Merge branch 'develop' into fix-cmake-python-install

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.

cmake/CMakeLists.txt

@@ -12,6 +12,11 @@ endif()
 if(POLICY CMP0109)
   cmake_policy(SET CMP0109 OLD)
 endif()
+# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
+if(POLICY CMP0135)
+  cmake_policy(SET CMP0135 OLD)
+endif()
+
 ########################################
 
 project(lammps CXX)

cmake/Modules/Packages/MDI.cmake

@@ -49,6 +49,14 @@ if(DOWNLOAD_MDI)
       set(MDI_USE_PYTHON_PLUGINS ON)
     endif()
   endif()
+  # python plugins are not supported and thus must be always off on Windows
+  if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+    unset(Python_Development_FOUND)
+    set(MDI_USE_PYTHON_PLUGINS OFF)
+    if(CMAKE_CROSSCOMPILING)
+      set(CMAKE_INSTALL_LIBDIR lib)
+    endif()
+  endif()
 
   # download/ build MDI library
   # always build static library with -fpic
@@ -57,8 +65,9 @@ if(DOWNLOAD_MDI)
   ExternalProject_Add(mdi_build
     URL     ${MDI_URL}
     URL_MD5 ${MDI_MD5}
+    PREFIX ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
     CMAKE_ARGS
-    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+    -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
     -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
     -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
@@ -70,23 +79,23 @@ if(DOWNLOAD_MDI)
     -Dplugins=ON
     -Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
     UPDATE_COMMAND ""
-    INSTALL_COMMAND ""
+    INSTALL_COMMAND ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/src/mdi_build-build --target install
-    BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
+    BUILD_BYPRODUCTS "${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
     )
 
   # where is the compiled library?
-  ExternalProject_get_property(mdi_build BINARY_DIR)
+  ExternalProject_get_property(mdi_build PREFIX)
-  set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
   # workaround for older CMake versions
-  file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
+  file(MAKE_DIRECTORY ${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi)
+  file(MAKE_DIRECTORY ${PREFIX}/include/mdi)
 
   # create imported target for the MDI library
   add_library(LAMMPS::MDI UNKNOWN IMPORTED)
   add_dependencies(LAMMPS::MDI mdi_build)
   set_target_properties(LAMMPS::MDI PROPERTIES
-    IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
+    IMPORTED_LOCATION "${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
-    INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
+    INTERFACE_INCLUDE_DIRECTORIES ${PREFIX}/include/mdi
-    )
+  )
 
   set(MDI_DEP_LIBS "")
   # if compiling with python plugins we need

cmake/Modules/Packages/ML-IAP.cmake

@@ -25,16 +25,18 @@ if(MLIAP_ENABLE_PYTHON)
   endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
-  set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/mliap_model_python_couple.pyx)
+  file(GLOB MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
-  get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE)
   file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
-  add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
+  foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
-          COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_SRC} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+    get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
-          COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+    add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
-          WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
+            COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_FILE} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
-          MAIN_DEPENDENCY    ${MLIAP_CYTHON_SRC}
+            COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
-          COMMENT "Generating C++ sources with cythonize...")
+            WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
+            MAIN_DEPENDENCY    ${MLIAP_CYTHON_FILE}
+            COMMENT "Generating C++ sources with cythonize...")
+    target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
+  endforeach()
   target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
-  target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
   target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
 endif()

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,6 +1,6 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2022.09.27.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "32394d799bc282bb57696c78c456e64f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "ad6c8597076479bd55059f5947d51acc" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 
@@ -15,23 +15,9 @@ execute_process(
 )
 get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
 
-# enforce building libyaml-cpp as static library and turn off optional features
+add_subdirectory(${lib-pace} build-pace)
-set(YAML_BUILD_SHARED_LIBS OFF)
-set(YAML_CPP_BUILD_CONTRIB OFF)
-set(YAML_CPP_BUILD_TOOLS OFF)
-add_subdirectory(${lib-pace}/yaml-cpp build-yaml-cpp)
-set(YAML_CPP_INCLUDE_DIR ${lib-pace}/yaml-cpp/include)
-
-file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${lib-pace}/ML-PACE)
-file(GLOB PACE_EVALUATOR_SOURCES ${lib-pace}/ML-PACE/*.cpp)
-list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
-
-add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
 set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
-target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR})
 
-
-target_link_libraries(pace PRIVATE yaml-cpp-pace)
 if(CMAKE_PROJECT_NAME STREQUAL "lammps")
   target_link_libraries(lammps PRIVATE pace)
 endif()

