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Merge branch 'master' into pair-style-nnp

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This commit is contained in:
Axel Kohlmeyer
2021-05-25 16:44:55 -04:00
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parent a50c980595 92e995d3a2
commit 9e1db61b41
3336 changed files with 3641 additions and 3482 deletions
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1
.gitattributes vendored
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@ -2,3 +2,4 @@
.gitignore export-ignore
.github export-ignore
.lgtm.yml export-ignore
SECURITY.md export-ignore

20
README
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@ -14,10 +14,10 @@ LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
under the terms of the GNU Public License (GPL) version 2.
The primary author of the code is Steve Plimpton, who can be emailed
at sjplimp@sandia.gov. The LAMMPS WWW Site at lammps.sandia.gov has
at sjplimp@sandia.gov. The LAMMPS WWW Site at www.lammps.org has
more information about the code and its uses.
The LAMMPS distribution includes the following files and directories:
@ -37,14 +37,14 @@ tools pre- and post-processing tools
Point your browser at any of these files to get started:
https://lammps.sandia.gov/doc/Manual.html LAMMPS manual
https://lammps.sandia.gov/doc/Intro.html hi-level introduction
https://lammps.sandia.gov/doc/Build.html how to build LAMMPS
https://lammps.sandia.gov/doc/Run_head.html how to run LAMMPS
https://lammps.sandia.gov/doc/Commands_all.html Table of available commands
https://lammps.sandia.gov/doc/Library.html LAMMPS library interfaces
https://lammps.sandia.gov/doc/Modify.html how to modify and extend LAMMPS
https://lammps.sandia.gov/doc/Developer.html LAMMPS developer info
https://docs.lammps.org/Manual.html LAMMPS manual
https://docs.lammps.org/Intro.html hi-level introduction
https://docs.lammps.org/Build.html how to build LAMMPS
https://docs.lammps.org/Run_head.html how to run LAMMPS
https://docs.lammps.org/Commands_all.html Table of available commands
https://docs.lammps.org/Library.html LAMMPS library interfaces
https://docs.lammps.org/Modify.html how to modify and extend LAMMPS
https://docs.lammps.org/Developer.html LAMMPS developer info
You can also create these doc pages locally:

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bench/POTENTIALS/README
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@ -1,7 +1,7 @@
These are input scripts used to run benchmark tests for many of the
interatomic potentials in LAMMPS. The results of running these
scripts on different machines are shown on the Potentials section of
the Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
the Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
Examples are shown below of how to run these scripts. Log files for
running them on 1 and 4 processors of a Linux box are included in the

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bench/README
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@ -2,7 +2,7 @@ LAMMPS benchmark problems
This directory contains 5 benchmark problems which are discussed in
the Benchmark section of the LAMMPS documentation, and on the
Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
This directory also has several sub-directories:
@ -11,7 +11,7 @@ KEPLER benchmark scripts for GPU cluster with Kepler GPUs
POTENTIALS benchmarks scripts for various potentials in LAMMPS
The results for all of these benchmarks are displayed and discussed on
the Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench.
the Benchmark page of the LAMMPS WWW site: https://www.lammps.org/bench.html
The remainder of this file refers to the 5 problems in the top-level
of this directory and how to run them on CPUs, either in serial or

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cmake/Modules/CodingStandard.cmake
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@ -15,6 +15,11 @@ if(Python3_EXECUTABLE)
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for whitespace errors")
add_custom_target(
check-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for homepage URL errors")
add_custom_target(
check-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
@ -25,6 +30,11 @@ if(Python3_EXECUTABLE)
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix whitespace errors")
add_custom_target(
fix-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix homepage URL errors")
add_custom_target(
fix-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .

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cmake/pkgconfig/liblammps.pc.in
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@ -24,7 +24,7 @@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
Name: liblammps@LAMMPS_MACHINE@
Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
URL: http://lammps.sandia.gov
URL: https://www.lammps.org
Version: @PROJECT_VERSION@
Requires:
Libs: -L${libdir} -llammps@LAMMPS_MACHINE@

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doc/Makefile
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@ -68,7 +68,6 @@ help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html create HTML pages in html dir"
@echo " pdf create Manual.pdf in this dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@echo " (requires ebook-convert tool from calibre)"
@ -185,13 +184,6 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@rm -rf latex/PDF/.[sg]*
@echo "Build finished. Manual.pdf is in this directory."
fetch:
@rm -rf html_www Manual_www.pdf
@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
@tar xzf lammps-doc.tar.gz
@rm -f lammps-doc.tar.gz
anchor_check : $(ANCHORCHECK)
@(\
. $(VENV)/bin/activate ;\

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doc/README
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@ -25,16 +25,11 @@ github-development-workflow.md notes on the LAMMPS development workflow
include-file-conventions.md notes on LAMMPS' include file conventions
documentation_conventions.md notes on writing documentation for LAMMPS
If you downloaded a LAMMPS tarball from lammps.sandia.gov, then the html
If you downloaded a LAMMPS tarball from www.lammps.org, then the html
folder and the PDF manual should be included. If you downloaded LAMMPS
from GitHub then you either need to download them or build them.
from GitHub then you either need to build them.
(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
site. Just type "make fetch". This should create a html_www directory
and Manual_www.pdf file. These will always represent the latest published
patch/development version of LAMMPS.
(b) You can build the HTML and PDF files yourself, by typing "make html"
You can build the HTML and PDF files yourself, by typing "make html"
or by "make pdf", respectively. This requires various tools and files.
Some of them have to be installed (more on that below). For the rest the
build process will attempt to download and install into a python virtual
@ -78,4 +73,4 @@ the tool 'ebook-convert' from the 'calibre' e-book management software
----------------
More details this can be found in the manual itself. The online
version is at: https://lammps.sandia.gov/doc/Manual_build.html
version is at: https://docs.lammps.org/Build_manual.html

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doc/src/Build_development.rst
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@ -28,7 +28,7 @@ variable VERBOSE set to 1:
----------
.. _clang-tidy
.. _clang-tidy:
Enable static code analysis with clang-tidy
-------------------------------------------
@ -469,12 +469,24 @@ The following options are available.
.. code-block:: bash
make check-whitespace # generate coverage report in HTML format
make fix-whitespace # generate coverage report in XML format
make check-permissions # delete folder with HTML format coverage report
make fix-permissions # delete all collected coverage data and HTML output
make check-whitespace # search for files with whitespace issues
make fix-whitespace # correct whitespace issues in files
make check-homepage # search for files with old LAMMPS homepage URLs
make fix-homepage # correct LAMMPS homepage URLs in files
make check-permissions # search for files with permissions issues
make fix-permissions # correct permissions issues in files
For the code in the ``unittest`` tree we are using the `clang-format`
tool (Clang version 8.0 or later is required). If available, the source
code files in the ``unittest`` tree can be updated to conform to the
formatting settings using ``make format-tests``.
For the code in the ``unittest`` and ``src`` trees we are transitioning
to use the `clang-format` tool to assist with having a consistent source
code style. The `clang-format` command bundled with Clang version 8.0
or later is required. The configuration is in files ``.clang-format``
in the respective folders. Since the modifications from `clang-format`
can be significant and - especially for "legacy style code" - also is
not always improving readability, a large number of files currently have
a ``// clang-format off`` at the top, which will disable the processing.
Over time, files will be refactored and updated to that `clang-format`
may be applied to them (at least in part).
If `clang-format` is available, the source code files in the ``unittest``
tree can be updated to conform to the formatting settings using
``make format-tests`` and the files in ``src`` with ``make format-src``.

