Merge branch 'lammps:develop' into fortran-further-tinkering

SECURITY.md

@@ -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
+either a user mistake or a bug in the code.  Bugs can be reported in the
-the LAMMPS project
+LAMMPS project [issue tracker on
-[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
+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
+LAMMPS follows continuous release development model.  We aim to keep to
-release versions (stable or patch) fully functional and employ a variety
+keep the development version (develop branch) always fully functional
-of automatic testing procedures to detect failures of existing
+and employ a variety of automatic testing procedures to detect failures
-functionality from adding new features before releases are made.  Thus
+of existing functionality from adding or modifying features.  Most of
-bugfixes and updates are only integrated into the current development
+those tests are run on pull requests *before* merging to the development
-branch and thus the next (patch) release and users are recommended to
+branch.  The develop branch is protected, so all changes *must* be
-update regularly.
+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.

doc/src/Bibliography.rst

@@ -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 and Fincham)**
-   Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993).
+   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)

doc/src/Build_development.rst

@@ -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

doc/src/Build_extras.rst

@@ -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::

doc/src/Build_manual.rst

@@ -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.

doc/src/Build_settings.rst

@@ -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
+The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
-distribution.  It is portable across all platforms.  Depending on the size
+included in the LAMMPS distribution.  It is portable across all
-of the FFTs and the number of processors used, the other libraries listed
+platforms.  Depending on the size of the FFTs and the number of
-here can be faster.
+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
+per-timestep CPU cost, FFTs are only a portion of long-range Coulombics,
-Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
+and 1d FFTs are only a portion of the FFT cost (parallel communication
-communication can be costly).  A breakdown of these timings is printed
+can be costly).  A breakdown of these timings is printed to the screen
-to the screen at the end of a run when using the
+at the end of a run when using the :doc:`kspace_style pppm
-:doc:`kspace_style pppm <kspace_style>` command. The
+<kspace_style>` command. The :doc:`Screen and logfile output
-:doc:`Screen and logfile output <Run_output>`
+<Run_output>` page gives more details.  A more detailed (and time
-page gives more details.  A more detailed (and time consuming)
+consuming) report of the FFT performance is generated with the
-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
+platform and can be faster than the KISS FFT library.  You can download
-download it from `www.fftw.org <http://www.fftw.org>`_.  LAMMPS requires
+it from `www.fftw.org <https://www.fftw.org>`_.  LAMMPS requires version
-version 3.X; the legacy version 2.1.X is no longer supported.
+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

doc/src/Errors_debug.rst

@@ -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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/src/Howto.rst

@@ -85,6 +85,7 @@ Packages howto
    Howto_coreshell
    Howto_drude
    Howto_drude2
+   Howto_peri
    Howto_manifold
    Howto_spins
 

doc/src/Howto_amoeba.rst

@@ -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>`_
 

doc/src/Howto_bioFF.rst

@@ -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
+formulas implemented in LAMMPS that correspond to formulas commonly used
-used in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
+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
+commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
-:doc:`bond_coeff <bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc
+<bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc page for
-page for additional tools that can use CHARMM, AMBER, or Materials
+additional tools that can use CHARMM, AMBER, or Materials Studio
-Studio generated files to assign force field coefficients and convert
+generated files to assign force field coefficients and convert their
-their output into LAMMPS input.
+output into LAMMPS input.
 
-See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM force
+See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
-field.  See :ref:`(Cornell) <howto-Cornell>` for a description of the AMBER
+force field.  See :ref:`(Cornell) <howto-Cornell>` for a description of
-force field.  See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS
+the AMBER force field.  See :ref:`(Sun) <howto-Sun>` for a description
-force field.
+of the COMPASS force field.
-
-.. _charmm: http://www.scripps.edu/brooks
-
-.. _amber: http://amber.scripps.edu
 
 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
+   For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
-   in March 2017.  We recommend they be used instead of the older *charmm*
+   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
+   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

doc/src/Howto_github.rst

@@ -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

doc/src/Howto_manifold.rst

@@ -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/>`_.

doc/src/Howto_spc.rst

@@ -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>`_.
 
 ----------
 

doc/src/Howto_tip3p.rst

@@ -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>`_.
 
 ----------
 

doc/src/Howto_tip4p.rst

@@ -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>`_.
 
