jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge pull request #1855 from akohlmey/remove-txt-files 

Remove txt sources of rst files from doc folder
This commit is contained in:
Axel Kohlmeyer 2020-01-27 12:04:37 -05:00 committed by GitHub
parent 4134d7fddd ec381964e4
commit 5eef3b1828
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
1209 changed files with 2874 additions and 101243 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

23
doc/Makefile
View File

@ -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

2
doc/src/Build_extras.rst
View File

@ -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 <kim_commands>`
use with LAMMPS. If you want to use the :doc:`kim_query <kim_commands>`
command, you also need to have libcurl installed with the matching
development headers and the curl-config tool.

10
doc/src/Build_settings.rst
View File

@ -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 <cxx11>` when building all of LAMMPS
| :ref:`FFT library <fft>` for use with the :doc:`kspace\_style pppm <kspace_style>` command
| :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
| :ref:`Size of LAMMPS data types <size>`
| :ref:`Read or write compressed files <gzip>`
| :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
| :ref:`Output of movie files <graphics>` via the :doc:`dump\_movie <dump_image>` command
| :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
| :ref:`Memory allocation alignment <align>`
| :ref:`Workaround for long long integers <longlong>`
| :ref:`Error handling exceptions <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 <kspace_style>` command performs 3d FFTs which
:doc:`kspace_style pppm <kspace_style>` 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 <atom_modify>` command will turn them off. Atom
:doc:`atom_modify id no <atom_modify>` 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 <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
**CMake variables**\ :

2
doc/src/Commands_bond.rst
View File

@ -131,7 +131,7 @@ OPT.
Improper_style potentials
=========================
All LAMMPS :doc:`improper\_style <improper_style>` commands. Some styles
All LAMMPS :doc:`improper_style <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.

90
doc/src/Commands_category.rst
View File

@ -18,73 +18,73 @@ Setup simulation box:
* :doc:`boundary <boundary>`,
* :doc:`box <box>`,
* :doc:`change\_box <change_box>`,
* :doc:`create\_box <create_box>`,
* :doc:`change_box <change_box>`,
* :doc:`create_box <create_box>`,
* :doc:`dimension <dimension>`,
* :doc:`lattice <lattice>`,
* :doc:`region <region>`
Setup atoms:
* :doc:`atom\_modify <atom_modify>`,
* :doc:`atom\_style <atom_style>`,
* :doc:`atom_modify <atom_modify>`,
* :doc:`atom_style <atom_style>`,
* :doc:`balance <balance>`,
* :doc:`create\_atoms <create_atoms>`,
* :doc:`create\_bonds <create_bonds>`,
* :doc:`delete\_atoms <delete_atoms>`,
* :doc:`delete\_bonds <delete_bonds>`,
* :doc:`displace\_atoms <displace_atoms>`,
* :doc:`create_atoms <create_atoms>`,
* :doc:`create_bonds <create_bonds>`,
* :doc:`delete_atoms <delete_atoms>`,
* :doc:`delete_bonds <delete_bonds>`,
* :doc:`displace_atoms <displace_atoms>`,
* :doc:`group <group>`,
* :doc:`mass <mass>`,
* :doc:`molecule <molecule>`,
* :doc:`read\_data <read_data>`,
* :doc:`read\_dump <read_dump>`,
* :doc:`read\_restart <read_restart>`,
* :doc:`read_data <read_data>`,
* :doc:`read_dump <read_dump>`,
* :doc:`read_restart <read_restart>`,
* :doc:`replicate <replicate>`,
* :doc:`set <set>`,
* :doc:`velocity <velocity>`
Force fields:
* :doc:`angle\_coeff <angle_coeff>`,
* :doc:`angle\_style <angle_style>`,
* :doc:`bond\_coeff <bond_coeff>`,
* :doc:`bond\_style <bond_style>`,
* :doc:`bond\_write <bond_write>`,
* :doc:`angle_coeff <angle_coeff>`,
* :doc:`angle_style <angle_style>`,
* :doc:`bond_coeff <bond_coeff>`,
* :doc:`bond_style <bond_style>`,
* :doc:`bond_write <bond_write>`,
* :doc:`dielectric <dielectric>`,
* :doc:`dihedral\_coeff <dihedral_coeff>`,
* :doc:`dihedral\_style <dihedral_style>`,
* :doc:`improper\_coeff <improper_coeff>`,
* :doc:`improper\_style <improper_style>`,
* :doc:`kspace\_modify <kspace_modify>`,
* :doc:`kspace\_style <kspace_style>`,
* :doc:`pair\_coeff <pair_coeff>`,
* :doc:`pair\_modify <pair_modify>`,
* :doc:`pair\_style <pair_style>`,
* :doc:`pair\_write <pair_write>`,
* :doc:`special\_bonds <special_bonds>`
* :doc:`dihedral_coeff <dihedral_coeff>`,
* :doc:`dihedral_style <dihedral_style>`,
* :doc:`improper_coeff <improper_coeff>`,
* :doc:`improper_style <improper_style>`,
* :doc:`kspace_modify <kspace_modify>`,
* :doc:`kspace_style <kspace_style>`,
* :doc:`pair_coeff <pair_coeff>`,
* :doc:`pair_modify <pair_modify>`,
* :doc:`pair_style <pair_style>`,
* :doc:`pair_write <pair_write>`,
* :doc:`special_bonds <special_bonds>`
Settings:
* :doc:`comm\_modify <comm_modify>`,
* :doc:`comm\_style <comm_style>`,
* :doc:`comm_modify <comm_modify>`,
* :doc:`comm_style <comm_style>`,
* :doc:`info <info>`,
* :doc:`min\_modify <min_modify>`,
* :doc:`min\_style <min_style>`,
* :doc:`neigh\_modify <neigh_modify>`,
* :doc:`min_modify <min_modify>`,
* :doc:`min_style <min_style>`,
* :doc:`neigh_modify <neigh_modify>`,
* :doc:`neighbor <neighbor>`,
* :doc:`partition <partition>`,
* :doc:`reset\_timestep <reset_timestep>`,
* :doc:`run\_style <run_style>`,
* :doc:`reset_timestep <reset_timestep>`,
* :doc:`run_style <run_style>`,
* :doc:`timer <timer>`,
* :doc:`timestep <timestep>`
Operations within timestepping (fixes) and diagnostics (computes):
* :doc:`compute <compute>`,
* :doc:`compute\_modify <compute_modify>`,
* :doc:`compute_modify <compute_modify>`,
* :doc:`fix <fix>`,
* :doc:`fix\_modify <fix_modify>`,
* :doc:`fix_modify <fix_modify>`,
* :doc:`uncompute <uncompute>`,
* :doc:`unfix <unfix>`
@ -93,22 +93,22 @@ Output:
* :doc:`dump image <dump_image>`,
* :doc:`dump movie <dump_image>`,
* :doc:`dump <dump>`,
* :doc:`dump\_modify <dump_modify>`,
* :doc:`dump_modify <dump_modify>`,
* :doc:`restart <restart>`,
* :doc:`thermo <thermo>`,
* :doc:`thermo\_modify <thermo_modify>`,
* :doc:`thermo\_style <thermo_style>`,
* :doc:`thermo_modify <thermo_modify>`,
* :doc:`thermo_style <thermo_style>`,
* :doc:`undump <undump>`,
* :doc:`write\_coeff <write_coeff>`,
* :doc:`write\_data <write_data>`,
* :doc:`write\_dump <write_dump>`,
* :doc:`write\_restart <write_restart>`
* :doc:`write_coeff <write_coeff>`,
* :doc:`write_data <write_data>`,
* :doc:`write_dump <write_dump>`,
* :doc:`write_restart <write_restart>`
Actions:
* :doc:`minimize <minimize>`,
* :doc:`neb <neb>`,
* :doc:`neb\_spin <neb_spin>`,
* :doc:`neb_spin <neb_spin>`,
* :doc:`prd <prd>`,
* :doc:`rerun <rerun>`,
* :doc:`run <run>`,

2
doc/src/Commands_input.rst
View File

@ -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 <read_data>` command initializes the system by setting
:doc:`read_data <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 <processors>` and
:doc:`boundary <boundary>` commands need to be used before read\_data to

2
doc/src/Commands_kspace.rst
View File

@ -14,7 +14,7 @@
KSpace solvers
==============
All LAMMPS :doc:`kspace\_style <kspace_style>` solvers. Some styles have
All LAMMPS :doc:`kspace_style <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.

4
doc/src/Commands_removed.rst
View File

@ -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 <read_restart>` and
:doc:`write\_data <write_data>` can be used to the same effect. For added
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For added
convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`

36
doc/src/Commands_structure.rst
View File

@ -26,23 +26,23 @@ read-in from a file.
The relevant commands are :doc:`units <units>`,
:doc:`dimension <dimension>`, :doc:`newton <newton>`,
:doc:`processors <processors>`, :doc:`boundary <boundary>`,
:doc:`atom\_style <atom_style>`, :doc:`atom\_modify <atom_modify>`.
:doc:`atom_style <atom_style>`, :doc:`atom_modify <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 <pair_style>`, :doc:`bond\_style <bond_style>`,
:doc:`angle\_style <angle_style>`, :doc:`dihedral\_style <dihedral_style>`,
:doc:`improper\_style <improper_style>`.
:doc:`pair_style <pair_style>`, :doc:`bond_style <bond_style>`,
:doc:`angle_style <angle_style>`, :doc:`dihedral_style <dihedral_style>`,
:doc:`improper_style <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 <read_data>` or
:doc:`read\_restart <read_restart>` commands. These files can contain
or restart file via the :doc:`read_data <read_data>` or
:doc:`read_restart <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 <lattice>`,
:doc:`region <region>`, :doc:`create\_box <create_box>`,
:doc:`create\_atoms <create_atoms>`. The entire set of atoms can be
:doc:`region <region>`, :doc:`create_box <create_box>`,
:doc:`create_atoms <create_atoms>`. The entire set of atoms can be
duplicated to make a larger simulation using the
:doc:`replicate <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 <pair_coeff>`,
:doc:`bond\_coeff <bond_coeff>`, :doc:`angle\_coeff <angle_coeff>`,
:doc:`dihedral\_coeff <dihedral_coeff>`,
:doc:`improper\_coeff <improper_coeff>`,
:doc:`kspace\_style <kspace_style>`, :doc:`dielectric <dielectric>`,
:doc:`special\_bonds <special_bonds>`.
set in the read-in files): :doc:`pair_coeff <pair_coeff>`,
:doc:`bond_coeff <bond_coeff>`, :doc:`angle_coeff <angle_coeff>`,
:doc:`dihedral_coeff <dihedral_coeff>`,
:doc:`improper_coeff <improper_coeff>`,
:doc:`kspace_style <kspace_style>`, :doc:`dielectric <dielectric>`,
:doc:`special_bonds <special_bonds>`.
Various simulation parameters are set by these commands:
:doc:`neighbor <neighbor>`, :doc:`neigh\_modify <neigh_modify>`,
:doc:`neighbor <neighbor>`, :doc:`neigh_modify <neigh_modify>`,
:doc:`group <group>`, :doc:`timestep <timestep>`,
:doc:`reset\_timestep <reset_timestep>`, :doc:`run\_style <run_style>`,
:doc:`min\_style <min_style>`, :doc:`min\_modify <min_modify>`.
:doc:`reset_timestep <reset_timestep>`, :doc:`run_style <run_style>`,
:doc:`min_style <min_style>`, :doc:`min_modify <min_modify>`.
Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The :doc:`fix <fix>` command comes in many flavors.
Various computations can be specified for execution during a
simulation using the :doc:`compute <compute>`,
:doc:`compute\_modify <compute_modify>`, and :doc:`variable <variable>`
:doc:`compute_modify <compute_modify>`, and :doc:`variable <variable>`
commands.
Output options are set by the :doc:`thermo <thermo>`, :doc:`dump <dump>`,

2
doc/src/Errors_common.rst
View File

@ -18,7 +18,7 @@ the two simulations will rapidly diverge. See the discussion of the
*loop* option in the :doc:`velocity <velocity>` command for details and
options that avoid this issue.
Similarly, the :doc:`create\_atoms <create_atoms>` command generates a
Similarly, the :doc:`create_atoms <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.