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doc/src/Build_manual.rst
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@ -28,29 +28,18 @@ If you downloaded LAMMPS as a tarball from `the LAMMPS website <lws_>`_,
the html folder and the PDF files should be included.
If you downloaded LAMMPS from the public git repository, then the HTML
and PDF files are not included. Instead you need to create them, in one
of two ways:
a. You can "fetch" the current HTML and PDF files from the LAMMPS web
site. Just type ``make fetch``. This should download a ``html_www``
directory and a ``Manual_www.pdf`` file. Note that if new LAMMPS features
have been added more recently than the date of your LAMMPS version, the
fetched documentation will include those changes (but your source code
will not, unless you update your local repository).
b. You can build the HTML or PDF files yourself, by typing ``make html``
or ``make pdf`` in the ``doc`` folder. This requires various tools
and files. Some of them have to be installed (see below). For the
rest the build process will attempt to download and install them into
a python virtual environment and local folders.
and PDF files are not included. You can build the HTML or PDF files yourself,
by typing ``make html`` or ``make pdf`` in the ``doc`` folder. This requires
various tools and files. Some of them have to be installed (see below). For
the rest the build process will attempt to download and install them into
a python virtual environment and local folders.
A current version of the manual (latest patch release, aka unstable
branch) is is available online at:
`https://lammps.sandia.gov/doc/Manual.html
<https://lammps.sandia.gov/doc/Manual.html>`_ A version of the manual
corresponding to the ongoing development (aka master branch) is
available online at: `https://docs.lammps.org/
<https://docs.lammps.org/>`_
`https://docs.lammps.org/Manual.html <https://docs.lammps.org/Manual.html>`_.
A version of the manual corresponding to the ongoing development (aka master branch)
is available online at: `https://docs.lammps.org/latest/
<https://docs.lammps.org/latest/>`_
Build using GNU make
--------------------
@ -257,4 +246,4 @@ the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org

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doc/src/Errors_bugs.rst
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@ -5,8 +5,8 @@ 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
<https://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site
<https://lammps.sandia.gov>`_ or the
<https://www.lammps.org/bug.html>`_ section of the `LAMMPS WWW site
<https://www.lammps.org>`_ or the
`GitHub Releases page <https://github.com/lammps/lammps/releases>`_ to
see if the bug has already been addressed in a patch release.
* Check that your issue can be reproduced with the latest development
@ -17,7 +17,7 @@ the steps outlined below:
if your issue has already been reported and if it is still open.
* Check the `GitHub Pull Requests page <https://github.com/lammps/lammps/pulls>`_
to see if there is already a fix for your bug pending.
* Check the `mailing list archives <https://lammps.sandia.gov/mail.html>`_
* Check the `mailing list archives <https://www.lammps.org/mail.html>`_
to see if the issue has been discussed before.
If none of these steps yields any useful information, please file a new

2
doc/src/Errors_common.rst
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@ -39,7 +39,7 @@ figure out your physics or numerical mistakes, like choosing too big a
timestep, specifying erroneous force field coefficients, or putting 2
atoms on top of each other! If you run into errors that LAMMPS
does not catch that you think it should flag, please send an email to
the `developers <https://lammps.sandia.gov/authors.html>`_.
the `developers <https://www.lammps.org/authors.html>`_.
If you get an error message about an invalid command in your input
script, you can determine what command is causing the problem by

2
doc/src/Errors_messages.rst
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@ -3871,7 +3871,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Fix orient/fcc found self twice*
The neighbor lists used by fix orient/fcc are messed up. If this
error occurs, it is likely a bug, so send an email to the
`developers <https://lammps.sandia.gov/authors.html>`_.
`developers <https://www.lammps.org/authors.html>`_.
*Fix peri neigh does not exist*
Somehow a fix that the pair style defines has been deleted.

6
doc/src/Examples.rst
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@ -18,7 +18,7 @@ files and image files.
If you uncomment the :doc:`dump <dump>` command in the input script, a
text dump file will be produced, which can be animated by various
`visualization programs <https://lammps.sandia.gov/viz.html>`_.
`visualization programs <https://www.lammps.org/viz.html>`_.
If you uncomment the :doc:`dump image <dump>` command in the input
script, and assuming you have built LAMMPS with a JPG library, JPG
@ -27,7 +27,7 @@ be quickly post-processed into a movie using commands described on the
:doc:`dump image <dump_image>` doc page.
Animations of many of the examples can be viewed on the Movies section
of the `LAMMPS web site <https://lammps.sandia.gov/movies.html>`_.
of the `LAMMPS web site <https://www.lammps.org/movies.html>`_.
There are two kinds of sub-directories in the examples folder. Lower
case named directories contain one or a few simple, quick-to-run
@ -166,7 +166,7 @@ Here is how you can run and visualize one of the sample problems:
Running the simulation produces the files *dump.indent* and
*log.lammps*\ . You can visualize the dump file of snapshots with a
variety of third-party tools highlighted on the
`Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
`Visualization <https://www.lammps.org/viz.html>`_ page of the LAMMPS
web site.
If you uncomment the :doc:`dump image <dump_image>` line(s) in the input

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doc/src/Howto.rst
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@ -3,7 +3,7 @@ Howto discussions
These doc pages describe how to perform various tasks with LAMMPS,
both for users and developers. The
`glossary <https://lammps.sandia.gov/glossary.html>`_ website page also lists MD
`glossary <https://www.lammps.org/glossary.html>`_ website page also lists MD
terminology with links to corresponding LAMMPS manual pages. The
example input scripts included in the examples directory of the LAMMPS
distribution and highlighted on the :doc:`Examples <Examples>` doc page

2
doc/src/Howto_wsl.rst
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@ -201,7 +201,7 @@ build configuration and any binaries generated during compilation.
There are countless ways to compile LAMMPS. It is beyond the scope of this
tutorial. If you want to find out more about what can be enabled, please
consult the extensive `documentation <https://lammps.sandia.gov/doc/Build_cmake.html>`_.
consult the extensive `documentation <https://docs.lammps.org/Build_cmake.html>`_.
To compile a minimal version of LAMMPS, we're going to use a preset.
Presets are a way to specify a collection of CMake options using a file.

