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update lammps.sandia.gov URLs to use https://

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Axel Kohlmeyer 2020-03-12 00:28:28 -04:00
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2
doc/src/Build_basics.rst
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@ -412,7 +412,7 @@ your system.
You can also download a tarball of the documentation for the
current LAMMPS version (HTML and PDF files), from the website
`download page <http://lammps.sandia.gov/download.html>`_.
`download page <https://lammps.sandia.gov/download.html>`_.
**CMake build option**\ :

6
doc/src/Errors_bugs.rst
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@ -4,7 +4,7 @@ Reporting bugs
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
<https://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.
@ -14,7 +14,7 @@ If you are confident that you have found a bug in LAMMPS, please follow the step
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>`_
* Check the `mailing list archives <https://lammps.sandia.gov/mail.html>`_
to see if the issue has been discussed before.
If none of these steps yields any useful information, please file
@ -41,5 +41,5 @@ 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
.. _lws: https://lammps.sandia.gov
.. _gip: https://github.com/lammps/issues

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
doesn't catch that you think it should flag, please send an email to
the `developers <http://lammps.sandia.gov/authors.html>`_.
the `developers <https://lammps.sandia.gov/authors.html>`_.
If you get an error message about an invalid command in your input
script, you can determine what command is causing the problem by

2
doc/src/Errors_messages.rst
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@ -3845,7 +3845,7 @@ 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 <http://lammps.sandia.gov/authors.html>`_.
`developers <https://lammps.sandia.gov/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 <http://lammps.sandia.gov/viz.html>`_.
`visualization programs <https://lammps.sandia.gov/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
@ -164,7 +164,7 @@ 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 3rd-party tools highlighted on the
`Visualization <http://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
`Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
web site.
If you uncomment the :doc:`dump image <dump_image>` line(s) in the input
@ -223,4 +223,4 @@ 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
.. _lws: https://lammps.sandia.gov

2
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 <http://lammps.sandia.gov>`_ website page also lists MD
`glossary <https://lammps.sandia.gov>`_ 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_bash.rst
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@ -122,7 +122,7 @@ Option 1: Downloading LAMMPS tarball using wget
.. code-block:: bash
wget http://lammps.sandia.gov/tars/lammps-stable.tar.gz
wget https://lammps.sandia.gov/tars/lammps-stable.tar.gz
tar xvzf lammps-stable.tar.gz
cd lammps-31Mar17

2
doc/src/Install_patch.rst
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@ -8,7 +8,7 @@ how to stay current are on the
If you prefer to download a tarball, as described on the :doc:`Install git <Install_tarball>` doc page, you can stay current by
downloading "patch files" when new patch releases are made. A link to
a patch file is posted on the `bug and feature page <http://lammps.sandia.gov/bug.html>`_ of the LAMMPS website, along
a patch file is posted on the `bug and feature page <https://lammps.sandia.gov/bug.html>`_ of the LAMMPS website, along
with a list of changed files and details about what is in the new patch
release. This page explains how to apply the patch file to your local
LAMMPS directory.

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: http://lammps.sandia.gov/download.html
.. _bug: http://lammps.sandia.gov/bug.html
.. _older: http://lammps.sandia.gov/tars
.. _lws: http://lammps.sandia.gov
.. _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
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: http://lammps.sandia.gov
.. _lws: https://lammps.sandia.gov
Past developers include Paul Crozier and Mark Stevens, both at Sandia,
and Ray Shan, now at Materials Design.
----------
The `Authors page <http://lammps.sandia.gov/authors.html>`_ of the
The `Authors page <https://lammps.sandia.gov/authors.html>`_ of the
`LAMMPS website <lws_>`_ has a comprehensive list of all the individuals
who have contributed code for a new feature or command or tool to
LAMMPS.
@ -46,7 +46,7 @@ general-purpose as it is without their expertise and efforts.
----------
As discussed on the `History page <http://lammps.sandia.gov/history.html>`_ of the website, LAMMPS
As discussed on the `History page <https://lammps.sandia.gov/history.html>`_ of the website, LAMMPS
originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:

2
doc/src/Intro_nonfeatures.rst
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@ -66,7 +66,7 @@ Here are suggestions on how to perform these tasks:
on-the-fly via its :doc:`dump image <dump_image>` command and pass
them to an external program, `FFmpeg <https://www.ffmpeg.org>`_ to generate
movies from them. For high-quality, interactive visualization there are
many excellent and free tools available. See the `Other Codes page <http://lammps.sandia.gov/viz.html>`_ page of the LAMMPS website for
many excellent and free tools available. See the `Other Codes page <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS website for
visualization packages that can use LAMMPS output data.
* **Plotting:** See the next bullet about Pizza.py as well as the
:doc:`Python <Python_head>` doc page for examples of plotting LAMMPS

4
doc/src/Intro_overview.rst
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@ -16,10 +16,10 @@ shared-memory boxes and distributed-memory clusters and
supercomputers.
.. _mpi: http://www-unix.mcs.anl.gov/mpi
.. _lws: http://lammps.sandia.gov
.. _lws: https://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
F90. See the `History page <https://lammps.sandia.gov/history.html>`_ of
the website for details. All versions can be downloaded from the
`LAMMPS website <lws_>`_.

42
doc/src/Intro_website.rst
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@ -5,32 +5,32 @@ 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
.. _lws: https://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>`_
* `Recent bug fixes and new features <http://lammps.sandia.gov/bug.html>`_
* `List of features <https://lammps.sandia.gov/features.html>`_
* `List of non-features <https://lammps.sandia.gov/non_features.html>`_
* `Recent bug fixes and new features <https://lammps.sandia.gov/bug.html>`_
* `Download info <http://lammps.sandia.gov/download.html>`_
* `Download info <https://lammps.sandia.gov/download.html>`_
* `GitHub site <https://github.com/lammps/lammps>`_
* `SourceForge site <https://sourceforge.net/projects/lammps>`_
* `LAMMPS open-source license <http://lammps.sandia.gov/open_source.html>`_
* `LAMMPS open-source license <https://lammps.sandia.gov/open_source.html>`_
* `Glossary of MD terms relevant to LAMMPS <http://lammps.sandia.gov/glossary.html>`_
* `LAMMPS highlights with images <http://lammps.sandia.gov/pictures.html>`_
* `LAMMPS highlights with movies <http://lammps.sandia.gov/movies.html>`_
* `Mail list <http://lammps.sandia.gov/mail.html>`_
* `Workshops <http://lammps.sandia.gov/workshops.html>`_
* `Tutorials <http://lammps.sandia.gov/tutorials.html>`_
* `Developer guide <http://lammps.sandia.gov/Developer.pdf>`_
* `Glossary of MD 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>`_
* `Developer guide <https://lammps.sandia.gov/Developer.pdf>`_
* `Pre- and post-processing tools for LAMMPS <http://lammps.sandia.gov/prepost.html>`_
* `Other software usable with LAMMPS <http://lammps.sandia.gov/offsite.html>`_
* `Viz tools usable with LAMMPS <http://lammps.sandia.gov/viz.html>`_
* `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>`_
* `Benchmark performance <http://lammps.sandia.gov/bench.html>`_
* `Publications that have cited LAMMPS <http://lammps.sandia.gov/papers.html>`_
* `Authors of LAMMPS <http://lammps.sandia.gov/authors.html>`_
* `History of LAMMPS development <http://lammps.sandia.gov/history.html>`_
* `Funding for LAMMPS <http://lammps.sandia.gov/funding.html>`_
* `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>`_

4
doc/src/Manual.rst
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@ -18,7 +18,7 @@ LAMMPS is an open-source code, distributed freely under the terms of
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 <http://lammps.sandia.gov/mail.html>`_ where users can post
It includes links to an on-line version of this manual, a `mailing list <https://lammps.sandia.gov/mail.html>`_ where users can post
questions, and a `GitHub site <https://github.com/lammps/lammps>`_ where
all LAMMPS development is coordinated.
@ -35,7 +35,7 @@ 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
.. _lws: https://lammps.sandia.gov
.. toctree::
:maxdepth: 2