6
doc/src/Errors_messages.rst
View File

@ -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 <neigh_modify>` command. The safest settings are
:doc:`neigh_modify <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 <neigh_modify>` command. The safest settings are
:doc:`neigh_modify <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 <neigh_modify>` command. The safest settings are
:doc:`neigh_modify <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

4
doc/src/Errors_warnings.rst
View File

@ -118,10 +118,10 @@ Doc page with :doc:`ERROR messages <Errors_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 <comm_modify>` (defaults to 0.0). If this results
via :doc:`comm_modify cutoff <comm_modify>` (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 <pair_zero>` with a suitable cutoff or use :doc:`comm\_modify cutoff <comm_modify>`.
:doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.
*Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
Self-explanatory.

2
doc/src/Howto_2d.rst
View File

@ -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 <atom_style>` and :doc:`fix nve/sphere <fix_nve_sphere>`
opposed to point particles. See the :doc:`atom_style sphere <atom_style>` and :doc:`fix nve/sphere <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

10
doc/src/Howto_barostat.rst
View File

@ -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 <fix_modify>` command for instructions on how to assign
:doc:`fix_modify <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 <thermo_style>` command, often includes pressure
:doc:`thermo_style <thermo_style>` command, often includes pressure
values. As explained on the doc page for the
:doc:`thermo\_style <thermo_style>` command, the default pressure is
:doc:`thermo_style <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 <thermo_style>` command.
Or you can use the :doc:`thermo\_modify <thermo_modify>` command to
explicitly via the :doc:`thermo_style custom <thermo_style>` command.
Or you can use the :doc:`thermo_modify <thermo_modify>` command to
re-define what pressure compute is used for default thermodynamic
output.

76
doc/src/Howto_bioFF.rst
View File

@ -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 <read_data>` command or in the input script with
commands like :doc:`pair\_coeff <pair_coeff>` or
:doc:`bond\_coeff <bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc
via the :doc:`read_data <read_data>` command or in the input script with
commands like :doc:`pair_coeff <pair_coeff>` or
:doc:`bond_coeff <bond_coeff>` and so on. See the :doc:`Tools <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 <bond_harmonic>` harmonic
* :doc:`angle\_style <angle_charmm>` charmm
* :doc:`dihedral\_style <dihedral_charmm>` charmmfsh
* :doc:`dihedral\_style <dihedral_charmm>` charmm
* :doc:`pair\_style <pair_charmm>` lj/charmmfsw/coul/charmmfsh
* :doc:`pair\_style <pair_charmm>` lj/charmmfsw/coul/long
* :doc:`pair\_style <pair_charmm>` lj/charmm/coul/charmm
* :doc:`pair\_style <pair_charmm>` lj/charmm/coul/charmm/implicit
* :doc:`pair\_style <pair_charmm>` lj/charmm/coul/long
* :doc:`bond_style <bond_harmonic>` harmonic
* :doc:`angle_style <angle_charmm>` charmm
* :doc:`dihedral_style <dihedral_charmm>` charmmfsh
* :doc:`dihedral_style <dihedral_charmm>` charmm
* :doc:`pair_style <pair_charmm>` lj/charmmfsw/coul/charmmfsh
* :doc:`pair_style <pair_charmm>` lj/charmmfsw/coul/long
* :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm
* :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm/implicit
* :doc:`pair_style <pair_charmm>` lj/charmm/coul/long
* :doc:`special\_bonds <special_bonds>` charmm
* :doc:`special\_bonds <special_bonds>` amber
* :doc:`special_bonds <special_bonds>` charmm
* :doc:`special_bonds <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 <bond_class2>` class2
* :doc:`angle\_style <angle_class2>` class2
* :doc:`dihedral\_style <dihedral_class2>` class2
* :doc:`improper\_style <improper_class2>` class2
* :doc:`bond_style <bond_class2>` class2
* :doc:`angle_style <angle_class2>` class2
* :doc:`dihedral_style <dihedral_class2>` class2
* :doc:`improper_style <improper_class2>` class2
* :doc:`pair\_style <pair_class2>` lj/class2
* :doc:`pair\_style <pair_class2>` lj/class2/coul/cut
* :doc:`pair\_style <pair_class2>` lj/class2/coul/long
* :doc:`pair_style <pair_class2>` lj/class2
* :doc:`pair_style <pair_class2>` lj/class2/coul/cut
* :doc:`pair_style <pair_class2>` lj/class2/coul/long
* :doc:`special\_bonds <special_bonds>` lj/coul 0 0 1
* :doc:`special_bonds <special_bonds>` lj/coul 0 0 1
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
@ -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 <bond_harmonic>` harmonic
* :doc:`bond\_style <bond_morse>` morse
* :doc:`bond_style <bond_harmonic>` harmonic
* :doc:`bond_style <bond_morse>` morse
* :doc:`angle\_style <angle_harmonic>` harmonic
* :doc:`angle\_style <angle_cosine>` cosine
* :doc:`angle\_style <angle_cosine_periodic>` cosine/periodic
* :doc:`angle_style <angle_harmonic>` harmonic
* :doc:`angle_style <angle_cosine>` cosine
* :doc:`angle_style <angle_cosine_periodic>` cosine/periodic
* :doc:`dihedral\_style <dihedral_charmm>` charmm
* :doc:`improper\_style <improper_umbrella>` umbrella
* :doc:`dihedral_style <dihedral_charmm>` charmm
* :doc:`improper_style <improper_umbrella>` umbrella
* :doc:`pair\_style <pair_buck>` buck
* :doc:`pair\_style <pair_buck>` buck/coul/cut
* :doc:`pair\_style <pair_buck>` buck/coul/long
* :doc:`pair\_style <pair_lj>` lj/cut
* :doc:`pair\_style <pair_lj>` lj/cut/coul/cut
* :doc:`pair\_style <pair_lj>` lj/cut/coul/long
* :doc:`pair_style <pair_buck>` buck
* :doc:`pair_style <pair_buck>` buck/coul/cut
* :doc:`pair_style <pair_buck>` buck/coul/long
* :doc:`pair_style <pair_lj>` lj/cut
* :doc:`pair_style <pair_lj>` lj/cut/coul/cut
* :doc:`pair_style <pair_lj>` lj/cut/coul/long
* :doc:`pair\_style <pair_hbond_dreiding>` hbond/dreiding/lj
* :doc:`pair\_style <pair_hbond_dreiding>` hbond/dreiding/morse
* :doc:`pair_style <pair_hbond_dreiding>` hbond/dreiding/lj
* :doc:`pair_style <pair_hbond_dreiding>` hbond/dreiding/morse
* :doc:`special\_bonds <special_bonds>` dreiding
* :doc:`special_bonds <special_bonds>` dreiding
----------

24
doc/src/Howto_body.rst
View File

@ -12,10 +12,10 @@ as spheres, ellipsoids, line segments, and triangles, but they are
simpler entities that body particles. See the :doc:`Howto spherical <Howto_spherical>` doc page for a general overview of all
these particle types.
Body particles are used via the :doc:`atom\_style body <atom_style>`
Body particles are used via the :doc:`atom_style body <atom_style>`
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 <atom_style>` command.
column is used as the *bstyle* argument for the :doc:`atom_style body <atom_style>` 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 <read_data>` command reads a data file for this
When the :doc:`read_data <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 <read_data>` command
as many lines as you wish; see the :doc:`read_data <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 <pair_body_nparticle>` command can be used
The :doc:`pair_style body/nparticle <pair_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 <compute_body_local>` and :doc:`dump local <dump>`
@ -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 <read_data>` command reads a data file for this
When the :doc:`read_data <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 <read_data>` command
as many lines as you wish; see the :doc:`read_data <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 <pair_body_rounded_polygon>`
The :doc:`pair_style body/rounded/polygon <pair_body_rounded_polygon>`
command can be used with this body style to compute body/body
interactions. The :doc:`fix wall/body/polygon <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 <read_data>` command reads a data file for this
When the :doc:`read_data <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 <read_data>` command for more details. Because the
:doc:`read_data <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 <pair_body_rounded_polyhedron>` command can
The :doc:`pair_style body/rounded/polhedron <pair_body_rounded_polyhedron>` command can
be used with this body style to compute body/body interactions. The
:doc:`fix wall/body/polyhedron <fix_wall_body_polygon>` 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 <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 <pair_body_rounded_polygon>` defines finite-size
physical extent of the body (because the :doc:`pair_style rounded/polygon <pair_body_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

16
doc/src/Howto_coreshell.rst
View File

@ -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 <atom_style>` *full* can
To run this model in LAMMPS, :doc:`atom_style <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 <special_bonds>` command should be used to
The :doc:`special_bonds <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 <special_bonds>` command with a 1-2 weight = 0.0,
:doc:`special_bonds <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 <special_bonds>` weighting according
to adjust the :doc:`special_bonds <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 <pair_cs>` 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 <kspace_style>` command. Either the PPPM or
by the :doc:`kspace_style <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*\ <group>` command.
Note that to perform thermostatting using this definition of
temperature, the :doc:`fix modify temp <fix_modify>` command should be
used to assign the compute to the thermostat fix. Likewise the
:doc:`thermo\_modify temp <thermo_modify>` command can be used to make
:doc:`thermo_modify temp <thermo_modify>` 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_pressure>` compute based on
the default :doc:`temperature <compute_temp>` and specifying it as a
second argument in :doc:`fix modify <fix_modify>` and
:doc:`thermo\_modify <thermo_modify>` resulting in:
:doc:`thermo_modify <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 <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 <read_data>` command. This field can then be
by the :doc:`read_data <read_data>` command. This field can then be
accessed by the :doc:`compute property/atom <compute_property_atom>`
command, to use as input to the :doc:`compute chunk/atom <compute_chunk_atom>` command to define the core/shell
pairs as chunks.

6
doc/src/Howto_drude.rst
View File

@ -39,19 +39,19 @@ specified via the :doc:`fix drude <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 <read_data>` command. If using :doc:`fix shake <fix_shake>`, make sure no Drude particle is in this fix
keyword of the :doc:`read_data <read_data>` command. If using :doc:`fix shake <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 <fix_langevin_drude>`
for a Langevin thermostat, or :doc:`fix drude/transform/\* <fix_drude_transform>` for a Nose-Hoover
thermostat. The former requires use of the command :doc:`comm\_modify vel yes <comm_modify>`. The latter requires two separate integration
thermostat. The former requires use of the command :doc:`comm_modify vel yes <comm_modify>`. 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 <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 <pair_thole>` in :doc:`pair\_style hybrid/overlay <pair_hybrid>`
using Thole functions through the :doc:`pair style thole <pair_thole>` in :doc:`pair_style hybrid/overlay <pair_hybrid>`
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.

2
doc/src/Howto_drude2.rst
View File

@ -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 <read_data>` or :doc:`create\_box <create_box>`
the :doc:`read_data <read_data>` or :doc:`create_box <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.

2
doc/src/Howto_elastic.rst
View File

@ -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 <change_box>` command and measuring the change in the
:doc:`change_box <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 <Examples>`
doc page.

