Merge branch 'develop' into gran-temp

.github/CODEOWNERS

@@ -63,6 +63,7 @@ src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
 src/REPLICA/*_grem.*                @dstelter92
 src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
+src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
 src/MISC/*_tracker.*                @jtclemm
 src/MC/fix_gcmc.*                   @athomps
 src/MC/fix_sgcmc.*                  @athomps
@@ -149,12 +150,12 @@ tools/vim/*           @hammondkd
 unittest/*            @akohlmey
 
 # cmake
-cmake/*               @junghans @rbberger
+cmake/*               @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/COLVARS.cmake @rbberger @giacomofiorin
-cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
+cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
 cmake/presets/*.cmake @akohlmey
 
 # python

.github/workflows/codeql-analysis.yml

@@ -49,7 +49,9 @@ jobs:
       shell: bash
       working-directory: build
       run: |
-        cmake -C ../cmake/presets/most.cmake ../cmake
+        cmake -C ../cmake/presets/most.cmake \
+              -D DOWNLOAD_POTENTIALS=off \
+              ../cmake
         cmake --build . --parallel 2
 
     - name: Perform CodeQL Analysis

.github/workflows/compile-msvc.yml

@@ -36,6 +36,7 @@ jobs:
         nuget install MSMPIsdk
         nuget install MSMPIDIST
         cmake -C cmake/presets/windows.cmake \
+              -D DOWNLOAD_POTENTIALS=off \
               -D PKG_PYTHON=on \
               -D WITH_PNG=off \
               -D WITH_JPEG=off \
@@ -43,7 +44,7 @@ jobs:
               -D BUILD_SHARED_LIBS=on \
               -D LAMMPS_EXCEPTIONS=on \
               -D ENABLE_TESTING=on
-        cmake --build build --config Release
+        cmake --build build --config Release --parallel 2
 
     - name: Run LAMMPS executable
       shell: bash

.github/workflows/unittest-macos.yml

@@ -47,6 +47,7 @@ jobs:
         python3 -m pip install pyyaml
         cmake -C ../cmake/presets/clang.cmake \
               -C ../cmake/presets/most.cmake \
+              -D DOWNLOAD_POTENTIALS=off \
               -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
               -D CMAKE_C_COMPILER_LAUNCHER=ccache \
               -D ENABLE_TESTING=on \

.gitignore

@@ -55,3 +55,5 @@ out/RelWithDebInfo
 out/Release
 out/x86
 out/x64
+src/Makefile.package-e
+src/Makefile.package.settings-e

SECURITY.md

@@ -30,18 +30,23 @@ for unicode characters and only all-ASCII source code is accepted.
 
 # Version Updates
 
-LAMMPS follows continuous release development model.  We aim to keep to
+LAMMPS follows a continuous release development model.  We aim to keep
-keep the development version (develop branch) always fully functional
+the development version (`develop` branch) always fully functional and
-and employ a variety of automatic testing procedures to detect failures
+employ a variety of automatic testing procedures to detect failures of
-of existing functionality from adding or modifying features.  Most of
+existing functionality from adding or modifying features.  Most of those
-those tests are run on pull requests *before* merging to the development
+tests are run on pull requests and must be passed *before* merging to
-branch.  The develop branch is protected, so all changes *must* be
+the `develop` branch.  The `develop` branch is protected, so all changes
-submitted as a pull request and thus cannot avoid the automated tests.
+*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
+`release` branch is fast-forwarded to that tag.  This is referred to to
-applied to the current development branch and thus will be available in
+as a "feature release".  Bug fixes and updates are applied first to the
-the next (patch) release.  For stable releases, selected bug fixes are
+`develop` branch.  Later, they appear in the `release` branch when the
-back-ported and occasionally published as update releases.  There are
+next patch release occurs.  For stable releases, backported bug fixes
-only updates to the latest stable release.
+and infrastructure updates are first applied to the `maintenance` branch
+and then merged to `stable` and published as "updates".  For a new
+stable release the `stable` branch is updated to the corresponding state
+of the `release` branch and a new stable tag is applied in addition to
+the release tag.

cmake/CMakeLists.txt

@@ -168,8 +168,8 @@ endif()
 ########################################################################
 # User input options                                                   #
 ########################################################################
-# set path to python interpreter and thus enforcing python version if
+# set path to python interpreter and thus enforcing python version when
-# when in a virtual environment and PYTHON_EXECUTABLE is not set on command line
+# in a virtual environment and PYTHON_EXECUTABLE is not set on command line
 if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
   if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
     set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
@@ -265,6 +265,7 @@ set(STANDARD_PACKAGES
   MC
   MDI
   MEAM
+  MESONT
   MGPT
   MISC
   ML-HDNNP
@@ -308,9 +309,8 @@ set(STANDARD_PACKAGES
   YAFF)
 
 set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT INTEL OPENMP)
-set(EXTRA_PACKAGES MESONT)
 
-foreach(PKG ${STANDARD_PACKAGES} ${EXTRA_PACKAGES} ${SUFFIX_PACKAGES})
+foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
@@ -520,7 +520,7 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE MESONT NETCDF
+foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
         PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MSCG COMPRESS ML-PACE LEPTON)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
@@ -538,7 +538,10 @@ set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine
 separate_arguments(CMAKE_TUNE_FLAGS)
 foreach(_FLAG ${CMAKE_TUNE_FLAGS})
   target_compile_options(lammps PRIVATE ${_FLAG})
+  # skip these flags when linking the main executable
+  if(NOT (("${_FLAG}" STREQUAL "-Xcudafe") OR (("${_FLAG}" STREQUAL "--diag_suppress=unrecognized_pragma"))))
     target_compile_options(lmp PRIVATE ${_FLAG})
+  endif()
 endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
@@ -566,7 +569,9 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
 ########################################################
 # Fetch missing external files and archives for packages
 ########################################################
-foreach(PKG ${STANDARD_PACKAGES} ${EXTRA_PACKAGES} ${SUFFIX_PACKAGES})
+option(DOWNLOAD_POTENTIALS "Automatically download large potential files" ON)
+mark_as_advanced(DOWNLOAD_POTENTIALS)
+foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   if(PKG_${PKG})
     FetchPotentials(${LAMMPS_SOURCE_DIR}/${PKG} ${LAMMPS_POTENTIALS_DIR})
   endif()
@@ -706,7 +711,7 @@ target_include_directories(lammps PRIVATE ${LAMMPS_STYLE_HEADERS_DIR})
 ######################################
 set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")
 set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] =  {\n")
-set(temp_PKG_LIST ${STANDARD_PACKAGES} ${EXTRA_PACKAGES} ${SUFFIX_PACKAGES})
+set(temp_PKG_LIST ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
 list(SORT temp_PKG_LIST)
 foreach(PKG ${temp_PKG_LIST})
     if(PKG_${PKG})
@@ -851,35 +856,6 @@ else()
     ${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
 endif()
 
-###############################################################################
-# Add LAMMPS python module to "install" target. This is taylored for building
-# LAMMPS for package managers and with different prefix settings.
-# This requires either a shared library or that the PYTHON package is included.
-###############################################################################
-if(BUILD_SHARED_LIBS OR PKG_PYTHON)
-  if(CMAKE_VERSION VERSION_LESS 3.12)
-    # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
-    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
-    find_package(PythonInterp) # Deprecated since version 3.12
-    if(PYTHONINTERP_FOUND)
-      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
-  else()
-    # backward compatibility
-    if(PYTHON_EXECUTABLE)
-      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
-    find_package(Python COMPONENTS Interpreter)
-  endif()
-  if(Python_EXECUTABLE)
-    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()
-
 include(Testing)
 include(CodeCoverage)
 include(CodingStandard)
@@ -891,6 +867,23 @@ if(ClangFormat_FOUND)
     WORKING_DIRECTORY ${LAMMPS_SOURCE_DIR})
 endif()
 
+# extract Kokkos compilation settings
+get_cmake_property(_allvars VARIABLES)
+foreach(_var ${_allvars})
+  if(${_var})
+    string(REGEX MATCH "Kokkos_ENABLE_(SERIAL|THREADS|OPENMP|CUDA|HIP|SYCL|OPENMPTARGET|HPX)" _match ${_var})
+    if(_match)
+      string(REGEX REPLACE "Kokkos_ENABLE_(OPENMP|SERIAL|CUDA|HIP|SYCL)" "\\1" _match ${_var})
+      list(APPEND KOKKOS_DEVICE ${_match})
+    endif()
+    string(REGEX MATCH "Kokkos_ARCH" _match ${_var})
+    if(_match)
+      string(REGEX REPLACE "Kokkos_ARCH_(.*)" "\\1" _match ${_var})
+      list(APPEND KOKKOS_ARCH ${_match})
+    endif()
+  endif()
+endforeach()
+
 get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
 if(BUILD_IS_MULTI_CONFIG)
   set(LAMMPS_BUILD_TYPE "Multi-Config")
@@ -910,7 +903,7 @@ message(STATUS "<<< Build configuration >>>
 # Print package summary
 ###############################################################################
 set(ENABLED_PACKAGES)
-foreach(PKG ${STANDARD_PACKAGES} ${EXTRA_PACKAGES} ${SUFFIX_PACKAGES})
+foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   if(PKG_${PKG})
     list(APPEND ENABLED_PACKAGES ${PKG})
   endif()
@@ -988,6 +981,12 @@ if(PKG_GPU)
   endif()
   message(STATUS "GPU precision:            ${GPU_PREC}")
 endif()
+if(PKG_KOKKOS)
+  message(STATUS "Kokkos Devices: ${KOKKOS_DEVICE}")
+  if(KOKKOS_ARCH)
+    message(STATUS "Kokkos Architecture: ${KOKKOS_ARCH}")
+  endif()
+endif()
 if(PKG_KSPACE)
   message(STATUS "<<< FFT settings >>>
 -- Primary FFT lib:  ${FFT}")

cmake/Modules/Documentation.cmake

@@ -56,14 +56,25 @@ if(BUILD_DOC)
   )
 
   set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
-  set(MATHJAX_MD5 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball")
+  set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball")
   mark_as_advanced(MATHJAX_URL)
+  GetFallbackURL(MATHJAX_URL MATHJAX_FALLBACK)
 
   # download mathjax distribution and unpack to folder "mathjax"
   if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
-    file(DOWNLOAD ${MATHJAX_URL}
+    if(EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
-      "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
+      file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
-      EXPECTED_MD5 ${MATHJAX_MD5})
+    endif()
+    if(NOT "${DL_MD5}" STREQUAL "${MATHJAX_MD5}")
+      file(DOWNLOAD ${MATHJAX_URL} "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz" STATUS DL_STATUS SHOW_PROGRESS)
+      file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz DL_MD5)
+      if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${MATHJAX_MD5}"))
+        message(WARNING "Download from primary URL ${MATHJAX_URL} failed\nTrying fallback URL ${MATHJAX_FALLBACK}")
+        file(DOWNLOAD ${MATHJAX_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${MATHJAX_MD5} SHOW_PROGRESS)
+      endif()
+    else()
+      message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+    endif()
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
     file(GLOB MATHJAX_VERSION_DIR ${CONFIGURE_DEPENDS} ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
     execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)

cmake/Modules/ExternalCMakeProject.cmake

@@ -9,8 +9,22 @@ function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
 
   get_filename_component(archive ${url} NAME)
   file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)
+  if(EXISTS ${CMAKE_BINARY_DIR}/_deps/${archive})
+    file(MD5 ${CMAKE_BINARY_DIR}/_deps/${archive} DL_MD5)
+  endif()
+  if(NOT "${DL_MD5}" STREQUAL "${hash}")
     message(STATUS "Downloading ${url}")
-  file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
+    file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} STATUS DL_STATUS SHOW_PROGRESS)
+    file(MD5 ${CMAKE_BINARY_DIR}/_deps/${archive} DL_MD5)
+    if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${hash}"))
+      set(${target}_URL ${url})
+      GetFallbackURL(${target}_URL fallback)
+      message(WARNING "Download from primary URL ${url} failed\nTrying fallback URL ${fallback}")
+      file(DOWNLOAD ${fallback} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
+    endif()
+  else()
+    message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/_deps/${archive}")
+  endif()
   message(STATUS "Unpacking and configuring ${archive}")
   execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ${CMAKE_BINARY_DIR}/_deps/${archive}
     WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)

cmake/Modules/LAMMPSInterfacePlugin.cmake

@@ -88,6 +88,18 @@ function(get_lammps_version version_header variable)
     set(${variable} "${date}" PARENT_SCOPE)
 endfunction()
 
+# determine canonical URL for downloading backup copy from download.lammps.org/thirdparty
+function(GetFallbackURL input output)
+  string(REPLACE "_URL" "" _tmp ${input})
+  string(TOLOWER ${_tmp} libname)
+  string(REGEX REPLACE "^https://.*/([^/]+gz)" "${LAMMPS_THIRDPARTY_URL}/${libname}-\\1" newurl "${${input}}")
+  if ("${newurl}" STREQUAL "${${input}}")
+    set(${output} "" PARENT_SCOPE)
+  else()
+    set(${output} ${newurl} PARENT_SCOPE)
+  endif()
+endfunction(GetFallbackURL)
+
 #################################################################################
 # LAMMPS C++ interface. We only need the header related parts except on windows.
 add_library(lammps INTERFACE)

cmake/Modules/LAMMPSUtils.cmake

@@ -99,8 +99,15 @@ function(check_for_autogen_files source_dir)
 endfunction()
 
 macro(pkg_depends PKG1 PKG2)
-  if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
+  if(DEFINED BUILD_${PKG2})
-    message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be built with the ${PKG2} package")
+    if(PKG_${PKG1} AND NOT BUILD_${PKG2})
+      message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be built with -D BUILD_${PKG2}=ON")
+    endif()
+  elseif(DEFINED PKG_${PKG2})
+    if(PKG_${PKG1} AND NOT PKG_${PKG2})
+      message(WARNING "The ${PKG1} package depends on the ${PKG2} package. Enabling it.")
+      set(PKG_${PKG2} ON CACHE BOOL "" FORCE)
+    endif()
   endif()
 endmacro()
 
@@ -118,6 +125,7 @@ endfunction(GenerateBinaryHeader)
 
 # fetch missing potential files
 function(FetchPotentials pkgfolder potfolder)
+  if(DOWNLOAD_POTENTIALS)
     if(EXISTS "${pkgfolder}/potentials.txt")
       file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
       foreach(line ${linelist})
@@ -130,7 +138,7 @@ function(FetchPotentials pkgfolder potfolder)
         endif()
         if(NOT sum STREQUAL oldsum)
           message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
-        string(MD5 TMP_EXT "${CMAKE_BINARY_DIR}")
+          string(RANDOM LENGTH 10 TMP_EXT)
           file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}"
             EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
           file(COPY "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}" DESTINATION "${LAMMPS_POTENTIALS_DIR}")
@@ -138,6 +146,7 @@ function(FetchPotentials pkgfolder potfolder)
         endif()
       endforeach()
     endif()
+  endif()
 endfunction(FetchPotentials)
 
 # set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
@@ -149,3 +158,15 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
   set(CMAKE_LINUX_DISTRO ${distro})
   set(CMAKE_DISTRO_VERSION ${disversion})
 endif()
+
+# determine canonical URL for downloading backup copy from download.lammps.org/thirdparty
+function(GetFallbackURL input output)
+  string(REPLACE "_URL" "" _tmp ${input})
+  string(TOLOWER ${_tmp} libname)
+  string(REGEX REPLACE "^https://.*/([^/]+gz)" "${LAMMPS_THIRDPARTY_URL}/${libname}-\\1" newurl "${${input}}")
+  if ("${newurl}" STREQUAL "${${input}}")
+    set(${output} "" PARENT_SCOPE)
+  else()
+    set(${output} ${newurl} PARENT_SCOPE)
+  endif()
+endfunction(GetFallbackURL)

cmake/Modules/Packages/COMPRESS.cmake

@@ -1,4 +1,9 @@
-find_package(ZLIB REQUIRED)
+find_package(ZLIB)
+if(NOT ZLIB_FOUND)
+  message(WARNING "No Zlib development support found. Disabling COMPRESS package...")
+  set(PKG_COMPRESS OFF CACHE BOOL "" FORCE)
+  return()
+endif()
 target_link_libraries(lammps PRIVATE ZLIB::ZLIB)
 
 find_package(PkgConfig QUIET)

cmake/Modules/Packages/GPU.cmake

@@ -26,6 +26,19 @@ elseif(GPU_PREC STREQUAL "SINGLE")
   set(GPU_PREC_SETTING "SINGLE_SINGLE")
 endif()
 
+option(GPU_DEBUG "Enable debugging code of the GPU package" OFF)
+mark_as_advanced(GPU_DEBUG)
+
+if(PKG_AMOEBA AND FFT_SINGLE)
+  message(FATAL_ERROR "GPU acceleration of AMOEBA is not (yet) compatible with single precision FFT")
+endif()
+
+if (PKG_AMOEBA)
+  list(APPEND GPU_SOURCES
+              ${GPU_SOURCES_DIR}/amoeba_convolution_gpu.h
+              ${GPU_SOURCES_DIR}/amoeba_convolution_gpu.cpp)
+endif()
+
 file(GLOB GPU_LIB_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
 file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
@@ -47,9 +60,9 @@ if(GPU_API STREQUAL "CUDA")
   option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
   if(CUDA_MPS_SUPPORT)
     if(CUDPP_OPT)
-      message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DGPU_CUDA_MPS_SUPPORT=ON")
+      message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DCUDA_MPS_SUPPORT=ON")
     endif()
-    set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
+    set(GPU_CUDA_MPS_FLAGS "-DCUDA_MPS_SUPPORT")
   endif()
 
   set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
@@ -85,9 +98,11 @@ if(GPU_API STREQUAL "CUDA")
   # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
   if(CUDA_VERSION VERSION_LESS 8.0)
     message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
-  elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+  elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0")
     message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
     set(GPU_CUDA_GENCODE "-arch=all")
+  elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+    set(GPU_CUDA_GENCODE "-arch=all")
   else()
     # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
     if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
@@ -151,7 +166,12 @@ if(GPU_API STREQUAL "CUDA")
   add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
   target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
   target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
-  target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
+  target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} ${GPU_CUDA_MPS_FLAGS})
+  if(GPU_DEBUG)
+    target_compile_definitions(gpu PRIVATE -DUCL_DEBUG -DGERYON_KERNEL_DUMP)
+  else()
+    target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DUCL_NO_EXIT)
+  endif()
   if(CUDPP_OPT)
     target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
     target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
@@ -192,6 +212,7 @@ elseif(GPU_API STREQUAL "OPENCL")
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
+    ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_hippo.cu
   )
 
   foreach(GPU_KERNEL ${GPU_LIB_CU})
@@ -208,6 +229,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
   GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
   GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
+  GenerateOpenCLHeader(hippo ${CMAKE_CURRENT_BINARY_DIR}/gpu/hippo_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_hippo_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_hippo.cu)
 
   list(APPEND GPU_LIB_SOURCES
     ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
@@ -217,14 +239,18 @@ elseif(GPU_API STREQUAL "OPENCL")
     ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
     ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
     ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
+    ${CMAKE_CURRENT_BINARY_DIR}/gpu/hippo_cl.h
   )
 
   add_library(gpu STATIC ${GPU_LIB_SOURCES})
   target_link_libraries(gpu PRIVATE OpenCL::OpenCL)
   target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu)
-  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
+  target_compile_definitions(gpu PRIVATE -DUSE_OPENCL -D_${GPU_PREC_SETTING})
-  target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
+  if(GPU_DEBUG)
-
+    target_compile_definitions(gpu PRIVATE -DUCL_DEBUG -DGERYON_KERNEL_DUMP)
+  else()
+    target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
+  endif()
   target_link_libraries(lammps PRIVATE gpu)
 
   add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
@@ -261,7 +287,7 @@ elseif(GPU_API STREQUAL "HIP")
 
   set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
 
-  if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
+  if(HIP_PLATFORM STREQUAL "amd")
     set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
   elseif(HIP_PLATFORM STREQUAL "spirv")
     set(HIP_ARCH "spirv" CACHE STRING "HIP target architecture")
@@ -334,7 +360,7 @@ elseif(GPU_API STREQUAL "HIP")
     set(CUBIN_FILE   "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
     set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
 
-    if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
+    if(HIP_PLATFORM STREQUAL "amd")
         configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
 
         if(HIP_COMPILER STREQUAL "clang")
@@ -374,8 +400,12 @@ elseif(GPU_API STREQUAL "HIP")
 
   add_library(gpu STATIC ${GPU_LIB_SOURCES})
   target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu)
-  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
+  target_compile_definitions(gpu PRIVATE -DUSE_HIP -D_${GPU_PREC_SETTING})
-  target_compile_definitions(gpu PRIVATE -DUSE_HIP)
+  if(GPU_DEBUG)
+    target_compile_definitions(gpu PRIVATE -DUCL_DEBUG -DGERYON_KERNEL_DUMP)
+  else()
+    target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DUCL_NO_EXIT)
+  endif()
   target_link_libraries(gpu PRIVATE hip::host)
 
   if(HIP_USE_DEVICE_SORT)
@@ -384,7 +414,8 @@ elseif(GPU_API STREQUAL "HIP")
       set_property(TARGET gpu PROPERTY CXX_STANDARD 14)
     endif()
     # add hipCUB
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
+    find_package(hipcub REQUIRED)
+    target_link_libraries(gpu PRIVATE hip::hipcub)
     target_compile_definitions(gpu PRIVATE -DUSE_HIP_DEVICE_SORT)
 
     if(HIP_PLATFORM STREQUAL "nvcc")
@@ -400,15 +431,17 @@ elseif(GPU_API STREQUAL "HIP")
 
       if(DOWNLOAD_CUB)
         message(STATUS "CUB download requested")
-        set(CUB_URL "https://github.com/NVlabs/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
+        # TODO: test update to current version 1.17.2
+        set(CUB_URL "https://github.com/nvidia/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
         set(CUB_MD5 "1cf595beacafff104700921bac8519f3" CACHE STRING "MD5 checksum of CUB tarball")
         mark_as_advanced(CUB_URL)
         mark_as_advanced(CUB_MD5)
+        GetFallbackURL(CUB_URL CUB_FALLBACK)
 
         include(ExternalProject)
 
         ExternalProject_Add(CUB
-          URL     ${CUB_URL}
+          URL     ${CUB_URL} ${CUB_FALLBACK}
           URL_MD5 ${CUB_MD5}
           PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
           CONFIGURE_COMMAND ""
@@ -431,30 +464,16 @@ elseif(GPU_API STREQUAL "HIP")
 
   add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(hip_get_devices PRIVATE -DUCL_HIP)
-  target_link_libraries(hip_get_devices hip::host)
+  target_link_libraries(hip_get_devices PRIVATE hip::host)
 
   if(HIP_PLATFORM STREQUAL "nvcc")
     target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
     target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS})
     target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
 
     target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_NVCC__)
-    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/include)
     target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
     target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
-  elseif(HIP_PLATFORM STREQUAL "hcc")
-    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_HCC__)
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
-
-    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
-    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
-  elseif(HIP_PLATFORM STREQUAL "amd")
-    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__)
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
-
-    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__)
-    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
   endif()
 
   target_link_libraries(lammps PRIVATE gpu)

cmake/Modules/Packages/KOKKOS.cmake

@@ -49,12 +49,14 @@ 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/3.7.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "84991eca9f066383abe119a5bc7a11c4" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_MD5 "f140e02b826223b1045207d9bc10d404" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
+  GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
+
   ExternalProject_Add(kokkos_build
-    URL     ${KOKKOS_URL}
+    URL     ${KOKKOS_URL} ${KOKKOS_FALLBACK}
     URL_MD5 ${KOKKOS_MD5}
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a <INSTALL_DIR>/lib/libkokkoscontainers.a
@@ -70,13 +72,11 @@ if(DOWNLOAD_KOKKOS)
   set_target_properties(LAMMPS::KOKKOSCONTAINERS PROPERTIES
     IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscontainers.a")
   target_link_libraries(lammps PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
-  target_link_libraries(lmp PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.7.00 REQUIRED CONFIG)
+  find_package(Kokkos 3.7.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
-  target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
   set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
@@ -96,7 +96,6 @@ else()
                           ${LAMMPS_LIB_KOKKOS_BIN_DIR})
   target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
   target_link_libraries(lammps PRIVATE kokkos)
-  target_link_libraries(lmp PRIVATE kokkos)
   if(BUILD_SHARED_LIBS_WAS_ON)
     set(BUILD_SHARED_LIBS ON)
   endif()
@@ -144,6 +143,7 @@ if(PKG_ML-IAP)
                                  ${KOKKOS_PKG_SOURCES_DIR}/mliap_descriptor_so3_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/mliap_model_linear_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/mliap_model_python_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_unified_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/mliap_so3_kokkos.cpp)
 
   # Add KOKKOS version of ML-IAP Python coupling if non-KOKKOS version is included

cmake/Modules/Packages/LATTE.cmake

@@ -19,6 +19,7 @@ if(DOWNLOAD_LATTE)
   set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
   mark_as_advanced(LATTE_URL)
   mark_as_advanced(LATTE_MD5)
+  GetFallbackURL(LATTE_URL LATTE_FALLBACK)
 
   # CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
   list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
@@ -30,7 +31,7 @@ if(DOWNLOAD_LATTE)
 
   include(ExternalProject)
   ExternalProject_Add(latte_build
-    URL     ${LATTE_URL}
+    URL     ${LATTE_URL} ${LATTE_FALLBACK}
     URL_MD5 ${LATTE_MD5}
     SOURCE_SUBDIR cmake
     CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib

cmake/Modules/Packages/LEPTON.cmake

@@ -4,7 +4,7 @@ if(LEPTON_SOURCE_DIR)
 endif()
 set(LEPTON_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/lepton)
 
-file(GLOB LEPTON_SOURCES ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp)
+file(GLOB LEPTON_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp)
 
 if((CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "amd64") OR
    (CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "AMD64") OR
@@ -15,7 +15,7 @@ else()
 endif()
 
 if(LEPTON_ENABLE_JIT)
-  file(GLOB ASMJIT_SOURCES ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
+  file(GLOB ASMJIT_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
 endif()
 
 add_library(lepton STATIC ${LEPTON_SOURCES} ${ASMJIT_SOURCES})

cmake/Modules/Packages/MDI.cmake

@@ -12,6 +12,7 @@ if(DOWNLOAD_MDI)
   set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
+  GetFallbackURL(MDI_URL MDI_FALLBACK)
   enable_language(C)
 
   # only ON/OFF are allowed for "mpi" flag when building MDI library
@@ -63,7 +64,7 @@ if(DOWNLOAD_MDI)
   # support cross-compilation and ninja-build
   include(ExternalProject)
   ExternalProject_Add(mdi_build
-    URL     ${MDI_URL}
+    URL     ${MDI_URL} ${MDI_FALLBACK}
     URL_MD5 ${MDI_MD5}
     PREFIX ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
     CMAKE_ARGS

cmake/Modules/Packages/MESONT.cmake

@@ -1,73 +0,0 @@
-
-
-set(MESONT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/MESONT)
-include(StyleHeaderUtils)
-include(CheckLanguage)
-
-# always include C++-only sources
-file(GLOB MESONT_SOURCES ${CONFIGURE_DEPENDS} ${MESONT_SOURCES_DIR}/[^.]*mesocnt*.cpp)
-file(GLOB MESONT_HEADERS ${CONFIGURE_DEPENDS} ${MESONT_SOURCES_DIR}/[^.]*mesocnt*.h)
-# remove derived class when base class is not available
-if(NOT PKG_MOLECULE)
-  list(REMOVE_ITEM MESONT_SOURCES ${MESONT_SOURCES_DIR}/bond_mesocnt.cpp)
-  list(REMOVE_ITEM MESONT_HEADERS ${MESONT_SOURCES_DIR}/bond_mesocnt.h)
-endif()
-
-# include styles dependent on Fortran library only when Fortran is available.
-check_language(Fortran)
-if(CMAKE_Fortran_COMPILER)
-  enable_language(Fortran)
-  file(GLOB MESONT_LIB_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/mesont/[^.]*.f90)
-  add_library(mesont STATIC ${MESONT_LIB_SOURCES})
-  set_target_properties(mesont PROPERTIES OUTPUT_NAME lammps_mesont${LAMMPS_MACHINE})
-  target_link_libraries(lammps PRIVATE mesont)
-
-  list(APPEND MESONT_SOURCES ${MESONT_SOURCES_DIR}/pair_mesont_tpm.cpp)
-  list(APPEND MESONT_SOURCES ${MESONT_SOURCES_DIR}/atom_vec_mesont.cpp)
-  list(APPEND MESONT_SOURCES ${MESONT_SOURCES_DIR}/compute_mesont.cpp)
-  list(APPEND MESONT_HEADERS ${MESONT_SOURCES_DIR}/pair_mesont_tpm.h)
-  list(APPEND MESONT_HEADERS ${MESONT_SOURCES_DIR}/atom_vec_mesont.h)
-  list(APPEND MESONT_HEADERS ${MESONT_SOURCES_DIR}/compute_mesont.h)
-endif()
-
-# check for package files in src directory due to old make system
-DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${MESONT_SOURCES} ${MESONT_HEADERS})
-
-# manually register style headers
-get_property(alist GLOBAL PROPERTY ANGLE)
-get_property(blist GLOBAL PROPERTY BOND)
-get_property(clist GLOBAL PROPERTY COMPUTE)
-get_property(plist GLOBAL PROPERTY PAIR)
-get_property(vlist GLOBAL PROPERTY ATOM_VEC)
-foreach(fname ${MESONT_HEADERS})
-  file(STRINGS ${fname} is_style LIMIT_COUNT 1 REGEX ANGLE_CLASS)
-  if(is_style)
-    list(APPEND alist ${fname})
-  endif()
-  file(STRINGS ${fname} is_style LIMIT_COUNT 1 REGEX BOND_CLASS)
-  if(is_style)
-    list(APPEND blist ${fname})
-  endif()
-  file(STRINGS ${fname} is_style LIMIT_COUNT 1 REGEX COMPUTE_CLASS)
-  if(is_style)
-    list(APPEND clist ${fname})
-  endif()
-  file(STRINGS ${fname} is_style LIMIT_COUNT 1 REGEX PAIR_CLASS)
-  if(is_style)
-    list(APPEND plist ${fname})
-  endif()
-  file(STRINGS ${fname} is_style LIMIT_COUNT 1 REGEX ATOM_CLASS)
-  if(is_style)
-    list(APPEND vlist ${fname})
-  endif()
-endforeach()
-set_property(GLOBAL PROPERTY ANGLE "${alist}")
-set_property(GLOBAL PROPERTY BOND "${blist}")
-set_property(GLOBAL PROPERTY COMPUTE "${clist}")
-set_property(GLOBAL PROPERTY PAIR "${plist}")
-set_property(GLOBAL PROPERTY ATOM_VEC "${vlist}")
-
-target_sources(lammps PRIVATE ${MESONT_SOURCES})
-target_include_directories(lammps PRIVATE ${MESONT_SOURCES_DIR})
-
-RegisterPackages(${MESONT_SOURCES_DIR})

cmake/Modules/Packages/ML-HDNNP.cmake

@@ -6,10 +6,11 @@ else()
 endif()
 option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT})
 if(DOWNLOAD_N2P2)
-  set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.4.tar.gz" CACHE STRING "URL for n2p2 tarball")
+  set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.2.0.tar.gz" CACHE STRING "URL for n2p2 tarball")
-  set(N2P2_MD5 "9595b066636cd6b90b0fef93398297a5" CACHE STRING "MD5 checksum of N2P2 tarball")
+  set(N2P2_MD5 "a2d9ab7f676b3a74a324fc1eda0a911d" CACHE STRING "MD5 checksum of N2P2 tarball")
   mark_as_advanced(N2P2_URL)
   mark_as_advanced(N2P2_MD5)
+  GetFallbackURL(N2P2_URL N2P2_FALLBACK)
 
   # adjust settings from detected compiler to compiler platform in n2p2 library
   # set compiler specific flag to turn on C++11 syntax (required on macOS and CentOS 7)
@@ -72,7 +73,7 @@ if(DOWNLOAD_N2P2)
   # download compile n2p2 library. much patch MPI calls in LAMMPS interface to accommodate MPI-2 (e.g. for cross-compiling)
   include(ExternalProject)
   ExternalProject_Add(n2p2_build
-    URL     ${N2P2_URL}
+    URL     ${N2P2_URL} ${N2P2_FALLBACK}
     URL_MD5 ${N2P2_MD5}
     UPDATE_COMMAND ""
     CONFIGURE_COMMAND ""

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,11 +1,25 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "f418d32b60e531063ac4285bf702b468" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "4f0b3b5b14456fe9a73b447de3765caa" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
+GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
 
 # download library sources to build folder
-file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5}) #SHOW_PROGRESS
+if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
+  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+endif()
+if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
+  message(STATUS "Downloading ${PACELIB_URL}")
+  file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
+  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+  if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
+    message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
+    file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
+  endif()
+else()
+  message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+endif()
 
 # uncompress downloaded sources
 execute_process(

cmake/Modules/Packages/ML-QUIP.cmake

@@ -16,6 +16,7 @@ if(DOWNLOAD_QUIP)
     set(temp "${temp}DEFINES += -DGETARG_F2003 -DFORTRAN_UNDERSCORE\n")
     set(temp "${temp}F95FLAGS += -fpp -free -fPIC\n")
     set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
+    set(temp "${temp}F95_PRE_FILENAME_FLAG = -Tf\n")
   elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
     set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
     set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")

cmake/Modules/Packages/PLUMED.cmake

@@ -59,10 +59,11 @@ if(DOWNLOAD_PLUMED)
 
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)
+  GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
 
   include(ExternalProject)
   ExternalProject_Add(plumed_build
-    URL     ${PLUMED_URL}
+    URL     ${PLUMED_URL} ${PLUMED_FALLBACK}
     URL_MD5 ${PLUMED_MD5}
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>

cmake/Modules/Packages/SCAFACOS.cmake

@@ -18,6 +18,8 @@ if(DOWNLOAD_SCAFACOS)
   set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball")
   mark_as_advanced(SCAFACOS_URL)
   mark_as_advanced(SCAFACOS_MD5)
+  GetFallbackURL(SCAFACOS_URL SCAFACOS_FALLBACK)
+
 
   # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
   file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
@@ -30,7 +32,7 @@ if(DOWNLOAD_SCAFACOS)
 
   include(ExternalProject)
   ExternalProject_Add(scafacos_build
-    URL     ${SCAFACOS_URL}
+    URL     ${SCAFACOS_URL} ${SCAFACOS_FALLBACK}
     URL_MD5 ${SCAFACOS_MD5}
     PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc

cmake/Modules/Tools.cmake

@@ -50,12 +50,16 @@ if(BUILD_LAMMPS_SHELL)
 
   add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp ${ICON_RC_FILE})
   target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
+  target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
 
   # workaround for broken readline pkg-config file on FreeBSD
   if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD")
     target_include_directories(lammps-shell PRIVATE /usr/local/include)
   endif()
-  target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
+  if(CMAKE_SYSTEM_NAME STREQUAL "LinuxMUSL")
+    pkg_check_modules(TERMCAP IMPORTED_TARGET REQUIRED termcap)
+    target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::TERMCAP)
+  endif()
   install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
   install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)

cmake/presets/most.cmake

@@ -40,6 +40,7 @@ set(ALL_PACKAGES
   MANYBODY
   MC
   MEAM
+  MESONT
   MISC
   ML-IAP
   ML-POD

cmake/presets/nolib.cmake

@@ -16,7 +16,6 @@ set(PACKAGES_WITH_LIB
   LEPTON
   MACHDYN
   MDI
-  MESONT
   ML-HDNNP
   ML-PACE
   ML-QUIP

cmake/presets/windows.cmake

@@ -36,6 +36,7 @@ set(WIN_PACKAGES
   MANYBODY
   MC
   MEAM
+  MESONT
   MISC
   ML-IAP
   ML-POD

doc/Makefile

@@ -86,18 +86,19 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
-		touch $(RSTDIR)/Fortran.rst ;\
+		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		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;\
-		echo "############################################" ;\
+		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\
-		python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
+		$(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 ;\
+		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -114,9 +115,9 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@mkdir -p fasthtml
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
-		touch $(RSTDIR)/Fortran.rst ;\
+		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
 		deactivate ;\
 	)
@@ -131,8 +132,8 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		. $(VENV)/bin/activate ; \
-		cp $(SPHINXCONFIG)/false_positives.txt $(RSTDIR)/ ; env PYTHONWARNINGS= \
+		cp $(SPHINXCONFIG)/false_positives.txt $(RSTDIR)/;  env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -b spelling -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
@@ -146,9 +147,9 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@rm -f LAMMPS.epub
 	@cp src/JPG/*.* epub/JPG
 	@(\
-		. $(VENV)/bin/activate ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
-		touch $(RSTDIR)/Fortran.rst ;\
+		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
@@ -167,17 +168,18 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@if [ "$(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= \
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-		touch $(RSTDIR)/Fortran.rst ;\
+		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build  $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
-		echo "############################################" ;\
+		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\
-		python utils/check-packages.py -s ../src -d src ;\
+		$(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 ;\
+		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -200,22 +202,22 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 
 anchor_check : $(ANCHORCHECK)
 	@(\
-		. $(VENV)/bin/activate ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\
 		deactivate ;\
 	)
 
 style_check : $(VENV)
 	@(\
-		. $(VENV)/bin/activate ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		python utils/check-styles.py -s ../src -d src ;\
+		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
 package_check : $(VENV)
 	@(\
-		. $(VENV)/bin/activate ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		python utils/check-packages.py -s ../src -d src ;\
+		$(PYTHON) utils/check-packages.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
@@ -224,6 +226,14 @@ char_check :
 
 role_check :
 	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
+
+link_check : $(VENV) html
+	@(\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		linkchecker -F html --check-extern html/Manual.html ;\
+		deactivate ;\
+	)
 
 xmlgen : doxygen/xml/index.xml
 
@@ -252,7 +262,7 @@ $(MATHJAX):
 
 $(ANCHORCHECK): $(VENV)
 	@( \
-		. $(VENV)/bin/activate; \
+		. $(VENV)/bin/activate; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		pip $(PIP_OPTIONS) install -e utils/converters;\
 		deactivate;\
 	)

doc/github-development-workflow.md

@@ -1,12 +1,12 @@
 # Outline of the GitHub Development Workflow
 
-This purpose of this document is to provide a point of reference for the
+The purpose of this document is to provide a point of reference for the
 core LAMMPS developers and other LAMMPS contributors to understand the
 choices the LAMMPS developers have agreed on. Git and GitHub provide the
 tools, but do not set policies, so it is up to the developers to come to
 an agreement as to how to define and interpret policies. This document
-is likely to change as our experiences and needs change and we try to
+is likely to change as our experiences and needs change, and we try to
-adapt accordingly. Last change 2021-09-02.
+adapt it accordingly. Last change 2023-02-10.
 
