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recover building the manual

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Axel Kohlmeyer 2021-06-29 21:49:21 -04:00
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26
doc/src/Build_extras.rst
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@ -1056,7 +1056,7 @@ binary package provided by your operating system.
----------
.. _user-adios:
.. _adios:
ADIOS package
-----------------------------------
@ -1097,7 +1097,7 @@ systems.
----------
.. _user-atc:
.. _atc:
ATC package
-------------------------------
@ -1151,7 +1151,7 @@ The ATC package requires the MANYBODY package also be installed.
----------
.. _user-awpmd:
.. _awpmd:
AWPMD package
------------------
@ -1202,7 +1202,7 @@ AWPMD package
----------
.. _user-colvars:
.. _colvars:
COLVARS package
---------------------------------------
@ -1301,7 +1301,7 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
----------
.. _user-plumed:
.. _plumed:
PLUMED package
-------------------------------------
@ -1431,7 +1431,7 @@ LAMMPS build.
----------
.. _user-h5md:
.. _h5md:
H5MD package
---------------------------------
@ -1600,7 +1600,7 @@ TBB and MKL.
----------
.. _user-mdi:
.. _mdi:
MDI package
-----------------------------
@ -1629,7 +1629,7 @@ MDI package
----------
.. _user-mesont:
.. _mesont:
MESONT package
-------------------------
@ -1671,7 +1671,7 @@ they will be downloaded the first time this package is installed.
----------
.. _user-molfile:
.. _molfile:
MOLFILE package
---------------------------------------
@ -1709,7 +1709,7 @@ MOLFILE package
----------
.. _user-netcdf:
.. _netcdf:
NETCDF package
-------------------------------------
@ -1773,7 +1773,7 @@ OPENMP package
----------
.. _user-qmmm:
.. _qmmm:
QMMM package
---------------------------------
@ -1883,7 +1883,7 @@ to be downloaded and configured. See step 1 and step 1.1 in the
----------
.. _user-scafacos:
.. _scafacos:
SCAFACOS package
-----------------------------------------
@ -1974,7 +1974,7 @@ Eigen3 is a template library, so you do not need to build it.
----------
.. _user-vtk:
.. _vtk:
VTK package
-------------------------------

2
doc/src/Build_manual.rst
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@ -204,7 +204,7 @@ be multiple tests run automatically:
.. parsed-literal::
Found 33 standard and 41 user packages
Found 74 packages
Standard package NEWPACKAGE missing in Packages_standard.rst
Standard package NEWPACKAGE missing in Packages_details.rst

26
doc/src/Build_package.rst
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@ -33,13 +33,13 @@ packages:
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`ADIOS <adios>` |
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`ADIOS <adios>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`ATC <atc>` | :ref:`AWPMD <awpmd>` | :ref:`COLVARS <colvars>` | :ref:`H5MD <h5md>` | :ref:`ML-HDNNP <ml-hdnnp>` | :ref:`INTEL <intel>` |
| :ref:`ATC <atc>` | :ref:`AWPMD <awpmd>` | :ref:`COLVARS <colvars>` | :ref:`H5MD <h5md>` | :ref:`ML-HDNNP <ml-hdnnp>` | :ref:`INTEL <intel>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`MOLFILE <molfile>` | :ref:`NETCDF <netcdf>` | :ref:`ML-PACE <ml-pace>` | :ref:`PLUMED <plumed>` | :ref:`OPENMP <openmp>` | :ref:`QMMM <qmmm>` |
| :ref:`MOLFILE <molfile>` | :ref:`NETCDF <netcdf>` | :ref:`ML-PACE <ml-pace>` | :ref:`PLUMED <plumed>` | :ref:`OPENMP <openmp>` | :ref:`QMMM <qmmm>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`ML-QUIP <ml-quip>` | :ref:`SCAFACOS <scafacos>` | :ref:`MACHDYN <machdyn>` | :ref:`VTK <vtk>` | | |
| :ref:`ML-QUIP <ml-quip>` | :ref:`SCAFACOS <scafacos>` | :ref:`MACHDYN <machdyn>` | :ref:`VTK <vtk>` | | |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
The mechanism for including packages is simple but different for CMake
@ -60,12 +60,8 @@ versus make.
-D PKG_MANYBODY=yes
-D PKG_INTEL=yes
All standard and user packages are included the same way. Note
that USER packages have a hyphen between USER and the rest of the
package name, not an underscore.
See the shortcut section below for how to install many packages at
once with CMake.
All packages are included the same way. See the shortcut section
below for how to install many packages at once with CMake.
.. note::
@ -91,10 +87,8 @@ versus make.
make no-rigid
make yes-intel
All standard and user packages are included the same way.
See the shortcut section below for how to install many packages at
once with make.
All packages are included the same way. See the shortcut section
below for how to install many packages at once with make.
.. note::
@ -208,10 +202,6 @@ These commands install/un-install sets of packages:
make yes-all # install all packages
make no-all # uninstall all packages
make yes-standard or make yes-std # install standard packages
make no-standard or make no-std # uninstall standard packages
make yes-user # install user packages
make no-user # uninstall user packages
make yes-lib # install packages that require extra libraries
make no-lib # uninstall packages that require extra libraries
make yes-ext # install packages that require external libraries

