Merge pull request #2999 from akohlmey/maintenance-2021-09-29

Maintenance fixes for the stable release

.github/CODEOWNERS

@@ -83,7 +83,7 @@ src/library.*             @sjplimp
 src/main.cpp              @sjplimp
 src/min_*.*               @sjplimp
 src/memory.*              @sjplimp
-src/modify.*              @sjplimp @stanmoore1
+src/modify.*              @sjplimp
 src/molecule.*            @sjplimp
 src/my_page.h             @sjplimp
 src/my_pool_chunk.h       @sjplimp

.github/workflows/codeql-analysis.yml

@@ -3,7 +3,7 @@ name: "CodeQL Code Analysis"
 
 on:
   push:
-    branches: [develop]
+    branches: [master]
 
 jobs:
   analyze:

.github/workflows/compile-msvc.yml

@@ -1,46 +0,0 @@
-# GitHub action to build LAMMPS on Windows with Visual C++
-name: "Native Windows Compilation and Unit Tests"
-
-on:
-  push:
-    branches: [develop]
-
-jobs:
-  build:
-    name: Windows Compilation Test
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: windows-latest
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
-      with:
-        fetch-depth: 2
-
-    - name: Select Python version
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.10'
-
-    - name: Building LAMMPS via CMake
-      shell: bash
-      run: |
-        python3 -m pip install numpy
-        cmake -C cmake/presets/windows.cmake \
-              -D PKG_PYTHON=on \
-              -S cmake -B build \
-              -D BUILD_SHARED_LIBS=on \
-              -D LAMMPS_EXCEPTIONS=on \
-              -D ENABLE_TESTING=on
-        cmake --build build --config Release
-
-    - name: Run LAMMPS executable
-      shell: bash
-      run: |
-        ./build/Release/lmp.exe -h
-        ./build/Release/lmp.exe -in bench/in.lj
-
-    - name: Run Unit Tests
-      working-directory: build
-      shell: bash
-      run: ctest -V -C Release

.github/workflows/unittest-macos.yml

@@ -3,7 +3,7 @@ name: "Unittest for MacOS"
 
 on:
   push:
-    branches: [develop]
+    branches: [master]
 
 jobs:
   build:

.gitignore

@@ -37,8 +37,8 @@ vgcore.*
 .Trashes
 ehthumbs.db
 Thumbs.db
+.clang-format
 .lammps_history
-.vs
 
 #cmake
 /build*
@@ -49,8 +49,3 @@ Thumbs.db
 /Testing
 /cmake_install.cmake
 /lmp
-out/Debug
-out/RelWithDebInfo
-out/Release
-out/x86
-out/x64

SECURITY.md

@@ -23,10 +23,6 @@ either a user mistake or a bug in the code.  Bugs can be reported in
 the LAMMPS project
 [issue tracker on GitHub](https://github.com/lammps/lammps/issues).
 
-To mitigate issues with using homoglyphs or bidirectional reordering in
-unicode, which have been demonstrated as a vector to obfuscate and hide
-malicious changes to the source code, all LAMMPS submissions are checked
-for unicode characters and only all-ASCII source code is accepted.
 
 # Version Updates
 

cmake/CMakeLists.txt

@@ -19,9 +19,6 @@ set(SOVERSION 0)
 
 get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
-# collect all executables and shared libs in the top level build folder
-set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
-set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 
 set(LAMMPS_SOURCE_DIR     ${LAMMPS_DIR}/src)
 set(LAMMPS_LIB_SOURCE_DIR ${LAMMPS_DIR}/lib)
@@ -84,40 +81,22 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckIncludeFileCXX)
 
 # set required compiler flags and compiler/CPU arch specific optimizations
-if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-  if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
-    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Qrestrict")
-    endif()
-    if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-      set(CMAKE_TUNE_DEFAULT "/QxCOMMON-AVX512")
-    else()
-      set(CMAKE_TUNE_DEFAULT "/QxHost")
-    endif()
+if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+  if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
+    set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
   else()
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
-    if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-      set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
-    else()
-      set(CMAKE_TUNE_DEFAULT "-xHost")
-    endif()
+    set(CMAKE_TUNE_DEFAULT "-xHost")
   endif()
 endif()
 
-# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
+# we require C++11 without extensions
 set(CMAKE_CXX_STANDARD 11)
-if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
-  set(CMAKE_CXX_STANDARD 14)
-endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
-# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
-# and prints lots of pointless warnings about "unsafe" functions
+# ugly hack for MSVC which by default always reports an old C++ standard in the __cplusplus macro
 if(MSVC)
   add_compile_options(/Zc:__cplusplus)
-  add_compile_options(/wd4244)
-  add_compile_options(/wd4267)
-  add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
 # export all symbols when building a .dll file on windows
@@ -136,7 +115,10 @@ endif()
 set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
 
 option(BUILD_SHARED_LIBS "Build shared library" OFF)
-option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
+if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
+  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+endif()
+
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
 option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
 
@@ -283,19 +265,28 @@ if(BUILD_MPI)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
     include(MPI4WIN)
+    target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
   else()
     find_package(MPI REQUIRED)
+    target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
     option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
     if(LAMMPS_LONGLONG_TO_LONG)
       target_compile_definitions(lammps PRIVATE -DLAMMPS_LONGLONG_TO_LONG)
     endif()
   endif()
-  target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
 else()
-  target_sources(lammps PRIVATE ${LAMMPS_SOURCE_DIR}/STUBS/mpi.cpp)
-  add_library(mpi_stubs INTERFACE)
-  target_include_directories(mpi_stubs INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
-  target_link_libraries(lammps PUBLIC mpi_stubs)
+  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.cpp)
+  add_library(mpi_stubs STATIC ${MPI_SOURCES})
+  set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
+  target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
+  if(BUILD_SHARED_LIBS)
+    target_link_libraries(lammps PRIVATE mpi_stubs)
+    target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
+    target_compile_definitions(lammps INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
+  else()
+    target_link_libraries(lammps PUBLIC mpi_stubs)
+  endif()
+  add_library(MPI::MPI_CXX ALIAS mpi_stubs)
 endif()
 
 set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
@@ -326,6 +317,7 @@ pkg_depends(ML-IAP ML-SNAP)
 pkg_depends(MPIIO MPI)
 pkg_depends(ATC MANYBODY)
 pkg_depends(LATBOLTZ MPI)
+pkg_depends(PHONON KSPACE)
 pkg_depends(SCAFACOS MPI)
 pkg_depends(DIELECTRIC KSPACE)
 pkg_depends(DIELECTRIC EXTRA-PAIR)
@@ -359,13 +351,11 @@ if(BUILD_OMP)
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
     # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
     # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
-    set(LAMMPS_OMP_COMPAT_LEVEL 4)
+    target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=4)
   else()
-    set(LAMMPS_OMP_COMPAT_LEVEL 3)
+    target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=3)
   endif()
-  target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=${LAMMPS_OMP_COMPAT_LEVEL})
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
-  target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
 if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE)
@@ -478,12 +468,9 @@ foreach(HEADER cmath)
   endif(NOT FOUND_${HEADER})
 endforeach(HEADER)
 
-# make the standard math library overrideable and autodetected (for systems that don't have it)
-find_library(STANDARD_MATH_LIB m DOC "Standard Math library")
-mark_as_advanced(STANDARD_MATH_LIB)
-if(STANDARD_MATH_LIB)
-  target_link_libraries(lammps PRIVATE ${STANDARD_MATH_LIB})
-endif()
+set(MATH_LIBRARIES "m" CACHE STRING "math library")
+mark_as_advanced( MATH_LIBRARIES )
+target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
 
 ######################################
 # Generate Basic Style files
@@ -579,10 +566,11 @@ if(PKG_ATC)
   if(LAMMPS_SIZES STREQUAL "BIGBIG")
     message(FATAL_ERROR "The ATC Package is not compatible with -DLAMMPS_BIGBIG")
   endif()
+  target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
   if(BUILD_MPI)
-    target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES} MPI::MPI_CXX)
+    target_link_libraries(atc PRIVATE MPI::MPI_CXX)
   else()
-    target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES} mpi_stubs)
+    target_link_libraries(atc PRIVATE mpi_stubs)
   endif()
   target_include_directories(atc PRIVATE ${LAMMPS_SOURCE_DIR})
   target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
@@ -596,19 +584,22 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
 endforeach()
 
 if(PKG_PLUGIN)
-  target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
-endif()
-
-# link with -ldl or equivalent for plugin loading; except on Windows
-if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-   target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
+  if(BUILD_SHARED_LIBS)
+    target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
+  else()
+    message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled")
+  endif()
+  # link with -ldl or equivalent for plugin loading; except on Windows
+  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
+  endif()
 endif()
 
 ######################################################################
@@ -617,7 +608,7 @@ endif()
 # and after everything else that is compiled locally
 ######################################################################
 if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
-  target_link_libraries(lammps PRIVATE "wsock32;psapi")
+  target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi)
 endif()
 
 ######################################################
@@ -678,7 +669,6 @@ endif()
 
 set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
 set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
-set_target_properties(lammps PROPERTIES PREFIX "lib")
 target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps>)
 file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
 foreach(_HEADER ${LAMMPS_CXX_HEADERS})
@@ -698,9 +688,6 @@ foreach(_DEF ${LAMMPS_DEFINES})
 endforeach()
 if(BUILD_SHARED_LIBS)
   install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-  if(NOT BUILD_MPI)
-    install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-  endif()
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
   install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
@@ -740,7 +727,7 @@ install(
 if(BUILD_SHARED_LIBS)
   if(CMAKE_VERSION VERSION_LESS 3.12)
     # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
-    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
+    set(Python_ADDITIONAL_VERSIONS 3.9 3.8 3.7 3.6 3.5)
     find_package(PythonInterp) # Deprecated since version 3.12
     if(PYTHONINTERP_FOUND)
         set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
@@ -799,17 +786,11 @@ if(ClangFormat_FOUND)
 endif()
 
 get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
-get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
-if(BUILD_IS_MULTI_CONFIG)
-  set(LAMMPS_BUILD_TYPE "Multi-Config")
-else()
-  set(LAMMPS_BUILD_TYPE ${CMAKE_BUILD_TYPE})
-endif()
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
 message(STATUS "<<< Build configuration >>>
    Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
-   Build type:       ${LAMMPS_BUILD_TYPE}
+   Build type:       ${CMAKE_BUILD_TYPE}
    Install path:     ${CMAKE_INSTALL_PREFIX}
    Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
 ###############################################################################

cmake/CMakeSettings.json

@@ -1,204 +0,0 @@
-{
-  "configurations": [
-    {
-      "name": "x64-Debug-MSVC",
-      "generator": "Ninja",
-      "configurationType": "Debug",
-      "buildRoot": "${workspaceRoot}\\build\\${name}",
-      "installRoot": "${workspaceRoot}\\install\\${name}",
-      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
-      "buildCommandArgs": "",
-      "ctestCommandArgs": "",
-      "inheritEnvironments": [ "msvc_x64_x64" ],
-      "variables": [
-        {
-          "name": "BUILD_SHARED_LIBS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "BUILD_TOOLS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "LAMMPS_EXCEPTIONS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "PKG_PYTHON",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "ENABLE_TESTING",
-          "value": "True",
-          "type": "BOOL"
-        }
-      ]
-    },
-    {
-      "name": "x64-Release-MSVC",
-      "generator": "Ninja",
-      "configurationType": "Release",
-      "buildRoot": "${workspaceRoot}\\build\\${name}",
-      "installRoot": "${workspaceRoot}\\install\\${name}",
-      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
-      "buildCommandArgs": "",
-      "ctestCommandArgs": "",
-      "inheritEnvironments": [ "msvc_x64_x64" ],
-      "variables": [
-        {
-          "name": "BUILD_SHARED_LIBS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "BUILD_TOOLS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "LAMMPS_EXCEPTIONS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "PKG_PYTHON",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "ENABLE_TESTING",
-          "value": "True",
-          "type": "BOOL"
-        }
-      ]
-    },
-    {
-      "name": "x64-Debug-Clang",
-      "generator": "Ninja",
-      "configurationType": "Debug",
-      "buildRoot": "${workspaceRoot}\\build\\${name}",
-      "installRoot": "${workspaceRoot}\\install\\${name}",
-      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
-      "buildCommandArgs": "",
-      "ctestCommandArgs": "",
-      "inheritEnvironments": [ "clang_cl_x64" ],
-      "variables": [
-        {
-          "name": "BUILD_SHARED_LIBS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "BUILD_TOOLS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "LAMMPS_EXCEPTIONS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "PKG_PYTHON",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "ENABLE_TESTING",
-          "value": "True",
-          "type": "BOOL"
-        }
-      ]
-    },
-    {
-      "name": "x64-Debug-OneAPI",
-      "generator": "Ninja",
-      "configurationType": "Debug",
-      "buildRoot": "${workspaceRoot}\\build\\${name}",
-      "installRoot": "${workspaceRoot}\\install\\${name}",
-      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_CXX_COMPILER=icx -DCMAKE_C_COMPILER=icx",
-      "buildCommandArgs": "",
-      "ctestCommandArgs": "",
-      "inheritEnvironments": [ "msvc_x64_x64" ],
-      "variables": [
-        {
-          "name": "BUILD_SHARED_LIBS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "BUILD_TOOLS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "LAMMPS_EXCEPTIONS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "PKG_PYTHON",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "ENABLE_TESTING",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "BUILD_MPI",
-          "value": "False",
-          "type": "BOOL"
-        }
-      ]
-    },
-    {
-      "name": "x64-Debug-Intel",
-      "generator": "Ninja",
-      "configurationType": "Debug",
-      "buildRoot": "${workspaceRoot}\\build\\${name}",
-      "installRoot": "${workspaceRoot}\\install\\${name}",
-      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_CXX_COMPILER=icl -DCMAKE_C_COMPILER=icl -DCMAKE_Fortran_COMPILER=ifort",
-      "buildCommandArgs": "",
-      "ctestCommandArgs": "",
-      "inheritEnvironments": [ "msvc_x64_x64" ],
-      "variables": [
-        {
-          "name": "BUILD_SHARED_LIBS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "BUILD_TOOLS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "LAMMPS_EXCEPTIONS",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "PKG_PYTHON",
-          "value": "True",
-          "type": "BOOL"
-        },
-        {
-          "name": "ENABLE_TESTING",
-          "value": "False",
-          "type": "BOOL"
-        },
-        {
-          "name": "BUILD_MPI",
-          "value": "False",
-          "type": "BOOL"
-        }
-      ]
-    }
-  ]
-}

cmake/Modules/ExternalCMakeProject.cmake

@@ -1,33 +0,0 @@
-# Build a CMake based external library as subdirectory.
-# The sources will be unpacked to ${CMAKE_BINARY_DIR}/_deps/${target}-src
-# The binaries will be built in ${CMAKE_BINARY_DIR}/_deps/${target}-build
-#
-function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
-  # change settings locally
-  set(BUILD_SHARED_LIBS OFF)
-  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-
-  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)
-  message(STATUS "Unpacking and configuring ${archive}")
-  execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ${CMAKE_BINARY_DIR}/_deps/${archive}
-    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)
-  file(GLOB TARGET_SOURCE "${CMAKE_BINARY_DIR}/_deps/src/${basedir}*")
-  list(LENGTH TARGET_SOURCE _num)
-  if(_num GREATER 1)
-    message(FATAL_ERROR "Inconsistent ${target} library sources. "
-      "Please delete ${CMAKE_BINARY_DIR}/_deps/src and re-run cmake")
-  endif()
-  file(REMOVE_RECURSE ${CMAKE_BINARY_DIR}/_deps/${target}-src)
-  file(RENAME ${TARGET_SOURCE} ${CMAKE_BINARY_DIR}/_deps/${target}-src)
-  if(NOT (cmakefile STREQUAL ""))
-    file(COPY ${cmakefile} DESTINATION ${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/)
-    get_filename_component(_cmakefile ${cmakefile} NAME)
-    file(RENAME "${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/${_cmakefile}"
-      "${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/CMakeLists.txt")
-  endif()
-  add_subdirectory("${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}"
-    "${CMAKE_BINARY_DIR}/_deps/${target}-build")
-endfunction(ExternalCMakeProject)

cmake/Modules/FindCythonize.cmake

@@ -8,19 +8,18 @@
 #=============================================================================
 
 if(CMAKE_VERSION VERSION_LESS 3.12)
-    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
     find_package(PythonInterp 3.6 QUIET) # Deprecated since version 3.12
     if(PYTHONINTERP_FOUND)
-        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+        set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
     endif()
 else()
-    find_package(Python 3.6 COMPONENTS Interpreter QUIET)
+    find_package(Python3 3.6 COMPONENTS Interpreter QUIET)
 endif()
 
 # Use the Cython executable that lives next to the Python executable
 # if it is a local installation.
-if(Python_EXECUTABLE)
-  get_filename_component(_python_path ${Python_EXECUTABLE} PATH)
+if(Python3_EXECUTABLE)
+  get_filename_component(_python_path ${Python3_EXECUTABLE} PATH)
   find_program(Cythonize_EXECUTABLE
     NAMES cythonize3 cythonize cythonize.bat
     HINTS ${_python_path})

cmake/Modules/GTest.cmake

@@ -0,0 +1,81 @@
+message(STATUS "Downloading and building Google Test library")
+
+if(CMAKE_BUILD_TYPE STREQUAL "Debug")
+  set(GTEST_LIB_POSTFIX d)
+else()
+  set(GTEST_LIB_POSTFIX)
+endif()
+
+include(ExternalProject)
+set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")
+set(GTEST_MD5 "ecd1fa65e7de707cd5c00bdac56022cd" CACHE STRING "MD5 checksum of GTest tarball")
+mark_as_advanced(GTEST_URL)
+mark_as_advanced(GTEST_MD5)
+ExternalProject_Add(googletest
+                    URL             ${GTEST_URL}
+                    URL_MD5         ${GTEST_MD5}
+                    SOURCE_DIR      "${CMAKE_BINARY_DIR}/gtest-src"
+                    BINARY_DIR      "${CMAKE_BINARY_DIR}/gtest-build"
+                    CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}
+                                    -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                                    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                                    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+                                    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+                    BUILD_BYPRODUCTS <BINARY_DIR>/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                                     <BINARY_DIR>/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                                     <BINARY_DIR>/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                                     <BINARY_DIR>/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                    LOG_DOWNLOAD ON
+                    LOG_CONFIGURE ON
+                    LOG_BUILD ON
+                    INSTALL_COMMAND ""
+                    TEST_COMMAND    "")
+
+ExternalProject_Get_Property(googletest SOURCE_DIR)
+set(GTEST_INCLUDE_DIR ${SOURCE_DIR}/googletest/include)
+set(GMOCK_INCLUDE_DIR ${SOURCE_DIR}/googlemock/include)
+
+# workaround for CMake 3.10 on ubuntu 18.04
+file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
+file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
+
+ExternalProject_Get_Property(googletest BINARY_DIR)
+set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+
+# Prevent GoogleTest from overriding our compiler/linker options
+# when building with Visual Studio
+set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
+
+find_package(Threads QUIET)
+
+add_library(GTest::GTest UNKNOWN IMPORTED)
+set_target_properties(GTest::GTest PROPERTIES
+        IMPORTED_LOCATION ${GTEST_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
+        INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
+add_dependencies(GTest::GTest googletest)
+
+add_library(GTest::GMock UNKNOWN IMPORTED)
+set_target_properties(GTest::GMock PROPERTIES
+        IMPORTED_LOCATION ${GMOCK_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
+        INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
+add_dependencies(GTest::GMock googletest)
+
+add_library(GTest::GTestMain UNKNOWN IMPORTED)
+set_target_properties(GTest::GTestMain PROPERTIES
+        IMPORTED_LOCATION ${GTEST_MAIN_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
+        INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
+add_dependencies(GTest::GTestMain googletest)
+
+add_library(GTest::GMockMain UNKNOWN IMPORTED)
+set_target_properties(GTest::GMockMain PROPERTIES
+        IMPORTED_LOCATION ${GMOCK_MAIN_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
+        INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
+add_dependencies(GTest::GMockMain googletest)

cmake/Modules/LAMMPSUtils.cmake

@@ -25,7 +25,7 @@ function(validate_option name values)
 endfunction(validate_option)
 
 function(get_lammps_version version_header variable)
-    file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
+    file(READ ${version_header} line)
     set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
     string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
     string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")
@@ -85,7 +85,7 @@ endfunction(GenerateBinaryHeader)
 
 # fetch missing potential files
 function(FetchPotentials pkgfolder potfolder)
-  if(EXISTS "${pkgfolder}/potentials.txt")
+  if (EXISTS "${pkgfolder}/potentials.txt")
     file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
     foreach(line ${linelist})
       string(FIND ${line} " " blank)

cmake/Modules/OpenCLLoader.cmake

@@ -1,11 +1,50 @@
 message(STATUS "Downloading and building OpenCL loader library")
-set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2022.01.04.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "8d3a801e87a2c6653bf0e27707063914" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.09.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "3b3882627964bd02e5c3b02065daac3c" CACHE STRING "MD5 checksum of OpenCL loader tarball")
 mark_as_advanced(OPENCL_LOADER_URL)
 mark_as_advanced(OPENCL_LOADER_MD5)
 
-set(INSTALL_LIBOPENCL OFF CACHE BOOL "" FORCE)
-include(ExternalCMakeProject)
-ExternalCMakeProject(opencl_loader ${OPENCL_LOADER_URL} ${OPENCL_LOADER_MD5} opencl-loader . "")
+include(ExternalProject)
+ExternalProject_Add(opencl_loader
+                    URL             ${OPENCL_LOADER_URL}
+                    URL_MD5         ${OPENCL_LOADER_MD5}
+                    SOURCE_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-src"
+                    BINARY_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-build"
+                    CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS}
+                                    -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                                    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                                    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+                                    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+                    BUILD_BYPRODUCTS <BINARY_DIR>/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}
+                    LOG_DOWNLOAD ON
+                    LOG_CONFIGURE ON
+                    LOG_BUILD ON
+                    INSTALL_COMMAND ""
+                    TEST_COMMAND    "")
+
+ExternalProject_Get_Property(opencl_loader SOURCE_DIR)
+set(OPENCL_LOADER_INCLUDE_DIR ${SOURCE_DIR}/inc)
+
+# workaround for CMake 3.10 on ubuntu 18.04
+file(MAKE_DIRECTORY ${OPENCL_LOADER_INCLUDE_DIR})
+
+ExternalProject_Get_Property(opencl_loader BINARY_DIR)
+set(OPENCL_LOADER_LIBRARY_PATH "${BINARY_DIR}/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}")
+
+find_package(Threads QUIET)
+if(NOT WIN32)
+  set(OPENCL_LOADER_DEP_LIBS "Threads::Threads;${CMAKE_DL_LIBS}")
+else()
+  set(OPENCL_LOADER_DEP_LIBS "cfgmgr32;runtimeobject")
+endif()
+
+add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
+add_dependencies(OpenCL::OpenCL opencl_loader)
+
+set_target_properties(OpenCL::OpenCL PROPERTIES
+  IMPORTED_LOCATION ${OPENCL_LOADER_LIBRARY_PATH}
+  INTERFACE_INCLUDE_DIRECTORIES ${OPENCL_LOADER_INCLUDE_DIR}
+  INTERFACE_LINK_LIBRARIES "${OPENCL_LOADER_DEP_LIBS}")
+
 
-add_library(OpenCL::OpenCL ALIAS OpenCL)

cmake/Modules/Packages/COMPRESS.cmake

@@ -1,11 +1,10 @@
 find_package(ZLIB REQUIRED)
 target_link_libraries(lammps PRIVATE ZLIB::ZLIB)
 
-find_package(PkgConfig QUIET)
-if(PkgConfig_FOUND)
-  pkg_check_modules(Zstd IMPORTED_TARGET libzstd>=1.4)
-  if(Zstd_FOUND)
+find_package(PkgConfig REQUIRED)
+pkg_check_modules(Zstd IMPORTED_TARGET libzstd>=1.4)
+
+if(Zstd_FOUND)
     target_compile_definitions(lammps PRIVATE -DLAMMPS_ZSTD)
     target_link_libraries(lammps PRIVATE PkgConfig::Zstd)
-  endif()
 endif()

cmake/Modules/Packages/GPU.cmake

@@ -306,12 +306,12 @@ elseif(GPU_API STREQUAL "HIP")
 
         if(HIP_COMPILER STREQUAL "clang")
           add_custom_command(OUTPUT ${CUBIN_FILE}
-            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
             DEPENDS ${CU_CPP_FILE}
             COMMENT "Generating ${CU_NAME}.cubin")
         else()
           add_custom_command(OUTPUT ${CUBIN_FILE}
-            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
             DEPENDS ${CU_CPP_FILE}
             COMMENT "Generating ${CU_NAME}.cubin")
         endif()
@@ -422,12 +422,13 @@ RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
 RegisterFixStyle(${GPU_SOURCES_DIR}/fix_gpu.h)
 
 get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
-if(BUILD_MPI)
-  target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
-else()
-  target_link_libraries(gpu PRIVATE mpi_stubs)
-endif()
 
+if(NOT BUILD_MPI)
+  # mpistubs is aliased to MPI::MPI_CXX, but older versions of cmake won't work forward the include path
+  target_link_libraries(gpu PRIVATE mpi_stubs)
+else()
+  target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
+endif()
 target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
 target_sources(lammps PRIVATE ${GPU_SOURCES})

cmake/Modules/Packages/KOKKOS.cmake

@@ -1,7 +1,7 @@
 ########################################################################
 # As of version 3.3.0 Kokkos requires C++14
 if(CMAKE_CXX_STANDARD LESS 14)
-  message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
+  set(CMAKE_CXX_STANDARD 14)
 endif()
 ########################################################################
 # consistency checks and Kokkos options/settings required by LAMMPS
@@ -11,14 +11,8 @@ if(Kokkos_ENABLE_CUDA)
 endif()
 # Adding OpenMP compiler flags without the checks done for
 # BUILD_OMP can result in compile failures. Enforce consistency.
-if(Kokkos_ENABLE_OPENMP)
-  if(NOT BUILD_OMP)
-    message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
-  else()
-    if(LAMMPS_OMP_COMPAT_LEVEL LESS 4)
-      message(FATAL_ERROR "Compiler must support OpenMP 4.0 or later with Kokkos_ENABLE_OPENMP")
-    endif()
-  endif()
+if(Kokkos_ENABLE_OPENMP AND NOT BUILD_OMP)
+  message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
 endif()
 ########################################################################
 
@@ -33,8 +27,6 @@ if(DOWNLOAD_KOKKOS)
   endforeach()
   message(STATUS "KOKKOS download requested - we will build our own")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>")
-  # build KOKKOS downloaded libraries as static libraries but with PIC, if needed
-  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DBUILD_SHARED_LIBS=OFF")
   if(CMAKE_REQUEST_PIC)
     list(APPEND KOKKOS_LIB_BUILD_ARGS ${CMAKE_REQUEST_PIC})
   endif()
@@ -47,48 +39,35 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${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/3.5.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "079323d973ae0e1c38c0a54a150c674e" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "4c84698917c93a18985b311bb6caf84f" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   ExternalProject_Add(kokkos_build
     URL     ${KOKKOS_URL}
     URL_MD5 ${KOKKOS_MD5}
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
-    BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a <INSTALL_DIR>/lib/libkokkoscontainers.a
+    BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
   )
   ExternalProject_get_property(kokkos_build INSTALL_DIR)
   file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
-  add_library(LAMMPS::KOKKOSCORE UNKNOWN IMPORTED)
-  add_library(LAMMPS::KOKKOSCONTAINERS UNKNOWN IMPORTED)
-  set_target_properties(LAMMPS::KOKKOSCORE PROPERTIES
+  add_library(LAMMPS::KOKKOS UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::KOKKOS PROPERTIES
     IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscore.a"
     INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include"
     INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
-  set_target_properties(LAMMPS::KOKKOSCONTAINERS PROPERTIES
-    IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscontainers.a")
-  target_link_libraries(lammps PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
-  target_link_libraries(lmp PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
-  add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
-  add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
+  target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
+  target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
+  add_dependencies(LAMMPS::KOKKOS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.5.00 REQUIRED CONFIG)
+  find_package(Kokkos 3.4.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
   target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
   set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
-  # build KOKKOS internal libraries as static libraries but with PIC, if needed
-  if(BUILD_SHARED_LIBS)
-    set(BUILD_SHARED_LIBS_WAS_ON YES)
-    set(BUILD_SHARED_LIBS OFF)
-  endif()
-  if(CMAKE_REQUEST_PIC)
-    set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-  endif()
   add_subdirectory(${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
@@ -96,9 +75,6 @@ else()
   target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
   target_link_libraries(lammps PRIVATE kokkos)
   target_link_libraries(lmp PRIVATE kokkos)
-  if(BUILD_SHARED_LIBS_WAS_ON)
-    set(BUILD_SHARED_LIBS ON)
-  endif()
 endif()
 target_compile_definitions(lammps PUBLIC $<BUILD_INTERFACE:LMP_KOKKOS>)
 
@@ -133,12 +109,6 @@ if(PKG_KSPACE)
   endif()
 endif()
 
-
-if(PKG_PHONON)
-  list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/dynamical_matrix_kokkos.cpp)
-  list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/third_order_kokkos.cpp)
-endif()
-
 set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
 
 # detects styles which have KOKKOS version

cmake/Modules/Packages/MACHDYN.cmake

@@ -8,7 +8,7 @@ option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed on
 if(DOWNLOAD_EIGEN3)
   message(STATUS "Eigen3 download requested - we will build our own")
 
-  set(EIGEN3_URL "${LAMMPS_THIRDPARTY_URL}/eigen-3.4.0.tar.gz" CACHE STRING "URL for Eigen3 tarball")
+  set(EIGEN3_URL "https://download.lammps.org/thirdparty/eigen-3.4.0.tar.gz" CACHE STRING "URL for Eigen3 tarball")
   set(EIGEN3_MD5 "4c527a9171d71a72a9d4186e65bea559" CACHE STRING "MD5 checksum of Eigen3 tarball")
   mark_as_advanced(EIGEN3_URL)
   mark_as_advanced(EIGEN3_MD5)

cmake/Modules/Packages/ML-HDNNP.cmake

@@ -46,10 +46,12 @@ if(DOWNLOAD_N2P2)
     if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
       get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
       set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
+      set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
     endif()
     if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
       get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
       set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
+      set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
     endif()
   endif()
 