 ## Table of Contents
 
@@ -22,47 +22,50 @@ adapt accordingly. Last change 2021-09-02.
 ## GitHub Merge Management
 
 In the interest of consistency, ONLY ONE of the core LAMMPS developers
-should doing the merging itself.  This is currently
+should do the merging.  This is currently
 [@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).  If this
 assignment needs to be changed, it shall be done right after a stable
 release.  If the currently assigned developer cannot merge outstanding
 pull requests in a timely manner, or in other extenuating circumstances,
-other core LAMMPS developers with merge rights can merge pull requests,
+other core LAMMPS developers with merge permission may merge pull
-when necessary.
+requests.
 
 ## Pull Requests
 
-ALL changes to the LAMMPS code and documentation, however trivial, MUST
+*ALL* changes to the LAMMPS code and documentation, however trivial,
-be submitted as a pull request to GitHub. All changes to the "develop"
+MUST be submitted as a pull request to GitHub.  All changes to the
-branch must be made exclusively through merging pull requests. The
+"develop" branch must be made exclusively through merging pull requests.
-"release" and "stable" branches, respectively are only to be updated
+The "release" and "stable" branches, respectively, are only to be
-upon patch or stable releases with fast-forward merges based on the
+updated upon feature or stable releases based on the associated
-associated tags. Pull requests may also be submitted to (long-running)
+tags.  Updates to the stable release in between stable releases
-feature branches created by LAMMPS developers inside the LAMMPS project,
+(for example, back-ported bug fixes) are first merged into the "maintenance"
-if needed. Those are not subject to the merge and review restrictions
+branch and then into the "stable" branch as update releases.
-discussed in this document, though, but get managed as needed on a
+
-case-by-case basis.
+Pull requests may also be submitted to (long-running) feature branches
+created by LAMMPS developers inside the LAMMPS project, if needed. Those
+are not subject to the merge and review restrictions discussed in this
+document, though, but get managed as needed on a case-by-case basis.
 
 ### Pull Request Assignments
 
 Pull requests can be "chaperoned" by one of the LAMMPS core developers.
-This is indicated by who the pull request is assigned to. LAMMPS core
+This is indicated by whom the pull request is assigned to.  LAMMPS core
-developers can self-assign or they can decide to assign a pull request
+developers can self-assign, or they can decide to assign a pull request
 to a different LAMMPS developer. Being assigned to a pull request means,
 that this pull request may need some work and the assignee is tasked to
-determine whether this might be needed or not, and may either implement
+determine whether this might be needed or not. The assignee may either
-the required changes or ask the submitter of the pull request to implement
+choose to implement required changes or ask the submitter of the pull
-them.  Even though, all LAMMPS developers may have write access to pull
+request to implement them.  Even though, all LAMMPS developers may have
-requests (if enabled by the submitter, which is the default), only the
+write access to pull requests (if enabled by the submitter, which is the
-submitter or the assignee of a pull request may do so.  During this
+default), only the submitter or the assignee of a pull request should do
-period the `work_in_progress` label may be applied to the pull
+so.  During this period, the `work_in_progress` label may be applied to
-request.  The assignee gets to decide what happens to the pull request
+the pull request.  The assignee gets to decide what happens to the pull
-next, e.g. whether it should be assigned to a different developer for
+request next, e.g. whether it should be assigned to a different
-additional checks and changes, or is recommended to be merged.  Removing
+developer for additional checks and changes, or is recommended to be
-the `work_in_progress` label and assigning the pull request to the
+merged.  Removing the `work_in_progress` label and assigning the pull
-developer tasked with merging signals that a pull request is ready to be
+request to the developer tasked with merging signals that a pull request
-merged. In addition, a `ready_for_merge` label may also be assigned
+is ready to be merged. In addition, a `ready_for_merge` label may also
-to signal urgency to merge this pull request quickly.
+be assigned to signal urgency to merge this pull request quickly.
 
 ### Pull Request Reviews
 
@@ -70,32 +73,33 @@ People can be assigned to review a pull request in two ways:
 
   * They can be assigned manually to review a pull request
     by the submitter or a LAMMPS developer
-  * They can be automatically assigned, because a developers matches
+  * They can be automatically assigned, because a developer's GitHub
-    a file pattern in the `.github/CODEOWNERS` file, which associates
+    handle matches a file pattern in the `.github/CODEOWNERS` file,
-    developers with the code they contributed and maintain.
+    which associates developers with the code they contributed and
+    maintain.
 
 Reviewers are requested to state their appraisal of the proposed changes
 and either approve or request changes. People may unassign themselves
 from review, if they feel not competent about the changes proposed. At
-least two approvals from LAMMPS developers with write access are required
+least two approvals from LAMMPS developers with write access are
-before merging in addition to the automated compilation tests.
+required before merging, in addition to passing all automated
-Merging counts as implicit approval, so does submission of a pull request
+compilation and unit tests.  Merging counts as implicit approval, so
-(by a LAMMPS developer). So the person doing the merge may not also submit
+does submission of a pull request (by a LAMMPS developer). So the person
-an approving review. The feature, that reviews from code owners are "hard"
+doing the merge may not also submit an approving review.  The GitHub
-reviews (i.e. they must all be approved before merging is allowed), is
+feature, that reviews from code owners are "hard" reviews (i.e. they
-currently disabled and it is in the discretion of the merge maintainer to
+must all approve before merging is allowed), is currently disabled.
-assess when a sufficient degree of approval, especially from external
+It is in the discretion of the merge maintainer to assess when a
-contributors, has been reached in these cases.  Reviews may be
+sufficient degree of approval has been reached, especially from external
-(automatically) dismissed, when the reviewed code has been changed,
+collaborators.  Reviews may be (automatically) dismissed, when the
-and then approval is required a second time.
+reviewed code has been changed. Review may be requested a second time.
 
 ### Pull Request Discussions
 
 All discussions about a pull request should be kept as much as possible
 on the pull request discussion page on GitHub, so that other developers
 can later review the entire discussion after the fact and understand the
-rationale behind choices made.  Exceptions to this policy are technical
+rationale behind choices that were made.  Exceptions to this policy are
-discussions, that are centered on tools or policies themselves
+technical discussions, that are centered on tools or policies themselves
 (git, GitHub, c++) rather than on the content of the pull request.
 
 ## GitHub Issues
@@ -109,39 +113,43 @@ marker in the subject. This is automatically done when using the
 corresponding template for submitting an issue.  Issues may be assigned
 to one or more developers, if they are working on this feature or
 working to resolve an issue.  Issues that have nobody working
-on them at the moment or in the near future, have the label
+on them at the moment, or in the near future, have the label
 `volunteer needed` attached.
 
-When an issue, say `#125` is resolved by a specific pull request,
+When an issue, say `#125` is resolved by a specific pull request, the
-the comment for the pull request shall contain the text `closes #125`
+comment for the pull request shall contain the text `closes #125` or
-or `fixes #125`, so that the issue is automatically deleted when
+`fixes #125`, so that the issue is automatically deleted when the pull
-the pull request is merged.  The template for pull requests includes
+request is merged.  The template for pull requests includes a header
-a header where connections between pull requests and issues can be listed
+where connections between pull requests and issues can be listed, and
-and thus were this comment should be placed.
+thus where this comment should be placed.
 
 ## Milestones and Release Planning
 
 LAMMPS uses a continuous release development model with incremental
-changes, i.e. significant effort is made - including automated pre-merge
+changes, i.e. significant effort is made -- including automated pre-merge
-testing - that the code in the branch "develop" does not get easily
+testing -- that the code in the branch "develop" does not get easily
 broken.  These tests are run after every update to a pull request.  More
-extensive and time consuming tests (including regression testing) are
+extensive and time-consuming tests (including regression testing) are
-performed after code is merged to the "develop" branch. There are patch
+performed after code is merged to the "develop" branch.  There are feature
-releases of LAMMPS every 3-5 weeks at a point, when the LAMMPS
+releases of LAMMPS made about every 4-6 weeks at a point, when the LAMMPS
-developers feel, that a sufficient amount of changes have happened, and
+developers feel, that a sufficient number of changes has been included
-the post-merge testing has been successful. These patch releases are
+and all post-merge testing has been successful.  These feature releases are
 marked with a `patch_<version date>` tag and the "release" branch
-follows only these versions (and thus is always supposed to be of
+follows only these versions with fast-forward merges.  While "develop" may
-production quality, unlike "develop", which may be temporary broken, in
+be temporarily broken through issues only detected by the post-merge tests,
-the case of larger change sets or unexpected incompatibilities or side
+The "release" branch is always supposed to be of production quality.
-effects.
 
-About 1-2 times each year, there are going to be "stable" releases of
+About once each year, there is a "stable" release of LAMMPS.
-LAMMPS.  These have seen additional, manual testing and review of
+These have seen additional, manual testing and review of
 results from testing with instrumented code and static code analysis.
-Also, the last 1-3 patch releases before a stable release are "release
+Also, the last few feature releases before a stable release are "release
-candidate" versions which only contain bugfixes and documentation
+candidate" versions which only contain bug fixes, feature additions to
-updates.  For release planning and the information of code contributors,
+peripheral functionality, and documentation updates.  In between stable
-issues and pull requests being actively worked on are assigned a
+releases, bug fixes and infrastructure updates are back-ported from the
-"milestone", which corresponds to the next stable release or the stable
+"develop" branch to the "maintenance" branch and occasionally merged
-release after that, with a tentative release date.
+into "stable" and published as update releases.
+
+For release planning and the information of code contributors, issues
+and pull requests being actively worked on are assigned a "milestone",
+which corresponds to the next stable release or the stable release after
+that, with a tentative release date.

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "22 December 2022" "2022-12-22"
+.TH LAMMPS "1" "8 February 2023" "2023-02-08"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 22 December 2022
+\- Molecular Dynamics Simulator.  Version 8 February 2023
 
 .SH SYNOPSIS
 .B lmp

doc/msi2lmp.1

@@ -1,11 +1,11 @@
-.TH MSI2LMP "1" "v3.9.9" "2018-11-05"
+.TH MSI2LMP "1" "v3.9.10" "2023-03-10"
 .SH NAME
 .B MSI2LMP
 \- Converter for Materials Studio files to LAMMPS
 
 .SH SYNOPSIS
 .B msi2lmp
-<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
+[-help] <ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
 
 .SH DESCRIPTION
 .PP
@@ -22,6 +22,9 @@ needed between .frc and .car/.mdf files are the atom types.
 
 .SH OPTIONS
 .TP
+\fB\-h\fR, \fB\-help\fR,
+Print detailed help message to the screen and stop.
+.TP
 \fB\<ROOTNAME>\fR
 This has to be the first argument and is a
 .B mandatory

doc/src/2001/basics.html

@@ -63,7 +63,7 @@ In the src directory, there is one top-level Makefile and several
 low-level machine-specific files named Makefile.xxx where xxx = the
 machine name. If a low-level Makefile exists for your platform, you do
 not need to edit the top-level Makefile.  However you should check the
-system-specific section of the low-level Makefile to insure the
+system-specific section of the low-level Makefile to ensure the
 various paths are correct for your environment. If a low-level
 Makefile does not exist for your platform, you will need to add a
 suitable target to the top-level Makefile. You will also need to

doc/src/2001/input_commands.html

@@ -1206,7 +1206,7 @@ this command is not typically needed if the "nonbond style" and "
 an exception to this is if a short cutoff is used initially,
   but a longer cutoff will be used for a subsequent run (in the same
   input script), in this case the "maximum cutoff" command should be
-  used to insure enough memory is allocated for the later run
+  used to ensure enough memory is allocated for the later run
 note that a restart file contains nonbond cutoffs (so it is not necessary
   to use a "nonbond style" command before "read restart"), but LAMMPS
   still needs to know what the maximum cutoff will be before the

doc/src/Build.rst

@@ -6,9 +6,9 @@ either traditional makefiles for use with GNU make (which may require
 manual editing), or using a build environment generated by CMake (Unix
 Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
 
-As an alternative you can download a package with pre-built executables
+As an alternative, you can download a package with pre-built executables
-or automated build trees as described on the :doc:`Install <Install>`
+or automated build trees, as described in the :doc:`Install <Install>`
-page.
+section of the manual.
 
 .. toctree::
    :maxdepth: 1

doc/src/Build_basics.rst

@@ -44,7 +44,7 @@ standard. A more detailed discussion of that is below.
 
       The executable created by CMake (after running make) is named
       ``lmp`` unless the ``LAMMPS_MACHINE`` option is set.  When setting
-      ``LAMMPS_MACHINE=name`` the executable will be called
+      ``LAMMPS_MACHINE=name``, the executable will be called
       ``lmp_name``.  Using ``BUILD_MPI=no`` will enforce building a
       serial executable using the MPI STUBS library.
 
@@ -60,7 +60,7 @@ standard. A more detailed discussion of that is below.
 
       Any ``make machine`` command will look up the make settings from a
       file ``Makefile.machine`` in the folder ``src/MAKE`` or one of its
-      sub-directories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a
+      subdirectories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a
       folder ``Obj_machine`` with all objects and generated files and an
       executable called ``lmp_machine``\ .  The standard parallel build
       with ``make mpi`` assumes a standard MPI installation with MPI
@@ -107,9 +107,9 @@ MPI and OpenMP support in LAMMPS
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 If you are installing MPI yourself to build a parallel LAMMPS
-executable, we recommend either MPICH or OpenMPI which are regularly
+executable, we recommend either MPICH or OpenMPI, which are regularly
 used and tested with LAMMPS by the LAMMPS developers.  MPICH can be
-downloaded from the `MPICH home page <https://www.mpich.org>`_ and
+downloaded from the `MPICH home page <https://www.mpich.org>`_, and
 OpenMPI can be downloaded correspondingly from the `OpenMPI home page
 <https://www.open-mpi.org>`_.  Other MPI packages should also work.  No
 specific vendor provided and standard compliant MPI library is currently
@@ -130,12 +130,12 @@ package can be compiled to include OpenMP threading.
 
 In addition, there are a few commands in LAMMPS that have native OpenMP
 support included as well.  These are commands in the ``MPIIO``,
-``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.  In addition
+``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.  Furthermore,
 some packages support OpenMP threading indirectly through the libraries
-they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``.
+they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``.  See the
-See the :doc:`Packages details <Packages_details>` page for more
+:doc:`Packages details <Packages_details>` page for more info on these
-info on these packages and the pages for their respective commands
+packages, and the pages for their respective commands for OpenMP
-for OpenMP threading info.
+threading info.
 
 For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
 and turn on their native OpenMP support and turn on their native OpenMP
@@ -144,9 +144,9 @@ variable before you launch LAMMPS.
 
 For building via conventional make, the ``CCFLAGS`` and ``LINKFLAGS``
 variables in Makefile.machine need to include the compiler flag that
-enables OpenMP. For GNU compilers it is ``-fopenmp``\ .  For (recent) Intel
+enables OpenMP. For the GNU compilers or Clang, it is ``-fopenmp``\ .
-compilers it is ``-qopenmp``\ .  If you are using a different compiler,
+For (recent) Intel compilers, it is ``-qopenmp``\ .  If you are using a
-please refer to its documentation.
+different compiler, please refer to its documentation.
 
 .. _default-none-issues:
 
@@ -174,15 +174,16 @@ Choice of compiler and compile/link options
 The choice of compiler and compiler flags can be important for maximum
 performance.  Vendor provided compilers for a specific hardware can
 produce faster code than open-source compilers like the GNU compilers.
-On the most common x86 hardware most popular C++ compilers are quite
+On the most common x86 hardware, the most popular C++ compilers are
-similar in performance of C/C++ code at high optimization levels.  When
+quite similar in their ability to optimize regular C/C++ source code at
-using the ``INTEL`` package, there is a distinct advantage in using
+high optimization levels.  When using the ``INTEL`` package, there is a
-the `Intel C++ compiler <intel_>`_ due to much improved vectorization
+distinct advantage in using the `Intel C++ compiler <intel_>`_ due to
-through SSE and AVX instructions on compatible hardware as the source
+much improved vectorization through SSE and AVX instructions on
-code includes changes and Intel compiler specific directives to enable
+compatible hardware.  The source code in that package conditionally
-high degrees of vectorization.  This may change over time as equivalent
+includes compiler specific directives to enable these high degrees of
-vectorization directives are included into OpenMP standard revisions and
+vectorization.  This may change over time as equivalent vectorization
-other compilers adopt them.
+directives are included into the OpenMP standard and other compilers
+adopt them.
 
 .. _intel: https://software.intel.com/en-us/intel-compilers
 
@@ -196,7 +197,7 @@ LAMMPS.
    .. tab:: CMake build
 
       By default CMake will use the compiler it finds according to
-      internal preferences and it will add optimization flags
+      internal preferences, and it will add optimization flags
       appropriate to that compiler and any :doc:`accelerator packages
       <Speed_packages>` you have included in the build.  CMake will
       check if the detected or selected compiler is compatible with the
@@ -250,9 +251,9 @@ LAMMPS.
       and `-C ../cmake/presets/pgi.cmake`
       will switch the compiler to the PGI compilers.
 
-      In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
+      Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
-      compiler flags to tune for optimal performance on given hosts. By
+      compiler flags to tune for optimal performance on given hosts.
-      default this variable is empty.
+      This variable is empty by default.
 
       .. note::
 
@@ -368,10 +369,10 @@ running LAMMPS from Python via its library interface.
                                       # no default value
 
       The compilation will always produce a LAMMPS library and an
-      executable linked to it.  By default this will be a static library
+      executable linked to it.  By default, this will be a static
-      named ``liblammps.a`` and an executable named ``lmp`` Setting
+      library named ``liblammps.a`` and an executable named ``lmp``
-      ``BUILD_SHARED_LIBS=yes`` will instead produce a shared library
+      Setting ``BUILD_SHARED_LIBS=yes`` will instead produce a shared
-      called ``liblammps.so`` (or ``liblammps.dylib`` or
+      library called ``liblammps.so`` (or ``liblammps.dylib`` or
       ``liblammps.dll`` depending on the platform) If
       ``LAMMPS_MACHINE=name`` is set in addition, the name of the
       generated libraries will be changed to either ``liblammps_name.a``
@@ -429,7 +430,7 @@ You may need to use ``sudo make install`` in place of the last line if
 you do not have write privileges for ``/usr/local/lib`` or use the
 ``--prefix`` configuration option to select an installation folder,
 where you do have write access.  The end result should be the file
-``/usr/local/lib/libmpich.so``.  On many Linux installations the folder
+``/usr/local/lib/libmpich.so``.  On many Linux installations, the folder
 ``${HOME}/.local`` is an alternative to using ``/usr/local`` and does
 not require superuser or sudo access.  In that case the configuration
 step becomes:
@@ -438,9 +439,10 @@ step becomes:
 
   ./configure --enable-shared --prefix=${HOME}/.local
 
-Avoiding to use "sudo" for custom software installation (i.e. from source
+Avoiding the use of "sudo" for custom software installation (i.e. from
-and not through a package manager tool provided by the OS) is generally
+source and not through a package manager tool provided by the OS) is
-recommended to ensure the integrity of the system software installation.
+generally recommended to ensure the integrity of the system software
+installation.
 
 ----------
 
@@ -514,11 +516,11 @@ using CMake or Make.
 Install LAMMPS after a build
 ------------------------------------------
 
-After building LAMMPS, you may wish to copy the LAMMPS executable of
+After building LAMMPS, you may wish to copy the LAMMPS executable or
-library, along with other LAMMPS files (library header, doc files) to
+library, along with other LAMMPS files (library header, doc files), to a
-a globally visible place on your system, for others to access.  Note
+globally visible place on your system, for others to access.  Note that
-that you may need super-user privileges (e.g. sudo) if the directory
+you may need super-user privileges (e.g. sudo) if the directory you want
-you want to copy files to is protected.
+to copy files to is protected.
 
 .. tabs::
 
@@ -536,7 +538,7 @@ you want to copy files to is protected.
       environment variable, if you are installing LAMMPS into a non-system
       location and/or are linking to libraries in a non-system location that
       depend on such runtime path settings.
-      As an alternative you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
+      As an alternative, you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
       to ``on`` and then the runtime paths for any linked shared libraries
       and the library installation folder for the LAMMPS library will be
       embedded and thus the requirement to set environment variables is avoided.

doc/src/Build_cmake.rst

@@ -9,10 +9,10 @@ page.
 
 The following text assumes some familiarity with CMake and focuses on
 using the command line tool ``cmake`` and what settings are supported
-for building LAMMPS.  A more detailed tutorial on how to use ``cmake``
+for building LAMMPS.  A more detailed tutorial on how to use CMake
-itself, the text mode or graphical user interface, change the generated
+itself, the text mode or graphical user interface, to change the
-output files for different build tools and development environments is
+generated output files for different build tools and development
-on a :doc:`separate page <Howto_cmake>`.
+environments is on a :doc:`separate page <Howto_cmake>`.
 
 .. note::
 
@@ -22,12 +22,12 @@ on a :doc:`separate page <Howto_cmake>`.
 .. warning::
 
    You must not mix the :doc:`traditional make based <Build_make>`
-   LAMMPS build procedure with using CMake.  Thus no packages may be
+   LAMMPS build procedure with using CMake.  No packages may be
    installed or a build been previously attempted in the LAMMPS source
    directory by using ``make <machine>``.  CMake will detect if this is
    the case and generate an error.  To remove conflicting files from the
    ``src`` you can use the command ``make no-all purge`` which will
-   un-install all packages and delete all auto-generated files.
+   uninstall all packages and delete all auto-generated files.
 
 
 Advantages of using CMake
@@ -44,9 +44,9 @@ software or for people that want to modify or extend LAMMPS.
   and adapt the LAMMPS default build configuration accordingly.
 - CMake can generate files for different build tools and integrated
   development environments (IDE).
-- CMake supports customization of settings with a text mode or graphical
+- CMake supports customization of settings with a command line, text
-  user interface. No knowledge of file formats or and complex command
+  mode, or graphical user interface.  No knowledge of file formats or
-  line syntax required.
+  complex command line syntax is required.
 - All enabled components are compiled in a single build operation.
 - Automated dependency tracking for all files and configuration options.
 - Support for true out-of-source compilation. Multiple configurations
@@ -55,23 +55,23 @@ software or for people that want to modify or extend LAMMPS.
   source tree.
 - Simplified packaging of LAMMPS for Linux distributions, environment
   modules, or automated build tools like `Homebrew <https://brew.sh/>`_.
-- Integration of automated regression testing (the LAMMPS side for that
+- Integration of automated unit and regression testing (the LAMMPS side
-  is still under development).
+  of this is still under active development).
 
 .. _cmake_build:
 
 Getting started
 ^^^^^^^^^^^^^^^
 
-Building LAMMPS with CMake is a two-step process.  First you use CMake
+Building LAMMPS with CMake is a two-step process.  In the first step,
-to generate a build environment in a new directory.  For that purpose
+you use CMake to generate a build environment in a new directory.  For
-you can use either the command-line utility ``cmake`` (or ``cmake3``),
+that purpose you can use either the command-line utility ``cmake`` (or
-the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the graphical
+``cmake3``), the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the
-utility ``cmake-gui``, or use them interchangeably.  The second step is
+graphical utility ``cmake-gui``, or use them interchangeably.  The
-then the compilation and linking of all objects, libraries, and
+second step is then the compilation and linking of all objects,
-executables. Here is a minimal example using the command line version of
+libraries, and executables using the selected build tool.  Here is a
-CMake to build LAMMPS with no add-on packages enabled and no
+minimal example using the command line version of CMake to build LAMMPS
-customization:
+with no add-on packages enabled and no customization:
 
 .. code-block:: bash
 
@@ -96,17 +96,17 @@ Compilation can take a long time, since LAMMPS is a large project with
 many features. If your machine has multiple CPU cores (most do these
 days), you can speed this up by compiling sources in parallel with
 ``make -j N`` (with N being the maximum number of concurrently executed
-tasks).  Also installation of the `ccache <https://ccache.dev/>`_ (=
+tasks).  Installation of the `ccache <https://ccache.dev/>`_ (= Compiler
-Compiler Cache) software may speed up repeated compilation even more,
+Cache) software may speed up repeated compilation even more, e.g. during
-e.g. during code development.
+code development, especially when repeatedly switching between branches.
 
 After the initial build, whenever you edit LAMMPS source files, enable
 or disable packages, change compiler flags or build options, you must
 re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
 ``make``).  If the compilation fails for some reason, try running
 ``cmake .`` and then compile again. The included dependency tracking
-should make certain that only the necessary subset of files are
+should make certain that only the necessary subset of files is
-re-compiled.  You can also delete compiled objects, libraries and
+re-compiled.  You can also delete compiled objects, libraries, and
 executables with ``cmake --build . --target clean`` (or ``make clean``).
 
 After compilation, you may optionally install the LAMMPS executable into
@@ -132,12 +132,12 @@ file called ``CMakeLists.txt`` (for LAMMPS it is located in the
 ``CMakeCache.txt``, which is generated at the end of the CMake
 configuration step.  The cache file contains all current CMake settings.
 
-To modify settings, enable or disable features, you need to set *variables*
+To modify settings, enable or disable features, you need to set
-with either the *-D* command line flag (``-D VARIABLE1_NAME=value``) or
+*variables* with either the *-D* command line flag (``-D
-change them in the text mode of graphical user interface.  The *-D* flag
+VARIABLE1_NAME=value``) or change them in the text mode of the graphical
-can be used several times in one command.
+user interface.  The *-D* flag can be used several times in one command.
 
-For your convenience we provide :ref:`CMake presets <cmake_presets>`
+For your convenience, we provide :ref:`CMake presets <cmake_presets>`
 that combine multiple settings to enable optional LAMMPS packages or use
 a different compiler tool chain.  Those are loaded with the *-C* flag
 (``-C ../cmake/presets/basic.cmake``).  This step would only be needed
@@ -155,22 +155,23 @@ specific CMake version is given when running ``cmake --help``.
 Multi-configuration build systems
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Throughout this manual it is mostly assumed that LAMMPS is being built
+Throughout this manual, it is mostly assumed that LAMMPS is being built
 on a Unix-like operating system with "make" as the underlying "builder",
-since this is the most common case.  In this case the build "configuration"
+since this is the most common case.  In this case the build
-is chose using ``-D CMAKE_BUILD_TYPE=<configuration>`` with ``<configuration>``
+"configuration" is chose using ``-D CMAKE_BUILD_TYPE=<configuration>``
-being one of "Release", "Debug", "RelWithDebInfo", or "MinSizeRel".
+with ``<configuration>`` being one of "Release", "Debug",
-Some build tools, however, can also use or even require to have a so-called
+"RelWithDebInfo", or "MinSizeRel".  Some build tools, however, can also
-multi-configuration build system setup.  For those the built type (or
+use or even require having a so-called multi-configuration build system
-configuration) is chosen at compile time using the same build files. E.g.
+setup.  For a multi-configuration build, the built type (or
-with:
+configuration) is selected at compile time using the same build
+files. E.g.  with:
 
 .. code-block:: bash
 
    cmake --build build-multi --config Release
 
 In that case the resulting binaries are not in the build folder directly
-but in sub-directories corresponding to the build type (i.e. Release in
+but in subdirectories corresponding to the build type (i.e. Release in
 the example from above).  Similarly, for running unit tests the
 configuration is selected with the *-C* flag:
 
@@ -184,7 +185,7 @@ particular applicable to compiling packages that require additional libraries
 that would be downloaded and compiled by CMake.  The "windows" preset file
 tries to keep track of which packages can be compiled natively with the
 MSVC compilers out-of-the box.  Not all of those external libraries are
-portable to Windows either.
+portable to Windows, either.
 
 
 Installing CMake

doc/src/Build_development.rst

@@ -46,7 +46,7 @@ It can be enabled for all C++ code with the following CMake flag
 
 With this flag enabled all source files will be processed twice, first to
 be compiled and then to be analyzed. Please note that the analysis can be
-significantly more time consuming than the compilation itself.
+significantly more time-consuming than the compilation itself.
 
 ----------
 

doc/src/Build_extras.rst

@@ -47,7 +47,6 @@ This is the list of packages that may require additional steps.
    * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
-   * :ref:`MESONT <mesont>`
    * :ref:`ML-HDNNP <ml-hdnnp>`
    * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
@@ -127,10 +126,11 @@ CMake build
    -D GPU_API=value             # value = opencl (default) or cuda or hip
    -D GPU_PREC=value            # precision setting
                                 # value = double or mixed (default) or single
-   -D HIP_PATH                  # path to HIP installation. Must be set if GPU_API=HIP
    -D GPU_ARCH=value            # primary GPU hardware choice for GPU_API=cuda
-                                # value = sm_XX, see below
+                                # value = sm_XX (see below, default is sm_50)
-                                # default is sm_50
+   -D GPU_DEBUG=value           # enable debug code in the GPU package library, mostly useful for developers
+                                # value = yes or no (default)
+   -D HIP_PATH=value            # value = path to HIP installation. Must be set if GPU_API=HIP
    -D HIP_ARCH=value            # primary GPU hardware choice for GPU_API=hip
                                 # value depends on selected HIP_PLATFORM
                                 # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
@@ -274,7 +274,7 @@ To enable GPU binning via CUDA performance primitives set the Makefile variable
 most modern GPUs.
 
 To support the CUDA multiprocessor server you can set the define
-``-DCUDA_PROXY``.  Please note that in this case you must **not** use
+``-DCUDA_MPS_SUPPORT``.  Please note that in this case you must **not** use
 the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
 to empty.
 
@@ -288,7 +288,7 @@ your machine are not correct, the LAMMPS build will fail, and
 .. note::
 
    If you re-build the GPU library in ``lib/gpu``, you should always
-   un-install the GPU package in ``lammps/src``, then re-install it and
+   uninstall the GPU package in ``lammps/src``, then re-install it and
    re-build LAMMPS.  This is because the compilation of files in the GPU
    package uses the library settings from the ``lib/gpu/Makefile.machine``
    used to build the GPU library.
@@ -606,6 +606,12 @@ They must be specified in uppercase.
    *  - AMPERE86
       - GPU
       - NVIDIA Ampere generation CC 8.6 GPU
+   *  - ADA89
+      - GPU
+      - NVIDIA Ada Lovelace generation CC 8.9 GPU
+   *  - HOPPER90
+      - GPU
+      - NVIDIA Hopper generation CC 9.0 GPU
    *  - VEGA900
       - GPU
       - AMD GPU MI25 GFX900
@@ -640,7 +646,7 @@ They must be specified in uppercase.
       - GPU
       - Intel GPU Ponte Vecchio
 
-This list was last updated for version 3.7.0 of the Kokkos library.
+This list was last updated for version 3.7.1 of the Kokkos library.
 
 .. tabs::
 
@@ -915,9 +921,9 @@ included in the LAMMPS source distribution in the ``lib/lepton`` folder.
 
       .. code-block:: bash
 
-         $ make lib-lepton                      # print help message
+         make lib-lepton                      # print help message
-         $ make lib-lepton args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
+         make lib-lepton args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
-         $ make lib-lepton args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+         make lib-lepton args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
 
       The "machine" argument of the "-m" flag is used to find a
       Makefile.machine to use as build recipe.
@@ -1129,7 +1135,7 @@ VORONOI package
 -----------------------------
 
 To build with this package, you must download and build the
-`Voro++ library <https://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::
@@ -1359,7 +1365,7 @@ module included in the LAMMPS source distribution.
       auto-generated consistent with those used in the core LAMMPS makefiles.
 
 
-      .. versionchanged:: TBD
+      .. versionchanged:: 8Feb2023
 
       Please note that Colvars uses the Lepton library, which is now
       included with the LEPTON package; if you use anything other than
@@ -1391,8 +1397,21 @@ This package depends on the KSPACE package.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_KSPACE=yes`` and
+      .. code-block:: bash
-      ``-D PKG_ELECTRODE=yes``.
+
+         -D PKG_ELECTRODE=yes          # enable the package itself
+         -D PKG_KSPACE=yes             # the ELECTRODE package requires KSPACE
+         -D USE_INTERNAL_LINALG=value  #
+
+      Features in the ELECTRODE package are dependent on code in the
+      KSPACE package so the latter one *must* be enabled.
+
+      The ELECTRODE package also requires LAPACK (and BLAS) and CMake
+      can identify their locations and pass that info to the LATTE build
+      script.  But on some systems this may cause problems when linking
+      or the dependency is not desired.  Try enabling
+      ``USE_INTERNAL_LINALG`` in those cases to use the bundled linear
+      algebra library and work around the limitation.
 