2
doc/src/Manual_version.rst
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@ -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 <http://lammps.sandia.gov/bug.html>`_. Every few
`this website page <https://lammps.sandia.gov/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
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@ -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 <http://lammps.sandia.gov/authors.html>`_ so they
to `the core developers <https://lammps.sandia.gov/authors.html>`_ so they
can be added to the LAMMPS distribution. The preferred way to manage
and coordinate this is as of Fall 2016 via the LAMMPS project on
`GitHub <https://github.com/lammps/lammps>`_. An alternative is to
@ -44,12 +44,12 @@ are listed and described on the :doc:`Packages details <Packages_details>` doc p
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
used as a license for the rest of LAMMPS. See the `Open source <http://lammps.sandia.gov/open_source.html>`_ page on the LAMMPS
used as a license for the rest of LAMMPS. See the `Open source <https://lammps.sandia.gov/open_source.html>`_ page on the LAMMPS
website for details.
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
code and on the `Authors page <http://lammps.sandia.gov/authors.html>`_
code and on the `Authors page <https://lammps.sandia.gov/authors.html>`_
of the `LAMMPS WWW site <lws_>`_), is a means for you to distribute your
work to the LAMMPS user community, and a mechanism for others to
easily try out your new feature. This may help you find bugs or make
@ -63,13 +63,13 @@ 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 <http://lammps.sandia.gov/offsite.html>`_ page of the LAMMPS web
their copy of LAMMPS. See the `Offsite LAMMPS packages and tools <https://lammps.sandia.gov/offsite.html>`_ page of the LAMMPS web
site for examples of groups that do this. We are happy to advertise
your package and web site from that page. Simply email the
`developers <http://lammps.sandia.gov/authors.html>`_ with info about
`developers <https://lammps.sandia.gov/authors.html>`_ with info about
your package and we will post it there.
.. _lws: http://lammps.sandia.gov
.. _lws: https://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
@ -78,7 +78,7 @@ 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 <http://lammps.sandia.gov/authors.html>`_, since we may or
developers <https://lammps.sandia.gov/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.

56
doc/src/Packages_details.rst
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@ -127,8 +127,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
* `doc/PDF/pair\_resquared\_extra.pdf <PDF/pair_resquared_extra.pdf>`_
* examples/ASPHERE
* examples/ellipse
* http://lammps.sandia.gov/movies.html#line
* http://lammps.sandia.gov/movies.html#tri
* https://lammps.sandia.gov/movies.html#line
* https://lammps.sandia.gov/movies.html#tri
----------
@ -322,7 +322,7 @@ 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 <http://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
----------
@ -348,11 +348,11 @@ potentials.
* examples/granregion
* examples/pour
* bench/in.chute
* http://lammps.sandia.gov/pictures.html#jamming
* http://lammps.sandia.gov/movies.html#hopper
* http://lammps.sandia.gov/movies.html#dem
* http://lammps.sandia.gov/movies.html#brazil
* http://lammps.sandia.gov/movies.html#granregion
* 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
----------
@ -461,7 +461,7 @@ 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 <http://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
----------
@ -581,7 +581,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
* :doc:`fix bond/swap <fix_bond_swap>`