@@ -62,8 +64,8 @@ if(DOWNLOAD_N2P2)
   string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
   set(N2P2_BUILD_FLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}} ${N2P2_CXX_STD}")
   set(N2P2_BUILD_OPTIONS INTERFACES=LAMMPS COMP=${N2P2_COMP} "PROJECT_OPTIONS=${N2P2_PROJECT_OPTIONS}" "PROJECT_DEBUG="
-    "PROJECT_CC=${CMAKE_CXX_COMPILER}" "PROJECT_MPICC=${CMAKE_CXX_COMPILER}" "PROJECT_CFLAGS=${N2P2_BUILD_FLAGS}"
-    "PROJECT_AR=${N2P2_AR}" "APP_CORE=nnp-convert" "APP_TRAIN=nnp-train" "APP=nnp-convert")
+    "PROJECT_CC=${CMAKE_CXX_COMPILER}" "PROJECT_MPICC=${MPI_CXX_COMPILER}" "PROJECT_CFLAGS=${N2P2_BUILD_FLAGS}"
+    "PROJECT_AR=${N2P2_AR}")
   # echo final flag for debugging
   message(STATUS "N2P2 BUILD OPTIONS: ${N2P2_BUILD_OPTIONS}")
 

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,11 +1,11 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "a2ac3315c41a1a4a5c912bcb1bc9c5cc" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 
 # download library sources to build folder
-file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5}) #SHOW_PROGRESS
+file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5})
 
 # uncompress downloaded sources
 execute_process(
@@ -14,19 +14,12 @@ execute_process(
   WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
 )
 
-file(GLOB lib-pace ${CMAKE_BINARY_DIR}/lammps-user-pace-*)
-add_subdirectory(${lib-pace}/yaml-cpp build-yaml-cpp)
-set(YAML_CPP_INCLUDE_DIR ${lib-pace}/yaml-cpp/include)
-
-file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${lib-pace}/ML-PACE)
-file(GLOB PACE_EVALUATOR_SOURCES ${lib-pace}/ML-PACE/*.cpp)
+file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
+file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
 list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
 
 add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
 set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
-target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR})
-
-
-target_link_libraries(pace PRIVATE yaml-cpp-pace)
-
+target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
 target_link_libraries(lammps PRIVATE pace)
+

cmake/Modules/Packages/ML-QUIP.cmake

@@ -32,8 +32,7 @@ if(DOWNLOAD_QUIP)
   foreach(flag ${LAPACK_LIBRARIES})
     set(temp "${temp} ${flag}")
   endforeach()
-  # Fix cmake crashing when MATH_LINKOPTS not set, required for e.g. recent Cray Programming Environment
-  set(temp "${temp} -L/_DUMMY_PATH_\n")
+  set(temp "${temp}\n")
   set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
   set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
   set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")

cmake/Modules/Packages/MSCG.cmake

@@ -12,12 +12,41 @@ if(DOWNLOAD_MSCG)
   mark_as_advanced(MSCG_URL)
   mark_as_advanced(MSCG_MD5)
 
-  include(ExternalCMakeProject)
-  ExternalCMakeProject(mscg ${MSCG_URL} ${MSCG_MD5} MSCG-release src/CMake "")
+  # CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
+  list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
+  list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
+  if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
+    message(FATAL_ERROR "Cannot compile downloaded MSCG library due to a technical limitation")
+  endif()
 
-  # set include and link library
-  target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/mscg-src/src")
-  target_link_libraries(lammps PRIVATE mscg)
+  include(ExternalProject)
+  ExternalProject_Add(mscg_build
+    URL     ${MSCG_URL}
+    URL_MD5 ${MSCG_MD5}
+    SOURCE_SUBDIR src/CMake
+    CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
+               -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+               -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+               -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
+               -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
+               -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+               -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+               -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+               -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+    BUILD_COMMAND ${CMAKE_COMMAND} --build . --target mscg
+    INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS <BINARY_DIR>/libmscg.a
+    )
+  ExternalProject_get_property(mscg_build BINARY_DIR)
+  ExternalProject_get_property(mscg_build SOURCE_DIR)
+  file(MAKE_DIRECTORY ${SOURCE_DIR}/src)
+  add_library(LAMMPS::MSCG UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::MSCG PROPERTIES
+    IMPORTED_LOCATION "${BINARY_DIR}/libmscg.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src"
+    INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
+  target_link_libraries(lammps PRIVATE LAMMPS::MSCG)
+  add_dependencies(LAMMPS::MSCG mscg_build)
 else()
   find_package(MSCG)
   if(NOT MSCG_FOUND)

cmake/Modules/Packages/PHONON.cmake

@@ -1,9 +0,0 @@
-# fix phonon may only be installed if also the FFT wrappers from KSPACE are installed
-if(NOT PKG_KSPACE)
-  get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
-  list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/PHONON/fix_phonon.h)
-  set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
-  get_target_property(LAMMPS_SOURCES lammps SOURCES)
-  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/PHONON/fix_phonon.cpp)
-  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
-endif()

cmake/Modules/Packages/PLUMED.cmake

@@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED)
     set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.3/plumed-src-2.7.3.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "f00cc82edfefe6bb3df934911dbe32fb" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.2/plumed-src-2.7.2.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "cfa0b4dd90a81c25d3302e8d97bfeaea" CACHE STRING "MD5 checksum of PLUMED tarball")
 
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)

cmake/Modules/Packages/PYTHON.cmake

@@ -3,7 +3,7 @@ if(CMAKE_VERSION VERSION_LESS 3.12)
   target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS})
   target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES})
 else()
-  find_package(Python REQUIRED COMPONENTS Interpreter Development)
+  find_package(Python REQUIRED COMPONENTS Development)
   target_link_libraries(lammps PRIVATE Python::Python)
 endif()
 target_compile_definitions(lammps PRIVATE -DLMP_PYTHON)

cmake/Modules/Tools.cmake

@@ -25,9 +25,7 @@ if(BUILD_TOOLS)
   get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
   file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
   add_executable(msi2lmp ${MSI2LMP_SOURCES})
-  if(STANDARD_MATH_LIB)
-    target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB})
-  endif()
+  target_link_libraries(msi2lmp PRIVATE ${MATH_LIBRARIES})
   install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
 endif()

cmake/Modules/YAML.cmake

@@ -0,0 +1,47 @@
+message(STATUS "Downloading and building YAML library")
+
+include(ExternalProject)
+set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball")
+set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of libyaml tarball")
+mark_as_advanced(YAML_URL)
+mark_as_advanced(YAML_MD5)
+
+# support cross-compilation to windows
+if(CMAKE_CROSSCOMPILING AND (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86")
+    set(YAML_CROSS_HOST --host=i686-mingw64)
+  elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    set(YAML_CROSS_HOST --host=x86_64-mingw64)
+  else()
+    message(FATAL_ERROR "Unsupported cross-compilation "
+      " for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}"
+      " on ${CMAKE_HOST_SYSTEM}/${CMAKE_HOST_SYSTEM_PROCESSOR}")
+  endif()
+endif()
+
+ExternalProject_Add(libyaml
+                    URL               ${YAML_URL}
+                    URL_MD5           ${YAML_MD5}
+                    SOURCE_DIR        "${CMAKE_BINARY_DIR}/yaml-src"
+                    BINARY_DIR        "${CMAKE_BINARY_DIR}/yaml-build"
+                    CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
+                                      CXX=${CMAKE_CXX_COMPILER} CC=${CMAKE_C_COMPILER}
+                                      --prefix=<INSTALL_DIR> --disable-shared ${YAML_CROSS_HOST}
+                    BUILD_BYPRODUCTS  <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
+                    TEST_COMMAND      "")
+
+ExternalProject_Get_Property(libyaml INSTALL_DIR)
+set(YAML_INCLUDE_DIR ${INSTALL_DIR}/include)
+set(YAML_LIBRARY_DIR ${INSTALL_DIR}/lib)
+
+# workaround for CMake 3.10 on ubuntu 18.04
+file(MAKE_DIRECTORY ${YAML_INCLUDE_DIR})
+file(MAKE_DIRECTORY ${YAML_LIBRARY_DIR})
+
+set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX})
+
+add_library(Yaml::Yaml UNKNOWN IMPORTED)
+set_target_properties(Yaml::Yaml PROPERTIES
+        IMPORTED_LOCATION ${YAML_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${YAML_INCLUDE_DIR})
+add_dependencies(Yaml::Yaml libyaml)

cmake/Modules/generate_lmpgitversion.cmake

@@ -24,10 +24,10 @@ if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
     OUTPUT_STRIP_TRAILING_WHITESPACE)
 endif()
 
-set(temp "${temp}bool LAMMPS_NS::LAMMPS::has_git_info() { return ${temp_git_info}; }\n")
-set(temp "${temp}const char *LAMMPS_NS::LAMMPS::git_commit() { return \"${temp_git_commit}\"; }\n")
-set(temp "${temp}const char *LAMMPS_NS::LAMMPS::git_branch() { return \"${temp_git_branch}\"; }\n")
-set(temp "${temp}const char *LAMMPS_NS::LAMMPS::git_descriptor() { return \"${temp_git_describe}\"; }\n")
+set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n")
 set(temp "${temp}#endif\n\n")
 
 message(STATUS "Generating lmpgitversion.h...")

cmake/iwyu/iwyu-extra-map.imp

@@ -20,14 +20,9 @@
   { include: [ "@\"kspace_.*.h\"", public, "\"style_kspace.h\"", public ] },
   { include: [ "@\"nbin_.*.h\"", public, "\"style_nbin.h\"", public ] },
   { include: [ "@\"npair_.*.h\"", public, "\"style_npair.h\"", public ] },
-  { include: [ "@\"nstencil_.*.h\"", public, "\"style_nstencil.h\"", public ] },
+  { include: [ "@\"nstenci_.*.h\"", public, "\"style_nstencil.h\"", public ] },
   { include: [ "@\"ntopo_.*.h\"", public, "\"style_ntopo.h\"", public ] },
-  { include: [ "\"fmt/core.h\"", private, "\"fmt/format.h\"", public ] },
   { include: [ "<float.h>",   public, "<cfloat>", public ] },
-  { include: [ "\"float.h\"",   public, "<cfloat>", public ] },
   { include: [ "<limits.h>",  public, "<climits>", public ] },
-  { include: [ "\"limits.h\"",  public, "<climits>", public ] },
-  { include: [ "<stdio.h>",  public, "<cstdio>", public ] },
-  { include: [ "<bits/types/struct_rusage.h>", private, "<sys/types.h>", public ] },
   { include: [ "<bits/types/struct_tm.h>", private, "<ctime>", public ] },
 ]

cmake/presets/gcc.cmake

@@ -3,19 +3,19 @@
 set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "gfortran" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Og -g" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 set(MPI_CXX "g++" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 set(MPI_C "gcc" CACHE STRING "" FORCE)
 set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE)
-set(CMAKE_C_FLAGS_DEBUG "-Wall -Og -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
 set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Og -g -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -g -std=f2003" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)

cmake/presets/most.cmake

@@ -48,6 +48,7 @@ set(ALL_PACKAGES
   PHONON
   PLUGIN
   POEMS
+  PYTHON
   QEQ
   REACTION
   REAXFF

cmake/presets/windows.cmake

@@ -1,64 +0,0 @@
-set(WIN_PACKAGES
-  ASPHERE
-  BOCS
-  BODY
-  BROWNIAN
-  CG-DNA
-  CG-SDK
-  CLASS2
-  COLLOID
-  COLVARS
-  CORESHELL
-  DIELECTRIC
-  DIFFRACTION
-  DIPOLE
-  DPD-BASIC
-  DPD-MESO
-  DPD-REACT
-  DPD-SMOOTH
-  DRUDE
-  EFF
-  EXTRA-COMPUTE
-  EXTRA-DUMP
-  EXTRA-FIX
-  EXTRA-MOLECULE
-  EXTRA-PAIR
-  FEP
-  GRANULAR
-  INTERLAYER
-  KSPACE
-  MANIFOLD
-  MANYBODY
-  MC
-  MEAM
-  MISC
-  ML-IAP
-  ML-SNAP
-  MOFFF
-  MOLECULE
-  MOLFILE
-  OPENMP
-  ORIENT
-  PERI
-  PHONON
-  POEMS
-  PTM
-  QEQ
-  QTB
-  REACTION
-  REAXFF
-  REPLICA
-  RIGID
-  SHOCK
-  SMTBQ
-  SPH
-  SPIN
-  SRD
-  TALLY
-  UEF
-  YAFF)
-
-foreach(PKG ${WIN_PACKAGES})
-  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
-endforeach()
-

doc/doxygen/Doxyfile.in

@@ -435,8 +435,6 @@ INPUT                  = @LAMMPS_SOURCE_DIR@/utils.cpp                 \
                          @LAMMPS_SOURCE_DIR@/my_pool_chunk.cpp         \
                          @LAMMPS_SOURCE_DIR@/my_pool_chunk.h           \
                          @LAMMPS_SOURCE_DIR@/math_eigen.h              \
-                         @LAMMPS_SOURCE_DIR@/platform.h                \
-                         @LAMMPS_SOURCE_DIR@/platform.cpp              \
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded

doc/github-development-workflow.md

@@ -33,9 +33,9 @@ when necessary.
 ## Pull Requests
 
 ALL changes to the LAMMPS code and documentation, however trivial, MUST
-be submitted as a pull request to GitHub. All changes to the "develop"
+be submitted as a pull request to GitHub. All changes to the "master"
 branch must be made exclusively through merging pull requests. The
-"release" and "stable" branches, respectively are only to be updated
+"unstable" and "stable" branches, respectively are only to be updated
 upon patch or stable releases with fast-forward merges based on the
 associated tags. Pull requests may also be submitted to (long-running)
 feature branches created by LAMMPS developers inside the LAMMPS project,
@@ -123,16 +123,16 @@ and thus were this comment should be placed.
 
 LAMMPS uses a continuous release development model with incremental
 changes, i.e. significant effort is made - including automated pre-merge
-testing - that the code in the branch "develop" does not get easily
+testing - that the code in the branch "master" does not get easily
 broken.  These tests are run after every update to a pull request.  More
 extensive and time consuming tests (including regression testing) are
-performed after code is merged to the "develop" branch. There are patch
+performed after code is merged to the "master" branch. There are patch
 releases of LAMMPS every 3-5 weeks at a point, when the LAMMPS
 developers feel, that a sufficient amount of changes have happened, and
 the post-merge testing has been successful. These patch releases are
-marked with a `patch_<version date>` tag and the "release" branch
+marked with a `patch_<version date>` tag and the "unstable" branch
 follows only these versions (and thus is always supposed to be of
-production quality, unlike "develop", which may be temporary broken, in
+production quality, unlike "master", which may be temporary broken, in
 the case of larger change sets or unexpected incompatibilities or side
 effects.
 

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "1" "17 February 2022" "2022-2-17"
+.TH LAMMPS "29 September 2021" "2021-09-29"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/msi2lmp.1

@@ -1,4 +1,4 @@
-.TH MSI2LMP "1" "v3.9.9" "2018-11-05"
+.TH MSI2LMP "v3.9.9" "2018-11-05"
 .SH NAME
 .B MSI2LMP
 \- Converter for Materials Studio files to LAMMPS

doc/src/Bibliography.rst

@@ -1123,12 +1123,9 @@ Bibliography
 **(Sun)**
    Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
 
-**(Surblys2019)**
+**(Surblys)**
    Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
 
-**(Surblys2021)**
-   Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).
-
 **(Sutmann)**
    Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
 

doc/src/Build_cmake.rst

@@ -150,42 +150,6 @@ for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the *-G*
 command line flag.  A list of available generator settings for your
 specific CMake version is given when running ``cmake --help``.
 
-.. _cmake_multiconfig:
-
-Multi-configuration build systems
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-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:
-
-.. 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
-the example from above).  Similarly, for running unit tests the
-configuration is selected with the *-C* flag:
-
-.. code-block:: bash
-
-   ctest -C Debug
-
-The CMake scripts in LAMMPS have basic support for being compiled using a
-multi-config build system, but not all of it has been ported.  This is in
-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.
-
 
 Installing CMake
 ^^^^^^^^^^^^^^^^

doc/src/Build_development.rst

@@ -185,10 +185,6 @@ The ``ctest`` command has many options, the most important ones are:
      - run subset of tests matching the regular expression <regex>
    * - -E <regex>
      - exclude subset of tests matching the regular expression <regex>
-   * - -L <regex>
-     - run subset of tests with a label matching the regular expression <regex>
-   * - -LE <regex>
-     - exclude subset of tests with a label matching the regular expression <regex>
    * - -N
      - dry-run: display list of tests without running them
    * - -T memcheck
@@ -303,12 +299,6 @@ will destroy the original file, if the generation run does not complete,
 so using *-g* is recommended unless the YAML file is fully tested
 and working.
 
-Some of the force style tests are rather slow to run and some are very
-sensitive to small differences like CPU architecture, compiler
-toolchain, compiler optimization. Those tests are flagged with a "slow"
-and/or "unstable" label, and thus those tests can be selectively
-excluded with the ``-LE`` flag or selected with the ``-L`` flag.
-
 .. admonition:: Recommendations and notes for YAML files
    :class: note
 

doc/src/Build_diskspace.rst

@@ -14,7 +14,7 @@ environments with restricted disk space capacity it may be needed to
 reduce the storage requirements. Here are some suggestions:
 
 - Create a so-called shallow repository by cloning only the last commit
-  instead of the full project history by using ``git clone git@github.com:lammps/lammps --depth=1 --branch=develop``.
+  instead of the full project history by using ``git clone git@github.com:lammps/lammps --depth=1 --branch=master``.
   This reduces the downloaded size to about half.  With ``--depth=1`` it is not possible to check out different
   versions/branches of LAMMPS, using ``--depth=1000`` will make multiple recent versions available at little
   extra storage needs (the entire git history had nearly 30,000 commits in fall 2021).

doc/src/Build_extras.rst

@@ -341,18 +341,6 @@ minutes to hours) to build.  Of course you only need to do that once.)
          $ 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
-      ``CMAKE`` environment variable if the cmake executable is named other
-      than ``cmake`` on your system.  Additional environment variables may be
-      provided on the command line for use by cmake.  For example, to use the
-      ``cmake3`` executable and tell it to use the gnu version 11 compilers
-      to build KIM, one could use the following command line.
-
-      .. 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
-
       Settings for debugging OpenKIM web queries discussed below need to
       be applied by adding them to the ``LMP_INC`` variable through
       editing the ``Makefile.machine`` you are using.  For example:
@@ -572,26 +560,11 @@ They must be specified in uppercase.
    *  - VEGA908
       - GPU
       - AMD GPU MI100 GFX908
-   *  - VEGA90A
+   *  - INTEL_GEN
       - GPU
-      - AMD GPU
-   *  - INTEL_DG1
-      - GPU
-      - Intel Iris XeMAX GPU
-   *  - INTEL_GEN9
-      - GPU
-      - Intel GPU Gen9
-   *  - INTEL_GEN11
-      - GPU
-      - Intel GPU Gen11
-   *  - INTEL_GEN12LP
-      - GPU
-      - Intel GPU Gen12LP
-   *  - INTEL_XEHP
-      - GPU
-      - Intel GPUs Xe-HP
+      - Intel GPUs Gen9+
 
-This list was last updated for version 3.5.0 of the Kokkos library.
+This list was last updated for version 3.4.1 of the Kokkos library.
 
 .. tabs::
 

doc/src/Build_manual.rst

@@ -33,15 +33,12 @@ various tools and files.  Some of them have to be installed (see below).  For
 the rest the build process will attempt to download and install them into
 a python virtual environment and local folders.
 
-A current version of the manual (latest patch release, that is the state
-of the *release* branch) is is available online at:
-`https://docs.lammps.org/ <https://docs.lammps.org/>`_.
-A version of the manual corresponding to the ongoing development (that is
-the state of the *develop* branch) is available online at:
-`https://docs.lammps.org/latest/ <https://docs.lammps.org/latest/>`_
-A version of the manual corresponding to the latest stable LAMMPS release
-(that is the state of the *stable* branch) is available online at:
-`https://docs.lammps.org/stable/ <https://docs.lammps.org/stable/>`_
+A current version of the manual (latest patch release, aka unstable
+branch) is is available online at:
+`https://docs.lammps.org/Manual.html <https://docs.lammps.org/Manual.html>`_.
+A version of the manual corresponding to the ongoing development (aka master branch)
+is available online at: `https://docs.lammps.org/latest/
+<https://docs.lammps.org/latest/>`_
 
 Build using GNU make
 --------------------

doc/src/Build_settings.rst

@@ -321,7 +321,9 @@ following settings:
 
       .. code-block:: make
 
-         LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG  <other LMP_INC settings>
+         LMP_INC = -DLAMMPS_JPEG
+         LMP_INC = -DLAMMPS_PNG
+         LMP_INC = -DLAMMPS_FFMPEG
 
          JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
          JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
@@ -352,10 +354,8 @@ 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:
-``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
+gzip compression by several LAMMPS commands, including
+:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
 
 .. tabs::
 
@@ -364,23 +364,23 @@ including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
       .. code-block:: bash
 
          -D WITH_GZIP=value       # yes or no
-                                  # default is yes if CMake can find the gzip program, else no
+                                  # default is yes if CMake can find gzip, else no
+         -D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it
 
    .. tab:: Traditional make
 
       .. code-block:: make
 
-         LMP_INC = -DLAMMPS_GZIP   <other LMP_INC settings>
+         LMP_INC = -DLAMMPS_GZIP
 
-This option requires that your operating system fully supports the
-"popen()" function in the standard runtime library and that a ``gzip``
-or other executable can be found by LAMMPS in the standard search path
-during a run.
+This option requires that your operating system fully supports the "popen()"
+function in the standard runtime library and that a ``gzip`` executable can be
+found by LAMMPS during a run.
 
 .. note::
 
-   On clusters with high-speed networks, using the "fork()" library call
-   (required by "popen()") can interfere with the fast communication
+   On some clusters with high-speed networks, using the "fork()" library
+   call (required by "popen()") can interfere with the fast communication
    library and lead to simulations using compressed output or input to
    hang or crash. For selected operations, compressed file I/O is also
    available using a compression library instead, which is what the
@@ -452,7 +452,7 @@ those systems:
 
       .. code-block:: make
 
-         LMP_INC = -DLAMMPS_LONGLONG_TO_LONG  <other LMP_INC settings>
+         LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
 
 ----------
 
@@ -479,7 +479,7 @@ e.g. to Python. Of course, the calling code has to be set up to
 
       .. code-block:: make
 
-         LMP_INC = -DLAMMPS_EXCEPTIONS   <other LMP_INC settings>
+         LMP_INC = -DLAMMPS_EXCEPTIONS
 
 .. note::
 
@@ -520,7 +520,7 @@ executable, not the library.
 
       .. code-block:: make
 
-         LMP_INC = -DLAMMPS_TRAP_FPE  <other LMP_INC settings>
+         LMP_INC = -DLAMMPS_TRAP_FPE
 
 After compilation with this flag set, the LAMMPS executable will stop
 and produce a core dump when a division by zero, overflow, illegal math

doc/src/Build_windows.rst

@@ -4,7 +4,6 @@ Notes for building LAMMPS on Windows
 * :ref:`General remarks <generic>`
 * :ref:`Running Linux on Windows <linux>`
 * :ref:`Using GNU GCC ported to Windows <gnu>`
-* :ref:`Using Visual Studio <msvc>`
 * :ref:`Using a cross-compiler <cross>`
 
 ----------
@@ -32,13 +31,13 @@ pre-compiled Windows binary packages are sufficient for your needs.  If
 it is necessary for you to compile LAMMPS on a Windows machine
 (e.g. because it is your main desktop), please also consider using a
 virtual machine software and compile and run LAMMPS in a Linux virtual
-machine, or - if you have a sufficiently up-to-date Windows 10 or
-Windows 11 installation - consider using the Windows subsystem for
-Linux.  This optional Windows feature allows you to run the bash shell
-from Ubuntu from within Windows and from there on, you can pretty much
-use that shell like you are running on an Ubuntu Linux machine
-(e.g. installing software via apt-get and more).  For more details on
-that, please see :doc:`this tutorial <Howto_wsl>`.
+machine, or - if you have a sufficiently up-to-date Windows 10
+installation - consider using the Windows subsystem for Linux.  This
+optional Windows feature allows you to run the bash shell from Ubuntu
+from within Windows and from there on, you can pretty much use that
+shell like you are running on an Ubuntu Linux machine (e.g. installing
+software via apt-get and more).  For more details on that, please see
+:doc:`this tutorial <Howto_wsl>`.
 
 .. _gnu:
 
@@ -68,40 +67,6 @@ requiring changes to the LAMMPS source code, or figure out corrections
 yourself, please report them on the lammps-users mailing list, or file
 them as an issue or pull request on the LAMMPS GitHub project.
 
-.. _msvc:
-
-Using Microsoft Visual Studio
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Following the integration of the :doc:`platform namespace
-<Developer_platform>` into the LAMMPS code base, portability of LAMMPS
-to be compiled on Windows using Visual Studio has been significantly
-improved.  This has been tested with Visual Studio 2019 (aka version
-16).  Not all features and packages in LAMMPS are currently supported
-out of the box, but a preset ``cmake/presets/windows.cmake`` is provided
-that contains the packages that have been compiled successfully.  You
-must use the CMake based build procedure, and either use the integrated
-CMake support of Visual Studio or use an external CMake installation to
-create build files for the Visual Studio build system.  Please note that
-on launching Visual Studio it will scan the directory tree and likely
-miss the correct master ``CMakeLists.txt``.  Try to open the
-``cmake/CMakeSettings.json`` and use those CMake configurations as a
-starting point.  It is also possible to configure and compile LAMMPS
-from the command line with a CMake binary from `cmake.org <https://cmake.org>`_.
-
-Please note, that for either approach CMake will create a so-called
-:ref:`"multi-configuration" build environment <cmake_multiconfig>`, and
-the command lines for building and testing LAMMPS must be adjusted
-accordingly.
-
-To support running in parallel you can compile with OpenMP enabled using
-the OPENMP package or install Microsoft MPI (including the SDK) and compile
-LAMMPS with MPI enabled.
-
-This is work in progress and you should contact the LAMMPS developers
-via GitHub, the forum, or the mailing list, if you have questions or
-LAMMPS specific problems.
-
 .. _cross:
 
 Using a cross-compiler

doc/src/Commands_all.rst

@@ -47,7 +47,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`displace_atoms <displace_atoms>`
    * :doc:`dump <dump>`
    * :doc:`dump_modify <dump_modify>`
-   * :doc:`dynamical_matrix (k) <dynamical_matrix>`
+   * :doc:`dynamical_matrix <dynamical_matrix>`
    * :doc:`echo <echo>`
    * :doc:`fix <fix>`
    * :doc:`fix_modify <fix_modify>`
@@ -117,7 +117,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`thermo <thermo>`
    * :doc:`thermo_modify <thermo_modify>`
    * :doc:`thermo_style <thermo_style>`
-   * :doc:`third_order (k) <third_order>`
+   * :doc:`third_order <third_order>`
    * :doc:`timer <timer>`
    * :doc:`timestep <timestep>`
    * :doc:`uncompute <uncompute>`

doc/src/Commands_bond.rst

@@ -35,7 +35,6 @@ OPT.
    * :doc:`class2 (ko) <bond_class2>`
    * :doc:`fene (iko) <bond_fene>`
    * :doc:`fene/expand (o) <bond_fene_expand>`
-   * :doc:`fene/nm <bond_fene>`
    * :doc:`gaussian <bond_gaussian>`
    * :doc:`gromos (o) <bond_gromos>`
    * :doc:`harmonic (iko) <bond_harmonic>`

doc/src/Commands_compute.rst

@@ -28,7 +28,6 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`angle <compute_angle>`
    * :doc:`angle/local <compute_angle_local>`
    * :doc:`angmom/chunk <compute_angmom_chunk>`
-   * :doc:`ave/sphere/atom (k) <compute_ave_sphere_atom>`
    * :doc:`basal/atom <compute_basal_atom>`
    * :doc:`body/local <compute_body_local>`
    * :doc:`bond <compute_bond>`

doc/src/Commands_fix.rst

@@ -23,7 +23,6 @@ OPT.
    :columns: 5
 
    * :doc:`accelerate/cos <fix_accelerate_cos>`
-   * :doc:`acks2/reaxff (k) <fix_acks2_reaxff>`
    * :doc:`adapt <fix_adapt>`
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`
@@ -104,7 +103,6 @@ OPT.
    * :doc:`manifoldforce <fix_manifoldforce>`
    * :doc:`mdi/engine <fix_mdi_engine>`
    * :doc:`meso/move <fix_meso_move>`
-   * :doc:`mol/swap <fix_mol_swap>`
    * :doc:`momentum (k) <fix_momentum>`
    * :doc:`momentum/chunk <fix_momentum>`
    * :doc:`move <fix_move>`
@@ -129,7 +127,6 @@ OPT.
    * :doc:`npt/sphere (o) <fix_npt_sphere>`
    * :doc:`npt/uef <fix_nh_uef>`
    * :doc:`numdiff <fix_numdiff>`
-   * :doc:`numdiff/virial <fix_numdiff_virial>`
    * :doc:`nve (giko) <fix_nve>`
    * :doc:`nve/asphere (gi) <fix_nve_asphere>`
    * :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`

doc/src/Commands_pair.rst

@@ -119,12 +119,10 @@ OPT.
    * :doc:`granular <pair_granular>`
    * :doc:`gw <pair_gw>`
    * :doc:`gw/zbl <pair_gw>`
-   * :doc:`harmonic/cut (o) <pair_harmonic_cut>`
    * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
    * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
    * :doc:`hdnnp <pair_hdnnp>`
    * :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
-   * :doc:`ilp/tmd <pair_ilp_tmd>`
    * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
    * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
    * :doc:`lcbop <pair_lcbop>`
@@ -212,7 +210,6 @@ OPT.
    * :doc:`nm/cut (o) <pair_nm>`
    * :doc:`nm/cut/coul/cut (o) <pair_nm>`
    * :doc:`nm/cut/coul/long (o) <pair_nm>`
-   * :doc:`nm/cut/split <pair_nm>`
    * :doc:`oxdna/coaxstk <pair_oxdna>`
    * :doc:`oxdna/excv <pair_oxdna>`
    * :doc:`oxdna/hbond <pair_oxdna>`
@@ -242,7 +239,6 @@ OPT.
    * :doc:`reaxff (ko) <pair_reaxff>`
    * :doc:`rebo (io) <pair_airebo>`
    * :doc:`resquared (go) <pair_resquared>`
-   * :doc:`saip/metal <pair_saip_metal>`
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
    * :doc:`smd/hertz <pair_smd_hertz>`
    * :doc:`smd/tlsph <pair_smd_tlsph>`
@@ -266,7 +262,6 @@ OPT.
    * :doc:`spin/neel <pair_spin_neel>`
    * :doc:`srp <pair_srp>`
    * :doc:`sw (giko) <pair_sw>`
-   * :doc:`sw/mod (o) <pair_sw>`
    * :doc:`table (gko) <pair_table>`
    * :doc:`table/rx (k) <pair_table_rx>`
    * :doc:`tdpd <pair_mesodpd>`

doc/src/Developer.rst

@@ -11,7 +11,6 @@ of time and requests from the LAMMPS user community.
    :maxdepth: 1
 