10
doc/src/Errors.rst
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@ -1,11 +1,11 @@
Errors
******
These doc pages describe the errors you can encounter when using
LAMMPS. The common problems include conceptual issues. The messages
and warnings doc pages give complete lists of all the messages the
code may generate (except those generated by USER packages), with
additional details for many of them.
These doc pages describe many of the error and warning message you can
encounter when using LAMMPS. The common problems include conceptual
issues. The messages and warnings doc pages give complete lists of all
the messages the code may generate, with additional details for many of
them.
.. toctree::
:maxdepth: 1

4
doc/src/Errors_messages.rst
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@ -14,10 +14,6 @@ For example, a message like this:
means that line #78 in the file src/velocity.cpp generated the error.
Looking in the source code may help you figure out what went wrong.
Note that error messages from :doc:`user-contributed packages <Packages_user>` are not listed here. If such an error
occurs and is not self-explanatory, you will need to look in the source
code or contact the author of the package.
Doc page with :doc:`WARNING messages <Errors_warnings>`
----------

4
doc/src/Errors_warnings.rst
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@ -14,10 +14,6 @@ generated. For example, a message like this:
means that line #187 in the file src/domain.cpp generated the error.
Looking in the source code may help you figure out what went wrong.
Note that warning messages from :doc:`user-contributed packages <Packages_user>` are not listed here. If such a warning
occurs and is not self-explanatory, you will need to look in the source
code or contact the author of the package.
Doc page with :doc:`ERROR messages <Errors_messages>`
----------