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.
@@ -216,9 +216,20 @@ be multiple tests run automatically:
 - A test that only standard, printable ASCII text characters are used.
   This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
   thus prints all offending lines with filename and line number
-  prepended to the screen.  Special characters like the Angstrom
+  prepended to the screen.  Special characters like Greek letters
-  :math:`\mathrm{\mathring{A}}` should be typeset with embedded math
+  (:math:`\alpha~~\sigma~~\epsilon`), super- or subscripts
-  (like this ``:math:`\mathrm{\mathring{A}}```\ ).
+  (:math:`x^2~~\mathrm{U}_{LJ}`), mathematical expressions
+  (:math:`\frac{1}{2}\mathrm{N}~~x\to\infty`), or the Angstrom symbol
+  (:math:`\AA`) should be typeset with embedded LaTeX (like this
+  ``:math:`\alpha \sigma \epsilon```, ``:math:`x^2 \mathrm{E}_{LJ}```,
+  ``:math:`\frac{1}{2}\mathrm{N} x\to\infty```, or ``:math:`\AA```\ ).
+
+- Embedded LaTeX is rendered in HTML output with `MathJax
+  <https://www.mathjax.org/>`_ and in PDF output by passing the embedded
+  text to LaTeX.  Some care has to be taken, though, since there are
+  limitations which macros and features can be used in either mode, so
+  it is recommended to always check whether any new or changed
+  documentation does translate and render correctly with either output.
 
 - A test whether all styles are documented and listed in their
   respective overview pages.  A typical output with warnings looks like this:

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/Commands_pair.rst

@@ -236,6 +236,7 @@ OPT.
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`pace (k) <pair_pace>`
+   * :doc:`pace/extrapolation <pair_pace>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`

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_spins.rst

@@ -30,9 +30,11 @@ can be coupled to another Langevin thermostat applied to the atoms
 using :doc:`fix langevin <fix_langevin>` in order to simulate
 thermostatted spin-lattice systems.
 
-The magnetic Gilbert damping can also be applied using :doc:`fix langevin/spin <fix_langevin_spin>`. It allows to either dissipate
+The magnetic damping can also be applied
-the thermal energy of the Langevin thermostat, or to perform a
+using :doc:`fix langevin/spin <fix_langevin_spin>`.
-relaxation of the magnetic configuration toward an equilibrium state.
+It allows to either dissipate the thermal energy of the Langevin
+thermostat, or to perform a relaxation of the magnetic configuration
+toward an equilibrium state.
 
 The command :doc:`fix setforce/spin <fix_setforce>` allows to set the
 components of the magnetic precession vectors (while erasing and
@@ -52,9 +54,11 @@ All the computed magnetic properties can be output by two main
 commands. The first one is :doc:`compute spin <compute_spin>`, that
 enables to evaluate magnetic averaged quantities, such as the total
 magnetization of the system along x, y, or z, the spin temperature, or
-the magnetic energy. The second command is :doc:`compute property/atom <compute_property_atom>`. It enables to output all the
+the magnetic energy. The second command
-per atom magnetic quantities. Typically, the orientation of a given
+is :doc:`compute property/atom <compute_property_atom>`.
-magnetic spin, or the magnetic force acting on this spin.
+It enables to output all the per atom magnetic quantities. Typically,
+the orientation of a given magnetic spin, or the magnetic force
+acting on this spin.
 
 ----------
 

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/Library_create.rst

@@ -11,6 +11,7 @@ This section documents the following functions:
 - :cpp:func:`lammps_mpi_finalize`
 - :cpp:func:`lammps_kokkos_finalize`
 - :cpp:func:`lammps_python_finalize`
+- :cpp:func:`lammps_error`
 
 --------------------
 
@@ -115,3 +116,8 @@ calling program.
 
 .. doxygenfunction:: lammps_python_finalize
    :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_error
+   :project: progguide

doc/src/Library_objects.rst

@@ -6,6 +6,7 @@ fixes, or variables in LAMMPS using the following functions:
 
 - :cpp:func:`lammps_extract_compute`
 - :cpp:func:`lammps_extract_fix`
+- :cpp:func:`lammps_extract_variable_datatype`
 - :cpp:func:`lammps_extract_variable`
 - :cpp:func:`lammps_set_variable`
 
@@ -21,6 +22,11 @@ fixes, or variables in LAMMPS using the following functions:
 
 -----------------------
 
+.. doxygenfunction:: lammps_extract_variable_datatype
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_extract_variable
    :project: progguide
 
@@ -36,3 +42,5 @@ fixes, or variables in LAMMPS using the following functions:
 .. doxygenenum:: _LMP_STYLE_CONST
 
 .. doxygenenum:: _LMP_TYPE_CONST
+
+.. doxygenenum:: _LMP_VAR_CONST

doc/src/Library_properties.rst

@@ -15,21 +15,21 @@ This section documents the following functions:
 