* :doc:`fix gcmc <fix_gcmc>`
* :doc:`pair_style dsmc <pair_dsmc>`
* http://lammps.sandia.gov/movies.html#gcmc
* https://lammps.sandia.gov/movies.html#gcmc
----------
@ -638,8 +638,8 @@ listing, "ls src/MISC", to see the list of commands.
* :doc:`fix viscosity <fix_viscosity>`
* examples/KAPPA
* examples/VISCOSITY
* http://lammps.sandia.gov/pictures.html#ttm
* http://lammps.sandia.gov/movies.html#evaporation
* https://lammps.sandia.gov/pictures.html#ttm
* https://lammps.sandia.gov/movies.html#evaporation
----------
@ -759,7 +759,7 @@ This package has :ref:`specific installation instructions <opt>` on the :doc:`Bu
* :doc:`Speed opt <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 <http://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
----------
@ -790,7 +790,7 @@ Foster (UTSA).
* :doc:`compute damage/atom <compute_damage_atom>`
* :doc:`compute plasticity/atom <compute_plasticity_atom>`
* examples/peri
* http://lammps.sandia.gov/movies.html#peri
* https://lammps.sandia.gov/movies.html#peri
----------
@ -929,8 +929,8 @@ Also several computes which calculate properties of rigid bodies.
* examples/ASPHERE
* examples/rigid
* bench/in.rhodo
* http://lammps.sandia.gov/movies.html#box
* http://lammps.sandia.gov/movies.html#star
* https://lammps.sandia.gov/movies.html#box
* https://lammps.sandia.gov/movies.html#star
----------
@ -1029,9 +1029,9 @@ colloidal particles.
* :doc:`fix wall/srd <fix_wall_srd>`
* examples/srd
* examples/ASPHERE
* http://lammps.sandia.gov/movies.html#tri
* http://lammps.sandia.gov/movies.html#line
* http://lammps.sandia.gov/movies.html#poly
* https://lammps.sandia.gov/movies.html#tri
* https://lammps.sandia.gov/movies.html#line
* https://lammps.sandia.gov/movies.html#poly
----------
@ -1123,7 +1123,7 @@ This package has :ref:`specific installation instructions <user-atc>` on the :do
* src/USER-ATC/README
* :doc:`fix atc <fix_atc>`
* examples/USER/atc
* http://lammps.sandia.gov/pictures.html#atc
* https://lammps.sandia.gov/pictures.html#atc
----------
@ -1236,7 +1236,7 @@ acids.
* :doc:`pair_style lj/sdk/\* <pair_sdk>`
* :doc:`angle_style sdk <angle_sdk>`
* examples/USER/cgsdk
* http://lammps.sandia.gov/pictures.html#cg
* https://lammps.sandia.gov/pictures.html#cg
----------
@ -1433,7 +1433,7 @@ tools/eff; see its README file.
* examples/USER/eff
* tools/eff/README
* tools/eff
* http://lammps.sandia.gov/movies.html#eff
* https://lammps.sandia.gov/movies.html#eff
----------
@ -1541,7 +1541,7 @@ 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 <http://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
----------
@ -1646,7 +1646,7 @@ Waltham, MA, USA)
* :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
* :doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>`
* examples/USER/manifold
* http://lammps.sandia.gov/movies.html#manifold
* https://lammps.sandia.gov/movies.html#manifold
----------
@ -1702,7 +1702,7 @@ algorithm.
* :doc:`pair_style tdpd <pair_mesodpd>`
* :doc:`fix mvv/dpd <fix_mvv_dpd>`
* examples/USER/mesodpd
* http://lammps.sandia.gov/movies.html#mesodpd
* https://lammps.sandia.gov/movies.html#mesodpd
----------
@ -1874,7 +1874,7 @@ 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 <http://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
----------
@ -2185,7 +2185,7 @@ 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
* http://lammps.sandia.gov/movies.html#smd
* https://lammps.sandia.gov/movies.html#smd
----------
@ -2242,7 +2242,7 @@ Dynamics, Ernst Mach Institute, Germany).
* src/USER-SPH/README
* doc/PDF/SPH\_LAMMPS\_userguide.pdf
* examples/USER/sph
* http://lammps.sandia.gov/movies.html#sph
* https://lammps.sandia.gov/movies.html#sph
----------