    .. tab:: Traditional make
 
@@ -1839,48 +1858,6 @@ MDI package
 
 ----------
 
-.. _mesont:
-
-MESONT package
--------------------------
-
-This package includes a library written in Fortran 90 in the
-``lib/mesont`` folder, so a working Fortran 90 compiler is required to
-compile it.  Also, the files with the force field data for running the
-bundled examples are not included in the source distribution. Instead
-they will be downloaded the first time this package is installed.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      No additional settings are needed besides ``-D PKG_MESONT=yes``
-
-   .. tab:: Traditional make
-
-      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
-      invokes the ``lib/mesont/Install.py`` script with the specified
-      args:
-
-      .. code-block:: bash
-
-         make lib-mesont                    # print help message
-         make lib-mesont args="-m gfortran" # build with GNU g++ compiler (settings as with "make serial")
-         make lib-mesont args="-m ifort"    # build with Intel icc compiler
-
-      The build should produce two files: ``lib/mesont/libmesont.a`` and
-      ``lib/mesont/Makefile.lammps``\ .  The latter is copied from an
-      existing ``Makefile.lammps.\*`` and has settings needed to build
-      LAMMPS with the *mesont* library (though typically the settings
-      contain only the Fortran runtime library).  If necessary, you can
-      edit/create a new ``lib/mesont/Makefile.machine`` file for your
-      system, which should define an ``EXTRAMAKE`` variable to specify a
-      corresponding ``Makefile.lammps.machine`` file.
-
-----------
-
 .. _molfile:
 
 MOLFILE package
@@ -1987,10 +1964,10 @@ OPENMP package
    Apple offers the `Xcode package and IDE
    <https://developer.apple.com/xcode/>`_ for compiling software on
    macOS, so you have likely installed it to compile LAMMPS.  Their
-   compiler is based on `Clang <https://clang.llvm.org/>`, but while it
+   compiler is based on `Clang <https://clang.llvm.org/>`_, but while it
    is capable of processing OpenMP directives, the necessary header
    files and OpenMP runtime library are missing.  The `R developers
-   <https://www.r-project.org/>` have figured out a way to build those
+   <https://www.r-project.org/>`_ have figured out a way to build those
    in a compatible fashion. One can download them from
    `https://mac.r-project.org/openmp/
    <https://mac.r-project.org/openmp/>`_.  Simply adding those files as

doc/src/Build_link.rst

@@ -1,33 +1,32 @@
 Link LAMMPS as a library to another code
 ========================================
 
-LAMMPS is designed as a library of C++ objects that can be
+LAMMPS is designed as a library of C++ objects that can be integrated
-integrated into other applications including Python scripts.
+into other applications, including Python scripts.  The files
-The files ``src/library.cpp`` and ``src/library.h`` define a
+``src/library.cpp`` and ``src/library.h`` define a C-style API for using
-C-style API for using LAMMPS as a library.  See the
+LAMMPS as a library.  See the :doc:`Howto_library` page for a
-:doc:`Howto_library` page
+description of the interface and how to use it for your needs.
-for a description of the interface and how to use it for your needs.
 
-The :doc:`Build_basics` page explains how to build
+The :doc:`Build_basics` page explains how to build LAMMPS as either a
-LAMMPS as either a shared or static library.  This results in a file
+shared or static library.  This results in a file in the compilation
-in the compilation folder called ``liblammps.a`` or ``liblammps_<name>.a``
+folder called ``liblammps.a`` or ``liblammps_<name>.a`` in case of
-in case of building a static library.  In case of a shared library
+building a static library.  In case of a shared library, the name is the
-the name is the same only that the suffix is going to be either ``.so``
+same only that the suffix is going to be either ``.so`` or ``.dylib`` or
-or ``.dylib`` or ``.dll`` instead of ``.a`` depending on the OS.
+``.dll`` instead of ``.a`` depending on the OS.  In some cases, the
-In some cases the ``.so`` file may be a symbolic link to a file with
+``.so`` file may be a symbolic link to a file with the suffix ``.so.0``
-the suffix ``.so.0`` (or some other number).
+(or some other number).
 
 .. note::
 
    Care should be taken to use the same MPI library for the calling code
-   and the LAMMPS library unless LAMMPS is to be compiled without (real)
+   and the LAMMPS library, unless LAMMPS is to be compiled without (real)
-   MPI support using the include STUBS MPI library.
+   MPI support using the included STUBS MPI library.
 
 Link with LAMMPS as a static library
 ------------------------------------
 
 The calling application can link to LAMMPS as a static library with
-compilation and link commands as in the examples shown below.  These
+compilation and link commands, as in the examples shown below.  These
 are examples for a code written in C in the file ``caller.c``.
 The benefit of linking to a static library is, that the resulting
 executable is independent of that library since all required
@@ -142,10 +141,10 @@ Link with LAMMPS as a shared library
 When linking to LAMMPS built as a shared library, the situation becomes
 much simpler, as all dependent libraries and objects are either included
 in the shared library or registered as a dependent library in the shared
-library file.  Thus those libraries need not to be specified when
+library file.  Thus, those libraries need not be specified when linking
-linking the calling executable.  Only the *-I* flags are needed.  So the
+the calling executable.  Only the *-I* flags are needed.  So the example
-example case from above of the serial version static LAMMPS library with
+case from above of the serial version static LAMMPS library with the
-the POEMS package installed becomes:
+POEMS package installed becomes:
 
 .. tabs::
 

doc/src/Build_make.rst

@@ -20,21 +20,22 @@ with :doc:`CMake <Build_cmake>`.  The makefiles of the traditional
 make based build process and the scripts they are calling expect a few
 additional tools to be available and functioning.
 
-  * a working C/C++ compiler toolchain supporting the C++11 standard; on
+  * A working C/C++ compiler toolchain supporting the C++11 standard; on
-    Linux these are often the GNU compilers. Some older compilers
+    Linux, these are often the GNU compilers. Some older compiler versions
     require adding flags like ``-std=c++11`` to enable the C++11 mode.
-  * a Bourne shell compatible "Unix" shell program (often this is ``bash``)
+  * A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
-  * a few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
+  * A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
-  * python (optional, required for ``make lib-<pkg>`` in the src folder).
+  * Python (optional, required for ``make lib-<pkg>`` in the src
-    python scripts are currently tested with python 2.7 and 3.6. The procedure
+    folder).  Python scripts are currently tested with python 2.7 and
-    for :doc:`building the documentation <Build_manual>` requires python 3.5 or later.
+    3.6 to 3.11. The procedure for :doc:`building the documentation
+    <Build_manual>` *requires* Python 3.5 or later.
 
 Getting started
 ^^^^^^^^^^^^^^^
 
 To include LAMMPS packages (i.e. optional commands and styles) you must
 enable (or "install") them first, as discussed on the :doc:`Build
-package <Build_package>` page.  If a packages requires (provided or
+package <Build_package>` page.  If a package requires (provided or
 external) libraries, you must configure and build those libraries
 **before** building LAMMPS itself and especially **before** enabling
 such a package with ``make yes-<package>``.  :doc:`Building LAMMPS with
@@ -56,36 +57,36 @@ Compilation can take a long time, since LAMMPS is a large project with
 many features. If your machine has multiple CPU cores (most do these
 days), you can speed this up by compiling sources in parallel with
 ``make -j N`` (with N being the maximum number of concurrently executed
-tasks).  Also installation of the `ccache <https://ccache.dev/>`_ (=
+tasks).  Installation of the `ccache <https://ccache.dev/>`_ (= Compiler
-Compiler Cache) software may speed up repeated compilation even more,
+Cache) software may speed up repeated compilation even more, e.g. during
-e.g. during code development.
+code development, especially when repeatedly switching between branches.
 
 After the initial build, whenever you edit LAMMPS source files, or add
 or remove new files to the source directory (e.g. by installing or
 uninstalling packages), you must re-compile and relink the LAMMPS
 executable with the same ``make <machine>`` command.  The makefile's
-dependency tracking should insure that only the necessary subset of
+dependency tracking should ensure that only the necessary subset of
-files are re-compiled.  If you change settings in the makefile, you have
+files is re-compiled.  If you change settings in the makefile, you have
-to recompile *everything*.  To delete all objects you can use ``make
+to recompile *everything*.  To delete all objects, you can use ``make
 clean-<machine>``.
 
 .. note::
 
    Before the actual compilation starts, LAMMPS will perform several
-   steps to collect information from the configuration and setup that
+   steps to collect information from the configuration and setup that is
-   is then embedded into the executable.  When you build LAMMPS for
+   then embedded into the executable.  When you build LAMMPS for the
-   the first time, it will also compile a tool to quickly assemble
+   first time, it will also compile a tool to quickly determine a list
-   a list of dependencies, that are required for the make program to
+   of dependencies.  Those are required for the make program to
-   correctly detect which parts need to be recompiled after changes
+   correctly detect, which files need to be recompiled or relinked
-   were made to the sources.
+   after changes were made to the sources.
 
 Customized builds and alternate makefiles
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The ``src/MAKE`` directory tree contains the ``Makefile.<machine>``
 files included in the LAMMPS distribution.  Typing ``make example`` uses
-``Makefile.example`` from one of those folders, if available.  Thus the
+``Makefile.example`` from one of those folders, if available.  The
-``make serial`` and ``make mpi`` lines above use
+``make serial`` and ``make mpi`` lines above, for example, use
 ``src/MAKE/Makefile.serial`` and ``src/MAKE/Makefile.mpi``,
 respectively.  Other makefiles are in these directories:
 
@@ -106,12 +107,13 @@ a new name, please edit the first line with the description and machine
 name, so you will not confuse yourself, when looking at the machine
 summary.
 
-Makefiles you may wish to try include these (some require a package
+Makefiles you may wish to try out, include those listed below (some
-first be installed).  Many of these include specific compiler flags
+require a package first be installed).  Many of these include specific
-for optimized performance.  Please note, however, that some of these
+compiler flags for optimized performance.  Please note, however, that
-customized machine Makefile are contributed by users.  Since both
+some of these customized machine Makefile are contributed by users, and
-compilers, OS configurations, and LAMMPS itself keep changing, their
+thus may have modifications specific to the systems of those users.
-settings may become outdated:
+Since compilers, OS configurations, and LAMMPS itself keep changing,
+their settings may become outdated, too:
 
 .. code-block:: bash
 

doc/src/Build_manual.rst

@@ -2,7 +2,7 @@ Build the LAMMPS documentation
 ==============================
 
 Depending on how you obtained LAMMPS and whether you have built the
-manual yourself, this directory has a number of sub-directories and
+manual yourself, this directory has a number of subdirectories and
 files. Here is a list with descriptions:
 
 .. code-block:: bash
@@ -33,7 +33,7 @@ various tools and files.  Some of them have to be installed (see below).  For
 the rest the build process will attempt to download and install them into
 a python virtual environment and local folders.
 
-A current version of the manual (latest patch release, that is the state
+A current version of the manual (latest feature release, that is the state
 of the *release* branch) is is available online at:
 `https://docs.lammps.org/ <https://docs.lammps.org/>`_.
 A version of the manual corresponding to the ongoing development (that is
@@ -48,9 +48,9 @@ Build using GNU make
 
 The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
 can be translated to different output format using the `Sphinx
-<https://sphinx-doc.org>`_ document generator tool.  It also
+<https://www.sphinx-doc.org/>`_ document generator tool.  It also
 incorporates programmer documentation extracted from the LAMMPS C++
-sources through the `Doxygen <https://doxygen.nl>`_ program.  Currently
+sources through the `Doxygen <https://doxygen.nl/>`_ program.  Currently
 the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
 and MOBI (for Amazon Kindle readers) are supported.  For that to work a
 Python 3 interpreter, the ``doxygen`` tools and internet access to
@@ -87,6 +87,7 @@ folder.  The following ``make`` commands are available:
    make anchor_check  # check for duplicate anchor labels
    make style_check   # check for complete and consistent style lists
    make package_check # check for complete and consistent package lists
+   make link_check    # check for broken or outdated URLs
    make spelling      # spell-check the manual
 
 ----------

doc/src/Build_package.rst

@@ -4,13 +4,14 @@ Include packages in build
 In LAMMPS, a package is a group of files that enable a specific set of
 features.  For example, force fields for molecular systems or
 rigid-body constraints are in packages.  In the src directory, each
-package is a sub-directory with the package name in capital letters.
+package is a subdirectory with the package name in capital letters.
 
 An overview of packages is given on the :doc:`Packages <Packages>` doc
-page.  Brief overviews of each package are on the :doc:`Packages details <Packages_details>` page.
+page.  Brief overviews of each package are on the :doc:`Packages details
+<Packages_details>` page.
 
 When building LAMMPS, you can choose to include or exclude each
-package.  In general there is no need to include a package if you
+package.  Generally, there is no need to include a package if you
 never plan to use its features.
 
 If you get a run-time error that a LAMMPS command or style is
@@ -49,7 +50,6 @@ packages:
    * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
-   * :ref:`MESONT <mesont>`
    * :ref:`ML-HDNNP <ml-hdnnp>`
    * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
@@ -94,7 +94,7 @@ versus make.
          If you switch between building with CMake and make builds, no
          packages in the src directory can be installed when you invoke
          ``cmake``.  CMake will give an error if that is not the case,
-         indicating how you can un-install all packages in the src dir.
+         indicating how you can uninstall all packages in the src dir.
 
    .. tab:: Traditional make
 
@@ -103,7 +103,7 @@ versus make.
          cd lammps/src
          make ps                    # check which packages are currently installed
          make yes-name              # install a package with name
-         make no-name               # un-install a package with name
+         make no-name               # uninstall a package with name
          make mpi                   # build LAMMPS with whatever packages are now installed
 
       Examples:
@@ -119,13 +119,13 @@ versus make.
       .. note::
 
          You must always re-build LAMMPS (via make) after installing or
-         un-installing a package, for the action to take effect. The
+         uninstalling a package, for the action to take effect. The
          included dependency tracking will make certain only files that
          are required to be rebuilt are recompiled.
 
       .. note::
 
-         You cannot install or un-install packages and build LAMMPS in a
+         You cannot install or uninstall packages and build LAMMPS in a
          single make command with multiple targets, e.g. ``make
          yes-colloid mpi``.  This is because the make procedure creates
          a list of source files that will be out-of-date for the build
@@ -150,7 +150,7 @@ other files dependent on that package are also excluded.
    if you downloaded a tarball, 3 packages (KSPACE, MANYBODY, MOLECULE)
    were pre-installed via the traditional make procedure in the ``src``
    directory.  That is no longer the case, so that CMake will build
-   as-is without needing to un-install those packages.
+   as-is without needing to uninstall those packages.
 
 ----------
 
@@ -167,9 +167,9 @@ control flow constructs for more complex operations.
 
 LAMMPS includes several of these files to define configuration
 "presets", similar to the options that exist for the Make based
-system. Using these files you can enable/disable portions of the
+system. Using these files, you can enable/disable portions of the
-available packages in LAMMPS. If you need a custom preset you can take
+available packages in LAMMPS. If you need a custom preset, you can
-one of them as a starting point and customize it to your needs.
+make a copy of one of them and modify it to suit your needs.
 
 .. code-block:: bash
 
@@ -183,7 +183,7 @@ one of them as a starting point and customize it to your needs.
     cmake -C ../cmake/presets/pgi.cmake      [OPTIONS] ../cmake  # change settings to use the PGI compilers by default
     cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake  # enable all packages
     cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
-    mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross compilers
+    mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross-compilers
 
 Presets that have names starting with "windows" are specifically for
 compiling LAMMPS :doc:`natively on Windows <Build_windows>` and
@@ -227,7 +227,7 @@ The following commands are useful for managing package source files
 and their installation when building LAMMPS via traditional make.
 Just type ``make`` in lammps/src to see a one-line summary.
 
-These commands install/un-install sets of packages:
+These commands install/uninstall sets of packages:
 
 .. code-block:: bash
 
@@ -243,40 +243,40 @@ These commands install/un-install sets of packages:
     make yes-ext                        # install packages that require external libraries
     make no-ext                         # uninstall packages that require external libraries
 
-which install/un-install various sets of packages.  Typing ``make
+which install/uninstall various sets of packages.  Typing ``make
 package`` will list all the these commands.
 
 .. note::
 
-   Installing or un-installing a package for the make based build process
+   Installing or uninstalling a package for the make based build process
    works by simply copying files back and forth between the main source
-   directory src and the sub-directories with the package name (e.g.
+   directory src and the subdirectories with the package name (e.g.
    src/KSPACE, src/ATC), so that the files are included or excluded
    when LAMMPS is built.  Only source files in the src folder will be
    compiled.
 
 The following make commands help manage files that exist in both the
-src directory and in package sub-directories.  You do not normally
+src directory and in package subdirectories.  You do not normally
 need to use these commands unless you are editing LAMMPS files or are
 updating LAMMPS via git.
 
 Type ``make package-status`` or ``make ps`` to show which packages are
 currently installed.  For those that are installed, it will list any
 files that are different in the src directory and package
-sub-directory.
+subdirectory.
 
 Type ``make package-installed`` or ``make pi`` to show which packages are
 currently installed, without listing the status of packages that are
 not installed.
 
 Type ``make package-update`` or ``make pu`` to overwrite src files with
-files from the package sub-directories if the package is installed.  It
+files from the package subdirectories if the package is installed.  It
 should be used after the checkout has been :doc:`updated or changed
-withy git <Install_git>`, this will only update the files in the package
+with git <Install_git>`, this will only update the files in the package
-sub-directories, but not the copies in the src folder.
+subdirectories, but not the copies in the src folder.
 
 Type ``make package-overwrite`` to overwrite files in the package
-sub-directories with src files.
+subdirectories with src files.
 
 Type ``make package-diff`` to list all differences between pairs of
 files in both the source directory and the package directory.

doc/src/Build_settings.rst

@@ -1,8 +1,8 @@
 Optional build settings
 =======================
 
-LAMMPS can be built with several optional settings.  Each sub-section
+LAMMPS can be built with several optional settings.  Each subsection
-explain how to do this for building both with CMake and make.
+explains how to do this for building both with CMake and make.
 
 * `C++11 standard compliance`_ when building all of LAMMPS
 * `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
@@ -41,7 +41,7 @@ FFT library
 When the KSPACE package is included in a LAMMPS build, the
 :doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
 require use of an FFT library to compute 1d FFTs.  The KISS FFT
-library is included with LAMMPS but other libraries can be faster.
+library is included with LAMMPS, but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
 
 .. tabs::
@@ -63,9 +63,9 @@ LAMMPS can use them if they are available on your system.
       Usually these settings are all that is needed.  If FFTW3 is
       selected, then CMake will try to detect, if threaded FFTW
       libraries are available and enable them by default.  This setting
-      is independent of whether OpenMP threads are enabled and a
+      is independent of whether OpenMP threads are enabled and a package
-      packages like KOKKOS or OPENMP is used.  If CMake cannot detect
+      like KOKKOS or OPENMP is used.  If CMake cannot detect the FFT
-      the FFT library, you can set these variables to assist:
+      library, you can set these variables to assist:
 
       .. code-block:: bash
 
@@ -141,18 +141,18 @@ The Intel MKL math library is part of the Intel compiler suite.  It
 can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
 above).
 
-Performing 3d FFTs in parallel can be time consuming due to data
+Performing 3d FFTs in parallel can be time-consuming due to data access
-access and required communication.  This cost can be reduced by
+and required communication.  This cost can be reduced by performing
-performing single-precision FFTs instead of double precision.  Single
+single-precision FFTs instead of double precision.  Single precision
-precision means the real and imaginary parts of a complex datum are
+means the real and imaginary parts of a complex datum are 4-byte floats.
-4-byte floats.  Double precision means they are 8-byte doubles.  Note
+Double precision means they are 8-byte doubles.  Note that Fourier
-that Fourier transform and related PPPM operations are somewhat less
+transform and related PPPM operations are somewhat less sensitive to
-sensitive to floating point truncation errors and thus the resulting
+floating point truncation errors, and thus the resulting error is
-error is less than the difference in precision. Using the ``-DFFT_SINGLE``
+generally less than the difference in precision. Using the
-setting trades off a little accuracy for reduced memory use and
+``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory
-parallel communication costs for transposing 3d FFT data.
+use and parallel communication costs for transposing 3d FFT data.
 
-When using ``-DFFT_SINGLE`` with FFTW3 you may need to build the FFTW
+When using ``-DFFT_SINGLE`` with FFTW3, you may need to build the FFTW
 library a second time with support for single-precision.
 
 For FFTW3, do the following, which should produce the additional
@@ -177,11 +177,11 @@ ARRAY mode.
 Size of LAMMPS integer types and size limits
 --------------------------------------------
 
-LAMMPS has a few integer data types which can be defined as either
+LAMMPS uses a few custom integer data types, which can be defined as
-4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
+either 4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
-This has an impact on the size of a system that can be simulated
+This has an impact on the size of a system that can be simulated, or how
-or how large counters can become before "rolling over".
+large counters can become before "rolling over".  The default setting of
-The default setting of "smallbig" is almost always adequate.
+"smallbig" is almost always adequate.
 
 .. tabs::
 
@@ -254,7 +254,7 @@ topology information, though IDs are enabled by default.  The
 :doc:`atom_modify id no <atom_modify>` command will turn them off.  Atom
 IDs are required for molecular systems with bond topology (bonds,
 angles, dihedrals, etc).  Similarly, some force or compute or fix styles
-require atom IDs.  Thus if you model a molecular system or use one of
+require atom IDs.  Thus, if you model a molecular system or use one of
 those styles with more than 2 billion atoms, you need the "bigbig"
 setting.
 
@@ -264,7 +264,7 @@ systems and 500 million for systems with bonds (the additional
 restriction is due to using the 2 upper bits of the local atom index
 in neighbor lists for storing special bonds info).
 
-Image flags store 3 values per atom in a single integer which count the
+Image flags store 3 values per atom in a single integer, which count the
 number of times an atom has moved through the periodic box in each
 dimension.  See the :doc:`dump <dump>` manual page for a discussion.  If
 an atom moves through the periodic box more than this limit, the value
@@ -285,7 +285,7 @@ Output of JPG, PNG, and movie files
 --------------------------------------------------
 
 The :doc:`dump image <dump_image>` command has options to output JPEG or
-PNG image files.  Likewise the :doc:`dump movie <dump_image>` command
+PNG image files.  Likewise, the :doc:`dump movie <dump_image>` command
 outputs movie files in a variety of movie formats.  Using these options
 requires the following settings:
 
@@ -354,7 +354,7 @@ Read or write compressed files
 If this option is enabled, large files can be read or written with
 compression by ``gzip`` or similar tools by several LAMMPS commands,
 including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
-:doc:`dump <dump>`.  Currently supported compression tools are:
+:doc:`dump <dump>`.  Supported compression tools are currently
 ``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
 
 .. tabs::
@@ -394,7 +394,7 @@ Memory allocation alignment
 ---------------------------------------
 
 This setting enables the use of the "posix_memalign()" call instead of
-"malloc()" when LAMMPS allocates large chunks or memory.  Vector
+"malloc()" when LAMMPS allocates large chunks of memory.  Vector
 instructions on CPUs may become more efficient, if dynamically allocated
 memory is aligned on larger-than-default byte boundaries.  On most
 current operating systems, the "malloc()" implementation returns
@@ -496,7 +496,7 @@ Trigger selected floating-point exceptions
 ------------------------------------------
 
 Many kinds of CPUs have the capability to detect when a calculation
-results in an invalid math operation like a division by zero or calling
+results in an invalid math operation, like a division by zero or calling
 the square root with a negative argument.  The default behavior on
 most operating systems is to continue and have values for ``NaN`` (= not
 a number) or ``Inf`` (= infinity).  This allows software to detect and

doc/src/Commands_bond.rst

@@ -42,6 +42,7 @@ OPT.
    * :doc:`gaussian <bond_gaussian>`
    * :doc:`gromos (o) <bond_gromos>`
    * :doc:`harmonic (iko) <bond_harmonic>`
+   * :doc:`harmonic/restrain <bond_harmonic_restrain>`
    * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
    * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
    * :doc:`lepton (o) <bond_lepton>`

doc/src/Commands_compute.rst

@@ -88,7 +88,6 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`ke/atom/eff <compute_ke_atom_eff>`
    * :doc:`ke/eff <compute_ke_eff>`
    * :doc:`ke/rigid <compute_ke_rigid>`
-   * :doc:`mesont <compute_mesont>`
    * :doc:`mliap <compute_mliap>`
    * :doc:`momentum <compute_momentum>`
    * :doc:`msd <compute_msd>`
@@ -105,6 +104,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`pe/tally <compute_tally>`
    * :doc:`plasticity/atom <compute_plasticity_atom>`
    * :doc:`pressure <compute_pressure>`
+   * :doc:`pressure/alchemy <compute_pressure_alchemy>`
    * :doc:`pressure/uef <compute_pressure_uef>`
    * :doc:`property/atom <compute_property_atom>`
    * :doc:`property/chunk <compute_property_chunk>`

doc/src/Commands_fix.rst

@@ -29,6 +29,7 @@ OPT.
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`
    * :doc:`addtorque <fix_addtorque>`
+   * :doc:`alchemy <fix_alchemy>`
    * :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
    * :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>`
    * :doc:`append/atoms <fix_append_atoms>`
@@ -44,9 +45,6 @@ OPT.
    * :doc:`ave/time <fix_ave_time>`
    * :doc:`aveforce <fix_aveforce>`
    * :doc:`balance <fix_balance>`
-   * :doc:`brownian <fix_brownian>`
-   * :doc:`brownian/asphere <fix_brownian>`
-   * :doc:`brownian/sphere <fix_brownian>`
    * :doc:`bocs <fix_bocs>`
    * :doc:`bond/break <fix_bond_break>`
    * :doc:`bond/create <fix_bond_create>`
@@ -54,6 +52,9 @@ OPT.
    * :doc:`bond/react <fix_bond_react>`
    * :doc:`bond/swap <fix_bond_swap>`
    * :doc:`box/relax <fix_box_relax>`
+   * :doc:`brownian <fix_brownian>`
+   * :doc:`brownian/asphere <fix_brownian>`
+   * :doc:`brownian/sphere <fix_brownian>`
    * :doc:`charge/regulation <fix_charge_regulation>`
    * :doc:`cmap <fix_cmap>`
    * :doc:`colvars <fix_colvars>`
@@ -169,7 +170,7 @@ OPT.
    * :doc:`pafi <fix_pafi>`
    * :doc:`pair <fix_pair>`
    * :doc:`phonon <fix_phonon>`
-   * :doc:`pimd <fix_pimd>`
+   * :doc:`pimd/nvt <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
    * :doc:`plumed <fix_plumed>`
    * :doc:`poems <fix_poems>`
@@ -264,6 +265,7 @@ OPT.
    * :doc:`wall/lj1043 <fix_wall>`
    * :doc:`wall/lj126 <fix_wall>`
    * :doc:`wall/lj93 (k) <fix_wall>`
+   * :doc:`wall/lepton <fix_wall>`
    * :doc:`wall/morse <fix_wall>`
    * :doc:`wall/piston <fix_wall_piston>`
    * :doc:`wall/reflect (k) <fix_wall_reflect>`
@@ -271,4 +273,5 @@ OPT.
    * :doc:`wall/region <fix_wall_region>`
    * :doc:`wall/region/ees <fix_wall_ees>`
    * :doc:`wall/srd <fix_wall_srd>`
+   * :doc:`wall/table <fix_wall>`
    * :doc:`widom <fix_widom>`

doc/src/Commands_pair.rst

@@ -39,7 +39,7 @@ OPT.
    * :doc:`agni (o) <pair_agni>`
    * :doc:`airebo (io) <pair_airebo>`
    * :doc:`airebo/morse (io) <pair_airebo>`
-   * :doc:`amoeba <pair_amoeba>`
+   * :doc:`amoeba (g) <pair_amoeba>`
    * :doc:`atm <pair_atm>`
    * :doc:`awpmd/cut <pair_awpmd>`
    * :doc:`beck (go) <pair_beck>`
@@ -126,7 +126,7 @@ OPT.
    * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
    * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
    * :doc:`hdnnp <pair_hdnnp>`
-   * :doc:`hippo <pair_amoeba>`
+   * :doc:`hippo (g) <pair_amoeba>`
    * :doc:`ilp/graphene/hbn (t) <pair_ilp_graphene_hbn>`
    * :doc:`ilp/tmd (t) <pair_ilp_tmd>`
    * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
@@ -166,7 +166,7 @@ OPT.
    * :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/msm/dielectric <pair_dielectric>`
    * :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
-   * :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
+   * :doc:`lj/cut/dipole/cut (gko) <pair_dipole>`
    * :doc:`lj/cut/dipole/long (g) <pair_dipole>`
    * :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/cut/soft (o) <pair_fep_soft>`
@@ -175,7 +175,7 @@ OPT.
    * :doc:`lj/cut/tip4p/long (got) <pair_lj_cut_tip4p>`
    * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
    * :doc:`lj/expand (gko) <pair_lj_expand>`
-   * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
+   * :doc:`lj/expand/coul/long (gk) <pair_lj_expand>`
    * :doc:`lj/gromacs (gko) <pair_gromacs>`
    * :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
    * :doc:`lj/long/coul/long (iot) <pair_lj_long>`
@@ -200,11 +200,11 @@ OPT.
    * :doc:`mdpd <pair_mesodpd>`
    * :doc:`mdpd/rhosum <pair_mesodpd>`
    * :doc:`meam (k) <pair_meam>`
+   * :doc:`meam/ms (k) <pair_meam>`
    * :doc:`meam/spline (o) <pair_meam_spline>`
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
    * :doc:`mesocnt <pair_mesocnt>`
    * :doc:`mesocnt/viscous <pair_mesocnt>`
-   * :doc:`mesont/tpm <pair_mesont_tpm>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
    * :doc:`mliap (k) <pair_mliap>`

doc/src/Commands_removed.rst

@@ -50,6 +50,27 @@ for some optimizations leading to better performance.  The pair style
 period the C++ version of MEAM was called USER-MEAMC so it could
 coexist with the Fortran version.
 
+Minimize style fire/old
+-----------------------
+
+.. deprecated:: 8Feb2023
+
+Minimize style *fire/old* has been removed. Its functionality can be
+reproduced with *fire* with specific options. Please see the
+:doc:`min_modify command <min_modify>` documentation for details.
+
+Pair style mesont/tpm, compute style mesont, atom style mesont
+--------------------------------------------------------------
+
+.. deprecated:: 8Feb2023
+
+Pair style *mesont/tpm*, compute style *mesont*, and atom style
+*mesont* have been removed from the :ref:`MESONT package <PKG-MESONT>`.
+The same functionality is available through
+:doc:`pair style mesocnt <pair_mesocnt>`,
+:doc:`bond style mesocnt <bond_mesocnt>` and
+:doc:`angle style mesocnt <angle_mesocnt>`.
+
 REAX package
 ------------
 

doc/src/Developer_code_design.rst

@@ -1,52 +1,53 @@
 Code design
 -----------
 
-This section explains some of the code design choices in LAMMPS with
+This section explains some code design choices in LAMMPS with the goal
-the goal of helping developers write new code similar to the existing
+of helping developers write new code similar to the existing code.
-code.  Please see the section on :doc:`Requirements for contributed
+Please see the section on :doc:`Requirements for contributed code
-code <Modify_style>` for more specific recommendations and guidelines.
+<Modify_style>` for more specific recommendations and guidelines.  While
-While that section is organized more in the form of a checklist for
+that section is organized more in the form of a checklist for code
-code contributors, the focus here is on overall code design strategy,
+contributors, the focus here is on overall code design strategy, choices
-choices made between possible alternatives, and discussing some
+made between possible alternatives, and discussing some relevant C++
-relevant C++ programming language constructs.
+programming language constructs.
 
 Historically, the basic design philosophy of the LAMMPS C++ code was a
 "C with classes" style.  The motivation was to make it easy to modify
-LAMMPS for people without significant training in C++ programming.
+LAMMPS for people without significant training in C++ programming.  Data
-Data structures and code constructs were used that resemble the
+structures and code constructs were used that resemble the previous
-previous implementation(s) in Fortran.  A contributing factor to this
+implementation(s) in Fortran.  A contributing factor to this choice was
-choice also was that at the time, C++ compilers were often not mature
+that at the time, C++ compilers were often not mature and some advanced
-and some of the advanced features contained bugs or did not function
+features contained bugs or did not function as the standard required.
-as the standard required.  There were also disagreements between
+There were also disagreements between compiler vendors as to how to
-compiler vendors as to how to interpret the C++ standard documents.
+interpret the C++ standard documents.
 
-However, C++ compilers have now advanced significantly.  In 2020 we
+However, C++ compilers and the C++ programming language have advanced
-decided to to require the C++11 standard as the minimum C++ language
+significantly.  In 2020, the LAMMPS developers decided to require the
-standard for LAMMPS.  Since then we have begun to also replace some of
+C++11 standard as the minimum C++ language standard for LAMMPS.  Since
-the C-style constructs with equivalent C++ functionality, either from
+then, we have begun to replace C-style constructs with equivalent C++
-the C++ standard library or as custom classes or functions, in order
+functionality.  This was taken either from the C++ standard library or
-to improve readability of the code and to increase code reuse through
+implemented as custom classes or functions.  The goal is to improve
-abstraction of commonly used functionality.
+readability of the code and to increase code reuse through abstraction
+of commonly used functionality.
 
 .. note::
 
-   Please note that as of spring 2022 there is still a sizable chunk
+   Please note that as of spring 2023 there is still a sizable chunk of
-   of legacy code in LAMMPS that has not yet been refactored to
+   legacy code in LAMMPS that has not yet been refactored to reflect
-   reflect these style conventions in full.  LAMMPS has a large code
+   these style conventions in full.  LAMMPS has a large code base and
-   base and many different contributors and there also is a hierarchy
+   many contributors.  There is also a hierarchy of precedence in which
-   of precedence in which the code is adapted.  Highest priority has
+   the code is adapted.  Highest priority has been the code in the
-   been the code in the ``src`` folder, followed by code in packages
+   ``src`` folder, followed by code in packages in order of their
-   in order of their popularity and complexity (simpler code is
+   popularity and complexity (simpler code gets adapted sooner), followed
-   adapted sooner), followed by code in the ``lib`` folder.  Source
+   by code in the ``lib`` folder.  Source code that is downloaded from
-   code that is downloaded from external packages or libraries during
+   external packages or libraries during compilation is not subject to
-   compilation is not subject to the conventions discussed here.
+   the conventions discussed here.
 
-Object oriented code
+Object-oriented code
 ^^^^^^^^^^^^^^^^^^^^
 
-LAMMPS is designed to be an object oriented code.  Each simulation is
+LAMMPS is designed to be an object-oriented code.  Each simulation is
 represented by an instance of the LAMMPS class.  When running in
-parallel each MPI process creates such an instance.  This can be seen
+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:
 
@@ -67,14 +68,14 @@ other special features.
 The basic LAMMPS class hierarchy which is created by the LAMMPS class
 constructor is shown in :ref:`class-topology`.  When input commands
 are processed, additional class instances are created, or deleted, or
-replaced.  Likewise specific member functions of specific classes are
+replaced.  Likewise, specific member functions of specific classes are
 called to trigger actions such creating atoms, computing forces,
 computing properties, time-propagating the system, or writing output.
 
 Compositing and Inheritance
 ===========================
 
-LAMMPS makes extensive use of the object oriented programming (OOP)
+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``,
@@ -83,7 +84,7 @@ 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
 composites, containing instances of classes describing different force
-interactions.  Similarly the ``Modify`` class contains a list of
+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*,
@@ -100,19 +101,18 @@ derived class variant was instantiated.  In LAMMPS these derived
 classes are often referred to as "styles", e.g.  pair styles, fix
 styles, atom styles and so on.
 
-This is the origin of the flexibility of LAMMPS.  For example pair
+This is the origin of the flexibility of LAMMPS.  For example, pair
 styles implement a variety of different non-bonded interatomic
 potentials functions.  All details for the implementation of a
 potential are stored and executed in a single class.
 
