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30
SECURITY.md
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@ -14,14 +14,14 @@ and tested by the LAMMPS developers, so it is easy to import bad
behavior from calling functions in one of those libraries.
Thus is is quite easy to crash LAMMPS through malicious input and do all
kinds of filesystem manipulations. And because of that LAMMPS should
kinds of file system manipulations. And because of that LAMMPS should
**NEVER** be compiled or **run** as superuser, either from a "root" or
"administrator" account directly or indirectly via "sudo" or "su".
Therefore what could be seen as a security vulnerability is usually
either a user mistake or a bug in the code. Bugs can be reported in
the LAMMPS project
[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
either a user mistake or a bug in the code. Bugs can be reported in the
LAMMPS project [issue tracker on
GitHub](https://github.com/lammps/lammps/issues).
To mitigate issues with using homoglyphs or bidirectional reordering in
unicode, which have been demonstrated as a vector to obfuscate and hide
@ -30,10 +30,18 @@ for unicode characters and only all-ASCII source code is accepted.
# Version Updates
LAMMPS follows continuous release development model. We aim to keep all
release versions (stable or patch) fully functional and employ a variety
of automatic testing procedures to detect failures of existing
functionality from adding new features before releases are made. Thus
bugfixes and updates are only integrated into the current development
branch and thus the next (patch) release and users are recommended to
update regularly.
LAMMPS follows continuous release development model. We aim to keep to
keep the development version (develop branch) always fully functional
and employ a variety of automatic testing procedures to detect failures
of existing functionality from adding or modifying features. Most of
those tests are run on pull requests *before* merging to the development
branch. The develop branch is protected, so all changes *must* be
submitted as a pull request and thus cannot avoid the automated tests.
Additional tests are run *after* merging. Before releases are made
*all* tests must have cleared. Then a release tag is applied and the
release branch fast-forwarded to that tag. Bug fixes and updates are
applied to the current development branch and thus will be available in
the next (patch) release. For stable releases, selected bug fixes are
back-ported and occasionally published as update releases. There are
only updates to the latest stable release.

24
doc/src/Bibliography.rst
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@ -314,7 +314,7 @@ Bibliography
Espanol, Revenga, Physical Review E, 67, 026705 (2003).
**(Espanol1997)**
Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI: 10.1209/epl/i1997-00515-8
Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI:10.1209/epl/i1997-00515-8
**(Evans and Morriss)**
Evans and Morriss, Phys Rev A, 30, 1528 (1984).
@ -368,7 +368,7 @@ Bibliography
Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.
**(GLE4MD)**
`http://gle4md.org/ <http://gle4md.org/>`_
`https://gle4md.org/ <https://gle4md.org/>`_
**(Gao)**
Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
@ -401,13 +401,13 @@ Bibliography
Hayre, and Farago, Comp Phys Comm, 185, 524 (2014)
**(Groot)**
Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI: 10.1063/1.474784
Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI:10.1063/1.474784
**(Guenole)**
Guenole, Noehring, Vaid, Houlle, Xie, Prakash, Bitzek, Comput Mater Sci, 175, 109584 (2020).
**(Gullet)**
Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). DOI:10.2172/918395
**(Guo)**
Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
@ -461,7 +461,7 @@ Bibliography
Hunt, Mol Simul, 42, 347 (2016).
**(IPI)**
`http://epfl-cosmo.github.io/gle4md/index.html?page=ipi <http://epfl-cosmo.github.io/gle4md/index.html?page=ipi>`_
`https://ipi-code.org/ <https://ipi-code.org/>`
**(IPI-CPC)**
Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).
@ -605,16 +605,16 @@ Bibliography
I.\ Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
**(Li2013_POF)**
Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). DOI: 10.1063/1.4812366.
Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). DOI:10.1063/1.4812366.
**(Li2014_JCP)**
Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003.
Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014). DOI:10.1016/j.jcp.2014.02.003.
**(Li2015_CC)**
Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 (2015). DOI: 10.1039/C5CC01684C.
Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 (2015). DOI:10.1039/C5CC01684C.
**(Li2015_JCP)**
Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI: 10.1063/1.4923254.
Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI:10.1063/1.4923254.
**(Lisal)**
M.\ Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.",
@ -733,8 +733,8 @@ Bibliography
**(Mishin)**
Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029 (2005).
**(Mitchell and Finchham)**
Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993).
**(Mitchell and Fincham)**
Mitchell, Fincham, J Phys Condensed Matter, 5, 1031-1038 (1993).
**(Mitchell2011)**
Mitchell. A non-local, ordinary-state-based viscoelasticity model for peridynamics. Sandia National Lab Report, 8064:1-28 (2011).
@ -875,7 +875,7 @@ Bibliography
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Paquay)**
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
**(Park)**
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)

2
doc/src/Build_development.rst
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@ -140,7 +140,7 @@ of the LAMMPS project on GitHub.
The unit testing facility is integrated into the CMake build process
of the LAMMPS source code distribution itself. It can be enabled by
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
It requires the `YAML <http://pyyaml.org/>`_ library and development
It requires the `YAML <https://pyyaml.org/>`_ library and development
headers (if those are not found locally a recent version will be
downloaded and compiled along with LAMMPS and the test program) to
compile and will download and compile a specific recent version of the

6
doc/src/Build_extras.rst
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@ -314,7 +314,7 @@ detailed information is available at:
In addition to installing the KIM API, it is also necessary to install the
library of KIM models (interatomic potentials).
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_ to
learn how to install a pre-build binary of the OpenKIM Repository of Models.
See the list of all KIM models here: https://openkim.org/browse/models
@ -432,7 +432,7 @@ Enabling the extra unit tests have some requirements,
``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_
to learn how to install a pre-built binary of the OpenKIM Repository of
Models or see
`Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
@ -1053,7 +1053,7 @@ VORONOI package
-----------------------------
To build with this package, you must download and build the
`Voro++ library <http://math.lbl.gov/voro++>`_ or install a
`Voro++ library <https://math.lbl.gov/voro++>`_ or install a
binary package provided by your operating system.
.. tabs::

2
doc/src/Build_manual.rst
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@ -176,7 +176,7 @@ math expressions transparently into embedded images.
For converting the generated ePUB file to a MOBI format file (for e-book
readers, like Kindle, that cannot read ePUB), you also need to have the
``ebook-convert`` tool from the "calibre" software
installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
installed. `https://calibre-ebook.com/ <https://calibre-ebook.com/>`_
Typing ``make mobi`` will first create the ePUB file and then convert
it. On the Kindle readers in particular, you also have support for PDF
files, so you could download and view the PDF version as an alternative.

29
doc/src/Build_settings.rst
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@ -111,26 +111,25 @@ LAMMPS can use them if they are available on your system.
files in its default search path. You must specify ``FFT_LIB``
with the appropriate FFT libraries to include in the link.
The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
distribution. It is portable across all platforms. Depending on the size
of the FFTs and the number of processors used, the other libraries listed
here can be faster.
The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
included in the LAMMPS distribution. It is portable across all
platforms. Depending on the size of the FFTs and the number of
processors used, the other libraries listed here can be faster.
However, note that long-range Coulombics are only a portion of the
per-timestep CPU cost, FFTs are only a portion of long-range
Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
communication can be costly). A breakdown of these timings is printed
to the screen at the end of a run when using the
:doc:`kspace_style pppm <kspace_style>` command. The
:doc:`Screen and logfile output <Run_output>`
page gives more details. A more detailed (and time consuming)
report of the FFT performance is generated with the
per-timestep CPU cost, FFTs are only a portion of long-range Coulombics,
and 1d FFTs are only a portion of the FFT cost (parallel communication
can be costly). A breakdown of these timings is printed to the screen
at the end of a run when using the :doc:`kspace_style pppm
<kspace_style>` command. The :doc:`Screen and logfile output
<Run_output>` page gives more details. A more detailed (and time
consuming) report of the FFT performance is generated with the
:doc:`kspace_modify fftbench yes <kspace_modify>` command.
FFTW is a fast, portable FFT library that should also work on any
platform and can be faster than the KISS FFT library. You can
download it from `www.fftw.org <http://www.fftw.org>`_. LAMMPS requires
version 3.X; the legacy version 2.1.X is no longer supported.
platform and can be faster than the KISS FFT library. You can download
it from `www.fftw.org <https://www.fftw.org>`_. LAMMPS requires version
3.X; the legacy version 2.1.X is no longer supported.
Building FFTW for your box should be as simple as ``./configure; make;
make install``. The install command typically requires root privileges

2
doc/src/Errors_debug.rst
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@ -75,7 +75,7 @@ Using the GDB debugger to get a stack trace
There are two options to use the GDB debugger for identifying the origin
of the segmentation fault or similar crash. The GDB debugger has many
more features and options, as can be seen for example its `online
documentation <http://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
documentation <https://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
Run LAMMPS from within the debugger
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

1
doc/src/Howto.rst
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@ -85,6 +85,7 @@ Packages howto
Howto_coreshell
Howto_drude
Howto_drude2
Howto_peri
Howto_manifold
Howto_spins

2
doc/src/Howto_amoeba.rst
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@ -281,7 +281,7 @@ Here is more information about the extended XYZ format defined and
used by Tinker, and links to programs that convert standard PDB files
to the extended XYZ format:
* `http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
* `https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
* `https://github.com/emleddin/pdbxyz-xyzpdb <https://github.com/emleddin/pdbxyz-xyzpdb>`_
* `https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f <https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f>`_

33
doc/src/Howto_bioFF.rst
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@ -3,24 +3,20 @@ CHARMM, AMBER, COMPASS, and DREIDING force fields
A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly
used in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting
formulas implemented in LAMMPS that correspond to formulas commonly used
in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting
coefficients is done either from special sections in an input data file
via the :doc:`read_data <read_data>` command or in the input script with
commands like :doc:`pair_coeff <pair_coeff>` or
:doc:`bond_coeff <bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc
page for additional tools that can use CHARMM, AMBER, or Materials
Studio generated files to assign force field coefficients and convert
their output into LAMMPS input.
commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
<bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc page for
additional tools that can use CHARMM, AMBER, or Materials Studio
generated files to assign force field coefficients and convert their
output into LAMMPS input.
See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM force
field. See :ref:`(Cornell) <howto-Cornell>` for a description of the AMBER
force field. See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS
force field.
.. _charmm: http://www.scripps.edu/brooks
.. _amber: http://amber.scripps.edu
See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
force field. See :ref:`(Cornell) <howto-Cornell>` for a description of
the AMBER force field. See :ref:`(Sun) <howto-Sun>` for a description
of the COMPASS force field.
The interaction styles listed below compute force field formulas that
are consistent with common options in CHARMM or AMBER. See each
@ -41,9 +37,10 @@ command's documentation for the formula it computes.
.. note::
For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released
in March 2017. We recommend they be used instead of the older *charmm*
styles. See discussion of the differences on the :doc:`pair charmm <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
March 2017. We recommend they be used instead of the older *charmm*
styles. See discussion of the differences on the :doc:`pair charmm
<pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
pages.
COMPASS is a general force field for atomistic simulation of common

2
doc/src/Howto_github.rst
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@ -10,7 +10,7 @@ changes or additions you have made to LAMMPS into the official LAMMPS
distribution. It uses the process of updating this very tutorial as an
example to describe the individual steps and options. You need to be
familiar with git and you may want to have a look at the `git book
<http://git-scm.com/book/>`_ to familiarize yourself with some of the
<https://git-scm.com/book/>`_ to familiarize yourself with some of the
more advanced git features used below.
As of fall 2016, submitting contributions to LAMMPS via pull requests

2
doc/src/Howto_manifold.rst
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@ -47,4 +47,4 @@ to the relevant fixes.
.. _Paquay1:
**(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.

