Merge pull request #3633 from akohlmey/next_patch_release

Update versions strings for the next patch release

.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

.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 +30,19 @@ for unicode characters and only all-ASCII source code is accepted.
 
 # Version Updates
 
-LAMMPS follows continuous release development model.  We aim to keep to
-keep the development version (develop branch) always fully functional
-and employ a variety of automatic testing procedures to detect failures
+LAMMPS follows a continuous release development model.  We aim to keep
+the development version (`develop` branch) always fully functional and
+employ a variety of automatic testing procedures to detect failures
 of existing functionality from adding or modifying features.  Most of
-those tests are run on pull requests *before* merging to the development
-branch.  The develop branch is protected, so all changes *must* be
+those tests are run on pull requests *before* merging to the `develop`
+branch.  The `develop` branch is protected, so all changes *must* be
 submitted as a pull request and thus cannot avoid the automated tests.
 
 Additional tests are run *after* merging.  Before releases are made
 *all* tests must have cleared.  Then a release tag is applied and the
-release branch fast-forwarded to that tag.  Bug fixes and updates are
-applied to the current development branch and thus will be available in
-the next (patch) release.  For stable releases, selected bug fixes are
-back-ported and occasionally published as update releases.  There are
-only updates to the latest stable release.
+`release` branch is fast-forwarded to that tag.  This is often referred
+to as a patch release. Bug fixes and updates are
+applied first to the `develop` branch.  Later, they appear in the `release`
+branch when the next patch release occurs.
+For stable releases, selected bug fixes, updates, and new functionality
+are pushed to the `stable` branch and a new stable tag is applied.

cmake/CMakeLists.txt

@@ -3,6 +3,7 @@
 # This file is part of LAMMPS
 # Created by Christoph Junghans and Richard Berger
 cmake_minimum_required(VERSION 3.10)
+########################################
 # set policy to silence warnings about ignoring <PackageName>_ROOT but use it
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
@@ -20,7 +21,13 @@ endif()
 if(POLICY CMP0135)
   cmake_policy(SET CMP0135 OLD)
 endif()
-
+########################################
+# Use CONFIGURE_DEPENDS as option for file(GLOB...) when available
+if(CMAKE_VERSION VERSION_LESS 3.12)
+  unset(CONFIGURE_DEPENDS)
+else()
+  set(CONFIGURE_DEPENDS CONFIGURE_DEPENDS)
+endif()
 ########################################
 
 project(lammps CXX)
@@ -161,8 +168,8 @@ endif()
 ########################################################################
 # User input options                                                   #
 ########################################################################
-# set path to python interpreter and thus enforcing python version if
-# when in a virtual environment and PYTHON_EXECUTABLE is not set on command line
+# set path to python interpreter and thus enforcing python version when
+# 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")
@@ -195,8 +202,8 @@ else()
 endif()
 
 include(GNUInstallDirs)
-file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
-file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
+file(GLOB ALL_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
+file(GLOB MAIN_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
 add_library(lammps ${ALL_SOURCES})
 
@@ -251,6 +258,7 @@ set(STANDARD_PACKAGES
   KSPACE
   LATBOLTZ
   LATTE
+  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY
@@ -440,16 +448,12 @@ if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_LATTE OR
     find_package(BLAS)
   endif()
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
-    include(CheckGeneratorSupport)
-    if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
-      status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
-    endif()
-    enable_language(Fortran)
-    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
-    add_library(linalg STATIC ${LAPACK_SOURCES})
+    file(GLOB LINALG_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
+    add_library(linalg STATIC ${LINALG_SOURCES})
     set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
     set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
     set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
+    target_link_libraries(lammps PRIVATE linalg)
   else()
     list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
   endif()
@@ -517,7 +521,7 @@ else()
 endif()
 
 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)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MSCG COMPRESS ML-PACE LEPTON)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -562,6 +566,8 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
 ########################################################
 # Fetch missing external files and archives for 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})
@@ -574,8 +580,8 @@ endforeach()
 foreach(PKG ${STANDARD_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
-  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
-  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
+  file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+  file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -602,8 +608,8 @@ endforeach()
 foreach(PKG ${SUFFIX_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
-  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
-  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
+  file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+  file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -614,18 +620,11 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
+foreach(PKG_LIB POEMS ATC AWPMD H5MD)
   if(PKG_${PKG_LIB})
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
-    if(PKG_LIB STREQUAL "mesont")
-      enable_language(Fortran)
-      file(GLOB_RECURSE ${PKG_LIB}_SOURCES
-        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
-    else()
-      file(GLOB_RECURSE ${PKG_LIB}_SOURCES
-        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
-        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
-    endif()
+    file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${CONFIGURE_DEPENDS}
+      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
     add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
     set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
     target_link_libraries(lammps PRIVATE ${PKG_LIB})
@@ -894,6 +893,23 @@ 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")
@@ -905,6 +921,7 @@ feature_summary(DESCRIPTION "The following tools and libraries have been found a
 message(STATUS "<<< Build configuration >>>
    LAMMPS Version:   ${PROJECT_VERSION}
    Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
+   CMake Version:    ${CMAKE_VERSION}
    Build type:       ${LAMMPS_BUILD_TYPE}
    Install path:     ${CMAKE_INSTALL_PREFIX}
    Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
@@ -990,6 +1007,12 @@ 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/CMakeSettings.json

@@ -72,7 +72,7 @@
       "configurationType": "Debug",
       "buildRoot": "${workspaceRoot}\\build\\${name}",
       "installRoot": "${workspaceRoot}\\install\\${name}",
-      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe -DBUILD_MPI=off",
       "buildCommandArgs": "",
       "ctestCommandArgs": "",
       "inheritEnvironments": [ "clang_cl_x64" ],
@@ -105,7 +105,7 @@
       "configurationType": "Release",
       "buildRoot": "${workspaceRoot}\\build\\${name}",
       "installRoot": "${workspaceRoot}\\install\\${name}",
-      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe -DBUILD_MPI=off",
       "buildCommandArgs": "",
       "ctestCommandArgs": "-V",
       "inheritEnvironments": [ "clang_cl_x64" ],
@@ -305,4 +305,4 @@
       ]
     }
   ]
-}
+}

cmake/Modules/Documentation.cmake

@@ -17,7 +17,7 @@ if(BUILD_DOC)
   endif()
   find_package(Doxygen 1.8.10 REQUIRED)
 
-  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
+  file(GLOB DOC_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
 
   add_custom_command(
@@ -56,16 +56,27 @@ 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 ${MATHJAX_URL}
-      "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
-      EXPECTED_MD5 ${MATHJAX_MD5})
+    if(EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
+      file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
+    endif()
+    if(NOT "${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 ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
+    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)
   endif()
 

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)
-  message(STATUS "Downloading ${url}")
-  file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
+  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} 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

@@ -65,7 +65,7 @@ endfunction(validate_option)
 
 # helper function for getting the most recently modified file or folder from a glob pattern
 function(get_newest_file path variable)
-  file(GLOB _dirs ${path})
+  file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
   set(_besttime 2000-01-01T00:00:00)
   set(_bestfile "<unknown>")
   foreach(_dir ${_dirs})

cmake/Modules/LAMMPSUtils.cmake

@@ -41,7 +41,7 @@ endfunction()
 
 # helper function for getting the most recently modified file or folder from a glob pattern
 function(get_newest_file path variable)
-  file(GLOB _dirs ${path})
+  file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
   set(_besttime 2000-01-01T00:00:00)
   set(_bestfile "<unknown>")
   foreach(_dir ${_dirs})
@@ -80,8 +80,8 @@ endfunction()
 
 function(check_for_autogen_files source_dir)
     message(STATUS "Running check for auto-generated files from make-based build system")
-    file(GLOB SRC_AUTOGEN_FILES ${source_dir}/style_*.h)
-    file(GLOB SRC_AUTOGEN_PACKAGES ${source_dir}/packages_*.h)
+    file(GLOB SRC_AUTOGEN_FILES ${CONFIGURE_DEPENDS} ${source_dir}/style_*.h)
+    file(GLOB SRC_AUTOGEN_PACKAGES ${CONFIGURE_DEPENDS} ${source_dir}/packages_*.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
     foreach(_SRC ${SRC_AUTOGEN_FILES})
@@ -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}))
-    message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be build with the ${PKG2} package")
+  if(DEFINED BUILD_${PKG2})
+    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()
 
@@ -118,25 +125,27 @@ endfunction(GenerateBinaryHeader)
 
 # fetch missing potential files
 function(FetchPotentials pkgfolder potfolder)
-  if(EXISTS "${pkgfolder}/potentials.txt")
-    file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
-    foreach(line ${linelist})
-      string(FIND ${line} " " blank)
-      math(EXPR plusone "${blank}+1")
-      string(SUBSTRING ${line} 0 ${blank} pot)
-      string(SUBSTRING ${line} ${plusone} -1 sum)
-      if(EXISTS "${LAMMPS_POTENTIALS_DIR}/${pot}")
-        file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
-      endif()
-      if(NOT sum STREQUAL oldsum)
-        message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
-        string(MD5 TMP_EXT "${CMAKE_BINARY_DIR}")
-        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 "${LAMMPS_POTENTIALS_DIR}")
-        file(RENAME "${LAMMPS_POTENTIALS_DIR}/${pot}.${TMP_EXT}" "${LAMMPS_POTENTIALS_DIR}/${pot}")
-      endif()
-    endforeach()
+  if(DOWNLOAD_POTENTIALS)
+    if(EXISTS "${pkgfolder}/potentials.txt")
+      file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
+      foreach(line ${linelist})
+        string(FIND ${line} " " blank)
+        math(EXPR plusone "${blank}+1")
+        string(SUBSTRING ${line} 0 ${blank} pot)
+        string(SUBSTRING ${line} ${plusone} -1 sum)
+        if(EXISTS "${LAMMPS_POTENTIALS_DIR}/${pot}")
+          file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
+        endif()
+        if(NOT sum STREQUAL oldsum)
+          message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
+          string(RANDOM LENGTH 10 TMP_EXT)
+          file(DOWNLOAD "${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}")
+          file(RENAME "${LAMMPS_POTENTIALS_DIR}/${pot}.${TMP_EXT}" "${LAMMPS_POTENTIALS_DIR}/${pot}")
+        endif()
+      endforeach()
+    endif()
   endif()
 endfunction(FetchPotentials)
 
@@ -149,3 +158,14 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
   set(CMAKE_LINUX_DISTRO ${distro})
   set(CMAKE_DISTRO_VERSION ${disversion})
 endif()
+
+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/COLVARS.cmake

@@ -1,20 +1,15 @@
 set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 
-file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
+file(GLOB COLVARS_SOURCES ${CONFIGURE_DEPENDS} ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
 
-option(COLVARS_DEBUG "Debugging messages for Colvars (quite verbose)" OFF)
+option(COLVARS_DEBUG "Enable debugging messages for Colvars (quite verbose)" OFF)
 
-# Build Lepton by default
-option(COLVARS_LEPTON "Build and link the Lepton library" ON)
+option(COLVARS_LEPTON "Use the Lepton library for custom expressions" ON)
 
 if(COLVARS_LEPTON)
-  set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
-  file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
-  add_library(lepton STATIC ${LEPTON_SOURCES})
-  # Change the define below to LEPTON_BUILDING_SHARED_LIBRARY when linking Lepton as a DLL with MSVC
-  target_compile_definitions(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
-  set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
-  target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
+  if(NOT LEPTON_SOURCE_DIR)
+    include(Packages/LEPTON)
+  endif()
 endif()
 
 add_library(colvars STATIC ${COLVARS_SOURCES})
@@ -30,14 +25,11 @@ target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
 target_link_libraries(lammps PRIVATE colvars)
 
 if(COLVARS_DEBUG)
-  # Need to export the macro publicly to also affect the proxy
+  # Need to export the define publicly to be valid in interface code
   target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)
 endif()
 
 if(COLVARS_LEPTON)
-  target_link_libraries(lammps PRIVATE lepton)
   target_compile_definitions(colvars PRIVATE -DLEPTON)
-  # Disable the line below when linking Lepton as a DLL with MSVC
-  target_compile_definitions(colvars PRIVATE -DLEPTON_USE_STATIC_LIBRARIES)
-  target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
+  target_link_libraries(colvars PUBLIC lepton)
 endif()

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

@@ -26,7 +26,20 @@ elseif(GPU_PREC STREQUAL "SINGLE")
   set(GPU_PREC_SETTING "SINGLE_SINGLE")
 endif()
 
-file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
+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)
 
 if(GPU_API STREQUAL "CUDA")
@@ -55,7 +68,7 @@ if(GPU_API STREQUAL "CUDA")
   set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
 
   # ensure that no *cubin.h files exist from a compile in the lib/gpu folder
-  file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
+  file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
   if(GPU_LIB_OLD_CUBIN_HEADERS)
     message(FATAL_ERROR "########################################################################\n"
       "Found file(s) generated by the make-based build system in lib/gpu\n"
@@ -65,15 +78,15 @@ if(GPU_API STREQUAL "CUDA")
       "########################################################################")
   endif()
 
-  file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
   cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
   if(CUDPP_OPT)
     cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-    file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
-    file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
+    file(GLOB GPU_LIB_CUDPP_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
+    file(GLOB GPU_LIB_CUDPP_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
   endif()
 
   # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
@@ -82,6 +95,7 @@ if(GPU_API STREQUAL "CUDA")
 
   # apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
   # only the Kepler achitecture and beyond is supported
+  # 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")
@@ -120,14 +134,14 @@ if(GPU_API STREQUAL "CUDA")
     if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
       string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
     endif()
-    # Hopper (GPU Arch 9.0) is supported by CUDA 12.0? and later
+    # Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
+      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+    endif()
+    # Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
     if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
       string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
     endif()
-    #    # Lovelace (GPU Arch 9.x) is supported by CUDA 12.0? and later
-    #if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-    #  string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_9x,code=[sm_9x,compute_9x]")
-    #endif()
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
@@ -150,7 +164,12 @@ 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)
@@ -182,7 +201,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   include(OpenCLUtils)
   set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
 
-  file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
@@ -191,6 +210,7 @@ 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})
@@ -207,6 +227,7 @@ 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
@@ -216,14 +237,18 @@ 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)
-
+  target_compile_definitions(gpu PRIVATE -DUSE_OPENCL -D_${GPU_PREC_SETTING})
+  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 ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
@@ -276,6 +301,7 @@ elseif(GPU_API STREQUAL "HIP")
     else()
       # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
       # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
+      # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
       set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH}")
       # 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"))
@@ -305,14 +331,22 @@ elseif(GPU_API STREQUAL "HIP")
       if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
         string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
       endif()
-      # Hopper (GPU Arch 9.0) is supported by CUDA 12.0? and later
+      # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
+        string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
+      endif()
+      # Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
+        string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+      endif()
+      # Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
       if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+        string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
       endif()
     endif()
   endif()
 
-  file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
   set(GPU_LIB_CU_HIP "")
@@ -364,8 +398,12 @@ 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)
+  target_compile_definitions(gpu PRIVATE -DUSE_HIP -D_${GPU_PREC_SETTING})
+  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)
@@ -390,15 +428,17 @@ 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 ""

cmake/Modules/Packages/INTEL.cmake

@@ -112,9 +112,5 @@ if(PKG_KSPACE)
   RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
 endif()
 
-if(PKG_ELECTRODE)
-  list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/electrode_accel_intel.cpp)
-endif()
-
 target_sources(lammps PRIVATE ${INTEL_SOURCES})
 target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

cmake/Modules/Packages/KOKKOS.cmake

@@ -3,6 +3,7 @@
 if(CMAKE_CXX_STANDARD LESS 14)
   message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
 endif()
+
 ########################################################################
 # consistency checks and Kokkos options/settings required by LAMMPS
 if(Kokkos_ENABLE_CUDA)
@@ -48,12 +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_MD5 "84991eca9f066383abe119a5bc7a11c4" CACHE STRING "MD5 checksum of 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 "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 ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a <INSTALL_DIR>/lib/libkokkoscontainers.a
@@ -73,7 +76,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.7.00 REQUIRED CONFIG)
+  find_package(Kokkos 3.7.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
   target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()
@@ -89,7 +92,6 @@ else()
   endif()
   add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
 
