whitespace

.github/release_steps.md

@@ -104,8 +104,8 @@ with a future release) from the `lammps-static` folder.
 rm -rf release-packages
 mkdir release-packages
 cd release-packages
-wget https://download.lammps.org/static/fedora41_musl_mingw.sif
-apptainer shell fedora41_musl_mingw.sif
+wget https://download.lammps.org/static/fedora41_musl.sif
+apptainer shell fedora41_musl.sif
 git clone -b release --depth 10 https://github.com/lammps/lammps.git lammps-release
 cmake -S lammps-release/cmake -B build-release -G Ninja -D CMAKE_INSTALL_PREFIX=$PWD/lammps-static -D CMAKE_TOOLCHAIN_FILE=/usr/musl/share/cmake/linux-musl.cmake -C lammps-release/cmake/presets/most.cmake -C lammps-release/cmake/presets/kokkos-openmp.cmake -D DOWNLOAD_POTENTIALS=OFF -D BUILD_MPI=OFF -D BUILD_TESTING=OFF -D CMAKE_BUILD_TYPE=Release -D PKG_ATC=ON -D PKG_AWPMD=ON -D PKG_MANIFOLD=ON -D PKG_MESONT=ON -D PKG_MGPT=ON -D PKG_ML-PACE=ON -D PKG_ML-RANN=ON -D PKG_MOLFILE=ON -D PKG_PTM=ON -D PKG_QTB=ON -D PKG_SMTBQ=ON
 cmake --build build-release --target all
@@ -204,7 +204,7 @@ cd ..
 rm -r release-packages
 ```
 
-#### Build Multi-arch App-bundle with GUI for macOS
+#### Build Multi-arch App-bundle for macOS
 
 Building app-bundles for macOS is not as easily automated and portable
 as some of the other steps.  It requires a machine actually running
@@ -251,7 +251,7 @@ attached to the GitHub release page.
 
 We are currently building the application images on macOS 12 (aka Monterey).
 
-#### Build Linux x86_64 binary tarball with GUI on Ubuntu 20.04LTS
+#### Build Linux x86_64 binary tarball on Ubuntu 20.04LTS
 
 While the flatpak Linux version uses portable runtime libraries provided
 by the flatpak environment, we also build regular Linux executables that

.github/workflows/check-cpp23.yml

@@ -1,4 +1,4 @@
-# GitHub action to build LAMMPS on Linux with gcc or clang and C++23
+# GitHub action to build LAMMPS on Linux with gcc and C++23
 name: "Check for C++23 Compatibility"
 
 on:
@@ -11,19 +11,11 @@ on:
 
   workflow_dispatch:
 
-concurrency:
-  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: ${{github.event_name == 'pull_request'}}
-
 jobs:
   build:
     name: Build with C++23 support enabled
     if: ${{ github.repository == 'lammps/lammps' }}
     runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 2
-      matrix:
-        idx: [ gcc, clang ]
     env:
       CCACHE_DIR: ${{ github.workspace }}/.ccache
 
@@ -37,11 +29,8 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get install -y ccache \
-                                clang \
-                                libcurl4-openssl-dev \
                                 libeigen3-dev \
-                                libfftw3-dev \
-                                libomp-dev \
+                                libcurl4-openssl-dev \
                                 mold \
                                 mpi-default-bin \
                                 mpi-default-dev \
@@ -69,14 +58,14 @@ jobs:
         cmake -S cmake -B build \
               -C cmake/presets/most.cmake \
               -C cmake/presets/kokkos-openmp.cmake \
-              -C cmake/presets/${{ matrix.idx }}.cmake \
               -D CMAKE_CXX_STANDARD=23 \
+              -D CMAKE_CXX_COMPILER=g++ \
+              -D CMAKE_C_COMPILER=gcc \
               -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
               -D CMAKE_C_COMPILER_LAUNCHER=ccache \
               -D CMAKE_BUILD_TYPE=Debug \
               -D CMAKE_CXX_FLAGS_DEBUG="-Og -g" \
               -D DOWNLOAD_POTENTIALS=off \
-              -D FFT=KISS \
               -D BUILD_MPI=on \
               -D BUILD_SHARED_LIBS=on \
               -D BUILD_TOOLS=off \

cmake/CMakeLists.txt

@@ -7,10 +7,6 @@ if(CMAKE_VERSION VERSION_LESS 3.20)
   message(WARNING "LAMMPS is planning to require at least CMake version 3.20 by Summer 2025. Please upgrade!")
 endif()
 ########################################
-# initialize version variables with project command
-if(POLICY CMP0048)
-  cmake_policy(SET CMP0048 NEW)
-endif()
 # set policy to silence warnings about ignoring <PackageName>_ROOT but use it
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
@@ -31,10 +27,7 @@ endif()
 
 ########################################
 
-project(lammps
-        DESCRIPTION "The LAMMPS Molecular Dynamics Simulator"
-        HOMEPAGE_URL "https://www.lammps.org"
-        LANGUAGES CXX C)
+project(lammps CXX)
 set(SOVERSION 0)
 get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
 
@@ -138,9 +131,7 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
 endif()
 
 # silence nvcc warnings
-if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT
-    ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
-    OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")))
+if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
 endif()
 
@@ -203,10 +194,6 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
   set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
 endif()
 
-# do not include the (obsolete) MPI C++ bindings which makes for leaner object files
-# and avoids namespace conflicts. Put this early to increase its visbility.
-set(MPI_CXX_SKIP_MPICXX TRUE CACHE BOOL "Skip MPI C++ Bindings" FORCE)
-
 ########################################################################
 # User input options                                                   #
 ########################################################################
@@ -390,6 +377,7 @@ if(PKG_ADIOS)
   # The search for ADIOS2 must come before MPI because
   # it includes its own MPI search with the latest FindMPI.cmake
   # script that defines the MPI::MPI_C target
+  enable_language(C)
   find_package(ADIOS2 REQUIRED)
   if(BUILD_MPI)
     if(NOT ADIOS2_HAVE_MPI)
@@ -404,18 +392,21 @@ if(PKG_ADIOS)
 endif()
 
 if(NOT CMAKE_CROSSCOMPILING)
-  find_package(MPI QUIET COMPONENTS CXX)
+  find_package(MPI QUIET)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()
   option(BUILD_MPI "Build MPI version" OFF)
 endif()
 
 if(BUILD_MPI)
+  # do not include the (obsolete) MPI C++ bindings which makes
+  # for leaner object files and avoids namespace conflicts
+  set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
     include(MPI4WIN)
   else()
-    find_package(MPI REQUIRED COMPONENTS CXX)
+    find_package(MPI REQUIRED)
     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)
@@ -542,6 +533,7 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUA
 endif()
 
 if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR PKG_RHEO OR BUILD_TOOLS)
+  enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
     find_package(BLAS)

cmake/Modules/LAMMPSInterfacePlugin.cmake

@@ -62,9 +62,6 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
 endif()
 set(CMAKE_POSITION_INDEPENDENT_CODE TRUE)
 
-# skip over obsolete MPI-2 C++ bindings
-set(MPI_CXX_SKIP_MPICXX TRUE)
-
 #######
 # helper functions from LAMMPSUtils.cmake
 function(validate_option name values)
@@ -131,7 +128,8 @@ endif()
 ################################################################################
 # MPI configuration
 if(NOT CMAKE_CROSSCOMPILING)
-  find_package(MPI QUIET COMPONENTS CXX)
+  set(MPI_CXX_SKIP_MPICXX TRUE)
+  find_package(MPI QUIET)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()
   option(BUILD_MPI "Build MPI version" OFF)
@@ -143,38 +141,78 @@ if(BUILD_MPI)
   set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
-    message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
-    set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
-    set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
-    mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-    mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+    # Download and configure MinGW compatible MPICH development files for Windows
+    option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
+    if(USE_MSMPI)
+      message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
+      set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
+      set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
+      mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+      mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
 
-    include(ExternalProject)
-    if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-      ExternalProject_Add(mpi4win_build
-        URL     ${MPICH2_WIN64_DEVEL_URL}
-        URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
-        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-        BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
+      include(ExternalProject)
+      if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+        ExternalProject_Add(mpi4win_build
+          URL     ${MPICH2_WIN64_DEVEL_URL}
+          URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
+      else()
+        message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
+      endif()
+
+      ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+      file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+      add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+      set_target_properties(MPI::MPI_CXX PROPERTIES
+        IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
+        INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+        INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+      # set variables for status reporting at the end of CMake run
+      set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+      set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
     else()
-      message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
+      # Download and configure custom MPICH files for Windows
+      message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
+      set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
+      set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
+      mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+      mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+
+      include(ExternalProject)
+      if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+        ExternalProject_Add(mpi4win_build
+          URL     ${MPICH2_WIN64_DEVEL_URL}
+          URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+      else()
+        ExternalProject_Add(mpi4win_build
+          URL     ${MPICH2_WIN32_DEVEL_URL}
+          URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
+          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+      endif()
+
+      ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+      file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+      add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+      set_target_properties(MPI::MPI_CXX PROPERTIES
+        IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
+        INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+        INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+      # set variables for status reporting at the end of CMake run
+      set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+      set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
     endif()
-
-    ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-    file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-    add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-    set_target_properties(MPI::MPI_CXX PROPERTIES
-      IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
-      INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
-      INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
-    add_dependencies(MPI::MPI_CXX mpi4win_build)
-
-    # set variables for status reporting at the end of CMake run
-    set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
-    set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
-    set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
   else()
-    find_package(MPI REQUIRED COMPONENTS CXX)
+    find_package(MPI REQUIRED)
     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 INTERFACE -DLAMMPS_LONGLONG_TO_LONG)

cmake/Modules/LAMMPSUtils.cmake

@@ -75,25 +75,13 @@ function(get_lammps_version version_header variable)
     list(FIND MONTHS "${month}" month)
     string(LENGTH ${day} day_length)
     string(LENGTH ${month} month_length)
-    # no leading zero needed for new version string with dots
-    # if(day_length EQUAL 1)
-    #   set(day "0${day}")
-    # endif()
-    # if(month_length EQUAL 1)
-    #   set(month "0${month}")
-    #endif()
-    file(STRINGS ${version_header} line REGEX LAMMPS_UPDATE)
-    string(REGEX REPLACE "#define LAMMPS_UPDATE \"Update ([0-9]+)\"" "\\1" tweak "${line}")
-    if (line MATCHES "#define LAMMPS_UPDATE \"(Maintenance|Development)\"")
-      set(tweak "99")
+    if(day_length EQUAL 1)
+        set(day "0${day}")
     endif()
-    if(NOT tweak)
-      set(tweak "0")
+    if(month_length EQUAL 1)
+        set(month "0${month}")
     endif()
-    # new version string with dots
-    set(${variable} "${year}.${month}.${day}.${tweak}" PARENT_SCOPE)
-    # old version string without dots
-    # set(${variable} "${year}${month}${day}" PARENT_SCOPE)
+    set(${variable} "${year}${month}${day}" PARENT_SCOPE)
 endfunction()
 
 function(check_for_autogen_files source_dir)

cmake/Modules/MPI4WIN.cmake

@@ -1,31 +1,74 @@
-# set-up MS-MPI library for Windows with MinGW compatibility
-message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
-set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
-set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
-mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+# Download and configure MinGW compatible MPICH development files for Windows
+option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
 
-include(ExternalProject)
-if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-  ExternalProject_Add(mpi4win_build
-    URL     ${MPICH2_WIN64_DEVEL_URL}
-    URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
-    CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-    BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
+if(USE_MSMPI)
+  message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
+  set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
+  set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
+  mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+  mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+
+  include(ExternalProject)
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    ExternalProject_Add(mpi4win_build
+      URL     ${MPICH2_WIN64_DEVEL_URL}
+      URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
+  else()
+    message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
+  endif()
+
+  ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+  file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+  add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+  set_target_properties(MPI::MPI_CXX PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+    INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+  add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+  # set variables for status reporting at the end of CMake run
+  set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+  set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+  set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
 else()
-  message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
+  message(STATUS "Downloading and configuring MPICH2-1.4.1 for Windows cross-compilation")
+  set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
+  set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
+  set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
+  set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
+  mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+  mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
+  mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+  mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
+
+  include(ExternalProject)
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    ExternalProject_Add(mpi4win_build
+      URL     ${MPICH2_WIN64_DEVEL_URL}
+      URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+  else()
+    ExternalProject_Add(mpi4win_build
+      URL     ${MPICH2_WIN32_DEVEL_URL}
+      URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+  endif()
+
+  ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+  file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+  add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+  set_target_properties(MPI::MPI_CXX PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+    INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+  add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+  # set variables for status reporting at the end of CMake run
+  set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+  set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+  set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
 endif()
-
-ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-set_target_properties(MPI::MPI_CXX PROPERTIES
-  IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
-  INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
-  INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
-add_dependencies(MPI::MPI_CXX mpi4win_build)
-
-# set variables for status reporting at the end of CMake run
-set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
-set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
-set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")

cmake/Modules/Packages/COLVARS.cmake

@@ -26,10 +26,6 @@ if(BUILD_OMP)
   target_link_libraries(colvars PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
-if(BUILD_MPI)
-  target_link_libraries(colvars PUBLIC MPI::MPI_CXX)
-endif()
-
 if(COLVARS_DEBUG)
   # Need to export the define publicly to be valid in interface code
   target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)

cmake/Modules/Packages/GPU.cmake

@@ -189,7 +189,7 @@ if(GPU_API STREQUAL "CUDA")
   endif()
 
   add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
-  target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR -DLAMMPS_${LAMMPS_SIZES})
+  target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
   target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
   target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
 
@@ -489,7 +489,7 @@ else()
   target_link_libraries(gpu PRIVATE mpi_stubs)
 endif()
 
-set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
 target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
+set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
 target_sources(lammps PRIVATE ${GPU_SOURCES})
 target_include_directories(lammps PRIVATE ${GPU_SOURCES_DIR})

cmake/Modules/Packages/MC.cmake

@@ -7,13 +7,3 @@ if(NOT PKG_MANYBODY)
   list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.cpp)
   set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
 endif()
-
-# fix neighbor/swap may only be installed if also the VORONOI package is installed
-if(NOT PKG_VORONOI)
-  get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
-  list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MC/fix_neighbor_swap.h)
-  set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
-  get_target_property(LAMMPS_SOURCES lammps SOURCES)
-  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_neighbor_swap.cpp)
-  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
-endif()

cmake/Modules/Packages/SCAFACOS.cmake

@@ -14,16 +14,27 @@ endif()
 option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
 if(DOWNLOAD_SCAFACOS)
   message(STATUS "ScaFaCoS download requested - we will build our own")
-  set(SCAFACOS_URL "https://github.com/scafacos/scafacos/releases/download/v1.0.4/scafacos-1.0.4.tar.gz" CACHE STRING "URL for SCAFACOS tarball")
-  set(SCAFACOS_MD5 "23867540ec32e63ce71d6ecc105278d2" CACHE STRING "MD5 checksum of SCAFACOS tarball")
+  set(SCAFACOS_URL "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" CACHE STRING "URL for SCAFACOS tarball")
+  set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball")
   mark_as_advanced(SCAFACOS_URL)
   mark_as_advanced(SCAFACOS_MD5)
   GetFallbackURL(SCAFACOS_URL SCAFACOS_FALLBACK)
 
+
+  # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
+  file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
+          EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
+
+  find_program(HAVE_PATCH patch)
+  if(NOT HAVE_PATCH)
+    message(FATAL_ERROR "The 'patch' program is required to build the ScaFaCoS library")
+  endif()
+
   include(ExternalProject)
   ExternalProject_Add(scafacos_build
     URL     ${SCAFACOS_URL} ${SCAFACOS_FALLBACK}
     URL_MD5 ${SCAFACOS_MD5}
+    PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
                                              --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
                                              --with-internal-fftw --with-internal-pfft

cmake/Modules/Testing.cmake

@@ -21,11 +21,11 @@ if(ENABLE_TESTING)
   # also only verified with Fedora Linux > 30 and Ubuntu 18.04 or 22.04+(Ubuntu 20.04 fails)
   if((CMAKE_SYSTEM_NAME STREQUAL "Linux")
       AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
-    if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04))
+    if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND
+          ((CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04) OR (CMAKE_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04)))
         OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
       include(CheckCXXCompilerFlag)
       set(CMAKE_CUSTOM_LINKER_DEFAULT default)
-      check_cxx_compiler_flag(--ld-path=${CMAKE_LINKER} HAVE_LD_PATH_FLAG)
       check_cxx_compiler_flag(-fuse-ld=mold HAVE_MOLD_LINKER_FLAG)
       check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
       check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
@@ -50,17 +50,6 @@ if(ENABLE_TESTING)
       if(NOT "${CMAKE_CUSTOM_LINKER}" STREQUAL "default")
         target_link_options(lammps PUBLIC -fuse-ld=${CMAKE_CUSTOM_LINKER})
       endif()
-      if(HAVE_LD_PATH_FLAG)
-        if("${CMAKE_CUSTOM_LINKER}" STREQUAL "mold")
-          target_link_options(lammps PUBLIC --ld-path=${HAVE_MOLD_LINKER_BIN})
-        elseif("${CMAKE_CUSTOM_LINKER}" STREQUAL "lld")
-          target_link_options(lammps PUBLIC --ld-path=${HAVE_LLD_LINKER_BIN})
-        elseif("${CMAKE_CUSTOM_LINKER}" STREQUAL "gold")
-          target_link_options(lammps PUBLIC --ld-path=${HAVE_GOLD_LINKER_BIN})
-        elseif("${CMAKE_CUSTOM_LINKER}" STREQUAL "bfd")
-          target_link_options(lammps PUBLIC --ld-path=${HAVE_BFD_LINKER_BIN})
-        endif()
-      endif()
     endif()
   endif()
 

cmake/Modules/Tools.cmake

@@ -6,10 +6,6 @@ if(BUILD_TOOLS)
   add_executable(stl_bin2txt ${LAMMPS_TOOLS_DIR}/stl_bin2txt.cpp)
   install(TARGETS stl_bin2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
 
-  add_executable(reformat-json ${LAMMPS_TOOLS_DIR}/json/reformat-json.cpp)
-  target_include_directories(reformat-json PRIVATE ${LAMMPS_SOURCE_DIR})
-  install(TARGETS reformat-json DESTINATION ${CMAKE_INSTALL_BINDIR})
-
   include(CheckGeneratorSupport)
   if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
     include(CheckLanguage)

cmake/presets/hip_amd.cmake

@@ -19,19 +19,12 @@ set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 
 set(MPI_CXX "hipcc" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-set(MPI_C "hipcc" CACHE STRING "" FORCE)
-set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE)
-
-# change as needed. This is for Fedora Linux 41 and 42
-set(_libomp_root "/usr/lib/clang/18")
-# we need to explicitly specify the include dir, since hipcc will
-# compile each file twice and doesn't find omp.h the second time
 
 unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "hipcc" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-fopenmp=libomp -I${_libomp_root}/include" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-fopenmp=libomp -I${_libomp_root}/include" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

cmake/presets/kokkos-cuda.cmake

@@ -1,8 +1,9 @@
 # preset that enables KOKKOS and selects CUDA compilation with OpenMP
-# enabled as well. The GPU architecture *must* match your hardware (If not manually set, Kokkos will try to autodetect it).
+# enabled as well. The GPU architecture *must* match your hardware
 set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)
+set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
 get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
 set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)

cmake/presets/kokkos-hip.cmake

@@ -1,8 +1,8 @@
-# preset that enables KOKKOS and selects HIP compilation withOUT OpenMP.
-# Kokkos OpenMP is not compatible with the second pass of hipcc.
+# preset that enables KOKKOS and selects HIP compilation with OpenMP
+# enabled as well. Also sets some performance related compiler flags.
 set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
-set(Kokkos_ENABLE_OPENMP OFF CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   OFF CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_HIP    ON CACHE BOOL "" FORCE)
 set(Kokkos_ARCH_VEGA90A on CACHE BOOL "" FORCE)
@@ -11,11 +11,11 @@ set(BUILD_OMP ON CACHE BOOL "" FORCE)
 
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -munsafe-fp-atomics" CACHE STRING "" FORCE)
 
-# If KSPACE is also enabled, use HIPFFT for FFTs
+# If KSPACE is also enabled, use CUFFT for FFTs
 set(FFT_KOKKOS "HIPFFT" CACHE STRING "" FORCE)
 
 # hide deprecation warnings temporarily for stable release
-#set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
 
 # these flags are needed to build with Cray MPICH on OLCF Crusher
 #-D CMAKE_CXX_FLAGS="-I/${MPICH_DIR}/include"

doc/graphviz/lammps-releases.dot

@@ -5,13 +5,13 @@ digraph releases {
     github -> develop [label="Merge commits"];
     {
         rank = "same";
-        work [shape="none" label="Development branches:" fontname="bold"]
+        work [shape="none" label="Development branches:"]
         develop [label="'develop' branch" height=0.75];
         maintenance [label="'maintenance' branch" height=0.75];
     };
     {
         rank = "same";
-        upload [shape="none" label="Release branches:" fontname="bold"]
+        upload [shape="none" label="Release branches:"]
         release [label="'release' branch" height=0.75];
         stable [label="'stable' branch" height=0.75];
     };
@@ -22,7 +22,7 @@ digraph releases {
     maintenance -> stable [label="Updates to stable release"];
     {
         rank = "same";
-        tag [shape="none" label="Applied tags:" fontname="bold"];
+        tag [shape="none" label="Applied tags:"];
         patchtag [shape="box" label="patch_<date>"];
         stabletag [shape="box" label="stable_<date>"];
         updatetag [shape="box" label="stable_<date>_update<num>"];

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "12 June 2025" "2025-06-12"
+.TH LAMMPS "1" "2 April 2025" "2025-04-02"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 12 June 2025
+\- Molecular Dynamics Simulator.  Version 2 April 2025
 
 .SH SYNOPSIS
 .B lmp

doc/src/Build.rst

@@ -14,10 +14,32 @@ As an alternative, you can download a package with pre-built executables
 or automated build trees, as described in the :doc:`Install <Install>`
 section of the manual.
 
+Prerequisites
+-------------
+
+Which software you need to compile and use LAMMPS strongly depends on
+which :doc:`features and settings <Build_settings>` and which
+:doc:`optional packages <Packages_list>` you are trying to include.
+Common to all is that you need a C++ and C compiler, where the C++
+compiler has to support at least the C++11 standard (note that some
+compilers require command-line flag to activate C++11 support).
+Furthermore, if you are building with CMake, you need at least CMake
+version 3.20 and a compatible build tool (make or ninja-build); if you
+are building the the legacy GNU make based build system you need GNU
+make (other make variants are not going to work since the build system
+uses features unique to GNU make) and a Unix-like build environment with
+a Bourne shell, and shell tools like "sed", "grep", "touch", "test",
+"tr", "cp", "mv", "rm", "ln", "diff" and so on. Parts of LAMMPS
+interface with or use Python version 3.6 or later.
+
+The LAMMPS developers aim to keep LAMMPS very portable and usable -
+at least in parts - on most operating systems commonly used for
+running MD simulations.  Please see the :doc:`section on portablility
+<Intro_portability>` for more details.
+
 .. toctree::
    :maxdepth: 1
 
-   Build_prerequisites
    Build_cmake
    Build_make
    Build_link

doc/src/Build_prerequisites.rst

@@ -1,22 +0,0 @@
-Prerequisites
--------------
-
-Which software you need to compile and use LAMMPS strongly depends on
-which :doc:`features and settings <Build_settings>` and which
-:doc:`optional packages <Packages_list>` you are trying to include.
-Common to all is that you need a C++ and C compiler, where the C++
-compiler has to support at least the C++11 standard (note that some
-compilers require command-line flag to activate C++11 support).
-Furthermore, if you are building with CMake, you need at least CMake
-version 3.20 and a compatible build tool (make or ninja-build); if you
-are building the the legacy GNU make based build system you need GNU
-make (other make variants are not going to work since the build system
-uses features unique to GNU make) and a Unix-like build environment with
-a Bourne shell, and shell tools like "sed", "grep", "touch", "test",
-"tr", "cp", "mv", "rm", "ln", "diff" and so on. Parts of LAMMPS
-interface with or use Python version 3.6 or later.
-
-The LAMMPS developers aim to keep LAMMPS very portable and usable -
-at least in parts - on most operating systems commonly used for
-running MD simulations.  Please see the :doc:`section on portablility
-<Intro_portability>` for more details.

doc/src/Commands_fix.rst

@@ -29,7 +29,6 @@ OPT.
    * :doc:`ave/grid <fix_ave_grid>`
    * :doc:`ave/histo <fix_ave_histo>`
    * :doc:`ave/histo/weight <fix_ave_histo>`
-   * :doc:`ave/moments <fix_ave_moments>`
    * :doc:`ave/time <fix_ave_time>`
    * :doc:`aveforce <fix_aveforce>`
    * :doc:`balance <fix_balance>`
@@ -78,7 +77,6 @@ OPT.
    * :doc:`flow/gauss <fix_flow_gauss>`
    * :doc:`freeze (k) <fix_freeze>`
    * :doc:`gcmc <fix_gcmc>`
-   * :doc:`gjf <fix_gjf>`
    * :doc:`gld <fix_gld>`
    * :doc:`gle <fix_gle>`
    * :doc:`gravity (ko) <fix_gravity>`
@@ -218,7 +216,6 @@ OPT.
    * :doc:`rigid/small (o) <fix_rigid>`
    * :doc:`rx (k) <fix_rx>`
    * :doc:`saed/vtk <fix_saed_vtk>`
-   * :doc:`set <fix_set>`
    * :doc:`setforce (k) <fix_setforce>`
    * :doc:`setforce/spin <fix_setforce>`
    * :doc:`sgcmc <fix_sgcmc>`

doc/src/Commands_kspace.rst

@@ -31,5 +31,3 @@ OPT.
    * :doc:`pppm/dielectric <kspace_style>`
    * :doc:`pppm/electrode (i) <kspace_style>`
    * :doc:`scafacos <kspace_style>`
-   * :doc:`zero <kspace_style>`
-

doc/src/Commands_removed.rst

@@ -1,7 +1,7 @@
 Removed commands and packages
 =============================
 
-.. contents::
+.. contents:: \
 
 ------
 
@@ -12,21 +12,10 @@ stop LAMMPS and print a suitable error message in most cases, when a
 style/command is used that has been removed or will replace the command
 with the direct alternative (if available) and print a warning.
 
-GJF formulation in fix langevin
--------------------------------
-
-.. deprecated:: 12Jun2025
-
-The *gjf* keyword in fix langevin is deprecated and will be removed
-soon.  The GJF functionality has been moved to its own fix style
-:doc:`fix gjf <fix_gjf>` and it is strongly recommended to use that
-fix instead.
-
-
 LAMMPS shell
 ------------
 
-.. deprecated:: 29Aug2024
+.. versionchanged:: 29Aug2024
 
 The LAMMPS shell has been removed from the LAMMPS distribution. Users
 are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
@@ -34,7 +23,7 @@ are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
 i-PI tool
 ---------
 
-.. deprecated:: 27Jun2024
+.. versionchanged:: 27Jun2024
 
 The i-PI tool has been removed from the LAMMPS distribution.  Instead,
 instructions to install i-PI from PyPI via pip are provided.

