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

Merge branch 'master' into fft-consistency

This commit is contained in:
Axel Kohlmeyer 2020-01-31 20:51:58 -05:00
parent 6369ab230e dd91d519e1
commit 2b6a022309
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
1515 changed files with 15580 additions and 106151 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
.gitignore vendored
View File

@ -26,6 +26,7 @@ vgcore.*
.vagrant
\#*#
.#*
.vscode
.DS_Store
.DS_Store?

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

5
doc/src/Build.rst
View File

@ -21,8 +21,3 @@ as described on the :doc:`Install <Install>` doc page.
Build_extras
Build_windows
Build_development
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_basics.rst
View File

@ -430,8 +430,3 @@ you want to copy files to is protected.
There is no "install" option in the src/Makefile for LAMMPS. If you
wish to do this you will need to first build LAMMPS, then manually
copy the desired LAMMPS files to the appropriate system directories.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_cmake.rst
View File

@ -238,8 +238,3 @@ enough version, you can download the latest version at
`https://cmake.org/download/ <https://cmake.org/download/>`_.
Instructions on how to install it on various platforms can be found
`on this page <https://cmake.org/install/>`_.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

6
doc/src/Build_development.rst
View File

@ -112,9 +112,3 @@ These reports require GCOVR to be installed. The easiest way to do this to insta
.. parsed-literal::
pip install git+https://github.com/gcovr/gcovr.git
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
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.
@ -1414,8 +1414,3 @@ the settings are not valid for your system, check if one of the other
lib/vtk/Makefile.lammps.\* files is compatible and copy it to
Makefile.lammps. If none of the provided files work, you will need to
edit the Makefile.lammps file. See lib/vtk/README for details.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_link.rst
View File

@ -84,8 +84,3 @@ See the sample codes in examples/COUPLE/simple for examples of C++ and
C and Fortran codes that invoke LAMMPS through its library interface.
Other examples in the COUPLE directory use coupling ideas discussed on
the :doc:`Howto couple <Howto_couple>` doc page.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_make.rst
View File

@ -87,8 +87,3 @@ settings may become outdated:
make kokkos_omp # build with the KOKKOS package for OpenMP
make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
make kokkos_phi # build with the KOKKOS package for KNLs
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_package.rst
View File

@ -258,8 +258,3 @@ sub-directories with src files.
Type "make package-diff" to list all differences between pairs of
files in both the src dir and a package dir.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

15
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.
@ -256,7 +256,7 @@ 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.
@ -362,7 +362,7 @@ 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**\ :
@ -493,8 +493,3 @@ e.g. to Python.
.. parsed-literal::
LMP_INC = -DLAMMPS_EXCEPTIONS
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_windows.rst
View File

@ -104,8 +104,3 @@ Support for the Visual C++ compilers is currently not available. The
CMake build system is capable of creating suitable a Visual Studio
style build environment, but the LAMMPS code itself is not fully ported
to support Visual C++. Volunteers to take on this task are welcome.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

1
doc/src/Commands_all.rst
View File

@ -136,4 +136,3 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`write_data <write_data>`
* :doc:`write_dump <write_dump>`
* :doc:`write_restart <write_restart>`

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>`,

1
doc/src/Commands_compute.rst
View File

@ -163,4 +163,3 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`vcm/chunk <compute_vcm_chunk>`
* :doc:`voronoi/atom <compute_voronoi_atom>`
* :doc:`xrd <compute_xrd>`

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.

