Merge pull request #3567 from akohlmey/next_patch_release

Set version strings for next patch release

.github/CODEOWNERS

@@ -13,40 +13,45 @@ lib/kim/*             @ellio167
 lib/mesont/*          @iafoss
 
 # whole packages
+src/ADIOS/*           @pnorbert
 src/AMOEBA/*          @sjplimp
-src/COMPRESS/*        @rbberger
-src/GPU/*             @ndtrung81
-src/KOKKOS/*          @stanmoore1
-src/KIM/*             @ellio167
-src/LATTE/*           @cnegre
-src/MLIAP/*           @athomps
-src/SNAP/*            @athomps
-src/SPIN/*            @julient31
+src/BPM/*             @jtclemm
 src/BROWNIAN/*        @samueljmcameron
 src/CG-DNA/*          @ohenrich
 src/CG-SPICA/*        @yskmiyazaki
 src/COLVARS/*         @giacomofiorin
+src/COMPRESS/*        @rbberger
 src/DIELECTRIC/*      @ndtrung81
 src/ELECTRODE/*       @ludwig-ahrens
 src/FEP/*             @agiliopadua
-src/ML-HDNNP/*        @singraber
+src/GPU/*             @ndtrung81
+src/GRANULAR/*        @jtclemm @dsbolin
 src/INTEL/*           @wmbrownintel
+src/KIM/*             @ellio167
+src/KOKKOS/*          @stanmoore1
+src/LATTE/*           @cnegre
 src/MANIFOLD/*        @Pakketeretet2
-src/MDI/*             @taylor-a-barnes
+src/MDI/*             @taylor-a-barnes @sjplimp
 src/MEAM/*            @martok
 src/MESONT/*          @iafoss
+src/ML-HDNNP/*        @singraber
+src/ML-IAP/*          @athomps
+src/ML-PACE/*         @yury-lysogorskiy
+src/ML-POD/*          @exapde @rohskopf
 src/MOFFF/*           @hheenen
 src/MOLFILE/*         @akohlmey
 src/NETCDF/*          @pastewka
-src/ML-PACE/*         @yury-lysogorskiy
-src/PLUMED/*          @gtribello
-src/PHONON/*          @lingtikong
-src/PTM/*             @pmla
 src/OPENMP/*          @akohlmey
+src/PHONON/*          @lingtikong
+src/PLUGIN/*          @akohlmey
+src/PLUMED/*          @gtribello
+src/PTM/*             @pmla
 src/QMMM/*            @akohlmey
-src/REAXFF/*          @hasanmetin @stanmoore1
 src/REACTION/*        @jrgissing
+src/REAXFF/*          @hasanmetin @stanmoore1
 src/SCAFACOS/*        @rhalver
+src/SNAP/*            @athomps
+src/SPIN/*            @julient31
 src/TALLY/*           @akohlmey
 src/UEF/*             @danicholson
 src/VTK/*             @rbberger
@@ -59,6 +64,8 @@ src/MANYBODY/pair_atm.*             @sergeylishchuk
 src/REPLICA/*_grem.*                @dstelter92
 src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
 src/MISC/*_tracker.*                @jtclemm
+src/MC/fix_gcmc.*                   @athomps
+src/MC/fix_sgcmc.*                  @athomps
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp
@@ -120,27 +127,32 @@ src/dump_movie.*          @akohlmey
 src/exceptions.h          @rbberger
 src/fix_nh.*              @athomps
 src/info.*                @akohlmey @rbberger
-src/timer.*               @akohlmey
 src/min*                  @sjplimp @stanmoore1
+src/platform.*            @akohlmey
+src/timer.*               @akohlmey
 src/utils.*               @akohlmey @rbberger
 src/verlet.*              @sjplimp @stanmoore1
 src/math_eigen_impl.h     @jewettaij
 
 # tools
-tools/msi2lmp/*       @akohlmey
+tools/coding_standard/* @akohlmey @rbberger
 tools/emacs/*         @HaoZeke
-tools/singularity/*   @akohlmey @rbberger
-tools/coding_standard/* @rbberger
-tools/valgrind/*      @akohlmey
-tools/swig/*          @akohlmey
+tools/lammps-shell/*  @akohlmey
+tools/msi2lmp/*       @akohlmey
 tools/offline/*       @rbberger
+tools/singularity/*   @akohlmey @rbberger
+tools/swig/*          @akohlmey
+tools/valgrind/*      @akohlmey
 tools/vim/*           @hammondkd
 
 # tests
-unittest/*            @akohlmey @rbberger
+unittest/*            @akohlmey
 
 # cmake
 cmake/*               @junghans @rbberger
+cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
+cmake/Modules/MPI4WIN.cmake @akohlmey
+cmake/Modules/OpenCLLoader.cmake @akohlmey
 cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
 cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
 cmake/presets/*.cmake @akohlmey
@@ -149,13 +161,12 @@ cmake/presets/*.cmake @akohlmey
 python/*              @rbberger
 
 # fortran
-fortran/*             @akohlmey
+fortran/*             @akohlmey @hammondkd
 
 # docs
-doc/utils/*/*         @rbberger
-doc/Makefile          @rbberger
-doc/README            @rbberger
+doc/*                 @akohlmey
 examples/plugin/*     @akohlmey
+examples/PACKAGES/pace/plugin/*     @akohlmey
 
 # for releases
 src/version.h         @sjplimp

.github/ISSUE_TEMPLATE/help_request.md

@@ -1,6 +1,6 @@
 ---
 name: Request for Help
-about: "Don't post help requests here, email the lammps-users mailing list"
+about: "Don't post help requests here, post in the LAMMPS forum"
 title: ""
 labels: invalid
 assignees: ''
@@ -8,8 +8,9 @@ assignees: ''
 ---
 
 Please **do not** post requests for help (e.g. with installing or using LAMMPS) here.
-Instead send an e-mail to the lammps-users mailing list.
+Instead, you can post to the LAMMPS category in the Materials Science Community
+Discourse forum at: https://matsci.org/lammps/
 
 This issue tracker is for tracking LAMMPS development related issues only.
 
-Thanks for your cooperation.
+Thank you in advance for your cooperation.

.github/workflows/compile-msvc.yml

@@ -26,15 +26,19 @@ jobs:
     - name: Select Python version
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.11'
 
     - name: Building LAMMPS via CMake
       shell: bash
       run: |
         python3 -m pip install numpy
         python3 -m pip install pyyaml
+        nuget install MSMPIsdk
+        nuget install MSMPIDIST
         cmake -C cmake/presets/windows.cmake \
               -D PKG_PYTHON=on \
+              -D WITH_PNG=off \
+              -D WITH_JPEG=off \
               -S cmake -B build \
               -D BUILD_SHARED_LIBS=on \
               -D LAMMPS_EXCEPTIONS=on \
@@ -50,4 +54,4 @@ jobs:
     - name: Run Unit Tests
       working-directory: build
       shell: bash
-      run: ctest -V -C Release
+      run: ctest -V -C Release -E FixTimestep:python_move_nve

README

@@ -16,8 +16,8 @@ National Laboratories, a US Department of Energy facility, with
 funding from the DOE.  It is an open-source code, distributed freely
 under the terms of the GNU Public License (GPL) version 2.
 
-The primary author of the code is Steve Plimpton, who can be emailed
-at sjplimp@sandia.gov.  The LAMMPS WWW Site at www.lammps.org has
+The code is maintained by the LAMMPS development team who can be emailed
+at developers@lammps.org.  The LAMMPS WWW Site at www.lammps.org has
 more information about the code and its uses.
 
 The LAMMPS distribution includes the following files and directories:

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
-the LAMMPS project
-[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
+either a user mistake or a bug in the code.  Bugs can be reported in the
+LAMMPS project [issue tracker on
+GitHub](https://github.com/lammps/lammps/issues).
 
 To mitigate issues with using homoglyphs or bidirectional reordering in
 unicode, which have been demonstrated as a vector to obfuscate and hide
@@ -30,10 +30,18 @@ for unicode characters and only all-ASCII source code is accepted.
 
 # Version Updates
 
-LAMMPS follows continuous release development model.  We aim to keep all
-release versions (stable or patch) fully functional and employ a variety
-of automatic testing procedures to detect failures of existing
-functionality from adding new features before releases are made.  Thus
-bugfixes and updates are only integrated into the current development
-branch and thus the next (patch) release and users are recommended to
-update regularly.
+LAMMPS follows continuous release development model.  We aim to keep to
+keep the development version (develop branch) always fully functional
+and employ a variety of automatic testing procedures to detect failures
+of existing functionality from adding or modifying features.  Most of
+those tests are run on pull requests *before* merging to the development
+branch.  The develop branch is protected, so all changes *must* be
+submitted as a pull request and thus cannot avoid the automated tests.
+
+Additional tests are run *after* merging.  Before releases are made
+*all* tests must have cleared.  Then a release tag is applied and the
+release branch fast-forwarded to that tag.  Bug fixes and updates are
+applied to the current development branch and thus will be available in
+the next (patch) release.  For stable releases, selected bug fixes are
+back-ported and occasionally published as update releases.  There are
+only updates to the latest stable release.

cmake/CMakeLists.txt

@@ -7,11 +7,20 @@ cmake_minimum_required(VERSION 3.10)
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
 endif()
+# set policy to silence warnings about ignoring  ${CMAKE_REQUIRED_LIBRARIES} but use it
+if(POLICY CMP0075)
+  cmake_policy(SET CMP0075 NEW)
+endif()
 # set policy to silence warnings about missing executable permissions in
 # pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
 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 +109,7 @@ 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()
@@ -257,6 +266,7 @@ set(STANDARD_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-POD
   MOFFF
   MOLECULE
   MOLFILE
@@ -307,6 +317,15 @@ if(PKG_ADIOS)
   # script that defines the MPI::MPI_C target
   enable_language(C)
   find_package(ADIOS2 REQUIRED)
+  if(BUILD_MPI)
+    if(NOT ADIOS2_HAVE_MPI)
+      message(FATAL_ERROR "ADIOS2 must be built with MPI support when LAMMPS has MPI enabled")
+    endif()
+  else()
+    if(ADIOS2_HAVE_MPI)
+      message(FATAL_ERROR "ADIOS2 must be built without MPI support when LAMMPS has MPI disabled")
+    endif()
+  endif()
   target_link_libraries(lammps PRIVATE adios2::adios2)
 endif()
 
@@ -380,9 +399,9 @@ pkg_depends(EXTRA-MOLECULE MOLECULE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
-find_package(OpenMP QUIET)
-if(OpenMP_FOUND)
-  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+find_package(OpenMP COMPONENTS CXX QUIET)
+if(OpenMP_CXX_FOUND)
+  check_omp_h_include()
   if(HAVE_OMP_H_INCLUDE)
     set(BUILD_OMP_DEFAULT ON)
   endif()
@@ -391,8 +410,8 @@ endif()
 option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
 
 if(BUILD_OMP)
-  find_package(OpenMP REQUIRED)
-  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  find_package(OpenMP COMPONENTS CXX REQUIRED)
+  check_omp_h_include()
   if(NOT HAVE_OMP_H_INCLUDE)
     message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
   endif()
@@ -414,7 +433,7 @@ if(BUILD_OMP)
   target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
-if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
+if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_LATTE OR PKG_ELECTRODE)
   enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
@@ -620,7 +639,7 @@ foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
   endif()
 endforeach()
 
-if(PKG_ELECTRODE)
+if(PKG_ELECTRODE OR PKG_ML-POD)
   target_link_libraries(lammps PRIVATE ${LAPACK_LIBRARIES})
 endif()
 
@@ -649,7 +668,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -722,18 +741,17 @@ list(FIND LANGUAGES "Fortran" _index)
 if(_index GREATER -1)
   target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
-set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
-  input.h info.h kspace.h lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h
-  pair.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
-if(LAMMPS_EXCEPTIONS)
-  list(APPEND LAMMPS_CXX_HEADERS exceptions.h)
-endif()
+set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h command.h compute.h dihedral.h domain.h
+  error.h exceptions.h fix.h force.h group.h improper.h input.h info.h kspace.h lammps.h lattice.h
+  library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h pair.h
+  platform.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
+set(LAMMPS_FMT_HEADERS core.h format.h)
 
 set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
 set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
 set_target_properties(lammps PROPERTIES PREFIX "lib")
 target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps>)
-file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt)
 foreach(_HEADER ${LAMMPS_CXX_HEADERS})
   add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
   add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
@@ -742,6 +760,14 @@ foreach(_HEADER ${LAMMPS_CXX_HEADERS})
     install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
   endif()
 endforeach()
+foreach(_HEADER ${LAMMPS_FMT_HEADERS})
+  add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER})
+  add_custom_target(fmt_${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER})
+  add_dependencies(lammps fmt_${_HEADER})
+  if(BUILD_SHARED_LIBS)
+    install(FILES ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/fmt)
+  endif()
+endforeach()
 target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
 add_library(LAMMPS::lammps ALIAS lammps)
 get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS)
@@ -849,8 +875,11 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
     find_package(Python COMPONENTS Interpreter)
   endif()
   if(Python_EXECUTABLE)
-    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
-    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/lib)
+    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()
 
@@ -961,9 +990,6 @@ if(PKG_GPU)
   endif()
   message(STATUS "GPU precision:            ${GPU_PREC}")
 endif()
-if(PKG_KOKKOS)
-  message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
-endif()
 if(PKG_KSPACE)
   message(STATUS "<<< FFT settings >>>
 -- Primary FFT lib:  ${FFT}")

cmake/Modules/FindClangFormat.cmake

@@ -1,5 +1,10 @@
 # Find clang-format
 find_program(ClangFormat_EXECUTABLE NAMES clang-format
+                                          clang-format-15.0
+                                          clang-format-14.0
+                                          clang-format-13.0
+                                          clang-format-12.0
+                                          clang-format-11.0
                                           clang-format-10.0
                                           clang-format-9.0
                                           clang-format-8.0
@@ -14,19 +19,27 @@ if(ClangFormat_EXECUTABLE)
                   OUTPUT_VARIABLE clang_format_version
                   ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-
-  if(clang_format_version MATCHES "^clang-format version .*")
-    # Arch Linux
+  if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*")
+    # Arch Linux output:
     # clang-format version 10.0.0
-
-    # Ubuntu 18.04 LTS Output
+    #
+    # Ubuntu 18.04 LTS output:
     # clang-format version 6.0.0-1ubuntu2 (tags/RELEASE_600/final)
-    string(REGEX REPLACE "clang-format version ([0-9.]+).*"
-                         "\\1"
+    #
+    # Ubuntu 20.04 LTS output:
+    # clang-format version 10.0.0-4ubuntu1
+    #
+    # Ubuntu 22.04 LTS output:
+    # Ubuntu clang-format version 14.0.0-1ubuntu1
+    #
+    # Fedora 36 output:
+    # clang-format version 14.0.5 (Fedora 14.0.5-1.fc36)
+    string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*"
+                         "\\2"
                          ClangFormat_VERSION
                          "${clang_format_version}")
   elseif(clang_format_version MATCHES ".*LLVM version .*")
-    # CentOS 7 Output
+    # CentOS 7 output:
     # LLVM (http://llvm.org/):
     #   LLVM version 3.4.2
     #   Optimized build.

cmake/Modules/FindCythonize.cmake

@@ -22,7 +22,7 @@ endif()
 if(Python_EXECUTABLE)
   get_filename_component(_python_path ${Python_EXECUTABLE} PATH)
   find_program(Cythonize_EXECUTABLE
-    NAMES cythonize3 cythonize cythonize.bat
+    NAMES cythonize-${Python_VERSION_MAJOR}.${Python_VERSION_MINOR} cythonize3 cythonize cythonize.bat
     HINTS ${_python_path})
 endif()
 

cmake/Modules/FindZMQ.cmake

@@ -1,19 +0,0 @@
-find_path(ZMQ_INCLUDE_DIR zmq.h)
-find_library(ZMQ_LIBRARY NAMES zmq)
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)
-
-# Copy the results to the output variables and target.
-if(ZMQ_FOUND)
-  set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
-  set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
-
-  if(NOT TARGET ZMQ::ZMQ)
-    add_library(ZMQ::ZMQ UNKNOWN IMPORTED)
-    set_target_properties(ZMQ::ZMQ PROPERTIES
-      IMPORTED_LINK_INTERFACE_LANGUAGES "C"
-      IMPORTED_LOCATION "${ZMQ_LIBRARY}"
-      INTERFACE_INCLUDE_DIRECTORIES "${ZMQ_INCLUDE_DIR}")
-  endif()
-endif()

cmake/Modules/LAMMPSInterfacePlugin.cmake

@@ -112,45 +112,76 @@ if(BUILD_MPI)
   set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
-    # Download and configure custom MPICH files for Windows
-    message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
-    set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
-    set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
-    set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
-    set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
-    mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-    mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
-    mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
-    mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
+    # Download and configure MinGW compatible MPICH development files for Windows
+    option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
+    if(USE_MSMPI)
+      message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
+      set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
+      set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
+      mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+      mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
 
-    include(ExternalProject)
-    if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-      ExternalProject_Add(mpi4win_build
-        URL     ${MPICH2_WIN64_DEVEL_URL}
-        URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
-        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-        BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+      include(ExternalProject)
+      if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+        ExternalProject_Add(mpi4win_build
+          URL     ${MPICH2_WIN64_DEVEL_URL}
+          URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
+      else()
+        message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
+      endif()
+
+      ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+      file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+      add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+      set_target_properties(MPI::MPI_CXX PROPERTIES
+        IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
+        INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+        INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+      # set variables for status reporting at the end of CMake run
+      set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+      set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
     else()
-      ExternalProject_Add(mpi4win_build
-        URL     ${MPICH2_WIN32_DEVEL_URL}
-        URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
-        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-        BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+      # Download and configure custom MPICH files for Windows
+      message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
+      set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
+      set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
+      mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+      mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+
+      include(ExternalProject)
+      if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+        ExternalProject_Add(mpi4win_build
+          URL     ${MPICH2_WIN64_DEVEL_URL}
+          URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+      else()
+        ExternalProject_Add(mpi4win_build
+          URL     ${MPICH2_WIN32_DEVEL_URL}
+          URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
+          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+      endif()
+
+      ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+      file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+      add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+      set_target_properties(MPI::MPI_CXX PROPERTIES
+        IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
+        INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+        INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+      # set variables for status reporting at the end of CMake run
+      set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+      set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
     endif()
-
-    ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-    file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-    add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-    set_target_properties(MPI::MPI_CXX PROPERTIES
-      IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
-      INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
-      INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-    add_dependencies(MPI::MPI_CXX mpi4win_build)
-
-    # set variables for status reporting at the end of CMake run
-    set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
-    set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-    set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
   else()
     find_package(MPI REQUIRED)
     option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)

cmake/Modules/LAMMPSUtils.cmake

@@ -24,6 +24,21 @@ function(validate_option name values)
     endif()
 endfunction(validate_option)
 
+# helper function to check for usable omp.h header
+function(check_omp_h_include)
+  find_package(OpenMP COMPONENTS CXX QUIET)
+  if(OpenMP_CXX_FOUND)
+    set(CMAKE_REQUIRED_FLAGS ${OpenMP_CXX_FLAGS})
+    set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
+    set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
+    set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
+    check_include_file_cxx(omp.h _have_omp_h)
+  else()
+    set(_have_omp_h FALSE)
+  endif()
+  set(HAVE_OMP_H_INCLUDE ${_have_omp_h} PARENT_SCOPE)
+endfunction()
+
 # helper function for getting the most recently modified file or folder from a glob pattern
 function(get_newest_file path variable)
   file(GLOB _dirs ${path})

cmake/Modules/MPI4WIN.cmake

@@ -1,39 +1,74 @@
-# Download and configure custom MPICH files for Windows
-message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
-set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
-set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
-set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
-set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
-mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
-mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
-mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
+# Download and configure MinGW compatible MPICH development files for Windows
+option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
 
-include(ExternalProject)
-if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-  ExternalProject_Add(mpi4win_build
-    URL     ${MPICH2_WIN64_DEVEL_URL}
-    URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
-    CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-    BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+if(USE_MSMPI)
+  message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
+  set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
+  set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
+  mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+  mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+
+  include(ExternalProject)
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    ExternalProject_Add(mpi4win_build
+      URL     ${MPICH2_WIN64_DEVEL_URL}
+      URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
+  else()
+    message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
+  endif()
+
+  ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+  file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+  add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+  set_target_properties(MPI::MPI_CXX PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+    INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+  add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+  # set variables for status reporting at the end of CMake run
+  set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+  set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+  set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
 else()
-  ExternalProject_Add(mpi4win_build
-    URL     ${MPICH2_WIN32_DEVEL_URL}
-    URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
-    CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-    BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+  message(STATUS "Downloading and configuring MPICH2-1.4.1 for Windows cross-compilation")
+  set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
+  set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
+  set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
+  set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
+  mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+  mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
+  mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+  mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
+
+  include(ExternalProject)
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    ExternalProject_Add(mpi4win_build
+      URL     ${MPICH2_WIN64_DEVEL_URL}
+      URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+  else()
+    ExternalProject_Add(mpi4win_build
+      URL     ${MPICH2_WIN32_DEVEL_URL}
+      URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+  endif()
+
+  ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+  file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+  add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+  set_target_properties(MPI::MPI_CXX PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+    INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+  add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+  # set variables for status reporting at the end of CMake run
+  set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+  set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+  set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
 endif()
-
-ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-set_target_properties(MPI::MPI_CXX PROPERTIES
-  IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
-  INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
-  INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-add_dependencies(MPI::MPI_CXX mpi4win_build)
-
-# set variables for status reporting at the end of CMake run
-set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
-set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")

cmake/Modules/Packages/KOKKOS.cmake

@@ -15,8 +15,9 @@ if(Kokkos_ENABLE_OPENMP)
   if(NOT BUILD_OMP)
     message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
   else()
-    if(LAMMPS_OMP_COMPAT_LEVEL LESS 4)
-      message(FATAL_ERROR "Compiler must support OpenMP 4.0 or later with Kokkos_ENABLE_OPENMP")
+    # NVHPC does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
+    if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
+      message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
     endif()
   endif()
 endif()
@@ -47,8 +48,8 @@ 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_MD5 "0ec97fc0c356dd65bd2487defe81a7bf" CACHE STRING "MD5 checksum of 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 "84991eca9f066383abe119a5bc7a11c4" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   ExternalProject_Add(kokkos_build
@@ -72,7 +73,7 @@ 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()
@@ -123,7 +124,7 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
 
 if(PKG_KSPACE)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
-                                 ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
   if(Kokkos_ENABLE_CUDA)
     if(NOT (FFT STREQUAL "KISS"))
@@ -138,6 +139,12 @@ if(PKG_KSPACE)
   endif()
 endif()
 