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2
doc/src/Howto_spc.rst
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@ -38,7 +38,7 @@ the partial charge assignments change:
See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
the SPC and SPC/E models.
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
----------

2
doc/src/Howto_tip3p.rst
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@ -49,7 +49,7 @@ details:
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
|
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
----------

2
doc/src/Howto_tip4p.rst
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@ -97,7 +97,7 @@ This leads to slightly larger cost for the long-range calculation, so
you can test the trade-off for your model. The OM distance and the LJ
and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>` command.
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
----------

7
doc/src/Howto_viz.rst
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@ -17,9 +17,10 @@ formats. See the :doc:`Tools <Tools>` page for details.
A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of
user-specified atom information, and convert them to various formats
or pipe them into visualization software directly. See the `Pizza.py WWW site <pizza_>`_ for details. Specifically, Pizza.py can convert
LAMMPS dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
user-specified atom information, and convert them to various formats or
pipe them into visualization software directly. See the `Pizza.py WWW
site <pizza_>`_ for details. Specifically, Pizza.py can convert LAMMPS
dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
RasMol visualization programs. Pizza.py has tools that do interactive
3d OpenGL visualization and one that creates SVG images of dump file

4
doc/src/Install_conda.rst
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@ -5,7 +5,7 @@ Binaries are available for MacOS or Linux via `Conda <conda_>`_.
First, one must setup the Conda package manager on your system. Follow the
instructions to install `Miniconda <mini_conda_install_>`_, then create a conda
environment (named `my-lammps-env` or whatever you prefer) for your lammps
environment (named `my-lammps-env` or whatever you prefer) for your LAMMPS
install:
.. code-block:: bash
@ -13,7 +13,7 @@ install:
% conda config --add channels conda-forge
% conda create -n my-lammps-env
Then, you can install lammps on your system with the following command:
Then, you can install LAMMPS on your system with the following command:
.. code-block:: bash

2
doc/src/Install_windows.rst
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@ -6,7 +6,7 @@ Windows system can be downloaded from this site:
.. parsed-literal::
`http://packages.lammps.org/windows.html <http://packages.lammps.org/windows.html>`_
`https://packages.lammps.org/windows.html <https://packages.lammps.org/windows.html>`_
Note that each installer package has a date in its name, which
corresponds to the LAMMPS version of the same date. Installers for

4
doc/src/Intro_authors.rst
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@ -4,13 +4,13 @@ Authors of LAMMPS
The primary LAMMPS developers are at Sandia National Labs and Temple
University:
* `Steve Plimpton <sjp_>`_, sjplimp at sandia.gov
* `Steve Plimpton <sjp_>`_, sjplimp at gmail.com
* Aidan Thompson, athomps at sandia.gov
* Stan Moore, stamoor at sandia.gov
* Axel Kohlmeyer, akohlmey at gmail.com
* Richard Berger, richard.berger at outlook.com
.. _sjp: http://www.cs.sandia.gov/~sjplimp
.. _sjp: https://sjplimp.github.io
.. _lws: https://www.lammps.org
Past developers include Paul Crozier and Mark Stevens, both at Sandia,

2
doc/src/Intro_citing.rst
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@ -27,7 +27,7 @@ namely https://www.lammps.org.
The original publication describing the parallel algorithms used in the
initial versions of LAMMPS is:
`S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <http://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf>`_
`S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <https://doi.org/10.1006/jcph.1995.1039>`_
DOI for the LAMMPS source code

4
doc/src/Intro_features.rst
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@ -95,7 +95,7 @@ commands)
* metal-organic framework potentials (QuickFF, MO-FF)
* implicit solvent potentials: hydrodynamic lubrication, Debye
* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim command <kim_commands>`
* access to the `OpenKIM Repository <https://openkim.org>`_ of potentials via the :doc:`kim command <kim_commands>`
* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
* overlaid potentials: superposition of multiple pair potentials (including many-body) with optional scale factor
@ -205,7 +205,7 @@ Pre- and post-processing
.. _pizza: https://lammps.github.io/pizza
.. _python: http://www.python.org
.. _python: https://www.python.org
.. _special:

6
doc/src/Intro_nonfeatures.rst
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@ -33,7 +33,7 @@ Here are suggestions on how to perform these tasks:
linear bead-spring polymer chains. The moltemplate program is a true
molecular builder that will generate complex molecular models. See
the :doc:`Tools <Tools>` page for details on tools packaged with
LAMMPS. The `Pre/post processing page <http:/www.lammps.org/prepost.html>`_ of the LAMMPS website
LAMMPS. The `Pre/post processing page <https:/www.lammps.org/prepost.html>`_ of the LAMMPS website
describes a variety of third party tools for this task. Furthermore,
some LAMMPS internal commands allow to reconstruct, or selectively add
topology information, as well as provide the option to insert molecule
@ -80,5 +80,5 @@ Here are suggestions on how to perform these tasks:
`Pizza.py <https://lammps.github.io/pizza>`_ which can do certain kinds of
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
simulations. It thus provides some functionality for several of the
above bullets. Pizza.py is written in `Python <http://www.python.org>`_
and is available for download from `this page <http://www.cs.sandia.gov/~sjplimp/download.html>`_.
above bullets. Pizza.py is written in `Python <https://www.python.org>`_
and is available for download from `this page <https://sjplimp.github.io/download.html>`_.

4
doc/src/Intro_opensource.rst
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@ -23,9 +23,9 @@ applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution.
.. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html
.. _gnuorg: http://www.gnu.org
.. _gnuorg: https://www.gnu.org
.. _opensource: http://www.opensource.org
.. _opensource: https://www.opensource.org
Here is a more specific summary of what the GPL means for LAMMPS users:

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doc/src/Packages_details.rst
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@ -134,6 +134,8 @@ commands to write and read data using the ADIOS library.
**Authors:** Norbert Podhorszki (ORNL) from the ADIOS developer team.
.. versionadded:: 28Feb2019
**Install:**
This package has :ref:`specific installation instructions <adios>` on the :doc:`Build extras <Build_extras>` page.
@ -364,6 +366,8 @@ and also support self-propelled particles.
**Authors:** Sam Cameron (University of Bristol),
Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
.. versionadded:: 14May2021
Example inputs are in the examples/PACKAGES/brownian folder.
----------
@ -592,6 +596,8 @@ To use this package, also the :ref:`KSPACE <PKG-KSPACE>` and
**Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U)
.. versionadded:: 2Jul2021
**Supporting info:**
* src/DIELECTRIC: filenames -> commands
@ -1071,7 +1077,7 @@ H5MD is a format for molecular simulations, built on top of HDF5.
This package implements a :doc:`dump h5md <dump_h5md>` command to output
LAMMPS snapshots in this format.
.. _HDF5: http://www.hdfgroup.org/HDF5
.. _HDF5: https://www.hdfgroup.org/solutions/hdf5
To use this package you must have the HDF5 library available on your
system.
@ -1512,6 +1518,8 @@ workflows via the `MolSSI Driver Interface
**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
.. versionadded:: 14May2021
**Install:**
This package has :ref:`specific installation instructions <mdi>` on
@ -1596,6 +1604,8 @@ of Alabama), Leonid V. Zhigilei (University of Virginia)
**Author of the *mesocnt* styles:**
Philipp Kloza (U Cambridge)
.. versionadded:: 15Jun2020
**Supporting info:**
* src/MESONT: filenames -> commands
@ -1688,6 +1698,8 @@ compiled on your system.
**Author:** Andreas Singraber
.. versionadded:: 27May2021
**Install:**
This package has :ref:`specific installation instructions <ml-hdnnp>` on the
@ -1722,6 +1734,10 @@ must be installed.
**Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
.. versionadded:: 30Jun2020
.. versionadded:: 30Jun2020
**Supporting info:**
* src/ML-IAP: filenames -> commands
@ -1766,6 +1782,8 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
^4: University of British Columbia, Vancouver, BC, Canada
.. versionadded:: 14May2021
**Install:**
This package has :ref:`specific installation instructions <ml-pace>` on the
@ -1829,6 +1847,8 @@ of a neural network.
This package was written by Christopher Barrett
with contributions by Doyl Dickel, Mississippi State University.
.. versionadded:: 27May2021
**Supporting info:**
* src/ML-RANN: filenames -> commands
@ -1954,7 +1974,7 @@ support for new file formats can be added to LAMMPS (or VMD or other
programs that use them) without having to re-compile the application
itself. More information about the VMD molfile plugins can be found
at
`http://www.ks.uiuc.edu/Research/vmd/plugins/molfile <http://www.ks.uiuc.edu/Research/vmd/plugins/molfile>`_.
`https://www.ks.uiuc.edu/Research/vmd/plugins/molfile <https://www.ks.uiuc.edu/Research/vmd/plugins/molfile>`_.
**Author:** Axel Kohlmeyer (Temple U).
@ -2045,7 +2065,7 @@ NETCDF package
Dump styles for writing NetCDF formatted dump files. NetCDF is a
portable, binary, self-describing file format developed on top of
HDF5. The file contents follow the AMBER NetCDF trajectory conventions
(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
(https://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
To use this package you must have the NetCDF library available on your
system.
@ -2056,7 +2076,7 @@ tools:
* `Ovito <ovito_>`_ (Ovito supports the AMBER convention and the extensions mentioned above)
* `VMD <vmd-home_>`_
.. _ovito: http://www.ovito.org
.. _ovito: https://www.ovito.org
.. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/
@ -2200,6 +2220,7 @@ Foster (UTSA).
**Supporting info:**
* src/PERI: filenames -> commands
* :doc:`Peridynamics Howto <Howto_peri>`
* `doc/PDF/PDLammps_overview.pdf <PDF/PDLammps_overview.pdf>`_
* `doc/PDF/PDLammps_EPS.pdf <PDF/PDLammps_EPS.pdf>`_
* `doc/PDF/PDLammps_VES.pdf <PDF/PDLammps_VES.pdf>`_
@ -2264,6 +2285,8 @@ try to load the contained plugins automatically at start-up.
**Authors:** Axel Kohlmeyer (Temple U)
.. versionadded:: 8Apr2021
**Supporting info:**
* src/PLUGIN: filenames -> commands
@ -2417,7 +2440,7 @@ A :doc:`fix qmmm <fix_qmmm>` command which allows LAMMPS to be used as
the MM code in a QM/MM simulation. This is currently only available
in combination with the `Quantum ESPRESSO <espresso_>`_ package.
.. _espresso: http://www.quantum-espresso.org
.. _espresso: https://www.quantum-espresso.org
To use this package you must have Quantum ESPRESSO (QE) available on
your system and include its coupling library in the compilation and
@ -2829,7 +2852,7 @@ collection of atoms by wrapping the `Voro++ library <voro-home_>`_. This
can be used to calculate the local volume or each atoms or its near
neighbors.
.. _voro-home: http://math.lbl.gov/voro++
.. _voro-home: https://math.lbl.gov/voro++
To use this package you must have the Voro++ library available on your
system.
@ -2863,9 +2886,9 @@ A :doc:`dump vtk <dump_vtk>` command which outputs snapshot info in the
`VTK format <vtk_>`_, enabling visualization by `Paraview <paraview_>`_ or
other visualization packages.
.. _vtk: http://www.vtk.org
.. _vtk: https://www.vtk.org
.. _paraview: http://www.paraview.org
.. _paraview: https://www.paraview.org
To use this package you must have VTK library available on your
system.
@ -2902,11 +2925,13 @@ which discuss the `QuickFF <quickff_>`_ methodology.
.. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877
.. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173
.. _quickff: http://molmod.github.io/QuickFF
.. _quickff: https://molmod.github.io/QuickFF
.. _yaff: https://github.com/molmod/yaff
**Author:** Steven Vandenbrande.
.. versionadded:: 1Feb2019
**Supporting info:**
* src/YAFF/README