-
   set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
                           ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
                           ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
@@ -143,7 +145,24 @@ if(PKG_ML-IAP)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/mliap_data_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/mliap_descriptor_so3_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/mliap_model_linear_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_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
+  if(MLIAP_ENABLE_PYTHON AND Cythonize_EXECUTABLE)
+    file(GLOB MLIAP_KOKKOS_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/KOKKOS/*.pyx)
+    foreach(MLIAP_CYTHON_FILE ${MLIAP_KOKKOS_CYTHON_SRC})
+      get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
+      add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
+              COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_FILE} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+              COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+              WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
+              MAIN_DEPENDENCY    ${MLIAP_CYTHON_FILE}
+              COMMENT "Generating C++ sources with cythonize...")
+      list(APPEND KOKKOS_PKG_SOURCES ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
+    endforeach()
+  endif()
 endif()
 
 if(PKG_PHONON)

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

@@ -0,0 +1,35 @@
+# avoid including this file twice
+if(LEPTON_SOURCE_DIR)
+   return()
+endif()
+set(LEPTON_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/lepton)
+
+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
+   (CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "x86_64"))
+   option(LEPTON_ENABLE_JIT "Enable Just-In-Time compiler for Lepton" ON)
+else()
+   option(LEPTON_ENABLE_JIT "Enable Just-In-Time compiler for Lepton" OFF)
+endif()
+
+if(LEPTON_ENABLE_JIT)
+  file(GLOB ASMJIT_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
+endif()
+
+add_library(lepton STATIC ${LEPTON_SOURCES} ${ASMJIT_SOURCES})
+set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
+target_compile_definitions(lepton PUBLIC LEPTON_BUILDING_STATIC_LIBRARY=1)
+target_include_directories(lepton PUBLIC ${LEPTON_SOURCE_DIR}/include)
+if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
+  find_library(LIB_RT rt QUIET)
+  target_link_libraries(lepton PUBLIC ${LIB_RT})
+endif()
+
+if(LEPTON_ENABLE_JIT)
+  target_compile_definitions(lepton PUBLIC "LEPTON_USE_JIT=1;ASMJIT_BUILD_X86=1;ASMJIT_STATIC=1;ASMJIT_BUILD_RELEASE=1")
+  target_include_directories(lepton PUBLIC ${LEPTON_SOURCE_DIR})
+endif()
+
+target_link_libraries(lammps PRIVATE lepton)

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/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_MD5 "9595b066636cd6b90b0fef93398297a5" CACHE STRING "MD5 checksum of 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 "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-IAP.cmake

@@ -34,7 +34,7 @@ if(MLIAP_ENABLE_PYTHON)
   endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
-  file(GLOB MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
+  file(GLOB MLIAP_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
   file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
   foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
     get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,11 +1,25 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2022.10.15.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_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 "848ad6a6cc79fa82745927001fb1c9b5" 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/StyleHeaderUtils.cmake

@@ -1,5 +1,5 @@
 function(FindStyleHeaders path style_class file_pattern headers)
-    file(GLOB files "${path}/${file_pattern}*.h")
+    file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
     get_property(hlist GLOBAL PROPERTY ${headers})
 
     foreach(file_name ${files})
@@ -184,7 +184,7 @@ endfunction(DetectBuildSystemConflict)
 
 
 function(FindPackagesHeaders path style_class file_pattern headers)
-    file(GLOB files "${path}/${file_pattern}*.h")
+    file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
     get_property(plist GLOBAL PROPERTY ${headers})
 
     foreach(file_name ${files})

cmake/Modules/Testing.cmake

@@ -6,7 +6,7 @@ if(ENABLE_TESTING)
   find_program(VALGRIND_BINARY NAMES valgrind)
   # generate custom suppression file
   file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
-  file(GLOB VALGRIND_SUPPRESSION_FILES ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
+  file(GLOB VALGRIND_SUPPRESSION_FILES ${CONFIGURE_DEPENDS} ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
   foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
     file(READ ${SUPP} SUPPRESSIONS)
     file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")

cmake/Modules/Tools.cmake

@@ -26,7 +26,7 @@ if(BUILD_TOOLS)
 
   enable_language(C)
   get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
-  file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
+  file(GLOB MSI2LMP_SOURCES ${CONFIGURE_DEPENDS} ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
   add_executable(msi2lmp ${MSI2LMP_SOURCES})
   if(STANDARD_MATH_LIB)
     target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB})
@@ -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/all_off.cmake

@@ -44,6 +44,7 @@ set(ALL_PACKAGES
   KSPACE
   LATBOLTZ
   LATTE
+  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY

cmake/presets/all_on.cmake

@@ -46,6 +46,7 @@ set(ALL_PACKAGES
   KSPACE
   LATBOLTZ
   LATTE
+  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY

cmake/presets/mingw-cross.cmake

@@ -36,6 +36,7 @@ set(WIN_PACKAGES
   INTERLAYER
   KSPACE
   LATTE
+  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY

cmake/presets/most.cmake

@@ -35,10 +35,12 @@ set(ALL_PACKAGES
   GRANULAR
   INTERLAYER
   KSPACE
+  LEPTON
   MACHDYN
   MANYBODY
   MC
   MEAM
+  MESONT
   MISC
   ML-IAP
   ML-POD

cmake/presets/nolib.cmake

@@ -13,9 +13,9 @@ set(PACKAGES_WITH_LIB
   KOKKOS
   LATBOLTZ
   LATTE
+  LEPTON
   MACHDYN
   MDI
-  MESONT
   ML-HDNNP
   ML-PACE
   ML-QUIP

cmake/presets/windows.cmake

@@ -1,6 +1,7 @@
 set(WIN_PACKAGES
   AMOEBA
   ASPHERE
+  AWPMD
   BOCS
   BODY
   BPM
@@ -20,6 +21,7 @@ set(WIN_PACKAGES
   DPD-SMOOTH
   DRUDE
   EFF
+  ELECTRODE
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -29,12 +31,15 @@ set(WIN_PACKAGES
   GRANULAR
   INTERLAYER
   KSPACE
+  LEPTON
   MANIFOLD
   MANYBODY
   MC
   MEAM
+  MESONT
   MISC
   ML-IAP
+  ML-POD
   ML-SNAP
   MOFFF
   MOLECULE

doc/Makefile

@@ -86,13 +86,13 @@ 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 ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
@@ -114,9 +114,9 @@ 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 +131,8 @@ 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= \
-		cp $(SPHINXCONFIG)/false_positives.txt $(RSTDIR)/ ; env PYTHONWARNINGS= \
+		. $(VENV)/bin/activate ; \
+		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 +146,9 @@ 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 ;\
@@ -167,12 +167,12 @@ 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 ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
@@ -200,21 +200,21 @@ 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 ;\
 		deactivate ;\
 	)
 
 package_check : $(VENV)
 	@(\
-		. $(VENV)/bin/activate ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \\
 		python utils/check-packages.py -s ../src -d src ;\
 		deactivate ;\
 	)
@@ -252,7 +252,7 @@ $(MATHJAX):
 
 $(ANCHORCHECK): $(VENV)
 	@( \
-		. $(VENV)/bin/activate; \
+		. $(VENV)/bin/activate; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		pip $(PIP_OPTIONS) install -e utils/converters;\
 		deactivate;\
 	)

doc/README

@@ -40,8 +40,9 @@ environment and local folders.
 Installing prerequisites for the documentation build
 
 To run the HTML documention build toolchain, python 3.x, doxygen, git,
-and virtualenv have to be installed.  Also internet access is initially
-required to download external files and tools.
+and the venv python module have to be installed if not already available.
+Also internet access is initially required to download external files
+and tools.
 
 Building the PDF format manual requires in addition a compatible LaTeX
 installation with support for PDFLaTeX and several add-on LaTeX packages

doc/documentation_conventions.md

@@ -4,45 +4,44 @@ This purpose of this document is to provide a point of reference
 for LAMMPS developers and contributors as to what conventions
 should be used to structure and format files in the LAMMPS manual.
 
-Last change: 2020-04-23
+Last change: 2022-12-30
 
 ## File format and tools
 
-In fall 2019, the LAMMPS documentation file format has changed from
-a home grown minimal markup designed to generate HTML format files
-from a mostly plain text format to using the reStructuredText file
-format.  For a transition period all files in the old .txt format
-were transparently converted to .rst and then processed.  The txt2rst
-tool is still included in the distribution to obtain an initial .rst
-file for integration into the manual.  Since the transition to
-reStructured text as source format, many of the artifacts or the
-translation have been removed though and parts of the documentation
-refactored and expanded to take advantage of the capabilities
-reStructuredText and associated tools.  The conversion from the
-source to the final formats (HTML, PDF, and optionally e-book
-reader formats ePUB and MOBI) is mostly automated and controlled
-by a Makefile in the `doc` folder. This makefile assumes that the
-processing is done on a Unix-like machine and Python 3.5 or later
-and a matching virtualenv module are available.  Additional Python
-packages (like the Sphinx tool and several extensions) are
-transparently installed into a virtual environment over the
-internet using the `pip` package manager.  Further requirements
-and details are discussed in the manual.
+In fall 2019, the LAMMPS documentation file format has changed from a
+home grown markup designed to generate HTML format files only, to
+[reStructuredText](https://docutils.sourceforge.io/rst.html>.  For a
+transition period all files in the old .txt format were transparently
+converted to .rst and then processed.  The `txt2rst tool` is still
+included in the distribution to obtain an initial .rst file for legacy
+integration into the manual.  Since that transition to reStructured
+text, many of the artifacts of the translation have been removed though,
+and parts of the documentation refactored and expanded to take advantage
+of the capabilities reStructuredText and associated tools.  The
+conversion from the source to the final formats (HTML, PDF, and
+optionally e-book reader formats ePUB and MOBI) is mostly automated and
+controlled by a Makefile in the `doc` folder. This makefile assumes that
+the processing is done on a Unix-like machine and Python 3.5 or later
+and a matching venv module are available.  Additional Python
+packages (like the Sphinx tool and several extensions) are transparently
+installed into a virtual environment over the internet using the `pip`
+package manager.  Further requirements and details are discussed in the
+manual.
 
 ## Work in progress
 
 The refactoring and improving of the documentation is an ongoing
 process, so statements in this document may not always be fully
-up-to-date.  If in doubt, contact the LAMMPS developers.
+up-to-date.  When in doubt, contact the LAMMPS developers.
 
 ## General structure
 
-The layout and formatting of added files should follow the example
-of the existing files.  Since those are directly derived from their
-former .txt format versions and the manual has been maintained in
+The layout and formatting of added files should follow the example of
+the existing files.  Since many of those were initially derived from
+their former .txt format versions and the manual has been maintained in
 that format for many years, there is a large degree of consistency
-already, so comparison with similar files should give you a good
-idea what kind of information and sections are needed.
+already, so comparison with similar files should give you a good idea
+what kind of information and sections are needed.
 
 ## Formatting conventions
 
@@ -52,21 +51,27 @@ It seems to be sufficient to have this consistent only within
 any single file and it is not (yet) enforced strictly, but making
 this globally consistent makes it easier to move sections around.
 
-Filenames, folders, paths, (shell) commands, definitions, makefile
+File names, folders, paths, (shell) commands, definitions, makefile
 settings and similar should be formatted as "literals" with
 double backward quotes bracketing the item: \`\`path/to/some/file\`\`
 
 Keywords and options are formatted in italics:  \*option\*
 
 Mathematical expressions, equations, symbols are typeset using
-either a `.. math:`` block or the `:math:` role.
+either a `.. math:` block or the `:math:` role.
 
-Groups of shell commands or LAMMPS input script or C/C++ source
+Groups of shell commands or LAMMPS input script or C/C++/Python source
 code should be typeset into a `.. code-block::` section. A syntax
-highlighting extension for LAMMPS input scripts is provided, so
-`LAMMPS` can be used to indicate the language in the code block
-in addition to `bash`, `c`, or `python`.  When no syntax style
-is indicated, no syntax highlighting is performed.
+highlighting extension for LAMMPS input scripts is provided, so `LAMMPS`
+can be used to indicate the language in the code block in addition to
+`bash`, `c`, `c++`, `console`, `csh`, `diff', `fortran`, `json`, `make`,
+`perl`, `powershell`, `python`, `sh`, or `tcl`, `text`, or `yaml`.  When
+no syntax style is indicated, no syntax highlighting is performed.  When
+typesetting commands executed on the shell, please do not prefix
+commands with a shell prompt and use `bash` highlighting, except when
+the block also shows the output from that command.  In the latter case,
+please use a dollar sign as the shell prompt and `console` for syntax
+highlighting.
 
 As an alternative, e.g. to typeset the syntax of file formats
 a `.. parsed-literal::` block can be used, which allows some
@@ -89,22 +94,30 @@ by `   :class: note`.
 
 ## Required steps when adding a custom style to LAMMPS
 
-When adding a new style (e.g. pair style or a compute or a fix)
-or a new command, it is **required** to include the corresponding
-documentation.  Those are often new files that need to be added.
-In order to be included in the documentation, those new files
-need to be reference in a `.. toctree::` block.  Most of those
-use patterns with wildcards, so the addition will be automatic.
-However, those additions also need to be added to some lists of
-styles or commands.  The `make style\_check` command will perform
-a test and report any missing entries and list the affected files.
-Any references defined with `.. \_refname:` have to be unique
-across all documentation files and this can be checked for with
-`make anchor\_check`.  Finally, a spell-check should be done,
-which is triggered via `make spelling`.  Any offenses need to
-be corrected and false positives should be added to the file
-`utils/sphinx-config/false\_positives.txt`.
+When adding a new style (e.g. pair style or a compute or a fix) or a new
+command, it is **required** to include the **corresponding documentation**
+in [reStructuredText format](https://docutils.sourceforge.io/rst.html).
+Those are often new files that need to be added.  In order to be
+included in the documentation, those new files need to be referenced in a
+`.. toctree::` block.  Most of those use patterns with wild cards, so the
+addition will be automatic.  However, those additions also need to be
+added to some lists of styles or commands.  The `make style\_check`
+command when executed in the `doc` folder will perform a test and report
+any missing entries and list the affected files.  Any references defined
+with `.. \_refname:` have to be unique across all documentation files
+and this can be checked for with `make anchor\_check`.  Finally, a
+spell-check should be done, which is triggered via `make spelling`.  Any
+offenses need to be corrected and false positives should be added to the
+file `utils/sphinx-config/false\_positives.txt`.
 
 ## Required additional steps when adding a new package to LAMMPS
 
-TODO
+When adding a new package, the package must be added to the list of
+packages in the `Packages_list.rst` file.  If additional build instructions
+need to be followed, a corresponding section should be added to the
+`Build_extras.rst` file and linked from the list at the top of the
+file as well as the equivalent list in the `Build_packages.rst` file.
+
+A detailed description of the package and pointers to configuration,
+included commands and examples, external pages, author information and
+more should be added to the `Packages_details.rst` file.

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/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
-or automated build trees as described on the :doc:`Install <Install>`
-page.
+As an alternative, you can download a package with pre-built executables
+or automated build trees, as described in the :doc:`Install <Install>`
+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``.
-See the :doc:`Packages details <Packages_details>` page for more
-info on these packages and the pages for their respective commands
-for OpenMP threading info.
+they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``.  See the
+:doc:`Packages details <Packages_details>` page for more info on these
+packages, and the pages for their respective commands for OpenMP
+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
-compilers it is ``-qopenmp``\ .  If you are using a different compiler,
-please refer to its documentation.
+enables OpenMP. For the GNU compilers or Clang, it is ``-fopenmp``\ .
+For (recent) Intel compilers, it is ``-qopenmp``\ .  If you are using a
+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
-similar in performance of C/C++ code at high optimization levels.  When
-using the ``INTEL`` package, there is a distinct advantage in using
-the `Intel C++ compiler <intel_>`_ due to much improved vectorization
-through SSE and AVX instructions on compatible hardware as the source
-code includes changes and Intel compiler specific directives to enable
-high degrees of vectorization.  This may change over time as equivalent
-vectorization directives are included into OpenMP standard revisions and
-other compilers adopt them.
+On the most common x86 hardware, the most popular C++ compilers are
+quite similar in their ability to optimize regular C/C++ source code at
+high optimization levels.  When using the ``INTEL`` package, there is a
+distinct advantage in using the `Intel C++ compiler <intel_>`_ due to
+much improved vectorization through SSE and AVX instructions on
+compatible hardware.  The source code in that package conditionally
+includes compiler specific directives to enable these high degrees of
+vectorization.  This may change over time as equivalent vectorization
+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
-      compiler flags to tune for optimal performance on given hosts. By
-      default this variable is empty.
+      Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
+      compiler flags to tune for optimal performance on given hosts.
+      This variable is empty by default.
 