+if(PKG_ML-IAP)
+  list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/mliap_data_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_descriptor_so3_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_model_linear_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_so3_kokkos.cpp)
+endif()
 
 if(PKG_PHONON)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/dynamical_matrix_kokkos.cpp)

cmake/Modules/Packages/MC.cmake

@@ -0,0 +1,9 @@
+# fix sgcmc may only be installed if also the EAM pair style from MANYBODY is installed
+if(NOT PKG_MANYBODY)
+  get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
+  list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.h)
+  set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
+endif()

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_MD5 "3791fe5081405c14aac07d4687f1cc58" CACHE STRING "MD5 checksum 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 "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=${CMAKE_MAKE_PROGRAM}
@@ -70,23 +79,23 @@ if(DOWNLOAD_MDI)
     -Dplugins=ON
     -Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
     UPDATE_COMMAND ""
-    INSTALL_COMMAND ""
-    BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
+    INSTALL_COMMAND ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/src/mdi_build-build --target install
+    BUILD_BYPRODUCTS "${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)
-  set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
+  ExternalProject_get_property(mdi_build PREFIX)
   # 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"
-    INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
-    )
+    IMPORTED_LOCATION "${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
+    INTERFACE_INCLUDE_DIRECTORIES ${PREFIX}/include/mdi
+  )
 
   set(MDI_DEP_LIBS "")
   # if compiling with python plugins we need

cmake/Modules/Packages/ML-IAP.cmake

@@ -2,7 +2,13 @@
 set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
 if(PKG_PYTHON)
   find_package(Cythonize QUIET)
-  if(Cythonize_FOUND)
+  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
+    find_package(Python COMPONENTS NumPy QUIET)
+  else()
+    # assume we have NumPy
+    set(Python_NumPy_FOUND ON)
+  endif()
+  if(Cythonize_FOUND AND Python_NumPy_FOUND)
     set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
   endif()
 endif()
@@ -11,6 +17,9 @@ option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_EN
 
 if(MLIAP_ENABLE_PYTHON)
   find_package(Cythonize REQUIRED)
+  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
+    find_package(Python COMPONENTS NumPy REQUIRED)
+  endif()
   if(NOT PKG_PYTHON)
     message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
   endif()
@@ -25,16 +34,18 @@ 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)
-  get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE)
+  file(GLOB MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
   file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
-  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            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
-          WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
-          MAIN_DEPENDENCY    ${MLIAP_CYTHON_SRC}
-          COMMENT "Generating C++ sources with cythonize...")
+  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_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_FILE}
+            COMMENT "Generating C++ sources with cythonize...")
+    target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
+  endforeach()
   target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
-  target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
   target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
 endif()

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,6 +1,6 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2022.10.15.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 "848ad6a6cc79fa82745927001fb1c9b5" 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
-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 ${PACE_EVALUATOR_SOURCES})
+add_subdirectory(${lib-pace} build-pace)
 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/Modules/Packages/ML-QUIP.cmake

@@ -58,12 +58,12 @@ if(DOWNLOAD_QUIP)
     BUILD_COMMAND env QUIP_ARCH=lammps make libquip
     INSTALL_COMMAND ""
     BUILD_IN_SOURCE YES
-    BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/libquip.a
+    BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}
   )
   ExternalProject_get_property(quip_build SOURCE_DIR)
   add_library(LAMMPS::QUIP UNKNOWN IMPORTED)
   set_target_properties(LAMMPS::QUIP PROPERTIES
-    IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/libquip.a"
+    IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}"
     INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
   target_link_libraries(lammps PRIVATE LAMMPS::QUIP)
   add_dependencies(LAMMPS::QUIP quip_build)

cmake/Modules/Packages/PLUMED.cmake

@@ -47,15 +47,15 @@ if(DOWNLOAD_PLUMED)
   endif()
   message(STATUS "PLUMED download requested - we will build our own")
   if(PLUMED_MODE STREQUAL "STATIC")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed.a")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
   elseif(PLUMED_MODE STREQUAL "SHARED")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.4/plumed-src-2.7.4.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "858e0b6aed173748fc85b6bc8a9dcb3e" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-src-2.8.1.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of PLUMED tarball")
 
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)
@@ -78,12 +78,12 @@ if(DOWNLOAD_PLUMED)
   add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
   add_dependencies(LAMMPS::PLUMED plumed_build)
   if(PLUMED_MODE STREQUAL "STATIC")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
   elseif(PLUMED_MODE STREQUAL "SHARED")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumedWrapper.a INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
   endif()
   set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
   file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
@@ -96,7 +96,7 @@ else()
   elseif(PLUMED_MODE STREQUAL "SHARED")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
   endif()
   set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")

cmake/Modules/Packages/VTK.cmake

@@ -1,4 +1,9 @@
 find_package(VTK REQUIRED NO_MODULE)
-include(${VTK_USE_FILE})
 target_compile_definitions(lammps PRIVATE -DLAMMPS_VTK)
-target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES})
+if (VTK_MAJOR_VERSION VERSION_LESS 9.0)
+  include(${VTK_USE_FILE})
+  target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES})
+else()
+  target_link_libraries(lammps PRIVATE VTK::CommonCore VTK::IOCore VTK::CommonDataModel VTK::IOXML VTK::IOLegacy VTK::IOParallelXML)
+  vtk_module_autoinit(TARGETS lammps MODULES VTK::CommonCore VTK::IOCore VTK::CommonDataModel VTK::IOXML VTK::IOLegacy VTK::IOParallelXML)
+endif()

cmake/presets/all_off.cmake

@@ -56,6 +56,7 @@ set(ALL_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
+  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP

cmake/presets/all_on.cmake

@@ -58,6 +58,7 @@ set(ALL_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
+  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP

cmake/presets/clang.cmake

@@ -28,10 +28,3 @@ set(MPI_CXX "clang++" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
 unset(HAVE_OMP_H_INCLUDE CACHE)
-set(OpenMP_C "clang" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
-set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
-set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

cmake/presets/gcc.cmake

@@ -19,11 +19,3 @@ set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Og -g -std=f2003" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
-
-set(OpenMP_C "gcc" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
-set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
-set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
-set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
-set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE)

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/mingw-cross.cmake

@@ -47,6 +47,7 @@ set(WIN_PACKAGES
   MISC
   ML-HDNNP
   ML-IAP
+  ML-POD
   ML-RANN
   ML-SNAP
   MOFFF

cmake/presets/most.cmake

@@ -41,6 +41,7 @@ set(ALL_PACKAGES
   MEAM
   MISC
   ML-IAP
+  ML-POD
   ML-SNAP
   MOFFF
   MOLECULE

cmake/presets/nvhpc.cmake

@@ -0,0 +1,9 @@
+# preset that will enable Nvidia HPC SDK compilers with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "nvc++" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "nvc" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "nvfortran" CACHE STRING "" FORCE)
+set(MPI_CXX "nvc++" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+

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)
 

cmake/presets/pedantic.cmake

@@ -1,4 +1,4 @@
-# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
+# preset that will set gcc/g++ with extra warnings enabled and support for MPI and OpenMP (on Linux boxes)
 
 set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
@@ -17,10 +17,3 @@ set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
 set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
 
-set(OpenMP_C "gcc" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
-set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
-set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
-set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
-set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE)

cmake/presets/pgi.cmake

@@ -7,10 +7,3 @@ set(MPI_CXX "pgc++" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
 
-set(OpenMP_C "pgcc" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-mp" CACHE STRING "" FORCE)
-set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_CXX "pgc++" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-mp" CACHE STRING "" FORCE)
-set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

doc/Makefile

@@ -38,16 +38,14 @@ endif
 # override settings for PIP commands
 # PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
 
-#SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
-
 # temporarily disable caching so that the hack for the sphinx-tabs extensions to get proper non-html output works
-SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
+SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
 
 # grab list of sources from doxygen config file.
 # we only want to use explicitly listed files.
 DOXYFILES      = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//') 
 
-.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen fasthtml
+.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml
 
 # ------------------------------------------
 
@@ -89,6 +87,8 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		ln -sf Manual.html html/index.html;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
@@ -96,6 +96,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 		rst_anchor_check src/*.rst ;\
 		python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -114,7 +115,9 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@mkdir -p fasthtml
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
-		sphinx-build -j 4 -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
+		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
+		touch $(RSTDIR)/Fortran.rst ;\
+		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
 		deactivate ;\
 	)
 	@rm -rf fasthtml/_sources
@@ -144,6 +147,8 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@cp src/JPG/*.* epub/JPG
 	@(\
 		. $(VENV)/bin/activate ;\
+		sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
+		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
@@ -163,12 +168,15 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
-		sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		touch $(RSTDIR)/Fortran.rst ;\
+		sphinx-build  $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ;\
 		rst_anchor_check src/*.rst ;\
 		python utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		python utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -214,6 +222,9 @@ package_check : $(VENV)
 char_check :
 	@( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : )
 
+role_check :
+	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
+
 xmlgen : doxygen/xml/index.xml
 
 doxygen/Doxyfile: doxygen/Doxyfile.in

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "15 September 2022" "2022-9-15"
+.TH LAMMPS "1" "22 December 2022" "2022-12-22"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 15 September 2022
+\- Molecular Dynamics Simulator.  Version 22 December 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, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993).
+**(Mitchell and Fincham)**
+   Mitchell, Fincham, J Phys Condensed Matter, 5, 1031-1038 (1993).
 
 **(Mitchell2011)**
    Mitchell. A non-local, ordinary-state-based viscoelasticity model for peridynamics. Sandia National Lab Report, 8064:1-28 (2011).
@@ -875,7 +875,7 @@ Bibliography
    G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
 
 **(Paquay)**
-   Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
+   Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
 
 **(Park)**
    Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)

doc/src/Build_development.rst

@@ -140,13 +140,23 @@ 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
 `Googletest <https://github.com/google/googletest/>`_ C++ test framework
 for implementing the tests.
 
+.. admonition:: Software version requirements for testing
+   :class: note
+
+   The compiler and library version requirements for the testing
+   framework are more strict than for the main part of LAMMPS.  For
+   example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
+   (version 4.8.x) are not sufficient.  The CMake configuration will try
+   to detect compatible versions and either skip incompatible tests or
+   stop with an error.
+
 After compilation is complete, the unit testing is started in the build
 folder using the ``ctest`` command, which is part of the CMake software.
 The output of this command will be looking something like this::

doc/src/Build_extras.rst

@@ -36,6 +36,7 @@ This is the list of packages that may require additional steps.
    * :ref:`AWPMD <awpmd>`
    * :ref:`COLVARS <colvars>`
    * :ref:`COMPRESS <compress>`
+   * :ref:`ELECTRODE <electrode>`
    * :ref:`GPU <gpu>`
    * :ref:`H5MD <h5md>`
    * :ref:`INTEL <intel>`
@@ -48,6 +49,7 @@ This is the list of packages that may require additional steps.
    * :ref:`ML-HDNNP <ml-hdnnp>`
    * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
+   * :ref:`ML-POD <ml-pod>`
    * :ref:`ML-QUIP <ml-quip>`
    * :ref:`MOLFILE <molfile>`
    * :ref:`MSCG <mscg>`
@@ -234,7 +236,7 @@ LAMMPS code.  This also applies to the ``-DLAMMPS_BIGBIG``\ ,
 Makefile you use.
 
 You can also build the library in one step from the ``lammps/src`` dir,
-using a command like these, which simply invoke the ``lib/gpu/Install.py``
+using a command like these, which simply invokes the ``lib/gpu/Install.py``
 script with the specified args:
 
 .. code-block:: bash
@@ -314,7 +316,7 @@ 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
 
@@ -350,7 +352,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
       You can download and build the KIM library manually if you prefer;
       follow the instructions in ``lib/kim/README``.  You can also do
       this in one step from the lammps/src directory, using a command like
-      these, which simply invoke the ``lib/kim/Install.py`` script with
+      these, which simply invokes the ``lib/kim/Install.py`` script with
       the specified args.
 
       .. code-block:: bash
@@ -432,7 +434,7 @@ 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 +485,9 @@ 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 +527,21 @@ 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 +613,10 @@ 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 +631,12 @@ 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::
 
@@ -933,7 +956,7 @@ more details.
       You can download and build the MS-CG library manually if you
       prefer; follow the instructions in ``lib/mscg/README``\ .  You can
       also do it in one step from the ``lammps/src`` dir, using a
-      command like these, which simply invoke the
+      command like these, which simply invokes the
       ``lib/mscg/Install.py`` script with the specified args:
 
       .. code-block:: bash
@@ -990,7 +1013,7 @@ POEMS package
       ``lib/poems``\ .  You can do this manually if you prefer; follow
       the instructions in ``lib/poems/README``\ .  You can also do it in
       one step from the ``lammps/src`` dir, using a command like these,
-      which simply invoke the ``lib/poems/Install.py`` script with the
+      which simply invokes the ``lib/poems/Install.py`` script with the
       specified args:
 
       .. code-block:: bash
@@ -1053,7 +1076,7 @@ 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::
@@ -1079,7 +1102,7 @@ binary package provided by your operating system.
       You can download and build the Voro++ library manually if you
       prefer; follow the instructions in ``lib/voronoi/README``.  You
       can also do it in one step from the ``lammps/src`` dir, using a
-      command like these, which simply invoke the
+      command like these, which simply invokes the
       ``lib/voronoi/Install.py`` script with the specified args:
 
       .. code-block:: bash
@@ -1158,7 +1181,7 @@ The ATC package requires the MANYBODY package also be installed.
       ``lib/atc``.  You can do this manually if you prefer; follow the
       instructions in ``lib/atc/README``.  You can also do it in one
       step from the ``lammps/src`` dir, using a command like these,
-      which simply invoke the ``lib/atc/Install.py`` script with the
+      which simply invokes the ``lib/atc/Install.py`` script with the
       specified args:
 
       .. code-block:: bash
@@ -1209,7 +1232,7 @@ AWPMD package
       ``lib/awpmd``.  You can do this manually if you prefer; follow the
       instructions in ``lib/awpmd/README``.  You can also do it in one
       step from the ``lammps/src`` dir, using a command like these,
-      which simply invoke the ``lib/awpmd/Install.py`` script with the
+      which simply invokes the ``lib/awpmd/Install.py`` script with the
       specified args:
 
       .. code-block:: bash
@@ -1272,7 +1295,7 @@ be built for the most part with all major versions of the C++ language.
 
       In general, it is safer to use build setting consistent with the
       rest of LAMMPS.  This is best carried out from the LAMMPS src
-      directory using a command like these, which simply invoke the
+      directory using a command like these, which simply invokes the
       ``lib/colvars/Install.py`` script with the specified args:
 
       .. code-block:: bash
@@ -1313,20 +1336,30 @@ This package depends on the KSPACE package.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_KSPACE=yes`` and ``-D
-      PKG_ELECTRODE=yes``.
+      No additional settings are needed besides ``-D PKG_KSPACE=yes`` and
+      ``-D PKG_ELECTRODE=yes``.
 
    .. tab:: Traditional make
 
-      The package is activated with ``make yes-KSPACE`` and ``make
-      yes-ELECTRODE``
+      Before building LAMMPS, you must configure the ELECTRODE support
+      libraries and settings in ``lib/electrode``.  You can do this
+      manually, if you prefer, or do it in one step from the
+      ``lammps/src`` dir, using a command like these, which simply
+      invokes the ``lib/electrode/Install.py`` script with the specified
+      args:
+
+      .. code-block:: bash
+
+         $ make lib-electrode                   # print help message
+         $ make lib-electrode args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         $ make lib-electrode args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
 
 
-      Note that the ``Makefile.lammps`` file has settings for the BLAS and
-      LAPACK linear algebra libraries.  As explained in ``lib/awpmd/README``
-      these can either exist on your system, or you can use the files provided
-      in ``lib/linalg``.  In the latter case you also need to build the library
-      in ``lib/linalg`` with a command like these:
+      Note that the ``Makefile.lammps`` file has settings for the BLAS
+      and LAPACK linear algebra libraries.  These can either exist on
+      your system, or you can use the files provided in ``lib/linalg``.
+      In the latter case you also need to build the library in
+      ``lib/linalg`` with a command like these:
 
       .. code-block:: bash
 
@@ -1335,6 +1368,9 @@ This package depends on the KSPACE package.
          $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
          $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
 
+      The package itself is activated with ``make yes-KSPACE`` and
+      ``make yes-ELECTRODE``
+
 ----------
 
 .. _ml-pace:
@@ -1377,6 +1413,49 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
 
 ----------
 
+.. _ml-pod:
+
+ML-POD package
+-----------------------------
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      No additional settings are needed besides ``-D PKG_ML-POD=yes``.
+
+   .. tab:: Traditional make
+
+      Before building LAMMPS, you must configure the ML-POD support
+      settings in ``lib/mlpod``.  You can do this manually, if you
+      prefer, or do it in one step from the ``lammps/src`` dir, using a
+      command like the following, which simply invoke the
+      ``lib/mlpod/Install.py`` script with the specified args:
+
+      .. code-block:: bash
+
+         $ make lib-mlpod                   # print help message
+         $ make lib-mlpod args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         $ make lib-mlpod args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+         $ make lib-mlpod args="-m mpi -e linalg"   # same as above but use the bundled linalg lib
+
+      Note that the ``Makefile.lammps`` file has settings to use the BLAS
+      and LAPACK linear algebra libraries.  These can either exist on
+      your system, or you can use the files provided in ``lib/linalg``.
+      In the latter case you also need to build the library in
+      ``lib/linalg`` with a command like these:
+
+      .. code-block:: bash
+
+         $ make lib-linalg                     # print help message
+         $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+         $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+         $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+
+      The package itself is activated with ``make yes-ML-POD``.
+
+----------
+
 .. _plumed:
 
 PLUMED package
@@ -1534,7 +1613,7 @@ the HDF5 library.
       ``lib/h5md``.  You can do this manually if you prefer; follow the
       instructions in ``lib/h5md/README``.  You can also do it in one
       step from the ``lammps/src`` dir, using a command like these,
-      which simply invoke the ``lib/h5md/Install.py`` script with the
+      which simply invokes the ``lib/h5md/Install.py`` script with the
       specified args:
 
       .. code-block:: bash
@@ -1590,7 +1669,7 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
       You can download and build the *n2p2* library manually if you prefer;
       follow the instructions in ``lib/hdnnp/README``\ . You can also do it in
       one step from the ``lammps/src`` dir, using a command like these, which
-      simply invoke the ``lib/hdnnp/Install.py`` script with the specified args:
+      simply invokes the ``lib/hdnnp/Install.py`` script with the specified args:
 
       .. code-block:: bash
 
@@ -1727,7 +1806,7 @@ they will be downloaded the first time this package is installed.
       Before building LAMMPS, you must build the *mesont* library in
       ``lib/mesont``\ .  You can also do it in one step from the
       ``lammps/src`` dir, using a command like these, which simply
-      invoke the ``lib/mesont/Install.py`` script with the specified
+      invokes the ``lib/mesont/Install.py`` script with the specified
       args:
 
       .. code-block:: bash
@@ -1896,7 +1975,7 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
       ``lib/qmmm``.  You can do this manually if you prefer; follow the
       first two steps explained in ``lib/qmmm/README``.  You can also do
       it in one step from the ``lammps/src`` dir, using a command like
-      these, which simply invoke the ``lib/qmmm/Install.py`` script with
+      these, which simply invokes the ``lib/qmmm/Install.py`` script with
       the specified args:
 
       .. code-block:: bash
@@ -2004,7 +2083,7 @@ To build with this package, you must download and build the
       You can download and build the ScaFaCoS library manually if you
       prefer; follow the instructions in ``lib/scafacos/README``.  You
       can also do it in one step from the ``lammps/src`` dir, using a
-      command like these, which simply invoke the
+      command like these, which simply invokes the
       ``lib/scafacos/Install.py`` script with the specified args:
 
       .. code-block:: bash
@@ -2048,7 +2127,7 @@ Eigen3 is a template library, so you do not need to build it.
       You can download the Eigen3 library manually if you prefer; follow
       the instructions in ``lib/smd/README``.  You can also do it in one
       step from the ``lammps/src`` dir, using a command like these,
-      which simply invoke the ``lib/smd/Install.py`` script with the
+      which simply invokes the ``lib/smd/Install.py`` script with the
       specified args:
 
       .. code-block:: bash

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
-  :math:`\mathrm{\mathring{A}}` should be typeset with embedded math
-  (like this ``:math:`\mathrm{\mathring{A}}```\ ).
+  prepended to the screen.  Special characters like Greek letters
+  (:math:`\alpha~~\sigma~~\epsilon`), super- or subscripts
+  (: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
-distribution.  It is portable across all platforms.  Depending on the size
-of the FFTs and the number of processors used, the other libraries listed
-here can be faster.
+The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
+included in the LAMMPS distribution.  It is portable across all
+platforms.  Depending on the size of the FFTs and the number of
+processors used, the other libraries listed here can be faster.
 