doc/src/Developer_plugins.rst

@@ -68,25 +68,24 @@ Members of ``lammpsplugin_t``
    * - author
      - String with the name and email of the author
    * - creator.v1
-     - Pointer to factory function for pair, bond, angle, dihedral, improper, kspace, command, or minimize styles
+     - Pointer to factory function for pair, bond, angle, dihedral, improper, kspace, or command styles
    * - creator.v2
-     - Pointer to factory function for compute, fix, region, or run styles
+     - Pointer to factory function for compute, fix, or region styles
    * - handle
      - Pointer to the open DSO file handle
 
 Only one of the two alternate creator entries can be used at a time and
 which of those is determined by the style of plugin. The "creator.v1"
 element is for factory functions of supported styles computing forces
-(i.e. pair, bond, angle, dihedral, or improper styles), command styles,
-or minimize styles and the function takes as single argument the pointer
-to the LAMMPS instance. The factory function is cast to the
-``lammpsplugin_factory1`` type before assignment.  The "creator.v2"
-element is for factory functions creating an instance of a fix, compute,
-region, or run style and takes three arguments: a pointer to the LAMMPS
-instance, an integer with the length of the argument list and a ``char
-**`` pointer to the list of arguments. The factory function pointer
-needs to be cast to the ``lammpsplugin_factory2`` type before
-assignment.
+(i.e. pair, bond, angle, dihedral, or improper styles) or command styles
+and the function takes as single argument the pointer to the LAMMPS
+instance. The factory function is cast to the ``lammpsplugin_factory1``
+type before assignment.  The "creator.v2" element is for factory
+functions creating an instance of a fix, compute, or region style and
+takes three arguments: a pointer to the LAMMPS instance, an integer with
+the length of the argument list and a ``char **`` pointer to the list of
+arguments. The factory function pointer needs to be cast to the
+``lammpsplugin_factory2`` type before assignment.
 
 Pair style example
 ^^^^^^^^^^^^^^^^^^
@@ -248,8 +247,8 @@ DSO handle.  The registration function is called with a pointer to the address
 of this struct and the pointer of the LAMMPS class.  The registration function
 will then add the factory function of the plugin style to the respective
 style map under the provided name.  It will also make a copy of the struct
-in a global list of all loaded plugins and update the reference counter for
-loaded plugins from this specific DSO file.
+in a list of all loaded plugins and update the reference counter for loaded
+plugins from this specific DSO file.
 
 The pair style itself (i.e. the PairMorse2 class in this example) can be
 written just like any other pair style that is included in LAMMPS.  For
@@ -264,21 +263,6 @@ the plugin will override the existing code.  This can be used to modify
 the behavior of existing styles or to debug new versions of them without
 having to re-compile or re-install all of LAMMPS.
 
-.. versionchanged:: 12Jun2025
-
-When using the :doc:`clear <clear>` command, plugins are not unloaded
-but restored to their respective style maps.  This also applies when
-multiple LAMMPS instances are created and deleted through the library
-interface.  The :doc:`plugin load <plugin>` load command may be issued
-again, but for existing plugins they will be skipped.  To replace
-plugins they must be explicitly unloaded with :doc:`plugin unload
-<plugin>`.  When multiple LAMMPS instances are created concurrently, any
-loaded plugins will be added to the global list of plugins, but are not
-immediately available to any LAMMPS instance that was created before
-loading the plugin.  To "import" such plugins, the :doc:`plugin restore
-<plugin>` may be used.  Plugins are only removed when they are explicitly
-unloaded or the LAMMPS interface is "finalized".
-
 Compiling plugins
 ^^^^^^^^^^^^^^^^^
 

doc/src/Developer_updating.rst

@@ -29,7 +29,6 @@ Available topics in mostly chronological order are:
 - `Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments`_
 - `Use Output::get_dump_by_id() instead of Output::find_dump()`_
 - `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
-- `FLERR as first argument to minimum image functions in Domain class`_
 
 ----
 
@@ -611,47 +610,3 @@ KSpace solvers which use distributed FFT grids:
 - ``src/KSPACE/pppm.cpp``
 
 This change is **required** or else the code will not compile.
-
-FLERR as first argument to minimum image functions in Domain class
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. versionchanged:: 12Jun2025
-
-The ``Domain::minimum_image()`` and ``Domain::minimum_image_big()``
-functions were changed to take the ``FLERR`` macros as first argument.
-This way the error message indicates *where* the function was called
-instead of pointing to the implementation of the function.  Example:
-
-Old:
-
-.. code-block:: c++
-
-   double delx1 = x[i1][0] - x[i2][0];
-   double dely1 = x[i1][1] - x[i2][1];
-   double delz1 = x[i1][2] - x[i2][2];
-   domain->minimum_image(delx1, dely1, delz1);
-   double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
-
-   double delx2 = x[i3][0] - x[i2][0];
-   double dely2 = x[i3][1] - x[i2][1];
-   double delz2 = x[i3][2] - x[i2][2];
-   domain->minimum_image_big(delx2, dely2, delz2);
-   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
-
-New:
-
-.. code-block:: c++
-
-   double delx1 = x[i1][0] - x[i2][0];
-   double dely1 = x[i1][1] - x[i2][1];
-   double delz1 = x[i1][2] - x[i2][2];
-   domain->minimum_image(FLERR, delx1, dely1, delz1);
-   double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
-
-   double delx2 = x[i3][0] - x[i2][0];
-   double dely2 = x[i3][1] - x[i2][1];
-   double delz2 = x[i3][2] - x[i2][2];
-   domain->minimum_image_big(FLERR, delx2, dely2, delz2);
-   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
-
-This change is **required** or else the code will not compile.

doc/src/Errors_details.rst

@@ -159,17 +159,13 @@ angle, dihedral, or improper with just one atom in the actual
 sub-domain.  Typically, this cutoff is set to the largest cutoff from
 the :doc:`pair style(s) <pair_style>` plus the :doc:`neighbor list skin
 distance <neighbor>` and will typically be sufficient for all bonded
-interactions.  But if the pair style cutoff is small (e.g. with a
-repulsive-only Lennard-Jones potential) this may not be enough.  It is
-even worse if there is no pair style defined (or the pair style is set
-to "none"), since then there will be no ghost atoms created at all.
-
-The communication cutoff can be set or adjusted with :doc:`comm_modify
-cutoff \<value\> <comm_modify>`, but setting this too large will waste
-CPU time and memory.  LAMMPS will print warnings in these cases.  For
-bonds it uses some heuristic based on the equilibrium bond length, but
-that still may not be sufficient for cases where the force constants are
-small and thus bonds may be stretched very far.
+interactions.  But if the pair style cutoff is small, this may not be
+enough.  LAMMPS will print a warning in this case using some heuristic
+based on the equilibrium bond length, but that still may not be
+sufficient for cases where the force constants are small and thus bonds
+may be stretched very far.  The communication cutoff can be adjusted
+with :doc:`comm_modify cutoff \<value\> <comm_modify>`, but setting this
+too large will waste CPU time and memory.
 
 .. _hint09:
 

doc/src/Fortran.rst

@@ -69,11 +69,10 @@ statement.  Internally, it will call either
 :cpp:func:`lammps_open_fortran` or :cpp:func:`lammps_open_no_mpi` from
 the C library API to create the class instance.  All arguments are
 optional and :cpp:func:`lammps_mpi_init` will be called automatically
-if it is needed.  Similarly, optional calls to
-:cpp:func:`lammps_mpi_finalize`, :cpp:func:`lammps_kokkos_finalize`,
-:cpp:func:`lammps_python_finalize`, and :cpp:func:`lammps_plugin_finalize`
-are integrated into the :f:func:`close` function and triggered with the
-optional logical argument set to ``.TRUE.``. Here is a simple example:
+if it is needed.  Similarly, a possible call to
+:cpp:func:`lammps_mpi_finalize` is integrated into the :f:func:`close`
+function and triggered with the optional logical argument set to
+``.TRUE.``. Here is a simple example:
 
 .. code-block:: fortran
 
@@ -522,8 +521,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    This method will close down the LAMMPS instance through calling
    :cpp:func:`lammps_close`.  If the *finalize* argument is present and
    has a value of ``.TRUE.``, then this subroutine also calls
-   :cpp:func:`lammps_kokkos_finalize`, :cpp:func:`lammps_mpi_finalize`,
-   :cpp:func:`lammps_python_finalize`, and :cpp:func:`lammps_plugin_finalize`.
+   :cpp:func:`lammps_kokkos_finalize` and
+   :cpp:func:`lammps_mpi_finalize`.
 
    :o finalize: shut down the MPI environment of the LAMMPS
     library if ``.TRUE.``.
@@ -531,8 +530,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    :to: :cpp:func:`lammps_close`
    :to: :cpp:func:`lammps_mpi_finalize`
    :to: :cpp:func:`lammps_kokkos_finalize`
-   :to: :cpp:func:`lammps_python_finalize`
-   :to: :cpp:func:`lammps_plugin_finalize`
 
 --------
 

doc/src/Howto.rst

@@ -66,7 +66,6 @@ Force fields howto
    :name: force_howto
    :maxdepth: 1
 
-   Howto_FFgeneral
    Howto_bioFF
    Howto_amoeba
    Howto_tip3p

doc/src/Howto_FFgeneral.rst

@@ -1,55 +0,0 @@
-Some general force field considerations
-=======================================
-
-A compact summary of the concepts, definitions, and properties of force
-fields with explicit bonded interactions (like the ones discussed in
-this HowTo) is given in :ref:`(Gissinger) <Typelabel2>`.
-
-A force field has 2 parts: the formulas that define its potential
-functions and the coefficients used for a particular system.  To assign
-parameters it is first required to assign atom types.  Those are not
-only based on the elements, but also on the chemical environment due to
-the atoms bound to them.  This often follows the chemical concept of
-*functional groups*.  Example: a carbon atom bound with a single bond to
-a single OH-group (alcohol) would be a different atom type than a carbon
-atom bound to a methyl CH3 group (aliphatic carbon).  The atom types
-usually then determine the non-bonded Lennard-Jones parameters and the
-parameters for bonds, angles, dihedrals, and impropers.  On top of that,
-partial charges have to be applied.  Those are usually independent of
-the atom types and are determined either for groups of atoms called
-residues with some fitting procedure based on quantum mechanical
-calculations, or based on some increment system that add or subtract
-increments from the partial charge of an atom based on the types of
-the neighboring atoms.
-
-Force fields differ in the strategies they employ to determine the
-parameters and charge distribution in how generic or specific they are
-which in turn has an impact on the accuracy (compare for example
-CGenFF to CHARMM and GAFF to Amber).  Because of the different
-strategies, it is not a good idea to use a mix of parameters from
-different force field *families* (like CHARMM, Amber, or GROMOS)
-and that extends to the parameters for the solvent, especially
-water.  The publication describing the parameterization of a force
-field will describe which water model to use.  Changing the water
-model usually leads to overall worse results (even if it may improve
-on the water itself).
-
-In addition, one has to consider that *families* of force fields like
-CHARMM, Amber, OPLS, or GROMOS have evolved over time and thus provide
-different *revisions* of the force field parameters.  These often
-corresponds to changes in the functional form or the parameterization
-strategies.  This may also result in changes required for simulation
-settings like the preferred cutoff or how Coulomb interactions are
-computed (cutoff, smoothed/shifted cutoff, or long-range with Ewald
-summation or equivalent).  Unless explicitly stated in the publication
-describing the force field, the Coulomb interaction cannot be chosen at
-will but must match the revision of the force field.  That said,
-liberties may be taken during the initial equilibration of a system to
-speed up the process, but not for production simulations.
-
-----------
-
-.. _Typelabel2:
-
-**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).
-

doc/src/Howto_bioFF.rst

@@ -1,16 +1,22 @@
 CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields
 =======================================================
 
-Here we only discuss formulas implemented in LAMMPS that correspond to
-formulas commonly used in the CHARMM, AMBER, COMPASS, and DREIDING force
-fields.  Setting coefficients is done either from special sections in an
-input data file via the :doc:`read_data <read_data>` command or in the
-input script with commands like :doc:`pair_coeff <pair_coeff>` or
-:doc:`bond_coeff <bond_coeff>` and so on.  See the :doc:`Tools <Tools>`
-doc page for additional tools that can use CHARMM, AMBER, or Materials
-Studio generated files to assign force field coefficients and convert
-their output into LAMMPS input. LAMMPS input scripts can also be
-generated by `charmm-gui.org <https://charmm-gui.org/>`_.
+A compact summary of the concepts, definitions, and properties of
+force fields with explicit bonded interactions (like the ones discussed
+in this HowTo) is given in :ref:`(Gissinger) <Typelabel2>`.
+
+A force field has 2 parts: the formulas that define it and the
+coefficients used for a particular system.  Here we only discuss
+formulas implemented in LAMMPS that correspond to formulas commonly used
+in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
+coefficients is done either from special sections in an input data file
+via the :doc:`read_data <read_data>` command or in the input script with
+commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
+<bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc page for
+additional tools that can use CHARMM, AMBER, or Materials Studio
+generated files to assign force field coefficients and convert their
+output into LAMMPS input. LAMMPS input scripts can also be generated by
+`charmm-gui.org <https://charmm-gui.org/>`_.
 
 CHARMM and AMBER
 ----------------
@@ -197,11 +203,9 @@ rather than individual force constants and geometric parameters that
 depend on the particular combinations of atoms involved in the bond,
 angle, or torsion terms.  DREIDING has an :doc:`explicit hydrogen bond
 term <pair_hbond_dreiding>` to describe interactions involving a
-hydrogen atom on very electronegative atoms (N, O, F).  Unlike CHARMM or
-AMBER, the DREIDING force field has not been parameterized for
-considering solvents (like water) and has no rules for assigning
-(partial) charges.  That will seriously limit its accuracy when used for
-simulating systems where those matter.
+hydrogen atom on very electronegative atoms (N, O, F).  Unlike CHARMM
+or AMBER, the DREIDING force field has not been parameterized for
+considering solvents (like water).
 
 See :ref:`(Mayo) <howto-Mayo>` for a description of the DREIDING force field
 
@@ -268,6 +272,10 @@ compatible with a subset of OPLS interactions.
 
 ----------
 
+.. _Typelabel2:
+
+**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).
+
 .. _howto-MacKerell:
 
 **(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al (1998).  J Phys Chem, 102, 3586 . https://doi.org/10.1021/jp973084f

doc/src/Howto_lammps_gui.rst

@@ -308,10 +308,7 @@ of the *Output* window showing how many warnings and errors were
 detected and how many lines the entire output has.  By clicking on the
 button on the right with the warning symbol or by using the keyboard
 shortcut `Ctrl-N` (`Command-N` on macOS), you can jump to the next
-line with a warning or error.  If there is a URL pointing to additional
-explanations in the online manual, that URL will be highlighted and
-double-clicking on it shall open the corresponding manual page in
-the web browser.  The option is also available from the context menu.
+line with a warning or error.
 
 By default, the *Output* window is replaced each time a run is started.
 The runs are counted and the run number for the current run is displayed

doc/src/Howto_spc.rst

@@ -1,5 +1,5 @@
-SPC and SPC/E water model
-=========================
+SPC water model
+===============
 
 The SPC water model specifies a 3-site rigid water molecule with
 charges and Lennard-Jones parameters assigned to each of the three atoms.

doc/src/Howto_thermostat.rst

@@ -21,14 +21,9 @@ can be invoked via the *dpd/tstat* pair style:
 * :doc:`fix nvt/sllod <fix_nvt_sllod>`
 * :doc:`fix temp/berendsen <fix_temp_berendsen>`
 * :doc:`fix temp/csvr <fix_temp_csvr>`
-* :doc:`fix ffl <fix_ffl>`
-* :doc:`fix gjf <fix_gjf>`
-* :doc:`fix gld <fix_gld>`
-* :doc:`fix gle <fix_gle>`
 * :doc:`fix langevin <fix_langevin>`
 * :doc:`fix temp/rescale <fix_temp_rescale>`
 * :doc:`pair_style dpd/tstat <pair_dpd>`
-* :doc:`pair_style dpd/ext/tstat <pair_dpd_ext>`
 
 :doc:`Fix nvt <fix_nh>` only thermostats the translational velocity of
 particles.  :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this,
@@ -87,10 +82,10 @@ that:
 
 .. note::
 
-   Not all thermostat fixes perform time integration, meaning they update
+   Only the nvt fixes perform time integration, meaning they update
    the velocities and positions of particles due to forces and velocities
    respectively.  The other thermostat fixes only adjust velocities; they
-   do NOT perform time integration updates.  Thus, they should be used in
+   do NOT perform time integration updates.  Thus they should be used in
    conjunction with a constant NVE integration fix such as these:
 
 * :doc:`fix nve <fix_nve>`

doc/src/Howto_tip4p.rst

@@ -1,5 +1,5 @@
-TIP4P and OPC water models
-==========================
+TIP4P water model
+=================
 
 The four-point TIP4P rigid water model extends the traditional
 :doc:`three-point TIP3P <Howto_tip3p>` model by adding an additional
@@ -9,11 +9,9 @@ the oxygen along the bisector of the HOH bond angle.  A bond style of
 :doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
 <angle_harmonic>` or :doc:`charmm <angle_charmm>` should also be used.
 In case of rigid bonds also bond style :doc:`zero <bond_zero>` and angle
-style :doc:`zero <angle_zero>` can be used.  Very similar to the TIP4P
-model is the OPC water model.  It can be realized the same way as TIP4P
-but has different geometry and force field parameters.
+style :doc:`zero <angle_zero>` can be used.
 
-There are two ways to implement TIP4P-like water in LAMMPS:
+There are two ways to implement TIP4P water in LAMMPS:
 
 #. Use a specially written pair style that uses the :ref:`TIP3P geometry
    <tip3p_molecule>` without the point M. The point M location is then
@@ -23,10 +21,7 @@ There are two ways to implement TIP4P-like water in LAMMPS:
    computationally very efficient, but the charge distribution in space
    is only correct within the tip4p labeled styles.  So all other
    computations using charges will "see" the negative charge incorrectly
-   located on the oxygen atom unless they are specially written for using
-   the TIP4P geometry internally as well, e.g. :doc:`compute dipole/tip4p
-   <compute_dipole>`, :doc:`fix efield/tip4p <fix_efield>`, or
-   :doc:`kspace_style pppm/tip4p <kspace_style>`.
+   on the oxygen atom.
 
    This can be done with the following pair styles for Coulomb with a cutoff:
 
@@ -73,90 +68,77 @@ TIP4P/2005 model :ref:`(Abascal2) <Abascal2>` and a version of TIP4P
 parameters adjusted for use with a long-range Coulombic solver
 (e.g. Ewald or PPPM in LAMMPS).  Note that for implicit TIP4P models the
 OM distance is specified in the :doc:`pair_style <pair_style>` command,
-not as part of the pair coefficients. Also parameters for the OPC
-model (:ref:`Izadi <Izadi>`) are provided.
+not as part of the pair coefficients.
 
 .. list-table::
       :header-rows: 1
-      :widths: 40 12 12 14 11 11
+      :widths: 36 19 13 15 17
 
       * - Parameter
         - TIP4P (original)
         - TIP4P/Ice
         - TIP4P/2005
         - TIP4P (Ewald)
-        - OPC
       * - O mass (amu)
         - 15.9994
         - 15.9994
         - 15.9994
         - 15.9994
-        - 15.9994
       * - H mass (amu)
         - 1.008
         - 1.008
         - 1.008
         - 1.008
-        - 1.008
       * - O or M charge (:math:`e`)
         - -1.040
         - -1.1794
         - -1.1128
         - -1.04844
-        - -1.3582
       * - H charge (:math:`e`)
         - 0.520
         - 0.5897
         - 0.5564
         - 0.52422
-        - 0.6791
       * - LJ :math:`\epsilon` of OO (kcal/mole)
         - 0.1550
         - 0.21084
         - 0.1852
         - 0.16275
-        - 0.21280
       * - LJ :math:`\sigma` of OO (:math:`\AA`)
         - 3.1536
         - 3.1668
         - 3.1589
         - 3.16435
-        - 3.1660
       * - LJ :math:`\epsilon` of HH, MM, OH, OM, HM (kcal/mole)
         - 0.0
         - 0.0
         - 0.0
         - 0.0
-        - 0.0
       * - LJ :math:`\sigma` of HH, MM, OH, OM, HM (:math:`\AA`)
         - 1.0
         - 1.0
         - 1.0
         - 1.0
-        - 1.0
       * - :math:`r_0` of OH bond (:math:`\AA`)
         - 0.9572
         - 0.9572
         - 0.9572
         - 0.9572
-        - 0.8724
       * - :math:`\theta_0` of HOH angle
         - 104.52\ :math:`^{\circ}`
         - 104.52\ :math:`^{\circ}`
         - 104.52\ :math:`^{\circ}`
         - 104.52\ :math:`^{\circ}`
-        - 103.60\ :math:`^{\circ}`
       * - OM distance (:math:`\AA`)
         - 0.15
         - 0.1577
         - 0.1546
         - 0.1250
-        - 0.1594
 
-Note that the when using a TIP4P pair style, the neighbor list cutoff
+Note that the when using the TIP4P pair style, the neighbor list cutoff
 for Coulomb interactions is effectively extended by a distance 2 \* (OM
 distance), to account for the offset distance of the fictitious charges
-on O atoms in water molecules.  Thus, it is typically best in an
+on O atoms in water molecules.  Thus it is typically best in an
 efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2\*(OM
 distance), to shrink the size of the neighbor list.  This leads to
 slightly larger cost for the long-range calculation, so you can test the
@@ -210,94 +192,6 @@ file changed):
     run 20000
     write_data tip4p-implicit.data nocoeff
 
-When constructing an OPC model, we cannot use the ``tip3p.mol`` file due
-to the different geometry.  Below is a molecule file providing the 3
-sites of an implicit OPC geometry for use with TIP4P styles.  Note, that
-the "Shake" and "Special" sections are missing here.  Those will be
-auto-generated by LAMMPS when the molecule file is loaded *after* the
-simulation box has been created.  These sections are required only when
-the molecule file is loaded *before*.
-
-.. _opc3p_molecule:
-.. code-block::
-
-   # Water molecule. 3 point geometry for OPC model
-
-   3 atoms
-   2 bonds
-   1 angles
-
-   Coords
-
-   1    0.00000  -0.06037   0.00000
-   2    0.68558   0.50250   0.00000
-   3   -0.68558   0.50250   0.00000
-
-   Types
-
-   1        1   # O
-   2        2   # H
-   3        2   # H
-
-   Charges
-
-   1       -1.3582
-   2        0.6791
-   3        0.6791
-
-   Bonds
-
-   1   1      1      2
-   2   1      1      3
-
-   Angles
-
-   1   1      2      1      3
-
-Below is a LAMMPS input file using the implicit method to implement
-the OPC model using the molecule file from above and including the
-PPPM long-range Coulomb solver.
-
-.. code-block:: LAMMPS
-
-    units real
-    atom_style full
-    region box block -5 5 -5 5 -5 5
-    create_box 2 box bond/types 1 angle/types 1 &
-                extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
-
-    mass 1 15.9994
-    mass 2 1.008
-
-    pair_style lj/cut/tip4p/long 1 2 1 1 0.1594 12.0
-    pair_coeff 1 1 0.2128 3.166
-    pair_coeff 2 2 0.0    1.0
-
-    bond_style zero
-    bond_coeff 1 0.8724
-
-    angle_style zero
-    angle_coeff 1 103.6
-
-    kspace_style pppm/tip4p 1.0e-5
-
-    molecule water opc3p.mol  # this file has the OPC geometry but is without M
-    create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
-
-    fix rigid all shake 0.001 10 10000 b 1 a 1
-    minimize 0.0 0.0 1000 10000
-
-    reset_timestep 0
-    timestep 1.0
-    velocity all create 300.0 5463576
-    fix integrate all nvt temp 300 300 100.0
-
-    thermo_style custom step temp press etotal pe
-
-    thermo 1000
-    run 20000
-    write_data opc-implicit.data nocoeff
-
 Below is the code for a LAMMPS input file using the explicit method and
 a TIP4P molecule file.  Because of using :doc:`fix rigid/small
 <fix_rigid>` no bonds need to be defined and thus no extra storage needs
@@ -385,8 +279,3 @@ Phys, 79, 926 (1983).
 
 **(Abascal2)** Abascal, J Chem Phys, 123, 234505 (2005)
    https://doi.org/10.1063/1.2121687
-
-.. _Izadi:
-
-**(Izadi)** Izadi, Anandakrishnan, Onufriev, J. Phys. Chem. Lett., 5, 21, 3863 (2014)
-   https://doi.org/10.1021/jz501780a

doc/src/Install_git.rst

@@ -21,8 +21,8 @@ You can follow the LAMMPS development on 4 different git branches:
 
 * **develop** : this branch follows the ongoing development and is
   updated with every merge commit of a pull request
-* **release** : this branch is updated with every "feature release"
-  and updates are always "fast-forward" merges from *develop*
+* **release** : this branch is updated with every "feature release";
+   updates are always "fast-forward" merges from *develop*
 * **maintenance** : this branch collects back-ported bug fixes from the
   *develop* branch to the *stable* branch.  It is used to update the
   *stable* branch for "stable update releases".

doc/src/Intro_authors.rst

@@ -84,9 +84,8 @@ lammps.org".  General questions about LAMMPS should be posted in the
 
    \normalsize
 
-Past core developers include Paul Crozier and Mark Stevens, both at SNL,
-and Ray Shan while at SNL and later at Materials Design, now at Thermo
-Fisher Scientific.
+Past developers include Paul Crozier and Mark Stevens, both at SNL,
+and Ray Shan, now at Materials Design.
 
 ----------
 

doc/src/Intro_portability.rst

@@ -28,9 +28,8 @@ Build systems
 LAMMPS can be compiled from source code using a (traditional) build
 system based on shell scripts, a few shell utilities (grep, sed, cat,
 tr) and the GNU make program. This requires running within a Bourne
-shell (``/bin/sh`` or ``/bin/bash``).  Alternatively, a build system
-with different back ends can be created using CMake.  CMake must be
-at least version 3.16.
+shell (``/bin/sh``).  Alternatively, a build system with different back
+ends can be created using CMake.  CMake must be at least version 3.16.
 
 Operating systems
 ^^^^^^^^^^^^^^^^^
@@ -41,18 +40,11 @@ Also, compilation and correct execution on macOS and Windows (using
 Microsoft Visual C++) is checked automatically for the largest part of
 the source code.  Some (optional) features are not compatible with all
 operating systems, either through limitations of the corresponding
-LAMMPS source code or through incompatibilities or build system
-limitations of required external libraries or packages.
+LAMMPS source code or through incompatibilities of source code or
+build system of required external libraries or packages.
 
-Executables for Windows may be created either natively using Cygwin,
-MinGW, Intel, Clang, or Microsoft Visual C++ compilers, or with a Linux
-to Windows MinGW cross-compiler.  Native compilation is supported using
-Microsoft Visual Studio or a terminal window (using the CMake build
-system).
-
-Executables for macOS may be created either using Xcode or GNU compilers
-installed with Homebrew.  In the latter case, building of LAMMPS through
-Homebrew instead of a manual compile is also possible.
+Executables for Windows may be created natively using either Cygwin or
+Visual Studio or with a Linux to Windows MinGW cross-compiler.
 
 Additionally, FreeBSD and Solaris have been tested successfully to
 run LAMMPS and produce results consistent with those on Linux.
@@ -69,9 +61,8 @@ CPU architectures
 ^^^^^^^^^^^^^^^^^
 
 The primary CPU architecture for running LAMMPS is 64-bit x86, but also
-64-bit ARM and PowerPC (64-bit, Little Endian) are currently regularly
-tested.  Further architectures are tested by Linux distributions that
-bundle LAMMPS.
+32-bit x86, and 64-bit ARM and PowerPC (64-bit, Little Endian) are
+regularly tested.
 
 Portability compliance
 ^^^^^^^^^^^^^^^^^^^^^^

doc/src/Library_create.rst

@@ -11,7 +11,6 @@ This section documents the following functions:
 - :cpp:func:`lammps_mpi_finalize`
 - :cpp:func:`lammps_kokkos_finalize`
 - :cpp:func:`lammps_python_finalize`
-- :cpp:func:`lammps_plugin_finalize`
 - :cpp:func:`lammps_error`
 
 --------------------
@@ -120,10 +119,5 @@ calling program.
