Update from master

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)
@@ -100,7 +105,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
       set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "-xHost")
+      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
     endif()
   endif()
 endif()
@@ -849,8 +854,11 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
     find_package(Python COMPONENTS Interpreter)
   endif()
   if(Python_EXECUTABLE)
-    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
+    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/lib)
-    install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})")
+    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/src)
+    file(COPY ${LAMMPS_SOURCE_DIR}/version.h  DESTINATION ${CMAKE_BINARY_DIR}/python/src)
+    file(COPY ${LAMMPS_PYTHON_DIR}/README ${LAMMPS_PYTHON_DIR}/pyproject.toml ${LAMMPS_PYTHON_DIR}/setup.py ${LAMMPS_PYTHON_DIR}/lammps  DESTINATION ${CMAKE_BINARY_DIR}/python/lib)
+    install(CODE "if(\"\$ENV{DESTDIR}\" STREQUAL \"\")\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX})\n else()\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR})\n endif()")
   endif()
 endif()
 

cmake/Modules/Packages/KOKKOS.cmake

@@ -47,8 +47,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.6.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "0ec97fc0c356dd65bd2487defe81a7bf" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_MD5 "84991eca9f066383abe119a5bc7a11c4" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   ExternalProject_Add(kokkos_build
@@ -72,7 +72,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.6.01 REQUIRED CONFIG)
+  find_package(Kokkos 3.7.00 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
   target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.11.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.12.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "3791fe5081405c14aac07d4687f1cc58" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   enable_language(C)
@@ -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=${CMAKE_MAKE_PROGRAM}
@@ -70,22 +79,22 @@ if(DOWNLOAD_MDI)
     -Dplugins=ON
     -Dpython_plugins=${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 "")

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})
+  foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
+    get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
     add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
-          COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_SRC} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+            COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_FILE} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
             COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
             WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
-          MAIN_DEPENDENCY    ${MLIAP_CYTHON_SRC}
+            MAIN_DEPENDENCY    ${MLIAP_CYTHON_FILE}
             COMMENT "Generating C++ sources with cythonize...")
-  target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
     target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
+  endforeach()
+  target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
   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.fix10Oct.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 "766cebcc0e5c4b8430c2f3cd202d9905" 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()

cmake/presets/intel.cmake

@@ -1,4 +1,4 @@
-# preset that will enable Intel compilers with support for MPI and OpenMP (on Linux boxes)
+# preset that will enable the classic Intel compilers with support for MPI and OpenMP (on Linux boxes)
 
 set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
@@ -18,11 +18,11 @@ set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
 unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icc" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "icpc" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-qopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_Fortran_FLAGS "-qopenmp" CACHE STRING "" FORCE)
+set(OpenMP_Fortran_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
 

cmake/presets/oneapi.cmake

@@ -18,11 +18,11 @@ set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
 unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icx" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-qopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_Fortran_FLAGS "-qopenmp" CACHE STRING "" FORCE)
+set(OpenMP_Fortran_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
 

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "3 August 2022" "2022-8-3"
+.TH LAMMPS "1" "15 September 2022" "2022-9-15"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 3 August 2022
+\- Molecular Dynamics Simulator.  Version 15 September 2022
 
 .SH SYNOPSIS
 .B lmp

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)
@@ -1373,7 +1373,7 @@ Bibliography
    Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).
 
 **(Ziegler)**
-   J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
+   J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985.
 