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doc/src/Install_git.rst
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@ -78,7 +78,7 @@ this is as follows.
$ git checkout tagID
Stable versions and what tagID to use for a particular stable version
are discussed on `this page <https://lammps.sandia.gov/bug.html#version>`_.
are discussed on `this page <https://www.lammps.org/bug.html#version>`_.
Note that this command will print some warnings, because in order to get
back to the latest revision and to be able to update with ``git pull``
again, you will need to do ``git checkout unstable`` (or

2
doc/src/Install_patch.rst
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@ -10,7 +10,7 @@ If you prefer to download a tarball, as described on the
:doc:`tarball download <Install_tarball>` page, you can stay current by
downloading "patch files" when new patch releases are made. A link to
a patch file is posted on the
`bug fixes and new feature page <https://lammps.sandia.gov/bug.html>`_
`bug fixes and new feature page <https://www.lammps.org/bug.html>`_
of the LAMMPS website, along
with a list of changed files and details about what is in the new patch
release. This page explains how to apply the patch file to your local

8
doc/src/Install_tarball.rst
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@ -4,10 +4,10 @@ Download source and documentation as a tarball
You can download a current LAMMPS tarball from the `download page <download_>`_
of the `LAMMPS website <lws_>`_.
.. _download: https://lammps.sandia.gov/download.html
.. _bug: https://lammps.sandia.gov/bug.html
.. _older: https://lammps.sandia.gov/tars
.. _lws: https://lammps.sandia.gov
.. _download: https://www.lammps.org/download.html
.. _bug: https://www.lammps.org/bug.html
.. _older: https://www.lammps.org/tars
.. _lws: https://www.lammps.org
You have two choices of tarballs, either the most recent stable
release or the most current patch release. Stable releases occur a

6
doc/src/Intro_authors.rst
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@ -11,14 +11,14 @@ University:
* Richard Berger, richard.berger at temple.edu
.. _sjp: http://www.cs.sandia.gov/~sjplimp
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
Past developers include Paul Crozier and Mark Stevens, both at Sandia,
and Ray Shan, now at Materials Design.
----------
The `Authors page <https://lammps.sandia.gov/authors.html>`_ of the
The `Authors page <https://www.lammps.org/authors.html>`_ of the
`LAMMPS website <lws_>`_ has a comprehensive list of all the individuals
who have contributed code for a new feature or command or tool to
LAMMPS.
@ -46,7 +46,7 @@ general-purpose as it is without their expertise and efforts.
----------
As discussed on the `History page <https://lammps.sandia.gov/history.html>`_ of the website, LAMMPS
As discussed on the `History page <https://www.lammps.org/history.html>`_ of the website, LAMMPS
originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:

4
doc/src/Intro_citing.rst
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@ -38,8 +38,8 @@ In addition there are DOIs for individual stable releases. Currently there are:
Home page
^^^^^^^^^
The LAMMPS website at `https://lammps.sandia.gov/
<https://lammps.sandia.gov>`_ is the canonical location for information
The LAMMPS website at `https://www.lammps.org/
<https://www.lammps.org>`_ is the canonical location for information
about LAMMPS and its features.
Citing contributions

4
doc/src/Intro_nonfeatures.rst
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@ -33,7 +33,7 @@ Here are suggestions on how to perform these tasks:
linear bead-spring polymer chains. The moltemplate program is a true
molecular builder that will generate complex molecular models. See
the :doc:`Tools <Tools>` doc page for details on tools packaged with
LAMMPS. The `Pre/post processing page <http:/lammps.sandia.gov/prepost.html>`_ of the LAMMPS website
LAMMPS. The `Pre/post processing page <http:/www.lammps.org/prepost.html>`_ of the LAMMPS website
describes a variety of third party tools for this task. Furthermore,
some LAMMPS internal commands allow to reconstruct, or selectively add
topology information, as well as provide the option to insert molecule
@ -67,7 +67,7 @@ Here are suggestions on how to perform these tasks:
them to an external program, `FFmpeg <https://www.ffmpeg.org>`_ to generate
movies from them. For high-quality, interactive visualization there are
many excellent and free tools available. See the
`Visualization Tools <https://lammps.sandia.gov/viz.html>`_ page of the
`Visualization Tools <https://www.lammps.org/viz.html>`_ page of the
LAMMPS website for
visualization packages that can process LAMMPS output data.
* **Plotting:** See the next bullet about Pizza.py as well as the

4
doc/src/Intro_overview.rst
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@ -16,10 +16,10 @@ shared-memory boxes and distributed-memory clusters and
supercomputers.
.. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
LAMMPS is written in C++. Earlier versions were written in F77 and
F90. See the `History page <https://lammps.sandia.gov/history.html>`_ of
F90. See the `History page <https://www.lammps.org/history.html>`_ of
the website for details. All versions can be downloaded from the
`LAMMPS website <lws_>`_.

40
doc/src/Intro_website.rst
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@ -5,31 +5,31 @@ The `LAMMPS website <lws_>`_ has a variety of additional info about
LAMMPS, beyond what is in this manual. Some other useful resources
available online are listed below.
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
* `Brief intro and recently added significant features <lws_>`_
* `List of features <https://lammps.sandia.gov/doc/Intro_features.html>`_
* `List of non-features <https://lammps.sandia.gov/doc/Intro_nonfeatures.html>`_
* `Recent bug fixes and new features <https://lammps.sandia.gov/bug.html>`_
* `List of features <https://docs.lammps.org/Intro_features.html>`_
* `List of non-features <https://docs.lammps.org/Intro_nonfeatures.html>`_
* `Recent bug fixes and new features <https://www.lammps.org/bug.html>`_
* `Download info <https://lammps.sandia.gov/download.html>`_
* `Download info <https://www.lammps.org/download.html>`_
* `GitHub site <https://github.com/lammps/lammps>`_
* `SourceForge site <https://sourceforge.net/projects/lammps>`_
* `LAMMPS open-source license <https://lammps.sandia.gov/doc/Intro_opensource.html>`_
* `LAMMPS open-source license <https://docs.lammps.org/Intro_opensource.html>`_
* `Glossary of terms relevant to LAMMPS <https://lammps.sandia.gov/glossary.html>`_
* `LAMMPS highlights with images <https://lammps.sandia.gov/pictures.html>`_
* `LAMMPS highlights with movies <https://lammps.sandia.gov/movies.html>`_
* `Mail list <https://lammps.sandia.gov/mail.html>`_
* `Workshops <https://lammps.sandia.gov/workshops.html>`_
* `Tutorials <https://lammps.sandia.gov/tutorials.html>`_
* `Glossary of terms relevant to LAMMPS <https://www.lammps.org/glossary.html>`_
* `LAMMPS highlights with images <https://www.lammps.org/pictures.html>`_
* `LAMMPS highlights with movies <https://www.lammps.org/movies.html>`_
* `Mail list <https://www.lammps.org/mail.html>`_
* `Workshops <https://www.lammps.org/workshops.html>`_
* `Tutorials <https://www.lammps.org/tutorials.html>`_
* `Pre- and post-processing tools for LAMMPS <https://lammps.sandia.gov/prepost.html>`_
* `Other software usable with LAMMPS <https://lammps.sandia.gov/offsite.html>`_
* `Viz tools usable with LAMMPS <https://lammps.sandia.gov/viz.html>`_
* `Pre- and post-processing tools for LAMMPS <https://www.lammps.org/prepost.html>`_
* `Other software usable with LAMMPS <https://www.lammps.org/offsite.html>`_
* `Viz tools usable with LAMMPS <https://www.lammps.org/viz.html>`_
* `Benchmark performance <https://lammps.sandia.gov/bench.html>`_
* `Publications that have cited LAMMPS <https://lammps.sandia.gov/papers.html>`_
* `Authors of LAMMPS <https://lammps.sandia.gov/authors.html>`_
* `History of LAMMPS development <https://lammps.sandia.gov/history.html>`_
* `Funding for LAMMPS <https://lammps.sandia.gov/funding.html>`_
* `Benchmark performance <https://www.lammps.org/bench.html>`_
* `Publications that have cited LAMMPS <https://www.lammps.org/papers.html>`_
* `Authors of LAMMPS <https://www.lammps.org/authors.html>`_
* `History of LAMMPS development <https://www.lammps.org/history.html>`_
* `Funding for LAMMPS <https://www.lammps.org/funding.html>`_