    Developer_org
-   Developer_cxx_vs_c_style
    Developer_parallel
    Developer_flow
    Developer_write
@@ -19,5 +18,4 @@ of time and requests from the LAMMPS user community.
    Developer_plugins
    Developer_unittest
    Classes
-   Developer_platform
    Developer_utils

doc/src/Developer_cxx_vs_c_style.rst

@@ -1,384 +0,0 @@
-Code design
------------
-
-This section discusses some of the code design choices in LAMMPS and
-overall strategy in order to assist developers to write new code that
-will fit well with the remaining 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 to discuss of some relevant C++ programming
-language constructs.
-
-Historically, the basic design philosophy of the LAMMPS C++ code was
-that of a "C with classes" style.  The was motivated by the desire to
-make it easier to modify LAMMPS for people without significant training
-in C++ programming and by trying to use data structures and code constructs
-that somewhat resemble the previous implementation(s) in Fortran.
-A contributing factor for this choice also was that at the time the
-implementation of C++ compilers was not always very mature and some of
-the advanced features contained bugs or were not functioning exactly
-as the standard required; plus there was some disagreement between
-compiler vendors about how to interpret the C++ standard documents.
-
-However, C++ compilers have advanced a lot since then and with the
-transition to requiring the C++11 standard in 2020 as the minimum C++ language
-standard for LAMMPS, the decision was made to also replace some of the
-C-style constructs with equivalent C++ functionality, either from the
-C++ standard library or as custom classes or function, in order 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 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 during compilation
-   is not subject to the conventions discussed here.
-
-Object oriented code
-^^^^^^^^^^^^^^^^^^^^
-
-LAMMPS is designed to be an object oriented code, that is each
-simulation is represented by an instance of the LAMMPS class.  When
-running in parallel, of course, each MPI process will create such an
-instance.  This can be seen in the ``main.cpp`` file where the core
-steps of running a LAMMPS simulation are the following 3 lines of code:
-
-.. code-block:: C++
-
-    LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
-    lammps->input->file();
-    delete lammps;
-
-The first line creates a LAMMPS class instance and passes the command
-line arguments and the global communicator to its constructor.  The
-second line tells the LAMMPS instance to process the input (either from
-standard input or the provided input file) until the end.  And the third
-line deletes that instance again.  The remainder of the main.cpp file
-are for error handling, MPI configuration and other special features.
-
-In the constructor of the LAMMPS class instance the basic LAMMPS class hierarchy
-is created as shown in :ref:`class-topology`.  While processing the input further
-class instances are created, or deleted, or replaced and specific member functions
-of specific classes are called to trigger actions like creating atoms, computing
-forces, computing properties, propagating the system, or writing output.
-
-Compositing and Inheritance
-===========================
-
-LAMMPS makes extensive use of the object oriented programming (OOP)
-principles of *compositing* and *inheritance*. Classes like the
-``LAMMPS`` class are a **composite** containing pointers to instances of
-other classes like ``Atom``, ``Comm``, ``Force``, ``Neighbor``,
-``Modify``, and so on.  Each of these classes implement certain
-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 a composite again containing instances
-of classes describing the force interactions or ``Modify`` containing
-and calling fixes and computes.  In most cases (e.g. ``AtomVec``, ``Comm``,
-``Pair``, or ``Bond``) there is only one instance of those member classes
-allowed, but in a few cases (e.g. ``Region``, ``Fix``, ``Compute``, or
-``Dump``) there can be multiple instances and the parent class is
-maintaining a list of the pointers of instantiated classes instead
-of a single pointer.
-
-Changing behavior or adjusting how LAMMPS handles a simulation is
-implemented via **inheritance** where different variants of the
-functionality are realized by creating *derived* classes that can share
-common functionality in their base class and provide a consistent
-interface where the derived classes replace (dummy or pure) functions in
-the base class.  The higher level classes can then call those methods of
-the instantiated classes without having to know which specific derived
-class variant was instantiated.  In the LAMMPS documentation those
-derived classes are usually referred to a "styles", e.g.  pair styles,
-fix styles, atom styles and so on.
-
-This is the origin of the flexibility of LAMMPS and facilitates for
-example to compute forces for very different non-bonded potential
-functions by having different pair styles (implemented as different
-classes derived from the ``Pair`` class) where the evaluation of the
-potential function is confined to the implementation of the individual
-classes.  Whenever a new :doc:`pair_style` or :doc:`bond_style` or
-:doc:`comm_style` or similar command is processed in the LAMMPS input
-any existing class instance is deleted and a new instance created in
-it place.
-
-Classes derived from ``Fix`` or ``Compute`` represent a different facet
-of LAMMPS' flexibility as there can be multiple instances of them an
-their member functions will be called at different phases of the time
-integration process (as explained in `Developer_flow`).  This way
-multiple manipulations of the entire or parts of the system can be
-programmed (with fix styles) or different computations can be performed
-and accessed and further processed or output through a common interface
-(with compute styles).
-
-Further code sharing is possible by creating derived classes from the
-derived classes (for instance to implement an accelerated version of a
-pair style) where then only a subset of the methods are replaced with
-the accelerated versions.
-
-Polymorphism
-============
-
-Polymorphism and dynamic dispatch are another OOP feature that play an
-important part of how LAMMPS selects which code to execute.  In a nutshell,
-this is a mechanism where the decision of which member function to call
-from a class is determined at runtime and not when the code is compiled.
-To enable it, the function has to be declared as ``virtual`` and all
-corresponding functions in derived classes should be using the ``override``
-property. Below is a brief example.
-
-.. code-block:: c++
-
-   class Base {
-   public:
-    virtual ~Base() = default;
-    void call();
-    void normal();
-    virtual void poly();
-   };
-
-   void Base::call() {
-    normal();
-    poly();
-   }
-
-   class Derived : public Base {
-   public:
-    ~Derived() override = default;
-    void normal();
-    void poly() override;
-   };
-
-   // [....]
-
-   Base *base1 = new Base();
-   Base *base2 = new Derived();
-
-   base1->call();
-   base2->call();
-
-The difference in behavior of the ``normal()`` and the ``poly()`` member
-functions is in which of the two member functions is called when
-executing `base1->call()` and `base2->call()`.  Without polymorphism, a
-function within the base class will call only member functions within
-the same scope, that is ``Base::call()`` will always call
-``Base::normal()``.  But for the `base2->call()` the call for the
-virtual member function will be dispatched to ``Derived::poly()``
-instead.  This mechanism allows to always call functions within the
-scope of the class type that was used to create the class instance, even
-if they are assigned to a pointer using the type of a base class. This
-is the desired behavior, and thanks to dynamic dispatch, 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
-(see example below).
-
-.. code-block:: c++
-
-   class Base {
-   public:
-    virtual void pure() = 0;
-   };
-
-This has the effect that it will no longer be possible to create an
-instance of the base class and that derived classes **must** implement
-these functions.  Many of the functions listed with the various class
-styles in the section :doc:`Modify` are such pure functions.  The
-motivation for this is to define the interface or API of the functions
-but defer the 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
-or to provide an explicit scope like in ``Base::poly()``.  Furthermore,
-any destructors in classes containing virtual functions should be
-declared virtual, too, so they are processed in the expected order
-before types are removed from dynamic dispatch.
-
-.. admonition:: Important Notes
-
-   In order to be able to detect incompatibilities and to avoid unexpected
-   behavior already at compile time, it is crucial that all member functions
-   that are intended to replace a virtual or pure function use the ``override``
-   property keyword.  For the same reason it should be avoided to use overloads
-   or default arguments for virtual functions as they lead to confusion over
-   which function is supposed to override which and which arguments need to be
-   declared.
-
-Style Factories
-===============
-
-In order to create class instances of the different styles, LAMMPS often
-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 in which function pointers are indexed by their keyword
-(for example "lj/cut" for ``PairLJCut`` and "morse" ``PairMorse``).
-A couple of typedefs help to keep the code readable and a template function
-is used to implement the actual factory functions for the individual classes.
-
-I/O and output formatting
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-C-style stdio versus C++ style iostreams
-========================================
-
-LAMMPS chooses to use the "stdio" library of the standard C library for
-reading from and writing to files and console instead of C++
-"iostreams".  This is mainly motivated by the better performance, better
-control over formatting, and less effort to achieve specific formatting.
-
-Since mixing "stdio" and "iostreams" can lead to unexpected behavior using
-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 only be done by MPI rank 0 (``comm->me == 0``) and output that is
-send to both ``screen`` and ``logfile`` should use the
-:cpp:func:`utils::logmesg() convenience function <LAMMPS_NS::utils::logmesg>`.
-
-We also discourage the use for stringstreams as the bundled {fmt} library
-and the customized tokenizer classes can provide the same functionality
-in a cleaner way with better performance. This will also help to retain
-a consistent programming style despite the 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
-"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
-64-bit) which may require different format strings depending on compile
-time settings or compilers/operating systems.  Furthermore, {fmt} gives
-better performance, has more functionality, a familiar formatting syntax
-that has similarities to ``format()`` in Python, and provides a facility
-that can be used to integrate format strings and a variable number of
-arguments into custom functions in a much simpler way that the varargs
-mechanism of the C library.  Finally, {fmt} has 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 ``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. Alternatively
-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 arguments 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
-==================================
-
-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.
-
-More common is the use of the format specifier, which starts with a
-colon.  This may optionally be followed by a fill character (default is
-' '). If provided, the fill character **must** be followed by an
-alignment character ('<', '^', '>' for left, centered, or right
-alignment (default)). The alignment character may be used without a fill
-character. The next important format parameter would be the minimum
-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
-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:
-
-.. code-block:: C
-
-   auto mesg = fmt::format("  CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus);
-   mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n",
-                      label, time_min, time, time_max, time_sq, tmp);
-   utils::logmesg(lmp,"{:>6} = max # of 1-2 neighbors\n",maxall);
-   utils::logmesg(lmp,"Lattice spacing in x,y,z = {:.8} {:.8} {:.8}\n",
-                  xlattice,ylattice,zlattice);
-
-which will create the following output lines:
-
-.. parsed-literal::
-
-     CPU time:    0:02:16
-     Pair    | 2.0133     | 2.0133     | 2.0133     |   0.0 | 84.21
-          4 = max # of 1-2 neighbors
-     Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
-
-A special feature of the {fmt} library is that format parameters like
-the width or the precision may be also provided as arguments. In that
-case a nested format is used where a pair of curly braces (with an
-optional argument id) "{}" are used instead of the value, for example
-"{:{}d}" will consume two integer arguments, the first will be the value
-shown and the second the minimum width.
-
-For more details and examples, please consult the `{fmt} syntax
-documentation <https://fmt.dev/latest/syntax.html>`_ website.
-
-
-Memory management
-^^^^^^^^^^^^^^^^^
-
-Dynamical allocation of data and objects should be done with either the
-C++ commands "new" and "delete/delete[]" or using member functions of
-the ``Memory`` class, most commonly, ``Memory::create()``,
-``Memory::grow()``, and ``Memory::destroy()``.  The use of ``malloc()``,
-``calloc()``, ``realloc()`` and ``free()`` directly is strongly
-discouraged.  To simplify adapting legacy code into the LAMMPS code base
-the member functions ``Memory::smalloc()``, ``Memory::srealloc()``, and
-``Memory::sfree()`` are available.
-
-Using those 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 consecutive block and thus when MPI communication is needed,
-  only this storage needs to be communicated (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
-  all operating systems, since the allocated storage pointers must be
-  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 would be safe to call ``Memory::destroy()``
-or ``delete[]`` on them before *any* allocation outside the constructor.
-This helps to prevent memory leaks.

doc/src/Developer_notes.rst

@@ -7,61 +7,6 @@ typically document what a variable stores, what a small section of
 code does, or what a function does and its input/outputs.  The topics
 on this page are intended to document code functionality at a higher level.
 
-Reading and parsing of text and text files
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-It is frequently required for a class in LAMMPS to read in additional
-data from a file, most commonly potential parameters from a potential
-file for manybody potentials.  LAMMPS provides several custom classes
-and convenience functions to simplify the process.  This offers the
-following benefits:
-
-- better code reuse and fewer lines of code needed to implement reading
-  and parsing data from a file
-- better detection of format errors, incompatible data, and better error messages
-- exit with an error message instead of silently converting only part of the
-  text to a number or returning a 0 on unrecognized text and thus reading incorrect values
-- re-entrant code through avoiding global static variables (as used by ``strtok()``)
-- transparent support for translating unsupported UTF-8 characters to their ASCII equivalents
-  (the text to value conversion functions **only** accept ASCII characters)
-
-In most cases (e.g. potential files) the same data is needed on all MPI
-ranks.  Then it is best to do the reading and parsing only on MPI rank
-0, and communicate the data later with one or more ``MPI_Bcast()``
-calls.  For reading generic text and potential parameter files the
-custom classes :cpp:class:`TextFileReader <LAMMPS_NS::TextFileReader>`
-and :cpp:class:`PotentialFileReader <LAMMPS_NS::PotentialFileReader>`
-are available. Those classes allow to read the file as individual lines
-for which they can return a tokenizer class (see below) for parsing the
-line, or they can return blocks of numbers as a vector directly.  The
-documentation on `File reader classes <file-reader-classes>`_ contains
-an example for a typical case.
-
-When reading per-atom data, the data in the file usually needs include
-an atom ID so it can be associated with a particular atom.  In that case
-the data can be read in multi-line chunks and broadcast to all MPI ranks
-with :cpp:func:`utils::read_lines_from_file()
-<LAMMPS_NS::utils::read_lines_from_file>`.  Those chunks are then
-split into lines, parsed, and applied only to atoms the MPI rank
-"owns".
-
-For splitting a string (incrementally) into words and optionally
-converting those to numbers, the :cpp:class:`Tokenizer
-<LAMMPS_NS::Tokenizer>` and :cpp:class:`ValueTokenizer
-<LAMMPS_NS::ValueTokenizer>` can be used.  Those provide a superset of
-the functionality of ``strtok()`` from the C-library and the latter also
-includes conversion to different types.  Any errors while processing the
-string in those classes will result in an exception, which can be caught
-and the error processed as needed.  Unlike the C-library functions
-``atoi()``, ``atof()``, ``strtol()``, or ``strtod()`` the conversion
-will check if the converted text is a valid integer of floating point
-number and will not silently return an unexpected or incorrect value.
-For example, ``atoi()`` will return 12 when converting "12.5" while the
-ValueTokenizer class will throw an :cpp:class:`InvalidIntegerException
-<LAMMPS_NS::InvalidIntegerException>` if
-:cpp:func:`ValueTokenizer::next_int()
-<LAMMPS_NS::ValueTokenizer::next_int>` is called on the same string.
-
 Fix contributions to instantaneous energy, virial, and cumulative energy
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Developer_org.rst

@@ -225,7 +225,7 @@ follows:
   commands in an input script.
 
 - The Force class computes various forces between atoms.  The Pair
-  parent class is for non-bonded or pairwise forces, which in LAMMPS
+  parent class is for non-bonded or pair-wise forces, which in LAMMPS
   also includes many-body forces such as the Tersoff 3-body potential if
   those are computed by walking pairwise neighbor lists.  The Bond,
   Angle, Dihedral, Improper parent classes are styles for bonded

doc/src/Developer_platform.rst

@@ -1,155 +0,0 @@
-Platform abstraction functions
-------------------------------
-
-The ``platform`` sub-namespace inside the ``LAMMPS_NS`` namespace
-provides a collection of wrapper and convenience functions and utilities
-that perform common tasks for which platform specific code would be
-required or for which a more high-level abstraction would be convenient
-and reduce duplicated code.  This reduces redundant implementations and
-encourages consistent behavior and thus has some overlap with the
-:doc:`"utils" sub-namespace <Developer_utils>`.
-
-Time functions
-^^^^^^^^^^^^^^
-
-.. doxygenfunction:: cputime
-   :project: progguide
-
-.. doxygenfunction:: walltime
-   :project: progguide
-
-.. doxygenfunction:: usleep
-   :project: progguide
-
-Platform information functions
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. doxygenfunction:: os_info
-   :project: progguide
-
-.. doxygenfunction:: compiler_info
-   :project: progguide
-
-.. doxygenfunction:: cxx_standard
-   :project: progguide
-
-.. doxygenfunction:: openmp_standard
-   :project: progguide
-
-.. doxygenfunction:: mpi_vendor
-   :project: progguide
-
-.. doxygenfunction:: mpi_info
-   :project: progguide
-
-.. doxygenfunction:: compress_info
-   :project: progguide
-
-
-File and path functions and global constants
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. doxygenvariable:: filepathsep
-   :project: progguide
-
-.. doxygenvariable:: pathvarsep
-   :project: progguide
-
-.. doxygenfunction:: guesspath
-   :project: progguide
-
-.. doxygenfunction:: path_basename
-   :project: progguide
-
-.. doxygenfunction:: path_join
-   :project: progguide
-
-.. doxygenfunction:: file_is_readable
-   :project: progguide
-
-.. doxygenfunction:: is_console
-   :project: progguide
-
-.. doxygenfunction:: path_is_directory
-   :project: progguide
-
-.. doxygenfunction:: current_directory
-   :project: progguide
-
-.. doxygenfunction:: list_directory
-   :project: progguide
-
-.. doxygenfunction:: chdir
-   :project: progguide
-
-.. doxygenfunction:: mkdir
-   :project: progguide
-
-.. doxygenfunction:: rmdir
-   :project: progguide
-
-.. doxygenfunction:: unlink
-   :project: progguide
-
-Standard I/O function wrappers
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. doxygenvariable:: END_OF_FILE
-   :project: progguide
-
-.. doxygenfunction:: ftell
-   :project: progguide
-
-.. doxygenfunction:: fseek
-   :project: progguide
-
-.. doxygenfunction:: ftruncate
-   :project: progguide
-
-.. doxygenfunction:: popen
-   :project: progguide
-
-.. doxygenfunction:: pclose
-   :project: progguide
-
-Environment variable functions
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. doxygenfunction:: putenv
-   :project: progguide
-
-.. doxygenfunction:: unsetenv
-   :project: progguide
-
-.. doxygenfunction:: list_pathenv
-   :project: progguide
-
-.. doxygenfunction:: find_exe_path
-   :project: progguide
-
-Dynamically loaded object or library functions
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. doxygenfunction:: dlopen
-   :project: progguide
-
-.. doxygenfunction:: dlclose
-   :project: progguide
-
-.. doxygenfunction:: dlsym
-   :project: progguide
-
-.. doxygenfunction:: dlerror
-   :project: progguide
-
-Compressed file I/O functions
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. doxygenfunction:: has_compress_extension
-   :project: progguide
-
-.. doxygenfunction:: compressed_read
-   :project: progguide
-
-.. doxygenfunction:: compressed_write
-   :project: progguide

doc/src/Developer_utils.rst

@@ -7,9 +7,7 @@ a collection of convenience functions and utilities that perform common
 tasks that are required repeatedly throughout the LAMMPS code like
 reading or writing to files with error checking or translation of
 strings into specific types of numbers with checking for validity.  This
-reduces redundant implementations and encourages consistent behavior and
-thus has some overlap with the :doc:`"platform" sub-namespace
-<Developer_platform>`.
+reduces redundant implementations and encourages consistent behavior.
 
 I/O with status check and similar functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -21,21 +19,18 @@ In that case, the functions will stop with an error message, indicating
 the name of the problematic file, if possible unless the *error* argument
 is a NULL pointer.
 
-The :cpp:func:`utils::fgets_trunc() <LAMMPS_NS::utils::fgets_trunc>`
-function will work similar for ``fgets()`` but it will read in a whole
-line (i.e. until the end of line or end of file), but store only as many
-characters as will fit into the buffer including a final newline
-character and the terminating NULL byte.  If the line in the file is
-longer it will thus be truncated in the buffer.  This function is used
-by :cpp:func:`utils::read_lines_from_file()
-<LAMMPS_NS::utils::read_lines_from_file>` to read individual lines but
-make certain they follow the size constraints.
+The :cpp:func:`fgets_trunc` function will work similar for ``fgets()``
+but it will read in a whole line (i.e. until the end of line or end
+of file), but store only as many characters as will fit into the buffer
+including a final newline character and the terminating NULL byte.
+If the line in the file is longer it will thus be truncated in the buffer.
+This function is used by :cpp:func:`read_lines_from_file` to read individual
+lines but make certain they follow the size constraints.
 
-The :cpp:func:`utils::read_lines_from_file()
-<LAMMPS_NS::utils::read_lines_from_file>` function will read the
-requested number of lines of a maximum length into a buffer and will
-return 0 if successful or 1 if not. It also guarantees that all lines
-are terminated with a newline character and the entire buffer with a
+The :cpp:func:`read_lines_from_file` function will read the requested
+number of lines of a maximum length into a buffer and will return 0
+if successful or 1 if not. It also guarantees that all lines are
+terminated with a newline character and the entire buffer with a
 NULL character.
 
 ----------
@@ -59,54 +54,33 @@ String to number conversions with validity check
 
 These functions should be used to convert strings to numbers. They are
 are strongly preferred over C library calls like ``atoi()`` or
-``atof()`` since they check if the **entire** string is a valid
+``atof()`` since they check if the **entire** provided string is a valid
 (floating-point or integer) number, and will error out instead of
 silently returning the result of a partial conversion or zero in cases
-where the string is not a valid number.  This behavior improves
-detecting typos or issues when processing input files.
-
-Similarly the :cpp:func:`utils::logical() <LAMMPS_NS::utils::logical>` function
-will convert a string into a boolean and will only accept certain words.
+where the string is not a valid number.  This behavior allows to more
+easily detect typos or issues when processing input files.
 
 The *do_abort* flag should be set to ``true`` in case  this function
 is called only on a single MPI rank, as that will then trigger the
 a call to ``Error::one()`` for errors instead of ``Error::all()``
 and avoids a "hanging" calculation when run in parallel.
 
-Please also see :cpp:func:`utils::is_integer() <LAMMPS_NS::utils::is_integer>`
-and :cpp:func:`utils::is_double() <LAMMPS_NS::utils::is_double>` for testing
+Please also see :cpp:func:`is_integer() <LAMMPS_NS::utils::is_integer>`
+and :cpp:func:`is_double() <LAMMPS_NS::utils::is_double>` for testing
 strings for compliance without conversion.
 
 ----------
 
-.. doxygenfunction:: numeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
+.. doxygenfunction:: numeric
    :project: progguide
 
-.. doxygenfunction:: numeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
+.. doxygenfunction:: inumeric
    :project: progguide
 
-.. doxygenfunction:: inumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
+.. doxygenfunction:: bnumeric
    :project: progguide
 
-.. doxygenfunction:: inumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
-   :project: progguide
-
-.. doxygenfunction:: bnumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
-   :project: progguide
-
-.. doxygenfunction:: bnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
-   :project: progguide
-
-.. doxygenfunction:: tnumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
-   :project: progguide
-
-.. doxygenfunction:: tnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
-   :project: progguide
-
-.. doxygenfunction:: logical(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
-   :project: progguide
-
-.. doxygenfunction:: logical(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
+.. doxygenfunction:: tnumeric
    :project: progguide
 
 
@@ -121,12 +95,6 @@ and parsing files or arguments.
 .. doxygenfunction:: strdup
    :project: progguide
 
-.. doxygenfunction:: lowercase
-   :project: progguide
-
-.. doxygenfunction:: uppercase
-   :project: progguide
-
 .. doxygenfunction:: trim
    :project: progguide
 
@@ -169,6 +137,21 @@ and parsing files or arguments.
 .. doxygenfunction:: is_double
    :project: progguide
 
+File and path functions
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. doxygenfunction:: guesspath
+   :project: progguide
+
+.. doxygenfunction:: path_basename
+   :project: progguide
+
+.. doxygenfunction:: path_join
+   :project: progguide
+
+.. doxygenfunction:: file_is_readable
+   :project: progguide
+
 Potential file functions
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -208,9 +191,6 @@ Convenience functions
 .. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
    :project: progguide
 
-.. doxygenfunction:: flush_buffers(LAMMPS *lmp)
-   :project: progguide
-
 .. doxygenfunction:: getsyserror
    :project: progguide
 
@@ -343,11 +323,11 @@ This code example should produce the following output:
 
 .. doxygenclass:: LAMMPS_NS::InvalidIntegerException
    :project: progguide
-   :members:
+   :members: what
 
 .. doxygenclass:: LAMMPS_NS::InvalidFloatException
    :project: progguide
-   :members:
+   :members: what
 
 ----------
 
@@ -396,26 +376,21 @@ A typical code segment would look like this:
 
 ----------
 
-.. file-reader-classes:
-
 File reader classes
 -------------------
 
 The purpose of the file reader classes is to simplify the recurring task
 of reading and parsing files. They can use the
-:cpp:class:`ValueTokenizer <LAMMPS_NS::ValueTokenizer>` class to process
-the read in text.  The :cpp:class:`TextFileReader
-<LAMMPS_NS::TextFileReader>` is a more general version while
-:cpp:class:`PotentialFileReader <LAMMPS_NS::PotentialFileReader>` is
-specialized to implement the behavior expected for looking up and
-reading/parsing files with potential parameters in LAMMPS.  The
-potential file reader class requires a LAMMPS instance, requires to be
-run on MPI rank 0 only, will use the
-:cpp:func:`utils::get_potential_file_path
-<LAMMPS_NS::utils::get_potential_file_path>` function to look up and
-open the file, and will call the :cpp:class:`LAMMPS_NS::Error` class in
-case of failures to read or to convert numbers, so that LAMMPS will be
-aborted.
+:cpp:class:`LAMMPS_NS::ValueTokenizer` class to process the read in
+text.  The :cpp:class:`LAMMPS_NS::TextFileReader` is a more general
+version while :cpp:class:`LAMMPS_NS::PotentialFileReader` is specialized
+to implement the behavior expected for looking up and reading/parsing
+files with potential parameters in LAMMPS.  The potential file reader
+class requires a LAMMPS instance, requires to be run on MPI rank 0 only,
+will use the :cpp:func:`LAMMPS_NS::utils::get_potential_file_path`
+function to look up and open the file, and will call the
+:cpp:class:`LAMMPS_NS::Error` class in case of failures to read or to
+convert numbers, so that LAMMPS will be aborted.
 
 .. code-block:: C++
    :caption: Use of PotentialFileReader class in pair style coul/streitz
@@ -490,10 +465,10 @@ provided, as that is used to determine whether a new page of memory
 must be used.
 
 The :cpp:class:`MyPage <LAMMPS_NS::MyPage>` class offers two ways to
-reserve a chunk: 1) with :cpp:func:`MyPage::get() <LAMMPS_NS::MyPage::get>` the
-chunk size needs to be known in advance, 2) with :cpp:func:`MyPage::vget()
+reserve a chunk: 1) with :cpp:func:`get() <LAMMPS_NS::MyPage::get>` the
+chunk size needs to be known in advance, 2) with :cpp:func:`vget()
 <LAMMPS_NS::MyPage::vget>` a pointer to the next chunk is returned, but
-its size is registered later with :cpp:func:`MyPage::vgot()
+its size is registered later with :cpp:func:`vgot()
 <LAMMPS_NS::MyPage::vgot>`.
 
 .. code-block:: C++
@@ -596,3 +571,4 @@ the communication buffers.
 
 .. doxygenunion:: LAMMPS_NS::ubuf
    :project: progguide
+

doc/src/Developer_write.rst

@@ -29,9 +29,7 @@ of code in the header before include guards:
 .. code-block:: c
 
    #ifdef FIX_CLASS
-   // clang-format off
-   FixStyle(print/vel,FixPrintVel);
-   // clang-format on
+   FixStyle(print/vel,FixPrintVel)
    #else
    /* the definition of the FixPrintVel class comes here */
    ...
@@ -55,7 +53,7 @@ of each timestep. First of all, implement a constructor:
      if (narg < 4)
        error->all(FLERR,"Illegal fix print/vel command");
 
-     nevery = utils::inumeric(FLERR,arg[3],false,lmp);
+     nevery = force->inumeric(FLERR,arg[3]);
      if (nevery <= 0)
        error->all(FLERR,"Illegal fix print/vel command");
    }

doc/src/Errors_messages.rst

@@ -1941,9 +1941,6 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Compute ID for fix numdiff does not exist*
    Self-explanatory.
 
-*Compute ID for fix numdiff/virial does not exist*
-   Self-explanatory.
-
 *Compute ID for fix store/state does not exist*
    Self-explanatory.
 
@@ -3799,10 +3796,6 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Self-explanatory. Efficient loop over all atoms for numerical
    difference requires consecutive atom IDs.
 
-*Fix numdiff/virial must use group all*
-   Virial contributions computed by this fix are
-   computed on all atoms.
-
 *Fix nve/asphere requires extended particles*
    This fix can only be used for particles with a shape setting.
 