105
doc/src/Modify_contribute.rst
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@ -49,13 +49,11 @@ with gzip. Please only use gzip compression, as this works well and is
available on all platforms.
If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a :doc:`standard package <Packages_standard>`. Else we will add them as a
user-contributed file or :doc:`user package <Packages_user>`. Examples
of user packages are in src sub-directories that start with USER. The
files to LAMMPS or as part of a :doc:`package <Packages_list>`. The
USER-MISC package is simply a collection of (mostly) unrelated single
files, which is the simplest way to have your contribution quickly
added to the LAMMPS distribution. All the standard and user packages
are listed and described on the :doc:`Packages details <Packages_details>` doc page.
files, which is the simplest way to have your contribution quickly added
to the LAMMPS distribution. All packages are listed and described
on the :doc:`Packages details <Packages_details>` doc page.
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
@ -65,27 +63,19 @@ on request only and with files that are authorized for that kind of
distribution removed (e.g. interface to FFTW). See the
:doc:`LAMMPS license <Intro_opensource>` doc page 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 <https://www.lammps.org/authors.html>`_
of the `LAMMPS WWW site <lws_>`_), is a means for you to distribute your
work to the LAMMPS user community, and a mechanism for others to
easily try out your new feature. This may help you find bugs or make
contact with new collaborators. Note that you're also implicitly
agreeing to support your code which means answer questions, fix bugs,
and maintain it if LAMMPS changes in some way that breaks it (an
unusual event).
.. note::
If you prefer to actively develop and support your add-on
feature yourself, then you may wish to make it available for download
from your own website, as a user package that LAMMPS users can add to
their copy of LAMMPS. See the `Offsite LAMMPS packages and tools <https://www.lammps.org/offsite.html>`_ page of the LAMMPS web
site for examples of groups that do this. We are happy to advertise
your package and web site from that page. Simply email the
`developers <https://www.lammps.org/authors.html>`_ with info about
your package and we will post it there.
If you prefer to actively develop and support your add-on feature
yourself, then you may wish to make it available for download from
your own website, as a user package that LAMMPS users can add to
their copy of LAMMPS. See the `Offsite LAMMPS packages and tools
<https://www.lammps.org/offsite.html>`_ page of the LAMMPS web site
for examples of groups that do this. We are happy to advertise your
package and web site from that page. Simply email the `developers
<https://www.lammps.org/authors.html>`_ with info about your package
and we will post it there. We recommend to name external packages
USER-\<name\> so they can be easily distinguished from bundled packages
that do not have the USER- prefix.
.. _lws: https://www.lammps.org
@ -167,17 +157,20 @@ packages in the src directory for examples. If you are uncertain, please ask.
2 source files. You can do this multiple times if you wish to
contribute several individual features.
* If you want your contribution to be added as a user-contribution and
it is several related features, it is probably best to make it a user
package directory with a name like FOO. In addition to your new
files, the directory should contain a README text file. The README
should contain your name and contact information and a brief
* If you want your contribution to be added and it has several related
features or is dependent on an external or bundled library, it is best
to make it a package directory with a name like FOO. In addition to
your new files, the directory should contain a README text file. The
README should contain your name and contact information and a brief
description of what your new package does. If your files depend on
other LAMMPS style files also being installed (e.g. because your file
is a derived class from the other LAMMPS class), then an Install.sh
file is also needed to check for those dependencies. See other README
and Install.sh files in other USER directories as examples. Send us a
tarball of this FOO directory.
and Install.sh files in other directories as examples. Submit a pull
request on GitHub or send us a tarball of this FOO directory. Pull
requests are strongly encouraged since the greatly reduce the effort
to integrate a contribution and simplify the process of adjusting the
contributed code to cleanly integrate into the LAMMPS distribution.
* Your new source files need to have the LAMMPS copyright, GPL notice,
and your name and email address at the top, like other
@ -190,21 +183,21 @@ packages in the src directory for examples. If you are uncertain, please ask.
code.
* You **must** also create a **documentation** file for each new command
or style you are adding to LAMMPS. For simplicity and convenience, the
documentation of groups of closely related commands or styles may be
combined into a single file. This will be one file for a single-file
feature. For a package, it might be several files. These are text
files with a .rst extension using the `reStructuredText <rst_>`_
markup language, that are then converted to HTML and PDF using the
`Sphinx <sphinx_>`_ documentation generator tool. Running Sphinx with
the included configuration requires Python 3.x. Configuration
settings and custom extensions for this conversion are included in the
source distribution, and missing python packages will be transparently
downloaded into a virtual environment via pip. Thus, if your local
system is missing required packages, you need access to the
internet. The translation can be as simple as doing "make html pdf" in
the doc folder. As appropriate, the text files can include inline
mathematical expression or figures (see doc/JPG for examples).
or style you are adding to LAMMPS. For simplicity and convenience,
the documentation of groups of closely related commands or styles may
be combined into a single file. This will be one file for a
single-file feature. For a package, it might be several files. These
are text files with a .rst extension using the `reStructuredText
<rst_>`_ markup language, that are then converted to HTML and PDF
using the `Sphinx <sphinx_>`_ documentation generator tool. Running
Sphinx with the included configuration requires Python 3.x.
Configuration settings and custom extensions for this conversion are
included in the source distribution, and missing python packages will
be transparently downloaded into a virtual environment via pip. Thus,
if your local system is missing required packages, you need access to
the internet. The translation can be as simple as doing "make html
pdf" in the doc folder. As appropriate, the text files can include
inline mathematical expression or figures (see doc/JPG for examples).
Additional PDF files with further details (see doc/PDF for examples)
may also be included. The doc page should also include literature
citations as appropriate; see the bottom of doc/fix_nh.rst for
@ -212,15 +205,15 @@ packages in the src directory for examples. If you are uncertain, please ask.
cite itself. Citation labels must be unique across all .rst files.
The "Restrictions" section of the doc page should indicate if your
command is only available if LAMMPS is built with the appropriate
USER-MISC or FOO package. See other user package doc files for
examples of how to do this. Please run at least "make html" and "make
spelling" and carefully inspect and proofread the resulting HTML
format doc page before submitting your code. Upon submission of a
pull request, checks for error free completion of the HTML and PDF
build will be performed and also a spell check, a check for correct
anchors and labels, and a check for completeness of references all
styles in their corresponding tables and lists is run. In case the
spell check reports false positives they can be added to the file
USER-MISC or FOO package. See other package doc files for examples of
how to do this. Please run at least "make html" and "make spelling"
and carefully inspect and proofread the resulting HTML format doc page
before submitting your code. Upon submission of a pull request,
checks for error free completion of the HTML and PDF build will be
performed and also a spell check, a check for correct anchors and
labels, and a check for completeness of references all styles in their
corresponding tables and lists is run. In case the spell check
reports false positives they can be added to the file
doc/utils/sphinx-config/false_positives.txt
* For a new package (or even a single command) you should include one or

3
doc/src/Packages.rst
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@ -14,6 +14,5 @@ LAMMPS build process.
.. toctree::
:maxdepth: 1
Packages_standard
Packages_user
Packages_list
Packages_details