 ----------
 

doc/src/Howto_viz.rst

@@ -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
+user-specified atom information, and convert them to various formats or
-or pipe them into visualization software directly.  See the `Pizza.py WWW site <pizza_>`_ for details.  Specifically, Pizza.py can convert
+pipe them into visualization software directly.  See the `Pizza.py WWW
-LAMMPS dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
+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

doc/src/Install_conda.rst

@@ -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
 

doc/src/Install_windows.rst

@@ -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

doc/src/Intro_authors.rst

@@ -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,

doc/src/Intro_citing.rst

@@ -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

doc/src/Intro_features.rst

@@ -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:
 

doc/src/Intro_nonfeatures.rst

@@ -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>`_
+  above bullets.  Pizza.py is written in `Python <https://www.python.org>`_
-  and is available for download from `this page <http://www.cs.sandia.gov/~sjplimp/download.html>`_.
+  and is available for download from `this page <https://sjplimp.github.io/download.html>`_.

doc/src/Intro_opensource.rst

@@ -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:
 

doc/src/Packages_details.rst

@@ -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

doc/src/Python_examples.rst

@@ -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/A/ <http://li.mit.edu/Archive/Graphics/A/>`_
-* `http://li.mit.edu/Archive/Graphics/A3/A3.html <atomeye3_>`_
+* `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/
+The latter link is to AtomEye 3 which has the scripting capability
-
+needed by these Python scripts.
-.. _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.
 
 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://www.pymol.org <https://www.pymol.org>`_
- * `https://github.com/schrodinger/pymol-open-source <pymolopen_>`_
+ * `https://github.com/schrodinger/pymol-open-source <https://github.com/schrodinger/pymol-open-source>`_
-
-.. _pymolhome: https://www.pymol.org
-
-.. _pymolopen: https://github.com/schrodinger/pymol-open-source
 
 The latter link is to the open-source version.
 

doc/src/Python_head.rst

@@ -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
+the script code is interfaced to optimized compiled code, performance
-be on par with a standalone executable, for as long as the scripting is
+can be on par with a standalone executable, for as long as the scripting
-restricted to high-level operations.  Thus Python is also convenient to
+is restricted to high-level operations.  Thus Python is also convenient
-use as a "glue" language to "drive" a program through its library
+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.

doc/src/Run_windows.rst

@@ -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 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 <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.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

doc/src/Speed_gpu.rst

@@ -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

doc/src/Speed_intel.rst

@@ -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.

doc/src/Speed_omp.rst

@@ -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
 """""""""""""""""""""""""""""""

doc/src/Tools.rst

@@ -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
+https://www.gnu.org/software/readline/
-<http://www.gnu.org/s/readline/#Documentation>`_
+
 
 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

doc/src/compute_ave_sphere_atom.rst

@@ -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

doc/src/compute_damage_atom.rst

@@ -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>`_
+in a group.  This is a quantity relevant for :doc:`Peridynamics models
-for an overview of LAMMPS commands for Peridynamics modeling.
+<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
+See the :doc:`Peridynamics Howto <Howto_peri>` for a formal definition
-definition of "damage" and more details about Peridynamics as it is
+of "damage" and more details about Peridynamics as it is implemented in
-implemented in LAMMPS.
+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
+This compute is part of the PERI package.  It is only enabled if LAMMPS
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/compute_dilatation_atom.rst

@@ -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
+contribution of the :math:`ij` pair is a function of the change in bond
-(versus the initial length in the reference state), the volume
+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
+:doc:`Peridynamics Howto <Howto_peri>` for a formal definition of
-a formal definition of dilatation.
+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
+This compute is part of the PERI package.  It is only enabled if LAMMPS
-LAMMPS was built with that package.  See the
+was built with that package.  See the :doc:`Build package
-:doc:`Build package <Build_package>` page for more info.
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/compute_fep_ta.rst

@@ -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

doc/src/compute_sna_atom.rst

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

doc/src/compute_temp_cs.rst

@@ -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).