10
doc/src/Howto_granular.rst
View File

@ -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 <atom_style>`
* :doc:`atom_style sphere <atom_style>`
* :doc:`fix nve/sphere <fix_nve_sphere>`
* :doc:`fix gravity <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 <pair_style>` gran/history
* :doc:`pair\_style <pair_style>` gran/no\_history
* :doc:`pair\_style <pair_style>` gran/hertzian
* :doc:`pair_style <pair_style>` gran/history
* :doc:`pair_style <pair_style>` gran/no\_history
* :doc:`pair_style <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 <neigh_modify>` exclude
* :doc:`neigh_modify <neigh_modify>` exclude
.. note::

16
doc/src/Howto_output.rst
View File

@ -88,21 +88,21 @@ Thermodynamic output
---------------------------------
The frequency and format of thermodynamic output is set by the
:doc:`thermo <thermo>`, :doc:`thermo\_style <thermo_style>`, and
:doc:`thermo\_modify <thermo_modify>` commands. The
:doc:`thermo\_style <thermo_style>` command also specifies what values
:doc:`thermo <thermo>`, :doc:`thermo_style <thermo_style>`, and
:doc:`thermo_modify <thermo_modify>` commands. The
:doc:`thermo_style <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 <compute>`
or :doc:`fix <fix>` or :doc:`variable <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 <dump>`
global values for input to the :doc:`thermo_style custom <dump>`
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 <thermo_modify>` determines whether
setting for :doc:`thermo_modify norm <thermo_modify>` 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 <variable>` produce only
@ -116,7 +116,7 @@ Dump file output
---------------------------
Dump file output is specified by the :doc:`dump <dump>` and
:doc:`dump\_modify <dump_modify>` commands. There are several
:doc:`dump_modify <dump_modify>` commands. There are several
pre-defined formats (dump atom, dump xtc, etc).
There is also a :doc:`dump custom <dump>` format where the user
@ -151,7 +151,7 @@ specifies one or more quantities as input. These can be global
:doc:`compute <compute>` values, global :doc:`fix <fix>` values, or
:doc:`variables <variable>` 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 <thermo_style>` command (like temp or
by the :doc:`thermo_style custom <thermo_style>` 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 <thermo_style>` | global scalars | screen, log file |
| :doc:`thermo_style custom <thermo_style>` | global scalars | screen, log file |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`dump custom <dump>` | per-atom vectors | dump file |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+

2
doc/src/Howto_replica.rst
View File

@ -9,7 +9,7 @@ periodically.
These are the relevant commands:
* :doc:`neb <neb>` for nudged elastic band calculations
* :doc:`neb\_spin <neb_spin>` for magnetic nudged elastic band calculations
* :doc:`neb_spin <neb_spin>` for magnetic nudged elastic band calculations
* :doc:`prd <prd>` for parallel replica dynamics
* :doc:`tad <tad>` for temperature accelerated dynamics
* :doc:`temper <temper>` for parallel tempering

10
doc/src/Howto_restart.rst
View File

@ -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 <restart>`
command. At a later time, these binary files can be read via a
:doc:`read\_restart <read_restart>` command in a new script. Or they can
be converted to text data files using the :doc:`-r command-line switch <Run_options>` and read by a :doc:`read\_data <read_data>`
:doc:`read_restart <read_restart>` command in a new script. Or they can
be converted to text data files using the :doc:`-r command-line switch <Run_options>` and read by a :doc:`read_data <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 <read_restart>` and
:doc:`read\_data <read_data>` commands.
documentation for the :doc:`read_restart <read_restart>` and
:doc:`read_data <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 <reset_timestep>` command is used to tell
Also, the :doc:`reset_timestep <reset_timestep>` command is used to tell
LAMMPS the current timestep. This value is stored in restart files,
but not in data files.

36
doc/src/Howto_spherical.rst
View File

@ -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 <atom_style>` command for details. The "set" command can be
inertia) in order to respond and rotate. See the :doc:`atom_style dipole <atom_style>` 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 <pair_peri>` and
defines particles as having a volume, that is used internally in the
:doc:`pair\_style peri <pair_peri>` potentials.
:doc:`pair_style peri <pair_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 <Howto_body>` doc
page.
Note that if one of these atom styles is used (or multiple styles via
the :doc:`atom\_style hybrid <atom_style>` command), not all particles in
the :doc:`atom_style hybrid <atom_style>` 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 <pair_hybrid>` can be used to insure the correct
:doc:`pair_style hybrid <pair_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 <pair_style>` that generate torque:
* :doc:`pair\_style gran/history <pair_gran>`
* :doc:`pair\_style gran/hertzian <pair_gran>`
* :doc:`pair\_style gran/no\_history <pair_gran>`
* :doc:`pair\_style dipole/cut <pair_dipole>`
* :doc:`pair\_style gayberne <pair_gayberne>`
* :doc:`pair\_style resquared <pair_resquared>`
* :doc:`pair\_style brownian <pair_brownian>`
* :doc:`pair\_style lubricate <pair_lubricate>`
* :doc:`pair\_style line/lj <pair_line_lj>`
* :doc:`pair\_style tri/lj <pair_tri_lj>`
* :doc:`pair\_style body/nparticle <pair_body_nparticle>`
* :doc:`pair_style gran/history <pair_gran>`
* :doc:`pair_style gran/hertzian <pair_gran>`
* :doc:`pair_style gran/no\_history <pair_gran>`
* :doc:`pair_style dipole/cut <pair_dipole>`
* :doc:`pair_style gayberne <pair_gayberne>`
* :doc:`pair_style resquared <pair_resquared>`
* :doc:`pair_style brownian <pair_brownian>`
* :doc:`pair_style lubricate <pair_lubricate>`
* :doc:`pair_style line/lj <pair_line_lj>`
* :doc:`pair_style tri/lj <pair_tri_lj>`
* :doc:`pair_style body/nparticle <pair_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 <thermo_modify>` command used. Note that by default
:doc:`thermo_modify <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 <thermo_style>` command for details.
:doc:`thermo_style <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 <fix_ri
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 :doc:`fix nve/body <fix_nve_body>`. Interactions between pairs of body
particles are computed via a command like :doc:`pair\_style body/nparticle <pair_body_nparticle>`.
particles are computed via a command like :doc:`pair_style body/nparticle <pair_body_nparticle>`.
.. _lws: http://lammps.sandia.gov

12
doc/src/Howto_thermostat.rst
View File

@ -23,7 +23,7 @@ can be invoked via the *dpd/tstat* pair style:
* :doc:`fix temp/csvr <fix_temp_csvr>`
* :doc:`fix langevin <fix_langevin>`
* :doc:`fix temp/rescale <fix_temp_rescale>`
* :doc:`pair\_style dpd/tstat <pair_dpd>`
* :doc:`pair_style dpd/tstat <pair_dpd>`
:doc:`Fix nvt <fix_nh>` only thermostats the translational velocity of
particles. :doc:`Fix nvt/sllod <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 <fix_modify>` command for
fixes and for the :doc:`fix_modify <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 <fix_nve_asphere>`
Thermodynamic output, which can be setup via the
:doc:`thermo\_style <thermo_style>` command, often includes temperature
:doc:`thermo_style <thermo_style>` command, often includes temperature
values. As explained on the doc page for the
:doc:`thermo\_style <thermo_style>` command, the default temperature is
:doc:`thermo_style <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 <thermo_style>` command. Or you can use the
:doc:`thermo\_modify <thermo_modify>` command to re-define what
specify them explicitly via the :doc:`thermo_style custom <thermo_style>` command. Or you can use the
:doc:`thermo_modify <thermo_modify>` command to re-define what
temperature compute is used for default thermodynamic output.

10
doc/src/Howto_tip4p.rst
View File

@ -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 <pair_lj>`
:doc:`pair_style lj/cut/tip4p/cut <pair_lj>`
or these two commands for a long-range model:
* :doc:`pair\_style lj/cut/tip4p/long <pair_lj>`
* :doc:`kspace\_style pppm/tip4p <kspace_style>`
* :doc:`pair_style lj/cut/tip4p/long <pair_lj>`
* :doc:`kspace_style pppm/tip4p <kspace_style>`
For both models, the bond lengths and bond angles should be held fixed
using the :doc:`fix shake <fix_shake>` command.
@ -24,7 +24,7 @@ using the :doc:`fix shake <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) <Jorgensen5>`. Note that the OM distance is specified in
the :doc:`pair\_style <pair_style>` command, not as part of the pair
the :doc:`pair_style <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 <pair_lj>` command.
and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj>` command.
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.

24
doc/src/Howto_triclinic.rst
View File

@ -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 <create_box>` or
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
is created, e.g. by the :doc:`create_box <create_box>` or
:doc:`read_data <read_data>` or :doc:`read_restart <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 <thermo_style>` command.
parameters, as well as lx,ly,lz, can be output via the :doc:`thermo_style custom <thermo_style>` 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 <create_box>` command is used with a region of
If the :doc:`create_box <create_box>` command is used with a region of
style *prism*\ , then a triclinic box is setup. See the
:doc:`region <region>` command for details. If the
:doc:`read\_data <read_data>` command is used to define the simulation
:doc:`read_data <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 <read_data>` command for details. Finally, if the
:doc:`read\_restart <read_restart>` command reads a restart file which
:doc:`read_data <read_data>` command for details. Finally, if the
:doc:`read_restart <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 <fix_nh>` or
:doc:`fix deform <fix_deform>` commands. Alternatively, you can use the
:doc:`change\_box <change_box>` command to convert a simulation box from
:doc:`change_box <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 <thermo_style>` command.
:doc:`thermo_style custom <thermo_style>` 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 <create_box>` or :doc:`read\_data <read_data>` commands,
:doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands,
as well as when the box shape changes dynamically during a simulation,
e.g. via the :doc:`fix deform <fix_deform>` or :doc:`fix npt <fix_nh>`
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 <thermo_style>` keywords
:doc:`thermo_style custom <thermo_style>` 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 <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 <create_atoms>` command.
:doc:`create_atoms <create_atoms>` command.
A second use is to run Parrinello-Rahman dynamics via the :doc:`fix npt <fix_nh>` command, which will adjust the xy, xz, yz tilt
factors to compensate for off-diagonal components of the pressure

10
doc/src/Howto_walls.rst
View File

@ -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 <lattice>` and :doc:`create\_atoms <create_atoms>` commands,
or read in via the :doc:`read\_data <read_data>` command.
:doc:`lattice <lattice>` and :doc:`create_atoms <create_atoms>` commands,
or read in via the :doc:`read_data <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 <neigh_modify>` command.
between wall particles via the :doc:`neigh_modify exclude <neigh_modify>` 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 <fix_wall_reflect>` - reflective flat walls
* :doc:`fix wall/lj93 <fix_wall>` - flat walls, with Lennard-Jones 9/3 potential
* :doc:`fix wall/lj126 <fix_wall>` - flat walls, with Lennard-Jones 12/6 potential
* :doc:`fix wall/colloid <fix_wall>` - flat walls, with :doc:`pair\_style colloid <pair_colloid>` potential
* :doc:`fix wall/colloid <fix_wall>` - flat walls, with :doc:`pair_style colloid <pair_colloid>` potential
* :doc:`fix wall/harmonic <fix_wall>` - flat walls, with repulsive harmonic spring potential
* :doc:`fix wall/morse <fix_wall>` - flat walls, with Morse potential
* :doc:`fix wall/region <fix_wall_region>` - use region surface as wall
* :doc:`fix wall/gran <fix_wall_gran>` - flat or curved walls with :doc:`pair\_style granular <pair_gran>` potential
* :doc:`fix wall/gran <fix_wall_gran>` - flat or curved walls with :doc:`pair_style granular <pair_gran>` potential
The *lj93*\ , *lj126*\ , *colloid*\ , *harmonic*\ , and *morse* styles all
allow the flat walls to move with a constant velocity, or oscillate in

8
doc/src/Intro_features.rst
View File

@ -96,9 +96,9 @@ commands)
Atom creation
--------------------------
(:doc:`read\_data <read_data>`, :doc:`lattice <lattice>`,
:doc:`create\_atoms <create_atoms>`, :doc:`delete\_atoms <delete_atoms>`,
:doc:`displace\_atoms <displace_atoms>`, :doc:`replicate <replicate>` commands)
(:doc:`read_data <read_data>`, :doc:`lattice <lattice>`,
:doc:`create_atoms <create_atoms>`, :doc:`delete_atoms <delete_atoms>`,
:doc:`displace_atoms <displace_atoms>`, :doc:`replicate <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 <run>`, :doc:`run\_style <run_style>`, :doc:`minimize <minimize>` commands)
(:doc:`run <run>`, :doc:`run_style <run_style>`, :doc:`minimize <minimize>` commands)
* velocity-Verlet integrator
* Brownian dynamics

2
doc/src/Modify_fix.rst
View File

@ -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 <run_style>`
constraint fix to work with rRESPA (see the :doc:`run_style <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

4
doc/src/Modify_thermo.rst
View File

@ -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 <thermo_style>` command for a list
output. See the :doc:`thermo_style <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 <thermo>` command already allows
Note that the :doc:`thermo_style custom <thermo>` command already allows
for thermo output of quantities calculated by :doc:`fixes <fix>`,
:doc:`computes <compute>`, and :doc:`variables <variable>`. Thus, it may
be simpler to compute what you wish via one of those constructs, than

4
doc/src/Modify_variable.rst
View File

@ -5,7 +5,7 @@ There is one class that computes and stores :doc:`variable <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 <print>`, :doc:`fix print <fix_print>`, or
:doc:`thermo\_style custom <thermo_style>` commands. Variables of style
:doc:`thermo_style custom <thermo_style>` 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 <thermo_style>`
Adding keywords for the :doc:`thermo_style custom <thermo_style>`
command (which can then be accessed by variables) is discussed on the
:doc:`Modify thermo <Modify_thermo>` doc page.