14
doc/src/Manual.rst
View File

@ -15,7 +15,7 @@ the GNU Public License (GPL).
The `LAMMPS website <lws_>`_ has a variety of information about the
code. It includes links to an on-line version of this manual, a
`mailing list <https://lammps.sandia.gov/mail.html>`_ where users can
`mailing list <https://www.lammps.org/mail.html>`_ where users can
post questions, and a `GitHub site <https://github.com/lammps/lammps>`_
where all LAMMPS development is coordinated.
@ -30,11 +30,13 @@ please :ref:`see this note <webbrowser>`.
-----------
The manual is organized in two parts:
The manual is organized in three parts:
1) the :ref:`User Guide <user_documentation>` for how to install
and use LAMMPS and 2) the :ref:`Programmer Guide <programmer_documentation>`
and use LAMMPS, 2) the :ref:`Programmer Guide <programmer_documentation>`
for how to write programs using the LAMMPS library from different
programming languages and how to modify and extend LAMMPS.
programming languages and how to modify and extend LAMMPS, and 3) the
:ref:`Command Reference <command_reference>` which includes detailed
descriptions of all commands included in the LAMMPS code.
.. only:: html
@ -42,7 +44,7 @@ programming languages and how to modify and extend LAMMPS.
:doc:`this page <Commands_all>` since it gives quick access
the documentation for all LAMMPS commands.
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
----------
@ -129,4 +131,4 @@ Indices and tables
where parts of the pages are not rendered as expected (e.g. the layout is
broken or mathematical expressions not typeset). In that case we
recommend to install/use a different/newer web browser or use
the `PDF version of the manual <https://lammps.sandia.gov/doc/Manual.pdf>`_.
the `PDF version of the manual <https://docs.lammps.org/Manual.pdf>`_.

2
doc/src/Manual_version.rst
View File

@ -5,7 +5,7 @@ The LAMMPS "version" is the date when it was released, such as 1 May
2014. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it in the next *patch* release, which are
typically made every couple of weeks. Info on patch releases are on
`this website page <https://lammps.sandia.gov/bug.html>`_. Every few
`this website page <https://www.lammps.org/bug.html>`_. Every few
months, the latest patch release is subjected to more thorough testing
and labeled as a *stable* version.

14
doc/src/Modify_contribute.rst
View File

@ -2,7 +2,7 @@ Submitting new features for inclusion in LAMMPS
===============================================
We encourage users to submit new features or modifications for LAMMPS to
`the core developers <https://lammps.sandia.gov/authors.html>`_ so they
`the core developers <https://www.lammps.org/authors.html>`_ so they
can be added to the LAMMPS distribution. The preferred way to manage and
coordinate this is via the LAMMPS project on `GitHub
<https://github.com/lammps/lammps>`_. Please see the :doc:`GitHub
@ -31,7 +31,7 @@ send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS
you are working on. Only discussions related to LAMMPS development are
tolerated, so this is **NOT** for people that look for help with compiling,
installing, or using LAMMPS. Please contact the `lammps-users mailing
list <https://lammps.sandia.gov/mail.html>`_ for those purposes instead.
list <https://www.lammps.org/mail.html>`_ for those purposes instead.
How quickly your contribution will be integrated depends largely on how
much effort it will cause to integrate and test it, how many and what
@ -67,7 +67,7 @@ distribution removed (e.g. interface to FFTW). See the
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
code and on the `Authors page <https://lammps.sandia.gov/authors.html>`_
code and on the `Authors page <https://www.lammps.org/authors.html>`_
of the `LAMMPS WWW site <lws_>`_), is a means for you to distribute your
work to the LAMMPS user community, and a mechanism for others to
easily try out your new feature. This may help you find bugs or make
@ -81,13 +81,13 @@ unusual event).
If you prefer to actively develop and support your add-on
feature yourself, then you may wish to make it available for download
from your own website, as a user package that LAMMPS users can add to
their copy of LAMMPS. See the `Offsite LAMMPS packages and tools <https://lammps.sandia.gov/offsite.html>`_ page of the LAMMPS web
their copy of LAMMPS. See the `Offsite LAMMPS packages and tools <https://www.lammps.org/offsite.html>`_ page of the LAMMPS web
site for examples of groups that do this. We are happy to advertise
your package and web site from that page. Simply email the
`developers <https://lammps.sandia.gov/authors.html>`_ with info about
`developers <https://www.lammps.org/authors.html>`_ with info about
your package and we will post it there.
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
The previous sections of this doc page describe how to add new "style"
files of various kinds to LAMMPS. Packages are simply collections of
@ -96,7 +96,7 @@ LAMMPS input script. If designed correctly, these additions typically
do not require changes to the main core of LAMMPS; they are simply
add-on files. If you think your new feature requires non-trivial
changes in core LAMMPS files, you should `communicate with the
developers <https://lammps.sandia.gov/authors.html>`_, since we may or
developers <https://www.lammps.org/authors.html>`_, since we may or
may not want to include those changes for some reason. An example of a
trivial change is making a parent-class method "virtual" when you derive
a new child class from it.