doc/src/compute_voronoi_atom.rst

@@ -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
+   The calculation of Voronoi volumes is performed by each processor for
-   processor for the atoms it owns, and includes the effect of ghost
+   the atoms it owns, and includes the effect of ghost atoms stored by
-   atoms stored by the processor.  This assumes that the Voronoi cells of
+   the processor.  This assumes that the Voronoi cells of owned atoms
-   owned atoms are not affected by atoms beyond the ghost atom cut-off
+   are not affected by atoms beyond the ghost atom cut-off distance.
-   distance.  This is usually a good assumption for liquid and solid
+   This is usually a good assumption for liquid and solid systems, but
-   systems, but may lead to underestimation of Voronoi volumes in low
+   may lead to underestimation of Voronoi volumes in low density
-   density systems.  By default, the set of ghost atoms stored by each
+   systems.  By default, the set of ghost atoms stored by each processor
-   processor is determined by the cutoff used for
+   is determined by the cutoff used for :doc:`pair_style <pair_style>`
-   :doc:`pair_style <pair_style>` interactions.  The cutoff can be set
+   interactions.  The cutoff can be set explicitly via the
-   explicitly via the :doc:`comm_modify cutoff <comm_modify>` command.  The
+   :doc:`comm_modify cutoff <comm_modify>` command.  The Voronoi cells
-   Voronoi cells for atoms adjacent to empty regions will extend into
+   for atoms adjacent to empty regions will extend into those regions up
-   those regions up to the communication cutoff in :math:`x`, :math:`y`, or
+   to the communication cutoff in :math:`x`, :math:`y`, or :math:`z`.
-   :math:`z`.  In that situation, an exterior face is created at the cutoff
+   In that situation, an exterior face is created at the cutoff distance
-   distance normal to the :math:`x`, :math:`y`, or :math:`z` direction.
+   normal to the :math:`x`, :math:`y`, or :math:`z` direction.  For
-   For triclinic systems, the exterior face is parallel to the corresponding
+   triclinic systems, the exterior face is parallel to the corresponding
    reciprocal lattice vector.
 
 .. note::

doc/src/create_atoms.rst

@@ -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

doc/src/delete_atoms.rst

@@ -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

doc/src/dump.rst

@@ -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.
 
 ----------

doc/src/dump_h5md.rst

@@ -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/>`_.

doc/src/dump_image.rst

@@ -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/>`_
 
 ----------
 

doc/src/dump_modify.rst

@@ -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

doc/src/dump_molfile.rst

@@ -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

doc/src/dump_netcdf.rst

@@ -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
+* Ovito (https://www.ovito.org/). Ovito supports the AMBER convention and
-all extensions of this dump style.
+  all extensions of this dump style.
-
+* VMD (https://www.ks.uiuc.edu/Research/vmd/).
-* 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.
 
 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/
 
 ----------
 

doc/src/dump_vtk.rst

@@ -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,
+timesteps in a format readable by the `VTK visualization toolkit
-such as `ParaView <http://www.paraview.org>`_.  The time steps on which dump
+<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
+respectively, for XML format; see the `VTK homepage
-`VTK homepage <http://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
+<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
+   Unless the :doc:`dump_modify sort <dump_modify>` option is invoked,
-   is invoked, the lines of atom information written to dump files will
+   the lines of atom information written to dump files will be in an
-   be in an indeterminate order for each snapshot.  This is even true
+   indeterminate order for each snapshot.  This is even true when
-   when running on a single processor, if the :doc:`atom_modify sort <atom_modify>` option is on, which it is by default.  In this
+   running on a single processor, if the :doc:`atom_modify sort
-   case atoms are re-ordered periodically during a simulation, due to
+   <atom_modify>` option is on, which it is by default.  In this case
-   spatial sorting.  It is also true when running in parallel, because
+   atoms are re-ordered periodically during a simulation, due to spatial
-   data for a single snapshot is collected from multiple processors, each
+   sorting.  It is also true when running in parallel, because data for
-   of which owns a subset of the atoms.
+   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.