196
doc/src/Packages_details.rst
View File

@ -72,8 +72,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
* src/ASPHERE: filenames -> commands
* :doc:`Howto spherical <Howto_spherical>`
* :doc:`pair\_style gayberne <pair_gayberne>`
* :doc:`pair\_style resquared <pair_resquared>`
* :doc:`pair_style gayberne <pair_gayberne>`
* :doc:`pair_style resquared <pair_resquared>`
* `doc/PDF/pair\_gayberne\_extra.pdf <PDF/pair_gayberne_extra.pdf>`_
* `doc/PDF/pair\_resquared\_extra.pdf <PDF/pair_resquared_extra.pdf>`_
* examples/ASPHERE
@ -101,9 +101,9 @@ overview.
* src/BODY filenames -> commands
* :doc:`Howto\_body <Howto_body>`
* :doc:`atom\_style body <atom_style>`
* :doc:`atom_style body <atom_style>`
* :doc:`fix nve/body <fix_nve_body>`
* :doc:`pair\_style body/nparticle <pair_body_nparticle>`
* :doc:`pair_style body/nparticle <pair_body_nparticle>`
* examples/body
@ -123,11 +123,11 @@ CLASS2 molecular force field.
**Supporting info:**
* src/CLASS2: filenames -> commands
* :doc:`bond\_style class2 <bond_class2>`
* :doc:`angle\_style class2 <angle_class2>`
* :doc:`dihedral\_style class2 <dihedral_class2>`
* :doc:`improper\_style class2 <improper_class2>`
* :doc:`pair\_style lj/class2 <pair_class2>`
* :doc:`bond_style class2 <bond_class2>`
* :doc:`angle_style class2 <angle_class2>`
* :doc:`dihedral_style class2 <dihedral_class2>`
* :doc:`improper_style class2 <improper_class2>`
* :doc:`pair_style lj/class2 <pair_class2>`
----------
@ -153,11 +153,11 @@ Higdon's group at UIUC.
* src/COLLOID: filenames -> commands
* :doc:`fix wall/colloid <fix_wall>`
* :doc:`pair\_style colloid <pair_colloid>`
* :doc:`pair\_style yukawa/colloid <pair_yukawa_colloid>`
* :doc:`pair\_style brownian <pair_brownian>`
* :doc:`pair\_style lubricate <pair_lubricate>`
* :doc:`pair\_style lubricateU <pair_lubricateU>`
* :doc:`pair_style colloid <pair_colloid>`
* :doc:`pair_style yukawa/colloid <pair_yukawa_colloid>`
* :doc:`pair_style brownian <pair_brownian>`
* :doc:`pair_style lubricate <pair_lubricate>`
* :doc:`pair_style lubricateU <pair_lubricateU>`
* examples/colloid
* examples/srd
@ -219,9 +219,9 @@ this package.
* :doc:`Howto coreshell <Howto_coreshell>`
* :doc:`Howto polarizable <Howto_polarizable>`
* :doc:`compute temp/cs <compute_temp_cs>`
* :doc:`pair\_style born/coul/long/cs <pair_cs>`
* :doc:`pair\_style buck/coul/long/cs <pair_cs>`
* :doc:`pair\_style lj/cut/coul/long/cs <pair_lj>`
* :doc:`pair_style born/coul/long/cs <pair_cs>`
* :doc:`pair_style buck/coul/long/cs <pair_cs>`
* :doc:`pair_style lj/cut/coul/long/cs <pair_lj>`
* examples/coreshell
@ -241,10 +241,10 @@ short-range or long-range interactions.
**Supporting info:**
* src/DIPOLE: filenames -> commands
* :doc:`atom\_style dipole <atom_style>`
* :doc:`pair\_style lj/cut/dipole/cut <pair_dipole>`
* :doc:`pair\_style lj/cut/dipole/long <pair_dipole>`
* :doc:`pair\_style lj/long/dipole/long <pair_dipole>`
* :doc:`atom_style dipole <atom_style>`
* :doc:`pair_style lj/cut/dipole/cut <pair_dipole>`
* :doc:`pair_style lj/cut/dipole/long <pair_dipole>`
* :doc:`pair_style lj/long/dipole/long <pair_dipole>`
* examples/dipole
@ -309,8 +309,8 @@ potentials.
* :doc:`Howto granular <Howto_granular>`
* :doc:`fix pour <fix_pour>`
* :doc:`fix wall/gran <fix_wall_gran>`
* :doc:`pair\_style gran/hooke <pair_gran>`
* :doc:`pair\_style gran/hertz/history <pair_gran>`
* :doc:`pair_style gran/hooke <pair_gran>`
* :doc:`pair_style gran/hertz/history <pair_gran>`
* 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) <https://openkim.org>`_
repository of interatomic models (IMs)
enabling compatible ones to be used in LAMMPS simulations.
This includes :doc:`kim\_init and kim\_interactions <kim_commands>`
This includes :doc:`kim_init and kim\_interactions <kim_commands>`
commands to select, initialize and instantiate the IM, and a
:doc:`kim\_query <kim_commands>` command to perform web queries
:doc:`kim_query <kim_commands>` 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) <https://openkim.org/kim-api/>`_
is provided by the :doc:`pair\_style kim <pair_kim>` command.
is provided by the :doc:`pair_style kim <pair_kim>` command.
.. note::
@ -361,7 +361,7 @@ and is funded by the `National Science Foundation <https://www.nsf.gov/>`_.
**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 <kim_commands>`
Ellad Tadmor (U Minnesota) contributed to the :doc:`kim_commands <kim_commands>`
interface in close collaboration with Ryan Elliott.
**Install:**
@ -370,8 +370,8 @@ This package has :ref:`specific installation instructions <kim>` on the :doc:`Bu
**Supporting info:**
* :doc:`kim\_commands <kim_commands>`
* :doc:`pair\_style kim <pair_kim>`
* :doc:`kim_commands <kim_commands>`
* :doc:`pair_style kim <pair_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 <kspace_style>`
* :doc:`kspace_style <kspace_style>`
* `doc/PDF/kspace.pdf <PDF/kspace.pdf>`_
* :doc:`Howto tip3p <Howto_tip3p>`
* :doc:`Howto tip4p <Howto_tip4p>`
* :doc:`Howto spc <Howto_spc>`
* :doc:`pair\_style coul <pair_coul>`
* :doc:`pair_style coul <pair_coul>`
* :doc:`Commands pair <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 <fix_bond_create>`
* :doc:`fix bond/swap <fix_bond_swap>`
* :doc:`fix gcmc <fix_gcmc>`
* :doc:`pair\_style dsmc <pair_dsmc>`
* :doc:`pair_style dsmc <pair_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 <atom_style>`
* :doc:`bond\_style <bond_style>`
* :doc:`angle\_style <angle_style>`
* :doc:`dihedral\_style <dihedral_style>`
* :doc:`improper\_style <improper_style>`
* :doc:`pair\_style hbond/dreiding/lj <pair_hbond_dreiding>`
* :doc:`pair\_style lj/charmm/coul/charmm <pair_charmm>`
* :doc:`atom_style <atom_style>`
* :doc:`bond_style <bond_style>`
* :doc:`angle_style <angle_style>`
* :doc:`dihedral_style <dihedral_style>`
* :doc:`improper_style <improper_style>`
* :doc:`pair_style hbond/dreiding/lj <pair_hbond_dreiding>`
* :doc:`pair_style lj/charmm/coul/charmm <pair_charmm>`
* :doc:`Howto bioFF <Howto_bioFF>`
* examples/cmap
* examples/dreiding
@ -678,8 +678,8 @@ written and read in parallel.
* src/MPIIO: filenames -> commands
* :doc:`dump <dump>`
* :doc:`restart <restart>`
* :doc:`write\_restart <write_restart>`
* :doc:`read\_restart <read_restart>`
* :doc:`write_restart <write_restart>`
* :doc:`read_restart <read_restart>`
----------
@ -779,8 +779,8 @@ Foster (UTSA).
* `doc/PDF/PDLammps\_overview.pdf <PDF/PDLammps_overview.pdf>`_
* `doc/PDF/PDLammps\_EPS.pdf <PDF/PDLammps_EPS.pdf>`_
* `doc/PDF/PDLammps\_VES.pdf <PDF/PDLammps_VES.pdf>`_
* :doc:`atom\_style peri <atom_style>`
* :doc:`pair\_style peri/\* <pair_peri>`
* :doc:`atom_style peri <atom_style>`
* :doc:`pair_style peri/\* <pair_peri>`
* :doc:`compute damage/atom <compute_damage_atom>`
* :doc:`compute plasticity/atom <compute_plasticity_atom>`
* examples/peri
@ -902,7 +902,7 @@ another set.
* :doc:`prd <prd>`
* :doc:`tad <tad>`
* :doc:`temper <temper>`,
* :doc:`run\_style verlet/split <run_style>`
* :doc:`run_style verlet/split <run_style>`
* 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 <pair_snap>`
* :doc:`pair_style snap <pair_snap>`
* :doc:`compute sna/atom <compute_sna_atom>`
* :doc:`compute snad/atom <compute_sna_atom>`
* :doc:`compute snav/atom <compute_sna_atom>`
@ -1007,12 +1007,12 @@ the usual manner via MD. Various pair, fix, and compute styles.
* src/SPIN: filenames -> commands
* :doc:`Howto spins <Howto_spins>`
* :doc:`pair\_style spin/dipole/cut <pair_spin_dipole>`
* :doc:`pair\_style spin/dipole/long <pair_spin_dipole>`
* :doc:`pair\_style spin/dmi <pair_spin_dmi>`
* :doc:`pair\_style spin/exchange <pair_spin_exchange>`
* :doc:`pair\_style spin/magelec <pair_spin_magelec>`
* :doc:`pair\_style spin/neel <pair_spin_neel>`
* :doc:`pair_style spin/dipole/cut <pair_spin_dipole>`
* :doc:`pair_style spin/dipole/long <pair_spin_dipole>`
* :doc:`pair_style spin/dmi <pair_spin_dmi>`
* :doc:`pair_style spin/exchange <pair_spin_exchange>`
* :doc:`pair_style spin/magelec <pair_spin_magelec>`
* :doc:`pair_style spin/neel <pair_spin_neel>`
* :doc:`fix nve/spin <fix_nve_spin>`
* :doc:`fix precession/spin <fix_precession_spin>`
* :doc:`compute spin <compute_spin>`
@ -1172,7 +1172,7 @@ This package has :ref:`specific installation instructions <user-awpmd>` on the :
* src/USER-AWPMD: filenames -> commands
* src/USER-AWPMD/README
* :doc:`pair\_style awpmd/cut <pair_awpmd>`
* :doc:`pair_style awpmd/cut <pair_awpmd>`
* examples/USER/awpmd
@ -1233,10 +1233,10 @@ stability.
* src/USER-CGDNA: filenames -> commands
* /src/USER-CGDNA/README
* :doc:`pair\_style oxdna/\* <pair_oxdna>`
* :doc:`pair\_style oxdna2/\* <pair_oxdna2>`
* :doc:`bond\_style oxdna/\* <bond_oxdna>`
* :doc:`bond\_style oxdna2/\* <bond_oxdna>`
* :doc:`pair_style oxdna/\* <pair_oxdna>`
* :doc:`pair_style oxdna2/\* <pair_oxdna2>`
* :doc:`bond_style oxdna/\* <bond_oxdna>`
* :doc:`bond_style oxdna2/\* <bond_oxdna>`
* :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
@ -1261,8 +1261,8 @@ acids.
* src/USER-CGSDK: filenames -> commands
* src/USER-CGSDK/README
* :doc:`pair\_style lj/sdk/\* <pair_sdk>`
* :doc:`angle\_style sdk <angle_sdk>`
* :doc:`pair_style lj/sdk/\* <pair_sdk>`
* :doc:`angle_style sdk <angle_sdk>`
* examples/USER/cgsdk
* http://lammps.sandia.gov/pictures.html#cg
@ -1397,12 +1397,12 @@ Brennan (ARL).
* :doc:`fix eos/table/rx <fix_eos_table_rx>`
* :doc:`fix shardlow <fix_shardlow>`
* :doc:`fix rx <fix_rx>`
* :doc:`pair\_style table/rx <pair_table_rx>`
* :doc:`pair\_style dpd/fdt <pair_dpd_fdt>`
* :doc:`pair\_style dpd/fdt/energy <pair_dpd_fdt>`
* :doc:`pair\_style exp6/rx <pair_exp6_rx>`
* :doc:`pair\_style multi/lucy <pair_multi_lucy>`
* :doc:`pair\_style multi/lucy/rx <pair_multi_lucy_rx>`
* :doc:`pair_style table/rx <pair_table_rx>`
* :doc:`pair_style dpd/fdt <pair_dpd_fdt>`
* :doc:`pair_style dpd/fdt/energy <pair_dpd_fdt>`
* :doc:`pair_style exp6/rx <pair_exp6_rx>`
* :doc:`pair_style multi/lucy <pair_multi_lucy>`
* :doc:`pair_style multi/lucy/rx <pair_multi_lucy_rx>`
* examples/USER/dpd
@ -1434,8 +1434,8 @@ Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
* :doc:`fix drude <fix_drude>`
* :doc:`fix drude/transform/\* <fix_drude_transform>`
* :doc:`compute temp/drude <compute_temp_drude>`
* :doc:`pair\_style thole <pair_thole>`
* :doc:`pair\_style lj/cut/thole/long <pair_thole>`
* :doc:`pair_style thole <pair_thole>`
* :doc:`pair_style lj/cut/thole/long <pair_thole>`
* 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 <atom_style>`
* :doc:`atom_style electron <atom_style>`
* :doc:`fix nve/eff <fix_nve_eff>`
* :doc:`fix nvt/eff <fix_nh_eff>`
* :doc:`fix npt/eff <fix_nh_eff>`
* :doc:`fix langevin/eff <fix_langevin_eff>`
* :doc:`compute temp/eff <compute_temp_eff>`
* :doc:`pair\_style eff/cut <pair_eff>`
* :doc:`pair\_style eff/inline <pair_eff>`
* :doc:`pair_style eff/cut <pair_eff>`
* :doc:`pair_style eff/inline <pair_eff>`
* 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 <fix_adapt_fep>`
* :doc:`compute fep <compute_fep>`
* :doc:`pair\_style \*/soft <pair_fep_soft>`
* :doc:`pair_style \*/soft <pair_fep_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 <pair_mgpt>`
* :doc:`pair_style mgpt <pair_mgpt>`
* examples/USER/mgpt
@ -1729,7 +1729,7 @@ Sandia.
* src/USER-MEAMC: filenames -> commands
* src/USER-MEAMC/README
* :doc:`pair\_style meam/c <pair_meamc>`
* :doc:`pair_style meam/c <pair_meamc>`
* examples/meamc
@ -1757,10 +1757,10 @@ algorithm.
* src/USER-MESO: filenames -> commands
* src/USER-MESO/README
* :doc:`atom\_style edpd <atom_style>`
* :doc:`pair\_style edpd <pair_meso>`
* :doc:`pair\_style mdpd <pair_meso>`
* :doc:`pair\_style tdpd <pair_meso>`
* :doc:`atom_style edpd <atom_style>`
* :doc:`pair_style edpd <pair_meso>`
* :doc:`pair_style mdpd <pair_meso>`
* :doc:`pair_style tdpd <pair_meso>`
* :doc:`fix mvv/dpd <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 <pair_buck6d_coul_gauss>`
* :doc:`angle\_style class2 <angle_class2>`
* :doc:`angle\_style cosine/buck6d <angle_cosine_buck6d>`
* :doc:`improper\_style inversion/harmonic <improper_inversion_harmonic>`
* :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>`
* :doc:`angle_style class2 <angle_class2>`
* :doc:`angle_style cosine/buck6d <angle_cosine_buck6d>`
* :doc:`improper_style inversion/harmonic <improper_inversion_harmonic>`
* examples/USER/mofff
@ -1965,8 +1965,8 @@ USER-PHONON package
A :doc:`fix phonon <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 <dynamical_matrix>` as well as a
:doc:`third\_order <third_order>` command to compute the dynamical matrix
And a :doc:`dynamical_matrix <dynamical_matrix>` as well as a
:doc:`third_order <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 <fix_phonon>`
* :doc:`dynamical\_matrix <dynamical_matrix>`
* :doc:`third\_order <third_order>`
* :doc:`dynamical_matrix <dynamical_matrix>`
* :doc:`third_order <third_order>`
* examples/USER/phonon
@ -2088,7 +2088,7 @@ USER-QUIP package
**Contents:**
A :doc:`pair\_style quip <pair_quip>` command which wraps the `QUIP libAtoms library <quip_>`_, which includes a variety of interatomic
A :doc:`pair_style quip <pair_quip>` command which wraps the `QUIP libAtoms library <quip_>`_, 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 <user-quip>` on the :d
* src/USER-QUIP: filenames -> commands
* src/USER-QUIP/README
* :doc:`pair\_style quip <pair_quip>`
* :doc:`pair_style quip <pair_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 <pair_reaxc>`
* :doc:`pair_style reax/c <pair_reaxc>`
* :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
* :doc:`fix reax/c/species <fix_reaxc_species>`
* examples/reax
@ -2172,8 +2172,8 @@ This package has :ref:`specific installation instructions <user-scafacos>` on th
* src/USER-SCAFACOS: filenames -> commands
* src/USER-SCAFACOS/README
* :doc:`kspace\_style scafacos <kspace_style>`
* :doc:`kspace\_modify <kspace_modify>`
* :doc:`kspace_style scafacos <kspace_style>`
* :doc:`kspace_modify <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 <pair_sdpd_taitwater_isothermal>`
* :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
* :doc:`fix meso/move <fix_meso_move>`
* :doc:`fix rigid/meso <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 <pair_smtbq>`
* :doc:`pair_style smtbq <pair_smtbq>`
* examples/USER/smtbq
@ -2438,13 +2438,13 @@ which discuss the `QuickFF <quickff_>`_ methodology.
**Supporting info:**
* src/USER-YAFF/README
* :doc:`angle\_style cross <angle_cross>`
* :doc:`angle\_style mm3 <angle_mm3>`
* :doc:`bond\_style mm3 <bond_mm3>`
* :doc:`improper\_style distharm <improper_distharm>`
* :doc:`improper\_style sqdistharm <improper_sqdistharm>`
* :doc:`pair\_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
* :doc:`pair\_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`angle_style cross <angle_cross>`
* :doc:`angle_style mm3 <angle_mm3>`
* :doc:`bond_style mm3 <bond_mm3>`
* :doc:`improper_style distharm <improper_distharm>`
* :doc:`improper_style sqdistharm <improper_sqdistharm>`
* :doc:`pair_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
* :doc:`pair_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* examples/USER/yaff