9
doc/src/Commands_removed.rst
View File

@ -57,11 +57,6 @@ 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>`
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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>`,

5
doc/src/Errors.rst
View File

@ -15,8 +15,3 @@ additional details for many of them.
Errors_bugs
Errors_messages
Errors_warnings
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

59
doc/src/Errors_bugs.rst
View File

@ -1,32 +1,45 @@
Reporting bugs
==============
If you are confident that you have found a bug in LAMMPS, follow these
steps.
If you are confident that you have found a bug in LAMMPS, please follow the steps outlined below:
Check the `New features and bug fixes <http://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site <lws_>`_ to see if the bug has already been reported or fixed or the
`Unfixed bug <http://lammps.sandia.gov/unbug.html>`_ to see if a fix is
pending.
* Check the `New features and bug fixes
<http://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site
<lws_>`_ to see if the bug has already been addressed in a patch.
* Check that your issue can be reproduced with the latest development
version of LAMMPS.
* Check the manual carefully to verify that the unexpected behavior you
are observing is indeed in conflict with the documentation
* Check the `GitHub Issue page <gip_>`_
if your issue has already been reported and if it is still open.
* Check the `GitHub Pull Requests page <https://github.com/lammps/pulls>`_
if there is already a fix for your bug pending.
* Check the `mailing list archives <http://lammps.sandia.gov/mail.html>`_
to see if the issue has been discussed before.
Check the `mailing list <http://lammps.sandia.gov/mail.html>`_ to see if
it has been discussed before.
If none of these steps yields any useful information, please file
a new bug report on the `GitHub Issue page <gip_>`_\ .
The website will offer you to select a suitable template with explanations
and then you should replace those explanations with the information
that you can provide to reproduce your issue.
If not, send an email to the mailing list describing the problem with
any ideas you have as to what is causing it or where in the code the
problem might be. The developers will ask for more info if needed,
such as an input script or data files.
The most useful thing you can do to help us fix the bug is to isolate
the problem. Run it on the smallest number of atoms and fewest number
of processors and with the simplest input script that reproduces the
bug and try to identify what command or combination of commands is
causing the problem.
.. note::
this page needs to have GitHub issues info added
The most useful thing you can do to help us verify and fix a bug is to
isolate the problem. Run it on the smallest number of atoms and fewest
number of processors with the simplest input script that reproduces the
bug. Try to identify what command or combination of commands is
causing the problem and upload the complete input deck as a tar or zip
archive. Please avoid using binary restart files unless the issue requires
it. In the latter case you should also include an input deck to quickly
generate this restart from a data file or a simple additional input.
You may also send an email to the LAMMPS mailing list at
"lammps-users at lists.sourceforge.net" describing the problem with the
same kind of information. The mailing list can provide a faster response,
especially if the bug reported is actually expected behavior. But because
of the high volume of the mailing list, it can happen that your e-mail
is overlooked and then forgotten. Issues on GitHub have to be explicitly
closed, so that will *guarantee* that at least one LAMMPS developer will
have looked at it.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
.. _gip: https://github.com/lammps/issues

7
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.
@ -121,8 +121,3 @@ implementations handle buffering of messages. If the code hangs
without an error message, it may be that you need to specify an MPI
setting or two (usually via an environment variable) to enable
buffering or boost the sizes of messages that can be buffered.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

13
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
@ -8415,10 +8415,3 @@ keyword to allow for additional bonds to be formed
*Zero-length lattice orient vector*
Self-explanatory.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

11
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.
@ -796,10 +796,3 @@ This will most likely cause errors in kinetic fluctuations.
*pair style reax is now deprecated and will soon be retired. Users should switch to pair\_style reax/c*
Self-explanatory.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

6
doc/src/Examples.rst
View File

@ -228,10 +228,4 @@ instructions. See the :doc:`Packages\_details <Packages_details>` doc
page for more info on specific USER packages.
.. _openkim: https://openkim.org
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto.rst
View File

@ -99,8 +99,3 @@ Packages howto
Howto_drude2
Howto_manifold
Howto_spins
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
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
@ -41,8 +41,3 @@ are for 2d models.
and the *disc* option for the :doc:`fix nve/sphere <fix_nve_sphere>`,
:doc:`fix nvt/sphere <fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere <fix_npt_sphere>`
commands.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

15
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::
@ -49,20 +49,15 @@ 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.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_bash.rst
View File