doc/src/fix_adapt.rst

@@ -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

doc/src/fix_external.rst

@@ -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
 
 ----------
 

doc/src/fix_gle.rst

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

doc/src/fix_imd.rst

@@ -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
+The source code for this fix includes code developed by the Theoretical
-examples/PACKAGES/imd. Additional examples and a driver for use with the
+and Computational Biophysics Group in the Beckman Institute for Advanced
-Novint Falcon game controller as haptic device can be found at:
+Science and Technology at the University of Illinois at
-http://sites.google.com/site/akohlmey/software/vrpn-icms.
+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
+apply forces to your simulation. Click on an atom, residue, or fragment
-fragment and drag to apply a force. Click quickly without moving the
+and drag to apply a force. Click quickly without moving the mouse to
-mouse to turn the force off. You can also use a variety of 3D position
+turn the force off. You can also use a variety of 3D position trackers
-trackers to apply forces to your simulation. Game controllers or haptic
+to apply forces to your simulation. Game controllers or haptic devices
-devices with force-feedback such as the Novint Falcon or Sensable
+with force-feedback such as the Novint Falcon or Sensable PHANTOM allow
-PHANTOM allow you to feel the resistance due to inertia or interactions
+you to feel the resistance due to inertia or interactions with neighbors
-with neighbors that the atoms experience you are trying to move, as if
+that the atoms experience you are trying to move, as if they were real
-they were real objects. See the `VMD IMD Homepage <imdvmd_>`_ and the
+objects. See the `VMD IMD Homepage <imdvmd_>`_ for more details.
-`VRPN-ICMS Homepage <vrpnicms_>`_ 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/
+.. _imdvmd: https://www.ks.uiuc.edu/Research/vmd/imd/
-
-.. _vrpnicms: http://sites.google.com/site/akohlmey/software/vrpn-icms
 
 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
+No information about this fix is written to :doc:`binary restart files
-are relevant to this fix.  No global scalar or vector or per-atom
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
-quantities are stored by this fix for access by various :doc:`output commands <Howto_output>`.  No parameter of this fix can be used
+relevant to this fix.  No global scalar or vector or per-atom quantities
-with the *start/stop* keywords of the :doc:`run <run>` command.  This
+are stored by this fix for access by various :doc:`output commands
-fix is not invoked during :doc:`energy minimization <minimize>`.
+<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
+This fix is part of the MISC package.  It is only enabled if LAMMPS was
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+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

doc/src/fix_ipi.rst

@@ -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>`_

doc/src/fix_latte.rst

@@ -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.

doc/src/fix_mdi_qm.rst

@@ -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

doc/src/fix_nh_uef.rst

@@ -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.
 

doc/src/fix_numdiff_virial.rst

@@ -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

doc/src/fix_nve_manifold_rattle.rst

@@ -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/>`_.

doc/src/fix_nvt_manifold_rattle.rst

@@ -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/>`_.

doc/src/fix_phonon.rst

@@ -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*

doc/src/fix_qmmm.rst

@@ -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

doc/src/fix_shake.rst

@@ -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
+enables a longer timestep.  The SHAKE or RATTLE constraint algorithms,
-*only* be applied during molecular dynamics runs.  When this fix is used
+however, can *only* be applied during molecular dynamics runs.
-during a minimization, the constraints are *approximated* by strong
+
-harmonic restraints.
+.. versionchanged:: 15Sep2022
+
+These fixes may still be used during minimization.  In that case the
+constraints are *approximated* by strong harmonic restraints.
 
 **SHAKE vs RATTLE:**
 

doc/src/kspace_style.rst

@@ -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
+The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver
-methods which can be used with LAMMPS.  The paper by :ref:`(Sutman) <Sutmann2014>`
+library <http://www.scafacos.de>`_ which provides a variety of solver
-gives an overview of ScaFaCoS.
+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

doc/src/pair_adp.rst

@@ -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

doc/src/pair_charmm.rst

@@ -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.
 

doc/src/pair_cs.rst

@@ -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).

doc/src/pair_eam.rst

@@ -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
+There are web sites that distribute and document EAM potentials stored
-potentials stored in DYNAMO or other formats:
+in DYNAMO or other formats:
 
-.. parsed-literal::
+* https://www.ctcms.nist.gov/potentials
-
+* https://openkim.org
-   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
 
 These potentials should be usable with LAMMPS, though the alternate
 formats would need to be converted to the DYNAMO format used by LAMMPS

doc/src/pair_gromacs.rst

@@ -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::

doc/src/pair_harmonic_cut.rst

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

doc/src/pair_ilp_tmd.rst

@@ -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>`.

doc/src/pair_meam.rst

@@ -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 previous versions of LAMMPS (before January 2011).  Newer versions
-of lammps, by default, use the single-element values of the *t*
+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).
+**(Gullet)** Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). DOI:10.2172/918395
-This report may be accessed on-line via `this link <sandreport_>`_.
+This report may be accessed on-line via `this link <https://download.lammps.org/pdfs/MEAM_report_2003.pdf>`_.
-
-.. _sandreport: http://infoserve.sandia.gov/sand_doc/2003/038782.pdf
 