20
doc/src/Python_examples.rst
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@ -43,26 +43,18 @@ Note that for AtomEye, you need version 3, and there is a line in the
scripts that specifies the path and name of the executable. See the
AtomEye web pages for more details:
* `http://li.mit.edu/Archive/Graphics/A/ <atomeye_>`_
* `http://li.mit.edu/Archive/Graphics/A3/A3.html <atomeye3_>`_
* `http://li.mit.edu/Archive/Graphics/A/ <http://li.mit.edu/Archive/Graphics/A/>`_
* `http://li.mit.edu/Archive/Graphics/A3/A3.html <http://li.mit.edu/Archive/Graphics/A3/A3.html>`_
.. _atomeye: http://li.mit.edu/Archive/Graphics/A/
.. _atomeye3: http://li.mit.edu/Archive/Graphics/A3/A3.html
The latter link is to AtomEye 3 which has the scripting
capability needed by these Python scripts.
The latter link is to AtomEye 3 which has the scripting capability
needed by these Python scripts.
Note that for PyMol, you need to have built and installed the
open-source version of PyMol in your Python, so that you can import it
from a Python script. See the PyMol web pages for more details:
* `https://www.pymol.org <pymolhome_>`_
* `https://github.com/schrodinger/pymol-open-source <pymolopen_>`_
.. _pymolhome: https://www.pymol.org
.. _pymolopen: https://github.com/schrodinger/pymol-open-source
* `https://www.pymol.org <https://www.pymol.org>`_
* `https://github.com/schrodinger/pymol-open-source <https://github.com/schrodinger/pymol-open-source>`_
The latter link is to the open-source version.

10
doc/src/Python_head.rst
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@ -18,17 +18,17 @@ together.
Python_error
Python_trouble
If you are not familiar with `Python <http://www.python.org>`_, it is a
If you are not familiar with `Python <https://www.python.org>`_, it is a
powerful scripting and programming language which can do almost
everything that compiled languages like C, C++, or Fortran can do in
fewer lines of code. It also comes with a large collection of add-on
modules for many purposes (either bundled or easily installed from
Python code repositories). The major drawback is slower execution speed
of the script code compared to compiled programming languages. But when
the script code is interfaced to optimized compiled code, performance can
be on par with a standalone executable, for as long as the scripting is
restricted to high-level operations. Thus Python is also convenient to
use as a "glue" language to "drive" a program through its library
the script code is interfaced to optimized compiled code, performance
can be on par with a standalone executable, for as long as the scripting
is restricted to high-level operations. Thus Python is also convenient
to use as a "glue" language to "drive" a program through its library
interface, or to hook multiple pieces of software together, such as a
simulation code and a visualization tool, or to run a coupled
multi-scale or multi-physics model.

4
doc/src/Run_windows.rst
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@ -25,8 +25,8 @@ in parallel, follow these steps.
Download and install a compatible MPI library binary package:
* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
The LAMMPS Windows installer packages will automatically adjust your
path for the default location of this MPI package. After the

2
doc/src/Speed_gpu.rst
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@ -39,7 +39,7 @@ toolkit software on your system (this is only tested on Linux
and unsupported on Windows):
* Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/\*/information
* Go to http://www.nvidia.com/object/cuda_get.html
* Go to https://developer.nvidia.com/cuda-downloads
* Install a driver and toolkit appropriate for your system (SDK is not necessary)
* Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
list supported devices and properties

2
doc/src/Speed_intel.rst
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@ -537,5 +537,5 @@ References
""""""""""
* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS", in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <https://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
* Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101.

2
doc/src/Speed_omp.rst
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@ -97,7 +97,7 @@ sub-section.
A description of the multi-threading strategy used in the OPENMP
package and some performance examples are
`presented here <http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1>`_.
`presented here <https://drive.google.com/file/d/1d1gLK6Ru6aPYB50Ld2tO10Li8zgPVNB8/view?usp=sharing>`_.
Guidelines for best performance
"""""""""""""""""""""""""""""""

13
doc/src/Tools.rst
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@ -205,6 +205,7 @@ scripts are available:
whitespace.py # detects TAB characters and trailing whitespace
homepage.py # detects outdated LAMMPS homepage URLs (pointing to sandia.gov instead of lammps.org)
errordocs.py # detects deprecated error docs in header files
versiontags.py # detects .. versionadded:: or .. versionchanged:: with pending version date
The tools need to be given the main folder of the LAMMPS distribution
or individual file names as argument and will by default check them
@ -397,7 +398,7 @@ ipp tool
------------------
The tools/ipp directory contains a Perl script ipp which can be used
to facilitate the creation of a complicated file (say, a lammps input
to facilitate the creation of a complicated file (say, a LAMMPS input
script or tools/createatoms input file) using a template file.
ipp was created and is maintained by Reese Jones (Sandia), rjones at
@ -512,8 +513,8 @@ with an ``.inputrc`` file in the home directory. For application
specific customization, the LAMMPS shell uses the name "lammps-shell".
For more information about using and customizing an application using
readline, please see the available documentation at:
`http://www.gnu.org/s/readline/#Documentation
<http://www.gnu.org/s/readline/#Documentation>`_
https://www.gnu.org/software/readline/
Additional commands
^^^^^^^^^^^^^^^^^^^
@ -715,7 +716,7 @@ See the README.pdf file for more information.
These scripts were written by Arun Subramaniyan at Purdue Univ
(asubrama at purdue.edu).
.. _matlabhome: http://www.mathworks.com
.. _matlabhome: https://www.mathworks.com
----------
@ -1046,7 +1047,7 @@ the binary file. This usually is a so-called little endian hardware
SWIG interface
--------------
The `SWIG tool <http://swig.org>`_ offers a mostly automated way to
The `SWIG tool <https://swig.org>`_ offers a mostly automated way to
incorporate compiled code modules into scripting languages. It
processes the function prototypes in C and generates wrappers for a wide
variety of scripting languages from it. Thus it can also be applied to
@ -1126,7 +1127,7 @@ data passed or returned as pointers are included in the ``lammps.i``
file. So most of the functionality of the library interface should be
accessible. What works and what does not depends a bit on the
individual language for which the wrappers are built and how well SWIG
supports those. The `SWIG documentation <http://swig.org/doc.html>`_
supports those. The `SWIG documentation <https://swig.org/doc.html>`_
has very detailed instructions and recommendations.
Usage examples

2
doc/src/compute_ave_sphere_atom.rst
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@ -35,6 +35,8 @@ Examples
Description
"""""""""""
.. versionadded:: 7Jan2022
Define a computation that calculates the local mass density and
temperature for each atom based on its neighbors inside a spherical
cutoff. If an atom has :math:`M` neighbors, then its local mass density is

16
doc/src/compute_damage_atom.rst
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@ -24,16 +24,17 @@ Description
"""""""""""
Define a computation that calculates the per-atom damage for each atom
in a group. This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`. See `this document <PDF/PDLammps_overview.pdf>`_
for an overview of LAMMPS commands for Peridynamics modeling.
in a group. This is a quantity relevant for :doc:`Peridynamics models
<pair_peri>`. See `this document <PDF/PDLammps_overview.pdf>`_ for an
overview of LAMMPS commands for Peridynamics modeling.
The "damage" of a Peridynamics particles is based on the bond breakage
between the particle and its neighbors. If all the bonds are broken
the particle is considered to be fully damaged.
See the `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for a formal
definition of "damage" and more details about Peridynamics as it is
implemented in LAMMPS.
See the :doc:`Peridynamics Howto <Howto_peri>` for a formal definition
of "damage" and more details about Peridynamics as it is implemented in
LAMMPS.
This command can be used with all the Peridynamic pair styles.
@ -53,8 +54,9 @@ The per-atom vector values are unitless numbers (damage) :math:`\ge 0.0`.
Restrictions
""""""""""""
This compute is part of the PERI package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
This compute is part of the PERI package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""

20
doc/src/compute_dilatation_atom.rst
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@ -24,7 +24,8 @@ Description
"""""""""""
Define a computation that calculates the per-atom dilatation for each
atom in a group. This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`. See `this document <PDF/PDLammps_overview.pdf>`_
atom in a group. This is a quantity relevant for :doc:`Peridynamics
models <pair_peri>`. See `this document <PDF/PDLammps_overview.pdf>`_
for an overview of LAMMPS commands for Peridynamics modeling.
For small deformation, dilatation of is the measure of the volumetric
@ -32,13 +33,14 @@ strain.
The dilatation :math:`\theta` for each peridynamic particle :math:`i` is
calculated as a sum over its neighbors with unbroken bonds, where the
contribution of the :math:`ij` pair is a function of the change in bond length
(versus the initial length in the reference state), the volume
contribution of the :math:`ij` pair is a function of the change in bond
length (versus the initial length in the reference state), the volume
fraction of the particles and an influence function. See the
`PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for
a formal definition of dilatation.
:doc:`Peridynamics Howto <Howto_peri>` for a formal definition of
dilatation.
This command can only be used with a subset of the Peridynamic :doc:`pair styles <pair_peri>`: peri/lps, peri/ves and peri/eps.
This command can only be used with a subset of the Peridynamic
:doc:`pair styles <pair_peri>`: *peri/lps*, *peri/ves*, and *peri/eps*.
The dilatation value will be 0.0 for atoms not in the specified
compute group.
@ -56,9 +58,9 @@ The per-atom vector values are unitless numbers :math:`(\theta \ge 0.0)`.
Restrictions
""""""""""""
This compute is part of the PERI package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
This compute is part of the PERI package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""