 However, note that long-range Coulombics are only a portion of the
-per-timestep CPU cost, FFTs are only a portion of long-range
-Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
-communication can be costly).  A breakdown of these timings is printed
-to the screen at the end of a run when using the
-:doc:`kspace_style pppm <kspace_style>` command. The
-:doc:`Screen and logfile output <Run_output>`
-page gives more details.  A more detailed (and time consuming)
-report of the FFT performance is generated with the
+per-timestep CPU cost, FFTs are only a portion of long-range Coulombics,
+and 1d FFTs are only a portion of the FFT cost (parallel communication
+can be costly).  A breakdown of these timings is printed to the screen
+at the end of a run when using the :doc:`kspace_style pppm
+<kspace_style>` command. The :doc:`Screen and logfile output
+<Run_output>` page gives more details.  A more detailed (and time
+consuming) report of the FFT performance is generated with the
 :doc:`kspace_modify fftbench yes <kspace_modify>` command.
 
 FFTW is a fast, portable FFT library that should also work on any
-platform and can be faster than the KISS FFT library.  You can
-download it from `www.fftw.org <http://www.fftw.org>`_.  LAMMPS requires
-version 3.X; the legacy version 2.1.X is no longer supported.
+platform and can be faster than the KISS FFT library.  You can download
+it from `www.fftw.org <https://www.fftw.org>`_.  LAMMPS requires version
+3.X; the legacy version 2.1.X is no longer supported.
 
 Building FFTW for your box should be as simple as ``./configure; make;
 make install``.  The install command typically requires root privileges

doc/src/Commands_all.rst

@@ -31,7 +31,6 @@ table above.
    * :doc:`bond_style <bond_style>`
    * :doc:`bond_write <bond_write>`
    * :doc:`boundary <boundary>`
-   * :doc:`box <box>`
    * :doc:`change_box <change_box>`
    * :doc:`clear <clear>`
    * :doc:`comm_modify <comm_modify>`
@@ -90,8 +89,7 @@ table above.
    * :doc:`region <region>`
    * :doc:`replicate <replicate>`
    * :doc:`rerun <rerun>`
-   * :doc:`reset_atom_ids <reset_atom_ids>`
-   * :doc:`reset_mol_ids <reset_mol_ids>`
+   * :doc:`reset_atoms <reset_atoms>`
    * :doc:`reset_timestep <reset_timestep>`
    * :doc:`restart <restart>`
    * :doc:`run <run>`
@@ -127,6 +125,7 @@ additional letter in parenthesis: k = KOKKOS.
    * :doc:`group2ndx <group2ndx>`
    * :doc:`hyper <hyper>`
    * :doc:`kim <kim_commands>`
+   * :doc:`fitpod <fitpod_command>`
    * :doc:`mdi <mdi>`
    * :doc:`ndx2group <group2ndx>`
    * :doc:`neb <neb>`

doc/src/Commands_category.rst

@@ -25,7 +25,6 @@ Setup simulation box:
    :columns: 4
 
    * :doc:`boundary <boundary>`
-   * :doc:`box <box>`
    * :doc:`change_box <change_box>`
    * :doc:`create_box <create_box>`
    * :doc:`dimension <dimension>`

doc/src/Commands_compute.rst

@@ -107,6 +107,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`pressure/uef <compute_pressure_uef>`
    * :doc:`property/atom <compute_property_atom>`
    * :doc:`property/chunk <compute_property_chunk>`
+   * :doc:`property/grid <compute_property_grid>`
    * :doc:`property/local <compute_property_local>`
    * :doc:`ptm/atom <compute_ptm_atom>`
    * :doc:`rdf <compute_rdf>`

doc/src/Commands_dump.rst

@@ -36,7 +36,8 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
    * :doc:`custom/mpiio <dump>`
    * :doc:`custom/zstd <dump>`
    * :doc:`dcd <dump>`
-   * :doc:`deprecated <dump>`
+   * :doc:`grid <dump>`
+   * :doc:`grid/vtk <dump>`
    * :doc:`h5md <dump_h5md>`
    * :doc:`image <dump_image>`
    * :doc:`local <dump>`

doc/src/Commands_fix.rst

@@ -38,6 +38,7 @@ OPT.
    * :doc:`ave/chunk <fix_ave_chunk>`
    * :doc:`ave/correlate <fix_ave_correlate>`
    * :doc:`ave/correlate/long <fix_ave_correlate_long>`
+   * :doc:`ave/grid <fix_ave_grid>`
    * :doc:`ave/histo <fix_ave_histo>`
    * :doc:`ave/histo/weight <fix_ave_histo>`
    * :doc:`ave/time <fix_ave_time>`
@@ -65,13 +66,13 @@ OPT.
    * :doc:`drude <fix_drude>`
    * :doc:`drude/transform/direct <fix_drude_transform>`
    * :doc:`drude/transform/inverse <fix_drude_transform>`
-   * :doc:`dt/reset <fix_dt_reset>`
+   * :doc:`dt/reset (k) <fix_dt_reset>`
    * :doc:`edpd/source <fix_dpd_source>`
    * :doc:`efield <fix_efield>`
    * :doc:`ehex <fix_ehex>`
-   * :doc:`electrode/conp (i) <fix_electrode_conp>`
-   * :doc:`electrode/conq (i) <fix_electrode_conp>`
-   * :doc:`electrode/thermo (i) <fix_electrode_conp>`
+   * :doc:`electrode/conp (i) <fix_electrode>`
+   * :doc:`electrode/conq (i) <fix_electrode>`
+   * :doc:`electrode/thermo (i) <fix_electrode>`
    * :doc:`electron/stopping <fix_electron_stopping>`
    * :doc:`electron/stopping/fit <fix_electron_stopping>`
    * :doc:`enforce2d (k) <fix_enforce2d>`
@@ -213,6 +214,7 @@ OPT.
    * :doc:`saed/vtk <fix_saed_vtk>`
    * :doc:`setforce (k) <fix_setforce>`
    * :doc:`setforce/spin <fix_setforce>`
+   * :doc:`sgcmc <fix_sgcmc>`
    * :doc:`shake (k) <fix_shake>`
    * :doc:`shardlow (k) <fix_shardlow>`
    * :doc:`smd <fix_smd>`
@@ -249,7 +251,7 @@ OPT.
    * :doc:`tune/kspace <fix_tune_kspace>`
    * :doc:`vector <fix_vector>`
    * :doc:`viscosity <fix_viscosity>`
-   * :doc:`viscous <fix_viscous>`
+   * :doc:`viscous (k) <fix_viscous>`
    * :doc:`viscous/sphere <fix_viscous_sphere>`
    * :doc:`wall/body/polygon <fix_wall_body_polygon>`
    * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`

doc/src/Commands_pair.rst

@@ -93,8 +93,8 @@ OPT.
    * :doc:`coul/wolf/cs <pair_cs>`
    * :doc:`dpd (giko) <pair_dpd>`
    * :doc:`dpd/fdt <pair_dpd_fdt>`
-   * :doc:`dpd/ext (k) <pair_dpd_ext>`
-   * :doc:`dpd/ext/tstat (k) <pair_dpd_ext>`
+   * :doc:`dpd/ext (ko) <pair_dpd_ext>`
+   * :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
    * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
    * :doc:`dpd/tstat (gko) <pair_dpd>`
    * :doc:`dsmc <pair_dsmc>`
@@ -205,7 +205,7 @@ OPT.
    * :doc:`mesont/tpm <pair_mesont_tpm>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
-   * :doc:`mliap <pair_mliap>`
+   * :doc:`mliap (k) <pair_mliap>`
    * :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
@@ -236,6 +236,8 @@ OPT.
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`pace (k) <pair_pace>`
+   * :doc:`pace/extrapolation <pair_pace>`
+   * :doc:`pod <pair_pod>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`
@@ -294,6 +296,7 @@ OPT.
    * :doc:`vashishta (gko) <pair_vashishta>`
    * :doc:`vashishta/table (o) <pair_vashishta>`
    * :doc:`wf/cut <pair_wf_cut>`
+   * :doc:`ylz <pair_ylz>`
    * :doc:`yukawa (gko) <pair_yukawa>`
    * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
    * :doc:`zbl (gko) <pair_zbl>`

doc/src/Commands_removed.rst

@@ -2,14 +2,17 @@ Removed commands and packages
 =============================
 
 This page lists LAMMPS commands and packages that have been removed from
-the distribution and provides suggestions for alternatives or replacements.
-LAMMPS has special dummy styles implemented, that will stop LAMMPS and
-print a suitable error message in most cases, when a style/command is used
-that has been removed.
+the distribution and provides suggestions for alternatives or
+replacements.  LAMMPS has special dummy styles implemented, that will
+stop LAMMPS and print a suitable error message in most cases, when a
+style/command is used that has been removed or will replace the command
+with the direct alternative (if available) and print a warning.
 
 Fix ave/spatial and fix ave/spatial/sphere
 ------------------------------------------
 
+.. deprecated:: 11Dec2015
+
 The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
 since they were superseded by the more general and extensible "chunk
 infrastructure".  Here the system is partitioned in one of many possible
@@ -17,10 +20,23 @@ ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
 and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
 Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
 
-Reset_ids command
------------------
+Box command
+-----------
 
-The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`.
+.. deprecated:: 22Dec2022
+
+The *box* command has been removed and the LAMMPS code changed so it won't
+be needed.  If present, LAMMPS will ignore the command and print a warning.
+
+Reset_ids, reset_atom_ids, reset_mol_ids commands
+-------------------------------------------------
+
+.. deprecated:: 22Dec2022
+
+The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
+been folded into the :doc:`reset_atoms <reset_atoms>` command.  If
+present, LAMMPS will replace the commands accordingly and print a
+warning.
 
 MEAM package
 ------------
@@ -30,18 +46,21 @@ The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
 Fortran code of MEAM into C++, which removes several restrictions
 (e.g. there can be multiple instances in hybrid pair styles) and allows
 for some optimizations leading to better performance.  The pair style
-:doc:`meam <pair_meam>` has the exact same syntax.
+:doc:`meam <pair_meam>` has the exact same syntax.  For a transition
+period the C++ version of MEAM was called USER-MEAMC so it could
+coexist with the Fortran version.
 
 REAX package
 ------------
 
 The REAX package has been removed since it was superseded by the
-:ref:`REAXFF package <PKG-REAXFF>`.  The REAXFF
-package has been tested to yield equivalent results to the REAX package,
-offers better performance, supports OpenMP multi-threading via OPENMP,
-and GPU and threading parallelization through KOKKOS.  The new pair styles
-are not syntax compatible with the removed reax pair style, so input
-files will have to be adapted.
+:ref:`REAXFF package <PKG-REAXFF>`.  The REAXFF package has been tested
+to yield equivalent results to the REAX package, offers better
+performance, supports OpenMP multi-threading via OPENMP, and GPU and
+threading parallelization through KOKKOS.  The new pair styles are not
+syntax compatible with the removed reax pair style, so input files will
+have to be adapted.  The REAXFF package was originally called
+USER-REAXC.
 
 USER-CUDA package
 -----------------
@@ -60,5 +79,6 @@ restart2data tool
 The functionality of the restart2data tool has been folded into the
 LAMMPS executable directly instead of having a separate tool.  A
 combination of the commands :doc:`read_restart <read_restart>` and
-:doc:`write_data <write_data>` can be used to the same effect.  For added
-convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
+:doc:`write_data <write_data>` can be used to the same effect.  For
+added convenience this conversion can also be triggered by
+:doc:`command line flags <Run_options>`

doc/src/Developer.rst

@@ -23,3 +23,4 @@ of time and requests from the LAMMPS user community.
    Classes
    Developer_platform
    Developer_utils
+   Developer_grid

doc/src/Developer_code_design.rst

@@ -50,7 +50,7 @@ parallel each MPI process creates such an instance.  This can be seen
 in the ``main.cpp`` file where the core steps of running a LAMMPS
 simulation are the following 3 lines of code:
 
-.. code-block:: C++
+.. code-block:: c++
 
     LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
     lammps->input->file();
@@ -78,7 +78,7 @@ LAMMPS makes extensive use of the object oriented programming (OOP)
 principles of *compositing* and *inheritance*. Classes like the
 ``LAMMPS`` class are a **composite** containing pointers to instances
 of other classes like ``Atom``, ``Comm``, ``Force``, ``Neighbor``,
-``Modify``, and so on.  Each of these classes implement certain
+``Modify``, and so on.  Each of these classes implements certain
 functionality by storing and manipulating data related to the
 simulation and providing member functions that trigger certain
 actions.  Some of those classes like ``Force`` are themselves
@@ -87,9 +87,9 @@ interactions.  Similarly the ``Modify`` class contains a list of
 ``Fix`` and ``Compute`` classes.  If the input commands that
 correspond to these classes include the word *style*, then LAMMPS
 stores only a single instance of that class.  E.g. *atom_style*,
-*comm_style*, *pair_style*, *bond_style*.  It the input command does
-not include the word *style*, there can be many instances of that
-class defined.  E.g. *region*, *fix*, *compute*, *dump*.
+*comm_style*, *pair_style*, *bond_style*.  If the input command does
+**not** include the word *style*, then there may be many instances of
+that class defined, for example *region*, *fix*, *compute*, *dump*.
 
 **Inheritance** enables creation of *derived* classes that can share
 common functionality in their base class while providing a consistent
@@ -232,7 +232,7 @@ macro ``PairStyle()`` will associate the style name "lj/cut"
 with a factory function creating an instance of the ``PairLJCut``
 class.
 
-.. code-block:: C++
+.. code-block:: c++
 
    // from force.h
    typedef Pair *(*PairCreator)(LAMMPS *);
@@ -360,7 +360,7 @@ characters; "{:<8}" would do this as left aligned, "{:^8}" as centered,
 argument type must be compatible or else the {fmt} formatting code will
 throw an exception. Some format string examples are given below:
 
-.. code-block:: C
+.. code-block:: c++
 
    auto mesg = fmt::format("  CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus);
    mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n",