       .. note::
 
@@ -276,7 +277,7 @@ LAMMPS.
 
       Parallel build (see ``src/MAKE/Makefile.mpi``):
 
-      .. code-block:: bash
+      .. code-block:: make
 
          CC =            mpicxx
          CCFLAGS =       -g -O3
@@ -296,7 +297,7 @@ LAMMPS.
 
          If compilation stops with a message like the following:
 
-         .. code-block::
+         .. code-block:: output
 
             g++ -g -O3  -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64    -I../STUBS     -c ../main.cpp
             In file included from ../pointers.h:24:0,
@@ -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
-      named ``liblammps.a`` and an executable named ``lmp`` Setting
-      ``BUILD_SHARED_LIBS=yes`` will instead produce a shared library
-      called ``liblammps.so`` (or ``liblammps.dylib`` or
+      executable linked to it.  By default, this will be a static
+      library named ``liblammps.a`` and an executable named ``lmp``
+      Setting ``BUILD_SHARED_LIBS=yes`` will instead produce a shared
+      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
-and not through a package manager tool provided by the OS) is generally
-recommended to ensure the integrity of the system software installation.
+Avoiding the use of "sudo" for custom software installation (i.e. from
+source and not through a package manager tool provided by the OS) is
+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
-library, along with other LAMMPS files (library header, doc files) to
-a globally visible place on your system, for others to access.  Note
-that you may need super-user privileges (e.g. sudo) if the directory
-you want to copy files to is protected.
+After building LAMMPS, you may wish to copy the LAMMPS executable or
+library, along with other LAMMPS files (library header, doc files), to a
+globally visible place on your system, for others to access.  Note that
+you may need super-user privileges (e.g. sudo) if the directory you want
+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``
-itself, the text mode or graphical user interface, change the generated
-output files for different build tools and development environments is
-on a :doc:`separate page <Howto_cmake>`.
+for building LAMMPS.  A more detailed tutorial on how to use CMake
+itself, the text mode or graphical user interface, to change the
+generated output files for different build tools and development
+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
-  user interface. No knowledge of file formats or and complex command
-  line syntax required.
+- CMake supports customization of settings with a command line, text
+  mode, or graphical user interface.  No knowledge of file formats or
+  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
-  is still under development).
+- Integration of automated unit and regression testing (the LAMMPS side
+  of this is still under active development).
 
 .. _cmake_build:
 
 Getting started
 ^^^^^^^^^^^^^^^
 
-Building LAMMPS with CMake is a two-step process.  First you use CMake
-to generate a build environment in a new directory.  For that purpose
-you can use either the command-line utility ``cmake`` (or ``cmake3``),
-the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the graphical
-utility ``cmake-gui``, or use them interchangeably.  The second step is
-then the compilation and linking of all objects, libraries, and
-executables. Here is a minimal example using the command line version of
-CMake to build LAMMPS with no add-on packages enabled and no
-customization:
+Building LAMMPS with CMake is a two-step process.  In the first step,
+you use CMake to generate a build environment in a new directory.  For
+that purpose you can use either the command-line utility ``cmake`` (or
+``cmake3``), the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the
+graphical utility ``cmake-gui``, or use them interchangeably.  The
+second step is then the compilation and linking of all objects,
+libraries, and executables using the selected build tool.  Here is a
+minimal example using the command line version of CMake to build LAMMPS
+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/>`_ (=
-Compiler Cache) software may speed up repeated compilation even more,
-e.g. during code development.
+tasks).  Installation of the `ccache <https://ccache.dev/>`_ (= Compiler
+Cache) software may speed up repeated compilation even more, e.g. during
+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
-re-compiled.  You can also delete compiled objects, libraries and
+should make certain that only the necessary subset of files is
+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*
-with either the *-D* command line flag (``-D VARIABLE1_NAME=value``) or
-change them in the text mode of graphical user interface.  The *-D* flag
-can be used several times in one command.
+To modify settings, enable or disable features, you need to set
+*variables* with either the *-D* command line flag (``-D
+VARIABLE1_NAME=value``) or change them in the text mode of the graphical
+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"
-is chose using ``-D CMAKE_BUILD_TYPE=<configuration>`` with ``<configuration>``
-being one of "Release", "Debug", "RelWithDebInfo", or "MinSizeRel".
-Some build tools, however, can also use or even require to have a so-called
-multi-configuration build system setup.  For those the built type (or
-configuration) is chosen at compile time using the same build files. E.g.
-with:
+since this is the most common case.  In this case the build
+"configuration" is chose using ``-D CMAKE_BUILD_TYPE=<configuration>``
+with ``<configuration>`` being one of "Release", "Debug",
+"RelWithDebInfo", or "MinSizeRel".  Some build tools, however, can also
+use or even require having a so-called multi-configuration build system
+setup.  For a multi-configuration build, the built type (or
+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.
 
 ----------
 
@@ -154,32 +154,48 @@ for implementing the tests.
    framework are more strict than for the main part of LAMMPS.  For
    example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
    (version 4.8.x) are not sufficient.  The CMake configuration will try
-   to detect compatible versions and either skip incompatible tests or
-   stop with an error.
+   to detect incompatible versions and either skip incompatible tests or
+   stop with an error.  Also the number of tests will depend on
+   installed LAMMPS packages, development environment, operating system,
+   and configuration settings.
 
 After compilation is complete, the unit testing is started in the build
 folder using the ``ctest`` command, which is part of the CMake software.
-The output of this command will be looking something like this::
+The output of this command will be looking something like this:
 
-   [...]$ ctest
-   Test project /home/akohlmey/compile/lammps/build-testing
-         Start  1: MolPairStyle:hybrid-overlay
-   1/109 Test  #1: MolPairStyle:hybrid-overlay .........   Passed    0.02 sec
-         Start  2: MolPairStyle:hybrid
-   2/109 Test  #2: MolPairStyle:hybrid .................   Passed    0.01 sec
-         Start  3: MolPairStyle:lj_class2
-    [...]
-         Start 107: PotentialFileReader
- 107/109 Test #107: PotentialFileReader ................   Passed    0.04 sec
-         Start 108: EIMPotentialFileReader
- 108/109 Test #108: EIMPotentialFileReader .............   Passed    0.03 sec
-         Start 109: TestSimpleCommands
- 109/109 Test #109: TestSimpleCommands .................   Passed    0.02 sec
+.. code-block:: console
 
-   100% tests passed, 0 tests failed out of 26
+    $ ctest
+    Test project /home/akohlmey/compile/lammps/build-testing
+         Start   1: RunLammps
+   1/563 Test   #1: RunLammps ..........................................   Passed    0.28 sec
+         Start   2: HelpMessage
+   2/563 Test   #2: HelpMessage ........................................   Passed    0.06 sec
+         Start   3: InvalidFlag
+   3/563 Test   #3: InvalidFlag ........................................   Passed    0.06 sec
+         Start   4: Tokenizer
+   4/563 Test   #4: Tokenizer ..........................................   Passed    0.05 sec
+         Start   5: MemPool
+   5/563 Test   #5: MemPool ............................................   Passed    0.05 sec
+         Start   6: ArgUtils
+   6/563 Test   #6: ArgUtils ...........................................   Passed    0.05 sec
+       [...]
+         Start 561: ImproperStyle:zero
+ 561/563 Test #561: ImproperStyle:zero .................................   Passed    0.07 sec
+         Start 562: TestMliapPyUnified
+ 562/563 Test #562: TestMliapPyUnified .................................   Passed    0.16 sec
+         Start 563: TestPairList
+ 563/563 Test #563: TestPairList .......................................   Passed    0.06 sec
 
-   Total Test time (real) =  25.57 sec
+ 100% tests passed, 0 tests failed out of 563
 
+ Label Time Summary:
+ generated    =   0.85 sec*proc (3 tests)
+ noWindows    =   4.16 sec*proc (2 tests)
+ slow         =  78.33 sec*proc (67 tests)
+ unstable     =  28.23 sec*proc (34 tests)
+
+ Total Test time (real) = 132.34 sec
 
 The ``ctest`` command has many options, the most important ones are:
 
@@ -210,11 +226,13 @@ Fortran) and testing different aspects of the LAMMPS software and its features.
 The tests will adapt to the compilation settings of LAMMPS, so that tests
 will be skipped if prerequisite features are not available in LAMMPS.
 
-.. note::
+.. admonition:: Work in Progress
+   :class: note
 
    The unit test framework was added in spring 2020 and is under active
    development.  The coverage is not complete and will be expanded over
-   time.
+   time.  Preference is given to parts of the code base that are easy to
+   test or commonly used.
 
 Tests for styles of the same kind of style (e.g. pair styles or bond
 styles) are performed with the same test executable using different
@@ -248,9 +266,9 @@ the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
 since this will skip the MPI initialization for each test run.
 Below is an example command and output:
 
-.. parsed-literal::
+.. code-block:: console
 
-   [tests]$ test_pair_style mol-pair-lj_cut.yaml
+   $ test_pair_style mol-pair-lj_cut.yaml
    [==========] Running 6 tests from 1 test suite.
    [----------] Global test environment set-up.
    [----------] 6 tests from PairStyle
@@ -530,7 +548,7 @@ commands like the following:
 
 .. code-block:: bash
 
-   $ clang-format -i some_file.cpp
+   clang-format -i some_file.cpp
 
 
 The following target are available for both, GNU make and CMake:
@@ -539,3 +557,19 @@ The following target are available for both, GNU make and CMake:
 
    make format-src       # apply clang-format to all files in src and the package folders
    make format-tests     # apply clang-format to all files in the unittest tree
+
+----------
+
+.. _gh-cli:
+
+GitHub command line interface
+-----------------------------
+
+GitHub is developing a `tool for the command line
+<https://cli.github.com>`_ that interacts with the GitHub website via a
+command called ``gh``.  This can be extremely convenient when working
+with a Git repository hosted on GitHub (like LAMMPS).  It is thus highly
+recommended to install it when doing LAMMPS development.
+
+The capabilities of the ``gh`` command is continually expanding, so
+please see the documentation at https://cli.github.com/manual/

doc/src/Build_extras.rst

@@ -12,11 +12,11 @@ in addition to
      - Traditional make
    * - .. code-block:: bash
 
-          $ cmake -D PKG_NAME=yes
+          cmake -D PKG_NAME=yes
 
-     - .. code-block:: bash
+     - .. code-block:: console
 
-          $ make yes-name
+          make yes-name
 
 as described on the :doc:`Build_package <Build_package>` page.
 
@@ -28,13 +28,14 @@ You may need to tell LAMMPS where it is found on your system.
 
 This is the list of packages that may require additional steps.
 
+.. this list must be kept in sync with its counterpart in Build_package.rst
 .. table_from_list::
    :columns: 6
 
    * :ref:`ADIOS <adios>`
    * :ref:`ATC <atc>`
    * :ref:`AWPMD <awpmd>`
-   * :ref:`COLVARS <colvars>`
+   * :ref:`COLVARS <colvar>`
    * :ref:`COMPRESS <compress>`
    * :ref:`ELECTRODE <electrode>`
    * :ref:`GPU <gpu>`
@@ -43,9 +44,9 @@ This is the list of packages that may require additional steps.
    * :ref:`KIM <kim>`
    * :ref:`KOKKOS <kokkos>`
    * :ref:`LATTE <latte>`
+   * :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>`
@@ -125,10 +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
-                                # default is sm_50
+                                # value = sm_XX (see below, 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
@@ -150,7 +152,9 @@ CMake build
 * sm_60 or sm_61 for Pascal (supported since CUDA 8)
 * sm_70 for Volta (supported since CUDA 9)
 * sm_75 for Turing (supported since CUDA 10)
-* sm_80 for Ampere (supported since CUDA 11)
+* sm_80 or sm_86 for Ampere (supported since CUDA 11, sm_86 since CUDA 11.1)
+* sm_89 for Lovelace (supported since CUDA 11.8)
+* sm_90 for Hopper (supported since CUDA 12.0)
 
 A more detailed list can be found, for example,
 at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
@@ -241,10 +245,10 @@ script with the specified args:
 
 .. code-block:: bash
 
-  $ make lib-gpu               # print help message
-  $ make lib-gpu args="-b"     # build GPU library with default Makefile.linux
-  $ make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
-  $ make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
+  make lib-gpu               # print help message
+  make lib-gpu args="-b"     # build GPU library with default Makefile.linux
+  make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
+  make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
 
 Note that this procedure starts with a Makefile.machine in lib/gpu, as
 specified by the "-m" switch.  For your convenience, machine makefiles
@@ -284,7 +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.
@@ -357,13 +361,13 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: bash
 
-         $ make lib-kim              # print help message
-         $ make lib-kim args="-b "   # (re-)install KIM API lib with only example models
-         $ make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
-         $ make lib-kim args="-b -a everything"     # install KIM API lib with all models
-         $ make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
-         $ make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
-         $ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
+         make lib-kim              # print help message
+         make lib-kim args="-b "   # (re-)install KIM API lib with only example models
+         make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
+         make lib-kim args="-b -a everything"     # install KIM API lib with all models
+         make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
+         make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
+         make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
 
       When using the "-b " option, the KIM library is built using its native
       cmake build system.  The ``lib/kim/Install.py`` script supports a
@@ -375,7 +379,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: bash
 
-         $ CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b "  # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
+         CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b "  # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
 
       Settings for debugging OpenKIM web queries discussed below need to
       be applied by adding them to the ``LMP_INC`` variable through
@@ -602,6 +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
@@ -636,7 +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::
 
@@ -858,11 +868,11 @@ library.
 
       .. code-block:: bash
 
-         $ make lib-latte                          # print help message
-         $ make lib-latte args="-b"                # download and build in lib/latte/LATTE-master
-         $ make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
-         $ make lib-latte args="-b -m gfortran"    # download and build in lib/latte and
-                                                   #   copy Makefile.lammps.gfortran to Makefile.lammps
+         make lib-latte                        # print help message
+         make lib-latte args="-b"              # download and build in lib/latte/LATTE-master
+         make lib-latte args="-p $HOME/latte"  # use existing LATTE installation in $HOME/latte
+         make lib-latte args="-b -m gfortran"  # download and build in lib/latte and
+                                               #   copy Makefile.lammps.gfortran to Makefile.lammps
 
       Note that 3 symbolic (soft) links, ``includelink`` and ``liblink``
       and ``filelink.o``, are created in ``lib/latte`` to point to
@@ -873,6 +883,55 @@ library.
 
 ----------
 
+.. _lepton:
+
+LEPTON package
+--------------
+
+To build with this package, you must build the Lepton library which is
+included in the LAMMPS source distribution in the ``lib/lepton`` folder.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      This is the recommended build procedure for using Lepton in
+      LAMMPS. No additional settings are normally needed besides
+      ``-D PKG_LEPTON=yes``.
+
+      On x86 hardware the Lepton library will also include a just-in-time
+      compiler for faster execution.  This is auto detected but can
+      be explicitly disabled by setting ``-D LEPTON_ENABLE_JIT=no``
+      (or enabled by setting it to yes).
+
+   .. tab:: Traditional make
+
+      Before building LAMMPS, one must build the Lepton library in lib/lepton.
+
+      This can be done manually in the same folder by using or adapting
+      one of the provided Makefiles: for example, ``Makefile.serial`` for
+      the GNU C++ compiler, or ``Makefile.mpi`` for the MPI compiler wrapper.
+      The Lepton library is written in C++-11 and thus the C++ compiler
+      may need to be instructed to enable support for that.
+
+      In general, it is safer to use build setting consistent with the
+      rest of LAMMPS.  This is best carried out from the LAMMPS src
+      directory using a command like these, which simply invokes the
+      ``lib/lepton/Install.py`` script with the specified args:
+
+      .. code-block:: bash
+
+         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 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.
+
+      The build should produce a ``build`` folder and the library ``lib/lepton/liblmplepton.a``
+
+----------
+
 .. _mliap:
 
 ML-IAP package
@@ -961,12 +1020,12 @@ more details.
 