 **(Zimmerman2004)**
    Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319.

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>`_
@@ -483,6 +483,9 @@ They must be specified in uppercase.
    *  - **Arch-ID**
       - **HOST or GPU**
       - **Description**
+   *  - NATIVE
+      - HOST
+      - Local machine
    *  - AMDAVX
       - HOST
       - AMD 64-bit x86 CPU (AVX 1)
@@ -522,9 +525,21 @@ They must be specified in uppercase.
    *  - BDW
       - HOST
       - Intel Broadwell Xeon E-class CPU (AVX 2 + transactional mem)
+   *  - SKL
+      - HOST
+      - Intel Skylake Client CPU
    *  - SKX
       - HOST
-      - Intel Sky Lake Xeon E-class HPC CPU (AVX512 + transactional mem)
+      - Intel Skylake Xeon Server CPU (AVX512)
+   *  - ICL
+      - HOST
+      - Intel Ice Lake Client CPU (AVX512)
+   *  - ICX
+      - HOST
+      - Intel Ice Lake Xeon Server CPU (AVX512)
+   *  - SPR
+      - HOST
+      - Intel Sapphire Rapids Xeon Server CPU (AVX512)
    *  - KNC
       - HOST
       - Intel Knights Corner Xeon Phi
@@ -596,7 +611,10 @@ They must be specified in uppercase.
       - AMD GPU MI100 GFX908
    *  - VEGA90A
       - GPU
-      - AMD GPU
+      - AMD GPU MI200 GFX90A
+   *  - INTEL_GEN
+      - GPU
+      - SPIR64-based devices, e.g. Intel GPUs, using JIT
    *  - INTEL_DG1
       - GPU
       - Intel Iris XeMAX GPU
@@ -611,9 +629,12 @@ They must be specified in uppercase.
       - Intel GPU Gen12LP
    *  - INTEL_XEHP
       - GPU
-      - Intel GPUs Xe-HP
+      - Intel GPU Xe-HP
+   *  - INTEL_PVC
+      - GPU
+      - Intel GPU Ponte Vecchio
 
-This list was last updated for version 3.5.0 of the Kokkos library.
+This list was last updated for version 3.7.0 of the Kokkos library.
 
 .. tabs::
 
@@ -1053,7 +1074,7 @@ 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_all.rst

@@ -15,7 +15,9 @@
 General commands
 ================
 
-An alphabetic list of general LAMMPS commands.
+An alphabetic list of general LAMMPS commands.  Note that style
+commands with many variants, can be more easily accessed via the small
+table above.
 
 .. table_from_list::
    :columns: 5

doc/src/Commands_fix.rst

@@ -166,6 +166,7 @@ OPT.
    * :doc:`orient/fcc <fix_orient>`
    * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`pafi <fix_pafi>`
+   * :doc:`pair <fix_pair>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`

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/Developer_updating.rst

@@ -328,7 +328,7 @@ removed so this update is **required** to avoid compilation failure.
 Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. versionchanged:: TBD
+.. versionchanged:: 15Sep2022
 
 This change splits the GLOBAL and PERATOM modes of fix STORE into two
 separate fixes STORE/GLOBAL and STORE/PERATOM.  There was very little
@@ -387,7 +387,7 @@ This change is **required** or else the code will not compile.
 Use Output::get_dump_by_id() instead of Output::find_dump()
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. versionchanged:: TBD
+.. versionchanged:: 15Sep2022
 
 The accessor function to individual dump style instances has been changed
 from ``Output::find_dump()`` returning the index of the dump instance in

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

@@ -86,6 +86,7 @@ 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_bpm.rst

@@ -33,46 +33,6 @@ reference state of a bond. Bonds that are created midway into a run,
 such as those created by pouring grains using :doc:`fix pour
 <fix_pour>`, are initialized on that timestep.
 
-As bonds can be broken between neighbor list builds, the
-:doc:`special_bonds <special_bonds>` command works differently for BPM
-bond styles. There are two possible settings which determine how pair
-interactions work between bonded particles.  First, one can turn off
-all pair interactions between bonded particles.  Unlike :doc:`bond
-quartic <bond_quartic>`, this is not done by subtracting pair forces
-during the bond computation but rather by dynamically updating the
-special bond list. This is the default behavior of BPM bond styles and
-is done by updating the 1-2 special bond list as bonds break.  To do
-this, LAMMPS requires :doc:`newton <newton>` bond off such that all
-processors containing an atom know when a bond breaks. Additionally,
-one must do either (A) or (B).
-
-A) Use the following special bond settings
-
-   .. code-block:: LAMMPS
-
-      special_bonds lj 0 1 1 coul 1 1 1
-
-   These settings accomplish two goals. First, they turn off 1-3 and 1-4
-   special bond lists, which are not currently supported for BPMs. As
-   BPMs often have dense bond networks, generating 1-3 and 1-4 special
-   bond lists is expensive.  By setting the lj weight for 1-2 bonds to
-   zero, this turns off pairwise interactions.  Even though there are no
-   charges in BPM models, setting a nonzero coul weight for 1-2 bonds
-   ensures all bonded neighbors are still included in the neighbor list
-   in case bonds break between neighbor list builds.
-
-B) Alternatively, one can simply overlay pair interactions such that all
-   bonded particles also feel pair interactions. This can be
-   accomplished by using the *overlay/pair* keyword present in all bpm
-   bond styles and by using the following special bond settings
-
-   .. code-block:: LAMMPS
-
-      special_bonds lj/coul 1 1 1
-
-See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
-more information.
-
 ----------
 