 As mentioned above, there can be multiple instances of classes derived
 from the ``Fix`` or ``Compute`` base classes.  They represent a
-different facet of LAMMPS flexibility as they provide methods which
+different facet of LAMMPS' flexibility, as they provide methods which
-can be called at different points in time within a timestep, as
+can be called at different points within a timestep, as explained in
-explained in `Developer_flow`.  This allows the input script to tailor
+`Developer_flow`.  This allows the input script to tailor how a specific
-how a specific simulation is run, what diagnostic computations are
+simulation is run, what diagnostic computations are performed, and how
-performed, and how the output of those computations is further
+the output of those computations is further processed or output.
-processed or output.
 
 Additional code sharing is possible by creating derived classes from the
 derived classes (e.g., to implement an accelerated version of a pair
@@ -164,15 +164,15 @@ The difference in behavior of the ``normal()`` and the ``poly()`` member
 functions is which of the two member functions is called when executing
 `base1->call()` versus `base2->call()`.  Without polymorphism, a
 function within the base class can only call member functions within the
-same scope, that is ``Base::call()`` will always call
+same scope: that is, ``Base::call()`` will always call
-``Base::normal()``.  But for the `base2->call()` case the call of the
+``Base::normal()``.  But for the `base2->call()` case, the call of the
 virtual member function will be dispatched to ``Derived::poly()``
-instead.  This mechanism means that functions are called within the
+instead.  This mechanism results in calling functions that are within
-scope of the class type that was used to *create* the class instance are
+the scope of the class that was used to *create* the instance, even if
-invoked; even if they are assigned to a pointer using the type of a base
+they are assigned to a pointer for their base class.  This is the
-class.  This is the desired behavior and this way LAMMPS can even use
+desired behavior, and this way LAMMPS can even use styles that are loaded
-styles that are loaded at runtime from a shared object file with the
+at runtime from a shared object file with the :doc:`plugin command
-:doc:`plugin command <plugin>`.
+<plugin>`.
 
 A special case of virtual functions are so-called pure functions.  These
 are virtual functions that are initialized to 0 in the class declaration
@@ -189,12 +189,12 @@ This has the effect that an instance of the base class cannot be
 created and that derived classes **must** implement these functions.
 Many of the functions listed with the various class styles in the
 section :doc:`Modify` are pure functions.  The motivation for this is
-to define the interface or API of the functions but defer their
+to define the interface or API of the functions, but defer their
 implementation to the derived classes.
 
 However, there are downsides to this. For example, calls to virtual
-functions from within a constructor, will not be in the scope of the
+functions from within a constructor, will *not* be in the scope of the
-derived class and thus it is good practice to either avoid calling them
+derived class, and thus it is good practice to either avoid calling them
 or to provide an explicit scope such as ``Base::poly()`` or
 ``Derived::poly()``.  Furthermore, any destructors in classes containing
 virtual functions should be declared virtual too, so they will be
@@ -208,8 +208,8 @@ dispatch.
    that are intended to replace a virtual or pure function use the
    ``override`` property keyword.  For the same reason, the use of
    overloads or default arguments for virtual functions should be
-   avoided as they lead to confusion over which function is supposed to
+   avoided, as they lead to confusion over which function is supposed to
-   override which and which arguments need to be declared.
+   override which, and which arguments need to be declared.
 
 Style Factories
 ===============
@@ -219,10 +219,10 @@ uses a programming pattern called `Factory`.  Those are functions that
 create an instance of a specific derived class, say ``PairLJCut`` and
 return a pointer to the type of the common base class of that style,
 ``Pair`` in this case.  To associate the factory function with the
-style keyword, an ``std::map`` class is used with function pointers
+style keyword, a ``std::map`` class is used with function pointers
 indexed by their keyword (for example "lj/cut" for ``PairLJCut`` and
 "morse" for ``PairMorse``).  A couple of typedefs help keep the code
-readable and a template function is used to implement the actual
+readable, and a template function is used to implement the actual
 factory functions for the individual classes.  Below is an example
 of such a factory function from the ``Force`` class as declared in
 ``force.h`` and implemented in ``force.cpp``.  The file ``style_pair.h``
@@ -279,26 +279,26 @@ from and writing to files and console instead of C++ "iostreams".
 This is mainly motivated by better performance, better control over
 formatting, and less effort to achieve specific formatting.
 
-Since mixing "stdio" and "iostreams" can lead to unexpected
+Since mixing "stdio" and "iostreams" can lead to unexpected behavior,
-behavior. use of the latter is strongly discouraged.  Also output to
+use of the latter is strongly discouraged.  Output to the screen should
-the screen should not use the predefined ``stdout`` FILE pointer, but
+*not* use the predefined ``stdout`` FILE pointer, but rather the
-rather the ``screen`` and ``logfile`` FILE pointers managed by the
+``screen`` and ``logfile`` FILE pointers managed by the LAMMPS class.
-LAMMPS class.  Furthermore, output should generally only be done by
+Furthermore, output should generally only be done by MPI rank 0
-MPI rank 0 (``comm->me == 0``).  Output that is sent to both
+(``comm->me == 0``).  Output that is sent to both ``screen`` and
-``screen`` and ``logfile`` should use the :cpp:func:`utils::logmesg()
+``logfile`` should use the :cpp:func:`utils::logmesg() convenience
-convenience function <LAMMPS_NS::utils::logmesg>`.
+function <LAMMPS_NS::utils::logmesg>`.
 
-We also discourage the use of stringstreams because the bundled {fmt}
+We discourage the use of stringstreams because the bundled {fmt} library
-library and the customized tokenizer classes can provide the same
+and the customized tokenizer classes provide the same functionality in a
-functionality in a cleaner way with better performance.  This also
+cleaner way with better performance.  This also helps maintain a
-helps maintain a consistent programming syntax with code from many
+consistent programming syntax with code from many different
-different contributors.
+contributors.
 
 Formatting with the {fmt} library
 ===================================
 
 The LAMMPS source code includes a copy of the `{fmt} library
-<https://fmt.dev>`_ which is preferred over formatting with the
+<https://fmt.dev>`_, which is preferred over formatting with the
 "printf()" family of functions.  The primary reason is that it allows
 a typesafe default format for any type of supported data.  This is
 particularly useful for formatting integers of a given size (32-bit or
@@ -313,17 +313,16 @@ been included into the C++20 language standard, so changes to adopt it
 are future-proof.
 
 Formatted strings are frequently created by calling the
-``fmt::format()`` function which will return a string as a
+``fmt::format()`` function, which will return a string as a
-``std::string`` class instance.  In contrast to the ``%`` placeholder
+``std::string`` class instance.  In contrast to the ``%`` placeholder in
-in ``printf()``, the {fmt} library uses ``{}`` to embed format
+``printf()``, the {fmt} library uses ``{}`` to embed format descriptors.
-descriptors.  In the simplest case, no additional characters are
+In the simplest case, no additional characters are needed, as {fmt} will
-needed as {fmt} will choose the default format based on the data type
+choose the default format based on the data type of the argument.
-of the argument.  Otherwise the ``fmt::print()`` function may be
+Otherwise, the ``fmt::print()`` function may be used instead of
-used instead of ``printf()`` or ``fprintf()``.  In addition, several
+``printf()`` or ``fprintf()``.  In addition, several LAMMPS output
-LAMMPS output functions, that originally accepted a single string as
+functions, that originally accepted a single string as argument have
-argument have been overloaded to accept a format string with optional
+been overloaded to accept a format string with optional arguments as
-arguments as well (e.g., ``Error::all()``, ``Error::one()``,
+well (e.g., ``Error::all()``, ``Error::one()``, ``utils::logmesg()``).
-``utils::logmesg()``).
 
 Summary of the {fmt} format syntax
 ==================================
@@ -332,10 +331,11 @@ The syntax of the format string is "{[<argument id>][:<format spec>]}",
 where either the argument id or the format spec (separated by a colon
 ':') is optional.  The argument id is usually a number starting from 0
 that is the index to the arguments following the format string.  By
-default these are assigned in order (i.e. 0, 1, 2, 3, 4 etc.).  The most
+default, these are assigned in order (i.e. 0, 1, 2, 3, 4 etc.).  The
-common case for using argument id would be to use the same argument in
+most common case for using argument id would be to use the same argument
-multiple places in the format string without having to provide it as an
+in multiple places in the format string without having to provide it as
-argument multiple times. In LAMMPS the argument id is rarely used.
+an argument multiple times. The argument id is rarely used in the LAMMPS
+source code.
 
 More common is the use of a format specifier, which starts with a colon.
 This may optionally be followed by a fill character (default is ' '). If
@@ -347,18 +347,19 @@ width, which may be followed by a dot '.' and a precision for floating
 point numbers.  The final character in the format string would be an
 indicator for the "presentation", i.e. 'd' for decimal presentation of
 integers, 'x' for hexadecimal, 'o' for octal, 'c' for character etc.
-This mostly follows the "printf()" scheme but without requiring an
+This mostly follows the "printf()" scheme, but without requiring an
 additional length parameter to distinguish between different integer
 widths.  The {fmt} library will detect those and adapt the formatting
 accordingly.  For floating point numbers there are correspondingly, 'g'
 for generic presentation, 'e' for exponential presentation, and 'f' for
 fixed point presentation.
 
-Thus "{:8}" would represent *any* type argument using at least 8
+The format string "{:8}" would thus represent *any* type argument and be
-characters; "{:<8}" would do this as left aligned, "{:^8}" as centered,
+replaced by at least 8 characters; "{:<8}" would do this as left
-"{:>8}" as right aligned.  If a specific presentation is selected, the
+aligned, "{:^8}" as centered, "{:>8}" as right aligned.  If a specific
-argument type must be compatible or else the {fmt} formatting code will
+presentation is selected, the argument type must be compatible or else
-throw an exception. Some format string examples are given below:
+the {fmt} formatting code will throw an exception.  Some format string
+examples are given below:
 
 .. code-block:: c++
 
@@ -392,12 +393,12 @@ documentation <https://fmt.dev/latest/syntax.html>`_ website.
 Memory management
 ^^^^^^^^^^^^^^^^^
 
-Dynamical allocation of small data and objects can be done with the
+Dynamical allocation of small data and objects can be done with the C++
-the C++ commands "new" and "delete/delete[].  Large data should use
+commands "new" and "delete/delete[]".  Large data should use the member
-the member functions of the ``Memory`` class, most commonly,
+functions of the ``Memory`` class, most commonly, ``Memory::create()``,
-``Memory::create()``, ``Memory::grow()``, and ``Memory::destroy()``,
+``Memory::grow()``, and ``Memory::destroy()``, which provide variants
-which provide variants for vectors, 2d arrays, 3d arrays, etc.
+for vectors, 2d arrays, 3d arrays, etc.  These can also be used for
-These can also be used for small data.
+small data.
 
 The use of ``malloc()``, ``calloc()``, ``realloc()`` and ``free()``
 directly is strongly discouraged.  To simplify adapting legacy code
@@ -408,26 +409,24 @@ perform additional error checks for safety.
 Use of these custom memory allocation functions is motivated by the
 following considerations:
 
-- memory allocation failures on *any* MPI rank during a parallel run
+- Memory allocation failures on *any* MPI rank during a parallel run
-  will trigger an immediate abort of the entire parallel calculation
+  will trigger an immediate abort of the entire parallel calculation.
-  instead of stalling it
+- A failing "new" will trigger an exception, which is also captured by
-- a failing "new" will trigger an exception which is also captured by
+  LAMMPS and triggers a global abort.
-  LAMMPS and triggers a global abort
+- Allocation of multidimensional arrays will be done in a C compatible
-- allocation of multi-dimensional arrays will be done in a C compatible
+  fashion, but such that the storage of the actual data is stored in one
-  fashion but so that the storage of the actual data is stored in one
+  large contiguous block.  Thus, when MPI communication is needed,
-  large contiguous block.  Thus when MPI communication is needed,
   the data can be communicated directly (similar to Fortran arrays).
-- the "destroy()" and "sfree()" functions may safely be called on NULL
+- The "destroy()" and "sfree()" functions may safely be called on NULL
-  pointers
+  pointers.
-- the "destroy()" functions will nullify the pointer variables making
+- The "destroy()" functions will nullify the pointer variables, thus
-  "use after free" errors easy to detect
+  making "use after free" errors easy to detect.
-- it is possible to use a larger than default memory alignment (not on
+- It is possible to use a larger than default memory alignment (not on
   all operating systems, since the allocated storage pointers must be
-  compatible with ``free()`` for technical reasons)
+  compatible with ``free()`` for technical reasons).
 
-In the practical implementation of code this means that any pointer
+In the practical implementation of code this means, that any pointer
-variables that are class members should be initialized to a
+variables, that are class members should be initialized to a ``nullptr``
-``nullptr`` value in their respective constructors.  That way it is
+value in their respective constructors.  That way, it is safe to call
-safe to call ``Memory::destroy()`` or ``delete[]`` on them before
+``Memory::destroy()`` or ``delete[]`` on them before *any* allocation
-*any* allocation outside the constructor.  This helps prevent memory
+outside the constructor.  This helps prevent memory leaks.
-leaks.

doc/src/Developer_comm_ops.rst

@@ -14,8 +14,8 @@ Owned and ghost atoms
 As described on the :doc:`parallel partitioning algorithms
 <Developer_par_part>` page, LAMMPS spatially decomposes the simulation
 domain, either in a *brick* or *tiled* manner.  Each processor (MPI
-task) owns atoms within its sub-domain and additionally stores ghost
+task) owns atoms within its subdomain and additionally stores ghost
-atoms within a cutoff distance of its sub-domain.
+atoms within a cutoff distance of its subdomain.
 
 Forward and reverse communication
 =================================
@@ -28,7 +28,7 @@ The need to do this communication arises when data from the owned atoms
 is updated (e.g. their positions) and this updated information needs to
 be **copied** to the corresponding ghost atoms.
 
-And second, *reverse communication* which sends ghost atom information
+And second, *reverse communication*, which sends ghost atom information
 from each processor to the owning processor to **accumulate** (sum)
 the values with the corresponding owned atoms.  The need for this
 arises when data is computed and also stored with ghost atoms
@@ -58,7 +58,7 @@ embedded-atom method (EAM) which compute intermediate values in the
 first part of the compute() function that need to be stored by both
 owned and ghost atoms for the second part of the force computation.
 The *Comm* class methods perform the MPI communication for buffers of
-per-atom data.  They "call back" to the *Pair* class so it can *pack*
+per-atom data.  They "call back" to the *Pair* class, so it can *pack*
 or *unpack* the buffer with data the *Pair* class owns.  There are 4
 such methods that the *Pair* class must define, assuming it uses both
 forward and reverse communication:
@@ -70,22 +70,22 @@ forward and reverse communication:
 
 The arguments to these methods include the buffer and a list of atoms
 to pack or unpack.  The *Pair* class also must set the *comm_forward*
-and *comm_reverse* variables which store the number of values stored
+and *comm_reverse* variables, which store the number of values stored
 in the communication buffers for each operation.  This means, if
 desired, it can choose to store multiple per-atom values in the
 buffer, and they will be communicated together to minimize
 communication overhead.  The communication buffers are defined vectors
 containing ``double`` values.  To correctly store integers that may be
 64-bit (bigint, tagint, imageint) in the buffer, you need to use the
-`ubuf union <Communication buffer coding with ubuf>`_ construct.
+:ref:`ubuf union <communication_buffer_coding_with_ubuf>` construct.
 
 The *Fix*, *Compute*, and *Dump* classes can also invoke the same kind
 of forward and reverse communication operations using the same *Comm*
-class methods.  Likewise the same pack/unpack methods and
+class methods.  Likewise, the same pack/unpack methods and
 comm_forward/comm_reverse variables must be defined by the calling
 *Fix*, *Compute*, or *Dump* class.
 
-For *Fix* classes there is an optional second argument to the
+For *Fix* classes, there is an optional second argument to the
 *forward_comm()* and *reverse_comm()* call which can be used when the
 fix performs multiple modes of communication, with different numbers
 of values per atom.  The fix should set the *comm_forward* and
@@ -150,7 +150,7 @@ latter case, when the *ring* operation is complete, each processor can
 examine its original buffer to extract modified values.
 
 Note that the *ring* operation is similar to an MPI_Alltoall()
-operation where every processor effectively sends and receives data to
+operation, where every processor effectively sends and receives data to
 every other processor.  The difference is that the *ring* operation
 does it one step at a time, so the total volume of data does not need
 to be stored by every processor.  However, the *ring* operation is
@@ -184,8 +184,8 @@ The *exchange_data()* method triggers the communication to be
 performed.  Each processor provides the vector of *N* datums to send,
 and the size of each datum.  All datums must be the same size.
 
-The *create_atom()* and *exchange_atom()* methods are similar except
+The *create_atom()* and *exchange_atom()* methods are similar, except
-that the size of each datum can be different.  Typically this is used
+that the size of each datum can be different.  Typically, this is used
 to communicate atoms, each with a variable amount of per-atom data, to
 other processors.
 

doc/src/Developer_flow.rst

@@ -45,9 +45,9 @@ other methods in the class.
   zero before each timestep, so that forces (torques, etc) can be
   accumulated.
 
-Now for the ``Verlet::run()`` method.  Its basic structure in hi-level pseudo
+Now for the ``Verlet::run()`` method.  Its basic structure in hi-level
-code is shown below.  In the actual code in ``src/verlet.cpp`` some of
+pseudocode is shown below.  In the actual code in ``src/verlet.cpp``
-these operations are conditionally invoked.
+some of these operations are conditionally invoked.
 
 .. code-block:: python
 
@@ -105,17 +105,17 @@ need it.  These flags are passed to the various methods that compute
 particle interactions, so that they either compute and tally the
 corresponding data or can skip the extra calculations if the energy and
 virial are not needed.  See the comments for the ``Integrate::ev_set()``
-method which document the flag values.
+method, which document the flag values.
 
 At various points of the timestep, fixes are invoked,
 e.g. ``fix->initial_integrate()``.  In the code, this is actually done
-via the Modify class which stores all the Fix objects and lists of which
+via the Modify class, which stores all the Fix objects and lists of which
 should be invoked at what point in the timestep.  Fixes are the LAMMPS
 mechanism for tailoring the operations of a timestep for a particular
 simulation.  As described elsewhere, each fix has one or more methods,
 each of which is invoked at a specific stage of the timestep, as show in
-the timestep pseudo-code.  All the active fixes defined in an input
+the timestep pseudocode.  All the active fixes defined in an input
-script, that are flagged to have an ``initial_integrate()`` method are
+script, that are flagged to have an ``initial_integrate()`` method, are
 invoked at the beginning of each timestep.  Examples are :doc:`fix nve
 <fix_nve>` or :doc:`fix nvt or fix npt <fix_nh>` which perform the
 start-of-timestep velocity-Verlet integration operations to update
@@ -131,15 +131,15 @@ can be changed using the :doc:`neigh_modify every/delay/check
 <neigh_modify>` command.  If not, coordinates of ghost atoms are
 acquired by each processor via the ``forward_comm()`` method of the Comm
 class.  If neighbor lists need to be built, several operations within
-the inner if clause of the pseudo-code are first invoked.  The
+the inner if clause of the pseudocode are first invoked.  The
 ``pre_exchange()`` method of any defined fixes is invoked first.
-Typically this inserts or deletes particles from the system.
+Typically, this inserts or deletes particles from the system.
 
 Periodic boundary conditions are then applied by the Domain class via
 its ``pbc()`` method to remap particles that have moved outside the
 simulation box back into the box.  Note that this is not done every
 timestep, but only when neighbor lists are rebuilt.  This is so that
-each processor's sub-domain will have consistent (nearby) atom
+each processor's subdomain will have consistent (nearby) atom
 coordinates for its owned and ghost atoms.  It is also why dumped atom
 coordinates may be slightly outside the simulation box if not dumped
 on a step where the neighbor lists are rebuilt.
@@ -148,15 +148,15 @@ The box boundaries are then reset (if needed) via the ``reset_box()``
 method of the Domain class, e.g. if box boundaries are shrink-wrapped to
 current particle coordinates.  A change in the box size or shape
 requires internal information for communicating ghost atoms (Comm class)
-and neighbor list bins (Neighbor class) be updated.  The ``setup()``
+and neighbor list bins (Neighbor class) to be updated.  The ``setup()``
 method of the Comm class and ``setup_bins()`` method of the Neighbor
 class perform the update.
 
 The code is now ready to migrate atoms that have left a processor's
-geometric sub-domain to new processors.  The ``exchange()`` method of
+geometric subdomain to new processors.  The ``exchange()`` method of
 the Comm class performs this operation.  The ``borders()`` method of the
 Comm class then identifies ghost atoms surrounding each processor's
-sub-domain and communicates ghost atom information to neighboring
+subdomain and communicates ghost atom information to neighboring
 processors.  It does this by looping over all the atoms owned by a
 processor to make lists of those to send to each neighbor processor.  On
 subsequent timesteps, the lists are used by the ``Comm::forward_comm()``
@@ -217,20 +217,21 @@ file, and restart files.  See the :doc:`thermo_style <thermo_style>`,
 :doc:`dump <dump>`, and :doc:`restart <restart>` commands for more
 details.
 
-The the flow of control during energy minimization iterations is
+The flow of control during energy minimization iterations is similar to
-similar to that of a molecular dynamics timestep.  Forces are computed,
+that of a molecular dynamics timestep.  Forces are computed, neighbor
-neighbor lists are built as needed, atoms migrate to new processors, and
+lists are built as needed, atoms migrate to new processors, and atom
-atom coordinates and forces are communicated to neighboring processors.
+coordinates and forces are communicated to neighboring processors.  The
-The only difference is what Fix class operations are invoked when.  Only
+only difference is what Fix class operations are invoked when.  Only a
-a subset of LAMMPS fixes are useful during energy minimization, as
+subset of LAMMPS fixes are useful during energy minimization, as
 explained in their individual doc pages.  The relevant Fix class methods
-are ``min_pre_exchange()``, ``min_pre_force()``, and ``min_post_force()``.
+are ``min_pre_exchange()``, ``min_pre_force()``, and
-Each fix is invoked at the appropriate place within the minimization
+``min_post_force()``.  Each fix is invoked at the appropriate place
-iteration.  For example, the ``min_post_force()`` method is analogous to
+within the minimization iteration.  For example, the
-the ``post_force()`` method for dynamics; it is used to alter or constrain
+``min_post_force()`` method is analogous to the ``post_force()`` method
-forces on each atom, which affects the minimization procedure.
+for dynamics; it is used to alter or constrain forces on each atom,
+which affects the minimization procedure.
 
-After all iterations are completed there is a ``cleanup`` step which
+After all iterations are completed, there is a ``cleanup`` step which
 calls the ``post_run()`` method of fixes to perform operations only required
-at the end of a calculations (like freeing temporary storage or creating
+at the end of a calculation (like freeing temporary storage or creating
 final outputs).

doc/src/Developer_grid.rst

@@ -28,9 +28,9 @@ 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
+within the processor's spatial subdomain.  The union of processor
-sub-domains is the global simulation box.  If a grid point is on the
+subdomains 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
+boundary of two subdomains, the lower processor owns the grid cell.  A
 processor may also store copies of ghost cells which surround its
 owned cells.
 
@@ -62,7 +62,7 @@ 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
+processors or their layout in a grid of processor subdomains which
 overlays the simulations domain.  Depending on the distributed grid
 size, a single processor may own many 1000s or no grid cells.
 
@@ -70,7 +70,7 @@ 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
+creates and it allocates the multidimensional array(s) needed to
 store the data.  No grid cell data is stored within the Grid2d or
 Grid3d classes.
 
@@ -115,7 +115,7 @@ which stores *Nvalues* per grid cell.
                                 nyhi_out, nxlo_out, nxhi_out, nvalues,
                                 "data3d_multi");
 
-Note that these multi-dimensional arrays are allocated as contiguous
+Note that these multidimensional 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
@@ -160,7 +160,7 @@ cells (the entire allocated grid).
 Grid class constructors
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-The following sub-sections describe the public methods of the Grid3d
+The following subsections 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.
 
@@ -235,7 +235,7 @@ invoked, because they influence its operation.
    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
+the processor's subdomain.  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
@@ -245,9 +245,9 @@ 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
+its particles being outside its subdomain 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.
+distance outside a processor's subdomain 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
@@ -295,7 +295,7 @@ 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
+are assigned to processors whose subdomains are adjacent to the upper
 z boundary of the simulation box.
 
 ----------
@@ -533,7 +533,7 @@ 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
+global grid size to ensure 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
@@ -549,13 +549,13 @@ 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.
+domain into processor subdomains.
 
 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.
+subdomains 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()*
@@ -564,7 +564,7 @@ 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
+new processor subdomains.  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.
@@ -753,7 +753,7 @@ their input script syntax, as described on the :doc:`Howto_grid
 * f_ID:gname:dname
 * f_ID:gname:dname[I]
 
-Each grid a command instantiates has a unique *gname*, defined by the
+Each grid 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.
@@ -784,8 +784,7 @@ 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
+global size of the grid, to ensure it is of the expected size.
-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
@@ -799,7 +798,7 @@ 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.
+multidimensional 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

doc/src/Developer_notes.rst

@@ -11,6 +11,7 @@ Available topics are:
 
 - `Reading and parsing of text and text files`_
 - `Requesting and accessing neighbor lists`_
+- `Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM`_
 - `Fix contributions to instantaneous energy, virial, and cumulative energy`_
 - `KSpace PPPM FFT grids`_
 
@@ -102,7 +103,7 @@ build is then :doc:`processed in parallel <Developer_par_neigh>`.
 The most commonly required neighbor list is a so-called "half" neighbor
 list, where each pair of atoms is listed only once (except when the
 :doc:`newton command setting <newton>` for pair is off; in that case
-pairs straddling sub-domains or periodic boundaries will be listed twice).
+pairs straddling subdomains or periodic boundaries will be listed twice).
 Thus these are the default settings when a neighbor list request is created in:
 
 .. code-block:: c++
@@ -216,6 +217,30 @@ command:
 
    neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
 
+Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+There are multiple ways to manage per-atom data within LAMMPS.  Often
+the per-atom storage is only used locally and managed by the class that
+uses it.  If the data has to persist between multiple time steps and
+migrate with atoms when they move from sub-domain to sub-domain or
+across periodic boundaries, then using a custom atom style, or :doc:`fix
+property/atom <fix_property_atom>`, or the internal fix STORE/ATOM are
+possible options.
+
+- Using the atom style is usually the most programming effort and mostly
+  needed when the per-atom data is an integral part of the model like a
+  per-atom charge or diameter and thus should be part of the Atoms
+  section of a :doc:`data file <read_data>`.
+
+- Fix property/atom is useful if the data is optional or should be
+  entered by the user, or accessed as a (named) custom property. In this
+  case the fix should be entered as part of the input (and not
+  internally) which allows to enter and store its content with data files.
+
+- Fix STORE/ATOM should be used when the data should be accessed internally
+  only and thus the fix can be created internally.
+
 Fix contributions to instantaneous energy, virial, and cumulative energy
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -361,7 +386,7 @@ allocated as a 1d vector or 3d array.  Either way, the ordering of
 values within contiguous memory x fastest, then y, z slowest.
 
 For the ``3d decomposition`` of the grid, the global grid is
-partitioned into bricks that correspond to the sub-domains of the
+partitioned into bricks that correspond to the subdomains of the
 simulation box that each processor owns.  Often, this is a regular 3d
 array (Px by Py by Pz) of bricks, where P = number of processors =
 Px * Py * Pz.  More generally it can be a tiled decomposition, where

doc/src/Developer_org.rst

@@ -7,7 +7,7 @@ but there are small a number of files in several other languages like C,
 Fortran, Shell script, or Python.
 
 The core of the code is located in the ``src`` folder and its
-sub-directories.  A sizable number of these files are in the ``src``
+subdirectories.  A sizable number of these files are in the ``src``
 directory itself, but there are plenty of :doc:`packages <Packages>`,
 which can be included or excluded when LAMMPS is built.  See the
 :doc:`Include packages in build <Build_package>` section of the manual
@@ -15,42 +15,42 @@ for more information about that part of the build process.  LAMMPS
 currently supports building with :doc:`conventional makefiles
 <Build_make>` and through :doc:`CMake <Build_cmake>`.  Those procedures
 differ in how packages are enabled or disabled for inclusion into a
-LAMMPS binary so they cannot be mixed.  The source files for each
+LAMMPS binary, so they cannot be mixed.  The source files for each
-package are in all-uppercase sub-directories of the ``src`` folder, for
+package are in all-uppercase subdirectories of the ``src`` folder, for
 example ``src/MOLECULE`` or ``src/EXTRA-MOLECULE``.  The ``src/STUBS``
-sub-directory is not a package but contains a dummy MPI library, that is
+subdirectory is not a package but contains a dummy MPI library, that is
 used when building a serial version of the code. The ``src/MAKE``
-directory and its sub-directories contain makefiles with settings and
+directory and its subdirectories contain makefiles with settings and
 flags for a variety of configuration and machines for the build process
 with traditional makefiles.
 
 The ``lib`` directory contains the source code for several supporting
 libraries or files with configuration settings to use globally installed
-libraries, that are required by some of the optional packages.  They may
+libraries, that are required by some optional packages.  They may
 include python scripts that can transparently download additional source
-code on request.  Each sub-directory, like ``lib/poems`` or ``lib/gpu``,
+code on request.  Each subdirectory, like ``lib/poems`` or ``lib/gpu``,
 contains the source files, some of which are in different languages such
-as Fortran or CUDA. These libraries included in the LAMMPS build,
+as Fortran or CUDA. These libraries included in the LAMMPS build, if the
-if the corresponding package is installed.
+corresponding package is installed.
 
 LAMMPS C++ source files almost always come in pairs, such as
 ``src/run.cpp`` (implementation file) and ``src/run.h`` (header file).
 Each pair of files defines a C++ class, for example the
-:cpp:class:`LAMMPS_NS::Run` class which contains the code invoked by the
+:cpp:class:`LAMMPS_NS::Run` class, which contains the code invoked by
-:doc:`run <run>` command in a LAMMPS input script.  As this example
+the :doc:`run <run>` command in a LAMMPS input script.  As this example
 illustrates, source file and class names often have a one-to-one
 correspondence with a command used in a LAMMPS input script.  Some
 source files and classes do not have a corresponding input script
-command, e.g. ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force`
+command, for example ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force`
 class.  They are discussed in the next section.
 
 The names of all source files are in lower case and may use the
-underscore character '_' to separate words. Outside of bundled libraries
+underscore character '_' to separate words. Apart from bundled,
-which may have different conventions, all C and C++ header files have a
+externally maintained libraries, which may have different conventions,
-``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a
+all C and C++ header files have a ``.h`` extension, all C++ files have a
-``.c`` extension. A small number of C++ classes and utility functions
+``.cpp`` extension, and C files a ``.c`` extension.  A few C++ classes
-are implemented with only a ``.h`` file. Examples are the Pointers and
+and utility functions are implemented with only a ``.h`` file. Examples
-Commands classes or the MathVec functions.
+are the Pointers and Commands classes or the MathVec functions.
 
 Class topology
 --------------
@@ -62,35 +62,36 @@ associated source files in the ``src`` folder, for example the class
 :cpp:class:`LAMMPS_NS::Memory` corresponds to the files ``memory.cpp``
 and ``memory.h``, or the class :cpp:class:`LAMMPS_NS::AtomVec`
 corresponds to the files ``atom_vec.cpp`` and ``atom_vec.h``.  Full
-lines in the figure represent compositing: that is the class at the base
+lines in the figure represent compositing: that is, the class at the
-of the arrow holds a pointer to an instance of the class at the tip.
+base of the arrow holds a pointer to an instance of the class at the
-Dashed lines instead represent inheritance: the class to the tip of the
+tip.  Dashed lines instead represent inheritance: the class at the tip
-arrow is derived from the class at the base.  Classes with a red boundary
+of the arrow is derived from the class at the base.  Classes with a red
-are not instantiated directly, but they represent the base classes for
+boundary are not instantiated directly, but they represent the base
-"styles".  Those "styles" make up the bulk of the LAMMPS code and only
+classes for "styles".  Those "styles" make up the bulk of the LAMMPS
-a few representative examples are included in the figure so it remains
+code and only a few representative examples are included in the figure,
-readable.
+so it remains readable.
 
 .. _class-topology:
 .. figure:: JPG/lammps-classes.png
 
    LAMMPS class topology
 
-   This figure shows some of the relations of the base classes of the
+      This figure shows relations of base classes of the LAMMPS
-   LAMMPS simulation package.  Full lines indicate that a class holds an
+      simulation package.  Full lines indicate that a class holds an
       instance of the class it is pointing to; dashed lines point to
       derived classes that are given as examples of what classes may be
       instantiated during a LAMMPS run based on the input commands and
-   accessed through the API define by their respective base classes.  At
+      accessed through the API define by their respective base classes.
-   the core is the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class, which
+      At the core is the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class,
-   holds pointers to class instances with specific purposes.  Those may
+      which holds pointers to class instances with specific purposes.
-   hold instances of other classes, sometimes directly, or only
+      Those may hold instances of other classes, sometimes directly, or
-   temporarily, sometimes as derived classes or derived classes of
+      only temporarily, sometimes as derived classes or derived classes
-   derived classes, which may also hold instances of other classes.
+      of derived classes, which may also hold instances of other
+      classes.
 
 The :cpp:class:`LAMMPS_NS::LAMMPS` class is the topmost class and
-represents what is generally referred to an "instance" of LAMMPS.  It is
+represents what is generally referred to as an "instance of LAMMPS".  It
-a composite holding pointers to instances of other core classes
+is a composite holding pointers to instances of other core classes
 providing the core functionality of the MD engine in LAMMPS and through
 them abstractions of the required operations.  The constructor of the
 LAMMPS class will instantiate those instances, process the command line
@@ -102,42 +103,44 @@ LAMMPS while passing it the command line flags and input script. It
 deletes the LAMMPS instance after the method reading the input returns
 and shuts down the MPI environment before it exits the executable.
 
-The :cpp:class:`LAMMPS_NS::Pointers` is not shown in the
+The :cpp:class:`LAMMPS_NS::Pointers` class is not shown in the
 :ref:`class-topology` figure for clarity.  It holds references to many
 of the members of the `LAMMPS_NS::LAMMPS`, so that all classes derived
 from :cpp:class:`LAMMPS_NS::Pointers` have direct access to those
-reference.  From the class topology all classes with blue boundary are
+references.  From the class topology all classes with blue boundary are
 referenced in the Pointers class and all classes in the second and third
-columns, that are not listed as derived classes are instead derived from
+columns, that are not listed as derived classes, are instead derived
-:cpp:class:`LAMMPS_NS::Pointers`.  To initialize the pointer references
+from :cpp:class:`LAMMPS_NS::Pointers`.  To initialize the pointer
-in Pointers, a pointer to the LAMMPS class instance needs to be passed
+references in Pointers, a pointer to the LAMMPS class instance needs to
-to the constructor and thus all constructors for classes derived from it
+be passed to the constructor. All constructors for classes derived from
-must do so and pass this pointer to the constructor for Pointers.
+it, must do so and thus pass that pointer to the constructor for
+:cpp:class:`LAMMPS_NS::Pointers`.  The default constructor for
+:cpp:class:`LAMMPS_NS::Pointers` is disabled to enforce this.
 
 Since all storage is supposed to be encapsulated (there are a few
 exceptions), the LAMMPS class can also be instantiated multiple times by
-a calling code.  Outside of the aforementioned exceptions, those LAMMPS
+a calling code.  Outside the aforementioned exceptions, those LAMMPS
 instances can be used alternately.  As of the time of this writing
-(early 2021) LAMMPS is not yet sufficiently thread-safe for concurrent
+(early 2023) LAMMPS is not yet sufficiently thread-safe for concurrent
 execution.  When running in parallel with MPI, care has to be taken,
 that suitable copies of communicators are used to not create conflicts
 between different instances.
 