@@ -7779,6 +7772,9 @@ keyword to allow for additional bonds to be formed
    The system size must fit in a 32-bit integer to use this dump
    style.
 
+*Too many atoms to dump sort*
+   Cannot sort when running with more than 2\^31 atoms.
+
 *Too many elements extracted from MEAM library.*
    Increase 'maxelt' in meam.h and recompile.
 

doc/src/Errors_warnings.rst

@@ -416,7 +416,7 @@ This will most likely cause errors in kinetic fluctuations.
    not defined for the specified atom style.
 
 *Molecule has bond topology but no special bond settings*
-   This means the bonded atoms will not be excluded in pairwise
+   This means the bonded atoms will not be excluded in pair-wise
    interactions.
 
 *Molecule template for create_atoms has multiple molecules*

doc/src/Examples.rst

@@ -80,7 +80,7 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | friction    | frictional contact of spherical asperities between 2d surfaces   |
 +-------------+------------------------------------------------------------------+
-| mc          | Monte Carlo features via fix gcmc, widom and other commands      |
+| gcmc        | Grand Canonical Monte Carlo (GCMC) via the fix gcmc command      |
 +-------------+------------------------------------------------------------------+
 | granregion  | use of fix wall/region/gran as boundary on granular particles    |
 +-------------+------------------------------------------------------------------+
@@ -205,7 +205,7 @@ Uppercase directories
 +------------+--------------------------------------------------------------------------------------------------+
 | KAPPA      | compute thermal conductivity via several methods                                                 |
 +------------+--------------------------------------------------------------------------------------------------+
-| MC-LOOP    | using LAMMPS in a Monte Carlo mode to relax the energy of a system in a input script loop        |
+| MC         | using LAMMPS in a Monte Carlo mode to relax the energy of a system                               |
 +------------+--------------------------------------------------------------------------------------------------+
 | PACKAGES   | examples for specific packages and contributed commands                                          |
 +------------+--------------------------------------------------------------------------------------------------+

doc/src/Howto_drude2.rst

@@ -491,6 +491,11 @@ NPT ensemble using Nose-Hoover thermostat:
 **(Schroeder)**  Schroeder and Steinhauser, J Chem Phys, 133,
 154511 (2010).
 
+.. _Jiang2:
+
+**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,
+ J Phys Chem Lett, 2, 87-92 (2011).
+
 .. _Thole2:
 
 **(Thole)** Chem Phys, 59, 341 (1981).

doc/src/Howto_github.rst

@@ -7,11 +7,11 @@ LAMMPS GitHub tutorial
 
 This document describes the process of how to use GitHub to integrate
 changes or additions you have made to LAMMPS into the official LAMMPS
-distribution.  It uses the process of updating this very tutorial as an
-example to describe the individual steps and options.  You need to be
-familiar with git and you may want to have a look at the `git book
-<http://git-scm.com/book/>`_ to familiarize yourself with some of the
-more advanced git features used below.
+distribution.  It uses the process of updating this very tutorial as
+an example to describe the individual steps and options.  You need to
+be familiar with git and you may want to have a look at the
+`git book <http://git-scm.com/book/>`_ to reacquaint yourself with some
+of the more advanced git features used below.
 
 As of fall 2016, submitting contributions to LAMMPS via pull requests
 on GitHub is the preferred option for integrating contributed features
@@ -37,15 +37,15 @@ username or e-mail address and password.
 **Forking the repository**
 
 To get changes into LAMMPS, you need to first fork the `lammps/lammps`
-repository on GitHub. At the time of writing, *develop* is the preferred
+repository on GitHub. At the time of writing, *master* is the preferred
 target branch. Thus go to `LAMMPS on GitHub <https://github.com/lammps/lammps>`_
-and make sure branch is set to "develop", as shown in the figure below.
+and make sure branch is set to "master", as shown in the figure below.
 
 .. image:: JPG/tutorial_branch.png
    :align: center
 
-If it is not, use the button to change it to *develop*. Once it is, use
-the fork button to create a fork.
+If it is not, use the button to change it to *master*\ . Once it is, use the
+fork button to create a fork.
 
 .. image:: JPG/tutorial_fork.png
    :align: center
@@ -64,12 +64,11 @@ LAMMPS development.
 **Adding changes to your own fork**
 
 Additions to the upstream version of LAMMPS are handled using *feature
-branches*.  For every new feature, a so-called feature branch is
+branches*\ .  For every new feature, a so-called feature branch is
 created, which contains only those modification relevant to one specific
 feature. For example, adding a single fix would consist of creating a
 branch with only the fix header and source file and nothing else.  It is
-explained in more detail here: `feature branch workflow
-<https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow>`_.
+explained in more detail here: `feature branch workflow <https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow>`_.
 
 **Feature branches**
 
@@ -95,8 +94,8 @@ The above command copies ("clones") the git repository to your local
 machine to a directory with the name you chose. If none is given, it will
 default to "lammps". Typical names are "mylammps" or something similar.
 
-You can use this local clone to make changes and test them without
-interfering with the repository on GitHub.
+You can use this local clone to make changes and
+test them without interfering with the repository on GitHub.
 
 To pull changes from upstream into this copy, you can go to the directory
 and use git pull:
@@ -104,46 +103,28 @@ and use git pull:
 .. code-block:: bash
 
      $ cd mylammps
-     $ git checkout develop
-     $ git pull https://github.com/lammps/lammps develop
+     $ git checkout master
+     $ git pull https://github.com/lammps/lammps
 
 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 lammps_upstream https://www.github.com/lammps/lammps
 
-From then on you can update your upstream branches with:
-
-.. code-block:: bash
-
-     $ git fetch upstream
-
-and then refer to the upstream repository branches with
-`upstream/develop` or `upstream/release` and so on.
-
-At this point, you typically make a feature branch from the updated
+At this point, you typically make a feature branch from the updated master
 branch for the feature you want to work on. This tutorial contains the
 workflow that updated this tutorial, and hence we will call the branch
 "github-tutorial-update":
 
 .. code-block:: bash
 
-    $ git fetch upstream
-    $ git checkout -b github-tutorial-update upstream/develop
+    $ git checkout -b github-tutorial-update master
 
 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,
 unrelated feature, you should switch branches!
 
-.. note::
-
-   Committing changes to the *develop*, *release*, or *stable* branches
-   is strongly discouraged.  While it may be convenient initially, it
-   will create more work in the long run.  Various texts and tutorials
-   on using git effectively discuss the motivation for using feature
-   branches instead.
-
 **After changes are made**
 
 After everything is done, add the files to the branch and commit them:
@@ -306,32 +287,28 @@ After each push, the automated checks are run again.
 
 LAMMPS developers may add labels to your pull request to assign it to
 categories (mostly for bookkeeping purposes), but a few of them are
-important: *needs_work*, *work_in_progress*, *run_tests*,
-*test_for_regression*, and *ready_for_merge*.  The first two indicate,
-that your pull request is not considered to be complete. With
-"needs_work" the burden is on exclusively on you; while
-"work_in_progress" can also mean, that a LAMMPS developer may want to
-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
-*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.
+important: needs_work, work_in_progress, test-for-regression, and
+full-regression-test. The first two indicate, that your pull request
+is not considered to be complete. With "needs_work" the burden is on
+exclusively on you; while "work_in_progress" can also mean, that a
+LAMMPS developer may want to 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.
 
 **Reviews**
 
-As of Fall 2021, a pull request needs to pass all automatic tests and at
-least 1 approving review from a LAMMPS developer with write access to
-the repository before it is eligible for merging.  In case your changes
-touch code that certain developers are associated with, they are
-auto-requested by the GitHub software.  Those associations are set in
-the file `.github/CODEOWNERS
-<https://github.com/lammps/lammps/blob/develop/.github/CODEOWNERS>`_ Thus
-if you want to be automatically notified to review when anybody changes
-files or packages, that **you** have contributed to LAMMPS, you can add
-suitable patterns to that file, or a LAMMPS developer may add you.
+As of Summer 2018, a pull request needs at least 1 approving review
+from a LAMMPS developer with write access to the repository.
+In case your changes touch code that certain developers are associated
+with, they are auto-requested by the GitHub software.  Those associations
+are set in the file
+`.github/CODEOWNERS <https://github.com/lammps/lammps/blob/master/.github/CODEOWNERS>`_
+Thus if you want to be automatically notified to review when anybody
+changes files or packages, that you have contributed to LAMMPS, you can
+add suitable patterns to that file, or a LAMMPS developer may add you.
 
 Otherwise, you can also manually request reviews from specific developers,
 or LAMMPS developers - in their assessment of your pull request - may
@@ -352,7 +329,7 @@ LAMMPS developer (including him/herself) or c) Axel Kohlmeyer (akohlmey).
   After the review, the developer can choose to implement changes directly
   or suggest them to you.
 * Case c) means that the pull request has been assigned to the developer
-  overseeing the merging of pull requests into the *develop* branch.
+  overseeing the merging of pull requests into the master branch.
 
 In this case, Axel assigned the tutorial to Steve:
 
@@ -374,11 +351,11 @@ Sometimes, however, you might not feel comfortable having other people
 push changes into your own branch, or maybe the maintainers are not sure
 their idea was the right one.  In such a case, they can make changes,
 reassign you as the assignee, and file a "reverse pull request", i.e.
-file a pull request in **your** forked GitHub repository to include
-changes in the branch, that you have submitted as a pull request
-yourself.  In that case, you can choose to merge their changes back into
-your branch, possibly make additional changes or corrections and proceed
-from there.  It looks something like this:
+file a pull request in your GitHub repository to include changes in the
+branch, that you have submitted as a pull request yourself.  In that
+case, you can choose to merge their changes back into your branch,
+possibly make additional changes or corrections and proceed from there.
+It looks something like this:
 
 .. image:: JPG/tutorial_reverse_pull_request.png
    :align: center
@@ -442,7 +419,7 @@ This merge also shows up on the lammps GitHub page:
 
 **After a merge**
 
-When everything is fine, the feature branch is merged into the *develop* branch:
+When everything is fine, the feature branch is merged into the master branch:
 
 .. image:: JPG/tutorial_merged.png
    :align: center
@@ -456,8 +433,8 @@ branch!
 
 .. code-block:: bash
 
-   $ git checkout develop
-   $ git pull https://github.com/lammps/lammps develop
+   $ git checkout master
+   $ git pull master
    $ git branch -d github-tutorial-update
 
 If you do not pull first, it is not really a problem but git will warn
@@ -465,7 +442,6 @@ you at the next statement that you are deleting a local branch that
 was not yet fully merged into HEAD. This is because git does not yet
 know your branch just got merged into LAMMPS upstream. If you
 first delete and then pull, everything should still be fine.
-You can display all branches that are fully merged by:
 
 Finally, if you delete the branch locally, you might want to push this
 to your remote(s) as well:
@@ -477,14 +453,14 @@ to your remote(s) as well:
 **Recent changes in the workflow**
 
 Some changes to the workflow are not captured in this tutorial.  For
-example, in addition to the *develop* branch, to which all new features
-should be submitted, there is also a *release* and a *stable* branch;
-these have the same content as *develop*, but are only updated after a
-patch release or stable release was made.  Furthermore, the naming of
-the patches now follow the pattern "patch_<Day><Month><Year>" to
-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.
+example, in addition to the master branch, to which all new features
+should be submitted, there is now also an "unstable" and a "stable"
+branch; these have the same content as "master", but are only updated
+after a patch release or stable release was made.
+Furthermore, the naming of the patches now follow the pattern
+"patch_<Day><Month><Year>" to 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>`_
+`doc/github-development-workflow.md <https://github.com/lammps/lammps/blob/master/doc/github-development-workflow.md>`_

doc/src/Howto_pylammps.rst

@@ -545,6 +545,6 @@ Feedback and Contributing
 -------------------------
 
 If you find this Python interface useful, please feel free to provide feedback
-and ideas on how to improve it to Richard Berger (richard.berger@outlook.com). We also
+and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
 want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
 and maybe their latest research results.

doc/src/Howto_thermostat.rst

@@ -2,8 +2,8 @@ Thermostats
 ===========
 
 Thermostatting means controlling the temperature of particles in an MD
-simulation.  :doc:`Barostatting <Howto_barostat>` means controlling
-the pressure.  Since the pressure includes a kinetic component due to
+simulation.  :doc:`Barostatting <Howto_barostat>` means controlling the
+pressure.  Since the pressure includes a kinetic component due to
 particle velocities, both these operations require calculation of the
 temperature.  Typically a target temperature (T) and/or pressure (P)
 is specified by the user, and the thermostat or barostat attempts to
@@ -26,13 +26,11 @@ can be invoked via the *dpd/tstat* pair style:
 * :doc:`pair_style dpd/tstat <pair_dpd>`
 
 :doc:`Fix nvt <fix_nh>` only thermostats the translational velocity of
-particles.  :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this,
-except that it subtracts out a velocity bias due to a deforming box
-and integrates the SLLOD equations of motion.  See the :doc:`Howto
-nemd <Howto_nemd>` page for further details.  :doc:`Fix nvt/sphere
-<fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>`
-thermostat not only translation velocities but also rotational
-velocities for spherical and aspherical particles.
+particles.  :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this, except
+that it subtracts out a velocity bias due to a deforming box and
+integrates the SLLOD equations of motion.  See the :doc:`Howto nemd <Howto_nemd>` page for further details.  :doc:`Fix nvt/sphere <fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>` thermostat not only translation
+velocities but also rotational velocities for spherical and aspherical
+particles.
 
 .. note::
 
@@ -42,31 +40,25 @@ velocities for spherical and aspherical particles.
    e.g. molecular systems.  The latter can be tricky to do correctly.
 
 DPD thermostatting alters pairwise interactions in a manner analogous
-to the per-particle thermostatting of :doc:`fix langevin
-<fix_langevin>`.
+to the per-particle thermostatting of :doc:`fix langevin <fix_langevin>`.
 
-Any of the thermostatting fixes can be instructed to use custom
-temperature computes that remove bias which has two effects: first,
-the current calculated temperature, which is compared to the requested
-target temperature, is calculated with the velocity bias removed;
-second, the thermostat adjusts only the thermal temperature component
-of the particle's velocities, which are the velocities with the bias
-removed.  The removed bias is then added back to the adjusted
-velocities.  See the doc pages for the individual fixes and for the
-:doc:`fix_modify <fix_modify>` command for instructions on how to
-assign a temperature compute to a thermostatting fix.
+Any of the thermostatting fixes can be instructed to use custom temperature
+computes that remove bias which has two effects:  first, the current
+calculated temperature, which is compared to the requested target temperature,
+is calculated with the velocity bias removed;  second, the thermostat adjusts
+only the thermal temperature component of the particle's velocities, which are
+the velocities with the bias removed.  The removed bias is then added back
+to the adjusted velocities.  See the doc pages for the individual
+fixes and for the :doc:`fix_modify <fix_modify>` command for
+instructions on how to assign a temperature compute to a
+thermostatting fix.  For example, you can apply a thermostat to only
+the x and z components of velocity by using it in conjunction with
+:doc:`compute temp/partial <compute_temp_partial>`.  Of you could
+thermostat only the thermal temperature of a streaming flow of
+particles without affecting the streaming velocity, by using
+:doc:`compute temp/profile <compute_temp_profile>`.
 
-For example, you can apply a thermostat only to atoms in a spatial
-region by using it in conjunction with :doc:`compute temp/region
-<compute_temp_region>`.  Or you can apply a thermostat to only the x
-and z components of velocity by using it with :doc:`compute
-temp/partial <compute_temp_partial>`.  Of you could thermostat only
-the thermal temperature of a streaming flow of particles without
-affecting the streaming velocity, by using :doc:`compute temp/profile
-<compute_temp_profile>`.
-
-Below is a list of custom temperature computes that can be used like
-that:
+Below is a list of some custom temperature computes that can be used like that:
 
 * :doc:`compute_temp_asphere`
 * :doc:`compute_temp_body`
@@ -80,6 +72,8 @@ that:
 * :doc:`compute_temp_rotate`
 * :doc:`compute_temp_sphere`
 
+
+
 .. note::
 
    Only the nvt fixes perform time integration, meaning they update
@@ -92,17 +86,17 @@ that:
 * :doc:`fix nve/sphere <fix_nve_sphere>`
 * :doc:`fix nve/asphere <fix_nve_asphere>`
 
-Thermodynamic output, which can be setup via the :doc:`thermo_style
-<thermo_style>` command, often includes temperature values.  As
-explained on the page for the :doc:`thermo_style <thermo_style>`
-command, the default temperature is setup by the thermo command
-itself.  It is NOT the temperature associated with any thermostatting
-fix you have defined or with any compute you have defined that
-calculates a temperature.  The doc pages for the thermostatting fixes
-explain the ID of the temperature compute they create.  Thus if you
-want to view these temperatures, you need to specify them explicitly
-via the :doc:`thermo_style custom <thermo_style>` command.  Or you can
-use the :doc:`thermo_modify <thermo_modify>` command to re-define what
+Thermodynamic output, which can be setup via the
+:doc:`thermo_style <thermo_style>` command, often includes temperature
+values.  As explained on the page for the
+:doc:`thermo_style <thermo_style>` command, the default temperature is
+setup by the thermo command itself.  It is NOT the temperature
+associated with any thermostatting fix you have defined or with any
+compute you have defined that calculates a temperature.  The doc pages
+for the thermostatting fixes explain the ID of the temperature compute
+they create.  Thus if you want to view these temperatures, you need to
+specify them explicitly via the :doc:`thermo_style custom <thermo_style>` command.  Or you can use the
+:doc:`thermo_modify <thermo_modify>` command to re-define what
 temperature compute is used for default thermodynamic output.
 
 ----------

doc/src/Install_git.rst

@@ -9,8 +9,7 @@ has several advantages:
   command.
 * You can create your own development branches to add code to LAMMPS.
 * You can submit your new features back to GitHub for inclusion in
-  LAMMPS.  For that you should first create your own :doc:`fork on
-  GitHub <Howto_github>`.
+  LAMMPS.
 
 You must have `git <git_>`_ installed on your system to use the
 commands explained below to communicate with the git servers on
@@ -21,56 +20,35 @@ provides `limited support for subversion clients <svn_>`_.
 
    As of October 2016, the official home of public LAMMPS development is
    on GitHub.  The previously advertised LAMMPS git repositories on
-   git.lammps.org and bitbucket.org are now offline or deprecated.
+   git.lammps.org and bitbucket.org are now deprecated or offline.
 
 .. _git: https://git-scm.com
 .. _svn: https://help.github.com/en/github/importing-your-projects-to-github/working-with-subversion-on-github
 
-You can follow the LAMMPS development on 3 different git branches:
+You can follow LAMMPS development on 3 different git branches:
 
-* **stable**   :  this branch is updated from the *release* branch with
-  every stable release version and also has selected bug fixes and updates
-  back-ported from the *develop* branch
-* **release**  :  this branch is updated with every patch release;
-  updates are always "fast forward" merges from *develop*
-* **develop**  :  this branch follows the ongoing development and
-  is updated with every merge commit of a pull request
+* **stable**   :  this branch is updated with every stable release
+* **unstable** :  this branch is updated with every patch release
+* **master**   :  this branch continuously follows ongoing development
 
 To access the git repositories on your box, use the clone command to
 create a local copy of the LAMMPS repository with a command like:
 
 .. code-block:: bash
 
-   $ git clone -b release https://github.com/lammps/lammps.git mylammps
+   $ git clone -b unstable https://github.com/lammps/lammps.git mylammps
 
 where "mylammps" is the name of the directory you wish to create on
-your machine and "release" is one of the 3 branches listed above.
+your machine and "unstable" is one of the 3 branches listed above.
 (Note that you actually download all 3 branches; you can switch
 between them at any time using "git checkout <branch name>".)
 
-.. admonition:: Saving time and disk space when using ``git clone``
-
-   The complete git history of the LAMMPS project is quite large because
-   it contains the entire commit history of the project since fall 2006,
-   which includes the time when LAMMPS was managed with subversion.
-   This includes a few commits that have added and removed some large
-   files (mostly by accident).  If you do not need access to the entire
-   commit history (most people don't), you can speed up the "cloning"
-   process and reduce local disk space requirements by using the
-   *--depth* git command line flag.  That will create a "shallow clone"
-   of the repository containing only a subset of the git history.  Using
-   a depth of 1000 is usually sufficient to include the head commits of
-   the *develop* and the *release* branches.  To include the head commit
-   of the *stable* branch you may need a depth of up to 10000.  If you
-   later need more of the git history, you can always convert the
-   shallow clone into a "full clone".
-
 Once the command completes, your directory will contain the same files
 as if you unpacked a current LAMMPS tarball, with the exception, that
 the HTML documentation files are not included.  They can be fetched
 from the LAMMPS website by typing ``make fetch`` in the doc directory.
-Or they can be generated from the content provided in ``doc/src`` by
-typing ``make html`` from the ``doc`` directory.
+Or they can be generated from the content provided in doc/src by
+typing ``make html`` from the doc directory.
 
 After initial cloning, as bug fixes and new features are added to
 LAMMPS you can stay up-to-date by typing the following git commands
@@ -78,9 +56,9 @@ from within the "mylammps" directory:
 
 .. code-block:: bash
 
-   $ git checkout release      # not needed if you always stay in this branch
-   $ git checkout stable       # use one of these 3 checkout commands
-   $ git checkout develop      # to choose the branch to follow
+   $ git checkout unstable      # not needed if you always stay in this branch
+   $ git checkout stable        # use one of these 3 checkout commands
+   $ git checkout master        # to choose the branch to follow
    $ git pull
 
 Doing a "pull" will not change any files you have added to the LAMMPS
@@ -103,7 +81,7 @@ Stable versions and what tagID to use for a particular stable version
 are discussed on `this page <https://www.lammps.org/bug.html#version>`_.
 Note that this command will print some warnings, because in order to get
 back to the latest revision and to be able to update with ``git pull``
-again, you will need to do ``git checkout release`` (or
+again, you will need to do ``git checkout unstable`` (or
 check out any other desired branch) first.
 
 Once you have updated your local files with a ``git pull`` (or ``git

doc/src/Intro_authors.rst

@@ -8,7 +8,7 @@ University:
 * Aidan Thompson, athomps at sandia.gov
 * Stan Moore, stamoor at sandia.gov
 * Axel Kohlmeyer, akohlmey at gmail.com
-* Richard Berger, richard.berger at outlook.com
+* Richard Berger, richard.berger at temple.edu
 
 .. _sjp: http://www.cs.sandia.gov/~sjplimp
 .. _lws: https://www.lammps.org

doc/src/Intro_opensource.rst

@@ -19,7 +19,7 @@ software and open-source distribution, see `www.gnu.org <gnuorg_>`_
 or `www.opensource.org <opensource_>`_.  The legal text of the GPL as it
 applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution.
 
-.. _gpl: https://github.com/lammps/lammps/blob/develop/LICENSE
+.. _gpl: https://github.com/lammps/lammps/blob/master/LICENSE
 
 .. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html
 

doc/src/Library_utility.rst

@@ -13,7 +13,6 @@ functions.  They do not directly call the LAMMPS library.
 - :cpp:func:`lammps_fix_external_set_virial_peratom`
 - :cpp:func:`lammps_fix_external_set_vector_length`
 - :cpp:func:`lammps_fix_external_set_vector`
-- :cpp:func:`lammps_flush_buffers`
 - :cpp:func:`lammps_free`
 - :cpp:func:`lammps_is_running`
 - :cpp:func:`lammps_force_timeout`
@@ -73,11 +72,6 @@ where such memory buffers were allocated that require the use of
 
 -----------------------
 
-.. doxygenfunction:: lammps_flush_buffers
-   :project: progguide
-
------------------------
-
 .. doxygenfunction:: lammps_free
    :project: progguide
 

doc/src/Manual_version.rst

@@ -7,34 +7,26 @@ correctly and reliably at all times.  You can follow its development
 in a public `git repository on GitHub <https://github.com/lammps/lammps>`_.
 
 Whenever we fix a bug or update or add a feature, it will be merged into
-the *develop* branch of the git repository.  When a sufficient number of
+the `master` branch of the git repository.  When a sufficient number of
 changes have accumulated *and* the software passes a set of automated
 tests, we release it in the next *patch* release, which are made every
-few weeks.  The *release* branch of the git repository is updated with
-every such release.  Info on patch releases are on `this website page
+few weeks.  Info on patch releases are on `this website page
 <https://www.lammps.org/bug.html>`_.
 
-Once or twice a year, we apply only bug fixes and small, non-intrusive
-changes to the *develop* branch and the code is subjected to more detailed
+Once or twice a year, only bug fixes and small, non-intrusive changes are
+included for a period of time, and the code is subjected to more detailed
 and thorough testing than the default automated testing.  The latest
-patch release after such a period is then also labeled as a *stable* version
-and the *stable* branch is updated with it.  Between stable releases
-we occasionally release some updates to the stable release containing
-only bug fixes and updates back-ported from *develop* but no new features
-and update the *stable* branch accordingly.
+patch release after such a period is then labeled as a *stable* version.
 
-Each version of LAMMPS contains all the documented features up to and
-including its version date.
+Each version of LAMMPS contains all the features and bug-fixes up to
+and including its version date.
 
 The version date is printed to the screen and logfile every time you
 run LAMMPS. It is also in the file src/version.h and in the LAMMPS
 directory name created when you unpack a tarball.  And it is on the
 first page of the :doc:`manual <Manual>`.
 
-* If you browse the HTML pages on the LAMMPS WWW site, they will by
-  default describe the most current patch release version of LAMMPS.
-  In the navigation bar on the bottom left, there is the option to
-  view instead the documentation for the most recent *stable* version
-  or the latest version from the current development branch.
+* If you browse the HTML pages on the LAMMPS WWW site, they always
+  describe the most current patch release of LAMMPS.
 * If you browse the HTML pages included in your tarball, they
   describe the version you have, which may be older.

doc/src/Modify_pair.rst

@@ -12,24 +12,24 @@ includes some optional methods to enable its use with rRESPA.
 
 Here is a brief description of the class methods in pair.h:
 
-+---------------------------------+---------------------------------------------------------------------+
-| compute                         | workhorse routine that computes pairwise interactions               |
-+---------------------------------+---------------------------------------------------------------------+
-| settings                        | reads the input script line with arguments you define               |
-+---------------------------------+---------------------------------------------------------------------+
-| coeff                           | set coefficients for one i,j type pair                              |
-+---------------------------------+---------------------------------------------------------------------+
-| init_one                        | perform initialization for one i,j type pair                        |
-+---------------------------------+---------------------------------------------------------------------+
-| init_style                      | initialization specific to this pair style                          |
-+---------------------------------+---------------------------------------------------------------------+
-| write & read_restart            | write/read i,j pair coeffs to restart files                         |
-+---------------------------------+---------------------------------------------------------------------+
-| write & read_restart_settings   | write/read global settings to restart files                         |
-+---------------------------------+---------------------------------------------------------------------+
-| single                          | force/r and energy of a single pairwise interaction between 2 atoms |
-+---------------------------------+---------------------------------------------------------------------+
-| compute_inner/middle/outer      | versions of compute used by rRESPA                                  |
-+---------------------------------+---------------------------------------------------------------------+
++---------------------------------+-------------------------------------------------------------------+
+| compute                         | workhorse routine that computes pairwise interactions             |
++---------------------------------+-------------------------------------------------------------------+
+| settings                        | reads the input script line with arguments you define             |
++---------------------------------+-------------------------------------------------------------------+
+| coeff                           | set coefficients for one i,j type pair                            |
++---------------------------------+-------------------------------------------------------------------+
+| init_one                        | perform initialization for one i,j type pair                      |
++---------------------------------+-------------------------------------------------------------------+
+| init_style                      | initialization specific to this pair style                        |
++---------------------------------+-------------------------------------------------------------------+
+| write & read_restart            | write/read i,j pair coeffs to restart files                       |
++---------------------------------+-------------------------------------------------------------------+
+| write & read_restart_settings   | write/read global settings to restart files                       |
++---------------------------------+-------------------------------------------------------------------+
+| single                          | force and energy of a single pairwise interaction between 2 atoms |
++---------------------------------+-------------------------------------------------------------------+
+| compute_inner/middle/outer      | versions of compute used by rRESPA                                |
++---------------------------------+-------------------------------------------------------------------+
 
 The inner/middle/outer routines are optional.

doc/src/Modify_style.rst

@@ -305,40 +305,6 @@ you are uncertain, please ask.
   FILE pointers and only be done on MPI rank 0.  Use the :cpp:func:`utils::logmesg`
   convenience function where possible.
 
-- Usage of C++11 `virtual`, `override`, `final` keywords: Please follow the
-  `C++ Core Guideline C.128 <https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#Rh-override>`_.
-  That means, you should only use `virtual` to declare a new virtual
-  function, `override` to indicate you are overriding an existing virtual
-  function, and `final` to prevent any further overriding.
-
-- Trivial destructors: Prefer not writing destructors when they are empty and `default`.
-
-  .. code-block:: c++
-
-     // don't write destructors for A or B like this
-     class A : protected Pointers {
-      public:
-        A();
-        ~A() override {}
-     };
-
-     class B : protected Pointers {
-      public:
-        B();
-        ~B() override = default;
-     };
-
-     // instead, let the compiler create the implicit default destructor by not writing it
-     class A : protected Pointers {
-      public:
-        A();
-     };
-
-     class B : protected Pointers {
-      public:
-        B();
-     };
-
 - Header files, especially those defining a "style", should only use
   the absolute minimum number of include files and **must not** contain
   any ``using`` statements. Typically that would be only the header for

doc/src/Packages_details.rst

@@ -1880,12 +1880,6 @@ MPIIO library.  It adds :doc:`dump styles <dump>` with a "mpiio" in
 their style name.  Restart files with an ".mpiio" suffix are also
 written and read in parallel.
 