       .. code-block:: bash
 
-         $ make lib-mscg             # print help message
-         $ make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
-                                               # with the settings compatible with "make serial"
-         $ make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
-                                               # with the settings compatible with "make mpi"
-         $ make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
+         make lib-mscg             # print help message
+         make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
+                                             # with the settings compatible with "make serial"
+         make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
+                                             # with the settings compatible with "make mpi"
+         make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
 
       Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``,
       will be created in ``lib/mscg`` to point to the MS-CG
@@ -1018,10 +1077,10 @@ POEMS package
 
       .. code-block:: bash
 
-         $ make lib-poems                   # print help message
-         $ make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
-         $ make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-         $ make lib-poems args="-m icc"     # build with Intel icc compiler
+         make lib-poems                   # print help message
+         make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
+         make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-poems args="-m icc"     # build with Intel icc compiler
 
       The build should produce two files: ``lib/poems/libpoems.a`` and
       ``lib/poems/Makefile.lammps``.  The latter is copied from an
@@ -1107,10 +1166,10 @@ binary package provided by your operating system.
 
       .. code-block:: bash
 
-         $ make lib-voronoi                          # print help message
-         $ make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
-         $ make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
-         $ make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
+         make lib-voronoi                          # print help message
+         make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
+         make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
+         make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
 
       Note that 2 symbolic (soft) links, ``includelink`` and
       ``liblink``, are created in lib/voronoi to point to the Voro++
@@ -1151,13 +1210,13 @@ systems.
 
       .. code-block:: bash
 
-         $ make yes-adios
+         make yes-adios
 
       otherwise, set ADIOS2_DIR environment variable when turning on the package:
 
       .. code-block:: bash
 
-         $ ADIOS2_DIR=path make yes-adios   # path is where ADIOS 2.x is installed
+         ADIOS2_DIR=path make yes-adios   # path is where ADIOS 2.x is installed
 
 ----------
 
@@ -1186,10 +1245,10 @@ The ATC package requires the MANYBODY package also be installed.
 
       .. code-block:: bash
 
-         $ make lib-atc                      # print help message
-         $ make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         $ make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
-         $ make lib-atc args="-m icc"        # build with Intel icc compiler
+         make lib-atc                      # print help message
+         make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+         make lib-atc args="-m icc"        # build with Intel icc compiler
 
       The build should produce two files: ``lib/atc/libatc.a`` and
       ``lib/atc/Makefile.lammps``.  The latter is copied from an
@@ -1208,17 +1267,17 @@ The ATC package requires the MANYBODY package also be installed.
 
       .. code-block:: bash
 
-         $ make lib-linalg                     # print help message
-         $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
-         $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
-         $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+         make lib-linalg                   # print help message
+         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
+         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-linalg args="-m g++"     # build with GNU Fortran compiler
 
 ----------
 
 .. _awpmd:
 
 AWPMD package
-------------------
+-------------
 
 .. tabs::
 
@@ -1237,10 +1296,10 @@ AWPMD package
 
       .. code-block:: bash
 
-         $ make lib-awpmd                   # print help message
-         $ make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         $ make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
-         $ make lib-awpmd args="-m icc"     # build with Intel icc compiler
+         make lib-awpmd                   # print help message
+         make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+         make lib-awpmd args="-m icc"     # build with Intel icc compiler
 
       The build should produce two files: ``lib/awpmd/libawpmd.a`` and
       ``lib/awpmd/Makefile.lammps``.  The latter is copied from an
@@ -1259,21 +1318,20 @@ AWPMD package
 
       .. code-block:: bash
 
-         $ make lib-linalg                     # print help message
-         $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
-         $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
-         $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+         make lib-linalg                   # print help message
+         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
+         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-linalg args="-m g++"     # build with GNU C++ compiler
 
 ----------
 
-.. _colvars:
+.. _colvar:
 
 COLVARS package
----------------------------------------
+---------------
 
-This package includes the `Colvars library
-<https://colvars.github.io/>`_ into the LAMMPS distribution, which can
-be built for the most part with all major versions of the C++ language.
+This package enables the use of the `Colvars <https://colvars.github.io/>`_
+module included in the LAMMPS source distribution.
 
 
 .. tabs::
@@ -1286,42 +1344,45 @@ be built for the most part with all major versions of the C++ language.
 
    .. tab:: Traditional make
 
-      Before building LAMMPS, one must build the Colvars library in lib/colvars.
+      As with other libraries distributed with LAMMPS, the Colvars library
+      needs to be built before building the LAMMPS program with the COLVARS
+      package enabled.
 
-      This can be done manually in the same folder by using or adapting
-      one of the provided Makefiles: for example, ``Makefile.g++`` for
-      the GNU C++ compiler.  C++11 compatibility may need to be enabled
-      for some older compilers (as is done in the example makefile).
-
-      In general, it is safer to use build setting consistent with the
-      rest of LAMMPS.  This is best carried out from the LAMMPS src
-      directory using a command like these, which simply invokes the
-      ``lib/colvars/Install.py`` script with the specified args:
+      From the LAMMPS ``src`` directory, this is most easily and safely done
+      via one of the following commands, which implicitly rely on the
+      ``lib/colvars/Install.py`` script with optional arguments:
 
       .. code-block:: bash
 
-         $ make lib-colvars                      # print help message
-         $ make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
-         $ make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
-         $ make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled
+         make lib-colvars                      # print help message
+         make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
+         make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+         make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled
 
       The "machine" argument of the "-m" flag is used to find a
-      Makefile.machine to use as build recipe.  If it does not already
-      exist in ``lib/colvars``, it will be auto-generated by using
-      compiler flags consistent with those parsed from the core LAMMPS
-      makefiles.
+      ``Makefile.machine`` file to use as build recipe.  If such recipe does
+      not already exist in ``lib/colvars``, suitable settings will be
+      auto-generated consistent with those used in the core LAMMPS makefiles.
+
+
+      .. versionchanged:: 8Feb2023
+
+      Please note that Colvars uses the Lepton library, which is now
+      included with the LEPTON package; if you use anything other than
+      the ``make lib-colvars`` command, please make sure to :ref:`build
+      Lepton beforehand <lepton>`.
 
       Optional flags may be specified as environment variables:
 
       .. code-block:: bash
 
-         $ COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
-         $ COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
+         COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
+         COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
 
-      The build should produce two files: the library ``lib/colvars/libcolvars.a``
-      (which also includes Lepton objects if enabled) and the specification file
-      ``lib/colvars/Makefile.lammps``.  The latter is auto-generated, and normally does
-      not need to be edited.
+      The build should produce two files: the library
+      ``lib/colvars/libcolvars.a`` and the specification file
+      ``lib/colvars/Makefile.lammps``.  The latter is auto-generated,
+      and normally does not need to be edited.
 
 ----------
 
@@ -1336,8 +1397,21 @@ This package depends on the KSPACE package.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_KSPACE=yes`` and
-      ``-D PKG_ELECTRODE=yes``.
+      .. code-block:: bash
+
+         -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
 
@@ -1350,9 +1424,9 @@ This package depends on the KSPACE package.
 
       .. code-block:: bash
 
-         $ make lib-electrode                   # print help message
-         $ make lib-electrode args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         $ make lib-electrode args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+         make lib-electrode                   # print help message
+         make lib-electrode args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         make lib-electrode args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
 
 
       Note that the ``Makefile.lammps`` file has settings for the BLAS
@@ -1363,10 +1437,10 @@ This package depends on the KSPACE package.
 
       .. code-block:: bash
 
-         $ make lib-linalg                     # print help message
-         $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
-         $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
-         $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+         make lib-linalg                   # print help message
+         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
+         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-linalg args="-m g++"     # build with GNU C++ compiler
 
       The package itself is activated with ``make yes-KSPACE`` and
       ``make yes-ELECTRODE``
@@ -1406,8 +1480,8 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
 
       .. code-block:: bash
 
-         $ make lib-pace                          # print help message
-         $ make lib-pace args="-b"                # download and build the default version in lib/pace
+         make lib-pace                          # print help message
+         make lib-pace args="-b"                # download and build the default version in lib/pace
 
       You should not need to edit the ``lib/pace/Makefile.lammps`` file.
 
@@ -1434,10 +1508,10 @@ ML-POD package
 
       .. code-block:: bash
 
-         $ make lib-mlpod                   # print help message
-         $ make lib-mlpod args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         $ make lib-mlpod args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
-         $ make lib-mlpod args="-m mpi -e linalg"   # same as above but use the bundled linalg lib
+         make lib-mlpod                   # print help message
+         make lib-mlpod args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         make lib-mlpod args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+         make lib-mlpod args="-m mpi -e linalg"   # same as above but use the bundled linalg lib
 
       Note that the ``Makefile.lammps`` file has settings to use the BLAS
       and LAPACK linear algebra libraries.  These can either exist on
@@ -1447,10 +1521,10 @@ ML-POD package
 
       .. code-block:: bash
 
-         $ make lib-linalg                     # print help message
-         $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
-         $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
-         $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+         make lib-linalg                   # print help message
+         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
+         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-linalg args="-m g++"     # build with GNU C++ compiler
 
       The package itself is activated with ``make yes-ML-POD``.
 
@@ -1549,10 +1623,10 @@ LAMMPS build.
 
       .. code-block:: bash
 
-         $ make lib-plumed                         # print help message
-         $ make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
-         $ make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
-         $ make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
+         make lib-plumed                         # print help message
+         make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
+         make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
+         make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
                                                            # /usr/local and use shared linkage mode
 
       Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``
@@ -1565,8 +1639,8 @@ LAMMPS build.
 
       .. code-block:: bash
 
-         $ make yes-plumed
-         $ make machine
+         make yes-plumed
+         make machine
 
       Once this compilation completes you should be able to run LAMMPS
       in the usual way.  For shared linkage mode, libplumed.so must be
@@ -1618,8 +1692,8 @@ the HDF5 library.
 
       .. code-block:: bash
 
-         $ make lib-h5md                     # print help message
-         $ make lib-h5md args="-m h5cc"      # build with h5cc compiler
+         make lib-h5md                     # print help message
+         make lib-h5md args="-m h5cc"      # build with h5cc compiler
 
       The build should produce two files: ``lib/h5md/libch5md.a`` and
       ``lib/h5md/Makefile.lammps``.  The latter is copied from an
@@ -1673,10 +1747,10 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
 
       .. code-block:: bash
 
-         $ make lib-hdnnp             # print help message
-         $ make lib-hdnnp args="-b"   # download and build in lib/hdnnp/n2p2-...
-         $ make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
-         $ make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
+         make lib-hdnnp             # print help message
+         make lib-hdnnp args="-b"   # download and build in lib/hdnnp/n2p2-...
+         make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
+         make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
 
       Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and
       ``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
@@ -1776,56 +1850,14 @@ MDI package
 
       .. code-block:: bash
 
-         $ python Install.py -m gcc       # build using gcc compiler
-         $ python Install.py -m icc       # build using icc compiler
+         python Install.py -m gcc       # build using gcc compiler
+         python Install.py -m icc       # build using icc compiler
 
       The build should produce two files: ``lib/mdi/includelink/mdi.h``
       and ``lib/mdi/liblink/libmdi.so``\ .
 
 ----------
 
-.. _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
@@ -1926,6 +1958,22 @@ OPENMP package
       For other platforms and compilers, please consult the
       documentation about OpenMP support for your compiler.
 
+.. admonition:: Adding OpenMP support on macOS
+   :class: note
+
+   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
+   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
+   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
+   instructed enables the Xcode C++ compiler to compile LAMMPS with ``-D
+   BUILD_OMP=yes``.
+
 ----------
 
 .. _qmmm:
@@ -1980,10 +2028,10 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
       .. code-block:: bash
 
-         $ make lib-qmmm                      # print help message
-         $ make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
-         $ make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
-         $ make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler
+         make lib-qmmm                      # print help message
+         make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
+         make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
+         make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler
 
       The build should produce two files: ``lib/qmmm/libqmmm.a`` and
       ``lib/qmmm/Makefile.lammps``.  The latter is copied from an
@@ -2132,9 +2180,9 @@ Eigen3 is a template library, so you do not need to build it.
 
       .. code-block:: bash
 
-         $ make lib-smd                         # print help message
-         $ make lib-smd args="-b"               # download to lib/smd/eigen3
-         $ make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
+         make lib-smd                         # print help message
+         make lib-smd args="-b"               # download to lib/smd/eigen3
+         make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
 
       Note that a symbolic (soft) link named ``includelink`` is created
       in ``lib/smd`` to point to the Eigen dir.  When LAMMPS builds it

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
-integrated into other applications including Python scripts.
-The files ``src/library.cpp`` and ``src/library.h`` define a
-C-style API for using LAMMPS as a library.  See the
-:doc:`Howto_library` page
-for a description of the interface and how to use it for your needs.
+LAMMPS is designed as a library of C++ objects that can be integrated
+into other applications, including Python scripts.  The files
+``src/library.cpp`` and ``src/library.h`` define a C-style API for using
+LAMMPS as a library.  See the :doc:`Howto_library` page for a
+description of the interface and how to use it for your needs.
 
-The :doc:`Build_basics` page explains how to build
-LAMMPS as either a shared or static library.  This results in a file
-in the compilation folder called ``liblammps.a`` or ``liblammps_<name>.a``
-in case of building a static library.  In case of a shared library
-the name is the same only that the suffix is going to be either ``.so``
-or ``.dylib`` or ``.dll`` instead of ``.a`` depending on the OS.
-In some cases the ``.so`` file may be a symbolic link to a file with
-the suffix ``.so.0`` (or some other number).
+The :doc:`Build_basics` page explains how to build LAMMPS as either a
+shared or static library.  This results in a file in the compilation
+folder called ``liblammps.a`` or ``liblammps_<name>.a`` in case of
+building a static library.  In case of a shared library, the name is the
+same only that the suffix is going to be either ``.so`` or ``.dylib`` or
+``.dll`` instead of ``.a`` depending on the OS.  In some cases, the
+``.so`` file may be a symbolic link to a file with the suffix ``.so.0``
+(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)
-   MPI support using the include STUBS MPI library.
+   and the LAMMPS library, unless LAMMPS is to be compiled without (real)
+   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
-linking the calling executable.  Only the *-I* flags are needed.  So the
-example case from above of the serial version static LAMMPS library with
-the POEMS package installed becomes:
+library file.  Thus, those libraries need not be specified when linking
+the calling executable.  Only the *-I* flags are needed.  So the example
+case from above of the serial version static LAMMPS library with the
+POEMS package installed becomes:
 
 .. tabs::
 
@@ -209,7 +208,7 @@ You can verify whether all required shared libraries are found with the
 
 .. code-block:: bash
 
-   $ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
+   LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
         linux-vdso.so.1 (0x00007ffe729e0000)
         liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000)
         libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000)
@@ -222,7 +221,7 @@ If a required library is missing, you would get a 'not found' entry:
 
 .. code-block:: bash
 
-   $  ldd caller
+   ldd caller
         linux-vdso.so.1 (0x00007ffd672fe000)
         liblammps.so => not found
         libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000)

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
-    Linux these are often the GNU compilers. Some older compilers
+  * A working C/C++ compiler toolchain supporting the C++11 standard; on
+    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 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 scripts are currently tested with python 2.7 and 3.6. The procedure
-    for :doc:`building the documentation <Build_manual>` requires python 3.5 or later.
+  * 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``
+  * Python (optional, required for ``make lib-<pkg>`` in the src
+    folder).  Python scripts are currently tested with python 2.7 and
+    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/>`_ (=
-Compiler Cache) software may speed up repeated compilation even more,
-e.g. during code development.
+tasks).  Installation of the `ccache <https://ccache.dev/>`_ (= Compiler
+Cache) software may speed up repeated compilation even more, e.g. during
+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
-files are re-compiled.  If you change settings in the makefile, you have
-to recompile *everything*.  To delete all objects you can use ``make
+dependency tracking should ensure that only the necessary subset of
+files is re-compiled.  If you change settings in the makefile, you have
+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
-   is then embedded into the executable.  When you build LAMMPS for
-   the first time, it will also compile a tool to quickly assemble
-   a list of dependencies, that are required for the make program to
-   correctly detect which parts need to be recompiled after changes
-   were made to the sources.
+   steps to collect information from the configuration and setup that is
+   then embedded into the executable.  When you build LAMMPS for the
+   first time, it will also compile a tool to quickly determine a list
+   of dependencies.  Those are required for the make program to
+   correctly detect, which files need to be recompiled or relinked
+   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
-``make serial`` and ``make mpi`` lines above use
+``Makefile.example`` from one of those folders, if available.  The
+``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
-first be installed).  Many of these include specific compiler flags
-for optimized performance.  Please note, however, that some of these
-customized machine Makefile are contributed by users.  Since both
-compilers, OS configurations, and LAMMPS itself keep changing, their
-settings may become outdated:
+Makefiles you may wish to try out, include those listed below (some
+require a package first be installed).  Many of these include specific
+compiler flags for optimized performance.  Please note, however, that
+some of these customized machine Makefile are contributed by users, and
+thus may have modifications specific to the systems of those users.
+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
@@ -125,38 +125,29 @@ common setups:
 
       .. code-block:: bash
 
-         sudo apt-get install python-virtualenv git doxygen
+         sudo apt-get install git doxygen
 
    .. tab:: RHEL or CentOS (Version 7.x)
 
       .. code-block:: bash
 
-         sudo yum install python3-virtualenv git doxygen
+         sudo yum install git doxygen
 
    .. tab:: Fedora or RHEL/CentOS (8.x or later)
 
       .. code-block:: bash
 
-         sudo dnf install python3-virtualenv git doxygen
+         sudo dnf install git doxygen
 
-   .. tab:: MacOS X
+   .. tab:: macOS
 
       *Python 3*
 
-      Download the latest Python 3 MacOS X package from
+      If Python 3 is not available on your macOS system, you can
+      download the latest Python 3 macOS package from
       `https://www.python.org <https://www.python.org>`_ and install it.
       This will install both Python 3 and pip3.
 