 --------------------
 
-The library interface allows extraction of different kinds of
+The library interface allows the extraction of different kinds of
-information about the active simulation instance and also
+information about the active simulation instance and also---in some
-modifications to it.  This enables combining of a LAMMPS simulation
+cases---to apply modifications to it.  This enables combining of a
-with other processing and simulation methods computed by the calling
+LAMMPS simulation with other processing and simulation methods computed
-code, or by another code that is coupled to LAMMPS via the library
+by the calling code, or by another code that is coupled to LAMMPS via
-interface.  In some cases the data returned is direct reference to the
+the library interface.  In some cases the data returned is direct
-original data inside LAMMPS, cast to a void pointer.  In that case the
+reference to the original data inside LAMMPS, cast to a void pointer.
-data needs to be cast to a suitable pointer for the calling program to
+In that case the data needs to be cast to a suitable pointer for the
-access it, and you may need to know the correct dimensions and
+calling program to access it, and you may need to know the correct
-lengths.  This also means you can directly change those value(s) from
+dimensions and lengths.  This also means you can directly change those
-the calling program, e.g. to modify atom positions.  Of course, this
+value(s) from the calling program (e.g., to modify atom positions).  Of
-should be done with care.  When accessing per-atom data, please note
+course, changing values should be done with care.  When accessing per-atom
-that this data is the per-processor **local** data and is indexed
+data, please note that these data are the per-processor **local** data and are
-accordingly. Per-atom data can change sizes and ordering at every
+indexed accordingly. Per-atom data can change sizes and ordering at
-neighbor list rebuild or atom sort event as atoms migrate between
+every neighbor list rebuild or atom sort event as atoms migrate between
 sub-domains and processors.
 
 .. code-block:: C

doc/src/Library_utility.rst

@@ -19,6 +19,7 @@ functions.  They do not directly call the LAMMPS library.
 - :cpp:func:`lammps_force_timeout`
 - :cpp:func:`lammps_has_error`
 - :cpp:func:`lammps_get_last_error_message`
+- :cpp:func:`lammps_python_api_version`
 
 The :cpp:func:`lammps_free` function is a clean-up function to free
 memory that the library had allocated previously via other function
@@ -100,3 +101,9 @@ where such memory buffers were allocated that require the use of
 
 .. doxygenfunction:: lammps_get_last_error_message
    :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_python_api_version
+   :project: progguide
+

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/Python_neighbor.rst

@@ -38,6 +38,40 @@ using the NumPy access method.
            for n in np.nditer(nlist):
                print("  atom {} with ID {}".format(n,tags[n]))
 
+Another example for extracting a full neighbor list without evaluating a
+potential is shown below.
+
+.. code-block:: python
+
+    from lammps import lammps
+    import numpy as np
+
+    lmp = lammps()
+    lmp.commands_string("""
+    newton off
+    region box block -2 2 -2 2 -2 2
+    lattice fcc 1.0
+    create_box 1 box
+    create_atoms 1 box
+    mass 1 1.0
+    pair_style zero 1.0 full
+    pair_coeff * *
+    run 0 post no""")
+
+    # look up the neighbor list
+    nlidx = lmp.find_pair_neighlist('zero')
+    nl = lmp.numpy.get_neighlist(nlidx)
+    tags = lmp.extract_atom('id')
+    print("full neighbor list with {} entries".format(nl.size))
+    # print neighbor list contents
+    for i in range(0,nl.size):
+        idx, nlist  = nl.get(i)
+        print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size))
+        if nlist.size > 0:
+            for n in np.nditer(nlist):
+                pass
+                print("  atom {} with ID {}".format(n,tags[n]))
+
 **Methods:**
 
 * :py:meth:`lammps.get_neighlist() <lammps.lammps.get_neighlist()>`: Get neighbor list for given index

doc/src/Run_basics.rst

@@ -30,12 +30,13 @@ executable itself can be placed elsewhere.
 
 .. note::
 
-   The redirection operator "<" will not always work when running
+   The redirection operator "<" will not always work when running in
-   in parallel with mpirun or mpiexec; for those systems the -in form is required.
+   parallel with ``mpirun`` or ``mpiexec``; for those systems the -in
+   form is required.
 
 As LAMMPS runs it prints info to the screen and a logfile named
-*log.lammps*\ .  More info about output is given on the
+*log.lammps*\ .  More info about output is given on the :doc:`screen and
-:doc:`screen and logfile output <Run_output>` page.
+logfile output <Run_output>` page.
 
 If LAMMPS encounters errors in the input script or while running a
 simulation it will print an ERROR message and stop or a WARNING

doc/src/Run_options.rst

@@ -93,13 +93,13 @@ switch is not set (the default), LAMMPS will operate as if the KOKKOS
 package were not installed; i.e. you can run standard LAMMPS or with
 the GPU or OPENMP packages, for testing or benchmarking purposes.
 