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doc/src/Packages_list.rst Normal file
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@ -0,0 +1,192 @@
Available Packages
==================
This is the list of packages included in LAMMPS. The link for each
package name gives more details.
Packages are supported by either the LAMMPS developers or the
contributing authors and written in a syntax and style consistent with
the rest of LAMMPS.
The "Example" column is a sub-directory in the examples directory of the
distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory; PACKAGES/atc refers
to the examples/PACKAGES/atc directory. The "Library" column indicates
whether an extra library is needed to build and use the package:
* no = no library
* sys = system library: you likely have it on your machine
* 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:`ADIOS <PKG-ADIOS>` | dump output via ADIOS | :doc:`dump adios <dump_adios>` | PACKAGES/adios | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ASPHERE <PKG-ASPHERE>` | aspherical particle models | :doc:`Howto spherical <Howto_spherical>` | ellipse | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ATC <PKG-ATC>` | Atom-to-Continuum coupling | :doc:`fix atc <fix_atc>` | PACKAGES/atc | int |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`AWPMD <PKG-AWPMD>` | wave packet MD | :doc:`pair_style awpmd/cut <pair_awpmd>` | PACKAGES/awpmd | int |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`BOCS <PKG-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | PACKAGES/bocs | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`BODY <PKG-BODY>` | body-style particles | :doc:`Howto body <Howto_body>` | body | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`BROWNIAN <PKG-BROWNIAN>` | Brownian dynamics and self-propelled particles | :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>` | PACKAGES/brownian | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`CG-DNA <PKG-CG-DNA>` | coarse-grained DNA force fields | src/CG-DNA/README | PACKAGES/cgdna | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`CG-SDK <PKG-CG-SDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | PACKAGES/cgsdk | 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:`COLVARS <PKG-COLVARS>` | collective variables library | :doc:`fix colvars <fix_colvars>` | PACKAGES/colvars | int |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :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:`DIELECTRIC <PKG-DIELECTRIC>` | dielectric boundary solvers and force styles | :doc:`compute efield/atom <compute_efield_atom>` | PACKAGES/dielectric | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DIFFRACTION <PKG-DIFFRACTION>` | virtual x-ray and electron diffraction | :doc:`compute xrd <compute_xrd>` | PACKAGES/diffraction | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair_style lj/.../dipole <pair_dipole>` | dipole | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DPD-MESO <PKG-DPD-MESO>` | mesoscale DPD models | :doc:`pair_style edpd <pair_mesodpd>` | PACKAGES/dpd-meso | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DPD-REACT <PKG-DPD-REACT>` | reactive dissipative particle dynamics | src/DPD-REACT/README | PACKAGES/dpd-react | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DPD-SMOOTH <PKG-DPD-SMOOTH>` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | PACKAGES/dpd-smooth | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DRUDE <PKG-DRUDE>` | Drude oscillators | :doc:`Howto drude <Howto_drude>` | PACKAGES/drude | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`EFF <PKG-EFF>` | electron force field | :doc:`pair_style eff/cut <pair_eff>` | PACKAGES/eff | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`FEP <PKG-FEP>` | free energy perturbation | :doc:`compute fep <compute_fep>` | PACKAGES/fep | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | int |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`GRANULAR <PKG-GRANULAR>` | granular systems | :doc:`Howto granular <Howto_granular>` | pour | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`H5MD <PKG-H5MD>` | dump output via HDF5 | :doc:`dump h5md <dump_h5md>` | n/a | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`INTEL <PKG-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | 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://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KSPACE <PKG-KSPACE>` | long-range Coulombic solvers | :doc:`kspace_style <kspace_style>` | peptide | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`LATBOLTZ <PKG-LATBOLTZ>` | Lattice Boltzmann fluid | :doc:`fix lb/fluid <fix_lb_fluid>` | PACKAGES/latboltz | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`LATTE <PKG-LATTE>` | quantum DFTB forces via LATTE | :doc:`fix latte <fix_latte>` | latte | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MACHDYN <PKG-MACHDYN>` | smoothed Mach dynamics | `SMD User Guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ | PACKAGES/machdyn | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MANIFOLD <PKG-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | PACKAGES/manifold | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MANYBODY <PKG-MANYBODY>` | many-body potentials | :doc:`pair_style tersoff <pair_tersoff>` | shear | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MC <PKG-MC>` | Monte Carlo options | :doc:`fix gcmc <fix_gcmc>` | n/a | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MDI <PKG-MDI>` | client-server coupling | :doc:`MDI Howto <Howto_mdi>` | PACKAGES/mdi | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MEAM <PKG-MEAM>` | modified EAM potential (C++) | :doc:`pair_style meam <pair_meam>` | meam | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MESONT <PKG-MESONT>` | mesoscopic tubular potential model for nanotubes | pair style :doc:`mesont/tpm <pair_mesont_tpm>`, :doc:`mesocnt <pair_mesocnt>` | PACKAGES/mesont | int |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MESSAGE <PKG-MESSAGE>` | client/server messaging | :doc:`message <message>` | message | int |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MGPT <PKG-MGPT>` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt <pair_mgpt>` | PACKAGES/mgpt | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MISC <PKG-MISC>` | miscellaneous single-file commands | n/a | no | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-HDNNP <PKG-ML-HDNNP>` | High-dimensional neural network potentials | :doc:`pair_style hdnnp <pair_hdnnp>` | PACKAGES/hdnnp | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-IAP <PKG-ML-IAP>` | multiple machine learning potentials | :doc:`pair_style mliap <pair_mliap>` | mliap | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-PACE <PKG-ML-PACE>` | Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | PACKAGES/pace | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-QUIP <PKG-ML-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | PACKAGES/quip | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-RANN <PKG-ML-RANN>` | rapid atomistic neural network (RANN) potentials | :doc:`pair rann <pair_rann>` | PACKAGES/rann | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-SNAP <PKG-ML-SNAP>` | quantum-fitted potential | :doc:`pair_style snap <pair_snap>` | snap | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MOFFF <PKG-MOFFF>` | styles for `MOF-FF <MOFplus_>`_ force field | :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` | PACKAGES/mofff | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MOLECULE <PKG-MOLECULE>` | molecular system force fields | :doc:`Howto bioFF <Howto_bioFF>` | peptide | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MOLFILE <PKG-MOLFILE>` | `VMD <VMD_>`_ molfile plug-ins | :doc:`dump molfile <dump_molfile>` | n/a | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :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:`NETCDF <PKG-NETCDF>` | dump output via NetCDF | :doc:`dump netcdf <dump_netcdf>` | n/a | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`OPENMP <PKG-OPENMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`OPT <PKG-OPT>` | optimized pair styles | :doc:`Speed opt <Speed_opt>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PHONON <PKG-PHONON>` | phonon dynamical matrix | :doc:`fix phonon <fix_phonon>` | PACKAGES/phonon | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PLUGIN <PKG-PLUGIN>` | Plugin loader command | :doc:`plugin <plugin>` | plugins | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PLUMED <PKG-PLUMED>` | :ref:`PLUMED <PLUMED>` free energy library | :doc:`fix plumed <fix_plumed>` | PACKAGES/plumed | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`POEMS <PKG-POEMS>` | coupled rigid body motion | :doc:`fix poems <fix_poems>` | rigid | int |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PTM <PKG-PTM>` | Polyhedral Template Matching | :doc:`compute ptm/atom <compute_ptm_atom>` | n/a | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :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:`QMMM <PKG-QMMM>` | QM/MM coupling | :doc:`fix qmmm <fix_qmmm>` | PACKAGES/qmmm | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`QTB <PKG-QTB>` | quantum nuclear effects | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`REACTION <PKG-REACTION>` | chemical reactions in classical MD | :doc:`fix bond/react <fix_bond_react>` | PACKAGES/reaction | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`REAXFF <PKG-REAXFF>` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc <pair_reaxc>` | reax | 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:`SCAFACOS <PKG-SCAFACOS>` | wrapper for ScaFaCoS Kspace solver | :doc:`kspace_style scafacos <kspace_style>` | PACKAGES/scafacos | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`SHOCK <PKG-SHOCK>` | shock loading methods | :doc:`fix msst <fix_msst>` | n/a | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`SMTBQ <PKG-SMTBQ>` | second moment tight binding QEq potential | :doc:`pair_style smtbq <pair_smtbq>` | PACKAGES/smtbq | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`SPH <PKG-SPH>` | smoothed particle hydrodynamics | `SPH User Guide <PDF/SPH_LAMMPS_userguide.pdf>`_ | PACKAGES/sph | 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:`TALLY <PKG-TALLY>` | pairwise tally computes | :doc:`compute XXX/tally <compute_tally>` | PACKAGES/tally | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`UEF <PKG-UEF>` | extensional flow | :doc:`fix nvt/uef <fix_nh_uef>` | PACKAGES/uef | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MISC <PKG-USER-MISC>` | single-file contributions | USER-MISC/README | USER-MISC | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`VORONOI <PKG-VORONOI>` | Voronoi tesselation | :doc:`compute voronoi/atom <compute_voronoi_atom>` | n/a | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`VTK <PKG-VTK>` | dump output via VTK | :doc:`compute vtk <dump_vtk>` | n/a | ext |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`YAFF <PKG-YAFF>` | additional styles implemented in YAFF | :doc:`angle_style cross <angle_cross>` | PACKAGES/yaff | no |
+------------------------------------------------+---------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF
.. _PLUMED: https://www.plumed.org
.. _VMD: https://www.ks.uiuc.edu/Research/vmd/