-      *virtualenv*
-
-      Once Python 3 is installed, open a Terminal and type
-
-      .. code-block:: bash
-
-         pip3 install virtualenv
-
-      This will install virtualenv from the Python Package Index.
-
 Prerequisites for PDF
 ---------------------
 

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
@@ -30,23 +31,29 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
 These links take you to the extra instructions for those select
 packages:
 
+.. this list must be kept in sync with its counterpart in Build_extras.rst
 .. table_from_list::
    :columns: 6
 
    * :ref:`ADIOS <adios>`
    * :ref:`ATC <atc>`
    * :ref:`AWPMD <awpmd>`
-   * :ref:`COLVARS <colvars>`
+   * :ref:`COLVARS <colvar>`
    * :ref:`COMPRESS <compress>`
+   * :ref:`ELECTRODE <electrode>`
    * :ref:`GPU <gpu>`
    * :ref:`H5MD <h5md>`
    * :ref:`INTEL <intel>`
    * :ref:`KIM <kim>`
    * :ref:`KOKKOS <kokkos>`
    * :ref:`LATTE <latte>`
+   * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
+   * :ref:`MDI <mdi>`
    * :ref:`ML-HDNNP <ml-hdnnp>`
+   * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
+   * :ref:`ML-POD <ml-pod>`
    * :ref:`ML-QUIP <ml-quip>`
    * :ref:`MOLFILE <molfile>`
    * :ref:`MSCG <mscg>`
@@ -87,7 +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
 
@@ -96,7 +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:
@@ -112,13 +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
@@ -143,7 +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.
 
 ----------
 
@@ -160,9 +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
-available packages in LAMMPS. If you need a custom preset you can take
-one of them as a starting point and customize it to your needs.
+system. Using these files, you can enable/disable portions of the
+available packages in LAMMPS. If you need a custom preset, you can
+make a copy of one of them and modify it to suit your needs.
 
 .. code-block:: bash
 
@@ -176,7 +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
@@ -220,7 +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
 
@@ -236,40 +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
-sub-directories, but not the copies in the src folder.
+with git <Install_git>`, this will only update the files in the package
+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
-explain how to do this for building both with CMake and make.
+LAMMPS can be built with several optional settings.  Each subsection
+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
-      packages like KOKKOS or OPENMP is used.  If CMake cannot detect
-      the FFT library, you can set these variables to assist:
+      is independent of whether OpenMP threads are enabled and a package
+      like KOKKOS or OPENMP is used.  If CMake cannot detect the FFT
+      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
-access and required communication.  This cost can be reduced by
-performing single-precision FFTs instead of double precision.  Single
-precision means the real and imaginary parts of a complex datum are
-4-byte floats.  Double precision means they are 8-byte doubles.  Note
-that Fourier transform and related PPPM operations are somewhat less
-sensitive to floating point truncation errors and thus the resulting
-error is less than the difference in precision. Using the ``-DFFT_SINGLE``
-setting trades off a little accuracy for reduced memory use and
-parallel communication costs for transposing 3d FFT data.
+Performing 3d FFTs in parallel can be time-consuming due to data access
+and required communication.  This cost can be reduced by performing
+single-precision FFTs instead of double precision.  Single precision
+means the real and imaginary parts of a complex datum are 4-byte floats.
+Double precision means they are 8-byte doubles.  Note that Fourier
+transform and related PPPM operations are somewhat less sensitive to
+floating point truncation errors, and thus the resulting error is
+generally less than the difference in precision. Using the
+``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory
+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
-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
-or how large counters can become before "rolling over".
-The default setting of "smallbig" is almost always adequate.
+LAMMPS uses a few custom integer data types, which can be defined as
+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, or how
+large counters can become before "rolling over".  The default setting of
+"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_all.rst

@@ -24,6 +24,7 @@ table above.
 
    * :doc:`angle_coeff <angle_coeff>`
    * :doc:`angle_style <angle_style>`
+   * :doc:`angle_write <angle_write>`
    * :doc:`atom_modify <atom_modify>`
    * :doc:`atom_style <atom_style>`
    * :doc:`balance <balance>`
@@ -45,6 +46,7 @@ table above.
    * :doc:`dielectric <dielectric>`
    * :doc:`dihedral_coeff <dihedral_coeff>`
    * :doc:`dihedral_style <dihedral_style>`
+   * :doc:`dihedral_write <dihedral_write>`
    * :doc:`dimension <dimension>`
    * :doc:`displace_atoms <displace_atoms>`
    * :doc:`dump <dump>`

doc/src/Commands_bond.rst

@@ -44,6 +44,7 @@ OPT.
    * :doc:`harmonic (iko) <bond_harmonic>`
    * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
    * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
+   * :doc:`lepton (o) <bond_lepton>`
    * :doc:`mesocnt <bond_mesocnt>`
    * :doc:`mm3 <bond_mm3>`
    * :doc:`morse (o) <bond_morse>`
@@ -93,6 +94,7 @@ OPT.
    * :doc:`fourier/simple (o) <angle_fourier_simple>`
    * :doc:`gaussian <angle_gaussian>`
    * :doc:`harmonic (iko) <angle_harmonic>`
+   * :doc:`lepton (o) <angle_lepton>`
    * :doc:`mesocnt <angle_mesocnt>`
    * :doc:`mm3 <angle_mm3>`
    * :doc:`quartic (o) <angle_quartic>`
@@ -127,6 +129,7 @@ OPT.
    * :doc:`fourier (io) <dihedral_fourier>`
    * :doc:`harmonic (iko) <dihedral_harmonic>`
    * :doc:`helix (o) <dihedral_helix>`
+   * :doc:`lepton (o) <dihedral_lepton>`
    * :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
    * :doc:`nharmonic (o) <dihedral_nharmonic>`
    * :doc:`opls (iko) <dihedral_opls>`

doc/src/Commands_compute.rst

@@ -57,6 +57,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`dpd/atom <compute_dpd_atom>`
    * :doc:`edpd/temp/atom <compute_edpd_temp_atom>`
    * :doc:`efield/atom <compute_efield_atom>`
+   * :doc:`efield/wolf/atom <compute_efield_wolf_atom>`
    * :doc:`entropy/atom <compute_entropy_atom>`
    * :doc:`erotate/asphere <compute_erotate_asphere>`
    * :doc:`erotate/rigid <compute_erotate_rigid>`
@@ -87,7 +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>`

doc/src/Commands_fix.rst

@@ -44,9 +44,6 @@ 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 +51,9 @@ 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>`

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>`
@@ -134,6 +134,8 @@ OPT.
    * :doc:`lcbop <pair_lcbop>`
    * :doc:`lebedeva/z <pair_lebedeva_z>`
    * :doc:`lennard/mdf <pair_mdf>`
+   * :doc:`lepton (o) <pair_lepton>`
+   * :doc:`lepton/coul (o) <pair_lepton>`
    * :doc:`line/lj <pair_line_lj>`
    * :doc:`lj/charmm/coul/charmm (giko) <pair_charmm>`
    * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
@@ -164,7 +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>`
@@ -173,7 +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>`
@@ -198,11 +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>`
@@ -236,7 +238,7 @@ OPT.
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`pace (k) <pair_pace>`
-   * :doc:`pace/extrapolation <pair_pace>`
+   * :doc:`pace/extrapolation (k) <pair_pace>`
    * :doc:`pod <pair_pod>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`

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
-the goal of helping developers write new code similar to the existing
-code.  Please see the section on :doc:`Requirements for contributed
-code <Modify_style>` for more specific recommendations and guidelines.
-While that section is organized more in the form of a checklist for
-code contributors, the focus here is on overall code design strategy,
-choices made between possible alternatives, and discussing some
-relevant C++ programming language constructs.
+This section explains some code design choices in LAMMPS with the goal
+of helping developers write new code similar to the existing code.
+Please see the section on :doc:`Requirements for contributed code
+<Modify_style>` for more specific recommendations and guidelines.  While
+that section is organized more in the form of a checklist for code
+contributors, the focus here is on overall code design strategy, choices
+made between possible alternatives, and discussing some relevant C++
+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.
-Data structures and code constructs were used that resemble the
-previous implementation(s) in Fortran.  A contributing factor to this
-choice also was that at the time, C++ compilers were often not mature
-and some of the advanced features contained bugs or did not function
-as the standard required.  There were also disagreements between
-compiler vendors as to how to interpret the C++ standard documents.
+LAMMPS for people without significant training in C++ programming.  Data
+structures and code constructs were used that resemble the previous
+implementation(s) in Fortran.  A contributing factor to this choice was
+that at the time, C++ compilers were often not mature and some advanced
+features contained bugs or did not function as the standard required.
+There were also disagreements between compiler vendors as to how to
+interpret the C++ standard documents.
 
-However, C++ compilers have now advanced significantly.  In 2020 we
-decided to to require the C++11 standard as the minimum C++ language
-standard for LAMMPS.  Since then we have begun to also replace some of
-the C-style constructs with equivalent C++ functionality, either from
-the C++ standard library or as custom classes or functions, in order
-to improve readability of the code and to increase code reuse through
-abstraction of commonly used functionality.
+However, C++ compilers and the C++ programming language have advanced
+significantly.  In 2020, the LAMMPS developers decided to require the
+C++11 standard as the minimum C++ language standard for LAMMPS.  Since
+then, we have begun to replace C-style constructs with equivalent C++
+functionality.  This was taken either from the C++ standard library or
+implemented as custom classes or functions.  The goal is to improve
+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
-   of legacy code in LAMMPS that has not yet been refactored to
-   reflect these style conventions in full.  LAMMPS has a large code
-   base and many different contributors and there also is a hierarchy
-   of precedence in which the code is adapted.  Highest priority has
-   been the code in the ``src`` folder, followed by code in packages
-   in order of their popularity and complexity (simpler code is
-   adapted sooner), followed by code in the ``lib`` folder.  Source
-   code that is downloaded from external packages or libraries during
-   compilation is not subject to the conventions discussed here.
+   Please note that as of spring 2023 there is still a sizable chunk of
+   legacy code in LAMMPS that has not yet been refactored to reflect
+   these style conventions in full.  LAMMPS has a large code base and
+   many contributors.  There is also a hierarchy of precedence in which
+   the code is adapted.  Highest priority has been the code in the
+   ``src`` folder, followed by code in packages in order of their
+   popularity and complexity (simpler code gets adapted sooner), followed
+   by code in the ``lib`` folder.  Source code that is downloaded from
+   external packages or libraries during compilation is not subject to
+   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
-can be called at different points in time within a timestep, as
-explained in `Developer_flow`.  This allows the input script to tailor
-how a specific simulation is run, what diagnostic computations are
-performed, and how the output of those computations is further
-processed or output.
+different facet of LAMMPS' flexibility, as they provide methods which
+can be called at different points within a timestep, as explained in
+`Developer_flow`.  This allows the input script to tailor how a specific
+simulation is run, what diagnostic computations are performed, and how
+the output of those computations is further 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
-``Base::normal()``.  But for the `base2->call()` case the call of the
+same scope: that is, ``Base::call()`` will always call
+``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
-scope of the class type that was used to *create* the class instance are
-invoked; even if they are assigned to a pointer using the type of a base
-class.  This is the desired behavior and this way LAMMPS can even use
-styles that are loaded at runtime from a shared object file with the
-:doc:`plugin command <plugin>`.
+instead.  This mechanism results in calling functions that are within
+the scope of the class that was used to *create* the instance, even if
+they are assigned to a pointer for their base class.  This is the
+desired behavior, and this way LAMMPS can even use styles that are loaded
+at runtime from a shared object file with the :doc:`plugin command
+<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
-derived class and thus it is good practice to either avoid calling them
+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
 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
-   override which and which arguments need to be declared.
+   avoided, as they lead to confusion over which function is supposed to
+   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
-behavior. use of the latter is strongly discouraged.  Also output to
-the screen should not use the predefined ``stdout`` FILE pointer, but
-rather the ``screen`` and ``logfile`` FILE pointers managed by the
-LAMMPS class.  Furthermore, output should generally only be done by
-MPI rank 0 (``comm->me == 0``).  Output that is sent to both
-``screen`` and ``logfile`` should use the :cpp:func:`utils::logmesg()
-convenience function <LAMMPS_NS::utils::logmesg>`.
+Since mixing "stdio" and "iostreams" can lead to unexpected behavior,
+use of the latter is strongly discouraged.  Output to the screen should
+*not* use the predefined ``stdout`` FILE pointer, but rather the
+``screen`` and ``logfile`` FILE pointers managed by the LAMMPS class.
+Furthermore, output should generally only be done by MPI rank 0
+(``comm->me == 0``).  Output that is sent to both ``screen`` and
+``logfile`` should use the :cpp:func:`utils::logmesg() convenience
+function <LAMMPS_NS::utils::logmesg>`.
 
