance units) -cs_re,cs_im = real/imaginary parts of wave packet coefficients -cv = heat capacity (need units) for SPH particles -density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) -diameter = diameter of spherical atom (distance units) -e = energy (need units) for SPH particles -edpd_temp = temperature for eDPD particles (temperature units) -edpd_cv = volumetric heat capacity for eDPD particles (energy/temperature/volume units) -ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles -eradius = electron radius (or fixed-core radius) -etag = integer ID of electron that each wave packet belongs to -kernel-radius = ??? (distance units) -lineflag = 1 for line segment particles, 0 for point or spherical particles -mass = mass of particle (mass units) -molecule-ID = integer ID of molecule the atom belongs to -mux,muy,muz = components of dipole moment of atom (dipole units) -q = charge on atom (charge units) -rho = density (need units) for SPH particles -spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP) -sp = norm of magnetic spin of atom (in number of Bohr magnetons) -spx,spy,spz = components of magnetic spin of atom (adim normalized vector) -template-atom = which atom within a template molecule the atom is -template-index = which molecule within the molecule template the atom is part of -theta = internal temperature of a DPD particle -triangleflag = 1 for triangular particles, 0 for point or spherical particles -volume = volume of Peridynamic particle (distance^3 units) -x,y,z = coordinates of atom (distance units) :ul - -The units for these quantities depend on the unit style; see the -"units"_units.html command for details. - -For 2d simulations specify z as 0.0, or a value within the {zlo zhi} -setting in the data file header. - -The atom-ID is used to identify the atom throughout the simulation and -in dump files. Normally, it is a unique value from 1 to Natoms for -each atom. Unique values larger than Natoms can be used, but they -will cause extra memory to be allocated on each processor, if an atom -map array is used, but not if an atom map hash is used; see the -"atom_modify"_atom_modify.html command for details. If an atom map is -not used (e.g. an atomic system with no bonds), and you don't care if -unique atom IDs appear in dump files, then the atom-IDs can all be set -to 0. - -The molecule ID is a 2nd identifier attached to an atom. Normally, it -is a number from 1 to N, identifying which molecule the atom belongs -to. It can be 0 if it is a non-bonded atom or if you don't care to -keep track of molecule assignments. - -The diameter specifies the size of a finite-size spherical particle. -It can be set to 0.0, which means that atom is a point particle. - -The ellipsoidflag, lineflag, triangleflag, and bodyflag determine -whether the particle is a finite-size ellipsoid or line or triangle or -body of finite size, or whether the particle is a point particle. -Additional attributes must be defined for each ellipsoid, line, -triangle, or body in the corresponding {Ellipsoids}, {Lines}, -{Triangles}, or {Bodies} section. - -The {template-index} and {template-atom} are only defined used by -"atom_style template"_atom_style.html. In this case the -"molecule"_molecule.html command is used to define a molecule template -which contains one or more molecules. If an atom belongs to one of -those molecules, its {template-index} and {template-atom} are both set -to positive integers; if not the values are both 0. The -{template-index} is which molecule (1 to Nmols) the atom belongs to. -The {template-atom} is which atom (1 to Natoms) within the molecule -the atom is. - -Some pair styles and fixes and computes that operate on finite-size -particles allow for a mixture of finite-size and point particles. See -the doc pages of individual commands for details. - -For finite-size particles, the density is used in conjunction with the -particle volume to set the mass of each particle as mass = density * -volume. In this context, volume can be a 3d quantity (for spheres or -ellipsoids), a 2d quantity (for triangles), or a 1d quantity (for line -segments). If the volume is 0.0, meaning a point particle, then the -density value is used as the mass. One exception is for the body atom -style, in which case the mass of each particle (body or point -particle) is specified explicitly. This is because the volume of the -body is unknown. - -Note that for 2d simulations of spheres, this command will treat them -as spheres when converting density to mass. However, they can also be -modeled as 2d discs (circles) if the "set density/disc"_set.html -command is used to reset their mass after the read_data command is -used. A {disc} keyword can also be used with time integration fixes, -such as "fix nve/sphere"_fix_nve_sphere.html and "fix -nvt/sphere"_fix_nve_sphere.html to time integrate their motion as 2d -discs (not 3d spheres), by changing their moment of inertia. - -For atom_style hybrid, following the 5 initial values (ID,type,x,y,z), -specific values for each sub-style must be listed. The order of the -sub-styles is the same as they were listed in the -"atom_style"_atom_style.html command. The sub-style specific values -are those that are not the 5 standard ones (ID,type,x,y,z). For -example, for the "charge" sub-style, a "q" value would appear. For -the "full" sub-style, a "molecule-ID" and "q" would appear. These are -listed in the same order they appear as listed above. Thus if - -atom_style hybrid charge sphere :pre - -were used in the input script, each atom line would have these fields: - -atom-ID atom-type x y z q diameter density :pre - -Note that if a non-standard value is defined by multiple sub-styles, -it must appear multiple times in the atom line. E.g. the atom line -for atom_style hybrid dipole full would list "q" twice: - -atom-ID atom-type x y z q mux muy myz molecule-ID q :pre - -Atom lines specify the (x,y,z) coordinates of atoms. These can be -inside or outside the simulation box. When the data file is read, -LAMMPS wraps coordinates outside the box back into the box for -dimensions that are periodic. As discussed above, if an atom is -outside the box in a non-periodic dimension, it will be lost. - -LAMMPS always stores atom coordinates as values which are inside the -simulation box. It also stores 3 flags which indicate which image of -the simulation box (in each dimension) the atom would be in if its -coordinates were unwrapped across periodic boundaries. An image flag -of 0 means the atom is still inside the box when unwrapped. A value -of 2 means add 2 box lengths to get the unwrapped coordinate. A value -of -1 means subtract 1 box length to get the unwrapped coordinate. -LAMMPS updates these flags as atoms cross periodic boundaries during -the simulation. The "dump"_dump.html command can output atom -coordinates in wrapped or unwrapped form, as well as the 3 image -flags. - -In the data file, atom lines (all lines or none of them) can -optionally list 3 trailing integer values (nx,ny,nz), which are used -to initialize the atom's image flags. If nx,ny,nz values are not -listed in the data file, LAMMPS initializes them to 0. Note that the -image flags are immediately updated if an atom's coordinates need to -wrapped back into the simulation box. - -It is only important to set image flags correctly in a data file if a -simulation model relies on unwrapped coordinates for some calculation; -otherwise they can be left unspecified. Examples of LAMMPS commands -that use unwrapped coordinates internally are as follows: - -Atoms in a rigid body (see "fix rigid"_fix_rigid.html, "fix -rigid/small"_fix_rigid.html) must have consistent image flags, so that -when the atoms are unwrapped, they are near each other, i.e. as a -single body. :ulb,l - -If the "replicate"_replicate.html command is used to generate a larger -system, image flags must be consistent for bonded atoms when the bond -crosses a periodic boundary. I.e. the values of the image flags -should be different by 1 (in the appropriate dimension) for the two -atoms in such a bond. :l - -If you plan to "dump"_dump.html image flags and perform post-analysis -that will unwrap atom coordinates, it may be important that a -continued run (restarted from a data file) begins with image flags -that are consistent with the previous run. :l -:ule - -NOTE: If your system is an infinite periodic crystal with bonds then -it is impossible to have fully consistent image flags. This is because -some bonds will cross periodic boundaries and connect two atoms with the -same image flag. - -Atom velocities and other atom quantities not defined above are set to -0.0 when the {Atoms} section is read. Velocities can be set later by -a {Velocities} section in the data file or by a -"velocity"_velocity.html or "set"_set.html command in the input -script. - -:line - -{Bodies} section: - -one or more lines per body :ulb,l -first line syntax: atom-ID Ninteger Ndouble :l - Ninteger = # of integer quantities for this particle - Ndouble = # of floating-point quantities for this particle :pre -0 or more integer lines with total of Ninteger values :l -0 or more double lines with total of Ndouble values :l -example: :l - 12 3 6 - 2 3 2 - 1.0 2.0 3.0 1.0 2.0 4.0 :pre -example: :l - 12 0 14 - 1.0 2.0 3.0 1.0 2.0 4.0 1.0 - 2.0 3.0 1.0 2.0 4.0 4.0 2.0 :pre -:ule - -The {Bodies} section must appear if "atom_style body"_atom_style.html -is used and any atoms listed in the {Atoms} section have a bodyflag = -1. The number of bodies should be specified in the header section via -the "bodies" keyword. - -Each body can have a variable number of integer and/or floating-point -values. The number and meaning of the values is defined by the body -style, as described in the "Howto body"_Howto_body.html doc page. The -body style is given as an argument to the "atom_style -body"_atom_style.html command. - -The Ninteger and Ndouble values determine how many integer and -floating-point values are specified for this particle. Ninteger and -Ndouble can be as large as needed and can be different for every body. -Integer values are then listed next on subsequent lines. Lines are -read one at a time until Ninteger values are read. Floating-point -values follow on subsequent lines, Again lines are read one at a time -until Ndouble values are read. Note that if there are no values of a -particular type, no lines appear for that type. - -The {Bodies} section must appear after the {Atoms} section. - -:line - -{Bond Coeffs} section: - -one line per bond type :ulb,l -line syntax: ID coeffs :l - ID = bond type (1-N) - coeffs = list of coeffs :pre -example: :l - 4 250 1.49 :pre -:ule - -The number and meaning of the coefficients are specific to the defined -bond style. See the "bond_style"_bond_style.html and -"bond_coeff"_bond_coeff.html commands for details. Coefficients can -also be set via the "bond_coeff"_bond_coeff.html command in the input -script. - -:line - -{BondAngle Coeffs} section: - -one line per angle type :ulb,l -line syntax: ID coeffs :l - ID = angle type (1-N) - coeffs = list of coeffs (see class 2 section of "angle_coeff"_angle_coeff.html) :pre -:ule - -:line - -{BondBond Coeffs} section: - -one line per angle type :ulb,l -line syntax: ID coeffs :l - ID = angle type (1-N) - coeffs = list of coeffs (see class 2 section of "angle_coeff"_angle_coeff.html) :pre -:ule - -:line - -{BondBond13 Coeffs} section: - -one line per dihedral type :ulb,l -line syntax: ID coeffs :l - ID = dihedral type (1-N) - coeffs = list of coeffs (see class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre -:ule - -:line - -{Bonds} section: - -one line per bond :ulb,l -line syntax: ID type atom1 atom2 :l - ID = bond number (1-Nbonds) - type = bond type (1-Nbondtype) - atom1,atom2 = IDs of 1st,2nd atoms in bond :pre -example: :l - 12 3 17 29 :pre -:ule - -The {Bonds} section must appear after the {Atoms} section. All values -in this section must be integers (1, not 1.0). - -:line - -{Dihedral Coeffs} section: - -one line per dihedral type :ulb,l -line syntax: ID coeffs :l - ID = dihedral type (1-N) - coeffs = list of coeffs :pre -example: :l - 3 0.6 1 0 1 :pre -:ule - -The number and meaning of the coefficients are specific to the defined -dihedral style. See the "dihedral_style"_dihedral_style.html and -"dihedral_coeff"_dihedral_coeff.html commands for details. -Coefficients can also be set via the -"dihedral_coeff"_dihedral_coeff.html command in the input script. - -:line - -{Dihedrals} section: - -one line per dihedral :ulb,l -line syntax: ID type atom1 atom2 atom3 atom4 :l - ID = number of dihedral (1-Ndihedrals) - type = dihedral type (1-Ndihedraltype) - atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral :pre -example: :l - 12 4 17 29 30 21 :pre -:ule - -The 4 atoms are ordered linearly within the dihedral. The {Dihedrals} -section must appear after the {Atoms} section. All values in this -section must be integers (1, not 1.0). - -:line - -{Ellipsoids} section: - -one line per ellipsoid :ulb,l -line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk :l - atom-ID = ID of atom which is an ellipsoid - shapex,shapey,shapez = 3 diameters of ellipsoid (distance units) - quatw,quati,quatj,quatk = quaternion components for orientation of atom :pre -example: :l - 12 1 2 1 1 0 0 0 :pre -:ule - -The {Ellipsoids} section must appear if "atom_style -ellipsoid"_atom_style.html is used and any atoms are listed in the -{Atoms} section with an ellipsoidflag = 1. The number of ellipsoids -should be specified in the header section via the "ellipsoids" -keyword. - -The 3 shape values specify the 3 diameters or aspect ratios of a -finite-size ellipsoidal particle, when it is oriented along the 3 -coordinate axes. They must all be non-zero values. - -The values {quatw}, {quati}, {quatj}, and {quatk} set the orientation -of the atom as a quaternion (4-vector). Note that the shape -attributes specify the aspect ratios of an ellipsoidal particle, which -is oriented by default with its x-axis along the simulation box's -x-axis, and similarly for y and z. If this body is rotated (via the -right-hand rule) by an angle theta around a unit vector (a,b,c), then -the quaternion that represents its new orientation is given by -(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These -4 components are quatw, quati, quatj, and quatk as specified above. -LAMMPS normalizes each atom's quaternion in case (a,b,c) is not -specified as a unit vector. - -The {Ellipsoids} section must appear after the {Atoms} section. - -:line - -{EndBondTorsion Coeffs} section: - -one line per dihedral type :ulb,l -line syntax: ID coeffs :l - ID = dihedral type (1-N) - coeffs = list of coeffs (see class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre -:ule - -:line - -{Improper Coeffs} section: - -one line per improper type :ulb,l -line syntax: ID coeffs :l - ID = improper type (1-N) - coeffs = list of coeffs :pre -example: :l - 2 20 0.0548311 :pre -:ule - -The number and meaning of the coefficients are specific to the defined -improper style. See the "improper_style"_improper_style.html and -"improper_coeff"_improper_coeff.html commands for details. -Coefficients can also be set via the -"improper_coeff"_improper_coeff.html command in the input script. - -:line - -{Impropers} section: - -one line per improper :ulb,l -line syntax: ID type atom1 atom2 atom3 atom4 :l - ID = number of improper (1-Nimpropers) - type = improper type (1-Nimpropertype) - atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper :pre -example: :l - 12 3 17 29 13 100 :pre -:ule - -The ordering of the 4 atoms determines the definition of the improper -angle used in the formula for each "improper -style"_improper_style.html. See the doc pages for individual styles -for details. - -The {Impropers} section must appear after the {Atoms} section. All -values in this section must be integers (1, not 1.0). - -:line - -{Lines} section: - -one line per line segment :ulb,l -line syntax: atom-ID x1 y1 x2 y2 :l - atom-ID = ID of atom which is a line segment - x1,y1 = 1st end point - x2,y2 = 2nd end point :pre -example: :l - 12 1.0 0.0 2.0 0.0 :pre -:ule - -The {Lines} section must appear if "atom_style line"_atom_style.html -is used and any atoms are listed in the {Atoms} section with a -lineflag = 1. The number of lines should be specified in the header -section via the "lines" keyword. - -The 2 end points are the end points of the line segment. The ordering -of the 2 points should be such that using a right-hand rule to cross -the line segment with a unit vector in the +z direction, gives an -"outward" normal vector perpendicular to the line segment. -I.e. normal = (c2-c1) x (0,0,1). This orientation may be important -for defining some interactions. - -The {Lines} section must appear after the {Atoms} section. - -:line - -{Masses} section: - -one line per atom type :ulb,l -line syntax: ID mass :l - ID = atom type (1-N) - mass = mass value :pre -example: :l - 3 1.01 :pre -:ule - -This defines the mass of each atom type. This can also be set via the -"mass"_mass.html command in the input script. This section cannot be -used for atom styles that define a mass for individual atoms - -e.g. "atom_style sphere"_atom_style.html. - -:line - -{MiddleBondTorsion Coeffs} section: - -one line per dihedral type :ulb,l -line syntax: ID coeffs :l - ID = dihedral type (1-N) - coeffs = list of coeffs (see class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre -:ule - -:line - -{Pair Coeffs} section: - -one line per atom type :ulb,l -line syntax: ID coeffs :l - ID = atom type (1-N) - coeffs = list of coeffs :pre -example: :l - 3 0.022 2.35197 0.022 2.35197 :pre -:ule - -The number and meaning of the coefficients are specific to the defined -pair style. See the "pair_style"_pair_style.html and -"pair_coeff"_pair_coeff.html commands for details. Since pair -coefficients for types I != J are not specified, these will be -generated automatically by the pair style's mixing rule. See the -individual pair_style doc pages and the "pair_modify -mix"_pair_modify.html command for details. Pair coefficients can also -be set via the "pair_coeff"_pair_coeff.html command in the input -script. - -:line - -{PairIJ Coeffs} section: - -one line per pair of atom types for all I,J with I <= J :ulb,l -line syntax: ID1 ID2 coeffs :l - ID1 = atom type I = 1-N - ID2 = atom type J = I-N, with I <= J - coeffs = list of coeffs :pre -examples: :l - 3 3 0.022 2.35197 0.022 2.35197 - 3 5 0.022 2.35197 0.022 2.35197 :pre -:ule - -This section must have N*(N+1)/2 lines where N = # of atom types. The -number and meaning of the coefficients are specific to the defined -pair style. See the "pair_style"_pair_style.html and -"pair_coeff"_pair_coeff.html commands for details. Since pair -coefficients for types I != J are all specified, these values will -turn off the default mixing rule defined by the pair style. See the -individual pair_style doc pages and the "pair_modify -mix"_pair_modify.html command for details. Pair coefficients can also -be set via the "pair_coeff"_pair_coeff.html command in the input -script. - -:line - -{Triangles} section: - -one line per triangle :ulb,l -line syntax: atom-ID x1 y1 z1 x2 y2 z2 x3 y3 z3 :l - atom-ID = ID of atom which is a line segment - x1,y1,z1 = 1st corner point - x2,y2,z2 = 2nd corner point - x3,y3,z3 = 3rd corner point :pre -example: :l - 12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0 :pre -:ule - -The {Triangles} section must appear if "atom_style -tri"_atom_style.html is used and any atoms are listed in the {Atoms} -section with a triangleflag = 1. The number of lines should be -specified in the header section via the "triangles" keyword. - -The 3 corner points are the corner points of the triangle. The -ordering of the 3 points should be such that using a right-hand rule -to go from point1 to point2 to point3 gives an "outward" normal vector -to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). This -orientation may be important for defining some interactions. - -The {Triangles} section must appear after the {Atoms} section. - -:line - -{Velocities} section: - -one line per atom -line syntax: depends on atom style :ul - -all styles except those listed: atom-ID vx vy vz -electron: atom-ID vx vy vz ervel -ellipsoid: atom-ID vx vy vz lx ly lz -sphere: atom-ID vx vy vz wx wy wz -hybrid: atom-ID vx vy vz sub-style1 sub-style2 ... :tb(s=:) - -where the keywords have these meanings: - -vx,vy,vz = translational velocity of atom -lx,ly,lz = angular momentum of aspherical atom -wx,wy,wz = angular velocity of spherical atom -ervel = electron radial velocity (0 for fixed-core):ul - -The velocity lines can appear in any order. This section can only be -used after an {Atoms} section. This is because the {Atoms} section -must have assigned a unique atom ID to each atom so that velocities -can be assigned to them. - -Vx, vy, vz, and ervel are in "units"_units.html of velocity. Lx, ly, -lz are in units of angular momentum (distance-velocity-mass). Wx, Wy, -Wz are in units of angular velocity (radians/time). - -For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz), -specific values for each sub-style must be listed. The order of the -sub-styles is the same as they were listed in the -"atom_style"_atom_style.html command. The sub-style specific values -are those that are not the 5 standard ones (ID,vx,vy,vz). For -example, for the "sphere" sub-style, "wx", "wy", "wz" values would -appear. These are listed in the same order they appear as listed -above. Thus if - -atom_style hybrid electron sphere :pre - -were used in the input script, each velocity line would have these -fields: - -atom-ID vx vy vz ervel wx wy wz :pre - -Translational velocities can also be set by the -"velocity"_velocity.html command in the input script. - -:line - -[Restrictions:] - -To read gzipped data files, you must compile LAMMPS with the --DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html -doc page for details. - -[Related commands:] - -"read_dump"_read_dump.html, "read_restart"_read_restart.html, -"create_atoms"_create_atoms.html, "write_data"_write_data.html - -[Default:] - -The default for all the {extra} keywords is 0. diff --git a/doc/txt/read_dump.txt b/doc/txt/read_dump.txt deleted file mode 100644 index df357a5018..0000000000 --- a/doc/txt/read_dump.txt +++ /dev/null @@ -1,343 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -read_dump command :h3 - -[Syntax:] - -read_dump file Nstep field1 field2 ... keyword values ... :pre - -file = name of dump file to read :ulb,l -Nstep = snapshot timestep to read from file :l -one or more fields may be appended :l -field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {q} or {ix} or {iy} or {iz} or {fx} or {fy} or {fz} - {x},{y},{z} = atom coordinates - {vx},{vy},{vz} = velocity components - {q} = charge - {ix},{iy},{iz} = image flags in each dimension - {fx},{fy},{fz} = force components :pre -zero or more keyword/value pairs may be appended :l -keyword = {nfile} or {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l - {nfile} value = Nfiles = how many parallel dump files exist - {box} value = {yes} or {no} = replace simulation box with dump box - {replace} value = {yes} or {no} = overwrite atoms with dump atoms - {purge} value = {yes} or {no} = delete all atoms before adding dump atoms - {trim} value = {yes} or {no} = trim atoms not in dump snapshot - {add} value = {yes} or {keep} or {no} = add new dump atoms to system - {label} value = field column - field = one of the listed fields or {id} or {type} - column = label on corresponding column in dump file - {scaled} value = {yes} or {no} = coords in dump file are scaled/unscaled - {wrapped} value = {yes} or {no} = coords in dump file are wrapped/unwrapped - {format} values = format of dump file, must be last keyword if used - {native} = native LAMMPS dump file - {xyz} = XYZ file - {molfile} style path = VMD molfile plugin interface - style = {dcd} or {xyz} or others supported by molfile plugins - path = optional path for location of molfile plugins :pre -:ule - -[Examples:] - -read_dump dump.file 5000 x y z -read_dump dump.xyz 5 x y z box no format xyz -read_dump dump.xyz 10 x y z box no format molfile xyz "../plugins" -read_dump dump.dcd 0 x y z box yes format molfile dcd -read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile -read_dump dump.file 5000 x y vx vy trim yes -read_dump ../run7/dump.file.gz 10000 x y z box yes -read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins -read_dump dump.dcd 0 x y z format molfile dcd -read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile :pre - -[Description:] - -Read atom information from a dump file to overwrite the current atom -coordinates, and optionally the atom velocities and image flags and -the simulation box dimensions. This is useful for restarting a run -from a particular snapshot in a dump file. See the -"read_restart"_read_restart.html and "read_data"_read_data.html -commands for alternative methods to do this. Also see the -"rerun"_rerun.html command for a means of reading multiple snapshots -from a dump file. - -Note that a simulation box must already be defined before using the -read_dump command. This can be done by the -"create_box"_create_box.html, "read_data"_read_data.html, or -"read_restart"_read_restart.html commands. The read_dump command can -reset the simulation box dimensions, as explained below. - -Also note that reading per-atom information from a dump snapshot is -limited to the atom coordinates, velocities and image flags, as -explained below. Other atom properties, which may be necessary to run -a valid simulation, such as atom charge, or bond topology information -for a molecular system, are not read from (or even contained in) dump -files. Thus this auxiliary information should be defined in the usual -way, e.g. in a data file read in by a "read_data"_read_data.html -command, before using the read_dump command, or by the "set"_set.html -command, after the dump snapshot is read. - -:line - -If the dump filename specified as {file} ends with ".gz", the dump -file is read in gzipped format. You cannot (yet) read a dump file -that was written in binary format with a ".bin" suffix. - -You can read dump files that were written (in parallel) to multiple -files via the "%" wild-card character in the dump file name. If any -specified dump file name contains a "%", they must all contain it. -See the "dump"_dump.html command for details. -The "%" wild-card character is only supported by the {native} format -for dump files, described next. - -If reading parallel dump files, you must also use the {nfile} keyword -to tell LAMMPS how many parallel files exist, via its specified -{Nfiles} value. - -The format of the dump file is selected through the {format} keyword. -If specified, it must be the last keyword used, since all remaining -arguments are passed on to the dump reader. The {native} format is -for native LAMMPS dump files, written with a "dump atom"_dump.html or -"dump custom"_dump.html command. The {xyz} format is for generic XYZ -formatted dump files. These formats take no additional values. - -The {molfile} format supports reading data through using the "VMD"_vmd -molfile plugin interface. This dump reader format is only available, -if the USER-MOLFILE package has been installed when compiling -LAMMPS. - -The {molfile} format takes one or two additional values. The {style} -value determines the file format to be used and can be any format that -the molfile plugins support, such as DCD or XYZ. Note that DCD dump -files can be written by LAMMPS via the "dump dcd"_dump.html command. -The {path} value specifies a list of directories which LAMMPS will -search for the molfile plugins appropriate to the specified {style}. -The syntax of the {path} value is like other search paths: it can -contain multiple directories separated by a colon (or semi-colon on -windows). The {path} keyword is optional and defaults to ".", -i.e. the current directory. - -Support for other dump format readers may be added in the future. - -:line - -Global information is first read from the dump file, namely timestep -and box information. - -The dump file is scanned for a snapshot with a timestamp that matches -the specified {Nstep}. This means the LAMMPS timestep the dump file -snapshot was written on for the {native} format. Note that the {xyz} -and {molfile} formats do not store the timestep. For these formats, -timesteps are numbered logically, in a sequential manner, starting -from 0. Thus to access the 10th snapshot in an {xyz} or {mofile} -formatted dump file, use {Nstep} = 9. - -The dimensions of the simulation box for the selected snapshot are -also read; see the {box} keyword discussion below. For the {native} -format, an error is generated if the snapshot is for a triclinic box -and the current simulation box is orthogonal or vice versa. A warning -will be generated if the snapshot box boundary conditions (periodic, -shrink-wrapped, etc) do not match the current simulation boundary -conditions, but the boundary condition information in the snapshot is -otherwise ignored. See the "boundary" command for more details. - -For the {xyz} format, no information about the box is available, so -you must set the {box} flag to {no}. See details below. - -For the {molfile} format, reading simulation box information is -typically supported, but the location of the simulation box origin is -lost and no explicit information about periodicity or -orthogonal/triclinic box shape is available. The USER-MOLFILE package -makes a best effort to guess based on heuristics, but this may not -always work perfectly. - -:line - -Per-atom information from the dump file snapshot is then read from the -dump file snapshot. This corresponds to the specified {fields} listed -in the read_dump command. It is an error to specify a z-dimension -field, namely {z}, {vz}, or {iz}, for a 2d simulation. - -For dump files in {native} format, each column of per-atom data has a -text label listed in the file. A matching label for each field must -appear, e.g. the label "vy" for the field {vy}. For the {x}, {y}, {z} -fields any of the following labels are considered a match: - -x, xs, xu, xsu for field {x} -y, ys, yu, ysu for field {y} -z, zs, zu, zsu for field {z} :pre - -The meaning of xs (scaled), xu (unwrapped), and xsu (scaled and -unwrapped) is explained on the "dump"_dump.html command doc page. -These labels are searched for in the list of column labels in the dump -file, in order, until a match is found. - -The dump file must also contain atom IDs, with a column label of "id". - -If the {add} keyword is specified with a value of {yes} or {keep}, as -discussed below, the dump file must contain atom types, with a column -label of "type". - -If a column label you want to read from the dump file is not a match -to a specified field, the {label} keyword can be used to specify the -specific column label from the dump file to associate with that field. -An example is if a time-averaged coordinate is written to the dump -file via the "fix ave/atom"_fix_ave_atom.html command. The column -will then have a label corresponding to the fix-ID rather than "x" or -"xs". The {label} keyword can also be used to specify new column -labels for fields {id} and {type}. - -For dump files in {xyz} format, only the {x}, {y}, and {z} fields are -supported. The dump file does not store atom IDs, so these are -assigned consecutively to the atoms as they appear in the dump file, -starting from 1. Thus you should insure that order of atoms is -consistent from snapshot to snapshot in the XYZ dump file. See -the "dump_modify sort"_dump_modify.html command if the XYZ dump file -was written by LAMMPS. - -For dump files in {molfile} format, the {x}, {y}, {z}, {vx}, {vy}, and -{vz} fields can be specified. However, not all molfile formats store -velocities, or their respective plugins may not support reading of -velocities. The molfile dump files do not store atom IDs, so these -are assigned consecutively to the atoms as they appear in the dump -file, starting from 1. Thus you should insure that order of atoms are -consistent from snapshot to snapshot in the molfile dump file. -See the "dump_modify sort"_dump_modify.html command if the dump file -was written by LAMMPS. - -:line - -Information from the dump file snapshot is used to overwrite or -replace properties of the current system. There are various options -for how this is done, determined by the specified fields and optional -keywords. - -The timestep of the snapshot becomes the current timestep for the -simulation. See the "reset_timestep"_reset_timestep.html command if -you wish to change this after the dump snapshot is read. - -If the {box} keyword is specified with a {yes} value, then the current -simulation box dimensions are replaced by the dump snapshot box -dimensions. If the {box} keyword is specified with a {no} value, the -current simulation box is unchanged. - -If the {purge} keyword is specified with a {yes} value, then all -current atoms in the system are deleted before any of the operations -invoked by the {replace}, {trim}, or {add} keywords take place. - -If the {replace} keyword is specified with a {yes} value, then atoms -with IDs that are in both the current system and the dump snapshot -have their properties overwritten by field values. If the {replace} -keyword is specified with a {no} value, atoms with IDs that are in -both the current system and the dump snapshot are not modified. - -If the {trim} keyword is specified with a {yes} value, then atoms with -IDs that are in the current system but not in the dump snapshot are -deleted. These atoms are unaffected if the {trim} keyword is -specified with a {no} value. - -If the {add} keyword is specified with a {no} value (default), then -dump file atoms with IDs that are not in the current system are not -added to the system. They are simply ignored. - -If a {yes} value is specified, the atoms with new IDs are added to the -system but their atom IDs are not preserved. Instead, after all the -atoms are added, new IDs are assigned to them in the same manner as is -described for the "create_atoms"_create_atoms.html command. Basically -the largest existing atom ID in the system is identified, and all the -added atoms are assigned IDs that consecutively follow the largest ID. - -If a {keep} value is specified, the atoms with new IDs are added to -the system and their atom IDs are preserved. This may lead to -non-contiguous IDs for the combined system. - -Note that atoms added via the {add} keyword will only have the -attributes read from the dump file due to the {field} arguments. For -example, if {x} or {y} or {z} or {q} is not specified as a field, a -value of 0.0 is used for added atoms. Added atoms must have an atom -type, so this value must appear in the dump file. - -Any other attributes (e.g. charge or particle diameter for spherical -particles) will be set to default values, the same as if the -"create_atoms"_create_atoms.html command were used. - -:line - -Atom coordinates read from the dump file are first converted into -unscaled coordinates, relative to the box dimensions of the snapshot. -These coordinates are then be assigned to an existing or new atom in -the current simulation. The coordinates will then be remapped to the -simulation box, whether it is the original box or the dump snapshot -box. If periodic boundary conditions apply, this means the atom will -be remapped back into the simulation box if necessary. If shrink-wrap -boundary conditions apply, the new coordinates may change the -simulation box dimensions. If fixed boundary conditions apply, the -atom will be lost if it is outside the simulation box. - -For {native} format dump files, the 3 xyz image flags for an atom in -the dump file are set to the corresponding values appearing in the -dump file if the {ix}, {iy}, {iz} fields are specified. If not -specified, the image flags for replaced atoms are not changed and -image flags for new atoms are set to default values. If coordinates -read from the dump file are in unwrapped format (e.g. {xu}) then the -image flags for read-in atoms are also set to default values. The -remapping procedure described in the previous paragraph will then -change images flags for all atoms (old and new) if periodic boundary -conditions are applied to remap an atom back into the simulation box. - -NOTE: If you get a warning about inconsistent image flags after -reading in a dump snapshot, it means one or more pairs of bonded atoms -now have inconsistent image flags. As discussed on the "Errors -common"_Errors_common.html doc page this may or may not cause problems -for subsequent simulations. One way this can happen is if you read -image flag fields from the dump file but do not also use the dump file -box parameters. - -LAMMPS knows how to compute unscaled and remapped coordinates for the -snapshot column labels discussed above, e.g. {x}, {xs}, {xu}, {xsu}. -If another column label is assigned to the {x} or {y} or {z} field via -the {label} keyword, e.g. for coordinates output by the "fix -ave/atom"_fix_ave_atom.html command, then LAMMPS needs to know whether -the coordinate information in the dump file is scaled and/or wrapped. -This can be set via the {scaled} and {wrapped} keywords. Note that -the value of the {scaled} and {wrapped} keywords is ignored for fields -{x} or {y} or {z} if the {label} keyword is not used to assign a -column label to that field. - -The scaled/unscaled and wrapped/unwrapped setting must be identical -for any of the {x}, {y}, {z} fields that are specified. Thus you -cannot read {xs} and {yu} from the dump file. Also, if the dump file -coordinates are scaled and the simulation box is triclinic, then all 3 -of the {x}, {y}, {z} fields must be specified, since they are all -needed to generate absolute, unscaled coordinates. - -:line - -[Restrictions:] - -To read gzipped dump files, you must compile LAMMPS with the --DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html -doc page for details. - -The {molfile} dump file formats are part of the USER-MOLFILE package. -They are only enabled if LAMMPS was built with that packages. See the -"Build package"_Build_package.html doc page for more info. - -[Related commands:] - -"dump"_dump.html, "dump molfile"_dump_molfile.html, -"read_data"_read_data.html, "read_restart"_read_restart.html, -"rerun"_rerun.html - -[Default:] - -The option defaults are box = yes, replace = yes, purge = no, trim = -no, add = no, scaled = no, wrapped = yes, and format = native. - -:link(vmd,http://www.ks.uiuc.edu/Research/vmd) - diff --git a/doc/txt/read_restart.txt b/doc/txt/read_restart.txt deleted file mode 100644 index 08cb6a2e6c..0000000000 --- a/doc/txt/read_restart.txt +++ /dev/null @@ -1,270 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -read_restart command :h3 - -[Syntax:] - -read_restart file flag :pre - -file = name of binary restart file to read in -flag = remap (optional) :ul - -[Examples:] - -read_restart save.10000 -read_restart save.10000 remap -read_restart restart.* -read_restart restart.*.mpiio -read_restart poly.*.% remap :pre - -[Description:] - -Read in a previously saved system configuration from a restart file. -This allows continuation of a previous run. Details about what -information is stored (and not stored) in a restart file is given -below. Basically this operation will re-create the simulation box -with all its atoms and their attributes as well as some related global -settings, at the point in time it was written to the restart file by a -previous simulation. The simulation box will be partitioned into a -regular 3d grid of rectangular bricks, one per processor, based on the -number of processors in the current simulation and the settings of the -"processors"_processors.html command. The partitioning can later be -changed by the "balance"_balance.html or "fix -balance"_fix_balance.html commands. - -NOTE: Normally, restart files are written by the -"restart"_restart.html or "write_restart"_write_restart.html commands -so that all atoms in the restart file are inside the simulation box. -If this is not the case, the read_restart command will print an error -that atoms were "lost" when the file is read. This error should be -reported to the LAMMPS developers so the invalid writing of the -restart file can be fixed. If you still wish to use the restart file, -the optional {remap} flag can be appended to the read_restart command. -This should avoid the error, by explicitly remapping each atom back -into the simulation box, updating image flags for the atom -appropriately. - -Restart files are saved in binary format to enable exact restarts, -meaning that the trajectories of a restarted run will precisely match -those produced by the original run had it continued on. - -Several things can prevent exact restarts due to round-off effects, in -which case the trajectories in the 2 runs will slowly diverge. These -include running on a different number of processors or changing -certain settings such as those set by the "newton"_newton.html or -"processors"_processors.html commands. LAMMPS will issue a warning in -these cases. - -Certain fixes will not restart exactly, though they should provide -statistically similar results. These include "fix -shake"_fix_shake.html and "fix langevin"_fix_langevin.html. - -Certain pair styles will not restart exactly, though they should -provide statistically similar results. This is because the forces -they compute depend on atom velocities, which are used at half-step -values every timestep when forces are computed. When a run restarts, -forces are initially evaluated with a full-step velocity, which is -different than if the run had continued. These pair styles include -"granular pair styles"_pair_gran.html, "pair dpd"_pair_dpd.html, and -"pair lubricate"_pair_lubricate.html. - -If a restarted run is immediately different than the run which -produced the restart file, it could be a LAMMPS bug, so consider -"reporting it"_Errors_bugs.html if you think the behavior is a bug. - -Because restart files are binary, they may not be portable to other -machines. In this case, you can use the "-restart command-line -switch"_Run_options.html to convert a restart file to a data file. - -Similar to how restart files are written (see the -"write_restart"_write_restart.html and "restart"_restart.html -commands), the restart filename can contain two wild-card characters. -If a "*" appears in the filename, the directory is searched for all -filenames that match the pattern where "*" is replaced with a timestep -value. The file with the largest timestep value is read in. Thus, -this effectively means, read the latest restart file. It's useful if -you want your script to continue a run from where it left off. See -the "run"_run.html command and its "upto" option for how to specify -the run command so it doesn't need to be changed either. - -If a "%" character appears in the restart filename, LAMMPS expects a -set of multiple files to exist. The "restart"_restart.html and -"write_restart"_write_restart.html commands explain how such sets are -created. Read_restart will first read a filename where "%" is -replaced by "base". This file tells LAMMPS how many processors -created the set and how many files are in it. Read_restart then reads -the additional files. For example, if the restart file was specified -as save.