-Additional optional keyword/value pairs can be specified which
+Additional optional keyword/value pairs can be specified which determine
-determine how Kokkos will use the underlying hardware on your
+how Kokkos will use the underlying hardware on your platform.  These
-platform.  These settings apply to each MPI task you launch via the
+settings apply to each MPI task you launch via the ``mpirun`` or
-"mpirun" or "mpiexec" command.  You may choose to run one or more MPI
+``mpiexec`` command.  You may choose to run one or more MPI tasks per
-tasks per physical node.  Note that if you are running on a desktop
+physical node.  Note that if you are running on a desktop machine, you
-machine, you typically have one physical node.  On a cluster or
+typically have one physical node.  On a cluster or supercomputer there
-supercomputer there may be dozens or 1000s of physical nodes.
+may be dozens or 1000s of physical nodes.
 
 Either the full word or an abbreviation can be used for the keywords.
 Note that the keywords do not use a leading minus sign.  I.e. the
@@ -148,9 +148,9 @@ one of these 4 environment variables
    MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
    OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
 
-which are initialized by the "srun", "mpirun" or "mpiexec" commands.
+which are initialized by the ``srun``, ``mpirun``, or ``mpiexec``
-The environment variable setting for each MPI rank is used to assign a
+commands.  The environment variable setting for each MPI rank is used to
-unique GPU ID to the MPI task.
+assign a unique GPU ID to the MPI task.
 
 .. parsed-literal::
 

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
@@ -76,10 +76,11 @@ instructions.
 
 **Run with the GPU package from the command line:**
 
-The mpirun or mpiexec command sets the total number of MPI tasks used
+The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks
-by LAMMPS (one or multiple per compute node) and the number of MPI
+used by LAMMPS (one or multiple per compute node) and the number of MPI
-tasks used per node.  E.g. the mpirun command in MPICH does this via
+tasks used per node.  E.g. the ``mpirun`` command in MPICH does this via
-its -np and -ppn switches.  Ditto for OpenMPI via -np and -npernode.
+its ``-np`` and ``-ppn`` switches.  Ditto for OpenMPI via ``-np`` and
+``-npernode``.
 
 When using the GPU package, you cannot assign more than one GPU to a
 single MPI task.  However multiple MPI tasks can share the same GPU,
@@ -129,8 +130,8 @@ GPU package pair styles.
 
 **Or run with the GPU package by editing an input script:**
 
-The discussion above for the mpirun/mpiexec command, MPI tasks/node,
+The discussion above for the ``mpirun`` or ``mpiexec`` command, MPI
-and use of multiple MPI tasks/GPU is the same.
+tasks/node, and use of multiple MPI tasks/GPU is the same.
 
 Use the :doc:`suffix gpu <suffix>` command, or you can explicitly add an
 "gpu" suffix to individual styles in your input script, e.g.

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_kokkos.rst

@@ -72,12 +72,12 @@ See the :ref:`Build extras <kokkos>` page for instructions.
 Running LAMMPS with the KOKKOS package
 """"""""""""""""""""""""""""""""""""""
 
-All Kokkos operations occur within the context of an individual MPI
+All Kokkos operations occur within the context of an individual MPI task
-task running on a single node of the machine. The total number of MPI
+running on a single node of the machine. The total number of MPI tasks
-tasks used by LAMMPS (one or multiple per compute node) is set in the
+used by LAMMPS (one or multiple per compute node) is set in the usual
-usual manner via the mpirun or mpiexec commands, and is independent of
+manner via the ``mpirun`` or ``mpiexec`` commands, and is independent of
-Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
+Kokkos. E.g. the mpirun command in OpenMPI does this via its ``-np`` and
--npernode switches. Ditto for MPICH via -np and -ppn.
+``-npernode`` switches. Ditto for MPICH via ``-np`` and ``-ppn``.
 
 Running on a multi-core CPU
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -168,7 +168,7 @@ for your MPI installation), binding can be forced with these flags:
 
 .. parsed-literal::
 
-   OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
+   OpenMPI 1.8:  mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
    Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ...
 
 For binding threads with KOKKOS OpenMP, use thread affinity environment
@@ -310,7 +310,8 @@ Alternatively the effect of the "-sf" or "-pk" switches can be
 duplicated by adding the :doc:`package kokkos <package>` or :doc:`suffix kk <suffix>` commands to your input script.
 
 The discussion above for building LAMMPS with the KOKKOS package, the
-mpirun/mpiexec command, and setting appropriate thread are the same.
+``mpirun`` or ``mpiexec`` command, and setting appropriate thread
+properties are the same.
 