134
doc/src/Packages_standard.rst
View File

@ -22,70 +22,70 @@ package:
* int = internal library: provided with LAMMPS, but you may need to build it
* ext = external library: you will need to download and install it on your machine
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| Package | Description | Doc page | Example | Library |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`ASPHERE <PKG-ASPHERE>` | aspherical particle models | :doc:`Howto spherical <Howto_spherical>` | ellipse | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`BODY <PKG-BODY>` | body-style particles | :doc:`Howto body <Howto_body>` | body | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`CLASS2 <PKG-CLASS2>` | class 2 force fields | :doc:`pair_style lj/class2 <pair_class2>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`COLLOID <PKG-COLLOID>` | colloidal particles | :doc:`atom_style colloid <atom_style>` | colloid | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`COMPRESS <PKG-COMPRESS>` | I/O compression | :doc:`dump \*/gz <dump>` | n/a | sys |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`CORESHELL <PKG-CORESHELL>` | adiabatic core/shell model | :doc:`Howto coreshell <Howto_coreshell>` | coreshell | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair_style dipole/cut <pair_dipole>` | dipole | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`GRANULAR <PKG-GRANULAR>` | granular systems | :doc:`Howto granular <Howto_granular>` | pour | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`KIM <PKG-KIM>` | OpenKIM wrapper | :doc:`pair_style kim <pair_kim>` | kim | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`KOKKOS <PKG-KOKKOS>` | Kokkos-enabled styles | :doc:`Speed kokkos <Speed_kokkos>` | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`KSPACE <PKG-KSPACE>` | long-range Coulombic solvers | :doc:`kspace_style <kspace_style>` | peptide | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`LATTE <PKG-LATTE>` | quantum DFTB forces via LATTE | :doc:`fix latte <fix_latte>` | latte | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`MANYBODY <PKG-MANYBODY>` | many-body potentials | :doc:`pair_style tersoff <pair_tersoff>` | shear | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`MC <PKG-MC>` | Monte Carlo options | :doc:`fix gcmc <fix_gcmc>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`MESSAGE <PKG-MESSAGE>` | client/server messaging | :doc:`message <message>` | message | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`MISC <PKG-MISC>` | miscellaneous single-file commands | n/a | no | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`MOLECULE <PKG-MOLECULE>` | molecular system force fields | :doc:`Howto bioFF <Howto_bioFF>` | peptide | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`MPIIO <PKG-MPIIO>` | MPI parallel I/O dump and restart | :doc:`dump <dump>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :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 <http://lammps.sandia.gov/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`POEMS <PKG-POEMS>` | coupled rigid body motion | :doc:`fix poems <fix_poems>` | rigid | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`PYTHON <PKG-PYTHON>` | embed Python code in an input script | :doc:`python <python>` | python | sys |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`QEQ <PKG-QEQ>` | QEq charge equilibration | :doc:`fix qeq <fix_qeq>` | qeq | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`REPLICA <PKG-REPLICA>` | multi-replica methods | :doc:`Howto replica <Howto_replica>` | tad | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`RIGID <PKG-RIGID>` | rigid bodies and constraints | :doc:`fix rigid <fix_rigid>` | rigid | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`SHOCK <PKG-SHOCK>` | shock loading methods | :doc:`fix msst <fix_msst>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`SNAP <PKG-SNAP>` | quantum-fitted potential | :doc:`pair_style snap <pair_snap>` | snap | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`SPIN <PKG-SPIN>` | magnetic atomic spin dynamics | :doc:`Howto spins <Howto_spins>` | SPIN | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`SRD <PKG-SRD>` | stochastic rotation dynamics | :doc:`fix srd <fix_srd>` | srd | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`VORONOI <PKG-VORONOI>` | Voronoi tesselation | :doc:`compute voronoi/atom <compute_voronoi_atom>` | n/a | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| Package | Description | Doc page | Example | Library |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ASPHERE <PKG-ASPHERE>` | aspherical particle models | :doc:`Howto spherical <Howto_spherical>` | ellipse | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`BODY <PKG-BODY>` | body-style particles | :doc:`Howto body <Howto_body>` | body | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`CLASS2 <PKG-CLASS2>` | class 2 force fields | :doc:`pair_style lj/class2 <pair_class2>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`COLLOID <PKG-COLLOID>` | colloidal particles | :doc:`atom_style colloid <atom_style>` | colloid | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`COMPRESS <PKG-COMPRESS>` | I/O compression | :doc:`dump \*/gz <dump>` | n/a | sys |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`CORESHELL <PKG-CORESHELL>` | adiabatic core/shell model | :doc:`Howto coreshell <Howto_coreshell>` | coreshell | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair_style dipole/cut <pair_dipole>` | dipole | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`GRANULAR <PKG-GRANULAR>` | granular systems | :doc:`Howto granular <Howto_granular>` | pour | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KIM <PKG-KIM>` | OpenKIM wrapper | :doc:`pair_style kim <pair_kim>` | kim | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KOKKOS <PKG-KOKKOS>` | Kokkos-enabled styles | :doc:`Speed kokkos <Speed_kokkos>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KSPACE <PKG-KSPACE>` | long-range Coulombic solvers | :doc:`kspace_style <kspace_style>` | peptide | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`LATTE <PKG-LATTE>` | quantum DFTB forces via LATTE | :doc:`fix latte <fix_latte>` | latte | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MANYBODY <PKG-MANYBODY>` | many-body potentials | :doc:`pair_style tersoff <pair_tersoff>` | shear | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MC <PKG-MC>` | Monte Carlo options | :doc:`fix gcmc <fix_gcmc>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MESSAGE <PKG-MESSAGE>` | client/server messaging | :doc:`message <message>` | message | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MISC <PKG-MISC>` | miscellaneous single-file commands | n/a | no | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MOLECULE <PKG-MOLECULE>` | molecular system force fields | :doc:`Howto bioFF <Howto_bioFF>` | peptide | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MPIIO <PKG-MPIIO>` | MPI parallel I/O dump and restart | :doc:`dump <dump>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :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:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`POEMS <PKG-POEMS>` | coupled rigid body motion | :doc:`fix poems <fix_poems>` | rigid | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PYTHON <PKG-PYTHON>` | embed Python code in an input script | :doc:`python <python>` | python | sys |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`QEQ <PKG-QEQ>` | QEq charge equilibration | :doc:`fix qeq <fix_qeq>` | qeq | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`REPLICA <PKG-REPLICA>` | multi-replica methods | :doc:`Howto replica <Howto_replica>` | tad | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`RIGID <PKG-RIGID>` | rigid bodies and constraints | :doc:`fix rigid <fix_rigid>` | rigid | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`SHOCK <PKG-SHOCK>` | shock loading methods | :doc:`fix msst <fix_msst>` | n/a | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`SNAP <PKG-SNAP>` | quantum-fitted potential | :doc:`pair_style snap <pair_snap>` | snap | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`SPIN <PKG-SPIN>` | magnetic atomic spin dynamics | :doc:`Howto spins <Howto_spins>` | SPIN | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`SRD <PKG-SRD>` | stochastic rotation dynamics | :doc:`fix srd <fix_srd>` | srd | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`VORONOI <PKG-VORONOI>` | Voronoi tesselation | :doc:`compute voronoi/atom <compute_voronoi_atom>` | n/a | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+