% when it was written, then read_restart reads the files -save.base, save.0, save.1, ... save.P-1, where P is the number of -processors that created the restart file. - -Note that P could be the total number of processors in the previous -simulation, or some subset of those processors, if the {fileper} or -{nfile} options were used when the restart file was written; see the -"restart"_restart.html and "write_restart"_write_restart.html commands -for details. The processors in the current LAMMPS simulation share -the work of reading these files; each reads a roughly equal subset of -the files. The number of processors which created the set can be -different the number of processors in the current LAMMPS simulation. -This can be a fast mode of input on parallel machines that support -parallel I/O. - -A restart file can also be read in parallel as one large binary file -via the MPI-IO library, assuming it was also written with MPI-IO. -MPI-IO is part of the MPI standard for versions 2.0 and above. Using -MPI-IO requires two steps. First, build LAMMPS with its MPIIO package -installed, e.g. - -make yes-mpiio # installs the MPIIO package -make mpi # build LAMMPS for your platform :pre - -Second, use a restart filename which contains ".mpiio". Note that it -does not have to end in ".mpiio", just contain those characters. -Unlike MPI-IO dump files, a particular restart file must be both -written and read using MPI-IO. - -:line - -Here is the list of information included in a restart file, which -means these quantities do not need to be re-specified in the input -script that reads the restart file, though you can redefine many of -these settings after the restart file is read. - -"units"_units.html -"newton bond"_newton.html (see discussion of newton command below) -"atom style"_atom_style.html and "atom_modify"_atom_modify.html settings id, map, sort -"comm style"_comm_style.html and "comm_modify"_comm_modify.html settings mode, cutoff, vel -"timestep"_timestep.html -simulation box size and shape and "boundary"_boundary.html settings -atom "group"_group.html definitions -per-type atom settings such as "mass"_mass.html -per-atom attributes including their group assignments and molecular topology attributes (bonds, angles, etc) -force field styles ("pair"_pair_style.html, "bond"_bond_style.html, "angle"_angle_style.html, etc) -force field coefficients ("pair"_pair_coeff.html, "bond"_bond_coeff.html, "angle"_angle_coeff.html, etc) in some cases (see below) -"pair_modify"_pair_modify.html settings, except the compute option -"special_bonds"_special_bonds.html settings :ul - -Here is a list of information not stored in a restart file, which -means you must re-issue these commands in your input script, after -reading the restart file. - -"newton pair"_newton.html (see discussion of newton command below) -"fix"_fix.html commands (see below) -"compute"_compute.html commands (see below) -"variable"_variable.html commands -"region"_region.html commands -"neighbor list"_neighbor.html criteria including "neigh_modify"_neigh_modify.html settings -"kspace_style"_kspace_style.html and "kspace_modify"_kspace_modify.html settings -info for "thermodynamic"_thermo_style.html, "dump"_dump.html, or "restart"_restart.html output :ul - -The "newton"_newton.html command has two settings, one for pairwise -interactions, the other for bonded. Both settings are stored in the -restart file. For the bond setting, the value in the file will -overwrite the current value (at the time the read_restart command is -issued) and warn if the two values are not the same and the current -value is not the default. For the pair setting, the value in the file -will not overwrite the current value (so that you can override the -previous run's value), but a warning is issued if the two values are -not the same and the current value is not the default. - -Note that some force field styles (pair, bond, angle, etc) do not -store their coefficient info in restart files. Typically these are -many-body or tabulated potentials which read their parameters from -separate files. In these cases you will need to re-specify the -"pair_coeff"_pair_coeff.html, "bond_coeff"_bond_coeff.html, etc -commands in your restart input script. The doc pages for individual -force field styles mention if this is the case. This is also true of -"pair_style hybrid"_pair_hybrid.html (bond hybrid, angle hybrid, etc) -commands; they do not store coefficient info. - -As indicated in the above list, the "fixes"_fix.html used for a -simulation are not stored in the restart file. This means the new -input script should specify all fixes it will use. However, note that -some fixes store an internal "state" which is written to the restart -file. This allows the fix to continue on with its calculations in a -restarted simulation. To re-enable such a fix, the fix command in the -new input script must be of the same style and use the same fix-ID as -was used in the input script that wrote the restart file. - -If a match is found, LAMMPS prints a message indicating that the fix -is being re-enabled. If no match is found before the first run or -minimization is performed by the new script, the "state" information -for the saved fix is discarded. At the time the discard occurs, -LAMMPS will also print a list of fixes for which the information is -being discarded. See the doc pages for individual fixes for info on -which ones can be restarted in this manner. Note that fixes which are -created internally by other LAMMPS commands (computes, fixes, etc) -will have style names which are all-capitalized, and IDs which are -generated internally. - -Likewise, the "computes"_fix.html used for a simulation are not stored -in the restart file. This means the new input script should specify -all computes it will use. However, some computes create a fix -internally to store "state" information that persists from timestep to -timestep. An example is the "compute msd"_compute_msd.html command -which uses a fix to store a reference coordinate for each atom, so -that a displacement can be calculated at any later time. If the -compute command in the new input script uses the same compute-ID and -group-ID as was used in the input script that wrote the restart file, -then it will create the same fix in the restarted run. This means the -re-created fix will be re-enabled with the stored state information as -described in the previous paragraph, so that the compute can continue -its calculations in a consistent manner. - -NOTE: There are a handful of commands which can be used before or -between runs which may require a system initialization. Examples -include the "balance", "displace_atoms", "delete_atoms", "set" (some -options), and "velocity" (some options) commands. This is because -they can migrate atoms to new processors. Thus they will also discard -unused "state" information from fixes. You will know the discard has -occurred because a list of discarded fixes will be printed to the -screen and log file, as explained above. This means that if you wish -to retain that info in a restarted run, you must re-specify the -relevant fixes and computes (which create fixes) before those commands -are used. - -Some pair styles, like the "granular pair styles"_pair_gran.html, also -use a fix to store "state" information that persists from timestep to -timestep. In the case of granular potentials, it is contact -information between pairs of touching particles. This info will also -be re-enabled in the restart script, assuming you re-use the same -granular pair style. - -LAMMPS allows bond interactions (angle, etc) to be turned off or -deleted in various ways, which can affect how their info is stored in -a restart file. - -If bonds (angles, etc) have been turned off by the "fix -shake"_fix_shake.html or "delete_bonds"_delete_bonds.html command, -their info will be written to a restart file as if they are turned on. -This means they will need to be turned off again in a new run after -the restart file is read. - -Bonds that are broken (e.g. by a bond-breaking potential) are written -to the restart file as broken bonds with a type of 0. Thus these -bonds will still be broken when the restart file is read. - -Bonds that have been broken by the "fix -bond/break"_fix_bond_break.html command have disappeared from the -system. No information about these bonds is written to the restart -file. - -:line - -[Restrictions:] - -To write and read restart files in parallel with MPI-IO, the MPIIO -package must be installed. - -[Related commands:] - -"read_data"_read_data.html, "read_dump"_read_dump.html, -"write_restart"_write_restart.html, "restart"_restart.html - -[Default:] none diff --git a/doc/txt/region.txt b/doc/txt/region.txt deleted file mode 100644 index d163f62dcb..0000000000 --- a/doc/txt/region.txt +++ /dev/null @@ -1,405 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -region command :h3 - -[Syntax:] - -region ID style args keyword arg ... :pre - -ID = user-assigned name for the region :ulb,l -style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sphere} or {union} or {intersect} :l - {delete} = no args - {block} args = xlo xhi ylo yhi zlo zhi - xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units) - {cone} args = dim c1 c2 radlo radhi lo hi - dim = {x} or {y} or {z} = axis of cone - c1,c2 = coords of cone axis in other 2 dimensions (distance units) - radlo,radhi = cone radii at lo and hi end (distance units) - lo,hi = bounds of cone in dim (distance units) - {cylinder} args = dim c1 c2 radius lo hi - dim = {x} or {y} or {z} = axis of cylinder - c1,c2 = coords of cylinder axis in other 2 dimensions (distance units) - radius = cylinder radius (distance units) - c1,c2, and radius can be a variable (see below) - lo,hi = bounds of cylinder in dim (distance units) - {plane} args = px py pz nx ny nz - px,py,pz = point on the plane (distance units) - nx,ny,nz = direction normal to plane (distance units) - {prism} args = xlo xhi ylo yhi zlo zhi xy xz yz - xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units) - xy = distance to tilt y in x direction (distance units) - xz = distance to tilt z in x direction (distance units) - yz = distance to tilt z in y direction (distance units) - {sphere} args = x y z radius - x,y,z = center of sphere (distance units) - radius = radius of sphere (distance units) - x,y,z, and radius can be a variable (see below) - {union} args = N reg-ID1 reg-ID2 ... - N = # of regions to follow, must be 2 or greater - reg-ID1,reg-ID2, ... = IDs of regions to join together - {intersect} args = N reg-ID1 reg-ID2 ... - N = # of regions to follow, must be 2 or greater - reg-ID1,reg-ID2, ... = IDs of regions to intersect :pre -zero or more keyword/arg pairs may be appended :l -keyword = {side} or {units} or {move} or {rotate} or {open} :l - {side} value = {in} or {out} - {in} = the region is inside the specified geometry - {out} = the region is outside the specified geometry - {units} value = {lattice} or {box} - {lattice} = the geometry is defined in lattice units - {box} = the geometry is defined in simulation box units - {move} args = v_x v_y v_z - v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time - {rotate} args = v_theta Px Py Pz Rx Ry Rz - v_theta = equal-style variable for rotaton of region over time (in radians) - Px,Py,Pz = origin for axis of rotation (distance units) - Rx,Ry,Rz = axis of rotation vector - {open} value = integer from 1-6 corresponding to face index (see below) -:pre - -accelerated styles (with same args) = {block/kk} :l -:ule - -[Examples:] - -region 1 block -3.0 5.0 INF 10.0 INF INF -region 2 sphere 0.0 0.0 0.0 5 side out -region void cylinder y 2 3 5 -5.0 EDGE units box -region 1 prism 0 10 0 10 0 10 2 0 0 -region outside union 4 side1 side2 side3 side4 -region 2 sphere 0.0 0.0 0.0 5 side out move v_left v_up NULL -region openbox block 0 10 0 10 0 10 open 5 open 6 units box -region funnel cone z 10 10 2 5 0 10 open 1 units box :pre - - -[Description:] - -This command defines a geometric region of space. Various other -commands use regions. For example, the region can be filled with -atoms via the "create_atoms"_create_atoms.html command. Or a bounding -box around the region, can be used to define the simulation box via -the "create_box"_create_box.html command. Or the atoms in the region -can be identified as a group via the "group"_group.html command, or -deleted via the "delete_atoms"_delete_atoms.html command. Or the -surface of the region can be used as a boundary wall via the "fix -wall/region"_fix_wall_region.html command. - -Commands which use regions typically test whether an atom's position -is contained in the region or not. For this purpose, coordinates -exactly on the region boundary are considered to be interior to the -region. This means, for example, for a spherical region, an atom on -the sphere surface would be part of the region if the sphere were -defined with the {side in} keyword, but would not be part of the -region if it were defined using the {side out} keyword. See more -details on the {side} keyword below. - -Normally, regions in LAMMPS are "static", meaning their geometric -extent does not change with time. If the {move} or {rotate} keyword -is used, as described below, the region becomes "dynamic", meaning -it's location or orientation changes with time. This may be useful, -for example, when thermostatting a region, via the compute temp/region -command, or when the fix wall/region command uses a region surface as -a bounding wall on particle motion, i.e. a rotating container. - -The {delete} style removes the named region. Since there is little -overhead to defining extra regions, there is normally no need to do -this, unless you are defining and discarding large numbers of regions -in your input script. - -The lo/hi values for {block} or {cone} or {cylinder} or {prism} styles -can be specified as EDGE or INF. EDGE means they extend all the way -to the global simulation box boundary. Note that this is the current -box boundary; if the box changes size during a simulation, the region -does not. INF means a large negative or positive number (1.0e20), so -it should encompass the simulation box even if it changes size. If a -region is defined before the simulation box has been created (via -"create_box"_create_box.html or "read_data"_read_data.html or -"read_restart"_read_restart.html commands), then an EDGE or INF -parameter cannot be used. For a {prism} region, a non-zero tilt -factor in any pair of dimensions cannot be used if both the lo/hi -values in either of those dimensions are INF. E.g. if the xy tilt is -non-zero, then xlo and xhi cannot both be INF, nor can ylo and yhi. - -NOTE: Regions in LAMMPS do not get wrapped across periodic boundaries, -as specified by the "boundary"_boundary.html command. For example, a -spherical region that is defined so that it overlaps a periodic -boundary is not treated as 2 half-spheres, one on either side of the -simulation box. - -NOTE: Regions in LAMMPS are always 3d geometric objects, regardless of -whether the "dimension"_dimension.html of a simulation is 2d or 3d. -Thus when using regions in a 2d simulation, you should be careful to -define the region so that its intersection with the 2d x-y plane of -the simulation has the 2d geometric extent you want. - -For style {cone}, an axis-aligned cone is defined which is like a -{cylinder} except that two different radii (one at each end) can be -defined. Either of the radii (but not both) can be 0.0. - -For style {cone} and {cylinder}, the c1,c2 params are coordinates in -the 2 other dimensions besides the cylinder axis dimension. For dim = -x, c1/c2 = y/z; for dim = y, c1/c2 = x/z; for dim = z, c1/c2 = x/y. -Thus the third example above specifies a cylinder with its axis in the -y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and -extending in the y-direction from -5.0 to the upper box boundary. - -For style {plane}, a plane is defined which contain the point -(px,py,pz) and has a normal vector (nx,ny,nz). The normal vector does -not have to be of unit length. The "inside" of the plane is the -half-space in the direction of the normal vector; see the discussion -of the {side} option below. - -For style {prism}, a parallelepiped is defined (it's too hard to spell -parallelepiped in an input script!). The parallelepiped has its -"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting -from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C = -(xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or positive or negative values -and are called "tilt factors" because they are the amount of -displacement applied to faces of an originally orthogonal box to -transform it into the parallelepiped. - -A prism region that will be used with the "create_box"_create_box.html -command to define a triclinic simulation box must have tilt factors -(xy,xz,yz) that do not skew the box more than half the distance of -corresponding the parallel box length. For example, if xlo = 2 and -xhi = 12, then the x box length is 10 and the xy tilt factor must be -between -5 and 5. Similarly, both xz and yz must be between --(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation, -since if the maximum tilt factor is 5 (as in this example), then -configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all -geometrically equivalent. - -The {radius} value for style {sphere} and {cylinder} can be specified -as an equal-style "variable"_variable.html. If the value is a -variable, it should be specified as v_name, where name is the variable -name. In this case, the variable will be evaluated each timestep, and -its value used to determine the radius of the region. For style {sphere} -also the x-, y-, and z- coordinate of the center of the sphere and for -style {cylinder} the two center positions c1 and c2 for the location of -the cylinder axes can be a variable with the same kind of effect and -requirements than for the radius. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent radius or have -a time dependent position of the sphere or cylinder region. - -See the "Howto tricilinc"_Howto_triclinic.html doc page for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used -triclinic representations. - -The {union} style creates a region consisting of the volume of all the -listed regions combined. The {intersect} style creates a region -consisting of the volume that is common to all the listed regions. - -NOTE: The {union} and {intersect} regions operate by invoking methods -from their list of sub-regions. Thus you cannot delete the -sub-regions after defining a {union} or {intersection} region. - -:line - -The {side} keyword determines whether the region is considered to be -inside or outside of the specified geometry. Using this keyword in -conjunction with {union} and {intersect} regions, complex geometries -can be built up. For example, if the interior of two spheres were -each defined as regions, and a {union} style with {side} = out was -constructed listing the region-IDs of the 2 spheres, the resulting -region would be all the volume in the simulation box that was outside -both of the spheres. - -The {units} keyword determines the meaning of the distance units used -to define the region for any argument above listed as having distance -units. It also affects the scaling of the velocity vector specified -with the {vel} keyword, the amplitude vector specified with the -{wiggle} keyword, and the rotation point specified with the {rotate} -keyword, since they each involve a distance metric. - -A {box} value selects standard distance units as defined by the -"units"_units.html command, e.g. Angstroms for units = real or metal. -A {lattice} value means the distance units are in lattice spacings. -The "lattice"_lattice.html command must have been previously used to -define the lattice spacings which are used as follows: - -For style {block}, the lattice spacing in dimension x is applied to -xlo and xhi, similarly the spacings in dimensions y,z are applied to -ylo/yhi and zlo/zhi. :ulb,l - -For style {cone}, the lattice spacing in argument {dim} is applied to -lo and hi. The spacings in the two radial dimensions are applied to -c1 and c2. The two cone radii are scaled by the lattice -spacing in the dimension corresponding to c1. :l - -For style {cylinder}, the lattice spacing in argument {dim} is applied -to lo and hi. The spacings in the two radial dimensions are applied -to c1 and c2. The cylinder radius is scaled by the lattice -spacing in the dimension corresponding to c1. :l - -For style {plane}, the lattice spacing in dimension x is applied to -px and nx, similarly the spacings in dimensions y,z are applied to -py/ny and pz/nz. :l - -For style {prism}, the lattice spacing in dimension x is applied to -xlo and xhi, similarly for ylo/yhi and zlo/zhi. The lattice spacing -in dimension x is applied to xy and xz, and the spacing in dimension y -to yz. :l - -For style {sphere}, the lattice spacing in dimensions x,y,z are -applied to the sphere center x,y,z. The spacing in dimension x is -applied to the sphere radius. :l,ule - -:line - -If the {move} or {rotate} keywords are used, the region is "dynamic", -meaning its location or orientation changes with time. These keywords -cannot be used with a {union} or {intersect} style region. Instead, -the keywords should be used to make the individual sub-regions of the -{union} or {intersect} region dynamic. Normally, each sub-region -should be "dynamic" in the same manner (e.g. rotate around the same -point), though this is not a requirement. - -The {move} keyword allows one or more "equal-style -variables"_variable.html to be used to specify the x,y,z displacement -of the region, typically as a function of time. A variable is -specified as v_name, where name is the variable name. Any of the -three variables can be specified as NULL, in which case no -displacement is calculated in that dimension. - -Note that equal-style variables can specify formulas with various -mathematical functions, and include "thermo_style"_thermo_style.html -command keywords for the simulation box parameters and timestep and -elapsed time. Thus it is easy to specify a region displacement that -change as a function of time or spans consecutive runs in a continuous -fashion. For the latter, see the {start} and {stop} keywords of the -"run"_run.html command and the {elaplong} keyword of "thermo_style -custom"_thermo_style.html for details. - -For example, these commands would displace a region from its initial -position, in the positive x direction, effectively at a constant -velocity: - -variable dx equal ramp(0,10) -region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL :pre - -Note that the initial displacement is 0.0, though that is not required. - -Either of these variables would "wiggle" the region back and forth in -the y direction: - -variable dy equal swiggle(0,5,100) -variable dysame equal 5*sin(2*PI*elaplong*dt/100) -region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL :pre - -The {rotate} keyword rotates the region around a rotation axis {R} = -(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz). The rotation -angle is calculated, presumably as a function of time, by a variable -specified as v_theta, where theta is the variable name. The variable -should generate its result in radians. The direction of rotation for -the region around the rotation axis is consistent with the right-hand -rule: if your right-hand thumb points along {R}, then your fingers -wrap around the axis in the direction of rotation. - -The {move} and {rotate} keywords can be used together. In this case, -the displacement specified by the {move} keyword is applied to the {P} -point of the {rotate} keyword. - -:line - -The {open} keyword can be used (multiple times) to indicate that one -or more faces of the region are ignored for purposes of particle/wall -interactions. This keyword is only relevant for regions used by the -{fix wall/region} and {fix wall/gran/region} commands. It can be used -to create "open" containers where only some of the region faces are -walls. For example, a funnel can be created with a {cone} style -region that has an open face at the smaller radius for particles to -flow out, or at the larger radius for pouring particles into the cone, -or both. - -Note that using the {open} keyword partly overrides the {side} -keyword, since both exterior and interior surfaces of an open region -are tested for particle contacts. The exception to this is a {union} -or {intersect} region which includes an open sub-region. In that case -the {side} keyword is still used to define the union/intersect region -volume, and the {open} settings are only applied to the individual -sub-regions that use them. - -The indices specified as part of the {open} keyword have the following -meanings: - -For style {block}, indices 1-6 correspond to the xlo, xhi, ylo, yhi, -zlo, zhi surfaces of the block. I.e. 1 is the yz plane at x = xlo, 2 -is the yz-plane at x = xhi, 3 is the xz plane at y = ylo, 4 is the xz -plane at y = yhi, 5 is the xy plane at z = zlo, 6 is the xy plane at z -= zhi). In the second-to-last example above, the region is a box open -at both xy planes. - -For style {prism}, values 1-6 have the same mapping as for style -{block}. I.e. in an untilted {prism}, {open} indices correspond to -the xlo, xhi, ylo, yhi, zlo, zhi surfaces. - -For style {cylinder}, index 1 corresponds to the flat end cap at the -low coordinate along the cylinder axis, index 2 corresponds to the -high-coordinate flat end cap along the cylinder axis, and index 3 is -the curved cylinder surface. For example, a {cylinder} region with -{open 1 open 2} keywords will be open at both ends (e.g. a section of -pipe), regardless of the cylinder orientation. - -For style {cone}, the mapping is the same as for style {cylinder}. -Index 1 is the low-coordinate flat end cap, index 2 is the -high-coordinate flat end cap, and index 3 is the curved cone surface. -In the last example above, a {cone} region is defined along the z-axis -that is open at the zlo value (e.g. for use as a funnel). - -For all other styles, the {open} keyword is ignored. As indicated -above, this includes the {intersect} and {union} regions, though their -sub-regions can be defined with the {open} keyword. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -The code using the region (such as a fix or compute) must also be supported -by Kokkos or no acceleration will occur. Currently, only {block} style -regions are supported by Kokkos. - -These accelerated styles are part of the Kokkos package. They are -only enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -A prism cannot be of 0.0 thickness in any dimension; use a small z -thickness for 2d simulations. For 2d simulations, the xz and yz -parameters must be 0.0. - -[Related commands:] - -"lattice"_lattice.html, "create_atoms"_create_atoms.html, -"delete_atoms"_delete_atoms.html, "group"_group.html - -[Default:] - -The option defaults are side = in, units = lattice, and no move or -rotation. diff --git a/doc/txt/replicate.txt b/doc/txt/replicate.txt deleted file mode 100644 index 50e6e4c6d2..0000000000 --- a/doc/txt/replicate.txt +++ /dev/null @@ -1,99 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -replicate command :h3 - -[Syntax:] - -replicate nx ny nz {keyword} :pre - -nx,ny,nz = replication factors in each dimension :ulb -optional {keyword} = {bbox} :l - {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :pre -:ule - -[Examples:] - -replicate 2 3 2 :pre - -[Description:] - -Replicate the current simulation one or more times in each dimension. -For example, replication factors of 2,2,2 will create a simulation -with 8x as many atoms by doubling the simulation domain in each -dimension. A replication factor of 1 in a dimension leaves the -simulation domain unchanged. When the new simulation box is created -it is also partitioned into a regular 3d grid of rectangular bricks, -one per processor, based on the number of processors being used and -the settings of the "processors"_processors.html command. The -partitioning can later be changed by the "balance"_balance.html or -"fix balance"_fix_balance.html commands. - -All properties of the atoms are replicated, including their -velocities, which may or may not be desirable. New atom IDs are -assigned to new atoms, as are molecule IDs. Bonds and other topology -interactions are created between pairs of new atoms as well as between -old and new atoms. This is done by using the image flag for each atom -to "unwrap" it out of the periodic box before replicating it. - -This means that any molecular bond you specify in the original data -file that crosses a periodic boundary should be between two atoms with -image flags that differ by 1. This will allow the bond to be -unwrapped appropriately. - -The optional keyword {bbox} uses a bounding box to only check atoms in -replicas that overlap with a processor's sub-domain when assigning -atoms to processors. It typically results in a substantial speedup -when using the replicate command on a large number of processors. It -does require temporary use of more memory, specifically that each -processor can store all atoms in the entire system before it is -replicated. - -[Restrictions:] - -A 2d simulation cannot be replicated in the z dimension. - -If a simulation is non-periodic in a dimension, care should be used -when replicating it in that dimension, as it may put atoms nearly on -top of each other. - -NOTE: You cannot use the replicate command on a system which has a -molecule that spans the box and is bonded to itself across a periodic -boundary, so that the molecule is effectively a loop. A simple -example would be a linear polymer chain that spans the simulation box -and bonds back to itself across the periodic boundary. More realistic -examples would be a CNT (meant to be an infinitely long CNT) or a -graphene sheet or a bulk periodic crystal where there are explicit -bonds specified between near neighbors. (Note that this only applies -to systems that have permanent bonds as specified in the data file. A -CNT that is just atoms modeled with the "AIREBO -potential"_pair_airebo.html has no such permanent bonds, so it can be -replicated.) The reason replication does not work with those systems -is that the image flag settings described above cannot be made -consistent. I.e. it is not possible to define images flags so that -when every pair of bonded atoms is unwrapped (using the image flags), -they will be close to each other. The only way the replicate command -could work in this scenario is for it to break a bond, insert more -atoms, and re-connect the loop for the larger simulation box. But it -is not clever enough to do this. So you will have to construct a -larger version of your molecule as a pre-processing step and input a -new data file to LAMMPS. - -If the current simulation was read in from a restart file (before a -run is performed), there must not be any fix information stored in -the file for individual atoms. Similarly, no fixes can be defined at -the time the replicate command is used that require vectors of atom -information to be stored. This is because the replicate command does -not know how to replicate that information for new atoms it creates. -To work around this restriction, restart files may be converted into -data files and fixes may be undefined via the "unfix"_unfix.html -command before and redefined after the replicate command. - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/rerun.txt b/doc/txt/rerun.txt deleted file mode 100644 index 3d5cdfff3c..0000000000 --- a/doc/txt/rerun.txt +++ /dev/null @@ -1,222 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -rerun command :h3 - -[Syntax:] - -rerun file1 file2 ... keyword args ... :pre - -file1,file2,... = dump file(s) to read :ulb,l -one or more keywords may be appended, keyword {dump} must appear and be last :l -keyword = {first} or {last} or {every} or {skip} or {start} or {stop} or {dump} - {first} args = Nfirst - Nfirst = dump timestep to start on - {last} args = Nlast - Nlast = dumptimestep to stop on - {every} args = Nevery - Nevery = read snapshots matching every this many timesteps - {skip} args = Nskip - Nskip = read one out of every Nskip snapshots - {start} args = Nstart - Nstart = timestep on which pseudo run will start - {stop} args = Nstop - Nstop = timestep to which pseudo run will end - {dump} args = same as "read_dump"_read_dump.html command starting with its field arguments :pre -:ule - -[Examples:] - -rerun dump.file dump x y z vx vy vz -rerun dump1.txt dump2.txt first 10000 every 1000 dump x y z -rerun dump.vels dump x y z vx vy vz box yes format molfile lammpstrj -rerun dump.dcd dump x y z box no format molfile dcd -rerun ../run7/dump.file.gz skip 2 dump x y z box yes :pre - -[Description:] - -Perform a pseudo simulation run where atom information is read one -snapshot at a time from a dump file(s), and energies and forces are -computed on the shapshot to produce thermodynamic or other output. - -This can be useful in the following kinds of scenarios, after an -initial simulation produced the dump file: - -Compute the energy and forces of snaphots using a different potential. -:ulb,l - -Calculate one or more diagnostic quantities on the snapshots that -weren't computed in the initial run. These can also be computed with -settings not used in the initial run, e.g. computing an RDF via the -"compute rdf"_compute_rdf.html command with a longer cutoff than was -used initially. :l - -Calculate the portion of per-atom forces resulting from a subset of -the potential. E.g. compute only Coulombic forces. This can be done -by only defining only a Coulombic pair style in the rerun script. -Doing this in the original script would result in different (bad) -dynamics. :l -:ule - -Conceptually, using the rerun command is like running an input script -that has a loop in it (see the "next"_next.html and "jump"_jump.html -commands). Each iteration of the loop reads one snapshot from the -dump file via the "read_dump"_read_dump.html command, sets the -timestep to the appropriate value, and then invokes a "run"_run.html -command for zero timesteps to simply compute energy and forces, and -any other "thermodynamic output"_thermo_style.html or diagnostic info -you have defined. This computation also invokes any fixes you have -defined that apply constraints to the system, such as "fix -shake"_fix_shake.html or "fix indent"_fix_indent.html. - -Note that a simulation box must already be defined before using the -rerun command. This can be done by the "create_box"_create_box.html, -"read_data"_read_data.html, or "read_restart"_read_restart.html -commands. - -Also note that reading per-atom information from dump snapshots is -limited to the atom coordinates, velocities and image flags as -explained in the "read_dump"_read_dump.html command. Other atom -properties, which may be necessary to compute energies and forces, -such as atom charge, or bond topology information for a molecular -system, are not read from (or even contained in) dump files. Thus -this auxiliary information should be defined in the usual way, e.g. in -a data file read in by a "read_data"_read_data.html command, before -using the rerun command. - -Also note that the frequency of thermodynamic or dump output from the -rerun simulation will depend on settings made in the rerun script, the -same as for output from any LAMMPS simulation. See further info below -as to what that means if the timesteps for snapshots read from dump -files do not match the specified output frequency. - -:line - -If more than one dump file is specified, the dump files are read one -after the other. It is assumed that snapshot timesteps will be in -ascending order. If a snapshot is encountered that is not in -ascending order, it will skip the snapshot until it reads one that is. -This allows skipping of a duplicate snapshot (same timestep), -e.g. that appeared at the end of one file and beginning of the next. -However if you specify a series of dump files in an incorrect order -(with respect to the timesteps they contain), you may skip large -numbers of snapshots - -Note that the dump files specified as part of the {dump} keyword can -be parallel files, i.e. written as multiple files either per processor -and/or per snapshot. If that is the case they will also be read in -parallel which can make the rerun command operate dramatically faster -for large systems. See the doc page for the "read_dump"_read_dump and -"dump"_dump.html commands which describe how to read and write -parallel dump files. - -The {first}, {last}, {every}, {skip} keywords determine which -snapshots are read from the dump file(s). Snapshots are skipped until -they have a timestamp >= {Nfirst}. When a snapshot with a timestamp > -{Nlast} is encountered, the rerun command finishes. Note below that -the defaults for {first} and {last} are to read all snapshots. If the -{every} keyword is set to a value > 0, then only snapshots with -timestamps that are a multiple of {Nevery} are read (the first -snapshot is always read). If {Nevery} = 0, then this criterion is -ignored, i.e. every snapshot is read that meets the other criteria. -If the {skip} keyword is used, then after the first snapshot is read, -every Nth snapshot is read, where N = {Nskip}. E.g. if {Nskip} = 3, -then only 1 out of every 3 snapshots is read, assuming the snapshot -timestamp is also consistent with the other criteria. - -The {start} and {stop} keywords do not affect which snapshots are read -from the dump file(s). Rather, they have the same meaning that they -do for the "run"_run.html command. They only need to be defined if -(a) you are using a "fix"_fix.html command that changes some value -over time, and (b) you want the reference point for elapsed time (from -start to stop) to be different than the {first} and {last} settings. -See the doc page for individual fixes to see which ones can be used -with the {start/stop} keywords. Note that if you define neither of -the {start}/{stop} or {first}/{last} keywords, then LAMMPS treats the -pseudo run as going from 0 to a huge value (effectively infinity). -This means that any quantity that a fix scales as a fraction of -elapsed time in the run, will essentially remain at its initial value. -Also note that an error will occur if you read a snapshot from the -dump file with a timestep value larger than the {stop} setting you -have specified. - -The {dump} keyword is required and must be the last keyword specified. -Its arguments are passed internally to the "read_dump"_read_dump.html -command. The first argument following the {dump} keyword should be -the {field1} argument of the "read_dump"_read_dump.html command. See -the "read_dump"_read_dump.html doc page for details on the various -options it allows for extracting information from the dump file -snapshots, and for using that information to alter the LAMMPS -simulation. - -:line - -In general, a LAMMPS input script that uses a rerun command can -include and perform all the usual operations of an input script that -uses the "run"_run.html command. There are a few exceptions and -points to consider, as discussed here. - -Fixes that perform time integration, such as "fix nve"_fix_nve.html or -"fix npt"_fix_nh.html are not invoked, since no time integration is -performed. Fixes that perturb or constrain the forces on atoms will -be invoked, just as they would during a normal run. Examples are "fix -indent"_fix_indent.html and "fix langevin"_fix_langevin.html. So you -should think carefully as to whether that makes sense for the manner -in which you are reprocessing the dump snapshots. - -If you only want the rerun script to perform an analysis that does -not involve pair interactions, such as use compute msd to calculated -displacements over time, you do not need to define a "pair -style"_pair_style.html, which may also mean neighbor lists will not -need to be calculated which saves time. The "comm_modify -cutoff"_comm_modify.html command can also be used to insure ghost -atoms are acquired from far enough away for operations like bond and -angle evaluations, if no pair style is being used. - -Every time a snapshot is read, the timestep for the simulation is -reset, as if the "reset_timestep"_reset_timestep.html command were -used. This command has some restrictions as to what fixes can be -defined. See its doc page for details. For example, the "fix -deposit"_fix_deposit.html and "fix dt/reset"_fix_dt_reset.html fixes -are in this category. They also make no sense to use with a rerun -command. - -If time-averaging fixes like "fix ave/time"_fix_ave_time.html are -used, they are invoked on timesteps that are a function of their -{Nevery}, {Nrepeat}, and {Nfreq} settings. As an example, see the -"fix ave/time"_fix_ave_time.html doc page for details. You must -insure those settings are consistent with the snapshot timestamps that -are read from the dump file(s). If an averaging fix is not invoked on -a timestep it expects to be, LAMMPS will flag an error. - -The various forms of LAMMPS output, as defined by the -"thermo_style"_thermo_style.html, "thermo"_thermo.html, -"dump"_dump.html, and "restart"_restart.html commands occur with -specified frequency, e.g. every N steps. If the timestep for a dump -snapshot is not a multiple of N, then it will be read and processed, -but no output will be produced. If you want output for every dump -snapshot, you can simply use N=1 for an output frequency, e.g. for -thermodynamic output or new dump file output. - -:line - -[Restrictions:] - -To read gzipped dump files, you must compile LAMMPS with the --DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html -doc page for details. - -[Related commands:] - -"read_dump"_read_dump.html - -[Default:] - -The option defaults are first = 0, last = a huge value (effectively -infinity), start = same as first, stop = same as last, every = 0, skip -= 1; diff --git a/doc/txt/reset_ids.txt b/doc/txt/reset_ids.txt deleted file mode 100644 index 8b217c7b1c..0000000000 --- a/doc/txt/reset_ids.txt +++ /dev/null @@ -1,56 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -reset_ids command :h3 - -[Syntax:] - -reset_ids :pre - -[Examples:] - -reset_ids :pre - -[Description:] - -Reset atom IDs for the system, including all the global IDs stored -for bond, angle, dihedral, improper topology data. This will -create a set of IDs that are numbered contiguously from 1 to N -for a N atoms system. - -This can be useful to do after performing a "delete_atoms" command for -a molecular system. The delete_atoms compress yes option will not -perform this operation due to the existence of bond topology. It can -also be useful to do after any simulation which has lost atoms, -e.g. due to atoms moving outside a simulation box with fixed -boundaries (see the "boundary command"), or due to evaporation (see -the "fix evaporate" command). - -Note that the resetting of IDs is not really a compression, where gaps -in atom IDs are removed by decrementing atom IDs that are larger. -Instead the IDs for all atoms are erased, and new IDs are assigned so -that the atoms owned by an individual processor have consecutive IDs, -as the "create_atoms"_create_atoms.html command explains. - -NOTE: If this command is used before a "pair style"_pair_style.html is -defined, an error about bond topology atom IDs not being found may -result. This is because the cutoff distance for ghost atom -communication was not sufficient to find atoms in bonds, angles, etc -that are owned by other processors. The "comm_modify -cutoff"_comm_modify.html command can be used to correct this issue. -Or you can define a pair style before using this command. If you do -the former, you should unset the comm_modify cutoff after using -reset_ids so that subsequent communication is not inefficient. - -[Restrictions:] none - -[Related commands:] - -"delete_atoms"_delete_atoms.html - -[Default:] none diff --git a/doc/txt/reset_timestep.txt b/doc/txt/reset_timestep.txt deleted file mode 100644 index 0d518655fb..0000000000 --- a/doc/txt/reset_timestep.txt +++ /dev/null @@ -1,61 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -reset_timestep command :h3 - -[Syntax:] - -reset_timestep N :pre - -N = timestep number :ul - -[Examples:] - -reset_timestep 0 -reset_timestep 4000000 :pre - -[Description:] - -Set the timestep counter to the specified value. This command -normally comes after the timestep has been set by reading a restart -file via the "read_restart"_read_restart.html command, or a previous -simulation advanced the timestep. - -The "read_data"_read_data.html and "create_box"_create_box.html -commands set the timestep to 0; the "read_restart"_read_restart.html -command sets the timestep to the value it had when the restart file -was written. - -[Restrictions:] none - -This command cannot be used when any fixes are defined that keep track -of elapsed time to perform certain kinds of time-dependent operations. -Examples are the "fix deposit"_fix_deposit.html and "fix -dt/reset"_fix_dt_reset.html commands. The former adds atoms on -specific timesteps. The latter keeps track of accumulated time. - -Various fixes use the current timestep to calculate related -quantities. If the timestep is reset, this may produce unexpected -behavior, but LAMMPS allows the fixes to be defined even if the -timestep is reset. For example, commands which thermostat the system, -e.g. "fix nvt"_fix_nh.html, allow you to specify a target temperature -which ramps from Tstart to Tstop which may persist over several runs. -If you change the timestep, you may induce an instantaneous change in -the target temperature. - -Resetting the timestep clears flags for "computes"_compute.html that -may have calculated some quantity from a previous run. This means -these quantity cannot be accessed by a variable in between runs until -a new run is performed. See the "variable"_variable.html command for -more details. - -[Related commands:] - -"rerun"_rerun.html - -[Default:] none diff --git a/doc/txt/restart.txt b/doc/txt/restart.txt deleted file mode 100644 index e0fae3909d..0000000000 --- a/doc/txt/restart.txt +++ /dev/null @@ -1,173 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -restart command :h3 - -[Syntax:] - -restart 0 -restart N root keyword value ... -restart N file1 file2 keyword value ... :pre - -N = write a restart file every this many timesteps :ulb,l -N can be a variable (see below) :l -root = filename to which timestep # is appended :l -file1,file2 = two full filenames, toggle between them when writing file :l -zero or more keyword/value pairs may be appended :l -keyword = {fileper} or {nfile} :l - {fileper} arg = Np - Np = write one file for every this many processors - {nfile} arg = Nf - Nf = write this many files, one from each of Nf processors :pre -:ule - -[Examples:] - -restart 0 -restart 1000 poly.restart -restart 1000 poly.restart.mpiio -restart 1000 restart.