-We also discourage the use of stringstreams because the bundled {fmt}
-library and the customized tokenizer classes can provide the same
-functionality in a cleaner way with better performance.  This also
-helps maintain a consistent programming syntax with code from many
-different contributors.
+We discourage the use of stringstreams because the bundled {fmt} library
+and the customized tokenizer classes provide the same functionality in a
+cleaner way with better performance.  This also helps maintain a
+consistent programming syntax with code from many different
+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
-``std::string`` class instance.  In contrast to the ``%`` placeholder
-in ``printf()``, the {fmt} library uses ``{}`` to embed format
-descriptors.  In the simplest case, no additional characters are
-needed as {fmt} will choose the default format based on the data type
-of the argument.  Otherwise the ``fmt::print()`` function may be
-used instead of ``printf()`` or ``fprintf()``.  In addition, several
-LAMMPS output functions, that originally accepted a single string as
-argument have been overloaded to accept a format string with optional
-arguments as well (e.g., ``Error::all()``, ``Error::one()``,
-``utils::logmesg()``).
+``fmt::format()`` function, which will return a string as a
+``std::string`` class instance.  In contrast to the ``%`` placeholder in
+``printf()``, the {fmt} library uses ``{}`` to embed format descriptors.
+In the simplest case, no additional characters are needed, as {fmt} will
+choose the default format based on the data type of the argument.
+Otherwise, the ``fmt::print()`` function may be used instead of
+``printf()`` or ``fprintf()``.  In addition, several LAMMPS output
+functions, that originally accepted a single string as argument have
+been overloaded to accept a format string with optional arguments as
+well (e.g., ``Error::all()``, ``Error::one()``, ``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
-common case for using argument id would be to use the same argument in
-multiple places in the format string without having to provide it as an
-argument multiple times. In LAMMPS the argument id is rarely used.
+default, these are assigned in order (i.e. 0, 1, 2, 3, 4 etc.).  The
+most common case for using argument id would be to use the same argument
+in multiple places in the format string without having to provide it as
+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
-characters; "{:<8}" would do this as left aligned, "{:^8}" as centered,
-"{:>8}" as right aligned.  If a specific presentation is selected, the
-argument type must be compatible or else the {fmt} formatting code will
-throw an exception. Some format string examples are given below:
+The format string "{:8}" would thus represent *any* type argument and be
+replaced by at least 8 characters; "{:<8}" would do this as left
+aligned, "{:^8}" as centered, "{:>8}" as right aligned.  If a specific
+presentation is selected, the argument type must be compatible or else
+the {fmt} formatting code will throw an exception.  Some format string
+examples are given below:
 
 .. code-block:: c++
 
@@ -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
-the C++ commands "new" and "delete/delete[].  Large data should use
-the member functions of the ``Memory`` class, most commonly,
-``Memory::create()``, ``Memory::grow()``, and ``Memory::destroy()``,
-which provide variants for vectors, 2d arrays, 3d arrays, etc.
-These can also be used for small data.
+Dynamical allocation of small data and objects can be done with the C++
+commands "new" and "delete/delete[]".  Large data should use the member
+functions of the ``Memory`` class, most commonly, ``Memory::create()``,
+``Memory::grow()``, and ``Memory::destroy()``, which provide variants
+for vectors, 2d arrays, 3d arrays, etc.  These can also be used for
+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
-  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
-  LAMMPS and triggers a global abort
-- allocation of multi-dimensional arrays will be done in a C compatible
-  fashion but so that the storage of the actual data is stored in one
-  large contiguous block.  Thus when MPI communication is needed,
+- Memory allocation failures on *any* MPI rank during a parallel run
+  will trigger an immediate abort of the entire parallel calculation.
+- A failing "new" will trigger an exception, which is also captured by
+  LAMMPS and triggers a global abort.
+- Allocation of multidimensional arrays will be done in a C compatible
+  fashion, but such that the storage of the actual data is stored in one
+  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
-  pointers
-- the "destroy()" functions will nullify the pointer variables making
-  "use after free" errors easy to detect
-- it is possible to use a larger than default memory alignment (not on
+- The "destroy()" and "sfree()" functions may safely be called on NULL
+  pointers.
+- The "destroy()" functions will nullify the pointer variables, thus
+  making "use after free" errors easy to detect.
+- 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
-variables that are class members should be initialized to a
-``nullptr`` value in their respective constructors.  That way it is
-safe to call ``Memory::destroy()`` or ``delete[]`` on them before
-*any* allocation outside the constructor.  This helps prevent memory
-leaks.
+In the practical implementation of code this means, that any pointer
+variables, that are class members should be initialized to a ``nullptr``
+value in their respective constructors.  That way, it is safe to call
+``Memory::destroy()`` or ``delete[]`` on them before *any* allocation
+outside the constructor.  This helps prevent memory 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
-atoms within a cutoff distance of its sub-domain.
+task) owns atoms within its subdomain and additionally stores ghost
+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:
@@ -70,7 +70,7 @@ 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
@@ -81,11 +81,11 @@ containing ``double`` values.  To correctly store integers that may be
 
 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
-that the size of each datum can be different.  Typically this is used
+The *create_atom()* and *exchange_atom()* methods are similar, except
+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
-code is shown below.  In the actual code in ``src/verlet.cpp`` some of
-these operations are conditionally invoked.
+Now for the ``Verlet::run()`` method.  Its basic structure in hi-level
+pseudocode is shown below.  In the actual code in ``src/verlet.cpp``
+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
-script, that are flagged to have an ``initial_integrate()`` method are
+the timestep pseudocode.  All the active fixes defined in an input
+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
-similar to that of a molecular dynamics timestep.  Forces are computed,
-neighbor lists are built as needed, atoms migrate to new processors, and
-atom coordinates and forces are communicated to neighboring processors.
-The only difference is what Fix class operations are invoked when.  Only
-a subset of LAMMPS fixes are useful during energy minimization, as
+The flow of control during energy minimization iterations is similar to
+that of a molecular dynamics timestep.  Forces are computed, neighbor
+lists are built as needed, atoms migrate to new processors, and atom
+coordinates and forces are communicated to neighboring processors.  The
+only difference is what Fix class operations are invoked when.  Only a
+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()``.
-Each fix is invoked at the appropriate place within the minimization
-iteration.  For example, the ``min_post_force()`` method is analogous to
-the ``post_force()`` method for dynamics; it is used to alter or constrain
-forces on each atom, which affects the minimization procedure.
+are ``min_pre_exchange()``, ``min_pre_force()``, and
+``min_post_force()``.  Each fix is invoked at the appropriate place
+within the minimization iteration.  For example, the
+``min_post_force()`` method is analogous to the ``post_force()`` method
+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
-sub-domains is the global simulation box.  If a grid point is on the
-boundary of two sub-domains, the lower processor owns the grid cell.  A
+within the processor's spatial subdomain.  The union of processor
+subdomains is the global simulation box.  If a grid point is on the
+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
-its grid reference arguments are for grids of the same size.
+global size of the grid, to ensure it is of the expected 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

@@ -102,7 +102,7 @@ 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++
@@ -361,7 +361,7 @@ 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
-package are in all-uppercase sub-directories of the ``src`` folder, for
+LAMMPS binary, so they cannot be mixed.  The source files for each
+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,
-if the corresponding package is installed.
+as Fortran or CUDA. These libraries included in the LAMMPS build, if the
+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
-:doc:`run <run>` command in a LAMMPS input script.  As this example
+:cpp:class:`LAMMPS_NS::Run` class, which contains the code invoked by
+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
-which may have different conventions, all C and C++ header files have a
-``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a
-``.c`` extension. A small number of C++ classes and utility functions
-are implemented with only a ``.h`` file. Examples are the Pointers and
-Commands classes or the MathVec functions.
+underscore character '_' to separate words. Apart from bundled,
+externally maintained libraries, which may have different conventions,
+all C and C++ header files have a ``.h`` extension, all C++ files have a
+``.cpp`` extension, and C files a ``.c`` extension.  A few C++ classes
+and utility functions are implemented with only a ``.h`` file. Examples
+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
-of the arrow holds a pointer to an instance of the class at the tip.
-Dashed lines instead represent inheritance: the class to the tip of the
-arrow is derived from the class at the base.  Classes with a red boundary
-are not instantiated directly, but they represent the base classes for
-"styles".  Those "styles" make up the bulk of the LAMMPS code and only
-a few representative examples are included in the figure so it remains
-readable.
+lines in the figure represent compositing: that is, the class at the
+base of the arrow holds a pointer to an instance of the class at the
+tip.  Dashed lines instead represent inheritance: the class at the tip
+of the arrow is derived from the class at the base.  Classes with a red
+boundary are not instantiated directly, but they represent the base
+classes for "styles".  Those "styles" make up the bulk of the LAMMPS
+code and only a few representative examples are included in the figure,
+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
-   LAMMPS 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
-   the core is the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class, which
-   holds pointers to class instances with specific purposes.  Those may
-   hold instances of other classes, sometimes directly, or only
-   temporarily, sometimes as derived classes or derived classes of
-   derived classes, which may also hold instances of other classes.
+      This figure shows relations of base classes of the LAMMPS
+      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 the core is the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class,
+      which holds pointers to class instances with specific purposes.
+      Those may hold instances of other classes, sometimes directly, or
+      only temporarily, sometimes as derived classes or derived 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
-a composite holding pointers to instances of other core classes
+represents what is generally referred to as an "instance of LAMMPS".  It
+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
-:cpp:class:`LAMMPS_NS::Pointers`.  To initialize the pointer references
-in Pointers, a pointer to the LAMMPS class instance needs to be passed
-to the constructor and thus all constructors for classes derived from it
-must do so and pass this pointer to the constructor for Pointers.
+columns, that are not listed as derived classes, are instead derived
+from :cpp:class:`LAMMPS_NS::Pointers`.  To initialize the pointer
+references in Pointers, a pointer to the LAMMPS class instance needs to
+be passed to the constructor. All constructors for classes derived from
+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
-representing the core functionality.  There are a handful of virtual
-parent classes in LAMMPS that define what LAMMPS calls ``styles``.  They
-are shaded red in the :ref:`class-topology` figure.  Each of these are
-parents of a number of child classes that implement the interface
-defined by the parent class.  There are two main categories of these
-``styles``: some may only have one instance active at a time (e.g. atom,
-pair, bond, angle, dihedral, improper, kspace, comm) and there is a
-dedicated pointer variable for each of them in the composite class.
+The LAMMPS class currently holds instances of 19 classes representing
+the core functionality.  There are a handful of virtual parent classes
+in LAMMPS that define what LAMMPS calls ``styles``.  These are shaded
+red in the :ref:`class-topology` figure.  Each of these are parents of a
+number of child classes that implement the interface defined by the
+parent class.  There are two main categories of these ``styles``: some
+may only have one instance active at a time (e.g. atom, pair, bond,
+angle, dihedral, improper, kspace, comm) and there is a dedicated
+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
-manages and forwards calls to the corresponding sub-styles for the
-designated subset of atoms or data.  The composite class may also have
-lists of class instances, e.g. Modify handles lists of compute and fix
-styles, while Output handles a list of dump class instances.
+*hybrid* class instance that acts as a proxy, and manages and forwards
+calls to the corresponding sub-style class instances for the designated
+subset of atoms or data.  The composite class may also have lists of
+class instances, e.g. ``Modify`` handles lists of compute and fix
+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,
-  stores variables, and invokes :doc:`commands <Commands_all>`.
+- The Input class reads and processes input (strings and files), stores
+  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.
 
@@ -206,18 +209,22 @@ follows:
   class stores a single list (for all atoms).  A NeighRequest class
   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
-  will try to optimize how they are computed by creating copies or
-  sub-lists where possible.
+  to select the neighbor list settings for the given request.  There can
+  be multiple instances of the NeighRequest class. The Neighbor class
+  will try to optimize how the requests are processed.  Depending on the
+  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.
-  Sometimes the Irregular class is used, when atoms may migrate to
-  arbitrary processors.
+  <comm_style>`, enabling different ways to perform the domain
+  decomposition.
+
+- 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
-processes need not only access to data of atoms they "own" but also
-information about atoms from neighboring sub-domains, in LAMMPS referred
+types, etc.)  To be able to compute the short-range interactions, MPI
+processes need not only access to the data of atoms they "own" but also
+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
-   dashed-line box is the extended sub-domain of processor 0 which
+   subdomains are drawn spatially separated for clarity.  The
+   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
-   with an 8x8x8 3d FFT grid, partitioned across 64 processors.
-   Within each of the 4 diagrams, grid cells of the same color are
-   owned by a single processor; for simplicity only cells owned by 4
-   or 8 of 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.
+      Stages of a parallel FFT for a simulation domain overlaid with an
+      8x8x8 3d FFT grid, partitioned across 64 processors.  Within each
+      of the 4 diagrams, grid cells of the same color are owned by a
+      single processor; for simplicity, only cells owned by 4 or 8 of
+      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
-grid cannot be decomposed like atoms into 3 dimensions for parallel
+along the *x-*, *y-*, and *z-*\ direction of the FFT grid.  Thus, the
+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,
-  the dominant cost for parallel FFTs is often the communication, not
-  the computation of 1d FFTs, even though the latter scales as :math:`N
-  \log(N)` in the number of grid points *N* per grid direction.  This is
-  due to the fact that only a 2d decomposition into pencils is possible
-  while atom data (and their corresponding short-range force and energy
-  computations) can be decomposed efficiently in 3d.
+- For large systems and particularly many MPI processes, the dominant
+  cost for parallel FFTs is often the communication, not the computation
+  of 1d FFTs, even though the latter scales as :math:`N \log(N)` in the
+  number of grid points *N* per grid direction.  This is due to the fact
+  that only a 2d decomposition into pencils is possible while atom data
+  (and their corresponding short-range force and energy computations)
+  can be decomposed efficiently in 3d.
 
-  This can be addressed by reducing the number of MPI processes involved
-  in the MPI communication by using :doc:`hybrid MPI + OpenMP
-  parallelization <Speed_omp>`.  This will use OpenMP parallelization
-  inside the MPI domains and while that may have a lower parallel
-  efficiency, it reduces the communication overhead.
+  Reducing the number of MPI processes involved in the MPI communication
+  will reduce this kind of overhead.  By using a :doc:`hybrid MPI +
+  OpenMP parallelization <Speed_omp>` it is still possible to use all
+  processes for parallel computation.  It will use OpenMP
+  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
-  sub-domain of the FFT grid decomposition and where pairwise non-bonded
+  "1:*p*" mapping of *p* subdomains of the atom decomposition to one
+  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
-neighbor list cutoff distance.  In LAMMPS the neighbor lists are stored
-in a multiple-page data structure; each page is a contiguous chunk of
-memory which stores vectors of neighbor atoms *j* for many *i* atoms.
-This allows pages to be incrementally allocated or deallocated in blocks
-as needed.  Neighbor lists typically consume the most memory of any data
+*j* = owned or ghost) with separation less than the applicable neighbor
+list cutoff distance.  In LAMMPS, the neighbor lists are stored in a
+multiple-page data structure; each page is a contiguous chunk of memory
+which stores vectors of neighbor atoms *j* for many *i* atoms.  This
+allows pages to be incrementally allocated or deallocated in blocks as
+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
-   augmented sub-domain is shown.  In the triclinic case it overlaps the
+   align with subdomain boundaries; only the portion overlapping 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
-neighbor bins which overlap its sub-domain extended by the neighbor
+single MPI processor's subdomain.  Each processor stores a set of
+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
-bounding box of the entire triclinic domain and thus are not periodic
-with respect to the simulation box itself.  The stencil and logic for
-determining which *i,j* pairs to include in the neighbor list are
-altered slightly to account for this.
+triclinic stencil has extra bins because the bins tile the bounding box
+of the entire triclinic domain, and thus are not periodic with respect
+to the simulation box itself.  The stencil and logic for determining
+which *i,j* pairs to include in the neighbor list are altered slightly
+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
-  depends only on the distance between two atoms and the cutoff
+  criteria for inclusion of a pairwise interaction.  Typically, this
+  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
-  and thus reduce the chance of a load imbalance.
+  "owned" atom, and thus it should lead to similar length neighbor lists
+  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.
-It is used instead of extending the corresponding storage to per-thread
-arrays to avoid slowdowns due to "false sharing" when multiple threads
-update adjacent elements in an array and thus force the CPU cache lines
-to be reset and re-fetched.  ``FixOMP`` finally manages the "multi-thread
+``ThrData`` is a class that manages per-thread data structures.  It is
+used instead of extending the corresponding storage to per-thread arrays
+to avoid slowdowns due to "false sharing" when multiple threads update
+adjacent elements in an array and thus force the CPU cache lines to be
+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
-   could happen
-4) use atomic operations when updating per-atom properties
-5) use replicated per-thread data structures to accumulate data without
+3. Use mutexes around functions and regions of code where the data race
+   could happen.
+4. Use atomic operations when updating per-atom properties.
+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
-   MPI process. The green dashed lines indicate how sub-domains are
-   extended with "ghost" atoms up to the communication cutoff distance.
+      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
+      subdomains, and the contained atoms are "owned" by the
+      corresponding MPI process. The green dashed lines indicate how
+      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
-or triclinic in shape, as illustrated in the :ref:`domain-decomposition`
-figure for the 2d case.  Orthogonal means the box edges are aligned with
-the *x*, *y*, *z* Cartesian axes, and the box faces are thus all
-rectangular.  Triclinic allows for a more general parallelepiped shape
-in which edges are aligned with three arbitrary vectors and the box
-faces are parallelograms.  In each dimension box faces can be periodic,
-or non-periodic with fixed or shrink-wrapped boundaries.  In the fixed
-case, atoms which move outside the face are deleted; shrink-wrapped
-means the position of the box face adjusts continuously to enclose all
-the atoms.
+The LAMMPS simulation box is a 3d or 2d volume, which can be of
+orthogonal or triclinic shape, as illustrated in the
+:ref:`domain-decomposition` figure for the 2d case.  Orthogonal means
+the box edges are aligned with the *x*, *y*, *z* Cartesian axes, and the
+box faces are thus all rectangular.  Triclinic allows for a more general
+parallelepiped shape in which edges are aligned with three arbitrary
+vectors and the box faces are parallelograms.  In each dimension, box
+faces can be periodic, or non-periodic with fixed or shrink-wrapped
+boundaries.  In the fixed case, atoms which move outside the face are
+deleted; shrink-wrapped means the position of the box face adjusts
+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
-grid and all sub-domains are identical in size and shape.  Both the
+:ref:`domain-decomposition` figure.  The subdomains comprise a regular
+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
-with several MPI ranks without atoms (left). By forcing a 1x12x1
-processor grid, every MPI rank does computations now, but number of
-atoms per sub-domain is still uneven and the thin slice shape increases
-the amount of communication between sub-domains (center left). With a
-2x6x1 processor grid and shifting the sub-domain divisions, the load
-imbalance is further reduced and the amount of communication required
-between sub-domains is less (center right).  And using the recursive
-bisectioning leads to further improved decomposition (right).
+Due to the vacuum in the system, the default decomposition is
+unbalanced, with several MPI ranks without atoms (left). By forcing a
+1x12x1 processor grid, every MPI rank does computations now, but the
+number of atoms per subdomain is still uneven, and the thin slice shape
+increases the amount of communication between subdomains (center
+left). With a 2x6x1 processor grid and shifting the subdomain divisions,
+the load imbalance is further reduced and the amount of communication
+required between subdomains is less (center right).  And using the
+recursive bisectioning leads to further improved decomposition (right).

doc/src/Developer_parallel.rst

@@ -3,11 +3,11 @@ Parallel algorithms
 
 LAMMPS is designed to enable running simulations in parallel using the
 MPI parallel communication standard with distributed data via domain
-decomposition.  The parallelization aims to be efficient result in good
-strong scaling (= good speedup for the same system) and good weak
-scaling (= the computational cost of enlarging the system is
+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_unittest.rst

@@ -489,7 +489,7 @@ to update the YAML files. Running a command like
 
 .. code-block:: bash
 
-   $ test_pair_style mol-pair-lennard_mdf.yaml -g new.yaml
+   test_pair_style mol-pair-lennard_mdf.yaml -g new.yaml
 
 will read the settings from the ``mol-pair-lennard_mdf.yaml`` file and then compute
 the reference data and write a new file with to ``new.yaml``.  If this step fails,
@@ -500,13 +500,13 @@ It is also possible to do an update in place with:
 
 .. code-block:: bash
 
-   $ test_pair_style mol-pair-lennard_mdf.yaml -u
+   test_pair_style mol-pair-lennard_mdf.yaml -u
 
 And one can finally run the full set of tests with:
 
 .. code-block:: bash
 
-   $ test_pair_style mol-pair-lennard_mdf.yaml
+   test_pair_style mol-pair-lennard_mdf.yaml
 
 This will just print a summary of the groups of tests.  When using the "-v" flag
 the test will also keep any LAMMPS output and when using the "-s" flag, there

doc/src/Developer_utils.rst

@@ -647,7 +647,7 @@ 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

@@ -40,7 +40,7 @@ We use it to show how to identify the origin of a segmentation fault.
 