 Currently there are two types of bonds included in the BPM
@@ -91,12 +51,6 @@ This also requires a unique integrator :doc:`fix nve/bpm/sphere
 <fix_nve_bpm_sphere>` which numerically integrates orientation similar
 to :doc:`fix nve/asphere <fix_nve_asphere>`.
 
-To monitor the fracture of bonds in the system, all BPM bond styles
-have the ability to record instances of bond breakage to output using
-the :doc:`dump local <dump>` command. Additionally, one can use
-:doc:`compute nbond/atom <compute_nbond_atom>` to tally the current
-number of bonds per atom.
-
 In addition to bond styles, a new pair style :doc:`pair bpm/spring
 <pair_bpm_spring>` was added to accompany the bpm/spring bond
 style. This pair style is simply a hookean repulsion with similar
@@ -104,6 +58,73 @@ velocity damping as its sister bond style.
 
 ----------
 
+Bond data can be output using a combination of standard LAMMPS commands.
+A list of IDs for bonded atoms can be generated using the
+:doc:`compute property/local <compute_property_local>` command.
+Various properties of bonds can be computed using the
+:doc:`compute bond/local <compute_bond_local>` command. This
+command allows one to access data saved to the bond's history
+such as the reference length of the bond. More information on
+bond history data can be found on the documentation pages for the specific
+BPM bond styles. Finally, this data can be output using a :doc:`dump local <dump>`
+command. As one may output many columns from the same compute, the
+:doc:`dump modify <dump_modify>` *colname* option may be used to provide
+more helpful column names. An example of this procedure is found in
+/examples/bpm/pour/. External software, such as OVITO, can read these dump
+files to render bond data.
+
+----------
+
+As bonds can be broken between neighbor list builds, the
+:doc:`special_bonds <special_bonds>` command works differently for BPM
+bond styles. There are two possible settings which determine how pair
+interactions work between bonded particles.  First, one can overlay
+pair forces with bond forces such that all bonded particles also
+feel pair interactions. This can be accomplished by using the *overlay/pair*
+keyword present in all bpm bond styles and by using the following special
+bond settings
+
+   .. code-block:: LAMMPS
+
+      special_bonds lj/coul 1 1 1
+
+Alternatively, one can turn off all pair interactions between bonded
+particles. Unlike :doc:`bond quartic <bond_quartic>`, this is not done
+by subtracting pair forces during the bond computation but rather by
+dynamically updating the special bond list. This is the default behavior
+of BPM bond styles and is done by updating the 1-2 special bond list as
+bonds break.  To do this, LAMMPS requires :doc:`newton <newton>` bond off
+such that all processors containing an atom know when a bond breaks.
+Additionally, one must use the following special bond settings
+
+   .. code-block:: LAMMPS
+
+      special_bonds lj 0 1 1 coul 1 1 1
+
+These settings accomplish two goals. First, they turn off 1-3 and 1-4
+special bond lists, which are not currently supported for BPMs. As
+BPMs often have dense bond networks, generating 1-3 and 1-4 special
+bond lists is expensive.  By setting the lj weight for 1-2 bonds to
+zero, this turns off pairwise interactions.  Even though there are no
+charges in BPM models, setting a nonzero coul weight for 1-2 bonds
+ensures all bonded neighbors are still included in the neighbor list
+in case bonds break between neighbor list builds.
+
+To monitor the fracture of bonds in the system, all BPM bond styles
+have the ability to record instances of bond breakage to output using
+the :doc:`dump local <dump>` command. Since one may frequently output
+a list of broken bonds and the time they broke, the
+:doc:`dump modify <dump_modify>` option *header no* may be useful to
+avoid repeatedly printing the header of the dump file. An example of
+this procedure is found in /examples/bpm/impact/. Additionally,
+one can use :doc:`compute nbond/atom <compute_nbond_atom>` to tally the
+current number of bonds per atom.
+
+See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
+more information.
+
+----------
+
 While LAMMPS has many utilities to create and delete bonds, *only*
 the following are currently compatible with BPM bond styles:
 