doc/src/Developer_grid.rst

@@ -0,0 +1,846 @@
+Use of distributed grids within style classes
+---------------------------------------------
+
+.. versionadded:: 22Dec2022
+
+The LAMMPS source code includes two classes which facilitate the
+creation and use of distributed grids.  These are the Grid2d and
+Grid3d classes in the src/grid2d.cpp.h and src/grid3d.cpp.h files
+respectively.  As the names imply, they are used for 2d or 3d
+simulations, as defined by the :doc:`dimension <dimension>` command.
+
+The :doc:`Howto_grid <Howto_grid>` page gives an overview of how
+distributed grids are defined from a user perspective, lists LAMMPS
+commands which use them, and explains how grid cell data is referenced
+from an input script.  Please read that page first as it motivates the
+coding details discussed here.
+
+This doc page is for users who wish to write new styles (input script
+commands) which use distributed grids.  There are a variety of
+material models and analysis methods which use atoms (or
+coarse-grained particles) and grids in tandem.
+
+A *distributed* grid means each processor owns a subset of the grid
+cells.  In LAMMPS, the subset for each processor will be a sub-block
+of grid cells with low and high index bounds in each dimension of the
+grid.  The union of the sub-blocks across all processors is the global
+grid.
+
+More specifically, a grid point is defined for each cell (by default
+the center point), and a processor owns a grid cell if its point is
+within the processor's spatial sub-domain.  The union of processor
+sub-domains is the global simulation box.  If a grid point is on the
+boundary of two sub-domains, the lower processor owns the grid cell.  A
+processor may also store copies of ghost cells which surround its
+owned cells.
+
+----------
+
+Style commands
+^^^^^^^^^^^^^^
+
+Style commands which can define and use distributed grids include the
+:doc:`compute <compute>`, :doc:`fix <fix>`, :doc:`pair <pair_style>`,
+and :doc:`kspace <kspace_style>` styles.  If you wish grid cell data
+to persist across timesteps, then use a fix.  If you wish grid cell
+data to be accessible by other commands, then use a fix or compute.
+Currently in LAMMPS, the :doc:`pair_style amoeba <pair_amoeba>`,
+:doc:`kspace_style pppm <kspace_style>`, and :doc:`kspace_style msm
+<kspace_style>` commands use distributed grids but do not require
+either of these capabilities; they thus create and use distributed
+grids internally.  Note that a pair style which needs grid cell data
+to persist could be coded to work in tandem with a fix style which
+provides that capability.
+
+The *size* of a grid is specified by the number of grid cells in each
+dimension of the simulation domain.  In any dimension the size can be
+any value >= 1.  Thus a 10x10x1 grid for a 3d simulation is
+effectively a 2d grid, where each grid cell spans the entire
+z-dimension.  A 1x100x1 grid for a 3d simulation is effectively a 1d
+grid, where grid cells are a series of thin xz slabs in the
+y-dimension.  It is even possible to define a 1x1x1 3d grid, though it
+may be inefficient to use it in a computational sense.
+
+Note that the choice of grid size is independent of the number of
+processors or their layout in a grid of processor sub-domains which
+overlays the simulations domain.  Depending on the distributed grid
+size, a single processor may own many 1000s or no grid cells.
+
+A command can define multiple grids, each of a different size.  Each
+grid is an instantiation of the Grid2d or Grid3d class.
+
+The command also defines what data it will store for each grid it
+creates and it allocates the multi-dimensional array(s) needed to
+store the data.  No grid cell data is stored within the Grid2d or
+Grid3d classes.
+
+If a single value per grid cell is needed, the data array will have
+the same dimension as the grid, i.e. a 2d array for a 2d grid,
+likewise for 3d.  If multiple values per grid cell are needed, the
+data array will have one more dimension than the grid, i.e. a 3d array
+for a 2d grid, or 4d array for a 3d grid.  A command can choose to
+define multiple data arrays for each grid it defines.
+
+----------
+
+Grid data allocation and access
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The simplest way for a command to allocate and access grid cell data
+is to use the *create_offset()* methods provided by the Memory class.
+Arguments for these methods can be values returned by the
+*setup_grid()* method (described below), which define the extent of
+the grid cells (owned+ghost) the processor owns.  These 4 methods
+allocate memory for 2d (first two) and 3d (second two) grid data.  The
+two methods that end in "_one" allocate an array which stores a single
+value per grid cell.  The two that end in "_multi" allocate an array
+which stores *Nvalues* per grid cell.
+
+.. code-block:: c++
+
+   // single value per cell for a 2d grid = 2d array
+   memory->create2d_offset(data2d_one, nylo_out, nyhi_out,
+                           nxlo_out, nxhi_out, "data2d_one");
+
+   // nvalues per cell for a 2d grid = 3d array
+   memory->create3d_offset_last(data2d_multi, nylo_out, nyhi_out,
+                                nxlo_out, nxhi_out, nvalues, "data2d_multi");
+
+   // single value per cell for a 3d grid = 3d array
+   memory->create3d_offset(data3d_one, nzlo_out, nzhi_out, nylo_out,
+                           nyhi_out, nxlo_out, nxhi_out, "data3d_one");
+
+   // nvalues per cell for a 3d grid = 4d array
+   memory->create4d_offset_last(data3d_multi, nzlo_out, nzhi_out, nylo_out,
+                                nyhi_out, nxlo_out, nxhi_out, nvalues,
+                                "data3d_multi");
+
+Note that these multi-dimensional arrays are allocated as contiguous
+chunks of memory where the x-index of the grid varies fastest, then y,
+and the z-index slowest.  For multiple values per grid cell, the
+Nvalues are contiguous, so their index varies even faster than the
+x-index.
+
+The key point is that the "offset" methods create arrays which are
+indexed by the range of indices which are the bounds of the sub-block
+of the global grid owned by this processor.  This means loops like
+these can be written in the caller code to loop over owned grid cells,
+where the "i" loop bounds are the range of owned grid cells for the
+processor.  These are the bounds returned by the *setup_grid()*
+method:
+
+.. code-block:: c++
+
+    for (int iy = iylo; iy <= iyhi; iy++)
+      for (int ix = ixlo; ix <= ixhi; ix++)
+        data2d_one[iy][ix] = 0.0;
+
+    for (int iy = iylo; iy <= iyhi; iy++)
+      for (int ix = ixlo; ix <= ixhi; ix++)
+        for (int m = 0; m < nvalues; m++)
+          data2d_multi[iy][ix][m] = 0.0;
+
+    for (int iz = izlo; iz <= izhi; iz++)
+      for (int iy = iylo; iy <= iyhi; iy++)
+        for (int ix = ixlo; ix <= ixhi; ix++)
+          data3d_one[iz][iy][ix] = 0.0;
+
+    for (int iz = izlo; iz <= izhi; iz++)
+      for (int iy = iylo; iy <= iyhi; iy++)
+        for (int ix = ixlo; ix <= ixhi; ix++)
+           for (int m = 0; m < nvalues; m++)
+              data3d_multi[iz][iy][ix][m] = 0.0;
+
+Simply replacing the "i" bounds with "o" bounds, also returned by the
+*setup_grid()* method, would alter this code to loop over owned+ghost
+cells (the entire allocated grid).
+
+----------
+
+Grid class constructors
+^^^^^^^^^^^^^^^^^^^^^^^
+
+The following sub-sections describe the public methods of the Grid3d
+class which a style command can invoke.  The Grid2d methods are
+similar; simply remove arguments which refer to the z-dimension.
+
+There are 2 constructors which can be used.  They differ in the extra
+i/o xyz lo/hi arguments:
+
+.. code-block:: c++
+
+   Grid3d(class LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz)
+   Grid3d(class LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz,
+          int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi,
+          int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi)
+
+Both constructors take the LAMMPS instance pointer and a communicator
+over which the grid will be distributed.  Typically this is the
+*world* communicator the LAMMPS instance is using.  The
+:doc:`kspace_style msm <kspace_style>` command creates a series of
+grids, each of different size, which are partitioned across different
+sub-communicators of processors.  Both constructors are also passed
+the global grid size: *gnx* by *gny* by *gnz*.
+
+The first constructor is used when the caller wants the Grid class to
+partition the global grid across processors; the Grid class defines
+which grid cells each processor owns and also which it stores as ghost
+cells.  A subsequent call to *setup_grid()*, discussed below, returns
+this info to the caller.
+
+The second constructor allows the caller to define the extent of owned
+and ghost cells, and pass them to the Grid class.  The 6 arguments
+which start with "i" are the inclusive lower and upper index bounds of
+the owned (inner) grid cells this processor owns in each of the 3
+dimensions within the global grid.  Owned grid cells are indexed from
+0 to N-1 in each dimension.
+
+The 6 arguments which start with "o" are the inclusive bounds of the
+owned+ghost (outer) grid cells it stores.  If the ghost cells are on
+the other side of a periodic boundary, then these indices may be < 0
+or >= N in any dimension, so that oxlo <= ixlo and ixhi >= ixhi is
+always the case.
+
+For example, if Nx = 100, then a processor might pass ixlo=50,
+ixhi=60, oxlo=48, oxhi=62 to the Grid class.  Or ixlo=0, ixhi=10,
+oxlo=-2, oxhi=13.  If a processor owns no grid cells in a dimension,
+then the ihi value should be specified as one less than the ilo value.
+
+Note that the only reason to use the second constructor is if the
+logic for assigning ghost cells is too complex for the Grid class to
+compute, using the various set() methods described next.  Currently
+only the kspace_style pppm/electrode and kspace_style msm commands use
+the second constructor.
+
+----------
+
+Grid class set methods
+^^^^^^^^^^^^^^^^^^^^^^
+
+The following methods affect how the Grid class computes which owned
+and ghost cells are assigned to each processor.  *Set_shift_grid()* is
+the only method which influences owned cell assignment; all the rest
+influence ghost cell assignment.  These methods are only used with the
+first constructor; they are ignored if the second constructor is used.
+These methods must be called before the *setup_grid()* method is
+invoked, because they influence its operation.
+
+.. code-block:: c++
+
+   void set_shift_grid(double shift);
+   void set_distance(double distance);
+   void set_stencil_atom(int lo, int hi);
+   void set_shift_atom(double shift_lo, double shift_hi);
+   void set_stencil_grid(int lo, int hi);
+   void set_zfactor(double factor);
+
+Processors own a grid cell if a point within the grid cell is inside
+the processor's sub-domain.  By default this is the center point of the
+grid cell.  The *set_shift_grid()* method can change this.  The *shift*
+argument is a value from 0.0 to 1.0 (inclusive) which is the offset of
+the point within the grid cell in each dimension.  The default is 0.5
+for the center of the cell.  A value of 0.0 is the lower left corner
+point; a value of 1.0 is the upper right corner point.  There is
+typically no need to change the default as it is optimal for
+minimizing the number of ghost cells needed.
+
+If a processor maps its particles to grid cells, it needs to allow for
+its particles being outside its sub-domain between reneighboring.  The
+*distance* argument of the *set_distance()* method sets the furthest
+distance outside a processor's sub-domain which a particle can move.
+Typically this is half the neighbor skin distance, assuming
+reneighboring is done appropriately.  This distance is used in
+determining how many ghost cells a processor needs to store to enable
+its particles to be mapped to grid cells.  The default value is 0.0.
+
+Some commands, like the :doc:`kspace_style pppm <kspace_style>`
+command, map values (charge in the case of PPPM) to a stencil of grid
+cells beyond the grid cell the particle is in.  The stencil extent may
+be different in the low and high directions.  The *set_stencil_atom()*
+method defines the maximum values of those 2 extents, assumed to be
+the same in each of the 3 dimensions.  Both the lo and hi values are
+specified as positive integers.  The default values are both 0.
+
+Some commands, like the :doc:`kspace_style pppm <kspace_style>`
+command, shift the position of an atom when mapping it to a grid cell,
+based on the size of the stencil used to map values to the grid
+(charge in the case of PPPM).  The lo and hi arguments of the
+*set_shift_atom()* method are the minimum shift in the low direction
+and the maximum shift in the high direction, assumed to be the same in
+each of the 3 dimensions.  The shifts should be fractions of a grid
+cell size with values between 0.0 and 1.0 inclusive.  The default
+values are both 0.0.  See the src/pppm.cpp file for examples of these
+lo/hi values for regular and staggered grids.
+
+Some methods like the :doc:`fix ttm/grid <fix_ttm>` command, perform
+finite difference kinds of operations on the grid, to diffuse electron
+heat in the case of the two-temperature model (TTM).  This operation
+uses ghost grid values beyond the owned grid values the processor
+updates.  The *set_stencil_grid()* method defines the extent of this
+stencil in both directions, assumed to be the same in each of the 3
+dimensions.  Both the lo and hi values are specified as positive
+integers.  The default values are both 0.
+
+The kspace_style pppm commands allow a grid to be defined which
+overlays a volume which extends beyond the simulation box in the z
+dimension.  This is for the purpose of modeling a 2d-periodic slab
+(non-periodic in z) as if it were a larger 3d periodic system,
+extended (with empty space) in the z dimension.  The
+:doc:`kspace_modify slab <kspace_modify>` command is used to specify
+the ratio of the larger volume to the simulation volume; a volume
+ratio of ~3 is typical.  For this kind of model, the PPPM caller sets
+the global grid size *gnz* ~3x larger than it would be otherwise.
+This same ratio is passed by the PPPM caller as the *factor* argument
+to the Grid class via the *set_zfactor()* method (*set_yfactor()* for
+2d grids).  The Grid class will then assign ownership of the 1/3 of
+grid cells that overlay the simulation box to the processors which
+also overlay the simulation box.  The remaining 2/3 of the grid cells
+are assigned to processors whose sub-domains are adjacent to the upper
+z boundary of the simulation box.
+
+----------
+
+Grid class setup_grid method
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The *setup_grid()* method is called after the first constructor
+(above) to partition the grid across processors, which determines
+which grid cells each processor owns.  It also calculates how many
+ghost grid cells in each dimension and each direction each processor
+needs to store.
+
+Note that this method is NOT called if the second constructor above is
+used.  In that case, the caller assigns owned and ghost cells to each
+processor.
+
+Also note that this method must be invoked after any *set_*()* methods have
+been used, since they can influence the assignment of owned and ghost
+cells.
+
+.. code-block:: c++
+
+   void setup_grid(int &ixlo, int &ixhi, int &iylo, int &iyhi, int &izlo, int &izhi,
+                   int &oxlo, int &oxhi, int &oylo, int &oyhi, int &ozlo, int &ozhi)
+
+The 6 return arguments which start with "i" are the inclusive lower
+and upper index bounds of the owned (inner) grid cells this processor
+owns in each of the 3 dimensions within the global grid.  Owned grid
+cells are indexed from 0 to N-1 in each dimension.
+
+The 6 return arguments which start with "o" are the inclusive bounds of
+the owned+ghost cells it owns.  If the ghost cells are on the other
+side of a periodic boundary, then these indices may be < 0 or >= N in
+any dimension, so that oxlo <= ixlo and ixhi >= ixhi is always the
+case.
+
+----------
+
+More grid class set methods
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following 2 methods can be used to override settings made by the
+constructors above.  If used, they must be called called before the
+*setup_comm()* method is invoked, since it uses the settings that
+these methods override.  In LAMMPS these methods are called by by the
+:doc:`kspace_style msm <kspace_style>` command for the grids it
+instantiates using the 2nd constructor above.
+
+.. code-block:: c++
+
+   void set_proc_neighs(int pxlo, int pxhi, int pylo, int pyhi, int pzlo, int pzhi)
+   void set_caller_grid(int fxlo, int fxhi, int fylo, int fyhi, int fzlo, int fzhi)
+
+The *set_proc_neighs()* method sets the processor IDs of the 6
+neighboring processors for each processor.  Normally these would match
+the processor grid neighbors which LAMMPS creates to overlay the
+simulation box (the default).  However, MSM excludes non-participating
+processors from coarse grid communication when less processors are
+used.  This method allows MSM to override the default values.
+
+The *set_caller_grid()* method species the size of the data arrays the
+caller allocates.  Normally these would match the extent of the ghost
+grid cells (the default).  However the MSM caller allocates a larger
+data array (more ghost cells) for its finest-level grid, for use in
+other operations besides owned/ghost cell communication.  This method
+allows MSM to override the default values.
+
+
+----------
+
+Grid class get methods
+^^^^^^^^^^^^^^^^^^^^^^
+
+The following methods allow the caller to query the settings for a
+specific grid, whether it created the grid or another command created
+it.
+
+.. code-block:: c++
+
+   void get_size(int &nxgrid, int &nygrid, int &nzgrid);
+   void get_bounds_owned(int &xlo, int &xhi, int &ylo, int &yhi, int &zlo, int &zhi)
+   void get_bounds_ghost(int &xlo, int &xhi, int &ylo, int &yhi, int &zlo, int &zhi)
+
+The *get_size()* method returns the size of the global grid in each dimension.
+
+The *get_bounds_owned()* method return the inclusive index bounds of
+the grid cells this processor owns.  The values range from 0 to N-1 in
+each dimension.  These values are the same as the "i" values returned
+by *setup_grid()*.
+
+The *get_bounds_ghost()* method return the inclusive index bounds of
+the owned+ghost grid cells this processor stores.  The owned cell
+indices range from 0 to N-1, so these indices may be less than 0 or
+greater than or equal to N in each dimension.  These values are the
+same as the "o" values returned by *setup_grid()*.
+
+----------
+
+Grid class owned/ghost communication
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If needed by the command, the following methods setup and perform
+communication of grid data to/from neighboring processors.  The
+*forward_comm()* method sends owned grid cell data to the
+corresponding ghost grid cells on other processors.  The
+*reverse_comm()* method sends ghost grid cell data to the
+corresponding owned grid cells on another processor.  The caller can
+choose to sum ghost grid cell data to the owned grid cell or simply
+copy it.
+
+.. code-block:: c++
+
+   void setup_comm(int &nbuf1, int &nbuf2)
+   void forward_comm(int caller, void *ptr, int which, int nper, int nbyte,
+                     void *buf1, void *buf2, MPI_Datatype datatype);
+   void reverse_comm(int caller, void *ptr, int which, int nper, int nbyte,
+                     void *buf1, void *buf2, MPI_Datatype datatype)
+   int ghost_adjacent();
+
+The *setup_comm()* method must be called one time before performing
+*forward* or *reverse* communication (multiple times if needed).  It
+returns two integers, which should be used to allocate two buffers.
+The *nbuf1* and *nbuf2* values are the number of grid cells whose data
+will be stored in two buffers by the Grid class when *forward* or
+*reverse* communication is performed.  The caller should thus allocate
+them to a size large enough to hold all the data used in any single
+forward or reverse communication operation it performs.  Note that the
+caller may allocate and communicate multiple data arrays for a grid it
+instantiates.  This size includes the bytes needed for the data type
+of the grid data it stores, e.g. double precision values.
+
+The *forward_comm()* and *reverse_comm()* methods send grid cell data
+from owned to ghost cells, or ghost to owned cells, respectively, as
+described above.  The *caller* argument should be one of these values
+-- Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR --
+depending on the style of the caller class.  The *ptr* argument is the
+"this" pointer to the caller class.  These 2 arguments are used to
+call back to pack()/unpack() functions in the caller class, as
+explained below.
+
+The *which* argument is a flag the caller can set which is passed to
+the caller's pack()/unpack() methods.  This allows a single callback
+method to pack/unpack data for several different flavors of
+forward/reverse communication, e.g. operating on different grids or
+grid data.
+
+The *nper* argument is the number of values per grid cell to be
+communicated.  The *nbyte* argument is the number of bytes per value,
+e.g. 8 for double-precision values.  The *buf1* and *buf2* arguments
+are the two allocated buffers described above.  So long as they are
+allocated for the maximum size communication, they can be re-used for
+any *forward_comm()/reverse_comm()* call.  The *datatype* argument is
+the MPI_Datatype setting, which should match the buffer allocation and
+the *nbyte* argument.  E.g. MPI_DOUBLE for buffers storing double
+precision values.
+
+To use the *forward_grid()* method, the caller must provide two
+callback functions; likewise for use of the *reverse_grid()* methods.
+These are the 4 functions, their arguments are all the same.
+
+.. code-block:: c++
+
+   void pack_forward_grid(int which, void *vbuf, int nlist, int *list);
+   void unpack_forward_grid(int which, void *vbuf, int nlist, int *list);
+   void pack_reverse_grid(int which, void *vbuf, int nlist, int *list);
+   void unpack_reverse_grid(int which, void *vbuf, int nlist, int *list);
+
+The *which* argument is set to the *which* value of the
+*forward_comm()* or *reverse_comm()* calls.  It allows the pack/unpack
+function to select what data values to pack/unpack.  *Vbuf* is the
+buffer to pack/unpack the data to/from.  It is a void pointer so that
+the caller can cast it to whatever data type it chooses, e.g. double
+precision values.  *Nlist* is the number of grid cells to pack/unpack
+and *list* is a vector (nlist in length) of offsets to where the data
+for each grid cell resides in the caller's data arrays, which is best
+illustrated with an example from the src/EXTRA-FIX/fix_ttm_grid.cpp
+class which stores the scalar electron temperature for 3d system in a
+3d grid (one value per grid cell):
+
+.. code-block:: c++
+
+   void FixTTMGrid::pack_forward_grid(int /*which*/, void *vbuf, int nlist, int *list)
+   {
+     auto buf = (double *) vbuf;
+     double *src = &T_electron[nzlo_out][nylo_out][nxlo_out];
+     for (int i = 0; i < nlist; i++) buf[i] = src[list[i]];
+   }
+
+In this case, the *which* argument is not used, *vbuf* points to a
+buffer of doubles, and the electron temperature is stored by the
+FixTTMGrid class in a 3d array of owned+ghost cells called T_electron.
+That array is allocated by the *memory->create_3d_offset()* method
+described above so that the first grid cell it stores is indexed as
+T_electron[nzlo_out][nylo_out][nxlo_out].  The *nlist* values in
+*list* are integer offsets from that first grid cell.  Setting *src*
+to the address of the first cell allows those offsets to be used to
+access the temperatures to pack into the buffer.
+
+Here is a similar portion of code from the src/fix_ave_grid.cpp class
+which can store two kinds of data, a scalar count of atoms in a grid
+cell, and one or more grid-cell-averaged atom properties.  The code
+from its *unpack_reverse_grid()* function for 2d grids and multiple
+per-atom properties per grid cell (*nvalues*) is shown here:
+
+.. code-block:: c++
+
+   void FixAveGrid::unpack_reverse_grid(int /*which*/, void *vbuf, int nlist, int *list)
+   {
+     auto buf = (double *) vbuf;
+     double *count,*data,*values;
+     count = &count2d[nylo_out][nxlo_out];
+     data = &array2d[nylo_out][nxlo_out][0];
+     m = 0;
+     for (i = 0; i < nlist; i++) {
+       count[list[i]] += buf[m++];
+       values = &data[nvalues*list[i]];
+       for (j = 0; j < nvalues; j++)
+        values[j] += buf[m++];
+     }
+   }
+
+Both the count and the multiple values per grid cell are communicated
+in *vbuf*.  Note that *data* is now a pointer to the first value in
+the first grid cell.  And *values* points to where the first value in
+*data* is for an offset of grid cells, calculated by multiplying
+*nvalues* by *list[i]*.  Finally, because this is reverse
+communication, the communicated buffer values are summed to the caller
+values.
+
+The *ghost_adjacent()* method returns a 1 if every processor can
+perform the necessary owned/ghost communication with only its nearest
+neighbor processors (4 in 2d, 6 in 3d).  It returns a 0 if any
+processor's ghost cells extend further than nearest neighbor
+processors.
+
+This can be checked by callers who have the option to change the
+global grid size to insure more efficient nearest-neighbor-only
+communication if they wish.  In this case, they instantiate a grid of
+a given size (resolution), then invoke *setup_comm()* followed by
+*ghost_adjacent()*.  If the ghost cells are not adjacent, they destroy
+the grid instance and start over with a higher-resolution grid.
+Several of the :doc:`kspace_style pppm <kspace_style>` command
+variants have this option.
+
+----------
+
+Grid class remap methods for load balancing
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following methods are used when a load-balancing operation,
+triggered by the :doc:`balance <balance>` or :doc:`fix balance
+<fix_balance>` commands, changes the partitioning of the simulation
+domain into processor sub-domains.
+
+In order to work with load-balancing, any style command (compute, fix,
+pair, or kspace style) which allocates a grid and stores per-grid data
+should define a *reset_grid()* method; it takes no arguments.  It will
+be called by the two balance commands after they have reset processor
+sub-domains and migrated atoms (particles) to new owning processors.
+The *reset_grid()* method will typically perform some or all of the
+following operations.  See the src/fix_ave_grid.cpp and
+src/EXTRA_FIX/fix_ttm_grid.cpp files for examples of *reset_grid()*
+methods, as well as the *pack_remap_grid()* and *unpack_remap_grid()*
+functions.
+
+First, the *reset_grid()* method can instantiate new grid(s) of the
+same global size, then call *setup_grid()* to partition them via the
+new processor sub-domains.  At this point, it can invoke the
+*identical()* method which compares the owned and ghost grid cell
+index bounds between two grids, the old grid passed as a pointer
+argument, and the new grid whose *identical()* method is being called.
+It returns 1 if the indices match on all processors, otherwise 0.  If
+they all match, then the new grids can be deleted; the command can
+continue to use the old grids.
+
+If not, then the command should allocate new grid data array(s) which
+depend on the new partitioning.  If the command does not need to
+persist its grid data from the old partitioning to the new one, then
+the command can simply delete the old data array(s) and grid
+instance(s).  It can then return.
+
+If the grid data does need to persist, then the data for each grid
+needs to be "remapped" from the old grid partitioning to the new grid
+partitioning.  The *setup_remap()* and *remap()* methods are used for
+that purpose.
+
+.. code-block:: c++
+
+   int identical(Grid3d *old);
+   void setup_remap(Grid3d *old, int &nremap_buf1, int &nremap_buf2)
+   void remap(int caller, void *ptr, int which, int nper, int nbyte,
+              void *buf1, void *buf2, MPI_Datatype datatype)
+
+The arguments to these methods are identical to those for
+the *setup_comm()* and *forward_comm()* or *reverse_comm()* methods.
+However the returned *nremap_buf1* and *nremap2_buf* values will be
+different than the *nbuf1* and *nbuf2* values.  They should be used to
+allocate two different remap buffers, separate from the owned/ghost
+communication buffers.
+
+To use the *remap()* method, the caller must provide two
+callback functions:
+
+.. code-block:: c++
+
+   void pack_remap_grid(int which, void *vbuf, int nlist, int *list);
+   void unpack_remap_grid(int which, void *vbuf, int list, int *list);
+
+Their arguments are identical to those for the *pack_forward_grid()*
+and *unpack_forward_grid()* callback functions (or the reverse
+variants) discussed above.  Normally, both these methods pack/unpack
+all the data arrays for a given grid.  The *which* argument of the
+*remap()* method sets the *which* value for the pack/unpack functions.
+If the command instantiates multiple grids (of different sizes), it
+can be used within the pack/unpack methods to select which grid's data
+is being remapped.
+
+Note that the *pack_remap_grid()* function must copy values from the
+OLD grid data arrays into the *vbuf* buffer. The *unpack_remap_grid()*
+function must copy values from the *vbuf* buffer into the NEW grid
+data arrays.
+
+After the remap operation for grid cell data has been performed, the
+*reset_grid()* method can deallocate the two remap buffers it created,
+and can then exit.
+
+----------
+
+Grid class I/O methods
+^^^^^^^^^^^^^^^^^^^^^^
+
+There are two I/O methods in the Grid classes which can be used to
+read and write grid cell data to files.  The caller can decide on the
+precise format of each file, e.g. whether header lines are prepended
+or comment lines are allowed.  Fundamentally, the file should contain
+one line per grid cell for the entire global grid.  Each line should
+contain identifying info as to which grid cell it is, e.g. a unique
+grid cell ID or the ix,iy,iz indices of the cell within a 3d grid.
+The line should also contain one or more data values which are stored
+within the grid data arrays created by the command
+
+For grid cell IDs, the LAMMPS convention is that the IDs run from 1 to
+N, where N = Nx * Ny for 2d grids and N = Nx * Ny * Nz for 3d grids.
+The x-index of the grid cell varies fastest, then y, and the z-index
+varies slowest.  So for a 10x10x10 grid the cell IDs from 901-1000
+would be in the top xy layer of the z dimension.
+
+The *read_file()* method does something simple.  It reads a chunk of
+consecutive lines from the file and passes them back to the caller to
+process.  The caller provides a *unpack_read_grid()* function for this
+purpose.  The function checks the grid cell ID or indices and only
+stores grid cell data for the grid cells it owns.
+
+The *write_file()* method does something slightly more complex.  Each
+processor packs the data for its owned grid cells into a buffer.  The
+caller provides a *pack_write_grid()* function for this purpose.  The
+*write_file()* method then loops over all processors and each sends
+its buffer one at a time to processor 0, along with the 3d (or 2d)
+index bounds of its grid cell data within the global grid.  Processor
+0 calls back to the *unpack_write_grid()* function provided by the
+caller with the buffer.  The function writes one line per grid cell to
+the file.
+
+See the src/EXTRA_FIX/fix_ttm_grid.cpp file for examples of now both
+these methods are used to read/write electron temperature values
+from/to a file, as well as for implementations of the the pack/unpack
+functions described below.
+
+Here are the details of the two I/O methods and the 3 callback
+functions.  See the src/fix_ave_grid.cpp file for examples of all of
+them.
+
+.. code-block:: c++
+
+   void read_file(int caller, void *ptr, FILE *fp, int nchunk, int maxline)
+   void write_file(int caller, void *ptr, int which,
+                   int nper, int nbyte, MPI_Datatype datatype
+
+The *caller* argument in both methods should be one of these values --
+Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR --
+depending on the style of the caller class.  The *ptr* argument in
+both methods is the "this" pointer to the caller class.  These 2
+arguments are used to call back to pack()/unpack() functions in the
+caller class, as explained below.
+
+For the *read_file()* method, the *fp* argument is a file pointer to
+the file to be read from, opened on processor 0 by the caller.
+*Nchunk* is the number of lines to read per chunk, and *maxline* is
+the maximum number of characters per line.  The Grid class will
+allocate a buffer for storing chunks of lines based on these values.
+
+For the *write_file()* method, the *which* argument is a flag the
+caller can set which is passed back to the caller's pack()/unpack()
+methods.  If the command instantiates multiple grids (of different
+sizes), this flag can be used within the pack/unpack methods to select
+which grid's data is being written out (presumably to different
+files).  the *nper* argument is the number of values per grid cell to
+be written out.  The *nbyte* argument is the number of bytes per
+value, e.g. 8 for double-precision values.  The *datatype* argument is
+the MPI_Datatype setting, which should match the *nbyte* argument.
+E.g. MPI_DOUBLE for double precision values.
+
+To use the *read_grid()* method, the caller must provide one callback
+function.  To use the *write_grid()* method, it provides two callback
+functions:
+
+.. code-block:: c++
+
+   int unpack_read_grid(int nlines, char *buffer)
+   void pack_write_grid(int which, void *vbuf)
+   void unpack_write_grid(int which, void *vbuf, int *bounds)
+
+For *unpack_read_grid()* the *nlines* argument is the number of lines
+of character data read from the file and contained in *buffer*.  The
+lines each include a newline character at the end.  When the function
+processes the lines, it may choose to skip some of them (header or
+comment lines).  It returns an integer count of the number of grid
+cell lines it processed.  This enables the Grid class *read_file()*
+method to know when it has read the correct number of lines.
+
+For *pack_write_grid()* and *unpack_write_grid()*, the *vbuf* argument
+is the buffer to pack/unpack data to/from.  It is a void pointer so
+that the caller can cast it to whatever data type it chooses,
+e.g. double precision values.  the *which* argument is set to the
+*which* value of the *write_file()* method.  It allows the caller to
+choose which grid data to operate on.
+
+For *unpack_write_grid()*, the *bounds* argument is a vector of 4 or 6
+integer grid indices (4 for 2d, 6 for 3d).  They are the
+xlo,xhi,ylo,yhi,zlo,zhi index bounds of the portion of the global grid
+which the *vbuf* holds owned grid cell data values for.  The caller
+should loop over the values in *vbuf* with a double loop (2d) or
+triple loop (3d), similar to the code snippets listed above.  The
+x-index varies fastest, then y, and the z-index slowest.  If there are
+multiple values per grid cell, the index for those values varies
+fastest of all.  The caller can add the x,y,z indices of the grid cell
+(or the corresponding grid cell ID) to the data value(s) written as
+one line to the output file.
+
+----------
+
+Style class grid access methods
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A style command can enable its grid cell data to be accessible from
+other commands.  For example :doc:`fix ave/grid <fix_ave_grid>` or
+:doc:`dump grid <dump>` or :doc:`dump grid/vtk <dump>`.  Those
+commands access the grid cell data by using a *grid reference* in
+their input script syntax, as described on the :doc:`Howto_grid
+<Howto_grid>` doc page.  They look like this:
+
+* c_ID:gname:dname
+* c_ID:gname:dname[I]
+* f_ID:gname:dname
+* f_ID:gname:dname[I]
+
+Each grid a command instantiates has a unique *gname*, defined by the
+command.  Likewise each grid cell data structure (scalar or vector)
+associated with a grid has a unique *dname*, also defined by the
+command.
+
+To provide access to its grid cell data, a style command needs to
+implement the following 4 methods:
+
+.. code-block:: c++
+
+   int get_grid_by_name(const std::string &name, int &dim);
+   void *get_grid_by_index(int index);
+   int get_griddata_by_name(int igrid, const std::string &name, int &ncol);
+   void *get_griddata_by_index(int index);
+
+Currently only computes and fixes can implement these methods.  If it
+does so, the compute of fix should also set the variable
+*pergrid_flag* to 1.  See any of the compute or fix commands which set
+"pergrid_flag = 1" for examples of how these 4 functions can be
+implemented.
+
+The *get_grid_by_name()* method takes a grid name as input and returns
+two values.  The *dim* argument is returned as 2 or 3 for the
+dimensionality of the grid.  The function return is a grid index from
+0 to G-1 where *G* is the number of grids the command instantiates.  A
+value of -1 is returned if the grid name is not recognized.
+
+The *get_grid_by_index()* method is called after the
+*get_grid_by_name()* method, using the grid index it returned as its
+argument.  This method will return a pointer to the Grid2d or Grid3d
+class.  The caller can use this to query grid attributes, such as the
+global size of the grid.  The :doc:`dump grid <dump>` to insure each
+its grid reference arguments are for grids of the same size.
+
+The *get_griddata_by_name()* method takes a grid index *igrid* and a
+data name as input.  It returns two values.  The *ncol* argument is
+returned as a 0 if the grid data is a single value (scalar) per grid
+cell, or an integer M > 0 if there are M values (vector) per grid
+cell.  Note that even if M = 1, it is still a 1-length vector, not a
+scalar.  The function return is a data index from 0 to D-1 where *D*
+is the number of data sets associated with that grid by the command.
+A value of -1 is returned if the data name is not recognized.
+
+The *get_griddata_by_index()* method is called after the
+*get_griddata_by_name()* method, using the data index it returned as
+its argument.  This method will return a pointer to the
+multi-dimensional array which stores the requested data.
+
+As in the discussion above of the Memory class *create_offset()*
+methods, the dimensionality of the array associated with the returned
+pointer depends on whether it is a 2d or 3d grid and whether there is
+a single or multiple values stored for each grid cell:
+
+* single value per cell for a 2d grid = 2d array pointer
+* multiple values per cell for a 2d grid = 3d array pointer
+* single value per cell for a 3d grid = 3d array pointer
+* multiple values per cell for a 3d grid = 4d array pointer
+
+The caller will typically access the data by casting the void pointer
+to the corresponding array pointer and using nested loops in x,y,z
+between owned or ghost index bounds returned by the
+*get_bounds_owned()* or *get_bounds_ghost()* methods to index into the
+array.  Example code snippets with this logic were listed above,
+
+----------
+
+Final notes
+^^^^^^^^^^^
+
+Finally, here are some additional issues to pay attention to for
+writing any style command which uses distributed grids via the Grid2d
+or Grid3d class.
+
+The command destructor should delete all instances of the Grid class,
+any buffers it allocated for forward/reverse or remap communication,
+and any data arrays it allocated to store grid cell data.
+
+If a command is intended to work for either 2d or 3d simulations, then
+it should have logic to instantiate either 2d or 3d grids and their
+associated data arrays, depending on the dimension of the simulation
+box.  The :doc:`fix ave/grid <fix_ave_grid>` command is an example of
+such a command.
+
+When a command maps its particles to the grid and updates grid cell
+values, it should check that it is not updating or accessing a grid
+cell value outside the range of its owned+ghost cells, and generate an
+error message if that is the case.  This could happen, for example, if
+a particle has moved further than half the neighbor skin distance,
+because the neighbor list update criterion are not adequate to prevent
+it from happening.  See the src/KSPACE/pppm.cpp file and its
+*particle_map()* method for an example of this kind of error check.