62
doc/src/Packages_details.rst
View File

@ -134,8 +134,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
* `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_
* examples/ASPHERE
* examples/ellipse
* https://lammps.sandia.gov/movies.html#line
* https://lammps.sandia.gov/movies.html#tri
* https://www.lammps.org/movies.html#line
* https://www.lammps.org/movies.html#tri
----------
@ -331,7 +331,7 @@ This package has :ref:`specific installation instructions <gpu>` on the :doc:`Bu
* :doc:`package gpu <package>`
* :doc:`Commands <Commands_all>` pages (:doc:`pair <Commands_pair>`, :doc:`kspace <Commands_kspace>`)
for styles followed by (g)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -357,11 +357,11 @@ potentials.
* examples/granregion
* examples/pour
* bench/in.chute
* https://lammps.sandia.gov/pictures.html#jamming
* https://lammps.sandia.gov/movies.html#hopper
* https://lammps.sandia.gov/movies.html#dem
* https://lammps.sandia.gov/movies.html#brazil
* https://lammps.sandia.gov/movies.html#granregion
* https://www.lammps.org/pictures.html#jamming
* https://www.lammps.org/movies.html#hopper
* https://www.lammps.org/movies.html#dem
* https://www.lammps.org/movies.html#brazil
* https://www.lammps.org/movies.html#granregion
----------
@ -480,7 +480,7 @@ This package has :ref:`specific installation instructions <kokkos>` on the :doc:
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
:doc:`kspace <Commands_kspace>`) for styles followed by (k)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -604,7 +604,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
* :doc:`fix tfmc <fix_tfmc>`
* :doc:`fix widom <fix_widom>`
* :doc:`pair_style dsmc <pair_dsmc>`
* https://lammps.sandia.gov/movies.html#gcmc
* https://www.lammps.org/movies.html#gcmc
----------
@ -661,8 +661,8 @@ listing, "ls src/MISC", to see the list of commands.
* :doc:`fix viscosity <fix_viscosity>`
* examples/KAPPA
* examples/VISCOSITY
* https://lammps.sandia.gov/pictures.html#ttm
* https://lammps.sandia.gov/movies.html#evaporation
* https://www.lammps.org/pictures.html#ttm
* https://www.lammps.org/movies.html#evaporation
----------
@ -817,7 +817,7 @@ This package has :ref:`specific installation instructions <opt>` on the :doc:`Bu
* :doc:`OPT package <Speed_opt>`
* :doc:`Section 2.6 -sf opt <Run_options>`
* Search the :doc:`pair style <Commands_pair>` page for styles followed by (t)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -848,7 +848,7 @@ Foster (UTSA).
* :doc:`compute damage/atom <compute_damage_atom>`
* :doc:`compute plasticity/atom <compute_plasticity_atom>`
* examples/peri
* https://lammps.sandia.gov/movies.html#peri
* https://www.lammps.org/movies.html#peri
----------
@ -1009,8 +1009,8 @@ Also several computes which calculate properties of rigid bodies.
* examples/ASPHERE
* examples/rigid
* bench/in.rhodo
* https://lammps.sandia.gov/movies.html#box
* https://lammps.sandia.gov/movies.html#star
* https://www.lammps.org/movies.html#box
* https://www.lammps.org/movies.html#star
----------
@ -1111,9 +1111,9 @@ colloidal particles.
* :doc:`fix wall/srd <fix_wall_srd>`
* examples/srd
* examples/ASPHERE
* https://lammps.sandia.gov/movies.html#tri
* https://lammps.sandia.gov/movies.html#line
* https://lammps.sandia.gov/movies.html#poly
* https://www.lammps.org/movies.html#tri
* https://www.lammps.org/movies.html#line
* https://www.lammps.org/movies.html#poly
----------
@ -1205,7 +1205,7 @@ This package has :ref:`specific installation instructions <user-atc>` on the :do
* src/USER-ATC/README
* :doc:`fix atc <fix_atc>`
* examples/USER/atc
* https://lammps.sandia.gov/pictures.html#atc
* https://www.lammps.org/pictures.html#atc
----------
@ -1338,7 +1338,7 @@ acids.
* :doc:`pair_style lj/sdk/\* <pair_sdk>`
* :doc:`angle_style sdk <angle_sdk>`
* examples/USER/cgsdk
* https://lammps.sandia.gov/pictures.html#cg
* https://www.lammps.org/pictures.html#cg
----------
@ -1575,7 +1575,7 @@ tools/eff; see its README file.
* examples/USER/eff
* tools/eff/README
* tools/eff
* https://lammps.sandia.gov/movies.html#eff
* https://www.lammps.org/movies.html#eff
----------
@ -1717,7 +1717,7 @@ This package has :ref:`specific installation instructions <user-intel>` on the :
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`kspace <Commands_kspace>`) for styles followed by (i)
* src/USER-INTEL/TEST
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -1822,7 +1822,7 @@ Waltham, MA, USA)
* :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
* :doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>`
* examples/USER/manifold
* https://lammps.sandia.gov/movies.html#manifold
* https://www.lammps.org/movies.html#manifold
----------
@ -1900,10 +1900,10 @@ algorithm.
* :doc:`pair_style tdpd <pair_mesodpd>`
* :doc:`fix mvv/dpd <fix_mvv_dpd>`
* examples/USER/mesodpd
* https://lammps.sandia.gov/movies.html#mesodpd
* https://www.lammps.org/movies.html#mesodpd
* examples/USER/meso
* http://lammps.sandia.gov/movies.html#mesodpd
* http://www.lammps.org/movies.html#mesodpd
----------
@ -2119,7 +2119,7 @@ This package has :ref:`specific installation instructions <user-omp>` on the :do
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
:doc:`kspace <Commands_kspace>`) for styles followed by (o)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -2302,8 +2302,8 @@ molecules, and chiral-sensitive reactions.
* src/USER-REACTION/README
* :doc:`fix bond/react <fix_bond_react>`
* examples/USER/reaction
* `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_
* `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_
* `2017 LAMMPS Workshop <https://www.lammps.org/workshops/Aug17/pdf/gissinger.pdf>`_
* `2019 LAMMPS Workshop <https://www.lammps.org/workshops/Aug19/talk_gissinger.pdf>`_
* reacter.org
----------
@ -2430,7 +2430,7 @@ This package has :ref:`specific installation instructions <user-smd>` on the :do
* src/USER-SMD/README
* doc/PDF/SMD_LAMMPS_userguide.pdf
* examples/USER/smd
* https://lammps.sandia.gov/movies.html#smd
* https://www.lammps.org/movies.html#smd
----------
@ -2487,7 +2487,7 @@ Dynamics, Ernst Mach Institute, Germany).
* src/USER-SPH/README
* doc/PDF/SPH_LAMMPS_userguide.pdf
* examples/USER/sph
* https://lammps.sandia.gov/movies.html#sph
* https://www.lammps.org/movies.html#sph
----------