 You must still use the "-k on" :doc:`command-line switch <Run_options>`
 to enable the KOKKOS package, and specify its additional arguments for

doc/src/Speed_omp.rst

@@ -33,8 +33,8 @@ These examples assume one or more 16-core nodes.
    mpirun -np 4 lmp_omp -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task
    mpirun -np 32 -ppn 4 lmp_omp -sf omp -pk omp 4 -in in.script   # 8 nodes, 4 MPI tasks/node, 4 threads/task
 
-The mpirun or mpiexec command sets the total number of MPI tasks used
+The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks
-by LAMMPS (one or multiple per compute node) and the number of MPI
+used by LAMMPS (one or multiple per compute node) and the number of MPI
 tasks used per node.  E.g. the mpirun command in MPICH does this via
 its -np and -ppn switches.  Ditto for OpenMPI via -np and -npernode.
 
@@ -58,8 +58,8 @@ OMP_NUM_THREADS environment variable.
 Or run with the OPENMP package by editing an input script
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-The discussion above for the mpirun/mpiexec command, MPI tasks/node,
+The discussion above for the ``mpirun`` or ``mpiexec`` command, MPI
-and threads/MPI task is the same.
+tasks/node, and threads/MPI task is the same.
 
 Use the :doc:`suffix omp <suffix>` command, or you can explicitly add an
 "omp" suffix to individual styles in your input script, e.g.
@@ -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/Speed_packages.rst

@@ -117,33 +117,15 @@ script.
    with all its accelerator packages installed.  Note however that the
    INTEL and KOKKOS packages require you to choose one of their
    hardware options when building for a specific platform.  I.e. CPU or
-   Phi option for the INTEL package.  Or the OpenMP, Cuda, or Phi
+   Phi option for the INTEL package.  Or the OpenMP, CUDA, HIP, SYCL,
-   option for the KOKKOS package.
+   or Phi option for the KOKKOS package.  Or the OpenCL, HIP, or CUDA
+   option for the GPU package.
 
 These are the exceptions.  You cannot build a single executable with:
 
 * both the INTEL Phi and KOKKOS Phi options
 * the INTEL Phi or Kokkos Phi option, and the GPU package
 
-See the examples/accelerate/README and make.list files for sample
-Make.py commands that build LAMMPS with any or all of the accelerator
-packages.  As an example, here is a command that builds with all the
-GPU related packages installed (GPU, KOKKOS with Cuda), including
-settings to build the needed auxiliary GPU libraries for Kepler GPUs:
-
-.. code-block:: bash
-
-   Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi   -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi
-
-The examples/accelerate directory also has input scripts that can be
-used with all of the accelerator packages.  See its README file for
-details.
-
-Likewise, the bench directory has FERMI and KEPLER and PHI
-sub-directories with Make.py commands and input scripts for using all
-the accelerator packages on various machines.  See the README files in
-those directories.
-
 As mentioned above, the `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS website gives
 performance results for the various accelerator packages for several
 of the standard LAMMPS benchmark problems, as a function of problem

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/bond_mm3.rst

@@ -26,14 +26,14 @@ as defined in :ref:`(Allinger) <mm3-allinger1989>`
 
 .. math::
 
-   E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
+   E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + \frac{7}{12} 2.55^2(r-r_0)^2 \right]
 
 where :math:`r_0` is the equilibrium value of the bond, and :math:`K` is a
-prefactor. The anharmonic prefactors have units angstrom\^(-n):
+prefactor. The anharmonic prefactors have units :math:`\AA^{-n}`:
--2.55 angstrom\^(-1) and (7/12)2.55\^2 angstrom\^(-2). The code takes
+:math:`-2.55 \AA^{-1}` and :math:`\frac{7}{12} 2.55^2 \AA^{-2}`. The code takes
 care of the necessary unit conversion for these factors internally.
-Note that the MM3 papers contains an error in Eq (1):
+Note that the MM3 papers contain an error in Eq (1):
-(7/12)2.55 should be replaced with (7/12)2.55\^2
+:math:`\frac{7}{12} 2.55` should be replaced with :math:`\frac{7}{12} 2.55^2`
 
 The following coefficients must be defined for each bond type via the
 :doc:`bond_coeff <bond_coeff>` command as in the example above, or in

doc/src/bond_quartic.rst

@@ -28,11 +28,18 @@ The *quartic* bond style uses the potential
 
 .. math::
 
-   E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
+   E      & = E_q + E_{LJ} \\
+   E_q    & = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 \\
+   E_{LJ} & = \left\{ \begin{array} {l@{\quad:\quad}l}
+   4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon & r < 2^{\frac{1}{6}}, \epsilon = 1, \sigma = 1 \\
+                                                  0 & r >= 2^{\frac{1}{6}}
+                         \end{array} \right.
 
 to define a bond that can be broken as the simulation proceeds (e.g.
-due to a polymer being stretched).  The :math:`\sigma` and :math:`\epsilon` used in the
+due to a polymer being stretched).  The :math:`\sigma` and
-LJ portion of the formula are both set equal to 1.0 by LAMMPS.
+:math:`\epsilon` used in the LJ portion of the formula are both set
+equal to 1.0 by LAMMPS and the LJ portion is cut off at its minimum,
+i.e. at :math:`r_c = 2^{\frac{1}{6}}`.
 