doc/src/Developer_notes.rst

@@ -105,7 +105,7 @@ list, where each pair of atoms is listed only once (except when the
 pairs straddling sub-domains or periodic boundaries will be listed twice).
 Thus these are the default settings when a neighbor list request is created in:
 
-.. code-block:: C++
+.. code-block:: c++
 
    void Pair::init_style()
    {
@@ -129,7 +129,7 @@ neighbor list request to the specific needs of a style an additional
 request flag is needed.  The :doc:`tersoff <pair_tersoff>` pair style,
 for example, needs a "full" neighbor list:
 
-.. code-block:: C++
+.. code-block:: c++
 
    void PairTersoff::init_style()
    {
@@ -141,7 +141,7 @@ When a pair style supports r-RESPA time integration with different cutoff region
 the request flag may depend on the corresponding r-RESPA settings. Here an example
 from pair style lj/cut:
 
-.. code-block:: C++
+.. code-block:: c++
 
    void PairLJCut::init_style()
    {
@@ -160,7 +160,7 @@ Granular pair styles need neighbor lists based on particle sizes and not cutoff
 and also may require to have the list of previous neighbors available ("history").
 For example with:
 
-.. code-block:: C++
+.. code-block:: c++
 
    if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY);
    else neighbor->add_request(this, NeighConst::REQ_SIZE);
@@ -170,7 +170,7 @@ settings each request can set an id which is then used in the corresponding
 ``init_list()`` function to assign it to the suitable pointer variable. This is
 done for example by the :doc:`pair style meam <pair_meam>`:
 
-.. code-block:: C++
+.. code-block:: c++
 
    void PairMEAM::init_style()
    {
@@ -189,7 +189,7 @@ just once) and this can also be indicated by a flag.  As an example here
 is the request from the ``FixPeriNeigh`` class which is created
 internally by :doc:`Peridynamics pair styles <pair_peri>`:
 
-.. code-block:: C++
+.. code-block:: c++
 
    neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
 
@@ -198,7 +198,7 @@ than what is usually inferred from the pair style settings (largest cutoff of
 all pair styles plus neighbor list skin).  The following is used in the
 :doc:`compute rdf <compute_rdf>` command implementation:
 
-.. code-block:: C++
+.. code-block:: c++
 
   if (cutflag)
     neighbor->add_request(this, NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh);
@@ -212,7 +212,7 @@ for printing the neighbor list summary the name of the requesting command
 should be set.  Below is the request from the :doc:`delete atoms <delete_atoms>`
 command:
 
-.. code-block:: C++
+.. code-block:: c++
 
    neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
 

doc/src/Developer_plugins.rst

@@ -95,7 +95,7 @@ a class ``PairMorse2`` in the files ``pair_morse2.h`` and
 ``pair_morse2.cpp`` with the factory function and initialization
 function would look like this:
 
-.. code-block:: C++
+.. code-block:: c++
 
   #include "lammpsplugin.h"
   #include "version.h"
@@ -141,7 +141,7 @@ list of argument strings), then the pointer type is ``lammpsplugin_factory2``
 and it must be assigned to the *creator.v2* member of the plugin struct.
 Below is an example for that:
 
-.. code-block:: C++
+.. code-block:: c++
 
   #include "lammpsplugin.h"
   #include "version.h"
@@ -176,7 +176,7 @@ demonstrated in the following example, which also shows that the
 implementation of the plugin class may be within the same source
 file as the plugin interface code:
 
-.. code-block:: C++
+.. code-block:: c++
 
    #include "lammpsplugin.h"
 

doc/src/Developer_unittest.rst

@@ -194,7 +194,7 @@ macro. These tests operate by capturing the screen output when executing
 the failing command and then comparing that with a provided regular
 expression string pattern.  Example:
 
-.. code-block:: C++
+.. code-block:: c++
 
    TEST_F(SimpleCommandsTest, UnknownCommand)
    {
@@ -226,9 +226,9 @@ The following test programs are currently available:
    * - ``test_kim_commands.cpp``
      - KimCommands
      - Tests for several commands from the :ref:`KIM package <PKG-KIM>`
-   * - ``test_reset_ids.cpp``
-     - ResetIDs
-     - Tests to validate the :doc:`reset_atom_ids <reset_atom_ids>` and :doc:`reset_mol_ids <reset_mol_ids>` commands
+   * - ``test_reset_atoms.cpp``
+     - ResetAtoms
+     - Tests to validate the :doc:`reset_atoms <reset_atoms>` sub-commands
 
 
 Tests for the C-style library interface
@@ -249,7 +249,7 @@ MPI support.  These include tests where LAMMPS is run in multi-partition
 mode or only on a subset of the MPI world communicator.  The CMake
 script code for adding this kind of test looks like this:
 
-.. code-block:: CMake
+.. code-block:: cmake
 
    if (BUILD_MPI)
      add_executable(test_library_mpi test_library_mpi.cpp)

doc/src/Developer_updating.rst

@@ -7,7 +7,7 @@ source files provided as a supplement to a publication) that are written
 for an older version of LAMMPS and thus need to be updated to be
 compatible with the current version of LAMMPS.  Due to the active
 development of LAMMPS it is likely to always be incomplete.  Please
-contact developer@lammps.org in case you run across an issue that is not
+contact developers@lammps.org in case you run across an issue that is not
 (yet) listed here.  Please also review the latest information about the
 LAMMPS :doc:`programming style conventions <Modify_style>`, especially
 if you are considering to submit the updated version for inclusion into
@@ -25,6 +25,7 @@ Available topics in mostly chronological order are:
 - `Simplified and more compact neighbor list requests`_
 - `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
 - `Use Output::get_dump_by_id() instead of Output::find_dump()`_
+- `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
 
 ----
 
@@ -61,7 +62,7 @@ header file needs to be updated accordingly.
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
    {
@@ -75,7 +76,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    int PairEAM::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
    {
@@ -112,14 +113,14 @@ Example from a pair style:
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    if (eflag || vflag) ev_setup(eflag, vflag);
    else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    ev_init(eflag, vflag);
 
@@ -142,14 +143,14 @@ when they are called from only one or a subset of the MPI processes.
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
     val = force->numeric(FLERR, arg[1]);
     num = force->inumeric(FLERR, arg[2]);
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
     val = utils::numeric(FLERR, true, arg[1], lmp);
     num = utils::inumeric(FLERR, false, arg[2], lmp);
@@ -183,14 +184,14 @@ copy them around for simulations.
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    fp = force->open_potential(filename);
    fp = fopen(filename, "r");
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    fp = utils::open_potential(filename, lmp);
 
@@ -207,7 +208,7 @@ Example:
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    if (fptr == NULL) {
      char str[128];
@@ -217,7 +218,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    if (fptr == nullptr)
      error->one(FLERR, "Cannot open AEAM potential file {}: {}", filename, utils::getsyserror());
@@ -237,7 +238,7 @@ an example from the ``FixWallReflect`` class:
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    FixWallReflect(class LAMMPS *, int, char **);
    virtual ~FixWallReflect();
@@ -247,7 +248,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    FixWallReflect(class LAMMPS *, int, char **);
    ~FixWallReflect() override;
@@ -271,7 +272,7 @@ the type of the "this" pointer argument.
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    comm->forward_comm_pair(this);
    comm->forward_comm_fix(this);
@@ -284,7 +285,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    comm->forward_comm(this);
    comm->reverse_comm(this);
@@ -304,7 +305,7 @@ requests can be :doc:`found here <Developer_notes>`. Example from the
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    int irequest = neighbor->request(this,instance_me);
    neighbor->requests[irequest]->pair = 0;
@@ -317,7 +318,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
    if (cutflag) req->set_cutoff(mycutneigh);
@@ -340,7 +341,7 @@ these are internal fixes, there is no user visible change.
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    #include "fix_store.h"
 
@@ -351,7 +352,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    #include "fix_store_peratom.h"
 
@@ -362,7 +363,7 @@ New:
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    #include "fix_store.h"
 
@@ -373,7 +374,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    #include "fix_store_global.h"
 
@@ -396,7 +397,7 @@ the dump directly.  Example:
 
 Old:
 
-.. code-block:: C++
+.. code-block:: c++
 
    int idump = output->find_dump(arg[iarg+1]);
    if (idump < 0)
@@ -412,7 +413,7 @@ Old:
 
 New:
 
-.. code-block:: C++
+.. code-block:: c++
 
    auto idump = output->get_dump_by_id(arg[iarg+1]);
    if (!idump) error->all(FLERR,"Dump ID {} in hyper command does not exist", arg[iarg+1]);
@@ -423,3 +424,56 @@ New:
    if (dumpflag) for (auto idump : dumplist) idump->write();
 
 This change is **required** or else the code will not compile.
+
+Refactored grid communication using Grid3d/Grid2d classes instead of GridComm
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 22Dec2022
+
+The ``GridComm`` class was for creating and communicating distributed
+grids was replaced by the ``Grid3d`` class with added functionality.
+A ``Grid2d`` class was also added for additional flexibility.
+
+The new functionality and commands using the two grid classes are
+discussed on the following documentation pages:
+
+- :doc:`Howto_grid`
+- :doc:`Developer_grid`
+
+If you have custom LAMMPS code, which uses the GridComm class, here are some notes
+on how to adapt it for using the Grid3d class.
+
+(1) The constructor has changed to allow the ``Grid3d`` / ``Grid2d``
+    classes to partition the global grid across processors, both for
+    owned and ghost grid cells.  Previously any class which called
+    ``GridComm`` performed the partitioning itself and that information
+    was passed in the ``GridComm::GridComm()`` constructor.  There are
+    several "set" functions which can be called to alter how ``Grid3d``
+    / ``Grid2d`` perform the partitioning.  They should be sufficient
+    for most use cases of the grid classes.
+
+(2) The partitioning is triggered by the ``setup_grid()`` method.
+
+(3) The ``setup()`` method of the ``GridComm`` class has been replaced
+    by the ``setup_comm()`` method in the new grid classes.  The syntax
+    for the ``forward_comm()`` and ``reverse_comm()`` methods is
+    slightly altered as is the syntax of the associated pack/unpack
+    callback methods.  But the functionality of these operations is the
+    same as before.
+
+(4) The new ``Grid3d`` / ``Grid2d`` classes have additional
+    functionality for dynamic load-balancing of grids and their
+    associated data across processors.  This did not exist in the
+    ``GridComm`` class.
+
+This and more is explained in detail on the :doc:`Developer_grid` page.
+The following LAMMPS source files can be used as illustrative examples
+for how the new grid classes are used by computes, fixes, and various
+KSpace solvers which use distributed FFT grids:
+
+- ``src/fix_ave_grid.cpp``
+- ``src/compute_property_grid.cpp``
+- ``src/EXTRA-FIX/fix_ttm_grid.cpp``
+- ``src/KSPACE/pppm.cpp``
+
+This change is **required** or else the code will not compile.

doc/src/Developer_utils.rst

@@ -133,6 +133,9 @@ and parsing files or arguments.
 .. doxygenfunction:: trim_comment
    :project: progguide
 
+.. doxygenfunction:: strip_style_suffix
+   :project: progguide
+
 .. doxygenfunction:: star_subst
    :project: progguide
 
@@ -211,6 +214,9 @@ Argument processing
 .. doxygenfunction:: expand_args
    :project: progguide
 
+.. doxygenfunction:: parse_grid_id
+   :project: progguide
+
 .. doxygenfunction:: expand_type
    :project: progguide
 
@@ -317,7 +323,7 @@ are all "whitespace" characters, i.e. the space character, the tabulator
 character, the carriage return character, the linefeed character, and
 the form feed character.
 
-.. code-block:: C++
+.. code-block:: c++
    :caption: Tokenizer class example listing entries of the PATH environment variable
 
    #include "tokenizer.h"
@@ -349,7 +355,7 @@ tokenizer into a ``try`` / ``catch`` block to handle errors.  The
 when a (type of) number is requested as next token that is not
 compatible with the string representing the next word.
 
-.. code-block:: C++
+.. code-block:: c++
    :caption: ValueTokenizer class example with exception handling
 
    #include "tokenizer.h"
@@ -427,7 +433,7 @@ one or two array indices "[<number>]" with numbers > 0.
 
 A typical code segment would look like this:
 
-.. code-block:: C++
+.. code-block:: c++
    :caption: Usage example for ArgInfo class
 
    int nvalues = 0;
@@ -476,7 +482,7 @@ open the file, and will call the :cpp:class:`LAMMPS_NS::Error` class in
 case of failures to read or to convert numbers, so that LAMMPS will be
 aborted.
 
-.. code-block:: C++
+.. code-block:: c++
    :caption: Use of PotentialFileReader class in pair style coul/streitz
 
     PotentialFileReader reader(lmp, file, "coul/streitz");
@@ -555,7 +561,7 @@ chunk size needs to be known in advance, 2) with :cpp:func:`MyPage::vget()
 its size is registered later with :cpp:func:`MyPage::vgot()
 <LAMMPS_NS::MyPage::vgot>`.
 