2
doc/src/compute_fep_ta.rst
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@ -34,6 +34,8 @@ Examples
Description
"""""""""""
.. versionadded:: 4May2022
Define a computation that calculates the change in the free energy due
to a test-area (TA) perturbation :ref:`(Gloor) <Gloor>`. The test-area
approach can be used to determine the interfacial tension of the system

24
doc/src/compute_sna_atom.rst
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@ -228,18 +228,20 @@ command:
See section below on output for a detailed explanation of the data
layout in the global array.
.. versionadded:: 3Aug2022
The compute *sna/grid* and *sna/grid/local* commands calculate
bispectrum components for a regular grid of points.
These are calculated from the local density of nearby atoms *i'*
around each grid point, as if there was a central atom *i*
at the grid point. This is useful for characterizing fine-scale
structure in a configuration of atoms, and it is used
in the `MALA package <https://github.com/casus/mala>`_
to build machine-learning surrogates for finite-temperature Kohn-Sham
density functional theory (:ref:`Ellis et al. <Ellis2021>`)
Neighbor atoms not in the group do not contribute to the
bispectrum components of the grid points. The distance cutoff :math:`R_{ii'}`
assumes that *i* has the same type as the neighbor atom *i'*.
bispectrum components for a regular grid of points. These are
calculated from the local density of nearby atoms *i'* around each grid
point, as if there was a central atom *i* at the grid point. This is
useful for characterizing fine-scale structure in a configuration of
atoms, and it is used in the `MALA package
<https://github.com/casus/mala>`_ to build machine-learning surrogates
for finite-temperature Kohn-Sham density functional theory (:ref:`Ellis
et al. <Ellis2021>`) Neighbor atoms not in the group do not contribute
to the bispectrum components of the grid points. The distance cutoff
:math:`R_{ii'}` assumes that *i* has the same type as the neighbor atom
*i'*.
Compute *sna/grid* calculates a global array containing bispectrum
components for a regular grid of points.

6
doc/src/compute_temp_cs.rst
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@ -29,7 +29,7 @@ Description
Define a computation that calculates the temperature of a system based
on the center-of-mass velocity of atom pairs that are bonded to each
other. This compute is designed to be used with the adiabatic
core/shell model of :ref:`(Mitchell and Finchham) <MitchellFinchham1>`.
core/shell model of :ref:`(Mitchell and Fincham) <MitchellFincham1>`.
See the :doc:`Howto coreshell <Howto_coreshell>` page for an overview of
the model as implemented in LAMMPS. Specifically, this compute
enables correct temperature calculation and thermostatting of
@ -127,7 +127,7 @@ none
----------
.. _MitchellFinchham1:
.. _MitchellFincham1:
**(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter,
**(Mitchell and Fincham)** Mitchell, Fincham, J Phys Condensed Matter,
5, 1031-1038 (1993).

32
doc/src/compute_voronoi_atom.rst
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@ -154,25 +154,25 @@ which must be installed on your system when building LAMMPS for use
with this compute. See instructions on obtaining and installing the
Voro++ software in the src/VORONOI/README file.
.. _voronoi: http://math.lbl.gov/voro++/
.. _voronoi: https://math.lbl.gov/voro++/
.. note::
The calculation of Voronoi volumes is performed by each
processor for the atoms it owns, and includes the effect of ghost
atoms stored by the processor. This assumes that the Voronoi cells of
owned atoms are not affected by atoms beyond the ghost atom cut-off
distance. This is usually a good assumption for liquid and solid
systems, but may lead to underestimation of Voronoi volumes in low
density systems. By default, the set of ghost atoms stored by each
processor is determined by the cutoff used for
:doc:`pair_style <pair_style>` interactions. The cutoff can be set
explicitly via the :doc:`comm_modify cutoff <comm_modify>` command. The
Voronoi cells for atoms adjacent to empty regions will extend into
those regions up to the communication cutoff in :math:`x`, :math:`y`, or
:math:`z`. In that situation, an exterior face is created at the cutoff
distance normal to the :math:`x`, :math:`y`, or :math:`z` direction.
For triclinic systems, the exterior face is parallel to the corresponding
The calculation of Voronoi volumes is performed by each processor for
the atoms it owns, and includes the effect of ghost atoms stored by
the processor. This assumes that the Voronoi cells of owned atoms
are not affected by atoms beyond the ghost atom cut-off distance.
This is usually a good assumption for liquid and solid systems, but
may lead to underestimation of Voronoi volumes in low density
systems. By default, the set of ghost atoms stored by each processor
is determined by the cutoff used for :doc:`pair_style <pair_style>`
interactions. The cutoff can be set explicitly via the
:doc:`comm_modify cutoff <comm_modify>` command. The Voronoi cells
for atoms adjacent to empty regions will extend into those regions up
to the communication cutoff in :math:`x`, :math:`y`, or :math:`z`.
In that situation, an exterior face is created at the cutoff distance
normal to the :math:`x`, :math:`y`, or :math:`z` direction. For
triclinic systems, the exterior face is parallel to the corresponding
reciprocal lattice vector.
.. note::

4
doc/src/create_atoms.rst
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@ -189,6 +189,10 @@ to the area of that triangle.
beneficial to exclude computing interactions between the created
particles using :doc:`neigh_modify exclude <neigh_modify>`.
.. versionchanged:: 2Jun2022
The *porosity* style has been renamed to *random* with added functionality.
For the *random* style, *N* particles are added to the system at
randomly generated coordinates, which can be useful for generating an
amorphous system. The particles are created one by one using the

2
doc/src/delete_atoms.rst
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@ -116,6 +116,8 @@ must be in both the specified group and region. If *group-ID* = all,
there is effectively no group criterion. If *region-ID* is specified
as NULL, no region criterion is imposed.
.. versionadded:: 4May2022
For style *variable*, all atoms for which the atom-style variable with
the given name evaluates to non-zero will be deleted. Additional atoms
can be deleted if they are in a molecule for which one or more atoms

2
doc/src/dump.rst
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@ -480,7 +480,7 @@ style.
----------
Note that *atom*, *custom*, *dcd*, *xtc*, and *xyz* style dump files
can be read directly by `VMD <http://www.ks.uiuc.edu/Research/vmd>`_, a
can be read directly by `VMD <https://www.ks.uiuc.edu/Research/vmd>`_, a
popular molecular viewing program.
----------

6
doc/src/dump_h5md.rst
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@ -64,7 +64,7 @@ stored within the same file by defining several dumps. A dump that
refers (via *file_from*) to an already open dump ID and that concerns
another particle group must specify *create_group yes*.
.. _h5md: http://nongnu.org/h5md/
.. _h5md: https://nongnu.org/h5md/
Each data element is written every N\*N_element steps. For *image*, no
sub-interval is needed as it must be present at the same interval as
@ -113,7 +113,7 @@ the `HDF5 <HDF5-ws_>`_ library installed (C bindings are sufficient) on
your system. The library ch5md is compiled with the h5cc wrapper
provided by the HDF5 library.
.. _HDF5-ws: http://www.hdfgroup.org/HDF5/
.. _HDF5-ws: https://www.hdfgroup.org/solutions/hdf5/
----------
@ -129,4 +129,4 @@ Related commands
**(de Buyl)** de Buyl, Colberg and Hofling, H5MD: A structured,
efficient, and portable file format for molecular data,
Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
`[arXiv:1308.6382] <http://arxiv.org/abs/1308.6382/>`_.
`[arXiv:1308.6382] <https://arxiv.org/abs/1308.6382/>`_.

4
doc/src/dump_image.rst
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@ -212,7 +212,7 @@ is used.
Similarly, the format of the resulting movie is chosen with the
*movie* dump style. This is handled by the underlying FFmpeg converter
and thus details have to be looked up in the `FFmpeg documentation
<http://ffmpeg.org/ffmpeg.html>`_. Typical examples are: .avi, .mpg,
<https://ffmpeg.org/ffmpeg.html>`_. Typical examples are: .avi, .mpg,
.m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie
compression like bitrate and framerate can be set using the
dump_modify command as described below.
@ -642,7 +642,7 @@ MPEG or other movie file you can use:
cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
Front ends for FFmpeg exist for multiple platforms. For more
information see the `FFmpeg homepage <http://www.ffmpeg.org/>`_
information see the `FFmpeg homepage <https://www.ffmpeg.org/>`_
----------

2
doc/src/dump_modify.rst
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@ -881,7 +881,7 @@ levels that sacrifice compression for performance. 0 is the default,
positive levels are 1 to 22, with 22 being the most expensive
compression. Zstd promises higher compression/decompression speeds for
similar compression ratios. For more details see
`http://facebook.github.io/zstd/`.
`https://facebook.github.io/zstd/`.
In addition, Zstd compressed files can include a checksum of the
entire contents. The Zstd enabled dump styles enable this feature by

2
doc/src/dump_molfile.rst
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@ -34,7 +34,7 @@ Dump a snapshot of atom coordinates and selected additional quantities
to one or more files every N timesteps in one of several formats.
Only information for atoms in the specified group is dumped. This
specific dump style uses molfile plugins that are bundled with the
`VMD <http://www.ks.uiuc.edu/Research/vmd>`_ molecular visualization and
`VMD <https://www.ks.uiuc.edu/Research/vmd>`_ molecular visualization and
analysis program.
Unless the filename contains a \* character, the output will be written

14
doc/src/dump_netcdf.rst
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@ -48,21 +48,17 @@ rank.
NetCDF files can be directly visualized via the following tools:
Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and
all extensions of this dump style.
* VMD (http://www.ks.uiuc.edu/Research/vmd/).
* AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye
contains a NetCDF reader that is not present in the standard
distribution of AtomEye.
* Ovito (https://www.ovito.org/). Ovito supports the AMBER convention and
all extensions of this dump style.
* VMD (https://www.ks.uiuc.edu/Research/vmd/).
In addition to per-atom data, :doc:`thermo <thermo>` data can be included in the
dump file. The data included in the dump file is identical to the data specified
by :doc:`thermo_style <thermo_style>`.
.. _netcdf-home: http://www.unidata.ucar.edu/software/netcdf/
.. _netcdf-home: https://www.unidata.ucar.edu/software/netcdf/
.. _pnetcdf-home: http://trac.mcs.anl.gov/projects/parallel-netcdf/
.. _pnetcdf-home: https://trac.mcs.anl.gov/projects/parallel-netcdf/
----------