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_type_labels.rst

@@ -1,7 +1,7 @@
 Type labels
 ===========
 
-.. versionadded:: TBD
+.. versionadded:: 15Sep2022
 
 Each atom in LAMMPS has an associated numeric atom type. Similarly,
 each bond, angle, dihedral, and improper is assigned a bond type,

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.
@@ -276,7 +278,7 @@ the barostat as outlined in:
 
 N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
 accurately describe the structure, pressure, and compressibility of
-molecular liquids," J. Chem. Phys. 143, 243148 (2015).
+molecular liquids", J. Chem. Phys. 143, 243148 (2015).
 
 **Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The
 Pennsylvania State University)
@@ -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::
 
@@ -495,7 +495,7 @@ run:
    write_dump group-ID dumpstyle dumpfile arg1 arg2 ...
 
 Note that the specified restartfile and dumpfile names may contain
-wild-card characters ("\*","%") as explained on the
+wild-card characters ("\*" or "%") as explained on the
 :doc:`read_restart <read_restart>` and :doc:`write_dump <write_dump>` doc
 pages.  The use of "%" means that a parallel restart file and/or
 parallel dump file can be read and/or written.  Note that a filename

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

@@ -536,6 +536,6 @@ supported.
 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., 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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -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/angle_mesocnt.rst

@@ -24,7 +24,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 15Sep2022
 
 The *mesocnt* angle style uses the potential
 

doc/src/atom_style.rst

@@ -91,7 +91,7 @@ quantities.
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *charge*     | charge                                              | atomic system with charges           |
 +--------------+-----------------------------------------------------+--------------------------------------+
-| *dielectric* | dipole, area, curvature                             | system with surface polarization     |
+| *dielectric* | normx normy normz area/patch ed em epsilon curv     | system with surface polarization     |
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *dipole*     | charge and dipole moment                            | system with dipolar particles        |
 +--------------+-----------------------------------------------------+--------------------------------------+
@@ -180,16 +180,21 @@ vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
 with its orientation.
 
 For the *dielectric* style, each particle can be either a physical
-particle (e.g. an ion), or an interface particle representing a
+particle (e.g. an ion), or an interface particle representing a boundary
-boundary element. For physical particles, the per-particle properties
+element between two regions of different dielectric constant. For
-are the same as atom_style full.  For interface particles, in addition
+interface particles, in addition to the properties associated with
-to these properties, each particle also has an area, a normal unit
+atom_style full, each particle also should be assigned a normal unit
-vector, a mean local curvature, the mean and difference of the
+vector (defined by normx, normy, normz), an area (area/patch), the
-dielectric constants of two sides of the interface, and the local
+difference and mean of the dielectric constants of two sides of the
-dielectric constant at the boundary element.  The distinction between
+interface along the direction of the normal vector (ed and em), the
-the physical and interface particles is only meaningful when :doc:`fix
+local dielectric constant at the boundary element (epsilon), and a mean
-polarize <fix_polarize>` commands are applied to the interface
+local curvature (curv).  Physical particles must be assigned these
-particles.
+values, as well, but only their local dielectric constants will be used;
+see documentation for associated :doc:`pair styles <pair_dielectric>`
+and :doc:`fixes <fix_polarize>`.  The distinction between the physical
+and interface particles is only meaningful when :doc:`fix polarize
+<fix_polarize>` commands are applied to the interface particles. This
+style is part of the DIELECTRIC package.
 
 For the *dipole* style, a point dipole is defined for each point
 particle.  Note that if you wish the particles to be finite-size

doc/src/bond_bpm_rotational.rst

@@ -138,15 +138,14 @@ the *overlay/pair* keyword. These settings require specific
 restrictions.  Further details can be found in the `:doc: how to
 <Howto_BPM>` page on BPMs.
 