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Standard packages
=================
This is the list of standard packages in LAMMPS. The link for each
package name gives more details.
Standard packages are supported by the LAMMPS developers and are
written in a syntax and style consistent with the rest of LAMMPS.
This means the developers will answer questions about them, debug and
fix them if necessary, and keep them compatible with future changes to
LAMMPS.
The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory; USER/atc
refers to the examples/PACKAGES/atc directory. The "Library" column
indicates whether an extra library is needed to build and use the
package:
* no = no library
* sys = system library: you likely have it on your machine
* 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 lj/.../dipole <pair_dipole>` | dipole | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`GRANULAR <PKG-GRANULAR>` | granular systems | :doc:`Howto granular <Howto_granular>` | pour | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KIM <PKG-KIM>` | OpenKIM wrapper | :doc:`pair_style kim <pair_kim>` | kim | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KOKKOS <PKG-KOKKOS>` | Kokkos-enabled styles | :doc:`Speed kokkos <Speed_kokkos>` | `Benchmarks <https://www.lammps.org/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:`ML-IAP <PKG-ML-IAP>` | multiple machine learning potentials | :doc:`pair_style mliap <pair_mliap>` | mliap | 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://www.lammps.org/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PLUGIN <PKG-PLUGIN>` | Plugin loader command | :doc:`plugin <plugin>` | plugins | 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:`ML-SNAP <PKG-ML-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 |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+