 
 -----------------------
 
-.. doxygenfunction:: lammps_plugin_finalize
-   :project: progguide
-
------------------------
-
 .. doxygenfunction:: lammps_error
    :project: progguide

doc/src/Python_call.rst

@@ -5,28 +5,18 @@ LAMMPS has several commands which can be used to invoke Python
 code directly from an input script:
 
 * :doc:`python <python>`
-* :doc:`python-style variables <variable>`
-* :doc:`equal-style and atom-style variables with formulas containing Python function wrappers <variable>`
+* :doc:`variable python <variable>`
 * :doc:`fix python/invoke <fix_python_invoke>`
 * :doc:`pair_style python <pair_python>`
 
-The :doc:`python <python>` command can be used to define and execute a
-Python function that you write the code for.  The Python function can
-also be assigned to a LAMMPS python-style variable via the
-:doc:`variable <variable>` command.  Each time the variable is
+The :doc:`python <python>` command which can be used to define and
+execute a Python function that you write the code for.  The Python
+function can also be assigned to a LAMMPS python-style variable via
+the :doc:`variable <variable>` command.  Each time the variable is
 evaluated, either in the LAMMPS input script itself, or by another
 LAMMPS command that uses the variable, this will trigger the Python
 function to be invoked.
 
-The Python function can also be referenced in the formula used to
-define an :doc:`equal-style or atom-style variable <variable>`, using
-the syntax for a :doc:`Python function wrapper <variable>`.  This make
-it easy to pass LAMMPS-related arguments to the Python function, as
-well as to invoke it whenever the equal- or atom-style variable is
-evaluated.  For an atom-style variable it means the Python function
-can be invoked once per atom, using per-atom properties as arguments
-to the function.
-
 The Python code for the function can be included directly in the input
 script or in an auxiliary file.  The function can have arguments which
 are mapped to LAMMPS variables (also defined in the input script) and

doc/src/Speed_compare.rst

@@ -75,34 +75,15 @@ section below for examples where this has been done.
 **Differences between the GPU and KOKKOS packages:**
 
 * The GPU package accelerates only pair force, neighbor list, and (parts
-  of) PPPM calculations (and runs the remaining force computations on
-  the CPU concurrently).  The KOKKOS package attempts to run most of the
+  of) PPPM calculations. The KOKKOS package attempts to run most of the
   calculation on the GPU, but can transparently support non-accelerated
   code (with a performance penalty due to having data transfers between
   host and GPU).
-* The list of which styles are accelerated by the GPU or KOKKOS package
-  differs with some overlap.
 * The GPU package requires neighbor lists to be built on the CPU when using
   hybrid pair styles, exclusion lists, or a triclinic simulation box.
-* The GPU package benefits from running multiple MPI processes (2-8) per
-  GPU to parallelize the non-GPU accelerated styles.  The KOKKOS package
-  usually not, especially when all parts of the calculation have KOKKOS
-  support.
-* The GPU package can be compiled for CUDA, HIP, or OpenCL and thus
-  supports NVIDIA, AMD, and Intel GPUs well. On NVIDIA or AMD hardware,
-  using native CUDA or HIP compilation, respectively, with either GPU or
-  KOKKOS results in equal or better performance over OpenCL.
-* OpenCL in the GPU package supports NVIDIA, AMD, and Intel GPUs at the
-  *same time* and with the *same executable*.  KOKKOS currently does not
-  support OpenCL.
-* The GPU package supports single precision floating point, mixed
-  precision floating point, and double precision floating point math on
-  the GPU.  This must be chosen at compile time.  KOKKOS currently only
-  supports double precision floating point math.  Using single or mixed
-  precision (recommended) results in significantly improved performance
-  on consumer GPUs for some loss in accuracy (which is rather small with
-  mixed precision).  Single and mixed precision support for KOKKOS is in
-  development (no ETA yet).
-* Some pair styles (for example :doc:`snap <pair_snap>`, :doc:`mliap
-  <pair_mliap>` or :doc:`reaxff <pair_reaxff>` in the KOKKOS package have
-  seen extensive optimizations and specializations for GPUs and CPUs.
+* The GPU package can be compiled for CUDA, HIP, or OpenCL and thus supports
+  NVIDIA, AMD, and Intel GPUs well. On NVIDIA hardware, using CUDA is
+  typically resulting in equal or better performance over OpenCL.
+* OpenCL in the GPU package does theoretically also support Intel CPUs or
+  Intel Xeon Phi, but the native support for those in KOKKOS (or INTEL)
+  is superior.

doc/src/Speed_measure.rst

@@ -1,218 +1,16 @@
 Measuring performance
 =====================
 
-Factors that influence performance
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Before trying to make your simulation run faster, you should
+understand how it currently performs and where the bottlenecks are.
 
-Before trying to make your simulation run faster, you should understand
-how it currently performs and where the bottlenecks are.  We generally
-distinguish between serial performance (how fast can a single process do
-the calculations?) and parallel efficiency (how much faster does a
-calculation get by using more processes?).  There are many factors
-affecting either and below are some lists discussing some commonly
-known but also some less known factors.
-
-Factors affecting serial performance (in no specific order):
-
-* CPU hardware: clock rate, cache sizes, CPU architecture (instructions
-  per clock, vectorization support, fused multiply-add support and more)
-* RAM speed and number of channels that the CPU can use to access RAM
-* Cooling: CPUs can change the CPU clock based on thermal load, thus the
-  degree of cooling can affect the speed of a CPU.  Sometimes even the
-  temperature of neighboring compute nodes in a cluster can make a
-  difference.
-* Compiler optimization: most of LAMMPS is written to be easy to modify
-  and thus compiler optimization can speed up calculations. However, too
-  aggressive compiler optimization can produce incorrect results or
-  crashes (during compilation or at runtime).
-* Source code improvements: styles in the OPT, OPENMP, and INTEL package
-  can be faster than their base implementation due to improved data
-  access patterns, cache efficiency, or vectorization. Compiler optimization
-  is required to take full advantage of these.
-* Number and kind of fixes, computes, or variables used during a simulation,
-  especially if they result in collective communication operations
-* Pair style cutoffs and system density: calculations get slower the more
-  neighbors are in the neighbor list and thus for which interactions need
-  to be computed.  Force fields with pair styles that compute interactions
-  between triples or quadruples of atoms or that use embedding energies or
-  charge equilibration will need to walk the neighbor lists multiple times.
-* Neighbor list settings: tradeoff between neighbor list skin (larger
-  skin = more neighbors, more distances to compute before applying the
-  cutoff) and frequency of neighbor list builds (larger skin = fewer
-  neighbor list builds).
-* Proximity of per-atom data in physical memory that for atoms that are
-  close in space improves cache efficiency (thus LAMMPS will by default
-  sort atoms in local storage accordingly)
-* Using r-RESPA multi-timestepping or a SHAKE or RATTLE fix to constrain
-  bonds with higher-frequency vibrations may allow a larger (outer) timestep
-  and thus fewer force evaluations (usually the most time consuming step in
-  MD) for the same simulated time (with some tradeoff in accuracy).
-
-Factors affecting parallel efficiency (in no specific order):
-
-* Bandwidth and latency of communication between processes. This can vary a
-  lot between processes on the same CPU or physical node and processes
-  on different physical nodes and there vary between different
-  communication technologies (like Ethernet or InfiniBand or other
-  high-speed interconnects)
-* Frequency and complexity of communication patterns required
-* Number of "work units" (usually correlated with the number of atoms
-  and choice of force field) per MPI-process required for one time step
-  (if this number becomes too small, the cost of communication becomes
-  dominant).
-* Choice of parallelization method (MPI-only, OpenMP-only, MPI+OpenMP,
-  MPI+GPU, MPI+GPU+OpenMP)
-* Algorithmic complexity of the chosen force field (pair-wise vs. many-body
-  potential, Ewald vs. PPPM vs. (compensated or smoothed) cutoff-Coulomb)
-* Communication cutoff: a larger cutoff results in more ghost atoms and
-  thus more data that needs to be communicated
-* Frequency of neighbor list builds: during a neighbor list build the
-  domain decomposition is updated and the list of ghost atoms rebuilt
-  which requires multiple global communication steps
-* FFT-grid settings and number of MPI processes for kspace style PPPM:
-  PPPM uses parallel 3d FFTs which will drop much faster in parallel
-  efficiency with respect to the number of MPI processes than other
-  parts of the force computation.  Thus using MPI+OpenMP parallelization
-  or :doc:`run style verlet/split <run_style>` can improve parallel
-  efficiency by limiting the number of MPI processes used for the FFTs.
-* Load (im-)balance: LAMMPS' domain decomposition assumes that atoms are
-  evenly distributed across the entire simulation box. If there are
-  areas of vacuum, this may lead to different amounts of work for
-  different MPI processes. Using the :doc:`processors command
-  <processors>` to change the spatial decomposition, or MPI+OpenMP
-  parallelization instead of only-MPI to have larger sub-domains, or the
-  (fix) balance command (without or with switching to communication style
-  tiled) to change the sub-domain volumes are all methods that
-  can help to avoid load imbalances.
-
-Examples comparing serial performance
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Before looking at your own input deck(s), you should get some reference
-data from a known input so that you know what kind of performance you
-should expect from your input.  For the following we therefore use the
-``in.rhodo.scaled`` input file and ``data.rhodo`` data file from the
-``bench`` folder. This is a system of 32000 atoms using the CHARMM force
-field and long-range electrostatics running for 100 MD steps.  The
-performance data is printed at the end of a run and only measures the
-performance during propagation and excludes the setup phase.
-
-Running with a single MPI process on an AMD Ryzen Threadripper PRO
-9985WX CPU (64 cores, 128 threads, base clock: 3.2GHz, max. clock
-5.4GHz, L1/L2/L3 cache 5MB/64MB/256MB, 8 DDR5-6400 memory channels) one
-gets the following performance report:
-
-.. code-block::
-
-   Performance: 1.232 ns/day, 19.476 hours/ns, 7.131 timesteps/s, 228.197 katom-step/s
-   99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-The %CPU value should be at 100% or very close.  Lower values would
-be an indication that there are *other* processes also using the same
-CPU core and thus invalidating the performance data.  The katom-step/s
-value is best suited for comparisons, since it is fairly independent
-from the system size. The `in.rhodo.scaled` input can be easily made
-larger through replication in the three dimensions by settings variables
-"x", "y", "z" to values other than 1 from the command line with the
-"-var" flag. Example:
-
-- 32000 atoms: 228.8 katom-step/s
-- 64000 atoms: 231.6 katom-step/s
-- 128000 atoms: 231.1 katom-step/s
-- 256000 atoms: 226.4 katom-step/s
-- 864000 atoms: 229.6 katom-step/s
-
-Comparing to an AMD Ryzen 7 7840HS CPU (8 cores, 16 threads, base clock
-3.8GHz, max. clock 5.1GHz, L1/L2/L3 cache 512kB/8MB/16MB, 2 DDR5-5600
-memory channels), we get similar single core performance (~220
-katom-step/s vs. ~230 katom-step/s) due to the similar clock and
-architecture:
-
-- 32000 atoms: 219.8 katom-step/s
-- 64000 atoms: 222.5 katom-step/s
-- 128000 atoms: 216.8 katom-step/s
-- 256000 atoms: 221.0 katom-step/s
-- 864000 atoms: 221.1 katom-step/s
-
-Switching to an older Intel Xeon E5-2650 v4 CPU (12 cores, 12 threads,
-base clock 2.2GHz, max. clock 2.9GHz, L1/L2/L3 cache (64kB/256kB/30MB, 4
-DDR4-2400 memory channels) leads to a lower performance of approximately
-109 katom-step/s due to differences in architecture and clock.  In all
-cases, when looking at multiple runs, the katom-step/s property
-fluctuates by approximately 1% around the average.
-
-From here on we are looking at the performance for the 256000 atom system only
-and change several settings incrementally:
-
-#. No compiler optimization GCC (-Og -g): 183.8 katom-step/s
-#. Moderate optimization with debug info GCC (-O2 -g): 231.1 katom-step/s
-#. Full compiler optimization GCC (-DNDEBUG -O3): 236.0 katom-step/s
-#. Aggressive compiler optimization GCC (-O3 -ffast-math -march=native): 239.9 katom-step/s
-#. Source code optimization in OPENMP package (1 thread): 266.7 katom-step/s
-#. Use *fix nvt* instead of *fix npt* (compute virial only every 50 steps): 272.9 katom-step/s
-#. Increase pair style cutoff by 2 :math:`\AA`: 181.2 katom-step/s
-#. Use tight PPPM convergence (1.0e-6 instead of 1.0e-4): 161.9 katom-step/s
-#. Use Ewald summation instead of PPPM (at 1.0e-4 convergence): 19.9 katom-step/s
-
-The numbers show that gains from aggressive compiler optimizations are
-rather small in LAMMPS, the data access optimizations in the OPENMP (and
-OPT) packages are more prominent.  On the other side, using more
-accurate force field settings causes, not unexpectedly, a significant
-slowdown (to about half the speed).  Finally, using regular Ewald
-summation causes a massive slowdown due to the bad algorithmic scaling
-with system size.
-
-Examples comparing parallel performance
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The parallel performance usually goes on top of the serial performance.
-Using twice as many processors should increase the performance metric
-by up to a factor of two.  With the number of processors *N* and the
-serial performance :math:`p_1` and the performance for *N* processors
-:math:`p_N` we can define a *parallel efficiency* in percent as follows:
-
-.. math::
-
-   P_{eff} = \frac{p_N}{p_1 \cdot N} \cdot 100\%
-
-For the AMD Ryzen Threadripper PRO 9985WX CPU and the serial
-simulation settings of point 6. from above, we get the following
-parallel efficiency data for the 256000 atom system:
-
-- 1 MPI task: 273.6 katom-step/s, :math:`P_{eff} = 100\%`
-- 2 MPI tasks: 530.6 katom-step/s, :math:`P_{eff} = 97\%`
-- 4 MPI tasks: 1.021 Matom-step/s, :math:`P_{eff} = 93\%`
-- 8 MPI tasks: 1.837 Matom-step/s, :math:`P_{eff} = 84\%`
-- 16 MPI tasks: 3.574 Matom-step/s, :math:`P_{eff} = 82\%`
-- 32 MPI tasks: 6.479 Matom-step/s, :math:`P_{eff} = 74\%`
-- 64 MPI tasks: 9.032 Matom-step/s, :math:`P_{eff} = 52\%`
-- 128 MPI tasks: 12.03 Matom-step/s, :math:`P_{eff} = 34\%`
-
-The 128 MPI tasks run uses CPU cores from hyper-threading.
-
-For a small system with only 32000 atoms the parallel efficiency
-drops off earlier when the number of work units is too small relative
-to the communication overhead:
-
-- 1 MPI task:  270.8  katom-step/s, :math:`P_{eff} = 100\%`
-- 2 MPI tasks: 529.3  katom-step/s, :math:`P_{eff} = 98\%`
-- 4 MPI tasks: 989.8  katom-step/s, :math:`P_{eff} = 91\%`
-- 8 MPI tasks: 1.832  Matom-step/s, :math:`P_{eff} = 85\%`
-- 16 MPI tasks: 3.463 Matom-step/s, :math:`P_{eff} = 80\%`
-- 32 MPI tasks: 5.970 Matom-step/s, :math:`P_{eff} = 69\%`
-- 64 MPI tasks: 7.477 Matom-step/s, :math:`P_{eff} = 42\%`
-- 128 MPI tasks: 8.069 Matom-step/s, :math:`P_{eff} = 23\%`
-
-Measuring performance of your input deck
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The best way to do this is run the your system (actual number of atoms)
-for a modest number of timesteps (say 100 steps) on several different
-processor counts, including a single processor if possible.  Do this for
-an equilibrium version of your system, so that the 100-step timings are
-representative of a much longer run.  There is typically no need to run
-for 1000s of timesteps to get accurate timings; you can simply
-extrapolate from short runs.
+The best way to do this is run the your system (actual number of
+atoms) for a modest number of timesteps (say 100 steps) on several
+different processor counts, including a single processor if possible.
+Do this for an equilibrium version of your system, so that the
+100-step timings are representative of a much longer run.  There is
+typically no need to run for 1000s of timesteps to get accurate
+timings; you can simply extrapolate from short runs.
 
 For the set of runs, look at the timing data printed to the screen and
 log file at the end of each LAMMPS run.  The
@@ -230,15 +28,12 @@ breakdown and relative percentages.  For example, trying different
 options for speeding up the long-range solvers will have little impact
 if they only consume 10% of the run time.  If the pairwise time is
 dominating, you may want to look at GPU or OMP versions of the pair
-style, as discussed below.  Comparing how the percentages change as you
-increase the processor count gives you a sense of how different
-operations within the timestep are scaling.  If you are using PPPM as
-Kspace solver, you can turn on an additional output with
-:doc:`kspace_modify fftbench yes <kspace_modify>` which measures the
-time spent during PPPM on the 3d FFTs, which can be communication
-intensive for larger processor counts.  This provides an indication
-whether it is worth trying out alternatives to the default FFT settings
-for additional performance.
+style, as discussed below.  Comparing how the percentages change as
+you increase the processor count gives you a sense of how different
+operations within the timestep are scaling.  Note that if you are
+running with a Kspace solver, there is additional output on the
+breakdown of the Kspace time.  For PPPM, this includes the fraction
+spent on FFTs, which can be communication intensive.
 
 Another important detail in the timing info are the histograms of
 atoms counts and neighbor counts.  If these vary widely across

doc/src/Tools.rst

@@ -92,7 +92,6 @@ Miscellaneous tools
    * :ref:`LAMMPS coding standards <coding_standard>`
    * :ref:`emacs <emacs>`
    * :ref:`i-PI <ipi>`
-   * :ref:`JSON support <json>`
    * :ref:`kate <kate>`
    * :ref:`LAMMPS-GUI <lammps_gui>`
    * :ref:`LAMMPS magic patterns for file(1) <magic>`
@@ -365,7 +364,7 @@ These tools were provided by Aidan Thompson at Sandia
 .. _fep:
 
 fep tool
---------
+------------------
 
 The tools/fep directory contains Python scripts useful for
 post-processing results from performing free-energy perturbation
@@ -380,7 +379,7 @@ See README file in the tools/fep directory.
 .. _ipi:
 
 i-PI tool
----------
+-------------------
 
 .. versionchanged:: 27June2024
 
@@ -433,87 +432,6 @@ tools/createatoms tool's input file.
 
 ----------
 
-.. _json:
-
-JSON support files
-------------------
-
-.. versionadded:: 12June2025
-
-The ``tools/json`` directory contains files and tools to support
-using `JSON format <https://www.json.org/>`_ files in LAMMPS.
-Currently only the :doc:`molecule command <molecule>` supports
-files in JSON format directly, but this is planned to be expanded
-in the future.
-
-JSON file validation
-^^^^^^^^^^^^^^^^^^^^
-
-The JSON syntax is independent of its content, and thus the data in the
-file must follow suitable conventions to be correctly parsed during
-input.  This can be done in a portable fashion using a `JSON schema file
-<https://json-schema.org/>`_ (which is in JSON format as well) to define
-those conventions.  A suitable JSON validator software can then validate
-JSON files against the requirements.  Validating a particular JSON file
-against a schema ensures that both, the syntax *and* the conventions
-are followed.  This is useful when writing or editing JSON files in a
-text editor or when writing a pre-processing script or tool to create
-JSON files for a specific purpose in LAMMPS.  It **cannot** check
-whether the file contents are physically meaningful, though.
-
-One such validator tool is `check-jsonschema
-<https://check-jsonschema.readthedocs.io/>`_ which is written in Python
-and can be installed using the `pip Python package manager
-<https://pypi.org/>`_, best in a virtual environment as shown below (for
-a Bourne Shell command line):
-
-.. code-block:: sh
-
-   python -m venv validate-json
-   source validate-json/bin/activate
-   pip install --upgrade pip
-   pip install check-jsonschema
-
-To validate a specific JSON file against a provided schema (here for
-a :doc:`molecule command file <molecule>` you would then run for example:
-
-.. code-block:: sh
-
-   check-jsonschema --schemafile molecule-schema.json tip3p.json
-
-The latest schema files are also maintained and available for download
-at https://download.lammps.org/json .  This enables validation of JSON
-files even if the LAMMPS sources are not locally available. Example:
-
-.. code-block:: sh
-
-   check-jsonschema --schemafile https://download.lammps.org/json/molecule-schema.json tip3p.json
-
-JSON file format normalization
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-There are extensions to the strict JSON format that allow for comments
-or ignore additional (dangling) commas. The ``reformat-json.cpp`` tool
-will read JSON files in relaxed format, but write it out in strict format.
-It is also possible to change the level of indentation from -1 (all data
-one long line) to any positive integer value.  The original file will be
-backed up (.bak added to file name) and then overwritten.
-
-Manual compilation (it will be automatically included in the CMake build
-if building tools is requested during CMake configuration):
-
-.. code-block:: sh
-
-   g++ -I <path/to/lammps/src> -o reformat-json reformat-json.cpp
-
-Usage:
-
-.. parsed-literal::
-
-   reformat-json <indent-width> <json-file-1> [<json-file-2> ...]
-
-----------
-
 .. _kate:
 
 kate tool
@@ -557,13 +475,9 @@ beginners to start with LAMMPS, it is also the expectation that
 LAMMPS-GUI users will eventually transition to workflows that most
 experienced LAMMPS users employ.
 
-.. image:: JPG/lammps-gui-screen.png
-   :align: center
-   :scale: 50%
-
-Features have been extensively exposed to keyboard shortcuts, so that
-there is also appeal for experienced LAMMPS users for prototyping and
-testing simulation setups.
+All features have been extensively exposed to keyboard shortcuts, so
+that there is also appeal for experienced LAMMPS users for prototyping
+and testing simulation setups.
 
 Features
 ^^^^^^^^
@@ -588,7 +502,7 @@ Here are a few highlights of LAMMPS-GUI
 - Visualization of current state in Image Viewer (via calling :doc:`write_dump image <dump_image>`)
 - Capture of images created via :doc:`dump image <dump_image>` in Slide show window
 - Dialog to set variables, similar to the LAMMPS command-line flag '-v' / '-var'
-- Support for GPU, INTEL, KOKKOS/OpenMP, OPENMP, and OPT accelerator packages
+- Support for GPU, INTEL, KOKKOS/OpenMP, OPENMAP, and OPT and accelerator packages
 
 Parallelization
 ^^^^^^^^^^^^^^^
@@ -609,8 +523,8 @@ with CMake is required.
 The LAMMPS-GUI has been successfully compiled and tested on:
 
 - Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
-- Fedora Linux 41 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS
-- Fedora Linux 41 x86\_64 using GCC 14, Qt version 6.8
+- Fedora Linux 40 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS
+- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.7
 - Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
 - Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
 - Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.40, Qt version 6.7

doc/src/compute_angle_local.rst

@@ -53,17 +53,15 @@ The value *eng* is the interaction energy for the angle.
 
 The value *v_name* can be used together with the *set* keyword to
 compute a user-specified function of the angle theta.  The *name*
-specified for the *v_name* value is the name of an :doc:`equal-style
-variable <variable>` which should evaluate a formula based on a
+specified for the *v_name* value is the name of an :doc:`equal-style variable <variable>` which should evaluate a formula based on a
 variable which will store the angle theta.  This other variable must
-be an :doc:`internal-style variable <variable>` specified by the *set*
-keyword.  It is an internal-style variable, because this command
-resets its value directly.  The internal-style variable does not need
-to be defined in the input script (though it can be); if it is not
-defined, then the *set* option creates an :doc:`internal-style
-variable <variable>` with the specified name.
+be an :doc:`internal-style variable <variable>` defined in the input
+script; its initial numeric value can be anything.  It must be an
+internal-style variable, because this command resets its value
+directly.  The *set* keyword is used to identify the name of this
+other variable associated with theta.
 
-Note that the value of theta for each angle which is stored in the
+Note that the value of theta for each angle which stored in the
 internal variable is in radians, not degrees.
 
 As an example, these commands can be added to the bench/in.rhodo
@@ -72,6 +70,7 @@ system and output the statistics in various ways:
 
 .. code-block:: LAMMPS
 
+   variable t internal 0.0
    variable cos equal cos(v_t)
    variable cossq equal cos(v_t)*cos(v_t)
 

doc/src/compute_bond_local.rst

@@ -64,32 +64,20 @@ All these properties are computed for the pair of atoms in a bond,
 whether the two atoms represent a simple diatomic molecule, or are part
 of some larger molecule.
 
-.. versionchanged:: 12Jun2025
-
-   The sign of *dx*, *dy*, *dz* is no longer determined by the atom IDs
-   of the bonded atoms but by their order in the bond list to be
-   consistent with *fx*, *fy*, and *fz*.
-
-The value *dist* is the current length of the bond.  The values *dx*,
-*dy*, and *dz* are the :math:`(x,y,z)` components of the distance vector
-:math:`\vec{x_i} - \vec{x_j}` between the atoms in the bond.  The order
-of the atoms is determined by the bond list and the respective atom-IDs
-can be output with :doc:`compute property/local
-<compute_property_local>`.
+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.
 
-The value *force* is the magnitude of the force acting between the pair
-of atoms in the bond, which is positive for a repulsive force and
-negative for an attractive force.
+The value *force* is the magnitude of the force acting between the
+pair of atoms in the bond.
 
-The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
-the force on the first atom *i* in the bond due to the second atom *j*.
-Mathematically, they are obtained by multiplying the value of *force*
-from above with a unit vector created from the *dx*, *dy*, and *dz*
-components of the distance vector also described above.  For bond styles
-that apply non-central forces, such as :doc:`bond_style bpm/rotational
+The values *fx*, *fy*, and *fz* are the xyz components of
+*force* between the pair of atoms in the bond. For bond styles that apply
+non-central forces, such as :doc:`bond_style bpm/rotational
 <bond_bpm_rotational>`, these values only include the :math:`(x,y,z)`
 components of the normal force component.
 
@@ -130,15 +118,13 @@ moving apart.
 
 The value *v_name* can be used together with the *set* keyword to
 compute a user-specified function of the bond distance.  The *name*
-specified for the *v_name* value is the name of an :doc:`equal-style
-variable <variable>` which should evaluate a formula based on a
-variable which stores the bond distance.  This other variable must be
-the :doc:`internal-style variable <variable>` specified by the *set*
-keyword.  It is an internal-style variable, because this command
-resets its value directly.  The internal-style variable does not need
-to be defined in the input script (though it can be); if it is not
-defined, then the *set* option creates an :doc:`internal-style
-variable <variable>` with the specified name.
+specified for the *v_name* value is the name of an :doc:`equal-style variable <variable>` which should evaluate a formula based on a
+variable which will store the bond distance.  This other variable must
+be an :doc:`internal-style variable <variable>` defined in the input
+script; its initial numeric value can be anything.  It must be an
+internal-style variable, because this command resets its value
+directly.  The *set* keyword is used to identify the name of this
+other variable associated with theta.
 
 As an example, these commands can be added to the bench/in.rhodo
 script to compute the length\ :math:`^2` of every bond in the system and
@@ -146,6 +132,7 @@ output the statistics in various ways:
 
 .. code-block:: LAMMPS
 
+   variable d internal 0.0
    variable dsq equal v_d*v_d
 
    compute 1 all property/local batom1 batom2 btype

doc/src/compute_dihedral_local.rst

@@ -45,31 +45,30 @@ interactions.  The number of datums generated, aggregated across all
 processors, equals the number of dihedral angles in the system, modified
 by the group parameter as explained below.
 
-The value *phi* (:math:`\phi`) is the dihedral angle, as defined in
-the diagram on the :doc:`dihedral_style <dihedral_style>` doc page.
+The value *phi* (:math:`\phi`) is the dihedral angle, as defined in the diagram
+on the :doc:`dihedral_style <dihedral_style>` doc page.
 
-The value *v_name* can be used together with the *set* keyword to
-compute a user-specified function of the dihedral angle :math:`\phi`.