26
doc/src/dump_vtk.rst
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@ -29,8 +29,9 @@ Description
"""""""""""
Dump a snapshot of atom quantities to one or more files every :math:`N`
timesteps in a format readable by the `VTK visualization toolkit <http://www.vtk.org>`_ or other visualization tools that use it,
such as `ParaView <http://www.paraview.org>`_. The time steps on which dump
timesteps in a format readable by the `VTK visualization toolkit
<https://www.vtk.org>`_ or other visualization tools that use it, such
as `ParaView <https://www.paraview.org>`_. The time steps on which dump
output is written can also be controlled by a variable; see the
:doc:`dump_modify every <dump_modify>` command for details.
@ -38,8 +39,8 @@ This dump style is similar to :doc:`dump_style custom <dump>` but uses
the VTK library to write data to VTK simple legacy or XML format,
depending on the filename extension specified for the dump file. This
can be either *\*.vtk* for the legacy format or *\*.vtp* and *\*.vtu*,
respectively, for XML format; see the
`VTK homepage <http://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
respectively, for XML format; see the `VTK homepage
<https://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
description of these formats. Since this naming convention conflicts
with the way binary output is usually specified (see below), the
:doc:`dump_modify binary <dump_modify>` command allows setting of a
@ -61,14 +62,15 @@ determine the kind of output.
.. warning::
Unless the :doc:`dump_modify sort <dump_modify>` option
is invoked, the lines of atom information written to dump files will
be in an indeterminate order for each snapshot. This is even true
when running on a single processor, if the :doc:`atom_modify sort <atom_modify>` option is on, which it is by default. In this
case atoms are re-ordered periodically during a simulation, due to
spatial sorting. It is also true when running in parallel, because
data for a single snapshot is collected from multiple processors, each
of which owns a subset of the atoms.
Unless the :doc:`dump_modify sort <dump_modify>` option is invoked,
the lines of atom information written to dump files will be in an
indeterminate order for each snapshot. This is even true when
running on a single processor, if the :doc:`atom_modify sort
<atom_modify>` option is on, which it is by default. In this case
atoms are re-ordered periodically during a simulation, due to spatial
sorting. It is also true when running in parallel, because data for
a single snapshot is collected from multiple processors, each of
which owns a subset of the atoms.
For the *vtk* style, sorting is off by default. See the
:doc:`dump_modify <dump_modify>` page for details.

2
doc/src/fix_adapt.rst
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@ -319,6 +319,8 @@ with fix_adapt are
----------
.. versionadded:: 4May2022
The *angle* keyword uses the specified variable to change the value of
an angle coefficient over time, very similar to how the *pair* keyword
operates. The only difference is that now an angle coefficient for a

2
doc/src/fix_external.rst
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@ -78,7 +78,7 @@ example of how this is done. This sample application performs
classical MD using quantum forces computed by a density functional
code `Quest <quest_>`_.
.. _quest: http://dft.sandia.gov/Quest
.. _quest: https://dft.sandia.gov/Quest
----------

2
doc/src/fix_gle.rst
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@ -159,7 +159,7 @@ Related commands
.. _GLE4MD:
**(GLE4MD)** `http://gle4md.org/ <http://gle4md.org/>`_
**(GLE4MD)** `https://gle4md.org/ <https://gle4md.org/>`_
.. _Ceriotti2:

55
doc/src/fix_imd.rst
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@ -51,16 +51,11 @@ from the main execution thread and potentially lower the inferred
latencies for slow communication links. This feature has only been
tested under linux.
There are example scripts for using this package with LAMMPS in
examples/PACKAGES/imd. Additional examples and a driver for use with the
Novint Falcon game controller as haptic device can be found at:
http://sites.google.com/site/akohlmey/software/vrpn-icms.
The source code for this fix includes code developed by the
Theoretical and Computational Biophysics Group in the Beckman
Institute for Advanced Science and Technology at the University of
Illinois at Urbana-Champaign. We thank them for providing a software
interface that allows codes like LAMMPS to hook to `VMD <VMD_>`_.
The source code for this fix includes code developed by the Theoretical
and Computational Biophysics Group in the Beckman Institute for Advanced
Science and Technology at the University of Illinois at
Urbana-Champaign. We thank them for providing a software interface that
allows codes like LAMMPS to hook to `VMD <VMD_>`_.
Upon initialization of the fix, it will open a communication port on
the node with MPI task 0 and wait for an incoming connection. As soon
@ -117,40 +112,40 @@ VMD are the following:
In the Mouse menu of the VMD Main window, select "Mouse -> Force ->
Atom". You may alternately select "Residue", or "Fragment" to apply
forces to whole residues or fragments. Your mouse can now be used to
apply forces to your simulation. Click on an atom, residue, or
fragment and drag to apply a force. Click quickly without moving the
mouse to turn the force off. You can also use a variety of 3D position
trackers to apply forces to your simulation. Game controllers or haptic
devices with force-feedback such as the Novint Falcon or Sensable
PHANTOM allow you to feel the resistance due to inertia or interactions
with neighbors that the atoms experience you are trying to move, as if
they were real objects. See the `VMD IMD Homepage <imdvmd_>`_ and the
`VRPN-ICMS Homepage <vrpnicms_>`_ for more details.
apply forces to your simulation. Click on an atom, residue, or fragment
and drag to apply a force. Click quickly without moving the mouse to
turn the force off. You can also use a variety of 3D position trackers
to apply forces to your simulation. Game controllers or haptic devices
with force-feedback such as the Novint Falcon or Sensable PHANTOM allow
you to feel the resistance due to inertia or interactions with neighbors
that the atoms experience you are trying to move, as if they were real
objects. See the `VMD IMD Homepage <imdvmd_>`_ for more details.
If IMD control messages are received, a line of text describing the
message and its effect will be printed to the LAMMPS output screen, if
screen output is active.
.. _VMD: http://www.ks.uiuc.edu/Research/vmd
.. _VMD: https://www.ks.uiuc.edu/Research/vmd
.. _imdvmd: http://www.ks.uiuc.edu/Research/vmd/imd/
.. _vrpnicms: http://sites.google.com/site/akohlmey/software/vrpn-icms
.. _imdvmd: https://www.ks.uiuc.edu/Research/vmd/imd/
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various :doc:`output commands <Howto_output>`. No parameter of this fix can be used
with the *start/stop* keywords of the :doc:`run <run>` command. This
fix is not invoked during :doc:`energy minimization <minimize>`.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix. No global scalar or vector or per-atom quantities
are stored by this fix for access by various :doc:`output commands
<Howto_output>`. No parameter of this fix can be used with the
*start/stop* keywords of the :doc:`run <run>` command. This fix is not
invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the MISC package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
This fix is part of the MISC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
page for more info.
When used in combination with VMD, a topology or coordinate file has
to be loaded, which matches (in number and ordering of atoms) the

2
doc/src/fix_ipi.rst
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@ -111,4 +111,4 @@ Related commands
.. _ipihome:
**(IPI)**
`http://epfl-cosmo.github.io/gle4md/index.html?page=ipi <http://epfl-cosmo.github.io/gle4md/index.html?page=ipi>`_
`https://ipi-code.org <https://ipi-code.org>`_

2
doc/src/fix_latte.rst
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@ -81,6 +81,8 @@ The *coulomb* argument is not yet supported by fix latte (as of Sept
Coulomb potential as an alternative to LATTE performing the
calculation.
.. versionadded:: 15Sep2022
The *exclude* argument allows this fix to work in tandem with another
fix which may decide to delete one or more atoms of molecules. The
specified fixID is the ID of the other fix.

2
doc/src/fix_mdi_qm.rst
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@ -43,6 +43,8 @@ Examples
Description
"""""""""""
.. versionadded:: 3Aug2022
This command enables LAMMPS to act as a client with another server
code that will compute the total energy, per-atom forces, and total
virial for atom conformations and simulation box size/shapes that

3
doc/src/fix_nh_uef.rst
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@ -210,7 +210,8 @@ use :doc:`change_box <change_box>` before invoking the fix.
.. note::
When resuming from restart files, you may need to use :doc:`box tilt large <box>` since lammps has internal criteria from lattice
When resuming from restart files, you may need to use :doc:`box tilt
large <box>` since LAMMPS has internal criteria from lattice
reduction that are not the same as the criteria in the numerical
lattice reduction algorithm.

2
doc/src/fix_numdiff_virial.rst
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@ -25,6 +25,8 @@ Examples
Description
"""""""""""
.. versionadded:: 17Feb2022
Calculate the virial stress tensor through a finite difference calculation of
energy versus strain. These values can be compared to the analytic virial
tensor computed by pair styles, bond styles, etc. This can be useful for

2
doc/src/fix_nve_manifold_rattle.rst
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@ -108,4 +108,4 @@ every = 0, tchain = 3
.. _Paquay2:
**(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.

2
doc/src/fix_nvt_manifold_rattle.rst
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@ -82,4 +82,4 @@ Related commands
.. _Paquay3:
**(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.