-.. warning::
-
-   The MPIIO package is currently unmaintained and has become
-   unreliable. Use with caution.
-
-
 **Install:**
 
 The MPIIO package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.

doc/src/Run_output.rst

@@ -106,7 +106,7 @@ individual ranks. Here is an example output for this section:
 ----------
 
 The third section above lists the number of owned atoms (Nlocal),
-ghost atoms (Nghost), and pairwise neighbors stored per processor.
+ghost atoms (Nghost), and pair-wise neighbors stored per processor.
 The max and min values give the spread of these values across
 processors with a 10-bin histogram showing the distribution. The total
 number of histogram counts is equal to the number of processors.
@@ -114,7 +114,7 @@ number of histogram counts is equal to the number of processors.
 ----------
 
 The last section gives aggregate statistics (across all processors)
-for pairwise neighbors and special neighbors that LAMMPS keeps track
+for pair-wise neighbors and special neighbors that LAMMPS keeps track
 of (see the :doc:`special_bonds <special_bonds>` command).  The number
 of times neighbor lists were rebuilt is tallied, as is the number of
 potentially *dangerous* rebuilds.  If atom movement triggered neighbor

doc/src/Speed.rst

@@ -14,7 +14,7 @@ Intel Xeon Phi co-processors.
 
 The `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS
 website gives performance results for the various accelerator
-packages discussed on the :doc:`Accelerator packages <Speed_packages>`
+packages discussed on the :doc:`Speed packages <Speed_packages>` doc
 page, for several of the standard LAMMPS benchmark problems, as a
 function of problem size and number of compute nodes, on different
 hardware platforms.

doc/src/Speed_kokkos.rst

@@ -214,7 +214,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
    The default for the :doc:`package kokkos <package>` command when
    running on KNL is to use "half" neighbor lists and set the Newton flag
    to "on" for both pairwise and bonded interactions. This will typically
-   be best for many-body potentials. For simpler pairwise potentials, it
+   be best for many-body potentials. For simpler pair-wise potentials, it
    may be faster to use a "full" neighbor list with Newton flag to "off".
    Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to change
    the default :doc:`package kokkos <package>` options. See its page for

doc/src/Tools.rst

@@ -277,34 +277,17 @@ at ens-lyon.fr, alain.dequidt at uca.fr
 eam database tool
 -----------------------------
 
-The tools/eam_database directory contains a Fortran and a Python program
-that will generate EAM alloy setfl potential files for any combination
-of the 17 elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg,
-Co, Ti, Zr, Cr.  The files can then be used with the :doc:`pair_style
-eam/alloy <pair_eam>` command.
+The tools/eam_database directory contains a Fortran program that will
+generate EAM alloy setfl potential files for any combination of 16
+elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
+Zr.  The files can then be used with the :doc:`pair_style eam/alloy <pair_eam>` command.
 
-The Fortran version of the tool was authored by Xiaowang Zhou (Sandia),
-xzhou at sandia.gov, with updates from Lucas Hale (NIST) lucas.hale at
-nist.gov and is based on his paper:
+The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
+and is based on his paper:
 
 X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
 144113 (2004).
 
-The parameters for Cr were taken from:
-
-Lin Z B, Johnson R A and Zhigilei L V, Phys. Rev. B 77 214108 (2008).
-
-The Python version of the tool was authored  by Germain Clavier
-(TU Eindhoven) g.m.g.c.clavier at tue.nl or germain.clavier at gmail.com
-
-.. note::
-
-   The parameters in the database are only optimized for individual
-   elements. The mixed parameters for interactions between different
-   elements generated by this tool are derived from simple mixing rules
-   and are thus inferior to parameterizations that are specifically
-   optimized for specific mixtures and combinations of elements.
-
 ----------
 
 .. _eamgn:

doc/src/accel_styles.rst

@@ -1,7 +1,7 @@
 Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Accelerator packages <Speed_packages>`
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 
@@ -13,5 +13,5 @@ You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
 :doc:`suffix <suffix>` command in your input script.
 
-See the :doc:`Accelerator packages <Speed_packages>` page for more
+See the :doc:`Speed packages <Speed_packages>` page for more
 instructions on how to use the accelerated styles effectively.

doc/src/angle_charmm.rst

@@ -56,7 +56,23 @@ radian\^2.
 
 ----------
 
-.. include:: accel_styles.rst
+Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, INTEL, KOKKOS,
+OPENMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See :doc:`Speed packages <Speed_packages>` page for more
+instructions on how to use the accelerated styles effectively.
 
 ----------
 

doc/src/angle_class2.rst

@@ -64,44 +64,34 @@ These are the 4 coefficients for the :math:`E_a` formula:
 radians internally; hence the various :math:`K` are effectively energy
 per radian\^2 or radian\^3 or radian\^4.
 
-For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff
-<angle_coeff>` command in the input script lists 4 coefficients, the
-first of which is "bb" to indicate they are BondBond coefficients.  In
-a data file, these coefficients should be listed under a "BondBond
-Coeffs" heading and you must leave out the "bb", i.e. only list 3
-coefficients after the angle type.
+For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff <angle_coeff>`
+command in the input script lists 4 coefficients, the first of which
+is "bb" to indicate they are BondBond coefficients.  In a data file,
+these coefficients should be listed under a "BondBond Coeffs" heading
+and you must leave out the "bb", i.e. only list 3 coefficients after
+the angle type.
 
 * bb
 * :math:`M` (energy/distance\^2)
 * :math:`r_1` (distance)
 * :math:`r_2` (distance)
 
-For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff
-<angle_coeff>` command in the input script lists 5 coefficients, the
-first of which is "ba" to indicate they are BondAngle coefficients.
-In a data file, these coefficients should be listed under a "BondAngle
-Coeffs" heading and you must leave out the "ba", i.e. only list 4
-coefficients after the angle type.
+For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff <angle_coeff>`
+command in the input script lists 5 coefficients, the first of which
+is "ba" to indicate they are BondAngle coefficients.  In a data file,
+these coefficients should be listed under a "BondAngle Coeffs" heading
+and you must leave out the "ba", i.e. only list 4 coefficients after
+the angle type.
 
 * ba
-* :math:`N_1` (energy/distance)
-* :math:`N_2` (energy/distance)
+* :math:`N_1` (energy/distance\^2)
+* :math:`N_2` (energy/distance\^2)
 * :math:`r_1` (distance)
 * :math:`r_2` (distance)
 
 The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified,
 since it is the same value from the :math:`E_a` formula.
 
-.. note::
-
-   It is important that the order of the I,J,K atoms in each angle
-   listed in the Angles section of the data file read by the
-   :doc:`read_data <read_data>` command be consistent with the order
-   of the :math:`r_1` and :math:`r_2` BondBond and BondAngle
-   coefficients.  This is because the terms in the formulas for
-   :math:`E_{bb}` and :math:`E_{ba}` will use the I,J atoms to compute
-   :math:`r_{ij}` and the J,K atoms to compute :math:`r_{jk}`.
-
 ----------
 
 .. include:: accel_styles.rst

doc/src/atom_style.rst

@@ -319,9 +319,28 @@ styles; see the :doc:`Modify <Modify>` doc page.
 
 ----------
 
-.. include:: accel_styles.rst
+Styles with a *kk* suffix are functionally the same as the
+corresponding style without the suffix.  They have been optimized to
+run faster, depending on your available hardware, as discussed in on
+the :doc:`Speed packages <Speed_packages>` doc page.  The accelerated
+styles take the same arguments and should produce the same results,
+except for round-off and precision issues.
 
-----------
+Note that other acceleration packages in LAMMPS, specifically the GPU,
+INTEL, OPENMP, and OPT packages do not use accelerated atom
+styles.
+
+The accelerated styles are part of the KOKKOS package.  They are only
+enabled if LAMMPS was built with those packages.  See the :doc:`Build
+package <Build_package>` page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line
+switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` page for more
+instructions on how to use the accelerated styles effectively.
 
 Restrictions
 """"""""""""

doc/src/balance.rst

@@ -383,7 +383,7 @@ multiple groups, its weight is the product of the weight factors.
 
 This weight style is useful in combination with pair style
 :doc:`hybrid <pair_hybrid>`, e.g. when combining a more costly many-body
-potential with a fast pairwise potential.  It is also useful when
+potential with a fast pair-wise potential.  It is also useful when
 using :doc:`run_style respa <run_style>` where some portions of the
 system have many bonded interactions and others none.  It assumes that
 the computational cost for each group remains constant over time.

doc/src/bond_fene.rst

@@ -1,5 +1,4 @@
 .. index:: bond_style fene
-.. index:: bond_style fene/nm
 .. index:: bond_style fene/intel
 .. index:: bond_style fene/kk
 .. index:: bond_style fene/omp
@@ -9,16 +8,12 @@ bond_style fene command
 
 Accelerator Variants: *fene/intel*, *fene/kk*, *fene/omp*
 
-bond_style fene/nm command
-==========================
-
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
    bond_style fene
-   bond_style fene/nm
 
 Examples
 """"""""
@@ -28,9 +23,6 @@ Examples
    bond_style fene
    bond_coeff 1 30.0 1.5 1.0 1.0
 
-   bond_style fene/nm
-   bond_coeff 1 2.25344 1.5 1.0 1.12246 2 6
-
 Description
 """""""""""
 
@@ -46,36 +38,16 @@ term is attractive, the second Lennard-Jones term is repulsive.  The
 first term extends to :math:`R_0`, the maximum extent of the bond.  The second
 term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.
 
-The *fene/nm* bond style substitutes the standard LJ potential with the generalized LJ potential
-in the same form as in pair style :doc:`nm/cut <pair_nm>`. The bond energy is then given by
-
-.. math::
-
-  E = -0.5 K r_0^2  \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + \frac{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n - n \left(\frac{r_0}{r}\right)^m \right]
-
-Similar to the *fene* style, the generalized Lennard-Jones is cut off at
-the potential minimum, :math:`r_0`, to be repulsive only.  The following
-coefficients must be defined for each bond type via the :doc:`bond_coeff
-<bond_coeff>` command as in the example above, or in the data file or
-restart files read by the :doc:`read_data <read_data>` or
-:doc:`read_restart <read_restart>` commands:
+The following coefficients must be defined for each bond type via the
+:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read_data <read_data>`
+or :doc:`read_restart <read_restart>` commands:
 
 * :math:`K` (energy/distance\^2)
 * :math:`R_0` (distance)
 * :math:`\epsilon` (energy)
 * :math:`\sigma` (distance)
 
-For the *fene/nm* style, the following coefficients are used.  Please
-note, that the standard LJ potential and thus the regular FENE potential
-is recovered for (n=12 m=6) and :math:`r_0 = 2^\frac{1}{6} \sigma`.
-
-* :math:`K` (energy/distance\^2)
-* :math:`R_0` (distance)
-* :math:`E_0` (energy)
-* :math:`r_0` (distance)
-* :math:`n` (unitless)
-* :math:`m` (unitless)
-
 ----------
 
 .. include:: accel_styles.rst
@@ -85,10 +57,9 @@ is recovered for (n=12 m=6) and :math:`r_0 = 2^\frac{1}{6} \sigma`.
 Restrictions
 """"""""""""
 
-The *fene* bond style can only be used if LAMMPS was built with the MOLECULE
-package; the *fene/nm* bond style can only be used if LAMMPS was built
-with the EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
-page for more info.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package.  See the :doc:`Build package <Build_package>` page for more
+info.
 
 You typically should specify :doc:`special_bonds fene <special_bonds>`
 or :doc:`special_bonds lj/coul 0 1 1 <special_bonds>` to use this bond
@@ -97,8 +68,7 @@ style.  LAMMPS will issue a warning it that's not the case.
 Related commands
 """"""""""""""""
 
-:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
-:doc:`pair style lj/cut <pair_lj>`, :doc:`pair style nm/cut <pair_nm>`.
+:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
 
 Default
 """""""

doc/src/bond_style.rst

@@ -87,7 +87,6 @@ accelerated styles exist.
 * :doc:`class2 <bond_class2>` - COMPASS (class 2) bond
 * :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond
 * :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles
-* :doc:`fene/nm <bond_fene>` - FENE bonds with a generalized Lennard-Jones potential
 * :doc:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
 * :doc:`gromos <bond_gromos>` - GROMOS force field bond
 * :doc:`harmonic <bond_harmonic>` - harmonic bond

doc/src/compute.rst

@@ -174,7 +174,6 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`angle <compute_angle>` - energy of each angle sub-style
 * :doc:`angle/local <compute_angle_local>` - theta and energy of each angle
 * :doc:`angmom/chunk <compute_angmom_chunk>` - angular momentum for each chunk
-* :doc:`ave/sphere/atom <compute_ave_sphere_atom>` - compute local density and temperature around each atom
 * :doc:`basal/atom <compute_basal_atom>` - calculates the hexagonal close-packed "c" lattice vector of each atom
 * :doc:`body/local <compute_body_local>` - attributes of body sub-particles
 * :doc:`bond <compute_bond>` - energy of each bond sub-style

doc/src/compute_ave_sphere_atom.rst

@@ -1,101 +0,0 @@
-.. index:: compute ave/sphere/atom
-.. index:: compute ave/sphere/atom/kk
-
-compute ave/sphere/atom command
-================================
-
-Accelerator Variants: *ave/sphere/atom/kk*
-
-Syntax
-""""""
-
-.. parsed-literal::
-
-   compute ID group-ID ave/sphere/atom keyword values ...
-
-* ID, group-ID are documented in :doc:`compute <compute>` command
-* ave/sphere/atom = style name of this compute command
-* one or more keyword/value pairs may be appended
-
-  .. parsed-literal::
-
-     keyword = *cutoff*
-       *cutoff* value = distance cutoff
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   compute 1 all ave/sphere/atom
-
-   compute 1 all ave/sphere/atom cutoff 5.0
-   comm_modify cutoff 5.0
-
-Description
-"""""""""""
-
-Define a computation that calculates the local density and temperature
-for each atom and neighbors inside a spherical cutoff.
-
-The optional keyword *cutoff* defines the distance cutoff
-used when searching for neighbors. The default value is the cutoff
-specified by the pair style. If no pair style is defined, then a cutoff
-must be defined using this keyword. If the specified cutoff is larger than
-that of the pair_style plus neighbor skin (or no pair style is defined),
-the *comm_modify cutoff* option must also be set to match that of the
-*cutoff* keyword.
-
-The neighbor list needed to compute this quantity is constructed each
-time the calculation is performed (i.e. each time a snapshot of atoms
-is dumped).  Thus it can be inefficient to compute/dump this quantity
-too frequently.
-
-.. note::
-
-   If you have a bonded system, then the settings of
-   :doc:`special_bonds <special_bonds>` command can remove pairwise
-   interactions between atoms in the same bond, angle, or dihedral.  This
-   is the default setting for the :doc:`special_bonds <special_bonds>`
-   command, and means those pairwise interactions do not appear in the
-   neighbor list.  Because this fix uses the neighbor list, it also means
-   those pairs will not be included in the order parameter.  This
-   difficulty can be circumvented by writing a dump file, and using the
-   :doc:`rerun <rerun>` command to compute the order parameter for
-   snapshots in the dump file.  The rerun script can use a
-   :doc:`special_bonds <special_bonds>` command that includes all pairs in
-   the neighbor list.
-
-----------
-
-
-.. include:: accel_styles.rst
-
-
-----------
-
-Output info
-"""""""""""
-
-This compute calculates a per-atom array with two columns: density and temperature.
-
-These values can be accessed by any command that uses per-atom values
-from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
-page for an overview of LAMMPS output options.
-
-Restrictions
-""""""""""""
-
-This compute is part of the EXTRA-COMPUTE package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
-
-Related commands
-""""""""""""""""
-
-:doc:`comm_modify <comm_modify>`
-
-Default
-"""""""
-
-The option defaults are *cutoff* = pair style cutoff
-

doc/src/compute_bond_local.rst

@@ -13,7 +13,7 @@ Syntax
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * bond/local = style name of this compute command
 * one or more values may be appended
-* value = *dist* or *dx* or *dy* or *dz* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name*
+* value = *dist* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name*
 
 .. parsed-literal::
 
@@ -21,7 +21,6 @@ Syntax
      *engpot* = bond potential energy
      *force* = bond force
 
-     *dx*,\ *dy*,\ *dz* = components of pairwise distance
      *fx*,\ *fy*,\ *fz* = components of bond force
      *engvib* = bond kinetic energy of vibration
      *engrot* = bond kinetic energy of rotation
@@ -64,9 +63,6 @@ whether the 2 atoms represent a simple diatomic molecule, or are part
 of some larger molecule.
 
 The value *dist* is the current length of the bond.
-The values *dx*, *dy*, and *dz* are the xyz components of the
-*distance* between the pair of atoms. This value is always the
-distance from the atom of lower to the one with the higher id.
 
 The value *engpot* is the potential energy for the bond,
 based on the current separation of the pair of atoms in the bond.

doc/src/compute_heat_flux.rst

@@ -89,20 +89,13 @@ included in the calculation.
 .. warning::
 
    The compute *heat/flux* has been reported to produce unphysical
-   values for angle, dihedral, improper and constraint force contributions
+   values for angle, dihedral and improper contributions
    when used with :doc:`compute stress/atom <compute_stress_atom>`,
-   as discussed in :ref:`(Surblys2019) <Surblys3>`, :ref:`(Boone) <Boone>`
-   and :ref:`(Surblys2021) <Surblys4>`. You are strongly advised to
+   as discussed in :ref:`(Surblys) <Surblys2>` and :ref:`(Boone) <Boone>`.
+   You are strongly advised to
    use :doc:`compute centroid/stress/atom <compute_stress_atom>`,
    which has been implemented specifically for such cases.
 
-.. warning::
-
-   Due to an implementation detail, the :math:`y` and :math:`z`
-   components of heat flux from :doc:`fix rigid <fix_rigid>`
-   contribution when computed via :doc:`compute stress/atom <compute_stress_atom>`
-   are highly unphysical and should not be used.
-
 The Green-Kubo formulas relate the ensemble average of the
 auto-correlation of the heat flux :math:`\mathbf{J}`
 to the thermal conductivity :math:`\kappa`:
@@ -239,14 +232,10 @@ none
 
 ----------
 
-.. _Surblys3:
+.. _Surblys2:
 
-**(Surblys2019)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
+**(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
 
 .. _Boone:
 
 **(Boone)** Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019).
-
-.. _Surblys4:
-
-**(Surblys2021)** Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).

doc/src/compute_pair_local.rst

@@ -13,12 +13,11 @@ Syntax
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * pair/local = style name of this compute command
 * one or more values may be appended
-* value = *dist* or *dx* or *dy* or *dz* or *eng* or *force* or *fx* or *fy* or *fz* or *pN*
+* value = *dist* or *eng* or *force* or *fx* or *fy* or *fz* or *pN*
 
   .. parsed-literal::
 
        *dist* = pairwise distance
-       *dx*,\ *dy*,\ *dz* = components of pairwise distance
        *eng* = pairwise energy
        *force* = pairwise force
        *fx*,\ *fy*,\ *fz* = components of pairwise force
@@ -57,9 +56,6 @@ force cutoff distance for that interaction, as defined by the
 commands.
 
 The value *dist* is the distance between the pair of atoms.
-The values *dx*, *dy*, and *dz* are the xyz components of the
-*distance* between the pair of atoms. This value is always the
-distance from the atom of lower to the one with the higher id.
 
 The value *eng* is the interaction energy for the pair of atoms.
 
@@ -93,10 +89,10 @@ from the second of the two sub-styles.  If the referenced *pN*
 is not computed for the specific pairwise interaction (based on
 atom types), then the output will be 0.0.
 
-The value *dist*, *dx*, *dy* and *dz* will be in distance :doc:`units <units>`.
-The value *eng* will be in energy :doc:`units <units>`.
-The values *force*, *fx*, *fy*, and *fz* will be in force :doc:`units <units>`.
-The values *pN* will be in whatever units the pair style defines.
+The value *dist* will be in distance :doc:`units <units>`.  The value
+*eng* will be in energy :doc:`units <units>`.  The values *force*, *fx*,
+*fy*, and *fz* will be in force :doc:`units <units>`.  The values *pN*
+will be in whatever units the pair style defines.
 
 The optional *cutoff* keyword determines how the force cutoff distance
 for an interaction is determined.  For the default setting of *type*,

doc/src/compute_pressure.rst

@@ -141,7 +141,7 @@ Related commands
 """"""""""""""""
 
 :doc:`compute temp <compute_temp>`, :doc:`compute stress/atom <compute_stress_atom>`,
-:doc:`thermo_style <thermo_style>`, :doc:`fix numdiff/virial <fix_numdiff_virial>`,
+:doc:`thermo_style <thermo_style>`,
 
 Default
 """""""

doc/src/compute_pressure_cylinder.rst

@@ -61,7 +61,7 @@ Restrictions
 This compute currently calculates the pressure tensor contributions
 for pair styles only (i.e. no bond, angle, dihedral, etc. contributions
 and in the presence of bonded interactions, the result will be incorrect
-due to exclusions for special bonds)  and requires pairwise force
+due to exclusions for special bonds)  and requires pair-wise force
 calculations not available for most many-body pair styles. K-space
 calculations are also excluded. Note that this pressure compute outputs
 the configurational terms only; the kinetic contribution is not included

doc/src/compute_stress_atom.rst

@@ -87,10 +87,6 @@ Tersoff 3-body interaction) is assigned in equal portions to each atom
 in the set.  E.g. 1/4 of the dihedral virial to each of the 4 atoms,
 or 1/3 of the fix virial due to SHAKE constraints applied to atoms in
 a water molecule via the :doc:`fix shake <fix_shake>` command.
-As an exception, the virial contribution from
-constraint forces in :doc:`fix rigid <fix_rigid>` on each atom
-is computed from the constraint force acting on the corresponding atom
-and its position, i.e. the total virial is not equally distributed.
 
 In case of compute *centroid/stress/atom*, the virial contribution is:
 
@@ -107,25 +103,13 @@ atom :math:`I` due to the interaction and the relative position
 :math:`\mathbf{r}_{I0}` of the atom :math:`I` to the geometric center
 of the interacting atoms, i.e. centroid, is used.  As the geometric
 center is different for each interaction, the :math:`\mathbf{r}_{I0}`
-also differs. The sixth term, Kspace contribution,
-is computed identically to compute *stress/atom*.
-The seventh term is handed differently depending on
-if the constraint forces are due to :doc:`fix shake <fix_shake>`
-or :doc:`fix rigid <fix_rigid>`.
-In case of SHAKE constraints, each distance constraint is
-handed as a pairwise interaction.
-E.g. in case of a water molecule, two OH and one HH distance
-constraints are treated as three pairwise interactions.
-In case of :doc:`fix rigid <fix_rigid>`,
-all constraint forces in the molecule are treated
-as a single many-body interaction with a single centroid position.
-In case of water molecule, the formula expression would become
-identical to that of the three-body angle interaction.
-Although the total system virial is the same as
+also differs.  The sixth and seventh terms, Kspace and :doc:`fix
+<fix>` contribution respectively, are computed identical to compute
+*stress/atom*.  Although the total system virial is the same as
 compute *stress/atom*, compute *centroid/stress/atom* is know to
-result in more consistent heat flux values for angle, dihedrals,
-improper and constraint force contributions
-when computed via :doc:`compute heat/flux <compute_heat_flux>`.
+result in more consistent heat flux values for angle, dihedrals and
+improper contributions when computed via :doc:`compute heat/flux
+<compute_heat_flux>`.
 
 If no extra keywords are listed, the kinetic contribution all of the
 virial contribution terms are included in the per-atom stress tensor.
@@ -150,8 +134,7 @@ contribution for the cluster interaction is divided evenly among those
 atoms.
 
 Details of how compute *centroid/stress/atom* obtains the virial for
-individual atoms are given in :ref:`(Surblys2019) <Surblys1>` and
-:ref:`(Surblys2021) <Surblys2>`, where the
+individual atoms is given in :ref:`(Surblys) <Surblys1>`, where the
 idea is that the virial of the atom :math:`I` is the result of only
 the force :math:`\mathbf{F}_I` on the atom due to the interaction and
 its positional vector :math:`\mathbf{r}_{I0}`, relative to the
@@ -252,10 +235,10 @@ between the pair of particles.  All bond styles are supported.  All
 angle, dihedral, improper styles are supported with the exception of
 INTEL and KOKKOS variants of specific styles.  It also does not
 support models with long-range Coulombic or dispersion forces,
-i.e. the kspace_style command in LAMMPS.  It also does not implement the
-following fixes which add rigid-body constraints:
-:doc:`fix rigid/* <fix_rigid>` and the OpenMP accelerated version of :doc:`fix rigid/small <fix_rigid>`,
-while all other :doc:`fix rigid/*/small <fix_rigid>` are implemented.
+i.e. the kspace_style command in LAMMPS.  It also does not support the
+following fixes which add rigid-body constraints: :doc:`fix shake
+<fix_shake>`, :doc:`fix rattle <fix_shake>`, :doc:`fix rigid
+<fix_rigid>`, :doc:`fix rigid/small <fix_rigid>`.
 
 LAMMPS will generate an error if one of these options is included in
 your model.  Extension of centroid stress calculations to these force
@@ -287,8 +270,4 @@ none
 
 .. _Surblys1:
 
-**(Surblys2019)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
-
-.. _Surblys2:
-
-**(Surblys2021)** Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).
+**(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).

doc/src/delete_atoms.rst

@@ -20,10 +20,8 @@ Syntax
          cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
          group1-ID = one atom in pair must be in this group
          group2-ID = other atom in pair must be in this group
-       *porosity* args = group-ID region-ID fraction seed
-         group-ID = group within which to perform deletions
+       *porosity* args = region-ID fraction seed
          region-ID = region within which to perform deletions
-                     or NULL to only impose the group criterion
          fraction = delete this fraction of atoms
          seed = random number seed (positive integer)
 
@@ -45,8 +43,7 @@ Examples
    delete_atoms region sphere compress no
    delete_atoms overlap 0.3 all all
    delete_atoms overlap 0.5 solvent colloid
-   delete_atoms porosity all cube 0.1 482793 bond yes
-   delete_atoms porosity polymer cube 0.1 482793 bond yes
+   delete_atoms porosity cube 0.1 482793 bond yes
 
 Description
 """""""""""
@@ -79,17 +76,12 @@ have occurred that no atom pairs within the cutoff will remain
 minimum number of atoms will be deleted, or that the same atoms will
 be deleted when running on different numbers of processors.
 
-For style *porosity* a specified *fraction* of atoms are deleted which
-are both in the specified group and within the specified region.  The
-region-ID can be specified as NULL to only impose the group criterion.
-Likewise, specifying the group-ID as *all* will only impose the region
-criterion.
-
-For example, if fraction is 0.1, then 10% of the eligible atoms will
-be deleted.  The atoms to delete are chosen randomly.  There is no
-guarantee that the exact fraction of atoms will be deleted, or that
-the same atoms will be deleted when running on different numbers of
-processors.
+For style *porosity* a specified *fraction* of atoms are deleted
+within the specified region.  For example, if fraction is 0.1, then
+10% of the atoms will be deleted.  The atoms to delete are chosen
+randomly.  There is no guarantee that the exact fraction of atoms will
+be deleted, or that the same atoms will be deleted when running on
+different numbers of processors.
 
 If the *compress* keyword is set to *yes*, then after atoms are
 deleted, then atom IDs are re-assigned so that they run from 1 to the
@@ -97,8 +89,8 @@ number of atoms in the system.  Note that this is not done for
 molecular systems (see the :doc:`atom_style <atom_style>` command),
 regardless of the *compress* setting, since it would foul up the bond
 connectivity that has already been assigned.  However, the
-:doc:`reset_atom_ids <reset_atom_ids>` command can be used after this
-command to accomplish the same thing.
+:doc:`reset_atom_ids <reset_atom_ids>` command can be used after this command to
+accomplish the same thing.
 
 Note that the re-assignment of IDs is not really a compression, where
 gaps in atom IDs are removed by decrementing atom IDs that are larger.
@@ -108,15 +100,15 @@ the :doc:`create_atoms <create_atoms>` command explains.
 
 A molecular system with fixed bonds, angles, dihedrals, or improper
 interactions, is one where the topology of the interactions is
-typically defined in the data file read by the :doc:`read_data
-<read_data>` command, and where the interactions themselves are
-defined with the :doc:`bond_style <bond_style>`, :doc:`angle_style
-<angle_style>`, etc commands.  If you delete atoms from such a system,
-you must be careful not to end up with bonded interactions that are
-stored by remaining atoms but which include deleted atoms.  This will
-cause LAMMPS to generate a "missing atoms" error when the bonded
-interaction is computed.  The *bond* and *mol* keywords offer two ways
-to do that.
+typically defined in the data file read by the
+:doc:`read_data <read_data>` command, and where the interactions
+themselves are defined with the :doc:`bond_style <bond_style>`,
+:doc:`angle_style <angle_style>`, etc commands.  If you delete atoms
+from such a system, you must be careful not to end up with bonded
+interactions that are stored by remaining atoms but which include
+deleted atoms.  This will cause LAMMPS to generate a "missing atoms"
+error when the bonded interaction is computed.  The *bond* and *mol*
+keywords offer two ways to do that.
 
 It the *bond* keyword is set to *yes* then any bond or angle or
 dihedral or improper interaction that includes a deleted atom is also

doc/src/dump.rst

@@ -137,7 +137,7 @@ Examples
    dump myDump all atom/gz 100 dump.atom.gz
    dump myDump all atom/zstd 100 dump.atom.zst
    dump 2 subgroup atom 50 dump.run.bin
-   dump 2 subgroup atom/mpiio 50 dump.run.mpiio.bin
+   dump 2 subgroup atom 50 dump.run.mpiio.bin
    dump 4a all custom 100 dump.myforce.* id type x y vx fx
    dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
    dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
@@ -169,12 +169,11 @@ or multiple smaller files).
 
 .. note::
 
-   Because periodic boundary conditions are enforced only on timesteps
-   when neighbor lists are rebuilt, the coordinates of an atom written
-   to a dump file may be slightly outside the simulation box.
-   Re-neighbor timesteps will not typically coincide with the
-   timesteps dump snapshots are written.  See the :doc:`dump_modify
-   pbc <dump_modify>` command if you with to force coordinates to be
+   Because periodic boundary conditions are enforced only on
+   timesteps when neighbor lists are rebuilt, the coordinates of an atom
+   written to a dump file may be slightly outside the simulation box.
+   Re-neighbor timesteps will not typically coincide with the timesteps
+   dump snapshots are written.  See the :doc:`dump_modify pbc <dump_modify>` command if you with to force coordinates to be
    strictly inside the simulation box.
 