16
doc/src/Packages_standard.rst
View File

@ -29,29 +29,29 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`BODY <PKG-BODY>` | body-style particles | :doc:`Howto body <Howto_body>` | body | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`CLASS2 <PKG-CLASS2>` | class 2 force fields | :doc:`pair\_style lj/class2 <pair_class2>` | n/a | no |
| :ref:`CLASS2 <PKG-CLASS2>` | class 2 force fields | :doc:`pair_style lj/class2 <pair_class2>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`COLLOID <PKG-COLLOID>` | colloidal particles | :doc:`atom\_style colloid <atom_style>` | colloid | no |
| :ref:`COLLOID <PKG-COLLOID>` | colloidal particles | :doc:`atom_style colloid <atom_style>` | colloid | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`COMPRESS <PKG-COMPRESS>` | I/O compression | :doc:`dump \*/gz <dump>` | n/a | sys |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`CORESHELL <PKG-CORESHELL>` | adiabatic core/shell model | :doc:`Howto coreshell <Howto_coreshell>` | coreshell | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair\_style dipole/cut <pair_dipole>` | dipole | no |
| :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair_style dipole/cut <pair_dipole>` | dipole | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`GRANULAR <PKG-GRANULAR>` | granular systems | :doc:`Howto granular <Howto_granular>` | pour | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`KIM <PKG-KIM>` | OpenKIM wrapper | :doc:`pair\_style kim <pair_kim>` | kim | ext |
| :ref:`KIM <PKG-KIM>` | OpenKIM wrapper | :doc:`pair_style kim <pair_kim>` | kim | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`KOKKOS <PKG-KOKKOS>` | Kokkos-enabled styles | :doc:`Speed kokkos <Speed_kokkos>` | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`KSPACE <PKG-KSPACE>` | long-range Coulombic solvers | :doc:`kspace\_style <kspace_style>` | peptide | no |
| :ref:`KSPACE <PKG-KSPACE>` | long-range Coulombic solvers | :doc:`kspace_style <kspace_style>` | peptide | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`LATTE <PKG-LATTE>` | quantum DFTB forces via LATTE | :doc:`fix latte <fix_latte>` | latte | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`MANYBODY <PKG-MANYBODY>` | many-body potentials | :doc:`pair\_style tersoff <pair_tersoff>` | shear | no |
| :ref:`MANYBODY <PKG-MANYBODY>` | many-body potentials | :doc:`pair_style tersoff <pair_tersoff>` | shear | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`MC <PKG-MC>` | Monte Carlo options | :doc:`fix gcmc <fix_gcmc>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
@ -67,7 +67,7 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`OPT <PKG-OPT>` | optimized pair styles | :doc:`Speed opt <Speed_opt>` | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair\_style peri <pair_peri>` | peri | no |
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`POEMS <PKG-POEMS>` | coupled rigid body motion | :doc:`fix poems <fix_poems>` | rigid | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
@ -81,7 +81,7 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`SHOCK <PKG-SHOCK>` | shock loading methods | :doc:`fix msst <fix_msst>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`SNAP <PKG-SNAP>` | quantum-fitted potential | :doc:`pair\_style snap <pair_snap>` | snap | no |
| :ref:`SNAP <PKG-SNAP>` | quantum-fitted potential | :doc:`pair_style snap <pair_snap>` | snap | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`SPIN <PKG-SPIN>` | magnetic atomic spin dynamics | :doc:`Howto spins <Howto_spins>` | SPIN | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+