6
doc/src/Packages_standard.rst
View File

@ -39,13 +39,13 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair_style lj/.../dipole <pair_dipole>` | dipole | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | int |
| :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`GRANULAR <PKG-GRANULAR>` | granular systems | :doc:`Howto granular <Howto_granular>` | pour | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KIM <PKG-KIM>` | OpenKIM wrapper | :doc:`pair_style kim <pair_kim>` | kim | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KOKKOS <PKG-KOKKOS>` | Kokkos-enabled styles | :doc:`Speed kokkos <Speed_kokkos>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
| :ref:`KOKKOS <PKG-KOKKOS>` | Kokkos-enabled styles | :doc:`Speed kokkos <Speed_kokkos>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KSPACE <PKG-KSPACE>` | long-range Coulombic solvers | :doc:`kspace_style <kspace_style>` | peptide | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
@ -67,7 +67,7 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MSCG <PKG-MSCG>` | multi-scale coarse-graining wrapper | :doc:`fix mscg <fix_mscg>` | mscg | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`OPT <PKG-OPT>` | optimized pair styles | :doc:`Speed opt <Speed_opt>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
| :ref:`OPT <PKG-OPT>` | optimized pair styles | :doc:`Speed opt <Speed_opt>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+

4
doc/src/Packages_user.rst
View File

@ -61,7 +61,7 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-HDNNP <PKG-USER-HDNNP>` | High-dimensional neural network potentials | :doc:`pair_style hdnnp <pair_hdnnp>` | USER/hdnnp | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-INTEL <PKG-USER-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
| :ref:`USER-INTEL <PKG-USER-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-LB <PKG-USER-LB>` | Lattice Boltzmann fluid | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
@ -85,7 +85,7 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-NETCDF <PKG-USER-NETCDF>` | dump output via NetCDF | :doc:`dump netcdf <dump_netcdf>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
| :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PACE <PKG-USER-PACE>` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | USER/pace | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+

2
doc/src/Speed.rst
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@ -12,7 +12,7 @@ accelerator packages provided with LAMMPS that contain code optimized
for certain kinds of hardware, including multi-core CPUs, GPUs, and
Intel Xeon Phi co-processors.
The `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the LAMMPS
The `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS
web site gives performance results for the various accelerator
packages discussed on the :doc:`Speed packages <Speed_packages>` doc
page, for several of the standard LAMMPS benchmark problems, as a

8
doc/src/Speed_bench.rst
View File

@ -1,7 +1,7 @@
Benchmarks
==========
Current LAMMPS performance is discussed on the `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of the `LAMMPS website <lws_>`_
Current LAMMPS performance is discussed on the `Benchmarks page <https://www.lammps.org/bench.html>`_ of the `LAMMPS website <lws_>`_
where timings and parallel efficiency are listed. The page has
several sections, which are briefly described below:
@ -43,11 +43,11 @@ to build LAMMPS and run on that kind of hardware.
The bench/POTENTIALS directory has input files which correspond to the
table of results on the
`Potentials <https://lammps.sandia.gov/bench.html#potentials>`_ section of
`Potentials <https://www.lammps.org/bench.html#potentials>`_ section of
the Benchmarks web page. So you can also run those test problems on
your machine.
The `billion-atom <https://lammps.sandia.gov/bench.html#billion>`_ section
The `billion-atom <https://www.lammps.org/bench.html#billion>`_ section
of the Benchmarks web page has performance data for very large
benchmark runs of simple Lennard-Jones (LJ) models, which use the
bench/in.lj input script.
@ -73,4 +73,4 @@ estimate parallel performance for multi-node runs using the same logic
as for all-MPI mode, except that now you will typically need many more
atoms/node to achieve good scalability.
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org

2
doc/src/Speed_gpu.rst
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@ -152,7 +152,7 @@ in OpenCL mode on CPUs (which uses vectorization and multithreading) is
usually resulting in inferior performance compared to using LAMMPS' native
threading and vectorization support in the USER-OMP and USER-INTEL packages.
See the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the
See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
LAMMPS web site for performance of the GPU package on various
hardware, including the Titan HPC platform at ORNL.

2
doc/src/Speed_kokkos.rst
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@ -406,7 +406,7 @@ Generally speaking, the following rules of thumb apply:
package also can increase the vector length of vector instructions
by switching to single or mixed precision mode.
See the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the
See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
LAMMPS web site for performance of the KOKKOS package on different
hardware.

2
doc/src/Speed_packages.rst
View File

@ -145,7 +145,7 @@ sub-directories with Make.py commands and input scripts for using all
the accelerator packages on various machines. See the README files in
those directories.
As mentioned above, the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the LAMMPS web site gives
As mentioned above, the `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS web site gives
performance results for the various accelerator packages for several
of the standard LAMMPS benchmark problems, as a function of problem
size and number of compute nodes, on different hardware platforms.

6
doc/src/Tools.rst
View File

@ -6,15 +6,15 @@ molecular dynamics computations. Additional pre- and post-processing
steps are often necessary to setup and analyze a simulation. A list
of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links:
* `Pre/Post processing <https://lammps.sandia.gov/prepost.html>`_
* `Offsite LAMMPS packages & tools <https://lammps.sandia.gov/offsite.html>`_
* `Pre/Post processing <https://www.lammps.org/prepost.html>`_
* `Offsite LAMMPS packages & tools <https://www.lammps.org/offsite.html>`_
* `Pizza.py toolkit <pizza_>`_
The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at
Sandia which provides tools for doing setup, analysis, plotting, and
visualization for LAMMPS simulations.
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
.. _pizza: https://pizza.sandia.gov
.. _python: https://www.python.org

2
doc/src/atom_modify.rst
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@ -80,7 +80,7 @@ LAMMPS commands require a map, even for atomic systems, and will
generate an error if one does not exist. The *map* keyword thus
allows you to force the creation of a map. The *yes* value will
create either an *array* or *hash* style map, as explained in the next
paragraph. The *array* and *hash* values create an atom-style or
paragraph. The *array* and *hash* values create an array-style or
hash-style map respectively.
For an *array*\ -style map, each processor stores a lookup table of

2
doc/src/fix_wall_gran_region.rst
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@ -65,7 +65,7 @@ non-granular particles and simpler wall geometries, respectively.
Here are snapshots of example models using this command. Corresponding
input scripts can be found in examples/granregion. Movies of these
simulations are `here on the Movies page <https://lammps.sandia.gov/movies.html#granregion>`_
simulations are `here on the Movies page <https://www.lammps.org/movies.html#granregion>`_
of the LAMMPS web site.
.. |wallgran1| image:: img/gran_funnel.png

4
examples/ASPHERE/README
View File

@ -10,7 +10,7 @@ systems. Some of the directories include a Python script, which can
be used with the Pizza.py tool to create the data file, e.g. for
collections of rigid bodies.
The web site for Pizza.py is http://pizza.sandia.gov
The web site for Pizza.py is https://pizza.sandia.gov
For example, If you have Pizza.py installed you can type "pizza.py -f
box.py", which creates the data.box data file in the box dir.
@ -18,7 +18,7 @@ box.py", which creates the data.box data file in the box dir.
If you uncomment the dump or dump image lines in the input scripts the
runs will produce dump files or JPG images which you can view or
animate. See the Movies page of the LAMMPS web site
(http://lammps.sandia.gov/movies.html), for animations of these
(https://www.lammps.org/movies.html), for animations of these
scripts. Most were done using the dump image command. A few were
done using the gl tool in Pizza.py; the Pizza.py scripts that do the
animation are given in the directory, e.g. as line.viz.py.