-.. code-block:: C++
+.. code-block:: c++
    :caption: Example of using :cpp:class:`MyPage <LAMMPS_NS::MyPage>`
 
       #include "my_page.h"

doc/src/Developer_write.rst

@@ -26,7 +26,7 @@ constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``.
 Every fix must be registered in LAMMPS by writing the following lines
 of code in the header before include guards:
 
-.. code-block:: c
+.. code-block:: c++
 
    #ifdef FIX_CLASS
    // clang-format off
@@ -47,7 +47,7 @@ keyword when it parses the input script.
 Let's write a simple fix which will print the average velocity at the end
 of each timestep. First of all, implement a constructor:
 
-.. code-block:: C++
+.. code-block:: c++
 
    FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
    : Fix(lmp, narg, arg)
@@ -72,7 +72,7 @@ in the Fix class called ``nevery`` which specifies how often the method
 
 The next method we need to implement is ``setmask()``:
 
-.. code-block:: C++
+.. code-block:: c++
 
    int FixPrintVel::setmask()
    {
@@ -87,7 +87,7 @@ during execution. The constant ``END_OF_STEP`` corresponds to the
 are called during a timestep and the order in which they are called
 are shown in the previous section.
 
-.. code-block:: C++
+.. code-block:: c++
 
    void FixPrintVel::end_of_step()
    {
@@ -143,7 +143,7 @@ The group membership information of an atom is contained in the *mask*
 property of and atom and the bit corresponding to a given group is
 stored in the groupbit variable which is defined in Fix base class:
 
-.. code-block:: C++
+.. code-block:: c++
 
    for (int i = 0; i < nlocal; ++i) {
      if (atom->mask[i] & groupbit) {
@@ -174,7 +174,7 @@ to store positions of atoms from previous timestep, we need to add
 ``double** xold`` to the header file. Than add allocation code
 to the constructor:
 
-.. code-block:: C++
+.. code-block:: c++
 
    FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr)
    {
@@ -190,7 +190,7 @@ to the constructor:
 
 Implement the aforementioned methods:
 
-.. code-block:: C++
+.. code-block:: c++
 
    double FixSavePos::memory_usage()
    {

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

@@ -51,6 +51,7 @@ Analysis howto
 
    Howto_output
    Howto_chunk
+   Howto_grid
    Howto_temperature
    Howto_elastic
    Howto_kappa
@@ -85,6 +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
-used in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
+formulas implemented in LAMMPS that correspond to formulas commonly used
+in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
 coefficients is done either from special sections in an input data file
 via the :doc:`read_data <read_data>` command or in the input script with
-commands like :doc:`pair_coeff <pair_coeff>` or
-:doc:`bond_coeff <bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc
-page for additional tools that can use CHARMM, AMBER, or Materials
-Studio generated files to assign force field coefficients and convert
-their output into LAMMPS input.
+commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
+<bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc page for
+additional tools that can use CHARMM, AMBER, or Materials Studio
+generated files to assign force field coefficients and convert their
+output into LAMMPS input.
 
-See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM force
-field.  See :ref:`(Cornell) <howto-Cornell>` for a description of the AMBER
-force field.  See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS
-force field.
-
-.. _charmm: http://www.scripps.edu/brooks
-
-.. _amber: http://amber.scripps.edu
+See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
+force field.  See :ref:`(Cornell) <howto-Cornell>` for a description of
+the AMBER force field.  See :ref:`(Sun) <howto-Sun>` for a description
+of the COMPASS force field.
 
 The interaction styles listed below compute force field formulas that
 are consistent with common options in CHARMM or AMBER.  See each
@@ -41,9 +37,10 @@ command's documentation for the formula it computes.
 
 .. note::
 
-   For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released
-   in March 2017.  We recommend they be used instead of the older *charmm*
-   styles.  See discussion of the differences on the :doc:`pair charmm <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
+   For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
+   March 2017.  We recommend they be used instead of the older *charmm*
+   styles.  See discussion of the differences on the :doc:`pair charmm
+   <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
    pages.
 
 COMPASS is a general force field for atomistic simulation of common

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_grid.rst

@@ -0,0 +1,102 @@
+Using distributed grids
+=======================
+
+.. versionadded:: 22Dec2022
+
+LAMMPS has internal capabilities to create uniformly spaced grids
+which overlay the simulation domain.  For 2d and 3d simulations these
+are 2d and 3d grids respectively.  Conceptually a grid can be thought
+of as a collection of grid cells.  Each grid cell can store one or
+more values (data).
+
+The grid cells and data they store are distributed across processors.
+Each processor owns the grid cells (and data) whose center points lie
+within the spatial sub-domain of the processor.  If needed for its
+computations, a processor may also store ghost grid cells with their
+data.
+
+Distributed grids can overlay orthogonal or triclinic simulation
+boxes; see the :doc:`Howto triclinic <Howto_triclinic>` doc page for
+an explanation of the latter.  For a triclinic box, the grid cell
+shape conforms to the shape of the simulation domain,
+e.g. parallelograms instead of rectangles in 2d.
+
+If the box size or shape changes during a simulation, the grid changes
+with it, so that it always overlays the entire simulation domain.  For
+non-periodic dimensions, the grid size in that dimension matches the
+box size, as set by the :doc:`boundary <boundary>` command for fixed
+or shrink-wrapped boundaries.
+
+If load-balancing is invoked by the :doc:`balance <balance>` or
+:doc:`fix balance <fix_balance>` commands, then the sub-domain owned
+by a processor can change which may also change which grid cells they
+own.
+
+Post-processing and visualization of grid cell data can be enabled by
+the :doc:`dump grid <dump>`, :doc:`dump grid/vtk <dump>`, and
+:doc:`dump image <dump_image>` commands.  The latter has an optional
+*grid* keyword.  The `OVITO visualization tool
+<https://www.ovito.org>`_ also plans (as of Nov 2022) to add support
+for visualizing grid cell data (along with atoms) using :doc:`dump
+grid <dump>` output files as input.
+
+.. note::
+
+   For developers, distributed grids are implemented within the code via
+   two classes: Grid2d and Grid3d.  These partition the grid across
+   processors and have methods which allow forward and reverse
+   communication of ghost grid data as well as load balancing.  If you
+   write a new compute or fix which needs a distributed grid, these are
+   the classes to look at.  A new pair style could use a distributed
+   grid by having a fix define it.  Please see the section on
+   :doc:`using distributed grids within style classes <Developer_grid>`
+   for a detailed description.
+
+----------
+
+These are the commands which currently define or use distributed
+grids:
+
+* :doc:`fix ttm/grid <fix_ttm>` - store electron temperature on grid
+* :doc:`fix ave/grid <fix_ave_grid>` - time average per-atom or per-grid values
+* :doc:`compute property/grid <compute_property_grid>` - generate grid IDs and coords
+* :doc:`dump grid <dump>` - output per-grid values in LAMMPS format
+* :doc:`dump grid/vtk <dump>` - output per-grid values in VTK format
+* :doc:`dump image grid <dump_image>` - include colored grid in output images
+* :doc:`pair_style amoeba <pair_amoeba>` - FFT grids
+* :doc:`kspace_style pppm <kspace_style>` (and variants) - FFT grids
+* :doc:`kspace_style msm <kspace_style>` (and variants) - MSM grids
+
+The grids used by the :doc:`kspace_style <kspace_style>` can not be
+referenced by an input script.  However the grids and data created and
+used by the other commands can be.
+
+A compute or fix command may create one or more grids (of different
+sizes).  Each grid can store one or more data fields.  A data field
+can be a single value per grid point (per-grid vector) or multiple
+values per grid point (per-grid array).  See the :doc:`Howto output
+<Howto_output>` doc page for an explanation of how per-grid data can
+be generated by some commands and used by other commands.
+
+A command accesses grid data from a compute or fix using a *grid
+reference* with the following syntax:
+
+* c_ID:gname:dname
+* c_ID:gname:dname[I]
+* f_ID:gname:dname
+* f_ID:gname:dname[I]
+
+The prefix "c\_" or "f\_" refers to the ID of the compute or fix; gname is
+the name of the grid, which is assigned by the compute or fix; dname is
+the name of the data field, which is also assigned by the compute or
+fix.
+
+If the data field is a per-grid vector (one value per grid point),
+then no brackets are used to access the values.  If the data field is
+a per-grid array (multiple values per grid point), then brackets are
+used to specify the column I of the array.  I ranges from 1 to Ncol
+inclusive, where Ncol is the number of columns in the array and is
+defined by the compute or fix.
+
+Currently, there are no per-grid variables implemented in LAMMPS.  We
+may add this feature at some point.

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_output.rst

@@ -22,14 +22,17 @@ commands you specify.
 As discussed below, LAMMPS gives you a variety of ways to determine
 what quantities are computed and printed when the thermodynamics,
 dump, or fix commands listed above perform output.  Throughout this
-discussion, note that users can also :doc:`add their own computes and fixes to LAMMPS <Modify>` which can then generate values that can then be
-output with these commands.
+discussion, note that users can also :doc:`add their own computes and
+fixes to LAMMPS <Modify>` which can then generate values that can then
+be output with these commands.
 
-The following sub-sections discuss different LAMMPS command related
+The following sub-sections discuss different LAMMPS commands related
 to output and the kind of data they operate on and produce:
 
-* :ref:`Global/per-atom/local data <global>`
+* :ref:`Global/per-atom/local/per-grid data <global>`
 * :ref:`Scalar/vector/array data <scalar>`
+* :ref:`Per-grid data <grid>`
+* :ref:`Disambiguation <disambiguation>`
 * :ref:`Thermodynamic output <thermo>`
 * :ref:`Dump file output <dump>`
 * :ref:`Fixes that write output files <fixoutput>`
@@ -42,27 +45,32 @@ to output and the kind of data they operate on and produce:
 
 .. _global:
 
-Global/per-atom/local data
---------------------------
+Global/per-atom/local/per-grid data
+-----------------------------------
 
-Various output-related commands work with three different styles of
-data: global, per-atom, or local.  A global datum is one or more
-system-wide values, e.g. the temperature of the system.  A per-atom
-datum is one or more values per atom, e.g. the kinetic energy of each
-atom.  Local datums are calculated by each processor based on the
-atoms it owns, but there may be zero or more per atom, e.g. a list of
-bond distances.
+Various output-related commands work with four different styles of
+data: global, per-atom, local, and per-grid.  A global datum is one or
+more system-wide values, e.g. the temperature of the system.  A
+per-atom datum is one or more values per atom, e.g. the kinetic energy
+of each atom.  Local datums are calculated by each processor based on
+the atoms it owns, but there may be zero or more per atom, e.g. a list
+of bond distances.
+
+A per-grid datum is one or more values per grid cell, for a grid which
+overlays the simulation domain.  The grid cells and the data they
+store are distributed across processors; each processor owns the grid
+cells whose center point falls within its sub-domain.
 
 .. _scalar:
 
 Scalar/vector/array data
 ------------------------
 
-Global, per-atom, and local datums can each come in three kinds: a
-single scalar value, a vector of values, or a 2d array of values.  The
-doc page for a "compute" or "fix" or "variable" that generates data
-will specify both the style and kind of data it produces, e.g. a
-per-atom vector.
+Global, per-atom, and local datums can come in three kinds: a single
+scalar value, a vector of values, or a 2d array of values.  The doc
+page for a "compute" or "fix" or "variable" that generates data will
+specify both the style and kind of data it produces, e.g. a per-atom
+vector.
 
 When a quantity is accessed, as in many of the output commands
 discussed below, it can be referenced via the following bracket
@@ -83,6 +91,18 @@ the dimension twice (array -> scalar).  Thus a command that uses
 scalar values as input can typically also process elements of a vector
 or array.
 
+.. _grid:
+
+Per-grid data
+------------------------
+
+Per-grid data can come in two kinds: a vector of values (one per grid
+cekk), or a 2d array of values (multiple values per grid ckk).  The
+doc page for a "compute" or "fix" that generates data will specify
+names for both the grid(s) and datum(s) it produces, e.g. per-grid
+vectors or arrays, which can be referenced by other commands.  See the
+:doc:`Howto grid <Howto_grid>` doc page for more details.
+
 .. _disambiguation:
 
 Disambiguation
@@ -90,15 +110,15 @@ Disambiguation
 
 Some computes and fixes produce data in multiple styles, e.g. a global
 scalar and a per-atom vector. Usually the context in which the input
-script references the data determines which style is meant. Example: if
-a compute provides both a global scalar and a per-atom vector, the
+script references the data determines which style is meant. Example:
+if a compute provides both a global scalar and a per-atom vector, the
 former will be accessed by using ``c_ID`` in an equal-style variable,
 while the latter will be accessed by using ``c_ID`` in an atom-style
-variable.  Note that atom-style variable formulas can also access global
-scalars, but in this case it is not possible to do directly because of
-the ambiguity.  Instead, an equal-style variable can be defined which
-accesses the global scalar, and that variable used in the atom-style
-variable formula in place of ``c_ID``.
+variable.  Note that atom-style variable formulas can also access
+global scalars, but in this case it is not possible to do this
+directly because of the ambiguity.  Instead, an equal-style variable
+can be defined which accesses the global scalar, and that variable can
+be used in the atom-style variable formula in place of ``c_ID``.
 
 .. _thermo:
 
@@ -107,15 +127,14 @@ Thermodynamic output
 
 The frequency and format of thermodynamic output is set by the
 :doc:`thermo <thermo>`, :doc:`thermo_style <thermo_style>`, and
-:doc:`thermo_modify <thermo_modify>` commands.  The
-:doc:`thermo_style <thermo_style>` command also specifies what values
-are calculated and written out.  Pre-defined keywords can be specified
-(e.g. press, etotal, etc).  Three additional kinds of keywords can
-also be specified (c_ID, f_ID, v_name), where a :doc:`compute <compute>`
-or :doc:`fix <fix>` or :doc:`variable <variable>` provides the value to be
-output.  In each case, the compute, fix, or variable must generate
-global values for input to the :doc:`thermo_style custom <dump>`
-command.
+:doc:`thermo_modify <thermo_modify>` commands.  The :doc:`thermo_style
+<thermo_style>` command also specifies what values are calculated and
+written out.  Pre-defined keywords can be specified (e.g. press, etotal,
+etc).  Three additional kinds of keywords can also be specified (c_ID,
+f_ID, v_name), where a :doc:`compute <compute>` or :doc:`fix <fix>` or
+:doc:`variable <variable>` provides the value to be output.  In each
+case, the compute, fix, or variable must generate global values for
+input to the :doc:`thermo_style custom <dump>` command.
 
 Note that thermodynamic output values can be "extensive" or
 "intensive".  The former scale with the number of atoms in the system
@@ -141,9 +160,10 @@ There is also a :doc:`dump custom <dump>` format where the user
 specifies what values are output with each atom.  Pre-defined atom
 attributes can be specified (id, x, fx, etc).  Three additional kinds
 of keywords can also be specified (c_ID, f_ID, v_name), where a
-:doc:`compute <compute>` or :doc:`fix <fix>` or :doc:`variable <variable>`
-provides the values to be output.  In each case, the compute, fix, or
-variable must generate per-atom values for input to the :doc:`dump custom <dump>` command.
+:doc:`compute <compute>` or :doc:`fix <fix>` or :doc:`variable
+<variable>` provides the values to be output.  In each case, the
+compute, fix, or variable must generate per-atom values for input to
+the :doc:`dump custom <dump>` command.
 
 There is also a :doc:`dump local <dump>` format where the user specifies
 what local values to output.  A pre-defined index keyword can be
@@ -154,18 +174,23 @@ provides the values to be output.  In each case, the compute or fix
 must generate local values for input to the :doc:`dump local <dump>`
 command.
 
+There is also a :doc:`dump grid <dump>` format where the user
+specifies what per-grid values to output from computes or fixes that
+generate per-grid data.
+
 .. _fixoutput:
 
 Fixes that write output files
 -----------------------------
 
 Several fixes take various quantities as input and can write output
-files: :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
-:doc:`fix ave/correlate <fix_ave_correlate>`, and :doc:`fix print <fix_print>`.
+files: :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/chunk
+<fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix
+ave/correlate <fix_ave_correlate>`, and :doc:`fix print <fix_print>`.
 
-The :doc:`fix ave/time <fix_ave_time>` command enables direct output to
-a file and/or time-averaging of global scalars or vectors.  The user
-specifies one or more quantities as input.  These can be global
+The :doc:`fix ave/time <fix_ave_time>` command enables direct output
+to a file and/or time-averaging of global scalars or vectors.  The
+user specifies one or more quantities as input.  These can be global
 :doc:`compute <compute>` values, global :doc:`fix <fix>` values, or
 :doc:`variables <variable>` of any style except the atom style which
 produces per-atom values.  Since a variable can refer to keywords used
@@ -184,8 +209,14 @@ atoms, e.g. individual molecules.  The per-atom quantities can be atom
 density (mass or number) or atom attributes such as position,
 velocity, force.  They can also be per-atom quantities calculated by a
 :doc:`compute <compute>`, by a :doc:`fix <fix>`, or by an atom-style
-:doc:`variable <variable>`.  The chunk-averaged output of this fix can
-also be used as input to other output commands.
+:doc:`variable <variable>`.  The chunk-averaged output of this fix is
+global and can also be used as input to other output commands.
+
+Note that the :doc:`fix ave/grid <fix_ave_grid>` command can also
+average the same per-atom quantities within spatial bins, but it does
+this for a distributed grid whose grid cells are owned by different
+processors.  It outputs per-grid data, not global data, so it is more
+efficient for large numbers of averaging bins.
 
 The :doc:`fix ave/histo <fix_ave_histo>` command enables direct output
 to a file of histogrammed quantities, which can be global or per-atom
@@ -202,38 +233,53 @@ written to the screen and log file or to a separate file, periodically
 during a running simulation.  The line can contain one or more
 :doc:`variable <variable>` values for any style variable except the
 vector or atom styles).  As explained above, variables themselves can
-contain references to global values generated by :doc:`thermodynamic keywords <thermo_style>`, :doc:`computes <compute>`,
-:doc:`fixes <fix>`, or other :doc:`variables <variable>`, or to per-atom
-values for a specific atom.  Thus the :doc:`fix print <fix_print>`
-command is a means to output a wide variety of quantities separate
-from normal thermodynamic or dump file output.
+contain references to global values generated by :doc:`thermodynamic
+keywords <thermo_style>`, :doc:`computes <compute>`, :doc:`fixes
+<fix>`, or other :doc:`variables <variable>`, or to per-atom values
+for a specific atom.  Thus the :doc:`fix print <fix_print>` command is
+a means to output a wide variety of quantities separate from normal
+thermodynamic or dump file output.
 
 .. _computeoutput:
 
 Computes that process output quantities
 ---------------------------------------
 
-The :doc:`compute reduce <compute_reduce>` and :doc:`compute reduce/region <compute_reduce>` commands take one or more per-atom
-or local vector quantities as inputs and "reduce" them (sum, min, max,
+The :doc:`compute reduce <compute_reduce>` and :doc:`compute
+reduce/region <compute_reduce>` commands take one or more per-atom or
+local vector quantities as inputs and "reduce" them (sum, min, max,
 ave) to scalar quantities.  These are produced as output values which
 can be used as input to other output commands.
 
-The :doc:`compute slice <compute_slice>` command take one or more global
-vector or array quantities as inputs and extracts a subset of their
-values to create a new vector or array.  These are produced as output
-values which can be used as input to other output commands.
+The :doc:`compute slice <compute_slice>` command take one or more
+global vector or array quantities as inputs and extracts a subset of
+their values to create a new vector or array.  These are produced as
+output values which can be used as input to other output commands.
 
-The :doc:`compute property/atom <compute_property_atom>` command takes a
-list of one or more pre-defined atom attributes (id, x, fx, etc) and
+The :doc:`compute property/atom <compute_property_atom>` command takes
+a list of one or more pre-defined atom attributes (id, x, fx, etc) and
 stores the values in a per-atom vector or array.  These are produced
 as output values which can be used as input to other output commands.
-The list of atom attributes is the same as for the :doc:`dump custom <dump>` command.
+The list of atom attributes is the same as for the :doc:`dump custom
+<dump>` command.
 
-The :doc:`compute property/local <compute_property_local>` command takes
-a list of one or more pre-defined local attributes (bond info, angle
-info, etc) and stores the values in a local vector or array.  These
-are produced as output values which can be used as input to other
-output commands.
+The :doc:`compute property/local <compute_property_local>` command
+takes a list of one or more pre-defined local attributes (bond info,
+angle info, etc) and stores the values in a local vector or array.
+These are produced as output values which can be used as input to
+other output commands.
+
+The :doc:`compute property/grid <compute_property_grid>` command takes
+a list of one or more pre-defined per-grid attributes (id, grid cell
+coords, etc) and stores the values in a per-grid vector or array.
+These are produced as output values which can be used as input to the
+:doc:`dump grid <dump>` command.
+
+The :doc:`compute property/chunk <compute_property_chunk>` command
+takes a list of one or more pre-defined chunk attributes (id, count,
+coords for spatial bins) and stores the values in a global vector or
+array.  These are produced as output values which can be used as input
+to other output commands.
 
 .. _fixprocoutput:
 
@@ -247,18 +293,42 @@ a time.
 The :doc:`fix ave/atom <fix_ave_atom>` command performs time-averaging
 of per-atom vectors.  The per-atom quantities can be atom attributes
 such as position, velocity, force.  They can also be per-atom
-quantities calculated by a :doc:`compute <compute>`, by a
-:doc:`fix <fix>`, or by an atom-style :doc:`variable <variable>`.  The
+quantities calculated by a :doc:`compute <compute>`, by a :doc:`fix
+<fix>`, or by an atom-style :doc:`variable <variable>`.  The
 time-averaged per-atom output of this fix can be used as input to
 other output commands.
 