 .. note::
@@ -190,21 +189,20 @@ or multiple smaller files).
    multiple processors, each of which owns a subset of the atoms.
 
 For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by
-default.  For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting
-by atom ID is on by default. See the :doc:`dump_modify <dump_modify>`
-doc page for details.
+default.  For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting by
+atom ID is on by default. See the :doc:`dump_modify <dump_modify>` doc
+page for details.
 
-The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles
-are identical in command syntax to the corresponding styles without
-"gz", however, they generate compressed files using the zlib
-library. Thus the filename suffix ".gz" is mandatory. This is an
-alternative approach to writing compressed files via a pipe, as done
-by the regular dump styles, which may be required on clusters where
-the interface to the high-speed network disallows using the fork()
-library call (which is needed for a pipe).  For the remainder of this
-doc page, you should thus consider the *atom* and *atom/gz* styles
-(etc) to be inter-changeable, with the exception of the required
-filename suffix.
+The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles are identical
+in command syntax to the corresponding styles without "gz", however,
+they generate compressed files using the zlib library. Thus the filename
+suffix ".gz" is mandatory. This is an alternative approach to writing
+compressed files via a pipe, as done by the regular dump styles, which
+may be required on clusters where the interface to the high-speed network
+disallows using the fork() library call (which is needed for a pipe).
+For the remainder of this doc page, you should thus consider the *atom*
+and *atom/gz* styles (etc) to be inter-changeable, with the exception
+of the required filename suffix.
 
 Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*,
 and *xyz/zstd* styles are identical to the gz styles, but use the Zstd
@@ -221,11 +219,6 @@ you should thus consider the *atom* and *atom/mpiio* styles (etc) to
 be inter-changeable.  The one exception is how the filename is
 specified for the MPI-IO styles, as explained below.
 
-.. warning::
-
-   The MPIIO package is currently unmaintained and has become
-   unreliable. Use with caution.
-
 The precision of values output to text-based dump files can be
 controlled by the :doc:`dump_modify format <dump_modify>` command and
 its options.
@@ -282,11 +275,10 @@ This bounding box is convenient for many visualization programs.  The
 meaning of the 6 character flags for "xx yy zz" is the same as above.
 
 Note that the first two numbers on each line are now xlo_bound instead
-of xlo, etc, since they represent a bounding box.  See the :doc:`Howto
-triclinic <Howto_triclinic>` page for a geometric description of
-triclinic boxes, as defined by LAMMPS, simple formulas for how the 6
-bounding box extents (xlo_bound,xhi_bound,etc) are calculated from the
-triclinic parameters, and how to transform those parameters to and
+of xlo, etc, since they represent a bounding box.  See the :doc:`Howto triclinic <Howto_triclinic>` page for a geometric description
+of triclinic boxes, as defined by LAMMPS, simple formulas for how the
+6 bounding box extents (xlo_bound,xhi_bound,etc) are calculated from
+the triclinic parameters, and how to transform those parameters to and
 from other commonly used triclinic representations.
 
 The "ITEM: ATOMS" line in each snapshot lists column descriptors for
@@ -318,24 +310,23 @@ written to the dump file.  This local data is typically calculated by
 each processor based on the atoms it owns, but there may be zero or
 more entities per atom, e.g. a list of bond distances.  An explanation
 of the possible dump local attributes is given below.  Note that by
-using input from the :doc:`compute property/local
-<compute_property_local>` command with dump local, it is possible to
-generate information on bonds, angles, etc that can be cut and pasted
-directly into a data file read by the :doc:`read_data <read_data>`
-command.
+using input from the :doc:`compute property/local <compute_property_local>` command with dump local,
+it is possible to generate information on bonds, angles, etc that can
+be cut and pasted directly into a data file read by the
+:doc:`read_data <read_data>` command.
 
 Style *cfg* has the same command syntax as style *custom* and writes
-extended CFG format files, as used by the `AtomEye
-<http://li.mit.edu/Archive/Graphics/A/>`_ visualization package.
-Since the extended CFG format uses a single snapshot of the system per
-file, a wildcard "\*" must be included in the filename, as discussed
-below.  The list of atom attributes for style *cfg* must begin with
-either "mass type xs ys zs" or "mass type xsu ysu zsu" since these
-quantities are needed to write the CFG files in the appropriate format
-(though the "mass" and "type" fields do not appear explicitly in the
-file).  Any remaining attributes will be stored as "auxiliary
-properties" in the CFG files.  Note that you will typically want to
-use the :doc:`dump_modify element <dump_modify>` command with
+extended CFG format files, as used by the
+`AtomEye <http://li.mit.edu/Archive/Graphics/A/>`_ visualization
+package.  Since the extended CFG format uses a single snapshot of the
+system per file, a wildcard "\*" must be included in the filename, as
+discussed below.  The list of atom attributes for style *cfg* must
+begin with either "mass type xs ys zs" or "mass type xsu ysu zsu"
+since these quantities are needed to write the CFG files in the
+appropriate format (though the "mass" and "type" fields do not appear
+explicitly in the file).  Any remaining attributes will be stored as
+"auxiliary properties" in the CFG files.  Note that you will typically
+want to use the :doc:`dump_modify element <dump_modify>` command with
 CFG-formatted files, to associate element names with atom types, so
 that AtomEye can render atoms appropriately. When unwrapped
 coordinates *xsu*, *ysu*, and *zsu* are requested, the nominal AtomEye
@@ -461,11 +452,6 @@ use the :doc:`read_dump <read_dump>` command or perform other
 post-processing, just as if the dump file was not written using
 MPI-IO.
 
-.. warning::
-
-   The MPIIO package is currently unmaintained and has become
-   unreliable. Use with caution.
-
 Note that MPI-IO dump files are one large file which all processors
 write to.  You thus cannot use the "%" wildcard character described
 above in the filename since that specifies generation of multiple
@@ -722,9 +708,8 @@ are part of the MPIIO package.  They are only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 doc page for more info.
 
-The *xtc* and *dcd* styles are part of the EXTRA-DUMP package.  They
-are only enabled if LAMMPS was built with that package.  See the
-:doc:`Build package <Build_package>` page for more info.
+The *xtc* style is part of the MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/dump_image.rst

@@ -6,8 +6,6 @@ dump image command
 dump movie command
 ==================
 
-(see below for :ref:`dump_modify options <dump_modify_image>` specific to dump image/movie)
-
 Syntax
 """"""
 
@@ -17,7 +15,7 @@ Syntax
 
 * ID = user-assigned name for the dump
 * group-ID = ID of the group of atoms to be imaged
-* style = *image* or *movie* = style of dump command (other styles such as *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
+* style = *image* or *movie* = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump <dump>` doc page)
 * N = dump every this many timesteps
 * file = name of file to write image to
 * color = atom attribute that determines color of each atom
@@ -81,69 +79,6 @@ Syntax
          seed = random # seed (positive integer)
          dfactor = strength of shading from 0.0 to 1.0
 
-
-.. _dump_modify_image:
-
-dump_modify options for dump image/movie
-========================================
-
-Syntax
-""""""
-
-.. parsed-literal::
-
-   dump_modify dump-ID keyword values ...
-
-* these keywords apply only to the *image* and *movie* styles and are documented on this page
-* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
-* see the :doc:`dump modify <dump_modify>` doc page for more general keywords
-
-  .. parsed-literal::
-
-       *acolor* args = type color
-         type = atom type or range of types (see below)
-         color = name of color or color1/color2/...
-       *adiam* args = type diam
-         type = atom type or range of types (see below)
-         diam = diameter of atoms of that type (distance units)
-       *amap* args = lo hi style delta N entry1 entry2 ... entryN
-         lo = number or *min* = lower bound of range of color map
-         hi = number or *max* = upper bound of range of color map
-         style = 2 letters = "c" or "d" or "s" plus "a" or "f"
-           "c" for continuous
-           "d" for discrete
-           "s" for sequential
-           "a" for absolute
-           "f" for fractional
-         delta = binsize (only used for style "s", otherwise ignored)
-           binsize = range is divided into bins of this width
-         N = # of subsequent entries
-         entry = value color (for continuous style)
-           value = number or *min* or *max* = single value within range
-           color = name of color used for that value
-         entry = lo hi color (for discrete style)
-           lo/hi = number or *min* or *max* = lower/upper bound of subset of range
-           color = name of color used for that subset of values
-         entry = color (for sequential style)
-           color = name of color used for a bin of values
-       *backcolor* arg = color
-         color = name of color for background
-       *bcolor* args = type color
-         type = bond type or range of types (see below)
-         color = name of color or color1/color2/...
-       *bdiam* args = type diam
-         type = bond type or range of types (see below)
-         diam = diameter of bonds of that type (distance units)
-       *boxcolor* arg = color
-         color = name of color for simulation box lines and processor sub-domain lines
-       *color* args = name R G B
-         name = name of color
-         R,G,B = red/green/blue numeric values from 0.0 to 1.0
-       *bitrate* arg = rate
-         rate = target bitrate for movie in kbps
-       *framerate* arg = fps
-         fps = frames per second for movie
-
 Examples
 """"""""
 
@@ -156,8 +91,6 @@ Examples
    dump m1 all movie 1000 movie.avi type type size 640 480
    dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720
 
-   dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
-
 Description
 """""""""""
 
@@ -212,10 +145,10 @@ is used.
 Similarly, the format of the resulting movie is chosen with the
 *movie* dump style. This is handled by the underlying FFmpeg converter
 and thus details have to be looked up in the `FFmpeg documentation
-<http://ffmpeg.org/ffmpeg.html>`_.  Typical examples are: .avi, .mpg,
-.m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie
-compression like bitrate and framerate can be set using the
-dump_modify command as described below.
+<http://ffmpeg.org/ffmpeg.html>`_.
+Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
+Additional settings of the movie compression like bitrate and
+framerate can be set using the :doc:`dump_modify <dump_modify>` command.
 
 To write out JPEG and PNG format files, you must build LAMMPS with
 support for the corresponding JPEG or PNG library. To convert images
@@ -277,20 +210,19 @@ to colors is as follows:
 * type 6 = cyan
 
 and repeats itself for types > 6.  This mapping can be changed by the
-"dump_modify acolor" command, as described below.
+:doc:`dump_modify acolor <dump_modify>` command.
 
 If *type* is specified for the *diameter* setting then the diameter of
 each atom is determined by its atom type.  By default all types have
-diameter 1.0.  This mapping can be changed by the "dump_modify adiam"
-command, as described below.
+diameter 1.0.  This mapping can be changed by the :doc:`dump_modify adiam <dump_modify>` command.
 
 If *element* is specified for the *color* and/or *diameter* setting,
 then the color and/or diameter of each atom is determined by which
 element it is, which in turn is specified by the element-to-type
-mapping specified by the "dump_modify element" command, as described
-below.  By default every atom type is C (carbon).  Every element has a
-color and diameter associated with it, which is the same as the colors
-and sizes used by the `AtomEye <atomeye_>`_ visualization package.
+mapping specified by the "dump_modify element" command.  By default
+every atom type is C (carbon).  Every element has a color and diameter
+associated with it, which is the same as the colors and sizes used by
+the `AtomEye <atomeye_>`_ visualization package.
 
 .. _atomeye: http://li.mit.edu/Archive/Graphics/A/
 
@@ -300,13 +232,13 @@ settings, they are interpreted in the following way.
 If "vx", for example, is used as the *color* setting, then the color
 of the atom will depend on the x-component of its velocity.  The
 association of a per-atom value with a specific color is determined by
-a "color map", which can be specified via the dump_modify command, as
-described below.  The basic idea is that the atom-attribute will be
-within a range of values, and every value within the range is mapped
-to a specific color.  Depending on how the color map is defined, that
-mapping can take place via interpolation so that a value of -3.2 is
-halfway between "red" and "blue", or discretely so that the value of
--3.2 is "orange".
+a "color map", which can be specified via the
+:doc:`dump_modify <dump_modify>` command.  The basic idea is that the
+atom-attribute will be within a range of values, and every value
+within the range is mapped to a specific color.  Depending on how the
+color map is defined, that mapping can take place via interpolation so
+that a value of -3.2 is halfway between "red" and "blue", or
+discretely so that the value of -3.2 is "orange".
 
 If "vx", for example, is used as the *diameter* setting, then the atom
 will be rendered using the x-component of its velocity as the
@@ -319,10 +251,9 @@ diameter, which can be used as the *diameter* setting.
 
 The various keywords listed above control how the image is rendered.
 As listed below, all of the keywords have defaults, most of which you
-will likely not need to change.  As described below, the dump modify
-command also has options specific to the dump image style,
-particularly for assigning colors to atoms, bonds, and other image
-features.
+will likely not need to change.  The :doc:`dump modify <dump_modify>`
+also has options specific to the dump image style, particularly for
+assigning colors to atoms, bonds, and other image features.
 
 ----------
 
@@ -364,7 +295,7 @@ types to colors is as follows:
 * type 6 = cyan
 
 and repeats itself for bond types > 6.  This mapping can be changed by
-the "dump_modify bcolor" command, as described below.
+the :doc:`dump_modify bcolor <dump_modify>` command.
 
 The bond *width* value can be a numeric value or *atom* or *type* (or
 *none* as indicated above).
@@ -379,8 +310,7 @@ of the 2 atoms in the bond.
 
 If *type* is specified for the *width* value then the diameter of each
 bond is determined by its bond type.  By default all types have
-diameter 0.5.  This mapping can be changed by the "dump_modify bdiam" command,
-as described below.
+diameter 0.5.  This mapping can be changed by the :doc:`dump_modify bdiam <dump_modify>` command.
 
 ----------
 
@@ -400,7 +330,7 @@ mapping of types to colors is as follows:
 * type 6 = cyan
 
 and repeats itself for types > 6.  There is not yet an option to
-change this via the dump_modify command.
+change this via the :doc:`dump_modify <dump_modify>` command.
 
 The line *width* can only be a numeric value, which specifies that all
 lines will be drawn as cylinders with that diameter, e.g. 1.0, which
@@ -427,7 +357,7 @@ default the mapping of types to colors is as follows:
 * type 6 = cyan
 
 and repeats itself for types > 6.  There is not yet an option to
-change this via the dump_modify command.
+change this via the :doc:`dump_modify <dump_modify>` command.
 
 ----------
 
@@ -460,7 +390,7 @@ particle.  By default the mapping of types to colors is as follows:
 * type 6 = cyan
 
 and repeats itself for types > 6.  There is not yet an option to
-change this via the dump_modify command.
+change this via the :doc:`dump_modify <dump_modify>` command.
 
 ----------
 
@@ -484,7 +414,7 @@ the mapping of types to colors is as follows:
 * type 6 = cyan
 
 and repeats itself for types > 6.  There is not yet an option to
-change this via the dump_modify command.
+change this via the :doc:`dump_modify <dump_modify>` command.
 
 ----------
 
@@ -558,8 +488,7 @@ are rendered as thin cylinders in the image.  If *no* is set, then the
 box boundaries are not drawn and the *diam* setting is ignored.  If
 *yes* is set, the 12 edges of the box are drawn, with a diameter that
 is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
-2d).  The color of the box boundaries can be set with the "dump_modify
-boxcolor" command.
+2d).  The color of the box boundaries can be set with the :doc:`dump_modify boxcolor <dump_modify>` command.
 
 The *axes* keyword determines if and how the coordinate axes are
 rendered as thin cylinders in the image.  If *no* is set, then the
@@ -578,8 +507,7 @@ set (default), then the sub-domain boundaries are not drawn and the
 *diam* setting is ignored.  If *yes* is set, the 12 edges of each
 processor sub-domain are drawn, with a diameter that is a fraction of
 the shortest box length in x,y,z (for 3d) or x,y (for 2d).  The color
-of the sub-domain boundaries can be set with the "dump_modify
-boxcolor" command.
+of the sub-domain boundaries can be set with the :doc:`dump_modify boxcolor <dump_modify>` command.
 
 ----------
 
@@ -679,272 +607,9 @@ Play the movie:
 
 ----------
 
-Dump_modify keywords for dump image and dump movie
-""""""""""""""""""""""""""""""""""""""""""""""""""
-
-The following dump_modify keywords apply only to the dump image and
-dump movie styles.  Any keyword that works with dump image also works
-with dump movie, since the movie is simply a collection of images.
-Some of the keywords only affect the dump movie style.  The
-descriptions give details.
-
-----------
-
-The *acolor* keyword can be used with the dump image command, when its
-atom color setting is *type*, to set the color that atoms of each type
-will be drawn in the image.
-
-The specified *type* should be an integer from 1 to Ntypes = the
-number of atom types.  A wildcard asterisk can be used in place of or
-in conjunction with the *type* argument to specify a range of atom
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
-the number of atom types, then an asterisk with no numeric values
-means all types from 1 to N.  A leading asterisk means all types from
-1 to n (inclusive).  A trailing asterisk means all types from n to N
-(inclusive).  A middle asterisk means all types from m to n
-(inclusive).
-
-The specified *color* can be a single color which is any of the 140
-pre-defined colors (see below) or a color name defined by the
-"dump_modify color" command, as described below.  Or it can be two or
-more colors separated by a "/" character, e.g. red/green/blue.  In the
-former case, that color is assigned to all the specified atom types.
-In the latter case, the list of colors are assigned in a round-robin
-fashion to each of the specified atom types.
-
-----------
-
-The *adiam* keyword can be used with the dump image command, when its
-atom diameter setting is *type*, to set the size that atoms of each
-type will be drawn in the image.  The specified *type* should be an
-integer from 1 to Ntypes.  As with the *acolor* keyword, a wildcard
-asterisk can be used as part of the *type* argument to specify a range
-of atom types.  The specified *diam* is the size in whatever distance
-:doc:`units <units>` the input script is using, e.g. Angstroms.
-
-----------
-
-The *amap* keyword can be used with the dump image command, with its
-*atom* keyword, when its atom setting is an atom-attribute, to setup a
-color map.  The color map is used to assign a specific RGB
-(red/green/blue) color value to an individual atom when it is drawn,
-based on the atom's attribute, which is a numeric value, e.g. its
-x-component of velocity if the atom-attribute "vx" was specified.
-
-The basic idea of a color map is that the atom-attribute will be
-within a range of values, and that range is associated with a series
-of colors (e.g. red, blue, green).  An atom's specific value (vx =
--3.2) can then mapped to the series of colors (e.g. halfway between
-red and blue), and a specific color is determined via an interpolation
-procedure.
-
-There are many possible options for the color map, enabled by the
-*amap* keyword.  Here are the details.
-
-The *lo* and *hi* settings determine the range of values allowed for
-the atom attribute.  If numeric values are used for *lo* and/or *hi*,
-then values that are lower/higher than that value are set to the
-value.  I.e. the range is static.  If *lo* is specified as *min* or
-*hi* as *max* then the range is dynamic, and the lower and/or
-upper bound will be calculated each time an image is drawn, based
-on the set of atoms being visualized.
-
-The *style* setting is two letters, such as "ca".  The first letter is
-either "c" for continuous, "d" for discrete, or "s" for sequential.
-The second letter is either "a" for absolute, or "f" for fractional.
-
-A continuous color map is one in which the color changes continuously
-from value to value within the range.  A discrete color map is one in
-which discrete colors are assigned to sub-ranges of values within the
-range.  A sequential color map is one in which discrete colors are
-assigned to a sequence of sub-ranges of values covering the entire
-range.
-
-An absolute color map is one in which the values to which colors are
-assigned are specified explicitly as values within the range.  A
-fractional color map is one in which the values to which colors are
-assigned are specified as a fractional portion of the range.  For
-example if the range is from -10.0 to 10.0, and the color red is to be
-assigned to atoms with a value of 5.0, then for an absolute color map
-the number 5.0 would be used.  But for a fractional map, the number
-0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.
-
-The *delta* setting must be specified for all styles, but is only used
-for the sequential style; otherwise the value is ignored.  It
-specifies the bin size to use within the range for assigning
-consecutive colors to.  For example, if the range is from -10.0 to
-10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
-the range.  The first will be from -10.0 <= color1 < -9.0, then second
-from -9.0 <= color2 < -8.0, etc.
-
-The *N* setting is how many entries follow.  The format of the entries
-depends on whether the color map style is continuous, discrete or
-sequential.  In all cases the *color* setting can be any of the 140
-pre-defined colors (see below) or a color name defined by the
-dump_modify color option.
-
-For continuous color maps, each entry has a *value* and a *color*\ .
-The *value* is either a number within the range of values or *min* or
-*max*\ .  The *value* of the first entry must be *min* and the *value*
-of the last entry must be *max*\ .  Any entries in between must have
-increasing values.  Note that numeric values can be specified either
-as absolute numbers or as fractions (0.0 to 1.0) of the range,
-depending on the "a" or "f" in the style setting for the color map.
-
-Here is how the entries are used to determine the color of an
-individual atom, given the value X of its atom attribute.  X will fall
-between 2 of the entry values.  The color of the atom is linearly
-interpolated (in each of the RGB values) between the 2 colors
-associated with those entries.  For example, if X = -5.0 and the 2
-surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
-atom's color will be halfway between "red" and "blue", which happens
-to be "purple".
-
-For discrete color maps, each entry has a *lo* and *hi* value and a
-*color*\ .  The *lo* and *hi* settings are either numbers within the
-range of values or *lo* can be *min* or *hi* can be *max*\ .  The *lo*
-and *hi* settings of the last entry must be *min* and *max*\ .  Other
-entries can have any *lo* and *hi* values and the sub-ranges of
-different values can overlap.  Note that numeric *lo* and *hi* values
-can be specified either as absolute numbers or as fractions (0.0 to
-1.0) of the range, depending on the "a" or "f" in the style setting
-for the color map.
-
-Here is how the entries are used to determine the color of an
-individual atom, given the value X of its atom attribute.  The entries
-are scanned from first to last.  The first time that *lo* <= X <=
-*hi*, X is assigned the color associated with that entry.  You can
-think of the last entry as assigning a default color (since it will
-always be matched by X), and the earlier entries as colors that
-override the default.  Also note that no interpolation of a color RGB
-is done.  All atoms will be drawn with one of the colors in the list
-of entries.
-
-For sequential color maps, each entry has only a *color*\ .  Here is how
-the entries are used to determine the color of an individual atom,
-given the value X of its atom attribute.  The range is partitioned
-into N bins of width *binsize*\ .  Thus X will fall in a specific bin
-from 1 to N, say the Mth bin.  If it falls on a boundary between 2
-bins, it is considered to be in the higher of the 2 bins.  Each bin is
-assigned a color from the E entries.  If E < N, then the colors are
-repeated.  For example if 2 entries with colors red and green are
-specified, then the odd numbered bins will be red and the even bins
-green.  The color of the atom is the color of its bin.  Note that the
-sequential color map is really a shorthand way of defining a discrete
-color map without having to specify where all the bin boundaries are.
-
-Here is an example of using a sequential color map to color all the
-atoms in individual molecules with a different color.  See the
-examples/pour/in.pour.2d.molecule input script for an example of how
-this is used.
-
-.. code-block:: LAMMPS
-
-   variable        colors string &
-                   "red green blue yellow white &
-                   purple pink orange lime gray"
-   variable        mol atom mol%10
-   dump            1 all image 250 image.*.jpg v_mol type &
-                   zoom 1.6 adiam 1.5
-   dump_modify     1 pad 5 amap 0 10 sa 1 10 ${colors}
-
-In this case, 10 colors are defined, and molecule IDs are
-mapped to one of the colors, even if there are 1000s of molecules.
-
-----------
-
-The *backcolor* sets the background color of the images.  The color
-name can be any of the 140 pre-defined colors (see below) or a color
-name defined by the dump_modify color option.
-
-----------
-
-The *bcolor* keyword can be used with the dump image command, with its
-*bond* keyword, when its color setting is *type*, to set the color
-that bonds of each type will be drawn in the image.
-
-The specified *type* should be an integer from 1 to Nbondtypes = the
-number of bond types.  A wildcard asterisk can be used in place of or
-in conjunction with the *type* argument to specify a range of bond
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
-the number of bond types, then an asterisk with no numeric values
-means all types from 1 to N.  A leading asterisk means all types from
-1 to n (inclusive).  A trailing asterisk means all types from n to N
-(inclusive).  A middle asterisk means all types from m to n
-(inclusive).
-
-The specified *color* can be a single color which is any of the 140
-pre-defined colors (see below) or a color name defined by the
-dump_modify color option.  Or it can be two or more colors separated
-by a "/" character, e.g. red/green/blue.  In the former case, that
-color is assigned to all the specified bond types.  In the latter
-case, the list of colors are assigned in a round-robin fashion to each
-of the specified bond types.
-
-----------
-
-The *bdiam* keyword can be used with the dump image command, with its
-*bond* keyword, when its diam setting is *type*, to set the diameter
-that bonds of each type will be drawn in the image.  The specified
-*type* should be an integer from 1 to Nbondtypes.  As with the
-*bcolor* keyword, a wildcard asterisk can be used as part of the
-*type* argument to specify a range of bond types.  The specified
-*diam* is the size in whatever distance :doc:`units <units>` you are
-using, e.g. Angstroms.
-
-----------
-
-The *bitrate* keyword can be used with the :doc:`dump movie
-<dump_image>` command to define the size of the resulting movie file
-and its quality via setting how many kbits per second are to be used
-for the movie file. Higher bitrates require less compression and will
-result in higher quality movies.  The quality is also determined by
-the compression format and encoder.  The default setting is 2000
-kbit/s, which will result in average quality with older compression
-formats.
-
-.. note::
-
-   Not all movie file formats supported by dump movie allow the
-   bitrate to be set.  If not, the setting is silently ignored.
-
-----------
-
-The *boxcolor* keyword sets the color of the simulation box drawn
-around the atoms in each image as well as the color of processor
-sub-domain boundaries.  See the "dump image box" command for how to
-specify that a box be drawn via the *box* keyword, and the sub-domain
-boundaries via the *subbox* keyword.  The color name can be any of the
-140 pre-defined colors (see below) or a color name defined by the
-dump_modify color option.
-
-----------
-
-The *color* keyword allows definition of a new color name, in addition
-to the 140-predefined colors (see below), and associates 3
-red/green/blue RGB values with that color name.  The color name can
-then be used with any other dump_modify keyword that takes a color
-name as a value.  The RGB values should each be floating point values
-between 0.0 and 1.0 inclusive.
-
-When a color name is converted to RGB values, the user-defined color
-names are searched first, then the 140 pre-defined color names.  This
-means you can also use the *color* keyword to overwrite one of the
-pre-defined color names with new RBG values.
-
-----------
-
-The *framerate* keyword can be used with the :doc:`dump movie
-<dump_image>` command to define the duration of the resulting movie
-file.  Movie files written by the dump *movie* command have a default
-frame rate of 24 frames per second and the images generated will be
-converted at that rate.  Thus a sequence of 1000 dump images will
-result in a movie of about 42 seconds.  To make a movie run longer you
-can either generate images more frequently or lower the frame rate.
-To speed a movie up, you can do the inverse.  Using a frame rate
-higher than 24 is not recommended, as it will result in simply
-dropping the rendered images. It is more efficient to dump images less
-frequently.
+See the :doc:`Modify <Modify>` page for information on how to add
+new compute and fix styles to LAMMPS to calculate per-atom quantities
+which could then be output into dump files.
 