*.equil -restart 10000 poly.%.1 poly.%.2 nfile 10 -restart v_mystep poly.restart :pre - -[Description:] - -Write out a binary restart file with the current state of the -simulation every so many timesteps, in either or both of two modes, as -a run proceeds. A value of 0 means do not write out any restart -files. The two modes are as follows. If one filename is specified, a -series of filenames will be created which include the timestep in the -filename. If two filenames are specified, only 2 restart files will -be created, with those names. LAMMPS will toggle between the 2 names -as it writes successive restart files. - -Note that you can specify the restart command twice, once with a -single filename and once with two filenames. This would allow you, -for example, to write out archival restart files every 100000 steps -using a single filename, and more frequent temporary restart files -every 1000 steps, using two filenames. Using restart 0 will turn off -both modes of output. - -Similar to "dump"_dump.html files, the restart filename(s) can contain -two wild-card characters. - -If a "*" appears in the single filename, it is replaced with the -current timestep value. This is only recognized when a single -filename is used (not when toggling back and forth). Thus, the 3rd -example above creates restart files as follows: restart.1000.equil, -restart.2000.equil, etc. If a single filename is used with no "*", -then the timestep value is appended. E.g. the 2nd example above -creates restart files as follows: poly.restart.1000, -poly.restart.2000, etc. - -If a "%" character appears in the restart filename(s), then one file -is written for each processor and the "%" character is replaced with -the processor ID from 0 to P-1. An additional file with the "%" -replaced by "base" is also written, which contains global information. -For example, the files written on step 1000 for filename restart.% -would be restart.base.1000, restart.0.1000, restart.1.1000, ..., -restart.P-1.1000. This creates smaller files and can be a fast mode -of output and subsequent input on parallel machines that support -parallel I/O. The optional {fileper} and {nfile} keywords discussed -below can alter the number of files written. - -The restart file can also be written in parallel as one large binary -file via the MPI-IO library, which is part of the MPI standard for -versions 2.0 and above. Using MPI-IO requires two steps. First, -build LAMMPS with its MPIIO package installed, e.g. - -make yes-mpiio # installs the MPIIO package -make mpi # build LAMMPS for your platform :pre - -Second, use a restart filename which contains ".mpiio". Note that it -does not have to end in ".mpiio", just contain those characters. -Unlike MPI-IO dump files, a particular restart file must be both -written and read using MPI-IO. - -Restart files are written on timesteps that are a multiple of N but -not on the first timestep of a run or minimization. You can use the -"write_restart"_write_restart.html command to write a restart file -before a run begins. A restart file is not written on the last -timestep of a run unless it is a multiple of N. A restart file is -written on the last timestep of a minimization if N > 0 and the -minimization converges. - -Instead of a numeric value, N can be specified as an "equal-style -variable"_variable.html, which should be specified as v_name, where -name is the variable name. In this case, the variable is evaluated at -the beginning of a run to determine the next timestep at which a -restart file will be written out. On that timestep, the variable will -be evaluated again to determine the next timestep, etc. Thus the -variable should return timestep values. See the stagger() and -logfreq() and stride() math functions for "equal-style -variables"_variable.html, as examples of useful functions to use in -this context. Other similar math functions could easily be added as -options for "equal-style variables"_variable.html. - -For example, the following commands will write restart files -every step from 1100 to 1200, and could be useful for debugging -a simulation where something goes wrong at step 1163: - -variable s equal stride(1100,1200,1) -restart v_s tmp.restart :pre - -:line - -See the "read_restart"_read_restart.html command for information about -what is stored in a restart file. - -Restart files can be read by a "read_restart"_read_restart.html -command to restart a simulation from a particular state. Because the -file is binary (to enable exact restarts), it may not be readable on -another machine. In this case, you can use the "-r command-line -switch"_Run_options.html to convert a restart file to a data file. - -NOTE: Although the purpose of restart files is to enable restarting a -simulation from where it left off, not all information about a -simulation is stored in the file. For example, the list of fixes that -were specified during the initial run is not stored, which means the -new input script must specify any fixes you want to use. Even when -restart information is stored in the file, as it is for some fixes, -commands may need to be re-specified in the new input script, in order -to re-use that information. See the "read_restart"_read_restart.html -command for information about what is stored in a restart file. - -:line - -The optional {nfile} or {fileper} keywords can be used in conjunction -with the "%" wildcard character in the specified restart file name(s). -As explained above, the "%" character causes the restart file to be -written in pieces, one piece for each of P processors. By default P = -the number of processors the simulation is running on. The {nfile} or -{fileper} keyword can be used to set P to a smaller value, which can -be more efficient when running on a large number of processors. - -The {nfile} keyword sets P to the specified Nf value. For example, if -Nf = 4, and the simulation is running on 100 processors, 4 files will -be written, by processors 0,25,50,75. Each will collect information -from itself and the next 24 processors and write it to a restart file. - -For the {fileper} keyword, the specified value of Np means write one -file for every Np processors. For example, if Np = 4, every 4th -processor (0,4,8,12,etc) will collect information from itself and the -next 3 processors and write it to a restart file. - -:line - -[Restrictions:] - -To write and read restart files in parallel with MPI-IO, the MPIIO -package must be installed. - -[Related commands:] - -"write_restart"_write_restart.html, "read_restart"_read_restart.html - -[Default:] - -restart 0 :pre diff --git a/doc/txt/run.txt b/doc/txt/run.txt deleted file mode 100644 index c7c73463d9..0000000000 --- a/doc/txt/run.txt +++ /dev/null @@ -1,205 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -run command :h3 - -[Syntax:] - -run N keyword values ... :pre - -N = # of timesteps :ulb,l -zero or more keyword/value pairs may be appended :l -keyword = {upto} or {start} or {stop} or {pre} or {post} or {every} :l - {upto} value = none - {start} value = N1 - N1 = timestep at which 1st run started - {stop} value = N2 - N2 = timestep at which last run will end - {pre} value = {no} or {yes} - {post} value = {no} or {yes} - {every} values = M c1 c2 ... - M = break the run into M-timestep segments and invoke one or more commands between each segment - c1,c2,...,cN = one or more LAMMPS commands, each enclosed in quotes - c1 = NULL means no command will be invoked :pre -:ule - -[Examples:] - -run 10000 -run 1000000 upto -run 100 start 0 stop 1000 -run 1000 pre no post yes -run 100000 start 0 stop 1000000 every 1000 "print 'Protein Rg = $r'" -run 100000 every 1000 NULL :pre - -[Description:] - -Run or continue dynamics for a specified number of timesteps. - -When the "run style"_run_style.html is {respa}, N refers to outer -loop (largest) timesteps. - -A value of N = 0 is acceptable; only the thermodynamics of the system -are computed and printed without taking a timestep. - -The {upto} keyword means to perform a run starting at the current -timestep up to the specified timestep. E.g. if the current timestep -is 10,000 and "run 100000 upto" is used, then an additional 90,000 -timesteps will be run. This can be useful for very long runs on a -machine that allocates chunks of time and terminate your job when time -is exceeded. If you need to restart your script multiple times -(reading in the last restart file), you can keep restarting your -script with the same run command until the simulation finally -completes. - -The {start} or {stop} keywords can be used if multiple runs are being -performed and you want a "fix"_fix.html command that changes some -value over time (e.g. temperature) to make the change across the -entire set of runs and not just a single run. See the doc page for -individual fixes to see which ones can be used with the {start/stop} -keywords. - -For example, consider this fix followed by 10 run commands: - -fix 1 all nvt 200.0 300.0 1.0 -run 1000 start 0 stop 10000 -run 1000 start 0 stop 10000 -... -run 1000 start 0 stop 10000 :pre - -The NVT fix ramps the target temperature from 200.0 to 300.0 during a -run. If the run commands did not have the start/stop keywords (just -"run 1000"), then the temperature would ramp from 200.0 to 300.0 -during the 1000 steps of each run. With the start/stop keywords, the -ramping takes place over the 10000 steps of all runs together. - -The {pre} and {post} keywords can be used to streamline the setup, -clean-up, and associated output to the screen that happens before and -after a run. This can be useful if you wish to do many short runs in -succession (e.g. LAMMPS is being called as a library which is doing -other computations between successive short LAMMPS runs). - -By default (pre and post = yes), LAMMPS creates neighbor lists, -computes forces, and imposes fix constraints before every run. And -after every run it gathers and prints timings statistics. If a run is -just a continuation of a previous run (i.e. no settings are changed), -the initial computation is not necessary; the old neighbor list is -still valid as are the forces. So if {pre} is specified as "no" then -the initial setup is skipped, except for printing thermodynamic info. -Note that if {pre} is set to "no" for the very 1st run LAMMPS -performs, then it is overridden, since the initial setup computations -must be done. - -NOTE: If your input script changes the system between 2 runs, then the -initial setup must be performed to insure the change is recognized by -all parts of the code that are affected. Examples are adding a -"fix"_fix.html or "dump"_dump.html or "compute"_compute.html, changing -a "neighbor"_neigh_modify.html list parameter, or writing restart file -which can migrate atoms between processors. LAMMPS has no easy way to -check if this has happened, but it is an error to use the {pre no} -option in this case. - -If {post} is specified as "no", the full timing summary is skipped; -only a one-line summary timing is printed. - -The {every} keyword provides a means of breaking a LAMMPS run into a -series of shorter runs. Optionally, one or more LAMMPS commands (c1, -c2, ..., cN) will be executed in between the short runs. If used, the -{every} keyword must be the last keyword, since it has a variable -number of arguments. Each of the trailing arguments is a single -LAMMPS command, and each command should be enclosed in quotes, so that -the entire command will be treated as a single argument. This will -also prevent any variables in the command from being evaluated until -it is executed multiple times during the run. Note that if a command -itself needs one of its arguments quoted (e.g. the "print"_print.html -command), then you can use a combination of single and double quotes, -as in the example above or below. - -The {every} keyword is a means to avoid listing a long series of runs -and interleaving commands in your input script. For example, a -"print"_print.html command could be invoked or a "fix"_fix.html could -be redefined, e.g. to reset a thermostat temperature. Or this could -be useful for invoking a command you have added to LAMMPS that wraps -some other code (e.g. as a library) to perform a computation -periodically during a long LAMMPS run. See the "Modify"_Modify.html -doc page for info about how to add new commands to LAMMPS. See the -"Howto couple"_Howto_couple.html doc page for ideas about how to -couple LAMMPS to other codes. - -With the {every} option, N total steps are simulated, in shorter runs -of M steps each. After each M-length run, the specified commands are -invoked. If only a single command is specified as NULL, then no -command is invoked. Thus these lines: - -variable q equal x\[100\] -run 6000 every 2000 "print 'Coord = $q'" :pre - -are the equivalent of: - -variable q equal x\[100\] -run 2000 -print "Coord = $q" -run 2000 -print "Coord = $q" -run 2000 -print "Coord = $q" :pre - -which does 3 runs of 2000 steps and prints the x-coordinate of a -particular atom between runs. Note that the variable "$q" will -be evaluated afresh each time the print command is executed. - -Note that by using the line continuation character "&", the run every -command can be spread across many lines, though it is still a single -command: - -run 100000 every 1000 & - "print 'Minimum value = $a'" & - "print 'Maximum value = $b'" & - "print 'Temp = $c'" & - "print 'Press = $d'" :pre - -If the {pre} and {post} options are set to "no" when used with the -{every} keyword, then the 1st run will do the full setup and the last -run will print the full timing summary, but these operations will be -skipped for intermediate runs. - -NOTE: You might wish to specify a command that exits the run by -jumping out of the loop, e.g. - -variable t equal temp -run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'" :pre - -However, this will not work. The run command simply executes each -command one at a time each time it pauses, then continues the run. - -Instead, you should use the "fix halt"_fix_halt.html command, which -has additional options for how to exit the run. - -[Restrictions:] - -When not using the {upto} keyword, the number of specified timesteps N -must fit in a signed 32-bit integer, so you are limited to slightly -more than 2 billion steps (2^31) in a single run. When using {upto}, -N can be larger than a signed 32-bit integer, however the difference -between N and the current timestep must still be no larger than -2^31 steps. - -However, with or without the {upto} keyword, you can perform -successive runs to run a simulation for any number of steps (ok, up to -2^63 total steps). I.e. the timestep counter within LAMMPS is a -64-bit signed integer. - -[Related commands:] - -"minimize"_minimize.html, "run_style"_run_style.html, -"temper"_temper.html, "fix halt"_fix_halt.html - -[Default:] - -The option defaults are start = the current timestep, stop = current -timestep + N, pre = yes, and post = yes. diff --git a/doc/txt/run_style.txt b/doc/txt/run_style.txt deleted file mode 100644 index bf13d20439..0000000000 --- a/doc/txt/run_style.txt +++ /dev/null @@ -1,329 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -run_style command :h3 - -[Syntax:] - -run_style style args :pre - -style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l - {verlet} args = none - {verlet/split} args = none - {respa} args = N n1 n2 ... keyword values ... - N = # of levels of rRESPA - n1, n2, ... = loop factors between rRESPA levels (N-1 values) - zero or more keyword/value pairings may be appended to the loop factors - keyword = {bond} or {angle} or {dihedral} or {improper} or - {pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace} - {bond} value = M - M = which level (1-N) to compute bond forces in - {angle} value = M - M = which level (1-N) to compute angle forces in - {dihedral} value = M - M = which level (1-N) to compute dihedral forces in - {improper} value = M - M = which level (1-N) to compute improper forces in - {pair} value = M - M = which level (1-N) to compute pair forces in - {inner} values = M cut1 cut2 - M = which level (1-N) to compute pair inner forces in - cut1 = inner cutoff between pair inner and - pair middle or outer (distance units) - cut2 = outer cutoff between pair inner and - pair middle or outer (distance units) - {middle} values = M cut1 cut2 - M = which level (1-N) to compute pair middle forces in - cut1 = inner cutoff between pair middle and pair outer (distance units) - cut2 = outer cutoff between pair middle and pair outer (distance units) - {outer} value = M - M = which level (1-N) to compute pair outer forces in - {hybrid} values = M1 M2 ... (as many values as there are hybrid sub-styles - M1 = which level (1-N) to compute the first pair_style hybrid sub-style in - M2 = which level (1-N) to compute the second pair_style hybrid sub-style in - M3,etc - {kspace} value = M - M = which level (1-N) to compute kspace forces in :pre -:ule - -[Examples:] - -run_style verlet -run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4 -run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4 -run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3 :pre - -[Description:] - -Choose the style of time integrator used for molecular dynamics -simulations performed by LAMMPS. - -The {verlet} style is a standard velocity-Verlet integrator. - -:line - -The {verlet/split} style is also a velocity-Verlet integrator, but it -splits the force calculation within each timestep over 2 partitions of -processors. See the "-partition command-line switch"_Run_options.html -for info on how to run LAMMPS with multiple partitions. - -Specifically, this style performs all computation except the -"kspace_style"_kspace_style.html portion of the force field on the 1st -partition. This include the "pair style"_pair_style.html, "bond -style"_bond_style.html, "neighbor list building"_neighbor.html, -"fixes"_fix.html including time integration, and output. The -"kspace_style"_kspace_style.html portion of the calculation is -performed on the 2nd partition. - -This is most useful for the PPPM kspace_style when its performance on -a large number of processors degrades due to the cost of communication -in its 3d FFTs. In this scenario, splitting your P total processors -into 2 subsets of processors, P1 in the 1st partition and P2 in the -2nd partition, can enable your simulation to run faster. This is -because the long-range forces in PPPM can be calculated at the same -time as pair-wise and bonded forces are being calculated, and the FFTs -can actually speed up when running on fewer processors. - -To use this style, you must define 2 partitions where P1 is a multiple -of P2. Typically having P1 be 3x larger than P2 is a good choice. -The 3d processor layouts in each partition must overlay in the -following sense. If P1 is a Px1 by Py1 by Pz1 grid, and P2 = Px2 by -Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly -for Py1 a multiple of Py2, and Pz1 a multiple of Pz2. - -Typically the best way to do this is to let the 1st partition choose -its onn optimal layout, then require the 2nd partition's layout to -match the integer multiple constraint. See the -"processors"_processors.html command with its {part} keyword for a way -to control this, e.g. - -procssors * * * part 1 2 multiple :pre - -You can also use the "partition"_partition.html command to explicitly -specify the processor layout on each partition. E.g. for 2 partitions -of 60 and 15 processors each: - -partition yes 1 processors 3 4 5 -partition yes 2 processors 3 1 5 :pre - -When you run in 2-partition mode with the {verlet/split} style, the -thermodynamic data for the entire simulation will be output to the log -and screen file of the 1st partition, which are log.lammps.0 and -screen.0 by default; see the "-plog and -pscreen command-line -switches"_Run_options.html to change this. The log and screen file -for the 2nd partition will not contain thermodynamic output beyond the -1st timestep of the run. - -See the "Speed packages"_Speed_packages.html doc page for performance -details of the speed-up offered by the {verlet/split} style. One -important performance consideration is the assignment of logical -processors in the 2 partitions to the physical cores of a parallel -machine. The "processors"_processors.html command has options to -support this, and strategies are discussed in "Section -5"_Speed.html of the manual. - -:line - -The {respa} style implements the rRESPA multi-timescale integrator -"(Tuckerman)"_#Tuckerman3 with N hierarchical levels, where level 1 is -the innermost loop (shortest timestep) and level N is the outermost -loop (largest timestep). The loop factor arguments specify what the -looping factor is between levels. N1 specifies the number of -iterations of level 1 for a single iteration of level 2, N2 is the -iterations of level 2 per iteration of level 3, etc. N-1 looping -parameters must be specified. - -Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors, -you could choose to have bond interactions computed 8x per large -timestep, angle interactions computed 4x, pair interactions computed -2x, and long-range interactions once per large timestep. - -The "timestep"_timestep.html command sets the large timestep for the -outermost rRESPA level. Thus if the 3 loop factors are "2 2 2" for -4-level rRESPA, and the outer timestep is set to 4.0 fmsec, then the -inner timestep would be 8x smaller or 0.5 fmsec. All other LAMMPS -commands that specify number of timesteps (e.g. "thermo"_thermo.html -for thermo output every N steps, "neigh_modify -delay/every"_neigh_modify.html parameters, "dump"_dump.html every N -steps, etc) refer to the outermost timesteps. - -The rRESPA keywords enable you to specify at what level of the -hierarchy various forces will be computed. If not specified, the -defaults are that bond forces are computed at level 1 (innermost -loop), angle forces are computed where bond forces are, dihedral -forces are computed where angle forces are, improper forces are -computed where dihedral forces are, pair forces are computed at the -outermost level, and kspace forces are computed where pair forces are. -The inner, middle, outer forces have no defaults. - -For fixes that support it, the rRESPA level at which a given fix is -active, can be selected through the "fix_modify"_fix_modify.html command. - -The {inner} and {middle} keywords take additional arguments for -cutoffs that are used by the pairwise force computations. If the 2 -cutoffs for {inner} are 5.0 and 6.0, this means that all pairs up to -6.0 apart are computed by the inner force. Those between 5.0 and 6.0 -have their force go ramped to 0.0 so the overlap with the next regime -(middle or outer) is smooth. The next regime (middle or outer) will -compute forces for all pairs from 5.0 outward, with those from 5.0 to -6.0 having their value ramped in an inverse manner. - -Note that you can use {inner} and {outer} without using {middle} to -split the pairwise computations into two portions instead of three. -Unless you are using a very long pairwise cutoff, a 2-way split is -often faster than a 3-way split, since it avoids too much duplicate -computation of pairwise interactions near the intermediate cutoffs. - -Also note that only a few pair potentials support the use of the -{inner} and {middle} and {outer} keywords. If not, only the {pair} -keyword can be used with that pair style, meaning all pairwise forces -are computed at the same rRESPA level. See the doc pages for -individual pair styles for details. - -Another option for using pair potentials with rRESPA is with the -{hybrid} keyword, which requires the use of the "pair_style hybrid or -hybrid/overlay"_pair_hybrid.html command. In this scenario, different -sub-styles of the hybrid pair style are evaluated at different rRESPA -levels. This can be useful, for example, to set different timesteps -for hybrid coarse-grained/all-atom models. The {hybrid} keyword -requires as many level assignments as there are hybrid sub-styles, -which assigns each sub-style to a rRESPA level, following their order -of definition in the pair_style command. Since the {hybrid} keyword -operates on pair style computations, it is mutually exclusive with -either the {pair} or the {inner}/{middle}/{outer} keywords. - -When using rRESPA (or for any MD simulation) care must be taken to -choose a timestep size(s) that insures the Hamiltonian for the chosen -ensemble is conserved. For the constant NVE ensemble, total energy -must be conserved. Unfortunately, it is difficult to know {a priori} -how well energy will be conserved, and a fairly long test simulation -(~10 ps) is usually necessary in order to verify that no long-term -drift in energy occurs with the trial set of parameters. - -With that caveat, a few rules-of-thumb may be useful in selecting -{respa} settings. The following applies mostly to biomolecular -simulations using the CHARMM or a similar all-atom force field, but -the concepts are adaptable to other problems. Without SHAKE, bonds -involving hydrogen atoms exhibit high-frequency vibrations and require -a timestep on the order of 0.5 fmsec in order to conserve energy. The -relatively inexpensive force computations for the bonds, angles, -impropers, and dihedrals can be computed on this innermost 0.5 fmsec -step. The outermost timestep cannot be greater than 4.0 fmsec without -risking energy drift. Smooth switching of forces between the levels -of the rRESPA hierarchy is also necessary to avoid drift, and a 1-2 -angstrom "healing distance" (the distance between the outer and inner -cutoffs) works reasonably well. We thus recommend the following -settings for use of the {respa} style without SHAKE in biomolecular -simulations: - -timestep 4.0 -run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4 :pre - -With these settings, users can expect good energy conservation and -roughly a 2.5 fold speedup over the {verlet} style with a 0.5 fmsec -timestep. - -If SHAKE is used with the {respa} style, time reversibility is lost, -but substantially longer time steps can be achieved. For biomolecular -simulations using the CHARMM or similar all-atom force field, bonds -involving hydrogen atoms exhibit high frequency vibrations and require -a time step on the order of 0.5 fmsec in order to conserve energy. -These high frequency modes also limit the outer time step sizes since -the modes are coupled. It is therefore desirable to use SHAKE with -respa in order to freeze out these high frequency motions and increase -the size of the time steps in the respa hierarchy. The following -settings can be used for biomolecular simulations with SHAKE and -rRESPA: - -fix 2 all shake 0.000001 500 0 m 1.0 a 1 -timestep 4.0 -run_style respa 2 2 inner 1 4.0 5.0 outer 2 :pre - -With these settings, users can expect good energy conservation and -roughly a 1.5 fold speedup over the {verlet} style with SHAKE and a -2.0 fmsec timestep. - -For non-biomolecular simulations, the {respa} style can be -advantageous if there is a clear separation of time scales - fast and -slow modes in the simulation. For example, a system of slowly-moving -charged polymer chains could be setup as follows: - -timestep 4.0 -run_style respa 2 8 :pre - -This is two-level rRESPA with an 8x difference between the short and -long timesteps. The bonds, angles, dihedrals will be computed every -0.5 fs (assuming real units), while the pair and kspace interactions -will be computed once every 4 fs. These are the default settings for -each kind of interaction, so no additional keywords are necessary. - -Even a LJ system can benefit from rRESPA if the interactions are -divided by the inner, middle and outer keywords. A 2-fold or more -speedup can be obtained while maintaining good energy conservation. -In real units, for a pure LJ fluid at liquid density, with a sigma of -3.0 angstroms, and epsilon of 0.1 Kcal/mol, the following settings -seem to work well: - -timestep 36.0 -run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre - -:line - -The {respa/omp} style is a variant of {respa} adapted for use with -pair, bond, angle, dihedral, improper, or kspace styles with an {omp} -suffix. It is functionally equivalent to {respa} but performs -additional operations required for managing {omp} styles. For more on -{omp} styles see the "Speed omp"_Speed_omp.html doc page. Accelerated -styles take the same arguments and should produce the same results, -except for round-off and precision issues. - -You can specify {respa/omp} explicitly in your input script, or you -can use the "-suffix command-line switch"_Run_options.html when you -invoke LAMMPS, or you can use the "suffix"_suffix.html command in your -input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -The {verlet/split} style can only be used if LAMMPS was built with the -REPLICA package. Correspondingly the {respa/omp} style is available -only if the USER-OMP package was included. See the "Build -package"_Build_package.html doc page for more info. - -Whenever using rRESPA, the user should experiment with trade-offs in -speed and accuracy for their system, and verify that they are -conserving energy to adequate precision. - -[Related commands:] - -"timestep"_timestep.html, "run"_run.html - -[Default:] - -run_style verlet :pre - -For run_style respa, the default assignment of interactions -to rRESPA levels is as follows: - -bond forces = level 1 (innermost loop) -angle forces = same level as bond forces -dihedral forces = same level as angle forces -improper forces = same level as dihedral forces -pair forces = level N (outermost level) -kspace forces = same level as pair forces -inner, middle, outer forces = no default :ul - -:line - -:link(Tuckerman3) -[(Tuckerman)] Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990 -(1992). diff --git a/doc/txt/server_mc.txt b/doc/txt/server_mc.txt deleted file mode 100644 index ef3c56f886..0000000000 --- a/doc/txt/server_mc.txt +++ /dev/null @@ -1,116 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -server mc command :h3 - -[Syntax:] - -server mc :pre - -mc = the protocol argument to the "server"_server.html command - -[Examples:] - -server mc :pre - -[Description:] - -This command starts LAMMPS running in "server" mode, where it will -expect messages from a separate "client" code that match the {mc} -protocol for format and content explained below. For each message -LAMMPS receives it will send a message back to the client. - -The "Howto client/server"_Howto_client_server.html doc page gives an -overview of client/server coupling of LAMMPS with another code where -one code is the "client" and sends request messages to a "server" -code. The server responds to each request with a reply message. This -enables the two codes to work in tandem to perform a simulation. - -When this command is invoked, LAMMPS will run in server mode in an -endless loop, waiting for messages from the client code. The client -signals when it is done sending messages to LAMMPS, at which point the -loop will exit, and the remainder of the LAMMPS script will be -processed. - -The "server"_server.html doc page gives other options for using LAMMPS -See an example of how this command is used in -examples/COUPLE/lammps_mc/in.server. - -:line - -When using this command, LAMMPS (as the server code) receives -instructions from a Monte Carlo (MC) driver to displace random atoms, -compute the energy before and after displacement, and run dynamics to -equilibrate the system. - -The MC driver performs the random displacements on random atoms, -accepts or rejects the move in an MC sense, and orchestrates the MD -runs. - -The format and content of the exchanged messages are explained here in -a conceptual sense. Python-style pseudo code for the library calls to -the CSlib is shown, which performs the actual message exchange between -the two codes. See the "CSlib website"_http://cslib.sandia.gov doc -pages for more details on the actual library syntax. The "cs" object -in this pseudo code is a pointer to an instance of the CSlib. - -See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses -these messages. See the examples/COUPLE/lammps_mc/mc.cpp file for an -example of how an MC driver code can use these messages. - -Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5. - -[Client sends one of these kinds of message]: - -cs->send(NATOMS,0) # msgID = 1 with no fields :pre - -cs->send(EINIT,0) # msgID = 2 with no fields :pre - -cs->send(DISPLACE,2) # msgID = 3 with 2 fields -cs->pack_int(1,ID) # 1st field = ID of atom to displace -cs->pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom :pre - -cs->send(ACCEPT,1) # msgID = 4 with 1 field -cs->pack_int(1,flag) # 1st field = accept/reject flag :pre - -cs->send(RUN,1) # msgID = 5 with 1 field -cs->pack_int(1,nsteps) # 1st field = # of timesteps to run MD :pre - -[Server replies]: - -cs->send(NATOMS,1) # msgID = 1 with 1 field -cs->pack_int(1,natoms) # 1st field = number of atoms :pre - -cs->send(EINIT,2) # msgID = 2 with 2 fields -cs->pack_double(1,poteng) # 1st field = potential energy of system -cs->pack(2,3*natoms,x) # 2nd field = 3N coords of Natoms :pre - -cs->send(DISPLACE,1) # msgID = 3 with 1 field -cs->pack_double(1,poteng) # 1st field = new potential energy of system :pre - -cs->send(ACCEPT,0) # msgID = 4 with no fields :pre - -cs->send(RUN,0) # msgID = 5 with no fields :pre - -:line - -[Restrictions:] - -This command is part of the MESSAGE package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -A script that uses this command must also use the -"message"_message.html command to setup the messaging protocol with -the other client code. - -[Related commands:] - -"message"_message.html - -[Default:] none diff --git a/doc/txt/server_md.txt b/doc/txt/server_md.txt deleted file mode 100644 index 495c890c59..0000000000 --- a/doc/txt/server_md.txt +++ /dev/null @@ -1,149 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -server md command :h3 - -[Syntax:] - -server md :pre - -md = the protocol argument to the "server"_server.html command - -[Examples:] - -server md :pre - -[Description:] - -This command starts LAMMPS running in "server" mode, where it will -expect messages from a separate "client" code that match the {md} -protocol for format and content explained below. For each message -LAMMPS receives it will send a message back to the client. - -The "Howto client/server"_Howto_client_server.html doc page gives an -overview of client/server coupling of LAMMPS with another code where -one code is the "client" and sends request messages to a "server" -code. The server responds to each request with a reply message. This -enables the two codes to work in tandem to perform a simulation. - -When this command is invoked, LAMMPS will run in server mode in an -endless loop, waiting for messages from the client code. The client -signals when it is done sending messages to LAMMPS, at which point the -loop will exit, and the remainder of the LAMMPS script will be -processed. - -The "server"_server.html doc page gives other options for using LAMMPS -in server mode. See an example of how this command is used in -examples/message/in.message.server. - -:line - -When using this command, LAMMPS (as the server code) receives the -current coordinates of all particles from the client code each -timestep, computes their interaction, and returns the energy, forces, -and pressure for the interacting particles to the client code, so it -can complete the timestep. This command could also be used with a -client code that performs energy minimization, using the server to -compute forces and energy each iteration of its minimizer. - -When using the "fix client/md"_fix_client_md.html command, LAMMPS (as -the client code) does the timestepping and receives needed energy, -forces, and pressure values from the server code. - -The format and content of the exchanged messages are explained here in -a conceptual sense. Python-style pseudo code for the library calls to -the CSlib is shown, which performs the actual message exchange between -the two codes. See the "CSlib website"_http://cslib.sandia.gov doc -pages for more details on the actual library syntax. The "cs" object -in this pseudo code is a pointer to an instance of the CSlib. - -See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp -files for details on how LAMMPS uses these messages. See the -examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how -a quantum code (VASP) can use these messages. - -The following pseudo-code uses these values, defined as enums. - -Define: - -SETUP=1, STEP=2 -DIM=1, PERIODICITY=2, ORIGIN=3, BOX=4, NATOMS=5, NTYPES=6, TYPES=7, COORDS=8, UNITS-9, CHARGE=10 -FORCES=1, ENERGY=2, PRESSURE=3, ERROR=4 :pre - -[Client sends 2 kinds of messages]: - -# required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS -# optional fields: UNITS, CHARGE :pre - -cs->send(SETUP,nfields) # msgID with nfields :pre - -cs->pack_int(DIM,dim) # dimension (2,3) of simulation -cs->pack(PERIODICITY,3,xyz) # periodicity flags in 3 dims -cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box -cs->pack(BOX,9,box) # 3 edge vectors of simulation box -cs->pack_int(NATOMS,natoms) # total number of atoms -cs->pack_int(NTYPES,ntypes) # number of atom types -cs->pack(TYPES,natoms,type) # vector of per-atom types -cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords -cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc -cs->pack(CHARGE,natoms,q) # vector of per-atom charge :pre - -# required fields: COORDS -# optional fields: ORIGIN, BOX :pre - -cs->send(STEP,nfields) # msgID with nfields :pre - -cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords -cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box -cs->pack(BOX,9,box) # 3 edge vectors of simulation box :pre - -[Server replies to either kind of message]: - -# required fields: FORCES, ENERGY, PRESSURE -# optional fields: ERROR :pre - -cs->send(msgID,nfields) # msgID with nfields -cs->pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms -cs->pack(ENERGY,1,poteng) # total potential energy of system -cs->pack(PRESSURE,6,press) # global pressure tensor (6-vector) -cs->pack_int(ERROR,flag) # server had an error (e.g. DFT non-convergence) :pre - -:line - -The units for various quantities that are sent and received iva -messages are defined for atomic-scale simulations in the table below. -The client and server codes (including LAMMPS) can use internal units -different than these (e.g. "real units"_units.html in LAMMPS), so long -as they convert to these units for messaging. - -COORDS, ORIGIN, BOX = Angstroms -CHARGE = multiple of electron charge (1.0 is a proton) -ENERGY = eV -FORCES = eV/Angstrom -PRESSURE = bars :ul - -Note that these are "metal units"_units.html in LAMMPS. - -If