 The following coefficients must be defined for each bond type via the
 :doc:`bond_coeff <bond_coeff>` command as in the example above, or in
@@ -46,9 +53,9 @@ or :doc:`read_restart <read_restart>` commands:
 * :math:`U_0` (energy)
 
 This potential was constructed to mimic the FENE bond potential for
-coarse-grained polymer chains.  When monomers with :math:`\sigma = \epsilon = 1.0`
+coarse-grained polymer chains.  When monomers with :math:`\sigma =
-are used, the following choice of parameters gives a quartic potential that
+\epsilon = 1.0` are used, the following choice of parameters gives a
-looks nearly like the FENE potential:
+quartic potential that looks nearly like the FENE potential:
 
 .. math::
 

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_chunk_atom.rst

@@ -602,8 +602,7 @@ be used.  For non-orthogonal (triclinic) simulation boxes, only the
 *reduced* option may be used.
 
 A *box* value selects standard distance units as defined by the
-:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring A}`
+:doc:`units <units>` command (e.g., :math:`\AA` for units = *real* or *metal*).
-for units = *real* or *metal*).
 A *lattice* value means the distance units are in lattice spacings.
 The :doc:`lattice <lattice>` command must have been previously used to
 define the lattice spacing.  A *reduced* value means normalized

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_displace_atom.rst

@@ -95,7 +95,7 @@ something like the following commands:
                    refresh c_dsp delay 100
 
 The :doc:`dump_modify thresh <dump_modify>` command will only output
-atoms that have displaced more than :math:`0.6~\mathrm{\mathring A}` on each
+atoms that have displaced more than :math:`0.6~\AA` on each
 snapshot (assuming metal units).  The dump_modify *refresh* option triggers a
 call to this compute at the end of every dump.
 

doc/src/compute_entropy_atom.rst

@@ -97,13 +97,13 @@ by the corresponding volume. This option can be useful when dealing with
 inhomogeneous systems such as those that have surfaces.
 
 Here are typical input parameters for fcc aluminum (lattice
-constant :math:`4.05~\mathrm{\mathring A}`),
+constant :math:`4.05~\AA`),
 
 .. parsed-literal::
 
    compute 1 all entropy/atom 0.25 5.7 avg yes 3.7
 
-and for bcc sodium (lattice constant 4.23 Angstroms),
+and for bcc sodium (lattice constant :math:`4.23~\AA`),
 
 .. parsed-literal::
 

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_rigid_local.rst

@@ -109,8 +109,7 @@ The *mass* attribute is the total mass of the rigid body.
 There are two options for outputting the coordinates of the center of
 mass (COM) of the body.  The *x*, *y*, *z* attributes write the COM
 "unscaled", in the appropriate distance :doc:`units <units>`
-(:math:`\mathrm{\mathring A}`,
+(:math:`\AA`, :math:`\sigma`, etc).  Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by
-sigma, etc).  Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by
 the image flags for each body.  Unwrapped means that if the body
 COM has passed through a periodic boundary one or more times, the value
 is generated what the COM coordinate would be if it had not been

doc/src/compute_saed.rst

@@ -86,7 +86,7 @@ will defined using the *c* values for the spacing along each reciprocal
 lattice axis. Note that manual mapping of the reciprocal space mesh is
 good for comparing diffraction results from  multiple simulations; however
 it can reduce the likelihood that Bragg reflections will be satisfied
-unless small spacing parameters (:math:`<0.05~\mathrm{\mathring A}^-1`)
+unless small spacing parameters (:math:`<0.05~\AA^-1`)
 are implemented.  Meshes with manual spacing do not require a periodic
 boundary.
 

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_temp_ramp.rst

@@ -58,7 +58,7 @@ constant, and :math:`T` is the absolute temperature.
 The *units* keyword determines the meaning of the distance units used
 for coordinates (*clo*, *chi*) and velocities (*vlo*, *vhi*).  A *box* value
 selects standard distance units as defined by the :doc:`units <units>`
-command (e.g., :math:`\mathrm{\mathring{A}}` for units = real or metal).  A
+command (e.g., :math:`\AA` for units = real or metal).  A
 *lattice* value means the distance units are in lattice spacings (i.e.,
 velocity in lattice spacings per unit time).  The :doc:`lattice <lattice>`
 command must have been previously used to define the lattice spacing.