 .. _Lee:
 

doc/src/pair_mliap.rst

@@ -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>`.

doc/src/pair_modify.rst

@@ -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

doc/src/pair_peri.rst

@@ -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
+at the mesoscopic and macroscopic scales.  See `this document
-for Peridynamics modeling.
+<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>`
+The canonical papers on Peridynamics are :ref:`(Silling 2000)
-and :ref:`(Silling 2007) <Silling2007>`.  The implementation of Peridynamics
+<Silling2000>` and :ref:`(Silling 2007) <Silling2007>`.  The
-in LAMMPS is described in :ref:`(Parks) <Parks>`.  Also see the `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for
+implementation of Peridynamics in LAMMPS is described in :ref:`(Parks)
-more details about its implementation.
+<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
+that describe the VES and EPS implementations are include in the LAMMPS
-LAMMPS distribution in `doc/PDF/PDLammps_VES.pdf <PDF/PDLammps_VES.pdf>`_ and
+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
+or in the data file or restart files read by the :doc:`read_data
-:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
+<read_data>` or :doc:`read_restart <read_restart>` commands, or by
-commands, or by mixing as described below.
+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
+:math:`\alpha` are used as a bond breaking criteria.  The units of c are
-that c/distance = stiffness/volume\^2, where stiffness is
+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
+cutoff distance for truncating interactions, and s00 and :math:`\alpha`
-used as a bond breaking criteria. See the users guide for more
+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
+cutoff distance for truncating interactions, and s00 and :math:`\alpha`
-used as a bond breaking criteria. m_lambdai and m_taubi are the
+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
+respectively. m_lambdai varies within zero to one. For very small values
-values of m_lambdai the viscoelastic model responds very similar to a
+of m_lambdai the viscoelastic model responds very similar to a linear
-linear elastic model. For details please see the description in
+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
+These pair styles write their information to :doc:`binary restart files
-to be specified in an input script that reads a restart file.
+<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
+All of these styles are part of the PERI package. They are only enabled
-enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/pair_quip.rst

@@ -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
+GAP potentials can be obtained from the `GAP models and databases page
-`http://www.libatoms.org <http://www.libatoms.org>`_, where the
+on the libAtoms homepage `https://libatoms.github.io
-appropriate initialization strings are also advised. The list of
+<https://libatoms.github.io/GAP/data.html>`_, where the appropriate
-atomic numbers must be matched to the LAMMPS atom types specified in
+initialization strings are also advised. The list of atomic numbers must
-the LAMMPS data file or elsewhere.
+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.

doc/src/pair_saip_metal.rst

@@ -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>`.

doc/src/pair_srp.rst

@@ -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

doc/src/pair_sw.rst

@@ -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,

doc/src/plugin.rst

@@ -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``

doc/src/read_dump.rst

@@ -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

doc/src/region.rst

@@ -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

doc/utils/sphinx-config/_static/css/lammps.css

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

doc/utils/sphinx-config/false_positives.txt

@@ -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

lib/gpu/geryon/hip_device.h

@@ -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

lib/gpu/geryon/nvd_device.h

@@ -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
@@ -305,9 +309,9 @@ class UCL_Device {
 
   /// For compatability with OCL API
   inline int auto_set_platform(const enum UCL_DEVICE_TYPE type=UCL_GPU,
-			       const std::string vendor="",
+                               const std::string vendor="",
-			       const int ndevices=-1,
+                               const int ndevices=-1,
-			       const int first_device=-1)
+                               const int first_device=-1)
     { return set_platform(0); }
 
  private:

lib/gpu/geryon/ocl_device.h

@@ -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};
+    if (_cq_profiling) {
-    _cq.back()=clCreateCommandQueueWithProperties(_context, _cl_device, props, &errorv);
+      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_device_fp_config double_mask = (CL_FP_FMA|CL_FP_ROUND_TO_NEAREST|
-                                     CL_FP_ROUND_TO_INF|CL_FP_INF_NAN|CL_FP_DENORM);
+                                     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