 ----------
 
@@ -999,7 +664,7 @@ Related commands
 Default
 """""""
 
-The defaults for the dump image and dump movie keywords are as follows:
+The defaults for the keywords are as follows:
 
 * adiam = not specified (use diameter setting)
 * atom = yes
@@ -1017,101 +682,3 @@ The defaults for the dump image and dump movie keywords are as follows:
 * subbox no 0.0
 * shiny = 1.0
 * ssao = no
-
-----------
-
-The defaults for the dump_modify keywords specific to dump image and dump movie are as follows:
-
-* acolor = \* red/green/blue/yellow/aqua/cyan
-* adiam = \* 1.0
-* amap = min max cf 0.0 2 min blue max red
-* backcolor = black
-* bcolor = \* red/green/blue/yellow/aqua/cyan
-* bdiam = \* 0.5
-* bitrate = 2000
-* boxcolor = yellow
-* color = 140 color names are pre-defined as listed below
-* framerate = 24
-
-----------
-
-These are the standard 109 element names that LAMMPS pre-defines for
-use with the dump image and dump_modify commands.
-
-* 1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne"
-* 11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca"
-* 21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn"
-* 31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr"
-* 41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn"
-* 51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd"
-* 61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb"
-* 71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg"
-* 81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th"
-* 91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm"
-* 101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt"
-
-----------
-
-These are the 140 colors that LAMMPS pre-defines for use with the dump
-image and dump_modify commands.  Additional colors can be defined with
-the dump_modify color command.  The 3 numbers listed for each name are
-the RGB (red/green/blue) values.  Divide each value by 255 to get the
-equivalent 0.0 to 1.0 value.
-
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| aliceblue = 240, 248, 255     | antiquewhite = 250, 235, 215         | aqua = 0, 255, 255              | aquamarine = 127, 255, 212     | azure = 240, 255, 255          |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| beige = 245, 245, 220         | bisque = 255, 228, 196               | black = 0, 0, 0                 | blanchedalmond = 255, 255, 205 | blue = 0, 0, 255               |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| blueviolet = 138, 43, 226     | brown = 165, 42, 42                  | burlywood = 222, 184, 135       | cadetblue = 95, 158, 160       | chartreuse = 127, 255, 0       |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| chocolate = 210, 105, 30      | coral = 255, 127, 80                 | cornflowerblue = 100, 149, 237  | cornsilk = 255, 248, 220       | crimson = 220, 20, 60          |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| cyan = 0, 255, 255            | darkblue = 0, 0, 139                 | darkcyan = 0, 139, 139          | darkgoldenrod = 184, 134, 11   | darkgray = 169, 169, 169       |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| darkgreen = 0, 100, 0         | darkkhaki = 189, 183, 107            | darkmagenta = 139, 0, 139       | darkolivegreen = 85, 107, 47   | darkorange = 255, 140, 0       |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| darkorchid = 153, 50, 204     | darkred = 139, 0, 0                  | darksalmon = 233, 150, 122      | darkseagreen = 143, 188, 143   | darkslateblue = 72, 61, 139    |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| darkslategray = 47, 79, 79    | darkturquoise = 0, 206, 209          | darkviolet = 148, 0, 211        | deeppink = 255, 20, 147        | deepskyblue = 0, 191, 255      |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| dimgray = 105, 105, 105       | dodgerblue = 30, 144, 255            | firebrick = 178, 34, 34         | floralwhite = 255, 250, 240    | forestgreen = 34, 139, 34      |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| fuchsia = 255, 0, 255         | gainsboro = 220, 220, 220            | ghostwhite = 248, 248, 255      | gold = 255, 215, 0             | goldenrod = 218, 165, 32       |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| gray = 128, 128, 128          | green = 0, 128, 0                    | greenyellow = 173, 255, 47      | honeydew = 240, 255, 240       | hotpink = 255, 105, 180        |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| indianred = 205, 92, 92       | indigo = 75, 0, 130                  | ivory = 255, 240, 240           | khaki = 240, 230, 140          | lavender = 230, 230, 250       |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| lavenderblush = 255, 240, 245 | lawngreen = 124, 252, 0              | lemonchiffon = 255, 250, 205    | lightblue = 173, 216, 230      | lightcoral = 240, 128, 128     |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| lightcyan = 224, 255, 255     | lightgoldenrodyellow = 250, 250, 210 | lightgreen = 144, 238, 144      | lightgrey = 211, 211, 211      | lightpink = 255, 182, 193      |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| lightsalmon = 255, 160, 122   | lightseagreen = 32, 178, 170         | lightskyblue = 135, 206, 250    | lightslategray = 119, 136, 153 | lightsteelblue = 176, 196, 222 |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| lightyellow = 255, 255, 224   | lime = 0, 255, 0                     | limegreen = 50, 205, 50         | linen = 250, 240, 230          | magenta = 255, 0, 255          |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| maroon = 128, 0, 0            | mediumaquamarine = 102, 205, 170     | mediumblue = 0, 0, 205          | mediumorchid = 186, 85, 211    | mediumpurple = 147, 112, 219   |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| mediumseagreen = 60, 179, 113 | mediumslateblue = 123, 104, 238      | mediumspringgreen = 0, 250, 154 | mediumturquoise = 72, 209, 204 | mediumvioletred = 199, 21, 133 |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| midnightblue = 25, 25, 112    | mintcream = 245, 255, 250            | mistyrose = 255, 228, 225       | moccasin = 255, 228, 181       | navajowhite = 255, 222, 173    |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| navy = 0, 0, 128              | oldlace = 253, 245, 230              | olive = 128, 128, 0             | olivedrab = 107, 142, 35       | orange = 255, 165, 0           |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| orangered = 255, 69, 0        | orchid = 218, 112, 214               | palegoldenrod = 238, 232, 170   | palegreen = 152, 251, 152      | paleturquoise = 175, 238, 238  |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| palevioletred = 219, 112, 147 | papayawhip = 255, 239, 213           | peachpuff = 255, 239, 213       | peru = 205, 133, 63            | pink = 255, 192, 203           |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| plum = 221, 160, 221          | powderblue = 176, 224, 230           | purple = 128, 0, 128            | red = 255, 0, 0                | rosybrown = 188, 143, 143      |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| royalblue = 65, 105, 225      | saddlebrown = 139, 69, 19            | salmon = 250, 128, 114          | sandybrown = 244, 164, 96      | seagreen = 46, 139, 87         |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| seashell = 255, 245, 238      | sienna = 160, 82, 45                 | silver = 192, 192, 192          | skyblue = 135, 206, 235        | slateblue = 106, 90, 205       |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| slategray = 112, 128, 144     | snow = 255, 250, 250                 | springgreen = 0, 255, 127       | steelblue = 70, 130, 180       | tan = 210, 180, 140            |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| teal = 0, 128, 128            | thistle = 216, 191, 216              | tomato = 253, 99, 71            | turquoise = 64, 224, 208       | violet = 238, 130, 238         |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
-| wheat = 245, 222, 179         | white = 255, 255, 255                | whitesmoke = 245, 245, 245      | yellow = 255, 255, 0           | yellowgreen = 154, 205, 50     |
-+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+

doc/src/dump_modify.rst

@@ -3,9 +3,6 @@
 dump_modify command
 ===================
 
-:doc:`dump_modify <dump_image>` command for image/movie options
-===============================================================
-
 Syntax
 """"""
 
@@ -15,16 +12,14 @@ Syntax
 
 * dump-ID = ID of dump to modify
 * one or more keyword/value pairs may be appended
-
 * these keywords apply to various dump styles
-* keyword = *append* or *at* or *balance* or *buffer* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
+* keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *fileper* or *first* or *flush* or *format* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
 
   .. parsed-literal::
 
        *append* arg = *yes* or *no*
        *at* arg = N
          N = index of frame written upon first dump
-       *balance* arg = *yes* or *no*
        *buffer* arg = *yes* or *no*
        *delay* arg = Dstep
          Dstep = delay output until this timestep
@@ -33,9 +28,6 @@ Syntax
        *every* arg = N
          N = dump every this many timesteps
          N can be a variable (see below)
-       *every/time* arg = Delta
-         Delta = dump every this interval in simulation time (time units)
-         Delta can be a variable (see below)
        *fileper* arg = Np
          Np = write one file for every this many processors
        *first* arg = *yes* or *no*
@@ -43,9 +35,6 @@ Syntax
        *format* args = *line* string, *int* string, *float* string, M string, or *none*
          string = C-style format string
          M = integer from 1 to N, where N = # of per-atom quantities being output
-       *header* arg = *yes* or *no*
-         *yes* to write the header
-         *no* to not write the header
        *image* arg = *yes* or *no*
        *label* arg = string
          string = character string (e.g. BONDS) to use in header of dump local file
@@ -77,11 +66,56 @@ Syntax
        *unwrap* arg = *yes* or *no*
 
 * these keywords apply only to the *image* and *movie* :doc:`styles <dump_image>`
-* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate*
+* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* or *header*
 
   .. parsed-literal::
 
-       see the :doc:`dump image <dump_image>` doc page for details
+       *acolor* args = type color
+         type = atom type or range of types (see below)
+         color = name of color or color1/color2/...
+       *adiam* args = type diam
+         type = atom type or range of types (see below)
+         diam = diameter of atoms of that type (distance units)
+       *amap* args = lo hi style delta N entry1 entry2 ... entryN
+         lo = number or *min* = lower bound of range of color map
+         hi = number or *max* = upper bound of range of color map
+         style = 2 letters = "c" or "d" or "s" plus "a" or "f"
+           "c" for continuous
+           "d" for discrete
+           "s" for sequential
+           "a" for absolute
+           "f" for fractional
+         delta = binsize (only used for style "s", otherwise ignored)
+           binsize = range is divided into bins of this width
+         N = # of subsequent entries
+         entry = value color (for continuous style)
+           value = number or *min* or *max* = single value within range
+           color = name of color used for that value
+         entry = lo hi color (for discrete style)
+           lo/hi = number or *min* or *max* = lower/upper bound of subset of range
+           color = name of color used for that subset of values
+         entry = color (for sequential style)
+           color = name of color used for a bin of values
+       *backcolor* arg = color
+         color = name of color for background
+       *bcolor* args = type color
+         type = bond type or range of types (see below)
+         color = name of color or color1/color2/...
+       *bdiam* args = type diam
+         type = bond type or range of types (see below)
+         diam = diameter of bonds of that type (distance units)
+       *boxcolor* arg = color
+         color = name of color for simulation box lines and processor sub-domain lines
+       *color* args = name R G B
+         name = name of color
+         R,G,B = red/green/blue numeric values from 0.0 to 1.0
+       *bitrate* arg = rate
+         rate = target bitrate for movie in kbps
+       *framerate* arg = fps
+         fps = frames per second for movie
+       *header* arg = *yes* or *no*
+         *yes* to write the header
+         *no* to not write the header
 
 * these keywords apply only to the */gz* and */zstd* dump styles
 * keyword = *compression_level*
@@ -92,7 +126,7 @@ Syntax
          level = integer specifying the compression level that should be used (see below for supported levels)
 
 * these keywords apply only to the */zstd* dump styles
-* keyword = *checksum*
+* keyword = *compression_level*
 
   .. parsed-literal::
 
@@ -110,6 +144,7 @@ Examples
    dump_modify xtcdump precision 10000 sfactor 0.1
    dump_modify 1 every 1000 nfile 20
    dump_modify 1 every v_myVar
+   dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
 
 Description
 """""""""""
@@ -128,9 +163,8 @@ which allow for use of MPI-IO.
 
 ----------
 
-Unless otherwise noted, the following keywords apply to all the
-various dump styles, including the :doc:`dump image <dump_image>` and
-:doc:`dump movie <dump_image>` styles.
+These keywords apply to various dump styles, including the :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>` styles.  The
+description gives details.
 
 ----------
 
@@ -201,19 +235,11 @@ will be accepted.
 
 ----------
 
-The *every* keyword can be used with any dump style except the *dcd*
-and *xtc* styles.  It does two things.  It specifies that the interval
-between dump snapshots will be set in timesteps, which is the default
-if the *every* or *every/time* keywords are not used.  See the
-*every/time* keyword for how to specify the interval in simulation
-time, i.e. in time units of the :doc:`units <units>` command.  The
-*every* keyword also sets the interval value, which overrides the dump
-frequency originally specified by the :doc:`dump <dump>` command.
-
-The *every* keyword can be specified in one of two ways.  It can be a
-numeric value in which case it must be > 0.  Or it can be an
-:doc:`equal-style variable <variable>`, which should be specified as
-v_name, where name is the variable name.
+The *every* keyword changes the dump frequency originally specified by
+the :doc:`dump <dump>` command to a new value.  The every keyword can be
+specified in one of two ways.  It can be a numeric value in which case
+it must be > 0.  Or it can be an :doc:`equal-style variable <variable>`,
+which should be specified as v_name, where name is the variable name.
 
 In this case, the variable is evaluated at the beginning of a run to
 determine the next timestep at which a dump snapshot will be written
@@ -222,12 +248,11 @@ determine the next timestep, etc.  Thus the variable should return
 timestep values.  See the stagger() and logfreq() and stride() math
 functions for :doc:`equal-style variables <variable>`, as examples of
 useful functions to use in this context.  Other similar math functions
-could easily be added as options for :doc:`equal-style variables
-<variable>`.  Also see the next() function, which allows use of a
-file-style variable which reads successive values from a file, each
-time the variable is evaluated.  Used with the *every* keyword, if the
-file contains a list of ascending timesteps, you can output snapshots
-whenever you wish.
+could easily be added as options for :doc:`equal-style variables <variable>`.  Also see the next() function, which allows
+use of a file-style variable which reads successive values from a
+file, each time the variable is evaluated.  Used with the *every*
+keyword, if the file contains a list of ascending timesteps, you can
+output snapshots whenever you wish.
 
 Note that when using the variable option with the *every* keyword, you
 need to use the *first* option if you want an initial snapshot written
@@ -268,103 +293,14 @@ in file tmp.times:
 
 ----------
 
-The *every/time* keyword can be used with any dump style except the
-*dcd* and *xtc* styles.  It does two things.  It specifies that the
-interval between dump snapshots will be set in simulation time,
-i.e. in time units of the :doc:`units <units>` command.  This can be
-useful when the timestep size varies during a simulation run, e.g. by
-use of the :doc:`fix dt/reset <fix_dt_reset>` command.  The default is
-to specify the interval in timesteps; see the *every* keyword.  The
-*every/time* command also sets the interval value.
-
-.. note::
-
-   If you wish dump styles *atom*, *custom*, *local*, or *xyz* to
-   include the simulation time as a field in the header portion of
-   each snapshot, you also need to use the dump_modify *time* keyword
-   with a setting of *yes*.  See its documentation below.
-
-Note that since snapshots are output on simulation steps, each
-snapshot will be written on the first timestep whose associated
-simulation time is >= the exact snapshot time value.
-
-As with the *every* option, the *Delta* value can be specified in one
-of two ways.  It can be a numeric value in which case it must be >
-0.0.  Or it can be an :doc:`equal-style variable <variable>`, which
-should be specified as v_name, where name is the variable name.
-
-In this case, the variable is evaluated at the beginning of a run to
-determine the next simulation time at which a dump snapshot will be
-written out.  On that timestep the variable will be evaluated again to
-determine the next simulation time, etc.  Thus the variable should
-return values in time units.  Note the current timestep or simulation
-time can be used in an :doc:`equal-style variables <variable>` since
-they are both thermodynamic keywords.  Also see the next() function,
-which allows use of a file-style variable which reads successive
-values from a file, each time the variable is evaluated.  Used with
-the *every/time* keyword, if the file contains a list of ascending
-simulation times, you can output snapshots whenever you wish.
-
-Note that when using the variable option with the *every/time*
-keyword, you need to use the *first* option if you want an initial
-snapshot written to the dump file.  The *every/time* keyword cannot be
-used with the dump *dcd* style.
-
-For example, the following commands will write snapshots at successive
-simulation times which grow by a factor of 1.5 with each interval.
-The dt value used in the variable is to avoid a zero result when the
-initial simulation time is 0.0.
-
-.. code-block:: LAMMPS
-
-   variable        increase equal 1.5*(time+dt)
-   dump            1 all atom 100 tmp.dump
-   dump_modify     1 every/time v_increase first yes
-
-The following commands would write snapshots at the times listed in
-file tmp.times:
-
-.. code-block:: LAMMPS
-
-   variable        f file tmp.times
-   variable        s equal next(f)
-   dump            1 all atom 100 tmp.dump
-   dump_modify     1 every/time v_s
-
-.. note::
-
-   When using a file-style variable with the *every/time* keyword, the
-   file of timesteps must list a first time that is beyond the time
-   associated with the current timestep (e.g. it cannot be 0.0).  And
-   it must list one or more times beyond the length of the run you
-   perform.  This is because the dump command will generate an error
-   if the next time it reads from the file is not a value greater than
-   the current time.  Thus if you wanted output at times 0,15,100 of a
-   run of length 100 in simulation time, the file should contain the
-   values 15,100,101 and you should also use the dump_modify first
-   command.  Any final value > 100 could be used in place of 101.
-
-----------
-
 The *first* keyword determines whether a dump snapshot is written on
 the very first timestep after the dump command is invoked.  This will
-always occur if the current timestep is a multiple of $N$, the
-frequency specified in the :doc:`dump <dump>` command or
-:doc:`dump_modify every <dump_modify>` command, including timestep 0.
-It will also always occur if the current simulation time is a multiple
-of *Delta*, the time interval specified in the doc:`dump_modify
-every/time <dump_modify>` command.
-
-But if this is not the case, a dump snapshot will only be written if
-the setting of this keyword is *yes*\ .  If it is *no*, which is the
+always occur if the current timestep is a multiple of N, the frequency
+specified in the :doc:`dump <dump>` command, including timestep 0.  But
+if this is not the case, a dump snapshot will only be written if the
+setting of this keyword is *yes*\ .  If it is *no*, which is the
 default, then it will not be written.
 
-Note that if the argument to the :doc:`dump_modify every
-<dump_modify>` doc:`dump_modify every/time <dump_modify>` commands is
-a variable and not a numeric value, then specifying *first yes* is the
-only way to write a dump snapshot on the first timestep after the dump
-command is invoked.
-
 ----------
 
 The *flush* keyword determines whether a flush operation is invoked
@@ -444,13 +380,6 @@ The *fileper* keyword is documented below with the *nfile* keyword.
 
 ----------
 
-The *header* keyword toggles whether the dump file will include a
-header.  Excluding a header will reduce the size of the dump file for
-fixes such as :doc:`fix pair/tracker <fix_pair_tracker>` which do not
-require the information typically written to the header.
-
-----------
-
 The *image* keyword applies only to the dump *atom* style.  If the
 image value is *yes*, 3 flags are appended to each atom's coords which
 are the absolute box image of the atom in each dimension.  For
@@ -663,19 +592,9 @@ The dump *local* style cannot be sorted by atom ID, since there are
 typically multiple lines of output per atom.  Some dump styles, such
 as *dcd* and *xtc*, require sorting by atom ID to format the output
 file correctly.  If multiple processors are writing the dump file, via
-the "%" wildcard in the dump filename and the *nfile* or *fileper*
-keywords are set to non-default values (i.e. the number of dump file
-pieces is not equal to the number of procs), then sorting cannot be
+the "%" wildcard in the dump filename, then sorting cannot be
 performed.
 
-In a parallel run, the per-processor dump file pieces can have
-significant imbalance in number of lines of per-atom info. The *balance*
-keyword determines whether the number of lines in each processor
-snapshot are balanced to be nearly the same. A balance value of *no*
-means no balancing will be done, while *yes* means balancing will be
-performed. This balancing preserves dump sorting order. For a serial
-run, this option is ignored since the output is already balanced.
-
 .. note::
 
    Unless it is required by the dump style, sorting dump file
@@ -751,20 +670,16 @@ threshold criterion is met.  Otherwise it is not met.
 
 ----------
 
-The *time* keyword only applies to the dump *atom*, *custom*, *local*,
-and *xyz* styles (and their COMPRESS package versions *atom/gz*,
-*custom/gz* and *local/gz*\ ).  For the first 3 styles, if set to
-*yes*, each frame will will contain two extra lines before the "ITEM:
-TIMESTEP" entry:
+The *time* keyword only applies to the dump *atom*, *custom*, and
+*local* styles (and their COMPRESS package versions *atom/gz*,
+*custom/gz* and *local/gz*\ ). If set to *yes*, each frame will will
+contain two extra lines before the "ITEM: TIMESTEP" entry:
 
 .. parsed-literal::
 
    ITEM: TIME
    \<elapsed time\>
 
-For the *xyz* style, the simulation time is included on the same line
-as the timestep value.
-
 This will output the current elapsed simulation time in current
 time units equivalent to the :doc:`thermo keyword <thermo_style>` *time*\ .
 This is to simplify post-processing of trajectories using a variable time
@@ -800,35 +715,305 @@ box size stored with the snapshot.
 
 ----------
 
-The COMPRESS package offers both GZ and Zstd compression variants of
-styles atom, custom, local, cfg, and xyz. When using these styles the
-compression level can be controlled by the :code:`compression_level`
-keyword. File names with these styles have to end in either
-:code:`.gz` or :code:`.zst`.
+These keywords apply only to the :doc:`dump image <dump_image>` and
+:doc:`dump movie <dump_image>` styles.  Any keyword that affects an
+image, also affects a movie, since the movie is simply a collection of
+images.  Some of the keywords only affect the :doc:`dump movie <dump_image>` style.  The descriptions give details.
 
-GZ supports compression levels from -1 (default), 0 (no compression),
-and 1 to
-9. 9 being the best compression. The COMPRESS :code:`/gz` styles use 9
-as default compression level.
+----------
+
+The *acolor* keyword can be used with the :doc:`dump image <dump_image>`
+command, when its atom color setting is *type*, to set the color that
+atoms of each type will be drawn in the image.
+
+The specified *type* should be an integer from 1 to Ntypes = the
+number of atom types.  A wildcard asterisk can be used in place of or
+in conjunction with the *type* argument to specify a range of atom
+types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N.  A leading asterisk means all types from 1 to n
+(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+The specified *color* can be a single color which is any of the 140
+pre-defined colors (see below) or a color name defined by the
+dump_modify color option.  Or it can be two or more colors separated
+by a "/" character, e.g. red/green/blue.  In the former case, that
+color is assigned to all the specified atom types.  In the latter
+case, the list of colors are assigned in a round-robin fashion to each
+of the specified atom types.
+
+----------
+
+The *adiam* keyword can be used with the :doc:`dump image <dump_image>`
+command, when its atom diameter setting is *type*, to set the size
+that atoms of each type will be drawn in the image.  The specified
+*type* should be an integer from 1 to Ntypes.  As with the *acolor*
+keyword, a wildcard asterisk can be used as part of the *type*
+argument to specify a range of atom types.  The specified *diam* is
+the size in whatever distance :doc:`units <units>` the input script is
+using, e.g. Angstroms.
+
+----------
+
+The *amap* keyword can be used with the :doc:`dump image <dump_image>`
+command, with its *atom* keyword, when its atom setting is an
+atom-attribute, to setup a color map.  The color map is used to assign
+a specific RGB (red/green/blue) color value to an individual atom when
+it is drawn, based on the atom's attribute, which is a numeric value,
+e.g. its x-component of velocity if the atom-attribute "vx" was
+specified.
+
+The basic idea of a color map is that the atom-attribute will be
+within a range of values, and that range is associated with a series
+of colors (e.g. red, blue, green).  An atom's specific value (vx =
+-3.2) can then mapped to the series of colors (e.g. halfway between
+red and blue), and a specific color is determined via an interpolation
+procedure.
+
+There are many possible options for the color map, enabled by the
+*amap* keyword.  Here are the details.
+
+The *lo* and *hi* settings determine the range of values allowed for
+the atom attribute.  If numeric values are used for *lo* and/or *hi*,
+then values that are lower/higher than that value are set to the
+value.  I.e. the range is static.  If *lo* is specified as *min* or
+*hi* as *max* then the range is dynamic, and the lower and/or
+upper bound will be calculated each time an image is drawn, based
+on the set of atoms being visualized.
+
+The *style* setting is two letters, such as "ca".  The first letter is
+either "c" for continuous, "d" for discrete, or "s" for sequential.
+The second letter is either "a" for absolute, or "f" for fractional.
+
+A continuous color map is one in which the color changes continuously
+from value to value within the range.  A discrete color map is one in
+which discrete colors are assigned to sub-ranges of values within the
+range.  A sequential color map is one in which discrete colors are
+assigned to a sequence of sub-ranges of values covering the entire
+range.
+
+An absolute color map is one in which the values to which colors are
+assigned are specified explicitly as values within the range.  A
+fractional color map is one in which the values to which colors are
+assigned are specified as a fractional portion of the range.  For
+example if the range is from -10.0 to 10.0, and the color red is to be
+assigned to atoms with a value of 5.0, then for an absolute color map
+the number 5.0 would be used.  But for a fractional map, the number
+0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.
+
+The *delta* setting must be specified for all styles, but is only used
+for the sequential style; otherwise the value is ignored.  It
+specifies the bin size to use within the range for assigning
+consecutive colors to.  For example, if the range is from -10.0 to
+10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to
+the range.  The first will be from -10.0 <= color1 < -9.0, then second
+from -9.0 <= color2 < -8.0, etc.
+
+The *N* setting is how many entries follow.  The format of the entries
+depends on whether the color map style is continuous, discrete or
+sequential.  In all cases the *color* setting can be any of the 140
+pre-defined colors (see below) or a color name defined by the
+dump_modify color option.
+
+For continuous color maps, each entry has a *value* and a *color*\ .
+The *value* is either a number within the range of values or *min* or
+*max*\ .  The *value* of the first entry must be *min* and the *value*
+of the last entry must be *max*\ .  Any entries in between must have
+increasing values.  Note that numeric values can be specified either
+as absolute numbers or as fractions (0.0 to 1.0) of the range,
+depending on the "a" or "f" in the style setting for the color map.
+
+Here is how the entries are used to determine the color of an
+individual atom, given the value X of its atom attribute.  X will fall
+between 2 of the entry values.  The color of the atom is linearly
+interpolated (in each of the RGB values) between the 2 colors
+associated with those entries.  For example, if X = -5.0 and the 2
+surrounding entries are "red" at -10.0 and "blue" at 0.0, then the
+atom's color will be halfway between "red" and "blue", which happens
+to be "purple".
+
+For discrete color maps, each entry has a *lo* and *hi* value and a
+*color*\ .  The *lo* and *hi* settings are either numbers within the
+range of values or *lo* can be *min* or *hi* can be *max*\ .  The *lo*
+and *hi* settings of the last entry must be *min* and *max*\ .  Other
+entries can have any *lo* and *hi* values and the sub-ranges of
+different values can overlap.  Note that numeric *lo* and *hi* values
+can be specified either as absolute numbers or as fractions (0.0 to
+1.0) of the range, depending on the "a" or "f" in the style setting
+for the color map.
+
+Here is how the entries are used to determine the color of an
+individual atom, given the value X of its atom attribute.  The entries
+are scanned from first to last.  The first time that *lo* <= X <=
+*hi*, X is assigned the color associated with that entry.  You can
+think of the last entry as assigning a default color (since it will
+always be matched by X), and the earlier entries as colors that
+override the default.  Also note that no interpolation of a color RGB
+is done.  All atoms will be drawn with one of the colors in the list
+of entries.
+
+For sequential color maps, each entry has only a *color*\ .  Here is how
+the entries are used to determine the color of an individual atom,
+given the value X of its atom attribute.  The range is partitioned
+into N bins of width *binsize*\ .  Thus X will fall in a specific bin
+from 1 to N, say the Mth bin.  If it falls on a boundary between 2
+bins, it is considered to be in the higher of the 2 bins.  Each bin is
+assigned a color from the E entries.  If E < N, then the colors are
+repeated.  For example if 2 entries with colors red and green are
+specified, then the odd numbered bins will be red and the even bins
+green.  The color of the atom is the color of its bin.  Note that the
+sequential color map is really a shorthand way of defining a discrete
+color map without having to specify where all the bin boundaries are.
+
+Here is an example of using a sequential color map to color all the
+atoms in individual molecules with a different color.  See the
+examples/pour/in.pour.2d.molecule input script for an example of how
+this is used.
+
+.. code-block:: LAMMPS
+
+   variable        colors string &
+                   "red green blue yellow white &
+                   purple pink orange lime gray"
+   variable        mol atom mol%10
+   dump            1 all image 250 image.*.jpg v_mol type &
+                   zoom 1.6 adiam 1.5
+   dump_modify     1 pad 5 amap 0 10 sa 1 10 ${colors}
+
+In this case, 10 colors are defined, and molecule IDs are
+mapped to one of the colors, even if there are 1000s of molecules.
+
+----------
+
+The *backcolor* sets the background color of the images.  The color
+name can be any of the 140 pre-defined colors (see below) or a color
+name defined by the dump_modify color option.
+
+----------
+
+The *bcolor* keyword can be used with the :doc:`dump image <dump_image>`
+command, with its *bond* keyword, when its color setting is *type*, to
+set the color that bonds of each type will be drawn in the image.
+
+The specified *type* should be an integer from 1 to Nbondtypes = the
+number of bond types.  A wildcard asterisk can be used in place of or
+in conjunction with the *type* argument to specify a range of bond
+types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+number of bond types, then an asterisk with no numeric values means
+all types from 1 to N.  A leading asterisk means all types from 1 to n
+(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+The specified *color* can be a single color which is any of the 140
+pre-defined colors (see below) or a color name defined by the
+dump_modify color option.  Or it can be two or more colors separated
+by a "/" character, e.g. red/green/blue.  In the former case, that
+color is assigned to all the specified bond types.  In the latter
+case, the list of colors are assigned in a round-robin fashion to each
+of the specified bond types.
+
+----------
+
+The *bdiam* keyword can be used with the :doc:`dump image <dump_image>`
+command, with its *bond* keyword, when its diam setting is *type*, to
+set the diameter that bonds of each type will be drawn in the image.
+The specified *type* should be an integer from 1 to Nbondtypes.  As
+with the *bcolor* keyword, a wildcard asterisk can be used as part of
+the *type* argument to specify a range of bond types.  The specified
+*diam* is the size in whatever distance :doc:`units <units>` you are
+using, e.g. Angstroms.
+
+----------
+
+The *bitrate* keyword can be used with the :doc:`dump movie <dump_image>` command to define the size of the resulting
+movie file and its quality via setting how many kbits per second are
+to be used for the movie file. Higher bitrates require less
+compression and will result in higher quality movies.  The quality is
+also determined by the compression format and encoder.  The default
+setting is 2000 kbit/s, which will result in average quality with
+older compression formats.
+
+.. note::
+
+   Not all movie file formats supported by dump movie allow the
+   bitrate to be set.  If not, the setting is silently ignored.
+
+----------
+
+The *boxcolor* keyword sets the color of the simulation box drawn
+around the atoms in each image as well as the color of processor
+sub-domain boundaries.  See the "dump image box" command for how to
+specify that a box be drawn via the *box* keyword, and the sub-domain
+boundaries via the *subbox* keyword.  The color name can be any of the
+140 pre-defined colors (see below) or a color name defined by the
+dump_modify color option.
+
+----------
+
+The *color* keyword allows definition of a new color name, in addition
+to the 140-predefined colors (see below), and associates 3
+red/green/blue RGB values with that color name.  The color name can
+then be used with any other dump_modify keyword that takes a color
+name as a value.  The RGB values should each be floating point values
+between 0.0 and 1.0 inclusive.
+
+When a color name is converted to RGB values, the user-defined color
+names are searched first, then the 140 pre-defined color names.  This
+means you can also use the *color* keyword to overwrite one of the
+pre-defined color names with new RBG values.
+
+----------
+
+The *framerate* keyword can be used with the :doc:`dump movie <dump_image>` command to define the duration of the resulting
+movie file.  Movie files written by the dump *movie* command have a
+default frame rate of 24 frames per second and the images generated
+will be converted at that rate.  Thus a sequence of 1000 dump images
+will result in a movie of about 42 seconds.  To make a movie run
+longer you can either generate images more frequently or lower the
+frame rate.  To speed a movie up, you can do the inverse.  Using a
+frame rate higher than 24 is not recommended, as it will result in
+simply dropping the rendered images. It is more efficient to dump
+images less frequently.
+
+----------
+
+The *header* keyword toggles whether the dump file will include a header.
+Excluding a header will reduce the size of the dump file for fixes such as
+:doc:`fix pair/tracker <fix_pair_tracker>` which do not require the information
+typically written to the header.
+
+----------
+
+The COMPRESS package offers both GZ and Zstd compression variants of styles
+atom, custom, local, cfg, and xyz. When using these styles the compression
+level can be controlled by the :code:`compression_level` parameter. File names
+with these styles have to end in either :code:`.gz` or :code:`.zst`.
+
+GZ supports compression levels from -1 (default), 0 (no compression), and 1 to
+9. 9 being the best compression. The COMPRESS :code:`/gz` styles use 9 as
+default compression level.
 