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/compute_xrd.rst

@@ -91,7 +91,7 @@ reciprocal lattice axis. Note that manual mapping of the reciprocal
 space mesh is good for comparing diffraction results from multiple
 simulations; however, it can reduce the likelihood that Bragg
 reflections will be satisfied unless small spacing parameters
-(:math:`< 0.05~\mathrm{\mathring{A}}^{-1}`) are implemented.
+(:math:`< 0.05~\AA^{-1}`) are implemented.
 Meshes with manual spacing do not require a periodic boundary.
 
 The limits of the reciprocal lattice mesh are determined by range of

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
@@ -460,7 +464,7 @@ The *units* keyword determines the meaning of the distance units used
 to specify the coordinates of the one particle created by the *single*
 style, or the overlap distance *Doverlap* by the *overlap* keyword.  A
 *box* value selects standard distance units as defined by the
-:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring{A}}` for
+:doc:`units <units>` command (e.g., :math:`\AA` for
 units = *real* or *metal*\ .  A *lattice* value means the distance units are in
 lattice spacings.
 

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/displace_atoms.rst

@@ -104,7 +104,7 @@ atom's rotation.
 Distance units for displacements and the origin point of the *rotate*
 style are determined by the setting of *box* or *lattice* for the
 *units* keyword.  *Box* means distance units as defined by the
-:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring A}` for
+:doc:`units <units>` command (e.g., :math:`\AA` for
 *real* or *metal* units). *Lattice* means distance units are in lattice
 spacings.  The :doc:`lattice <lattice>` command must have been previously used
 to define the lattice spacing.

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.
 
 ----------
@@ -693,7 +693,7 @@ charge.
 
 There are several options for outputting atom coordinates.  The *x*,
 *y*, and *z* attributes write atom coordinates "unscaled", in the
-appropriate distance :doc:`units <units>` (:math:`\mathrm{\mathring A}`,
+appropriate distance :doc:`units <units>` (:math:`\AA`,
 :math:`\sigma`, etc.).  Use *xs*, *ys*, and *zs* if you want the
 coordinates "scaled" to the box size so that each value is 0.0 to 1.0.
 If the simulation box is triclinic (tilted), then all atom coords will

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

@@ -632,7 +632,7 @@ calculates the displacement of each atom from its reference position.
 The "4" index is the scalar displacement; 1, 2, and 3 are the :math:`xyz`
 components of the displacement.  The :doc:`dump_modify thresh <dump_modify>`
 command will cause only atoms that have displaced more than
-:math:`0.6~\mathrm{\mathring A}` to be output on a given snapshot (assuming
+:math:`0.6~\AA` to be output on a given snapshot (assuming
 metal units).  However, note that when an atom is output, we also need to
 update the reference position for that atom to its new coordinates.  So that it
 will not be output in every snapshot thereafter.  That reference position is
@@ -675,7 +675,7 @@ value of *yes* means atom coords are written in normalized units from
 0.0 to 1.0 in each box dimension.  If the simulation box is triclinic
 (tilted), then all atom coords will still be between 0.0 and 1.0.  A
 value of *no* means they are written in absolute distance units
-(e.g., :math:`\mathrm{\mathring A}` or :math:`\sigma`).
+(e.g., :math:`\AA` or :math:`\sigma`).
 Using this keyword will reset all custom header names set with
 *dump_modify colname* to their respective default values.
 
@@ -687,7 +687,7 @@ when writing to XTC files.  By default, they are initialized for
 whatever :doc:`units <units>` style is being used, to write out
 coordinates in nanometers and time in picoseconds.  For example, for *real*
 units, LAMMPS defines *sfactor* = 0.1 and *tfactor* = 0.001, since the
-:math:`\mathrm{\mathring A}` and fs used by *real* units are 0.1 nm and
+:math:`\AA` and fs used by *real* units are 0.1 nm and
 0.001 ps, respectively.  If you are using a units system with distance and time
 units far from nm and ps, you may wish to write XTC files with
 different units, since the compression algorithm used in XTC files is
@@ -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_acks2_reaxff.rst

@@ -71,7 +71,7 @@ potential in eV, *gamma*, the valence orbital exponent, and *bcut*, the
 bond cutoff distance.  Note that these 4 quantities are also in the
 ReaxFF potential file, except that eta is defined here as twice the eta
 value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
-of this fix are hard-coded to be :math:`\mathrm{\mathring{A}}`, eV, and
+of this fix are hard-coded to be :math:`\AA`, eV, and
 electronic charge.
 