@ -284,8 +284,3 @@ the PATH variable should be
This should give you a jump start when trying to run LAMMPS on Windows.
To become effective in this environment I encourage you to look into Linux
tutorials explaining Bash and Basic Unix commands (e.g., `Linux Journey <https://linuxjourney.com>`_)
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

81
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
----------
@ -144,8 +144,3 @@ Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

29
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
@ -512,8 +512,3 @@ Particuology, 6, 455 (2008).
**(Wang)** J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular
Matter, 13, 1 (2011).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_chunk.rst
View File

@ -212,8 +212,3 @@ using the :doc:`fix ave/chunk <fix_ave_chunk>` command to calculate an
average dipole moment vector for each bin. This example is explained
on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
command doc page.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

25
doc/src/Howto_client_server.rst
View File

@ -68,8 +68,8 @@ programs.
.. note::
For client/server coupling to work between LAMMPS and another
code, the other code also has to use the CSlib. This can often be
done without any modification to the other code by simply wrapping it
code, the other code also has to use the CSlib. This can sometimes be
done without any modifications to the other code by simply wrapping it
with a Python script that exchanges CSlib messages with LAMMPS and
prepares input for or processes output from the other code. The other
code also has to implement a matching protocol for the format and
@ -94,17 +94,23 @@ client or server code:
* examples/message
* examples/COUPLE/README
* examples/COUPLE/lammps\_mc
* examples/COUPLE/lammps\_nwchem
* examples/COUPLE/lammps\_vasp
The examples/message dir couples a client instance of LAMMPS to a
server instance of LAMMPS.
The lammps\_mc dir shows how to couple LAMMPS as a server to a simple
Monte Carlo client code as the driver.
The files in the *lammps\_mc* folder show how to couple LAMMPS as
a server to a simple Monte Carlo client code as the driver.
The lammps\_vasp dir shows how to couple LAMMPS as a client code
running MD timestepping to VASP acting as a server providing quantum
DFT forces, through a Python wrapper script on VASP.
The files in the *lammps\_nwchem* folder show how to couple LAMMPS
as a client code running MD timestepping to NWChem acting as a
server providing quantum DFT forces, through a Python wrapper script
on NWChem.
The files in the *lammps\_vasp* folder show how to couple LAMMPS as
a client code running MD timestepping to VASP acting as a server
providing quantum DFT forces, through a Python wrapper script on VASP.
Here is how to launch a client and server code together for any of the
4 modes of message exchange that the :doc:`message <message>` command
@ -157,8 +163,3 @@ command-line option as their its option, where color is an integer
label that will be used to distinguish one executable from another in
the multiple executables that the mpirun command launches. In this
example the client was colored with a 0, and the server with a 1.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

21
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.
@ -264,8 +264,3 @@ The additional section in the date file would be formatted like this:
**(Fincham)** Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
6, 393-404 (1994).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_couple.rst
View File

@ -118,8 +118,3 @@ instances of LAMMPS to perform different calculations.
(4) Couple LAMMPS with another code in a client/server mode. This is
described on the :doc:`Howto client/server <Howto_client_server>` doc
page.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

9
doc/src/Howto_diffusion.rst
View File

@ -21,12 +21,3 @@ diffusion coefficient. The instantaneous VACF values can be
accumulated in a vector via the :doc:`fix vector <fix_vector>` command,
and time integrated via the :doc:`variable trap <variable>` function,
and thus extract D.
----------
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_dispersion.rst
View File

@ -98,8 +98,3 @@ This can be achieved using the *kspace\_modify mix/disp none* command.
Note that the code does not check automatically whether any mixing
rule is fulfilled. If mixing rules do not apply, the user will have
to specify this command explicitly.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