you wish to run LAMMPS in another its non-atomic units, e.g. "lj -units"_units.html, then the client and server should exchange a UNITS -message as indicated above, and both the client and server should -agree on the units for the data they exchange. - -:line - -[Restrictions:] - -This command is part of the MESSAGE package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"message"_message.html, "fix client/md"_fix_client_md.html - -[Default:] none diff --git a/doc/txt/set.txt b/doc/txt/set.txt deleted file mode 100644 index 15c96071ae..0000000000 --- a/doc/txt/set.txt +++ /dev/null @@ -1,490 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -set command :h3 - -[Syntax:] - -set style ID keyword values ... :pre - -style = {atom} or {type} or {mol} or {group} or {region} :ulb,l -ID = atom ID range or type range or mol ID range or group ID or region ID :l -one or more keyword/value pairs may be appended :l -keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ - {charge} or {dipole} or {dipole/random} or {quat} or \ - {spin} or {spin/random} or {quat} or \ - {quat/random} or {diameter} or {shape} or \ - {length} or {tri} or {theta} or {theta/random} or \ - {angmom} or {omega} or \ - {mass} or {density} or {density/disc} or {volume} or {image} or \ - {bond} or {angle} or {dihedral} or {improper} or \ - {meso/e} or {meso/cv} or {meso/rho} or \ - {smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \ - {edpd/temp} or {edpd/cv} or {cc} or {i_name} or {d_name} :l - {type} value = atom type - value can be an atom-style variable (see below) - {type/fraction} values = type fraction seed - type = new atom type - fraction = fraction of selected atoms to set to new atom type - seed = random # seed (positive integer) - {mol} value = molecule ID - value can be an atom-style variable (see below) - {x},{y},{z} value = atom coordinate (distance units) - value can be an atom-style variable (see below) - {vx},{vy},{vz} value = atom velocity (velocity units) - value can be an atom-style variable (see below) - {charge} value = atomic charge (charge units) - value can be an atom-style variable (see below) - {dipole} values = x y z - x,y,z = orientation of dipole moment vector - any of x,y,z can be an atom-style variable (see below) - {dipole/random} value = seed Dlen - seed = random # seed (positive integer) for dipole moment orientations - Dlen = magnitude of dipole moment (dipole units) - {spin} values = g x y z - g = magnitude of magnetic spin vector (in Bohr magneton's unit) - x,y,z = orientation of magnetic spin vector - any of x,y,z can be an atom-style variable (see below) - {spin/random} value = seed Dlen - seed = random # seed (positive integer) for magnetic spin orientations - Dlen = magnitude of magnetic spin vector (in Bohr magneton's unit) - {quat} values = a b c theta - a,b,c = unit vector to rotate particle around via right-hand rule - theta = rotation angle (degrees) - any of a,b,c,theta can be an atom-style variable (see below) - {quat/random} value = seed - seed = random # seed (positive integer) for quaternion orientations - {diameter} value = diameter of spherical particle (distance units) - value can be an atom-style variable (see below) - {shape} value = Sx Sy Sz - Sx,Sy,Sz = 3 diameters of ellipsoid (distance units) - {length} value = len - len = length of line segment (distance units) - len can be an atom-style variable (see below) - {tri} value = side - side = side length of equilateral triangle (distance units) - side can be an atom-style variable (see below) - {theta} value = angle (degrees) - angle = orientation of line segment with respect to x-axis - angle can be an atom-style variable (see below) - {theta/random} value = seed - seed = random # seed (positive integer) for line segment orienations - {angmom} values = Lx Ly Lz - Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units) - any of Lx,Ly,Lz can be an atom-style variable (see below) - {omega} values = Wx Wy Wz - Wx,Wy,Wz = components of angular velocity vector (radians/time units) - any of wx,wy,wz can be an atom-style variable (see below) - {mass} value = per-atom mass (mass units) - value can be an atom-style variable (see below) - {density} value = particle density for a sphere or ellipsoid (mass/distance^3 units), or for a triangle (mass/distance^2 units) or line (mass/distance units) particle - value can be an atom-style variable (see below) - {density/disc} value = particle density for a 2d disc or ellipse (mass/distance^2 units) - value can be an atom-style variable (see below) - {volume} value = particle volume for Peridynamic particle (distance^3 units) - value can be an atom-style variable (see below) - {image} nx ny nz - nx,ny,nz = which periodic image of the simulation box the atom is in - any of nx,ny,nz can be an atom-style variable (see below) - {bond} value = bond type for all bonds between selected atoms - {angle} value = angle type for all angles between selected atoms - {dihedral} value = dihedral type for all dihedrals between selected atoms - {improper} value = improper type for all impropers between selected atoms - {meso/e} value = energy of SPH particles (need units) - value can be an atom-style variable (see below) - {meso/cv} value = heat capacity of SPH particles (need units) - value can be an atom-style variable (see below) - {meso/rho} value = density of SPH particles (need units) - value can be an atom-style variable (see below) - {smd/contact/radius} = radius for short range interactions, i.e. contact and friction - value can be an atom-style variable (see below) - {smd/mass/density} = set particle mass based on volume by providing a mass density - value can be an atom-style variable (see below) - {dpd/theta} value = internal temperature of DPD particles (temperature units) - value can be an atom-style variable (see below) - value can be NULL which sets internal temp of each particle to KE temp - {edpd/temp} value = temperature of eDPD particles (temperature units) - value can be an atom-style variable (see below) - {edpd/cv} value = volumetric heat capacity of eDPD particles (energy/temperature/volume units) - value can be an atom-style variable (see below) - {cc} values = index cc - index = index of a chemical species (1 to Nspecies) - cc = chemical concentration of tDPD particles for a species (mole/volume units) - {i_name} value = value for custom integer vector with name - {d_name} value = value for custom floating-point vector with name :pre -:ule - -[Examples:] - -set group solvent type 2 -set group solvent type/fraction 2 0.5 12393 -set group edge bond 4 -set region half charge 0.5 -set type 3 charge 0.5 -set type 1*3 charge 0.5 -set atom * charge v_atomfile -set atom 100*200 x 0.5 y 1.0 -set atom 100 vx 0.0 vy 0.0 vz -1.0 -set atom 1492 type 3 :pre - -[Description:] - -Set one or more properties of one or more atoms. Since atom -properties are initially assigned by the "read_data"_read_data.html, -"read_restart"_read_restart.html or "create_atoms"_create_atoms.html -commands, this command changes those assignments. This can be useful -for overriding the default values assigned by the -"create_atoms"_create_atoms.html command (e.g. charge = 0.0). It can -be useful for altering pairwise and molecular force interactions, -since force-field coefficients are defined in terms of types. It can -be used to change the labeling of atoms by atom type or molecule ID -when they are output in "dump"_dump.html files. It can also be useful -for debugging purposes; i.e. positioning an atom at a precise location -to compute subsequent forces or energy. - -Note that the {style} and {ID} arguments determine which atoms have -their properties reset. The remaining keywords specify which -properties to reset and what the new values are. Some strings like -{type} or {mol} can be used as a style and/or a keyword. - -:line - -This section describes how to select which atoms to change -the properties of, via the {style} and {ID} arguments. - -The style {atom} selects all the atoms in a range of atom IDs. The -style {type} selects all the atoms in a range of types. The style -{mol} selects all the atoms in a range of molecule IDs. - -In each of the range cases, the range can be specified as a single -numeric value, or a wildcard asterisk can be used to specify a range -of values. This takes the form "*" or "*n" or "n*" or "m*n". For -example, for the style {type}, if N = the number of atom types, then -an asterisk with no numeric values means all types from 1 to N. A -leading asterisk means all types from 1 to n (inclusive). A trailing -asterisk means all types from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). For all the styles except -{mol}, the lowest value for the wildcard is 1; for {mol} it is 0. - -The style {group} selects all the atoms in the specified group. The -style {region} selects all the atoms in the specified geometric -region. See the "group"_group.html and "region"_region.html commands -for details of how to specify a group or region. - -:line - -This section describes the keyword options for which properties to -change, for the selected atoms. - -Note that except where explicitly prohibited below, all of the -keywords allow an "atom-style or atomfile-style -variable"_variable.html to be used as the specified value(s). If the -value is a variable, it should be specified as v_name, where name is -the variable name. In this case, the variable will be evaluated, and -its resulting per-atom value used to determine the value assigned to -each selected atom. Note that the per-atom value from the variable -will be ignored for atoms that are not selected via the {style} and -{ID} settings explained above. A simple way to use per-atom values -from the variable to reset a property for all atoms is to use style -{atom} with {ID} = "*"; this selects all atom IDs. - -Atom-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters and timestep and elapsed -time. They can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a time-dependent or -spatially-dependent set of per-atom values. As explained on the -"variable"_variable.html doc page, atomfile-style variables can be -used in place of atom-style variables, and thus as arguments to the -set command. Atomfile-style variables read their per-atoms values -from a file. - -NOTE: Atom-style and atomfile-style variables return floating point -per-atom values. If the values are assigned to an integer variable, -such as the molecule ID, then the floating point value is truncated to -its integer portion, e.g. a value of 2.6 would become 2. - -Keyword {type} sets the atom type for all selected atoms. The -specified value must be from 1 to ntypes, where ntypes was set by the -"create_box"_create_box.html command or the {atom types} field in the -header of the data file read by the "read_data"_read_data.html -command. - -Keyword {type/fraction} sets the atom type for a fraction of the -selected atoms. The actual number of atoms changed is not guaranteed -to be exactly the requested fraction, but should be statistically -close. Random numbers are used in such a way that a particular atom -is changed or not changed, regardless of how many processors are being -used. This keyword does not allow use of an atom-style variable. - -Keyword {mol} sets the molecule ID for all selected atoms. The "atom -style"_atom_style.html being used must support the use of molecule -IDs. - -Keywords {x}, {y}, {z}, and {charge} set the coordinates or charge of -all selected atoms. For {charge}, the "atom style"_atom_style.html -being used must support the use of atomic charge. Keywords {vx}, {vy}, -and {vz} set the velocities of all selected atoms. - -Keyword {dipole} uses the specified x,y,z values as components of a -vector to set as the orientation of the dipole moment vectors of the -selected atoms. The magnitude of the dipole moment is set -by the length of this orientation vector. - -Keyword {dipole/random} randomizes the orientation of the dipole -moment vectors for the selected atoms and sets the magnitude of each -to the specified {Dlen} value. For 2d systems, the z component of the -orientation is set to 0.0. Random numbers are used in such a way that -the orientation of a particular atom is the same, regardless of how -many processors are being used. This keyword does not allow use of an -atom-style variable. - -Keyword {spin} uses the specified g value to set the magnitude of the -magnetic spin vectors, and the x,y,z values as components of a vector -to set as the orientation of the magnetic spin vectors of the selected -atoms. - -Keyword {spin/random} randomizes the orientation of the magnetic spin -vectors for the selected atoms and sets the magnitude of each to the -specified {Dlen} value. - -Keyword {quat} uses the specified values to create a quaternion -(4-vector) that represents the orientation of the selected atoms. The -particles must define a quaternion for their orientation -(e.g. ellipsoids, triangles, body particles) as defined by the -"atom_style"_atom_style.html command. Note that particles defined by -"atom_style ellipsoid"_atom_style.html have 3 shape parameters. The 3 -values must be non-zero for each particle set by this command. They -are used to specify the aspect ratios of an ellipsoidal particle, -which is oriented by default with its x-axis along the simulation -box's x-axis, and similarly for y and z. If this body is rotated (via -the right-hand rule) by an angle theta around a unit rotation vector -(a,b,c), then the quaternion that represents its new orientation is -given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2), -c*sin(theta/2)). The theta and a,b,c values are the arguments to the -{quat} keyword. LAMMPS normalizes the quaternion in case (a,b,c) was -not specified as a unit vector. For 2d systems, the a,b,c values are -ignored, since a rotation vector of (0,0,1) is the only valid choice. - -Keyword {quat/random} randomizes the orientation of the quaternion for -the selected atoms. The particles must define a quaternion for their -orientation (e.g. ellipsoids, triangles, body particles) as defined by -the "atom_style"_atom_style.html command. Random numbers are used in -such a way that the orientation of a particular atom is the same, -regardless of how many processors are being used. For 2d systems, -only orientations in the xy plane are generated. As with keyword -{quat}, for ellipsoidal particles, the 3 shape values must be non-zero -for each particle set by this command. This keyword does not allow -use of an atom-style variable. - -Keyword {diameter} sets the size of the selected atoms. The particles -must be finite-size spheres as defined by the "atom_style -sphere"_atom_style.html command. The diameter of a particle can be -set to 0.0, which means they will be treated as point particles. Note -that this command does not adjust the particle mass, even if it was -defined with a density, e.g. via the "read_data"_read_data.html -command. - -Keyword {shape} sets the size and shape of the selected atoms. The -particles must be ellipsoids as defined by the "atom_style -ellipsoid"_atom_style.html command. The {Sx}, {Sy}, {Sz} settings are -the 3 diameters of the ellipsoid in each direction. All 3 can be set -to the same value, which means the ellipsoid is effectively a sphere. -They can also all be set to 0.0 which means the particle will be -treated as a point particle. Note that this command does not adjust -the particle mass, even if it was defined with a density, e.g. via the -"read_data"_read_data.html command. - -Keyword {length} sets the length of selected atoms. The particles -must be line segments as defined by the "atom_style -line"_atom_style.html command. If the specified value is non-zero the -line segment is (re)set to a length = the specified value, centered -around the particle position, with an orientation along the x-axis. -If the specified value is 0.0, the particle will become a point -particle. Note that this command does not adjust the particle mass, -even if it was defined with a density, e.g. via the -"read_data"_read_data.html command. - -Keyword {tri} sets the size of selected atoms. The particles must be -triangles as defined by the "atom_style tri"_atom_style.html command. -If the specified value is non-zero the triangle is (re)set to be an -equilateral triangle in the xy plane with side length = the specified -value, with a centroid at the particle position, with its base -parallel to the x axis, and the y-axis running from the center of the -base to the top point of the triangle. If the specified value is 0.0, -the particle will become a point particle. Note that this command -does not adjust the particle mass, even if it was defined with a -density, e.g. via the "read_data"_read_data.html command. - -Keyword {theta} sets the orientation of selected atoms. The particles -must be line segments as defined by the "atom_style -line"_atom_style.html command. The specified value is used to set the -orientation angle of the line segments with respect to the x axis. - -Keyword {theta/random} randomizes the orientation of theta for the -selected atoms. The particles must be line segments as defined by the -"atom_style line"_atom_style.html command. Random numbers are used in -such a way that the orientation of a particular atom is the same, -regardless of how many processors are being used. This keyword does -not allow use of an atom-style variable. - -Keyword {angmom} sets the angular momentum of selected atoms. The -particles must be ellipsoids as defined by the "atom_style -ellipsoid"_atom_style.html command or triangles as defined by the -"atom_style tri"_atom_style.html command. The angular momentum vector -of the particles is set to the 3 specified components. - -Keyword {omega} sets the angular velocity of selected atoms. The -particles must be spheres as defined by the "atom_style sphere"_ -atom_style.html command. The angular velocity vector of the particles -is set to the 3 specified components. - -Keyword {mass} sets the mass of all selected particles. The particles -must have a per-atom mass attribute, as defined by the -"atom_style"_atom_style.html command. See the "mass" command for how -to set mass values on a per-type basis. - -Keyword {density} or {density/disc} also sets the mass of all selected -particles, but in a different way. The particles must have a per-atom -mass attribute, as defined by the "atom_style"_atom_style.html -command. If the atom has a radius attribute (see "atom_style -sphere"_atom_style.html) and its radius is non-zero, its mass is set -from the density and particle volume for 3d systems (the input density -is assumed to be in mass/distance^3 units). For 2d, the default is -for LAMMPS to model particles with a radius attribute as spheres. -However, if the {density/disc} keyword is used, then they can be -modeled as 2d discs (circles). Their mass is set from the density and -particle area (the input density is assumed to be in mass/distance^2 -units). - -If the atom has a shape attribute (see "atom_style -ellipsoid"_atom_style.html) and its 3 shape parameters are non-zero, -then its mass is set from the density and particle volume (the input -density is assumed to be in mass/distance^3 units). The -{density/disc} keyword has no effect; it does not (yet) treat 3d -ellipsoids as 2d ellipses. - -If the atom has a length attribute (see "atom_style -line"_atom_style.html) and its length is non-zero, then its mass is -set from the density and line segment length (the input density is -assumed to be in mass/distance units). If the atom has an area -attribute (see "atom_style tri"_atom_style.html) and its area is -non-zero, then its mass is set from the density and triangle area (the -input density is assumed to be in mass/distance^2 units). - -If none of these cases are valid, then the mass is set to the density -value directly (the input density is assumed to be in mass units). - -Keyword {volume} sets the volume of all selected particles. -Currently, only the "atom_style peri"_atom_style.html command defines -particles with a volume attribute. Note that this command does not -adjust the particle mass. - -Keyword {image} sets which image of the simulation box the atom is -considered to be in. An image of 0 means it is inside the box as -defined. A value of 2 means add 2 box lengths to get the true value. -A value of -1 means subtract 1 box length to get the true value. -LAMMPS updates these flags as atoms cross periodic boundaries during -the simulation. The flags can be output with atom snapshots via the -"dump"_dump.html command. If a value of NULL is specified for any of -nx,ny,nz, then the current image value for that dimension is unchanged. -For non-periodic dimensions only a value of 0 can be specified. -This command can be useful after a system has been equilibrated and -atoms have diffused one or more box lengths in various directions. -This command can then reset the image values for atoms so that they -are effectively inside the simulation box, e.g if a diffusion -coefficient is about to be measured via the "compute -msd"_compute_msd.html command. Care should be taken not to reset the -image flags of two atoms in a bond to the same value if the bond -straddles a periodic boundary (rather they should be different by +/- -1). This will not affect the dynamics of a simulation, but may mess -up analysis of the trajectories if a LAMMPS diagnostic or your own -analysis relies on the image flags to unwrap a molecule which -straddles the periodic box. - -Keywords {bond}, {angle}, {dihedral}, and {improper}, set the bond -type (angle type, etc) of all bonds (angles, etc) of selected atoms to -the specified value from 1 to nbondtypes (nangletypes, etc). All -atoms in a particular bond (angle, etc) must be selected atoms in -order for the change to be made. The value of nbondtype (nangletypes, -etc) was set by the {bond types} ({angle types}, etc) field in the -header of the data file read by the "read_data"_read_data.html -command. These keywords do not allow use of an atom-style variable. - -Keywords {meso/e}, {meso/cv}, and {meso/rho} set the energy, heat -capacity, and density of smoothed particle hydrodynamics (SPH) -particles. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to -using SPH in LAMMPS. - -Keyword {smd/mass/density} sets the mass of all selected particles, -but it is only applicable to the Smooth Mach Dynamics package -USER-SMD. It assumes that the particle volume has already been -correctly set and calculates particle mass from the provided mass -density value. - -Keyword {smd/contact/radius} only applies to simulations with the -Smooth Mach Dynamics package USER-SMD. Itsets an interaction radius -for computing short-range interactions, e.g. repulsive forces to -prevent different individual physical bodies from penetrating each -other. Note that the SPH smoothing kernel diameter used for computing -long range, nonlocal interactions, is set using the {diameter} -keyword. - -Keyword {dpd/theta} sets the internal temperature of a DPD particle as -defined by the USER-DPD package. If the specified value is a number -it must be >= 0.0. If the specified value is NULL, then the kinetic -temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2 -m v^2 = 1/2 m (vx*vx+vy*vy+vz*vz). Each particle's internal -temperature is set to Tkin. If the specified value is an atom-style -variable, then the variable is evaluated for each particle. If a -value >= 0.0, the internal temperature is set to that value. If it is -< 0.0, the computation of Tkin is performed and the internal -temperature is set to that value. - -Keywords {edpd/temp} and {edpd/cv} set the temperature and volumetric -heat capacity of an eDPD particle as defined by the USER-MESO package. -Currently, only "atom_style edpd"_atom_style.html defines particles -with these attributes. The values for the temperature and heat -capacity must be positive. - -Keyword {cc} sets the chemical concentration of a tDPD particle for a -specified species as defined by the USER-MESO package. Currently, only -"atom_style tdpd"_atom_style.html defines particles with this -attribute. An integer for "index" selects a chemical species (1 to -Nspecies) where Nspecies is set by the atom_style command. The value -for the chemical concentration must be >= 0.0. - -Keywords {i_name} and {d_name} refer to custom integer and -floating-point properties that have been added to each atom via the -"fix property/atom"_fix_property_atom.html command. When that command -is used specific names are given to each attribute which are what is -specified as the "name" portion of {i_name} or {d_name}. - -[Restrictions:] - -You cannot set an atom attribute (e.g. {mol} or {q} or {volume}) if -the "atom_style"_atom_style.html does not have that attribute. - -This command requires inter-processor communication to coordinate the -setting of bond types (angle types, etc). This means that your system -must be ready to perform a simulation before using one of these -keywords (force fields set, atom mass set, etc). This is not -necessary for other keywords. - -Using the {region} style with the bond (angle, etc) keywords can give -unpredictable results if there are bonds (angles, etc) that straddle -periodic boundaries. This is because the region may only extend up to -the boundary and partner atoms in the bond (angle, etc) may have -coordinates outside the simulation box if they are ghost atoms. - -[Related commands:] - -"create_box"_create_box.html, "create_atoms"_create_atoms.html, -"read_data"_read_data.html - -[Default:] none diff --git a/doc/txt/shell.txt b/doc/txt/shell.txt deleted file mode 100644 index d274f498e5..0000000000 --- a/doc/txt/shell.txt +++ /dev/null @@ -1,107 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -shell command :h3 - -[Syntax:] - -shell cmd args :pre - -cmd = {cd} or {mkdir} or {mv} or {rm} or {rmdir} or {putenv} or arbitrary command :ulb,l - {cd} arg = dir - dir = directory to change to - {mkdir} args = dir1 dir2 ... - dir1,dir2 = one or more directories to create - {mv} args = old new - old = old filename - new = new filename - {rm} args = file1 file2 ... - file1,file2 = one or more filenames to delete - {rmdir} args = dir1 dir2 ... - dir1,dir2 = one or more directories to delete - {putenv} args = var1=value1 var2=value2 - var=value = one of more definitions of environment variables - anything else is passed as a command to the shell for direct execution :pre -:ule - -[Examples:] - -shell cd sub1 -shell cd .. -shell mkdir tmp1 tmp2 tmp3 -shell rmdir tmp1 -shell mv log.lammps hold/log.1 -shell rm TMP/file1 TMP/file2 -shell putenv LAMMPS_POTENTIALS=../../potentials -shell my_setup file1 10 file2 -shell my_post_process 100 dump.out :pre - -[Description:] - -Execute a shell command. A few simple file-based shell commands are -supported directly, in Unix-style syntax. Any command not listed -above is passed as-is to the C-library system() call, which invokes -the command in a shell. - -This is means to invoke other commands from your input script. For -example, you can move files around in preparation for the next section -of the input script. Or you can run a program that pre-processes data -for input into LAMMPS. Or you can run a program that post-processes -LAMMPS output data. - -With the exception of {cd}, all commands, including ones invoked via a -system() call, are executed by only a single processor, so that -files/directories are not being manipulated by multiple processors. - -The {cd} cmd executes the Unix "cd" command to change the working -directory. All subsequent LAMMPS commands that read/write files will -use the new directory. All processors execute this command. - -The {mkdir} cmd executes the Unix "mkdir" command to create one or -more directories. - -The {mv} cmd executes the Unix "mv" command to rename a file and/or -move it to a new directory. - -The {rm} cmd executes the Unix "rm" command to remove one or more -files. - -The {rmdir} cmd executes the Unix "rmdir" command to remove one or -more directories. A directory must be empty to be successfully -removed. - -The {putenv} cmd defines or updates an environment variable directly. -Since this command does not pass through the shell, no shell variable -expansion or globbing is performed, only the usual substitution for -LAMMPS variables defined with the "variable"_variable.html command is -performed. The resulting string is then used literally. - -Any other cmd is passed as-is to the shell along with its arguments as -one string, invoked by the C-library system() call. For example, -these lines in your input script: - -variable n equal 10 -variable foo string file2 -shell my_setup file1 $n $\{foo\} :pre - -would be the same as invoking - -% my_setup file1 10 file2 :pre - -from a command-line prompt. The executable program "my_setup" is run -with 3 arguments: file1 10 file2. - -[Restrictions:] - -LAMMPS does not detect errors or print warnings when any of these -commands execute. E.g. if the specified directory does not exist, -executing the {cd} command will silently do nothing. - -[Related commands:] none - -[Default:] none diff --git a/doc/txt/special_bonds.txt b/doc/txt/special_bonds.txt deleted file mode 100644 index f8316a9bfb..0000000000 --- a/doc/txt/special_bonds.txt +++ /dev/null @@ -1,245 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -special_bonds command :h3 - -[Syntax:] - -special_bonds keyword values ... :pre - -one or more keyword/value pairs may be appended :ulb,l -keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} :l - {amber} values = none - {charmm} values = none - {dreiding} values = none - {fene} values = none - {lj/coul} values = w1,w2,w3 - w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions - {lj} values = w1,w2,w3 - w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions - {coul} values = w1,w2,w3 - w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions - {angle} value = {yes} or {no} - {dihedral} value = {yes} or {no} :pre -:ule - -Examples: - -special_bonds amber -special_bonds charmm -special_bonds fene dihedral no -special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes -special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes :pre - -[Description:] - -Set weighting coefficients for pairwise energy and force contributions -between pairs of atoms that are also permanently bonded to each other, -either directly or via one or two intermediate bonds. These weighting -factors are used by nearly all "pair styles"_pair_style.html in LAMMPS -that compute simple pairwise interactions. Permanent bonds between -atoms are specified by defining the bond topology in the data file -read by the "read_data"_read_data.html command. Typically a -"bond_style"_bond_style.html command is also used to define a bond -potential. The rationale for using these weighting factors is that -the interaction between a pair of bonded atoms is all (or mostly) -specified by the bond, angle, dihedral potentials, and thus the -non-bonded Lennard-Jones or Coulombic interaction between the pair of -atoms should be excluded (or reduced by a weighting factor). - -NOTE: These weighting factors are NOT used by "pair -styles"_pair_style.html that compute many-body interactions, since the -"bonds" that result from such interactions are not permanent, but are -created and broken dynamically as atom conformations change. Examples -of pair styles in this category are EAM, MEAM, Stillinger-Weber, -Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no -sense to define permanent bonds between atoms that interact via these -potentials, though such bonds may exist elsewhere in your system, -e.g. when using the "pair_style hybrid"_pair_hybrid.html command. -Thus LAMMPS ignores special_bonds settings when many-body potentials -are calculated. Please note, that the existence of explicit bonds -for atoms that are described by a many-body potential will alter the -neighbor list and thus can render the computation of those interactions -invalid, since those pairs are not only used to determine direct -pairwise interactions but also neighbors of neighbors and more. -The recommended course of action is to remove such bonds, or - if -that is not possible - use a special bonds setting of 1.0 1.0 1.0. - -NOTE: Unlike some commands in LAMMPS, you cannot use this command -multiple times in an incremental fashion: e.g. to first set the LJ -settings and then the Coulombic ones. Each time you use this command -it sets all the coefficients to default values and only overrides the -one you specify, so you should set all the options you need each time -you use it. See more details at the bottom of this page. - -The Coulomb factors are applied to any Coulomb (charge interaction) -term that the potential calculates. The LJ factors are applied to the -remaining terms that the potential calculates, whether they represent -LJ interactions or not. The weighting factors are a scaling -pre-factor on the energy and force between the pair of atoms. A value -of 1.0 means include the full interaction; a value of 0.0 means -exclude it completely. - -The 1st of the 3 coefficients (LJ or Coulombic) is the weighting -factor on 1-2 atom pairs, which are pairs of atoms directly bonded to -each other. The 2nd coefficient is the weighting factor on 1-3 atom -pairs which are those separated by 2 bonds (e.g. the two H atoms in a -water molecule). The 3rd coefficient is the weighting factor on 1-4 -atom pairs which are those separated by 3 bonds (e.g. the 1st and 4th -atoms in a dihedral interaction). Thus if the 1-2 coefficient is set -to 0.0, then the pairwise interaction is effectively turned off for -all pairs of atoms bonded to each other. If it is set to 1.0, then -that interaction will be at full strength. - -NOTE: For purposes of computing weighted pairwise interactions, 1-3 -and 1-4 interactions are not defined from the list of angles or -dihedrals used by the simulation. Rather, they are inferred -topologically from the set of bonds specified when the simulation is -defined from a data or restart file (see "read_data"_read_data.html or -"read_restart"_read_restart.html commands). Thus the set of -1-2,1-3,1-4 interactions that the weights apply to is the same whether -angle and dihedral potentials are computed or not, and remains the -same even if bonds are constrained, or turned off, or removed during a -simulation. - -The two exceptions to this rule are (a) if the {angle} or {dihedral} -keywords are set to {yes} (see below), or (b) if the -"delete_bonds"_delete_bonds.html command is used with the {special} -option that re-computes the 1-2,1-3,1-4 topologies after bonds are -deleted; see the "delete_bonds"_delete_bonds.html command for more -details. - -The {amber} keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ -interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which -is the default for a commonly used version of the AMBER force field, -where the last value is really 5/6. See "(Cornell)"_#Cornell for a -description of the AMBER force field. - -The {charmm} keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both -LJ and Coulombic interactions, which is the default for a commonly -used version of the CHARMM force field. Note that in pair styles -{lj/charmm/coul/charmm} and {lj/charmm/coul/long} the 1-4 coefficients -are defined explicitly, and these pairwise contributions are computed -as part of the charmm dihedral style - see the -"pair_coeff"_pair_coeff.html and "dihedral_style"_dihedral_style.html -commands for more information. See "(MacKerell)"_#MacKerell for a -description of the CHARMM force field. - -The {dreiding} keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both -LJ and Coulombic interactions, which is the default for the Dreiding -force field, as discussed in "(Mayo)"_#Mayo. - -The {fene} keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both -LJ and Coulombic interactions, which is consistent with a -coarse-grained polymer model with "FENE bonds"_bond_fene.html. See -"(Kremer)"_#Kremer for a description of FENE bonds. - -The {lj/coul}, {lj}, and {coul} keywords allow the 3 coefficients to -be set explicitly. The {lj/coul} keyword sets both the LJ and -Coulombic coefficients to the same 3 values. The {lj} and {coul} -keywords only set either the LJ or Coulombic coefficients. Use both -of them if you wish to set the LJ coefficients to different values -than the Coulombic coefficients. - -The {angle} keyword allows the 1-3 weighting factor to be ignored for -individual atom pairs if they are not listed as the first and last -atoms in any angle defined in the simulation or as 1,3 or 2,4 atoms in -any dihedral defined in the simulation. For example, imagine the 1-3 -weighting factor is set to 0.5 and you have a linear molecule with 4 -atoms and bonds as follows: 1-2-3-4. If your data file defines 1-2-3 -as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a -dihedral, then the pairwise interaction between atoms 1 and 3 will -always be weighted by 0.5, but different force fields use different -rules for weighting the pairwise interaction between atoms 2 and 4. -If the {angle} keyword is specified as {yes}, then the pairwise -interaction between atoms 2 and 4 will be unaffected (full weighting -of 1.0). If the {angle} keyword is specified as {no} which is the -default, then the 2,4 interaction will also be weighted by 0.5. - -The {dihedral} keyword allows the 1-4 weighting factor to be ignored -for individual atom pairs if they are not listed as the first and last -atoms in any dihedral defined in the simulation. For example, imagine -the 1-4 weighting factor is set to 0.5 and you have a linear molecule -with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file -defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a -dihedral, then the pairwise interaction between atoms 1 and 4 will -always be weighted by 0.5, but different force fields use different -rules for weighting the pairwise interaction between atoms 2 and 5. -If the {dihedral} keyword is specified as {yes}, then the pairwise -interaction between atoms 2 and 5 will be unaffected (full weighting -of 1.0). If the {dihedral} keyword is specified as {no} which is the -default, then the 2,5 interaction will also be weighted by 0.5. - -:line - -NOTE: LAMMPS stores and maintains a data structure with a list of the -1st, 2nd, and 3rd neighbors of each atom (within the bond topology of -the system). If new bonds are created (or molecules added containing -atoms with more special neighbors), the size of this list needs to -grow. Note that adding a single bond always adds a new 1st neighbor -but may also induce *many* new 2nd and 3rd neighbors, depending on the -molecular topology of your system. Using the {extra/special/per/atom} -keyword to either "read_data"_read_data.html or "create_box"_create_box.html -reserves empty space in the list for this N additional 1st, 2nd, or 3rd -neighbors to be added. If you do not do this, you may get an error -when bonds (or molecules) are added. - -:line - -NOTE: If you reuse this command in an input script, you should set all -the options you need each time. This command cannot be used a 2nd -time incrementally. E.g. these two commands: - -special_bonds lj 0.0 1.0 1.0 -special_bonds coul 0.0 0.0 1.0 :pre - -are not the same as - -special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0 :pre - -In the first case you end up with (after the 2nd command): - -LJ: 0.0 0.0 0.0 -Coul: 0.0 0.0 1.0 :pre - -while only in the second case, you get the desired settings of: - -LJ: 0.0 1.0 1.0 -Coul: 0.0 0.0 1.0 :pre - -This happens because the LJ (and Coul) settings are reset to -their default values before modifying them, each time the -{special_bonds} command is issued. - -[Restrictions:] none - -[Related commands:] - -"delete_bonds"_delete_bonds.html, "fix bond/create"_fix_bond_create.html - -[Default:] - -All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0, -angle = no, dihedral = no. - -:line - -:link(Cornell) -[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, -Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). - -:link(Kremer) -[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990). - -:link(MacKerell) -[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). - -:link(Mayo) -[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). diff --git a/doc/txt/suffix.txt b/doc/txt/suffix.txt deleted file mode 100644 index e9fae44088..0000000000 --- a/doc/txt/suffix.txt +++ /dev/null @@ -1,110 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -suffix command :h3 - -[Syntax:] - -suffix style args :pre - -style = {off} or {on} or {gpu} or {intel} or {kk} or {omp} or {opt} or {hybrid} -args = for hybrid style, default suffix to be used and alternative suffix :ul - -[Examples:] - -suffix off -suffix on -suffix gpu -suffix intel -suffix hybrid intel omp -suffix kk :pre - -[Description:] - -This command allows you to use variants of various styles if they -exist. In that respect it operates the same as the "-suffix -command-line switch"_Run_options.html. It also has options to turn -off or back on any suffix setting made via the command line. - -The specified style can be {gpu}, {intel}, {kk}, {omp}, {opt} or -{hybrid}. These refer to optional packages that LAMMPS can be built -with, as described on the "Build package"_Build_package.html doc page. -The "gpu" style corresponds to the GPU package, the "intel" style to -the USER-INTEL package, the "kk" style to the KOKKOS package, the -"omp" style to the USER-OMP package, and the "opt" style to the OPT -package. - -These are the variants these packages provide: - -GPU = a handful of pair styles and the PPPM kspace_style, optimized to -run on one or more GPUs or multicore CPU/GPU nodes :ulb,l - -USER-INTEL = a collection of pair styles and neighbor routines -optimized to run in single, mixed, or double precision on CPUs and -Intel(R) Xeon Phi(TM) co-processors. :l - -KOKKOS = a collection of atom, pair, and fix styles optimized to run -using the Kokkos library on various kinds of hardware, including GPUs -via CUDA and many-core chips via OpenMP or threading. :l - -USER-OMP = a collection of pair, bond, angle, dihedral, improper, -kspace, compute, and fix styles with support for OpenMP -multi-threading :l - -OPT = a handful of pair styles, cache-optimized for faster CPU -performance :l - -HYBRID = a combination of two packages can be specified (see below) :l -:ule - -As an example, all of the packages provide a "pair_style -lj/cut"_pair_lj.html variant, with style names lj/cut/opt, lj/cut/omp, -lj/cut/gpu, lj/cut/intel, or lj/cut/kk. A variant styles -can be specified explicitly in your input script, e.g. pair_style -lj/cut/gpu. If the suffix command is used with the appropriate style, -you do not need to modify your input script. The specified suffix -(opt,omp,gpu,intel,kk) is automatically appended whenever your -input script command creates a new "atom"_atom_style.html, -"pair"_pair_style.html, "bond"_bond_style.html, -"angle"_angle_style.html, "dihedral"_dihedral_style.html, -"improper"_improper_style.html, "kspace"_kspace_style.html, -"fix"_fix.html, "compute"_compute.html, or "run"_run_style.html style. -If the variant version does not exist, the standard version is -created. - -For "hybrid", two packages are specified. The first is used whenever -available. If a style with the first suffix is not available, the style -with the suffix for the second package will be used if available. For -example, "hybrid intel omp" will use styles from the USER-INTEL package -as a first choice and styles from the USER-OMP package as a second choice -if no USER-INTEL variant is available. - -If the specified style is {off}, then any previously specified suffix -is temporarily disabled, whether it was specified by a command-line -switch or a previous suffix command. If the specified style is {on}, -a disabled suffix is turned back on. The use of these 2 commands lets -your input script use a standard LAMMPS style (i.e. a non-accelerated -variant), which can be useful for testing or benchmarking purposes. -Of course this is also possible by not using any suffix commands, and -explicitly appending or not appending the suffix to the relevant -commands in your input script. - -NOTE: The default "run_style"_run_style.html verlet is invoked prior to -reading the input script and is therefore not affected by a suffix command -in the input script. The KOKKOS package requires "run_style verlet/kk", -so when using the KOKKOS package it is necessary to either use the command -line "-sf kk" command or add an explicit "run_style verlet" command to the -input script. - -[Restrictions:] none - -[Related commands:] - -"-suffix command-line switch"_Run_options.html - -[Default:] none diff --git a/doc/txt/tad.txt b/doc/txt/tad.txt deleted file mode 100644 index 62407532d6..0000000000 --- a/doc/txt/tad.txt +++ /dev/null @@ -1,311 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -tad command :h3 - -[Syntax:] - -tad N t_event T_lo T_hi delta tmax compute-ID \ -keyword value ... :pre - -N = # of timesteps to run (not including dephasing/quenching) :ulb,l -t_event = timestep interval between event checks :l -T_lo = temperature at which event times are desired :l -T_hi = temperature at which MD simulation is performed :l -delta = desired confidence level for stopping criterion :l -tmax = reciprocal of lowest expected pre-exponential factor (time units) :l -compute-ID = ID of the compute used for event detection :l -zero or more keyword/value pairs may be appended :l -keyword = {min} or {neb} or {min_style} or {neb_style} or {neb_log} :l - {min} values = etol ftol maxiter maxeval - etol = stopping tolerance for energy (energy units) - ftol = stopping tolerance for force (force units) - maxiter = max iterations of minimize - maxeval = max number of force/energy evaluations - {neb} values = ftol N1 N2 Nevery - etol = stopping tolerance for energy (energy units) - ftol = stopping tolerance for force (force units) - N1 = max # of iterations (timesteps) to run initial NEB - N2 = max # of iterations (timesteps) to run barrier-climbing NEB - Nevery = print NEB statistics every this many timesteps - {neb_style} value = {quickmin} or {fire} - {neb_step} value = dtneb - dtneb = timestep for NEB damped dynamics minimization - {neb_log} value = file where NEB statistics are printed :pre - -:ule - -[Examples:] - -tad 2000 50 1800 2300 0.01 0.01 event -tad 2000 50 1800 2300 0.01 0.01 event & - min 1e-05 1e-05 100 100 & - neb 0.0 0.01 200 200 20 & - min_style cg & - neb_style fire & - neb_log log.neb :pre - -[Description:] - -Run a temperature accelerated dynamics (TAD) simulation. This method -requires two or more partitions to perform NEB transition state -searches. - -TAD is described in "this paper"_#Voter2000 by Art Voter. It is a method -that uses accelerated dynamics at an elevated temperature to generate -results at a specified lower temperature. A good overview of -accelerated dynamics methods for such systems is given in "this review -paper"_#Voter2002 from the same group. In general, these methods assume -that the long-time dynamics is dominated by infrequent events i.e. the -system is confined to low energy basins for long periods, -punctuated by brief, randomly-occurring transitions to adjacent -basins. TAD is suitable for infrequent-event systems, where in -addition, the transition kinetics are well-approximated by harmonic -transition state theory (hTST). In hTST, the temperature dependence of -transition rates follows the Arrhenius relation. As a consequence a -set of event times generated in a high-temperature simulation can be -mapped to a set of much longer estimated times in the low-temperature -system. However, because this mapping involves the energy barrier of -the transition event, which is different for each event, the first -event at the high temperature may not be the earliest event at the low -temperature. TAD handles this by first generating a set of possible -events from the current basin. After each event, the simulation is -reflected backwards into the current basin. This is repeated until -the stopping criterion is satisfied, at which point the event with the -earliest low-temperature occurrence time is selected. The stopping -criterion is that the confidence measure be greater than -1-{delta}. The confidence measure is the probability that no earlier -low-temperature event will occur at some later time in the -high-temperature simulation. hTST provides an lower bound for this -probability, based on the user-specified minimum pre-exponential -factor (reciprocal of {tmax}). - -In order to estimate the energy barrier for each event, the TAD method -invokes the "NEB"_neb.html method. Each NEB replica runs on a -partition of processors. The current NEB implementation in LAMMPS -restricts you to having exactly one processor per replica. For more -information, see the documentation for the "neb"_neb.html command. In -the current LAMMPS implementation of TAD, all the non-NEB TAD -operations are performed on the first partition, while the other -partitions remain idle. See the "Howto replica"_Howto_replica.html doc -page for further discussion of multi-replica simulations. - -A TAD run has several stages, which are repeated each time an event is -performed. The logic for a TAD run is as follows: - -while (time remains): - while (time < tstop): - until (event occurs): - run dynamics for t_event steps - quench - run neb calculation using all replicas - compute tlo from energy barrier - update earliest event - update tstop - reflect back into current basin - execute earliest event :pre - -Before this outer loop begins, the initial potential energy basin is -identified by quenching (an energy minimization, see below) the -initial state and storing the resulting coordinates for reference. - -Inside the inner loop, dynamics is run continuously according to -whatever integrator has been specified by the user, stopping every -{t_event} steps to check if a transition event has occurred. This -check is performed by quenching the system and comparing the resulting -atom coordinates to the coordinates from the previous basin. - -A quench is an energy minimization and is performed by whichever -algorithm has been defined by the "min_style"_min_style.html command; -its default is the CG minimizer. The tolerances and limits for each -quench can be set by the {min} keyword. Note that typically, you do -not need to perform a highly-converged minimization to detect a -transition event. - -The event check is performed by a compute with the specified -{compute-ID}. Currently there is only one compute that works with the -TAD command, which is the "compute -event/displace"_compute_event_displace.html command. Other -event-checking computes may be added. "Compute -event/displace"_compute_event_displace.html checks whether any atom in -the compute group has moved further than a specified threshold -distance. If so, an "event" has occurred. - -The NEB calculation is similar to that invoked by the "neb"_neb.html -command, except that the final state is generated internally, instead -of being read in from a file. The style of minimization performed by -NEB is determined by the {neb_style} keyword and must be a damped -dynamics minimizer. The tolerances and limits for each NEB -calculation can be set by the {neb} keyword. As discussed on the -"neb"_neb.html, it is often advantageous to use a larger timestep for -NEB than for normal dynamics. Since the size of the timestep set by -the "timestep"_timestep.html command is used by TAD for performing -dynamics, there is a {neb_step} keyword which can be used to set a -larger timestep for each NEB calculation if desired. - -:line - -A key aspect of the TAD method is setting the stopping criterion -appropriately. If this criterion is too conservative, then many -events must be generated before one is finally executed. Conversely, -if this criterion is too aggressive, high-entropy high-barrier events -will be over-sampled, while low-entropy low-barrier events will be -under-sampled. If the lowest pre-exponential factor is known fairly -accurately, then it can be used to estimate {tmax}, and the value of -{delta} can be set to the desired confidence level e.g. {delta} = 0.05 -corresponds to 95% confidence. However, for systems where the dynamics -are not well characterized (the most common case), it will be -necessary to experiment with the values of {delta} and {tmax} to get a -good trade-off between accuracy and performance. - -A second key aspect is the choice of {t_hi}. A larger value greatly -increases the rate at which new events are generated. However, too -large a value introduces errors due to anharmonicity (not accounted -for within hTST). Once again, for any given system, experimentation is -necessary to determine the best value of {t_hi}. - -:line - -Five kinds of output can be generated during a TAD run: event -statistics, NEB statistics, thermodynamic output by each replica, dump -files, and restart files. - -Event statistics are printed to the screen and master log.lammps file -each time an event is executed. The quantities are the timestep, CPU -time, global event number {N}, local event number {M}, event status, -energy barrier, time margin, {t_lo} and {delt_lo}. The timestep is -the usual LAMMPS timestep, which corresponds to the high-temperature -time at which the event was detected, in units of timestep. The CPU -time is the total processor time since the start of the TAD run. The -global event number {N} is a counter that increments with each -executed event. The local event number {M} is a counter that resets to -zero upon entering each new basin. The event status is {E} when an -event is executed, and is {D} for an event that is detected, while -{DF} is for a detected event that is also the earliest (first) event -at the low temperature. - -The time margin is the ratio of the high temperature time in the -current basin to the stopping time. This last number can be used to -judge whether the stopping time is too short or too long (see above). - -{t_lo} is the low-temperature event time when the current basin was -entered, in units of timestep. del{t_lo} is the time of each detected -event, measured relative to {t_lo}. {delt_lo} is equal to the -high-temperature time since entering the current basin, scaled by an -exponential factor that depends on the hi/lo temperature ratio and the -energy barrier for that event. - -On lines for executed events, with status {E}, the global event number -is incremented by one, -the local event number and time margin are reset to zero, -while the global event number, energy barrier, and -{delt_lo} match the last event with status {DF} -in the immediately preceding block of detected events. -The low-temperature event time {t_lo} is incremented by {delt_lo}. - -NEB statistics are written to the file specified by the {neb_log} -keyword. If the keyword value is "none", then no NEB statistics are -printed out. The statistics are written every {Nevery} timesteps. See -the "neb"_neb.html command for a full description of the NEB -statistics. When invoked from TAD, NEB statistics are never printed to -the screen. - -Because the NEB calculation must run on multiple partitions, LAMMPS -produces additional screen and log files for each partition, -e.g. log.lammps.0, log.lammps.1, etc. For the TAD command, these -contain the thermodynamic output of each NEB replica. In addition, the -log file for the first partition, log.lammps.0, will contain -thermodynamic output from short runs and minimizations corresponding -to the dynamics and quench operations, as well as a line for each new -detected event, as described above. - -After the TAD command completes, timing statistics for the TAD run are -printed in each replica's log file, giving a breakdown of how much CPU -time was spent in each stage (NEB, dynamics, quenching, etc). - -Any "dump files"_dump.html defined in the input script will be written -to during a TAD run at timesteps when an event is executed. This -means the requested dump frequency in the "dump"_dump.html command -is ignored. There will be one dump file (per dump command) created -for all partitions. The atom coordinates of the dump snapshot are -those of the minimum energy configuration resulting from quenching -following the executed event. The timesteps written into the dump -files correspond to the timestep at which the event occurred and NOT -the clock. A dump snapshot corresponding to the initial minimum state -used for event detection is written to the dump file at the beginning -of each TAD run. - -If the "restart"_restart.html command is used, a single restart file -for all the partitions is generated, which allows a TAD run to be -continued by a new input script in the usual manner. The restart file -is generated after an event is executed. The restart file contains a -snapshot of the system in the new quenched state, including the event -number and the low-temperature time. The restart frequency specified -in the "restart"_restart.html command is interpreted differently when -performing a TAD run. It does not mean the timestep interval between -restart files. Instead it means an event interval for executed -events. Thus a frequency of 1 means write a restart file every time -an event is executed. A frequency of 10 means write a restart file -every 10th executed event. When an input script reads a restart file -from a previous TAD run, the new script can be run on a different -number of replicas or processors. - -Note that within a single state, the dynamics will typically -temporarily continue beyond the event that is ultimately chosen, until -the stopping criterion is satisfied. When the event is eventually -executed, the timestep counter is reset to the value when the event -was detected. Similarly, after each quench and NEB minimization, the -timestep counter is reset to the value at the start of the -minimization. This means that the timesteps listed in the replica log -files do not always increase monotonically. However, the timestep -values printed to the master log file, dump files, and restart files -are always monotonically increasing. - -:line - -[Restrictions:] - -This command can only be used if LAMMPS was built with the REPLICA -package. See the "Build package"_Build_package.html doc -page for more info. - -{N} setting must be integer multiple of {t_event}. - -Runs restarted from restart files written during a TAD run will only -produce identical results if the user-specified integrator supports -exact restarts. So "fix nvt"_fix_nh.html will produce an exact -restart, but "fix langevin"_fix_langevin.html will not. - -This command cannot be used when any fixes are defined that keep track -of elapsed time to perform time-dependent operations. Examples -include the "ave" fixes such as "fix ave/chunk"_fix_ave_chunk.html. -Also "fix dt/reset"_fix_dt_reset.html and "fix -deposit"_fix_deposit.html. - -[Related commands:] - -"compute event/displace"_compute_event_displace.html, -"min_modify"_min_modify.html, "min_style"_min_style.html, -"run_style"_run_style.html, "minimize"_minimize.html, -"temper"_temper.html, "neb"_neb.html, -"prd"_prd.html - -[Default:] - -The option defaults are {min} = 0.1 0.1 40 50, {neb} = 0.01 100 100 -10, {neb_style} = {quickmin}, {neb_step} = the same timestep set by -the "timestep"_timestep.html command, and {neb_log} = "none". - -:line - -:link(Voter2000) -[(Voter2000)] Sorensen and Voter, J Chem Phys, 112, 9599 (2000) - -:link(Voter2002) -[(Voter2002)] Voter, Montalenti, Germann, Annual Review of Materials -Research 32, 321 (2002). diff --git a/doc/txt/temper.txt b/doc/txt/temper.txt deleted file mode 100644 index 6a61dfa6dd..0000000000 --- a/doc/txt/temper.txt +++ /dev/null @@ -1,153 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -temper command :h3 - -[Syntax:] - -temper N M temp fix-ID seed1 seed2 index :pre - -N = total # of timesteps to run -M = attempt a tempering swap every this many steps -temp = initial temperature for this ensemble -fix-ID = ID of the fix that will control temperature during the run -seed1 = random # seed used to decide on adjacent temperature to partner with -seed2 = random # seed for Boltzmann factor in Metropolis swap -index = which temperature (0 to N-1) I am simulating (optional) :ul - -[Examples:] - -temper 100000 100 $t tempfix 0 58728 -temper 40000 100 $t tempfix 0 32285 $w :pre - -[Description:] - -Run a parallel tempering or replica exchange simulation using multiple -replicas (ensembles) of a system. Two or more replicas must be used. - -Each replica runs on a partition of one or more processors. Processor -partitions are defined at run-time using the "-partition command-line -switch"_Run_options.html. Note that if you have MPI installed, you -can run a multi-replica simulation with more replicas (partitions) -than you have physical processors, e.g you can run a 10-replica -simulation on one or two processors. You will simply not get the -performance speed-up you would see with one or more physical -processors per replica. See the "Howto replica"_Howto_replica.html -doc page for further discussion. - -Each replica's temperature is controlled at a different value by a fix -with {fix-ID} that controls temperature. Most thermostat fix styles -(with and without included time integration) are supported. The command -will print an error message and abort, if the chosen fix is unsupported. -The desired temperature is specified by {temp}, which is typically a -variable previously set in the input script, so that each partition is -assigned a different temperature. See the "variable"_variable.html -command for more details. For example: - -variable t world 300.0 310.0 320.0 330.0 -fix myfix all nvt temp $t $t 100.0 -temper 100000 100 $t myfix 3847 58382 :pre - -would define 4 temperatures, and assign one of them to the thermostat -used by each replica, and to the temper command. - -As the tempering simulation runs for {N} timesteps, a temperature swap -between adjacent ensembles will be attempted every {M} timesteps. If -{seed1} is 0, then the swap attempts will alternate between odd and -even pairings. If {seed1} is non-zero then it is used as a seed in a -random number generator to randomly choose an odd or even pairing each -time. Each attempted swap of temperatures is either accepted or -rejected based on a Boltzmann-weighted Metropolis criterion which uses -{seed2} in the random number generator. - -As a tempering run proceeds, multiple log files and screen output -files are created, one per replica. By default these files are named -log.lammps.M and screen.M where M is the replica number from 0 to N-1, -with N = # of replicas. See the "-log and -screen command-line -swiches"_Run_options.html for info on how to change these names. - -The main screen and log file (log.lammps) will list information about -which temperature is assigned to each replica at each thermodynamic -output timestep. E.g. for a simulation with 16 replicas: - -Running on 16 partitions of processors -Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15 -0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15 -1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15 -1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15 -2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15 -2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15 -... :pre - -The column headings T0 to TN-1 mean which temperature is currently -assigned to the replica 0 to N-1. Thus the columns represent replicas -and the value in each column is its temperature (also numbered 0 to -N-1). For example, a 0 in the 4th column (column T3, step 2500) means -that the 4th replica is assigned temperature 0, i.e. the lowest -temperature. You can verify this time sequence of temperature -assignments for the Nth replica by comparing the Nth column of screen -output to the thermodynamic data in the corresponding log.lammps.N or -screen.N files as time proceeds. - -You can have each replica create its own dump file in the following -manner: - -variable rep world 0 1 2 3 4 5 6 7 -dump 1 all atom 1000 dump.temper.${rep} :pre - -NOTE: Each replica's dump file will contain a continuous trajectory -for its atoms where the temperature varies over time as swaps take -place involving that replica. If you want a series of dump files, -each with snapshots (from all replicas) that are all at a single -temperature, then you will need to post-process the dump files using -the information from the log.lammps file. E.g. you could produce one -dump file with snapshots at 300K (from all replicas), another with -snapshots at 310K, etc. Note that these new dump files will not -contain "continuous trajectories" for individual atoms, because two -successive snapshots (in time) may be from different replicas. The -reorder_remd_traj python script can do the reordering for you -(and additionally also calculated configurational log-weights of -trajectory snapshots in the canonical ensemble). The script can be found -in the tools/replica directory while instructions on how to use it is -available in doc/Tools (in brief) and as a README file in tools/replica -(in detail). - -The last argument {index} in the temper command is optional and is -used when restarting a tempering run from a set of restart files (one -for each replica) which had previously swapped to new temperatures. -The {index} value (from 0 to N-1, where N is the # of replicas) -identifies which temperature the replica was simulating on the -timestep the restart files were written. Obviously, this argument -must be a variable so that each partition has the correct value. Set -the variable to the {N} values listed in the log file for the previous -run for the replica temperatures at that timestep. For example if the -log file listed the following for a simulation with 5 replicas: - -500000 2 4 0 1 3 :pre - -then a setting of - -variable w world 2 4 0 1 3 :pre - -would be used to restart the run with a tempering command like the -example above with $w as the last argument. - -:line - -[Restrictions:] - -This command can only be used if LAMMPS was built with the REPLICA -package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"variable"_variable.html, "prd"_prd.html, "neb"_neb.html - -[Default:] none diff --git a/doc/txt/temper_grem.txt b/doc/txt/temper_grem.txt deleted file mode 100644 index 7d22e46403..0000000000 --- a/doc/txt/temper_grem.txt +++ /dev/null @@ -1,109 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -temper/grem command :h3 - -[Syntax:] - -temper/grem N M lambda fix-ID thermostat-ID seed1 seed2 index :pre - -N = total # of timesteps to run -M = attempt a tempering swap every this many steps -lambda = initial lambda for this ensemble -fix-ID = ID of fix_grem -thermostat-ID = ID of the thermostat that controls kinetic temperature -seed1 = random # seed used to decide on adjacent temperature to partner with -seed2 = random # seed for Boltzmann factor in Metropolis swap -index = which temperature (0 to N-1) I am simulating (optional) :ul - -[Examples:] - -temper/grem 100000 1000 ${lambda} fxgREM fxnvt 0 58728 -temper/grem 40000 100 ${lambda} fxgREM fxnpt 0 32285 ${walkers} :pre - -[Description:] - -Run a parallel tempering or replica exchange simulation in LAMMPS -partition mode using multiple generalized replicas (ensembles) of a -system defined by "fix grem"_fix_grem.html, which stands for the -generalized replica exchange method (gREM) originally developed by -"(Kim)"_#KimStraub. It uses non-Boltzmann ensembles to sample over first -order phase transitions. The is done by defining replicas with an -enthalpy dependent effective temperature - -Two or more replicas must be used. See the "temper"_temper.html -command for an explanation of how to run replicas on multiple -partitions of one or more processors. - -This command is a modification of the "temper"_temper.html command and -has the same dependencies, restraints, and input variables which are -discussed there in greater detail. - -Instead of temperature, this command performs replica exchanges in -lambda as per the generalized ensemble enforced by "fix -grem"_fix_grem.html. The desired lambda is specified by {lambda}, -which is typically a variable previously set in the input script, so -that each partition is assigned a different temperature. See the -"variable"_variable.html command for more details. For example: - -variable lambda world 400 420 440 460 -fix fxnvt all nvt temp 300.0 300.0 100.0 -fix fxgREM all grem ${lambda} -0.05 -50000 fxnvt -temper 100000 100 ${lambda} fxgREM fxnvt 3847 58382 :pre - -would define 4 lambdas with constant kinetic temperature but unique -generalized temperature, and assign one of them to "fix -grem"_fix_grem.html used by each replica, and to the grem command. - -As the gREM simulation runs for {N} timesteps, a swap between adjacent -ensembles will be attempted every {M} timesteps. If {seed1} is 0, -then the swap attempts will alternate between odd and even pairings. -If {seed1} is non-zero then it is used as a seed in a random number -generator to randomly choose an odd or even pairing each time. Each -attempted swap of temperatures is either accepted or rejected based on -a Metropolis criterion, derived for gREM by "(Kim)"_#Kim, which uses -{seed2} in the random number generator. - -File management works identical to the "temper"_temper.html command. -Dump files created by this fix contain continuous trajectories and -require post-processing to obtain per-replica information. - -The last argument {index} in the grem command is optional and is used -when restarting a run from a set of restart files (one for each -replica) which had previously swapped to new lambda. This is done -using a variable. For example if the log file listed the following for -a simulation with 5 replicas: - -500000 2 4 0 1 3 :pre - -then a setting of - -variable walkers world 2 4 0 1 3 :pre - -would be used to restart the run with a grem command like the example -above with ${walkers} as the last argument. This functionality is -identical to "temper"_temper.html. - -:line - -[Restrictions:] - -This command can only be used if LAMMPS was built with the USER-MISC -package. See the "Build package"_Build_package.html doc -page for more info. - -This command must be used with "fix grem"_fix_grem.html. - -[Related commands:] - -"fix grem"_fix_grem.html, "temper"_temper.html, "variable"_variable.html - -[Default:] none - -:link(KimStraub) -[(Kim)] Kim, Keyes, Straub, J Chem Phys, 132, 224107 (2010). diff --git a/doc/txt/temper_npt.txt b/doc/txt/temper_npt.txt deleted file mode 100644 index 00a3e35ec3..0000000000 --- a/doc/txt/temper_npt.txt +++ /dev/null @@ -1,67 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line -temper/npt command :h3 - -[Syntax:] - -temper/npt N M temp fix-ID seed1 seed2 pressure index :pre - -N = total # of timesteps to run -M = attempt a tempering swap every this many steps -temp = initial temperature for this ensemble -fix-ID = ID of the fix that will control temperature and pressure during the run -seed1 = random # seed used to decide on adjacent temperature to partner with -seed2 = random # seed for Boltzmann factor in Metropolis swap -pressure = setpoint pressure for the ensemble -index = which temperature (0 to N-1) I am simulating (optional) :ul - -[Examples:] - -temper/npt 100000 100 $t nptfix 0 58728 1 -temper/npt 2500000 1000 300 nptfix 0 32285 $p -temper/npt 5000000 2000 $t nptfix 0 12523 1 $w :pre - -[Description:] - -Run a parallel tempering or replica exchange simulation using multiple -replicas (ensembles) of a system in the isothermal-isobaric (NPT) -ensemble. The command temper/npt works like "temper"_temper.html but -requires running replicas in the NPT ensemble instead of the canonical -(NVT) ensemble and allows for pressure to be set in the ensembles. -These multiple ensembles can run in parallel at different temperatures -or different pressures. The acceptance criteria for temper/npt is -specific to the NPT ensemble and can be found in references -"(Okabe)"_#Okabe2 and "(Mori)"_#Mori2. - -Apart from the difference in acceptance criteria and the specification -of pressure, this command works much like the "temper"_temper.html -command. See the documentation on "temper"_temper.html for information -on how the parallel tempering is handled in general. - -:line - -[Restrictions:] - -This command can only be used if LAMMPS was built with the USER-MISC -package. See the "Build package"_Build_package.html doc page for more -info. - -This command should be used with a fix that maintains the -isothermal-isobaric (NPT) ensemble. - -[Related commands:] - -"temper"_temper.html, "variable"_variable.html, "fix_npt"_fix_nh.html - -[Default:] none - -:link(Okabe2) -[(Okabe)] T. Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001). - -:link(Mori2) -[(Mori)] Y. Mori, Y. Okamoto, J. Phys. Soc. Jpn., 7, 074003 (2010). diff --git a/doc/txt/thermo.txt b/doc/txt/thermo.txt deleted file mode 100644 index 5f12f98707..0000000000 --- a/doc/txt/thermo.txt +++ /dev/null @@ -1,59 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -thermo command :h3 - -[Syntax:] - -thermo N :pre - -N = output thermodynamics every N timesteps -N can be a variable (see below) :ul - -[Examples:] - -thermo 100 :pre - -[Description:] - -Compute and print thermodynamic info (e.g. temperature, energy, -pressure) on timesteps that are a multiple of N and at the beginning -and end of a simulation. A value of 0 will only print thermodynamics -at the beginning and end. - -The content and format of what is printed is controlled by the -"thermo_style"_thermo_style.html and -"thermo_modify"_thermo_modify.html commands. - -Instead of a numeric value, N can be specified as an "equal-style -variable"_variable.html, which should be specified as v_name, where -name is the variable name. In this case, the variable is evaluated at -the beginning of a run to determine the next timestep at which -thermodynamic info will be written out. On that timestep, the -variable will be evaluated again to determine the next timestep, etc. -Thus the variable should return timestep values. See the stagger() -and logfreq() and stride() math functions for "equal-style -variables"_variable.html, as examples of useful functions to use in -this context. Other similar math functions could easily be added as -options for "equal-style variables"_variable.html. - -For example, the following commands will output thermodynamic info at -timesteps 0,10,20,30,100,200,300,1000,2000,etc: - -variable s equal logfreq(10,3,10) -thermo v_s :pre - -[Restrictions:] none - -[Related commands:] - -"thermo_style"_thermo_style.html, "thermo_modify"_thermo_modify.html - -[Default:] - -thermo 0 :pre diff --git a/doc/txt/thermo_modify.txt b/doc/txt/thermo_modify.txt deleted file mode 100644 index ca2957de77..0000000000 --- a/doc/txt/thermo_modify.txt +++ /dev/null @@ -1,179 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -thermo_modify command :h3 - -[Syntax:] - -thermo_modify keyword value ... :pre - -one or more keyword/value pairs may be listed :ulb,l -keyword = {lost} or {lost/bond} or {norm} or {flush} or {line} or {format} or {temp} or {press}:l - {lost} value = {error} or {warn} or {ignore} - {lost/bond} value = {error} or {warn} or {ignore} - {norm} value = {yes} or {no} - {flush} value = {yes} or {no} - {line} value = {one} or {multi} - {format} values = {line} string, {int} string, {float} string, M string, or {none} - string = C-style format string - M = integer from 1 to N, where N = # of quantities being output - {temp} value = compute ID that calculates a temperature - {press} value = compute ID that calculates a pressure :pre -:ule - -[Examples:] - -thermo_modify lost ignore flush yes -thermo_modify temp myTemp format 3 %15.8g -thermo_modify temp myTemp format line "%ld %g %g %15.8g" -thermo_modify line multi format float %g :pre - -[Description:] - -Set options for how thermodynamic information is computed and printed -by LAMMPS. - -NOTE: These options apply to the currently defined thermo style. When -you specify a "thermo_style"_thermo_style.html command, all -thermodynamic settings are restored to their default values, including -those previously reset by a thermo_modify command. Thus if your input -script specifies a thermo_style command, you should use the -thermo_modify command after it. - -The {lost} keyword determines whether LAMMPS checks for lost atoms -each time it computes thermodynamics and what it does if atoms are -lost. An atom can be "lost" if it moves across a non-periodic -simulation box "boundary"_boundary.html or if it moves more than a box -length outside the simulation domain (or more than a processor -sub-domain length) before reneighboring occurs. The latter case is -typically due to bad dynamics, e.g. too large a timestep or huge -forces and velocities. If the value is {ignore}, LAMMPS does not -check for lost atoms. If the value is {error} or {warn}, LAMMPS -checks and either issues an error or warning. The code will exit with -an error and continue with a warning. A warning will only be issued -once, the first time an atom is lost. This can be a useful debugging -option. - -The {lost/bond} keyword determines whether LAMMPS throws an error or -not if an atom in a bonded interaction (bond, angle, etc) cannot be -found when it creates bonded neighbor lists. By default this is a -fatal error. However in some scenarios it may be desirable to only -issue a warning or ignore it and skip the computation of the missing -bond, angle, etc. An example would be when gas molecules in a vapor -are drifting out of the box through a fixed boundary condition (see -the "boundary"_boundary.html command). In this case one atom may be -deleted before the rest of the molecule is, on a later timestep. - -The {norm} keyword determines whether various thermodynamic output -values are normalized by the number of atoms or not, depending on -whether it is set to {yes} or {no}. Different unit styles have -different defaults for this setting (see below). Even if {norm} is -set to {yes}, a value is only normalized if it is an "extensive" -quantity, meaning that it scales with the number of atoms in the -system. For the thermo keywords described by the doc page for the -"thermo_style"_thermo_style.html command, all energy-related keywords -are extensive, such as {pe} or {ebond} or {enthalpy}. Other keywords -such as {temp} or {press} are "intensive" meaning their value is -independent (in a statistical sense) of the number of atoms in the -system and thus are never normalized. For thermodynamic output values -extracted from fixes and computes in a "thermo_style -custom"_thermo_style.html command, the doc page for the individual -"fix"_fix.html or "compute"_compute.html lists whether the value is -"extensive" or "intensive" and thus whether it is normalized. -Thermodynamic output values calculated by a variable formula are -assumed to be "intensive" and thus are never normalized. You can -always include a divide by the number of atoms in the variable formula -if this is not the case. - -The {flush} keyword invokes a flush operation after thermodynamic info -is written to the log file. This insures the output in that file is -current (no buffering by the OS), even if LAMMPS halts before the -simulation completes. - -The {line} keyword determines whether thermodynamics will be output as -a series of numeric values on one line or in a multi-line format with -3 quantities with text strings per line and a dashed-line header -containing the timestep and CPU time. This modify option overrides -the {one} and {multi} thermo_style settings. - -The {format} keyword can be used to change the default numeric format -of any of quantities the "thermo_style"_thermo_style.html command -outputs. All the specified format strings are C-style formats, -e.g. as used by the C/C++ printf() command. The {line} keyword takes -a single argument which is the format string for the entire line of -thermo output, with N fields, which you must enclose in quotes if it -is more than one field. The {int} and {float} keywords take a single -format argument and are applied to all integer or floating-point -quantities output. The setting for {M string} also takes a single -format argument which is used for the Mth value output in each line, -e.g. the 5th column is output in high precision for "format 5 -%20.15g". - -The {format} keyword can be used multiple times. The precedence is -that for each value in a line of output, the {M} format (if specified) -is used, else the {int} or {float} setting (if specified) is used, -else the {line} setting (if specified) for that value is used, else -the default setting is used. A setting of {none} clears all previous -settings, reverting all values to their default format. - -NOTE: The thermo output values {step} and {atoms} are stored -internally as 8-byte signed integers, rather than the usual 4-byte -signed integers. When specifying the {format int} option you can use -a "%d"-style format identifier in the format string and LAMMPS will -convert this to the corresponding 8-byte form when it is applied to -those keywords. However, when specifying the {line} option or {format -M string} option for {step} and {natoms}, you should specify a format -string appropriate for an 8-byte signed integer, e.g. one with "%ld". - -The {temp} keyword is used to determine how thermodynamic temperature -is calculated, which is used by all thermo quantities that require a -temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx", etc). -The specified compute ID must have been previously defined by the user -via the "compute"_compute.html command and it must be a style of -compute that calculates a temperature. As described in the -"thermo_style"_thermo_style.html command, thermo output uses a default -compute for temperature with ID = {thermo_temp}. This option allows -the user to override the default. - -The {press} keyword is used to determine how thermodynamic pressure is -calculated, which is used by all thermo quantities that require a -pressure ("press", "enthalpy", "pxx", etc). The specified compute ID -must have been previously defined by the user via the -"compute"_compute.html command and it must be a style of compute that -calculates a pressure. As described in the -"thermo_style"_thermo_style.html command, thermo output uses a default -compute for pressure with ID = {thermo_press}. This option allows the -user to override the default. - -NOTE: If both the {temp} and {press} keywords are used in a single -thermo_modify command (or in two separate commands), then the order in -which the keywords are specified is important. Note that a "pressure -compute"_compute_pressure.html defines its own temperature compute as -an argument when it is specified. The {temp} keyword will override -this (for the pressure compute being used by thermodynamics), but only -if the {temp} keyword comes after the {press} keyword. If the {temp} -keyword comes before the {press} keyword, then the new pressure -compute specified by the {press} keyword will be unaffected by the -{temp} setting. - -[Restrictions:] none - -[Related commands:] - -"thermo"_thermo.html, "thermo_style"_thermo_style.html - -[Default:] - -The option defaults are lost = error, norm = yes for unit style of -{lj}, norm = no for unit style of {real} and {metal}, flush = no, -and temp/press = compute IDs defined by thermo_style. - -The defaults for the line and format options depend on the thermo -style. For styles "one" and "custom", the line and format defaults -are "one", "%8d", and "%12.8g". For style "multi", the line and -format defaults are "multi", "%8d", and "%14.4f". diff --git a/doc/txt/thermo_style.txt b/doc/txt/thermo_style.txt deleted file mode 100644 index 4d294c1df7..0000000000 --- a/doc/txt/thermo_style.txt +++ /dev/null @@ -1,407 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -thermo_style command :h3 - -[Syntax:] - -thermo_style style args :pre - -style = {one} or {multi} or {custom} :ulb,l -args = list of arguments for a particular style :l - {one} args = none - {multi} args = none - {custom} args = list of keywords - possible keywords = step, elapsed, elaplong, dt, time, - cpu, tpcpu, spcpu, cpuremain, part, timeremain, - atoms, temp, press, pe, ke, etotal, enthalpy, - evdwl, ecoul, epair, ebond, eangle, edihed, eimp, - emol, elong, etail, - vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi, - xy, xz, yz, xlat, ylat, zlat, - bonds, angles, dihedrals, impropers, - pxx, pyy, pzz, pxy, pxz, pyz, - fmax, fnorm, nbuild, ndanger, - cella, cellb, cellc, cellalpha, cellbeta, cellgamma, - c_ID, c_ID\[I\], c_ID\[I\]\[J\], - f_ID, f_ID\[I\], f_ID\[I\]\[J\], - v_name, v_name\[I\] - step = timestep - elapsed = timesteps since start of this run - elaplong = timesteps since start of initial run in a series of runs - dt = timestep size - time = simulation time - cpu = elapsed CPU time in seconds since start of this run - tpcpu = time per CPU second - spcpu = timesteps per CPU second - cpuremain = estimated CPU time remaining in run - part = which partition (0 to Npartition-1) this is - timeremain = remaining time in seconds on timer timeout. - atoms = # of atoms - temp = temperature - press = pressure - pe = total potential energy - ke = kinetic energy - etotal = total energy (pe + ke) - enthalpy = enthalpy (etotal + press*vol) - evdwl = VanderWaal pairwise energy (includes etail) - ecoul = Coulombic pairwise energy - epair = pairwise energy (evdwl + ecoul + elong) - ebond = bond energy - eangle = angle energy - edihed = dihedral energy - eimp = improper energy - emol = molecular energy (ebond + eangle + edihed + eimp) - elong = long-range kspace energy - etail = VanderWaal energy long-range tail correction - vol = volume - density = mass density of system - lx,ly,lz = box lengths in x,y,z - xlo,xhi,ylo,yhi,zlo,zhi = box boundaries - xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes - xlat,ylat,zlat = lattice spacings as calculated