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User packages
=============
This is a list of user packages in LAMMPS. The link for each package
name gives more details.
User packages have been contributed by users, and begin with the
"user" prefix. If a contribution is a single command (single file),
it is typically in the USER-MISC package. User packages don't
necessarily meet the requirements of the :doc:`standard packages <Packages_standard>`. This means the developers will try
to keep things working and usually can answer technical questions
about compiling the package. If you have problems using a specific
feature provided in a user package, you may need to contact the
contributor directly to get help. Information on how to submit
additions you make to LAMMPS as single files or as a standard or user
package is explained on the :doc:`Modify contribute <Modify_contribute>`
doc page.
The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory; USER/atc
refers to the examples/PACKAGES/atc directory. The "Library" column
indicates whether an extra library is needed to build and use the
package:
* no = no library
* sys = system library: you likely have it on your machine
* 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:`ADIOS <PKG-ADIOS>` | dump output via ADIOS | :doc:`dump adios <dump_adios>` | USER/adios | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ATC <PKG-ATC>` | Atom-to-Continuum coupling | :doc:`fix atc <fix_atc>` | USER/atc | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`AWPMD <PKG-AWPMD>` | wave packet MD | :doc:`pair_style awpmd/cut <pair_awpmd>` | USER/awpmd | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`BOCS <PKG-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`BROWNIAN <PKG-BROWNIAN>` | Brownian dynamics and self-propelled particles | :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>` | USER/brownian | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`CG-DNA <PKG-CG-DNA>` | coarse-grained DNA force fields | src/CG-DNA/README | USER/cgdna | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`CG-SDK <PKG-CG-SDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`COLVARS <PKG-COLVARS>` | collective variables library | :doc:`fix colvars <fix_colvars>` | USER/colvars | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DIELECTRIC <PKG-DIELECTRIC>` | dielectric boundary solvers and force styles | :doc:`compute efield/atom <compute_efield_atom>` | USER/dielectric | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DIFFRACTION <PKG-DIFFRACTION>` | virtual x-ray and electron diffraction | :doc:`compute xrd <compute_xrd>` | USER/diffraction | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DPD-REACT <PKG-DPD-REACT>` | reactive dissipative particle dynamics | src/DPD-REACT/README | USER/dpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DRUDE <PKG-DRUDE>` | Drude oscillators | :doc:`Howto drude <Howto_drude>` | USER/drude | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`EFF <PKG-EFF>` | electron force field | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`FEP <PKG-FEP>` | free energy perturbation | :doc:`compute fep <compute_fep>` | USER/fep | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`H5MD <PKG-H5MD>` | dump output via HDF5 | :doc:`dump h5md <dump_h5md>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-HDNNP <PKG-ML-HDNNP>` | High-dimensional neural network potentials | :doc:`pair_style hdnnp <pair_hdnnp>` | USER/hdnnp | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`INTEL <PKG-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`LATBOLTZ <PKG-LATBOLTZ>` | Lattice Boltzmann fluid | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MANIFOLD <PKG-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | USER/manifold | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MDI <PKG-MDI>` | client-server coupling | :doc:`MDI Howto <Howto_mdi>` | USER/mdi | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MEAM <PKG-MEAM>` | modified EAM potential (C++) | :doc:`pair_style meam <pair_meam>` | meam | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DPD-MESO <PKG-DPD-MESO>` | mesoscale DPD models | :doc:`pair_style edpd <pair_mesodpd>` | USER/mesodpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MESONT <PKG-MESONT>` | mesoscopic tubular potential model for nanotubes | pair style :doc:`mesont/tpm <pair_mesont_tpm>`, :doc:`mesocnt <pair_mesocnt>` | USER/mesont | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MGPT <PKG-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:`MOFFF <PKG-MOFFF>` | styles for `MOF-FF <MOFplus_>`_ force field | :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` | USER/mofff | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MOLFILE <PKG-MOLFILE>` | `VMD <https://www.ks.uiuc.edu/Research/vmd/>`_ molfile plug-ins | :doc:`dump molfile <dump_molfile>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`NETCDF <PKG-NETCDF>` | dump output via NetCDF | :doc:`dump netcdf <dump_netcdf>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`OPENMP <PKG-OPENMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-PACE <PKG-ML-PACE>` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | USER/pace | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PHONON <PKG-PHONON>` | phonon dynamical matrix | :doc:`fix phonon <fix_phonon>` | USER/phonon | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PLUMED <PKG-PLUMED>` | :ref:`PLUMED <PLUMED>` free energy library | :doc:`fix plumed <fix_plumed>` | USER/plumed | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PTM <PKG-PTM>` | Polyhedral Template Matching | :doc:`compute ptm/atom <compute_ptm_atom>` | n/a | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`QMMM <PKG-QMMM>` | QM/MM coupling | :doc:`fix qmmm <fix_qmmm>` | USER/qmmm | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`QTB <PKG-QTB>` | quantum nuclear effects | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-QUIP <PKG-ML-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | USER/quip | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`ML-RANN <PKG-ML-RANN>` | rapid atomistic neural network (RANN) potentials | :doc:`pair rann <pair_rann>` | USER/rann | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`REACTION <PKG-REACTION>` | chemical reactions in classical MD | :doc:`fix bond/react <fix_bond_react>` | USER/reaction | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`REAXFF <PKG-REAXFF>` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc <pair_reaxc>` | reax | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`SCAFACOS <PKG-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos <kspace_style>` | USER/scafacos | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DPD-SMOOTH <PKG-DPD-SMOOTH>` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | USER/sdpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MACHDYN <PKG-MACHDYN>` | smoothed Mach dynamics | `SMD User Guide <PDF/SMD_LAMMPS_userguide.pdf>`_ | USER/smd | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`SMTBQ <PKG-SMTBQ>` | second moment tight binding QEq potential | :doc:`pair_style smtbq <pair_smtbq>` | USER/smtbq | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`SPH <PKG-SPH>` | smoothed particle hydrodynamics | `SPH User Guide <PDF/SPH_LAMMPS_userguide.pdf>`_ | USER/sph | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`TALLY <PKG-TALLY>` | pairwise tally computes | :doc:`compute XXX/tally <compute_tally>` | USER/tally | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`UEF <PKG-UEF>` | extensional flow | :doc:`fix nvt/uef <fix_nh_uef>` | USER/uef | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`VTK <PKG-VTK>` | dump output via VTK | :doc:`compute vtk <dump_vtk>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`YAFF <PKG-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: https://www.plumed.org