11
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.
@ -65,8 +65,3 @@ too close, which can cause numerical issues.
**(Lamoureux and Roux)** G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
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.
@ -535,8 +535,3 @@ NPT ensemble using Nose-Hoover thermostat:
**(SWM4-NDP)** Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys
Let, 418, 245-249 (2006)
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
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.
@ -42,8 +42,3 @@ converge and requires careful post-processing :ref:`(Shinoda) <Shinoda1>`
**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_github.rst
View File

@ -492,8 +492,3 @@ and code checks to make sure they at the very least compile.
A discussion of the LAMMPS developer GitHub workflow can be found in the file
`doc/github-development-workflow.md <https://github.com/lammps/lammps/blob/master/doc/github-development-workflow.md>`_
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

15
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::
@ -48,8 +48,3 @@ computations between frozen atoms by using this command:
will be the same as in 3d. If you wish to model granular particles in
2d as 2d discs, see the note on this topic on the :doc:`Howto 2d <Howto_2d>`
doc page, where 2d simulations are discussed.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_kappa.rst
View File

@ -79,8 +79,3 @@ formalism.
**(Wirnsberger)** Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104
(2015).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_library.rst
View File

@ -245,8 +245,3 @@ lammps\_reset\_box()) to restore a previously extracted and saved state
of a simulation. Additional properties for the new atoms can then be
assigned via the lammps\_scatter\_atoms() or lammps\_extract\_atom()
functions.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_manifold.rst
View File

@ -50,8 +50,3 @@ to the relevant fixes.
**(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_multiple.rst
View File

@ -96,8 +96,3 @@ on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each
partition. When one finished, that partition would then start
the 4th simulation, and so forth, until all 8 were completed.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_nemd.rst
View File

@ -53,8 +53,3 @@ using the :doc:`fix flow/gauss <fix_flow_gauss>` command.
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

21
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 |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
@ -342,8 +342,3 @@ vector input could be a column of an array.
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`fix store/state <fix_store_state>` | per-atom vectors | per-atom vector/array |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_polarizable.rst
View File

@ -71,8 +71,3 @@ temperature is regulated using the velocities of the center of mass of
core+shell (or Drude) pairs, but in the Drude model the actual
relative core-Drude particle motion is thermostatted separately as
well.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_pylammps.rst
View File

@ -577,8 +577,3 @@ If you find this Python interface useful, please feel free to provide feedback
and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
and maybe their latest research results.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
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
@ -53,8 +53,3 @@ processors. Thus the above commands could be run on a
single-processor (or few-processor) desktop so that you can run
a multi-replica simulation on more replicas than you have
physical processors.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

15
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
@ -95,11 +95,6 @@ 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.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_spc.rst
View File

@ -50,8 +50,3 @@ Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki
**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

41
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:
@ -235,9 +235,4 @@ 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>`.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
particles are computed via a command like :doc:`pair_style body/nparticle <pair_body_nparticle>`.

5
doc/src/Howto_spins.rst
View File

@ -66,8 +66,3 @@ magnetic spin, or the magnetic force acting on this spin.
**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, 372, 406-425, (2018).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_temperature.rst
View File

@ -31,8 +31,3 @@ They both allow for velocity biases indirectly, via an optional extra
argument which is another temperature compute that subtracts a
velocity bias. This allows the translational velocity of spherical or
aspherical particles to be adjusted in prescribed ways.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

17
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.
@ -92,8 +92,3 @@ temperature compute is used for default thermodynamic output.
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_tip3p.rst
View File

@ -74,8 +74,3 @@ Phys, 79, 926 (1983).
**(Price)** Price and Brooks, J Chem Phys, 121, 10096 (2004).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

15
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>`_.
@ -109,8 +109,3 @@ Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

39
doc/src/Howto_triclinic.rst
View File

@ -1,17 +1,3 @@
:doc:`Higher level section <Howto>` - `LAMMPS WWW Site <lws_>`_ - `LAMMPS Documentation <ld_>`_ - `LAMMPS Commands <lc_>`_
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands\_all.html
Triclinic (non-orthogonal) simulation boxes
===========================================
@ -22,11 +8,11 @@ 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 +76,14 @@ 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 +91,20 @@ 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 +159,7 @@ 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 +199,7 @@ 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
@ -225,4 +211,3 @@ material. The :doc:`fix deform <fix_deform>` command can be used for
this purpose. It allows dynamic control of the xy, xz, yz tilt
factors as a simulation runs. This is discussed in the next section
on non-equilibrium MD (NEMD) simulations.