-The LAMMPS class currently (early 2021) holds instances of 19 classes
+The LAMMPS class currently holds instances of 19 classes representing
-representing the core functionality.  There are a handful of virtual
+the core functionality.  There are a handful of virtual parent classes
-parent classes in LAMMPS that define what LAMMPS calls ``styles``.  They
+in LAMMPS that define what LAMMPS calls ``styles``.  These are shaded
-are shaded red in the :ref:`class-topology` figure.  Each of these are
+red in the :ref:`class-topology` figure.  Each of these are parents of a
-parents of a number of child classes that implement the interface
+number of child classes that implement the interface defined by the
-defined by the parent class.  There are two main categories of these
+parent class.  There are two main categories of these ``styles``: some
-``styles``: some may only have one instance active at a time (e.g. atom,
+may only have one instance active at a time (e.g. atom, pair, bond,
-pair, bond, angle, dihedral, improper, kspace, comm) and there is a
+angle, dihedral, improper, kspace, comm) and there is a dedicated
-dedicated pointer variable for each of them in the composite class.
+pointer variable for each of them in the corresponding composite class.
 Setups that require a mix of different such styles have to use a
-*hybrid* class that takes the place of the one allowed instance and then
+*hybrid* class instance that acts as a proxy, and manages and forwards
-manages and forwards calls to the corresponding sub-styles for the
+calls to the corresponding sub-style class instances for the designated
-designated subset of atoms or data.  The composite class may also have
+subset of atoms or data.  The composite class may also have lists of
-lists of class instances, e.g. Modify handles lists of compute and fix
+class instances, e.g. ``Modify`` handles lists of compute and fix
-styles, while Output handles a list of dump class instances.
+styles, while ``Output`` handles a list of dump class instances.
 
 The exception to this scheme are the ``command`` style classes.  These
 implement specific commands that can be invoked before, after, or in
@@ -146,19 +149,19 @@ command() method called and then, after completion, the class instance
 deleted.  Examples for this are the create_box, create_atoms, minimize,
 run, set, or velocity command styles.
 
-For all those ``styles`` certain naming conventions are employed: for
+For all those ``styles``, certain naming conventions are employed: for
 the fix nve command the class is called FixNVE and the source files are
-``fix_nve.h`` and ``fix_nve.cpp``. Similarly for fix ave/time we have
+``fix_nve.h`` and ``fix_nve.cpp``. Similarly, for fix ave/time we have
 FixAveTime and ``fix_ave_time.h`` and ``fix_ave_time.cpp``.  Style names
 are lower case and without spaces or special characters. A suffix or
 words are appended with a forward slash '/' which denotes a variant of
 the corresponding class without the suffix.  To connect the style name
 and the class name, LAMMPS uses macros like: ``AtomStyle()``,
 ``PairStyle()``, ``BondStyle()``, ``RegionStyle()``, and so on in the
-corresponding header file.  During configuration or compilation files
+corresponding header file.  During configuration or compilation, files
 with the pattern ``style_<name>.h`` are created that consist of a list
 of include statements including all headers of all styles of a given
-type that are currently active (or "installed).
+type that are currently enabled (or "installed").
 
 
 More details on individual classes in the :ref:`class-topology` are as
@@ -172,8 +175,8 @@ follows:
   that one or multiple simulations can be run, on the processors
   allocated for a run, e.g. by the mpirun command.
 
-- The Input class reads and processes input input strings and files,
+- The Input class reads and processes input (strings and files), stores
-  stores variables, and invokes :doc:`commands <Commands_all>`.
+  variables, and invokes :doc:`commands <Commands_all>`.
 
 - Command style classes are derived from the Command class. They provide
   input script commands that perform one-time operations
@@ -192,7 +195,7 @@ follows:
 - The Atom class stores per-atom properties associated with atom styles.
   More precisely, they are allocated and managed by a class derived from
   the AtomVec class, and the Atom class simply stores pointers to them.
-  The classes derived from AtomVec represent the different atom styles
+  The classes derived from AtomVec represent the different atom styles,
   and they are instantiated through the :doc:`atom_style <atom_style>`
   command.
 
@@ -207,17 +210,21 @@ follows:
   instance is created by pair, fix, or compute styles when they need a
   particular kind of neighbor list and use the NeighRequest properties
   to select the neighbor list settings for the given request.  There can
-  be multiple instances of the NeighRequest class and the Neighbor class
+  be multiple instances of the NeighRequest class. The Neighbor class
-  will try to optimize how they are computed by creating copies or
+  will try to optimize how the requests are processed.  Depending on the
-  sub-lists where possible.
+  NeighRequest properties, neighbor lists are constructed from scratch,
+  aliased, or constructed by post-processing an existing list into
+  sub-lists.
 
 - The Comm class performs inter-processor communication, typically of
   ghost atom information.  This usually involves MPI message exchanges
   with 6 neighboring processors in the 3d logical grid of processors
   mapped to the simulation box. There are two :doc:`communication styles
-  <comm_style>` enabling different ways to do the domain decomposition.
+  <comm_style>`, enabling different ways to perform the domain
-  Sometimes the Irregular class is used, when atoms may migrate to
+  decomposition.
-  arbitrary processors.
+
+- The Irregular class is used, when atoms may migrate to arbitrary
+  processors.
 
 - The Domain class stores the simulation box geometry, as well as
   geometric Regions and any user definition of a Lattice.  The latter
@@ -246,7 +253,7 @@ follows:
   file, dump file snapshots, and restart files.  These correspond to the
   :doc:`Thermo <thermo_style>`, :doc:`Dump <dump>`, and
   :doc:`WriteRestart <write_restart>` classes respectively.  The Dump
-  class is a base class with several derived classes implementing
+  class is a base class, with several derived classes implementing
   various dump style variants.
 
 - The Timer class logs timing information, output at the end

doc/src/Developer_par_comm.rst

@@ -1,22 +1,22 @@
 Communication
 ^^^^^^^^^^^^^
 
-Following the partitioning scheme in use all per-atom data is
+Following the selected partitioning scheme, all per-atom data is
 distributed across the MPI processes, which allows LAMMPS to handle very
 large systems provided it uses a correspondingly large number of MPI
 processes.  Since The per-atom data (atom IDs, positions, velocities,
-types, etc.)  To be able to compute the short-range interactions MPI
+types, etc.)  To be able to compute the short-range interactions, MPI
-processes need not only access to data of atoms they "own" but also
+processes need not only access to the data of atoms they "own" but also
-information about atoms from neighboring sub-domains, in LAMMPS referred
+information about atoms from neighboring subdomains, in LAMMPS referred
 to as "ghost" atoms.  These are copies of atoms storing required
 per-atom data for up to the communication cutoff distance. The green
 dashed-line boxes in the :ref:`domain-decomposition` figure illustrate
-the extended ghost-atom sub-domain for one processor.
+the extended ghost-atom subdomain for one processor.
 
 This approach is also used to implement periodic boundary
 conditions: atoms that lie within the cutoff distance across a periodic
 boundary are also stored as ghost atoms and taken from the periodic
-replication of the sub-domain, which may be the same sub-domain, e.g. if
+replication of the subdomain, which may be the same subdomain, e.g. if
 running in serial.  As a consequence of this, force computation in
 LAMMPS is not subject to minimum image conventions and thus cutoffs may
 be larger than half the simulation domain.
@@ -28,10 +28,10 @@ be larger than half the simulation domain.
    ghost atom communication
 
    This figure shows the ghost atom communication patterns between
-   sub-domains for "brick" (left) and "tiled" communication styles for
+   subdomains for "brick" (left) and "tiled" communication styles for
    2d simulations.  The numbers indicate MPI process ranks.  Here the
-   sub-domains are drawn spatially separated for clarity.  The
+   subdomains are drawn spatially separated for clarity.  The
-   dashed-line box is the extended sub-domain of processor 0 which
+   dashed-line box is the extended subdomain of processor 0 which
    includes its ghost atoms.  The red- and blue-shaded boxes are the
    regions of communicated ghost atoms.
 
@@ -42,7 +42,7 @@ atom communication is performed in two stages for a 2d simulation (three
 in 3d) for both a regular and irregular partitioning of the simulation
 box.  For the regular case (left) atoms are exchanged first in the
 *x*-direction, then in *y*, with four neighbors in the grid of processor
-sub-domains.
+subdomains.
 
 In the *x* stage, processor ranks 1 and 2 send owned atoms in their
 red-shaded regions to rank 0 (and vice versa).  Then in the *y* stage,
@@ -55,11 +55,11 @@ For the irregular case (right) the two stages are similar, but a
 processor can have more than one neighbor in each direction.  In the
 *x* stage, MPI ranks 1,2,3 send owned atoms in their red-shaded regions to
 rank 0 (and vice versa).  These include only atoms between the lower
-and upper *y*-boundary of rank 0's sub-domain.  In the *y* stage, ranks
+and upper *y*-boundary of rank 0's subdomain.  In the *y* stage, ranks
 4,5,6 send atoms in their blue-shaded regions to rank 0.  This may
 include ghost atoms they received in the *x* stage, but only if they
 are needed by rank 0 to fill its extended ghost atom regions in the
-+/-*y* directions (blue rectangles).  Thus in this case, ranks 5 and
++/-*y* directions (blue rectangles).  Thus, in this case, ranks 5 and
 6 do not include ghost atoms they received from each other (in the *x*
 stage) in the atoms they send to rank 0.  The key point is that while
 the pattern of communication is more complex in the irregular
@@ -78,14 +78,14 @@ A "reverse" communication is when computed ghost atom attributes are
 sent back to the processor who owns the atom.  This is used (for
 example) to sum partial forces on ghost atoms to the complete force on
 owned atoms.  The order of the two stages described in the
-:ref:`ghost-atom-comm` figure is inverted and the same lists of atoms
+:ref:`ghost-atom-comm` figure is inverted, and the same lists of atoms
 are used to pack and unpack message buffers with per-atom forces.  When
 a received buffer is unpacked, the ghost forces are summed to owned atom
 forces.  As in forward communication, forces on atoms in the four blue
 corners of the diagrams are sent, received, and summed twice (once at
 each stage) before owning processors have the full force.
 
-These two operations are used many places within LAMMPS aside from
+These two operations are used in many places within LAMMPS aside from
 exchange of coordinates and forces, for example by manybody potentials
 to share intermediate per-atom values, or by rigid-body integrators to
 enable each atom in a body to access body properties.  Here are
@@ -105,16 +105,16 @@ performed in LAMMPS:
   atom pairs when building neighbor lists or computing forces.
 
 - The cutoff distance for exchanging ghost atoms is typically equal to
-  the neighbor cutoff.  But it can also chosen to be longer if needed,
+  the neighbor cutoff.  But it can also set to a larger value if needed,
   e.g. half the diameter of a rigid body composed of multiple atoms or
   over 3x the length of a stretched bond for dihedral interactions.  It
   can also exceed the periodic box size.  For the regular communication
   pattern (left), if the cutoff distance extends beyond a neighbor
-  processor's sub-domain, then multiple exchanges are performed in the
+  processor's subdomain, then multiple exchanges are performed in the
   same direction.  Each exchange is with the same neighbor processor,
   but buffers are packed/unpacked using a different list of atoms. For
-  forward communication, in the first exchange a processor sends only
+  forward communication, in the first exchange, a processor sends only
   owned atoms.  In subsequent exchanges, it sends ghost atoms received
   in previous exchanges.  For the irregular pattern (right) overlaps of
-  a processor's extended ghost-atom sub-domain with all other processors
+  a processor's extended ghost-atom subdomain with all other processors
   in each dimension are detected.

doc/src/Developer_par_long.rst

@@ -20,7 +20,7 @@ e) electric field values from grid points near each atom are interpolated to com
 
 For any of the spatial-decomposition partitioning schemes each processor
 owns the brick-shaped portion of FFT grid points contained within its
-sub-domain.  The two interpolation operations use a stencil of grid
+subdomain.  The two interpolation operations use a stencil of grid
 points surrounding each atom.  To accommodate the stencil size, each
 processor also stores a few layers of ghost grid points surrounding its
 brick.  Forward and reverse communication of grid point values is
@@ -40,31 +40,31 @@ orthogonal boxes.
 
 .. _fft-parallel:
 .. figure:: img/fft-decomp-parallel.png
-   :align: center
 
-   parallel FFT in PPPM
+   Parallel FFT in PPPM
 
-   Stages of a parallel FFT for a simulation domain overlaid
+      Stages of a parallel FFT for a simulation domain overlaid with an
-   with an 8x8x8 3d FFT grid, partitioned across 64 processors.
+      8x8x8 3d FFT grid, partitioned across 64 processors.  Within each
-   Within each of the 4 diagrams, grid cells of the same color are
+      of the 4 diagrams, grid cells of the same color are owned by a
-   owned by a single processor; for simplicity only cells owned by 4
+      single processor; for simplicity, only cells owned by 4 or 8 of
-   or 8 of the 64 processors are colored.  The two images on the left
+      the 64 processors are colored.  The two images on the left
       illustrate brick-to-pencil communication.  The two images on the
       right illustrate pencil-to-pencil communication, which in this
       case transposes the *y* and *z* dimensions of the grid.
 
 Parallel 3d FFTs require substantial communication relative to their
 computational cost.  A 3d FFT is implemented by a series of 1d FFTs
-along the *x-*, *y-*, and *z-*\ direction of the FFT grid.  Thus the FFT
+along the *x-*, *y-*, and *z-*\ direction of the FFT grid.  Thus, the
-grid cannot be decomposed like atoms into 3 dimensions for parallel
+FFT grid cannot be decomposed like atoms into 3 dimensions for parallel
 processing of the FFTs but only in 1 (as planes) or 2 (as pencils)
 dimensions and in between the steps the grid needs to be transposed to
 have the FFT grid portion "owned" by each MPI process complete in the
 direction of the 1d FFTs it has to perform. LAMMPS uses the
-pencil-decomposition algorithm as shown in the :ref:`fft-parallel` figure.
+pencil-decomposition algorithm as shown in the :ref:`fft-parallel`
+figure.
 
 Initially (far left), each processor owns a brick of same-color grid
-cells (actually grid points) contained within in its sub-domain.  A
+cells (actually grid points) contained within in its subdomain.  A
 brick-to-pencil communication operation converts this layout to 1d
 pencils in the *x*-dimension (center left).  Again, cells of the same
 color are owned by the same processor.  Each processor can then compute
@@ -97,7 +97,7 @@ across all $P$ processors with a single call to ``MPI_Alltoall()``, but
 this is typically much slower.  However, for the specialized brick and
 pencil tiling illustrated in :ref:`fft-parallel` figure, collective
 communication across the entire MPI communicator is not required.  In
-the example an :math:`8^3` grid with 512 grid cells is partitioned
+the example, an :math:`8^3` grid with 512 grid cells is partitioned
 across 64 processors; each processor owns a 2x2x2 3d brick of grid
 cells.  The initial brick-to-pencil communication (upper left to upper
 right) only requires collective communication within subgroups of 4
@@ -132,7 +132,7 @@ grid/particle operations that LAMMPS supports:
 - The fftMPI library allows each grid dimension to be a multiple of
   small prime factors (2,3,5), and allows any number of processors to
   perform the FFT.  The resulting brick and pencil decompositions are
-  thus not always as well-aligned but the size of subgroups of
+  thus not always as well-aligned, but the size of subgroups of
   processors for the two modes of communication (brick/pencil and
   pencil/pencil) still scale as :math:`O(P^{\frac{1}{3}})` and
   :math:`O(P^{\frac{1}{2}})`.
@@ -143,26 +143,28 @@ grid/particle operations that LAMMPS supports:
   in memory.  This reordering can be done during the packing or
   unpacking of buffers for MPI communication.
 
-- For large systems and particularly a large number of MPI processes,
+- For large systems and particularly many MPI processes, the dominant
-  the dominant cost for parallel FFTs is often the communication, not
+  cost for parallel FFTs is often the communication, not the computation
-  the computation of 1d FFTs, even though the latter scales as :math:`N
+  of 1d FFTs, even though the latter scales as :math:`N \log(N)` in the
-  \log(N)` in the number of grid points *N* per grid direction.  This is
+  number of grid points *N* per grid direction.  This is due to the fact
-  due to the fact that only a 2d decomposition into pencils is possible
+  that only a 2d decomposition into pencils is possible while atom data
-  while atom data (and their corresponding short-range force and energy
+  (and their corresponding short-range force and energy computations)
-  computations) can be decomposed efficiently in 3d.
+  can be decomposed efficiently in 3d.
 
-  This can be addressed by reducing the number of MPI processes involved
+  Reducing the number of MPI processes involved in the MPI communication
-  in the MPI communication by using :doc:`hybrid MPI + OpenMP
+  will reduce this kind of overhead.  By using a :doc:`hybrid MPI +
-  parallelization <Speed_omp>`.  This will use OpenMP parallelization
+  OpenMP parallelization <Speed_omp>` it is still possible to use all
-  inside the MPI domains and while that may have a lower parallel
+  processes for parallel computation.  It will use OpenMP
-  efficiency, it reduces the communication overhead.
+  parallelization inside the MPI domains. While that may have a lower
+  parallel efficiency for some part of the computation, that can be less
+  than the communication overhead in the 3d FFTs.
 
-  As an alternative it is also possible to start a :ref:`multi-partition
+  As an alternative, it is also possible to start a :ref:`multi-partition
   <partition>` calculation and then use the :doc:`verlet/split
   integrator <run_style>` to perform the PPPM computation on a
   dedicated, separate partition of MPI processes.  This uses an integer
-  "1:*p*" mapping of *p* sub-domains of the atom decomposition to one
+  "1:*p*" mapping of *p* subdomains of the atom decomposition to one
-  sub-domain of the FFT grid decomposition and where pairwise non-bonded
+  subdomain of the FFT grid decomposition and where pairwise non-bonded
   and bonded forces and energies are computed on the larger partition
   and the PPPM kspace computation concurrently on the smaller partition.
 
@@ -172,10 +174,10 @@ grid/particle operations that LAMMPS supports:
 
 - LAMMPS implements a ``GridComm`` class which overlays the simulation
   domain with a regular grid, partitions it across processors in a
-  manner consistent with processor sub-domains, and provides methods for
+  manner consistent with processor subdomains, and provides methods for
   forward and reverse communication of owned and ghost grid point
   values.  It is used for PPPM as an FFT grid (as outlined above) and
-  also for the MSM algorithm which uses a cascade of grid sizes from
+  also for the MSM algorithm, which uses a cascade of grid sizes from
   fine to coarse to compute long-range Coulombic forces.  The GridComm
   class is also useful for models where continuum fields interact with
   particles.  For example, the two-temperature model (TTM) defines heat

doc/src/Developer_par_neigh.rst

@@ -3,12 +3,12 @@ Neighbor lists
 
 To compute forces efficiently, each processor creates a Verlet-style
 neighbor list which enumerates all pairs of atoms *i,j* (*i* = owned,
-*j* = owned or ghost) with separation less than the applicable
+*j* = owned or ghost) with separation less than the applicable neighbor
-neighbor list cutoff distance.  In LAMMPS the neighbor lists are stored
+list cutoff distance.  In LAMMPS, the neighbor lists are stored in a
-in a multiple-page data structure; each page is a contiguous chunk of
+multiple-page data structure; each page is a contiguous chunk of memory
-memory which stores vectors of neighbor atoms *j* for many *i* atoms.
+which stores vectors of neighbor atoms *j* for many *i* atoms.  This
-This allows pages to be incrementally allocated or deallocated in blocks
+allows pages to be incrementally allocated or deallocated in blocks as
-as needed.  Neighbor lists typically consume the most memory of any data
+needed.  Neighbor lists typically consume the most memory of any data
 structure in LAMMPS.  The neighbor list is rebuilt (from scratch) once
 every few timesteps, then used repeatedly each step for force or other
 computations.  The neighbor cutoff distance is :math:`R_n = R_f +
@@ -16,20 +16,20 @@ computations.  The neighbor cutoff distance is :math:`R_n = R_f +
 the interatomic potential for computing short-range pairwise or manybody
 forces and :math:`\Delta_s` is a "skin" distance that allows the list to
 be used for multiple steps assuming that atoms do not move very far
-between consecutive time steps.  Typically the code triggers
+between consecutive time steps.  Typically, the code triggers
 reneighboring when any atom has moved half the skin distance since the
 last reneighboring; this and other options of the neighbor list rebuild
 can be adjusted with the :doc:`neigh_modify <neigh_modify>` command.
 
 On steps when reneighboring is performed, atoms which have moved outside
-their owning processor's sub-domain are first migrated to new processors
+their owning processor's subdomain are first migrated to new processors
 via communication.  Periodic boundary conditions are also (only)
 enforced on these steps to ensure each atom is re-assigned to the
 correct processor.  After migration, the atoms owned by each processor
-are stored in a contiguous vector.  Periodically each processor
+are stored in a contiguous vector.  Periodically, each processor
 spatially sorts owned atoms within its vector to reorder it for improved
 cache efficiency in force computations and neighbor list building.  For
-that atoms are spatially binned and then reordered so that atoms in the
+that, atoms are spatially binned and then reordered so that atoms in the
 same bin are adjacent in the vector.  Atom sorting can be disabled or
 its settings modified with the :doc:`atom_modify <atom_modify>` command.
 
@@ -39,12 +39,12 @@ its settings modified with the :doc:`atom_modify <atom_modify>` command.
 
    neighbor list stencils
 
-   A 2d simulation sub-domain (thick black line) and the corresponding
+   A 2d simulation subdomain (thick black line) and the corresponding
    ghost atom cutoff region (dashed blue line) for both orthogonal
    (left) and triclinic (right) domains.  A regular grid of neighbor
    bins (thin lines) overlays the entire simulation domain and need not
-   align with sub-domain boundaries; only the portion overlapping the
+   align with subdomain boundaries; only the portion overlapping the
-   augmented sub-domain is shown.  In the triclinic case it overlaps the
+   augmented subdomain is shown.  In the triclinic case, it overlaps the
    bounding box of the tilted rectangle.  The blue- and red-shaded bins
    represent a stencil of bins searched to find neighbors of a particular
    atom (black dot).
@@ -52,13 +52,13 @@ its settings modified with the :doc:`atom_modify <atom_modify>` command.
 To build a local neighbor list in linear time, the simulation domain is
 overlaid (conceptually) with a regular 3d (or 2d) grid of neighbor bins,
 as shown in the :ref:`neighbor-stencil` figure for 2d models and a
-single MPI processor's sub-domain.  Each processor stores a set of
+single MPI processor's subdomain.  Each processor stores a set of
-neighbor bins which overlap its sub-domain extended by the neighbor
+neighbor bins which overlap its subdomain, extended by the neighbor
 cutoff distance :math:`R_n`.  As illustrated, the bins need not align
 with processor boundaries; an integer number in each dimension is fit to
 the size of the entire simulation box.
 
-Most often LAMMPS builds what it calls a "half" neighbor list where
+Most often, LAMMPS builds what is called a "half" neighbor list where
 each *i,j* neighbor pair is stored only once, with either atom *i* or
 *j* as the central atom.  The build can be done efficiently by using a
 pre-computed "stencil" of bins around a central origin bin which
@@ -67,18 +67,18 @@ is simply a list of integer offsets in *x,y,z* of nearby bins
 surrounding the origin bin which are close enough to contain any
 neighbor atom *j* within a distance :math:`R_n` from any atom *i* in the
 origin bin.  Note that for a half neighbor list, the stencil can be
-asymmetric since each atom only need store half its nearby neighbors.
+asymmetric, since each atom only need store half its nearby neighbors.
 
 These stencils are illustrated in the figure for a half list and a bin
 size of :math:`\frac{1}{2} R_n`.  There are 13 red+blue stencil bins in
 2d (for the orthogonal case, 15 for triclinic).  In 3d there would be
 63, 13 in the plane of bins that contain the origin bin and 25 in each
 of the two planes above it in the *z* direction (75 for triclinic).  The
-reason the triclinic stencil has extra bins is because the bins tile the
+triclinic stencil has extra bins because the bins tile the bounding box
-bounding box of the entire triclinic domain and thus are not periodic
+of the entire triclinic domain, and thus are not periodic with respect
-with respect to the simulation box itself.  The stencil and logic for
+to the simulation box itself.  The stencil and logic for determining
-determining which *i,j* pairs to include in the neighbor list are
+which *i,j* pairs to include in the neighbor list are altered slightly
-altered slightly to account for this.
+to account for this.
 
 To build a neighbor list, a processor first loops over its "owned" plus
 "ghost" atoms and assigns each to a neighbor bin.  This uses an integer
@@ -95,7 +95,7 @@ supports:
   been found to be optimal for many typical cases.  Smaller bins incur
   additional overhead to loop over; larger bins require more distance
   calculations.  Note that for smaller bin sizes, the 2d stencil in the
-  figure would be more semi-circular in shape (hemispherical in 3d),
+  figure would be of a more semicircular shape (hemispherical in 3d),
   with bins near the corners of the square eliminated due to their
   distance from the origin bin.
 
@@ -111,8 +111,8 @@ supports:
   symmetric stencil.  It also includes lists with partial enumeration of
   ghost atom neighbors.  The full and ghost-atom lists are used by
   various manybody interatomic potentials.  Lists may also use different
-  criteria for inclusion of a pair interaction.  Typically this simply
+  criteria for inclusion of a pairwise interaction.  Typically, this
-  depends only on the distance between two atoms and the cutoff
+  simply depends only on the distance between two atoms and the cutoff
   distance.  But for finite-size coarse-grained particles with
   individual diameters (e.g. polydisperse granular particles), it can
   also depend on the diameters of the two particles.
@@ -121,11 +121,11 @@ supports:
   of the master neighbor list for the full system need to be generated,
   one for each sub-style, which contains only the *i,j* pairs needed to
   compute interactions between subsets of atoms for the corresponding
-  potential.  This means not all *i* or *j* atoms owned by a processor
+  potential.  This means, not all *i* or *j* atoms owned by a processor
   are included in a particular sub-list.
 
 - Some models use different cutoff lengths for pairwise interactions
-  between different kinds of particles which are stored in a single
+  between different kinds of particles, which are stored in a single
   neighbor list.  One example is a solvated colloidal system with large
   colloidal particles where colloid/colloid, colloid/solvent, and
   solvent/solvent interaction cutoffs can be dramatically different.
@@ -144,7 +144,7 @@ supports:
 
 - For small and sparse systems and as a fallback method, LAMMPS also
   supports neighbor list construction without binning by using a full
-  :math:`O(N^2)` loop over all *i,j* atom pairs in a sub-domain when
+  :math:`O(N^2)` loop over all *i,j* atom pairs in a subdomain when
   using the :doc:`neighbor nsq <neighbor>` command.
 
 - Dependent on the "pair" setting of the :doc:`newton <newton>` command,
@@ -153,7 +153,7 @@ supports:
   For the newton pair *on* setting the atom *j* is only added to the
   list if its *z* coordinate is larger, or if equal the *y* coordinate
   is larger, and that is equal, too, the *x* coordinate is larger.  For
-  homogeneously dense systems that will result in picking neighbors from
+  homogeneously dense systems, that will result in picking neighbors from
   a same size sector in always the same direction relative to the
-  "owned" atom and thus it should lead to similar length neighbor lists
+  "owned" atom, and thus it should lead to similar length neighbor lists
-  and thus reduce the chance of a load imbalance.
+  and reduce the chance of a load imbalance.

doc/src/Developer_par_openmp.rst

@@ -6,7 +6,7 @@ thread parallelism to predominantly distribute loops over local data
 and thus follow an orthogonal parallelization strategy to the
 decomposition into spatial domains used by the :doc:`MPI partitioning
 <Developer_par_part>`.  For clarity, this section discusses only the
-implementation in the OPENMP package as it is the simplest. The INTEL
+implementation in the OPENMP package, as it is the simplest. The INTEL
 and KOKKOS package offer additional options and are more complex since
 they support more features and different hardware like co-processors
 or GPUs.
@@ -14,7 +14,7 @@ or GPUs.
 One of the key decisions when implementing the OPENMP package was to
 keep the changes to the source code small, so that it would be easier to
 maintain the code and keep it in sync with the non-threaded standard
-implementation.  this is achieved by a) making the OPENMP version a
+implementation.  This is achieved by a) making the OPENMP version a
 derived class from the regular version (e.g. ``PairLJCutOMP`` from
 ``PairLJCut``) and overriding only methods that are multi-threaded or
 need to be modified to support multi-threading (similar to what was done
@@ -26,13 +26,13 @@ into three separate classes ``ThrOMP``, ``ThrData``, and ``FixOMP``.
 available in the corresponding base class (e.g. ``Pair`` for
 ``PairLJCutOMP``) like multi-thread aware variants of the "tally"
 functions. Those functions are made available through multiple
-inheritance so those new functions have to have unique names to avoid
+inheritance, so those new functions have to have unique names to avoid
 ambiguities; typically ``_thr`` is appended to the name of the function.
-``ThrData`` is a classes that manages per-thread data structures.
+``ThrData`` is a class that manages per-thread data structures.  It is
-It is used instead of extending the corresponding storage to per-thread
+used instead of extending the corresponding storage to per-thread arrays
-arrays to avoid slowdowns due to "false sharing" when multiple threads
+to avoid slowdowns due to "false sharing" when multiple threads update
-update adjacent elements in an array and thus force the CPU cache lines
+adjacent elements in an array and thus force the CPU cache lines to be
-to be reset and re-fetched.  ``FixOMP`` finally manages the "multi-thread
+reset and re-fetched.  ``FixOMP`` finally manages the "multi-thread
 state" like settings and access to per-thread storage, it is activated
 by the :doc:`package omp <package>` command.
 
@@ -46,24 +46,24 @@ involve multiple atoms and thus there are race conditions when multiple
 threads want to update per-atom data of the same atoms.  Five possible
 strategies have been considered to avoid this:
 
-1) restructure the code so that there is no overlapping access possible
+1. Restructure the code so that there is no overlapping access possible
    when computing in parallel, e.g. by breaking lists into multiple
    parts and synchronizing threads in between.
-2) have each thread be "responsible" for a specific group of atoms and
+2. Have each thread be "responsible" for a specific group of atoms and
    compute these interactions multiple times, once on each thread that
-   is responsible for a given atom and then have each thread only update
+   is responsible for a given atom, and then have each thread only update
    the properties of this atom.
-3) use mutexes around functions and regions of code where the data race
+3. Use mutexes around functions and regions of code where the data race
-   could happen
+   could happen.
-4) use atomic operations when updating per-atom properties
+4. Use atomic operations when updating per-atom properties.
-5) use replicated per-thread data structures to accumulate data without
+5. Use replicated per-thread data structures to accumulate data without
    conflicts and then use a reduction to combine those results into the
    data structures used by the regular style.
 
 Option 5 was chosen for the OPENMP package because it would retain the
-performance for the case of 1 thread and the code would be more
+performance for the case of a single thread and the code would be more
 maintainable.  Option 1 would require extensive code changes,
-particularly to the neighbor list code; options 2 would have incurred a
+particularly to the neighbor list code; option 2 would have incurred a
 2x or more performance penalty for the serial case; option 3 causes
 significant overhead and would enforce serialization of operations in
 inner loops and thus defeat the purpose of multi-threading; option 4
@@ -80,7 +80,7 @@ equivalent to the number of CPU cores per CPU socket on high-end
 supercomputers.
 
 Thus arrays like the force array are dimensioned to the number of atoms
-times the number of threads when enabling OpenMP support and inside the
+times the number of threads when enabling OpenMP support, and inside the
 compute functions a pointer to a different chunk is obtained by each thread.
 Similarly, accumulators like potential energy or virial are kept in
 per-thread instances of the ``ThrData`` class and then only reduced and
@@ -91,7 +91,7 @@ Loop scheduling
 """""""""""""""
 
 Multi-thread parallelization is applied by distributing (outer) loops
-statically across threads.  Typically this would be the loop over local
+statically across threads.  Typically, this would be the loop over local
 atoms *i* when processing *i,j* pairs of atoms from a neighbor list.
 The design of the neighbor list code results in atoms having a similar
 number of neighbors for homogeneous systems and thus load imbalances

doc/src/Developer_par_part.rst

@@ -7,39 +7,39 @@ distributed-memory parallelism is set with the :doc:`comm_style command
 
 .. _domain-decomposition:
 .. figure:: img/domain-decomp.png
-   :align: center
 
-   domain decomposition
+   Domain decomposition schemes
 
       This figure shows the different kinds of domain decomposition used
       for MPI parallelization: "brick" on the left with an orthogonal
       (left) and a triclinic (middle) simulation domain, and a "tiled"
       decomposition (right).  The black lines show the division into
-   sub-domains and the contained atoms are "owned" by the corresponding
+      subdomains, and the contained atoms are "owned" by the
-   MPI process. The green dashed lines indicate how sub-domains are
+      corresponding MPI process. The green dashed lines indicate how
-   extended with "ghost" atoms up to the communication cutoff distance.
+      subdomains are extended with "ghost" atoms up to the communication
+      cutoff distance.
 
-The LAMMPS simulation box is a 3d or 2d volume, which can be orthogonal
+The LAMMPS simulation box is a 3d or 2d volume, which can be of
-or triclinic in shape, as illustrated in the :ref:`domain-decomposition`
+orthogonal or triclinic shape, as illustrated in the
-figure for the 2d case.  Orthogonal means the box edges are aligned with
+:ref:`domain-decomposition` figure for the 2d case.  Orthogonal means
-the *x*, *y*, *z* Cartesian axes, and the box faces are thus all
+the box edges are aligned with the *x*, *y*, *z* Cartesian axes, and the
-rectangular.  Triclinic allows for a more general parallelepiped shape
+box faces are thus all rectangular.  Triclinic allows for a more general
-in which edges are aligned with three arbitrary vectors and the box
+parallelepiped shape in which edges are aligned with three arbitrary
-faces are parallelograms.  In each dimension box faces can be periodic,
+vectors and the box faces are parallelograms.  In each dimension, box
-or non-periodic with fixed or shrink-wrapped boundaries.  In the fixed
+faces can be periodic, or non-periodic with fixed or shrink-wrapped
-case, atoms which move outside the face are deleted; shrink-wrapped
+boundaries.  In the fixed case, atoms which move outside the face are
-means the position of the box face adjusts continuously to enclose all
+deleted; shrink-wrapped means the position of the box face adjusts
-the atoms.
+continuously to enclose all the atoms.
 
 For distributed-memory MPI parallelism, the simulation box is spatially
-decomposed (partitioned) into non-overlapping sub-domains which fill the
+decomposed (partitioned) into non-overlapping subdomains which fill the
 box. The default partitioning, "brick", is most suitable when atom
 density is roughly uniform, as shown in the left-side images of the
-:ref:`domain-decomposition` figure.  The sub-domains comprise a regular
+:ref:`domain-decomposition` figure.  The subdomains comprise a regular
-grid and all sub-domains are identical in size and shape.  Both the
+grid, and all subdomains are identical in size and shape.  Both the
 orthogonal and triclinic boxes can deform continuously during a
 simulation, e.g. to compress a solid or shear a liquid, in which case
-the processor sub-domains likewise deform.
+the processor subdomains likewise deform.
 
 
 For models with non-uniform density, the number of particles per
@@ -50,14 +50,14 @@ load.  For such models, LAMMPS supports multiple strategies to reduce
 the load imbalance:
 
 - The processor grid decomposition is by default based on the simulation
-  cell volume and tries to optimize the volume to surface ratio for the sub-domains.
+  cell volume and tries to optimize the volume to surface ratio for the subdomains.
   This can be changed with the :doc:`processors command <processors>`.
-- The parallel planes defining the size of the sub-domains can be shifted
+- The parallel planes defining the size of the subdomains can be shifted
   with the :doc:`balance command <balance>`. Which can be done in addition
   to choosing a more optimal processor grid.
 - The recursive bisectioning algorithm in combination with the "tiled"
   communication style can produce a partitioning with equal numbers of
-  particles in each sub-domain.
+  particles in each subdomain.
 