-The *name* specified for the *v_name* value is the name of an
-:doc:`equal-style variable <variable>` which should evaluate a formula
-based on a variable which will store the angle :math:`\phi`.  This
-other variable must be an :doc:`internal-style variable <variable>`
-specified by the *set* keyword.  It is an internal-style variable,
-because this command resets its value directly.  The internal-style
-variable does not need to be defined in the input script (though it
-can be); if it is not defined, then the *set* option creates an
-:doc:`internal-style variable <variable>` with the specified name.
+The value *v_name* can be used together with the *set* keyword to compute a
+user-specified function of the dihedral angle :math:`\phi`.  The *name*
+specified for the *v_name* value is the name of an
+:doc:`equal-style variable <variable>` which should evaluate a formula based on
+a variable which will store the angle :math:`\phi`.  This other variable must
+be an :doc:`internal-style variable <variable>` defined in the input
+script; its initial numeric value can be anything.  It must be an
+internal-style variable, because this command resets its value
+directly.  The *set* keyword is used to identify the name of this
+other variable associated with :math:`\phi`.
 
-Note that the value of :math:`\phi` for each angle which stored in the
-internal variable is in radians, not degrees.
+Note that the value of :math:`\phi` for each angle which stored in the internal
+variable is in radians, not degrees.
 
 As an example, these commands can be added to the bench/in.rhodo
-script to compute the :math:`\cos\phi` and :math:`\cos^2\phi` of every
-dihedral angle in the system and output the statistics in various
-ways:
+script to compute the :math:`\cos\phi` and :math:`\cos^2\phi` of every dihedral
+angle in the system and output the statistics in various ways:
 
 .. code-block:: LAMMPS
 
+   variable p internal 0.0
    variable cos equal cos(v_p)
    variable cossq equal cos(v_p)*cos(v_p)
 
@@ -101,10 +100,10 @@ no consistent ordering of the entries within the local vector or array
 from one timestep to the next.  The only consistency that is
 guaranteed is that the ordering on a particular timestep will be the
 same for local vectors or arrays generated by other compute commands.
-For example, dihedral output from the :doc:`compute property/local
-<compute_property_local>` command can be combined with data from this
-command and output by the :doc:`dump local <dump>` command in a
-consistent way.
+For example, dihedral output from the
+:doc:`compute property/local <compute_property_local>` command can be combined
+with data from this command and output by the :doc:`dump local <dump>`
+command in a consistent way.
 
 Here is an example of how to do this:
 

doc/src/compute_pair_local.rst

@@ -56,33 +56,19 @@ force cutoff distance for that interaction, as defined by the
 :doc:`pair_style <pair_style>` and :doc:`pair_coeff <pair_coeff>`
 commands.
 
-.. versionchanged:: 12Jun2025
-
-   The sign of *dx*, *dy*, *dz* is no longer determined by the value of
-   their atom-IDs but by their order in the neighbor list to be
-   consistent with *fx*, *fy*, and *fz*.
-
-The value *dist* is the distance between the pair of atoms.  The values
-*dx*, *dy*, and *dz* are the :math:`(x,y,z)` components of the distance
-vector :math:`\vec{x_i} - \vec{x_j}` between the pair of atoms.  The
-order of the atoms is determined by the neighbor list and the respective
-atom-IDs can be output with :doc:`compute property/local
-<compute_property_local>`.
+The value *dist* is the distance between the pair of atoms.
+The values *dx*, *dy*, and *dz* are the :math:`(x,y,z)` components of the
+*distance* between the pair of atoms. This value is always the
+distance from the atom of higher to the one with the lower atom ID.
 
 The value *eng* is the interaction energy for the pair of atoms.
 
 The value *force* is the force acting between the pair of atoms, which
 is positive for a repulsive force and negative for an attractive
-force.
-
-The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
-the force vector on the first atom *i* of a pair in the neighbor list
-due to the second atom *j*.  Mathematically, they are obtained by
-multiplying the value of *force* from above with a unit vector created
-from the *dx*, *dy*, and *dz* components of the distance vector also
-described above.  For pair styles that apply non-central forces, such as
-:doc:`granular pair styles <pair_gran>`, these values only include the
-:math:`(x,y,z)` components of the normal force component.
+force.  The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
+*force* on atom I. For pair styles that apply non-central forces,
+such as :doc:`granular pair styles <pair_gran>`, these values only include
+the :math:`(x,y,z)` components of the normal force component.
 
 A pair style may define additional pairwise quantities which can be
 accessed as *p1* to *pN*, where :math:`N` is defined by the pair style.

doc/src/create_atoms.rst

@@ -396,7 +396,7 @@ correct number of particles are inserted, in a perfectly random
 fashion.  Which lattice sites are selected will change with the number
 of processors used.
 
-.. versionadded:: 12Jun2025
+.. versionadded:: TBD
 
 The *group* keyword adds the newly created atoms to the named
 :doc:`group <group>`.  If the group does not yet exist it will be
@@ -416,23 +416,24 @@ atom, based on its coordinates.  They apply to all styles except
 *single*.  The *name* specified for the *var* keyword is the name of
 an :doc:`equal-style variable <variable>` that should evaluate to a
 zero or non-zero value based on one or two or three variables that
-will store the *x*, *y*, or *z* coordinates of an atom (one variable
-per coordinate).  If used, these other variables must be specified by
-the *set* keyword.  They are internal-style variable, because this
-command resets their values directly.  The internal-style variables do
-not need to be defined in the input script (though they can be); if
-one (or more) is not defined, then the *set* option creates an
-:doc:`internal-style variable <variable>` with the specified name.
+will store the *x*, *y*, or *z* coordinates of an atom (one variable per
+coordinate).  If used, these other variables must be
+:doc:`internal-style variables <variable>` defined in the input
+script; their initial numeric value can be anything.  They must be
+internal-style variables, because this command resets their values
+directly.  The *set* keyword is used to identify the names of these
+other variables, one variable for the *x*-coordinate of a created atom,
+one for *y*, and one for *z*.
 
 .. figure:: img/sinusoid.jpg
             :figwidth: 50%
             :align: right
             :target: _images/sinusoid.jpg
 
-When an atom is about to be created, its :math:`(x,y,z)` coordinates
-become the values for any *set* variable that is defined.  The *var*
-variable is then evaluated.  If the returned value is 0.0, the atom is
-not created.  If it is non-zero, the atom is created.
+When an atom is created, its :math:`(x,y,z)` coordinates become the values for
+any *set* variable that is defined.  The *var* variable is then
+evaluated.  If the returned value is 0.0, the atom is not created.  If
+it is non-zero, the atom is created.
 
 As an example, these commands can be used in a 2d simulation, to
 create a sinusoidal surface.  Note that the surface is "rough" due to
@@ -455,6 +456,8 @@ converts lattice spacings to distance.
    region      box block 0 $x 0 $y -0.5 0.5
    create_box  1 box
 
+   variable    xx internal 0.0
+   variable    yy internal 0.0
    variable    v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
    create_atoms  1 box var v set x xx set y yy
    write_dump  all atom sinusoid.lammpstrj

doc/src/dump_image.rst

@@ -783,109 +783,134 @@ 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.
+-3.2) can then be mapped to a specific color.  The details of the
+mapping procedure depend on the *style* of the color map, as explained
+below.
 
-There are many possible options for the color map, enabled by the
-*amap* keyword.  Here are the details.
+There are many possible options for defining a 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.
+then individual atom values which are lower/higher than lo/hi are set
+to lo/hi for purposes of determining the atom's color.  I.e. the range
+is static.  If *lo* is specified as *min* or *hi* as *max* then the
+range is dynamic.  The lower and/or upper bound will be calculated
+each time an image is drawn, based on the current atom values of all
+the 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.
+A *continuous* color map is one in which the color of an atom changes
+continuously as its attribute value increases within the range.
+Colors are assigned to specific values within the range; an atom with
+an attribue value between two adjacent specific values is assigned a
+color interpolated between the two adjacent colors.
 
-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.
+A *discrete* color map is one in which discrete colors are assigned to
+sub-ranges of values within the overall range.  Each sub-range can be
+of variable width and overlap with other sub-ranges.  An atom with an
+attribute value is mapped to one of the sub-ranges and assigned that
+color.
+
+A *sequential* color map is similar to a discrete color map except that
+all sub-ranges are of equal width and discrete colors are assigned to
+each sub-range in a round-robin fashion until the overall range is
+covered from *lo* to *hi*.
+
+An *absolute* color map is one in which the numeric settings
+associated with assigned colors are specified explicitly as values
+within the range.
+
+A *fractional* color map is one in which the numeric settings
+associated with assigned colors are specified as a fractional position
+within the range.
+
+For a continuous color map, the numeric settings are the specific
+values each color is assigned to.  For a discrete color map, the
+numeric settings are the bounds of each sub-range.  For a sequential
+color map, the numeric settings is the width of all the sub-ranges.
+For example if the overall range is from -10.0 to 10.0, and the color
+red is to be assigned to atoms with an attribute value of 5.0, then
+for an absolute color map the numeric value of 5.0 should map to red.
+But for a fractional map, the numeric value of 0.75 should map to red,
+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 :math:`-10.0` to
-:math:`10.0` and a *delta* of :math:`1.0` is used, then 20 colors will be
-assigned to the range.  The first will be from
-:math:`-10.0 \le \text{color1} < -9.0`, then second from
+for the *sequential* style; otherwise the setting is ignored.  It
+specifies the bin size of the sub-ranges of values described above,
+For example, if the overall range is from :math:`-10.0` to
+:math:`10.0` and a *delta* of :math:`1.0` is used, then 20 colors will
+be assigned to a series of sub-ranges.  The first sub-range will be
+from :math:`-10.0 \le \text{color1} < -9.0`, the second from
 :math:`-9.0 \le 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.
+The *N* setting is how many color entries follow.  The format of each
+color entry depends on whether the color map style is continuous,
+discrete, or sequential.  For each entry, the specified *color* 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.
+For *continuous* color maps, each entry has a *value* and a *color*\ .
+The *value* is either a number within the *lo/hi* range of values or
+*min* or *max*\ .  The *value* for the first entry must be *min* and
+the *value* for the last entry must be *max*\ .  In-between entries
+must have increasing numeric values.  There must be 2 or more entries.
+Note that numeric values are 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 :math:`X` of its atom attribute.  :math:`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 :math:`X = -5.0` and the two
-surrounding entries are "red" at :math:`-10.0` and "blue" at
-:math:`0.0`, then the atom's color will be halfway between "red" and
-"blue", which happens to be "purple".
+Here is how the *N* entries are used to determine the color of an
+individual atom, based on the value :math:`X` of its atom attribute.
+:math:`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 :math:`X =
+-5.0` and the two surrounding entries are "red" at :math:`-10.0` and
+"blue" at :math:`0.0`, then the atom's color will be halfway between
+"red" and "blue", which in this case is "purple".
 
-For discrete color maps, each entry has a *lo* and *hi* value and a
+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
+range of values or *min* (for *lo) or *max* (for *hi*).  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.
+different entries can overlap.  There must be one or more entries.
+Note that numeric *lo* and *hi* values are 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.  The lo/hi
+values in each sub-range must satisfy lo < hi.
 
-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.
+Here is how the *N* entries are used to determine the color of an
+individual atom, based on the value :math:`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.
+This means can the last entry can be thought of as a default color
+(since it will always be matched by X); the earlier entries override
+the default.  Note that for a *discrete* map, no interpolation of a
+color RGB values 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.
+For *sequential* color maps, each entry has only a *color*\ .  There
+must be 1 or more entries.  Here is how the *N* entries are used to
+determine the color of an individual atom, given the value X of its
+atom attribute.  The range is overlaid with M bins of width *delta*\ ,
+the last of which may extend beyond the *hi* boundary of the range.
+Thus X will fall in a specific bin from 1 to M.  If it falls on a
+boundary between 2 bins, it is considered to be in the higher of the 2
+bins (except in the case of 2 bins whose boundary is the *hi*
+boundary, it is considered to be in the lower of the 2 bins).  Each of
+the M bins is assigned a color from the *N* entries.  If M < *N*, then
+the colors are repeated in a round-robin fashion.  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.  An atom's color is the
+color of its bin.
 
 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.
+atoms in individual molecules with a different color based on its
+molecule ID.  See the examples/pour/in.pour.2d.molecule input script
+for an example of how this is used.
 
 .. code-block:: LAMMPS
 
@@ -897,8 +922,9 @@ this is used.
                    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.
+In this case, the sequential color map has 10 color entries, and
+molecule IDs are mapped to one of the colors, even if there are 1000s
+of molecules.
 
 ----------
 

doc/src/fix.rst

@@ -208,7 +208,6 @@ accelerated styles exist.
 * :doc:`ave/grid <fix_ave_grid>` - compute per-grid time-averaged quantities
 * :doc:`ave/histo <fix_ave_histo>` - compute/output time-averaged histograms
 * :doc:`ave/histo/weight <fix_ave_histo>` - weighted version of fix ave/histo
-* :doc:`ave/moments <fix_ave_moments>` - compute moments of scalar quantities
 * :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
 * :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
 * :doc:`balance <fix_balance>` - perform dynamic load-balancing
@@ -257,7 +256,6 @@ accelerated styles exist.
 * :doc:`flow/gauss <fix_flow_gauss>` - Gaussian dynamics for constant mass flux
 * :doc:`freeze <fix_freeze>` - freeze atoms in a granular simulation
 * :doc:`gcmc <fix_gcmc>` - grand canonical insertions/deletions
-* :doc:`gjf <fix_gjf>` - statistically correct Langevin temperature control using the GJ methods
 * :doc:`gld <fix_gld>` - generalized Langevin dynamics integrator
 * :doc:`gle <fix_gle>` - generalized Langevin equation thermostat
 * :doc:`gravity <fix_gravity>` - add gravity to atoms in a granular simulation
@@ -397,7 +395,6 @@ accelerated styles exist.
 * :doc:`rigid/small <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NVE integration
 * :doc:`rx <fix_rx>` - solve reaction kinetic ODEs for a defined reaction set
 * :doc:`saed/vtk <fix_saed_vtk>` - time-average the intensities from :doc:`compute saed <compute_saed>`
-* :doc:`set <fix_set>` - reset an atom property via an atom-style variable every N steps
 * :doc:`setforce <fix_setforce>` - set the force on each atom
 * :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
 * :doc:`sgcmc <fix_sgcmc>` - fix for hybrid semi-grand canonical MD/MC simulations

doc/src/fix_adapt.rst

@@ -440,7 +440,7 @@ this fix uses to reset theta0 needs to generate values in radians.
 
 ----------
 
-.. versionadded:: 12Jun2025
+.. versionadded:: TBD
 
 The *dihedral* keyword uses the specified variable to change the value of
 a dihedral coefficient over time, very similar to how the *angle* keyword

doc/src/fix_ave_correlate_long.rst

@@ -82,9 +82,10 @@ specified values may represent calculations performed by computes and
 fixes which store their own "group" definitions.
 
 Each listed value can be the result of a compute or fix or the
-evaluation of an equal-style or vector-style variable.  The specified
-indices can include a wildcard string.  See the
-:doc:`fix ave/correlate <fix_ave_correlate>` page for details on that.
+evaluation of an equal-style or vector-style variable.  For
+vector-style variables, the specified indices can include a wildcard
+character.  See the :doc:`fix ave/correlate <fix_ave_correlate>` page
+for details.
 
 The *Nevery* and *Nfreq* arguments specify on what time steps the input
 values will be used to calculate correlation data and the frequency

doc/src/fix_ave_moments.rst

@@ -1,296 +0,0 @@
-.. index:: fix ave/moments
-
-fix ave/moments command
-=======================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   fix ID group-ID ave/moments Nevery Nrepeat Nfreq value1 value2 ... moment1 moment2 ... keyword args ...
-
-* ID, group-ID are documented in :doc:`fix <fix>` command
-* ave/moments = style name of this fix command
-* Nevery = use input values every this many time steps
-* Nrepeat = # of times to use input values for calculating averages
-* Nfreq = calculate averages every this many time steps
-* one or more input variables can be listed
-* value = v_name
-
-  .. parsed-literal::
-
-       c_ID = global scalar calculated by a compute with ID
-       c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
-       f_ID = global scalar calculated by a fix with ID
-       f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
-       v_name = value calculated by an equal-style variable with name
-       v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
-
-* one or more moments to compute can be listed
-* moment = *mean* or *stddev* or *variance* or *skew* or *kurtosis*, see exact definitions below.
-* zero or more keyword/arg pairs may be appended
-* keyword = *start* or *history*
-
-  .. parsed-literal::
-
-       *start* args = Nstart
-         Nstart = invoke first after this time step
-       *history* args = Nrecent
-         Nrecent = keep a history of up to Nrecent outputs
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   fix 1 all ave/moments 1 1000 100 v_volume mean stddev
-   fix 1 all ave/moments 1 200 1000 v_volume variance kurtosis history 10
-
-Description
-"""""""""""
-
-.. versionadded:: 12Jun2025
-
-Using one or more values as input, calculate the moments of the underlying
-(population) distributions based on samples collected every few time
-steps over a time step window. The definitions of the moments calculated
-are given below.
-
-The group specified with this command is ignored.  However, note that
-specified values may represent calculations performed by computes and
-fixes which store their own "group" definitions.
-
-Each listed value can be the result of a :doc:`compute <compute>` or
-:doc:`fix <fix>` or the evaluation of an equal-style or vector-style
-:doc:`variable <variable>`.  In each case, the compute, fix, or variable
-must produce a global quantity, not a per-atom or local quantity.
-If you wish to spatial- or time-average or histogram per-atom
-quantities from a compute, fix, or variable, then see the :doc:`fix
-ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`, or
-:doc:`fix ave/histo <fix_ave_histo>` commands.  If you wish to sum a
-per-atom quantity into a single global quantity, see the :doc:`compute
-reduce <compute_reduce>` command.
-
-Many :doc:`computes <compute>` and :doc:`fixes <fix>` produce global
-quantities.  See their doc pages for details. :doc:`Variables <variable>`
-of style *equal* and *vector* are the only ones that can be used with
-this fix.  Variables of style *atom* cannot be used, since they produce
-per-atom values.
-
-The input values must all be scalars or vectors with a bracketed term
-appended, indicating the :math:`I^\text{th}` value of the vector is
-used.
-
-The result of this fix can be accessed as a vector, containing the
-interleaved moments of each input in order.  If M moments are requested,
-then the moments of input 1 will be the first M values in the vector
-output by this fix. The moments of input 2 will the next M values, etc.
-If there are N values, the vector length will be N*M.
-
-----------
-
-For input values from a compute or fix or variable, the bracketed index
-I can be specified using a wildcard asterisk with the index to
-effectively specify multiple values.  This takes the form "\*" or "\*n"
-or "m\*" or "m\*n".  If :math:`N` is the size of the vector, then an
-asterisk with no numeric values means all indices from 1 to :math:`N`.
-A leading asterisk means all indices from 1 to n (inclusive).  A
-trailing asterisk means all indices from n to :math:`N` (inclusive).  A
-middle asterisk means all indices from m to n (inclusive).
-
-Using a wildcard is the same as if the individual elements of the vector
-or cells of the array had been listed one by one.  For examples, see the
-description of this capability in :doc:`fix ave/time <fix_ave_time>`.
-
-----------
-
-The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and
-:math:`N_\text{freq}` arguments specify on what time steps the input
-values will be used in order to contribute to the average.  The final
-statistics are generated on time steps that are a multiple of
-:math:`N_\text{freq}`\ .  The average is over a window of up to
-:math:`N_\text{repeat}` quantities, computed in the preceding portion of
-the simulation once every :math:`N_\text{every}` time steps.
-
-.. note::
-
-    Contrary to most fix ave/* commands, it is not required that Nevery *
-    Nrepeat <= Nfreq.  This is to allow the user to choose the time
-    window and number of samples contributing to the output at each
-    Nfreq interval.
-
-For example, if :math:`N_\text{freq}=100` and :math:`N_\text{repeat}=5`
-(and :math:`N_\text{every}=1`), then on step 100 values from time steps
-96, 97, 98, 99, and 100 will be used. The fix does not compute its
-inputs on steps that are not required.  If :math:`N_\text{freq}=5`,
-:math:`N_\text{repeat}=8` and :math:`N_\text{every}=1`, then values
-will first be calculated on step 5 from steps 1-5, on step 10 from 3-10,
-on step 15 from 8-15 and so on, forming a rolling average over
-timesteps that span a time window larger than Nfreq.
-
-----------
-
-If a value begins with "c\_", a compute ID must follow which has been
-previously defined in the input script.  If no bracketed term is
-appended, the global scalar calculated by the compute is used.  If a
-bracketed term is appended, the Ith element of the global vector
-calculated by the compute is used.  See the discussion above for how I
-can be specified with a wildcard asterisk to effectively specify
-multiple values.
-
-If a value begins with "f\_", a fix ID must follow which has been
-previously defined in the input script.  If no bracketed term is
-appended, the global scalar calculated by the fix is used.  If a
-bracketed term is appended, the Ith element of the global vector
-calculated by the fix is used.  See the discussion above for how I can
-be specified with a wildcard asterisk to effectively specify multiple
-values.
-
-Note that some fixes only produce their values on certain time steps,
-which must be compatible with *Nevery*, else an error will result.
-Users can also write code for their own fix styles and :doc:`add them to
-LAMMPS <Modify>`.
-
-If a value begins with "v\_", a variable name must follow which has been
-previously defined in the input script. Only equal-style or vector-style
-variables can be used, which both produce global values.  Vector-style
-variables require a bracketed term to specify the Ith element of the
-vector calculated by the variable.
-
-Note that variables of style *equal* and *vector* define a formula which
-can reference individual atom properties or thermodynamic keywords, or
-they can invoke other computes, fixes, or variables when they are
-evaluated, so this is a very general means of specifying quantities to
-time average.
-
-----------
-
-The moments are output in the order requested in the arguments following
-the last input.  Any number and order of moments can be specified,
-although it does not make much sense to specify the same moment multiple
-times.  All moments are computed using a correction of the sample estimators
-used to obtain unbiased cumulants :math:`k_{1..4}` (see :ref:`(Cramer)
-<Cramer1>`). The correction for variance is the standard Bessel
-correction. For other moments, see :ref:`(Joanes)<Joanes1>`.
-
-For *mean*, the arithmetic mean :math:`\bar{x} = \frac{1}{n}
-\sum_{i=1}^{n} x_i` is calculated.
-
-For *variance*, the Bessel-corrected sample variance :math:`var = k_2 =
-\frac{1}{n - 1} \sum_{i=1}^{n} (x_i - \bar{x})^2` is calculated.
-
-For *stddev*, the Bessel-corrected sample standard deviation
-:math:`stddev = \sqrt{k_2}` is calculated.
-
-For *skew*, the adjusted Fisher--Pearson standardized moment :math:`G_1
-= \frac{k_3}{k_2^{3/2}} = \frac{k_3}{stddev^3}` is calculated.
-
-For *kurtosis*, the adjusted Fisher--Pearson standardized moment
-:math:`G_2 = \frac{k_4}{k_2^2}` is calculated.
-
-----------
-
-Fix invocation and output can be modified by optional keywords.
-
-The *start* keyword specifies that the first computation should be no
-earlier than the step number given (but will still occur on a multiple
-of *Nfreq*).  The default is step 0.  Often input values can be 0.0 at
-time 0, so setting *start* to a larger value can avoid including a 0.0
-in a longer series.
-
-The *history* keyword stores the Nrecent most recent outputs on Nfreq
-timesteps, so they can be accessed as global outputs of the fix.  Nrecent
-must be >= 1. The default is 1, meaning only the most recent output is
-accessible. For example, if history 10 is specified and Nfreq = 1000,
-then on timestep 20000, the Nfreq outputs from steps 20000, 19000, ...
-11000 are available for access.  See below for details on how to access
-the history values.
-
-For example, this will store the outputs of the previous 10 Nfreq
-time steps, i.e. a window of 10000 time steps:
-
-.. code-block:: LAMMPS
-
-   fix 1 all ave/moments 1 200 1000 v_volume mean history 10
-
-The previous results can be accessed as values in a global array output
-by this fix. Each column of the array is the vector output of the N-th
-preceding Nfreq timestep.  For example, assuming a single moment is
-calculated, the most recent result corresponding to the third input
-value would be accessed as "f_name[3][1]", "f_name[3][4]" is the 4th
-most recent and so on.  The current vector output is always the first
-column of the array, corresponding to the most recent result.
-
-To illustrate the utility of keeping output history, consider using
-this fix in conjunction with :doc:`fix halt <fix_halt>` to stop a run
-automatically if a quantity is converged to within some desired tolerance:
-
-.. code-block:: LAMMPS
-
-   variable target equal etot
-   fix aveg all ave/moments 1 200 1000 v_target mean stddev history 10
-   variable stopcond equal "abs(f_aveg[1]-f_aveg[1][10])<f_aveg[2]"
-   fix fhalt all halt 1000 v_stopcond == 1
-
-In this example, every 1000 time steps, the average and standard
-deviation of the total energy over the previous 200 time steps are
-calculated.  If the difference between the most recent and 10-th most
-recent average is lower than the most recent standard deviation, the run
-is stopped.
-
-----------
-
-Restart, fix_modify, output, run start/stop, minimize info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-No information about this fix is written to :doc:`binary restart files
-<restart>`.
-
-This fix produces a global vector and global array which can be accessed
-by various :doc:`output commands <Howto_output>`.  The values can be
-accessed on any time step, but may not be current.
-
-A global vector is produced with the # of elements = number of moments *
-number of inputs.  The moments are output in the order given in the fix
-definition.  An array is produced having # of rows = length of vector
-output (with an ordering which matches the vector) and # of columns =
-value of *history*. There is always at least one column.
-
-Each element of the global vector or array can be either "intensive" or
-"extensive", depending on whether the values contributing to the element
-are "intensive" or "extensive".  If a compute or fix provides the value
-being time averaged, then the compute or fix determines whether the value
-is intensive or extensive; see the page for that compute or fix for
-further info.  Values produced by a variable are treated as 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>`.
-
-Restrictions
-""""""""""""
-
-This compute is part of the EXTRA-FIX 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:`fix ave/time <fix_ave_time>`,
-
-Default
-"""""""
-
-The option defaults are history = 1, start = 0.
-
-----------
-
-.. _Cramer1:
-
-**(Cramer)** Cramer, Mathematical Methods of Statistics, Princeton University Press (1946).
-
-.. _Joanes1:
-
-**(Joanes)** Joanes, Gill, The Statistician, 47, 183--189 (1998).

doc/src/fix_controller.rst

@@ -98,53 +98,52 @@ the following dynamic equation:
 
    \frac{dc}{dt}  = -\alpha (K_p e + K_i \int_0^t e \, dt + K_d \frac{de}{dt} )
 
-where *c* is the continuous time analog of the control variable, *e*
-=\ *pvar*\ -\ *setpoint* is the error in the process variable, and
-:math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are
-constants set by the corresponding keywords described above. The
-discretized version of this equation is:
+where *c* is the continuous time analog of the control variable,
+*e* =\ *pvar*\ -\ *setpoint* is the error in the process variable, and
+:math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are constants
+set by the corresponding
+keywords described above. The discretized version of this equation is:
 
 .. math::
 
    c_n  = c_{n-1} -\alpha \left( K_p \tau e_n + K_i \tau^2 \sum_{i=1}^n e_i + K_d (e_n - e_{n-1}) \right)
 
-where :math:`\tau = \mathtt{Nevery} \cdot \mathtt{timestep}` is the
-time interval between updates, and the subscripted variables indicate
-the values of *c* and *e* at successive updates.
+where :math:`\tau = \mathtt{Nevery} \cdot \mathtt{timestep}` is the time
+interval between updates,
+and the subscripted variables indicate the values of *c* and *e* at
+successive updates.