5
doc/src/Howto_viscosity.rst
View File

@ -141,8 +141,3 @@ with time at sufficiently long times.
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
doc/src/Howto_viz.rst
View File

@ -34,10 +34,3 @@ snapshots.
.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

15
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
@ -69,8 +69,3 @@ The only frictional idealized walls currently in LAMMPS are flat or
curved surfaces specified by the :doc:`fix wall/gran <fix_wall_gran>`
command. At some point we plan to allow regoin surfaces to be used as
frictional walls, as well as triangulated surfaces.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Install.rst
View File

@ -51,8 +51,3 @@ These are the files and sub-directories in the LAMMPS distribution:
You will have all of these if you download source. You will only have
some of them if you download executables, as explained on the pages
listed above.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

4
doc/src/Install_conda.rst
View File

@ -42,7 +42,3 @@ up the Conda capability.
.. _conda: https://docs.conda.io/en/latest/index.html
.. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Install_git.rst
View File

@ -121,8 +121,3 @@ The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
gmail.com) and Richard Berger (Temple U, richard.berger at
temple.edu).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Install_linux.rst
View File

@ -262,8 +262,3 @@ Alternatively, you may use an AUR helper to install these packages.
Note that the AUR provides build-scripts that download the source and
the build the package on your machine.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

6
doc/src/Install_mac.rst
View File

@ -46,9 +46,3 @@ up the Homebrew capability.
.. _openkim: https://openkim.org
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Install_patch.rst
View File

@ -61,8 +61,3 @@ up to date.
sub-dir of src, then re-install the package. The version in the src
dir is merely a copy and will be wiped out if you type "make
package-update".
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Install_svn.rst
View File

@ -95,8 +95,3 @@ The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
gmail.com) and Richard Berger (Temple U, richard.berger at
temple.edu).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

13
doc/src/Install_tarball.rst
View File

@ -5,15 +5,9 @@ You can download a current LAMMPS tarball from the `download page <download_>`_
of the `LAMMPS website <lws_>`_.
.. _download: http://lammps.sandia.gov/download.html
.. _bug: http://lammps.sandia.gov/bug.html
.. _older: http://lammps.sandia.gov/tars
.. _lws: http://lammps.sandia.gov
You have two choices of tarballs, either the most recent stable
@ -77,8 +71,3 @@ The patch files are posted on the `bug and feature page <bug_>`_ of the
website, along with a list of changed files and details about what is
in the new patch release. Instructions for applying a patch file are
on the :doc:`Install patch <Install_patch>` doc page.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Install_windows.rst
View File

@ -42,8 +42,3 @@ automatically, so this should only be done for debugging purposes.
Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting
up this Windows capability.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Intro.rst
View File

@ -14,8 +14,3 @@ These pages provide a brief introduction to LAMMPS.
Intro_opensource
Intro_authors
Intro_website
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
doc/src/Intro_authors.rst
View File

@ -11,7 +11,7 @@ University:
* Richard Berger, richard.berger at temple.edu
.. _sjp: http://www.cs.sandia.gov/~sjplimp
.. _lws: http://lammps.sandia.gov
Past developers include Paul Crozier and Mark Stevens, both at Sandia,
@ -62,8 +62,3 @@ version of LAMMPS were the following:
* Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
* Steve Lustig (Dupont)
* Jim Belak and Roy Pollock (LLNL)
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