 
 .. |decomp1| image:: img/decomp-regular.png
@@ -76,14 +76,14 @@ the load imbalance:
 
 The pictures above demonstrate different decompositions for a 2d system
 with 12 MPI ranks.  The atom colors indicate the load imbalance of each
-sub-domain with green being optimal and red the least optimal.
+subdomain, with green being optimal and red the least optimal.
 
-Due to the vacuum in the system, the default decomposition is unbalanced
+Due to the vacuum in the system, the default decomposition is
-with several MPI ranks without atoms (left). By forcing a 1x12x1
+unbalanced, with several MPI ranks without atoms (left). By forcing a
-processor grid, every MPI rank does computations now, but number of
+1x12x1 processor grid, every MPI rank does computations now, but the
-atoms per sub-domain is still uneven and the thin slice shape increases
+number of atoms per subdomain is still uneven, and the thin slice shape
-the amount of communication between sub-domains (center left). With a
+increases the amount of communication between subdomains (center
-2x6x1 processor grid and shifting the sub-domain divisions, the load
+left). With a 2x6x1 processor grid and shifting the subdomain divisions,
-imbalance is further reduced and the amount of communication required
+the load imbalance is further reduced and the amount of communication
-between sub-domains is less (center right).  And using the recursive
+required between subdomains is less (center right).  And using the
-bisectioning leads to further improved decomposition (right).
+recursive bisectioning leads to further improved decomposition (right).

doc/src/Developer_parallel.rst

@@ -7,7 +7,7 @@ decomposition.  The parallelization aims to be efficient, and resulting
 in good strong scaling (= good speedup for the same system) and good
 weak scaling (= the computational cost of enlarging the system is
 proportional to the system size).  Additional parallelization using GPUs
-or OpenMP can also be applied within the sub-domain assigned to an MPI
+or OpenMP can also be applied within the subdomain assigned to an MPI
 process.  For clarity, most of the following illustrations show the 2d
 simulation case. The underlying algorithms in those cases, however,
 apply to both 2d and 3d cases equally well.

doc/src/Developer_updating.rst

@@ -24,6 +24,7 @@ Available topics in mostly chronological order are:
 - `Use of "override" instead of "virtual"`_
 - `Simplified and more compact neighbor list requests`_
 - `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
+- `Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments`_
 - `Use Output::get_dump_by_id() instead of Output::find_dump()`_
 - `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
 
@@ -385,6 +386,34 @@ New:
 
 This change is **required** or else the code will not compile.
 
+Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: TBD
+
+The available functionality of the internal fix to store per-atom
+properties was expanded to enable storing data with ghost atoms and to
+support binary restart files.  With those changes, the fix was renamed
+to fix STORE/ATOM and the number and order of (required) arguments has
+changed.
+
+Old syntax: ``ID group-ID STORE/PERATOM rflag n1 n2 [n3]``
+
+- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
+- :math:`n1 = 1, n2 = 1, \mathrm{no}\;n3 \to` per-atom vector, single value per atom
+- :math:`n1 = 1, n2 > 1, \mathrm{no}\;n3 \to` per-atom array, *n2* values per atom
+- :math:`n1 = 1, n2 > 0, n3 > 0 \to` per-atom tensor, *n2* x *n3* values per atom
+
+New syntax:  ``ID group-ID STORE/ATOM n1 n2 gflag rflag``
+
+- :math:`n1 = 1, n2 = 0 \to` per-atom vector, single value per atom
+- :math:`n1 > 1, n2 = 0 \to` per-atom array, *n1* values per atom
+- :math:`n1 > 0, n2 > 0 \to` per-atom tensor, *n1* x *n2* values per atom
+- *gflag* = 0/1, *no*/*yes* communicate per-atom values with ghost atoms
+- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
+
+Since this is an internal fix, there is no user visible change.
+
 Use Output::get_dump_by_id() instead of Output::find_dump()
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Developer_utils.rst

@@ -643,11 +643,13 @@ Tohoku University (under MIT license)
 
 ---------------------------
 
+.. _communication_buffer_coding_with_ubuf:
+
 Communication buffer coding with *ubuf*
 ---------------------------------------
 
 LAMMPS uses communication buffers where it collects data from various
-class instances and then exchanges the data with neighboring sub-domains.
+class instances and then exchanges the data with neighboring subdomains.
 For simplicity those buffers are defined as ``double`` buffers and
 used for doubles and integer numbers. This presents a unique problem
 when 64-bit integers are used.  While the storage needed for a ``double``

doc/src/Errors_common.rst

@@ -113,7 +113,7 @@ LAMMPS output, something is wrong with your simulation.  If you
 suspect this is happening, it is a good idea to print out
 thermodynamic info frequently (e.g. every timestep) via the
 :doc:`thermo <thermo>` so you can monitor what is happening.
-Visualizing the atom movement is also a good idea to insure your model
+Visualizing the atom movement is also a good idea to ensure your model
 is behaving as you expect.
 
 In parallel, one way LAMMPS can hang is due to how different MPI

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 <https://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
+documentation <https://www.sourceware.org/gdb/documentation/>`_.
 
 Run LAMMPS from within the debugger
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/src/Errors_messages.rst

@@ -5635,7 +5635,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Lost atoms are checked for each time thermo output is done.  See the
    thermo_modify lost command for options.  Lost atoms usually indicate
    bad dynamics, e.g. atoms have been blown far out of the simulation
-   box, or moved further than one processor's sub-domain away before
+   box, or moved further than one processor's subdomain away before
    reneighboring.
 
 *MEAM library error %d*
@@ -6092,7 +6092,7 @@ keyword to allow for additional bonds to be formed
    after a read_data, read_restart, or create_box command.
 
 *Next command must list all universe and uloop variables*
-   This is to insure they stay in sync.
+   This is to ensure they stay in sync.
 
 *No Kspace style defined for compute group/group*
    Self-explanatory.
@@ -6266,14 +6266,14 @@ keyword to allow for additional bonds to be formed
    One or more atoms are attempting to map their charge to a MSM grid point
    that is not owned by a processor.  This is likely for one of two
    reasons, both of them bad.  First, it may mean that an atom near the
-   boundary of a processor's sub-domain has moved more than 1/2 the
+   boundary of a processor's subdomain has moved more than 1/2 the
    :doc:`neighbor skin distance <neighbor>` without neighbor lists being
    rebuilt and atoms being migrated to new processors.  This also means
    you may be missing pairwise interactions that need to be computed.
    The solution is to change the re-neighboring criteria via the
    :doc:`neigh_modify <neigh_modify>` command.  The safest settings are
    "delay 0 every 1 check yes".  Second, it may mean that an atom has
-   moved far outside a processor's sub-domain or even the entire
+   moved far outside a processor's subdomain or even the entire
    simulation box. This indicates bad physics, e.g. due to highly
    overlapping atoms, too large a timestep, etc.
 
@@ -6281,14 +6281,14 @@ keyword to allow for additional bonds to be formed
    One or more atoms are attempting to map their charge to a PPPM grid
    point that is not owned by a processor.  This is likely for one of two
    reasons, both of them bad.  First, it may mean that an atom near the
-   boundary of a processor's sub-domain has moved more than 1/2 the
+   boundary of a processor's subdomain has moved more than 1/2 the
    :doc:`neighbor skin distance <neighbor>` without neighbor lists being
    rebuilt and atoms being migrated to new processors.  This also means
    you may be missing pairwise interactions that need to be computed.
    The solution is to change the re-neighboring criteria via the
    :doc:`neigh_modify <neigh_modify>` command.  The safest settings are
    "delay 0 every 1 check yes".  Second, it may mean that an atom has
-   moved far outside a processor's sub-domain or even the entire
+   moved far outside a processor's subdomain or even the entire
    simulation box. This indicates bad physics, e.g. due to highly
    overlapping atoms, too large a timestep, etc.
 
@@ -6296,14 +6296,14 @@ keyword to allow for additional bonds to be formed
    One or more atoms are attempting to map their charge to a PPPM grid
    point that is not owned by a processor.  This is likely for one of two
    reasons, both of them bad.  First, it may mean that an atom near the
-   boundary of a processor's sub-domain has moved more than 1/2 the
+   boundary of a processor's subdomain has moved more than 1/2 the
    :doc:`neighbor skin distance <neighbor>` without neighbor lists being
    rebuilt and atoms being migrated to new processors.  This also means
    you may be missing pairwise interactions that need to be computed.
    The solution is to change the re-neighboring criteria via the
    :doc:`neigh_modify <neigh_modify>` command.  The safest settings are
    "delay 0 every 1 check yes".  Second, it may mean that an atom has
-   moved far outside a processor's sub-domain or even the entire
+   moved far outside a processor's subdomain or even the entire
    simulation box. This indicates bad physics, e.g. due to highly
    overlapping atoms, too large a timestep, etc.
 
@@ -7231,7 +7231,7 @@ keyword to allow for additional bonds to be formed
 
 *Replacing a fix, but new style != old style*
    A fix ID can be used a second time, but only if the style matches the
-   previous fix.  In this case it is assumed you with to reset a fix's
+   previous fix.  In this case it is assumed you want to reset a fix's
    parameters.  This error may mean you are mistakenly re-using a fix ID
    when you do not intend to.
 
@@ -7337,7 +7337,7 @@ keyword to allow for additional bonds to be formed
 *Rigid body atoms %d %d missing on proc %d at step %ld*
    This means that an atom cannot find the atom that owns the rigid body
    it is part of, or vice versa.  The solution is to use the communicate
-   cutoff command to insure ghost atoms are acquired from far enough away
+   cutoff command to ensure ghost atoms are acquired from far enough away
    to encompass the max distance printed when the fix rigid/small command
    was invoked.
 

doc/src/Errors_warnings.rst

@@ -109,9 +109,9 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
 *Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
    Since LAMMPS stores topology data with individual atoms, all atoms
    comprising a bond, angle, dihedral or improper must be present on any
-   sub-domain that "owns" the atom with the information, either as a
+   subdomain that "owns" the atom with the information, either as a
    local or a ghost atom. The communication cutoff is what determines up
-   to what distance from a sub-domain boundary ghost atoms are created.
+   to what distance from a subdomain boundary ghost atoms are created.
    The communication cutoff is by default the largest non-bonded cutoff
    plus the neighbor skin distance, but for short or non-bonded cutoffs
    and/or long bonds, this may not be sufficient. This warning indicates
@@ -351,7 +351,7 @@ This will most likely cause errors in kinetic fluctuations.
    Self-explanatory.
 
 *Kspace_modify slab param < 2.0 may cause unphysical behavior*
-   The kspace_modify slab parameter should be larger to insure periodic
+   The kspace_modify slab parameter should be larger to ensure periodic
    grids padded with empty space do not overlap.
 
 *Less insertions than requested*
@@ -398,7 +398,7 @@ This will most likely cause errors in kinetic fluctuations.
    Lost atoms are checked for each time thermo output is done.  See the
    thermo_modify lost command for options.  Lost atoms usually indicate
    bad dynamics, e.g. atoms have been blown far out of the simulation
-   box, or moved further than one processor's sub-domain away before
+   box, or moved further than one processor's subdomain away before
    reneighboring.
 
 *MSM mesh too small, increasing to 2 points in each direction*
@@ -491,7 +491,7 @@ This will most likely cause errors in kinetic fluctuations.
 *Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies*
    This is because excluding specific pair interactions also excludes
    them from long-range interactions which may not be the desired effect.
-   The special_bonds command handles this consistently by insuring
+   The special_bonds command handles this consistently by ensuring
    excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated
    consistently by both the short-range pair style and the long-range
    solver.  This is not done for exclusions of charged atom pairs via the
@@ -545,7 +545,7 @@ This will most likely cause errors in kinetic fluctuations.
    If there are other fixes that act immediately after the initial stage
    of time integration within a timestep (i.e. after atoms move), then
    the command that sets up the dynamic group should appear after those
-   fixes.  This will insure that dynamic group assignments are made
+   fixes.  This will ensure that dynamic group assignments are made
    after all atoms have moved.
 
 *One or more respa levels compute no forces*
@@ -582,13 +582,13 @@ This will most likely cause errors in kinetic fluctuations.
    needed.  The requested volume fraction may be too high, or other atoms
    may be in the insertion region.
 
-*Proc sub-domain size < neighbor skin, could lead to lost atoms*
+*Proc subdomain size < neighbor skin, could lead to lost atoms*
    The decomposition of the physical domain (likely due to load
-   balancing) has led to a processor's sub-domain being smaller than the
+   balancing) has led to a processor's subdomain being smaller than the
    neighbor skin in one or more dimensions.  Since reneighboring is
    triggered by atoms moving the skin distance, this may lead to lost
    atoms, if an atom moves all the way across a neighboring processor's
-   sub-domain before reneighboring is triggered.
+   subdomain before reneighboring is triggered.
 
 *Reducing PPPM order b/c stencil extends beyond nearest neighbor processor*
    This may lead to a larger grid than desired.  See the kspace_modify overlap

doc/src/Examples.rst

@@ -1,7 +1,7 @@
 Example scripts
 ===============
 
-The LAMMPS distribution includes an examples sub-directory with many
+The LAMMPS distribution includes an examples subdirectory with many
 sample problems.  Many are 2d models that run quickly and are
 straightforward to visualize, requiring at most a couple of minutes to
 run on a desktop machine.  Each problem has an input script (in.\*) and
@@ -29,7 +29,7 @@ be quickly post-processed into a movie using commands described on the
 Animations of many of the examples can be viewed on the Movies section
 of the `LAMMPS website <https://www.lammps.org/movies.html>`_.
 
-There are two kinds of sub-directories in the examples folder.  Lower
+There are two kinds of subdirectories in the examples folder.  Lower
 case named directories contain one or a few simple, quick-to-run
 problems.  Upper case named directories contain up to several complex
 scripts that illustrate a particular kind of simulation method or
@@ -221,10 +221,10 @@ Uppercase directories
 Nearly all of these directories have README files which give more
 details on how to understand and use their contents.
 
-The PACKAGES directory has a large number of sub-directories which
+The PACKAGES directory has a large number of subdirectories which
 correspond by name to specific packages.  They contain scripts that
 illustrate how to use the command(s) provided in those packages.  Many
-of the sub-directories have their own README files which give further
+of the subdirectories have their own README files which give further
 instructions.  See the :doc:`Packages_details <Packages_details>` doc
 page for more info on specific packages.
 

doc/src/Fortran.rst

@@ -47,7 +47,16 @@ Fortran code in order to uses the Fortran interface.
 A working example can be found together with equivalent examples in C and
 C++ in the ``examples/COUPLE/simple`` folder of the LAMMPS distribution.
 
-.. versionchanged:: TBD
+.. admonition:: Fortran compiler compatibility
+   :class: note
+
+   A fully Fortran 2003 compatible Fortran compiler is required.
+   This means that currently only GNU Fortran 9 and later are
+   compatible and thus the default compilers of Red Hat or CentOS 7
+   and Ubuntu 18.04 LTS and not compatible.  Either newer compilers
+   need to be installed or the Linux updated.
+
+.. versionchanged:: 8Feb2023
 
 .. note::
 
@@ -303,6 +312,12 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype scatter_atoms_subset: subroutine
    :f gather_bonds: :f:subr:`gather_bonds`
    :ftype gather_bonds: subroutine
+   :f gather_angles: :f:subr:`gather_angles`
+   :ftype gather_angles: subroutine
+   :f gather_dihedrals: :f:subr:`gather_dihedrals`
+   :ftype gather_dihedrals: subroutine
+   :f gather_impropers: :f:subr:`gather_impropers`
+   :ftype gather_impropers: subroutine
    :f gather: :f:subr:`gather`
    :ftype gather: subroutine
    :f gather_concat: :f:subr:`gather_concat`
@@ -1532,6 +1547,51 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
 --------
 
+.. f:subroutine:: gather_angles(data)
+
+   Gather type and constituent atom information for all angles.
+
+   .. versionadded:: 8Feb2023
+
+   This function copies the list of all angles into an allocatable array.
+   The array will be filled with (angle type, angle atom 1, angle atom 2, angle atom 3)
+   for each angle. The array is allocated to the right length (i.e., four times the
+   number of angles). The array *data* must be of the same type as the LAMMPS
+   ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or
+   ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used
+   when LAMMPS was built. If the supplied array does not match, an error will
+   result at run-time.
+
+   An example of how to use this routine is below:
+
+   .. code-block:: fortran
+
+      PROGRAM angles
+        USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
+        USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
+        USE LIBLAMMPS
+        IMPLICIT NONE
+        INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: angles
+        INTEGER(c_int), DIMENSION(:,:), POINTER :: angles_array
+        TYPE(lammps) :: lmp
+        INTEGER :: i
+        ! other commands to initialize LAMMPS, create angles, etc.
+        CALL lmp%gather_angles(angles)
+        angles_array(1:4, 1:SIZE(angles)/4) => angles
+        DO i = 1, SIZE(angles)/4
+          WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4,1X,I4)') 'angle', angles_array(1,i), &
+            '; type = ', angles_array(2,i), angles_array(3,i), angles_array(4,i)
+        END DO
+      END PROGRAM angles
+
+   :p data: array into which to copy the result. \*The ``KIND`` parameter is
+    either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``,
+    kind ``c_int64_t``.
+   :ptype data: integer(kind=\*),allocatable
+   :to: :cpp:func:`lammps_gather_angles`
+
+--------
+
 .. f:subroutine:: gather(self, name, count, data)
 
    Gather the named per-atom, per-atom fix, per-atom compute, or fix
@@ -1574,6 +1634,98 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
 --------
 
+.. f:subroutine:: gather_dihedrals(data)
+
+   Gather type and constituent atom information for all dihedrals.
+
+   .. versionadded:: 8Feb2023
+
+   This function copies the list of all dihedrals into an allocatable array.
+   The array will be filled with (dihedral type, dihedral atom 1, dihedral atom 2,
+   dihedral atom 3, dihedral atom 4) for each dihedral. The array is allocated to
+   the right length (i.e., five times the number of dihedrals).
+   The array *data* must be of the same type as the LAMMPS
+   ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or
+   ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used
+   when LAMMPS was built. If the supplied array does not match, an error will
+   result at run-time.
+
+   An example of how to use this routine is below:
+
+   .. code-block:: fortran
+
+      PROGRAM dihedrals
+        USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
+        USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
+        USE LIBLAMMPS
+        IMPLICIT NONE
+        INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: dihedrals
+        INTEGER(c_int), DIMENSION(:,:), POINTER :: dihedrals_array
+        TYPE(lammps) :: lmp
+        INTEGER :: i
+        ! other commands to initialize LAMMPS, create dihedrals, etc.
+        CALL lmp%gather_dihedrals(dihedrals)
+        dihedrals_array(1:5, 1:SIZE(dihedrals)/5) => dihedrals
+        DO i = 1, SIZE(dihedrals)/5
+          WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4,1X,I4,1X,I4)') 'dihedral', dihedrals_array(1,i), &
+            '; type = ', dihedrals_array(2,i), dihedrals_array(3,i), dihedrals_array(4,i), dihedrals_array(5,i)
+        END DO
+      END PROGRAM dihedrals
+
+   :p data: array into which to copy the result. \*The ``KIND`` parameter is
+    either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``,
+    kind ``c_int64_t``.
+   :ptype data: integer(kind=\*),allocatable
+   :to: :cpp:func:`lammps_gather_dihedrals`
+
+--------
+
+.. f:subroutine:: gather_impropers(data)
+
+   Gather type and constituent atom information for all impropers.
+
+   .. versionadded:: 8Feb2023
+
+   This function copies the list of all impropers into an allocatable array.
+   The array will be filled with (improper type, improper atom 1, improper atom 2,
+   improper atom 3, improper atom 4) for each improper. The array is allocated to
+   the right length (i.e., five times the number of impropers).
+   The array *data* must be of the same type as the LAMMPS
+   ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or
+   ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used
+   when LAMMPS was built. If the supplied array does not match, an error will
+   result at run-time.
+
+   An example of how to use this routine is below:
+
+   .. code-block:: fortran
+
+      PROGRAM impropers
+        USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
+        USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
+        USE LIBLAMMPS
+        IMPLICIT NONE
+        INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: impropers
+        INTEGER(c_int), DIMENSION(:,:), POINTER :: impropers_array
+        TYPE(lammps) :: lmp
+        INTEGER :: i
+        ! other commands to initialize LAMMPS, create impropers, etc.
+        CALL lmp%gather_impropers(impropers)
+        impropers_array(1:5, 1:SIZE(impropers)/5) => impropers
+        DO i = 1, SIZE(impropers)/5
+          WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4,1X,I4,1X,I4)') 'improper', impropers_array(1,i), &
+            '; type = ', impropers_array(2,i), impropers_array(3,i), impropers_array(4,i), impropers_array(5,i)
+        END DO
+      END PROGRAM impropers
+
+   :p data: array into which to copy the result. \*The ``KIND`` parameter is
+    either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``,
+    kind ``c_int64_t``.
+   :ptype data: integer(kind=\*),allocatable
+   :to: :cpp:func:`lammps_gather_impropers`
+
+--------
+
 .. f:subroutine:: gather_concat(self, name, count, data)
 
    Gather the named per-atom, per-atom fix, per-atom compute, or fix
@@ -2003,7 +2155,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    The LAMMPS :doc:`dump style movie <dump_image>` supports generating movies
    from images on-the-fly via creating a pipe to the
-   `ffmpeg <https://ffmpeg.org/ffmpeg/>`_ program.
+   `ffmpeg <https://ffmpeg.org/>`_ program.
    This function checks whether this feature was
    :ref:`enabled at compile time <graphics>`.
    It does **not** check whether the ``ffmpeg`` itself is installed and usable.

doc/src/Howto.rst

@@ -4,9 +4,9 @@ Howto discussions
 These doc pages describe how to perform various tasks with LAMMPS,
 both for users and developers.  The
 `glossary <https://www.lammps.org/glossary.html>`_ website page also lists MD
-terminology with links to corresponding LAMMPS manual pages.  The
+terminology, with links to corresponding LAMMPS manual pages.  The
-example input scripts included in the examples directory of the LAMMPS
+example input scripts included in the ``examples`` directory of the LAMMPS
-distribution and highlighted on the :doc:`Examples <Examples>` doc page
+source code distribution and highlighted on the :doc:`Examples` page
 also show how to set up and run various kinds of simulations.
 
 General howto
@@ -70,6 +70,7 @@ Force fields howto
    Howto_amoeba
    Howto_tip3p
    Howto_tip4p
+   Howto_tip5p
    Howto_spc
 
 Packages howto

doc/src/Howto_2d.rst

@@ -22,7 +22,7 @@ atom in the file, assign a z coordinate so it falls inside the
 z-boundaries of the box - e.g. 0.0.
 
 Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last
-defined fix to insure that the z-components of velocities and forces
+defined fix to ensure that the z-components of velocities and forces
 are zeroed out every timestep.  The reason to make it the last fix is
 so that any forces induced by other fixes will be zeroed out.
 

doc/src/Howto_bpm.rst

@@ -3,16 +3,16 @@ Bonded particle models
 
 The BPM package implements bonded particle models which can be used to
 simulate mesoscale solids.  Solids are constructed as a collection of
-particles which each represent a coarse-grained region of space much
+particles, which each represent a coarse-grained region of space much
 larger than the atomistic scale.  Particles within a solid region are
 then connected by a network of bonds to provide solid elasticity.
 
 Unlike traditional bonds in molecular dynamics, the equilibrium bond
 length can vary between bonds. Bonds store the reference state.  This
 includes setting the equilibrium length equal to the initial distance
-between the two particles but can also include data on the bond
+between the two particles, but can also include data on the bond
-orientation for rotational models. This produces a stress free initial
+orientation for rotational models. This produces a stress-free initial
-state. Furthermore, bonds are allowed to break under large strains
+state. Furthermore, bonds are allowed to break under large strains,
 producing fracture. The examples/bpm directory has sample input scripts
 for simulations of the fragmentation of an impacted plate and the
 pouring of extended, elastic bodies.
@@ -22,8 +22,8 @@ pouring of extended, elastic bodies.
 Bonds can be created using a :doc:`read data <read_data>` or
 :doc:`create bonds <create_bonds>` command. Alternatively, a
 :doc:`molecule <molecule>` template with bonds can be used with
-:doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` to
+:doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` to create
-create solid grains.
+solid grains.
 
 In this implementation, bonds store their reference state when they are
 first computed in the setup of the first simulation run. Data is then
@@ -35,21 +35,20 @@ such as those created by pouring grains using :doc:`fix pour
 
 ----------
 
-Currently there are two types of bonds included in the BPM
+Currently, there are two types of bonds included in the BPM package. The
-package. The first bond style, :doc:`bond bpm/spring
+first bond style, :doc:`bond bpm/spring <bond_bpm_spring>`, only applies
-<bond_bpm_spring>`, only applies pairwise, central body forces. Point
+pairwise, central body forces. Point particles must have :doc:`bond atom
-particles must have :doc:`bond atom style <atom_style>` and may be
+style <atom_style>` and may be thought of as nodes in a spring
-thought of as nodes in a spring network. Alternatively, the second
+network. Alternatively, the second bond style, :doc:`bond bpm/rotational
-bond style, :doc:`bond bpm/rotational <bond_bpm_rotational>`, resolves
+<bond_bpm_rotational>`, resolves tangential forces and torques arising
-tangential forces and torques arising with the shearing, bending, and
+with the shearing, bending, and twisting of the bond due to rotation or
-twisting of the bond due to rotation or displacement of particles.
+displacement of particles.  Particles are similar to those used in the
-Particles are similar to those used in the :doc:`granular package
+:doc:`granular package <Howto_granular>`, :doc:`atom style sphere
-<Howto_granular>`, :doc:`atom style sphere <atom_style>`. However,
+<atom_style>`. However, they must also track the current orientation of
-they must also track the current orientation of particles and store bonds
+particles and store bonds, and therefore use a :doc:`bpm/sphere atom
-and therefore use a :doc:`bpm/sphere atom style <atom_style>`.
+style <atom_style>`.  This also requires a unique integrator :doc:`fix
-This also requires a unique integrator :doc:`fix nve/bpm/sphere
+nve/bpm/sphere <fix_nve_bpm_sphere>` which numerically integrates
-<fix_nve_bpm_sphere>` which numerically integrates orientation similar
+orientation similar to :doc:`fix nve/asphere <fix_nve_asphere>`.
-to :doc:`fix nve/asphere <fix_nve_asphere>`.
 
 In addition to bond styles, a new pair style :doc:`pair bpm/spring
 <pair_bpm_spring>` was added to accompany the bpm/spring bond
@@ -63,7 +62,7 @@ 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
+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>`
@@ -90,7 +89,7 @@ bond settings
 
 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
+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
@@ -134,7 +133,10 @@ the following are currently compatible with BPM bond styles:
 * :doc:`fix bond/break <fix_bond_break>`
 * :doc:`fix bond/swap <fix_bond_swap>`
 
-Note :doc:`create_bonds <create_bonds>` requires certain special_bonds settings.
+.. note::
-To subtract pair interactions, one will need to switch between different
+
-special_bonds settings in the input script. An example is found in
+   The :doc:`create_bonds <create_bonds>` command requires certain
-examples/bpm/impact.
+   :doc:`special_bonds <special_bonds>` settings.  To subtract pair
+   interactions, one will need to switch between different *special_bonds*
+   settings in the input script. An example is found in
+   ``examples/bpm/impact``.

doc/src/Howto_broken_bonds.rst

@@ -1,15 +1,15 @@
 Broken Bonds
 ============
 
-Typically, bond interactions persist for the duration of a simulation
+Typically, bond interactions persist for the duration of a simulation in
-in LAMMPS. However, there are some exceptions that allow for bonds to
+LAMMPS. However, there are some exceptions that allow for bonds to
-break including the :doc:`quartic bond style <bond_quartic>` and the
+break, including the :doc:`quartic bond style <bond_quartic>` and the
 bond styles in the :doc:`BPM package <Howto_bpm>` which contains the
-:doc:`bpm/spring <bond_bpm_spring>` and
+:doc:`bpm/spring <bond_bpm_spring>` and :doc:`bpm/rotational
-:doc:`bpm/rotational <bond_bpm_rotational>` bond styles. In these cases,
+<bond_bpm_rotational>` bond styles. In these cases, a bond can be broken
-a bond can be broken if it is stretched beyond a user-defined threshold.
+if it is stretched beyond a user-defined threshold.  LAMMPS accomplishes
-LAMMPS accomplishes this by setting the bond type to zero such that the
+this by setting the bond type to 0, such that the bond force is no
-bond force is no longer computed.
+longer computed.
 
 Users are normally able to weight the contribution of pair forces to atoms
 that are bonded using the :doc:`special_bonds command <special_bonds>`.

doc/src/Howto_cmake.rst

@@ -89,7 +89,7 @@ different options (``build-parallel``, ``build-serial``) or with
 different compilers (``build-gnu``, ``build-clang``, ``build-intel``)
 and so on.  All the auxiliary files created by one build process
 (executable, object files, log files, etc) are stored in this directory
-or sub-directories within it that CMake creates.
+or subdirectories within it that CMake creates.
 
 
 Running CMake

doc/src/Howto_coreshell.rst

@@ -111,7 +111,7 @@ Therefore it is typically desirable to decouple the relative motion of
 the core/shell pair, which is an imaginary degree of freedom, from the
 real physical system.  To do that, the :doc:`compute temp/cs <compute_temp_cs>` command can be used, in conjunction with
 any of the thermostat fixes, such as :doc:`fix nvt <fix_nh>` or :doc:`fix langevin <fix_langevin>`.  This compute uses the center-of-mass velocity
-of the core/shell pairs to calculate a temperature, and insures that
+of the core/shell pairs to calculate a temperature, and ensures that
 velocity is what is rescaled for thermostatting purposes.  This
 compute also works for a system with both core/shell pairs and
 non-polarized ions (ions without an attached satellite particle).  The

doc/src/Howto_couple.rst

@@ -1,27 +1,27 @@
 Coupling LAMMPS to other codes
 ==============================
 
-LAMMPS is designed to allow it to be coupled to other codes.  For
+LAMMPS is designed to support being coupled to other codes.  For
 example, a quantum mechanics code might compute forces on a subset of
 atoms and pass those forces to LAMMPS.  Or a continuum finite element
 (FE) simulation might use atom positions as boundary conditions on FE
 nodal points, compute a FE solution, and return interpolated forces on
 MD atoms.
 
-LAMMPS can be coupled to other codes in at least 4 ways.  Each has
+LAMMPS can be coupled to other codes in at least 4 different ways.  Each
-advantages and disadvantages, which you will have to think about in the
+has advantages and disadvantages, which you will have to think about in
-context of your application.
+the context of your application.
 
-1. Define a new :doc:`fix <fix>` command that calls the other code.
+1. Define a new :doc:`fix <fix>` command that calls the other code.  In
-   In this scenario, LAMMPS is the driver code.  During timestepping,
+   this scenario, LAMMPS is the driver code.  During timestepping, the
-   the fix is invoked, and can make library calls to the other code,
+   fix is invoked, and can make library calls to the other code, which
-   which has been linked to LAMMPS as a library.  This is the way the
+   has been linked to LAMMPS as a library.  This is the way the
    :ref:`LATTE <PKG-LATTE>` package, which performs density-functional
    tight-binding calculations using the `LATTE software
-   <https://github.com/lanl/LATTE>`_ to compute forces, is hooked to
+   <https://github.com/lanl/LATTE>`_ to compute forces, is interfaced to
    LAMMPS.  See the :doc:`fix latte <fix_latte>` command for more
-   details.  Also see the :doc:`Modify <Modify>` doc pages for info on
+   details.  Also see the :doc:`Modify <Modify>` pages for information
-   how to add a new fix to LAMMPS.
+   on how to add a new fix to LAMMPS.
 
 .. spacer
 
@@ -42,28 +42,26 @@ context of your application.
    stand-alone code could communicate with LAMMPS through files that the
    command writes and reads.
 
-   See the :doc:`Modify command <Modify_command>` page for info on how
+   See the :doc:`Modify command <Modify_command>` page for information
-   to add a new command to LAMMPS.
+   on how to add a new command to LAMMPS.
 
 .. spacer
 
-3. Use LAMMPS as a library called by another code.  In this case the
+3. Use LAMMPS as a library called by another code.  In this case, the
-   other code is the driver and calls LAMMPS as needed.  Or a wrapper
+   other code is the driver and calls LAMMPS as needed.  Alternately, a
-   code could link and call both LAMMPS and another code as libraries.
+   wrapper code could link and call both LAMMPS and another code as
-   Again, the :doc:`run <run>` command has options that allow it to be
+   libraries.  Again, the :doc:`run <run>` command has options that
-   invoked with minimal overhead (no setup or clean-up) if you wish to
+   allow it to be invoked with minimal overhead (no setup or clean-up)
-   do multiple short runs, driven by another program.  Details about
+   if you wish to do multiple short runs, driven by another program.
-   using the library interface are given in the :doc:`library API
+   Details about using the library interface are given in the
-   <Library>` documentation.
+   :doc:`library API <Library>` documentation.
 
 .. spacer
 
-4. Couple LAMMPS with another code in a client/server fashion, using
+4. Couple LAMMPS with another code in a client/server fashion, using the
-   using the `MDI Library
+   `MDI Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_
-   <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_
    developed by the `Molecular Sciences Software Institute (MolSSI)
-   <https://molssi.org>`_ to run LAMMPS as either an MDI driver
+   <https://molssi.org>`_ to run LAMMPS as either an MDI driver (client)
-   (client) or an MDI engine (server).  The MDI driver issues commands
+   or an MDI engine (server).  The MDI driver issues commands to the MDI
-   to the MDI server to exchange data between them.  See the
+   server to exchange data between them.  See the :doc:`Howto_mdi` page for
-   :doc:`Howto mdi <Howto_mdi>` page for more information about how
+   more information about how LAMMPS can operate in either of these modes.
-   LAMMPS can operate in either of these modes.

doc/src/Howto_github.rst

@@ -315,7 +315,7 @@ add changes. Please watch the comments to the pull requests. The two
 "test" labels are used to trigger extended tests before the code is
 merged. This is sometimes done by LAMMPS developers, if they suspect
 that there may be some subtle side effects from your changes. It is not
-done by default, because those tests are very time consuming.  The
+done by default, because those tests are very time-consuming.  The
 *ready_for_merge* label is usually attached when the LAMMPS developer
 assigned to the pull request considers this request complete and to
 trigger a final full test evaluation.
@@ -476,16 +476,25 @@ to your remote(s) as well:
 
 **Recent changes in the workflow**
 
-Some changes to the workflow are not captured in this tutorial.  For
+Some recent changes to the workflow are not captured in this tutorial.
-example, in addition to the *develop* branch, to which all new features
+For example, in addition to the *develop* branch, to which all new
-should be submitted, there is also a *release* and a *stable* branch;
+features should be submitted, there is also a *release*, a *stable*, and
-these have the same content as *develop*, but are only updated after a
+a *maintenance* branch; the *release* branch is updated from the
-patch release or stable release was made.  Furthermore, the naming of
+*develop* as part of a feature release, and *stable* (together with
-the patches now follow the pattern "patch_<Day><Month><Year>" to
+*release*) are updated from *develop* when a stable release is made. In
-simplify comparisons between releases.  Finally, all patches and
+between stable releases, selected bug fixes and infrastructure updates
-submissions are subject to automatic testing and code checks to make
+are back-ported from the *develop* branch to the *maintenance* branch
-sure they at the very least compile.
+and occasionally merged to *stable* as an update release.
 