2
examples/COUPLE/fortran2/LAMMPS-wrapper.cpp
View File

@ -1,6 +1,6 @@
/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp
View File

@ -1,6 +1,6 @@
/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp
View File

@ -1,6 +1,6 @@
/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/lammps_mc/mc.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
------------------------------------------------------------------------- */

2
examples/COUPLE/lammps_mc/mc.h
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
------------------------------------------------------------------------- */

2
examples/COUPLE/lammps_mc/random_park.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/lammps_mc/random_park.h
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/lammps_nwchem/nwchem_wrap.py
View File

@ -2,7 +2,7 @@
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# https://www.lammps.org/ Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
# ----------------------------------------------------------------------

2
examples/COUPLE/lammps_vasp/vasp_wrap.py
View File

@ -2,7 +2,7 @@
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# https://www.lammps.org/ Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
# ----------------------------------------------------------------------

2
examples/COUPLE/multiple/multiple.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/COUPLE/simple/simple.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/
https://www.lammps.org/
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/README
View File

@ -37,7 +37,7 @@ produce dump snapshots of the running simulation in any of 3 formats.
If you uncomment the dump command in the input script, a text dump
file will be produced, which can be animated by various visualization
programs (see http://lammps.sandia.gov/viz.html) such as Ovito, VMD,
programs (see https://www.lammps.org/viz.html) such as Ovito, VMD,
or AtomEye.
If you uncomment the dump image command in the input script, and

2
examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py
View File

@ -2,7 +2,7 @@
"""
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/USER/cgdna/util/generate.py
View File

@ -2,7 +2,7 @@
"""
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/USER/diffraction/Output/log.cite
View File

@ -1,5 +1,5 @@
This LAMMPS simulation made specific use of work described in the
following references. See http://lammps.sandia.gov/cite.html
following references. See https://www.lammps.org/cite.html
for details.
compute_xrd command:

2
examples/VISCOSITY/README
View File

@ -28,7 +28,7 @@ minute or so and produce the accompanying log files and profile files
(for velocity or momentum flux).
See the Movies page of the LAMMPS web site
(http://lammps.sandia.gov/movies.html), for animations of the NEMD
(https://www.lammps.org/movies.html), for animations of the NEMD
scripts, created using the dump image command.
The state point of the LJ fluid is rho* = 0.6, T* = 1.0, and Rcut =

6
examples/kim/in.kim-pm-property
View File

@ -11,18 +11,18 @@
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
# `https://docs.lammps.org/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
# installed. See the `https://docs.lammps.org/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
# `https://docs.lammps.org/Build_extras.html#kim` doc page for
# further details.
#
# This example requires that the KIM Portable Model (PM)

2
examples/kim/in.kim-query
View File

@ -6,7 +6,7 @@
# the KIM package, is the KIM API library that must be downloaded from the
# OpenKIM website and installed before LAMMPS is compiled. The 'kim query'
# command requires the libcurl library to be installed. See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for further
# `https://docs.lammps.org/Build_extras.html#kim` doc page for further
# details
#
# This example requires that the KIM Models

6
examples/kim/log.10Feb21.in.kim-pm-property.clang.1
View File

@ -12,18 +12,18 @@ LAMMPS (10 Feb 2021)
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
# `https://docs.lammps.org/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
# installed. See the `https://docs.lammps.org/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
# `https://docs.lammps.org/Build_extras.html#kim` doc page for
# further details.
#
# This example requires that the KIM Portable Model (PM)

6
examples/kim/log.10Feb21.in.kim-pm-property.clang.4
View File

@ -12,18 +12,18 @@ LAMMPS (10 Feb 2021)
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
# `https://docs.lammps.org/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
# installed. See the `https://docs.lammps.org/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
# `https://docs.lammps.org/Build_extras.html#kim` doc page for
# further details.
#
# This example requires that the KIM Portable Model (PM)

2
examples/kim/log.10Feb21.in.kim-query.clang.1
View File

@ -7,7 +7,7 @@ LAMMPS (10 Feb 2021)
# the KIM package, is the KIM API library that must be downloaded from the
# OpenKIM website and installed before LAMMPS is compiled. The 'kim query'
# command requires the libcurl library to be installed. See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for further
# `https://docs.lammps.org/Build_extras.html#kim` doc page for further
# details
#
# This example requires that the KIM Models

2
examples/plugins/angle_zero2.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/angle_zero2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/bond_zero2.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/bond_zero2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/dihedral_zero2.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/dihedral_zero2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/fix_nve2.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/fix_nve2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/improper_zero2.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/improper_zero2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/pair_morse2.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/pair_morse2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/pair_morse2_omp.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
This software is distributed under the GNU General Public License.

2
examples/plugins/pair_morse2_omp.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/pair_zero2.cpp
View File

@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

2
examples/plugins/pair_zero2.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract

4
examples/reax/HNS/README.txt
View File

@ -15,7 +15,7 @@ Questions: Mitchell Wood, mitwood@sandia.gov
The file is read line by line looking for keywords to set up this run.
It will read in the configuration given by the argument of the read_data command, which is supplied in this distribution.
The type of simulation is set by the 'fix' commands, dynamic charges are controlled with 'fix qeq' and the integration style is given as 'fix nve' here.
More information about each of the individual commands can be found online at lammps.sandia.gov in the user manual section.
More information about each of the individual commands can be found online at www.lammps.org in the user manual section.
*There are four free variables in this file, three of which control the size of the simulation and the last will dictate how many MD time steps are taken.
*The size of the system is controlled by the 'replicate' command given the values of $x, $y and $z.
@ -27,7 +27,7 @@ Questions: Mitchell Wood, mitwood@sandia.gov
lmp_serial -in in.reaxc.hns -v x 2 -v y 2 -v z 2 -v t 100
2) LAMMPS Data file for crystalline HNS
This file matches the LAMMPS data format, more information about this data structure can be found at lammps.sandia.gov
This file matches the LAMMPS data format, more information about this data structure can be found at www.lammps.org
This particular data file is of the energetic material Hexanitrostilbene (HNS) with atom_style charge (id type q x y z).
The file contains eight molecules (2 unit cells).