lib/gpu/geryon/ocl_memory.h

@@ -118,15 +118,19 @@ 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) {
-  cl_int error_flag;
+  // When viewing outside host allocation with discrete main memory on accelerator,
-  cl_buffer_region subbuffer;
+  // no cl_buffer object is created to avoid unnecessary creation of device allocs
-  subbuffer.origin = o;
+  if (cm.shared_mem_device()) {
-  subbuffer.size = n;
+    cl_int error_flag;
-  mat.cbegin()=clCreateSubBuffer(cm.cbegin(), 0,
+    cl_buffer_region subbuffer;
-                                 CL_BUFFER_CREATE_TYPE_REGION, &subbuffer,
+    subbuffer.origin = o;
-                                 &error_flag);
+    subbuffer.size = n;
-
+    mat.cbegin()=clCreateSubBuffer(cm.cbegin(), 0,
-  CL_CHECK_ERR(error_flag);
+                                   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) {
-  cl_int error_flag;
+  if (mat.shared_mem_device()) {
-  mat.cbegin()=clCreateBuffer(dev.context(), CL_MEM_USE_HOST_PTR,
+    cl_int error_flag;
-                              n,*mat.host_ptr(),&error_flag);
+    mat.cbegin()=clCreateBuffer(dev.context(), CL_MEM_USE_HOST_PTR,
-  CL_CHECK_ERR(error_flag);
+                                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;
 }
@@ -181,7 +188,10 @@ 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) {
-    CL_DESTRUCT_CALL(clReleaseMemObject(mat.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 (mat.cbegin()!=(cl_mem)(0))
+      CL_DESTRUCT_CALL(clReleaseMemObject(mat.cbegin()));
     CL_DESTRUCT_CALL(clReleaseCommandQueue(mat.cq()));
   }
 }

lib/gpu/geryon/ocl_timer.h

@@ -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
@@ -71,8 +75,12 @@ class UCL_Timer {
 
   /// Start timing on default command queue
   inline void start() {
+    if (has_measured_time) {
+      clReleaseEvent(start_event);
+      clReleaseEvent(stop_event);
+      has_measured_time = false;
+    }
     UCL_OCL_MARKER(_cq,&start_event);
-    has_measured_time = false;
   }
 
   /// Stop timing on default command queue
@@ -83,8 +91,12 @@ class UCL_Timer {
 
   /// Block until the start event has been reached on device
   inline void sync_start() {
+    if (has_measured_time) {
+      clReleaseEvent(start_event);
+      clReleaseEvent(stop_event);
+      has_measured_time = false;
+    }
     CL_SAFE_CALL(clWaitForEvents(1,&start_event));
-    has_measured_time = false;
   }
 
   /// Block until the stop event has been reached on device

lib/gpu/geryon/ucl_basemat.h

@@ -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
+    #endif
-    return false;
+
     #endif
   }
 

lib/gpu/geryon/ucl_h_mat.h

@@ -140,7 +140,10 @@ class UCL_H_Mat : public UCL_BaseMat {
     _end=_array+_cols;
     #ifdef _OCL_MAT
     _carray=input.cbegin();
-    CL_SAFE_CALL(clRetainMemObject(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
   }

lib/gpu/geryon/ucl_h_vec.h

@@ -139,7 +139,10 @@ class UCL_H_Vec : public UCL_BaseMat {
     _end=_array+_cols;
     #ifdef _OCL_MAT
     _carray=input.cbegin();
-    CL_SAFE_CALL(clRetainMemObject(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
   }

lib/gpu/lal_device.cpp

@@ -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
+  // Previous source of OCL memory leak when time_device=false
-  // XXX: the following setting triggers a memory leak with OpenCL and MPI
+  // - Logic added to release OCL events when timers are not invoked
-  //      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>
   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++)

lib/gpu/lal_pppm.cpp

@@ -304,7 +304,8 @@ int PPPMT::spread(const int ago, const int nlocal, const int nall,
                            const double delxinv, const double delyinv,
                            const double delzinv) {
   if (!_precompute_done) {
-    atom->acc_timers();
+    if (device->time_device())
+      atom->acc_timers();
     _precompute(ago,nlocal,nall,host_x,host_type,success,host_q,boxlo,delxinv,
                 delyinv,delzinv);
   }

python/lammps/mliap/mliap_unified_abc.py

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