-A discussion of the LAMMPS developer GitHub workflow can be found in the
+Furthermore, the naming of the release tags now follow the pattern
-file `doc/github-development-workflow.md
+"patch_<Day><Month><Year>" to simplify comparisons between releases.
+For stable releases additional "stable_<Day><Month><Year>" tags are
+applied and update releases are tagged with
+"stable_<Day><Month><Year>_update<Number>", Finally, all releases and
+submissions are subject to automatic testing and code checks to make
+sure they compile with a variety of compilers and popular operating
+systems.  Some unit and regression testing is applied as well.
+
+A detailed discussion of the LAMMPS developer GitHub workflow can be
+found in the file `doc/github-development-workflow.md
 <https://github.com/lammps/lammps/blob/develop/doc/github-development-workflow.md>`_

doc/src/Howto_grid.rst

@@ -11,7 +11,7 @@ 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
+within the spatial subdomain of the processor.  If needed for its
 computations, a processor may also store ghost grid cells with their
 data.
 
@@ -28,7 +28,7 @@ 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
+:doc:`fix balance <fix_balance>` commands, then the subdomain owned
 by a processor can change which may also change which grid cells they
 own.
 

doc/src/Howto_library.rst

@@ -6,22 +6,22 @@ can be built as a static or shared library, 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 interface <Python_head>`.
 
-At the core of LAMMPS is the ``LAMMPS`` class which encapsulates the
+At the core of LAMMPS is the ``LAMMPS`` class, which encapsulates the
 state of the simulation program through the state of the various class
 instances that it is composed of.  So a calculation using LAMMPS
-requires to create an instance of the ``LAMMPS`` class and then send it
+requires creating an instance of the ``LAMMPS`` class and then send it
 (text) commands, either individually or from a file, or perform other
 operations that modify the state stored inside that instance or drive
-simulations.  This is essentially what the ``src/main.cpp`` file does
+simulations.  This is essentially what the ``src/main.cpp`` file does as
-as well for the standalone LAMMPS executable with reading commands
+well for the standalone LAMMPS executable, reading commands either from
-either from an input file or stdin.
+an input file or the standard input.
 
 Creating a LAMMPS instance can be done by using C++ code directly or
 through a C-style interface library to LAMMPS that is provided in the
-files ``src/library.cpp`` and ``library.h``.  This
+files ``src/library.cpp`` and ``src/library.h``.  This :ref:`C language
-:ref:`C language API <lammps_c_api>`, can be used from C and C++,
+API <lammps_c_api>`, can be used from C and C++, and is also the basis
-and is also the basis for the :doc:`Python <Python_module>` and
+for the :doc:`Python <Python_module>` and :doc:`Fortran <Fortran>`
-:doc:`Fortran <Fortran>` interfaces or wrappers included in the
+interfaces or the :ref:`SWIG based wrappers <swig>` included in the
 LAMMPS source code.
 
 The ``examples/COUPLE`` and ``python/examples`` directories contain some

doc/src/Howto_mdi.rst

@@ -12,11 +12,11 @@ developed by the `Molecular Sciences Software Institute (MolSSI)
 <https://molssi.org>`_, which is supported by the :ref:`MDI <PKG-MDI>`
 package.
 
-Alternate methods for code coupling with LAMMPS are described on the
+Alternate methods for coupling codes with LAMMPS are described on the
-:doc:`Howto couple <Howto_couple>` doc page.
+:doc:`Howto_couple` page.
 
 Some advantages of client/server coupling are that the codes can run
-as stand-alone executables; they need not be linked together.  Thus
+as stand-alone executables; they need not be linked together.  Thus,
 neither code needs to have a library interface.  This also makes it
 easy to run the two codes on different numbers of processors.  If a
 message protocol (format and content) is defined for a particular kind
@@ -41,7 +41,7 @@ within that sub-communicator exchange messages with the corresponding
 engine instance, and can also send MPI messages to other processors in
 the driver.  The driver code can also destroy engine instances and
 re-instantiate them.  LAMMPS can operate as either a stand-alone or
-plugin MDI engine.  When it operates as a driver, if can use either
+plugin MDI engine.  When it operates as a driver, it can use either
 stand-alone or plugin MDI engines.
 
 The way in which an MDI driver communicates with an MDI engine is by
@@ -50,83 +50,83 @@ to MPI_Send() and MPI_Recv() calls.  Each send or receive operation
 uses a string to identify the command name, and optionally some data,
 which can be a single value or vector of values of any data type.
 Inside the MDI library, data is exchanged between the driver and
-engine via MPI calls or sockets.  This a run-time choice by the user.
+engine via MPI calls or sockets.  This is a run-time choice by the user.
 
 ----------
 
 The :ref:`MDI <PKG-MDI>` package provides a :doc:`mdi engine <mdi>`
-command which enables LAMMPS to operate as an MDI engine.  Its doc
+command, which enables LAMMPS to operate as an MDI engine.  Its doc
 page explains the variety of standard and custom MDI commands which
 the LAMMPS engine recognizes and can respond to.
 
-The package also provides a :doc:`mdi plugin <mdi>` command which
+The package also provides a :doc:`mdi plugin <mdi>` command, which
 enables LAMMPS to operate as an MDI driver and load an MDI engine as a
 plugin library.
 
-The package also has a `fix mdi/qm <fix_mdi_qm>` command in which
+The package furthermore includes a :doc:`fix mdi/qm <fix_mdi_qm>`
-LAMMPS operates as an MDI driver in conjunction with a quantum
+command, in which LAMMPS operates as an MDI driver in conjunction with a
-mechanics code as an MDI engine.  The post_force() method of the
+quantum mechanics code as an MDI engine.  The post_force() method of the
-fix_mdi_qm.cpp file shows how a driver issues MDI commands to another
+``fix_mdi_qm.cpp`` file shows how a driver issues MDI commands to
-code.  This command can be used to couple to an MDI engine which is
+another code.  This command can be used to couple to an MDI engine,
-either a stand-alone code or a plugin library.
+which is either a stand-alone code or a plugin library.
 
-As explained on the `fix mdi/qm <fix_mdi_qm>` command doc page, it can
+As explained in the :doc:`fix mdi/qm <fix_mdi_qm>` command
-be used to perform *ab initio* MD simulations or energy minimizations,
+documentation, it can be used to perform *ab initio* MD simulations or
-or to evaluate the quantum energy and forces for a series of
+energy minimizations, or to evaluate the quantum energy and forces for a
-independent systems.  The examples/mdi directory has example input
+series of independent systems.  The ``examples/mdi`` directory has
-scripts for all of these use cases.
+example input scripts for all of these use cases.
 
 ----------
 
 The examples/mdi directory contains Python scripts and LAMMPS input
-script which use LAMMPS as either an MDI driver or engine or both.
+script which use LAMMPS as either an MDI driver or engine, or both.
 Currently, 5 example use cases are provided:
 
-* Run ab initio MD (AIMD) using 2 instances of LAMMPS.  As a driver
+* Run ab initio MD (AIMD) using 2 instances of LAMMPS.  As a driver,
   LAMMPS performs the timestepping in either NVE or NPT mode.  As an
   engine, LAMMPS computes forces and is a surrogate for a quantum
   code.
 
-* As a driver, LAMMPS runs an MD simulation.  Every N steps it passes
+* LAMMPS runs an MD simulation as a driver.  Every N steps it passes the
-  the current snapshot to an MDI engine to evaluate the energy,
+  current snapshot to an MDI engine to evaluate the energy, virial, and
-  virial, and peratom forces.  As the engine LAMMPS is a surrogate for
+  peratom forces.  As the engine, LAMMPS is a surrogate for a quantum
-  a quantum code.
-
-* As a driver, LAMMPS loops over a series of data files and passes the
-  configuration to an MDI engine to evaluate the energy, virial, and
-  peratom forces.  As the engine LAMMPS is a surrogate for a quantum
   code.
 
+* LAMMPS loops over a series of data files and passes the configuration
+  to an MDI engine to evaluate the energy, virial, and peratom forces
+  and thus acts as a simulation driver.  As the engine, LAMMPS is used
+  as a surrogate for a quantum code.
+
 * A Python script driver invokes a sequence of unrelated LAMMPS
   calculations.  Calculations can be single-point energy/force
   evaluations, MD runs, or energy minimizations.
 
-* Run AIMD with a Python driver code and 2 LAMMPS instances as
+* Run AIMD with a Python driver code and 2 LAMMPS instances as engines.
-  engines.  The first LAMMPS instance performs MD timestepping.  The
+  The first LAMMPS instance performs MD timestepping.  The second LAMMPS
-  second LAMMPS instance acts as a surrogate QM code to compute
+  instance acts as a surrogate QM code to compute forces.
-  forces.
 
-Note that in any of these example where LAMMPS is used as an engine,
+.. note::
-an actual QM code (which supports MDI) could be used in its place,
+
+   In any of these examples where LAMMPS is used as an engine, an actual
+   QM code (provided it has support for MDI) could be used in its place,
    without modifying the input scripts or launch commands, except to
    specify the name of the QM code.
 
-The examples/mdi/Run.sh file illustrates how to launch both driver and
+The ``examples/mdi/Run.sh`` file illustrates how to launch both driver
-engine codes so that they communicate using the MDI library via either
+and engine codes so that they communicate using the MDI library via
-MPI or sockets.  Or using the engine as a stand-alone code or plugin
+either MPI or sockets, or using the engine as a stand-alone code, or
-library.
+as a plugin library.
 
 -------------
 
-Currently there are at least two quantum DFT codes which have direct
+Currently, there are at least two quantum DFT codes which have direct MDI
-MDI support, `Quantum ESPRESSO (QE)
+support, `Quantum ESPRESSO (QE) <https://www.quantum-espresso.org/>`_
-<https://www.quantum-espresso.org/>`_ and `INQ
+and `INQ <https://qsg.llnl.gov/node/101.html>`_.  There are also several
-<https://qsg.llnl.gov/node/101.html>`_.  There are also several QM
+QM codes which have indirect support through QCEngine or i-PI.  The
-codes which have indirect support through QCEngine or i-PI.  The
+former means they require a wrapper program (QCEngine) with MDI support
-former means they require a wrapper program (QCEngine) with MDI
+which writes/read files to pass data to the quantum code itself.  The
-support which writes/read files to pass data to the quantum code
+list of QCEngine-supported and i-PI-supported quantum codes is on the
-itself.  The list of QCEngine-supported and i-PI-supported quantum
+`MDI webpage
-codes is on the `MDI webpage
 <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
 
 Here is how to build QE as a stand-alone ``pw.x`` file which can be
@@ -138,7 +138,7 @@ used in stand-alone mode:
    build the executable pw.x, following the `QE build guide <https://gitlab.com/QEF/q-e/-/wikis/Developers/CMake-build-system>`_
 
 Here is how to build QE as a shared library which can be used in plugin mode,
-which results in a libqemdi.so file in <base_path>/q-e/MDI/src:
+which results in a ``libqemdi.so`` file in ``<base_path>/q-e/MDI/src``:
 
 .. code-block:: bash
 
@@ -149,8 +149,8 @@ which results in a libqemdi.so file in <base_path>/q-e/MDI/src:
 
 INQ cannot be built as a stand-alone code; it is by design a library.
 Here is how to build INQ as a shared library which can be used in
-plugin mode, which results in a libinqmdi.so file in
+plugin mode, which results in a ``libinqmdi.so`` file in
-<base_path>/inq/build/examples:
+``<base_path>/inq/build/examples``:
 
 .. code-block:: bash
 

doc/src/Howto_multiple.rst

@@ -4,7 +4,7 @@ Run multiple simulations from one input script
 This can be done in several ways.  See the documentation for
 individual commands for more details on how these examples work.
 
-If "multiple simulations" means continue a previous simulation for
+If "multiple simulations" means to continue a previous simulation for
 more timesteps, then you simply use the :doc:`run <run>` command
 multiple times.  For example, this script
 

doc/src/Howto_output.rst

@@ -26,7 +26,7 @@ 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 commands related
+The following subsections discuss different LAMMPS commands related
 to output and the kind of data they operate on and produce:
 
 * :ref:`Global/per-atom/local/per-grid data <global>`
@@ -59,7 +59,7 @@ 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.
+cells whose center point falls within its subdomain.
 
 .. _scalar:
 
@@ -322,7 +322,7 @@ 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
+subset of grid cells within its subdomain.  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.
 

doc/src/Howto_peri.rst

@@ -783,19 +783,19 @@ Pitfalls
 **Parallel Scalability**
 
 LAMMPS operates in parallel in a :doc:`spatial-decomposition mode
-<Developer_par_part>`, where each processor owns a spatial sub-domain of
+<Developer_par_part>`, where each processor owns a spatial subdomain of
 the overall simulation domain and communicates with its neighboring
 processors via distributed-memory message passing (MPI) to acquire ghost
 atom information to allow forces on the atoms it owns to be
 computed. LAMMPS also uses Verlet neighbor lists which are recomputed
 every few timesteps as particles move. On these timesteps, particles
 also migrate to new processors as needed. LAMMPS decomposes the overall
-simulation domain so that spatial sub-domains of nearly equal volume are
+simulation domain so that spatial subdomains of nearly equal volume are
-assigned to each processor. When each sub-domain contains nearly the
+assigned to each processor. When each subdomain contains nearly the
 same number of particles, this results in a reasonable load balance
 among all processors. As is more typical with some peridynamic
-simulations, some sub-domains may contain many particles while other
+simulations, some subdomains may contain many particles while other
-sub-domains contain few particles, resulting in a load imbalance that
+subdomains contain few particles, resulting in a load imbalance that
 impacts parallel scalability.
 
 **Setting the "skin" distance**

doc/src/Howto_pylammps.rst

@@ -392,7 +392,7 @@ IPyLammps Examples
 ------------------
 
 Examples of IPython notebooks can be found in the python/examples/pylammps
-sub-directory. To open these notebooks launch *jupyter notebook* inside this
+subdirectory. To open these notebooks launch *jupyter notebook* inside this
 directory and navigate to one of them. If you compiled and installed
 a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
 you should be able to rerun all of these notebooks.

doc/src/Howto_replica.rst

@@ -47,9 +47,9 @@ script which is required when running in multi-replica mode.
 
 Also note that with MPI installed on a machine (e.g. your desktop), you
 can run on more (virtual) processors than you have physical processors.
-Thus the above commands could be run on a single-processor (or
+Thus, the above commands could be run on a single-processor (or
 few-processor) desktop so that you can run a multi-replica simulation on
 more replicas than you have physical processors. This is useful for
 testing and debugging, since with most modern processors and MPI
-libraries the efficiency of a calculation can severely diminish when
+libraries, the efficiency of a calculation can severely diminish when
 oversubscribing processors.

doc/src/Howto_restart.rst

@@ -7,8 +7,9 @@ run will continue from where the previous run left off.  Or binary
 restart files can be saved to disk using the :doc:`restart <restart>`
 command.  At a later time, these binary files can be read via a
 :doc:`read_restart <read_restart>` command in a new script.  Or they can
-be converted to text data files using the :doc:`-r command-line switch <Run_options>` and read by a :doc:`read_data <read_data>`
+be converted to text data files using the :doc:`-r command-line switch
-command in a new script.
+<Run_options>` and read by a :doc:`read_data <read_data>` command in a
+new script.
 
 Here we give examples of 2 scripts that read either a binary restart
 file or a converted data file and then issue a new run command to
@@ -47,7 +48,7 @@ last 50 timesteps:
 
 Note that the following commands do not need to be repeated because
 their settings are included in the restart file: *units, atom_style,
-special_bonds, pair_style, bond_style*.  However these commands do
+special_bonds, pair_style, bond_style*.  However, these commands do
 need to be used, since their settings are not in the restart file:
 *neighbor, fix, timestep*\ .
 
@@ -90,7 +91,7 @@ Then, this script could be used to re-run the last 50 steps:
 
 Note that nearly all the settings specified in the original *in.chain*
 script must be repeated, except the *pair_coeff* and *bond_coeff*
-commands since the new data file lists the force field coefficients.
+commands, since the new data file lists the force field coefficients.
 Also, the :doc:`reset_timestep <reset_timestep>` command is used to tell
-LAMMPS the current timestep.  This value is stored in restart files,
+LAMMPS the current timestep.  This value is stored in restart files, but
-but not in data files.
+not in data files.

doc/src/Howto_spc.rst

@@ -20,7 +20,6 @@ atoms and the water molecule to run a rigid SPC model.
 | LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
 | :math:`r_0` of OH bond = 1.0
 | :math:`\theta_0` of HOH angle = 109.47\ :math:`^{\circ}`
-|
 
 Note that as originally proposed, the SPC model was run with a 9
 Angstrom cutoff for both LJ and Coulomb terms.  It can also be used
@@ -33,16 +32,123 @@ the partial charge assignments change:
 
 | O charge = -0.8476
 | H charge = 0.4238
-|
 
 See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
 the SPC and SPC/E models.
 
+Below is the code for a LAMMPS input file and a molecule file
+(``spce.mol``) of SPC/E water for use with the :doc:`molecule command
+<molecule>` demonstrating how to set up a small bulk water system for
+SPC/E with rigid bonds.
+
+.. code-block:: LAMMPS
+
+   units real
+   atom_style full
+   region box block -5 5 -5 5 -5 5
+   create_box 2 box  bond/types 1 angle/types 1 &
+                   extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
+
+   mass 1 15.9994
+   mass 2 1.008
+
+   pair_style lj/cut/coul/cut 10.0
+   pair_coeff 1 1 0.1553 3.166
+   pair_coeff 1 2 0.0    1.0
+   pair_coeff 2 2 0.0    1.0
+
+   bond_style zero
+   bond_coeff 1 1.0
+
+   angle_style zero
+   angle_coeff 1 109.47
+
+   molecule water spce.mol
+   create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
+
+   timestep 1.0
+   fix rigid     all shake 0.0001 10 10000 b 1 a 1
+   minimize 0.0 0.0 1000 10000
+   run 0 post no
+   reset_timestep 0
+   velocity all create 300.0 5463576
+   fix integrate all nvt temp 300.0 300.0 1.0
+
+   thermo_style custom step temp press etotal density pe ke
+   thermo 1000
+   run 20000 upto
+   write_data tip4p.data nocoeff
+
+.. _spce_molecule:
+.. code-block::
+
+   # Water molecule. SPC/E geometry
+
+   3 atoms
+   2 bonds
+   1 angles
+
+   Coords
+
+   1    0.00000  -0.06461   0.00000
+   2    0.81649   0.51275   0.00000
+   3   -0.81649   0.51275   0.00000
+
+   Types
+
+   1        1   # O
+   2        2   # H
+   3        2   # H
+
+   Charges
+
+   1       -0.8476
+   2        0.4238
+   3        0.4238
+
+   Bonds
+
+   1   1      1      2
+   2   1      1      3
+
+   Angles
+
+   1   1      2      1      3
+
+   Shake Flags
+
+   1 1
+   2 1
+   3 1
+
+   Shake Atoms
+
+   1 1 2 3
+   2 1 2 3
+   3 1 2 3
+
+   Shake Bond Types
+
+   1 1 1 1
+   2 1 1 1
+   3 1 1 1
+
+   Special Bond Counts
+
+   1 2 0 0
+   2 1 1 0
+   3 1 1 0
+
+   Special Bonds
+
+   1 2 3
+   2 1 3
+   3 1 2
+
 Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
 
 ----------
 
 .. _howto-Berendsen:
 
-**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91,
+**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
-6269-6271 (1987).

doc/src/Howto_spherical.rst

@@ -93,7 +93,7 @@ Some of the pair styles used to compute pairwise interactions between
 finite-size particles also compute the correct interaction with point
 particles as well, e.g. the interaction between a point particle and a
 finite-size particle or between two point particles.  If necessary,
-:doc:`pair_style hybrid <pair_hybrid>` can be used to insure the correct
+:doc:`pair_style hybrid <pair_hybrid>` can be used to ensure the correct
 interactions are computed for the appropriate style of interactions.
 Likewise, using groups to partition particles (ellipsoids versus
 spheres versus point particles) will allow you to use the appropriate

doc/src/Howto_tip3p.rst

@@ -1,53 +1,211 @@
 TIP3P water model
 =================
 
-The TIP3P water model as implemented in CHARMM
+The TIP3P water model as implemented in CHARMM :ref:`(MacKerell)
-:ref:`(MacKerell) <howto-tip3p>` specifies a 3-site rigid water molecule with
+<howto-tip3p>` specifies a 3-site rigid water molecule with charges and
-charges and Lennard-Jones parameters assigned to each of the 3 atoms.
+Lennard-Jones parameters assigned to each of the 3 atoms.
-In LAMMPS the :doc:`fix shake <fix_shake>` command can be used to hold
-the two O-H bonds and the H-O-H angle rigid.  A bond style of
-*harmonic* and an angle style of *harmonic* or *charmm* should also be
-used.
 
-These are the additional parameters (in real units) to set for O and H
+A suitable pair style with cutoff Coulomb would be:
-atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
-cutoff.  The K values can be used if a flexible TIP3P model (without
-fix shake) is desired.  If the LJ epsilon and sigma for HH and OH are
-set to 0.0, it corresponds to the original 1983 TIP3P model
-:ref:`(Jorgensen) <Jorgensen1>`.
 
-| O mass = 15.9994
+* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
-| H mass = 1.008
-| O charge = -0.834
-| H charge = 0.417
-| LJ :math:`\epsilon` of OO = 0.1521
-| LJ :math:`\sigma` of OO = 3.1507
-| LJ :math:`\epsilon` of HH = 0.0460
-| LJ :math:`\sigma` of HH = 0.4000
-| LJ :math:`\epsilon` of OH = 0.0836
-| LJ :math:`\sigma` of OH = 1.7753
-| K of OH bond = 450
-| :math:`r_0` of OH bond = 0.9572
-| K of HOH angle = 55
-| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
-|
 
-These are the parameters to use for TIP3P with a long-range Coulomb
+or these commands for a long-range Coulomb model:
-solver (e.g. Ewald or PPPM in LAMMPS), see :ref:`(Price) <Price1>` for
+
-details:
+* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
+* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
+* :doc:`kspace_style pppm <kspace_style>`
+* :doc:`kspace_style pppm/disp <kspace_style>`
+
+In LAMMPS the :doc:`fix shake or fix rattle <fix_shake>` command can be
+used to hold the two O-H bonds and the H-O-H angle rigid.  A bond style
+of :doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
+<angle_harmonic>` or :doc:`charmm <angle_charmm>` should also be used.
+In case of rigid bonds also bond style :doc:`zero <bond_zero>` and angle
+style :doc:`zero <angle_zero>` can be used.
+
+The table below lists the force field parameters (in real :doc:`units
+<units>`) to for the water molecule atoms to run a rigid or flexible
+TIP3P-CHARMM model with a cutoff, the original 1983 TIP3P model
+:ref:`(Jorgensen) <Jorgensen1>`, or a TIP3P model with parameters
+optimized for a long-range Coulomb solver (e.g. Ewald or PPPM in LAMMPS)
+:ref:`(Price) <Price1>`.   The K values can be used if a flexible TIP3P
+model (without fix shake) is desired, for rigid bonds/angles they are
+ignored.
+
+   .. list-table::
+      :header-rows: 1
+      :widths: auto
+
+      * - Parameter
+        - TIP3P-CHARMM
+        - TIP3P (original)
+        - TIP3P (Ewald)
+      * - O mass (amu)
+        - 15.9994
+        - 15.9994
+        - 15.9994
+      * - H mass (amu)
+        - 1.008
+        - 1.008
+        - 1.008
+      * - O charge (:math:`e`)
+        - -0.834
+        - -0.834
+        - -0.834
+      * - H charge (:math:`e`)
+        - 0.417
+        - 0.417
+        - 0.417
+      * - LJ :math:`\epsilon` of OO (kcal/mole)
+        - 0.1521
+        - 0.1521
+        - 0.1020
+      * - LJ :math:`\sigma` of OO (:math:`\AA`)
+        - 3.1507
+        - 3.1507
+        - 3.188
+      * - LJ :math:`\epsilon` of HH (kcal/mole)
+        - 0.0460
+        - 0.0
+        - 0.0
+      * - LJ :math:`\sigma` of HH (:math:`\AA`)
+        - 0.4
+        - 1.0
+        - 1.0
+      * - LJ :math:`\epsilon` of OH (kcal/mole)
+        - 0.0836
+        - 0.0
+        - 0.0
+      * - LJ :math:`\sigma` of OH (:math:`\AA`)
+        - 1.7753
+        - 1.0
+        - 1.0
+      * - K of OH bond (kcal/mole/:math:`\AA^2`)
+        - 450
+        - 450
+        - 450
+      * - :math:`r_0` of OH bond (:math:`\AA`)
+        - 0.9572
+        - 0.9572
+        - 0.9572
+      * - K of HOH angle (kcal/mole)
+        - 55.0
+        - 55.0
+        - 55.0
+      * - :math:`\theta_0` of HOH angle
+        - 104.52\ :math:`^{\circ}`
+        - 104.52\ :math:`^{\circ}`
+        - 104.52\ :math:`^{\circ}`
+
+Below is the code for a LAMMPS input file and a molecule file
+(``tip3p.mol``) of TIP3P water for use with the :doc:`molecule command
+<molecule>` demonstrating how to set up a small bulk water system for
+TIP3P with rigid bonds.
+
+.. code-block:: LAMMPS
+
+    units real
+    atom_style full
+    region box block -5 5 -5 5 -5 5
+    create_box 2 box bond/types 1 angle/types 1 &
+                extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
+
+    mass 1 15.9994
+    mass 2 1.008
+
+    pair_style lj/cut/coul/cut 8.0
+    pair_coeff 1 1 0.1521 3.1507
+    pair_coeff 2 2 0.0    1.0
+
+    bond_style zero
+    bond_coeff 1 0.9574
+
+    angle_style zero
+    angle_coeff 1 104.52
+
+    molecule water tip3p.mol
+    create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
+
+    fix rigid all shake 0.001 10 10000 b 1 a 1
+    minimize 0.0 0.0 1000 10000
+    run 0 post no
+
+    reset_timestep 0
+    velocity all create 300.0 5463576
+    fix integrate all nvt temp 300 300 1.0
+
+    thermo_style custom step temp press etotal pe
+
+    thermo 1000
+    run 20000
+    write_data tip3p.data nocoeff
+
+.. _tip3p_molecule:
+.. code-block::
+
+   # Water molecule. TIP3P geometry
+
+   3 atoms
+   2 bonds
+   1 angles
+
+   Coords
+
+   1    0.00000  -0.06556   0.00000
+   2    0.75695   0.52032   0.00000
+   3   -0.75695   0.52032   0.00000
+
+   Types
+
+   1        1   # O
+   2        2   # H
+   3        2   # H
+
+   Charges
+
+   1       -0.834
+   2        0.417
+   3        0.417
+
+   Bonds
+
+   1   1      1      2
+   2   1      1      3
+
+   Angles
+
+   1   1      2      1      3
+
+   Shake Flags
+
+   1 1
+   2 1
+   3 1
+
+   Shake Atoms
+
+   1 1 2 3
+   2 1 2 3
+   3 1 2 3
+
+   Shake Bond Types
+
+   1 1 1 1
+   2 1 1 1
+   3 1 1 1
+
+   Special Bond Counts
+
+   1 2 0 0
+   2 1 1 0
+   3 1 1 0
+
+   Special Bonds
+
+   1 2 3
+   2 1 3
+   3 1 2
 
-| O mass = 15.9994
-| H mass = 1.008
-| O charge = -0.830
-| H charge = 0.415
-| LJ :math:`\epsilon` of OO = 0.102
-| LJ :math:`\sigma` of OO = 3.188
-| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
-| K of OH bond = 450
-| :math:`r_0` of OH bond = 0.9572
-| K of HOH angle = 55
-| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
-|
 
 Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
 

doc/src/Howto_tip4p.rst

@@ -2,19 +2,33 @@ TIP4P water model
 =================
 
 The four-point TIP4P rigid water model extends the traditional
-three-point TIP3P model by adding an additional site, usually
+:doc:`three-point TIP3P <Howto_tip3p>` model by adding an additional
-massless, where the charge associated with the oxygen atom is placed.
+site M, usually massless, where the charge associated with the oxygen
-This site M is located at a fixed distance away from the oxygen along
+atom is placed.  This site M is located at a fixed distance away from
-the bisector of the HOH bond angle.  A bond style of *harmonic* and an
+the oxygen along the bisector of the HOH bond angle.  A bond style of
-angle style of *harmonic* or *charmm* should also be used.
+:doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
+<angle_harmonic>` or :doc:`charmm <angle_charmm>` should also be used.
+In case of rigid bonds also bond style :doc:`zero <bond_zero>` and angle
+style :doc:`zero <angle_zero>` can be used.
 
-A TIP4P model is run with LAMMPS using either these commands
+There are two ways to implement TIP4P water in LAMMPS:
-for a cutoff model:
+
+#. Use a specially written pair style that uses the :ref:`TIP3P geometry
+   <tip3p_molecule>` without the point M. The point M location is then
+   implicitly derived from the other atoms or each water molecule and
+   used during the force computation.  The forces on M are then
+   projected on the oxygen and the two hydrogen atoms.  This is
+   computationally very efficient, but the charge distribution in space
+   is only correct within the tip4p labeled styles.  So all other
+   computations using charges will "see" the negative charge incorrectly
+   on the oxygen atom.
+
+   This can be done with the following pair styles for Coulomb with a cutoff:
 
    * :doc:`pair_style tip4p/cut <pair_lj_cut_tip4p>`
    * :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
 
-or these commands for a long-range model:
+   or these commands for a long-range Coulomb treatment:
 
    * :doc:`pair_style tip4p/long <pair_coul>`
    * :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
@@ -31,71 +45,95 @@ 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
+#. Use an :ref:`explicit 4 point TIP4P geometry <tip4p_molecule>` where
-atoms and the water molecule to run a rigid TIP4P model with a cutoff
+   the oxygen atom carries no charge and the M point no Lennard-Jones
-:ref:`(Jorgensen) <Jorgensen5>`.  Note that the OM distance is specified in
+   interactions.  Since :doc:`fix shake <fix_shake>` or :doc:`fix rattle
-the :doc:`pair_style <pair_style>` command, not as part of the pair
+   <fix_shake>` may not be applied to this kind of geometry, :doc:`fix
-coefficients.
+   rigid or fix rigid/small <fix_rigid>` or its thermostatted variants
+   are required to maintain a rigid geometry.  This avoids some of the
+   issues with respect to analysis and non-tip4p styles, but it is a
+   more costly force computation (more atoms in the same volume and thus
+   more neighbors in the neighbor lists) and requires a much shorter
+   timestep for stable integration of the rigid body motion.  Since no
+   bonds or angles are required, they do not need to be defined and atom
+   style charge would be sufficient for a bulk TIP4P water system.  In
+   order to avoid that LAMMPS produces an error due to the massless M
+   site a tiny non-zero mass needs to be assigned.
 
-| O mass = 15.9994
+The table below lists the force field parameters (in real :doc:`units
-| H mass = 1.008
+<units>`) to for a selection of popular variants of the TIP4P model.
-| O charge = -1.040
+There is the rigid TIP4P model with a cutoff :ref:`(Jorgensen)
-| H charge = 0.520
+<Jorgensen5>`, the TIP4/Ice model :ref:`(Abascal1) <Abascal1>`, the
-| :math:`r_0` of OH bond = 0.9572
+TIP4P/2005 model :ref:`(Abascal2) <Abascal2>` and a version of TIP4P
-| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
+parameters adjusted for use with a long-range Coulombic solver
-| OM distance = 0.15
+(e.g. Ewald or PPPM in LAMMPS).  Note that for implicit TIP4P models the
-| LJ :math:`\epsilon` of O-O = 0.1550
+OM distance is specified in the :doc:`pair_style <pair_style>` command,
-| LJ :math:`\sigma` of O-O = 3.1536
+not as part of the pair coefficients.
-| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
-| Coulomb cutoff = 8.5
-|
 
-For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
+   .. list-table::
-https://doi.org/10.1063/1.1931662) these values can be used:
+      :header-rows: 1
+      :widths: auto
 
-| O mass = 15.9994
+      * - Parameter
-| H mass =  1.008
+        - TIP4P (original)
-| O charge = -1.1794
+        - TIP4P/Ice
-| H charge =  0.5897
+        - TIP4P/2005
-| :math:`r_0` of OH bond = 0.9572
+        - TIP4P (Ewald)
-| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
+      * - O mass (amu)
-| OM distance = 0.1577
+        - 15.9994
-| LJ :math:`\epsilon` of O-O = 0.21084
+        - 15.9994
-| LJ :math:`\sigma` of O-O = 3.1668
+        - 15.9994
-| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
+        - 15.9994
-| Coulomb cutoff = 8.5
+      * - H mass (amu)
-|
+        - 1.008
-
+        - 1.008
-For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
+        - 1.008
-https://doi.org/10.1063/1.2121687), these values can be used:
+        - 1.008
-
+      * - O or M charge (:math:`e`)
-| O mass = 15.9994
+        - -1.040
-| H mass =  1.008
+        - -1.1794
-| O charge = -1.1128
+        - -1.1128
-| H charge = 0.5564
+        - -1.04844
-| :math:`r_0` of OH bond = 0.9572
+      * - H charge (:math:`e`)
-| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
+        - 0.520
-| OM distance = 0.1546
+        - 0.5897
-| LJ :math:`\epsilon` of O-O = 0.1852
+        - 0.5564
-| LJ :math:`\sigma` of O-O = 3.1589
+        - 0.52422
-| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
+      * - LJ :math:`\epsilon` of OO (kcal/mole)
-| Coulomb cutoff = 8.5
+        - 0.1550
-|
+        - 0.1577
-
+        - 0.1852
-These are the parameters to use for TIP4P with a long-range Coulombic
+        - 0.16275
-solver (e.g. Ewald or PPPM in LAMMPS):
+      * - LJ :math:`\sigma` of OO (:math:`\AA`)
-
+        - 3.1536
-| O mass = 15.9994
+        - 3.1668
-| H mass = 1.008
+        - 3.1589
-| O charge = -1.0484
+        - 3.16435
-| H charge = 0.5242
+      * - LJ :math:`\epsilon` of HH, MM, OH, OM, HM (kcal/mole)
-| :math:`r_0` of OH bond = 0.9572
+        - 0.0
-| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
+        - 0.0
-| OM distance = 0.1250
+        - 0.0
-| LJ :math:`\epsilon` of O-O = 0.16275
+        - 0.0
-| LJ :math:`\sigma` of O-O = 3.16435
+      * - LJ :math:`\sigma` of HH, MM, OH, OM, HM (:math:`\AA`)
-| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
+        - 1.0
-|
+        - 1.0
+        - 1.0
+        - 1.0
+      * - :math:`r_0` of OH bond (:math:`\AA`)
+        - 0.9572
+        - 0.9572
+        - 0.9572
+        - 0.9572
+      * - :math:`\theta_0` of HOH angle
+        - 104.52\ :math:`^{\circ}`
+        - 104.52\ :math:`^{\circ}`
+        - 104.52\ :math:`^{\circ}`
+        - 104.52\ :math:`^{\circ}`
+      * - OM distance (:math:`\AA`)
+        - 0.15
+        - 0.1577
+        - 0.1546
+        - 0.1250
 
 Note that the when using the TIP4P pair style, the neighbor list cutoff
 for Coulomb interactions is effectively extended by a distance 2 \* (OM
@@ -108,6 +146,117 @@ 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.
 