 The optional *maxiter* keyword allows changing the max number
@@ -111,7 +111,7 @@ LAMMPS was built with that package. See the :doc:`Build package
 
 This fix does not correctly handle interactions involving multiple
 periodic images of the same atom.  Hence, it should not be used for
-periodic cell dimensions less than :math:`10~\mathrm{\mathring{A}}`.
+periodic cell dimensions less than :math:`10~\AA`.
 
 This fix may be used in combination with :doc:`fix efield <fix_efield>`
 and will apply the external electric field during charge equilibration,

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_append_atoms.rst

@@ -79,7 +79,7 @@ measured from zhi and is set with the *extent* argument.
 The *units* keyword determines the meaning of the distance units used
 to define a wall position, but only when a numeric constant is used.
 A *box* value selects standard distance units as defined by the
-:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring A}`
+:doc:`units <units>` command (e.g., :math:`\AA`
 for units = real or metal.
 A *lattice* value means the distance units are in lattice spacings.
 The :doc:`lattice <lattice>` command must have been previously used to

doc/src/fix_bocs.rst

@@ -59,7 +59,7 @@ Note both the COMMA and the SPACE separating the volume's
 value and its corresponding pressure correction. The volumes in the file
 must be uniformly spaced. Both the volumes and the pressure corrections
 should be provided in the proper units, e.g. if you are using *units real*,
-the volumes should all be in cubic angstroms, and the pressure corrections
+the volumes should all be in cubic Angstroms, and the pressure corrections
 should all be in atmospheres. Furthermore, the table should start/end at a
 volume considerably smaller/larger than you expect your system to sample
 during the simulation. If the system ever reaches a volume outside of the
@@ -72,8 +72,8 @@ With the *analytic* option, the arguments are as follows:
    ... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
 
 Note that *V_avg* and *Coeff_i* should all be in the proper units, e.g. if you
-are using *units real*, *V_avg* should be in cubic angstroms, and the
+are using *units real*, *V_avg* should be in cubic Angstroms, and the
-coefficients should all be in atmospheres \* cubic angstroms.
+coefficients should all be in atmospheres \* cubic Angstroms.
 
 ----------
 

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
@@ -93,8 +88,8 @@ to send "unwrapped" coordinates to the IMD client that undo the
 wrapping back of coordinates into the principle unit cell, as done by
 default in LAMMPS.  The *fscale* keyword allows to apply a scaling
 factor to forces transmitted by the IMD client. The IMD protocols
-stipulates that forces are transferred in kcal/mol/angstrom under the
+stipulates that forces are transferred in kcal/mol/Angstrom under the
-assumption that coordinates are given in angstrom. For LAMMPS runs
+assumption that coordinates are given in Angstrom. For LAMMPS runs
 with different units or as a measure to tweak the forces generated by
 the manipulation of the IMD client, this option allows to make
 adjustments.
@@ -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_langevin_spin.rst

@@ -40,7 +40,7 @@ the following stochastic differential equation:
   \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right) \right)
 
 with :math:`\lambda` the transverse damping, and :math:`\eta` a random vector.
-This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG)
+This equation is referred to as the stochastic Landau-Lifshitz (sLL)
 equation.
 
 The components of :math:`\eta` are drawn from a Gaussian probability
@@ -49,7 +49,7 @@ the external thermostat T (in K in metal units).
 
 More details about this implementation are reported in :ref:`(Tranchida) <Tranchida2>`.
 
-Note: due to the form of the sLLG equation, this fix has to be defined just
+Note: due to the form of the sLL equation, this fix has to be defined just
 before the nve/spin fix (and after all other magnetic fixes).
 As an example:
 

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_qeq_reaxff.rst

@@ -124,7 +124,7 @@ LAMMPS was built with that package. See the :doc:`Build package
 
 This fix does not correctly handle interactions involving multiple
 periodic images of the same atom.  Hence, it should not be used for
-periodic cell dimensions less than 10 angstroms.
+periodic cell dimensions less than 10 Angstroms.
 
 This fix may be used in combination with :doc:`fix efield <fix_efield>`
 and will apply the external electric field during charge equilibration,

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

@@ -301,7 +301,7 @@ and for mixed periodic and non-periodic boundaries.
 MSM is most competitive versus Ewald and PPPM when only relatively
 low accuracy forces, about 1e-4 relative error or less accurate,
 are needed. Note that use of a larger Coulombic cutoff (i.e. 15
-angstroms instead of 10 angstroms) provides better MSM accuracy for
+Angstroms instead of 10 Angstroms) provides better MSM accuracy for
 both the real space and grid computed forces.
 
 Currently calculation of the full pressure tensor in MSM is expensive.
@@ -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