15
doc/src/Intro_features.rst
View File

@ -87,7 +87,7 @@ commands)
* water potentials: TIP3P, TIP4P, SPC
* implicit solvent potentials: hydrodynamic lubrication, Debye
* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim\_init, kim\_interactions, and kim\_query <kim_commands>` commands
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim_init, kim_interactions, and kim_query <kim_commands>` commands
* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
* overlaid potentials: superposition of multiple pair potentials
@ -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
@ -224,8 +224,3 @@ classical MD options:
* :doc:`Lattice Boltzmann fluid <fix_lb_fluid>`
* :doc:`targeted <fix_tmd>` and :doc:`steered <fix_smd>` molecular dynamics
* :doc:`two-temperature electron model <fix_ttm>`
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Intro_nonfeatures.rst
View File

@ -80,8 +80,3 @@ Here are suggestions on how to perform these tasks:
simulations. It thus provides some functionality for several of the
above bullets. Pizza.py is written in `Python <http://www.python.org>`_
and is available for download from `this page <http://www.cs.sandia.gov/~sjplimp/download.html>`_.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Intro_opensource.rst
View File

@ -42,8 +42,3 @@ of the GPL.
(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
source file headers (including the copyright and GPL notices) should
remain part of the code.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

8
doc/src/Intro_overview.rst
View File

@ -16,8 +16,7 @@ shared-memory boxes and distributed-memory clusters and
supercomputers.
.. _mpi: http://www-unix.mcs.anl.gov/mpi
.. _lws: http://lammps.sandia.gov
LAMMPS is written in C++. Earlier versions were written in F77 and
F90. See the `History page <http://lammps.sandia.gov/history.html>`_ of
@ -47,8 +46,3 @@ partition the simulation domain into small sub-domains of equal
computational cost, one of which is assigned to each processor.
Processors communicate and store "ghost" atom information for atoms
that border their sub-domain.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
doc/src/Intro_website.rst
View File

@ -5,6 +5,8 @@ The `LAMMPS website <lws_>`_ has a variety of additional info about
LAMMPS, beyond what is in this manual. Some of the other pages in
this Intr are included in this list.
.. _lws: http://lammps.sandia.gov
* `Brief intro and recently added significant features <lws_>`_
* `List of features <http://lammps.sandia.gov/features.html>`_
* `List of non-features <http://lammps.sandia.gov/non_features.html>`_
@ -32,8 +34,3 @@ this Intr are included in this list.
* `Authors of LAMMPS <http://lammps.sandia.gov/authors.html>`_
* `History of LAMMPS development <http://lammps.sandia.gov/history.html>`_
* `Funding for LAMMPS <http://lammps.sandia.gov/funding.html>`_
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

11
doc/src/Manual.rst
View File

@ -22,23 +22,21 @@ It includes links to an on-line version of this manual, a `mailing list <http://
questions, and a `GitHub site <https://github.com/lammps/lammps>`_ where
all LAMMPS development is coordinated.
----------
The content for this manual is part of the LAMMPS distribution. You
can build a local copy of the Manual as HTML pages or a PDF file, by
following the steps on the :doc:`Manual build <Manual_build>` doc page.
There is also a `Developer.pdf <Developer.pdf>`_ document which gives
a brief description of the basic code structure of LAMMPS.
----------
Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands>` since it gives quick access to a doc page for
every LAMMPS command.
.. _lws: http://lammps.sandia.gov
.. _lc: Commands_all.html
.. toctree::
:maxdepth: 2
@ -85,8 +83,3 @@ Indices and tables
.. raw:: html
</BODY>
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Manual_build.rst
View File

@ -134,8 +134,3 @@ For converting the generated ePUB file to a MOBI format file
also need to have the 'ebook-convert' tool from the "calibre"
software installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
You first create the ePUB file and then convert it with 'make mobi'
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Manual_version.rst
View File

@ -21,8 +21,3 @@ first page of the :doc:`manual <Manual>`.
describe the most current patch release of LAMMPS.
* If you browse the HTML doc pages included in your tarball, they
describe the version you have, which may be older.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify.rst
View File