-The :doc:`fix store/state <fix_store_state>` command can archive one or
-more per-atom attributes at a particular time, so that the old values
-can be used in a future calculation or output.  The list of atom
-attributes is the same as for the :doc:`dump custom <dump>` command,
-including per-atom quantities calculated by a :doc:`compute <compute>`,
-by a :doc:`fix <fix>`, or by an atom-style :doc:`variable <variable>`.
-The output of this fix can be used as input to other output commands.
+The :doc:`fix store/state <fix_store_state>` command can archive one
+or more per-atom attributes at a particular time, so that the old
+values can be used in a future calculation or output.  The list of
+atom attributes is the same as for the :doc:`dump custom <dump>`
+command, including per-atom quantities calculated by a :doc:`compute
+<compute>`, by a :doc:`fix <fix>`, or by an atom-style :doc:`variable
+<variable>`.  The output of this fix can be used as input to other
+output commands.
+
+The :doc:`fix ave/grid <fix_ave_grid>` command performs time-averaging
+of either per-atom or per-grid data.
+
+For per-atom data it performs averaging for the atoms within each grid
+cell, similar to the :doc:`fix ave/chunk <fix_ave_chunk>` command when
+its chunks are defined as regular 2d or 3d bins.  The per-atom
+quantities can be atom density (mass or number) or atom attributes
+such as position, velocity, force.  They can also be per-atom
+quantities calculated by a :doc:`compute <compute>`, by a :doc:`fix
+<fix>`, or by an atom-style :doc:`variable <variable>`.
+
+The chief difference between the :doc:`fix ave/grid <fix_ave_grid>`
+and :doc:`fix ave/chunk <fix_ave_chunk>` commands when used in this
+context is that the former uses a distributed grid, while the latter
+uses a global grid.  Distributed means that each processor owns the
+subset of grid cells within its sub-domain.  Global means that each
+processor owns a copy of the entire grid.  The :doc:`fix ave/grid
+<fix_ave_grid>` command is thus more efficient for large grids.
+
+For per-grid data, the :doc:`fix ave/grid <fix_ave_grid>` command
+takes inputs for grid data produced by other computes or fixes and
+averages the values for each grid point over time.
 
 .. _compute:
 
@@ -266,24 +336,25 @@ Computes that generate values to output
 ---------------------------------------
 
 Every :doc:`compute <compute>` in LAMMPS produces either global or
-per-atom or local values.  The values can be scalars or vectors or
-arrays of data.  These values can be output using the other commands
-described in this section.  The page for each compute command
+per-atom or local or per-grid values.  The values can be scalars or
+vectors or arrays of data.  These values can be output using the other
+commands described in this section.  The page for each compute command
 describes what it produces.  Computes that produce per-atom or local
-values have the word "atom" or "local" in their style name.  Computes
-without the word "atom" or "local" produce global values.
+or per-grid values have the word "atom" or "local" or "grid as the
+last word in their style name.  Computes without the word "atom" or
+"local" or "grid" produce global values.
 
 .. _fix:
 
 Fixes that generate values to output
 ------------------------------------
 
-Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom or
-local values which can be accessed by other commands.  The values can
-be scalars or vectors or arrays of data.  These values can be output
-using the other commands described in this section.  The page for
-each fix command tells whether it produces any output quantities and
-describes them.
+Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom
+or local or per-grid values which can be accessed by other commands.
+The values can be scalars or vectors or arrays of data.  These values
+can be output using the other commands described in this section.  The
+page for each fix command tells whether it produces any output
+quantities and describes them.
 
 .. _variable:
 
@@ -300,6 +371,8 @@ computes, fixes, and other variables.  The values generated by
 variables can be used as input to and thus output by the other
 commands described in this section.
 
+Per-grid variables have not (yet) been implemented.
+
 .. _table:
 
 Summary table of output options and data flow between commands
@@ -319,44 +392,52 @@ Also note that, as described above, when a command takes a scalar as
 input, that could be an element of a vector or array.  Likewise a
 vector input could be a column of an array.
 
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| Command                                                | Input                                        | Output                                    |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`thermo_style custom <thermo_style>`              | global scalars                               | screen, log file                          |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`dump custom <dump>`                              | per-atom vectors                             | dump file                                 |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`dump local <dump>`                               | local vectors                                | dump file                                 |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`fix print <fix_print>`                           | global scalar from variable                  | screen, file                              |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`print <print>`                                   | global scalar from variable                  | screen                                    |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`computes <compute>`                              | N/A                                          | global/per-atom/local scalar/vector/array |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`fixes <fix>`                                     | N/A                                          | global/per-atom/local scalar/vector/array |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`variables <variable>`                            | global scalars and vectors, per-atom vectors | global scalar and vector, per-atom vector |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`compute reduce <compute_reduce>`                 | per-atom/local vectors                       | global scalar/vector                      |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`compute slice <compute_slice>`                   | global vectors/arrays                        | global vector/array                       |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`compute property/atom <compute_property_atom>`   | per-atom vectors                             | per-atom vector/array                     |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`compute property/local <compute_property_local>` | local vectors                                | local vector/array                        |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`fix vector <fix_vector>`                         | global scalars                               | global vector                             |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`fix ave/atom <fix_ave_atom>`                     | per-atom vectors                             | per-atom vector/array                     |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`fix ave/time <fix_ave_time>`                     | global scalars/vectors                       | global scalar/vector/array, file          |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`fix ave/chunk <fix_ave_chunk>`                   | per-atom vectors                             | global array, file                        |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`fix ave/histo <fix_ave_histo>`                   | global/per-atom/local scalars and vectors    | global array, file                        |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`fix ave/correlate <fix_ave_correlate>`           | global scalars                               | global array, file                        |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
-| :doc:`fix store/state <fix_store_state>`               | per-atom vectors                             | per-atom vector/array                     |
-+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| Command                                                | Input                                        | Output                                             |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`thermo_style custom <thermo_style>`              | global scalars                               | screen, log file                                   |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`dump custom <dump>`                              | per-atom vectors                             | dump file                                          |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`dump local <dump>`                               | local vectors                                | dump file                                          |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`dump grid <dump>`                                | per-grid vectors                             | dump file                                          |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`fix print <fix_print>`                           | global scalar from variable                  | screen, file                                       |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`print <print>`                                   | global scalar from variable                  | screen                                             |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`computes <compute>`                              | N/A                                          | global/per-atom/local/per-grid scalar/vector/array |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`fixes <fix>`                                     | N/A                                          | global/per-atom/local/per-grid scalar/vector/array |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`variables <variable>`                            | global scalars and vectors, per-atom vectors | global scalar and vector, per-atom vector          |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`compute reduce <compute_reduce>`                 | per-atom/local vectors                       | global scalar/vector                               |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`compute slice <compute_slice>`                   | global vectors/arrays                        | global vector/array                                |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`compute property/atom <compute_property_atom>`   | N/A                                          | per-atom vector/array                              |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`compute property/local <compute_property_local>` | N/A                                          | local vector/array                                 |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`compute property/grid <compute_property_grid>`   | N/A                                          | per-grid vector/array                              |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`compute property/chunk <compute_property_chunk>` | N/A                                          | global vector/array                                |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`fix vector <fix_vector>`                         | global scalars                               | global vector                                      |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`fix ave/atom <fix_ave_atom>`                     | per-atom vectors                             | per-atom vector/array                              |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`fix ave/time <fix_ave_time>`                     | global scalars/vectors                       | global scalar/vector/array, file                   |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`fix ave/chunk <fix_ave_chunk>`                   | per-atom vectors                             | global array, file                                 |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`fix ave/grid <fix_ave_grid>`                     | per-atom vectors or per-grid vectors         | per-grid vector/array                              |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`fix ave/histo <fix_ave_histo>`                   | global/per-atom/local scalars and vectors    | global array, file                                 |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`fix ave/correlate <fix_ave_correlate>`           | global scalars                               | global array, file                                 |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+
+| :doc:`fix store/state <fix_store_state>`               | per-atom vectors                             | per-atom vector/array                              |
++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+

doc/src/Howto_pylammps.rst

@@ -152,14 +152,14 @@ Creating a new instance of PyLammps
 To create a PyLammps object you need to first import the class from the lammps
 module. By using the default constructor, a new *lammps* instance is created.
 
-.. code-block:: Python
+.. code-block:: python
 
    from lammps import PyLammps
    L = PyLammps()
 
 You can also initialize PyLammps on top of this existing *lammps* object:
 
-.. code-block:: Python
+.. code-block:: python
 
    from lammps import lammps, PyLammps
    lmp = lammps()
@@ -180,14 +180,14 @@ For instance, let's take the following LAMMPS command:
 In the original interface this command can be executed with the following
 Python code if *L* was a lammps instance:
 
-.. code-block:: Python
+.. code-block:: python
 
    L.command("region box block 0 10 0 5 -0.5 0.5")
 
 With the PyLammps interface, any command can be split up into arbitrary parts
 separated by white-space, passed as individual arguments to a region method.
 
-.. code-block:: Python
+.. code-block:: python
 
    L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
 
@@ -199,14 +199,14 @@ The benefit of this approach is avoiding redundant command calls and easier
 parameterization. In the original interface parameterization needed to be done
 manually by creating formatted strings.
 
-.. code-block:: Python
+.. code-block:: python
 
    L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
 
 In contrast, methods of PyLammps accept parameters directly and will convert
 them automatically to a final command string.
 
-.. code-block:: Python
+.. code-block:: python
 
    L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
 
@@ -256,7 +256,7 @@ LAMMPS variables can be both defined and accessed via the PyLammps interface.
 
 To define a variable you can use the :doc:`variable <variable>` command:
 
-.. code-block:: Python
+.. code-block:: python
 
    L.variable("a index 2")
 
@@ -265,14 +265,14 @@ A dictionary of all variables is returned by L.variables
 you can access an individual variable by retrieving a variable object from the
 L.variables dictionary by name
 
-.. code-block:: Python
+.. code-block:: python
 
    a = L.variables['a']
 
 The variable value can then be easily read and written by accessing the value
 property of this object.
 
-.. code-block:: Python
+.. code-block:: python
 
    print(a.value)
    a.value = 4
@@ -284,7 +284,7 @@ LAMMPS expressions can be immediately evaluated by using the eval method. The
 passed string parameter can be any expression containing global thermo values,
 variables, compute or fix data.
 
-.. code-block:: Python
+.. code-block:: python
 
    result = L.eval("ke") # kinetic energy
    result = L.eval("pe") # potential energy
@@ -298,7 +298,7 @@ All atoms in the current simulation can be accessed by using the L.atoms list.
 Each element of this list is an object which exposes its properties (id, type,
 position, velocity, force, etc.).
 
-.. code-block:: Python
+.. code-block:: python
 
    # access first atom
    L.atoms[0].id
@@ -311,7 +311,7 @@ position, velocity, force, etc.).
 
 Some properties can also be used to set:
 
-.. code-block:: Python
+.. code-block:: python
 
    # set position in 2D simulation
    L.atoms[0].position = (1.0, 0.0)
@@ -328,7 +328,7 @@ after a run via the L.runs list. This list contains a growing list of run data.
 The first element is the output of the first run, the second element that of
 the second run.
 
-.. code-block:: Python
+.. code-block:: python
 
    L.run(1000)
    L.runs[0] # data of first 1000 time steps
@@ -339,14 +339,14 @@ the second run.
 Each run contains a dictionary of all trajectories. Each trajectory is
 accessible through its thermo name:
 
-.. code-block:: Python
+.. code-block:: python
 
    L.runs[0].thermo.Step # list of time steps in first run
    L.runs[0].thermo.Ke   # list of kinetic energy values in first run
 
 Together with matplotlib plotting data out of LAMMPS becomes simple:
 
-.. code-block:: Python
+.. code-block:: python
 
    import matplotlib.plot as plt
    steps = L.runs[0].thermo.Step
@@ -406,7 +406,7 @@ Four atoms are placed in the simulation and the dihedral potential is applied on
 them using a datafile. Then one of the atoms is rotated along the central axis by
 setting its position from Python, which changes the dihedral angle.
 
-.. code-block:: Python
+.. code-block:: python
 
    phi = [d \* math.pi / 180 for d in range(360)]
 
@@ -439,7 +439,7 @@ Initially, a 2D system is created in a state with minimal energy.
 
 It is then disordered by moving each atom by a random delta.
 
-.. code-block:: Python
+.. code-block:: python
 
    random.seed(27848)
    deltaperturb = 0.2
@@ -458,7 +458,7 @@ It is then disordered by moving each atom by a random delta.
 Finally, the Monte Carlo algorithm is implemented in Python. It continuously
 moves random atoms by a random delta and only accepts certain moves.
 
-.. code-block:: Python
+.. code-block:: python
 
    estart = L.eval("pe")
    elast = estart
@@ -517,7 +517,7 @@ PyLammps can be run in parallel using mpi4py. This python package can be install
 The following is a short example which reads in an existing LAMMPS input file and
 executes it in parallel.  You can find in.melt in the examples/melt folder.
 
-.. code-block:: Python
+.. code-block:: python
 
    from mpi4py import MPI
    from lammps import PyLammps

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 thermal energy of the Langevin thermostat, or to perform a
-relaxation of the magnetic configuration toward an equilibrium state.
+The magnetic damping can also be applied
+using :doc:`fix langevin/spin <fix_langevin_spin>`.
+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
-per atom magnetic quantities. Typically, the orientation of a given
-magnetic spin, or the magnetic force acting on this spin.
+the magnetic energy. The second command
+is :doc:`compute property/atom <compute_property_atom>`.
+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_structured_data.rst

@@ -43,7 +43,7 @@ JSON
      "ke": $(ke)
    }""" file current_state.json screen no
 
-.. code-block:: JSON
+.. code-block:: json
    :caption: current_state.json
 
    {

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

@@ -8,18 +8,28 @@ This site M is located at a fixed distance away from the oxygen along
 the bisector of the HOH bond angle.  A bond style of *harmonic* and an
 angle style of *harmonic* or *charmm* should also be used.
 
-A TIP4P model is run with LAMMPS using either this command
+A TIP4P model is run with LAMMPS using either these commands
 for a cutoff model:
 
+* :doc:`pair_style tip4p/cut <pair_lj_cut_tip4p>`
 * :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
 
-or these two commands for a long-range model:
+or these commands for a long-range model:
 
+* :doc:`pair_style tip4p/long <pair_coul>`
 * :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
+* :doc:`pair_style lj/long/tip4p/long <pair_lj_long>`
+* :doc:`pair_style tip4p/long/soft <pair_fep_soft>`
+* :doc:`pair_style lj/cut/tip4p/long/soft <pair_fep_soft>`
 * :doc:`kspace_style pppm/tip4p <kspace_style>`
+* :doc:`kspace_style pppm/disp/tip4p <kspace_style>`
 
-For both models, the bond lengths and bond angles should be held fixed
-using the :doc:`fix shake <fix_shake>` command.
+The bond lengths and bond angles should be held fixed using the
+:doc:`fix shake <fix_shake>` or :doc:`fix rattle <fix_shake>` command,
+unless a parameterization for a flexible TIP4P model is used.  The
+parameter sets listed below are all for rigid TIP4P model variants and
+thus the bond and angle force constants are not used and can be set to
+any legal value; only equilibrium length and angle are used.
 
 These are the additional parameters (in real units) to set for O and H
 atoms and the water molecule to run a rigid TIP4P model with a cutoff
@@ -87,17 +97,18 @@ solver (e.g. Ewald or PPPM in LAMMPS):
 | LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
 |
 
-Note that the when using the TIP4P pair style, the neighbor list
-cutoff for Coulomb interactions is effectively extended by a distance
-2 \* (OM distance), to account for the offset distance of the
-fictitious charges on O atoms in water molecules.  Thus it is
-typically best in an efficiency sense to use a LJ cutoff >= Coulomb
-cutoff + 2\*(OM distance), to shrink the size of the neighbor list.
-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.
+Note that the when using the TIP4P pair style, the neighbor list cutoff
+for Coulomb interactions is effectively extended by a distance 2 \* (OM
+distance), to account for the offset distance of the fictitious charges
+on O atoms in water molecules.  Thus it is typically best in an
+efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2\*(OM
+distance), to shrink the size of the neighbor list.  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_triclinic.rst

@@ -144,11 +144,6 @@ does not change the atom positions due to non-periodicity.  In this
 mode, if you tilt the system to extreme angles, the simulation will
 simply become inefficient, due to the highly skewed simulation box.
 
-The limitation on not creating a simulation box with a tilt factor
-skewing the box more than half the distance of the parallel box length
-can be overridden via the :doc:`box <box>` command.  Setting the *tilt*
-keyword to *large* allows any tilt factors to be specified.
-
 Box flips that may occur using the :doc:`fix deform <fix_deform>` or
 :doc:`fix npt <fix_nh>` commands can be turned off using the *flip no*
 option with either of the commands.

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
-or pipe them into visualization software directly.  See the `Pizza.py WWW site <pizza_>`_ for details.  Specifically, Pizza.py can convert
-LAMMPS dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
+user-specified atom information, and convert them to various formats or
+pipe them into visualization software directly.  See the `Pizza.py WWW
+site <pizza_>`_ for details.  Specifically, Pizza.py can convert LAMMPS
+dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
 Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
 RasMol visualization programs.  Pizza.py has tools that do interactive
 3d OpenGL visualization and one that creates SVG images of dump file

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

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.rst

@@ -2,12 +2,13 @@ LAMMPS Library Interfaces
 *************************
 
 As described on the :doc:`library interface to LAMMPS <Howto_library>`
-page, LAMMPS can be built as a library (static or shared), so that
-it can be called by another code, used in a :doc:`coupled manner
+page, LAMMPS can be built as a library (static or shared), so that it
+can be called by another code, used in a :doc:`coupled manner
 <Howto_couple>` with other codes, or driven through a :doc:`Python
-script <Python_head>`.  Even the LAMMPS standalone executable is
-essentially a thin wrapper on top of the LAMMPS library, creating a
-LAMMPS instance, processing input and then existing.
+script <Python_head>`.  The LAMMPS standalone executable itself is
+essentially a thin wrapper on top of the LAMMPS library, which creates a
+LAMMPS instance, passes the input for processing to that instance, and
+then exits.
 
 Most of the APIs described below are based on C language wrapper
 functions in the files ``src/library.h`` and ``src/library.cpp``, but
@@ -87,6 +88,18 @@ run LAMMPS in serial mode.
    message retrieved <lammps_get_last_error_message>`.  We thus
    recommend enabling C++ exceptions when using the library interface,
 
+.. admonition:: Using the C library interface as a plugin
+   :class: note
+
+   Rather than including the C library directly and link to the LAMMPS
+   library at compile time, you can use the ``liblammpsplugin.h`` header
+   file and the ``liblammpsplugin.c`` C code in the
+   ``examples/COUPLE/plugin`` folder for an interface to LAMMPS that is
+   largely identical to the regular library interface, only that it will
+   load a LAMMPS shared library file at runtime.  This can be useful for
+   applications where the interface to LAMMPS would be an optional
+   feature.
+
 .. warning::
 
    No checks are made on the arguments of the function calls of the C
@@ -163,5 +176,3 @@ The following links provide some examples and references to the C++ API.
    :maxdepth: 1
 
    Cplusplus
-
-

doc/src/Library_config.rst

@@ -39,7 +39,7 @@ crashes within LAMMPS may be recovered from by enabling
 :ref:`exceptions <exceptions>`, avoiding them proactively is a safer
 approach.
 
-.. code-block:: C
+.. code-block:: c
    :caption: Example for using configuration settings functions
 
    #include "library.h"

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`
 
 --------------------
 
@@ -21,7 +22,7 @@ as the "handle" argument in subsequent function calls until that
 instance is destroyed by calling :cpp:func:`lammps_close`.  Here is a
 simple example demonstrating its use:
 
-.. code-block:: C
+.. code-block:: c
 
    #include "library.h"
    #include <stdio.h>
@@ -115,3 +116,8 @@ calling program.
 
 .. doxygenfunction:: lammps_python_finalize
    :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_error
+   :project: progguide

doc/src/Library_execute.rst

@@ -30,7 +30,7 @@ be included in the file or strings, and expansion of variables with
 ``${name}`` or ``$(expression)`` syntax is performed.
 Below is a short example using some of these functions.
 
-.. code-block:: C
+.. code-block:: c
 
    /* define to make the otherwise hidden prototype for "lammps_open()" visible */
    #define LAMMPS_LIB_MPI

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

@@ -15,24 +15,24 @@ This section documents the following functions:
 
 --------------------
 
-The library interface allows extraction of different kinds of
-information about the active simulation instance and also
-modifications to it.  This enables combining of a LAMMPS simulation
-with other processing and simulation methods computed by the calling
-code, or by another code that is coupled to LAMMPS via the library
-interface.  In some cases the data returned is direct reference to the
-original data inside LAMMPS, cast to a void pointer.  In that case the
-data needs to be cast to a suitable pointer for the calling program to
-access it, and you may need to know the correct dimensions and
-lengths.  This also means you can directly change those value(s) from
-the calling program, e.g. to modify atom positions.  Of course, this
-should be done with care.  When accessing per-atom data, please note
-that this data is the per-processor **local** data and is indexed
-accordingly. Per-atom data can change sizes and ordering at every
-neighbor list rebuild or atom sort event as atoms migrate between
+The library interface allows the extraction of different kinds of
+information about the active simulation instance and also---in some
+cases---to apply modifications to it.  This enables combining of a
+LAMMPS simulation with other processing and simulation methods computed
+by the calling code, or by another code that is coupled to LAMMPS via
+the library interface.  In some cases the data returned is direct
+reference to the original data inside LAMMPS, cast to a void pointer.
+In that case the data needs to be cast to a suitable pointer for the
+calling program to access it, and you may need to know the correct
+dimensions and lengths.  This also means you can directly change those
+value(s) from the calling program (e.g., to modify atom positions).  Of
+course, changing values should be done with care.  When accessing per-atom
+data, please note that these data are the per-processor **local** data and are
+indexed accordingly. Per-atom data can change sizes and ordering at
+every neighbor list rebuild or atom sort event as atoms migrate between
 sub-domains and processors.
 