 
 From the first equation, it is clear that if the three gain values
 :math:`K_p`, :math:`K_i`, :math:`K_d` are dimensionless constants,
-then :math:`\alpha` must have units of [unit *cvar*\ ]/[unit *pvar*\
-]/[unit time] e.g. [ eV/K/ps ]. The advantage of this unit scheme is
-that the value of the constants should be invariant under a change of
-either the MD timestep size or the value of *Nevery*\ . Similarly, if
-the LAMMPS :doc:`unit style <units>` is changed, it should only be
-necessary to change the value of :math:`\alpha` to reflect this, while
-leaving :math:`K_p`, :math:`K_i`, and :math:`K_d` unaltered.
+then :math:`\alpha` must have
+units of [unit *cvar*\ ]/[unit *pvar*\ ]/[unit time] e.g. [ eV/K/ps
+]. The advantage of this unit scheme is that the value of the
+constants should be invariant under a change of either the MD timestep
+size or the value of *Nevery*\ . Similarly, if the LAMMPS :doc:`unit style <units>` is changed, it should only be necessary to change
+the value of :math:`\alpha` to reflect this, while leaving :math:`K_p`,
+:math:`K_i`, and :math:`K_d` unaltered.
 
 When choosing the values of the four constants, it is best to first
 pick a value and sign for :math:`\alpha` that is consistent with the
-magnitudes and signs of *pvar* and *cvar*\ .  The magnitude of
-:math:`K_p` should then be tested over a large positive range keeping
-:math:`K_i = K_d =0`.  A good value for :math:`K_p` will produce a
-fast response in *pvar*, without overshooting the *setpoint*\ .  For
-many applications, proportional feedback is sufficient, and so
-:math:`K_i = K_d =0` can be used. In cases where there is a
-substantial lag time in the response of *pvar* to a change in *cvar*,
-this can be counteracted by increasing :math:`K_d`. In situations
+magnitudes and signs of *pvar* and *cvar*\ .  The magnitude of :math:`K_p`
+should then be tested over a large positive range keeping :math:`K_i = K_d =0`.
+A good value for :math:`K_p` will produce a fast response in *pvar*,
+without overshooting the *setpoint*\ .  For many applications, proportional
+feedback is sufficient, and so :math:`K_i = K_d =0` can be used. In cases
+where there is a substantial lag time in the response of *pvar* to a change
+in *cvar*, this can be counteracted by increasing :math:`K_d`. In situations
 where *pvar* plateaus without reaching *setpoint*, this can be
-counteracted by increasing :math:`K_i`.  In the language of Charles
-Dickens, :math:`K_p` represents the error of the present, :math:`K_i`
-the error of the past, and :math:`K_d` the error yet to come.
+counteracted by increasing :math:`K_i`.  In the language of Charles Dickens,
+:math:`K_p` represents the error of the present, :math:`K_i` the error of
+the past, and :math:`K_d` the error yet to come.
 
 Because this fix updates *cvar*, but does not initialize its value,
-the initial value :math:`c_0` is that assigned by the user in the
-input script via the :doc:`internal-style variable <variable>`
-command.  This value is used (by every other LAMMPS command that uses
-the variable) until this fix performs its first update of *cvar* after
-*Nevery* timesteps.  On the first update, the value of the derivative
-term is set to zero, because the value of :math:`e_{n-1}` is not yet
-defined.
+the initial value :math:`c_0` is that assigned by the user in the input script via
+the :doc:`internal-style variable <variable>` command.  This value is
+used (by every other LAMMPS command that uses the variable) until this
+fix performs its first update of *cvar* after *Nevery* timesteps.  On
+the first update, the value of the derivative term is set to zero,
+because the value of :math:`e_{n-1}` is not yet defined.
 
 ----------
 
@@ -155,23 +154,21 @@ must produce a global quantity, not a per-atom or local quantity.
 
 If *pvar* begins with "c\_", a compute ID must follow which has been
 previously defined in the input script and which generates a global
-scalar or vector.  See the individual :doc:`compute <compute>` doc
-page for details.  If no bracketed integer is appended, the scalar
+scalar or vector.  See the individual :doc:`compute <compute>` doc page
+for details.  If no bracketed integer is appended, the scalar
 calculated by the compute is used.  If a bracketed integer is
 appended, the Ith value of the vector calculated by the compute is
-used.  Users can also write code for their own compute styles and
-:doc:`add them to LAMMPS <Modify>`.
+used.  Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
 
 If *pvar* begins with "f\_", a fix ID must follow which has been
 previously defined in the input script and which generates a global
 scalar or vector.  See the individual :doc:`fix <fix>` page for
 details.  Note that some fixes only produce their values on certain
 timesteps, which must be compatible with when fix controller
-references the values, or else an error results.  If no bracketed
-integer is appended, the scalar calculated by the fix is used.  If a
-bracketed integer is appended, the Ith value of the vector calculated
-by the fix is used.  Users can also write code for their own fix style
-and :doc:`add them to LAMMPS <Modify>`.
+references the values, or else an error results.  If no bracketed integer
+is appended, the scalar calculated by the fix is used.  If a bracketed
+integer is appended, the Ith value of the vector calculated by the fix
+is used.  Users can also write code for their own fix style and :doc:`add them to LAMMPS <Modify>`.
 
 If *pvar* begins with "v\_", a variable name must follow which has been
 previously defined in the input script.  Only equal-style variables
@@ -185,21 +182,19 @@ variable.
 The target value *setpoint* for the process variable must be a numeric
 value, in whatever units *pvar* is defined for.
 
-The control variable *cvar* must be the name of an
-:doc:`internal-style variable <variable>` previously defined in the
-input script.  Note that it is not specified with a "v\_" prefix, just
-the name of the variable.  It must be an internal-style variable,
-because this fix updates its value directly.  Note that other commands
-can use an equal-style versus internal-style variable interchangeably.
+The control variable *cvar* must be the name of an :doc:`internal-style variable <variable>` previously defined in the input script.  Note
+that it is not specified with a "v\_" prefix, just the name of the
+variable.  It must be an internal-style variable, because this fix
+updates its value directly.  Note that other commands can use an
+equal-style versus internal-style variable interchangeably.
 
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-Currently, 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.
+Currently, 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 produces a global vector with 3 values which can be accessed
 by various :doc:`output commands <Howto_output>`.  The values can be
@@ -216,8 +211,7 @@ variable is in.  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
 """"""""""""

doc/src/fix_deposit.rst

@@ -225,25 +225,22 @@ rotated configuration of the molecule.
 
 .. versionadded:: 21Nov2023
 
-The *var* and *set* keywords can be used together to provide a
-criterion for accepting or rejecting the addition of an individual
-atom, based on its coordinates.  The *name* specified for the *var*
-keyword is the name of an :doc:`equal-style variable <variable>` that
-should evaluate to a zero or non-zero value based on one or two or
-three variables that will store the *x*, *y*, or *z* coordinates of an
-atom (one variable per coordinate).  If used, these other variables
-must be :doc:`internal-style variables <variable>` specified by the
-*set* keyword.  They must be internal-style variables, because this
-command resets their values directly.  The internal-style variables do
-not need to be defined in the input script (though they can be); if
-one (or more) is not defined, then the *set* option creates an
-:doc:`internal-style variable <variable>` with the specified name.
-
-When an atom is about to be created, its :math:`(x,y,z)` coordinates
-become the values for any *set* variable that is defined.  The *var*
-variable is then evaluated.  If the returned value is 0.0, the atom is
-not created.  If it is non-zero, the atom is created.  For an example
-of how to use the set/var keywords in a similar context, see the
+The *var* and *set* keywords can be used together to provide a criterion
+for accepting or rejecting the addition of an individual atom, based on its
+coordinates.  The *name* specified for the *var* keyword is the name of an
+:doc:`equal-style variable <variable>` that should evaluate to a zero or
+non-zero value based on one or two or three variables that will store the
+*x*, *y*, or *z* coordinates of an atom (one variable per coordinate).  If
+used, these other variables must be :doc:`internal-style variables
+<variable>` defined in the input script; their initial numeric value can be
+anything. They must be internal-style variables, because this command
+resets their values directly.  The *set* keyword is used to identify the
+names of these other variables, one variable for the *x*-coordinate of a
+created atom, one for *y*, and one for *z*.  When an atom is created, its
+:math:`(x,y,z)` coordinates become the values for any *set* variable that
+is defined.  The *var* variable is then evaluated.  If the returned value
+is 0.0, the atom is not created.  If it is non-zero, the atom is created.
+For an example of how to use these keywords, see the
 :doc:`create_atoms <create_atoms>` command.
 
 The *rate* option moves the insertion volume in the z direction (3d)
@@ -307,13 +304,12 @@ units of distance or velocity.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the deposition to :doc:`binary restart
-files <restart>`.  This includes information about how many particles
-have been deposited, the random number generator seed, the next
-timestep for deposition, 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 deposition to :doc:`binary restart files <restart>`.  This includes information about how many
+particles have been deposited, the random number generator seed, the
+next timestep for deposition, 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::
 

doc/src/fix_gjf.rst

@@ -1,208 +0,0 @@
-.. index:: fix gjf
-
-fix gjf command
-========================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   fix ID group-ID gjf Tstart Tstop damp seed keyword values ...
-
-* ID, group-ID are documented in :doc:`fix <fix>` command
-* gjf = style name of this fix command
-* Tstart,Tstop = desired temperature at start/end of run (temperature units)
-* Tstart can be a variable (see below)
-* damp = damping parameter (time units)
-* seed = random number seed to use for white noise (positive integer)
-* zero or more keyword/value pairs may be appended
-* keyword = *vel* or *method*
-
-  .. parsed-literal::
-
-       *vel* value = *vfull* or *vhalf*
-         *vfull* = use on-site velocity
-         *vhalf* = use half-step velocity
-       *method* value = *1-8*
-         *1-8* = choose one of the many GJ formulations
-         *7*   = requires input of additional scalar between 0 and 1
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   fix 3 boundary gjf 10.0 10.0 1.0 699483
-   fix 1 all gjf 10.0 100.0 100.0 48279 vel vfull method 4
-   fix 2 all gjf 10.0 10.0 1.0 26488 method 7 0.95
-
-Description
-"""""""""""
-.. versionadded:: 12Jun2025
-
-Apply a Langevin thermostat as described in :ref:`(Gronbech-Jensen-2020) <Gronbech-Jensen-2020>`
-to a group of atoms which models an interaction with a background
-implicit solvent.  As described in the papers cited below, the GJ methods
-provide exact diffusion, drift, and Boltzmann sampling for linear systems for
-any time step within the stability limit. The purpose of this set of methods
-is therefore to significantly improve statistical accuracy at longer time steps
-compared to other thermostats.
-
-The current implementation provides the user with the option to output
-the velocity in one of two forms: *vfull* or *vhalf*. The option *vhalf*
-outputs the 2GJ half-step velocity given in :ref:`Gronbech Jensen/Gronbech-Jensen
-<Gronbech-Jensen-2019>`; for linear systems, this velocity is shown to not
-have any statistical errors for any stable time step. The option *vfull*
-outputs the on-site velocity given in :ref:`Gronbech-Jensen/Farago
-<Gronbech-Jensen-Farago>`; this velocity is shown to be systematically lower
-than the target temperature by a small amount, which grows
-quadratically with the timestep. An overview of statistically correct Boltzmann
-and Maxwell-Boltzmann sampling of true on-site and true half-step velocities is
-given in :ref:`Gronbech-Jensen-2020 <Gronbech-Jensen-2020>`.
-
-This fix allows the use of several GJ methods as listed in :ref:`Gronbech-Jensen-2020 <Gronbech-Jensen-2020>`.
-The GJ-VII method is described in :ref:`Finkelstein <Finkelstein>` and GJ-VIII
-is described in :ref:`Gronbech-Jensen-2024 <Gronbech-Jensen-2024>`.
-The implementation follows the splitting form provided in Eqs. (24) and (25)
-in :ref:`Gronbech-Jensen-2024 <Gronbech-Jensen-2024>`, including the application
-of Gaussian noise values, per the description in
-:ref:`Gronbech-Jensen-2023 <Gronbech-Jensen-2023>`.
-
-
-.. note::
-
-   Unlike the :doc:`fix langevin <fix_langevin>` command which performs force
-   modifications only, this fix performs thermostatting and time integration.
-   Thus you no longer need a separate time integration fix, like :doc:`fix nve <fix_nve>`.
-
-See the :doc:`Howto thermostat <Howto_thermostat>` page for
-a discussion of different ways to compute temperature and perform
-thermostatting.
-
-The desired temperature at each timestep is a ramped value during the
-run from *Tstart* to *Tstop*\ .
-
-*Tstart* can be specified as an equal-style or atom-style
-:doc:`variable <variable>`.  In this case, the *Tstop* setting is
-ignored.  If the value is a variable, it should be specified as
-v_name, where name is the variable name.  In this case, the variable
-will be evaluated each timestep, and its value used to determine the
-target temperature.
-
-Equal-style variables can specify formulas with various mathematical
-functions, and include :doc:`thermo_style <thermo_style>` command
-keywords for the simulation box parameters and timestep and elapsed
-time.  Thus it is easy to specify a time-dependent temperature.
-
-Atom-style variables can specify the same formulas as equal-style
-variables but can also include per-atom values, such as atom
-coordinates.  Thus it is easy to specify a spatially-dependent
-temperature with optional time-dependence as well.
-
-Like other fixes that perform thermostatting, this fix can be used
-with :doc:`compute commands <compute>` that remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.
-
-The *damp* parameter is specified in time units and determines how
-rapidly the temperature is relaxed.  For example, a value of 100.0 means
-to relax the temperature in a timespan of (roughly) 100 time units
-(:math:`\tau` or fs or ps - see the :doc:`units <units>` command).  The
-damp factor can be thought of as inversely related to the viscosity of
-the solvent.  I.e. a small relaxation time implies a high-viscosity
-solvent and vice versa.  See the discussion about :math:`\gamma` and
-viscosity in the documentation for the :doc:`fix viscous <fix_viscous>`
-command for more details.
-
-The random # *seed* must be a positive integer.  A Marsaglia random
-number generator is used.  Each processor uses the input seed to
-generate its own unique seed and its own stream of random numbers.
-Thus the dynamics of the system will not be identical on two runs on
-different numbers of processors.
-
-----------
-
-The keyword/value option pairs are used in the following ways.
-
-The keyword *vel* determines which velocity is used to determine
-quantities of interest in the simulation.
-
-The keyword *method* selects one of the eight GJ-methods implemented in LAMMPS.
-
-----------
-
-Restart, fix_modify, output, run start/stop, minimize info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-No information about this fix is written to :doc:`binary restart files <restart>`.
-Because the state of the random number generator is not saved in restart files,
-this means you cannot do "exact" restarts with this fix, where the simulation
-continues on the same as if no restart had taken place.  However, in a
-statistical sense, a restarted simulation should produce the same behavior.
-Additionally, the GJ methods implement noise exclusively within each time step
-(unlike the BBK thermostat of the fix-langevin). The restart is done with
-either vfull or vhalf velocity output for as long as the choice of vfull/vhalf
-is the same for the simulation as it is in the restart file.
-
-The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
-fix.  You can use it to assign a temperature :doc:`compute <compute>`
-you have defined to this fix which will be used in its thermostatting
-procedure, as described above.  For consistency, the group used by
-this fix and by the compute should be the same.
-
-This fix can ramp its target temperature over multiple runs, using the
-*start* and *stop* keywords of the :doc:`run <run>` command.  See the
-:doc:`run <run>` command for details of how to do this.
-
-This fix is not invoked during :doc:`energy minimization <minimize>`.
-
-Restrictions
-""""""""""""
-
-This fix is not compatible with run_style respa. It is not compatible with
-accelerated packages such as KOKKOS.
-
-Related commands
-""""""""""""""""
-
-:doc:`fix langevin <fix_langevin>`, :doc:`fix nvt <fix_nh>`
-
-Default
-"""""""
-
-The option defaults are vel = vhalf, method = 1.
-
-----------
-
-.. _Gronbech-Jensen-2020:
-
-**(Gronbech-Jensen-2020)** Gronbech-Jensen, Mol Phys 118, e1662506 (2020).
-
-.. _Gronbech-Jensen-2019:
-
-**(Gronbech Jensen/Gronbech-Jensen)** Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511 (2019)
-
-.. _Gronbech-Jensen-Farago:
-
-**(Gronbech-Jensen/Farago)** Gronbech-Jensen and Farago, Mol Phys, 111, 983 (2013).
-
-.. _Finkelstein:
-
-**(Finkelstein)** Finkelstein, Cheng, Florin, Seibold, Gronbech-Jensen, J. Chem. Phys., 155, 18 (2021)
-
-.. _Gronbech-Jensen-2024:
-
-**(Gronbech-Jensen-2024)** Gronbech-Jensen, J. Stat. Phys. 191, 137 (2024).
-
-.. _Gronbech-Jensen-2023:
-
-**(Gronbech-Jensen-2023)** Gronbech-Jensen, J. Stat. Phys. 190, 96 (2023).

doc/src/fix_langevin.rst

@@ -56,7 +56,7 @@ Examples
 Description
 """""""""""
 
-Apply a Langevin thermostat as described in :ref:`(Bruenger) <Bruenger1>`
+Apply a Langevin thermostat as described in :ref:`(Schneider) <Schneider1>`
 to a group of atoms which models an interaction with a background
 implicit solvent.  Used with :doc:`fix nve <fix_nve>`, this command
 performs Brownian dynamics (BD), since the total force on each atom
@@ -241,13 +241,6 @@ to zero by subtracting off an equal part of it from each atom in the
 group.  As a result, the center-of-mass of a system with zero initial
 momentum will not drift over time.
 
-.. deprecated:: TDB
-
-The *gjf* keyword in fix langevin is deprecated and will be removed
-soon.  The GJF functionality has been moved to its own fix style
-:doc:`fix gjf <fix_gjf>` and it is strongly recommended to use that
-fix instead.
-
 The keyword *gjf* can be used to run the :ref:`Gronbech-Jensen/Farago
 <Gronbech-Jensen>` time-discretization of the Langevin model.  As
 described in the papers cited below, the purpose of this method is to
@@ -331,16 +324,14 @@ types, tally = no, zero = no, gjf = no.
 
 ----------
 
-.. _Bruenger1:
-
-**(Bruenger)** Bruenger, Brooks, and Karplus, Chem. Phys. Lett. 105, 495 (1982).
-[Previously attributed to Schneider and Stoll, Phys. Rev. B 17, 1302 (1978).
-Implementation remains unchanged.]
-
 .. _Dunweg1:
 
 **(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
 
+.. _Schneider1:
+
+**(Schneider)** Schneider and Stoll, Phys Rev B, 17, 1302 (1978).
+
 .. _Gronbech-Jensen:
 
 **(Gronbech-Jensen)** Gronbech-Jensen and Farago, Mol Phys, 111, 983

doc/src/fix_qeq_rel_reaxff.rst

@@ -37,18 +37,18 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: 2Apr2025
+.. versionadded:: 19Nov2024
 
-This fix implements the QEqR method :ref:`(Lalli) <lalli2>` for charge
-equilibration, which differs from the QEq charge equilibration method
-:ref:`(Rappe and Goddard) <Rappe4>` only in how external electric fields
-are accounted for. This fix therefore raises a warning when used without
-:doc:`fix efield <fix_efield>` since :doc:`fix qeq/reaxff <fix_qeq_reaxff>`
-should be used when no external electric field is present.  Charges are
-computed with the QEqR method by minimizing the electrostatic energy of
-the system in the same way as the QEq method but where the absolute
-electronegativity, :math:`\chi_i`, of each atom in the QEq method is
-replaced with an effective electronegativity given by
+This fix implements the QEqR method for charge equilibration, which
+differs from the QEq charge equilibration method :ref:`(Rappe and
+Goddard) <Rappe4>` only in how external electric fields are accounted
+for.  This fix therefore raises a warning when used without :doc:`fix
+efield <fix_efield>` since :doc:`fix qeq/reaxff <fix_qeq_reaxff>` should
+be used without an external electric field.  Charges are computed with
+the QEqR method by minimizing the electrostatic energy of the system in
+the same way as the QEq method but where the absolute electronegativity,
+:math:`\chi_i`, of each atom in the QEq method is replaced with an
+effective electronegativity given by
 
 .. math::
    \chi_{\mathrm{r}i} = \chi_i + \frac{\sum_{j=1}^{N} \beta(\phi_i - \phi_j) S_{ij}}
@@ -61,9 +61,8 @@ external electric field and :math:`S_{ij}` is the overlap integral
 between atoms :math:`i` and :math:`j`.  This formulation is advantageous
 over the method used by :doc:`fix qeq/reaxff <fix_qeq_reaxff>` to
 account for an external electric field in that it permits periodic
-boundaries in the direction of an external electric field and in
-that it does not worsen long-range charge transfer seen with
-QEq. See :ref:`Lalli <lalli2>` for further details.
+boundaries in the direction of an external electric field and in that it
+does not worsen long-range charge transfer seen with QEq.
 
 This fix is typically used in conjunction with the ReaxFF force field
 model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
@@ -185,10 +184,6 @@ scale = 1.0 and maxiter = 200
 
 ----------
 
-.. _lalli2:
-
-**(Lalli)** Lalli and Giusti, Journal of Chemical Physics, 162, 174311 (2025).
-
 .. _Rappe4:
 
 **(Rappe)** Rappe and Goddard III, Journal of Physical Chemistry, 95,

doc/src/fix_qtpie_reaxff.rst

@@ -59,7 +59,8 @@ and atom :math:`j`.
 The effect of an external electric field can be incorporated into the QTPIE
 method by modifying the absolute or effective electronegativities of each
 atom :ref:`(Chen) <qtpie-Chen>`. This fix models the effect of an external
-electric field by using the effective electronegativity :ref:`(Lalli) <lalli>`
+electric field by using the effective electronegativity given in
+:ref:`(Gergs) <Gergs>`:
 
 .. math::
    \tilde{\chi}_{\mathrm{r}i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j + \beta(\phi_i - \phi_j)) S_{ij}}
@@ -67,8 +68,7 @@ electric field by using the effective electronegativity :ref:`(Lalli) <lalli>`
 
 where :math:`\beta` is a scaling factor and :math:`\phi_i` and :math:`\phi_j`
 are the electric potentials at the positions of atoms :math:`i` and :math:`j`
-due to the external electric field. Additional details regarding the
-implementation and performance of this fix are provided in :ref:`Lalli <lalli>`.
+due to the external electric field.
 
 This fix is typically used in conjunction with the ReaxFF force
 field model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
@@ -206,9 +206,10 @@ scale = 1.0 and maxiter = 200
 **(Chen)** Chen, Jiahao. Theory and applications of fluctuating-charge models.
 University of Illinois at Urbana-Champaign, 2009.
 
-.. _lalli:
+.. _Gergs:
 
-**(Lalli)** Lalli and Giusti, Journal of Chemical Physics, 162, 174311 (2025).
+**(Gergs)** Gergs, Dirkmann and Mussenbrock.
+Journal of Applied Physics 123.24 (2018).
 
 .. _qeq-Aktulga2:
 

doc/src/fix_set.rst

@@ -1,175 +0,0 @@
-.. index:: fix set
-
-fix set command
-===============
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   fix ID group-ID set Nfreq rnflag set-args
-
-* ID, group-ID are documented in :doc:`fix <fix>` command
-* set = style name of this fix command
-* Nfreq = reset per-atom properties every this many timesteps
-* rnflag = 1 to reneighbor on next timestep, 0 to not
-* set-args = identical to args for the :doc:`set <set>` command
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   fix 10 all set 1 0 group all i_dump v_new
-   fix 10 all set 1 0 group all i_dump v_turnoff
-
-Description
-"""""""""""
-
-.. versionadded:: 12Jun2025
-
-Reset one or more properties of one or more atoms once every *Nfreq*
-steps during a simulation.
-
-If the *rnflag* for reneighboring is set to 1, then a reneighboring
-will be triggered on the next timestep (since the fix set operation
-occurs at the end of the current timestep).  This is important to do
-if this command changes per-atom properties that need to be
-communicated to ghost atoms.  If this is not the case, an *rnflag*
-setting of 0 can be used; reneighboring will only be triggered on
-subsequent timesteps by the usual neighbor list criteria; see the
-:doc:`neigh_modify command <neigh_modify>`.
-
-Here are two examples where an *rnflag* setting of 1 are needed.  If a
-custom per-atom property is changed and the :doc:`fix property/atom
-<fix_property_atom>` command to create the property used the *ghost
-yes* keyword.  Or if per-atom charges are changed, all pair styles
-which compute Coulombic interactions require charge values for ghost
-atoms.  In both these examples, the re-neighboring will trigger the
-changes in the owned atom properties to be immediately communicated to
-ghost atoms.
-
-The arguments following *Nfreq* and *rnflag* are identical to those
-allowed for the :doc:`set <set>` command, as in the examples above and
-below.
-
-Note that the group-ID setting for this command is ignored.  The
-syntax for the :doc:`set <set>` arguments allows selection of which
-atoms have their properties reset.
-
-This command can only be used to reset an atom property using a
-per-atom variable.  This option in allowed by many, but not all, of
-the keyword/value pairs supported by the :doc:`set <set>` command.
-The reason for this restriction is that if a per-atom variable is not
-used, this command will typically not change atom properties during
-the simulation.
-
-The :doc:`set <set>` command can be used with similar syntax to this
-command to reset atom properties once before or between simulations.
-
-----------
-
-Here is an example of input script commands which will output atoms
-into a dump file only when their x-velocity crosses a threshold value
-*vthresh* for the first time.  Their position and x-velocity will then
-be output every step for *twindow* timesteps.
-
-.. code-block:: LAMMPS
-
-   variable        vthresh equal 2             # threshold velocity
-   variable        twindow equal 10            # dump for this many steps
-   #
-   # define custom property i_dump to store timestep threshold is crossed
-   #
-   fix             2 all property/atom i_dump
-   set             group all i_dump -1
-   #
-   # fix set command checks for threshold crossings every step
-   # resets i_dump from -1 to current timestep when crossing occurs
-   #
-   variable        start atom "vx > v_vthresh && i_dump == -1"
-   variable        new atom ternary(v_start,step,i_dump)
-   fix             3 all set 1 0 group all i_dump v_new
-   #
-   # dump command with thresh which enforces twindow
-   #
-   dump            1 all custom 1 tmp.dump id x y vx i_dump
-   variable        dumpflag atom "i_dump >= 0 && (step-i_dump) < v_twindow"
-   dump_modify     1 thresh v_dumpflag == 1
-   #
-   # run the simulation
-   # final dump with all atom IDs which crossed threshold on which timestep
-   #
-   run             1000
-   write_dump      all custom tmp.dump.final id i_dump modify thresh i_dump >= 0
-
-The tmp.dump.final file lists which atoms crossed the velocity
-threshold.  This command will print the *twindow* timesteps when a
-specific atom ID (104 in this case) was output in the tmp.dump file:
-
-.. code-block:: LAMMPS
-
-   % grep "^104 " tmp.dump
-
-If these commands are used instead of the above, then an atom can
-cross the velocity threshold multiple times, and will be output for
-*twindow* timesteps each time.  However the write_dump command is no
-longer useful.
-
-.. code-block:: LAMMPS
-
-   variable        vthresh equal 2             # threshold velocity
-   variable        twindow equal 10            # dump for this many steps
-   #
-   # define custom property i_dump to store timestep threshold is crossed
-   #
-   fix             2 all property/atom i_dump
-   set             group all i_dump -1
-   #
-   # fix set command checks for threshold crossings every step
-   # resets i_dump from -1 to current timestep when crossing occurs
-   #
-   variable        start atom "vx > v_vthresh && i_dump == -1"
-   variable        turnon atom ternary(v_start,step,i_dump)
-   variable        stop atom "v_turnon >= 0 && (step-v_turnon) < v_twindow"
-   variable        turnoff atom ternary(v_stop,v_turnon,-1)
-   fix             3 all set 1 0 group all i_dump v_turnoff
-   #
-   # dump command with thresh which enforces twindow
-   #
-   dump            1 all custom 1 tmp.dump id x y vx i_dump
-   variable        dumpflag atom "i_dump >= 0 && (step-i_dump) < v_twindow"
-   dump_modify     1 thresh v_dumpflag == 1
-   #
-   # run the simulation
-   #
-   run             1000
-
-----------
-
-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 global 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 not invoked during
-:doc:`energy minimization <minimize>`.