170
doc/src/Packages_user.rst
View File

@ -28,91 +28,91 @@ package:
* int = internal library: provided with LAMMPS, but you may need to build it
* ext = external library: you will need to download and install it on your machine
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| Package | Description | Doc page | Example | Library |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-ADIOS <PKG-USER-ADIOS>` | dump output via ADIOS | :doc:`dump adios <dump_adios>` | USER/adios | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-ATC <PKG-USER-ATC>` | Atom-to-Continuum coupling | :doc:`fix atc <fix_atc>` | USER/atc | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-AWPMD <PKG-USER-AWPMD>` | wave packet MD | :doc:`pair_style awpmd/cut <pair_awpmd>` | USER/awpmd | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-BOCS <PKG-USER-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-CGDNA <PKG-USER-CGDNA>` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-CGSDK <PKG-USER-CGSDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-COLVARS <PKG-USER-COLVARS>` | collective variables library | :doc:`fix colvars <fix_colvars>` | USER/colvars | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>` | virtual x-ray and electron diffraction | :doc:`compute xrd <compute_xrd>` | USER/diffraction | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-DPD <PKG-USER-DPD>` | reactive dissipative particle dynamics | src/USER-DPD/README | USER/dpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-DRUDE <PKG-USER-DRUDE>` | Drude oscillators | :doc:`Howto drude <Howto_drude>` | USER/drude | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-EFF <PKG-USER-EFF>` | electron force field | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-FEP <PKG-USER-FEP>` | free energy perturbation | :doc:`compute fep <compute_fep>` | USER/fep | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-H5MD <PKG-USER-H5MD>` | dump output via HDF5 | :doc:`dump h5md <dump_h5md>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-INTEL <PKG-USER-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <http://lammps.sandia.gov/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-LB <PKG-USER-LB>` | Lattice Boltzmann fluid | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | USER/manifold | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MEAMC <PKG-USER-MEAMC>` | modified EAM potential (C++) | :doc:`pair_style meam/c <pair_meamc>` | meamc | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MESODPD <PKG-USER-MESODPD>` | mesoscale DPD models | :doc:`pair_style edpd <pair_mesodpd>` | USER/mesodpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MGPT <PKG-USER-MGPT>` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MISC <PKG-USER-MISC>` | single-file contributions | USER-MISC/README | USER/misc | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MOFFF <PKG-USER-MOFFF>` | styles for `MOF-FF <MOFplus_>`_ force field | :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` | USER/mofff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-MOLFILE <PKG-USER-MOLFILE>` | `VMD <https://www.ks.uiuc.edu/Research/vmd/>`_ molfile plug-ins | :doc:`dump molfile <dump_molfile>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :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 <http://lammps.sandia.gov/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-PHONON <PKG-USER-PHONON>` | phonon dynamical matrix | :doc:`fix phonon <fix_phonon>` | USER/phonon | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-PLUMED <PKG-USER-PLUMED>` | :ref:`PLUMED <PLUMED>` free energy library | :doc:`fix plumed <fix_plumed>` | USER/plumed | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-PTM <PKG-USER-PTM>` | Polyhedral Template Matching | :doc:`compute ptm/atom <compute_ptm_atom>` | n/a | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-QMMM <PKG-USER-QMMM>` | QM/MM coupling | :doc:`fix qmmm <fix_qmmm>` | USER/qmmm | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-QTB <PKG-USER-QTB>` | quantum nuclear effects | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-QUIP <PKG-USER-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | USER/quip | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-REACTION <PKG-USER-REACTION>` | chemical reactions in classical MD | :doc:`fix bond/react <fix_bond_react>` | USER/reaction | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-REAXC <PKG-USER-REAXC>` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc <pair_reaxc>` | reax | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos <kspace_style>` | USER/scafacos | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SDPD <PKG-USER-SDPD>` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | USER/sdpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SMD <PKG-USER-SMD>` | smoothed Mach dynamics | `SMD User Guide <PDF/SMD_LAMMPS_userguide.pdf>`_ | USER/smd | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | second moment tight binding QEq potential | :doc:`pair_style smtbq <pair_smtbq>` | USER/smtbq | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-SPH <PKG-USER-SPH>` | smoothed particle hydrodynamics | `SPH User Guide <PDF/SPH_LAMMPS_userguide.pdf>`_ | USER/sph | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-TALLY <PKG-USER-TALLY>` | pairwise tally computes | :doc:`compute XXX/tally <compute_tally>` | USER/tally | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-UEF <PKG-USER-UEF>` | extensional flow | :doc:`fix nvt/uef <fix_nh_uef>` | USER/uef | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-VTK <PKG-USER-VTK>` | dump output via VTK | :doc:`compute vtk <dump_vtk>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`USER-YAFF <PKG-USER-YAFF>` | additional styles implemented in YAFF | :doc:`angle_style cross <angle_cross>` | USER/yaff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| Package | Description | Doc page | Example | Library |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-ADIOS <PKG-USER-ADIOS>` | dump output via ADIOS | :doc:`dump adios <dump_adios>` | USER/adios | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-ATC <PKG-USER-ATC>` | Atom-to-Continuum coupling | :doc:`fix atc <fix_atc>` | USER/atc | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-AWPMD <PKG-USER-AWPMD>` | wave packet MD | :doc:`pair_style awpmd/cut <pair_awpmd>` | USER/awpmd | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-BOCS <PKG-USER-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-CGDNA <PKG-USER-CGDNA>` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-CGSDK <PKG-USER-CGSDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-COLVARS <PKG-USER-COLVARS>` | collective variables library | :doc:`fix colvars <fix_colvars>` | USER/colvars | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>` | virtual x-ray and electron diffraction | :doc:`compute xrd <compute_xrd>` | USER/diffraction | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-DPD <PKG-USER-DPD>` | reactive dissipative particle dynamics | src/USER-DPD/README | USER/dpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-DRUDE <PKG-USER-DRUDE>` | Drude oscillators | :doc:`Howto drude <Howto_drude>` | USER/drude | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-EFF <PKG-USER-EFF>` | electron force field | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-FEP <PKG-USER-FEP>` | free energy perturbation | :doc:`compute fep <compute_fep>` | USER/fep | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-H5MD <PKG-USER-H5MD>` | dump output via HDF5 | :doc:`dump h5md <dump_h5md>` | n/a | 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-LB <PKG-USER-LB>` | Lattice Boltzmann fluid | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | USER/manifold | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MEAMC <PKG-USER-MEAMC>` | modified EAM potential (C++) | :doc:`pair_style meam/c <pair_meamc>` | meamc | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MESODPD <PKG-USER-MESODPD>` | mesoscale DPD models | :doc:`pair_style edpd <pair_mesodpd>` | USER/mesodpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MGPT <PKG-USER-MGPT>` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MISC <PKG-USER-MISC>` | single-file contributions | USER-MISC/README | USER/misc | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MOFFF <PKG-USER-MOFFF>` | styles for `MOF-FF <MOFplus_>`_ force field | :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` | USER/mofff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MOLFILE <PKG-USER-MOLFILE>` | `VMD <https://www.ks.uiuc.edu/Research/vmd/>`_ molfile plug-ins | :doc:`dump molfile <dump_molfile>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :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-PHONON <PKG-USER-PHONON>` | phonon dynamical matrix | :doc:`fix phonon <fix_phonon>` | USER/phonon | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PLUMED <PKG-USER-PLUMED>` | :ref:`PLUMED <PLUMED>` free energy library | :doc:`fix plumed <fix_plumed>` | USER/plumed | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PTM <PKG-USER-PTM>` | Polyhedral Template Matching | :doc:`compute ptm/atom <compute_ptm_atom>` | n/a | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-QMMM <PKG-USER-QMMM>` | QM/MM coupling | :doc:`fix qmmm <fix_qmmm>` | USER/qmmm | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-QTB <PKG-USER-QTB>` | quantum nuclear effects | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-QUIP <PKG-USER-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | USER/quip | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-REACTION <PKG-USER-REACTION>` | chemical reactions in classical MD | :doc:`fix bond/react <fix_bond_react>` | USER/reaction | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-REAXC <PKG-USER-REAXC>` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc <pair_reaxc>` | reax | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos <kspace_style>` | USER/scafacos | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-SDPD <PKG-USER-SDPD>` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | USER/sdpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-SMD <PKG-USER-SMD>` | smoothed Mach dynamics | `SMD User Guide <PDF/SMD_LAMMPS_userguide.pdf>`_ | USER/smd | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | second moment tight binding QEq potential | :doc:`pair_style smtbq <pair_smtbq>` | USER/smtbq | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-SPH <PKG-USER-SPH>` | smoothed particle hydrodynamics | `SPH User Guide <PDF/SPH_LAMMPS_userguide.pdf>`_ | USER/sph | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-TALLY <PKG-USER-TALLY>` | pairwise tally computes | :doc:`compute XXX/tally <compute_tally>` | USER/tally | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-UEF <PKG-USER-UEF>` | extensional flow | :doc:`fix nvt/uef <fix_nh_uef>` | USER/uef | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-VTK <PKG-USER-VTK>` | dump output via VTK | :doc:`compute vtk <dump_vtk>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-YAFF <PKG-USER-YAFF>` | additional styles implemented in YAFF | :doc:`angle_style cross <angle_cross>` | USER/yaff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF
.. _PLUMED: http://www.plumed.org