4
doc/src/fix_phonon.rst
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@ -134,7 +134,7 @@ for other systems, *nasr* = 10 is typically sufficient.
The *map_file* contains the mapping information between the lattice
indices and the atom IDs, which tells the code which atom sits at
which lattice point; the lattice indices start from 0. An auxiliary
code, `latgen <http://code.google.com/p/latgen>`_, can be employed to
code, `latgen <https://code.google.com/p/latgen>`_, can be employed to
generate the compatible map file for various crystals.
In case one simulates a non-periodic system, where the whole simulation
@ -143,7 +143,7 @@ that the mapping info will be generated internally and a file is not
needed. In this case, the dynamical matrix at only the gamma-point
will/can be evaluated. Please keep in mind that fix-phonon is designed
for cyrstals, it will be inefficient and even degrade the performance
of lammps in case the unit cell is too large.
of LAMMPS in case the unit cell is too large.
The calculated dynamical matrix elements are written out in
:doc:`energy/distance\^2/mass <units>` units. The coordinates for *q*

2
doc/src/fix_qmmm.rst
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@ -31,7 +31,7 @@ wave DFT package. Electrostatic coupling is in preparation and the
interface has been written in a manner that coupling to other QM codes
should be possible without changes to LAMMPS itself.
.. _espresso: http://www.quantum-espresso.org
.. _espresso: https://www.quantum-espresso.org
The interface code for this is in the lib/qmmm directory of the LAMMPS
distribution and is being made available at this early stage of

11
doc/src/fix_shake.rst
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@ -58,10 +58,13 @@ Description
Apply bond and angle constraints to specified bonds and angles in the
simulation by either the SHAKE or RATTLE algorithms. This typically
enables a longer timestep. The SHAKE or RATTLE algorithms, however, can
*only* be applied during molecular dynamics runs. When this fix is used
during a minimization, the constraints are *approximated* by strong
harmonic restraints.
enables a longer timestep. The SHAKE or RATTLE constraint algorithms,
however, can *only* be applied during molecular dynamics runs.
.. versionchanged:: 15Sep2022
These fixes may still be used during minimization. In that case the
constraints are *approximated* by strong harmonic restraints.
**SHAKE vs RATTLE:**

7
doc/src/kspace_style.rst
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@ -314,9 +314,10 @@ pressure simulation with MSM will cause the code to run slower.
----------
The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver library <http://www.scafacos.de>`_ which provides a variety of solver
methods which can be used with LAMMPS. The paper by :ref:`(Sutman) <Sutmann2014>`
gives an overview of ScaFaCoS.
The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver
library <http://www.scafacos.de>`_ which provides a variety of solver
methods which can be used with LAMMPS. The paper by :ref:`(Sutman)
<Sutmann2014>` gives an overview of ScaFaCoS.
ScaFaCoS was developed by a consortium of German research facilities
with a BMBF (German Ministry of Science and Education) funded project

2
doc/src/pair_adp.rst
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@ -54,7 +54,7 @@ command to specify them.
**ADP potentials are available from:**
* The NIST WWW site at http://www.ctcms.nist.gov/potentials.
* The NIST WWW site at https://www.ctcms.nist.gov/potentials.
Note that ADP potentials obtained from NIST must be converted
into the extended DYNAMO *setfl* format discussed below.
* The OpenKIM Project at

2
doc/src/pair_charmm.rst
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@ -110,7 +110,7 @@ These pair styles compute Lennard Jones (LJ) and Coulombic
interactions with additional switching or shifting functions that ramp
the energy and/or force smoothly to zero between an inner and outer
cutoff. They are implementations of the widely used CHARMM force
field used in the `CHARMM <http://www.scripps.edu/brooks>`_ MD code (and
field used in the `CHARMM <https://www.charmm.org>`_ MD code (and
others). See :ref:`(MacKerell) <pair-MacKerell>` for a description of the
CHARMM force field.

6
doc/src/pair_cs.rst
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@ -114,7 +114,7 @@ Description
"""""""""""
These pair styles are designed to be used with the adiabatic
core/shell model of :ref:`(Mitchell and Finchham) <MitchellFinchham2>`. See
core/shell model of :ref:`(Mitchell and Fincham) <MitchellFincham3>`. See
the :doc:`Howto coreshell <Howto_coreshell>` page for an overview of
the model as implemented in LAMMPS.
@ -196,7 +196,7 @@ none
----------
.. _MitchellFinchham2:
.. _MitchellFincham3:
**(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter,
**(Mitchell and Fincham)** Mitchell, Fincham, J Phys Condensed Matter,
5, 1031-1038 (1993).

12
doc/src/pair_eam.rst
View File

@ -122,15 +122,11 @@ are parameterized in terms of LAMMPS :doc:`metal units <units>`.
EAM potential files list atomic masses; thus you do not need to use
the :doc:`mass <mass>` command to specify them.
There are several WWW sites that distribute and document EAM
potentials stored in DYNAMO or other formats:
There are web sites that distribute and document EAM potentials stored
in DYNAMO or other formats:
.. parsed-literal::
http://www.ctcms.nist.gov/potentials
http://cst-www.nrl.navy.mil/ccm6/ap
http://enpub.fulton.asu.edu/cms/potentials/main/main.htm
https://openkim.org
* https://www.ctcms.nist.gov/potentials
* https://openkim.org
These potentials should be usable with LAMMPS, though the alternate
formats would need to be converted to the DYNAMO format used by LAMMPS

2
doc/src/pair_gromacs.rst
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@ -53,7 +53,7 @@ Description
The *lj/gromacs* styles compute shifted LJ and Coulombic interactions
with an additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cutoff. It is a commonly
used potential in the `GROMACS <http://www.gromacs.org>`_ MD code and for
used potential in the `GROMACS <https://www.gromacs.org>`_ MD code and for
the coarse-grained models of :ref:`(Marrink) <Marrink>`.
.. math::

2
doc/src/pair_harmonic_cut.rst
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@ -27,6 +27,8 @@ Examples
Description
"""""""""""
.. versionadded:: 17Feb2022
Style *harmonic/cut* computes pairwise repulsive-only harmonic interactions with the formula
.. math::

2
doc/src/pair_ilp_tmd.rst
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@ -32,6 +32,8 @@ Examples
Description
"""""""""""
.. versionadded:: 17Feb2022
The *ilp/tmd* style computes the registry-dependent interlayer
potential (ILP) potential for transition metal dichalcogenides (TMD)
as described in :ref:`(Ouyang7) <Ouyang7>`.

20
doc/src/pair_meam.rst
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@ -311,9 +311,9 @@ formulation of the partial electron density function. In recent
literature, an extra term is included in the expression for the
third-order density in order to make the densities orthogonal (see for
example :ref:`(Wang) <Wang2>`, equation 3d); this term is included in the
MEAM implementation in lammps. However, in earlier published work
MEAM implementation in LAMMPS. However, in earlier published work
this term was not included when deriving parameters, including most of
those provided in the ``library.meam`` file included with lammps, and to
those provided in the ``library.meam`` file included with LAMMPS, and to
account for this difference the parameter *t1* must be augmented by
3/5\**t3*. If *augt1* = 1, the default, this augmentation is done
automatically. When parameter values are fit using the modified
@ -321,16 +321,16 @@ density function, as in more recent literature, augt1 should be set to
0.
The *mixture_ref_t* parameter is available to match results with those
of previous versions of lammps (before January 2011). Newer versions
of lammps, by default, use the single-element values of the *t*
of previous versions of LAMMPS (before January 2011). Newer versions
of LAMMPS, by default, use the single-element values of the *t*
parameters to compute the background reference density. This is the
proper way to compute these parameters. Earlier versions of lammps
proper way to compute these parameters. Earlier versions of LAMMPS
used an alloy mixture averaged value of *t* to compute the background
reference density. Setting *mixture_ref_t* = 1 gives the old behavior.
WARNING: using *mixture_ref_t* = 1 will give results that are demonstrably
incorrect for second-neighbor MEAM, and non-standard for
first-neighbor MEAM; this option is included only for matching with
previous versions of lammps and should be avoided if possible.
previous versions of LAMMPS and should be avoided if possible.
The parameters *attrac* and *repuls*, along with the integer selection
parameter *erose_form*, can be used to modify the Rose energy function
@ -361,7 +361,7 @@ recent published MEAM parameter sets, such as :ref:`(Valone) <Valone>`
The default form of the *erose* expression in LAMMPS was corrected
in March 2009. The current version is correct, but may show different
behavior compared with earlier versions of lammps with the attrac
behavior compared with earlier versions of LAMMPS with the attrac
and/or repuls parameters are non-zero. To obtain the previous default
form, use *erose_form* = 1 (this form does not seem to appear in the
literature). An alternative form (see e.g. :ref:`(Lee2) <Lee2>`) is
@ -423,10 +423,8 @@ none
.. _Gullet:
**(Gullet)** Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
This report may be accessed on-line via `this link <sandreport_>`_.
.. _sandreport: http://infoserve.sandia.gov/sand_doc/2003/038782.pdf
**(Gullet)** Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). DOI:10.2172/918395
This report may be accessed on-line via `this link <https://download.lammps.org/pdfs/MEAM_report_2003.pdf>`_.
.. _Lee:

2
doc/src/pair_mliap.rst
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@ -62,6 +62,8 @@ useful to know the gradient or derivative of energy, force, and stress
w.r.t. model parameters. This information can be accessed using the
related :doc:`compute mliap <compute_mliap>` command.
.. versionadded:: 2Jun2022
The descriptor style *so3* is a descriptor that is derived from the
the smooth SO(3) power spectrum with the explicit inclusion of a radial
basis :ref:`(Bartok) <Bartok2013>` and :ref:`(Zagaceta) <Zagaceta2020>`.

2
doc/src/pair_modify.rst
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@ -284,6 +284,8 @@ the *pair* keyword. Use *no* to disable, or *yes* to enable.
The "pair_modify pair compute/tally" command must be issued
**before** the corresponding compute style is defined.
.. versionadded:: 3Aug2022
The *neigh/trim* keyword controls whether an explicit cutoff is set for
each neighbor list request issued by individual pair sub-styles when
using :doc:`pair hybrid/overlay <pair_hybrid>`. When this keyword is