-If the *store/local* keyword is used, this fix will track bonds that
+If the *store/local* keyword is used, an internal fix will track bonds that
 break during the simulation. Whenever a bond breaks, data is processed
 and transferred to an internal fix labeled *fix_ID*. This allows the
-local data to be accessed by other LAMMPS commands.
+local data to be accessed by other LAMMPS commands. Following this optional
-Following any optional keyword/value arguments, a list of one or more
+keyword, a list of one or more attributes is specified.  These include the
-attributes is specified.  These include the IDs of the two atoms in
+IDs of the two atoms in the bond. The other attributes for the two atoms
-the bond. The other attributes for the two atoms include the timestep
+include the timestep during which the bond broke and the current/initial
-during which the bond broke and the current/initial center of mass
+center of mass position of the two atoms.
-position of the two atoms.
 
 Data is continuously accumulated over intervals of *N*
 timesteps. At the end of each interval, all of the saved accumulated
@@ -177,29 +176,38 @@ Restart and other info
 
 This bond style writes the reference state of each bond to
 :doc:`binary restart files <restart>`. Loading a restart file will
-properly resume bonds.
+properly resume bonds. However, the reference state is NOT
+written to data files. Therefore reading a data file will not
+restore bonds and will cause their reference states to be redefined.
 
-The single() function of these pair styles returns 0.0 for the energy
+If the *store/local* option is used, an internal fix will calculate
-of a pairwise interaction, since energy is not conserved in these
+a local vector or local array depending on the number of input values.
-dissipative potentials.  It also returns only the normal component of
+The length of the vector or number of rows in the array is the number
-the pairwise interaction force.
+of recorded, broken bonds.  If a single input is specified, a local
-
+vector is produced. If two or more inputs are specified, a local array
-The accumulated data is not written to restart files and should be
+is produced where the number of columns = the number of inputs.  The
-output before a restart file is written to avoid missing data.
+vector or array can be accessed by any command that uses local values
-
+from a compute as input. See the :doc:`Howto output <Howto_output>` page
-The internal fix calculates a local vector or local array depending on the
+for an overview of LAMMPS output options.
-number of input values.  The length of the vector or number of rows in
-the array is the number of recorded, lost interactions.  If a single
-input is specified, a local vector is produced.  If two or more inputs
-are specified, a local array is produced where the number of columns =
-the number of inputs.  The vector or array can be accessed by any
-command that uses local values from a compute as input.  See the
-:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
-output options.
 
 The vector or array will be floating point values that correspond to
 the specified attribute.
 
+The single() function of this bond style returns 0.0 for the energy
+of a bonded interaction, since energy is not conserved in these
+dissipative potentials.  It also returns only the normal component of
+the bonded interaction force.  However, the single() function also
+calculates 7 extra bond quantities.  The first 4 are data from the
+reference state of the bond including the initial distance between particles
+:math:`r_0` followed by the :math:`x`, :math:`y`, and :math:`z` components
+of the initial unit vector pointing to particle I from particle J. The next 3
+quantities (5-7) are the  :math:`x`, :math:`y`, and :math:`z` components
+of the total force, including normal and tangential contributions, acting
+on particle I.
+
+These extra quantities can be accessed by the :doc:`compute bond/local <compute_bond_local>`
+command, as *b1*, *b2*, ..., *b7*\ .
+
 Restrictions
 """"""""""""
 

doc/src/bond_bpm_spring.rst

@@ -103,15 +103,14 @@ the *overlay/pair* keyword. These settings require specific
 restrictions.  Further details can be found in the `:doc: how to
 <Howto_BPM>` page on BPMs.
 
-If the *store/local* keyword is used, this fix will track bonds that
+If the *store/local* keyword is used, an internal fix will track bonds that
 break during the simulation. Whenever a bond breaks, data is processed
 and transferred to an internal fix labeled *fix_ID*. This allows the
-local data to be accessed by other LAMMPS commands.
+local data to be accessed by other LAMMPS commands. Following this optional
-Following any optional keyword/value arguments, a list of one or more
+keyword, a list of one or more attributes is specified.  These include the
-attributes is specified.  These include the IDs of the two atoms in
+IDs of the two atoms in the bond. The other attributes for the two atoms
-the bond. The other attributes for the two atoms include the timestep
+include the timestep during which the bond broke and the current/initial
-during which the bond broke and the current/initial center of mass
+center of mass position of the two atoms.
-position of the two atoms.
 
