diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index a03f101d79..1f457c6b38 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -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 `_. + `download page `_. **CMake build option**\ : diff --git a/doc/src/Errors_bugs.rst b/doc/src/Errors_bugs.rst index 6cb313db97..e169b93d81 100644 --- a/doc/src/Errors_bugs.rst +++ b/doc/src/Errors_bugs.rst @@ -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 - `_ section of the `LAMMPS WWW site + `_ section of the `LAMMPS WWW site `_ 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 `_ if there is already a fix for your bug pending. - * Check the `mailing list archives `_ + * Check the `mailing list archives `_ 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 diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst index 133890c961..0926e3a72c 100644 --- a/doc/src/Errors_common.rst +++ b/doc/src/Errors_common.rst @@ -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 `_. +the `developers `_. If you get an error message about an invalid command in your input script, you can determine what command is causing the problem by diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 4955af773b..da36f18d82 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -3845,7 +3845,7 @@ Doc page with :doc:`WARNING messages ` *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 `_. + `developers `_. *Fix peri neigh does not exist* Somehow a fix that the pair style defines has been deleted. diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 365ff21db5..b45be6bcf0 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -18,7 +18,7 @@ files and image files. If you uncomment the :doc:`dump ` command in the input script, a text dump file will be produced, which can be animated by various -`visualization programs `_. +`visualization programs `_. If you uncomment the :doc:`dump image ` 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 `_ page of the LAMMPS +`Visualization `_ page of the LAMMPS web site. If you uncomment the :doc:`dump image ` line(s) in the input @@ -223,4 +223,4 @@ instructions. See the :doc:`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 diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index b9109d921f..f4376898b1 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -3,7 +3,7 @@ Howto discussions These doc pages describe how to perform various tasks with LAMMPS, both for users and developers. The -`glossary `_ website page also lists MD +`glossary `_ 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 ` doc page diff --git a/doc/src/Howto_bash.rst b/doc/src/Howto_bash.rst index 4a84da2f85..2a182f5040 100644 --- a/doc/src/Howto_bash.rst +++ b/doc/src/Howto_bash.rst @@ -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 diff --git a/doc/src/Install_patch.rst b/doc/src/Install_patch.rst index 6ea0c01b09..3acd72753f 100644 --- a/doc/src/Install_patch.rst +++ b/doc/src/Install_patch.rst @@ -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 ` 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 `_ of the LAMMPS website, along +a patch file is posted on the `bug and feature page `_ 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. diff --git a/doc/src/Install_tarball.rst b/doc/src/Install_tarball.rst index 79dd9b9f2d..a3df478311 100644 --- a/doc/src/Install_tarball.rst +++ b/doc/src/Install_tarball.rst @@ -4,10 +4,10 @@ Download source and documentation as a tarball You can download a current LAMMPS tarball from the `download page `_ of the `LAMMPS website `_. -.. _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 diff --git a/doc/src/Intro_authors.rst b/doc/src/Intro_authors.rst index c34dafe069..fbf306a295 100644 --- a/doc/src/Intro_authors.rst +++ b/doc/src/Intro_authors.rst @@ -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 `_ of the +The `Authors page `_ of the `LAMMPS website `_ 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 `_ of the website, LAMMPS +As discussed on the `History page `_ 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: diff --git a/doc/src/Intro_nonfeatures.rst b/doc/src/Intro_nonfeatures.rst index daf23eaea9..feb35c7198 100644 --- a/doc/src/Intro_nonfeatures.rst +++ b/doc/src/Intro_nonfeatures.rst @@ -66,7 +66,7 @@ Here are suggestions on how to perform these tasks: on-the-fly via its :doc:`dump image ` command and pass them to an external program, `FFmpeg `_ to generate movies from them. For high-quality, interactive visualization there are - many excellent and free tools available. See the `Other Codes page `_ page of the LAMMPS website for + many excellent and free tools available. See the `Other Codes page `_ 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 ` doc page for examples of plotting LAMMPS diff --git a/doc/src/Intro_overview.rst b/doc/src/Intro_overview.rst index b661352d30..776002354a 100644 --- a/doc/src/Intro_overview.rst +++ b/doc/src/Intro_overview.rst @@ -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 `_ of +F90. See the `History page `_ of the website for details. All versions can be downloaded from the `LAMMPS website `_. diff --git a/doc/src/Intro_website.rst b/doc/src/Intro_website.rst index 82fa52e226..0999e90907 100644 --- a/doc/src/Intro_website.rst +++ b/doc/src/Intro_website.rst @@ -5,32 +5,32 @@ The `LAMMPS website `_ 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 `_ -* `List of features `_ -* `List of non-features `_ -* `Recent bug fixes and new features `_ +* `List of features `_ +* `List of non-features `_ +* `Recent bug fixes and new features `_ -* `Download info `_ +* `Download info `_ * `GitHub site `_ * `SourceForge site `_ -* `LAMMPS open-source license `_ +* `LAMMPS open-source license `_ -* `Glossary of MD terms relevant to LAMMPS `_ -* `LAMMPS highlights with images `_ -* `LAMMPS highlights with movies `_ -* `Mail list `_ -* `Workshops `_ -* `Tutorials `_ -* `Developer guide `_ +* `Glossary of MD terms relevant to LAMMPS `_ +* `LAMMPS highlights with images `_ +* `LAMMPS highlights with movies `_ +* `Mail list `_ +* `Workshops `_ +* `Tutorials `_ +* `Developer guide `_ -* `Pre- and post-processing tools for LAMMPS `_ -* `Other software usable with LAMMPS `_ -* `Viz tools usable with LAMMPS `_ +* `Pre- and post-processing tools for LAMMPS `_ +* `Other software usable with LAMMPS `_ +* `Viz tools usable with LAMMPS `_ -* `Benchmark performance `_ -* `Publications that have cited LAMMPS `_ -* `Authors of LAMMPS `_ -* `History of LAMMPS development `_ -* `Funding for LAMMPS `_ +* `Benchmark performance `_ +* `Publications that have cited LAMMPS `_ +* `Authors of LAMMPS `_ +* `History of LAMMPS development `_ +* `Funding for LAMMPS `_ diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index 08cfa862ab..f805c594c6 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -18,7 +18,7 @@ LAMMPS is an open-source code, distributed freely under the terms of the GNU Public License (GPL). The `LAMMPS website `_ has a variety of information about the code. -It includes links to an on-line version of this manual, a `mailing list `_ where users can post +It includes links to an on-line version of this manual, a `mailing list `_ where users can post questions, and a `GitHub site `_ 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 ` 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 diff --git a/doc/src/Manual_version.rst b/doc/src/Manual_version.rst index 7a76824d0c..a9a395a14d 100644 --- a/doc/src/Manual_version.rst +++ b/doc/src/Manual_version.rst @@ -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 `_. Every few +`this website page `_. Every few months, the latest patch release is subjected to more thorough testing and labeled as a *stable* version. diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst index 97eac24055..358861c720 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -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 `_ so they +to `the core developers `_ 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 `_. An alternative is to @@ -44,12 +44,12 @@ are listed and described on the :doc:`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 `_ page on the LAMMPS +used as a license for the rest of LAMMPS. See the `Open source `_ 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 `_ +code and on the `Authors page `_ of the `LAMMPS WWW site `_), 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 `_ page of the LAMMPS web + their copy of LAMMPS. See the `Offsite LAMMPS packages and tools `_ 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 `_ with info about + `developers `_ 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 `_, since we may or +developers `_, 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. diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 5ad6f16681..e343848295 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -127,8 +127,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles. * `doc/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 ` on the :doc:`Bu * :doc:`package gpu ` * :doc:`Commands ` pages (:doc:`pair `, :doc:`kspace `) for styles followed by (g) -* `Benchmarks page `_ of web site +* `Benchmarks page `_ 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 ` on the :doc: * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (k) -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of web site ---------- @@ -581,7 +581,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC * :doc:`fix bond/swap ` * :doc:`fix gcmc ` * :doc:`pair_style 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 ` * 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 ` on the :doc:`Bu * :doc:`Speed opt ` * :doc:`Section 2.6 -sf opt ` * Search the :doc:`pair style ` page for styles followed by (t) -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of web site ---------- @@ -790,7 +790,7 @@ Foster (UTSA). * :doc:`compute damage/atom ` * :doc:`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 ` * 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 ` on the :do * src/USER-ATC/README * :doc:`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/\* ` * :doc:`angle_style 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 ` on the : * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (i) * src/USER-INTEL/TEST -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of web site ---------- @@ -1646,7 +1646,7 @@ Waltham, MA, USA) * :doc:`fix nve/manifold/rattle ` * :doc:`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 ` * :doc:`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 ` on the :do * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (o) -* `Benchmarks page `_ of web site +* `Benchmarks page `_ of web site ---------- @@ -2185,7 +2185,7 @@ This package has :ref:`specific installation instructions ` 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 ---------- diff --git a/doc/src/Packages_standard.rst b/doc/src/Packages_standard.rst index 1e1daf69c6..74a567e0b9 100644 --- a/doc/src/Packages_standard.rst +++ b/doc/src/Packages_standard.rst @@ -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 ` | aspherical particle models | :doc:`Howto spherical ` | ellipse | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`BODY ` | body-style particles | :doc:`Howto body ` | body | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`CLASS2 ` | class 2 force fields | :doc:`pair_style lj/class2 ` | n/a | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`COLLOID ` | colloidal particles | :doc:`atom_style colloid ` | colloid | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`COMPRESS ` | I/O compression | :doc:`dump \*/gz ` | n/a | sys | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`CORESHELL ` | adiabatic core/shell model | :doc:`Howto coreshell ` | coreshell | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`DIPOLE ` | point dipole particles | :doc:`pair_style dipole/cut ` | dipole | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`GPU ` | GPU-enabled styles | :doc:`Section gpu ` | `Benchmarks `_ | int | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`GRANULAR ` | granular systems | :doc:`Howto granular ` | pour | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`KIM ` | OpenKIM wrapper | :doc:`pair_style kim ` | kim | ext | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`KOKKOS ` | Kokkos-enabled styles | :doc:`Speed kokkos ` | `Benchmarks `_ | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`KSPACE ` | long-range Coulombic solvers | :doc:`kspace_style ` | peptide | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`LATTE ` | quantum DFTB forces via LATTE | :doc:`fix latte ` | latte | ext | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`MANYBODY ` | many-body potentials | :doc:`pair_style tersoff ` | shear | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`MC ` | Monte Carlo options | :doc:`fix gcmc ` | n/a | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`MESSAGE ` | client/server messaging | :doc:`message ` | message | int | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`MISC ` | miscellaneous single-file commands | n/a | no | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`MOLECULE ` | molecular system force fields | :doc:`Howto bioFF ` | peptide | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`MPIIO ` | MPI parallel I/O dump and restart | :doc:`dump ` | n/a | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`MSCG ` | multi-scale coarse-graining wrapper | :doc:`fix mscg ` | mscg | ext | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`OPT ` | optimized pair styles | :doc:`Speed opt ` | `Benchmarks `_ | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`PERI ` | Peridynamics models | :doc:`pair_style peri ` | peri | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`POEMS ` | coupled rigid body motion | :doc:`fix poems ` | rigid | int | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`PYTHON ` | embed Python code in an input script | :doc:`python ` | python | sys | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`QEQ ` | QEq charge equilibration | :doc:`fix qeq ` | qeq | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`REPLICA ` | multi-replica methods | :doc:`Howto replica ` | tad | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`RIGID ` | rigid bodies and constraints | :doc:`fix rigid ` | rigid | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`SHOCK ` | shock loading methods | :doc:`fix msst ` | n/a | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`SNAP ` | quantum-fitted potential | :doc:`pair_style snap ` | snap | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`SPIN ` | magnetic atomic spin dynamics | :doc:`Howto spins ` | SPIN | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`SRD ` | stochastic rotation dynamics | :doc:`fix srd ` | srd | no | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`VORONOI ` | Voronoi tesselation | :doc:`compute voronoi/atom ` | n/a | ext | -+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+ ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| Package | Description | Doc page | Example | Library | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`ASPHERE ` | aspherical particle models | :doc:`Howto spherical ` | ellipse | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`BODY ` | body-style particles | :doc:`Howto body ` | body | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`CLASS2 ` | class 2 force fields | :doc:`pair_style lj/class2 ` | n/a | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`COLLOID ` | colloidal particles | :doc:`atom_style colloid ` | colloid | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`COMPRESS ` | I/O compression | :doc:`dump \*/gz ` | n/a | sys | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`CORESHELL ` | adiabatic core/shell model | :doc:`Howto coreshell ` | coreshell | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`DIPOLE ` | point dipole particles | :doc:`pair_style dipole/cut ` | dipole | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`GPU ` | GPU-enabled styles | :doc:`Section gpu ` | `Benchmarks `_ | int | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`GRANULAR ` | granular systems | :doc:`Howto granular ` | pour | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`KIM ` | OpenKIM wrapper | :doc:`pair_style kim ` | kim | ext | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`KOKKOS ` | Kokkos-enabled styles | :doc:`Speed kokkos ` | `Benchmarks `_ | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`KSPACE ` | long-range Coulombic solvers | :doc:`kspace_style ` | peptide | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`LATTE ` | quantum DFTB forces via LATTE | :doc:`fix latte ` | latte | ext | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`MANYBODY ` | many-body potentials | :doc:`pair_style tersoff ` | shear | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`MC ` | Monte Carlo options | :doc:`fix gcmc ` | n/a | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`MESSAGE ` | client/server messaging | :doc:`message ` | message | int | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`MISC ` | miscellaneous single-file commands | n/a | no | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`MOLECULE ` | molecular system force fields | :doc:`Howto bioFF ` | peptide | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`MPIIO ` | MPI parallel I/O dump and restart | :doc:`dump ` | n/a | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`MSCG ` | multi-scale coarse-graining wrapper | :doc:`fix mscg ` | mscg | ext | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`OPT ` | optimized pair styles | :doc:`Speed opt ` | `Benchmarks `_ | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`PERI ` | Peridynamics models | :doc:`pair_style peri ` | peri | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`POEMS ` | coupled rigid body motion | :doc:`fix poems ` | rigid | int | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`PYTHON ` | embed Python code in an input script | :doc:`python ` | python | sys | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`QEQ ` | QEq charge equilibration | :doc:`fix qeq ` | qeq | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`REPLICA ` | multi-replica methods | :doc:`Howto replica ` | tad | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`RIGID ` | rigid bodies and constraints | :doc:`fix rigid ` | rigid | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`SHOCK ` | shock loading methods | :doc:`fix msst ` | n/a | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`SNAP ` | quantum-fitted potential | :doc:`pair_style snap ` | snap | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`SPIN ` | magnetic atomic spin dynamics | :doc:`Howto spins ` | SPIN | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`SRD ` | stochastic rotation dynamics | :doc:`fix srd ` | srd | no | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`VORONOI ` | Voronoi tesselation | :doc:`compute voronoi/atom ` | n/a | ext | ++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 3c489564d7..ab276d79a4 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -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 ` | dump output via ADIOS | :doc:`dump adios ` | USER/adios | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-ATC ` | Atom-to-Continuum coupling | :doc:`fix atc ` | USER/atc | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-AWPMD ` | wave packet MD | :doc:`pair_style awpmd/cut ` | USER/awpmd | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-BOCS ` | BOCS bottom up coarse graining | :doc:`fix bocs ` | USER/bocs | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-CGDNA ` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-CGSDK ` | SDK coarse-graining model | :doc:`pair_style lj/sdk ` | USER/cgsdk | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-COLVARS ` | collective variables library | :doc:`fix colvars ` | USER/colvars | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-DIFFRACTION ` | virtual x-ray and electron diffraction | :doc:`compute xrd ` | USER/diffraction | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-DPD ` | reactive dissipative particle dynamics | src/USER-DPD/README | USER/dpd | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-DRUDE ` | Drude oscillators | :doc:`Howto drude ` | USER/drude | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-EFF ` | electron force field | :doc:`pair_style eff/cut ` | USER/eff | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-FEP ` | free energy perturbation | :doc:`compute fep ` | USER/fep | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-H5MD ` | dump output via HDF5 | :doc:`dump h5md ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-INTEL ` | optimized Intel CPU and KNL styles | :doc:`Speed intel ` | `Benchmarks `_ | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-LB ` | Lattice Boltzmann fluid | :doc:`fix lb/fluid ` | USER/lb | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MANIFOLD ` | motion on 2d surfaces | :doc:`fix manifoldforce ` | USER/manifold | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair_style meam/c ` | meamc | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MESODPD ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/mesodpd | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt ` | USER/mgpt | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MISC ` | single-file contributions | USER-MISC/README | USER/misc | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MOFFF ` | styles for `MOF-FF `_ force field | :doc:`pair_style buck6d/coul/gauss ` | USER/mofff | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MOLFILE ` | `VMD `_ molfile plug-ins | :doc:`dump molfile ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-NETCDF ` | dump output via NetCDF | :doc:`dump netcdf ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-PHONON ` | phonon dynamical matrix | :doc:`fix phonon ` | USER/phonon | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-PLUMED ` | :ref:`PLUMED ` free energy library | :doc:`fix plumed ` | USER/plumed | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-PTM ` | Polyhedral Template Matching | :doc:`compute ptm/atom ` | n/a | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-QMMM ` | QM/MM coupling | :doc:`fix qmmm ` | USER/qmmm | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-QTB ` | quantum nuclear effects | :doc:`fix qtb ` :doc:`fix qbmsst ` | qtb | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-REACTION ` | chemical reactions in classical MD | :doc:`fix bond/react ` | USER/reaction | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-REAXC ` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc ` | reax | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SCAFACOS ` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos ` | USER/scafacos | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SDPD ` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal ` | USER/sdpd | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SMD ` | smoothed Mach dynamics | `SMD User Guide `_ | USER/smd | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SMTBQ ` | second moment tight binding QEq potential | :doc:`pair_style smtbq ` | USER/smtbq | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SPH ` | smoothed particle hydrodynamics | `SPH User Guide `_ | USER/sph | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-TALLY ` | pairwise tally computes | :doc:`compute XXX/tally ` | USER/tally | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-UEF ` | extensional flow | :doc:`fix nvt/uef ` | USER/uef | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-VTK ` | dump output via VTK | :doc:`compute vtk ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-YAFF ` | additional styles implemented in YAFF | :doc:`angle_style cross ` | USER/yaff | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| Package | Description | Doc page | Example | Library | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-ADIOS ` | dump output via ADIOS | :doc:`dump adios ` | USER/adios | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-ATC ` | Atom-to-Continuum coupling | :doc:`fix atc ` | USER/atc | int | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-AWPMD ` | wave packet MD | :doc:`pair_style awpmd/cut ` | USER/awpmd | int | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-BOCS ` | BOCS bottom up coarse graining | :doc:`fix bocs ` | USER/bocs | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-CGDNA ` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-CGSDK ` | SDK coarse-graining model | :doc:`pair_style lj/sdk ` | USER/cgsdk | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-COLVARS ` | collective variables library | :doc:`fix colvars ` | USER/colvars | int | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-DIFFRACTION ` | virtual x-ray and electron diffraction | :doc:`compute xrd ` | USER/diffraction | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-DPD ` | reactive dissipative particle dynamics | src/USER-DPD/README | USER/dpd | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-DRUDE ` | Drude oscillators | :doc:`Howto drude ` | USER/drude | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-EFF ` | electron force field | :doc:`pair_style eff/cut ` | USER/eff | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-FEP ` | free energy perturbation | :doc:`compute fep ` | USER/fep | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-H5MD ` | dump output via HDF5 | :doc:`dump h5md ` | n/a | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-INTEL ` | optimized Intel CPU and KNL styles | :doc:`Speed intel ` | `Benchmarks `_ | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-LB ` | Lattice Boltzmann fluid | :doc:`fix lb/fluid ` | USER/lb | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MANIFOLD ` | motion on 2d surfaces | :doc:`fix manifoldforce ` | USER/manifold | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair_style meam/c ` | meamc | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MESODPD ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/mesodpd | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt ` | USER/mgpt | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MISC ` | single-file contributions | USER-MISC/README | USER/misc | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MOFFF ` | styles for `MOF-FF `_ force field | :doc:`pair_style buck6d/coul/gauss ` | USER/mofff | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MOLFILE ` | `VMD `_ molfile plug-ins | :doc:`dump molfile ` | n/a | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-NETCDF ` | dump output via NetCDF | :doc:`dump netcdf ` | n/a | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-PHONON ` | phonon dynamical matrix | :doc:`fix phonon ` | USER/phonon | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-PLUMED ` | :ref:`PLUMED ` free energy library | :doc:`fix plumed ` | USER/plumed | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-PTM ` | Polyhedral Template Matching | :doc:`compute ptm/atom ` | n/a | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-QMMM ` | QM/MM coupling | :doc:`fix qmmm ` | USER/qmmm | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-QTB ` | quantum nuclear effects | :doc:`fix qtb ` :doc:`fix qbmsst ` | qtb | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-REACTION ` | chemical reactions in classical MD | :doc:`fix bond/react ` | USER/reaction | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-REAXC ` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc ` | reax | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-SCAFACOS ` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos ` | USER/scafacos | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-SDPD ` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal ` | USER/sdpd | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-SMD ` | smoothed Mach dynamics | `SMD User Guide `_ | USER/smd | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-SMTBQ ` | second moment tight binding QEq potential | :doc:`pair_style smtbq ` | USER/smtbq | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-SPH ` | smoothed particle hydrodynamics | `SPH User Guide `_ | USER/sph | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-TALLY ` | pairwise tally computes | :doc:`compute XXX/tally ` | USER/tally | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-UEF ` | extensional flow | :doc:`fix nvt/uef ` | USER/uef | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-VTK ` | dump output via VTK | :doc:`compute vtk ` | n/a | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-YAFF ` | additional styles implemented in YAFF | :doc:`angle_style cross ` | USER/yaff | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ .. _MOFplus: https://www.mofplus.org/content/show/MOF-FF .. _PLUMED: http://www.plumed.org diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index 382381d432..989408a798 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -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 `_ for more +See the `citation page `_ for more details. ---------- diff --git a/doc/src/Speed.rst b/doc/src/Speed.rst index a409772655..0528ff32d8 100644 --- a/doc/src/Speed.rst +++ b/doc/src/Speed.rst @@ -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 `_ of the LAMMPS +The `Benchmark page `_ of the LAMMPS web site gives performance results for the various accelerator packages discussed on the :doc:`Speed packages ` doc page, for several of the standard LAMMPS benchmark problems, as a diff --git a/doc/src/Speed_bench.rst b/doc/src/Speed_bench.rst index c67842bcc0..45b5b21d8a 100644 --- a/doc/src/Speed_bench.rst +++ b/doc/src/Speed_bench.rst @@ -1,7 +1,7 @@ Benchmarks ========== -Current LAMMPS performance is discussed on the `Benchmarks page `_ of the `LAMMPS website `_ +Current LAMMPS performance is discussed on the `Benchmarks page `_ of the `LAMMPS website `_ 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 `_ section of +`Potentials `_ section of the Benchmarks web page. So you can also run those test problems on your machine. -The `billion-atom `_ section +The `billion-atom `_ 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 diff --git a/doc/src/Speed_gpu.rst b/doc/src/Speed_gpu.rst index 618b135620..eb03ff560c 100644 --- a/doc/src/Speed_gpu.rst +++ b/doc/src/Speed_gpu.rst @@ -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 `_ of the +See the `Benchmark page `_ of the LAMMPS web site for performance of the GPU package on various hardware, including the Titan HPC platform at ORNL. diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index 2a1e451d28..834aa70e61 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -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 `_ of the +See the `Benchmark page `_ of the LAMMPS web site for performance of the KOKKOS package on different hardware. diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst index d606d7497f..e515a89d19 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -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 `_ of the LAMMPS web site gives +As mentioned above, the `Benchmark page `_ 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. diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 9d9950e514..8144769270 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -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 `_ of the LAMMPS +simulations are `here on the Movies page `_ of the LAMMPS web site. .. image:: JPG/gran_funnel_small.jpg