 Zstd offers a wider range of compression levels, including negative
-levels that sacrifice compression for performance. 0 is the default,
-positive levels are 1 to 22, with 22 being the most expensive
+levels that sacrifice compression for performance. 0 is the
+default, positive levels are 1 to 22, with 22 being the most expensive
 compression. Zstd promises higher compression/decompression speeds for
 similar compression ratios. For more details see
 `http://facebook.github.io/zstd/`.
 
-In addition, Zstd compressed files can include a checksum of the
-entire contents. The Zstd enabled dump styles enable this feature by
-default and it can be disabled with the :code:`checksum` keyword.
+In addition, Zstd compressed files can have a checksum of the entire
+contents. The Zstd enabled dump styles enable this feature by default and it
+can be disabled with the :code:`checksum` parameter.
 
 ----------
 
 Restrictions
 """"""""""""
 
-Not all *dump_modify* options can be applied to all dump styles.
-Details are in the discussions of the individual options.
+*dump_modify sort* is not supported for dumps of groups containing
+more than 2 billion atoms.
 
 Related commands
 """"""""""""""""
@@ -841,7 +1026,6 @@ Default
 The option defaults are
 
 * append = no
-* balance = no
 * buffer = yes for dump styles *atom*, *custom*, *loca*, and *xyz*
 * element = "C" for every atom type
 * every = whatever it was set to via the :doc:`dump <dump>` command
@@ -864,7 +1048,100 @@ The option defaults are
 * units = no
 * unwrap = no
 
+* acolor = \* red/green/blue/yellow/aqua/cyan
+* adiam = \* 1.0
+* amap = min max cf 0.0 2 min blue max red
+* backcolor = black
+* bcolor = \* red/green/blue/yellow/aqua/cyan
+* bdiam = \* 0.5
+* bitrate = 2000
+* boxcolor = yellow
+* color = 140 color names are pre-defined as listed below
+* framerate = 24
+
 * compression_level = 9 (gz variants)
 * compression_level = 0 (zstd variants)
 * checksum = yes (zstd variants)
 
+----------
+
+These are the standard 109 element names that LAMMPS pre-defines for
+use with the :doc:`dump image <dump_image>` and dump_modify commands.
+
+* 1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne"
+* 11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca"
+* 21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn"
+* 31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr"
+* 41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn"
+* 51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd"
+* 61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb"
+* 71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg"
+* 81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th"
+* 91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm"
+* 101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt"
+
+----------
+
+These are the 140 colors that LAMMPS pre-defines for use with the
+:doc:`dump image <dump_image>` and dump_modify commands.  Additional
+colors can be defined with the dump_modify color command.  The 3
+numbers listed for each name are the RGB (red/green/blue) values.
+Divide each value by 255 to get the equivalent 0.0 to 1.0 value.
+
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| aliceblue = 240, 248, 255     | antiquewhite = 250, 235, 215         | aqua = 0, 255, 255              | aquamarine = 127, 255, 212     | azure = 240, 255, 255          |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| beige = 245, 245, 220         | bisque = 255, 228, 196               | black = 0, 0, 0                 | blanchedalmond = 255, 255, 205 | blue = 0, 0, 255               |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| blueviolet = 138, 43, 226     | brown = 165, 42, 42                  | burlywood = 222, 184, 135       | cadetblue = 95, 158, 160       | chartreuse = 127, 255, 0       |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| chocolate = 210, 105, 30      | coral = 255, 127, 80                 | cornflowerblue = 100, 149, 237  | cornsilk = 255, 248, 220       | crimson = 220, 20, 60          |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| cyan = 0, 255, 255            | darkblue = 0, 0, 139                 | darkcyan = 0, 139, 139          | darkgoldenrod = 184, 134, 11   | darkgray = 169, 169, 169       |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| darkgreen = 0, 100, 0         | darkkhaki = 189, 183, 107            | darkmagenta = 139, 0, 139       | darkolivegreen = 85, 107, 47   | darkorange = 255, 140, 0       |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| darkorchid = 153, 50, 204     | darkred = 139, 0, 0                  | darksalmon = 233, 150, 122      | darkseagreen = 143, 188, 143   | darkslateblue = 72, 61, 139    |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| darkslategray = 47, 79, 79    | darkturquoise = 0, 206, 209          | darkviolet = 148, 0, 211        | deeppink = 255, 20, 147        | deepskyblue = 0, 191, 255      |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| dimgray = 105, 105, 105       | dodgerblue = 30, 144, 255            | firebrick = 178, 34, 34         | floralwhite = 255, 250, 240    | forestgreen = 34, 139, 34      |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| fuchsia = 255, 0, 255         | gainsboro = 220, 220, 220            | ghostwhite = 248, 248, 255      | gold = 255, 215, 0             | goldenrod = 218, 165, 32       |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| gray = 128, 128, 128          | green = 0, 128, 0                    | greenyellow = 173, 255, 47      | honeydew = 240, 255, 240       | hotpink = 255, 105, 180        |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| indianred = 205, 92, 92       | indigo = 75, 0, 130                  | ivory = 255, 240, 240           | khaki = 240, 230, 140          | lavender = 230, 230, 250       |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| lavenderblush = 255, 240, 245 | lawngreen = 124, 252, 0              | lemonchiffon = 255, 250, 205    | lightblue = 173, 216, 230      | lightcoral = 240, 128, 128     |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| lightcyan = 224, 255, 255     | lightgoldenrodyellow = 250, 250, 210 | lightgreen = 144, 238, 144      | lightgrey = 211, 211, 211      | lightpink = 255, 182, 193      |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| lightsalmon = 255, 160, 122   | lightseagreen = 32, 178, 170         | lightskyblue = 135, 206, 250    | lightslategray = 119, 136, 153 | lightsteelblue = 176, 196, 222 |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| lightyellow = 255, 255, 224   | lime = 0, 255, 0                     | limegreen = 50, 205, 50         | linen = 250, 240, 230          | magenta = 255, 0, 255          |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| maroon = 128, 0, 0            | mediumaquamarine = 102, 205, 170     | mediumblue = 0, 0, 205          | mediumorchid = 186, 85, 211    | mediumpurple = 147, 112, 219   |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| mediumseagreen = 60, 179, 113 | mediumslateblue = 123, 104, 238      | mediumspringgreen = 0, 250, 154 | mediumturquoise = 72, 209, 204 | mediumvioletred = 199, 21, 133 |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| midnightblue = 25, 25, 112    | mintcream = 245, 255, 250            | mistyrose = 255, 228, 225       | moccasin = 255, 228, 181       | navajowhite = 255, 222, 173    |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| navy = 0, 0, 128              | oldlace = 253, 245, 230              | olive = 128, 128, 0             | olivedrab = 107, 142, 35       | orange = 255, 165, 0           |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| orangered = 255, 69, 0        | orchid = 218, 112, 214               | palegoldenrod = 238, 232, 170   | palegreen = 152, 251, 152      | paleturquoise = 175, 238, 238  |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| palevioletred = 219, 112, 147 | papayawhip = 255, 239, 213           | peachpuff = 255, 239, 213       | peru = 205, 133, 63            | pink = 255, 192, 203           |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| plum = 221, 160, 221          | powderblue = 176, 224, 230           | purple = 128, 0, 128            | red = 255, 0, 0                | rosybrown = 188, 143, 143      |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| royalblue = 65, 105, 225      | saddlebrown = 139, 69, 19            | salmon = 250, 128, 114          | sandybrown = 244, 164, 96      | seagreen = 46, 139, 87         |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| seashell = 255, 245, 238      | sienna = 160, 82, 45                 | silver = 192, 192, 192          | skyblue = 135, 206, 235        | slateblue = 106, 90, 205       |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| slategray = 112, 128, 144     | snow = 255, 250, 250                 | springgreen = 0, 255, 127       | steelblue = 70, 130, 180       | tan = 210, 180, 140            |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| teal = 0, 128, 128            | thistle = 216, 191, 216              | tomato = 253, 99, 71            | turquoise = 64, 224, 208       | violet = 238, 130, 238         |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+
+| wheat = 245, 222, 179         | white = 255, 255, 255                | whitesmoke = 245, 245, 245      | yellow = 255, 255, 0           | yellowgreen = 154, 205, 50     |
++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+

doc/src/dynamical_matrix.rst

@@ -1,11 +1,8 @@
 .. index:: dynamical_matrix
-.. index:: dynamical_matrix/kk
 
 dynamical_matrix command
 ========================
 
-Accelerator Variants: dynamical_matrix/kk
-
 Syntax
 """"""
 
@@ -59,12 +56,6 @@ If the style eskm is selected, the dynamical matrix will be in units of
 inverse squared femtoseconds. These units will then conveniently leave
 frequencies in THz.
 
-----------
-
-.. include:: accel_styles.rst
-
-----------
-
 Restrictions
 """"""""""""
 

doc/src/fix.rst

@@ -166,7 +166,6 @@ page are followed by one or more of (g,i,k,o,t) to indicate which
 accelerated styles exist.
 
 * :doc:`accelerate/cos <fix_accelerate_cos>` - apply cosine-shaped acceleration to atoms
-* :doc:`acks2/reaxff <fix_acks2_reaxff>` - apply ACKS2 charge equilibration
 * :doc:`adapt <fix_adapt>` - change a simulation parameter over time
 * :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
 * :doc:`addforce <fix_addforce>` - add a force to each atom
@@ -247,7 +246,6 @@ accelerated styles exist.
 * :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
 * :doc:`mdi/engine <fix_mdi_engine>` - connect LAMMPS to external programs via the MolSSI Driver Interface (MDI)
 * :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
-* :doc:`mol/swap <fix_mol_swap>` - Monte Carlo atom type swapping with a molecule
 * :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
 * :doc:`momentum/chunk <fix_momentum>` - zero the linear and/or angular momentum of a chunk of atoms
 * :doc:`move <fix_move>` - move atoms in a prescribed fashion
@@ -271,8 +269,7 @@ accelerated styles exist.
 * :doc:`npt/eff <fix_nh_eff>` - NPT for  nuclei and electrons in the electron force field model
 * :doc:`npt/sphere <fix_npt_sphere>` - NPT for spherical particles
 * :doc:`npt/uef <fix_nh_uef>` - NPT style time integration with diagonal flow
-* :doc:`numdiff <fix_numdiff>` - numerically approximate atomic forces using finite energy differences
-* :doc:`numdiff/virial <fix_numdiff_virial>` - numerically approximate virial stress tensor using finite energy differences
+* :doc:`numdiff <fix_numdiff>` - compute derivatives of per-atom data from finite differences
 * :doc:`nve <fix_nve>` - constant NVE time integration
 * :doc:`nve/asphere <fix_nve_asphere>` - NVE for aspherical particles
 * :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` - NVE for aspherical particles without forces

doc/src/fix_acks2_reaxff.rst

@@ -1,118 +0,0 @@
-.. index:: fix acks2/reaxff
-.. index:: fix acks2/reaxff/kk
-
-fix acks2/reaxff command
-========================
-
-Accelerator Variants: *acks2/reaxff/kk*
-
-Syntax
-""""""
-
-.. parsed-literal::
-
-   fix ID group-ID acks2/reaxff Nevery cutlo cuthi tolerance params args
-
-* ID, group-ID are documented in :doc:`fix <fix>` command
-* acks2/reaxff = style name of this fix command
-* Nevery = perform ACKS2 every this many steps
-* cutlo,cuthi = lo and hi cutoff for Taper radius
-* tolerance = precision to which charges will be equilibrated
-* params = reaxff or a filename
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff
-   fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 param.acks2
-
-Description
-"""""""""""
-
-Perform the atom-condensed Kohn-Sham DFT to second order (ACKS2) charge
-equilibration method as described in :ref:`(Verstraelen) <Verstraelen>`.
-ACKS2 impedes unphysical long-range charge transfer sometimes seen with
-QEq (e.g. for dissociation of molecules), at increased computational
-cost.  It is typically used in conjunction with the ReaxFF force field
-model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
-command, but it can be used with any potential in LAMMPS, so long as it
-defines and uses charges on each atom.  For more technical details about
-the charge equilibration performed by fix acks2/reaxff, see the
-:ref:`(O'Hearn) <O'Hearn>` paper.
-
-The ACKS2 method minimizes the electrostatic energy of the system by
-adjusting the partial charge on individual atoms based on interactions
-with their neighbors. It requires some parameters for each atom type.
-If the *params* setting above is the word "reaxff", then these are
-extracted from the :doc:`pair_style reaxff <pair_reaxff>` command and
-the ReaxFF force field file it reads in.  If a file name is specified
-for *params*\ , then the parameters are taken from the specified file
-and the file must contain one line for each atom type.  The latter form
-must be used when performing QeQ with a non-ReaxFF potential.  The lines
-should be formatted as follows:
-
-.. parsed-literal::
-
-   bond_softness
-   itype chi eta gamma bcut
-
-where the first line is the global parameter *bond_softness*. The
-remaining 1 to Ntypes lines include *itype*, the atom type from 1 to
-Ntypes, *chi*, the electronegativity in eV, *eta*, the self-Coulomb
-potential in eV, *gamma*, the valence orbital exponent, and *bcut*, the
-bond cutoff distance.  Note that these 4 quantities are also in the
-ReaxFF potential file, except that eta is defined here as twice the eta
-value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
-of this fix are hard-coded to be A, eV, and electronic charge.
-
-**Restart, fix_modify, output, run start/stop, minimize info:**
-
-No information about this fix is written to :doc:`binary restart files
-<restart>`.  No global scalar or vector or per-atom quantities are
-stored by this fix for access by various :doc:`output commands
-<Howto_output>`.  No parameter of this fix can be used with the
-*start/stop* keywords of the :doc:`run <run>` command.
-
-This fix is invoked during :doc:`energy minimization <minimize>`.
-
-----------
-
-.. include:: accel_styles.rst
-
-----------
-
-Restrictions
-""""""""""""
-
-This fix is part of the REAXFF package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package
-<Build_package>` doc page for more info.
-
-This fix does not correctly handle interactions involving multiple
-periodic images of the same atom. Hence, it should not be used for
-periodic cell dimensions less than 10 angstroms.
-
-This fix may be used in combination with :doc:`fix efield <fix_efield>`
-and will apply the external electric field during charge equilibration,
-but there may be only one fix efield instance used, it may only use a
-constant electric field, and the electric field vector may only have
-components in non-periodic directions.
-
-Related commands
-""""""""""""""""
-
-:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`
-
-**Default:** none
-
-----------
-
-.. _O'Hearn:
-
-**(O'Hearn)** O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1-C22 (2020).
-
-.. _Verstraelen:
-
-**(Verstraelen)** Verstraelen, Ayers, Speybroeck, Waroquier, J. Chem. Phys. 138, 074108 (2013).

doc/src/fix_addtorque.rst

@@ -99,7 +99,7 @@ invoked by the :doc:`minimize <minimize>` command.
 Restrictions
 """"""""""""
 
-This fix is part of the EXTRA-FIX package.  It is only enabled if
+This fix is part of the MISC package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 

doc/src/fix_atom_swap.rst

@@ -73,51 +73,51 @@ is the same after the swap as it was before the swap, even though the
 atom masses have changed.
 
 The *semi-grand* keyword can be set to *yes* to switch to the
-semi-grand canonical ensemble as discussed in :ref:`(Sadigh)
-<Sadigh>`. This means that the total number of each particle type does
-not need to be conserved. The default is *no*, which means that the
-only kind of swap allowed exchanges an atom of one type with an atom
-of a different given type. In other words, the relative mole fractions
-of the swapped atoms remains constant. Whereas in the semi-grand
-canonical ensemble, the composition of the system can change. Note
-that when using *semi-grand*, atoms in the fix group whose type is not
-listed in the *types* keyword are ineligible for attempted
-conversion. An attempt is made to switch the selected atom (if
-eligible) to one of the other listed types with equal
-probability. Acceptance of each attempt depends upon the Metropolis
-criterion.
+semi-grand canonical ensemble as discussed in :ref:`(Sadigh) <Sadigh>`. This
+means that the total number of each particle type does not need to be
+conserved. The default is *no*, which means that the only kind of swap
+allowed exchanges an atom of one type with an atom of a different
+given type. In other words, the relative mole fractions of the swapped
+atoms remains constant. Whereas in the semi-grand canonical ensemble,
+the composition of the system can change. Note that when using
+*semi-grand*, atoms in the fix group whose type is not listed
+in the *types* keyword are ineligible for attempted
+conversion. An attempt is made to switch
+the selected atom (if eligible) to one of the other listed types
+with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.
 
-The *mu* keyword allows users to specify chemical potentials. This is
-required and allowed only when using *semi-grand*\ .  All chemical
-potentials are absolute, so there is one for each swap type listed
-following the *types* keyword.  In semi-grand canonical ensemble
-simulations the chemical composition of the system is controlled by
-the difference in these values. So shifting all values by a constant
-amount will have no effect on the simulation.
+The *mu* keyword allows users to specify chemical
+potentials. This is required and allowed only when using *semi-grand*\ .
+All chemical potentials are absolute, so there is one for
+each swap type listed following the *types* keyword.
+In semi-grand canonical ensemble simulations the chemical composition
+of the system is controlled by the difference in these values. So
+shifting all values by a constant amount will have no effect
+on the simulation.
 
 This command may optionally use the *region* keyword to define swap
 volume.  The specified region must have been previously defined with a
-:doc:`region <region>` command.  It must be defined with side = *in*\
-.  Swap attempts occur only between atoms that are both within the
+:doc:`region <region>` command.  It must be defined with side = *in*\ .
+Swap attempts occur only between atoms that are both within the
 specified region. Swaps are not otherwise attempted.
 
 You should ensure you do not swap atoms belonging to a molecule, or
-LAMMPS will eventually generate an error when it tries to find those
-atoms.  LAMMPS will warn you if any of the atoms eligible for swapping
-have a non-zero molecule ID, but does not check for this at the time of
+LAMMPS will soon generate an error when it tries to find those atoms.
+LAMMPS will warn you if any of the atoms eligible for swapping have a
+non-zero molecule ID, but does not check for this at the time of
 swapping.
 
 If not using *semi-grand* this fix checks to ensure all atoms of the
 given types have the same atomic charge. LAMMPS does not enforce this
-in general, but it is needed for this fix to simplify the swapping
-procedure. Successful swaps will swap the atom type and charge of the
-swapped atoms. Conversely, when using *semi-grand*, it is assumed that
-all the atom types involved in switches have the same
-charge. Otherwise, charge would not be conserved. As a consequence, no
-checks on atomic charges are performed, and successful switches update
-the atom type but not the atom charge. While it is possible to use
-*semi-grand* with groups of atoms that have different charges, these
-charges will not be changed when the atom types change.
+in general, but it is needed for this fix to simplify the
+swapping procedure. Successful swaps will swap the atom type and charge
+of the swapped atoms. Conversely, when using *semi-grand*, it is assumed that all the atom
+types involved in switches have the same charge. Otherwise, charge
+would not be conserved. As a consequence, no checks on atomic charges are
+performed, and successful switches update the atom type but not the
+atom charge. While it is possible to use *semi-grand* with groups of
+atoms that have different charges, these charges will not be changed when the
+atom types change.
 
 Since this fix computes total potential energies before and after
 proposed swaps, so even complicated potential energy calculations are
@@ -133,24 +133,23 @@ OK, including the following:
 Some fixes have an associated potential energy. Examples of such fixes
 include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
 :doc:`addforce <fix_addforce>`, :doc:`langevin <fix_langevin>`,
-:doc:`restrain <fix_restrain>`, :doc:`temp/berendsen
-<fix_temp_berendsen>`, :doc:`temp/rescale <fix_temp_rescale>`, and
-:doc:`wall fixes <fix_wall>`.  For that energy to be included in the
-total potential energy of the system (the quantity used when
-performing GCMC moves), you MUST enable the :doc:`fix_modify
-<fix_modify>` *energy* option for that fix.  The doc pages for
-individual :doc:`fix <fix>` commands specify if this should be done.
+:doc:`restrain <fix_restrain>`, :doc:`temp/berendsen <fix_temp_berendsen>`,
+:doc:`temp/rescale <fix_temp_rescale>`, and :doc:`wall fixes <fix_wall>`.
+For that energy to be included in the total potential energy of the
+system (the quantity used when performing GCMC moves),
+you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for
+that fix.  The doc pages for individual :doc:`fix <fix>` commands
+specify if this should be done.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the fix to :doc:`binary restart files
-<restart>`.  This includes information about the random number
-generator seed, the next timestep for MC exchanges, the number of
-exchange attempts and successes etc.  See the :doc:`read_restart
-<read_restart>` command for info on how to re-specify a fix in an
-input script that reads a restart file, so that the operation of the
-fix continues in an uninterrupted fashion.
+This fix writes the state of the fix to :doc:`binary restart files <restart>`.  This includes information about the random
+number generator seed, the next timestep for MC exchanges, the number
+of exchange attempts and successes etc.  See
+the :doc:`read_restart <read_restart>` command for info on how to
+re-specify a fix in an input script that reads a restart file, so that
+the operation of the fix continues in an uninterrupted fashion.
 
 .. note::
 
@@ -166,13 +165,12 @@ by various :doc:`output commands <Howto_output>`.  The vector values are
 the following global cumulative quantities:
 
 * 1 = swap attempts
-* 2 = swap accepts
+* 2 = swap successes
 
 The vector values calculated by this fix are "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during
-:doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
@@ -186,8 +184,7 @@ Related commands
 
 :doc:`fix nvt <fix_nh>`, :doc:`neighbor <neighbor>`,
 :doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
-:doc:`delete_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`,
-:doc:`fix mol/swap <fix_mol_swap>`
+:doc:`delete_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`
 
 Default
 """""""

doc/src/fix_charge_regulation.rst

@@ -20,13 +20,13 @@ Syntax
 
   .. parsed-literal::
 
-     keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *rxd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
+     keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
      *pH* value = pH of the solution (can be specified as an equal-style variable)
-     *pKa* value = acid dissociation constant (in the -log10 representation)
-     *pKb* value = base dissociation constant (in the -log10 representation)
-     *pIp* value = activity (effective concentration) of free cations (in the -log10 representation)
-     *pIm* value = activity (effective concentration) of free anions (in the -log10 representation)
-     *pKs* value = solvent self-dissociation constant (in the -log10 representation)
+     *pKa* value = acid dissociation constant
+     *pKb* value = base dissociation constant
+     *pIp* value = chemical potential of free cations
+     *pIm* value = chemical potential of free anions
+     *pKs* value = solution self-dissociation constant
      *acid_type* = atom type of acid groups
      *base_type*  = atom type of base groups
      *lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers)
@@ -34,7 +34,7 @@ Syntax
      *tempfixid* value = fix ID of temperature thermostat
      *nevery* value = invoke this fix every nevery steps
      *nmc* value = number of charge regulation MC moves to attempt every nevery steps
-     *rxd* value = cutoff distance for acid/base reaction
+     *xrd* value = cutoff distance for acid/base reaction
      *seed* value = random # seed (positive integer)
      *tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0")
      *group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups.
@@ -47,7 +47,7 @@ Examples
 """"""""
 .. code-block:: LAMMPS
 
-    fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5.0 pKb 6.0 pH 7.0 pIp 3.0 pIm 3.0 nevery 200 nmc 200 seed 123 tempfixid fT
+    fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT
 
     fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0
 
@@ -92,11 +92,7 @@ where the fix attempts to charge :math:`\mathrm{A}` (discharge
 :math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and
 insert (delete) a proton (atom type 2). Besides, the fix implements
 self-ionization reaction of water :math:`\emptyset \rightleftharpoons
-\mathrm{H}^++\mathrm{OH}^-`.
-
-
-
-However, this approach is highly
+\mathrm{H}^++\mathrm{OH}^-`.  However, this approach is highly
 inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of
 both protons and hydroxyl ions is low, resulting in a relatively low
 acceptance rate of MC moves.
@@ -106,31 +102,24 @@ reactions, which can be easily achieved via
 
 .. code-block:: LAMMPS
 
-    fix acid_reaction2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
+    fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
 
-where particles of atom type 4 and 5 are the salt cations and anions, both at activity (effective concentration) of :math:`10^{-2}` mol/l, see :ref:`(Curk1) <Curk1>` and
+where particles of atom type 4 and 5 are the salt cations and anions,
+both at chemical potential pI=2.0, see :ref:`(Curk1) <Curk1>` and
 :ref:`(Landsgesell) <Landsgesell>` for more details.
 
-We could have simultaneously added a base ionization reaction (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
+
+ Similarly, we could have simultaneously added a base ionization reaction
+ (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
 
 .. code-block:: LAMMPS
 
-    fix acid_base_reaction all charge/regulation 2 3 acid_type 1 base_type 6 pH 7.0 pKa 5.0 pKb 6.0 pIp 7.0 pIm 7.0
+    fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0
 
 where the fix will attempt to charge :math:`\mathrm{B}` (discharge
 :math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and
-insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3.
-
-
-Dissociated ions and salt ions can be combined into a single particle type, which reduces the number of necessary MC moves and increases sampling performance, see :ref:`(Curk1) <Curk1>`. The :math:`\mathrm{H}^+` and monovalent salt cation (:math:`\mathrm{S}^+`) are combined into a single particle type, :math:`\mathrm{X}^+ = \{\mathrm{H}^+, \mathrm{S}^+\}`. In this case "pIp" refers to the effective concentration of the combined cation type :math:`\mathrm{X}^+` and its value is determined by :math:`10^{-\mathrm{pIp}} = 10^{-\mathrm{pH}} + 10^{-\mathrm{pSp}}`, where :math:`10^{-\mathrm{pSp}}` is the effective concentration of salt cations. For example, at pH=7 and pSp=6 we would find pIp~5.958 and the command that performs reactions with combined ions could read,
-
-.. code-block:: LAMMPS
-
-    fix acid_reaction_combined all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 5.958 pIm 5.958
-
-
-
-If neither the acid or the base type is specified, for example,
+insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3.  If
+neither the acid or the base type is specified, for example,
 
 .. code-block:: LAMMPS
 
@@ -138,11 +127,11 @@ If neither the acid or the base type is specified, for example,
 
 the fix simply inserts or deletes an ion pair of a free cation (atom
 type 4) and a free anion (atom type 5) as done in a conventional
-grand-canonical MC simulation. Multivalent ions can be inserted (deleted) by using the *onlysalt* keyword.
+grand-canonical MC simulation.
 
 
 The fix is compatible with LAMMPS sub-packages such as *molecule* or
-*rigid*. The acid and base particles can be part of larger
+*rigid*. That said, the acid and base particles can be part of larger
 molecules or rigid bodies. Free ions that are inserted to or deleted
 from the system must be defined as single particles (no bonded
 interactions allowed) and cannot be part of larger molecules or rigid
@@ -164,14 +153,14 @@ Langevin thermostat:
     fix fT all langevin 1.0 1.0 1.0 123
     fix_modify fT temp dtemp
 
-The units of  pH, pKa, pKb, pIp, pIm are considered to be in the standard -log10
+The chemical potential units (e.g. pH) are in the standard log10
 representation assuming reference concentration :math:`\rho_0 =
-\mathrm{mol}/\mathrm{l}`.  For example, in the dilute
-ideal solution limit, the concentration of free cations will be
-:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. To perform the internal unit
-conversion, the the value of the LAMMPS unit length must be
-specified in nanometers via *lunit_nm*. The default value is set to the Bjerrum length in water
-at room temperature (0.71 nm), *lunit_nm* = 0.71.
+\mathrm{mol}/\mathrm{l}`.  Therefore, to perform the internal unit
+conversion, the length (in nanometers) of the LAMMPS unit length must be
+specified via *lunit_nm* (default is set to the Bjerrum length in water
+at room temperature *lunit_nm* = 0.71nm). For example, in the dilute
+ideal solution limit, the concentration of free ions will be
+:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`.
 
 The temperature used in MC acceptance probability is set by *temp*. This
 temperature should be the same as the temperature set by the molecular
@@ -182,10 +171,10 @@ thermostat fix-ID is *fT*. The inserted particles attain a random
 velocity corresponding to the specified temperature. Using *tempfixid*
 overrides any fixed temperature set by *temp*.
 
-The *rxd* keyword can be used to restrict the inserted/deleted
+The *xrd* keyword can be used to restrict the inserted/deleted
 counterions to a specific radial distance from an acid or base particle
 that is currently participating in a reaction. This can be used to
-simulate more realist reaction dynamics. If *rxd* = 0 or *rxd* > *L* /
+simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* /
 2, where *L* is the smallest box dimension, the radial restriction is
 automatically turned off and free ion can be inserted or deleted
 anywhere in the simulation box.
@@ -269,18 +258,18 @@ Default
 
 pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0;
 acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery =
-100; nmc = 100; rxd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
+100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
 [1/3, 1/3, 1/3], group-ID = all
 
 ----------
 
 .. _Curk1:
 
-**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Accelerated simulation method for charge regulation effects", JCP 156 (2022).
+**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Coarse-grained simulation of charge regulation using LAMMPS", preprint (2021).
 
 .. _Curk2:
 
-**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL 126 (2021)
+**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL (2021)
 
 .. _Landsgesell:
 

doc/src/fix_dt_reset.rst

@@ -78,20 +78,13 @@ outer loop (largest) timestep, which is the same timestep that the
 
 Note that the cumulative simulation time (in time units), which
 accounts for changes in the timestep size as a simulation proceeds,
-can be accessed by the :doc:`thermo_style time <thermo_style>`
-keyword.
-
-Also note that the :doc:`dump_modify every/time <dump_modify>` option
-allows dump files to be written at intervals specified by simulation
-time, rather than by timesteps.  Simulation time is in time units;
-see the :doc:`units <units>` doc page for details.
+can be accessed by the :doc:`thermo_style time <thermo_style>` keyword.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files
-<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
-relevant to this fix.
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+are relevant to this fix.
 
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar stores the last
@@ -100,8 +93,7 @@ timestep on which the timestep was reset to a new value.
 The scalar value calculated by this fix is "intensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during
-:doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
@@ -110,7 +102,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`timestep <timestep>`, :doc:`dump_modify every/time <dump_modify>`
+:doc:`timestep <timestep>`
 
 Default
 """""""