-
-Restrictions
-""""""""""""
-
-none
-
-Related commands
-""""""""""""""""
-
-:doc:`set <set>`
-
-Default
-"""""""
-
-none

doc/src/kspace_style.rst

@@ -32,7 +32,6 @@
 .. index:: kspace_style msm/cg/omp
 .. index:: kspace_style msm/dielectric
 .. index:: kspace_style scafacos
-.. index:: kspace_style zero
 
 kspace_style command
 ====================
@@ -44,7 +43,7 @@ Syntax
 
    kspace_style style value
 
-* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/disp/dipole* or *ewald/omp* or *ewald/electrode* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *pppm/dielectic* or *pppm/disp/dielectric* or *pppm/electrode* or *pppm/electrode/intel* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *msm/dielectric* or *scafacos* or *zero*
+* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/disp/dipole* or *ewald/omp* or *ewald/electrode* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *pppm/dielectic* or *pppm/disp/dielectric* or *pppm/electrode* or *pppm/electrode/intel* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *msm/dielectric* or *scafacos*
 
   .. parsed-literal::
 
@@ -122,7 +121,6 @@ Syntax
        *scafacos* values = method accuracy
          method = fmm or p2nfft or p3m or ewald or direct
          accuracy = desired relative error in forces
-       *zero* value = none
 
 Examples
 """"""""
@@ -134,7 +132,6 @@ Examples
    kspace_style msm 1.0e-4
    kspace_style scafacos fmm 1.0e-4
    kspace_style none
-   kspace_style zero
 
 Used in input scripts:
 
@@ -378,13 +375,6 @@ other ScaFaCoS options currently exposed to LAMMPS.
 
 ----------
 
-.. versionadded:: 12Jun2025
-
-The *zero* style does not do any calculations, but is compatible
-with all pair styles that require some version of a kspace style.
-
-----------
-
 The specified *accuracy* determines the relative RMS error in per-atom
 forces calculated by the long-range solver.  It is set as a
 dimensionless number, relative to the force that two unit point

doc/src/molecule.rst

@@ -34,7 +34,7 @@ Syntax
        *ioff* value = Ioff
          Ioff = offset to add to improper types
        *scale* value = sfactor
-         sfactor = scale factor to apply to the size, mass, and dipole of the molecule
+         sfactor = scale factor to apply to the size and mass of the molecule
 
 Examples
 """"""""
@@ -42,7 +42,6 @@ Examples
 .. code-block:: LAMMPS
 
    molecule 1 mymol.txt
-   molecule water tip3p.json
    molecule 1 co2.txt h2o.txt
    molecule CO2 co2.txt boff 3 aoff 2
    molecule 1 mymol.txt offset 6 9 18 23 14
@@ -66,7 +65,7 @@ templates include:
 * :doc:`atom_style template <atom_style>`
 
 The ID of a molecule template can only contain alphanumeric characters
-and underscores, same as other IDs in LAMMPS.
+and underscores.
 
 A single template can contain multiple molecules, listed one per file.
 Some of the commands listed above currently use only the first
@@ -75,11 +74,6 @@ contains multiple molecules.  The :doc:`atom_style template
 <atom_style>` command allows multiple-molecule templates to define a
 system with more than one templated molecule.
 
-The molecule file can be either in a *native* format or in `JSON format
-<https://www.json.org/>`_.  The details of the two formats are described
-below.  When referencing multiple molecule files in a single *molecule*
-command, each of those files may be either format.
-
 Each filename can be followed by optional keywords which are applied
 only to the molecule in the file as used in this template.  This is to
 make it easy to use the same molecule file in different molecule
@@ -101,45 +95,40 @@ use that attribute (e.g. no bonds).
    labels will determine the actual types directly depending on the
    current :doc:`labelmap <labelmap>` settings.
 
-The *scale* keyword scales the size of the molecule.  This can be useful
-for modeling polydisperse granular rigid bodies.  The scale factor is
-applied to each of these properties in the molecule file, if they are
-defined: the individual particle coordinates (Coords or "coords"
-section), the individual mass of each particle (Masses or "masses"
-section), the individual diameters of each particle (Diameters or
-"diameters" section), the per-atom dipoles (Dipoles or "dipoles"
-section) the total mass of the molecule (header keyword = mass), the
-center-of-mass of the molecule (header keyword = com), and the moments
-of inertia of the molecule (header keyword = inertia).
+The *scale* keyword scales the size of the molecule.  This can be
+useful for modeling polydisperse granular rigid bodies.  The scale
+factor is applied to each of these properties in the molecule file, if
+they are defined: the individual particle coordinates (Coords
+section), the individual mass of each particle (Masses section), the
+individual diameters of each particle (Diameters section), the total
+mass of the molecule (header keyword = mass), the center-of-mass of
+the molecule (header keyword = com), and the moments of inertia of the
+molecule (header keyword = inertia).
 
 .. note::
 
    The molecule command can be used to define molecules with bonds,
-   angles, dihedrals, impropers, and special bond lists of neighbors
+   angles, dihedrals, impropers, or special bond lists of neighbors
    within a molecular topology, so that you can later add the molecules
    to your simulation, via one or more of the commands listed above.
-   Since this topology-related information requires that suitable
-   storage is reserved when LAMMPS creates the simulation box (e.g. when
-   using the :doc:`create_box <create_box>` command or the
-   :doc:`read_data <read_data>` command) suitable space has to be
-   reserved at that step so you do not overflow those pre-allocated data
-   structures when adding molecules later.  Both the :doc:`create_box
-   <create_box>` command and the :doc:`read_data <read_data>` command
-   have "extra" options which ensure extra space is allocated for
-   storing topology info for molecules that are added later.  This
-   feature is *not* available for the :doc:`read_restart command
-   <read_restart>`, thus binary restart files need to be converted
-   to data files first.
+   Since this topology-related information requires that suitable storage
+   is reserved when LAMMPS creates the simulation box (e.g. when using
+   the :doc:`create_box <create_box>` command or the
+   :doc:`read_data <read_data>` command) suitable space has to be reserved
+   so you do not overflow those pre-allocated data structures when adding
+   molecules later.  Both the :doc:`create_box <create_box>` command and
+   the :doc:`read_data <read_data>` command have "extra" options which
+   ensure space is allocated for storing topology info for molecules that
+   are added later.
 
 ----------
 
-Format of a native molecule file
-""""""""""""""""""""""""""""""""
+Format of a molecule file
+"""""""""""""""""""""""""
 
-The format of an "native" individual molecule file looks similar but is
-*different* from that of a data file read by the :doc:`read_data
-<read_data>` commands.  Here is a simple example for a TIP3P water
-molecule:
+The format of an individual molecule file looks similar but is
+different than that of a data file read by the :doc:`read_data <read_data>`
+commands.  Here is a simple example for a TIP3P water molecule:
 
 .. code-block::
 
@@ -680,191 +669,6 @@ the file format.
 
 ----------
 
-Format of a JSON molecule file
-""""""""""""""""""""""""""""""
-
-.. versionadded:: 12Jun2025
-
-The format of a JSON format individual molecule file must follow the
-`JSON format <https://www.json.org/>`_, which evolved from the
-JavaScript programming language as a programming-language-neutral data
-interchange language.  The JSON syntax is independent of its content,
-and thus the data in the file must follow suitable conventions to be
-correctly processed.  LAMMPS provides a `JSON schema file
-<https://json-schema.org/>`_ for JSON format molecule files in the
-:ref:`tools/json folder <json>` to represent those conventions.  Using
-the schema file any JSON format molecule files can be validated.
-Validating a particular JSON format molecule file against this schema
-ensures that both, the JSON syntax requirement *and* the LAMMPS
-conventions for molecule templates are followed.  This is a formal check
-only and thus it **cannot** check whether the file contents are
-physically meaningful.
-
-Here is a simple example for the same TIP3P water molecule from above in
-JSON format and also using :doc:`type labels <labelmap>` instead of
-numeric types:
-
-.. code-block:: json
-
-   {
-       "application": "LAMMPS",
-       "format": "molecule",
-       "revision": 1,
-       "title": "Water molecule. TIP3P geometry",
-       "schema": "https://download.lammps.org/json/molecule-schema.json",
-       "units": "real",
-       "coords": {
-           "format": ["atom-id", "x", "y", "z"],
-           "data": [
-               [1,  0.00000, -0.06556,  0.00000],
-               [2,  0.75695,  0.52032,  0.00000],
-               [3, -0.75695,  0.52032,  0.00000]
-           ]
-       },
-       "types": {
-           "format": ["atom-id", "type"],
-           "data": [
-               [1,  "OW"],
-               [2,  "HO1"],
-               [3,  "HO1"]
-           ]
-       },
-       "charges": {
-           "format": ["atom-id", "charge"],
-           "data": [
-               [1, -0.834],
-               [2,  0.417],
-               [3,  0.417]
-           ]
-       },
-       "bonds": {
-           "format": ["bond-type", "atom1", "atom2"],
-           "data": [
-               ["OW-HO1",  1,  2],
-               ["OW-HO1",  1,  3]
-           ]
-       },
-       "angles": {
-           "format": ["angle-type", "atom1", "atom2", "atom3"],
-           "data": [
-               ["HO1-OW-HO1",  2,  1,  3]
-           ]
-       }
-   }
-
-Unlike with the native molecule file format, there are no header or body
-sections, just a list of keywords with associated data.  JSON format
-data is read, parsed, and stored in an internal dictionary data
-structure in one step and thus the order of keywords is not relevant.
-
-Data for keywords is either provided directly following the keyword or
-as a *data block*.  A *data block* is a list that has to include two
-keywords, "format" and "data", where the former lists keywords of the
-properties that are stored in the columns of the "data" lists.  The
-names and order of entries in the "format" list (and thus how the data
-is interpreted) are currently fixed.
-
-Since the length of the various lists can be easily obtained from the
-internal data structure, several header keywords of the "native" molecule
-file are not needed.  On the other hand, some additional keywords are
-required to identify the conventions applied to the generic JSON file
-format.  The structure of the data itself mostly follows what is used
-for the "native" molecule file format.
-
-.. list-table::
-   :header-rows: 1
-
-   * - Keyword
-     - Argument(s)
-     - Required
-     - Description
-   * - application
-     - "LAMMPS"
-     - yes
-     - indicates a LAMMPS JSON file; files from other applications may be accepted in the future
-   * - format
-     - "molecule"
-     - yes
-     - indicates a molecule template file
-   * - revision
-     - an integer
-     - yes
-     - currently 1, to facility backward compatibility on changes to the conventions
-   * - title
-     - a string
-     - no
-     - information about the template which will echoed to the screen and log
-   * - schema
-     - URL as string
-     - no
-     - location of a JSON schema file for validating the molecule file format
-   * - units
-     - a string
-     - no
-     - indicates :doc:`units settings <units>` for this molecule template
-   * - com
-     - list with 3 doubles
-     - no
-     - overrides the auto-computed center-of-mass for the template
-   * - masstotal
-     - double
-     - no
-     - overrides the auto-computed total mass for the template
-   * - inertia
-     - list with 6 doubles
-     - no
-     - overrides the auto-computed moments of inertia
-   * - coords
-     - a data block
-     - no
-     - contains atom positions with the format "atom-id", "x", "y", "z" (same as Coords)
-   * - types
-     - a data block
-     - yes
-     - assigns atom types to atoms with the format "atom-id", "type" (same as Types)
-   * - molecule
-     - a data block
-     - no
-     - assigns molecule-IDs to atoms with the format "atom-id", "molecule-id" (same as Molecules)
-   * - fragments
-     - a data block
-     - no
-     - assigns atom-ids to fragment-IDs with the format "fragment-id", "atom-id-list" (same as Fragments)
-   * - charges
-     - a data block
-     - no
-     - assigns charges to atoms with the format "atom-id", "charge" (same as Charges)
-   * - dipoles
-     - a data block
-     - no
-     - assigns point dipoles to atoms with the format "atom-id", "mux", "muy", "muz" (same as Dipoles)
-   * - diameters
-     - a data block
-     - no
-     - assigns diameters to atoms with the format "atom-id", "diameter" (same as Diameters)
-   * - masses
-     - a data block
-     - no
-     - assigns per-atom masses to atoms with the format "atom-id", "mass" (same as Masses)
-   * - bonds
-     - a data block
-     - no
-     - defines bonds in the molecule template with the format "bond-type", "atom1", "atom2" (same as Bonds without bond-ID)
-   * - angles
-     - a data block
-     - no
-     - defines angles in the molecule template with the format "angle-type", "atom1", "atom2", "atom3" (same as Angles without angle-ID)
-   * - dihedrals
-     - a data block
-     - no
-     - defines dihedrals in the molecule template with the format "dihedral-type", "atom1", "atom2", "atom3", "atom4" (same as Dihedrals without dihedral-ID)
-   * - impropers
-     - a data block
-     - no
-     - defines impropers in the molecule template with the format "improper-type", "atom1", "atom2", "atom3", "atom4" (same as Impropers without improper-ID)
-
-----------
-
 Restrictions
 """"""""""""
 

doc/src/pair_granular.rst

@@ -44,7 +44,7 @@ Examples
    pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 heat area 0.1
 
    pair_style granular
-   pair_coeff * * mdr 5e6 0.4 1.9e5 2.0 0.5 0.5 tangential linear_history 940.0 1.0 0.7 rolling sds 2.7e5 0.0 0.6 damping mdr 1
+   pair_coeff * * mdr 5e6 0.4 1.9e5 2.0 0.5 0.5 tangential linear_history 940.0 0.0 0.7 rolling sds 2.7e5 0.0 0.6 damping none
 
 Description
 """""""""""
@@ -88,8 +88,7 @@ and their required arguments are:
 3. *hertz/material* : E, :math:`\eta_{n0}` (or :math:`e`), :math:`\nu`
 4. *dmt* : E, :math:`\eta_{n0}` (or :math:`e`), :math:`\nu`, :math:`\gamma`
 5. *jkr* : E, :math:`\eta_{n0}` (or :math:`e`), :math:`\nu`, :math:`\gamma`
-6. *mdr* : :math:`E`, :math:`\nu`, :math:`Y`, :math:`\Delta\gamma`,
-   :math:`\psi_b`, :math:`\eta_{n0}`
+6. *mdr* : :math:`E`, :math:`\nu`, :math:`Y`, :math:`\Delta\gamma`, :math:`\psi_b`, :math:`e`
 
 Here, :math:`k_n` is spring stiffness (with units that depend on model
 choice, see below); :math:`\eta_{n0}` is a damping prefactor (or, in its
@@ -178,8 +177,6 @@ two-part series :ref:`Zunker and Kamrin Part I <Zunker2024I>` and
 :ref:`Zunker and Kamrin Part II <Zunker2024II>`. Further development
 and demonstrations of its application to industrially relevant powder
 compaction processes are presented in :ref:`Zunker et al. <Zunker2025>`.
-If you use the *mdr* normal model the only supported damping option is
-the *mdr* damping class described below.
 
 The model requires the following inputs:
 
@@ -203,8 +200,8 @@ The model requires the following inputs:
    triggered. Lower values of :math:`\psi_b` delay the onset of the bulk elastic
    response.
 
-   6. *Damping coefficent* :math:`\eta_{n0} \ge 0` : The damping coefficient
-   is a tunable parameter that controls damping in the normal direction.
+   6. *Coefficient of restitution* :math:`0 \le e \le 1` : The coefficient of
+   restitution is a tunable parameter that controls damping in the normal direction.
 
 .. note::
 
@@ -216,12 +213,18 @@ The *mdr* model produces a nonlinear force-displacement response, therefore the
 critical timestep :math:`\Delta t` depends on the inputs and level of
 deformation. As a conservative starting point the timestep can be assumed to be
 dictated by the bulk elastic response such that
-:math:`\Delta t = 0.08\sqrt{m/k_\textrm{bulk}}`, where :math:`m` is the mass of
+:math:`\Delta t = 0.35\sqrt{m/k_\textrm{bulk}}`, where :math:`m` is the mass of
 the smallest particle and :math:`k_\textrm{bulk} = \kappa R_\textrm{min}` is an
 effective stiffness related to the bulk elastic response.
 Here, :math:`\kappa = E/(3(1-2\nu))` is the bulk modulus and
 :math:`R_\textrm{min}` is the radius of the smallest particle.
 
+.. note::
+
+   The *mdr* model requires some specific settings to function properly,
+   please read the following text carefully to ensure all requirements are
+   followed.
+
 The *atom_style* must be set to *sphere 1* to enable dynamic particle
 radii. The *mdr* model is designed to respect the incompressibility of
 plastic deformation and inherently tracks free surface displacements
@@ -250,6 +253,13 @@ algorithm see :ref:`Zunker et al. <Zunker2025>`.
 
    newton off
 
+The damping model must be set to *none*. The *mdr* model already has a built
+in damping model.
+
+.. code-block:: LAMMPS
+
+   pair_coeff * * mdr 5e6 0.4 1.9e5 2 0.5 0.5 damping none
+
 The definition of multiple *mdr* models in the *pair_style* is currently not
 supported. Similarly, the *mdr* model cannot be combined with a different normal
 model in the *pair_style*. Physically this means that only one homogeneous
@@ -260,7 +270,7 @@ The *mdr* model currently only supports *fix wall/gran/region*, not
 any *fix wall/gran/region* commands must also use the *mdr* model.
 Additionally, the following *mdr* inputs must match between the
 *pair_style* and *fix wall/gran/region* definitions: :math:`E`,
-:math:`\nu`, :math:`Y`, :math:`\psi_b`, and :math:`\eta_{n0}`. The exception
+:math:`\nu`, :math:`Y`, :math:`\psi_b`, and :math:`e`. The exception
 is :math:`\Delta\gamma`, which may vary, permitting different
 adhesive behaviors between particle-particle and particle-wall interactions.
 
@@ -326,7 +336,6 @@ for the damping model currently supported are:
 3. *viscoelastic*
 4. *tsuji*
 5. *coeff_restitution*
-6. *mdr* (class) : :math:`d_{type}`
 
 If the *damping* keyword is not specified, the *viscoelastic* model is
 used by default.
@@ -416,37 +425,6 @@ the damping coefficient, it accurately reproduces the specified coefficient of
 restitution for both monodisperse and polydisperse particle pairs.  This damping
 model is not compatible with cohesive normal models such as *JKR* or *DMT*.
 
-The *mdr* damping class contains multiple damping models that can be toggled between
-by specifying different integer values for the :math:`d_{type}` input parameter. This
-damping option is only compatible with the normal *mdr* contact model.
-
-Setting :math:`d_{type} = 1` is the suggested damping option. This specifies a damping
-model that takes into account the contact stiffness :math:`k_{mdr}` calculated
-by the normal *mdr* contact model to determine the damping coefficient:
-
-.. math::
-
-   \eta_n = \eta_{n0} (m_{eff}k_{mdr})^{1/2},
-
-where :math:`k_{mdr}` is proportional to contact radius :math:`a_{mdr}` tracked by the
-normal *mdr* contact model:
-
-.. math::
-
-   k_{mdr} = 2 E_{eff} a_{mdr}.
-
-In this case, :math:`\eta_{n0}` is simply a dimensionless coefficient that scales the
-the overall damping coefficient.
-
-The other supported option is :math:`d_{type} = 2`, which defines a simple damping model
-similar to the *velocity* option
-
-.. math::
-
-   \eta_n = \eta_{n0},
-
-but has additional checks to avoid non-physical damping after plastic deformation.
-
 The total normal force is computed as the sum of the elastic and
 damping components:
 
@@ -1090,8 +1068,8 @@ a bulk elastic response. Journal of the Mechanics and Physics of Solids,
 
 **(Zunker et al, 2025)** Zunker, W., Dunatunga, S., Thakur, S.,
 Tang, P., & Kamrin, K. (2025). Experimentally validated DEM for large
-deformation powder compaction: Mechanically-derived contact model and
-screening of non-physical contacts. Powder Technology, 120972.
+deformation powder compaction: mechanically-derived contact model and
+screening of non-physical contacts.
 
 .. _Luding2008:
 

doc/src/pair_hybrid.rst

@@ -100,56 +100,6 @@ first is assigned to intra-molecular interactions (i.e. both atoms
 have the same molecule ID), the second to inter-molecular interactions
 (i.e. interacting atoms have different molecule IDs).
 
-.. admonition:: When **NOT** to use a hybrid pair style
-   :class: warning
-
-   Using pair style *hybrid* can be very tempting to use if you need a
-   **many-body potential** supporting a mix of elements for which you
-   cannot find a potential file that covers *all* of them.  Regardless
-   of how this is set up, there will be *errors*.  The major use case
-   where the error is *small*, is when the many-body sub-styles are used
-   on different objects (for example a slab and a liquid, a metal and a
-   nano-machining work piece).  In that case the *mixed* terms
-   **should** be provided by a pair-wise additive potential (like
-   Lennard-Jones or Morse) to avoid unexpected behavior and reduce
-   errors.  LAMMPS cannot easily check for this condition and thus will
-   accept good and bad choices alike.
-
-   Outside of this, we *strongly* recommend *against* using pair style
-   hybrid with many-body potentials for the following reasons:
-
-   1. When trying to combine EAM or MEAM potentials, there is a *large*
-      error in the embedding term, since it is computed separately for
-      each sub-style only.
-
-   2. When trying to combine many-body potentials like Stillinger-Weber,
-      Tersoff, AIREBO, Vashishta, or similar, you have to understand
-      that the potential of a sub-style cannot be applied in a pair-wise
-      fashion but will need to be applied to multiples of atoms
-      (e.g. a Tersoff potential of elements A and B includes the
-      interactions A-A, B-B, A-B, A-A-A, A-A-B, A-B-B, A-B-A, B-A-A,
-      B-A-B, B-B-A, B-B-B; AIREBO also considers all quadruples of
-      atom elements).
-
-   3. When one of the sub-styles uses charge-equilibration (= QEq; like
-      in ReaxFF or COMB) you have inconsistent QEq behavior because
-      either you try to apply QEq to *all* atoms but then you are
-      missing the QEq parameters for the non-QEq pair style (and it
-      would be inconsistent to apply QEq for pair styles that are not
-      parameterized for QEq) or else you would have either no charges or
-      fixed charges interacting with the QEq which also leads to
-      inconsistent behavior between two sub-styles.  When attempting to
-      use multiple ReaxFF instances to combine different potential
-      files, you might be able to work around the QEq limitations, but
-      point 2. still applies.
-
-   We understand that it is frustrating to not be able to run simulations
-   due to lack of available potential files, but that does not justify
-   combining potentials in a broken way via pair style hybrid.  This is
-   not what the hybrid pair styles are designed for.
-
-----------
-
 Here are two examples of hybrid simulations.  The *hybrid* style could
 be used for a simulation of a metal droplet on a LJ surface.  The metal
 atoms interact with each other via an *eam* potential, the surface atoms
@@ -424,11 +374,12 @@ selected sub-style.
 
 ----------
 
-Even though the command name "pair_style" would suggest that these are
-pair-wise interactions, several of the potentials defined via the
-pair_style command in LAMMPS are really many-body potentials, such as
-Tersoff, AIREBO, MEAM, ReaxFF, etc.  The way to think about using these
-potentials in a hybrid setting is as follows.
+.. note::
+
+   Several of the potentials defined via the pair_style command in
+   LAMMPS are really many-body potentials, such as Tersoff, AIREBO, MEAM,
+   ReaxFF, etc.  The way to think about using these potentials in a
+   hybrid setting is as follows.
 
 A subset of atom types is assigned to the many-body potential with a
 single :doc:`pair_coeff <pair_coeff>` command, using "\* \*" to include

doc/src/pair_lj_pirani.rst

@@ -27,7 +27,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: 12Jun2025
+.. versionadded:: TBD
 
 Pair style *lj/pirani* computes pairwise interactions from an Improved
 Lennard-Jones (ILJ) potential according to :ref:`(Pirani) <Pirani>`.
@@ -74,7 +74,7 @@ electrostatic interactions.  If these are desired, this pair style
 should be used along with a Coulomb pair style like
 :doc:`pair styles coul/cut or coul/long <pair_coul>` by using
 :doc:`pair style hybrid/overlay <pair_hybrid>` and a suitable
-:doc:`kspace style <kspace_style>`, if needed.
+kspace style :doc:`<kspace_style>`, if needed.
 
 As discussed in :ref:`(Pirani) <Pirani>`, analysis of a variety of
 systems showed that :math:`\alpha= 4` generally works very well.  In

doc/src/pair_lj_smooth.rst

@@ -48,19 +48,13 @@ At the inner cutoff the force and its first derivative
 will match the non-smoothed LJ formula.  At the outer cutoff the force
 and its first derivative will be 0.0.  The inner cutoff cannot be 0.0.
 
-Explicit expressions for the coefficients C1, C2, C3, C4, as well as the
-energy discontinuity at the cutoff can be found here :ref:`(Leoni_1) <Leoni_1>`
-and here :ref:`(Leoni_2) <Leoni_2>`
-
 .. note::
 
    this force smoothing causes the energy to be discontinuous both
    in its values and first derivative.  This can lead to poor energy
-   conservation and may require the use of a thermostat.  The energy
-   value discontinuity can be eliminated by shifting the potential
-   energy to be zero at the outer cutoff using the pair_modify shift
-   option. With or without shifting, you can plot the resulting energy
-   and force via the :doc:`pair_write <pair_write>` command to see the effect.
+   conservation and may require the use of a thermostat.  Plot the energy
+   and force resulting from this formula via the
+   :doc:`pair_write <pair_write>` command to see the effect.
 
 The following coefficients must be defined for each pair of atoms
 types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@@ -128,14 +122,3 @@ Default
 """""""
 
 none
-
-----------
-
-.. _Leoni_1:
-
-**(Leoni_1)** F. Leoni et al., Phys Rev Lett, 134, 128201 (2025).
-
-.. _Leoni_2:
-
-**(Leoni_2)** F. Leoni et al., Phys Rev Lett, 134, Supplementary Material (2025).
-

doc/src/plugin.rst

@@ -10,17 +10,16 @@ Syntax
 
    plugin command args
 
-* command = *load* or *unload* or *list* or *clear* or *restore*
+* command = *load* or *unload* or *list* or *clear*
 * args = list of arguments for a particular plugin command
 
   .. parsed-literal::
 
      *load* file = load plugin(s) from shared object in *file*
      *unload* style name = unload plugin *name* of style *style*
-         *style* = *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *compute* or *fix* or *region* or *command* or *run* or *min*
+         *style* = *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *compute* or *fix* or *region* or *command*
      *list* = print a list of currently loaded plugins
      *clear* = unload all currently loaded plugins
-     *restore* = restore all loaded plugins
 
 Examples
 """"""""
@@ -32,7 +31,6 @@ Examples
    plugin unload command hello
    plugin list
    plugin clear
-   plugin restore
 
 Description
 """""""""""
@@ -42,46 +40,22 @@ commands into a LAMMPS binary from so-called dynamic shared object (DSO)
 files.  This enables to add new functionality to an existing LAMMPS
 binary without having to recompile and link the entire executable.
 
-.. admonition:: Plugins are a global, per-executable property
-   :class: Hint
-
-   Unlike most settings in LAMMPS, plugins are a per-executable global
-   property.  Loading a plugin means that it is not only available for
-   the current LAMMPS instance but for all *future* LAMMPS instances.
-
-   After a :doc:`clear <clear>` command, all currently loaded plugins
-   will be restored and do not need to be loaded again.
-
-   When using the library interface or the Python or Fortran module
-   to create multiple concurrent LAMMPS instances, all plugins should
-   be loaded by the first created LAMMPS instance as all future instances
-   will inherit them.  To import plugins that were loaded by a different
-   LAMMPS instance, use the *restore* command.