@ -33,8 +33,3 @@ as a pull request on our `GitHub site <https://github.com/lammps/lammps>`_, afte
Modify_body
Modify_thermo
Modify_variable
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_atom.rst
View File

@ -117,8 +117,3 @@ accessed using the returned index as
Ivector or dvector are vectors of length Nlocal = # of owned atoms,
which store the attributes of individual atoms.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_body.rst
View File

@ -33,8 +33,3 @@ class. See body.h for details.
+----------------------+-----------------------------------------------------------+
| unpack\_border\_body | unpacking of those attributes |
+----------------------+-----------------------------------------------------------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_bond.rst
View File

@ -34,8 +34,3 @@ for details and specific additional methods.
+-----------------------+---------------------------------------------------------------------------+
| memory\_usage | tally memory allocated by the style (optional) |
+-----------------------+---------------------------------------------------------------------------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_command.rst
View File

@ -18,8 +18,3 @@ The single method your new class must define is as follows:
Of course, the new class can define other methods and variables as
needed.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_compute.rst
View File

@ -55,8 +55,3 @@ each pair after force and energy has been computed for this pair. Then
the tallied values are retrieved with the standard compute\_scalar or
compute\_vector or compute\_peratom methods. The USER-TALLY package
provides *examples*\ \_compute\_tally.html for utilizing this mechanism.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
doc/src/Modify_contribute.rst
View File

@ -69,6 +69,8 @@ unusual event).
`developers <http://lammps.sandia.gov/authors.html>`_ with info about
your package and we will post it there.
.. _lws: http://lammps.sandia.gov
The previous sections of this doc page describe how to add new "style"
files of various kinds to LAMMPS. Packages are simply collections of
one or more new class files which are invoked as a new style within a
@ -196,8 +198,3 @@ Finally, as a general rule-of-thumb, the more clear and
self-explanatory you make your documentation and README files, and the
easier you make it for people to get started, e.g. by providing example
scripts, the more likely it is that users will try out your new feature.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_dump.rst
View File

@ -30,8 +30,3 @@ new quantities to dump.
Note that new keywords for atom properties are not typically
added to the :doc:`dump custom <dump>` command. Instead they are added
to the :doc:`compute property/atom <compute_property_atom>` command.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
doc/src/Modify_fix.rst
View File

@ -146,13 +146,8 @@ 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
quantities and/or to be summed to the potential energy of the system.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_kspace.rst
View File

@ -19,8 +19,3 @@ class. See kspace.h for details.
+---------------+----------------------------------------------+
| memory\_usage | tally of memory usage |
+---------------+----------------------------------------------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_min.rst
View File

@ -17,8 +17,3 @@ class. See min.h for details.
+---------------+------------------------------------------+
| memory\_usage | tally of memory usage |
+---------------+------------------------------------------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_overview.rst
View File

@ -100,8 +100,3 @@ functionality:
**(Foo)** Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_pair.rst
View File

@ -33,8 +33,3 @@ Here is a brief description of the class methods in pair.h:
+---------------------------------+-------------------------------------------------------------------+
The inner/middle/outer routines are optional.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_region.rst
View File

@ -20,8 +20,3 @@ class. See region.h for details.
+-------------------+---------------------------------------------------------------------+
| shape\_update | change region shape if set by time-dependent variable |
+-------------------+---------------------------------------------------------------------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

9
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.
@ -20,13 +20,8 @@ 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
by adding a new keyword to the thermo command.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

9
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.
@ -38,8 +38,3 @@ to find the appropriate location.
Adding new :doc:`compute styles <compute>` (whose calculated values can
then be accessed by variables) is discussed on the :doc:`Modify compute <Modify_compute>` doc page.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

BIN
doc/src/PDF/colvars-refman-lammps.pdf
View File

Binary file not shown.

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