 After recompiling LAMMPS and running the input you should get something like this:
 
-.. code-block::
+.. code-block:: console
 
    $ ./lmp -in in.melt
    LAMMPS (19 Mar 2020)
@@ -90,8 +90,9 @@ it.  When it reaches the code causing the segmentation fault, it will
 stop with a message why it stopped, print the current line of code, and
 drop back to the GDB prompt.
 
-.. code-block::
+.. code-block:: console
 
+   (gdb) run
    [...]
    Setting up Verlet run ...
      Unit style    : lj
@@ -106,7 +107,7 @@ drop back to the GDB prompt.
 Now typing the command "where" will show the stack of functions starting from
 the current function back to "main()".
 
-.. code-block::
+.. code-block:: console
 
    (gdb) where
    #0  0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x829740, eflag=1, vflag=<optimized out>) at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139
@@ -124,7 +125,7 @@ You can also print the value of variables and see if there is anything
 unexpected.  Segmentation faults, for example, commonly happen when a
 pointer variable is not assigned and still initialized to NULL.
 
-.. code-block::
+.. code-block:: console
 
    (gdb) print x
    $1 = (double **) 0x7ffff7ca1010
@@ -153,7 +154,7 @@ utility to the current folder. Example: ``coredumpctl -o core dump lmp``.
 Now you can launch the debugger to load the executable, its debug info
 and the core dump and drop you to a prompt like before.
 
-.. code-block::
+.. code-block:: console
 
    $ gdb lmp core
    Reading symbols from lmp...
@@ -186,7 +187,7 @@ recommended to redirect the valgrind output to a file (e.g. with
 process ID) so that the messages of the multiple valgrind instances to
 the console are not mixed.
 
-.. code-block::
+.. code-block:: console
 
    $ valgrind ./lmp -in in.melt
    ==1933642== Memcheck, a memory error detector

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

@@ -5,46 +5,67 @@ The :f:mod:`LIBLAMMPS` module provides an interface to call LAMMPS from
 Fortran.  It is based on the LAMMPS C library interface and requires a
 fully Fortran 2003-compatible compiler to be compiled.  It is designed
 to be self-contained and not require any support functions written in C,
-C++, or Fortran other than those in the C library interface and the module
-itself.
+C++, or Fortran other than those in the C library interface and the
+LAMMPS Fortran module itself.
 
 While C libraries have a defined binary interface (ABI) and can thus be
-used from multiple compiler versions from different vendors as long
-as they are compatible with the hosting operating system, the same is
-not true for Fortran programs.  Thus, the LAMMPS Fortran module needs to be
+used from multiple compiler versions from different vendors as long as
+they are compatible with the hosting operating system, the same is not
+true for Fortran programs.  Thus, the LAMMPS Fortran module needs to be
 compiled alongside the code using it from the source code in
-``fortran/lammps.f90``.  When linking, you also need to
-:doc:`link to the LAMMPS library <Build_link>`.  A typical command line
-for a simple program using the Fortran interface would be:
+``fortran/lammps.f90`` *and* with the same compiler used to build the
+rest of the Fortran code that interfaces to LAMMPS.  When linking, you
+also need to :doc:`link to the LAMMPS library <Build_link>`.  A typical
+command line for a simple program using the Fortran interface would be:
 
 .. code-block:: bash
 
    mpifort -o testlib.x lammps.f90 testlib.f90 -L. -llammps
 
 Please note that the MPI compiler wrapper is only required when the
-calling the library from an MPI-parallelized program.  Otherwise, using
-the plain Fortran compiler (gfortran, ifort, flang, etc.) will suffice.
-It may be necessary to link to additional libraries, depending on how
-LAMMPS was configured and whether the LAMMPS library :doc:`was compiled
-as a static or dynamic library <Build_link>`.
+calling the library *from* an MPI-parallelized program.  Otherwise,
+using the plain Fortran compiler (gfortran, ifort, flang, etc.) will
+suffice, since there are no direct references to MPI library features,
+definitions and subroutine calls; MPI communicators are referred to by
+their integer index representation as required by the Fortran MPI
+interface.  It may be necessary to link to additional libraries,
+depending on how LAMMPS was configured and whether the LAMMPS library
+:doc:`was compiled as a static or dynamic library <Build_link>`.
 
 If the LAMMPS library itself has been compiled with MPI support, the
-resulting executable will still be able to run LAMMPS in parallel with
-``mpirun``, ``mpiexec``, or equivalent.  Please also note that the order
-of the source files matters: the ``lammps.f90`` file needs to be
-compiled first, since it provides the :f:mod:`LIBLAMMPS` module that is
-imported by the Fortran code that uses the 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.
+resulting executable will be able to run LAMMPS in parallel with
+``mpirun``, ``mpiexec``, or equivalent.  This may be either on the
+"world" communicator or a sub-communicator created by the calling
+Fortran code.  If, on the other hand, the LAMMPS library has been
+compiled **without** MPI support, each LAMMPS instance will run
+independently using just one processor.
 
-.. versionadded:: 9Oct2020
+Please also note that the order of the source files matters: the
+``lammps.f90`` file needs to be compiled first, since it provides the
+:f:mod:`LIBLAMMPS` module that would need to be imported by the calling
+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.
+
+.. 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::
 
-   A contributed Fortran interface that more closely resembles the C library
-   interface is available in the ``examples/COUPLE/fortran2`` folder.  Please
-   see the ``README`` file in that folder for more information about it and how
-   to contact its author and maintainer.
+   A contributed Fortran interface is available in the
+   ``examples/COUPLE/fortran2`` folder.  However, since the completion
+   of the :f:mod:`LIBLAMMPS` module, this interface is now deprecated,
+   no longer actively maintained and will likely be removed in the
+   future.  Please see the ``README`` file in that folder for more
+   information about it and how to contact its author and maintainer.
 
 ----------
 
@@ -291,6 +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`
@@ -1520,6 +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
@@ -1562,6 +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
@@ -2391,7 +2555,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    mode. The function should have Fortran language bindings with the following
    interface, which depends on how LAMMPS was compiled:
 
-   .. code-block:: Fortran
+   .. code-block:: fortran
 
       ABSTRACT INTERFACE
         SUBROUTINE external_callback(caller, timestep, ids, x, fexternal)
@@ -2450,7 +2614,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
       with ``-DLAMMPS_SMALLBIG``) that applies something akin to Hooke's Law
       (with each atom having a different *k* value) is shown below.
 
-      .. code-block:: Fortran
+      .. code-block:: fortran
 
          MODULE stuff
            USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double, c_int64_t

doc/src/Howto.rst

@@ -4,10 +4,10 @@ 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
-example input scripts included in the examples directory of the LAMMPS
-distribution and highlighted on the :doc:`Examples <Examples>` doc page
-also show how to setup and run various kinds of simulations.
+terminology, with links to corresponding LAMMPS manual pages.  The
+example input scripts included in the ``examples`` directory of the LAMMPS
+source code distribution and highlighted on the :doc:`Examples` page
+also show how to set up and run various kinds of simulations.
 
 General 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_amoeba.rst

@@ -261,11 +261,11 @@ all the options available to use with the tinker2lmp.py script:
 
 .. code-block:: bash
 
-   % python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba                # AMOEBA non-periodic system
-   % python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo                   # HIPPO non-periodic system
-   % python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643    # AMOEBA periodic system
-   % python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643       # HIPPO periodic system
-   % python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin.new -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data.new   # system with bitorsions
+   python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba                # AMOEBA non-periodic system
+   python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo                   # HIPPO non-periodic system
+   python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643    # AMOEBA periodic system
+   python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643       # HIPPO periodic system
+   python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin.new -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data.new   # system with bitorsions
 
 Switches and their arguments may be specified in any order.
 

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
-larger than the atomistic scale. Particles within a solid region are
+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
-orientation for rotational models. This produces a stress free initial
-state. Furthermore, bonds are allowed to break under large strains
+between the two particles, but can also include data on the bond
+orientation for rotational models. This produces a stress-free initial
+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
-create solid grains.
+:doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` to create
+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
-package. The first bond style, :doc:`bond bpm/spring
-<bond_bpm_spring>`, only applies pairwise, central body forces. Point
-particles must have :doc:`bond atom style <atom_style>` and may be
-thought of as nodes in a spring network. Alternatively, the second
-bond style, :doc:`bond bpm/rotational <bond_bpm_rotational>`, resolves
-tangential forces and torques arising with the shearing, bending, and
-twisting of the bond due to rotation or displacement of particles.
-Particles are similar to those used in the :doc:`granular package
-<Howto_granular>`, :doc:`atom style sphere <atom_style>`. However,
-they must also track the current orientation of particles and store bonds
-and therefore use a :doc:`bpm/sphere atom style <atom_style>`.
-This also requires a unique integrator :doc:`fix nve/bpm/sphere
-<fix_nve_bpm_sphere>` which numerically integrates orientation similar
-to :doc:`fix nve/asphere <fix_nve_asphere>`.
+Currently, there are two types of bonds included in the BPM package. The
+first bond style, :doc:`bond bpm/spring <bond_bpm_spring>`, only applies
+pairwise, central body forces. Point particles must have :doc:`bond atom
+style <atom_style>` and may be thought of as nodes in a spring
+network. Alternatively, the second bond style, :doc:`bond bpm/rotational
+<bond_bpm_rotational>`, resolves tangential forces and torques arising
+with the shearing, bending, and twisting of the bond due to rotation or
+displacement of particles.  Particles are similar to those used in the
+:doc:`granular package <Howto_granular>`, :doc:`atom style sphere
+<atom_style>`. However, they must also track the current orientation of
+particles and store bonds, and therefore use a :doc:`bpm/sphere atom
+style <atom_style>`.  This also requires a unique integrator :doc:`fix
+nve/bpm/sphere <fix_nve_bpm_sphere>` which numerically integrates
+orientation similar to :doc:`fix nve/asphere <fix_nve_asphere>`.
 
 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.
-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.
+.. note::
+
+   The :doc:`create_bonds <create_bonds>` command requires certain
+   :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
-in LAMMPS. However, there are some exceptions that allow for bonds to
-break including the :doc:`quartic bond style <bond_quartic>` and the
+Typically, bond interactions persist for the duration of a simulation in
+LAMMPS. However, there are some exceptions that allow for bonds to
+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/rotational <bond_bpm_rotational>` bond styles. In these cases,
-a bond can be broken if it is stretched beyond a user-defined threshold.
-LAMMPS accomplishes this by setting the bond type to zero such that the
-bond force is no longer computed.
+:doc:`bpm/spring <bond_bpm_spring>` and :doc:`bpm/rotational
+<bond_bpm_rotational>` bond styles. In these cases, a bond can be broken
+if it is stretched beyond a user-defined threshold.  LAMMPS accomplishes
+this by setting the bond type to 0, such that the bond force is no
+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

@@ -46,7 +46,7 @@ This tutorial assumes that you are operating in a command-line environment
 using a shell like Bash.
 
 - Linux: any Terminal window will work
-- MacOS X: launch the Terminal application.
+- macOS: launch the Terminal application.
 - Windows 10: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>`
 
 We also assume that you have downloaded and unpacked a recent LAMMPS source code package
@@ -56,7 +56,7 @@ You should change into the top level directory of the LAMMPS source tree all
 paths mentioned in the tutorial are relative to that.  Immediately after downloading
 it should look like this:
 
-.. code-block:: bash
+.. code-block:: console
 
     $ ls
     bench  doc       lib      potentials  README  tools
@@ -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
@@ -104,7 +104,7 @@ the progress of the configuration printed to the screen followed by a
 summary of the enabled features, options and compiler settings. A typical
 summary screen will look like this:
 
-.. code-block::
+.. code-block:: console
 
    $ cmake ../cmake/
    -- The CXX compiler identification is GNU 8.2.0

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
-advantages and disadvantages, which you will have to think about in the
-context of your application.
+LAMMPS can be coupled to other codes in at least 4 different ways.  Each
+has advantages and disadvantages, which you will have to think about in
+the context of your application.
 
-1. Define a new :doc:`fix <fix>` command that calls the other code.
-   In this scenario, LAMMPS is the driver code.  During timestepping,
-   the fix is invoked, and can make library calls to the other code,
-   which has been linked to LAMMPS as a library.  This is the way the
+1. Define a new :doc:`fix <fix>` command that calls the other code.  In
+   this scenario, LAMMPS is the driver code.  During timestepping, the
+   fix is invoked, and can make library calls to the other code, which
+   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
-   how to add a new fix to LAMMPS.
+   details.  Also see the :doc:`Modify <Modify>` pages for information
+   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
-   to add a new command to LAMMPS.
+   See the :doc:`Modify command <Modify_command>` page for information
+   on how to add a new command to LAMMPS.
 
 .. spacer
 
-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
-   code could link and call both LAMMPS and another code as libraries.
-   Again, the :doc:`run <run>` command has options that allow it to be
-   invoked with minimal overhead (no setup or clean-up) if you wish to
-   do multiple short runs, driven by another program.  Details about
-   using the library interface are given in the :doc:`library API
-   <Library>` documentation.
+3. Use LAMMPS as a library called by another code.  In this case, the
+   other code is the driver and calls LAMMPS as needed.  Alternately, a
+   wrapper code could link and call both LAMMPS and another code as
+   libraries.  Again, the :doc:`run <run>` command has options that
+   allow it to be invoked with minimal overhead (no setup or clean-up)
+   if you wish to do multiple short runs, driven by another program.
+   Details about using the library interface are given in the
+   :doc:`library API <Library>` documentation.
 