32
doc/src/Packages_user.rst
View File

@ -35,13 +35,13 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-ATC <PKG-USER-ATC>` | Atom-to-Continuum coupling | :doc:`fix atc <fix_atc>` | USER/atc | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-AWPMD <PKG-USER-AWPMD>` | wave packet MD | :doc:`pair\_style awpmd/cut <pair_awpmd>` | USER/awpmd | int |
| :ref:`USER-AWPMD <PKG-USER-AWPMD>` | wave packet MD | :doc:`pair_style awpmd/cut <pair_awpmd>` | USER/awpmd | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-BOCS <PKG-USER-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-CGDNA <PKG-USER-CGDNA>` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-CGSDK <PKG-USER-CGSDK>` | SDK coarse-graining model | :doc:`pair\_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
| :ref:`USER-CGSDK <PKG-USER-CGSDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-COLVARS <PKG-USER-COLVARS>` | collective variables library | :doc:`fix colvars <fix_colvars>` | USER/colvars | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
@ -51,7 +51,7 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-DRUDE <PKG-USER-DRUDE>` | Drude oscillators | :doc:`Howto drude <Howto_drude>` | USER/drude | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-EFF <PKG-USER-EFF>` | electron force field | :doc:`pair\_style eff/cut <pair_eff>` | USER/eff | no |
| :ref:`USER-EFF <PKG-USER-EFF>` | electron force field | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-FEP <PKG-USER-FEP>` | free energy perturbation | :doc:`compute fep <compute_fep>` | USER/fep | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
@ -63,15 +63,15 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | USER/manifold | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MEAMC <PKG-USER-MEAMC>` | modified EAM potential (C++) | :doc:`pair\_style meam/c <pair_meamc>` | meamc | no |
| :ref:`USER-MEAMC <PKG-USER-MEAMC>` | modified EAM potential (C++) | :doc:`pair_style meam/c <pair_meamc>` | meamc | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MESO <PKG-USER-MESO>` | mesoscale DPD models | :doc:`pair\_style edpd <pair_meso>` | USER/meso | no |
| :ref:`USER-MESO <PKG-USER-MESO>` | mesoscale DPD models | :doc:`pair_style edpd <pair_meso>` | USER/meso | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MGPT <PKG-USER-MGPT>` | fast MGPT multi-ion potentials | :doc:`pair\_style mgpt <pair_mgpt>` | USER/mgpt | no |
| :ref:`USER-MGPT <PKG-USER-MGPT>` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MISC <PKG-USER-MISC>` | single-file contributions | USER-MISC/README | USER/misc | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MOFFF <PKG-USER-MOFFF>` | styles for `MOF-FF <MOFplus_>`_ force field | :doc:`pair\_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` | USER/mofff | no |
| :ref:`USER-MOFFF <PKG-USER-MOFFF>` | styles for `MOF-FF <MOFplus_>`_ force field | :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` | USER/mofff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MOLFILE <PKG-USER-MOLFILE>` | `VMD <https://www.ks.uiuc.edu/Research/vmd/>`_ molfile plug-ins | :doc:`dump molfile <dump_molfile>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
@ -89,17 +89,17 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-QTB <PKG-USER-QTB>` | quantum nuclear effects | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-QUIP <PKG-USER-QUIP>` | QUIP/libatoms interface | :doc:`pair\_style quip <pair_quip>` | USER/quip | ext |
| :ref:`USER-QUIP <PKG-USER-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | USER/quip | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-REAXC <PKG-USER-REAXC>` | ReaxFF potential (C/C++) | :doc:`pair\_style reaxc <pair_reaxc>` | reax | no |
| :ref:`USER-REAXC <PKG-USER-REAXC>` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc <pair_reaxc>` | reax | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace\_style scafacos <kspace_style>` | USER/scafacos | ext |
| :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos <kspace_style>` | USER/scafacos | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SDPD <PKG-USER-SDPD>` | smoothed dissipative particle dynamics | :doc:`pair\_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | USER/sdpd | no |
| :ref:`USER-SDPD <PKG-USER-SDPD>` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | USER/sdpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SMD <PKG-USER-SMD>` | smoothed Mach dynamics | `SMD User Guide <PDF/SMD_LAMMPS_userguide.pdf>`_ | USER/smd | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | second moment tight binding QEq potential | :doc:`pair\_style smtbq <pair_smtbq>` | USER/smtbq | no |
| :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | second moment tight binding QEq potential | :doc:`pair_style smtbq <pair_smtbq>` | USER/smtbq | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SPH <PKG-USER-SPH>` | smoothed particle hydrodynamics | `SPH User Guide <PDF/SPH_LAMMPS_userguide.pdf>`_ | USER/sph | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
@ -109,18 +109,12 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-VTK <PKG-USER-VTK>` | dump output via VTK | :doc:`compute vtk <dump_vtk>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-YAFF <PKG-USER-YAFF>` | additional styles implemented in YAFF | :doc:`angle\_style cross <angle_cross>` | USER/yaff | no |
| :ref:`USER-YAFF <PKG-USER-YAFF>` | additional styles implemented in YAFF | :doc:`angle_style cross <angle_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

4
doc/src/Python_call.rst
View File

@ -7,7 +7,7 @@ code directly from an input script:
* :doc:`python <python>`
* :doc:`variable python <variable>`
* :doc:`fix python/invoke <fix_python_invoke>`
* :doc:`pair\_style python <pair_python>`
* :doc:`pair_style python <pair_python>`
The :doc:`python <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 <fix_python_invoke>` command can execute
Python code at selected timesteps during a simulation run.
The :doc:`pair\_style python <pair_python>` command allows you to define
The :doc:`pair_style python <pair_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.

7
doc/src/Python_install.rst
View File

@ -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 <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

12
doc/src/Python_mpi.rst
View File

@ -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 <https://github.com/daleroberts/pypar>`_
* `MPI for Python <https://mpi4py.readthedocs.io/>`_
* `pypar <https://github.com/daleroberts/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

20
doc/src/Run_options.rst
View File

@ -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 <run_style>` command with 2 partitions
the :doc:`run_style verlet/split <run_style>` 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 <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 <run_style>` command with 2
when using the :doc:`run_style verlet/split <run_style>` 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 <read_restart>` and :doc:`write\_data <write_data>` doc
:doc:`read_restart <read_restart>` and :doc:`write_data <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 <read_restart>` command, and operates as explained on
:doc:`read_restart <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 <write_data>`
is identical to the arguments of the :doc:`write_data <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 <read_restart>` and :doc:`write\_dump <write_dump>` doc
:doc:`read_restart <read_restart>` and :doc:`write_dump <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 <read_restart>` command, as explained on its doc page.
:doc:`read_restart <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 <write_dump>`
is identical to the arguments of the :doc:`write_dump <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 <dump_modify>` doc page for details.
:doc:`dump_modify <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 <pair_lj>` variant, with style names lj/cut/gpu,
As an example, all of the packages provide a :doc:`pair_style lj/cut <pair_lj>` 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

6
doc/src/Run_output.rst
View File

@ -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 <special_bonds>` command). The number
of (see the :doc:`special_bonds <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 <neigh_modify>` command),
list rebuilding (see the :doc:`neigh_modify <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 <kspace_style>` long-range Coulombics solver
If a :doc:`kspace_style <kspace_style>` long-range Coulombics solver
that performs FFTs was used during the run (PPPM, Ewald), then
additional information is printed, e.g.

2
doc/src/Speed_gpu.rst
View File

@ -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 <kspace_style>` for long-range Coulombics.
:doc:`kspace_style pppm <kspace_style>` for long-range Coulombics.
It has the following general features:
* It is designed to exploit common GPU hardware configurations where one

4
doc/src/Speed_intel.rst
View File

@ -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 <kspace_style>` is used:
:doc:`kspace\_modify diff ad <kspace_modify>` should be added to the
:doc:`kspace_modify diff ad <kspace_modify>` should be added to the
input script.
Long-Range Thread (LRT) mode is an option to the :doc:`package intel <package>` 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 <run_style>` command; only the "pair" option is
:doc:`run_style respa <run_style>` command; only the "pair" option is
supported.
**References:**

4
doc/src/Speed_omp.rst
View File

@ -129,14 +129,14 @@ circumstances:
where MPI parallelism is maxed out. For example, this can happen when
using the :doc:`PPPM solver <kspace_style>` for long-range
electrostatics on large numbers of nodes. The scaling of the KSpace
calculation (see the :doc:`kspace\_style <kspace_style>` command) becomes
calculation (see the :doc:`kspace_style <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 <run_style>` command, which is compatible
:doc:`run_style verlet/split <run_style>` 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.

14
doc/src/Speed_packages.rst
View File

@ -1,7 +1,7 @@
Accelerator packages
====================
Accelerated versions of various :doc:`pair\_style <pair_style>`,
Accelerated versions of various :doc:`pair_style <pair_style>`,
:doc:`fixes <fix>`, :doc:`computes <compute>`, 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 <pair_lj>`:
Lennard-Jones :doc:`pair_style lj/cut <pair_lj>`:
* :doc:`pair\_style lj/cut/gpu <pair_lj>`
* :doc:`pair\_style lj/cut/intel <pair_lj>`
* :doc:`pair\_style lj/cut/kk <pair_lj>`
* :doc:`pair\_style lj/cut/omp <pair_lj>`
* :doc:`pair\_style lj/cut/opt <pair_lj>`
* :doc:`pair_style lj/cut/gpu <pair_lj>`
* :doc:`pair_style lj/cut/intel <pair_lj>`
* :doc:`pair_style lj/cut/kk <pair_lj>`
* :doc:`pair_style lj/cut/omp <pair_lj>`
* :doc:`pair_style lj/cut/opt <pair_lj>`
To see what accelerate styles are currently available for a particular
style, find the style name in the `Commands\_all <lc_>`_

6
doc/src/Tools.rst
View File

@ -60,7 +60,7 @@ Post-processing tools
+--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+
| :ref:`amber2lmp <amber>` | :ref:`binary2txt <binary>` | :ref:`ch2lmp <charmm>` | :ref:`colvars <colvars>` | :ref:`eff <eff>` | :ref:`fep <fep>` |
+--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+
| :ref:`lmp2arc <arc>` | :ref:`lmp2cfg <cfg>` | :ref:`matlab <matlab>` | :ref:`phonon <phonon>` | :ref:`pymol\_asphere <pymol>` | :ref:`python <pythontools>` |
| :ref:`lmp2arc <arc>` | :ref:`lmp2cfg <cfg>` | :ref:`matlab <matlab>` | :ref:`phonon <phonon>` | :ref:`pymol_asphere <pymol>` | :ref:`python <pythontools>` |
+--------------------------+----------------------------+------------------------+--------------------------+-------------------------------+-----------------------------+
| :ref:`reax <reax_tool>` | :ref:`replica <replica>` | :ref:`smd <smd>` | :ref:`spin <spin>` | :ref:`xmgrace <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 <pair_eam>` command.
Zr. The files can then be used with the :doc:`pair_style eam/alloy <pair_eam>` 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) <pair_eam>` setfl potential file. The potentials they
produce are in the potentials directory, and can be used with the
:doc:`pair\_style eam/alloy <pair_eam>` command.
:doc:`pair_style eam/alloy <pair_eam>` command.
The source files and potentials were provided by Gerolf Ziegenhain
(gerolf at ziegenhain.com).

8
doc/src/angle_charmm.rst
View File

@ -48,9 +48,9 @@ See :ref:`(MacKerell) <angle-MacKerell>` for a description of the CHARMM force
field.
The following coefficients must be defined for each angle type via the
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy/radian\^2)
* :math:`\theta_0` (degrees)
@ -97,7 +97,7 @@ for more info.
Related commands
""""""""""""""""
:doc:`angle\_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`
**Default:** none

10
doc/src/angle_class2.rst
View File

@ -51,9 +51,9 @@ the equilibrium bond lengths.
See :ref:`(Sun) <angle-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 <angle_coeff>` command as in
each angle type via the :doc:`angle_coeff <angle_coeff>` command as in
the example above, or in the data file or restart files read by the
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
:doc:`read_data <read_data>` or :doc:`read_restart <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 <angle_coeff>`
For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff <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 <angle_coeff>`
For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff <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 <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`
**Default:** none

8
doc/src/angle_cosine.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy)
@ -82,6 +82,6 @@ for more info.
Related commands
""""""""""""""""
:doc:`angle\_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`
**Default:** none

12
doc/src/angle_cosine_buck6d.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands in the following order:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <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 <pair_buck6d_coul_gauss>` between the end atoms of the
angle. For this reason this angle style only works in combination
with the :doc:`pair\_buck6d <pair_buck6d_coul_gauss>` styles and needs
the :doc:`special\_bonds <special_bonds>` 1-3 interactions to be weighted
the :doc:`special_bonds <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 <pair_buck6d_coul_gauss>` style and with a
:doc:`special\_bonds <special_bonds>` 0.0 weighting of 1-3 interactions.
:doc:`special_bonds <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 <Build_package>` doc
@ -71,6 +71,6 @@ page for more info.
Related commands
""""""""""""""""
:doc:`angle\_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`
**Default:** none

8
doc/src/angle_cosine_delta.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy)
* :math:`\theta_0` (degrees)
@ -84,6 +84,6 @@ for more info.
Related commands
""""""""""""""""
:doc:`angle\_coeff <angle_coeff>`, :doc:`angle\_style cosine/squared <angle_cosine_squared>`
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style cosine/squared <angle_cosine_squared>`
**Default:** none