+Below is the code for a LAMMPS input file using the implicit method and
+the :ref:`TIP3P molecule file <tip3p_molecule>`.  Because the TIP4P
+charges are different from TIP3P they need to be reset (or the molecule
+file changed):
+
+.. code-block:: LAMMPS
+
+    units real
+    atom_style full
+    region box block -5 5 -5 5 -5 5
+    create_box 2 box bond/types 1 angle/types 1 &
+                extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
+
+    mass 1 15.9994
+    mass 2 1.008
+
+    pair_style lj/cut/tip4p/cut 1 2 1 1 0.15 8.0
+    pair_coeff 1 1 0.1550 3.1536
+    pair_coeff 2 2 0.0    1.0
+
+    bond_style zero
+    bond_coeff 1 0.9574
+
+    angle_style zero
+    angle_coeff 1 104.52
+
+    molecule water tip3p.mol  # this uses the TIP3P geometry
+    create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
+    # must change charges for TIP4P
+    set type 1 charge -1.040
+    set type 2 charge  0.520
+
+    fix rigid all shake 0.001 10 10000 b 1 a 1
+    minimize 0.0 0.0 1000 10000
+    run 0 post no
+
+    reset_timestep 0
+    velocity all create 300.0 5463576
+    fix integrate all nvt temp 300 300 1.0
+
+    thermo_style custom step temp press etotal pe
+
+    thermo 1000
+    run 20000
+    write_data tip3p.data nocoeff
+
+Below is the code for a LAMMPS input file using the explicit method and
+a TIP4P molecule file.  Because of using :doc:`fix rigid/nvt/small
+<fix_rigid>` no bonds need to be defined and thus no extra storage needs
+to be reserved for them, but we need to switch to atom style full or use
+:doc:`fix property/atom mol <fix_property_atom>` so that fix
+rigid/nvt/small can identify rigid bodies by their molecule ID:
+
+.. code-block:: LAMMPS
+
+    units real
+    atom_style charge
+    region box block -5 5 -5 5 -5 5
+    create_box 3 box
+
+    mass 1 15.9994
+    mass 2 1.008
+    mass 3 1.0e-100
+
+    pair_style lj/cut/coul/cut 8.0
+    pair_coeff 1 1 0.1550 3.1536
+    pair_coeff 2 2 0.0    1.0
+    pair_coeff 3 3 0.0    1.0
+
+    fix mol all property/atom mol
+    molecule water tip4p.mol
+    create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
+
+    timestep 0.1
+    fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
+    velocity all create 300.0 5463576
+
+    thermo_style custom step temp press etotal density pe ke
+    thermo 1000
+    run 20000
+    write_data tip4p.data nocoeff
+
+.. _tip4p_molecule:
+.. code-block::
+
+   # Water molecule. Explicit TIP4P geometry for use with fix rigid
+
+   4 atoms
+
+   Coords
+
+   1    0.00000  -0.06556   0.00000
+   2    0.75695   0.52032   0.00000
+   3   -0.75695   0.52032   0.00000
+   4    0.00000   0.08444   0.00000
+
+   Types
+
+   1        1   # O
+   2        2   # H
+   3        2   # H
+   4        3   # M
+
+   Charges
+
+   1        0.000
+   2        0.520
+   3        0.520
+   4       -1.040
+
+
 Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
 
 ----------
@@ -116,3 +265,13 @@ Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wik
 
 **(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
 Phys, 79, 926 (1983).
+
+.. _Abascal1:
+
+**(Abascal1)** Abascal, Sanz, Fernandez, Vega, J Chem Phys, 122, 234511 (2005)
+   https://doi.org/10.1063/1.1931662
+
+.. _Abascal2:
+
+**(Abascal2)** Abascal, J Chem Phys, 123, 234505 (2005)
+   https://doi.org/10.1063/1.2121687

doc/src/Howto_tip5p.rst

@@ -0,0 +1,161 @@
+TIP5P water model
+=================
+
+The five-point TIP5P rigid water model extends the :doc:`three-point
+TIP3P model <Howto_tip3p>` by adding two additional sites L, usually
+massless, where the charge associated with the oxygen atom is placed.
+These sites L are located at a fixed distance away from the oxygen atom,
+forming a tetrahedral angle that is rotated by 90 degrees from the HOH
+plane.  Those sites thus somewhat approximate lone pairs of the oxygen
+and consequently improve the water structure to become even more
+"tetrahedral" in comparison to the :doc:`four-point TIP4P model
+<Howto_tip4p>`.
+
+A suitable pair style with cutoff Coulomb would be:
+
+* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
+
+or these commands for a long-range model:
+
+* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
+* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
+* :doc:`kspace_style pppm <kspace_style>`
+* :doc:`kspace_style pppm/disp <kspace_style>`
+
+A TIP5P model *must* be run using a :doc:`rigid fix <fix_rigid>` since
+there is no other option to keep this kind of structure rigid in LAMMPS.
+In order to avoid that LAMMPS produces an error due to the massless L
+sites, those need to be assigned a tiny non-zero mass.
+
+The table below lists the force field parameters (in real :doc:`units
+<units>`) to for a the TIP5P model with a cutoff :ref:`(Mahoney)
+<Mahoney>` and the TIP5P-E model :ref:`(Rick) <Rick>` for use with a
+long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS).
+
+   .. list-table::
+      :header-rows: 1
+      :widths: auto
+
+      * - Parameter
+        - TIP5P
+        - TIP5P-E
+      * - O mass (amu)
+        - 15.9994
+        - 15.9994
+      * - H mass (amu)
+        - 1.008
+        - 1.008
+      * - O charge (:math:`e`)
+        - 0.0
+        - 0.0
+      * - L charge (:math:`e`)
+        - -0.241
+        - -0.241
+      * - H charge (:math:`e`)
+        - 0.241
+        - 0.241
+      * - LJ :math:`\epsilon` of OO (kcal/mole)
+        - 0.1600
+        - 0.1780
+      * - LJ :math:`\sigma` of OO (:math:`\AA`)
+        - 3.1200
+        - 3.0970
+      * - LJ :math:`\epsilon` of HH, LL, OH, OL, HL (kcal/mole)
+        - 0.0
+        - 0.0
+      * - LJ :math:`\sigma` of HH, LL, OH, OL, HL (:math:`\AA`)
+        - 1.0
+        - 1.0
+      * - :math:`r_0` of OH bond (:math:`\AA`)
+        - 0.9572
+        - 0.9572
+      * - :math:`\theta_0` of HOH angle
+        - 104.52\ :math:`^{\circ}`
+        - 104.52\ :math:`^{\circ}`
+      * - OL distance (:math:`\AA`)
+        - 0.70
+        - 0.70
+      * - :math:`\theta_0` of LOL angle
+        - 109.47\ :math:`^{\circ}`
+        - 109.47\ :math:`^{\circ}`
+
+Below is the code for a LAMMPS input file for setting up a simulation of
+TIP5P water with a molecule file.  Because of using :doc:`fix
+rigid/nvt/small <fix_rigid>` no bonds need to be defined and thus no
+extra storage needs to be reserved for them, but we need to switch to
+atom style full or use :doc:`fix property/atom mol <fix_property_atom>`
+so that fix rigid/nvt/small can identify rigid bodies by their molecule
+ID:
+
+.. code-block:: LAMMPS
+
+    units real
+    atom_style charge
+    region box block -5 5 -5 5 -5 5
+    create_box 3 box
+
+    mass 1 15.9994
+    mass 2 1.008
+    mass 3 1.0e-100
+
+    pair_style lj/cut/coul/cut 8.0
+    pair_coeff 1 1 0.160  3.12
+    pair_coeff 2 2 0.0    1.0
+    pair_coeff 3 3 0.0    1.0
+
+    fix mol all property/atom mol
+    molecule water tip5p.mol
+    create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
+
+    timestep 0.20
+    fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
+    reset_timestep 0
+    velocity all create 300.0 5463576
+
+    thermo_style custom step temp press etotal density pe ke
+    thermo 1000
+    run 20000
+    write_data tip5p.data nocoeff
+
+.. _tip5p_molecule:
+.. code-block::
+
+   # Water molecule. Explicit TIP5P geometry for use with fix rigid
+
+   5 atoms
+
+   Coords
+
+   1    0.00000  -0.06556   0.00000
+   2    0.75695   0.52032   0.00000
+   3   -0.75695   0.52032   0.00000
+   4    0.00000  -0.46971   0.57154
+   5    0.00000  -0.46971  -0.57154
+
+   Types
+
+   1        1   # O
+   2        2   # H
+   3        2   # H
+   4        3   # L
+   5        3   # L
+
+   Charges
+
+   1        0.000
+   2        0.241
+   3        0.241
+   4       -0.241
+   5       -0.241
+
+Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
+
+----------
+
+.. _Mahoney:
+
+**(Mahoney)** Mahoney, Jorgensen, J Chem Phys 112, 8910 (2000)
+
+.. _Rick:
+
+**(Rick)** Rick, J Chem Phys 120, 6085 (2004)

doc/src/Howto_triclinic.rst

@@ -150,7 +150,7 @@ option with either of the commands.
 
 Note that if a simulation box has a large tilt factor, LAMMPS will run
 less efficiently, due to the large volume of communication needed to
-acquire ghost atoms around a processor's irregular-shaped sub-domain.
+acquire ghost atoms around a processor's irregular-shaped subdomain.
 For extreme values of tilt, LAMMPS may also lose atoms and generate an
 error.
 

doc/src/Howto_viz.rst

@@ -1,33 +1,21 @@
 Visualize LAMMPS snapshots
 ==========================
 
-LAMMPS itself does not do visualization, but snapshots from LAMMPS
+Snapshots from LAMMPS simulations can be viewed, visualized, and
-simulations can be visualized (and analyzed) in a variety of ways.
+analyzed in a variety of ways.
 
-Mention dump image and dump movie.
+LAMMPS snapshots are created by the :doc:`dump <dump>` command, which
+can create files in several formats. The native LAMMPS dump format is a
+text file (see "dump atom" or "dump custom") which can be visualized by
+`several visualization tools <https://www.lammps.org/viz.html>`_ for MD
+simulation trajectories.  `OVITO <https://www.ovito.org>`_ and `VMD
+<https://www.ks.uiuc.edu/Research/vmd>`_ seem to be the most popular
+choices among them.
 
-LAMMPS snapshots are created by the :doc:`dump <dump>` command which can
+The :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>`
-create files in several formats. The native LAMMPS dump format is a
+styles can output internally rendered images or convert them to a movie
-text file (see "dump atom" or "dump custom") which can be visualized
+during the MD run.
-by several popular visualization tools. The :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>` styles can
-output internally rendered images and convert a sequence of them to a
-movie during the MD run.  Several programs included with LAMMPS as
-auxiliary tools can convert between LAMMPS format files and other
-formats.  See the :doc:`Tools <Tools>` page for details.
 
-A Python-based toolkit distributed by our group can read native LAMMPS
+Programs included with LAMMPS as auxiliary tools can convert
-dump files, including custom dump files with additional columns of
+between LAMMPS format files and other formats.  See the :doc:`Tools
-user-specified atom information, and convert them to various formats or
+<Tools>` page for details.  These are rarely needed these days.
-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
-snapshots.
-
-.. _pizza: https://lammps.github.io/pizza
-
-.. _ensight: https://www.ansys.com/products/fluids/ansys-ensight
-
-.. _atomeye: http://li.mit.edu/Archive/Graphics/A/

doc/src/Howto_wsl.rst

@@ -11,12 +11,14 @@ LAMMPS in workshop settings, we had to redirect Windows users to
 Linux Virtual Machines such as VirtualBox or Unix-like compilation with
 Cygwin.
 
-With the latest updates in Windows 10 (Version 2004, Build 19041 or higher),
+With the latest updates in Windows 10 (Version 2004, Build 19041 or
-Microsoft has added a new way to work on Linux-based code. The Windows
+higher), Microsoft has added a new way to work on Linux-based code. The
-Subsystem for Linux (WSL). With WSL Version 2, you now get a Linux Virtual
+`Windows Subsystem for Linux (WSL)
-Machine that transparently integrates into Windows. All you need is to ensure
+<https://learn.microsoft.com/en-us/windows/wsl/>`_.  With WSL Version 2,
-you have the latest Windows updates installed and enable this new feature.
+you now get a Linux Virtual Machine that transparently integrates into
-Linux VMs are then easily installed using the Microsoft Store.
+Windows.  All you need is to ensure you have the latest Windows updates
+installed and enable this new feature.  Linux VMs are then easily
+installed using the Microsoft Store.
 
 In this tutorial, I'll show you how to set up and compile LAMMPS for both serial
 and MPI usage in WSL2.

doc/src/Install.rst

@@ -18,6 +18,8 @@ you **must** build LAMMPS from the source code.
    developers have no control over their choices of how they configure
    and build their packages and when they update them.
 
+----
+
 .. toctree::
    :maxdepth: 1
 
@@ -29,38 +31,40 @@ you **must** build LAMMPS from the source code.
    Install_tarball
    Install_git
 
-These are the files and sub-directories in the LAMMPS distribution:
+----
 
-+------------+-------------------------------------------+
+These are the files and subdirectories in the LAMMPS distribution:
+
++------------+---------------------------------------------+
 | README     | Short description of the LAMMPS package     |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
 | LICENSE    | GNU General Public License (GPL)            |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
-| SECURITY.md| Security Policy for the LAMMPS package    |
+| SECURITY.md| Security policy for the LAMMPS package      |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
-| bench      | benchmark problems                        |
+| bench      | benchmark inputs                            |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
 | cmake      | CMake build files                           |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
-| doc        | documentation                             |
+| doc        | documentation and tools to build the manual |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
-| examples   | simple test problems                      |
+| examples   | example input files                         |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
-| fortran    | Fortran wrapper for LAMMPS                |
+| fortran    | Fortran module for LAMMPS library interface |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
 | lib        | additional provided or external libraries   |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
-| potentials | interatomic potential files               |
+| potentials | selected interatomic potential files        |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
-| python     | Python wrappers for LAMMPS                |
+| python     | Python module for LAMMPS library interface  |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
-| src        | source files                              |
+| src        | LAMMPS source files                         |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
 | tools      | pre- and post-processing tools              |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
-| unittest   | sources and inputs for testing LAMMPS     |
+| unittest   | source code and inputs for testing LAMMPS   |
-+------------+-------------------------------------------+
++------------+---------------------------------------------+
 
-You will have all of these if you download source.  You will only have
+You will have all of these if you downloaded the LAMMPS source code.
-some of them if you download executables, as explained on the pages
+You will have only some of them if you downloaded executables, as
-listed above.
+explained on the pages listed above.

doc/src/Install_conda.rst

@@ -1,7 +1,7 @@
 Download an executable for Linux or Mac via Conda
 -------------------------------------------------
 
-Pre-compiled LAMMPS binaries are available for macOS or Linux via the
+Pre-compiled LAMMPS binaries are available for macOS and Linux via the
 `Conda <conda_>`_ package management system.
 
 First, one must set up the Conda package manager on your system.  Follow the
@@ -21,19 +21,19 @@ Then, you can install LAMMPS on your system with the following command:
    conda activate my-lammps-env
    conda install lammps
 
-The LAMMPS binary is built with the :ref:`KIM package <kim>` which
+The LAMMPS binary is built with the :ref:`KIM package <kim>`, which
 results in Conda also installing the `kim-api` binaries when LAMMPS is
-installed.  In order to use potentials from `openkim.org <openkim_>`_, you can
+installed.  In order to use potentials from `openkim.org <openkim_>`_,
-install the `openkim-models` package
+you can install the `openkim-models` package
 
 .. code-block:: bash
 
    conda install openkim-models
 
-If you have problems with the installation you can post issues to
+If you have problems with the installation, you can post issues to `this
-`this link <conda_forge_lammps_>`_.
+link <conda_forge_lammps_>`_.  Thanks to Jan Janssen
-Thanks to Jan Janssen (Max-Planck-Institut fuer Eisenforschung) for setting
+(Max-Planck-Institut fuer Eisenforschung) for setting up the Conda
-up the Conda capability.
+capability.
 
 .. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues
 .. _openkim: https://openkim.org

doc/src/Install_git.rst

@@ -1,16 +1,16 @@
 Download the LAMMPS source with git
 -----------------------------------
 
-All LAMMPS development is coordinated through the "LAMMPS GitHub
+LAMMPS development is coordinated through the "LAMMPS GitHub site".
-site".  If you clone the LAMMPS repository onto your local machine, it
+If you clone the LAMMPS repository onto your local machine, it has
-has several advantages:
+several advantages:
 
 * You can stay current with changes to LAMMPS with a single git
   command.
 * You can create your own development branches to add code to LAMMPS.
 * You can submit your new features back to GitHub for inclusion in
-  LAMMPS.  For that you should first create your own :doc:`fork on
+  LAMMPS.  For that, you should first create your own :doc:`fork on
-  GitHub <Howto_github>`.
+  GitHub <Howto_github>`, though.
 
 You must have `git <git_>`_ installed on your system to use the
 commands explained below to communicate with the git servers on
@@ -26,15 +26,18 @@ provides `limited support for subversion clients <svn_>`_.
 .. _git: https://git-scm.com
 .. _svn: https://help.github.com/en/github/importing-your-projects-to-github/working-with-subversion-on-github
 
-You can follow the LAMMPS development on 3 different git branches:
+You can follow the LAMMPS development on 4 different git branches:
 
-* **stable**   :  this branch is updated from the *release* branch with
+* **release**  :  this branch is updated with every patch or feature release;
-  every stable release version and also has selected bug fixes and updates
+  updates are always "fast-forward" merges from *develop*
-  back-ported from the *develop* branch
-* **release**  :  this branch is updated with every patch release;
-  updates are always "fast forward" merges from *develop*
 * **develop**  :  this branch follows the ongoing development and
   is updated with every merge commit of a pull request
+* **stable**   :  this branch is updated from the *release* branch with
+  every stable release version and also has selected bug fixes with every
+  update release when the *maintenance* branch is merged into it
+* **maintenance**  :  this branch collects back-ported bug fixes from the
+  *develop* branch to the *stable* branch. It is used to update *stable*
+  for update releases and it synchronized with *stable* at each stable release.
 
 To access the git repositories on your box, use the clone command to
 create a local copy of the LAMMPS repository with a command like:
@@ -58,19 +61,19 @@ between them at any time using "git checkout <branch name>".)
    commit history (most people don't), you can speed up the "cloning"
    process and reduce local disk space requirements by using the
    *--depth* git command line flag.  That will create a "shallow clone"
-   of the repository containing only a subset of the git history.  Using
+   of the repository, which contains only a subset of the git history.
-   a depth of 1000 is usually sufficient to include the head commits of
+   Using a depth of 1000 is usually sufficient to include the head
-   the *develop* and the *release* branches.  To include the head commit
+   commits of the *develop*, the *release*, and the *maintenance*
-   of the *stable* branch you may need a depth of up to 10000.  If you
+   branches.  To include the head commit of the *stable* branch you may
-   later need more of the git history, you can always convert the
+   need a depth of up to 10000.  If you later need more of the git
-   shallow clone into a "full clone".
+   history, you can always convert the shallow clone into a "full
+   clone".
 
 Once the command completes, your directory will contain the same files
 as if you unpacked a current LAMMPS tarball, with the exception, that
-the HTML documentation files are not included.  They can be fetched
+the HTML documentation files are not included. They can be generated
-from the LAMMPS website by typing ``make fetch`` in the doc directory.
+from the content provided in ``doc/src`` by typing ``make html`` from
-Or they can be generated from the content provided in ``doc/src`` by
+the ``doc`` directory.
-typing ``make html`` from the ``doc`` directory.
 
 After initial cloning, as bug fixes and new features are added to
 LAMMPS you can stay up-to-date by typing the following git commands
@@ -79,16 +82,17 @@ from within the "mylammps" directory:
 .. code-block:: bash
 
    git checkout release      # not needed if you always stay in this branch
-   git checkout stable       # use one of these 3 checkout commands
+   git checkout stable       # use one of these 4 checkout commands
    git checkout develop      # to choose the branch to follow
+   git checkout maintenance
    git pull
 
 Doing a "pull" will not change any files you have added to the LAMMPS
-directory structure.  It will also not change any existing LAMMPS
+directory structure.  It will also not change any existing LAMMPS files
-files you have edited, unless those files have changed in the
+you have edited, unless those files have changed in the repository.  In
-repository.  In that case, git will attempt to merge the new
+that case, git will attempt to merge the changes from the repository
-repository file with your version of the file and tell you if there
+file with your version of the file and tell you if there are any
-are any conflicts.  See the git documentation for details.
+conflicts.  See the git documentation for details.
 
 If you want to access a particular previous release version of LAMMPS,
 you can instead "check out" any version with a published tag. See the
@@ -145,24 +149,24 @@ changed.  How to do this depends on the build system you are using.
       to enforce consistency of the source between the src folder
       and package directories.  This is OK to do even if you don't
       use any packages. The ``make purge`` command removes any deprecated
-      src files if they were removed by the patch from a package
+      src files if they were removed by the update from a package
-      sub-directory.
+      subdirectory.
 
       .. warning::
 
          If you wish to edit/change a src file that is from a package,
          you should edit the version of the file inside the package
-         sub-directory with src, then re-install the package.  The
+         subdirectory with src, then re-install the package.  The
          version in the source directory is merely a copy and will be
          wiped out if you type "make package-update".
 
 .. admonition:: Git protocols
    :class: note
 
-   The servers at github.com support the "https://" access protocol for
+   The servers at github.com support the "https" access protocol for
    anonymous, read-only access.  If you have a suitably configured
    GitHub account, you may also use SSH protocol with the URL
-   "git@github.com:lammps/lammps.git".
+   ``git@github.com:lammps/lammps.git``.
 
-The LAMMPS GitHub project is currently managed by Axel Kohlmeyer
+The LAMMPS GitHub project is currently overseen by Axel Kohlmeyer
 (Temple U, akohlmey at gmail.com).

doc/src/Install_linux.rst

@@ -3,7 +3,8 @@ Download an executable for Linux
 
 Binaries are available for different versions of Linux:
 
-- :ref:`Pre-built Ubuntu Linux executables <ubuntu>`
+- :ref:`Pre-built static Linux x86_64 executables <static>`
+- :ref:`Pre-built Ubuntu and Debian Linux executables <ubuntu>`
 - :ref:`Pre-built Fedora Linux executables <fedora>`
 - :ref:`Pre-built EPEL Linux executables (RHEL, CentOS) <epel>`
 - :ref:`Pre-built OpenSuse Linux executables <opensuse>`
@@ -14,21 +15,50 @@ Binaries are available for different versions of Linux:
 
    If you have questions about these pre-compiled LAMMPS executables,
    you need to contact the people preparing those packages.  The LAMMPS
-   developers have no control over their choices of how they configure
+   developers have no control over how they configure and build their
-   and build their packages and when they update them.
+   packages and when they update them.  They may only provide packages
+   for stable release versions and not always update the packages in a
+   timely fashion after a new LAMMPS release is made.
+
+----------
+
+.. _static:
+
+Pre-built static Linux x86_64 executables
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Pre-built LAMMPS executables for Linux, that are statically linked and
+compiled for 64-bit x86 CPUs (x86_64 or AMD64) are available for download
+at `https://download.lammps.org/static/ <https://download.lammps.org/static/>`_.
+Because of that static linkage (and unlike the Linux distribution specific
+packages listed below), they do not depend on any installed software and
+thus should run on *any* 64-bit x86 machine with *any* Linux version.
+
+These executable include most of the available packages and multi-thread
+parallelization (via INTEL, KOKKOS, or OPENMP package).  They are **not**
+compatible with MPI.  Several of the LAMMPS tools executables (e.g. ``msi2lmp``)
+and the ``lammps-shell`` program are included as well.  Because of the
+static linkage, there is no ``liblammps.so`` library file and thus also the
+LAMMPS python module, which depends on it, is not included.
+
+The compressed tar archives available for download have names following
+the pattern ``lammps-linux-x86_64-<version>.tar.gz`` and will all unpack
+into a ``lammps-static`` folder.  The executables are then in the
+``lammps-static/bin/`` folder.  Since they do not depend on any other
+software, they may be freely moved or copied around.
 
 ----------
 
 .. _ubuntu:
 
-Pre-built Ubuntu Linux executables
+Pre-built Ubuntu and Debian Linux executables
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-A pre-built LAMMPS executable suitable for running on the latest Ubuntu
+A pre-built LAMMPS executable, suitable for running on the latest Ubuntu
-Linux versions, can be downloaded as a Debian package.  This allows you
+and Debian Linux versions, can be downloaded as a Debian package.  This
-to install LAMMPS with a single command, and stay (mostly) up-to-date
+allows you to install LAMMPS with a single command, and stay (mostly)
-with the current stable version of LAMMPS by simply updating your
+up-to-date with the current stable version of LAMMPS by simply updating
-operating system.
+your operating system.
 
 To install LAMMPS do the following once:
 
@@ -38,8 +68,22 @@ To install LAMMPS do the following once:
 
 This downloads an executable named ``lmp`` to your box and multiple
 packages with supporting data, examples and libraries as well as any
-missing dependencies.  This executable can then be used in the usual way
+missing dependencies.  For example, the LAMMPS binary in this package is
-to run input scripts:
+built with the :ref:`KIM package <kim>` enabled, which results in the
+above command also installing the ``kim-api`` binaries when LAMMPS is
+installed, unless they were installed already.  In order to use
+potentials from `openkim.org <openkim_>`_, you can also install the
+``openkim-models`` package:
+
+.. code-block:: bash
+
+   sudo apt-get install openkim-models
+
+Or use the `KIM-API commands <https://openkim.org/doc/usage/obtaining-models/#installing_api>`_
+to download and install individual models.
+
+This LAMMPS executable can then be used in the usual way to run input
+scripts:
 
 .. code-block:: bash
 
@@ -51,20 +95,9 @@ To update LAMMPS to the latest packaged version, do the following:
 
    sudo apt-get update
 
-which will also update other packages on your system.
+This will also update other packages on your system.
 
-The ``lmp`` binary is built with the :ref:`KIM package <kim>` included,
+To uninstall LAMMPS, do the following:
-which results in the above command also installing the ``kim-api``
-binaries when LAMMPS is installed.  In order to use potentials from
-`openkim.org <openkim_>`_, you can also install the ``openkim-models``
-package
-
-.. code-block:: bash
-
-   sudo apt-get install openkim-models
-
-Or use the KIM-API commands to download and install individual models.
-To un-install LAMMPS, do the following:
 
 .. code-block:: bash
 
@@ -83,8 +116,9 @@ Ubuntu package capability.
 Pre-built Fedora Linux executables
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pre-built LAMMPS packages for stable releases are available in the
+Pre-built `LAMMPS packages for stable releases
-Fedora Linux distribution as of Fedora version 28. The packages can be
+<https://packages.fedoraproject.org/pkgs/lammps/>`_ are available in the
+Fedora Linux distribution since Fedora version 28. The packages can be
 installed via the dnf package manager. There are 3 basic varieties
 (lammps = no MPI, lammps-mpich = MPICH MPI library, lammps-openmpi =
 OpenMPI MPI library) and for each support for linking to the C library
@@ -109,7 +143,7 @@ To install LAMMPS with OpenMPI and run an input ``in.lj`` with 2 CPUs do:
 
 The ``dnf install`` command is needed only once.  In case of a new LAMMPS
 stable release, ``dnf update`` will automatically update to the newer
-version as soon at the RPM files are built and uploaded to the download
+version as soon as the RPM files are built and uploaded to the download
 mirrors. The ``module load`` command is needed once per (shell) session
 or shell terminal instance, unless it is automatically loaded from the
 shell profile.
@@ -165,7 +199,7 @@ in OpenSuse as of Leap 15.0. You can install the package with:
    zypper install lammps
 
 This includes support for OpenMPI. The name of the LAMMPS executable
-is ``lmp``. Thus to run an input in parallel on 2 CPUs you would do:
+is ``lmp``. To run an input in parallel on 2 CPUs you would do:
 
 .. code-block:: bash
 
@@ -192,17 +226,18 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
 Gentoo Linux executable
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-LAMMPS is part of Gentoo's main package tree and can be installed by
+LAMMPS is part of `Gentoo's main package tree
-typing:
+<https://packages.gentoo.org/packages/sci-physics/lammps>`_ and can be
+installed by typing:
 
 .. code-block:: bash
 
    emerge --ask lammps
 
-Note that in Gentoo the LAMMPS source is downloaded and the package is
+Note that in Gentoo the LAMMPS source code is downloaded and the package is
-built on the your machine.
+then compiled and installed on your machine.
 
-Certain LAMMPS packages can be enable via USE flags, type
+Certain LAMMPS packages can be enabled via USE flags, type
 
 .. code-block:: bash
 
@@ -221,8 +256,11 @@ Archlinux build-script
 ^^^^^^^^^^^^^^^^^^^^^^
 
 LAMMPS is available via Arch's unofficial Arch User repository (AUR).
-There are three scripts available, named lammps, lammps-beta and lammps-git.
+There are three scripts available, named `lammps
-They respectively package the stable, patch and git releases.
+<https://aur.archlinux.org/packages/lammps>`_, `lammps-beta
+<https://aur.archlinux.org/packages/lammps>`_ and `lammps-git
+<https://aur.archlinux.org/packages/lammps>`_.  They respectively
+package the stable, feature, and git releases.
 
 To install, you will need to have the git package installed. You may use
 any of the above names in-place of lammps.
@@ -234,9 +272,9 @@ any of the above names in-place of lammps.
    makepkg -s
    makepkg -i
 
-To update, you may repeat the above, or change into the cloned directory,
+To update LAMMPS, you may repeat the above, or change into the cloned
-and execute the following, after which, if there are any changes, you may
+directory, and execute the following, after which, if there are any
-use makepkg as above.
+changes, you may use makepkg as above.
 
 .. code-block:: bash
 
@@ -244,12 +282,5 @@ use makepkg as above.
 
 Alternatively, you may use an AUR helper to install these packages.
 
-Note that the AUR provides build-scripts that download the source and
+Note that the AUR provides build-scripts that download the source code
-the build the package on your machine.
+and then build and install the package on your machine.
-
-.. note::
-
-   It looks like the Arch Linux AUR repository build scripts for LAMMPS
-   have not been updated since the 29 October 2020 version.  You may want
-   to consider installing a more current version of LAMMPS from source
-   directly.

doc/src/Install_mac.rst

@@ -2,10 +2,11 @@ Download an executable for Mac
 ------------------------------
 
 LAMMPS can be downloaded, built, and configured for OS X on a Mac with
-`Homebrew <homebrew_>`_.  (Alternatively, see the install instructions for
+`Homebrew <homebrew_>`_.  (Alternatively, see the installation
-:doc:`Download an executable via Conda <Install_conda>`.)  The following LAMMPS
+instructions for :doc:`downloading an executable via Conda
-packages are unavailable at this time because of additional needs not yet met:
+<Install_conda>`.)  The following LAMMPS packages are unavailable at
-GPU, KOKKOS, LATTE, MSCG, MPIIO, POEMS, VORONOI.
+this time because of additional requirements not yet met: GPU, KOKKOS,
+LATTE, MSCG, MPIIO, POEMS, VORONOI.
 
 After installing Homebrew, you can install LAMMPS on your system with
 the following commands:
@@ -24,16 +25,16 @@ Lennard-Jones benchmark file:
 
    brew test lammps -v
 
-The LAMMPS binary is built with the :ref:`KIM package <kim>` which
+The LAMMPS binary is built with the :ref:`KIM package <kim>`, which
-results in Homebrew also installing the `kim-api` binaries when LAMMPS is
+results in Homebrew also installing the `kim-api` binaries when LAMMPS
-installed.  In order to use potentials from `openkim.org <openkim_>`_, you can
+is installed.  In order to use potentials from `openkim.org
-install the `openkim-models` package
+<openkim_>`_, you can install the `openkim-models` package
 
 .. code-block:: bash
 
    brew install openkim-models
 
-If you have problems with the installation you can post issues to
+If you have problems with the installation, you can post issues to
 `this link <https://github.com/Homebrew/homebrew-core/issues>`_.
 
 .. _homebrew: https://brew.sh

doc/src/Install_tarball.rst

@@ -9,17 +9,19 @@ of the `LAMMPS website <lws_>`_.
 .. _older: https://download.lammps.org/tars/
 .. _lws: https://www.lammps.org
 
-You have two choices of tarballs, either the most recent stable
+You have two choices of tarballs, either the most recent stable release
-release or the most current patch release.  Stable releases occur a
+or the most recent feature release.  Stable releases occur a few times
-few times per year, and undergo more testing before release.  Patch
+per year, and undergo more testing before release.  Also, between stable
-releases occur a couple times per month.  The new contents in all
+releases bug fixes from the feature releases are back-ported and the
-releases are listed on the `bug and feature page <bug_>`_ of the website.
+tarball occasionally updated.  Feature releases occur every 4 to 8
+weeks.  The new contents in all feature releases are listed on the `bug
+and feature page <bug_>`_ of the LAMMPS homepage.
 
 Both tarballs include LAMMPS documentation (HTML and PDF files)
-corresponding to that version.  The download page also has an option
+corresponding to that version.
-to download the current-version LAMMPS documentation by itself.
 
-Older versions of LAMMPS can also be downloaded from `this page <older_>`_.
+Tarballs of older LAMMPS versions can also be downloaded from `this page
+<older_>`_.
 
 Once you have a tarball, unzip and untar it with the following
 command:
@@ -36,13 +38,13 @@ in its name, e.g. lammps-23Jun18.
 You can also download a compressed tar or zip archives from the
 "Assets" sections of the `LAMMPS GitHub releases site <git_>`_.
 The file name will be lammps-<version>.zip which can be unzipped
-with the following command, to create a lammps-<version> dir:
+with the following command, to create a lammps-<version> directory:
 
 .. code-block:: bash
 
    unzip lammps*.zip
 
-This version corresponds to the selected LAMMPS patch or stable
+This version corresponds to the selected LAMMPS feature or stable
 release.
 
 .. _git: https://github.com/lammps/lammps/releases

doc/src/Install_windows.rst

@@ -17,11 +17,12 @@ install the Windows MPI package (MPICH2 from Argonne National Labs),
 needed to run in parallel with MPI.
 
 The LAMMPS binaries contain *all* :doc:`optional packages <Packages>`
-included in the source distribution except: KIM, KOKKOS, MSCG, PYTHON,
+included in the source distribution except: ADIOS, H5MD, KIM, ML-PACE,
-ADIOS, H5MD, NETCDF, QMMM, ML-QUIP, and VTK.
+ML-QUIP, MSCG, NETCDF, PLUMED, QMMM, SCAFACOS, and VTK.  The serial
-The serial version also does not include the MPIIO and
+version also does not include the MPIIO and LATBOLTZ packages.  The
-LATBOLTZ packages.  The GPU package is compiled for OpenCL with
+PYTHON package is only available in the Python installers that bundle a
-mixed precision kernels.
+Python runtime.  The GPU package is compiled for OpenCL with mixed
+precision kernels.
 
 The LAMMPS library is compiled as a shared library and the
 :doc:`LAMMPS Python module <Python_module>` is installed, so that
@@ -33,7 +34,7 @@ Windows, once it is installed, in both serial and parallel.
 When you download the installer package, you run it on your Windows
 machine.  It will then prompt you with a dialog, where you can choose
 the installation directory, unpack and copy several executables,
-potential files, documentation pdfs, selected example files, etc.  It
+potential files, documentation PDFs, selected example files, etc.  It
 will then update a few system settings (e.g. PATH, LAMMPS_POTENTIALS)
 and add an entry into the Start Menu (with references to the
 documentation, LAMMPS homepage and more).  From that menu, there is
@@ -41,10 +42,10 @@ also a link to an uninstaller that removes the files and undoes the
 environment manipulations.
 
 Note that to update to a newer version of LAMMPS, you should typically
-uninstall the version you currently have, download a new installer,
+uninstall the version you currently have, download a new installer, and
-and go through the install procedure described above.  I.e. the same
+go through the installation procedure described above.  I.e. the same
 procedure for installing/updating most Windows programs.  You can
-install multiple versions of LAMMPS (in different directories), but
+install multiple versions of LAMMPS (in different directories), but only
-only the executable for the last-installed package will be found
+the executable for the last-installed package will be found
 automatically, so this should only be done for debugging purposes.