by "lattice"_lattice.html command - bonds,angles,dihedrals,impropers = # of these interactions defined - pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor - fmax = max component of force on any atom in any dimension - fnorm = length of force vector for all atoms - nbuild = # of neighbor list builds - ndanger = # of dangerous neighbor list builds - cella,cellb,cellc = periodic cell lattice constants a,b,c - cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma - c_ID = global scalar value calculated by a compute with ID - c_ID\[I\] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below) - c_ID\[I\]\[J\] = I,J component of global array calculated by a compute with ID - f_ID = global scalar value calculated by a fix with ID - f_ID\[I\] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below) - f_ID\[I\]\[J\] = I,J component of global array calculated by a fix with ID - v_name = value calculated by an equal-style variable with name - v_name\[I\] = value calculated by a vector-style variable with name :pre -:ule - -[Examples:] - -thermo_style multi -thermo_style custom step temp pe etotal press vol -thermo_style custom step temp etotal c_myTemp v_abc -thermo_style custom step temp etotal c_myTemp\[*\] v_abc :pre - -[Description:] - -Set the style and content for printing thermodynamic data to the -screen and log file. - -Style {one} prints a one-line summary of thermodynamic info that is -the equivalent of "thermo_style custom step temp epair emol etotal -press". The line contains only numeric values. - -Style {multi} prints a multiple-line listing of thermodynamic info -that is the equivalent of "thermo_style custom etotal ke temp pe ebond -eangle edihed eimp evdwl ecoul elong press". The listing contains -numeric values and a string ID for each quantity. - -Style {custom} is the most general setting and allows you to specify -which of the keywords listed above you want printed on each -thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are -references to "computes"_compute.html, "fixes"_fix.html, and -equal-style "variables"_variable.html that have been defined elsewhere -in the input script or can even be new styles which users have added -to LAMMPS. See the "Modify"_Modify.html doc page for details on the -latter. Thus the {custom} style provides a flexible means of -outputting essentially any desired quantity as a simulation proceeds. - -All styles except {custom} have {vol} appended to their list of -outputs if the simulation box volume changes during the simulation. - -The values printed by the various keywords are instantaneous values, -calculated on the current timestep. Time-averaged quantities, which -include values from previous timesteps, can be output by using the -f_ID keyword and accessing a fix that does time-averaging such as the -"fix ave/time"_fix_ave_time.html command. - -Options invoked by the "thermo_modify"_thermo_modify.html command can -be used to set the one- or multi-line format of the print-out, the -normalization of thermodynamic output (total values versus per-atom -values for extensive quantities (ones which scale with the number of -atoms in the system), and the numeric precision of each printed value. - -NOTE: When you use a "thermo_style" command, all thermodynamic -settings are restored to their default values, including those -previously set by a "thermo_modify"_thermo_modify.html command. Thus -if your input script specifies a thermo_style command, you should use -the thermo_modify command after it. - -:line - -Several of the thermodynamic quantities require a temperature to be -computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx", etc. By -default this is done by using a {temperature} compute which is created -when LAMMPS starts up, as if this command had been issued: - -compute thermo_temp all temp :pre - -See the "compute temp"_compute_temp.html command for details. Note -that the ID of this compute is {thermo_temp} and the group is {all}. -You can change the attributes of this temperature (e.g. its -degrees-of-freedom) via the "compute_modify"_compute_modify.html -command. Alternatively, you can directly assign a new compute (that -calculates temperature) which you have defined, to be used for -calculating any thermodynamic quantity that requires a temperature. -This is done via the "thermo_modify"_thermo_modify.html command. - -Several of the thermodynamic quantities require a pressure to be -computed: "press", "enthalpy", "pxx", etc. By default this is done by -using a {pressure} compute which is created when LAMMPS starts up, as -if this command had been issued: - -compute thermo_press all pressure thermo_temp :pre - -See the "compute pressure"_compute_pressure.html command for details. -Note that the ID of this compute is {thermo_press} and the group is -{all}. You can change the attributes of this pressure via the -"compute_modify"_compute_modify.html command. Alternatively, you can -directly assign a new compute (that calculates pressure) which you -have defined, to be used for calculating any thermodynamic quantity -that requires a pressure. This is done via the -"thermo_modify"_thermo_modify.html command. - -Several of the thermodynamic quantities require a potential energy to -be computed: "pe", "etotal", "ebond", etc. This is done by using a -{pe} compute which is created when LAMMPS starts up, as if this -command had been issued: - -compute thermo_pe all pe :pre - -See the "compute pe"_compute_pe.html command for details. Note that -the ID of this compute is {thermo_pe} and the group is {all}. You can -change the attributes of this potential energy via the -"compute_modify"_compute_modify.html command. - -:line - -The kinetic energy of the system {ke} is inferred from the temperature -of the system with 1/2 Kb T of energy for each degree of freedom. -Thus, using different "compute commands"_compute.html for calculating -temperature, via the "thermo_modify temp"_thermo_modify.html command, -may yield different kinetic energies, since different computes that -calculate temperature can subtract out different non-thermal -components of velocity and/or include different degrees of freedom -(translational, rotational, etc). - -The potential energy of the system {pe} will include contributions -from fixes if the "fix_modify thermo"_fix_modify.html option is set -for a fix that calculates such a contribution. For example, the "fix -wall/lj93"_fix_wall.html fix calculates the energy of atoms -interacting with the wall. See the doc pages for "individual fixes" -to see which ones contribute. - -A long-range tail correction {etail} for the VanderWaal pairwise -energy will be non-zero only if the "pair_modify -tail"_pair_modify.html option is turned on. The {etail} contribution -is included in {evdwl}, {epair}, {pe}, and {etotal}, and the -corresponding tail correction to the pressure is included in {press} -and {pxx}, {pyy}, etc. - -:line - -The {step}, {elapsed}, and {elaplong} keywords refer to timestep -count. {Step} is the current timestep, or iteration count when a -"minimization"_minimize.html is being performed. {Elapsed} is the -number of timesteps elapsed since the beginning of this run. -{Elaplong} is the number of timesteps elapsed since the beginning of -an initial run in a series of runs. See the {start} and {stop} -keywords for the "run"_run.html for info on how to invoke a series of -runs that keep track of an initial starting time. If these keywords -are not used, then {elapsed} and {elaplong} are the same value. - -The {dt} keyword is the current timestep size in time -"units"_units.html. The {time} keyword is the current elapsed -simulation time, also in time "units"_units.html, which is simply -(step*dt) if the timestep size has not changed and the timestep has -not been reset. If the timestep has changed (e.g. via "fix -dt/reset"_fix_dt_reset.html) or the timestep has been reset (e.g. via -the "reset_timestep" command), then the simulation time is effectively -a cumulative value up to the current point. - -The {cpu} keyword is elapsed CPU seconds since the beginning of this -run. The {tpcpu} and {spcpu} keywords are measures of how fast your -simulation is currently running. The {tpcpu} keyword is simulation -time per CPU second, where simulation time is in time -"units"_units.html. E.g. for metal units, the {tpcpu} value would be -picoseconds per CPU second. The {spcpu} keyword is the number of -timesteps per CPU second. Both quantities are on-the-fly metrics, -measured relative to the last time they were invoked. Thus if you are -printing out thermodynamic output every 100 timesteps, the two keywords -will continually output the time and timestep rate for the last 100 -steps. The {tpcpu} keyword does not attempt to track any changes in -timestep size, e.g. due to using the "fix dt/reset"_fix_dt_reset.html -command. - -The {cpuremain} keyword estimates the CPU time remaining in the -current run, based on the time elapsed thus far. It will only be a -good estimate if the CPU time/timestep for the rest of the run is -similar to the preceding timesteps. On the initial timestep the value -will be 0.0 since there is no history to estimate from. For a -minimization run performed by the "minimize" command, the estimate is -based on the {maxiter} parameter, assuming the minimization will -proceed for the maximum number of allowed iterations. - -The {part} keyword is useful for multi-replica or multi-partition -simulations to indicate which partition this output and this file -corresponds to, or for use in a "variable"_variable.html to append to -a filename for output specific to this partition. See discussion of -the "-partition command-line switch"_Run_options.html for details on -running in multi-partition mode. - -The {timeremain} keyword returns the remaining seconds when a -timeout has been configured via the "timer timeout"_timer.html command. -If the timeout timer is inactive, the value of this keyword is 0.0 and -if the timer is expired, it is negative. This allows for example to exit -loops cleanly, if the timeout is expired with: - -if "$(timeremain) < 0.0" then "quit 0" :pre - -The {fmax} and {fnorm} keywords are useful for monitoring the progress -of an "energy minimization"_minimize.html. The {fmax} keyword -calculates the maximum force in any dimension on any atom in the -system, or the infinity-norm of the force vector for the system. The -{fnorm} keyword calculates the 2-norm or length of the force vector. - -The {nbuild} and {ndanger} keywords are useful for monitoring neighbor -list builds during a run. Note that both these values are also -printed with the end-of-run statistics. The {nbuild} keyword is the -number of re-builds during the current run. The {ndanger} keyword is -the number of re-builds that LAMMPS considered potentially -"dangerous". If atom movement triggered neighbor list rebuilding (see -the "neigh_modify"_neigh_modify.html command), then dangerous -reneighborings are those that were triggered on the first timestep -atom movement was checked for. If this count is non-zero you may wish -to reduce the delay factor to insure no force interactions are missed -by atoms moving beyond the neighbor skin distance before a rebuild -takes place. - -The keywords {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, -{cellgamma}, correspond to the usual crystallographic quantities that -define the periodic unit cell of a crystal. See the "Howto -triclinic"_Howto_triclinic.html doc page for a geometric description -of triclinic periodic cells, including a precise definition of these -quantities in terms of the internal LAMMPS cell dimensions {lx}, {ly}, -{lz}, {yz}, {xz}, {xy}. - -:line - -For output values from a compute or fix, the bracketed index I used to -index a vector, as in {c_ID\[I\]} or {f_ID\[I\]}, can be specified -using a wildcard asterisk with the index to effectively specify -multiple values. This takes the form "*" or "*n" or "n*" or "m*n". -If N = the size of the vector (for {mode} = scalar) or the number of -columns in the array (for {mode} = vector), then an asterisk with no -numeric values means all indices from 1 to N. A leading asterisk -means all indices from 1 to n (inclusive). A trailing asterisk means -all indices from n to N (inclusive). A middle asterisk means all -indices from m to n (inclusive). - -Using a wildcard is the same as if the individual elements of the -vector had been listed one by one. E.g. these 2 thermo_style commands -are equivalent, since the "compute temp"_compute_temp.html command -creates a global vector with 6 values. - -compute myTemp all temp -thermo_style custom step temp etotal c_myTemp\[*\] -thermo_style custom step temp etotal & - c_myTemp\[1\] c_myTemp\[2\] c_myTemp\[3\] & - c_myTemp\[4\] c_myTemp\[5\] c_myTemp\[6\] :pre - -:line - -The {c_ID} and {c_ID\[I\]} and {c_ID\[I\]\[J\]} keywords allow global -values calculated by a compute to be output. As discussed on the -"compute"_compute.html doc page, computes can calculate global, -per-atom, or local values. Only global values can be referenced by -this command. However, per-atom compute values for an individual atom -can be referenced in a "variable"_variable.html and the variable -referenced by thermo_style custom, as discussed below. See the -discussion above for how the I in {c_ID\[I\]} can be specified with a -wildcard asterisk to effectively specify multiple values from a global -compute vector. - -The ID in the keyword should be replaced by the actual ID of a compute -that has been defined elsewhere in the input script. See the -"compute"_compute.html command for details. If the compute calculates -a global scalar, vector, or array, then the keyword formats with 0, 1, -or 2 brackets will reference a scalar value from the compute. - -Note that some computes calculate "intensive" global quantities like -temperature; others calculate "extensive" global quantities like -kinetic energy that are summed over all atoms in the compute group. -Intensive quantities are printed directly without normalization by -thermo_style custom. Extensive quantities may be normalized by the -total number of atoms in the simulation (NOT the number of atoms in -the compute group) when output, depending on the "thermo_modify -norm"_thermo_modify.html option being used. - -The {f_ID} and {f_ID\[I\]} and {f_ID\[I\]\[J\]} keywords allow global -values calculated by a fix to be output. As discussed on the -"fix"_fix.html doc page, fixes can calculate global, per-atom, or -local values. Only global values can be referenced by this command. -However, per-atom fix values can be referenced for an individual atom -in a "variable"_variable.html and the variable referenced by -thermo_style custom, as discussed below. See the discussion above for -how the I in {f_ID\[I\]} can be specified with a wildcard asterisk to -effectively specify multiple values from a global fix vector. - -The ID in the keyword should be replaced by the actual ID of a fix -that has been defined elsewhere in the input script. See the -"fix"_fix.html command for details. If the fix calculates a global -scalar, vector, or array, then the keyword formats with 0, 1, or 2 -brackets will reference a scalar value from the fix. - -Note that some fixes calculate "intensive" global quantities like -timestep size; others calculate "extensive" global quantities like -energy that are summed over all atoms in the fix group. Intensive -quantities are printed directly without normalization by thermo_style -custom. Extensive quantities may be normalized by the total number of -atoms in the simulation (NOT the number of atoms in the fix group) -when output, depending on the "thermo_modify norm"_thermo_modify.html -option being used. - -The {v_name} keyword allow the current value of a variable to be -output. The name in the keyword should be replaced by the variable -name that has been defined elsewhere in the input script. Only -equal-style and vector-style variables can be referenced; the latter -requires a bracketed term to specify the Ith element of the vector -calculated by the variable. However, an atom-style variable can be -referenced for an individual atom by an equal-style variable and that -variable referenced. See the "variable"_variable.html command for -details. Variables of style {equal} and {vector} and {atom} define a -formula which can reference per-atom properties or thermodynamic -keywords, or they can invoke other computes, fixes, or variables when -evaluated, so this is a very general means of creating thermodynamic -output. - -Note that equal-style and vector-style variables are assumed to -produce "intensive" global quantities, which are thus printed as-is, -without normalization by thermo_style custom. You can include a -division by "natoms" in the variable formula if this is not the case. - -:line - -[Restrictions:] - -This command must come after the simulation box is defined by a -"read_data"_read_data.html, "read_restart"_read_restart.html, or -"create_box"_create_box.html command. - -[Related commands:] - -"thermo"_thermo.html, "thermo_modify"_thermo_modify.html, -"fix_modify"_fix_modify.html, "compute temp"_compute_temp.html, -"compute pressure"_compute_pressure.html - -[Default:] - -thermo_style one :pre diff --git a/doc/txt/third_order.txt b/doc/txt/third_order.txt deleted file mode 100644 index 9636ec830e..0000000000 --- a/doc/txt/third_order.txt +++ /dev/null @@ -1,62 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -third_order command :h3 - -[Syntax:] - -third_order group-ID style delta args keyword value ... :pre - -group-ID = ID of group of atoms to displace :ulb,l -style = {regular} or {eskm} :l -delta = finite different displacement length (distance units) :l -one or more keyword/arg pairs may be appended :l - keyword = {file} or {binary} - {file} name = name of output file for the third order tensor - {binary} arg = {yes} or {no} or {gzip} :pre -:ule - -[Examples:] - -third_order 1 regular 0.000001 -third_order 1 eskm 0.000001 -third_order 3 regular 0.00004 file third_order.dat -third_order 5 eskm 0.00000001 file third_order.dat binary yes :pre - -[Description:] - -Calculate the third order force constant tensor by finite difference of the selected group, - -:c,image(JPG/third_order_force_constant.png)) - -where Phi is the third order force constant tensor. - -The output of the command is the tensor, three elements at a time. The -three elements correspond to the three gamma elements for a specific i/alpha/j/beta/k. -The initial five numbers are i, alpha, j, beta, and k respectively. - -If the style eskm is selected, the tensor will be using energy units of 10 J/mol. -These units conform to eskm style from the dynamical_matrix command, which -will simplify operations using dynamical matrices with third order tensors. - -[Restrictions:] - -The command collects a 9 times the number of atoms in the group on every single MPI rank, -so the memory requirements can be very significant for large systems. - -This command is part of the USER-PHONON package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix phonon"_fix_phonon.html "dynamical_matrix"_dynamical_matrix.html - -[Default:] - -The default settings are file = "third_order.dat", binary = no diff --git a/doc/txt/timer.txt b/doc/txt/timer.txt deleted file mode 100644 index 6da74ca153..0000000000 --- a/doc/txt/timer.txt +++ /dev/null @@ -1,121 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -timer command :h3 - -[Syntax:] - -timer args :pre - -{args} = one or more of {off} or {loop} or {normal} or {full} or {sync} or {nosync} or {timeout} or {every} :l - {off} = do not collect or print any timing information - {loop} = collect only the total time for the simulation loop - {normal} = collect timer information broken down by sections (default) - {full} = like {normal} but also include CPU and thread utilization - {sync} = explicitly synchronize MPI tasks between sections - {nosync} = do not synchronize MPI tasks between sections (default) - {timeout} elapse = set wall time limit to {elapse} - {every} Ncheck = perform timeout check every {Ncheck} steps :pre - -[Examples:] - -timer full sync -timer timeout 2:00:00 every 100 -timer loop :pre - -[Description:] - -Select the level of detail at which LAMMPS performs its CPU timings. -Multiple keywords can be specified with the {timer} command. For -keywords that are mutually exclusive, the last one specified takes -precedence. - -During a simulation run LAMMPS collects information about how much -time is spent in different sections of the code and thus can provide -information for determining performance and load imbalance problems. -This can be done at different levels of detail and accuracy. For more -information about the timing output, see the "Run -output"_Run_output.html doc page. - -The {off} setting will turn all time measurements off. The {loop} -setting will only measure the total time for a run and not collect any -detailed per section information. With the {normal} setting, timing -information for portions of the timestep (pairwise calculations, -neighbor list construction, output, etc) are collected as well as -information about load imbalances for those sections across -processors. The {full} setting adds information about CPU -utilization and thread utilization, when multi-threading is enabled. - -With the {sync} setting, all MPI tasks are synchronized at each timer -call which measures load imbalance for each section more accurately, -though it can also slow down the simulation by prohibiting overlapping -independent computations on different MPI ranks Using the {nosync} -setting (which is the default) turns this synchronization off. - -With the {timeout} keyword a wall time limit can be imposed, that -affects the "run"_run.html and "minimize"_minimize.html commands. -This can be convenient when calculations have to comply with execution -time limits, e.g. when running under a batch system when you want to -maximize the utilization of the batch time slot, especially for runs -where the time per timestep varies much and thus it becomes difficult -to predict how many steps a simulation can perform for a given wall time -limit. This also applies for difficult to converge minimizations. -The timeout {elapse} value should be somewhat smaller than the maximum -wall time requested from the batch system, as there is usually -some overhead to launch jobs, and it is advisable to write -out a restart after terminating a run due to a timeout. - -The timeout timer starts when the command is issued. When the time -limit is reached, the run or energy minimization will exit on the -next step or iteration that is a multiple of the {Ncheck} value -which can be set with the {every} keyword. Default is checking -every 10 steps. After the timer timeout has expired all subsequent -run or minimize commands in the input script will be skipped. -The remaining time or timer status can be accessed with the -"thermo"_thermo_style.html variable {timeremain}, which will be -zero, if the timeout is inactive (default setting), it will be -negative, if the timeout time is expired and positive if there -is time remaining and in this case the value of the variable are -the number of seconds remaining. - -When the {timeout} key word is used a second time, the timer is -restarted with a new time limit. The timeout {elapse} value can -be specified as {off} or {unlimited} to impose a no timeout condition -(which is the default). The {elapse} setting can be specified as -a single number for seconds, two numbers separated by a colon (MM:SS) -for minutes and seconds, or as three numbers separated by colons for -hours, minutes, and seconds (H:MM:SS). - -The {every} keyword sets how frequently during a run or energy -minimization the wall clock will be checked. This check count applies -to the outer iterations or time steps during minimizations or "r-RESPA -runs"_run_style.html, respectively. Checking for timeout too often, -can slow a calculation down. Checking too infrequently can make the -timeout measurement less accurate, with the run being stopped later -than desired. - -NOTE: Using the {full} and {sync} options provides the most detailed -and accurate timing information, but can also have a negative -performance impact due to the overhead of the many required system -calls. It is thus recommended to use these settings only when testing -tests to identify performance bottlenecks. For calculations with few -atoms or a very large number of processors, even the {normal} setting -can have a measurable negative performance impact. In those cases you -can just use the {loop} or {off} setting. - -[Restrictions:] none - -[Related commands:] - -"run post no"_run.html, "kspace_modify fftbench"_kspace_modify.html - -[Default:] - -timer normal nosync -timer timeout off -timer every 10 :pre diff --git a/doc/txt/timestep.txt b/doc/txt/timestep.txt deleted file mode 100644 index ee0ace05b9..0000000000 --- a/doc/txt/timestep.txt +++ /dev/null @@ -1,51 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -timestep command :h3 - -[Syntax:] - -timestep dt :pre - -dt = timestep size (time units) :ul - -[Examples:] - -timestep 2.0 -timestep 0.003 :pre - -[Description:] - -Set the timestep size for subsequent molecular dynamics simulations. -See the "units"_units.html command for the time units associated with -each choice of units that LAMMPS supports. - -The default value for the timestep size also depends on the choice of -units for the simulation; see the default values below. - -When the "run style"_run_style.html is {respa}, dt is the timestep for -the outer loop (largest) timestep. - -[Restrictions:] none - -[Related commands:] - -"fix dt/reset"_fix_dt_reset.html, "run"_run.html, -"run_style"_run_style.html respa, "units"_units.html - -[Default:] - -choice of "units"_units.html : time units : default timestep size -lj : tau : 0.005 tau -real : fmsec : 1.0 fmsec -metal : psec : 0.001 psec -si : sec : 1.0e-8 sec (10 nsec) -cgs : sec : 1.0e-8 sec (10 nsec) -electron : fmsec : 0.001 fmsec -micro : usec : 2.0 usec -nano : nsec : 0.00045 nsec :tb(s=:,a=l,ea=c) diff --git a/doc/txt/uncompute.txt b/doc/txt/uncompute.txt deleted file mode 100644 index 4c788d4722..0000000000 --- a/doc/txt/uncompute.txt +++ /dev/null @@ -1,34 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -uncompute command :h3 - -[Syntax:] - -uncompute compute-ID :pre - -compute-ID = ID of a previously defined compute :ul - -[Examples:] - -uncompute 2 -uncompute lower-boundary :pre - -[Description:] - -Delete a compute that was previously defined with a "compute"_compute.html -command. This also wipes out any additional changes made to the compute -via the "compute_modify"_compute_modify.html command. - -[Restrictions:] none - -[Related commands:] - -"compute"_compute.html - -[Default:] none diff --git a/doc/txt/undump.txt b/doc/txt/undump.txt deleted file mode 100644 index cc3d8b9103..0000000000 --- a/doc/txt/undump.txt +++ /dev/null @@ -1,33 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -undump command :h3 - -[Syntax:] - -undump dump-ID :pre - -dump-ID = ID of previously defined dump :ul - -[Examples:] - -undump mine -undump 2 :pre - -[Description:] - -Turn off a previously defined dump so that it is no longer active. -This closes the file associated with the dump. - -[Restrictions:] none - -[Related commands:] - -"dump"_dump.html - -[Default:] none diff --git a/doc/txt/unfix.txt b/doc/txt/unfix.txt deleted file mode 100644 index 9608b39c7e..0000000000 --- a/doc/txt/unfix.txt +++ /dev/null @@ -1,34 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -unfix command :h3 - -[Syntax:] - -unfix fix-ID :pre - -fix-ID = ID of a previously defined fix :ul - -[Examples:] - -unfix 2 -unfix lower-boundary :pre - -[Description:] - -Delete a fix that was previously defined with a "fix"_fix.html -command. This also wipes out any additional changes made to the fix -via the "fix_modify"_fix_modify.html command. - -[Restrictions:] none - -[Related commands:] - -"fix"_fix.html - -[Default:] none diff --git a/doc/txt/units.txt b/doc/txt/units.txt deleted file mode 100644 index 844504d977..0000000000 --- a/doc/txt/units.txt +++ /dev/null @@ -1,221 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -units command :h3 - -[Syntax:] - -units style :pre - -style = {lj} or {real} or {metal} or {si} or {cgs} or {electron} or {micro} or {nano} :ul - -[Examples:] - -units metal -units lj :pre - -[Description:] - -This command sets the style of units used for a simulation. It -determines the units of all quantities specified in the input script -and data file, as well as quantities output to the screen, log file, -and dump files. Typically, this command is used at the very beginning -of an input script. - -For all units except {lj}, LAMMPS uses physical constants from -www.physics.nist.gov. For the definition of Kcal in real units, -LAMMPS uses the thermochemical calorie = 4.184 J. - -The choice you make for units simply sets some internal conversion -factors within LAMMPS. This means that any simulation you perform for -one choice of units can be duplicated with any other unit setting -LAMMPS supports. In this context "duplicate" means the particles will -have identical trajectories and all output generated by the simulation -will be identical. This will be the case for some number of timesteps -until round-off effects accumulate, since the conversion factors for -two different unit systems are not identical to infinite precision. - -To perform the same simulation in a different set of units you must -change all the unit-based input parameters in your input script and -other input files (data file, potential files, etc) correctly to the -new units. And you must correctly convert all output from the new -units to the old units when comparing to the original results. That -is often not simple to do. - -:line - -For style {lj}, all quantities are unitless. Without loss of -generality, LAMMPS sets the fundamental quantities mass, sigma, -epsilon, and the Boltzmann constant = 1. The masses, distances, -energies you specify are multiples of these fundamental values. The -formulas relating the reduced or unitless quantity (with an asterisk) -to the same quantity with units is also given. Thus you can use the -mass & sigma & epsilon values for a specific material and convert the -results from a unitless LJ simulation into physical quantities. - -mass = mass or m -distance = sigma, where x* = x / sigma -time = tau, where t* = t (epsilon / m / sigma^2)^1/2 -energy = epsilon, where E* = E / epsilon -velocity = sigma/tau, where v* = v tau / sigma -force = epsilon/sigma, where f* = f sigma / epsilon -torque = epsilon, where t* = t / epsilon -temperature = reduced LJ temperature, where T* = T Kb / epsilon -pressure = reduced LJ pressure, where P* = P sigma^3 / epsilon -dynamic viscosity = reduced LJ viscosity, where eta* = eta sigma^3 / epsilon / tau -charge = reduced LJ charge, where q* = q / (4 pi perm0 sigma epsilon)^1/2 -dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2 -electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon -density = mass/volume, where rho* = rho sigma^dim :ul - -Note that for LJ units, the default mode of thermodynamic output via -the "thermo_style"_thermo_style.html command is to normalize all -extensive quantities by the number of atoms. E.g. potential energy is -extensive because it is summed over atoms, so it is output as -energy/atom. Temperature is intensive since it is already normalized -by the number of atoms, so it is output as-is. This behavior can be -changed via the "thermo_modify norm"_thermo_modify.html command. - -For style {real}, these are the units: - -mass = grams/mole -distance = Angstroms -time = femtoseconds -energy = Kcal/mole -velocity = Angstroms/femtosecond -force = Kcal/mole-Angstrom -torque = Kcal/mole -temperature = Kelvin -pressure = atmospheres -dynamic viscosity = Poise -charge = multiple of electron charge (1.0 is a proton) -dipole = charge*Angstroms -electric field = volts/Angstrom -density = gram/cm^dim :ul - -For style {metal}, these are the units: - -mass = grams/mole -distance = Angstroms -time = picoseconds -energy = eV -velocity = Angstroms/picosecond -force = eV/Angstrom -torque = eV -temperature = Kelvin -pressure = bars -dynamic viscosity = Poise -charge = multiple of electron charge (1.0 is a proton) -dipole = charge*Angstroms -electric field = volts/Angstrom -density = gram/cm^dim :ul - -For style {si}, these are the units: - -mass = kilograms -distance = meters -time = seconds -energy = Joules -velocity = meters/second -force = Newtons -torque = Newton-meters -temperature = Kelvin -pressure = Pascals -dynamic viscosity = Pascal*second -charge = Coulombs (1.6021765e-19 is a proton) -dipole = Coulombs*meters -electric field = volts/meter -density = kilograms/meter^dim :ul - -For style {cgs}, these are the units: - -mass = grams -distance = centimeters -time = seconds -energy = ergs -velocity = centimeters/second -force = dynes -torque = dyne-centimeters -temperature = Kelvin -pressure = dyne/cm^2 or barye = 1.0e-6 bars -dynamic viscosity = Poise -charge = statcoulombs or esu (4.8032044e-10 is a proton) -dipole = statcoul-cm = 10^18 debye -electric field = statvolt/cm or dyne/esu -density = grams/cm^dim :ul - -For style {electron}, these are the units: - -mass = atomic mass units -distance = Bohr -time = femtoseconds -energy = Hartrees -velocity = Bohr/atomic time units \[1.03275e-15 seconds\] -force = Hartrees/Bohr -temperature = Kelvin -pressure = Pascals -charge = multiple of electron charge (1.0 is a proton) -dipole moment = Debye -electric field = volts/cm :ul - -For style {micro}, these are the units: - -mass = picograms -distance = micrometers -time = microseconds -energy = picogram-micrometer^2/microsecond^2 -velocity = micrometers/microsecond -force = picogram-micrometer/microsecond^2 -torque = picogram-micrometer^2/microsecond^2 -temperature = Kelvin -pressure = picogram/(micrometer-microsecond^2) -dynamic viscosity = picogram/(micrometer-microsecond) -charge = picocoulombs (1.6021765e-7 is a proton) -dipole = picocoulomb-micrometer -electric field = volt/micrometer -density = picograms/micrometer^dim :ul - -For style {nano}, these are the units: - -mass = attograms -distance = nanometers -time = nanoseconds -energy = attogram-nanometer^2/nanosecond^2 -velocity = nanometers/nanosecond -force = attogram-nanometer/nanosecond^2 -torque = attogram-nanometer^2/nanosecond^2 -temperature = Kelvin -pressure = attogram/(nanometer-nanosecond^2) -dynamic viscosity = attogram/(nanometer-nanosecond) -charge = multiple of electron charge (1.0 is a proton) -dipole = charge-nanometer -electric field = volt/nanometer -density = attograms/nanometer^dim :ul - -The units command also sets the timestep size and neighbor skin -distance to default values for each style: - -For style {lj} these are dt = 0.005 tau and skin = 0.3 sigma. -For style {real} these are dt = 1.0 femtoseconds and skin = 2.0 Angstroms. -For style {metal} these are dt = 0.001 picoseconds and skin = 2.0 Angstroms. -For style {si} these are dt = 1.0e-8 seconds and skin = 0.001 meters. -For style {cgs} these are dt = 1.0e-8 seconds and skin = 0.1 centimeters. -For style {electron} these are dt = 0.001 femtoseconds and skin = 2.0 Bohr. -For style {micro} these are dt = 2.0 microseconds and skin = 0.1 micrometers. -For style {nano} these are dt = 0.00045 nanoseconds and skin = 0.1 nanometers. :ul - -[Restrictions:] - -This command cannot be used after the simulation box is defined by a -"read_data"_read_data.html or "create_box"_create_box.html command. - -[Related commands:] none - -[Default:] - -units lj :pre diff --git a/doc/txt/variable.txt b/doc/txt/variable.txt deleted file mode 100644 index b545f6cee2..0000000000 --- a/doc/txt/variable.txt +++ /dev/null @@ -1,1337 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -variable command :h3 - -[Syntax:] - -variable name style args ... :pre - -name = name of variable to define :ulb,l -style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {string} or {format} or {getenv} or {file} or {atomfile} or {python} or {internal} or {equal} or {vector} or {atom} :l - {delete} = no args - {index} args = one or more strings - {loop} args = N - N = integer size of loop, loop from 1 to N inclusive - {loop} args = N pad - N = integer size of loop, loop from 1 to N inclusive - pad = all values will be same length, e.g. 001, 002, ..., 100 - {loop} args = N1 N2 - N1,N2 = loop from N1 to N2 inclusive - {loop} args = N1 N2 pad - N1,N2 = loop from N1 to N2 inclusive - pad = all values will be same length, e.g. 050, 051, ..., 100 - {world} args = one string for each partition of processors - {universe} args = one or more strings - {uloop} args = N - N = integer size of loop - {uloop} args = N pad - N = integer size of loop - pad = all values will be same length, e.g. 001, 002, ..., 100 - {string} arg = one string - {format} args = vname fstr - vname = name of equal-style variable to evaluate - fstr = C-style format string - {getenv} arg = one string - {file} arg = filename - {atomfile} arg = filename - {python} arg = function - {internal} arg = numeric value - {equal} or {vector} or {atom} args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references - numbers = 0.0, 100, -5.4, 2.8e-4, etc - constants = PI, version, on, off, true, false, yes, no - thermo keywords = vol, ke, press, etc from "thermo_style"_thermo_style.html - math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y, - x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, x |^ y, !x - math functions = sqrt(x), exp(x), ln(x), log(x), abs(x), - sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), - random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x) - ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), - logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), - vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) - group functions = count(group), mass(group), charge(group), - xcm(group,dim), vcm(group,dim), fcm(group,dim), - bound(group,dir), gyration(group), ke(group), - angmom(group,dim), torque(group,dim), - inertia(group,dimdim), omega(group,dim) - region functions = count(group,region), mass(group,region), charge(group,region), - xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region), - bound(group,dir,region), gyration(group,region), ke(group,reigon), - angmom(group,dim,region), torque(group,dim,region), - inertia(group,dimdim,region), omega(group,dim,region) - special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x) - feature functions = is_active(category,feature,exact), is_defined(category,id,exact) - atom value = id\[i\], mass\[i\], type\[i\], mol\[i\], x\[i\], y\[i\], z\[i\], vx\[i\], vy\[i\], vz\[i\], fx\[i\], fy\[i\], fz\[i\], q\[i\] - atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q - compute references = c_ID, c_ID\[i\], c_ID\[i\]\[j\], C_ID, C_ID\[i\] - fix references = f_ID, f_ID\[i\], f_ID\[i\]\[j\], F_ID, F_ID\[i\] - variable references = v_name, v_name\[i\] :pre -:ule - -[Examples:] - -variable x index run1 run2 run3 run4 run5 run6 run7 run8 -variable LoopVar loop $n -variable beta equal temp/3.0 -variable b1 equal x\[234\]+0.5*vol -variable b1 equal "x\[234\] + 0.5*vol" -variable b equal xcm(mol1,x)/2.0 -variable b equal c_myTemp -variable b atom x*y/vol -variable foo string myfile -variable foo internal 3.5 -variable myPy python increase -variable f file values.txt -variable temp world 300.0 310.0 320.0 $\{Tfinal\} -variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -variable x uloop 15 pad -variable str format x %.6g -variable x delete :pre - -[Description:] - -This command assigns one or more strings to a variable name for -evaluation later in the input script or during a simulation. - -Variables can thus be useful in several contexts. A variable can be -defined and then referenced elsewhere in an input script to become -part of a new input command. For variable styles that store multiple -strings, the "next"_next.html command can be used to increment which -string is assigned to the variable. Variables of style {equal} store -a formula which when evaluated produces a single numeric value which -can be output either directly (see the "print"_print.html, "fix -print"_fix_print.html, and "run every"_run.html commands) or as part -of thermodynamic output (see the "thermo_style"_thermo_style.html -command), or used as input to an averaging fix (see the "fix -ave/time"_fix_ave_time.html command). Variables of style {vector} -store a formula which produces a vector of such values which can be -used as input to various averaging fixes, or elements of which can be -part of thermodynamic output. Variables of style {atom} store a -formula which when evaluated produces one numeric value per atom which -can be output to a dump file (see the "dump custom"_dump.html command) -or used as input to an averaging fix (see the "fix -ave/chunk"_fix_ave_chunk.html and "fix ave/atom"_fix_ave_atom.html -commands). Variables of style {atomfile} can be used anywhere in an -input script that atom-style variables are used; they get their -per-atom values from a file rather than from a formula. Variables of -style {python} can be hooked to Python functions using code you -provide, so that the variable gets its value from the evaluation of -the Python code. Variables of style {internal} are used by a few -commands which set their value directly. - -NOTE: As discussed on the "Commands parse"_Commands_parse.html doc -page, an input script can use "immediate" variables, specified as -$(formula) with parenthesis, where the formula has the same syntax as -equal-style variables described on this page. This is a convenient -way to evaluate a formula immediately without using the variable -command to define a named variable and then evaluate that -variable. See below for a more detailed discussion of this feature. - -In the discussion that follows, the "name" of the variable is the -arbitrary string that is the 1st argument in the variable command. -This name can only contain alphanumeric characters and underscores. -The "string" is one or more of the subsequent arguments. The "string" -can be simple text as in the 1st example above, it can contain other -variables as in the 2nd example, or it can be a formula as in the 3rd -example. The "value" is the numeric quantity resulting from -evaluation of the string. Note that the same string can generate -different values when it is evaluated at different times during a -simulation. - -NOTE: When an input script line is encountered that defines a variable -of style {equal} or {vector} or {atom} or {python} that contains a -formula or Python code, the formula is NOT immediately evaluated. It -will be evaluated every time when the variable is [used] instead. If -you simply want to evaluate a formula in place you can use as -so-called. See the section below about "Immediate Evaluation of -Variables" for more details on the topic. This is also true of a -{format} style variable since it