2
fortran/lammps.f90
View File

@ -1,6 +1,6 @@
! -------------------------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/gpu/README
View File

@ -29,7 +29,7 @@ LAMMPS styles and neighbor list builds using CUDA, OpenCL, or ROCm HIP.
Pair styles supported by this library are marked in the list of Pair style
potentials with a "g". See the online version at:
https://lammps.sandia.gov/doc/Commands_pair.html
https://docs.lammps.org/Commands_pair.html
In addition the (plain) pppm kspace style is supported as well.

2
lib/mesont/CNTPot.f90
View File

@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/mesont/ExportCNT.f90
View File

@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/mesont/LinFun2.f90
View File

@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/mesont/Spline1.f90
View File

@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/mesont/Spline2.f90
View File

@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/mesont/TPMForceField.f90
View File

@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/mesont/TPMGeom.f90
View File

@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/mesont/TPMLib.f90
View File

@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/mesont/TPMM0.f90
View File

@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/mesont/TPMM1.f90
View File

@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/mesont/TubePotBase.f90
View File

@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/mesont/TubePotMono.f90
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@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
lib/mesont/TubePotTrue.f90
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@ -1,6 +1,6 @@
! ------------ ----------------------------------------------------------
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
! http://lammps.sandia.gov, Sandia National Laboratories
! https://www.lammps.org/ Sandia National Laboratories
! Steve Plimpton, sjplimp@sandia.gov
!
! Copyright (2003) Sandia Corporation. Under the terms of Contract

2
python/examples/pylammps/README.md
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@ -4,7 +4,7 @@ This folder contains examples showcasing the usage of the PyLammps Python
interface and Jupyter notebooks. To use this you will need LAMMPS compiled as
a shared library and the LAMMPS Python package installed.
An extensive guide on how to achieve this is documented in the [LAMMPS manual](https://lammps.sandia.gov/doc/Python_install.html). There is also a [PyLammps tutorial](https://lammps.sandia.gov/doc/Howto_pylammps.html).
An extensive guide on how to achieve this is documented in the [LAMMPS manual](https://docs.lammps.org/Python_install.html). There is also a [PyLammps tutorial](https://docs.lammps.org/Howto_pylammps.html).
The following will show one way of creating a Python virtual environment
which has both LAMMPS and its Python package installed:

2
python/examples/pylammps/interface_usage.ipynb
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@ -13,7 +13,7 @@
"source": [
"## Prerequisites\n",
"\n",
"Before running this example, make sure your Python environment can find the LAMMPS shared library (`liblammps.so`) and the LAMMPS Python package is installed. If you followed the [README](README.md) in this folder, this should already be the case. You can also find more information about how to compile LAMMPS and install the LAMMPS Python package in the [LAMMPS manual](https://lammps.sandia.gov/doc/Python_install.html). There is also a dedicated [PyLammps HowTo](https://lammps.sandia.gov/doc/Howto_pylammps.html)."
"Before running this example, make sure your Python environment can find the LAMMPS shared library (`liblammps.so`) and the LAMMPS Python package is installed. If you followed the [README](README.md) in this folder, this should already be the case. You can also find more information about how to compile LAMMPS and install the LAMMPS Python package in the [LAMMPS manual](https://docs.lammps.org/Python_install.html). There is also a dedicated [PyLammps HowTo](https://docs.lammps.org/Howto_pylammps.html)."
]
},
{

2
python/examples/pylammps/interface_usage_bonds.ipynb
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@ -13,7 +13,7 @@
"source": [
"## Prerequisites\n",
"\n",
"Before running this example, make sure your Python environment can find the LAMMPS shared library (`liblammps.so`) and the LAMMPS Python package is installed. If you followed the [README](README.md) in this folder, this should already be the case. You can also find more information about how to compile LAMMPS and install the LAMMPS Python package in the [LAMMPS manual](https://lammps.sandia.gov/doc/Python_install.html). There is also a dedicated [PyLammps HowTo](https://lammps.sandia.gov/doc/Howto_pylammps.html)."
"Before running this example, make sure your Python environment can find the LAMMPS shared library (`liblammps.so`) and the LAMMPS Python package is installed. If you followed the [README](README.md) in this folder, this should already be the case. You can also find more information about how to compile LAMMPS and install the LAMMPS Python package in the [LAMMPS manual](https://docs.lammps.org/Python_install.html). There is also a dedicated [PyLammps HowTo](https://docs.lammps.org/Howto_pylammps.html)."
]
},
{

4
python/examples/pylammps/simple.ipynb
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@ -20,7 +20,7 @@
"source": [
"## Prerequisites\n",
"\n",
"Before Running this example, make sure your Python environment can find the LAMMPS shared library (`liblammps.so`) and the LAMMPS Python package is installed. If you followed the [README](README.md) in this folder, this should already be the case. You can also find more information about how to compile LAMMPS and install the LAMMPS Python package in the [LAMMPS manual](https://lammps.sandia.gov/doc/Python_install.html). There is also a dedicated [PyLammps HowTo](https://lammps.sandia.gov/doc/Howto_pylammps.html)."
"Before Running this example, make sure your Python environment can find the LAMMPS shared library (`liblammps.so`) and the LAMMPS Python package is installed. If you followed the [README](README.md) in this folder, this should already be the case. You can also find more information about how to compile LAMMPS and install the LAMMPS Python package in the [LAMMPS manual](https://docs.lammps.org/Python_install.html). There is also a dedicated [PyLammps HowTo](https://docs.lammps.org/Howto_pylammps.html)."
]
},
{
@ -111,7 +111,7 @@
"source": [
"## Visualizing the initial state\n",
"\n",
"`IPyLammps` allows you to visualize the current simulation state with the [image](https://lammps.sandia.gov/doc/Python_module.html#lammps.IPyLammps.image) command. Here we use it to create an image of the initial state of the system."
"`IPyLammps` allows you to visualize the current simulation state with the [image](https://docs.lammps.org/Python_module.html#lammps.IPyLammps.image) command. Here we use it to create an image of the initial state of the system."
]
},
{

2
python/install.py
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@ -112,7 +112,7 @@ setup_kwargs= dict(name="lammps",
version=verstr,
author="Steve Plimpton",
author_email="sjplimp@sandia.gov",
url="https://lammps.sandia.gov",
url="https://www.lammps.org",
description="LAMMPS Molecular Dynamics Python package",
license="GPL",
packages=pkgs,

2
python/lammps/constants.py
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@ -1,6 +1,6 @@
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# https://www.lammps.org/ Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract

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