4
doc/src/Run_options.rst
View File

@ -10,7 +10,7 @@ letter abbreviation can be used:
* :ref:`-i or -in <file>`
* :ref:`-k or -kokkos <run-kokkos>`
* :ref:`-l or -log <log>`
* :ref:`-mdi <mdi>`
* :ref:`-mdi <mdi_flags>`
* :ref:`-m or -mpicolor <mpicolor>`
* :ref:`-c or -cite <cite>`
* :ref:`-nc or -nocite <nocite>`
@ -197,7 +197,7 @@ Option -plog will override the name of the partition log files file.N.
----------
.. _mdi:
.. _mdi_flags:
**-mdi 'multiple flags'**

15
doc/src/Speed_packages.rst
View File

@ -12,17 +12,16 @@ All of these commands are in packages provided with LAMMPS. An
overview of packages is give on the :doc:`Packages <Packages>` doc
pages.
These are the accelerator packages currently in LAMMPS, either as
standard or user packages:
These are the accelerator packages currently in LAMMPS:
+-----------------------------------------+-------------------------------------------------------+
| :doc:`GPU Package <Speed_gpu>` | for GPUs via CUDA, OpenCL, or ROCm HIP |
+-----------------------------------------+-------------------------------------------------------+
| :doc:`INTEL Package <Speed_intel>` | for Intel CPUs and Intel Xeon Phi |
| :doc:`INTEL Package <Speed_intel>` | for Intel CPUs and Intel Xeon Phi |
+-----------------------------------------+-------------------------------------------------------+
| :doc:`KOKKOS Package <Speed_kokkos>` | for NVIDIA GPUs, Intel Xeon Phi, and OpenMP threading |
+-----------------------------------------+-------------------------------------------------------+
| :doc:`OPENMP Package <Speed_omp>` | for OpenMP threading and generic CPU optimizations |
| :doc:`OPENMP Package <Speed_omp>` | for OpenMP threading and generic CPU optimizations |
+-----------------------------------------+-------------------------------------------------------+
| :doc:`OPT Package <Speed_opt>` | generic CPU optimizations |
+-----------------------------------------+-------------------------------------------------------+
@ -41,11 +40,11 @@ Inverting this list, LAMMPS currently has acceleration support for
three kinds of hardware, via the listed packages:
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| Many-core CPUs | :doc:`INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>`, :doc:`OPENMP <Speed_omp>`, :doc:`OPT <Speed_opt>` packages |
| Many-core CPUs | :doc:`INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>`, :doc:`OPENMP <Speed_omp>`, :doc:`OPT <Speed_opt>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| GPUs | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| Intel Phi/AVX | :doc:`INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>` packages |
| Intel Phi/AVX | :doc:`INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
Which package is fastest for your hardware may depend on the size
@ -84,9 +83,9 @@ listed above:
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
| build the accelerator library | only for GPU package |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
| install the accelerator package | make yes-opt, make yes-intel, etc |
| install the accelerator package | make yes-opt, make yes-intel, etc |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
| add compile/link flags to Makefile.machine in src/MAKE | only for INTEL, KOKKOS, OPENMP, OPT packages |
| add compile/link flags to Makefile.machine in src/MAKE | only for INTEL, KOKKOS, OPENMP, OPT packages |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+
| re-build LAMMPS | make machine |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+