8
doc/src/angle_cosine_periodic.rst
View File

@ -42,9 +42,9 @@ where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle
See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field
The following coefficients must be defined for each angle type via the
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`C` (energy)
* :math:`B` = 1 or -1
@ -92,7 +92,7 @@ for more info.
Related commands
""""""""""""""""
:doc:`angle\_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`
**Default:** none

8
doc/src/angle_cosine_shift.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`U_{\text{min}}` (energy)
* :math:`\theta` (angle)
@ -82,7 +82,7 @@ USER-MISC package.
Related commands
""""""""""""""""
:doc:`angle\_coeff <angle_coeff>`,
:doc:`angle_coeff <angle_coeff>`,
:doc:`angle\_cosine\_shift\_exp <angle_cosine_shift_exp>`
**Default:** none

8
doc/src/angle_cosine_shift_exp.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`U_min` (energy)
* :math:`\theta` (angle)
@ -93,7 +93,7 @@ page for more info.
Related commands
""""""""""""""""
:doc:`angle\_coeff <angle_coeff>`,
:doc:`angle_coeff <angle_coeff>`,
:doc:`angle\_cosine\_shift <angle_cosine_shift>`,
:doc:`dihedral\_cosine\_shift\_exp <dihedral_cosine_shift_exp>`

8
doc/src/angle_cosine_squared.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy)
* :math:`\theta_0` (degrees)
@ -84,6 +84,6 @@ for more info.
Related commands
""""""""""""""""
:doc:`angle\_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`
**Default:** none

8
doc/src/angle_cross.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <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 <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`
**Default:** none

8
doc/src/angle_dipole.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <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 <angle_coeff>`, :doc:`angle\_hybrid <angle_hybrid>`
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_hybrid <angle_hybrid>`
**Default:** none

8
doc/src/angle_fourier.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy)
* :math:`C_0` (real)
@ -79,6 +79,6 @@ page for more info.
Related commands
""""""""""""""""
:doc:`angle\_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`
**Default:** none

8
doc/src/angle_fourier_simple.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy)
* :math:`c` (real)
@ -78,6 +78,6 @@ page for more info.
Related commands
""""""""""""""""
:doc:`angle\_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`
**Default:** none

8
doc/src/angle_harmonic.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <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 <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`
**Default:** none

8
doc/src/angle_mm3.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <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 <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`
**Default:** none

8
doc/src/angle_quartic.rst
View File

@ -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 <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <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 <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`
**Default:** none

8
doc/src/angle_sdk.rst
View File

@ -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 <pair_sdk>`. Relative to the pair\_style
:doc:`pair_style lj/sdk <pair_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 <angle_coeff>` command as in the example above:
:doc:`angle_coeff <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 <angle_coeff>`, :doc:`angle\_style harmonic <angle_harmonic>`, :doc:`pair\_style lj/sdk <pair_sdk>`,
:doc:`pair\_style lj/sdk/coul/long <pair_sdk>`
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/sdk <pair_sdk>`,
:doc:`pair_style lj/sdk/coul/long <pair_sdk>`
**Default:** none

8
doc/src/atom_modify.rst
View File

@ -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 <atom_style>`
in addition to what is specified by the :doc:`atom_style <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 <create_atoms>` or
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
:doc:`read_data <read_data>` or :doc:`read_restart <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 <atom_style>` for molecular
only creates a map for :doc:`atom_styles <atom_style>` 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 <neigh_modify>` and :doc:`comm\_modify group <comm_modify>`
this option will be a net slow-down. The :doc:`neigh_modify include <neigh_modify>` and :doc:`comm_modify group <comm_modify>`
commands are two examples of commands that require this setting to
work efficiently. Several :doc:`fixes <fix>`, most notably time
integration fixes like :doc:`fix nve <fix_nve>`, also take advantage of

16
doc/src/atom_style.rst
View File

@ -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 <read_data>`,
:doc:`read\_restart <read_restart>`, or :doc:`create\_box <create_box>`
used before a simulation is setup via a :doc:`read_data <read_data>`,
:doc:`read_restart <read_restart>`, or :doc:`create_box <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 <read_data>` command.
by the :doc:`read_data <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 <read_data>`, :doc:`create\_atoms <create_atoms>`, and
:doc:`read_data <read_data>`, :doc:`create_atoms <create_atoms>`, and
:doc:`set <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 <pair_dpd>` commands, which can
the :doc:`pair_style dpd or dpd/stat <pair_dpd>` 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 <read_data>` command. Rather the
defined, e.g. by the :doc:`read_data <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 <read_data>` or :doc:`create\_box <create_box>` command.
:doc:`read_data <read_data>` or :doc:`create_box <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 <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 <read_data>`, :doc:`pair\_style <pair_style>`
:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`
Default
"""""""

20
doc/src/balance.rst
View File

@ -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 <comm_style>` command can then
be used to replace a current :doc:`comm\_style tiled <comm_style>`
"grid" so that the :doc:`comm_style brick <comm_style>` command can then
be used to replace a current :doc:`comm_style tiled <comm_style>`
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 <create_atoms>` command, then "grid" methods may
the :doc:`create_atoms <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 <kspace_style>` command. Thus you should benchmark
:doc:`kspace_style <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 <comm_style>` command options, *brick* or *tiled*\ . The
"tiling" methods can only be used with :doc:`comm\_style tiled <comm_style>`. Note that it can be useful to use a "grid"
method with :doc:`comm\_style tiled <comm_style>` to return the domain
:doc:`comm_style <comm_style>` command options, *brick* or *tiled*\ . The
"tiling" methods can only be used with :doc:`comm_style tiled <comm_style>`. Note that it can be useful to use a "grid"
method with :doc:`comm_style tiled <comm_style>` 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 <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 <pair_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 <run_style>` where some portions of the
using :doc:`run_style respa <run_style>` 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 <comm_style>`
:doc:`comm_style tiled <comm_style>`
Related commands
""""""""""""""""
:doc:`group <group>`, :doc:`processors <processors>`,
:doc:`fix balance <fix_balance>`, :doc:`comm\_style <comm_style>`
:doc:`fix balance <fix_balance>`, :doc:`comm_style <comm_style>`
.. _pizza: http://pizza.sandia.gov

8
doc/src/bond_class2.rst
View File

@ -41,9 +41,9 @@ where :math:`r_0` is the equilibrium bond distance.
See :ref:`(Sun) <bond-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 <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`r_0` (distance)
* :math:`K_2` (energy/distance\^2)
@ -87,7 +87,7 @@ info.
Related commands
""""""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none

10
doc/src/bond_coeff.rst
View File

@ -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 <read_data>` command or in a restart file.
:doc:`read_data <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 <bond_style>` doc page. They are also listed in more
:doc:`bond_style <bond_style>` doc page. They are also listed in more
compact form on the :doc:`Commands bond <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 <read_data>`, :doc:`read\_restart <read_restart>`, or
:doc:`create\_box <create_box>` command.
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
:doc:`create_box <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 <bond_style>`
:doc:`bond_style <bond_style>`
**Default:** none

12
doc/src/bond_fene.rst
View File

@ -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 <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <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 <Build_package>` doc page for more
info.
You typically should specify :doc:`special\_bonds fene <special_bonds>`
or :doc:`special\_bonds lj/coul 0 1 1 <special_bonds>` to use this bond
You typically should specify :doc:`special_bonds fene <special_bonds>`
or :doc:`special_bonds lj/coul 0 1 1 <special_bonds>` to use this bond
style. LAMMPS will issue a warning it that's not the case.
Related commands
""""""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none

12
doc/src/bond_fene_expand.rst
View File

@ -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 <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <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 <Build_package>` doc page for more
info.
You typically should specify :doc:`special\_bonds fene <special_bonds>`
or :doc:`special\_bonds lj/coul 0 1 1 <special_bonds>` to use this bond
You typically should specify :doc:`special_bonds fene <special_bonds>`
or :doc:`special_bonds lj/coul 0 1 1 <special_bonds>` to use this bond
style. LAMMPS will issue a warning it that's not the case.
Related commands
""""""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none

8
doc/src/bond_gromos.rst
View File

@ -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 <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy/distance\^4)
* :math:`r_0` (distance)
@ -81,6 +81,6 @@ info.
Related commands
""""""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none

8
doc/src/bond_harmonic.rst
View File

@ -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 <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy/distance\^2)
* :math:`r_0` (distance)
@ -87,6 +87,6 @@ info.
Related commands
""""""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none

10
doc/src/bond_harmonic_shift.rst
View File

@ -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 <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`U_{\text{min}}` (energy)
@ -86,7 +86,7 @@ page for more info.
Related commands
""""""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`,
:doc:`bond\_harmonic <bond_harmonic>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
:doc:`bond_harmonic <bond_harmonic>`
**Default:** none

10
doc/src/bond_harmonic_shift_cut.rst
View File

@ -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 <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <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 <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`,
:doc:`bond\_harmonic <bond_harmonic>`,
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
:doc:`bond_harmonic <bond_harmonic>`,
:doc:`bond\_harmonic\_shift <bond_harmonic_shift>`
**Default:** none

8
doc/src/bond_mm3.rst
View File

@ -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 <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <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 <bond_coeff>`
:doc:`bond_coeff <bond_coeff>`
**Default:** none

8
doc/src/bond_morse.rst
View File

@ -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 <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`D` (energy)
* :math:`\alpha` (inverse distance)
@ -82,6 +82,6 @@ info.
Related commands
""""""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none

8
doc/src/bond_nonlinear.rst
View File

@ -37,9 +37,9 @@ to define an anharmonic spring :ref:`(Rector) <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 <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`\epsilon` (energy)
* :math:`r_0` (distance)
@ -82,7 +82,7 @@ info.
Related commands
""""""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none

10
doc/src/bond_oxdna.rst
View File

@ -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 <bond_coeff>` command as given in the above example, or
:doc:`bond_coeff <bond_coeff>` command as given in the above example, or
in the data file or restart files read by the
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
:doc:`read_data <read_data>` or :doc:`read_restart <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 <pair_oxdna>`). For the oxDNA2
:doc:`pair_style oxdna/excv <pair_oxdna>`). For the oxDNA2
:ref:`(Snodin) <Snodin0>` 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 <pair_oxdna>`, :doc:`pair\_style oxdna2/excv <pair_oxdna2>`, :doc:`pair\_style oxrna2/excv <pair_oxrna2>`,
:doc:`bond\_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
:doc:`pair_style oxdna/excv <pair_oxdna>`, :doc:`pair_style oxdna2/excv <pair_oxdna2>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`,
:doc:`bond_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
**Default:**

16
doc/src/bond_quartic.rst
View File

@ -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 <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <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 <pair_style>` command, whether the bond is broken or
not. This means that :doc:`special\_bonds <special_bonds>` must be set
:doc:`pair_style <pair_style>` command, whether the bond is broken or
not. This means that :doc:`special_bonds <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 <dump>` command, bonds with type 0 are not included. The
:doc:`delete\_bonds <delete_bonds>` command can also be used to query the
:doc:`delete_bonds <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 <Build_package>` doc page for more
info.
The *quartic* style requires that :doc:`special\_bonds <special_bonds>`
The *quartic* style requires that :doc:`special_bonds <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 <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none

16
doc/src/bond_style.rst
View File

@ -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 <pair_style>`
interaction, which are set via the :doc:`pair_style <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 <read_data>` or
:doc:`read\_restart <read_restart>` command from a data or restart file.
atoms is read in by a :doc:`read_data <read_data>` or
:doc:`read_restart <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 <bond_coeff>` command.
data or restart file or via the :doc:`bond_coeff <bond_coeff>` command.
All bond potentials store their coefficient data in binary restart
files which means bond\_style and :doc:`bond\_coeff <bond_coeff>` commands
files which means bond\_style and :doc:`bond_coeff <bond_coeff>` commands
do not need to be re-specified in an input script that restarts a
simulation. See the :doc:`read\_restart <read_restart>` command for
simulation. See the :doc:`read_restart <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 <special_bonds>` command often needs to be used to
:doc:`special_bonds <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 <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
Default
"""""""