 Data is continuously accumulated over intervals of *N*
 timesteps. At the end of each interval, all of the saved accumulated
@@ -141,28 +140,30 @@ Restart and other info
 
 This bond style writes the reference state of each bond to
 :doc:`binary restart files <restart>`. Loading a restart
-file will properly resume bonds.
+file will properly restore bonds. However, the reference state is NOT
+written to data files. Therefore reading a data file will not
+restore bonds and will cause their reference states to be redefined.
 
-The single() function of these pair styles returns 0.0 for the energy
+If the *store/local* option is used, an internal fix will calculate
-of a pairwise interaction, since energy is not conserved in these
+a local vector or local array depending on the number of input values.
-dissipative potentials.
+The length of the vector or number of rows in the array is the number
-
+of recorded, broken bonds.  If a single input is specified, a local
-The accumulated data is not written to restart files and should be
+vector is produced. If two or more inputs are specified, a local array
-output before a restart file is written to avoid missing data.
+is produced where the number of columns = the number of inputs.  The
-
+vector or array can be accessed by any command that uses local values
-The internal fix calculates a local vector or local array depending on the
+from a compute as input. See the :doc:`Howto output <Howto_output>` page
-number of input values.  The length of the vector or number of rows in
+for an overview of LAMMPS output options.
-the array is the number of recorded, lost interactions.  If a single
-input is specified, a local vector is produced.  If two or more inputs
-are specified, a local array is produced where the number of columns =
-the number of inputs.  The vector or array can be accessed by any
-command that uses local values from a compute as input.  See the
-:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
-output options.
 
 The vector or array will be floating point values that correspond to
 the specified attribute.
 
+The single() function of this bond style returns 0.0 for the energy
+of a bonded interaction, since energy is not conserved in these
+dissipative potentials.  The single() function also calculates an
+extra bond quantity, the initial distance :math:`r_0`. This
+extra quantity can be accessed by the
+:doc:`compute bond/local <compute_bond_local>` command as *b1*\ .
+
 Restrictions
 """"""""""""
 

doc/src/bond_mesocnt.rst

@@ -22,7 +22,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 15Sep2022
 
 The *mesocnt* bond style is a wrapper for the :doc:`harmonic
 <bond_harmonic>` style, and uses the potential

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_angmom_chunk.rst

@@ -78,7 +78,7 @@ These values can be accessed by any command that uses global array
 values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The array values are "intensive."  The array values will be in
+The array values are "intensive".  The array values will be in
 mass-velocity-distance :doc:`units <units>`.
 
 Restrictions

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_bond_local.rst

@@ -13,7 +13,7 @@ Syntax
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * bond/local = style name of this compute command
 * one or more values may be appended
-* value = *dist* or *dx* or *dy* or *dz* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name*
+* value = *dist* or *dx* or *dy* or *dz* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name* or *bN*
 
 .. parsed-literal::
 
@@ -29,6 +29,7 @@ Syntax
      *omega* = magnitude of bond angular velocity
      *velvib* = vibrational velocity along the bond length
      *v_name* = equal-style variable with name (see below)
+     *bN* = bond style specific quantities for allowed N values
 
 * zero or more keyword/args pairs may be appended
 * keyword = *set*
@@ -47,7 +48,7 @@ Examples
    compute 1 all bond/local engpot
    compute 1 all bond/local dist engpot force
 
-   compute 1 all bond/local dist fx fy fz
+   compute 1 all bond/local dist fx fy fz b1 b2
 
    compute 1 all bond/local dist v_distsq set dist d
 
@@ -147,6 +148,19 @@ those quantities via the :doc:`compute reduce <compute_reduce>` command
 with thermo output, and the :doc:`fix ave/histo <fix_ave_histo>`
 command will histogram the length\ :math:`^2` values and write them to a file.
 