4
doc/src/Tools.rst
View File

@ -67,7 +67,7 @@ Post-processing tools
* :ref:`amber2lmp <amber>`
* :ref:`binary2txt <binary>`
* :ref:`ch2lmp <charmm>`
* :ref:`colvars <colvars>`
* :ref:`colvars <colvars_tools>`
* :ref:`eff <eff>`
* :ref:`fep <fep>`
* :ref:`lmp2arc <arc>`
@ -214,7 +214,7 @@ tool and the specific name of the program used (e.g. ``ninja-v1.10`` or
----------
.. _colvars:
.. _colvars_tools:
colvars tools
---------------------------

40
doc/utils/check-packages.py
View File

@ -41,12 +41,10 @@ if not os.path.isdir(doc_dir):
pkgdirs = glob(os.path.join(src_dir, '[A-Z][A-Z]*'))
dirs = re.compile(".*/([0-9A-Z-]+)$")
user = re.compile(".*")
stdpkg = []
usrpkg = []
pkgs = []
# find package names and add to standard and user package lists.
# find package names and add package list.
# anything starting with at least two upper case characters, is a
# folder, and is not called 'MAKE' is a package
@ -54,47 +52,29 @@ for d in pkgdirs:
pkg = dirs.match(d).group(1)
if not os.path.isdir(os.path.join(src_dir, pkg)): continue
if pkg in ['DEPEND','MAKE','STUBS']: continue
if user.match(pkg):
usrpkg.append(pkg)
else:
stdpkg.append(pkg)
pkgs.append(pkg)
print(f"Found {len(stdpkg)} standard and {len(usrpkg)} user packages")
print(f"Found {len(pkgs)} packages")
counter = 0
with open(os.path.join(doc_dir, 'Packages_standard.rst')) as fp:
with open(os.path.join(doc_dir, 'Packages_list.rst')) as fp:
text = fp.read()
matches = set(re.findall(':ref:`([A-Z0-9-]+) <[A-Z0-9-]+>`', text, re.MULTILINE))
for p in stdpkg:
for p in pkgs:
if not p in matches:
counter += 1
print(f"Standard package {p} missing in Packages_standard.rst")
with open(os.path.join(doc_dir, 'Packages_user.rst')) as fp:
text = fp.read()
matches = set(re.findall(':ref:`([A-Z0-9-]+) <[A-Z0-9-]+>`', text, re.MULTILINE))
for p in usrpkg:
if not p in matches:
counter += 1
print(f"User package {p} missing in Packages_user.rst")
print(f"Package {p} missing in Packages_list.rst")
with open(os.path.join(doc_dir, 'Packages_details.rst')) as fp:
text = fp.read()
matches = set(re.findall(':ref:`([A-Z0-9]+) <PKG-\\1>`', text, re.MULTILINE))
for p in stdpkg:
matches = set(re.findall(':ref:`([A-Z0-9-]+) <PKG-\\1>`', text, re.MULTILINE))
for p in pkgs:
if not p in matches:
counter += 1
print(f"Standard package {p} missing in Packages_details.rst")
matches = set(re.findall(':ref:`([A-Z0-9]+) <PKG-\\1>`', text, re.MULTILINE))
for p in usrpkg:
if not p in matches:
counter +=1
print(f"User package {p} missing in Packages_details.rst")
print(f"Package {p} missing in Packages_details.rst")
if counter:
print(f"Found {counter} issue(s) with package lists")

6
doc/utils/check-styles.py
View File

@ -267,9 +267,9 @@ counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) <fix.+>`",
counter += check_style('fix.rst', doc_dir, ":doc:`(.+) <fix.+>` -",
fix,'Fix',skip=('python', 'NEIGH_HISTORY/omp'),suffix=False)
counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",
pair,'Pair',skip=('meam','lj/sf'),suffix=True)
pair,'Pair',skip=('meam/c','lj/sf'),suffix=True)
counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",
pair,'Pair',skip=('meam','lj/sf'),suffix=False)
pair,'Pair',skip=('meam/c','lj/sf'),suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",
bond,'Bond',suffix=True)
counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",
@ -301,7 +301,7 @@ counter += check_style_index("bond_style", bond, index["bond_style"])
counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])
counter += check_style_index("improper_style", improper, index["improper_style"])
counter += check_style_index("kspace_style", kspace, index["kspace_style"])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam', 'lj/sf'])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf'])
if counter:
print(f"Found {counter} issue(s) with style index")

7
doc/utils/sphinx-config/false_positives.txt
View File

@ -1325,6 +1325,7 @@ hyperradius
hyperspherical
hysteretic
hz
IAP
Ibanez
iatom
ibar
@ -1647,6 +1648,8 @@ larentzos
Larentzos
Laroche
lars
LATBOLTZ
latboltz
latencies
Latour
latourr
@ -1797,6 +1800,8 @@ Lysogorskiy
Lyulin
lz
Maaravi
MACHDYN
machdyn
Mackay
Mackrodt
Macromolecules
@ -2734,7 +2739,7 @@ README
realtime
reamin
reax
REAXC
REAXFF
ReaxFF
rebo
recursing