-
-
 The *load* command will load and initialize all plugins contained in the
-plugin DSO with the given filename.  A message with information about
-the plugin style and name and more will be printed.  Individual DSO
-files may contain multiple plugins.  If a plugin is already loaded
-it will be skipped.  More details about how to write and
+plugin DSO with the given filename.  A message with information the
+plugin style and name and more will be printed.  Individual DSO files
+may contain multiple plugins.  More details about how to write and
 compile the plugin DSO is given in programmer's guide part of the manual
 under :doc:`Developer_plugins`.
 
 The *unload* command will remove the given style or the given name from
 the list of available styles.  If the plugin style is currently in use,
-that style instance will be deleted and replaced by the default setting
-for that style.
+that style instance will be deleted.
 
 The *list* command will print a list of the loaded plugins and their
 styles and names.
 
 The *clear* command will unload all currently loaded plugins.
 
-.. versionadded:: 12Jun2025
-
-The *restore* command will restore all currently loaded plugins.
-This allows to "import" plugins into a different LAMMPS instance.
-
 .. admonition:: Automatic loading of plugins
    :class: note
 
@@ -105,7 +79,7 @@ If plugins access functions or classes from a package,
 LAMMPS must have been compiled with that package included.
 
 Plugins are dependent on the LAMMPS binary interface (ABI)
-and particularly the MPI library used.  So they are not guaranteed
+and particularly the MPI library used. So they are not guaranteed
 to work when the plugin was compiled with a different MPI library
 or different compilation settings or a different LAMMPS version.
 There are no checks, so if there is a mismatch the plugin object

doc/src/python.rst

@@ -10,7 +10,7 @@ Syntax
 
    python mode keyword args ...
 
-* mode = *source* or *name* of Python function
+* mode = *source* or name of Python function
 
   if mode is *source*:
 
@@ -18,39 +18,35 @@ Syntax
 
      keyword = *here* or name of a *Python file*
        *here* arg = inline
-         inline = one or more lines of Python code which will be executed immediately
+         inline = one or more lines of Python code which defines func
                   must be a single argument, typically enclosed between triple quotes
        *Python file* = name of a file with Python code which will be executed immediately
 
-* if *mode* is *name* of a Python function:
+* if *mode* is the name of a Python function, one or more keywords with/without arguments must be appended
 
   .. parsed-literal::
 
-     one or more keywords with/without arguments must be appended
      keyword = *invoke* or *input* or *return* or *format* or *length* or *file* or *here* or *exists*
-       *invoke* arg = logreturn (optional)
-         invoke the previously-defined Python function
-         if logreturn is specified, print the return value of the invoked function to the screen and logfile
+       *invoke* arg = none = invoke the previously defined Python function
        *input* args = N i1 i2 ... iN
          N = # of inputs to function
          i1,...,iN = value, SELF, or LAMMPS variable name
            value = integer number, floating point number, or string
-           SELF = reference to LAMMPS itself which can then be accessed by Python function
-           variable = v_name, where name = name of a LAMMPS variable, e.g. v_abc
-           internal variable = iv_name, where name = name of a LAMMPS internal-style variable, e.g. iv_xyz
+           SELF = reference to LAMMPS itself which can be accessed by Python function
+           variable = v_name, where name = name of LAMMPS variable, e.g. v_abc
        *return* arg = varReturn
          varReturn = v_name  = LAMMPS variable name which the return value of the Python function will be assigned to
        *format* arg = fstring with M characters
          M = N if no return value, where N = # of inputs
          M = N+1 if there is a return value
-         fstring = each character (i,f,s,p) corresponds (in order) to an input or return value
-           'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
+         fstring = each character (i,f,s,p) corresponds in order to an input or return value
+         'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
        *length* arg = Nlen
          Nlen = max length of string returned from Python function
        *file* arg = filename
-         filename = file of Python code, which defines the Python function
+         filename = file of Python code, which defines func
        *here* arg = inline
-         inline = one or more lines of Python code which defines the Python function
+         inline = one or more lines of Python code which defines func
                   must be a single argument, typically enclosed between triple quotes
        *exists* arg = none = Python code has been loaded by previous python command
 
@@ -60,7 +56,7 @@ Examples
 .. code-block:: LAMMPS
 
    python pForce input 2 v_x 20.0 return v_f format fff file force.py
-   python pForce invoke logreturn
+   python pForce invoke
 
    python factorial input 1 myN return v_fac format ii here """
    def factorial(n):
@@ -91,149 +87,75 @@ Examples
 Description
 """""""""""
 
-The *python* command interfaces LAMMPS with an embedded Python
-interpreter and enables executing arbitrary python code in that
-interpreter.  This can be done immediately, by using *mode* = *source*.
-Or execution can be deferred, by registering a Python function for later
-execution, by using *mode* = *name* of a Python function.
+The *python* command allows interfacing LAMMPS with an embedded Python
+interpreter and enables either executing arbitrary python code in that
+interpreter, registering a Python function for future execution (as a
+python style variable, from a fix interfaced with python, or for direct
+invocation), or invoking such a previously registered function.
 
-Later execution can be triggered in one of two ways.  One is to use the
-python command again with its *invoke* keyword.  The other is to trigger
-the evaluation of a python-style, equal-style, vector-style, or
-atom-style variable.  A python-style variable invokes its associated
-Python function; its return value becomes the value of the python-style
-variable.  Equal-, vector-, and atom-style variables can use a Python
-function wrapper in their formulas which encodes the python-style
-variable name, and specifies arguments (which themselves can be numeric
-formulas) to pass to the Python function associated with the
-python-style variable.
-
-As explained on the :doc:`variable <variable>` doc page, the definition
-of a python-style variable associates a Python function name with the
-variable.  Its specification must match the *mode* argument of the
-*python* command for the Python function name.  For example these two
-commands would be consistent:
-
-.. code-block:: LAMMPS
-
-   variable foo python myMultiply
-   python myMultiply return v_foo format f file funcs.py
-
-The two commands can appear in either order in the input script so long
-as both are specified before the Python function is invoked for the
-first time.
-
-Note that python-style, equal-style, vector-style, and atom-style
-variables can be used in many different ways within LAMMPS.  They can be
-evaluated directly in an input script, effectively replacing the
-variable with its value.  Or they can be passed to various commands as
-arguments, so that the variable is evaluated multiple times during a
-simulation run.  See the :doc:`variable <variable>` command doc page for
-more details on variable styles which enable Python function evaluation.
-
-The Python code for a Python function can be included directly in the
-input script or in a separate Python file.  The function can be standard
-Python code or it can make "callbacks" to LAMMPS through its library
-interface to query or set internal values within LAMMPS.  This is a
-powerful mechanism for performing complex operations in a LAMMPS input
-script that are not possible with the simple input script and variable
-syntax which LAMMPS defines.  Thus your input script can operate more
-like a true programming language.
+Arguments, including LAMMPS variables, can be passed to the function
+from the LAMMPS input script and a value returned by the Python function
+assigned to a LAMMPS variable.  The Python code for the function can be included
+directly in the input script or in a separate Python file.  The function
+can be standard Python code or it can make "callbacks" to LAMMPS through
+its library interface to query or set internal values within LAMMPS.
+This is a powerful mechanism for performing complex operations in a
+LAMMPS input script that are not possible with the simple input script
+and variable syntax which LAMMPS defines.  Thus your input script can
+operate more like a true programming language.
 
 Use of this command requires building LAMMPS with the PYTHON package
 which links to the Python library so that the Python interpreter is
 embedded in LAMMPS.  More details about this process are given below.
 
+There are two ways to invoke a Python function once it has been
+registered.  One is using the *invoke* keyword.  The other is to assign
+the function to a :doc:`python-style variable <variable>` defined in
+your input script.  Whenever the variable is evaluated, it will execute
+the Python function to assign a value to the variable.  Note that
+variables can be evaluated in many different ways within LAMMPS.  They
+can be substituted with their result directly in an input script, or
+they can be passed to various commands as arguments, so that the
+variable is evaluated during a simulation run.
+
 A broader overview of how Python can be used with LAMMPS is given in the
 :doc:`Use Python with LAMMPS <Python_head>` section of the
-documentation.  There is also an ``examples/python`` directory which
+documentation.  There also is an ``examples/python`` directory which
 illustrates use of the python command.
 
 ----------
 
-The first argument to the *python* command is the *mode* setting, which
-is either *source* or the *name* of a Python function.
+The first argument of the *python* command is either the *source*
+keyword or the name of a Python function.  This defines the mode
+of the python command.
 
 .. versionchanged:: 22Dec2022
 
-If *source* is used, it is followed by either the *here* keyword or a
-file name containing Python code.  The *here* keyword is followed by a
-single *inline* argument which is a string containing one or more python
-commands.  The string can either be on the same line as the *python*
-command, enclosed in quotes, or it can be multiple lines enclosed in
-triple quotes.
+If the *source* keyword is used, it is followed by either a file name or
+the *here* keyword.  No other keywords can be used.  The *here* keyword
+is followed by a string with python commands, either on a single line
+enclosed in quotes, or as multiple lines enclosed in triple quotes.
+These Python commands will be passed to the python interpreter and
+executed immediately without registering a Python function for future
+execution.  The code will be loaded into and run in the "main" module of
+the Python interpreter.  This allows running arbitrary Python code at
+any time while processing the LAMMPS input file.  This can be used to
+pre-load Python modules, initialize global variables, define functions
+or classes, or perform operations using the python programming language.
+The Python code will be executed in parallel on all MPI processes.  No
+arguments can be passed.
 
-In either case, the in-line code or the file contents are passed to the
-python interpreter and executed immediately.  The code will be loaded
-into and run in the "main" module of the Python interpreter.  This
-allows running arbitrary Python code at any time while processing the
-LAMMPS input file.  This can be used to pre-load Python modules,
-initialize global variables, define functions or classes, or perform
-operations using the Python programming language.  The Python code will
-be executed in parallel on all the MPI processes being used to run
-LAMMPS.  Note that no arguments can be passed to the executed Python
-code.
+In all other cases, the first argument is the name of a Python function
+that will be registered with LAMMPS for future execution.  The function
+may already be defined (see *exists* keyword) or must be defined using
+the *file* or *here* keywords as explained below.
 
-If the *mode* setting is the *name* of a Python function, then it will
-be registered with LAMMPS for future execution (or can already be
-defined, see the *exists* keyword).  One or more keywords must follow
-the *mode* function name.  One of the keywords must be *invoke*, *file*,
-*here*, or *exists*, which specifies what Python code to load into the
-Python interpreter.  Note that only one of those 4 keywords is allowed
-since their operations are mutually exclusive.
-
-----------
-
-If the *invoke* keyword is used, no other keywords can be used.  A
+If the *invoke* keyword is used, no other keywords can be used, and a
 previous *python* command must have registered the Python function
-referenced by this command, which can then be invoked multiple times in
-an input script via the *invoke* keyword.  Each invocation passes
-current values for arguments to the Python function.  A return value of
-the Python function will be ignored unless the Python function is linked
-to a :doc:`python style variable <variable>` with the *return* keyword.
-This return value can be logged to the screen and logfile by adding the
-optional *logreturn* argument to the *invoke* keyword.  In that case a
-message with the name of the python command and the return value is
-printed.  Note that return values of python functions are otherwise
-*only* accessible when the function is invoked indirectly by evaluating
-its associated :doc:`python style variable <variable>`, as described
-below.
-
-The *file* keyword gives the name of a file containing Python code,
-which should end with a ".py" suffix.  The code will be immediately
-loaded into and run in the "main" module of the Python interpreter.  The
-Python code will be executed in parallel on all MPI processes.  Note
-that Python code which contains a function definition does NOT "execute"
-the function when it is run; it simply defines the function so that it
-can be invoked later.
-
-The *here* keyword does the same thing, except that the Python code
-follows as a single argument to the *here* keyword.  This can be done
-using triple quotes as delimiters, as in the examples above and below.
-This allows Python code to be listed verbatim in your input script, with
-proper indentation, blank lines, and comments, as desired.  See the
-:doc:`Commands parse <Commands_parse>` doc page, for an explanation of
-how triple quotes can be used as part of input script syntax.
-
-The *exists* keyword takes no argument.  It simply means that Python
-code containing the needed Python function has already been loaded into
-the LAMMPS Python interpreter, for example by previous *python source*
-command or in a file that was loaded previously with the *file*
-keyword. This allows use of a single file of Python code which contains
-multiple functions, any of which can be used in the same (or different)
-input scripts (see below).
-
-Note that the Python code that is loaded and run by the *file* or *here*
-keyword must contain a function with the specified function *name*.  To
-operate properly when the function is later invoked, the code for the
-function must match the *input* and *return* and *format* keywords
-specified by the python command.  Otherwise Python will generate an
-error.
-
-----------
-
-The other keywords which can be used with the *python* command are
-*input*, *return*, *format*, and *length*.
+referenced by this command.  This invokes the Python function with the
+previously defined arguments and the return value is processed as
+explained below.  You can invoke the function as many times as you wish
+in your input script.
 
 The *input* keyword defines how many arguments *N* the Python function
 expects.  If it takes no arguments, then the *input* keyword should not
@@ -247,63 +169,35 @@ itself using the :doc:`LAMMPS Python module <Python_module>`.  This
 enables the function to call back to LAMMPS through its library
 interface as explained below.  This allows the Python function to query
 or set values internal to LAMMPS which can affect the subsequent
-execution of the input script.
-
-A LAMMPS variable can also be used as an *input* argument, specified as
-v_name, where "name" is the name of the variable defined in the input
-script.  Any style of LAMMPS variable returning a scalar or a string can
-be used, as defined by the :doc:`variable <variable>` command.  The
-style of variable must be consistent with the *format* keyword
-specification for the type of data that is passed to Python.  Each time
-the Python function is invoked, the LAMMPS variable is evaluated and its
-value is passed as an argument to the Python function.  Note that a
-python-style variable can be used as an argument, which means that the a
-Python function can use arguments which invoke other Python functions.
-
-A LAMMPS internal-style variable can also be used as an *input*
-argument, specified as iv_name, where "name" is the name of the
-internal-style variable.  The internal-style variable does not have to
-be defined in the input script (though it can be); if it is not defined,
-this command creates an :doc:`internal-style variable <variable>` with
-the specified name.
-
-An internal-style variable must be used when an equal-style,
-vector-style, or atom-style variable triggers the invocation of the
-Python function defined by this command, by including a Python function
-wrapper with arguments in its formula.  Each of the arguments must be
-specified as an internal-style variable via the *input* keyword.
-
-In brief, the syntax for a Python function wrapper in a variable formula
-is ``py_varname(arg1,arg2,...argN)``, where "varname" is the name of a
-python-style variable associated with a Python function defined by this
-command.  One or more arguments to the function wrapper can themselves
-be sub-formulas which the variable command will evaluate and pass as
-arguments to the Python function.  This is done by assigning the numeric
-result for each argument to an internal-style variable; thus the *input*
-keyword must specify the arguments as internal-style variables and their
-format (see below) as "f" for floating point.  This is because LAMMPS
-variable formulas are calculated with floating point arithmetic (any
-integer values are converted to floating point).  Note that the Python
-function can also have additional inputs, also specified by the *input*
-keyword, which are NOT arguments in the Python function wrapper.  See
-the example below for the ``mixedargs`` Python function.
-
-See the :doc:`variable <variable>` command doc page for full details on
-formula syntax including for Python function wrappers.  Examples using
-Python function wrappers are shown below.  Note that as explained above
-with python-style variables, Python function wrappers can be nested; a
-sub-formula for an argument can contain its own Python function wrapper
-which invokes another Python function.
+execution of the input script.  A LAMMPS variable can also be used as an
+argument, specified as v_name, where "name" is the name of the variable.
+Any style of LAMMPS variable returning a scalar or a string can be used,
+as defined by the :doc:`variable <variable>` command.  The *format*
+keyword must be used to set the type of data that is passed to Python.
+Each time the Python function is invoked, the LAMMPS variable is
+evaluated and its value is passed to the Python function.
 
 The *return* keyword is only needed if the Python function returns a
-value.  The specified *varReturn* is of the form v_name, where "name" is
-the name of a python-style LAMMPS variable, defined by the
+value.  The specified *varReturn* must be of the form v_name, where
+"name" is the name of a python-style LAMMPS variable, defined by the
 :doc:`variable <variable>` command.  The Python function can return a
-numeric or string value, as specified by the *format* keyword.  This
-return value is *only* accessible when its associated python-style
-variable is evaluated.  When the *invoke* keyword is used, the return
-value of the python function is ignored unless the optional *logreturn*
-argument is specified.
+numeric or string value, as specified by the *format* keyword.
+
+As explained on the :doc:`variable <variable>` doc page, the definition
+of a python-style variable associates a Python function name with the
+variable.  This must match the *Python function name* first argument of
+the *python* command.  For example these two commands would be
+consistent:
+
+.. code-block:: LAMMPS
+
+   variable foo python myMultiply
+   python myMultiply return v_foo format f file funcs.py
+
+The two commands can appear in either order in the input script so
+long as both are specified before the Python function is invoked for
+the first time.  Afterwards, the variable 'foo' is associated with
+the Python function 'myMultiply'.
 
 The *format* keyword must be used if the *input* or *return* keywords
 are used.  It defines an *fstring* with M characters, where M = sum of
@@ -320,16 +214,47 @@ but only if the output of the Python function is flagged as a numeric
 value ("i" or "f") via the *format* keyword.
 
 If the *return* keyword is used and the *format* keyword specifies the
-output as a string, then the default maximum length of that string is 63
-characters (64-1 for the string terminator).  If you want to return a
-longer string, the *length* keyword can be specified with its *Nlen*
-value set to a larger number.  LAMMPS will then allocate Nlen+1 space to
-include the string terminator.  If the Python function generates a
+output as a string, then the default maximum length of that string is
+63 characters (64-1 for the string terminator).  If you want to return
+a longer string, the *length* keyword can be specified with its *Nlen*
+value set to a larger number (the code allocates space for Nlen+1 to
+include the string terminator).  If the Python function generates a
 string longer than the default 63 or the specified *Nlen*, it will be
 truncated.
 
 ----------
 
+Either the *file*, *here*, or *exists* keyword must be used, but only
+one of them.  These keywords specify what Python code to load into the
+Python interpreter.  The *file* keyword gives the name of a file
+containing Python code, which should end with a ".py" suffix.  The code
+will be immediately loaded into and run in the "main" module of the
+Python interpreter.  The Python code will be executed in parallel on all
+MPI processes.  Note that Python code which contains a function
+definition does not "execute" the function when it is run; it simply
+defines the function so that it can be invoked later.
+
+The *here* keyword does the same thing, except that the Python code
+follows as a single argument to the *here* keyword.  This can be done
+using triple quotes as delimiters, as in the examples above.  This
+allows Python code to be listed verbatim in your input script, with
+proper indentation, blank lines, and comments, as desired.  See the
+:doc:`Commands parse <Commands_parse>` doc page, for an explanation of
+how triple quotes can be used as part of input script syntax.
+
+The *exists* keyword takes no argument.  It means that Python code
+containing the required Python function with the given name has already
+been executed, for example by a *python source* command or in the same
+file that was used previously with the *file* keyword.
+
+Note that the Python code that is loaded and run must contain a function
+with the specified function name.  To operate properly when later
+invoked, the function code must match the *input* and *return* and
+*format* keywords specified by the python command.  Otherwise Python
+will generate an error.
+
+----------
+
 This section describes how Python code can be written to work with
 LAMMPS.
 
@@ -350,16 +275,16 @@ keyword once to load several functions, and the *exists* keyword
 thereafter in subsequent python commands to register the other functions
 that were previously loaded with LAMMPS.
 
-A Python function you define (or more generally, the code you load) can
-import other Python modules or classes, it can make calls to other
+A Python function you define (or more generally, the code you load)
+can import other Python modules or classes, it can make calls to other
 system functions or functions you define, and it can access or modify
 global variables (in the "main" module) which will persist between
 successive function calls.  The latter can be useful, for example, to
 prevent a function from being invoke multiple times per timestep by
 different commands in a LAMMPS input script that access the returned
 python-style variable associated with the function.  For example,
-consider this function loaded with two global variables defined outside
-the function:
+consider this function loaded with two global variables defined
+outside the function:
 
 .. code-block:: python
 
@@ -383,33 +308,32 @@ previous value is simply returned, without re-computing it.  The
 "global" statement inside the Python function allows it to overwrite the
 global variables from within the local context of the function.
 
-Also note that if you load Python code multiple times (via multiple
-python commands), you can overwrite previously loaded variables and
-functions if you are not careful.  E.g. if the code above were loaded
-twice, the global variables would be re-initialized, which might not be
-what you want.  Likewise, if a function with the same name exists in two
-chunks of Python code you load, the function loaded second will override
-the function loaded first.
+Note that if you load Python code multiple times (via multiple python
+commands), you can overwrite previously loaded variables and functions
+if you are not careful.  E.g. if the code above were loaded twice, the
+global variables would be re-initialized, which might not be what you
+want.  Likewise, if a function with the same name exists in two chunks
+of Python code you load, the function loaded second will override the
+function loaded first.
 
 It's important to realize that if you are running LAMMPS in parallel,
-each MPI task will load the Python interpreter and execute a local copy
-of the Python function(s) you define.  There is no connection between
-the Python interpreters running on different processors.  This implies
-three important things.
+each MPI task will load the Python interpreter and execute a local
+copy of the Python function(s) you define.  There is no connection
+between the Python interpreters running on different processors.
+This implies three important things.
 
 First, if you put a print or other statement creating output to the
 screen in your Python function, you will see P copies of the output,
 when running on P processors.  If the prints occur at (nearly) the same
-time, the P copies of the output may be mixed together.
-
-It is possible to avoid this issue, by passing the pointer to the
-current LAMMPS class instance to the Python function via the {input}
-SELF argument described above.  The Python function can then use the
-Python interface to the LAMMPS library interface, and determine the MPI
-rank of the current process.  The Python code can then ensure output
-will only appear on MPI rank 0.  The following LAMMPS input demonstrates
-how this could be done. The text 'Hello, LAMPS!' should be printed only
-once, even when running LAMMPS in parallel.
+time, the P copies of the output may be mixed together.  When loading
+the LAMMPS Python module into the embedded Python interpreter, it is
+possible to pass the pointer to the current LAMMPS class instance and
+via the Python interface to the LAMMPS library interface, it is possible
+to determine the MPI rank of the current process and thus adapt the
+Python code so that output will only appear on MPI rank 0.  The
+following LAMMPS input demonstrates how this could be done. The text
+'Hello, LAMMPS!' should be printed only once, even when running LAMMPS
+in parallel.
 
 .. code-block:: LAMMPS
 
@@ -424,26 +348,27 @@ once, even when running LAMMPS in parallel.
 
    python python_hello invoke
 
-Second, if your Python code loads Python modules that are not pre-loaded
-by the Python library, then it will load the module from disk.  This may
-be a bottleneck if 1000s of processors try to load a module at the same
-time.  On some large supercomputers, loading of modules from disk by
-Python may be disabled.  In this case you would need to pre-build a
-Python library that has the required modules pre-loaded and link LAMMPS
-with that library.
+If your Python code loads Python modules that are not pre-loaded by the
+Python library, then it will load the module from disk.  This may be a
+bottleneck if 1000s of processors try to load a module at the same time.
+On some large supercomputers, loading of modules from disk by Python may
+be disabled.  In this case you would need to pre-build a Python library
+that has the required modules pre-loaded and link LAMMPS with that
+library.
 
-Third, if your Python code calls back to LAMMPS (discussed in the next
-section) and causes LAMMPS to perform an MPI operation requires global
-communication (e.g. via MPI_Allreduce), such as computing the global
-temperature of the system, then you must ensure all your Python
+Third, if your Python code calls back to LAMMPS (discussed in the
+next section) and causes LAMMPS to perform an MPI operation requires
+global communication (e.g. via MPI_Allreduce), such as computing the
+global temperature of the system, then you must ensure all your Python
 functions (running independently on different processors) call back to
 LAMMPS.  Otherwise the code may hang.
 
 ----------
 
-As mentioned above, a Python function can "call back" to LAMMPS through
-its library interface, if the SELF input is used to pass Python a
-pointer to LAMMPS.  The mechanism for doing this is as follows:
+Your Python function can "call back" to LAMMPS through its
+library interface, if you use the SELF input to pass Python
+a pointer to LAMMPS.  The mechanism for doing this in your
+Python function is as follows:
 
 .. code-block:: python
 
@@ -468,15 +393,15 @@ appeared in your input script.  In this case, LAMMPS should output
    Hello from inside Python
 
 to the screen and log file.  Note that since the LAMMPS print command
-itself takes a string in quotes as its argument, the Python string must
-be delimited with a different style of quotes.
+itself takes a string in quotes as its argument, the Python string
+must be delimited with a different style of quotes.
 
-The :doc:`Python_head` page describes the syntax for how Python wraps
-the various functions included in the LAMMPS library interface.
+The :doc:`Python_head` page describes the syntax
+for how Python wraps the various functions included in the LAMMPS
+library interface.
 
-A more interesting example is in the ``examples/python/in.python``
-script which loads and runs the following function from
-``examples/python/funcs.py``:
+A more interesting example is in the ``examples/python/in.python`` script
+which loads and runs the following function from ``examples/python/funcs.py``:
 
 .. code-block:: python
 
@@ -491,7 +416,7 @@ script which loads and runs the following function from
 
        lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
        lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command
-       #lmp.command("pair_style lj/cut %d" % cut)  # alternate form of LAMMPS command
+       #lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option
 
        lmp.command("pair_coeff * * 1.0 1.0")       # ditto
        lmp.command("run 10")                       # ditto
@@ -507,160 +432,51 @@ with these input script commands:
    python          loop invoke
 
 This has the effect of looping over a series of 10 short runs (10
-timesteps each) where the pair style cutoff is increased from a value of
-1.0 in distance units, in increments of 0.1.  The looping stops when the
-per-atom potential energy falls below a threshold of -4.0 in energy
-units.  More generally, Python can be used to implement a loop with
-complex logic, much more so than can be created using the LAMMPS
+timesteps each) where the pair style cutoff is increased from a value
+of 1.0 in distance units, in increments of 0.1.  The looping stops
+when the per-atom potential energy falls below a threshold of -4.0 in
+energy units.  More generally, Python can be used to implement a loop
+with complex logic, much more so than can be created using the LAMMPS
 :doc:`jump <jump>` and :doc:`if <if>` commands.
 
 Several LAMMPS library functions are called from the loop function.
 Get_natoms() returns the number of atoms in the simulation, so that it
 can be used to normalize the potential energy that is returned by
-extract_compute() for the "thermo_pe" compute that is defined by default
-for LAMMPS thermodynamic output.  Set_variable() sets the value of a
-string variable defined in LAMMPS.  This library function is a useful
-way for a Python function to return multiple values to LAMMPS, more than
-the single value that can be passed back via a return statement.  This
-cutoff value in the "cut" variable is then substituted (by LAMMPS) in
-the pair_style command that is executed next.  Alternatively, the
-"alternate form of LAMMPS command" line could be used in place of the 2
-preceding lines, to have Python insert the value into the LAMMPS command
-string.
+extract_compute() for the "thermo_pe" compute that is defined by
+default for LAMMPS thermodynamic output.  Set_variable() sets the
+value of a string variable defined in LAMMPS.  This library function
+is a useful way for a Python function to return multiple values to
+LAMMPS, more than the single value that can be passed back via a
+return statement.  This cutoff value in the "cut" variable is then
+substituted (by LAMMPS) in the pair_style command that is executed
+next.  Alternatively, the "LAMMPS command option" line could be used
+in place of the 2 preceding lines, to have Python insert the value
+into the LAMMPS command string.