+A bond style may define additional bond quantities which can be
+accessed as *b1* to *bN*, where N is defined by the bond style.  Most
+bond styles do not define any additional quantities, so N = 0.  An
+example of ones that do are the :doc:`BPM bond styles <Howto_bpm>`
+which store the reference state between two particles. See
+individual bond styles for details.
+
+When using *bN* with bond style *hybrid*, the output will be the Nth
+quantity from the sub-style that computes the bonded interaction
+(based on bond type).  If that sub-style does not define a *bN*,
+the output will be 0.0.  The maximum allowed N is the maximum number
+of quantities provided by any sub-style.
+
 ----------
 
 The local data stored by this command is generated by looping over all

doc/src/compute_born_matrix.rst

@@ -182,7 +182,7 @@ by any command that uses global values from a compute as input. See
 the :doc:`Howto output <Howto_output>` doc page for an overview of
 LAMMPS output options.
 
-The array values calculated by this compute are all "extensive."
+The array values calculated by this compute are all "extensive".
 
 Restrictions
 """"""""""""

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_com.rst

@@ -49,7 +49,7 @@ accessed by indices 1--3 by any command that uses global vector values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.
 
-The vector values are "intensive."  The vector values will be in
+The vector values are "intensive".  The vector values will be in
 distance :doc:`units <units>`.
 
 Restrictions

doc/src/compute_com_chunk.rst

@@ -77,7 +77,7 @@ values can be accessed by any command that uses global array values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.
 
-The array values are "intensive."  The array values will be in
+The array values are "intensive".  The array values will be in
 distance :doc:`units <units>`.
 
 Restrictions

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_dipole.rst

@@ -54,7 +54,7 @@ the computed dipole moment and a global vector of length 3 with the
 dipole vector.  See the :doc:`Howto output <Howto_output>` page for
 an overview of LAMMPS output options.
 
-The computed values are "intensive."  The array values will be in
+The computed values are "intensive".  The array values will be in
 dipole units (i.e., charge :doc:`units <units>` times distance
 :doc:`units <units>`).
 

doc/src/compute_dipole_chunk.rst

@@ -86,7 +86,7 @@ chunk. These values can be accessed by any command that uses global
 array values from a compute as input.  See the :doc:`Howto output
 <Howto_output>` page for an overview of LAMMPS output options.
 
-The array values are "intensive."  The array values will be in
+The array values are "intensive".  The array values will be in
 dipole units (i.e., charge :doc:`units <units>` times distance
 :doc:`units <units>`).
 

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_erotate_asphere.rst

@@ -48,7 +48,7 @@ used by any command that uses a global scalar value from a compute as
 input.  See the :doc:`Howto output <Howto_output>` page for an
 overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "extensive."  The
+The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_erotate_rigid.rst

@@ -48,7 +48,7 @@ of all the rigid bodies).  This value can be used by any command that
 uses a global scalar value from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "extensive."  The
+The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_erotate_sphere.rst

@@ -44,7 +44,7 @@ used by any command that uses a global scalar value from a compute as
 input.  See the :doc:`Howto output <Howto_output>` page for an
 overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "extensive."  The
+The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_event_displace.rst

@@ -40,7 +40,7 @@ further than the threshold distance.
    If the system is undergoing significant center-of-mass motion,
    due to thermal motion, an external force, or an initial net momentum,
    then this compute will not be able to distinguish that motion from
-   local atom displacements and may generate "false positives."
+   local atom displacements and may generate "false positives".
 
 Output info
 """""""""""
@@ -50,7 +50,7 @@ used by any command that uses a global scalar value from a compute as
 input.  See the :doc:`Howto output <Howto_output>` page for an
 overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "intensive."  The
+The scalar value calculated by this compute is "intensive".  The
 scalar value will be a 0 or 1 as explained above.
 
 Restrictions

doc/src/compute_fep.rst

@@ -299,7 +299,7 @@ These output results can be used by any command that uses a global
 scalar or vector from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options. For example, the computed values can be averaged using :doc:`fix ave/time <fix_ave_time>`.
 
-The values calculated by this compute are "extensive."
+The values calculated by this compute are "extensive".
 
 Restrictions
 """"""""""""

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_group_group.rst

@@ -140,7 +140,7 @@ vector values from a compute as input.  See the
 options.
 