2
doc/src/Run_options.rst
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@ -222,7 +222,7 @@ links with from the lib/message directory. See the
Disable writing the log.cite file which is normally written to list
references for specific cite-able features used during a LAMMPS run.
See the `citation page <http://lammps.sandia.gov/cite.html>`_ for more
See the `citation page <https://lammps.sandia.gov/cite.html>`_ for more
details.
----------

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 <http://lammps.sandia.gov/bench.html>`_ of the LAMMPS
The `Benchmark page <https://lammps.sandia.gov/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 <http://lammps.sandia.gov/bench.html>`_ of the `LAMMPS website <lws_>`_
Current LAMMPS performance is discussed on the `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of the `LAMMPS website <lws_>`_
where timings and parallel efficiency are listed. The page has
several sections, which are briefly described below:
@ -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 <http://lammps.sandia.gov/bench.html#potentials>`_ section of
`Potentials <https://lammps.sandia.gov/bench.html#potentials>`_ section of
the Benchmarks web page. So you can also run those test problems on
your machine.
The `billion-atom <http://lammps.sandia.gov/bench.html#billion>`_ section
The `billion-atom <https://lammps.sandia.gov/bench.html#billion>`_ section
of the Benchmarks web page has performance data for very large
benchmark runs of simple Lennard-Jones (LJ) models, which use the
bench/in.lj input script.
@ -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: http://lammps.sandia.gov
.. _lws: https://lammps.sandia.gov

2
doc/src/Speed_gpu.rst
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@ -123,7 +123,7 @@ 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 <http://lammps.sandia.gov/bench.html>`_ of the
See the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the
LAMMPS web site for performance of the GPU package on various
hardware, including the Titan HPC platform at ORNL.

2
doc/src/Speed_kokkos.rst
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@ -381,7 +381,7 @@ Generally speaking, the following rules of thumb apply:
* When running on Intel hardware, KOKKOS is not as fast as
the USER-INTEL package, which is optimized for that hardware.
See the `Benchmark page <http://lammps.sandia.gov/bench.html>`_ of the
See the `Benchmark page <https://lammps.sandia.gov/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 <http://lammps.sandia.gov/bench.html>`_ of the LAMMPS web site gives
As mentioned above, the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the LAMMPS web site gives
performance results for the various accelerator packages for several
of the standard LAMMPS benchmark problems, as a function of problem
size and number of compute nodes, on different hardware platforms.

2
doc/src/fix_wall_gran_region.rst
View File

@ -59,7 +59,7 @@ 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.
Click on the images to see a bigger picture. Movies of these
simulations are `here on the Movies page <http://lammps.sandia.gov/movies.html#granregion>`_ of the LAMMPS
simulations are `here on the Movies page <https://lammps.sandia.gov/movies.html#granregion>`_ of the LAMMPS
web site.
.. image:: JPG/gran_funnel_small.jpg