52
doc/src/pair_peri.rst
View File

@ -51,8 +51,9 @@ Description
"""""""""""
The peridynamic pair styles implement material models that can be used
at the mesoscopic and macroscopic scales. See `this document <PDF/PDLammps_overview.pdf>`_ for an overview of LAMMPS commands
for Peridynamics modeling.
at the mesoscopic and macroscopic scales. See `this document
<PDF/PDLammps_overview.pdf>`_ for an overview of LAMMPS commands for
Peridynamics modeling.
Style *peri/pmb* implements the Peridynamic bond-based prototype
microelastic brittle (PMB) model.
@ -66,26 +67,27 @@ peridynamic viscoelastic solid (VES) model.
Style *peri/eps* implements the Peridynamic state-based elastic-plastic
solid (EPS) model.
The canonical papers on Peridynamics are :ref:`(Silling 2000) <Silling2000>`
and :ref:`(Silling 2007) <Silling2007>`. The implementation of Peridynamics
in LAMMPS is described in :ref:`(Parks) <Parks>`. Also see the `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for
more details about its implementation.
The canonical papers on Peridynamics are :ref:`(Silling 2000)
<Silling2000>` and :ref:`(Silling 2007) <Silling2007>`. The
implementation of Peridynamics in LAMMPS is described in :ref:`(Parks)
<Parks>`. Also see the :doc:`Peridynamics Howto <Howto_peri>` for more
details about its implementation.
The peridynamic VES and EPS models in PDLAMMPS were implemented by
R. Rahman and J. T. Foster at University of Texas at San Antonio. The
original VES formulation is described in "(Mitchell2011)" and the
original EPS formulation is in "(Mitchell2011a)". Additional PDF docs
that describe the VES and EPS implementations are include in the
LAMMPS distribution in `doc/PDF/PDLammps_VES.pdf <PDF/PDLammps_VES.pdf>`_ and
that describe the VES and EPS implementations are include in the LAMMPS
distribution in `doc/PDF/PDLammps_VES.pdf <PDF/PDLammps_VES.pdf>`_ and
`doc/PDF/PDLammps_EPS.pdf <PDF/PDLammps_EPS.pdf>`_. For questions
regarding the VES and EPS models in LAMMPS you can contact R. Rahman
(rezwanur.rahman at utsa.edu).
The following coefficients must be defined for each pair of atom types
via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,
or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands, or by mixing as described below.
or in the data file or restart files read by the :doc:`read_data
<read_data>` or :doc:`read_restart <read_restart>` commands, or by
mixing as described below.
For the *peri/pmb* style:
@ -96,8 +98,8 @@ For the *peri/pmb* style:
C is the effectively a spring constant for Peridynamic bonds, the
horizon is a cutoff distance for truncating interactions, and s00 and
:math:`\alpha` are used as a bond breaking criteria. The units of c are such
that c/distance = stiffness/volume\^2, where stiffness is
:math:`\alpha` are used as a bond breaking criteria. The units of c are
such that c/distance = stiffness/volume\^2, where stiffness is
energy/distance\^2 and volume is distance\^3. See the users guide for
more details.
@ -110,8 +112,8 @@ For the *peri/lps* style:
* :math:`\alpha` (unitless)
K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance for truncating interactions, and s00 and :math:`\alpha` are
used as a bond breaking criteria. See the users guide for more
cutoff distance for truncating interactions, and s00 and :math:`\alpha`
are used as a bond breaking criteria. See the users guide for more
details.
For the *peri/ves* style:
@ -125,12 +127,12 @@ For the *peri/ves* style:
* m_taubi (unitless)
K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance for truncating interactions, and s00 and :math:`\alpha` are
used as a bond breaking criteria. m_lambdai and m_taubi are the
cutoff distance for truncating interactions, and s00 and :math:`\alpha`
are used as a bond breaking criteria. m_lambdai and m_taubi are the
viscoelastic relaxation parameter and time constant,
respectively. m_lambdai varies within zero to one. For very small
values of m_lambdai the viscoelastic model responds very similar to a
linear elastic model. For details please see the description in
respectively. m_lambdai varies within zero to one. For very small values
of m_lambdai the viscoelastic model responds very similar to a linear
elastic model. For details please see the description in
"(Mitchell2011)".
For the *peri/eps* style:
@ -165,8 +167,9 @@ shift option.
The :doc:`pair_modify <pair_modify>` table and tail options are not
relevant for these pair styles.
These pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
These pair styles write their information to :doc:`binary restart files
<restart>`, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file.
These pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
@ -177,8 +180,9 @@ These pair styles can only be used via the *pair* keyword of the
Restrictions
""""""""""""
All of these styles are part of the PERI package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
All of these styles are part of the PERI package. They are only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""

11
doc/src/pair_quip.rst
View File

@ -49,11 +49,12 @@ A QUIP potential is fully specified by the filename which contains the
parameters of the potential in XML format, the initialization string,
and the map of atomic numbers.
GAP potentials can be obtained from the Data repository section of
`http://www.libatoms.org <http://www.libatoms.org>`_, where the
appropriate initialization strings are also advised. The list of
atomic numbers must be matched to the LAMMPS atom types specified in
the LAMMPS data file or elsewhere.
GAP potentials can be obtained from the `GAP models and databases page
on the libAtoms homepage `https://libatoms.github.io
<https://libatoms.github.io/GAP/data.html>`_, where the appropriate
initialization strings are also advised. The list of atomic numbers must
be matched to the LAMMPS atom types specified in the LAMMPS data file or
elsewhere.
Two examples input scripts are provided in the examples/PACKAGES/quip
directory.

2
doc/src/pair_saip_metal.rst
View File

@ -32,6 +32,8 @@ Examples
Description
"""""""""""
.. versionadded:: 17Feb2022
The *saip/metal* style computes the registry-dependent interlayer
potential (ILP) potential for hetero-junctions formed with hexagonal
2D materials and metal surfaces, as described in :ref:`(Ouyang6) <Ouyang6>`.

2
doc/src/pair_srp.rst
View File

@ -132,6 +132,8 @@ at the cutoff distance :math:`r_c`.
----------
.. versionadded:: 3Aug2022
Pair style *srp/react* interfaces the pair style *srp* with the
bond breaking and formation mechanisms provided by fix *bond/break*
and fix *bond/create*, respectively. When using this pair style, whenever a

2
doc/src/pair_sw.rst
View File

@ -130,6 +130,8 @@ terms.
so the inconsistency between potential and force can be neglected in
actual simulations.
.. versionadded:: 3Aug2022
The *threebody* keyword is optional and determines whether or not the
three-body term of the potential is calculated. The default value is
"on" and it is only available for the plain *sw* pair style variants,

2
doc/src/plugin.rst
View File

@ -59,6 +59,8 @@ The *clear* command will unload all currently loaded plugins.
.. admonition:: Automatic loading of plugins
:class: note
.. versionadded:: 4May2022
When the environment variable ``LAMMPS_PLUGIN_PATH`` is set, then
LAMMPS will search the directory (or directories) listed in this path
for files with names that end in ``plugin.so``

4
doc/src/read_dump.rst
View File

@ -266,6 +266,8 @@ replace properties of the current system. There are various options
for how this is done, determined by the specified fields and optional
keywords.
.. versionchanged:: 3Aug2022
The timestep of the snapshot becomes the current timestep for the
simulation unless the *timestep* keyword is specified with a *no* value
(default setting is *yes*). See the :doc:`reset_timestep <reset_timestep>`
@ -397,4 +399,4 @@ Default
The option defaults are box = yes, timestep = yes, replace = yes, purge = no,
trim = no, add = no, scaled = no, wrapped = yes, and format = native.
.. _vmd: http://www.ks.uiuc.edu/Research/vmd
.. _vmd: https://www.ks.uiuc.edu/Research/vmd

2
doc/src/region.rst
View File

@ -162,6 +162,8 @@ Thus the third example above specifies a cylinder with its axis in the
y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
extending in the y-direction from -5.0 to the upper box boundary.
.. versionadded:: 4May2022
For style *ellipsoid*, an axis-aligned ellipsoid is defined. The
ellipsoid has its center at (x,y,z) and is defined by 3 axis-aligned
vectors given by A = (a,0,0); B = (0,b,0); C = (0,0,c). Note that

8
doc/utils/sphinx-config/_static/css/lammps.css
View File

@ -1,3 +1,11 @@
.math {
text-align: left;
}
.eqno {
float: right;
}
.wy-nav-content {
max-width: 100% !important;
}

11
doc/utils/sphinx-config/false_positives.txt
View File

@ -750,6 +750,7 @@ dirname
discoverable
discretization
discretized
discretizing
disp
dissipative
Dissipative
@ -918,6 +919,7 @@ emax
Emax
Embt
emi
Emmrich
emol
eN
endian
@ -1083,7 +1085,6 @@ filesystem
filesystems
Fily
Fincham
Finchham
Fint
fingerprintconstants
fingerprintsperelement
@ -2128,6 +2129,7 @@ modelled
modelling
Modelling
Modine
moduli
mofff
MOFFF
Mohd
@ -2143,6 +2145,7 @@ Monaghan
Monaghans
monodisperse
monodispersity
monolayer
monopole
monovalent
Montalenti
@ -2418,6 +2421,7 @@ normy
normz
Noskov
noslip
notational
noticable
Nout
noutcol
@ -2778,6 +2782,7 @@ ps
Ps
pscreen
pscrozi
Pseudocode
pseudodynamics
pseudopotential
pSp
@ -3137,6 +3142,7 @@ sectoring
sed
segmental
Seifert
Seleson
sellerio
Sellerio
Semaev
@ -3215,7 +3221,7 @@ slategray
slater
Slepoy
Sliozberg
sLLG
sLL
sllod
sm
smallbig
@ -3626,6 +3632,7 @@ unsmoothed
unsolvated
unsplit
unstrained
unstretched
untar
untilted
Unwin

4
lib/gpu/geryon/hip_device.h
View File

@ -81,6 +81,10 @@ class UCL_Device {
/// Return the number of devices that support CUDA
inline int num_devices() { return _properties.size(); }
/// Specify whether profiling (device timers) will be used for the device (yes=true)
/** No-op for CUDA and HIP **/
inline void configure_profiling(const bool profiling_on) {}
/// Set the CUDA device to the specified device number
/** A context and default command queue will be created for the device
* Returns UCL_SUCCESS if successful or UCL_ERROR if the device could not

4
lib/gpu/geryon/nvd_device.h
View File

@ -95,6 +95,10 @@ class UCL_Device {
/// Return the number of devices that support CUDA
inline int num_devices() { return _properties.size(); }
/// Specify whether profiling (device timers) will be used for the device (yes=true)
/** No-op for CUDA and HIP **/
inline void configure_profiling(const bool profiling_on) {}
/// Set the CUDA device to the specified device number
/** A context and default command queue will be created for the device
* Returns UCL_SUCCESS if successful or UCL_ERROR if the device could not