 Both the scalar and vector values calculated by this compute are
-"extensive."  The scalar value will be in energy :doc:`units <units>`.
+"extensive".  The scalar value will be in energy :doc:`units <units>`.
 The vector values will be in force :doc:`units <units>`.
 
 Restrictions

doc/src/compute_gyration.rst

@@ -69,7 +69,7 @@ vector values from a compute as input.  See the :doc:`Howto output <Howto_output
 options.
 
 The scalar and vector values calculated by this compute are
-"intensive."  The scalar and vector values will be in distance and
+"intensive".  The scalar and vector values will be in distance and
 distance\ :math:`^2` :doc:`units <units>`, respectively.
 
 Restrictions

doc/src/compute_gyration_shape.rst

@@ -78,7 +78,7 @@ vector values from a compute as input.  See the
 options.
 
 The vector values calculated by this compute are
-"intensive."  The first five vector values will be in
+"intensive".  The first five vector values will be in
 distance\ :math:`2` :doc:`units <units>` while the sixth one is dimensionless.
 
 Restrictions

doc/src/compute_gyration_shape_chunk.rst

@@ -80,7 +80,7 @@ See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
 output options.
 
 The array calculated by this compute is
-"intensive."  The first five columns will be in
+"intensive".  The first five columns will be in
 distance\ :math:`^2` :doc:`units <units>` while the sixth one is dimensionless.
 
 Restrictions

doc/src/compute_heat_flux.rst

@@ -142,14 +142,14 @@ command that uses global vector values from a compute as input.
 See the :doc:`Howto output <Howto_output>` documentation for an overview of
 LAMMPS output options.
 
-The vector values calculated by this compute are "extensive," meaning
+The vector values calculated by this compute are "extensive", meaning
 they scale with the number of atoms in the simulation.  They can be
-divided by the appropriate volume to get a flux, which would then be
+divided by the appropriate volume to get a flux, which would then be an
-an "intensive" value, meaning independent of the number of atoms in
+"intensive" value, meaning independent of the number of atoms in the
-the simulation.  Note that if the compute is "all," then the
+simulation.  Note that if the compute group is "all", then the
-appropriate volume to divide by is the simulation box volume.
+appropriate volume to divide by is the simulation box volume.  However,
-However, if a sub-group is used, it should be the volume containing
+if a group with a subset of atoms is used, it should be the volume
-those atoms.
+containing those atoms.
 
 The vector values will be in energy\*velocity :doc:`units <units>`.  Once
 divided by a volume the units will be that of flux, namely

doc/src/compute_hma.rst

@@ -172,7 +172,7 @@ requested as arguments to the command (the potential energy, pressure and/or hea
 capacity).  The elements of the vector can be accessed by indices 1--n by any
 command that uses global vector values as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options.
 
-The vector values calculated by this compute are "extensive."  The
+The vector values calculated by this compute are "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_inertia_chunk.rst

@@ -84,7 +84,7 @@ by any command that uses global array values from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The array values are "intensive."  The array values will be in
+The array values are "intensive".  The array values will be in
 mass\*distance\ :math:`^2` :doc:`units <units>`.
 
 Restrictions

doc/src/compute_ke.rst

@@ -52,7 +52,7 @@ can be used by any command that uses a global scalar value from a
 compute as input.  See the :doc:`Howto output <Howto_output>` doc page
 for an overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "extensive."  The
+The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_ke_rigid.rst

@@ -48,7 +48,7 @@ global scalar value from a compute as input.  See the
 :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "extensive."  The
+The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_momentum.rst

@@ -37,7 +37,7 @@ length 3. This value can be used by any command that uses a global
 vector value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The vector value calculated by this compute is "extensive." The vector
+The vector value calculated by this compute is "extensive". The vector
 value will be in mass\*velocity :doc:`units <units>`.
 
 Restrictions

doc/src/compute_msd.rst

@@ -105,7 +105,7 @@ accessed by indices 1--4 by any command that uses global vector values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.
 
-The vector values are "intensive."  The vector values will be in
+The vector values are "intensive".  The vector values will be in
 distance\ :math:`^2` :doc:`units <units>`.
 
 Restrictions