 .. spacer
 
-4. Couple LAMMPS with another code in a client/server fashion, using
-   using the `MDI Library
-   <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_
+4. Couple LAMMPS with another code in a client/server fashion, using the
+   `MDI Library <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
-   (client) or an MDI engine (server).  The MDI driver issues commands
-   to the MDI server to exchange data between them.  See the
-   :doc:`Howto mdi <Howto_mdi>` page for more information about how
-   LAMMPS can operate in either of these modes.
+   <https://molssi.org>`_ to run LAMMPS as either an MDI driver (client)
+   or an MDI engine (server).  The MDI driver issues commands to the MDI
+   server to exchange data between them.  See the :doc:`Howto_mdi` page for
+   more information about how LAMMPS can operate in either of these modes.

doc/src/Howto_github.rst

@@ -78,13 +78,13 @@ machine via HTTPS:
 
 .. code-block:: bash
 
-     $ git clone https://github.com/<your user name>/lammps.git <some name>
+     git clone https://github.com/<your user name>/lammps.git <some name>
 
 or, if you have set up your GitHub account for using SSH keys, via SSH:
 
 .. code-block:: bash
 
-     $ git clone git@github.com:<your user name>/lammps.git
+     git clone git@github.com:<your user name>/lammps.git
 
 You can find the proper URL by clicking the "Clone or download"-button:
 
@@ -103,21 +103,21 @@ and use git pull:
 
 .. code-block:: bash
 
-     $ cd mylammps
-     $ git checkout develop
-     $ git pull https://github.com/lammps/lammps develop
+     cd mylammps
+     git checkout develop
+     git pull https://github.com/lammps/lammps develop
 
 You can also add this URL as a remote:
 
 .. code-block:: bash
 
-     $ git remote add upstream https://www.github.com/lammps/lammps
+     git remote add upstream https://www.github.com/lammps/lammps
 
 From then on you can update your upstream branches with:
 
 .. code-block:: bash
 
-     $ git fetch upstream
+     git fetch upstream
 
 and then refer to the upstream repository branches with
 `upstream/develop` or `upstream/release` and so on.
@@ -129,8 +129,8 @@ workflow that updated this tutorial, and hence we will call the branch
 
 .. code-block:: bash
 
-    $ git fetch upstream
-    $ git checkout -b github-tutorial-update upstream/develop
+    git fetch upstream
+    git checkout -b github-tutorial-update upstream/develop
 
 Now that we have changed branches, we can make our changes to our local
 repository. Just remember that if you want to start working on another,
@@ -150,8 +150,8 @@ After everything is done, add the files to the branch and commit them:
 
 .. code-block:: bash
 
-    $ git add doc/src/Howto_github.txt
-    $ git add doc/src/JPG/tutorial*.png
+    git add doc/src/Howto_github.txt
+    git add doc/src/JPG/tutorial*.png
 
 .. warning::
 
@@ -174,13 +174,13 @@ useful message that explains the change.
 
 .. code-block:: bash
 
-     $ git commit -m 'Finally updated the GitHub tutorial'
+   git commit -m 'Finally updated the GitHub tutorial'
 
 After the commit, the changes can be pushed to the same branch on GitHub:
 
 .. code-block:: bash
 
-   $ git push
+   git push
 
 Git will ask you for your user name and password on GitHub if you have
 not configured anything. If your local branch is not present on GitHub yet,
@@ -188,7 +188,7 @@ it will ask you to add it by running
 
 .. code-block:: bash
 
-     $ git push --set-upstream origin github-tutorial-update
+   git push --set-upstream origin github-tutorial-update
 
 If you correctly type your user name and
 password, the feature branch should be added to your fork on GitHub.
@@ -198,13 +198,13 @@ If you want to make really sure you push to the right repository
 
 .. code-block:: bash
 
-   $ git push origin
+   git push origin
 
 or using an explicit URL:
 
 .. code-block:: bash
 
-   $ git push git@github.com:Pakketeretet2/lammps.git
+   git push git@github.com:Pakketeretet2/lammps.git
 
 ----------
 
@@ -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.
@@ -412,10 +412,10 @@ we need to pull Axel's change back into our branch, and merge them:
 
 .. code-block:: bash
 
-    $ git add Howto_github.txt
-    $ git add JPG/tutorial_reverse_pull_request*.png
-    $ git commit -m "Updated text and images on reverse pull requests"
-    $ git pull
+    git add Howto_github.txt
+    git add JPG/tutorial_reverse_pull_request*.png
+    git commit -m "Updated text and images on reverse pull requests"
+    git pull
 
 In this case, the merge was painless because git could auto-merge:
 
@@ -428,10 +428,10 @@ commit and push again:
 
 .. code-block:: bash
 
-    $ git add Howto_github.txt
-    $ git add JPG/tutorial_reverse_pull_request6.png
-    $ git commit -m "Merged Axel's suggestions and updated text"
-    $ git push git@github.com:Pakketeretet2/lammps
+    git add Howto_github.txt
+    git add JPG/tutorial_reverse_pull_request6.png
+    git commit -m "Merged Axel's suggestions and updated text"
+    git push git@github.com:Pakketeretet2/lammps
 
 This merge also shows up on the lammps GitHub page:
 
@@ -456,9 +456,9 @@ branch!
 
 .. code-block:: bash
 
-   $ git checkout develop
-   $ git pull https://github.com/lammps/lammps develop
-   $ git branch -d github-tutorial-update
+   git checkout develop
+   git pull https://github.com/lammps/lammps develop
+   git branch -d github-tutorial-update
 
 If you do not pull first, it is not really a problem but git will warn
 you at the next statement that you are deleting a local branch that
@@ -472,7 +472,7 @@ to your remote(s) as well:
 
 .. code-block:: bash
 
-   $ git push origin :github-tutorial-update
+   git push origin :github-tutorial-update
 
 **Recent changes in the workflow**
 
@@ -486,5 +486,6 @@ simplify comparisons between releases.  Finally, all patches and
 submissions are subject to automatic testing and code checks to make
 sure they at the very least compile.
 
-A 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>`_
+A 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
-as well for the standalone LAMMPS executable with reading commands
-either from an input file or stdin.
+simulations.  This is essentially what the ``src/main.cpp`` file does as
+well for the standalone LAMMPS executable, reading commands either from
+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
-:ref:`C language API <lammps_c_api>`, can be used from C and C++,
-and is also the basis for the :doc:`Python <Python_module>` and
-:doc:`Fortran <Fortran>` interfaces or wrappers included in the
+files ``src/library.cpp`` and ``src/library.h``.  This :ref:`C language
+API <lammps_c_api>`, can be used from C and C++, and is also the basis
+for the :doc:`Python <Python_module>` and :doc:`Fortran <Fortran>`
+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
-:doc:`Howto couple <Howto_couple>` doc page.
+Alternate methods for coupling codes with LAMMPS are described on the
+: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
-LAMMPS operates as an MDI driver in conjunction with a quantum
+The package furthermore includes a `fix mdi/qm <fix_mdi_qm>` command, in
+which LAMMPS operates as an MDI driver in conjunction with a 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
-code.  This command can be used to couple to an MDI engine which is
+``fix_mdi_qm.cpp`` file shows how a driver issues MDI commands to another
+code.  This command can be used to couple to an MDI engine, 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
-be used to perform *ab initio* MD simulations or energy minimizations,
-or to evaluate the quantum energy and forces for a series of
-independent systems.  The examples/mdi directory has example input
-scripts for all of these use cases.
+As explained in the `fix mdi/qm <fix_mdi_qm>` command documentation, it
+can be used to perform *ab initio* MD simulations or energy
+minimizations, or to evaluate the quantum energy and forces for a series
+of independent systems.  The ``examples/mdi`` directory has 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
-  the current snapshot to an MDI engine to evaluate the energy,
-  virial, and peratom forces.  As the engine LAMMPS is a surrogate for
-  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
+* LAMMPS runs an MD simulation as a driver.  Every N steps it passes the
+  current snapshot 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
-  engines.  The first LAMMPS instance performs MD timestepping.  The
-  second LAMMPS instance acts as a surrogate QM code to compute
-  forces.
+* Run AIMD with a Python driver code and 2 LAMMPS instances as engines.
+  The first LAMMPS instance performs MD timestepping.  The second LAMMPS
+  instance acts as a surrogate QM code to compute forces.
 
-Note that in any of these example where LAMMPS is used as an engine,
-an actual QM code (which supports MDI) could be used in its place,
-without modifying the input scripts or launch commands, except to
-specify the name of the QM code.
+.. note::
 
-The examples/mdi/Run.sh file illustrates how to launch both driver and
-engine codes so that they communicate using the MDI library via either
-MPI or sockets.  Or using the engine as a stand-alone code or plugin
-library.
+   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 engine codes so that they communicate using the MDI library via
+either MPI or sockets, or using the engine as a stand-alone code, or
+as a plugin library.
 
 -------------
 
-Currently there are at least two quantum DFT codes which have direct
-MDI support, `Quantum ESPRESSO (QE)
-<https://www.quantum-espresso.org/>`_ and `INQ
-<https://qsg.llnl.gov/node/101.html>`_.  There are also several QM
-codes which have indirect support through QCEngine or i-PI.  The
-former means they require a wrapper program (QCEngine) with MDI
-support which writes/read files to pass data to the quantum code
-itself.  The list of QCEngine-supported and i-PI-supported quantum
-codes is on the `MDI webpage
+Currently, there are at least two quantum DFT codes which have direct MDI
+support, `Quantum ESPRESSO (QE) <https://www.quantum-espresso.org/>`_
+and `INQ <https://qsg.llnl.gov/node/101.html>`_.  There are also several
+QM codes which have indirect support through QCEngine or i-PI.  The
+former means they require a wrapper program (QCEngine) with MDI support
+which writes/read files to pass data to the quantum code itself.  The
+list of QCEngine-supported and i-PI-supported quantum 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
@@ -134,30 +134,30 @@ used in stand-alone mode:
 
 .. code-block:: bash
 
-   % git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
-   % build the executable pw.x, following the `QE build guide <https://gitlab.com/QEF/q-e/-/wikis/Developers/CMake-build-system>`_
+   git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
+   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
 
-   % git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
-   % cd <base_path>/q-e
-   % ./configure --enable-parallel --enable-openmp --enable-shared FFLAGS="-fPIC" FCFLAGS="-fPIC" CFLAGS="-fPIC" foxflags="-fPIC" try_foxflags="-fPIC"
-   % make -j 4 mdi
+   git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
+   cd <base_path>/q-e
+   ./configure --enable-parallel --enable-openmp --enable-shared FFLAGS="-fPIC" FCFLAGS="-fPIC" CFLAGS="-fPIC" foxflags="-fPIC" try_foxflags="-fPIC"
+   make -j 4 mdi
 
 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
-<base_path>/inq/build/examples:
+plugin mode, which results in a ``libinqmdi.so`` file in
+``<base_path>/inq/build/examples``:
 
 .. code-block:: bash
 
-   % git clone --branch mdi --recurse-submodules https://gitlab.com/taylor-a-barnes/inq.git <base_path>/inq
-   % cd <base_path>/inq
-   % mkdir -p build
-   % cd build
-   % ../configure --prefix=<install_path>/install
-   % make -j 4
-   % make install
+   git clone --branch mdi --recurse-submodules https://gitlab.com/taylor-a-barnes/inq.git <base_path>/inq
+   cd <base_path>/inq
+   mkdir -p build
+   cd build
+   ../configure --prefix=<install_path>/install
+   make -j 4
+   make install

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
-assigned to each processor. When each sub-domain contains nearly the
+simulation domain so that spatial subdomains of nearly equal volume are
+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
-sub-domains contain few particles, resulting in a load imbalance that
+simulations, some subdomains may contain many particles while other
+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>`
-command in a new script.
+be converted to text data files using the :doc:`-r command-line switch
+<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,
-but not in data files.
+LAMMPS the current timestep.  This value is stored in restart files, but
+not in data files.

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_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
-simulations can be visualized (and analyzed) in a variety of ways.
+Snapshots from LAMMPS simulations can be viewed, visualized, and
+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
-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 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.
+The :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>`
+styles can output internally rendered images or convert them to a movie
+during the MD run.
 
-A Python-based toolkit distributed by our group can read native LAMMPS
-dump files, including custom dump files with additional columns of
-user-specified atom information, and convert them to various formats or
-pipe them into visualization software directly.  See the `Pizza.py WWW
-site <pizza_>`_ for details.  Specifically, Pizza.py can convert LAMMPS
-dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
-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/
+Programs included with LAMMPS as auxiliary tools can convert
+between LAMMPS format files and other formats.  See the :doc:`Tools
+<Tools>` page for details.  These are rarely needed these days.

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:
+----
 
-+------------+-------------------------------------------+
-| README     | Short description of the LAMMPS package   |
-+------------+-------------------------------------------+
-| LICENSE    | GNU General Public License (GPL)          |
-+------------+-------------------------------------------+
-| SECURITY.md| Security Policy for the LAMMPS package    |
-+------------+-------------------------------------------+
-| bench      | benchmark problems                        |
-+------------+-------------------------------------------+
-| cmake      | CMake build files                         |
-+------------+-------------------------------------------+
-| doc        | documentation                             |
-+------------+-------------------------------------------+
-| examples   | simple test problems                      |
-+------------+-------------------------------------------+
-| fortran    | Fortran wrapper for LAMMPS                |
-+------------+-------------------------------------------+
-| lib        | additional provided or external libraries |
-+------------+-------------------------------------------+
-| potentials | interatomic potential files               |
-+------------+-------------------------------------------+
-| python     | Python wrappers for LAMMPS                |
-+------------+-------------------------------------------+
-| src        | source files                              |
-+------------+-------------------------------------------+
-| tools      | pre- and post-processing tools            |
-+------------+-------------------------------------------+
-| unittest   | sources and inputs for testing LAMMPS     |
-+------------+-------------------------------------------+
+These are the files and subdirectories in the LAMMPS distribution:
 
-You will have all of these if you download source.  You will only have
-some of them if you download executables, as explained on the pages
-listed above.
++------------+---------------------------------------------+
+| README     | Short description of the LAMMPS package     |
++------------+---------------------------------------------+
+| LICENSE    | GNU General Public License (GPL)            |
++------------+---------------------------------------------+
+| SECURITY.md| Security policy for the LAMMPS package      |
++------------+---------------------------------------------+
+| bench      | benchmark inputs                            |
++------------+---------------------------------------------+
+| cmake      | CMake build files                           |
++------------+---------------------------------------------+
+| doc        | documentation and tools to build the manual |
++------------+---------------------------------------------+
+| examples   | example input files                         |
++------------+---------------------------------------------+
+| fortran    | Fortran module for LAMMPS library interface |
++------------+---------------------------------------------+
+| lib        | additional provided or external libraries   |
++------------+---------------------------------------------+
+| potentials | selected interatomic potential files        |
++------------+---------------------------------------------+
+| python     | Python module for LAMMPS library interface  |
++------------+---------------------------------------------+
+| src        | LAMMPS source files                         |
++------------+---------------------------------------------+
+| tools      | pre- and post-processing tools              |
++------------+---------------------------------------------+
+| unittest   | source code and inputs for testing LAMMPS   |
++------------+---------------------------------------------+
+
+You will have all of these if you downloaded the LAMMPS source code.
+You will have only some of them if you downloaded executables, as
+explained on the pages listed above.

doc/src/Install_conda.rst

@@ -1,38 +1,39 @@
 Download an executable for Linux or Mac via Conda
 -------------------------------------------------
 
-Binaries are available for MacOS or Linux via `Conda <conda_>`_.
+Pre-compiled LAMMPS binaries are available for macOS and Linux via the
+`Conda <conda_>`_ package management system.
 
-First, one must setup the Conda package manager on your system.  Follow the
+First, one must set up the Conda package manager on your system.  Follow the
 instructions to install `Miniconda <mini_conda_install_>`_, then create a conda
 environment (named `my-lammps-env` or whatever you prefer) for your LAMMPS
 install:
 
 .. code-block:: bash
 
-   % conda config --add channels conda-forge
-   % conda create -n my-lammps-env
+   conda config --add channels conda-forge
+   conda create -n my-lammps-env
 
 Then, you can install LAMMPS on your system with the following command:
 
 .. code-block:: bash
 
-   % conda activate my-lammps-env
-   % conda install lammps
+   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
-install the `openkim-models` package
+installed.  In order to use potentials from `openkim.org <openkim_>`_,
+you can install the `openkim-models` package
 
 .. code-block:: bash
 
-   % conda install openkim-models
+   conda install openkim-models
 
-If you have problems with the installation you can post issues to
-`this link <conda_forge_lammps_>`_.
-Thanks to Jan Janssen (Max-Planck-Institut fuer Eisenforschung) for setting
-up the Conda capability.
+If you have problems with the installation, you can post issues to `this
+link <conda_forge_lammps_>`_.  Thanks to Jan Janssen
+(Max-Planck-Institut fuer Eisenforschung) for setting up the Conda
+capability.
 
 .. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues
 .. _openkim: https://openkim.org