evaluates another variable when it is -invoked. - -Variables of style {equal} and {vector} and {atom} can be used as -inputs to various other commands which evaluate their formulas as -needed, e.g. at different timesteps during a "run"_run.html. - -Variables of style {internal} can be used in place of an equal-style -variable, except by commands that set the value stored by the -internal-style variable. Thus any command that states it can use an -equal-style variable as an argument, can also use an internal-style -variable. This means that when the command evaluates the variable, it -will use the value set (internally) by another command. - -Variables of style {python} can be used in place of an equal-style -variable so long as the associated Python function, as defined by the -"python"_python.html command, returns a numeric value. Thus any -command that states it can use an equal-style variable as an argument, -can also use such a python-style variable. This means that when the -LAMMPS command evaluates the variable, the Python function will be -executed. - -NOTE: When a variable command is encountered in the input script and -the variable name has already been specified, the command is ignored. -This means variables can NOT be re-defined in an input script (with -two exceptions, read further). This is to allow an input script to be -processed multiple times without resetting the variables; see the -"jump"_jump.html or "include"_include.html commands. It also means -that using the "command-line switch"_Run_options.html -var will -override a corresponding index variable setting in the input script. - -There are two exceptions to this rule. First, variables of style -{string}, {getenv}, {internal}, {equal}, {vector}, {atom}, and -{python} ARE redefined each time the command is encountered. This -allows these style of variables to be redefined multiple times in an -input script. In a loop, this means the formula associated with an -{equal} or {atom} style variable can change if it contains a -substitution for another variable, e.g. $x or v_x. - -Second, as described below, if a variable is iterated on to the end of -its list of strings via the "next"_next.html command, it is removed -from the list of active variables, and is thus available to be -re-defined in a subsequent variable command. The {delete} style does -the same thing. - -:line - -The "Commands parse"_Commands_parse.html doc page explains how -occurrences of a variable name in an input script line are replaced by -the variable's string. The variable name can be referenced as $x if -the name "x" is a single character, or as $\{LoopVar\} if the name -"LoopVar" is one or more characters. - -As described below, for variable styles {index}, {loop}, {file}, -{universe}, and {uloop}, which string is assigned to a variable can be -incremented via the "next"_next.html command. When there are no more -strings to assign, the variable is exhausted and a flag is set that -causes the next "jump"_jump.html command encountered in the input -script to be skipped. This enables the construction of simple loops -in the input script that are iterated over and then exited from. - -As explained above, an exhausted variable can be re-used in an input -script. The {delete} style also removes the variable, the same as if -it were exhausted, allowing it to be redefined later in the input -script or when the input script is looped over. This can be useful -when breaking out of a loop via the "if"_if.html and "jump"_jump.html -commands before the variable would become exhausted. For example, - -label loop -variable a loop 5 -print "A = $a" -if "$a > 2" then "jump in.script break" -next a -jump in.script loop -label break -variable a delete :pre - -:line - -This section describes how all the various variable styles are defined -and what they store. Except for the {equal} and {vector} and {atom} -styles, which are explained in the next section. - -Many of the styles store one or more strings. Note that a single -string can contain spaces (multiple words), if it is enclosed in -quotes in the variable command. When the variable is substituted for -in another input script command, its returned string will then be -interpreted as multiple arguments in the expanded command. - -For the {index} style, one or more strings are specified. Initially, -the 1st string is assigned to the variable. Each time a -"next"_next.html command is used with the variable name, the next -string is assigned. All processors assign the same string to the -variable. - -{Index} style variables with a single string value can also be set by -using the "command-line switch -var"_Run_options.html. - -The {loop} style is identical to the {index} style except that the -strings are the integers from 1 to N inclusive, if only one argument N -is specified. This allows generation of a long list of runs -(e.g. 1000) without having to list N strings in the input script. -Initially, the string "1" is assigned to the variable. Each time a -"next"_next.html command is used with the variable name, the next -string ("2", "3", etc) is assigned. All processors assign the same -string to the variable. The {loop} style can also be specified with -two arguments N1 and N2. In this case the loop runs from N1 to N2 -inclusive, and the string N1 is initially assigned to the variable. -N1 <= N2 and N2 >= 0 is required. - -For the {world} style, one or more strings are specified. There must -be one string for each processor partition or "world". LAMMPS can be -run with multiple partitions via the "-partition command-line -switch"_Run_options.html. This variable command assigns one string to -each world. All processors in the world are assigned the same string. -The next command cannot be used with {equal} style variables, since -there is only one value per world. This style of variable is useful -when you wish to run different simulations on different partitions, or -when performing a parallel tempering simulation (see the -"temper"_temper.html command), to assign different temperatures to -different partitions. - -For the {universe} style, one or more strings are specified. There -must be at least as many strings as there are processor partitions or -"worlds". LAMMPS can be run with multiple partitions via the -"-partition command-line switch"_Run_options.html. This variable -command initially assigns one string to each world. When a -"next"_next.html command is encountered using this variable, the first -processor partition to encounter it, is assigned the next available -string. This continues until all the variable strings are consumed. -Thus, this command can be used to run 50 simulations on 8 processor -partitions. The simulations will be run one after the other on -whatever partition becomes available, until they are all finished. -{Universe} style variables are incremented using the files -"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will -see in your directory during such a LAMMPS run. - -The {uloop} style is identical to the {universe} style except that the -strings are the integers from 1 to N. This allows generation of long -list of runs (e.g. 1000) without having to list N strings in the input -script. - -For the {string} style, a single string is assigned to the variable. -Two differences between this style and using the {index} style exist: -a variable with {string} style can be redefined, e.g. by another command later -in the input script, or if the script is read again in a loop. The other -difference is that {string} performs variable substitution even if the -string parameter is quoted. - -For the {format} style, an equal-style variable is specified along -with a C-style format string, e.g. "%f" or "%.10g", which must be -appropriate for formatting a double-precision floating-point value. -The default format is "%.15g". This variable style allows an -equal-style variable to be formatted precisely when it is evaluated. - -If you simply wish to print a variable value with desired precision to -the screen or logfile via the "print"_print.html or "fix -print"_fix_print.html commands, you can also do this by specifying an -"immediate" variable with a trailing colon and format string, as part -of the string argument of those commands. This is explained on the -"Commands parse"_Commands_parse.html doc page. - -For the {getenv} style, a single string is assigned to the variable -which should be the name of an environment variable. When the -variable is evaluated, it returns the value of the environment -variable, or an empty string if it not defined. This style of -variable can be used to adapt the behavior of LAMMPS input scripts via -environment variable settings, or to retrieve information that has -been previously stored with the "shell putenv"_shell.html command. -Note that because environment variable settings are stored by the -operating systems, they persist beyond a "clear"_clear.html command. - -For the {file} style, a filename is provided which contains a list of -strings to assign to the variable, one per line. The strings can be -numeric values if desired. See the discussion of the next() function -below for equal-style variables, which will convert the string of a -file-style variable into a numeric value in a formula. - -When a file-style variable is defined, the file is opened and the -string on the first line is read and stored with the variable. This -means the variable can then be evaluated as many times as desired and -will return that string. There are two ways to cause the next string -from the file to be read: use the "next"_next.html command or the -next() function in an equal- or atom-style variable, as discussed -below. - -The rules for formatting the file are as follows. A comment character -"#" can be used anywhere on a line; text starting with the comment -character is stripped. Blank lines are skipped. The first "word" of -a non-blank line, delimited by white-space, is the "string" assigned -to the variable. - -For the {atomfile} style, a filename is provided which contains one or -more sets of values, to assign on a per-atom basis to the variable. -The format of the file is described below. - -When an atomfile-style variable is defined, the file is opened and the -first set of per-atom values are read and stored with the variable. -This means the variable can then be evaluated as many times as desired -and will return those values. There are two ways to cause the next -set of per-atom values from the file to be read: use the -"next"_next.html command or the next() function in an atom-style -variable, as discussed below. - -The rules for formatting the file are as follows. Each time a set of -per-atom values is read, a non-blank line is searched for in the file. -A comment character "#" can be used anywhere on a line; text starting -with the comment character is stripped. Blank lines are skipped. The -first "word" of a non-blank line, delimited by white-space, is read as -the count N of per-atom lines to immediately follow. N can be the -total number of atoms in the system, or only a subset. The next N -lines have the following format - -ID value :pre - -where ID is an atom ID and value is the per-atom numeric value that -will be assigned to that atom. IDs can be listed in any order. - -NOTE: Every time a set of per-atom lines is read, the value for all -atoms is first set to 0.0. Thus values for atoms whose ID does not -appear in the set, will remain 0.0. - -For the {python} style a Python function name is provided. This needs -to match a function name specified in a "python"_python.html command -which returns a value to this variable as defined by its {return} -keyword. For example these two commands would be self-consistent: - -variable foo python myMultiply -python myMultiply return v_foo format f file funcs.py :pre - -The two commands can appear in either order so long as both are -specified before the Python function is invoked for the first time. - -Each time the variable is evaluated, the associated Python function is -invoked, and the value it returns is also returned by the variable. -Since the Python function can use other LAMMPS variables as input, or -query interal LAMMPS quantities to perform its computation, this means -the variable can return a different value each time it is evaluated. - -The type of value stored in the variable is determined by the {format} -keyword of the "python"_python.html command. It can be an integer -(i), floating point (f), or string (s) value. As mentioned above, if -it is a numeric value (integer or floating point), then the -python-style variable can be used in place of an equal-style variable -anywhere in an input script, e.g. as an argument to another command -that allows for equal-style variables. - -For the {internal} style a numeric value is provided. This value will -be assigned to the variable until a LAMMPS command sets it to a new -value. There are currently only two LAMMPS commands that require -{internal} variables as inputs, because they reset them: -"create_atoms"_create_atoms.html and "fix -controller"_fix_controller.html. As mentioned above, an -internal-style variable can be used in place of an equal-style -variable anywhere else in an input script, e.g. as an argument to -another command that allows for equal-style variables. - -:line - -For the {equal} and {vector} and {atom} styles, a single string is -specified which represents a formula that will be evaluated afresh -each time the variable is used. If you want spaces in the string, -enclose it in double quotes so the parser will treat it as a single -argument. For {equal}-style variables the formula computes a scalar -quantity, which becomes the value of the variable whenever it is -evaluated. For {vector}-style variables the formula must compute a -vector of quantities, which becomes the value of the variable whenever -it is evaluated. The calculated vector can be on length one, but it -cannot be a simple scalar value like that produced by an equal-style -compute. I.e. the formula for a vector-style variable must have at -least one quantity in it that refers to a global vector produced by a -compute, fix, or other vector-style variable. For {atom}-style -variables the formula computes one quantity for each atom whenever it -is evaluated. - -Note that {equal}, {vector}, and {atom} variables can produce -different values at different stages of the input script or at -different times during a run. For example, if an {equal} variable is -used in a "fix print"_fix_print.html command, different values could -be printed each timestep it was invoked. If you want a variable to be -evaluated immediately, so that the result is stored by the variable -instead of the string, see the section below on "Immediate Evaluation -of Variables". - -The next command cannot be used with {equal} or {vector} or {atom} -style variables, since there is only one string. - -The formula for an {equal}, {vector}, or {atom} variable can contain a -variety of quantities. The syntax for each kind of quantity is -simple, but multiple quantities can be nested and combined in various -ways to build up formulas of arbitrary complexity. For example, this -is a valid (though strange) variable formula: - -variable x equal "pe + c_MyTemp / vol^(1/3)" :pre - -Specifically, a formula can contain numbers, constants, thermo -keywords, math operators, math functions, group functions, region -functions, atom values, atom vectors, compute references, fix -references, and references to other variables. - -Number: 0.2, 100, 1.0e20, -15.4, etc -Constant: PI, version, on, off, true, false, yes, no -Thermo keywords: vol, pe, ebond, etc -Math operators: (), -x, x+y, x-y, x*y, x/y, x^y, x%y, \ - x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, x |^ y, !x -Math functions: sqrt(x), exp(x), ln(x), log(x), abs(x), \ - sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), \ - random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), \ - ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), \ - logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), \ - vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) -Group functions: count(ID), mass(ID), charge(ID), xcm(ID,dim), \ - vcm(ID,dim), fcm(ID,dim), bound(ID,dir), \ - gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), \ - inertia(ID,dimdim), omega(ID,dim) -Region functions: count(ID,IDR), mass(ID,IDR), charge(ID,IDR), \ - xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), \ - bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), \ - angmom(ID,dim,IDR), torque(ID,dim,IDR), \ - inertia(ID,dimdim,IDR), omega(ID,dim,IDR) -Special functions: sum(x), min(x), max(x), ave(x), trap(x), \ - slope(x), gmask(x), rmask(x), grmask(x,y), next(x) -Atom values: id\[i\], mass\[i\], type\[i\], mol\[i\], x\[i\], y\[i\], z\[i\], \ - vx\[i\], vy\[i\], vz\[i\], fx\[i\], fy\[i\], fz\[i\], q\[i\] -Atom vectors: id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q -Compute references: c_ID, c_ID\[i\], c_ID\[i\]\[j\], C_ID, C_ID\[i\] -Fix references: f_ID, f_ID\[i\], f_ID\[i\]\[j\], F_ID, F_ID\[i\] -Other variables: v_name, v_name\[i\] :tb(s=:) - -Most of the formula elements produce a scalar value. Some produce a -global or per-atom vector of values. Global vectors can be produced -by computes or fixes or by other vector-style variables. Per-atom -vectors are produced by atom vectors, compute references that -represent a per-atom vector, fix references that represent a per-atom -vector, and variables that are atom-style variables. Math functions -that operate on scalar values produce a scalar value; math function -that operate on global or per-atom vectors do so element-by-element -and produce a global or per-atom vector. - -A formula for equal-style variables cannot use any formula element -that produces a global or per-atom vector. A formula for a -vector-style variable can use formula elements that produce either a -scalar value or a global vector value, but cannot use a formula -element that produces a per-atom vector. A formula for an atom-style -variable can use formula elements that produce either a scalar value -or a per-atom vector, but not one that produces a global vector. -Atom-style variables are evaluated by other commands that define a -"group"_group.html on which they operate, e.g. a "dump"_dump.html or -"compute"_compute.html or "fix"_fix.html command. When they invoke -the atom-style variable, only atoms in the group are included in the -formula evaluation. The variable evaluates to 0.0 for atoms not in -the group. - -:line - -Numbers, constants, and thermo keywords :h4 - -Numbers can contain digits, scientific notation -(3.0e20,3.0e-20,3.0E20,3.0E-20), and leading minus signs. - -Constants are set at compile time and cannot be changed. {PI} will -return the number 3.14159265358979323846; {on}, {true} or {yes} will -return 1.0; {off}, {false} or {no} will return 0.0; {version} will -return a numeric version code of the current LAMMPS version (e.g. -version 2 Sep 2015 will return the number 20150902). The corresponding -value for newer versions of LAMMPS will be larger, for older versions -of LAMMPS will be smaller. This can be used to have input scripts -adapt automatically to LAMMPS versions, when non-backwards compatible -syntax changes are introduced. Here is an illustrative example (which -will not work, since the {version} has been introduced more recently): - -if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes" :pre - -The thermo keywords allowed in a formula are those defined by the -"thermo_style custom"_thermo_style.html command. Thermo keywords that -require a "compute"_compute.html to calculate their values such as -"temp" or "press", use computes stored and invoked by the -"thermo_style"_thermo_style.html command. This means that you can -only use those keywords in a variable if the style you are using with -the thermo_style command (and the thermo keywords associated with that -style) also define and use the needed compute. Note that some thermo -keywords use a compute indirectly to calculate their value (e.g. the -enthalpy keyword uses temp, pe, and pressure). If a variable is -evaluated directly in an input script (not during a run), then the -values accessed by the thermo keyword must be current. See the -discussion below about "Variable Accuracy". - -:line - -Math Operators :h4 - -Math operators are written in the usual way, where the "x" and "y" in -the examples can themselves be arbitrarily complex formulas, as in the -examples above. In this syntax, "x" and "y" can be scalar values or -per-atom vectors. For example, "ke/natoms" is the division of two -scalars, where "vy+vz" is the element-by-element sum of two per-atom -vectors of y and z velocities. - -Operators are evaluated left to right and have the usual C-style -precedence: unary minus and unary logical NOT operator "!" have the -highest precedence, exponentiation "^" is next; multiplication and -division and the modulo operator "%" are next; addition and -subtraction are next; the 4 relational operators "<", "<=", ">", and -">=" are next; the two remaining relational operators "==" and "!=" -are next; then the logical AND operator "&&"; and finally the logical -OR operator "||" and logical XOR (exclusive or) operator "|^" have the -lowest precedence. Parenthesis can be used to group one or more -portions of a formula and/or enforce a different order of evaluation -than what would occur with the default precedence. - -NOTE: Because a unary minus is higher precedence than exponentiation, -the formula "-2^2" will evaluate to 4, not -4. This convention is -compatible with some programming languages, but not others. As -mentioned, this behavior can be easily overridden with parenthesis; -the formula "-(2^2)" will evaluate to -4. - -The 6 relational operators return either a 1.0 or 0.0 depending on -whether the relationship between x and y is TRUE or FALSE. For -example the expression x<10.0 in an atom-style variable formula will -return 1.0 for all atoms whose x-coordinate is less than 10.0, and 0.0 -for the others. The logical AND operator will return 1.0 if both its -arguments are non-zero, else it returns 0.0. The logical OR operator -will return 1.0 if either of its arguments is non-zero, else it -returns 0.0. The logical XOR operator will return 1.0 if one of its -arguments is zero and the other non-zero, else it returns 0.0. The -logical NOT operator returns 1.0 if its argument is 0.0, else it -returns 0.0. - -These relational and logical operators can be used as a masking or -selection operation in a formula. For example, the number of atoms -whose properties satisfy one or more criteria could be calculated by -taking the returned per-atom vector of ones and zeroes and passing it -to the "compute reduce"_compute_reduce.html command. - -:line - -Math Functions :h4 - -Math functions are specified as keywords followed by one or more -parenthesized arguments "x", "y", "z", each of which can themselves be -arbitrarily complex formulas. In this syntax, the arguments can -represent scalar values or global vectors or per-atom vectors. In the -latter case, the math operation is performed on each element of the -vector. For example, "sqrt(natoms)" is the sqrt() of a scalar, where -"sqrt(y*z)" yields a per-atom vector with each element being the -sqrt() of the product of one atom's y and z coordinates. - -Most of the math functions perform obvious operations. The ln() is -the natural log; log() is the base 10 log. - -The random(x,y,z) function takes 3 arguments: x = lo, y = hi, and z = -seed. It generates a uniform random number between lo and hi. The -normal(x,y,z) function also takes 3 arguments: x = mu, y = sigma, and -z = seed. It generates a Gaussian variate centered on mu with -variance sigma^2. In both cases the seed is used the first time the -internal random number generator is invoked, to initialize it. For -equal-style and vector-style variables, every processor uses the same -seed so that they each generate the same sequence of random numbers. -For atom-style variables, a unique seed is created for each processor, -based on the specified seed. This effectively generates a different -random number for each atom being looped over in the atom-style -variable. - -NOTE: Internally, there is just one random number generator for all -equal-style and vector-style variables and another one for all -atom-style variables. If you define multiple variables (of each -style) which use the random() or normal() math functions, then the -internal random number generators will only be initialized once, which -means only one of the specified seeds will determine the sequence of -generated random numbers. - -The ceil(), floor(), and round() functions are those in the C math -library. Ceil() is the smallest integer not less than its argument. -Floor() if the largest integer not greater than its argument. Round() -is the nearest integer to its argument. - -The ramp(x,y) function uses the current timestep to generate a value -linearly interpolated between the specified x,y values over the course -of a run, according to this formula: - -value = x + (y-x) * (timestep-startstep) / (stopstep-startstep) :pre - -The run begins on startstep and ends on stopstep. Startstep and -stopstep can span multiple runs, using the {start} and {stop} keywords -of the "run"_run.html command. See the "run"_run.html command for -details of how to do this. - -The stagger(x,y) function uses the current timestep to generate a new -timestep. X,y > 0 and x > y are required. The generated timesteps -increase in a staggered fashion, as the sequence -x,x+y,2x,2x+y,3x,3x+y,etc. For any current timestep, the next -timestep in the sequence is returned. Thus if stagger(1000,100) is -used in a variable by the "dump_modify every"_dump_modify.html -command, it will generate the sequence of output timesteps: - -100,1000,1100,2000,2100,3000,etc :pre - -The logfreq(x,y,z) function uses the current timestep to generate a -new timestep. X,y,z > 0 and y < z are required. The generated -timesteps are on a base-z logarithmic scale, starting with x, and the -y value is how many of the z-1 possible timesteps within one -logarithmic interval are generated. I.e. the timesteps follow the -sequence x,2x,3x,...y*x,x*z,2x*z,3x*z,...y*x*z,x*z^2,2x*z^2,etc. For -any current timestep, the next timestep in the sequence is returned. -Thus if logfreq(100,4,10) is used in a variable by the "dump_modify -every"_dump_modify.html command, it will generate this sequence of -output timesteps: - -100,200,300,400,1000,2000,3000,4000,10000,20000,etc :pre - -The logfreq2(x,y,z) function is similar to logfreq, except a single -logarithmic interval is divided into y equally-spaced timesteps and -all of them are output. Y < z is not required. Thus, if -logfreq2(100,18,10) is used in a variable by the "dump_modify -every"_dump_modify.html command, then the interval between 100 and -1000 is divided as 900/18 = 50 steps, and it will generate the -sequence of output timesteps: - -100,150,200,...950,1000,1500,2000,...9500,10000,15000,etc :pre - -The logfreq3(x,y,z) function generates y points between x and z (inclusive), -that are separated by a multiplicative ratio: (z/x)^(1/(y-1)). Constraints -are: x,z > 0, y > 1, z-x >= y-1. For eg., if logfreq3(10,25,1000) is used in -a variable by the "fix print"_fix_print.html command, then the interval -between 10 and 1000 is divided into 24 parts with a multiplicative -separation of ~1.21, and it will generate the following sequence of output -timesteps: - -10, 13, 15, 18, 22, 27, 32,...384, 465, 563, 682, 826, 1000 :pre - -The stride(x,y,z) function uses the current timestep to generate a new -timestep. X,y >= 0 and z > 0 and x <= y are required. The generated -timesteps increase in increments of z, from x to y, i.e. it generates -the sequence x,x+z,x+2z,...,y. If y-x is not a multiple of z, then -similar to the way a for loop operates, the last value will be one -that does not exceed y. For any current timestep, the next timestep -in the sequence is returned. Thus if stride(1000,2000,100) is used -in a variable by the "dump_modify every"_dump_modify.html command, it -will generate the sequence of output timesteps: - -1000,1100,1200, ... ,1900,2000 :pre - -The stride2(x,y,z,a,b,c) function is similar to the stride() function -except it generates two sets of strided timesteps, one at a coarser -level and one at a finer level. Thus it is useful for debugging, -e.g. to produce output every timestep at the point in simulation when -a problem occurs. X,y >= 0 and z > 0 and x <= y are required, as are -a,b >= 0 and c > 0 and a < b. Also, a >= x and b <= y are required so -that the second stride is inside the first. The generated timesteps -increase in increments of z, starting at x, until a is reached. At -that point the timestep increases in increments of c, from a to b, -then after b, increments by z are resumed until y is reached. For any -current timestep, the next timestep in the sequence is returned. Thus -if stride2(1000,2000,100,1350,1360,1) is used in a variable by the -"dump_modify every"_dump_modify.html command, it will generate the -sequence of output timesteps: - -1000,1100,1200,1300,1350,1351,1352, ... 1359,1360,1400,1500, ... ,2000 :pre - -The vdisplace(x,y) function takes 2 arguments: x = value0 and y = -velocity, and uses the elapsed time to change the value by a linear -displacement due to the applied velocity over the course of a run, -according to this formula: - -value = value0 + velocity*(timestep-startstep)*dt :pre - -where dt = the timestep size. - -The run begins on startstep. Startstep can span multiple runs, using -the {start} keyword of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. Note that the -"thermo_style"_thermo_style.html keyword elaplong = -timestep-startstep. - -The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments: -x = value0, y = amplitude, z = period. They use the elapsed time to -oscillate the value by a sin() or cos() function over the course of a -run, according to one of these formulas, where omega = 2 PI / period: - -value = value0 + Amplitude * sin(omega*(timestep-startstep)*dt) -value = value0 + Amplitude * (1 - cos(omega*(timestep-startstep)*dt)) :pre - -where dt = the timestep size. - -The run begins on startstep. Startstep can span multiple runs, using -the {start} keyword of the "run"_run.html command. See the -"run"_run.html command for details of how to do this. Note that the -"thermo_style"_thermo_style.html keyword elaplong = -timestep-startstep. - -:line - -Group and Region Functions :h4 - -Group functions are specified as keywords followed by one or two -parenthesized arguments. The first argument {ID} is the group-ID. -The {dim} argument, if it exists, is {x} or {y} or {z}. The {dir} -argument, if it exists, is {xmin}, {xmax}, {ymin}, {ymax}, {zmin}, or -{zmax}. The {dimdim} argument, if it exists, is {xx} or {yy} or {zz} -or {xy} or {yz} or {xz}. - -The group function count() is the number of atoms in the group. The -group functions mass() and charge() are the total mass and charge of -the group. Xcm() and vcm() return components of the position and -velocity of the center of mass of the group. Fcm() returns a -component of the total force on the group of atoms. Bound() returns -the min/max of a particular coordinate for all atoms in the group. -Gyration() computes the radius-of-gyration of the group of atoms. See -the "compute gyration"_compute_gyration.html command for a definition -of the formula. Angmom() returns components of the angular momentum -of the group of atoms around its center of mass. Torque() returns -components of the torque on the group of atoms around its center of -mass, based on current forces on the atoms. Inertia() returns one of -6 components of the symmetric inertia tensor of the group of atoms -around its center of mass, ordered as Ixx,Iyy,Izz,Ixy,Iyz,Ixz. -Omega() returns components of the angular velocity of the group of -atoms around its center of mass. - -Region functions are specified exactly the same way as group functions -except they take an extra final argument {IDR} which is the region ID. -The function is computed for all atoms that are in both the group and -the region. If the group is "all", then the only criteria for atom -inclusion is that it be in the region. - -:line - -Special Functions :h4 - -Special functions take specific kinds of arguments, meaning their -arguments cannot be formulas themselves. - -The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions -each take 1 argument which is of the form "c_ID" or "c_ID\[N\]" or -"f_ID" or "f_ID\[N\]" or "v_name". The first two are computes and the -second two are fixes; the ID in the reference should be replaced by -the ID of a compute or fix defined elsewhere in the input script. The -compute or fix must produce either a global vector or array. If it -produces a global vector, then the notation without "\[N\]" should be -used. If it produces a global array, then the notation with "\[N\]" -should be used, when N is an integer, to specify which column of the -global array is being referenced. The last form of argument "v_name" -is for a vector-style variable where "name" is replaced by the name of -the variable. - -These functions operate on a global vector of inputs and reduce it to -a single scalar value. This is analogous to the operation of the -"compute reduce"_compute_reduce.html command, which performs similar -operations on per-atom and local vectors. - -The sum() function calculates the sum of all the vector elements. The -min() and max() functions find the minimum and maximum element -respectively. The ave() function is the same as sum() except that it -divides the result by the length of the vector. - -The trap() function is the same as sum() except the first and last -elements are multiplied by a weighting factor of 1/2 when performing -the sum. This effectively implements an integration via the -trapezoidal rule on the global vector of data. I.e. consider a set of -points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2), -..., (N,VN), where the Vi are the values in the global vector of -length N. The integral from 1 to N of these points is trap(). When -appropriately normalized by the timestep size, this function is useful -for calculating integrals of time-series data, like that generated by -the "fix ave/correlate"_fix_ave_correlate.html command. - -The slope() function uses linear regression to fit a line to the set -of points, equally spaced by 1 in their x coordinate: (1,V1), (2,V2), -..., (N,VN), where the Vi are the values in the global vector of -length N. The returned value is the slope of the line. If the line -has a single point or is vertical, it returns 1.0e20. - -The gmask(x) function takes 1 argument which is a group ID. It -can only be used in atom-style variables. It returns a 1 for -atoms that are in the group, and a 0 for atoms that are not. - -The rmask(x) function takes 1 argument which is a region ID. It can -only be used in atom-style variables. It returns a 1 for atoms that -are in the geometric region, and a 0 for atoms that are not. - -The grmask(x,y) function takes 2 arguments. The first is a group ID, -and the second is a region ID. It can only be used in atom-style -variables. It returns a 1 for atoms that are in both the group and -region, and a 0 for atoms that are not in both. - -The next(x) function takes 1 argument which is a variable ID (not -"v_foo", just "foo"). It must be for a file-style or atomfile-style -variable. Each time the next() function is invoked (i.e. each time -the equal-style or atom-style variable is evaluated), the following -steps occur. - -For file-style variables, the current string value stored by the -file-style variable is converted to a numeric value and returned by -the function. And the next string value in the file is read and -stored. Note that if the line previously read from the file was not a -numeric string, then it will typically evaluate to 0.0, which is -likely not what you want. - -For atomfile-style variables, the current per-atom values stored by -the atomfile-style variable are returned by the function. And the -next set of per-atom values in the file is read and stored. - -Since file-style and atomfile-style variables read and store the first -line of the file or first set of per-atoms values when they are -defined in the input script, these are the value(s) that will be -returned the first time the next() function is invoked. If next() is -invoked more times than there are lines or sets of lines in the file, -the variable is deleted, similar to how the "next"_next.html command -operates. - -:line - -Feature Functions :h4 - -Feature functions allow to probe the running LAMMPS executable for -whether specific features are either active, defined, or available. -The functions take two arguments, a {category} and a corresponding -{argument}. The arguments are strings thus cannot be formulas -themselves (only $-style immediate variable expansion is possible). -Return value is either 1.0 or 0.0 depending on whether the function -evaluates to true or false, respectively. - -The {is_active()} function allows to query for active settings which -are grouped by categories. Currently supported categories and -arguments are: - -{package} (argument = {gpu} or {intel} or {kokkos} or {omp}) -{newton} (argument = {pair} or {bond} or {any}) -{pair} (argument = {single} or {respa} or {manybody} or {tail} or {shift}) -{comm_style} (argument = {brick} or {tiled}) -{min_style} (argument = any of the compiled in minimizer styles) -{run_style} (argument = any of the compiled in run styles) -{atom_style} (argument = any of the compiled in atom styles) -{pair_style} (argument = any of the compiled in pair styles) -{bond_style} (argument = any of the compiled in bond styles) -{angle_style} (argument = any of the compiled in angle styles) -{dihedral_style} (argument = any of the compiled in dihedral styles) -{improper_style} (argument = any of the compiled in improper styles) -{kspace_style} (argument = any of the compiled in kspace styles) :ul - -Most of the settings are self-explanatory, the {single} argument in the -{pair} category allows to check whether a pair style supports a -Pair::single() function as needed by compute group/group and others -features or LAMMPS, {respa} allows to check whether the inner/middle/outer -mode of r-RESPA is supported. In the various style categories, -the checking is also done using suffix flags, if available and enabled. - -Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with USER-OMP). - -pair_style lj/cut/coul/long 14.0 -if $(is_active(package,gpu)) then "suffix off" -kspace_style pppm :pre - -Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step - -timestep $(2.0*(1.0+2.0*is_active(pair,respa)) -if $(is_active(pair,respa)) then "run_style respa 4 3 2 2 improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2 improper 1 pair 2 kspace 3" :pre - -The {is_defined()} function allows to query categories like {compute}, -{dump}, {fix}, {group}, {region}, and {variable} whether an entry -with the provided name or id is defined. - -The {is_available(category,name)} function allows to query whether -a specific optional feature is available, i.e. compiled in. -This currently works for the following categories: {command}, -{compute}, {fix}, {pair_style} and {feature}. For all categories -except {command} and {feature} also appending active suffixes is -tried before reporting failure. - -The {feature} category is used to check the availability of compiled in -features such as GZIP support, PNG support, JPEG support, FFMPEG support, -and C++ exceptions for error handling. Corresponding values for name are -{gzip}, {png}, {jpeg}, {ffmpeg} and {exceptions}. - -This enables writing input scripts which only dump using a given format if -the compiled binary supports it. - -if "$(is_available(feature,png))" then "print 'PNG supported'" else "print 'PNG not supported'" :pre - -if "$(is_available(feature,ffmpeg)" then "dump 3 all movie 25 movie.mp4 type type zoom 1.6 adiam 1.0" :pre - - -:line - -Atom Values and Vectors :h4 - -Atom values take an integer argument I from 1 to N, where I is the -atom-ID, e.g. x\[243\], which means use the x coordinate of the atom -with ID = 243. Or they can take a variable name, specified as v_name, -where name is the name of the variable, like x\[v_myIndex\]. The -variable can be of any style except {vector} or {atom} or {atomfile} -variables. The variable is evaluated and the result is expected to be -numeric and is cast to an integer (i.e. 3.4 becomes 3), to use an -index, which must be a value from 1 to N. Note that a "formula" -cannot be used as the argument between the brackets, e.g. x\[243+10\] -or x\[v_myIndex+1\] are not allowed. To do this a single variable can -be defined that contains the needed formula. - -Note that the 0 < atom-ID <= N, where N is the largest atom ID -in the system. If an ID is specified for an atom that does not -currently exist, then the generated value is 0.0. - -Atom vectors generate one value per atom, so that a reference like -"vx" means the x-component of each atom's velocity will be used when -evaluating the variable. - -The meaning of the different atom values and vectors is mostly -self-explanatory. {Mol} refers to the molecule ID of an atom, and is -only defined if an "atom_style"_atom_style.html is being used that -defines molecule IDs. - -Note that many other atom attributes can be used as inputs to a -variable by using the "compute -property/atom"_compute_property_atom.html command and then specifying -a quantity from that compute. - -:line - -Compute References :h4 - -Compute references access quantities calculated by a -"compute"_compute.html. The ID in the reference should be replaced by -the ID of a compute defined elsewhere in the input script. As -discussed in the doc page for the "compute"_compute.html command, -computes can produce global, per-atom, or local values. Only global -and per-atom values can be used in a variable. Computes can also -produce a scalar, vector, or array. - -An equal-style variable can only use scalar values, which means a -global scalar, or an element of a global or per-atom vector or array. -A vector-style variable can use scalar values or a global vector of -values, or a column of a global array of values. Atom-style variables -can use global scalar values. They can also use per-atom vector -values, or a column of a per-atom array. See the doc pages for -individual computes to see what kind of values they produce. - -Examples of different kinds of compute references are as follows. -There is typically no ambiguity (see exception below) as to what a -reference means, since computes only produce either global or per-atom -quantities, never both. - -c_ID: global scalar, or per-atom vector -c_ID\[I\]: Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array -c_ID\[I\]\[J\]: I,J element of global array, or atom I's Jth value