-.. code-block:: C
+.. code-block:: c
 
    #include "library.h"
    #include <stdio.h>

doc/src/Library_utility.rst

@@ -7,6 +7,7 @@ functions.  They do not directly call the LAMMPS library.
 - :cpp:func:`lammps_encode_image_flags`
 - :cpp:func:`lammps_decode_image_flags`
 - :cpp:func:`lammps_set_fix_external_callback`
+- :cpp:func:`lammps_fix_external_get_force`
 - :cpp:func:`lammps_fix_external_set_energy_global`
 - :cpp:func:`lammps_fix_external_set_energy_peratom`
 - :cpp:func:`lammps_fix_external_set_virial_global`
@@ -19,6 +20,7 @@ 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
@@ -43,6 +45,11 @@ where such memory buffers were allocated that require the use of
 
 -----------------------
 
+.. doxygenfunction:: lammps_fix_external_get_force
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_fix_external_set_energy_global
    :project: progguide
 
@@ -100,3 +107,9 @@ 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/Manual.rst

@@ -42,7 +42,7 @@ descriptions of all commands included in the LAMMPS code.
 .. only:: html
 
    Once you are familiar with LAMMPS, you may want to bookmark
-   :doc:`this page <Commands_all>` since it gives quick access
+   :doc:`this page <Commands_all>` since it gives quick access to
    the documentation for all LAMMPS commands.
 
 .. _lws: https://www.lammps.org

doc/src/Modify_bond.rst

@@ -13,24 +13,65 @@ Here is a brief description of common methods you define in your
 new derived class.  See bond.h, angle.h, dihedral.h, and improper.h
 for details and specific additional methods.
 
-+-----------------------+---------------------------------------------------------------------------------------+
-| init                  | check if all coefficients are set, calls *init_style* (optional)                      |
-+-----------------------+---------------------------------------------------------------------------------------+
-| init_style            | check if style specific conditions are met (optional)                                 |
-+-----------------------+---------------------------------------------------------------------------------------+
-| compute               | compute the molecular interactions (required)                                         |
-+-----------------------+---------------------------------------------------------------------------------------+
-| settings              | apply global settings for all types (optional)                                        |
-+-----------------------+---------------------------------------------------------------------------------------+
-| coeff                 | set coefficients for one type (required)                                              |
-+-----------------------+---------------------------------------------------------------------------------------+
-| equilibrium_distance  | length of bond, used by SHAKE (required, bond only)                                   |
-+-----------------------+---------------------------------------------------------------------------------------+
-| equilibrium_angle     | opening of angle, used by SHAKE (required, angle only)                                |
-+-----------------------+---------------------------------------------------------------------------------------+
-| write & read_restart  | writes/reads coeffs to restart files (required)                                       |
-+-----------------------+---------------------------------------------------------------------------------------+
-| single                | force (bond only) and energy of a single bond or angle (required, bond or angle only) |
-+-----------------------+---------------------------------------------------------------------------------------+
-| memory_usage          | tally memory allocated by the style (optional)                                        |
-+-----------------------+---------------------------------------------------------------------------------------+
++-----------------------+---------------------------------------------------------------------+
+| Required              | "pure" methods that *must* be overridden in a derived class         |
++=======================+=====================================================================+
+| compute               | compute the molecular interactions for all listed items             |
++-----------------------+---------------------------------------------------------------------+
+| coeff                 | set coefficients for one type                                       |
++-----------------------+---------------------------------------------------------------------+
+| equilibrium_distance  | length of bond, used by SHAKE (bond styles only)                    |
++-----------------------+---------------------------------------------------------------------+
+| equilibrium_angle     | opening of angle, used by SHAKE (angle styles only)                 |
++-----------------------+---------------------------------------------------------------------+
+| write & read_restart  | writes/reads coeffs to restart files                                |
++-----------------------+---------------------------------------------------------------------+
+| single                | force/r (bond styles only) and energy of a single bond or angle     |
++-----------------------+---------------------------------------------------------------------+
+
+
++--------------------------------+----------------------------------------------------------------------+
+| Optional                       | methods that have a default or dummy implementation                  |
++================================+======================================================================+
+| init                           | check if all coefficients are set, calls init_style()                |
++--------------------------------+----------------------------------------------------------------------+
+| init_style                     | check if style specific conditions are met                           |
++--------------------------------+----------------------------------------------------------------------+
+| settings                       | apply global settings for all types                                  |
++--------------------------------+----------------------------------------------------------------------+
+| write & read_restart_settings  | writes/reads global style settings to restart files                  |
++--------------------------------+----------------------------------------------------------------------+
+| write_data                     | write corresponding Coeffs section(s) in data file                   |
++--------------------------------+----------------------------------------------------------------------+
+| memory_usage                   | tally memory allocated by the style                                  |
++--------------------------------+----------------------------------------------------------------------+
+| extract                        | provide access to internal data  (bond or angle styles only)         |
++--------------------------------+----------------------------------------------------------------------+
+| reinit                         | reset all type-based parameters, called by fix adapt (bonds only)    |
++--------------------------------+----------------------------------------------------------------------+
+| pack & unpack_forward_comm     | copy data to and from buffer in forward communication (bonds only)   |
++--------------------------------+----------------------------------------------------------------------+
+| pack & unpack_reverse_comm     | copy data to and from buffer in reverse communication (bonds only)   |
++--------------------------------+----------------------------------------------------------------------+
+
+Here is a list of flags or settings that should be set in the
+constructor of the derived class when they differ from the default
+setting.
+
++---------------------------------+------------------------------------------------------------------------------+---------+
+| Name of flag                    | Description                                                                  | default |
++=================================+==============================================================================+=========+
+| writedata                       | 1 if write_data() is implemented                                             | 1       |
++---------------------------------+------------------------------------------------------------------------------+---------+
+| single_extra                    | number of extra single values calculated (bond styles only)                  | 0       |
++---------------------------------+------------------------------------------------------------------------------+---------+
+| partial_flag                    | 1 if bond type can be set to 0 and deleted (bond styles only)                | 0       |
++---------------------------------+------------------------------------------------------------------------------+---------+
+| reinitflag                      | 1 if style has reinit() and is compatible with fix adapt                     | 1       |
++---------------------------------+------------------------------------------------------------------------------+---------+
+| comm_forward                    | size of buffer (in doubles) for forward communication  (bond styles only)    | 0       |
++---------------------------------+------------------------------------------------------------------------------+---------+
+| comm_reverse                    | size of buffer (in doubles) for reverse communication  (bond styles only)    | 0       |
++---------------------------------+------------------------------------------------------------------------------+---------+
+| comm_reverse_off                | size of buffer for reverse communication with newton off (bond styles only)  | 0       |
++---------------------------------+------------------------------------------------------------------------------+---------+

doc/src/Modify_pair.rst

@@ -1,35 +1,121 @@
 Pair styles
 ===========
 
-Classes that compute pairwise interactions are derived from the Pair
-class.  In LAMMPS, pairwise calculation include many-body potentials
-such as EAM or Tersoff where particles interact without a static bond
-topology.  New styles can be created to add new pair potentials to
-LAMMPS.
+Classes that compute pairwise non-bonded interactions are derived from
+the Pair class.  In LAMMPS, pairwise calculation include many-body
+potentials such as EAM, Tersoff, or ReaxFF where particles interact
+without an explicit bond topology but include interactions beyond
+pairwise non-bonded contributions.  New styles can be created to add
+support for additional pair potentials to LAMMPS.  When the
+modifications are small, sometimes it is more effective to derive from
+an existing pair style class.  This latter approach is also used by
+:doc:`Accelerator packages <Speed_packages>` where the accelerated style
+names differ from their base classes by an appended suffix.
 
-Pair_lj_cut.cpp is a simple example of a Pair class, though it
-includes some optional methods to enable its use with rRESPA.
+The file ``src/pair_lj_cut.cpp`` is an example of a Pair class with a
+very simple potential function.  It includes several optional methods to
+enable its use with :doc:`run_style respa <run_style>` and :doc:`compute
+group/group <compute_group_group>`.
 
-Here is a brief description of the class methods in pair.h:
+Here is a brief list of some the class methods in the Pair class that
+*must* be or *may* be overridden in a derived class.
 
 +---------------------------------+---------------------------------------------------------------------+
+| Required                        | "pure" methods that *must* be overridden in a derived class         |
++=================================+=====================================================================+
 | compute                         | workhorse routine that computes pairwise interactions               |
 +---------------------------------+---------------------------------------------------------------------+
-| settings                        | reads the input script line with arguments you define               |
+| settings                        | processes the arguments to the pair_style command                   |
 +---------------------------------+---------------------------------------------------------------------+
-| coeff                           | set coefficients for one i,j type pair                              |
-+---------------------------------+---------------------------------------------------------------------+
-| init_one                        | perform initialization for one i,j type pair                        |
-+---------------------------------+---------------------------------------------------------------------+
-| init_style                      | initialization specific to this pair style                          |
-+---------------------------------+---------------------------------------------------------------------+
-| write & read_restart            | write/read i,j pair coeffs to restart files                         |
-+---------------------------------+---------------------------------------------------------------------+
-| write & read_restart_settings   | write/read global settings to restart files                         |
-+---------------------------------+---------------------------------------------------------------------+
-| single                          | force/r and energy of a single pairwise interaction between 2 atoms |
-+---------------------------------+---------------------------------------------------------------------+
-| compute_inner/middle/outer      | versions of compute used by rRESPA                                  |
+| coeff                           | set coefficients for one i,j type pair, called from pair_coeff      |
 +---------------------------------+---------------------------------------------------------------------+
 
-The inner/middle/outer routines are optional.
++---------------------------------+----------------------------------------------------------------------+
+| Optional                        | methods that have a default or dummy implementation                  |
++=================================+======================================================================+
+| init_one                        | perform initialization for one i,j type pair                         |
++---------------------------------+----------------------------------------------------------------------+
+| init_style                      | style initialization: request neighbor list(s), error checks         |
++---------------------------------+----------------------------------------------------------------------+
+| init_list                       | Neighbor class callback function to pass neighbor list to pair style |
++---------------------------------+----------------------------------------------------------------------+
+| single                          | force/r and energy of a single pairwise interaction between 2 atoms  |
++---------------------------------+----------------------------------------------------------------------+
+| compute_inner/middle/outer      | versions of compute used by rRESPA                                   |
++---------------------------------+----------------------------------------------------------------------+
+| memory_usage                    | return estimated amount of memory used by the pair style             |
++---------------------------------+----------------------------------------------------------------------+
+| modify_params                   | process arguments to pair_modify command                             |
++---------------------------------+----------------------------------------------------------------------+
+| extract                         | provide access to internal scalar or per-type data like cutoffs      |
++---------------------------------+----------------------------------------------------------------------+
+| extract_peratom                 | provide access to internal per-atom data                             |
++---------------------------------+----------------------------------------------------------------------+
+| setup                           | initialization at the beginning of a run                             |
++---------------------------------+----------------------------------------------------------------------+
+| finish                          | called at the end of a run, e.g. to print                            |
++---------------------------------+----------------------------------------------------------------------+
+| write & read_restart            | write/read i,j pair coeffs to restart files                          |
++---------------------------------+----------------------------------------------------------------------+
+| write & read_restart_settings   | write/read global settings to restart files                          |
++---------------------------------+----------------------------------------------------------------------+
+| write_data                      | write Pair Coeffs section to data file                               |
++---------------------------------+----------------------------------------------------------------------+
+| write_data_all                  | write PairIJ Coeffs section to data file                             |
++---------------------------------+----------------------------------------------------------------------+
+| pack & unpack_forward_comm      | copy data to and from buffer if style uses forward communication     |
++---------------------------------+----------------------------------------------------------------------+
+| pack & unpack_reverse_comm      | copy data to and from buffer if style uses reverse communication     |
++---------------------------------+----------------------------------------------------------------------+
+| reinit                          | reset all type-based parameters, called by fix adapt for example     |
++---------------------------------+----------------------------------------------------------------------+
+| reset_dt                        | called when the time step is changed by timestep or fix reset/dt     |
++---------------------------------+----------------------------------------------------------------------+
+
+Here is a list of flags or settings that should be set in the
+constructor of the derived pair class when they differ from the default
+setting.
+
++---------------------------------+-------------------------------------------------------------+---------+
+| Name of flag                    | Description                                                 | default |
++=================================+=============================================================+=========+
+| single_enable                   | 1 if single() method is implemented, 0 if missing           | 1       |
++---------------------------------+-------------------------------------------------------------+---------+
+| respa_enable                    | 1 if pair style has compute_inner/middle/outer()            | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| restartinfo                     | 1 if pair style writes its settings to a restart            | 1       |
++---------------------------------+-------------------------------------------------------------+---------+
+| one_coeff                       | 1 if only a pair_coeff * * command is allowed               | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| manybody_flag                   | 1 if pair style is a manybody potential                     | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| unit_convert_flag               | value != 0 indicates support for unit conversion            | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| no_virial_fdotr_compute         | 1 if pair style does not call virial_fdotr_compute()        | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| writedata                       | 1 if write_data() and write_data_all() are implemented      | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| comm_forward                    | size of buffer (in doubles) for forward communication       | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| comm_reverse                    | size of buffer (in doubles) for reverse communication       | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| ghostneigh                      | 1 if cutghost is set and style uses neighbors of ghosts     | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| finitecutflag                   | 1 if cutoff depends on diameter of atoms                    | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| reinitflag                      | 1 if style has reinit() and is compatible with fix adapt    | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| ewaldflag                       | 1 if compatible with kspace_style ewald                     | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| pppmflag                        | 1 if compatible with kspace_style pppm                      | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| msmflag                         | 1 if compatible with kspace_style msm                       | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| dispersionflag                  | 1 if compatible with ewald/disp or pppm/disp                | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| tip4pflag                       | 1 if compatible with kspace_style pppm/tip4p                | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| dipoleflag                      | 1 if compatible with dipole kspace_style                    | 0       |
++---------------------------------+-------------------------------------------------------------+---------+
+| spinflag                        | 1 if compatible with spin kspace_style                      | 0       |
++---------------------------------+-------------------------------------------------------------+---------+

doc/src/Modify_style.rst

@@ -359,6 +359,12 @@ you are uncertain, please ask.
 
 - I/O is done via the C-style stdio library and **not** iostreams.
 
+- Do not use so-called "alternative tokens" like ``and``, ``or``,
+  ``not`` and similar, but rather use the corresponding operators
+  ``&&``, ``||``, and ``!``.  The alternative tokens are not available
+  by default on all compilers, and also we want to maintain a consistent
+  programming style.
+
 - Output to the screen and the logfile should be using the corresponding
   FILE pointers and only be done on MPI rank 0.  Use the :cpp:func:`utils::logmesg`
   convenience function where possible.

doc/src/Packages_details.rst

@@ -80,6 +80,7 @@ page gives those details.
    * :ref:`ML-HDNNP <PKG-ML-HDNNP>`
    * :ref:`ML-IAP <PKG-ML-IAP>`
    * :ref:`ML-PACE <PKG-ML-PACE>`
+   * :ref:`ML-POD <PKG-ML-POD>`
    * :ref:`ML-QUIP <PKG-ML-QUIP>`
    * :ref:`ML-RANN <PKG-ML-RANN>`
    * :ref:`ML-SNAP <PKG-ML-SNAP>`
@@ -134,6 +135,8 @@ 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.
@@ -198,6 +201,7 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
 * :doc:`Howto spherical <Howto_spherical>`
 * :doc:`pair_style gayberne <pair_gayberne>`
 * :doc:`pair_style resquared <pair_resquared>`
+* :doc:`pair_style ylz <pair_ylz>`
 * `doc/PDF/pair_gayberne_extra.pdf <PDF/pair_gayberne_extra.pdf>`_
 * `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_
 * examples/ASPHERE
@@ -364,6 +368,8 @@ 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 +598,8 @@ 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
@@ -858,7 +866,7 @@ ELECTRODE package
 The ELECTRODE package allows the user to enforce a constant potential method for
 groups of atoms that interact with the remaining atoms as electrolyte.
 
-**Authors:** The ELECTRODE library is written and maintained by Ludwig
+**Authors:** The ELECTRODE package is written and maintained by Ludwig
 Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and
 Robert Meissner (TUHH, Hamburg, Germany).
 
@@ -871,7 +879,7 @@ This package has :ref:`specific installation instructions <electrode>` on the
 
 **Supporting info:**
 
-* :doc:`fix electrode/conp <fix_electrode_conp>`
+* :doc:`fix electrode/conp <fix_electrode>`
 
 ----------
 
@@ -1071,7 +1079,7 @@ 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.
@@ -1478,8 +1486,9 @@ MC package
 
 Several fixes and a pair style that have Monte Carlo (MC) or MC-like
 attributes.  These include fixes for creating, breaking, and swapping
-bonds, for performing atomic swaps, and performing grand-canonical MC
-(GCMC) or similar processes in conjunction with dynamics.
+bonds, for performing atomic swaps, and performing grand canonical
+MC (GCMC), semi-grand canonical MC (SGCMC), or similar processes in
+conjunction with molecular dynamics (MD).
 
 **Supporting info:**
 
@@ -1491,6 +1500,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
 * :doc:`fix bond/swap <fix_bond_swap>`
 * :doc:`fix charge/regulation <fix_charge_regulation>`
 * :doc:`fix gcmc <fix_gcmc>`
+* :doc:`fix sgcmc <fix_sgcmc>`
 * :doc:`fix tfmc <fix_tfmc>`
 * :doc:`fix widom <fix_widom>`
 * :doc:`pair_style dsmc <pair_dsmc>`
@@ -1512,6 +1522,8 @@ 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 +1608,8 @@ 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 +1702,8 @@ compiled on your system.
 
 **Author:** Andreas Singraber
 
+.. versionadded:: 27May2021
+
 **Install:**
 
 This package has :ref:`specific installation instructions <ml-hdnnp>` on the
@@ -1722,6 +1738,8 @@ must be installed.
 
 **Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
 
+.. versionadded:: 30Jun2020
+
 **Supporting info:**
 
 * src/ML-IAP: filenames -> commands
@@ -1766,6 +1784,8 @@ 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
@@ -1779,6 +1799,39 @@ This package has :ref:`specific installation instructions <ml-pace>` on the
 
 ----------
 
+.. _PKG-ML-POD:
+
+ML-POD package
+-------------------
+
+**Contents:**
+
+A pair style and fitpod style for Proper Orthogonal Descriptors
+(POD). POD is a methodology for deriving descriptors based on the proper
+orthogonal decomposition. The ML-POD package provides an efficient
+implementation for running simulations with POD potentials, along with
+fitting the potentials natively in LAMMPS.
+
+**Authors:**
+
+Ngoc Cuong Nguyen (MIT), Andrew Rohskopf (Sandia)
+
+.. versionadded:: 22Dec2022
+
+**Install:**
+
+This package has :ref:`specific installation instructions <ml-pod>` on the
+:doc:`Build extras <Build_extras>` page.
+
+**Supporting info:**
+
+* src/ML-POD: filenames -> commands
+* :doc:`pair_style pod <pair_pod>`
+* :doc:`command_style fitpod <fitpod_command>`
+* examples/PACKAGES/pod
+
+----------
+
 .. _PKG-ML-QUIP:
 
 ML-QUIP package
@@ -1829,6 +1882,8 @@ 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 +2009,7 @@ 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 +2100,7 @@ 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 +2111,7 @@ 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 +2255,7 @@ 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 +2320,8 @@ 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 +2475,7 @@ 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 +2887,7 @@ 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 +2921,9 @@ 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 +2960,13 @@ 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/Packages_list.rst

@@ -155,7 +155,7 @@ whether an extra library is needed to build and use the package:
      - no
    * - :ref:`ELECTRODE <PKG-ELECTRODE>`
      - electrode charges to match potential
-     - :doc:`fix electrode/conp <fix_electrode_conp>`
+     - :doc:`fix electrode/conp <fix_electrode>`
      - PACKAGES/electrode
      - no
    * - :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
@@ -298,6 +298,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`pair pace <pair_pace>`
      - PACKAGES/pace
      - ext
+   * - :ref:`ML-POD <PKG-ML-POD>`
+     - Proper orthogonal decomposition potentials
+     - :doc:`pair pod <pair_pod>`
+     - pod
+     - ext
    * - :ref:`ML-QUIP <PKG-ML-QUIP>`
      - QUIP/libatoms interface
      - :doc:`pair_style quip <pair_quip>`

doc/src/Python_atoms.rst

@@ -58,7 +58,7 @@ against invalid accesses.
       Each element of this list is a :py:class:`Atom <lammps.Atom>` or :py:class:`Atom2D <lammps.Atom2D>` object. The attributes of
       these objects provide access to their data (id, type, position, velocity, force, etc.):
 
-      .. code-block:: Python
+      .. code-block:: python
 
          # access first atom
          L.atoms[0].id
@@ -71,7 +71,7 @@ against invalid accesses.
 
       Some attributes can be changed:
 
-      .. code-block:: Python
+      .. code-block:: python
 
          # set position in 2D simulation
          L.atoms[0].position = (1.0, 0.0)