34
lib/gpu/geryon/ocl_device.h
View File

@ -99,6 +99,7 @@ struct OCLProperties {
int cl_device_version;
bool has_subgroup_support;
bool has_shuffle_support;
bool shared_main_memory;
};
/// Class for looking at data parallel device properties
@ -125,6 +126,11 @@ class UCL_Device {
/// Return the number of devices that support OpenCL
inline int num_devices() { return _num_devices; }
/// Specify whether profiling (device timers) will be used for the device (yes=true)
/** No-op for CUDA and HIP **/
inline void configure_profiling(const bool profiling_on)
{ _cq_profiling = profiling_on; }
/// Set the OpenCL device to the specified device number
/** A context and default command queue will be created for the device *
* Returns UCL_SUCCESS if successful or UCL_ERROR if the device could not
@ -169,10 +175,22 @@ class UCL_Device {
_cq.push_back(cl_command_queue());
#ifdef CL_VERSION_2_0
cl_queue_properties props[] = {CL_QUEUE_PROPERTIES, CL_QUEUE_PROFILING_ENABLE, 0};
_cq.back()=clCreateCommandQueueWithProperties(_context, _cl_device, props, &errorv);
if (_cq_profiling) {
cl_queue_properties props[] = {CL_QUEUE_PROPERTIES, CL_QUEUE_PROFILING_ENABLE,
0};
_cq.back()=clCreateCommandQueueWithProperties(_context, _cl_device, props,
&errorv);
} else {
cl_queue_properties props[] = {CL_QUEUE_PROPERTIES, 0};
_cq.back()=clCreateCommandQueueWithProperties(_context, _cl_device, props,
&errorv);
}
#else
_cq.back()=clCreateCommandQueue(_context, _cl_device, CL_QUEUE_PROFILING_ENABLE, &errorv);
if (_cq_profiling)
_cq.back()=clCreateCommandQueue(_context, _cl_device, CL_QUEUE_PROFILING_ENABLE,
&errorv);
else
_cq.back()=clCreateCommandQueue(_context, _cl_device, 0, &errorv);
#endif
if (errorv!=CL_SUCCESS) {
std::cerr << "Could not create command queue on device: " << name()
@ -209,7 +227,7 @@ class UCL_Device {
inline bool shared_memory() { return shared_memory(_device); }
/// Returns true if host memory is efficiently addressable from device
inline bool shared_memory(const int i)
{ return _shared_mem_device(_cl_devices[i]); }
{ return _properties[i].shared_main_memory; }
/// Returns preferred vector width
inline int preferred_fp32_width() { return preferred_fp32_width(_device); }
@ -370,6 +388,7 @@ class UCL_Device {
cl_platform_id _cl_platforms[20]; // OpenCL IDs for all platforms
cl_context _context; // Context used for accessing the device
std::vector<cl_command_queue> _cq;// The default command queue for this device
bool _cq_profiling; // True=create command queues w/ profiling support
int _device; // UCL_Device ID for current device
cl_device_id _cl_device; // OpenCL ID for current device
std::vector<cl_device_id> _cl_devices; // OpenCL IDs for all devices
@ -384,6 +403,7 @@ class UCL_Device {
// Grabs the properties for all devices
UCL_Device::UCL_Device() {
_device=-1;
_cq_profiling=true;
// --- Get Number of Platforms
cl_uint nplatforms;
@ -563,8 +583,9 @@ void UCL_Device::add_properties(cl_device_id device_list) {
op.preferred_vector_width64=double_width;
// Determine if double precision is supported: All bits in the mask must be set.
cl_device_fp_config double_mask = (CL_FP_FMA|CL_FP_ROUND_TO_NEAREST|CL_FP_ROUND_TO_ZERO|
CL_FP_ROUND_TO_INF|CL_FP_INF_NAN|CL_FP_DENORM);
cl_device_fp_config double_mask = (CL_FP_FMA|CL_FP_ROUND_TO_NEAREST|
CL_FP_ROUND_TO_ZERO|CL_FP_ROUND_TO_INF|
CL_FP_INF_NAN|CL_FP_DENORM);
cl_device_fp_config double_avail;
CL_SAFE_CALL(clGetDeviceInfo(device_list,CL_DEVICE_DOUBLE_FP_CONFIG,
sizeof(double_avail),&double_avail,nullptr));
@ -665,6 +686,7 @@ void UCL_Device::add_properties(cl_device_id device_list) {
double arch = static_cast<double>(minor)/10+major;
if (arch >= 3.0)
op.has_shuffle_support=true;
op.shared_main_memory=_shared_mem_device(device_list);
}
delete[] buffer2;
#endif

12
lib/gpu/geryon/ocl_memory.h
View File

@ -118,6 +118,9 @@ inline int _host_alloc(mat_type &mat, copy_type &cm, const size_t n,
template <class mat_type, class copy_type>
inline int _host_view(mat_type &mat, copy_type &cm, const size_t o,
const size_t n) {
// When viewing outside host allocation with discrete main memory on accelerator,
// no cl_buffer object is created to avoid unnecessary creation of device allocs
if (cm.shared_mem_device()) {
cl_int error_flag;
cl_buffer_region subbuffer;
subbuffer.origin = o;
@ -125,8 +128,9 @@ inline int _host_view(mat_type &mat, copy_type &cm, const size_t o,
mat.cbegin()=clCreateSubBuffer(cm.cbegin(), 0,
CL_BUFFER_CREATE_TYPE_REGION, &subbuffer,
&error_flag);
CL_CHECK_ERR(error_flag);
} else
mat.cbegin()=(cl_mem)0;
CL_SAFE_CALL(clRetainCommandQueue(mat.cq()));
return UCL_SUCCESS;
}
@ -170,10 +174,13 @@ inline int _host_alloc(mat_type &mat, UCL_Device &dev, const size_t n,
template <class mat_type>
inline int _host_view(mat_type &mat, UCL_Device &dev, const size_t n) {
if (mat.shared_mem_device()) {
cl_int error_flag;
mat.cbegin()=clCreateBuffer(dev.context(), CL_MEM_USE_HOST_PTR,
n,*mat.host_ptr(),&error_flag);
CL_CHECK_ERR(error_flag);
} else
mat.cbegin()=(cl_mem)0;
CL_SAFE_CALL(clRetainCommandQueue(mat.cq()));
return UCL_SUCCESS;
}
@ -181,6 +188,9 @@ inline int _host_view(mat_type &mat, UCL_Device &dev, const size_t n) {
template <class mat_type>
inline void _host_free(mat_type &mat) {
if (mat.cols()>0) {
// When viewing outside host allocation with discrete main memory on accelerator,
// no cl_buffer object is created to avoid unnecessary creation of device allocs
if (mat.cbegin()!=(cl_mem)(0))
CL_DESTRUCT_CALL(clReleaseMemObject(mat.cbegin()));
CL_DESTRUCT_CALL(clReleaseCommandQueue(mat.cq()));
}

18
lib/gpu/geryon/ocl_timer.h
View File

@ -50,11 +50,15 @@ class UCL_Timer {
/** \note init() must be called to reuse timer after a clear() **/
inline void clear() {
if (_initialized) {
if (has_measured_time) {
clReleaseEvent(start_event);
clReleaseEvent(stop_event);
has_measured_time = false;
}
CL_DESTRUCT_CALL(clReleaseCommandQueue(_cq));
_initialized=false;
_total_time=0.0;
}
has_measured_time = false;
}
/// Initialize default command queue for timing
@ -71,9 +75,13 @@ class UCL_Timer {
/// Start timing on default command queue
inline void start() {
UCL_OCL_MARKER(_cq,&start_event);
if (has_measured_time) {
clReleaseEvent(start_event);
clReleaseEvent(stop_event);
has_measured_time = false;
}
UCL_OCL_MARKER(_cq,&start_event);
}
/// Stop timing on default command queue
inline void stop() {
@ -83,9 +91,13 @@ class UCL_Timer {
/// Block until the start event has been reached on device
inline void sync_start() {
CL_SAFE_CALL(clWaitForEvents(1,&start_event));
if (has_measured_time) {
clReleaseEvent(start_event);
clReleaseEvent(stop_event);
has_measured_time = false;
}
CL_SAFE_CALL(clWaitForEvents(1,&start_event));
}
/// Block until the stop event has been reached on device
inline void sync_stop() {

14
lib/gpu/geryon/ucl_basemat.h
View File

@ -75,13 +75,21 @@ class UCL_BaseMat {
inline enum UCL_MEMOPT kind() const { return _kind; }
inline bool shared_mem_device() {
#ifdef _OCL_MAT
#ifndef _OCL_MAT
return false;
#else
#if defined(GERYON_FORCE_SHARED_MAIN_MEM_ON)
return true;
#elif defined(GERYON_FORCE_SHARED_MAIN_MEM_OFF)
return false;
#else
cl_device_id device;
CL_SAFE_CALL(clGetCommandQueueInfo(_cq,CL_QUEUE_DEVICE,
sizeof(cl_device_id),&device,NULL));
return _shared_mem_device(device);
#else
return false;
#endif
#endif
}

3
lib/gpu/geryon/ucl_h_mat.h
View File

@ -140,6 +140,9 @@ class UCL_H_Mat : public UCL_BaseMat {
_end=_array+_cols;
#ifdef _OCL_MAT
_carray=input.cbegin();
// When viewing outside host allocation with discrete main memory on accelerator,
// no cl_buffer object is created to avoid unnecessary creation of device allocs
if (_carray!=(cl_mem)(0))
CL_SAFE_CALL(clRetainMemObject(input.cbegin()));
CL_SAFE_CALL(clRetainCommandQueue(input.cq()));
#endif

3
lib/gpu/geryon/ucl_h_vec.h
View File

@ -139,6 +139,9 @@ class UCL_H_Vec : public UCL_BaseMat {
_end=_array+_cols;
#ifdef _OCL_MAT
_carray=input.cbegin();
// When viewing outside host allocation with discrete main memory on accelerator,
// no cl_buffer object is created to avoid unnecessary creation of device allocs
if (_carray!=(cl_mem)(0))
CL_SAFE_CALL(clRetainMemObject(input.cbegin()));
CL_SAFE_CALL(clRetainCommandQueue(input.cq()));
#endif

16
lib/gpu/lal_device.cpp
View File

@ -265,15 +265,13 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int ngpu,
// Time on the device only if 1 proc per gpu
_time_device=true;
#if 0
// XXX: the following setting triggers a memory leak with OpenCL and MPI
// setting _time_device=true for all processes doesn't seem to be a
// problem with either (no segfault, no (large) memory leak.
// thus keeping this disabled for now. may need to review later.
// 2018-07-23 <akohlmey@gmail.com>
// Previous source of OCL memory leak when time_device=false
// - Logic added to release OCL events when timers are not invoked
if (_procs_per_gpu>1)
_time_device=false;
#endif
if (!_time_device && _particle_split > 0)
gpu->configure_profiling(false);
// Set up a per device communicator
MPI_Comm_split(node_comm,my_gpu,0,&_comm_gpu);
@ -715,7 +713,9 @@ void DeviceT::estimate_gpu_overhead(const int kernel_calls,
dev_data_out[0].flush();
#endif
driver_time=MPI_Wtime()-driver_time;
double time=over_timer.seconds();
double time=0.0;
if (_time_device)
time=over_timer.seconds();
if (time_device()) {
for (int i=0; i<_data_in_estimate; i++)

1
lib/gpu/lal_pppm.cpp
View File

@ -304,6 +304,7 @@ int PPPMT::spread(const int ago, const int nlocal, const int nall,
const double delxinv, const double delyinv,
const double delzinv) {
if (!_precompute_done) {
if (device->time_device())
atom->acc_timers();
_precompute(ago,nlocal,nall,host_x,host_type,success,host_q,boxlo,delxinv,
delyinv,delzinv);

13
python/lammps/mliap/mliap_unified_abc.py
View File

@ -4,12 +4,13 @@ import pickle
class MLIAPUnified(ABC):
"""Abstract base class for MLIAPUnified."""
def __init__(self):
self.interface = None
self.element_types = None
self.ndescriptors = None
self.nparams = None
self.rcutfac = None
def __init__(self, interface = None, element_types = None,
ndescriptors = None, nparams = None, rcutfac = None):
self.interface = interface
self.element_types = element_types
self.ndescriptors = ndescriptors
self.nparams = nparams
self.rcutfac = rcutfac
@abstractmethod
def compute_gradients(self, data):

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