in per-atom array :tb(s=:) - -For I and J indices, integers can be specified or a variable name, -specified as v_name, where name is the name of the variable. The -rules for this syntax are the same as for the "Atom Values and -Vectors" discussion above. - -One source of ambiguity for compute references is when a vector-style -variable refers to a compute that produces both a global scalar and a -global vector. Consider a compute with ID "foo" that does this, -referenced as follows by variable "a", where "myVec" is another -vector-style variable: - -variable a vector c_foo*v_myVec :pre - -The reference "c_foo" could refer to either the global scalar or -global vector produced by compute "foo". In this case, "c_foo" will -always refer to the global scalar, and "C_foo" can be used to -reference the global vector. Similarly if the compute produces both a -global vector and global array, then "c_foo\[I\]" will always refer to -an element of the global vector, and "C_foo\[I\]" can be used to -reference the Ith column of the global array. - -Note that if a variable containing a compute is evaluated directly in -an input script (not during a run), then the values accessed by the -compute must be current. See the discussion below about "Variable -Accuracy". - -:line - -Fix References :h4 - -Fix references access quantities calculated by a "fix"_compute.html. -The ID in the reference should be replaced by the ID of a fix defined -elsewhere in the input script. As discussed in the doc page for the -"fix"_fix.html command, fixes can produce global, per-atom, or local -values. Only global and per-atom values can be used in a variable. -Fixes can also produce a scalar, vector, or array. An equal-style -variable can only use scalar values, which means a global scalar, or -an element of a global or per-atom vector or array. Atom-style -variables can use the same scalar values. They can also use per-atom -vector values. A vector value can be a per-atom vector itself, or a -column of an per-atom array. See the doc pages for individual fixes -to see what kind of values they produce. - -The different kinds of fix references are exactly the same as the -compute references listed in the above table, where "c_" is replaced -by "f_". Again, there is typically no ambiguity (see exception below) -as to what a reference means, since fixes only produce either global -or per-atom quantities, never both. - -f_ID: global scalar, or per-atom vector -f_ID\[I\]: Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array -f_ID\[I\]\[J\]: I,J element of global array, or atom I's Jth value in per-atom array :tb(s=:) - -For I and J indices, integers can be specified or a variable name, -specified as v_name, where name is the name of the variable. The -rules for this syntax are the same as for the "Atom Values and -Vectors" discussion above. - -One source of ambiguity for fix references is the same ambiguity -discussed for compute references above. Namely when a vector-style -variable refers to a fix that produces both a global scalar and a -global vector. The solution is the same as for compute references. -For a fix with ID "foo", "f_foo" will always refer to the global -scalar, and "F_foo" can be used to reference the global vector. And -similarly for distinguishing between a fix's global vector versus -global array with "f_foo\[I\]" versus "F_foo\[I\]". - -Note that if a variable containing a fix is evaluated directly in an -input script (not during a run), then the values accessed by the fix -should be current. See the discussion below about "Variable -Accuracy". - -Note that some fixes only generate quantities on certain timesteps. -If a variable attempts to access the fix on non-allowed timesteps, an -error is generated. For example, the "fix ave/time"_fix_ave_time.html -command may only generate averaged quantities every 100 steps. See -the doc pages for individual fix commands for details. - -:line - -Variable References :h4 - -Variable references access quantities stored or calculated by other -variables, which will cause those variables to be evaluated. The name -in the reference should be replaced by the name of a variable defined -elsewhere in the input script. - -As discussed on this doc page, equal-style variables generate a single -global numeric value, vector-style variables generate a vector of -global numeric values, and atom-style and atomfile-style variables -generate a per-atom vector of numeric values. All other variables -store one or more strings. - -The formula for an equal-style variable can use any style of variable -including a vector_style or atom-style or atomfile-style. For these -3 styles, a subscript must be used to access a single value from -the vector-, atom-, or atomfile-style variable. If a string-storing -variable is used, the string is converted to a numeric value. Note -that this will typically produce a 0.0 if the string is not a numeric -string, which is likely not what you want. - -The formula for a vector-style variable can use any style of variable, -including atom-style or atomfile-style variables. For these 2 styles, -a subscript must be used to access a single value from the atom-, or -atomfile-style variable. - -The formula for an atom-style variable can use any style of variable, -including other atom-style or atomfile-style variables. If it uses a -vector-style variable, a subscript must be used to access a single -value from the vector-style variable. - -Examples of different kinds of variable references are as follows. -There is no ambiguity as to what a reference means, since variables -produce only a global scalar or global vector or per-atom vector. - -v_name: global scalar from equal-style variable -v_name: global vector from vector-style variable -v_name: per-atom vector from atom-style or atomfile-style variable -v_name\[I\]: Ith element of a global vector from vector-style variable -v_name\[I\]: value of atom with ID = I from atom-style or atomfile-style variable :tb(s=:) - -For the I index, an integer can be specified or a variable name, -specified as v_name, where name is the name of the variable. The -rules for this syntax are the same as for the "Atom Values and -Vectors" discussion above. - -:line - -[Immediate Evaluation of Variables:] - -If you want an equal-style variable to be evaluated immediately, it -may be the case that you do not need to define a variable at all. See -the "Commands parse"_Commands_parse.html doc page for info on how to -use "immediate" variables in an input script, specified as $(formula) -with parenthesis, where the formula has the same syntax as equal-style -variables described on this page. This effectively evaluates a -formula immediately without using the variable command to define a -named variable. - -More generally, there is a difference between referencing a variable -with a leading $ sign (e.g. $x or $\{abc\}) versus with a leading "v_" -(e.g. v_x or v_abc). The former can be used in any input script -command, including a variable command. The input script parser -evaluates the reference variable immediately and substitutes its value -into the command. As explained on the "Commands -parse"_Commands_parse.html doc page, you can also use un-named -"immediate" variables for this purpose. For example, a string like -this $((xlo+xhi)/2+sqrt(v_area)) in an input script command evaluates -the string between the parenthesis as an equal-style variable formula. - -Referencing a variable with a leading "v_" is an optional or required -kind of argument for some commands (e.g. the "fix -ave/chunk"_fix_ave_chunk.html or "dump custom"_dump.html or -"thermo_style"_thermo_style.html commands) if you wish it to evaluate -a variable periodically during a run. It can also be used in a -variable formula if you wish to reference a second variable. The -second variable will be evaluated whenever the first variable is -evaluated. - -As an example, suppose you use this command in your input script to -define the variable "v" as - -variable v equal vol :pre - -before a run where the simulation box size changes. You might think -this will assign the initial volume to the variable "v". That is not -the case. Rather it assigns a formula which evaluates the volume -(using the thermo_style keyword "vol") to the variable "v". If you -use the variable "v" in some other command like "fix -ave/time"_fix_ave_time.html then the current volume of the box will be -evaluated continuously during the run. - -If you want to store the initial volume of the system, you can do it -this way: - -variable v equal vol -variable v0 equal $v :pre - -The second command will force "v" to be evaluated (yielding the -initial volume) and assign that value to the variable "v0". Thus the -command - -thermo_style custom step v_v v_v0 :pre - -would print out both the current and initial volume periodically -during the run. - -Note that it is a mistake to enclose a variable formula in double -quotes if it contains variables preceded by $ signs. For example, - -variable vratio equal "$\{vfinal\}/$\{v0\}" :pre - -This is because the quotes prevent variable substitution (explained on -the "Commands parse"_Commands_parse.html doc page), and thus an error -will occur when the formula for "vratio" is evaluated later. - -:line - -[Variable Accuracy:] - -Obviously, LAMMPS attempts to evaluate variables containing formulas -({equal} and {atom} style variables) accurately whenever the -evaluation is performed. Depending on what is included in the -formula, this may require invoking a "compute"_compute.html, either -directly or indirectly via a thermo keyword, or accessing a value -previously calculated by a compute, or accessing a value calculated -and stored by a "fix"_fix.html. If the compute is one that calculates -the pressure or energy of the system, then these quantities need to be -tallied during the evaluation of the interatomic potentials (pair, -bond, etc) on timesteps that the variable will need the values. - -LAMMPS keeps track of all of this during a "run"_run.html or "energy -minimization"_minimize.html. An error will be generated if you -attempt to evaluate a variable on timesteps when it cannot produce -accurate values. For example, if a "thermo_style -custom"_thermo_style.html command prints a variable which accesses -values stored by a "fix ave/time"_fix_ave_time.html command and the -timesteps on which thermo output is generated are not multiples of the -averaging frequency used in the fix command, then an error will occur. - -An input script can also request variables be evaluated before or -after or in between runs, e.g. by including them in a -"print"_print.html command. In this case, if a compute is needed to -evaluate a variable (either directly or indirectly), LAMMPS will not -invoke the compute, but it will use a value previously calculated by -the compute, and can do this only if it was invoked on the current -timestep. Fixes will always provide a quantity needed by a variable, -but the quantity may or may not be current. This leads to one of -three kinds of behavior: - -(1) The variable may be evaluated accurately. If it contains -references to a compute or fix, and these values were calculated on -the last timestep of a preceding run, then they will be accessed and -used by the variable and the result will be accurate. - -(2) LAMMPS may not be able to evaluate the variable and will generate -an error message stating so. For example, if the variable requires a -quantity from a "compute"_compute.html that has not been invoked on -the current timestep, LAMMPS will generate an error. This means, for -example, that such a variable cannot be evaluated before the first run -has occurred. Likewise, in between runs, a variable containing a -compute cannot be evaluated unless the compute was invoked on the last -timestep of the preceding run, e.g. by thermodynamic output. - -One way to get around this problem is to perform a 0-timestep run -before using the variable. For example, these commands - -variable t equal temp -print "Initial temperature = $t" -run 1000 :pre - -will generate an error if the run is the first run specified in the -input script, because generating a value for the "t" variable requires -a compute for calculating the temperature to be invoked. - -However, this sequence of commands would be fine: - -run 0 -variable t equal temp -print "Initial temperature = $t" -run 1000 :pre - -The 0-timestep run initializes and invokes various computes, including -the one for temperature, so that the value it stores is current and -can be accessed by the variable "t" after the run has completed. Note -that a 0-timestep run does not alter the state of the system, so it -does not change the input state for the 1000-timestep run that -follows. Also note that the 0-timestep run must actually use and -invoke the compute in question (e.g. via "thermo"_thermo_style.html or -"dump"_dump.html output) in order for it to enable the compute to be -used in a variable after the run. Thus if you are trying to print a -variable that uses a compute you have defined, you can insure it is -invoked on the last timestep of the preceding run by including it in -thermodynamic output. - -Unlike computes, "fixes"_fix.html will never generate an error if -their values are accessed by a variable in between runs. They always -return some value to the variable. However, the value may not be what -you expect if the fix has not yet calculated the quantity of interest -or it is not current. For example, the "fix indent"_fix_indent.html -command stores the force on the indenter. But this is not computed -until a run is performed. Thus if a variable attempts to print this -value before the first run, zeroes will be output. Again, performing -a 0-timestep run before printing the variable has the desired effect. - -(3) The variable may be evaluated incorrectly and LAMMPS may have no -way to detect this has occurred. Consider the following sequence of -commands: - -pair_coeff 1 1 1.0 1.0 -run 1000 -pair_coeff 1 1 1.5 1.0 -variable e equal pe -print "Final potential energy = $e" :pre - -The first run is performed using one setting for the pairwise -potential defined by the "pair_style"_pair_style.html and -"pair_coeff"_pair_coeff.html commands. The potential energy is -evaluated on the final timestep and stored by the "compute -pe"_compute_pe.html compute (this is done by the -"thermo_style"_thermo_style.html command). Then a pair coefficient is -changed, altering the potential energy of the system. When the -potential energy is printed via the "e" variable, LAMMPS will use the -potential energy value stored by the "compute pe"_compute_pe.html -compute, thinking it is current. There are many other commands which -could alter the state of the system between runs, causing a variable -to evaluate incorrectly. - -The solution to this issue is the same as for case (2) above, namely -perform a 0-timestep run before the variable is evaluated to insure -the system is up-to-date. For example, this sequence of commands -would print a potential energy that reflected the changed pairwise -coefficient: - -pair_coeff 1 1 1.0 1.0 -run 1000 -pair_coeff 1 1 1.5 1.0 -run 0 -variable e equal pe -print "Final potential energy = $e" :pre - -:line - -[Restrictions:] - -Indexing any formula element by global atom ID, such as an atom value, -requires the "atom style"_atom_style.html to use a global mapping in -order to look up the vector indices. By default, only atom styles -with molecular information create global maps. The "atom_modify -map"_atom_modify.html command can override the default, e.g. for -atomic-style atom styles. - -All {universe}- and {uloop}-style variables defined in an input script -must have the same number of values. - -[Related commands:] - -"next"_next.html, "jump"_jump.html, "include"_include.html, -"temper"_temper.html, "fix print"_fix_print.html, "print"_print.html - -[Default:] none diff --git a/doc/txt/velocity.txt b/doc/txt/velocity.txt deleted file mode 100644 index 4bbbc5ad45..0000000000 --- a/doc/txt/velocity.txt +++ /dev/null @@ -1,259 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -velocity command :h3 - -[Syntax:] - -velocity group-ID style args keyword value ... :pre - -group-ID = ID of group of atoms whose velocity will be changed :ulb,l -style = {create} or {set} or {scale} or {ramp} or {zero} :l - {create} args = temp seed - temp = temperature value (temperature units) - seed = random # seed (positive integer) - {set} args = vx vy vz - vx,vy,vz = velocity value or NULL (velocity units) - any of vx,vy,vz van be a variable (see below) - {scale} arg = temp - temp = temperature value (temperature units) - {ramp} args = vdim vlo vhi dim clo chi - vdim = {vx} or {vy} or {vz} - vlo,vhi = lower and upper velocity value (velocity units) - dim = {x} or {y} or {z} - clo,chi = lower and upper coordinate bound (distance units) - {zero} arg = {linear} or {angular} - {linear} = zero the linear momentum - {angular} = zero the angular momentum :pre - -zero or more keyword/value pairs may be appended :l -keyword = {dist} or {sum} or {mom} or {rot} or {temp} or {bias} or {loop} or {units} :l - {dist} value = {uniform} or {gaussian} - {sum} value = {no} or {yes} - {mom} value = {no} or {yes} - {rot} value = {no} or {yes} - {temp} value = temperature compute ID - {bias} value = {no} or {yes} - {loop} value = {all} or {local} or {geom} - {rigid} value = fix-ID - fix-ID = ID of rigid body fix - {units} value = {box} or {lattice} :pre -:ule - -[Examples:] - -velocity all create 300.0 4928459 rot yes dist gaussian -velocity border set NULL 4.0 v_vz sum yes units box -velocity flow scale 300.0 -velocity flow ramp vx 0.0 5.0 y 5 25 temp mytemp -velocity all zero linear :pre - -[Description:] - -Set or change the velocities of a group of atoms in one of several -styles. For each style, there are required arguments and optional -keyword/value parameters. Not all options are used by each style. -Each option has a default as listed below. - -The {create} style generates an ensemble of velocities using a random -number generator with the specified seed at the specified temperature. - -The {set} style sets the velocities of all atoms in the group to the -specified values. If any component is specified as NULL, then it is -not set. Any of the vx,vy,vz velocity components can be specified as -an equal-style or atom-style "variable"_variable.html. If the value -is a variable, it should be specified as v_name, where name is the -variable name. In this case, the variable will be evaluated, and its -value used to determine the velocity component. Note that if a -variable is used, the velocity it calculates must be in box units, not -lattice units; see the discussion of the {units} keyword below. - -Equal-style variables can specify formulas with various mathematical -functions, and include "thermo_style"_thermo_style.html command -keywords for the simulation box parameters or other parameters. - -Atom-style variables can specify the same formulas as equal-style -variables but can also include per-atom values, such as atom -coordinates. Thus it is easy to specify a spatially-dependent -velocity field. - -The {scale} style computes the current temperature of the group of -atoms and then rescales the velocities to the specified temperature. - -The {ramp} style is similar to that used by the "compute -temp/ramp"_compute_temp_ramp.html command. Velocities ramped -uniformly from vlo to vhi are applied to dimension vx, or vy, or vz. -The value assigned to a particular atom depends on its relative -coordinate value (in dim) from clo to chi. For the example above, an -atom with y-coordinate of 10 (1/4 of the way from 5 to 25), would be -assigned a x-velocity of 1.25 (1/4 of the way from 0.0 to 5.0). Atoms -outside the coordinate bounds (less than 5 or greater than 25 in this -case), are assigned velocities equal to vlo or vhi (0.0 or 5.0 in this -case). - -The {zero} style adjusts the velocities of the group of atoms so that -the aggregate linear or angular momentum is zero. No other changes -are made to the velocities of the atoms. If the {rigid} option is -specified (see below), then the zeroing is performed on individual -rigid bodies, as defined by the "fix rigid or fix -rigid/small"_fix_rigid.html commands. In other words, zero linear -will set the linear momentum of each rigid body to zero, and zero -angular will set the angular momentum of each rigid body to zero. -This is done by adjusting the velocities of the atoms in each rigid -body. - -All temperatures specified in the velocity command are in temperature -units; see the "units"_units.html command. The units of velocities and -coordinates depend on whether the {units} keyword is set to {box} or -{lattice}, as discussed below. - -For all styles, no atoms are assigned z-component velocities if the -simulation is 2d; see the "dimension"_dimension.html command. - -:line - -The keyword/value options are used in the following ways by the -various styles. - -The {dist} keyword is used by {create}. The ensemble of generated -velocities can be a {uniform} distribution from some minimum to -maximum value, scaled to produce the requested temperature. Or it can -be a {gaussian} distribution with a mean of 0.0 and a sigma scaled to -produce the requested temperature. - -The {sum} keyword is used by all styles, except {zero}. The new -velocities will be added to the existing ones if sum = yes, or will -replace them if sum = no. - -The {mom} and {rot} keywords are used by {create}. If mom = yes, the -linear momentum of the newly created ensemble of velocities is zeroed; -if rot = yes, the angular momentum is zeroed. - -:line - -If specified, the {temp} keyword is used by {create} and {scale} to -specify a "compute"_compute.html that calculates temperature in a -desired way, e.g. by first subtracting out a velocity bias, as -discussed on the "Howto thermostat"_Howto_thermostat.html doc page. -If this keyword is not specified, {create} and {scale} calculate -temperature using a compute that is defined internally as follows: - -compute velocity_temp group-ID temp :pre - -where group-ID is the same ID used in the velocity command. i.e. the -group of atoms whose velocity is being altered. This compute is -deleted when the velocity command is finished. See the "compute -temp"_compute_temp.html command for details. If the calculated -temperature should have degrees-of-freedom removed due to fix -constraints (e.g. SHAKE or rigid-body constraints), then the -appropriate fix command must be specified before the velocity command -is issued. - -The {bias} keyword with a {yes} setting is used by {create} and -{scale}, but only if the {temp} keyword is also used to specify a -"compute"_compute.html that calculates temperature in a desired way. -If the temperature compute also calculates a velocity bias, the -bias is subtracted from atom velocities before the {create} and -{scale} operations are performed. After the operations, the bias is -added back to the atom velocities. See the "Howto -thermostat"_Howto_thermostat.html doc page for more discussion of -temperature computes with biases. Note that the velocity bias is only -applied to atoms in the temperature compute specified with the {temp} -keyword. - -As an example, assume atoms are currently streaming in a flow -direction (which could be separately initialized with the {ramp} -style), and you wish to initialize their thermal velocity to a desired -temperature. In this context thermal velocity means the per-particle -velocity that remains when the streaming velocity is subtracted. This -can be done using the {create} style with the {temp} keyword -specifying the ID of a "compute temp/ramp"_compute_temp_ramp.html or -"compute temp/profile"_compute_temp_profile.html command, and the -{bias} keyword set to a {yes} value. - -:line - -The {loop} keyword is used by {create} in the following ways. - -If loop = all, then each processor loops over all atoms in the -simulation to create velocities, but only stores velocities for atoms -it owns. This can be a slow loop for a large simulation. If atoms -were read from a data file, the velocity assigned to a particular atom -will be the same, independent of how many processors are being used. -This will not be the case if atoms were created using the -"create_atoms"_create_atoms.html command, since atom IDs will likely -be assigned to atoms differently. - -If loop = local, then each processor loops over only its atoms to -produce velocities. The random number seed is adjusted to give a -different set of velocities on each processor. This is a fast loop, -but the velocity assigned to a particular atom will depend on which -processor owns it. Thus the results will always be different when a -simulation is run on a different number of processors. - -If loop = geom, then each processor loops over only its atoms. For -each atom a unique random number seed is created, based on the atom's -xyz coordinates. A velocity is generated using that seed. This is a -fast loop and the velocity assigned to a particular atom will be the -same, independent of how many processors are used. However, the set -of generated velocities may be more correlated than if the {all} or -{local} keywords are used. - -Note that the {loop geom} keyword will not necessarily assign -identical velocities for two simulations run on different machines. -This is because the computations based on xyz coordinates are -sensitive to tiny differences in the double-precision value for a -coordinate as stored on a particular machine. - -:line - -The {rigid} keyword only has meaning when used with the {zero} style. -It allows specification of a fix-ID for one of the "rigid-body -fix"_fix_rigid.html variants which defines a set of rigid bodies. The -zeroing of linear or angular momentum is then performed for each rigid -body defined by the fix, as described above. - -The {units} keyword is used by {set} and {ramp}. If units = box, -the velocities and coordinates specified in the velocity command are -in the standard units described by the "units"_units.html command -(e.g. Angstroms/fmsec for real units). If units = lattice, velocities -are in units of lattice spacings per time (e.g. spacings/fmsec) and -coordinates are in lattice spacings. The "lattice"_lattice.html -command must have been previously used to define the lattice spacing. - -:line - -[Restrictions:] - -Assigning a temperature via the {create} style to a system with "rigid -bodies"_fix_rigid.html or "SHAKE constraints"_fix_shake.html may not -have the desired outcome for two reasons. First, the velocity command -can be invoked before all of the relevant fixes are created and -initialized and the number of adjusted degrees of freedom (DOFs) is -known. Thus it is not possible to compute the target temperature -correctly. Second, the assigned velocities may be partially canceled -when constraints are first enforced, leading to a different -temperature than desired. A workaround for this is to perform a "run -0"_run.html command, which insures all DOFs are accounted for -properly, and then rescale the temperature to the desired value before -performing a simulation. For example: - -velocity all create 300.0 12345 -run 0 # temperature may not be 300K -velocity all scale 300.0 # now it should be :pre - -[Related commands:] - -"fix rigid"_fix_rigid.html, "fix shake"_fix_shake.html, -"lattice"_lattice.html - -[Default:] - -The keyword defaults are dist = uniform, sum = no, mom = yes, rot = -no, bias = no, loop = all, and units = lattice. The temp and rigid -keywords are not defined by default. diff --git a/doc/txt/write_coeff.txt b/doc/txt/write_coeff.txt deleted file mode 100644 index 74d19b5c3d..0000000000 --- a/doc/txt/write_coeff.txt +++ /dev/null @@ -1,44 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -write_coeff command :h3 - -[Syntax:] - -write_coeff file :pre - -file = name of data file to write out :pre - -[Examples:] - -write_coeff polymer.coeff :pre - -[Description:] - -Write a text format file with the currently defined force field -coefficients in a way, that it can be read by LAMMPS with the -"include"_include.html command. In combination with the nocoeff -option of "write_data"_write_data.html this can be used to move -the Coeffs sections from a data file into a separate file. - -NOTE: The write_coeff command is not yet fully implemented as -some pair styles do not output their coefficient information. -This means you will need to add/copy this information manually. - -:line - -[Restrictions:] - -none - -[Related commands:] - -"read_data"_read_data.html, "write_restart"_write_restart.html, -"write_data"_write_data.html - - diff --git a/doc/txt/write_data.txt b/doc/txt/write_data.txt deleted file mode 100644 index 79e855dff3..0000000000 --- a/doc/txt/write_data.txt +++ /dev/null @@ -1,129 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -write_data command :h3 - -[Syntax:] - -write_data file keyword value ... :pre - -file = name of data file to write out :ulb,l -zero or more keyword/value pairs may be appended :l -keyword = {pair} or {nocoeff} :l - {nocoeff} = do not write out force field info - {nofix} = do not write out extra sections read by fixes - {pair} value = {ii} or {ij} - {ii} = write one line of pair coefficient info per atom type - {ij} = write one line of pair coefficient info per IJ atom type pair :pre -:ule - -[Examples:] - -write_data data.polymer -write_data data.* :pre - -[Description:] - -Write a data file in text format of the current state of the -simulation. Data files can be read by the "read data"_read_data.html -command to begin a simulation. The "read_data"_read_data.html command -also describes their format. - -Similar to "dump"_dump.html files, the data filename can contain a "*" -wild-card character. The "*" is replaced with the current timestep -value. - -NOTE: The write-data command is not yet fully implemented in two -respects. First, most pair styles do not yet write their coefficient -information into the data file. This means you will need to specify -that information in your input script that reads the data file, via -the "pair_coeff"_pair_coeff.html command. Second, a few of the "atom -styles"_atom_style.html (body, ellipsoid, line, tri) that store -auxiliary "bonus" information about aspherical particles, do not yet -write the bonus info into the data file. Both these functionalities -will be added to the write_data command later. - -Because a data file is in text format, if you use a data file written -out by this command to restart a simulation, the initial state of the -new run will be slightly different than the final state of the old run -(when the file was written) which was represented internally by LAMMPS -in binary format. A new simulation which reads the data file will -thus typically diverge from a simulation that continued in the -original input script. - -If you want to do more exact restarts, using binary files, see the -"restart"_restart.html, "write_restart"_write_restart.html, and -"read_restart"_read_restart.html commands. You can also convert -binary restart files to text data files, after a simulation has run, -using the "-r command-line switch"_Run_options.html. - -NOTE: Only limited information about a simulation is stored in a data -file. For example, no information about atom "groups"_group.html and -"fixes"_fix.html are stored. "Binary restart files"_read_restart.html -store more information. - -Bond interactions (angle, etc) that have been turned off by the "fix -shake"_fix_shake.html or "delete_bonds"_delete_bonds.html command will -be written to a data file as if they are turned on. This means they -will need to be turned off again in a new run after the data file is -read. - -Bonds that are broken (e.g. by a bond-breaking potential) are not -written to the data file. Thus these bonds will not exist when the -data file is read. - -:line - -The {nocoeff} keyword requests that no force field parameters should -be written to the data file. This can be very helpful, if one wants -to make significant changes to the force field or if the parameters -are read in separately anyway, e.g. from an include file. - -The {nofix} keyword requests that no extra sections read by fixes -should be written to the data file (see the {fix} option of the -"read_data"_read_data.html command for details). For example, this -option excludes sections for user-created per-atom properties -from "fix property/atom"_fix_property_atom.html. - -The {pair} keyword lets you specify in what format the pair -coefficient information is written into the data file. If the value -is specified as {ii}, then one line per atom type is written, to -specify the coefficients for each of the I=J interactions. This means -that no cross-interactions for I != J will be specified in the data -file and the pair style will apply its mixing rule, as documented on -individual "pair_style"_pair_style.html doc pages. Of course this -behavior can be overridden in the input script after reading the data -file, by specifying additional "pair_coeff"_pair_coeff.html commands -for any desired I,J pairs. - -If the value is specified as {ij}, then one line of coefficients is -written for all I,J pairs where I <= J. These coefficients will -include any specific settings made in the input script up to that -point. The presence of these I != J coefficients in the data file -will effectively turn off the default mixing rule for the pair style. -Again, the coefficient values in the data file can be overridden -in the input script after reading the data file, by specifying -additional "pair_coeff"_pair_coeff.html commands for any desired I,J -pairs. - -:line - -[Restrictions:] - -This command requires inter-processor communication to migrate atoms -before the data file is written. This means that your system must be -ready to perform a simulation before using this command (force fields -setup, atom masses initialized, etc). - -[Related commands:] - -"read_data"_read_data.html, "write_restart"_write_restart.html - -[Default:] - -The option defaults are pair = ii. diff --git a/doc/txt/write_dump.txt b/doc/txt/write_dump.txt deleted file mode 100644 index e676979001..0000000000 --- a/doc/txt/write_dump.txt +++ /dev/null @@ -1,92 +0,0 @@ - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -write_dump command :h3 - -[Syntax:] - -write_dump group-ID style file dump-args modify dump_modify-args :pre - -group-ID = ID of the group of atoms to be dumped :ulb,l -style = any of the supported "dump styles"_dump.html :l -file = name of file to write dump info to :l -dump-args = any additional args needed for a particular "dump style"_dump.html :l -modify = all args after this keyword are passed to "dump_modify"_dump_modify.html (optional) :l -dump-modify-args = args for "dump_modify"_dump_modify.html (optional) :l -:ule - -[Examples:] - -write_dump all atom dump.atom -write_dump subgroup atom dump.run.bin -write_dump all custom dump.myforce.* id type x y vx fx -write_dump flow custom dump.%.myforce id type c_myF\[3\] v_ke modify sort id -write_dump all xyz system.xyz modify sort id element O H -write_dump all image snap*.jpg type type size 960 960 modify backcolor white -write_dump all image snap*.jpg element element & - bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600 & - modify backcolor white element C C O H N C C C O H H S O H :pre - -[Description:] - -Dump a single snapshot of atom quantities to one or more files for the -current state of the system. This is a one-time immediate operation, -in contrast to the "dump"_dump.html command which will will set up a -dump style to write out snapshots periodically during a running -simulation. - -The syntax for this command is mostly identical to that of the -"dump"_dump.html and "dump_modify"_dump_modify.html commands as if -they were concatenated together, with the following exceptions: There -is no need for a dump ID or dump frequency and the keyword {modify} is -added. The latter is so that the full range of -"dump_modify"_dump_modify.html options can be specified for the single -snapshot, just as they can be for multiple snapshots. The {modify} -keyword separates the arguments that would normally be passed to the -{dump} command from those that would be given the {dump_modify}. Both -support optional arguments and thus LAMMPS needs to be able to cleanly -separate the two sets of args. - -Note that if the specified filename uses wildcard characters "*" or -"%", as supported by the "dump"_dump.html command, they will operate -in the same fashion to create the new filename(s). Normally, "dump -image"_dump_image.html files require a filename with a "*" character -for the timestep. That is not the case for the write_dump command; no -wildcard "*" character is necessary. - -:line - -[Restrictions:] - -All restrictions for the "dump"_dump.html and -"dump_modify"_dump_modify.html commands apply to this command as well, -with the exception of the "dump image"_dump_image.html filename not -requiring a wildcard "*" character, as noted above. - -Since dumps are normally written during a "run"_run.html or "energy -minimization"_minimize.html, the simulation has to be ready to run -before this command can be used. Similarly, if the dump requires -information from a compute, fix, or variable, the information needs to -have been calculated for the current timestep (e.g. by a prior run), -else LAMMPS will generate an error message. - -For example, it is not possible to dump per-atom energy with this -command before a run has been performed, since no energies and forces -have yet been calculated. See the "variable"_variable.html doc page -section on Variable Accuracy for more information on this topic. - -[Related commands:] - -"dump"_dump.html, "dump image"_dump_image.html, -"dump_modify"_dump_modify.html - -[Default:] - -The defaults are listed on the doc pages for the "dump"_dump.html and -"dump image"_dump_image.html and "dump_modify"_dump_modify.html -commands. diff --git a/doc/txt/write_restart.txt b/doc/txt/write_restart.txt deleted file mode 100644 index c393c7f735..0000000000 --- a/doc/txt/write_restart.txt +++ /dev/null @@ -1,120 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -write_restart command :h3 - -[Syntax:] - -write_restart file keyword value ... :pre - -file = name of file to write restart information to :ulb,l -zero or more keyword/value pairs may be appended :l -keyword = {fileper} or {nfile} :l - {fileper} arg = Np - Np = write one file for every this many processors - {nfile} arg = Nf - Nf = write this many files, one from each of Nf processors :pre -:ule - -[Examples:] - -write_restart restart.equil -write_restart restart.equil.mpiio -write_restart poly.%.* nfile 10 :pre - -[Description:] - -Write a binary restart file of the current state of the simulation. - -During a long simulation, the "restart"_restart.html command is -typically used to output restart files periodically. The -write_restart command is useful after a minimization or whenever you -wish to write out a single current restart file. - -Similar to "dump"_dump.html files, the restart filename can contain -two wild-card characters. If a "*" appears in the filename, it is -replaced with the current timestep value. If a "%" character appears -in the filename, then one file is written by each processor and the -"%" character is replaced with the processor ID from 0 to P-1. An -additional file with the "%" replaced by "base" is also written, which -contains global information. For example, the files written for -filename restart.% would be restart.base, restart.0, restart.1, ... -restart.P-1. This creates smaller files and can be a fast mode of -output and subsequent input on parallel machines that support parallel -I/O. The optional {fileper} and {nfile} keywords discussed below can -alter the number of files written. - -The restart file can also be written in parallel as one large binary -file via the MPI-IO library, which is part of the MPI standard for -versions 2.0 and above. Using MPI-IO requires two steps. First, -build LAMMPS with its MPIIO package installed, e.g. - -make yes-mpiio # installs the MPIIO package -make mpi # build LAMMPS for your platform :pre - -Second, use a restart filename which contains ".mpiio". Note that it -does not have to end in ".mpiio", just contain those characters. -Unlike MPI-IO dump files, a particular restart file must be both -written and read using MPI-IO. - -Restart files can be read by a "read_restart"_read_restart.html -command to restart a simulation from a particular state. Because the -file is binary (to enable exact restarts), it may not be readable on -another machine. In this case, you can use the "-r command-line -switch"_Run_options.html to convert a restart file to a data file. - -NOTE: Although the purpose of restart files is to enable restarting a -simulation from where it left off, not all information about a -simulation is stored in the file. For example, the list of fixes that -were specified during the initial run is not stored, which means the -new input script must specify any fixes you want to use. Even when -restart information is stored in the file, as it is for some fixes, -commands may need to be re-specified in the new input script, in order -to re-use that information. Details are usually given in the -documentation of the respective command. Also, see the -"read_restart"_read_restart.html command for general information about -what is stored in a restart file. - -:line - -The optional {nfile} or {fileper} keywords can be used in conjunction -with the "%" wildcard character in the specified restart file name. -As explained above, the "%" character causes the restart file to be -written in pieces, one piece for each of P processors. By default P = -the number of processors the simulation is running on. The {nfile} or -{fileper} keyword can be used to set P to a smaller value, which can -be more efficient when running on a large number of processors. - -The {nfile} keyword sets P to the specified Nf value. For example, if -Nf = 4, and the simulation is running on 100 processors, 4 files will -be written, by processors 0,25,50,75. Each will collect information -from itself and the next 24 processors and write it to a restart file. - -For the {fileper} keyword, the specified value of Np means write one -file for every Np processors. For example, if Np = 4, every 4th -processor (0,4,8,12,etc) will collect information from itself and the -next 3 processors and write it to a restart file. - -:line - -[Restrictions:] - -This command requires inter-processor communication to migrate atoms -before the restart file is written. This means that your system must -be ready to perform a simulation before using this command (force -fields setup, atom masses initialized, etc). - -To write and read restart files in parallel with MPI-IO, the MPIIO -package must be installed. - -[Related commands:] - -"restart"_restart.html, "read_restart"_read_restart.html, -"write_data"_write_data.html - -[Default:] none