2
doc/src/bond_table.rst
View File

@ -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 <bond_style>` command. Let
specified in the :doc:`bond_style table <bond_style>` 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

6
doc/src/bond_zero.rst
View File

@ -31,14 +31,14 @@ commands.
As an example, the :doc:`compute bond/local <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 <read_data>`
atoms listed in the data file read by the :doc:`read_data <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 <bond_coeff>` command must be used for
Note that the :doc:`bond_coeff <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 <fix_shake>`.
@ -50,6 +50,6 @@ Restrictions
Related commands
""""""""""""""""
:doc:`bond\_style none <bond_none>`
:doc:`bond_style none <bond_none>`
**Default:** none

16
doc/src/boundary.rst
View File

@ -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 <read_data>`,
:doc:`read\_restart <read_restart>`, or :doc:`create\_box <create_box>`
of the simulation box is set by the :doc:`read_data <read_data>`,
:doc:`read_restart <read_restart>`, or :doc:`create_box <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 <thermo_modify>` option to
you have set the :doc:`thermo_modify lost <thermo_modify>` 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 <create_box>` command. For example, if the upper z
:doc:`create_box <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 <read_data>` or :doc:`create\_box <create_box>` command or
:doc:`read\_restart <read_restart>` command. See the
:doc:`change\_box <change_box>` command for how to change the simulation
:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command or
:doc:`read_restart <read_restart>` command. See the
:doc:`change_box <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 <thermo_modify>` command for a discussion
See the :doc:`thermo_modify <thermo_modify>` command for a discussion
of lost atoms.
Default

8
doc/src/box.rst
View File

@ -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 <create_box>` or
:doc:`read\_data <read_data>` commands. Tilt factors determine how
e.g. via the :doc:`create_box <create_box>` or
:doc:`read_data <read_data>` commands. Tilt factors determine how
skewed the triclinic box is; see the :doc:`Howto triclinic <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 <read_data>` or :doc:`create\_box <create_box>` command or
:doc:`read\_restart <read_restart>` command.
:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command or
:doc:`read_restart <read_restart>` command.
**Related commands:** none

20
doc/src/change_box.rst
View File

@ -77,12 +77,12 @@ conditions for the simulation box, similar to the
:doc:`boundary <boundary>` command.
The size and shape of the initial simulation box are specified by the
:doc:`create\_box <create_box>` or :doc:`read\_data <read_data>` or
:doc:`read\_restart <read_restart>` command used to setup the simulation.
:doc:`create_box <create_box>` or :doc:`read_data <read_data>` or
:doc:`read_restart <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 <fix_nh>` or :doc:`fix deform <fix_deform>` commands.
The :doc:`create\_box <create_box>`, :doc:`read data <read_data>`, and
:doc:`read\_restart <read_restart>` commands also determine whether the
The :doc:`create_box <create_box>`, :doc:`read data <read_data>`, and
:doc:`read_restart <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 <create_atoms>` command, because the simulation box
:doc:`create_atoms <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 <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 <read_data>` or
:doc:`create\_box <create_box>` or :doc:`read\_restart <read_restart>`
simulation box is defined via a :doc:`read_data <read_data>` or
:doc:`create_box <create_box>` or :doc:`read_restart <read_restart>`
command. This command allows the boundary conditions to be changed
later in your input script. Also note that the
:doc:`read\_restart <read_restart>` will change boundary conditions to
:doc:`read_restart <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 <create_box>`,
:doc:`read\_data <read_data>`, or :doc:`read\_restart <read_restart>`
it is created via the :doc:`create_box <create_box>`,
:doc:`read_data <read_data>`, or :doc:`read_restart <read_restart>`
commands.
These keywords allow you to toggle the existing simulation box from

14
doc/src/comm_modify.rst
View File

@ -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 <comm_style>` or
:doc:`read\_restart <read_restart>` command, all communication settings
you specify a :doc:`comm_style <comm_style>` or
:doc:`read_restart <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 <neigh_modify>` command.
:doc:`neigh_modify cluster <neigh_modify>` 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 <atom_modify>` command.
:doc:`atom_modify first <atom_modify>` command.
The *vel* keyword enables velocity information to be communicated with
ghost particles. Depending on the :doc:`atom\_style <atom_style>`,
ghost particles. Depending on the :doc:`atom_style <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 <comm_style>` *brick*\ .
:doc:`comm_style <comm_style>` *brick*\ .
Related commands
""""""""""""""""
:doc:`comm\_style <comm_style>`, :doc:`neighbor <neighbor>`
:doc:`comm_style <comm_style>`, :doc:`neighbor <neighbor>`
Default
"""""""

8
doc/src/comm_style.rst
View File

@ -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 <create_box>`
or :doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
simulation box is first created, via the :doc:`create_box <create_box>`
or :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands. For both the *brick* and *tiled* styles, the initial
decomposition will be the same, as described by
:doc:`create\_box <create_box>` and :doc:`processors <processors>`
:doc:`create_box <create_box>` and :doc:`processors <processors>`
commands. The decomposition can be changed via the
:doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
@ -64,7 +64,7 @@ cells.
Related commands
""""""""""""""""
:doc:`comm\_modify <comm_modify>`, :doc:`processors <processors>`,
:doc:`comm_modify <comm_modify>`, :doc:`processors <processors>`,
:doc:`balance <balance>`, :doc:`fix balance <fix_balance>`
Default

10
doc/src/compute.rst
View File

@ -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 <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
* Global values can be output via the :doc:`thermo_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
Or the values can be referenced in a :doc:`variable equal <variable>` or
:doc:`variable atom <variable>` command.
* Per-atom values can be output via the :doc:`dump custom <dump>` 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 <thermo_style>` command.
:doc:`thermo_style <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 <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 <thermo_modify>` and :doc:`fix modify <fix_modify>` commands.
described by the :doc:`thermo_modify <thermo_modify>` and :doc:`fix modify <fix_modify>` commands.
Properties of either a default or user-defined compute can be modified
via the :doc:`compute\_modify <compute_modify>` command.
via the :doc:`compute_modify <compute_modify>` command.
Computes can be deleted with the :doc:`uncompute <uncompute>` command.
@ -329,7 +329,7 @@ Restrictions
Related commands
""""""""""""""""
:doc:`uncompute <uncompute>`, :doc:`compute\_modify <compute_modify>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/histo <fix_ave_histo>`
:doc:`uncompute <uncompute>`, :doc:`compute_modify <compute_modify>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/histo <fix_ave_histo>`
**Default:** none

10
doc/src/compute_adf.rst
View File

@ -60,9 +60,9 @@ neighbor atom in each requested ADF.
.. note::
If you have a bonded system, then the settings of
:doc:`special\_bonds <special_bonds>` command can remove pairwise
:doc:`special_bonds <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 <special_bonds>`
is the default setting for the :doc:`special_bonds <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 <rerun>` command to compute the ADF for snapshots in
the dump file. The rerun script can use a
:doc:`special\_bonds <special_bonds>` command that includes all pairs in
:doc:`special_bonds <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 <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 <comm_modify>` command, else the ADF computation
:doc:`comm_modify cutoff <comm_modify>` 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 <neighbor>` command.
@ -221,7 +221,7 @@ your model.
Related commands
""""""""""""""""
:doc:`compute rdf <compute_rdf>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`compute\_modify <compute_modify>`
:doc:`compute rdf <compute_rdf>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`compute_modify <compute_modify>`
Default
"""""""

4
doc/src/compute_angle.rst
View File

@ -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 <angle_hybrid>` if you want to know the portion of the total
This compute is useful when using :doc:`angle_style hybrid <angle_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 <angle_style>` command, which can be accessed by indices
number of sub\_styles defined by the :doc:`angle_style hybrid <angle_style>` 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 <Howto_output>` doc page for an overview of LAMMPS output
options.

6
doc/src/compute_angle_local.rst
View File

@ -90,7 +90,7 @@ and output the statistics in various ways:
The :doc:`dump local <dump>` command will output the energy, angle,
cosine(angle), cosine\^2(angle) for every angle in the system. The
:doc:`thermo\_style <thermo_style>` command will print the average of
:doc:`thermo_style <thermo_style>` command will print the average of
those quantities via the :doc:`compute reduce <compute_reduce>` command
with thermo output. And the :doc:`fix ave/histo <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 <angle_style>` command) by setting their angle type to
0 are not included. Angles that have been turned off (see the :doc:`fix shake <fix_shake>` or :doc:`delete\_bonds <delete_bonds>` commands) by
:doc:`angle_style <angle_style>` command) by setting their angle type to
0 are not included. Angles that have been turned off (see the :doc:`fix shake <fix_shake>` or :doc:`delete_bonds <delete_bonds>` commands) by
setting their angle type negative are written into the file, but their
energy will be 0.0.

2
doc/src/compute_angmom_chunk.rst
View File

@ -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 <dump>` command for a discussion
of "unwrapped" coordinates. See the Atoms section of the
:doc:`read\_data <read_data>` command for a discussion of image flags and
:doc:`read_data <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 <set>` command.

2
doc/src/compute_body_local.rst
View File

@ -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 <atom_style>`, determines how many fields
by the :doc:`atom_style body <atom_style>`, determines how many fields
exist and what they are. See the :doc:`Howto\_body <Howto_body>` doc
page for details of the different styles.

6
doc/src/compute_bond.rst
View File

@ -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 <bond_hybrid>` command. These values are made accessible
of the bond sub-styles used in the :doc:`bond_style hybrid <bond_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 <bond_hybrid>`
This compute is useful when using :doc:`bond_style hybrid <bond_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 <bond_style>` command, which can be accessed by indices 1-N.
number of sub\_styles defined by the :doc:`bond_style hybrid <bond_style>` 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 <Howto_output>` doc page for an overview of LAMMPS output
options.

6
doc/src/compute_bond_local.rst
View File

@ -143,7 +143,7 @@ output the statistics in various ways:
The :doc:`dump local <dump>` command will output the energy, distance,
distance\^2 for every bond in the system. The
:doc:`thermo\_style <thermo_style>` command will print the average of
:doc:`thermo_style <thermo_style>` command will print the average of
those quantities via the :doc:`compute reduce <compute_reduce>` command
with thermo output. And the :doc:`fix ave/histo <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 <bond_style>`
Any bonds that have been broken (see the :doc:`bond_style <bond_style>`
command) by setting their bond type to 0 are not included. Bonds that
have been turned off (see the :doc:`fix shake <fix_shake>` or
:doc:`delete\_bonds <delete_bonds>` commands) by setting their bond type
:doc:`delete_bonds <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

2
doc/src/compute_chunk_atom.rst
View File

@ -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 <create_box>` or :doc:`read\_data <read_data>` commands.
:doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands.
----------

8
doc/src/compute_cluster_atom.rst
View File

@ -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 <read_data>`,
the :doc:`create\_bonds <create_bonds>` command, or through fixes like
the :doc:`create_bonds <create_bonds>` command, or through fixes like
:doc:`fix bond/create <fix_bond_create>`, :doc:`fix bond/swap <fix_bond_swap>`,
or :doc:`fix bond/break <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 <special_bonds>` command can remove pairwise
:doc:`special_bonds <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 <special_bonds>`
is the default setting for the :doc:`special_bonds <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 <rerun>` command to compute the clusters for
snapshots in the dump file. The rerun script can use a
:doc:`special\_bonds <special_bonds>` command that includes all pairs in
:doc:`special_bonds <special_bonds>` command that includes all pairs in
the neighbor list.
**Output info:**

2
doc/src/compute_com.rst
View File

@ -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 <dump>` command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
:doc:`read\_data <read_data>` command for a discussion of image flags and
:doc:`read_data <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 <set>` command.

2
doc/src/compute_com_chunk.rst
View File

@ -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 <dump>` command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the :doc:`read\_data <read_data>` command for a discussion of image flags
the :doc:`read_data <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 <set>` command.

2
doc/src/compute_contact_atom.rst
View File

@ -51,7 +51,7 @@ Restrictions
This compute requires that atoms store a radius as defined by the
:doc:`atom\_style sphere <atom_style>` command.
:doc:`atom_style sphere <atom_style>` command.
Related commands
""""""""""""""""

Some files were not shown because too many files have changed in this diff Show More