 
 .. note::
 
    When using the callback mechanism just described, recognize that
-   there are some operations you should not attempt because LAMMPS
-   cannot execute them correctly.  If the Python function is invoked
-   between runs in the LAMMPS input script, then it should be OK to
-   invoke any LAMMPS input script command via the library interface
-   command() or file() functions, so long as the command would work if
-   it were executed in the LAMMPS input script directly at the same
-   point.
+   there are some operations you should not attempt because LAMMPS cannot
+   execute them correctly.  If the Python function is invoked between
+   runs in the LAMMPS input script, then it should be OK to invoke any
+   LAMMPS input script command via the library interface command() or
+   file() functions, so long as the command would work if it were
+   executed in the LAMMPS input script directly at the same point.
 
+However, a Python function can also be invoked during a run, whenever
+an associated LAMMPS variable it is assigned to is evaluated.  If the
+variable is an input argument to another LAMMPS command (e.g. :doc:`fix setforce <fix_setforce>`), then the Python function will be invoked
+inside the class for that command, in one of its methods that is
+invoked in the middle of a timestep.  You cannot execute arbitrary
+input script commands from the Python function (again, via the
+command() or file() functions) at that point in the run and expect it
+to work.  Other library functions such as those that invoke computes
+or other variables may have hidden side effects as well.  In these
+cases, LAMMPS has no simple way to check that something illogical is
+being attempted.
 
-----------
-
-As noted above, a Python function can be invoked during a run, whenever
-an associated python-style variable it is assigned to is evaluated.
-
-If the variable is an input argument to another LAMMPS command
-(e.g. :doc:`fix setforce <fix_setforce>`), then the Python function will
-be invoked inside the class for that command, possibly in one of its
-methods that is invoked in the middle of a timestep.  You cannot execute
-arbitrary input script commands from the Python function (again, via the
-command() or file() functions) at that point in the run and expect it to
-work.  Other library functions such as those that invoke computes or
-other variables may have hidden side effects as well.  In these cases,
-LAMMPS has no simple way to check that something illogical is being
-attempted.
-
-The same constraints apply to Python functions called during a
-simulation run at each time step using the :doc:`fix python/invoke
-<fix_python_invoke>` command.
-
-----------
-
-As noted above, a Python function can also be invoked within the formula
-for an equal-style, vector-style, or atom-style variable.  This means
-the Python function will be invoked whenever that variable is invoked.
-In the case of a vector-style variable, the Python function can be
-invoked once per element of the global vector.  In the case of an
-atom-style variable, the Python function can be invoked once per atom.
-
-Here are three simple examples using equal-, vector-, and atom-style
-variables to trigger execution of a Python function:
-
-.. code-block:: LAMMPS
-
-   variable        foo python truncate
-   python          truncate return v_foo input 1 iv_arg format fi here """
-   def truncate(x):
-     return int(x)
-   """
-   variable        ptrunc equal py_foo(press)
-   print           "TRUNCATED pressure = ${ptrunc}"
-
-The Python ``truncate`` function simply converts a floating-point value
-to an integer value.  When the LAMMPS print command evaluates the
-equal-style ``ptrunc`` variable, the current thermodynamic pressure is
-passed to the Python function.  The truncated value is output to the
-screen and logfile by the print command.  Note that the *input* keyword
-for the *python* command, specifies an internal-style variable named
-"arg" as iv_arg which is required to invoke the Python function from a
-Python function wrapper.
-
-The last 2 lines can be replaced by these to define a vector-style
-variable which invokes the same Python ``truncate`` function:
-
-.. code-block:: LAMMPS
-
-  compute         ke all temp
-  variable        ke vector c_ke
-  variable        ketrunc vector py_foo(v_ke)
-  thermo_style    custom step temp epair v_ketrunc[*6]
-
-The vector-style variable ``ketrunc`` invokes the Python ``truncate``
-function on each of the 6 components of the global kinetic energy tensor
-calculated by the :doc:`compute ke <compute_ke>` command.  The 6
-truncated values will be printed with thermo output to the screen and
-log file.
-
-Or the last 2 lines of the equal-style variable example can be replaced
-by these to define atom-style variables which invoke the same Python
-``truncate`` function:
-
-.. code-block:: LAMMPS
-
-   variable        xtrunc atom py_foo(x)
-   variable        ytrunc atom py_foo(y)
-   variable        ztrunc atom py_foo(z)
-   dump            1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
-
-When the dump command invokes the 3 atom-style variables, their
-arguments x,y,z to the Python function wrapper are the current per-atom
-coordinates of each atom.  The Python ``truncate`` function is thus
-invoked 3 times for each atom, and the truncated coordinate values for
-each atom are written to the dump file.
-
-Note that when using a Python function wrapper in a variable, arguments
-can be passed to the Python function either from the variable formula or
-by *input* keyword to the :doc:`python command <python>`.  For example,
-consider these (made up) commands:
-
-.. code-block:: LAMMPS
-
-   variable        foo python mixedargs
-   python          mixedargs return v_foo input 6 7.5 v_myValue iv_arg1 iv_argy iv_argz v_flag &
-                   format fffffsf here """
-   def mixedargs(a,b,x,y,z,flag):
-     ...
-     return result
-   """
-   variable        flag string optionABC
-   variable        myValue equal "2.0*temp*c_pe"
-   compute         pe all pe
-   compute         peatom all pe/atom
-   variable        field atom py_foo(x+3.0,sqrt(y),(z-zlo)*c_peatom)
-
-They define a Python ``mixedargs`` function with 6 arguments.  Three of
-them are internal-style variables, which the variable formula calculates
-as numeric values for each atom and passes to the function.  In this
-example, these arguments are themselves small formulas containing the
-x,y,z coordinates of each atom as well as a per-atom compute (c_peratom)
-and thermodynamic keyword (zlo).
-
-The other three arguments ``(7.5,v_myValue,v_flag)`` are defined by the
-*python* command.  The first and last are constant values ("7.5" and the
-``optionABC`` string).  The second argument (``myValue``) is the result
-of an equal-style variable formula which accesses the system temperature
-and potential energy.
-
-The "result" returned by each invocation of the Python ``mixedargs``
-function becomes the per-atom value in the atom-style "field" variable,
-which could be output to a dump file or used elsewhere in the input
-script.
+The same applies to Python functions called during a simulation run at
+each time step using :doc:`fix python/invoke <fix_python_invoke>`.
 
 ----------
 
@@ -669,11 +485,12 @@ interactively or by using Python to launch a Python script stored in a
 file, and your code has an error, you will typically see informative
 error messages.  That is not the case when you run Python code from
 LAMMPS using an embedded Python interpreter.  The code will typically
-fail silently.  LAMMPS will catch some errors but cannot tell you where
-in the Python code the problem occurred.  For example, if the Python
-code cannot be loaded and run because it has syntax or other logic
-errors, you may get an error from Python pointing to the offending line,
-or you may get one of these generic errors from LAMMPS:
+fail silently.  LAMMPS will catch some errors but cannot tell you
+where in the Python code the problem occurred.  For example, if the
+Python code cannot be loaded and run because it has syntax or other
+logic errors, you may get an error from Python pointing to the
+offending line, or you may get one of these generic errors from
+LAMMPS:
 
 .. parsed-literal::
 
@@ -687,16 +504,16 @@ you will typically get this generic error from LAMMPS:
 
    Python function evaluation failed
 
-Here are three suggestions for debugging your Python code while running
-it under LAMMPS.
+Here are three suggestions for debugging your Python code while
+running it under LAMMPS.
 
 First, don't run it under LAMMPS, at least to start with!  Debug it
 using plain Python.  Load and invoke your function, pass it arguments,
 check return values, etc.
 
-Second, add Python print statements to the function to check how far it
-gets and intermediate values it calculates.  See the discussion above
-about printing from Python when running in parallel.
+Second, add Python print statements to the function to check how far
+it gets and intermediate values it calculates.  See the discussion
+above about printing from Python when running in parallel.
 
 Third, use Python exception handling.  For example, say this statement
 in your Python function is failing, because you have not initialized the
@@ -706,7 +523,8 @@ variable foo:
 
    foo += 1
 
-If you put one (or more) statements inside a "try" statement, like this:
+If you put one (or more) statements inside a "try" statement,
+like this:
 
 .. code-block:: python
 
@@ -745,15 +563,13 @@ If you use Python code which calls back to LAMMPS, via the SELF input
 argument explained above, there is an extra step required when building
 LAMMPS.  LAMMPS must also be built as a shared library and your Python
 function must be able to load the :doc:`"lammps" Python module
-<Python_module>` that wraps the LAMMPS library interface.
-
-These are the same steps required to use Python by itself to wrap
-LAMMPS.  Details on these steps are explained on the :doc:`Python
-<Python_head>` doc page.  Note that it is important that the stand-alone
-LAMMPS executable and the LAMMPS shared library be consistent (built
-from the same source code files) in order for this to work.  If the two
-have been built at different times using different source files,
-problems may occur.
+<Python_module>` that wraps the LAMMPS library interface.  These are the
+same steps required to use Python by itself to wrap LAMMPS.  Details on
+these steps are explained on the :doc:`Python <Python_head>` doc page.
+Note that it is important that the stand-alone LAMMPS executable and the
+LAMMPS shared library be consistent (built from the same source code
+files) in order for this to work.  If the two have been built at
+different times using different source files, problems may occur.
 
 Another limitation of calling back to Python from the LAMMPS module
 using the *python* command in a LAMMPS input is that both, the Python
@@ -767,8 +583,7 @@ global variables will become invisible.
 Related commands
 """"""""""""""""
 
-:doc:`shell <shell>`, :doc:`variable <variable>`,
-:doc:`fix python/invoke <fix_python_invoke>`
+:doc:`shell <shell>`, :doc:`variable <variable>`, :doc:`fix python/invoke <fix_python_invoke>`
 
 Default
 """""""

doc/src/run.rst

@@ -103,16 +103,14 @@ must be done.
 
 .. note::
 
-   If your input script "changes" the system between 2 runs, then the
-   initial setup typically needs to be performed to ensure the change
-   is recognized by all parts of the code that are affected.  Examples
-   are adding a :doc:`fix <fix>` or :doc:`dump <dump>` or
-   :doc:`compute <compute>`, changing a :doc:`neighbor <neigh_modify>`
-   list parameter, using the :doc:`set <set>` command, or writing a
-   restart file via the :doc:`write_restart <write_restart>` command,
-   which can migrate atoms between processors.  LAMMPS has no easy way
-   to check if this has happened, but it is an error to use the *pre
-   no* option in these cases.
+   If your input script changes the system between 2 runs, then the
+   initial setup must be performed to ensure the change is recognized by
+   all parts of the code that are affected.  Examples are adding a
+   :doc:`fix <fix>` or :doc:`dump <dump>` or :doc:`compute <compute>`, changing
+   a :doc:`neighbor <neigh_modify>` list parameter, or writing restart file
+   which can migrate atoms between processors.  LAMMPS has no easy way to
+   check if this has happened, but it is an error to use the *pre no*
+   option in this case.
 
 If *post* is specified as "no", the full timing summary is skipped;
 only a one-line summary timing is printed.

doc/src/set.rst

@@ -22,110 +22,21 @@ Syntax
        for style = *region*, ID = a region ID
 
 * one or more keyword/value pairs may be appended
-
-* keyword = *angle* or *angmom* or *bond* or *cc* or *charge* or
-  *density* or *density/disc* or *diameter* or *dihedral* or *dipole*
-  or *dipole/random* or *dpd/theta* or *edpd/cv* or *edpd/temp* or
-  *epsilon* or *image* or *improper* or *length* or *mass* or *mol* or
-  *omega* or *quat* or *quat/random* or *radius/electron* or *shape* or
-  *smd/contact/radius* or *smd/mass/density* or *sph/cv* or *sph/e* or
-  *sph/rho* or *spin/atom* or *spin/atom/random* or *spin/electron* or
-  *temperature* or *theta* or *theta/random* or *tri* or *type* or
-  *type/fraction* or *type/ratio* or *type/subset* or *volume* or *vx*
-  or *vy* or *vz* or *x* or *y* or *z* or *i_name* or *d_name* or
-  *i2_name* or *d2_name*
+* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset*
+  or *mol* or *x* or *y* or *z* or *vx* or *vy* or *vz* or *charge* or
+  *dipole* or *dipole/random* or *quat* or *spin/atom* or *spin/atom/random* or
+  *spin/electron* or *radius/electron* or
+  *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or
+  *theta* or *theta/random* or *angmom* or *omega* or
+  *mass* or *density* or *density/disc* or *temperature* or
+  *volume* or *image* or *bond* or *angle* or *dihedral* or
+  *improper* or *sph/e* or *sph/cv* or *sph/rho* or
+  *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or
+  *edpd/temp* or *edpd/cv* or *cc* or *epsilon* or
+  *i_name* or *d_name* or *i2_name* or *d2_name*
 
   .. parsed-literal::
 
-       *angle* value = numeric angle type or angle type label, for all angles between selected atoms
-       *angmom* values = Lx Ly Lz
-         Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
-         any of Lx,Ly,Lz can be an atom-style variable (see below)
-       *bond* value = numeric bond type or bond type label, for all bonds between selected atoms
-       *cc* values = index cc
-         index = index of a chemical species (1 to Nspecies)
-         cc = chemical concentration of tDPD particles for a species (mole/volume units)
-         cc can be an atom-style variable (see below)
-       *charge* value = atomic charge (charge units)
-         value can be an atom-style variable (see below)
-       *density* value = particle density for a sphere or ellipsoid (mass/distance\^3 units), or for a triangle (mass/distance\^2 units) or line (mass/distance units) particle
-         value can be an atom-style variable (see below)
-       *density/disc* value = particle density for a 2d disc or ellipse (mass/distance\^2 units)
-         value can be an atom-style variable (see below)
-       *diameter* value = diameter of spherical particle (distance units)
-         value can be an atom-style variable (see below)
-       *dihedral* value = numeric dihedral type or dihedral type label, for all dihedrals between selected atoms
-       *dipole* values = x y z
-         x,y,z = orientation of dipole moment vector
-         any of x,y,z can be an atom-style variable (see below)
-       *dipole/random* values = seed Dlen
-         seed = random # seed (positive integer) for dipole moment orientations
-         Dlen = magnitude of dipole moment (dipole units)
-       *dpd/theta* value = internal temperature of DPD particles (temperature units)
-         value can be an atom-style variable (see below)
-         value can be NULL which sets internal temp of each particle to KE temp
-       *edpd/cv* value = volumetric heat capacity of eDPD particles (energy/temperature/volume units)
-         value can be an atom-style variable (see below)
-       *edpd/temp* value = temperature of eDPD particles (temperature units)
-         value can be an atom-style variable (see below)
-       *epsilon* value = dielectric constant of the medium where the atoms reside
-         value can be an atom-style variable (see below)
-       *image* values = nx ny nz
-         nx,ny,nz = which periodic image of the simulation box the atom is in
-         any of nx,ny,nz can be an atom-style variable (see below)
-       *improper* value = numeric improper type or improper type label, for all impropers between selected atoms
-       *length* value = len
-         len = length of line segment (distance units)
-         len can be an atom-style variable (see below)
-       *mass* value = per-atom mass (mass units)
-         value can be an atom-style variable (see below)
-       *mol* value = molecule ID
-         the moleclue ID can be an atom-style variable (see below)
-       *omega* values = Wx Wy Wz
-         Wx,Wy,Wz = components of angular velocity vector (radians/time units)
-         any of Wx,Wy,Wz can be an atom-style variable (see below)
-       *quat* values = a b c theta
-         a,b,c = unit vector to rotate particle around via right-hand rule
-         theta = rotation angle (degrees)
-         any of a,b,c,theta values can be an atom-style variable (see below)
-       *quat/random* value = seed
-         seed = random # seed (positive integer) for quaternion orientations
-       *radius/electron* value = eradius
-         eradius = electron radius (or fixed-core radius) (distance units)
-         value can be an atom-style variable (see below)
-       *shape* values = Sx Sy Sz
-         Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
-         any of Sx,Sy,Sz can be an atom-style variable (see below)
-       *smd/contact/radius* value = radius for short range interactions, i.e. contact and friction
-         value can be an atom-style variable (see below)
-       *smd/mass/density* value = set particle mass based on volume by providing a mass density
-         value can be an atom-style variable (see below)
-       *sph/cv* value = heat capacity of SPH particles (need units)
-         value can be an atom-style variable (see below)
-       *sph/e* value = energy of SPH particles (need units)
-         value can be an atom-style variable (see below)
-       *sph/rho* value = density of SPH particles (need units)
-         value can be an atom-style variable (see below)
-       *spin/atom* values = g x y z
-         g = magnitude of magnetic spin vector (in Bohr magneton's unit)
-         x,y,z = orientation of magnetic spin vector
-         any of x,y,z can be an atom-style variable (see below)
-       *spin/atom/random* values = seed Dlen
-         seed = random # seed (positive integer) for magnetic spin orientations
-         Dlen = magnitude of magnetic spin vector (in Bohr magneton's unit)
-       *spin/electron* value = espin
-         espin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
-         value can be an atom-style variable (see below)
-       *temperature* value = temperature for finite-size particles (temperature units)
-         value can be an atom-style variable (see below)
-       *theta* value = angle (degrees)
-         angle = orientation of line segment with respect to x-axis
-         value can be an atom-style variable (see below)
-       *theta/random* value = seed
-         seed = random # seed (positive integer) for line segment orienations
-       *tri* value = side
-         side = side length of equilateral triangle (distance units)
-         value can be an atom-style variable (see below)
        *type* value = numeric atom type or type label
          value can be an atom-style variable (see below)
        *type/fraction* values = type fraction seed
@@ -140,22 +51,104 @@ Syntax
          type = numeric atom type or type label
          Nsubset = exact number of selected atoms to set to new atom type
          seed = random # seed (positive integer)
-       *volume* value = particle volume for Peridynamic particle (distance\^3 units)
+       *mol* value = molecule ID
+       value can be an atom-style variable (see below)
+       *x*,\ *y*,\ *z* value = atom coordinate (distance units)
          value can be an atom-style variable (see below)
        *vx*,\ *vy*,\ *vz* value = atom velocity (velocity units)
          value can be an atom-style variable (see below)
-       *x*,\ *y*,\ *z* value = atom coordinate (distance units)
+       *charge* value = atomic charge (charge units)
          value can be an atom-style variable (see below)
+       *dipole* values = x y z
+         x,y,z = orientation of dipole moment vector
+         any of x,y,z can be an atom-style variable (see below)
+       *dipole/random* value = seed Dlen
+         seed = random # seed (positive integer) for dipole moment orientations
+         Dlen = magnitude of dipole moment (dipole units)
+       *spin/atom* values = g x y z
+         g = magnitude of magnetic spin vector (in Bohr magneton's unit)
+         x,y,z = orientation of magnetic spin vector
+         any of x,y,z can be an atom-style variable (see below)
+       *spin/atom/random* value = seed Dlen
+         seed = random # seed (positive integer) for magnetic spin orientations
+         Dlen = magnitude of magnetic spin vector (in Bohr magneton's unit)
+       *radius/electron* values = eradius
+         eradius = electron radius (or fixed-core radius) (distance units)
+       *spin/electron* value = espin
+         espin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
+       *quat* values = a b c theta
+         a,b,c = unit vector to rotate particle around via right-hand rule
+         theta = rotation angle (degrees)
+         any of a,b,c,theta can be an atom-style variable (see below)
+       *quat/random* value = seed
+         seed = random # seed (positive integer) for quaternion orientations
+       *diameter* value = diameter of spherical particle (distance units)
+         value can be an atom-style variable (see below)
+       *shape* value = Sx Sy Sz
+         Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
+       *length* value = len
+         len = length of line segment (distance units)
+         len can be an atom-style variable (see below)
+       *tri* value = side
+         side = side length of equilateral triangle (distance units)
+         side can be an atom-style variable (see below)
+       *theta* value = angle (degrees)
+         angle = orientation of line segment with respect to x-axis
+         angle can be an atom-style variable (see below)
+       *theta/random* value = seed
+         seed = random # seed (positive integer) for line segment orienations
+       *angmom* values = Lx Ly Lz
+         Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
+         any of Lx,Ly,Lz can be an atom-style variable (see below)
+       *omega* values = Wx Wy Wz
+         Wx,Wy,Wz = components of angular velocity vector (radians/time units)
+         any of wx,wy,wz can be an atom-style variable (see below)
+       *mass* value = per-atom mass (mass units)
+         value can be an atom-style variable (see below)
+       *density* value = particle density for a sphere or ellipsoid (mass/distance\^3 units), or for a triangle (mass/distance\^2 units) or line (mass/distance units) particle
+         value can be an atom-style variable (see below)
+       *density/disc* value = particle density for a 2d disc or ellipse (mass/distance\^2 units)
+         value can be an atom-style variable (see below)
+       *temperature* value = temperature for finite-size particles (temperature units)
+         value can be an atom-style variable (see below)
+       *volume* value = particle volume for Peridynamic particle (distance\^3 units)
+         value can be an atom-style variable (see below)
+       *image* nx ny nz
+         nx,ny,nz = which periodic image of the simulation box the atom is in
+         any of nx,ny,nz can be an atom-style variable (see below)
+       *bond* value = numeric bond type or bond type label, for all bonds between selected atoms
+       *angle* value = numeric angle type or angle type label, for all angles between selected atoms
+       *dihedral* value = numeric dihedral type or dihedral type label, for all dihedrals between selected atoms
+       *improper* value = numeric improper type or improper type label, for all impropers between selected atoms
+       *rheo/rho* value = density of RHEO particles (mass/distance\^3)
+       *rheo/status* value = status or phase of RHEO particles (unitless)
+       *sph/e* value = energy of SPH particles (need units)
+         value can be an atom-style variable (see below)
+       *sph/cv* value = heat capacity of SPH particles (need units)
+         value can be an atom-style variable (see below)
+       *sph/rho* value = density of SPH particles (need units)
+         value can be an atom-style variable (see below)
+       *smd/contact/radius* = radius for short range interactions, i.e. contact and friction
+         value can be an atom-style variable (see below)
+       *smd/mass/density* = set particle mass based on volume by providing a mass density
+         value can be an atom-style variable (see below)
+       *dpd/theta* value = internal temperature of DPD particles (temperature units)
+         value can be an atom-style variable (see below)
+         value can be NULL which sets internal temp of each particle to KE temp
+       *edpd/temp* value = temperature of eDPD particles (temperature units)
+         value can be an atom-style variable (see below)
+       *edpd/cv* value = volumetric heat capacity of eDPD particles (energy/temperature/volume units)
+         value can be an atom-style variable (see below)
+       *cc* values = index cc
+         index = index of a chemical species (1 to Nspecies)
+         cc = chemical concentration of tDPD particles for a species (mole/volume units)
+       *epsilon* value = dielectric constant of the medium where the atoms reside
        *i_name* value = custom integer vector with name
-         value can be an atom-style variable (see below)
        *d_name* value = custom floating-point vector with name
-         value can be an atom-style variable (see below)
-       *i2_name* value = custom integer array with name
+       *i2_name* value = column of a custom integer array with name
                          column specified as i2_name[N] where N is 1 to Ncol
-         value can be an atom-style variable (see below)
-       *d2_name* value = custom floating-point array with name
+       *d2_name* value = column of a custom floating-point array with name
                          column specified as d2_name[N] where N is 1 to Ncol
-         value can be an atom-style variable (see below)
 
 Examples
 """"""""
@@ -184,26 +177,22 @@ Description
 
 Set one or more properties of one or more atoms.  Since atom
 properties are initially assigned by the :doc:`read_data <read_data>`,
-:doc:`read_restart <read_restart>` or :doc:`create_atoms
-<create_atoms>` commands, this command changes those assignments.
-This can be useful for overriding the default values assigned by the
-:doc:`create_atoms <create_atoms>` command (e.g. charge = 0.0).  It
-can be useful for altering pairwise and molecular force interactions,
+:doc:`read_restart <read_restart>` or :doc:`create_atoms <create_atoms>`
+commands, this command changes those assignments.  This can be useful
+for overriding the default values assigned by the
+:doc:`create_atoms <create_atoms>` command (e.g. charge = 0.0).  It can
+be useful for altering pairwise and molecular force interactions,
 since force-field coefficients are defined in terms of types.  It can
 be used to change the labeling of atoms by atom type or molecule ID
-when they are output in :doc:`dump <dump>` files.  It can also be
-useful for debugging purposes; i.e. positioning an atom at a precise
-location to compute subsequent forces or energy.
+when they are output in :doc:`dump <dump>` files.  It can also be useful
+for debugging purposes; i.e. positioning an atom at a precise location
+to compute subsequent forces or energy.
 
 Note that the *style* and *ID* arguments determine which atoms have
 their properties reset.  The remaining keywords specify which
 properties to reset and what the new values are.  Some strings like
 *type* or *mol* can be used as a style and/or a keyword.
 
-The :doc:`fix set <fix_set>` command can be used with similar syntax
-to this command to reset atom properties once every *N* steps during a
-simulation using via atom-style variables.
-
 ----------
 
 This section describes how to select which atoms to change
@@ -222,8 +211,8 @@ can be specified, e.g. "C".  The style *mol* selects all the atoms in
 a range of molecule IDs.
 
 In each of the range cases, the range can be specified as a single
-numeric value, or with a wildcard asterisk to specify a range of
-values.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  For
+numeric value, or a wildcard asterisk can be used to specify a range
+of values.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  For
 example, for the style *type*, 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
@@ -233,25 +222,25 @@ means all types from m to n (inclusive).  For all the styles except
 
 The style *group* selects all the atoms in the specified group.  The
 style *region* selects all the atoms in the specified geometric
-region.  See the :doc:`group <group>` and :doc:`region <region>`
-commands for details of how to specify a group or region.
+region.  See the :doc:`group <group>` and :doc:`region <region>` commands
+for details of how to specify a group or region.
 
 ----------
 
-The next section describes the keyword options for which properties to
+This section describes the keyword options for which properties to
 change, for the selected atoms.
 
 Note that except where explicitly prohibited below, all of the
 keywords allow an :doc:`atom-style or atomfile-style variable
 <variable>` to be used as the specified value(s).  If the value is a
-variable, it should be specified as v_name, where name is the variable
-name.  In this case, the variable will be evaluated, and its resulting
-per-atom value used to determine the value assigned to each selected
-atom.  Note that the per-atom value from the variable will be ignored
-for atoms that are not selected via the *style* and *ID* settings
-explained above.  A simple way to use per-atom values from the
-variable to reset a property for all atoms is to use style *atom* with
-*ID* = "\*"; this selects all atom IDs.
+variable, it should be specified as v_name, where name is the
+variable name.  In this case, the variable will be evaluated, and its
+resulting per-atom value used to determine the value assigned to each
+selected atom.  Note that the per-atom value from the variable will be
+ignored for atoms that are not selected via the *style* and *ID*
+settings explained above.  A simple way to use per-atom values from
+the variable to reset a property for all atoms is to use style *atom*
+with *ID* = "\*"; this selects all atom IDs.
 
 Atom-style variables can specify formulas with various mathematical
 functions, and include :doc:`thermo_style <thermo_style>` command
@@ -267,110 +256,52 @@ from a file.
 .. note::
 
    Atom-style and atomfile-style variables return floating point
-   per-atom values.  If the values are assigned to an integer
-   variable, such as the molecule ID, then the floating point value is
-   truncated to its integer portion, e.g. a value of 2.6 would
-   become 2.
-
-----------
+   per-atom values.  If the values are assigned to an integer variable,
+   such as the molecule ID, then the floating point value is truncated to
+   its integer portion, e.g. a value of 2.6 would become 2.
 
 .. versionchanged:: 28Mar2023
 
-   Support for type labels was added for setting angle types
+   Support for type labels was added for setting atom, bond, angle,
+   dihedral, and improper types
 
-Keyword *angle* sets the angle type of all angles of selected atoms to
-the specified value.  The value can be a numeric type from 1 to
-nangletypes.  Or it can be a angle type label.  See the :doc:`Howto
-type labels <Howto_type_labels>` doc page for the allowed syntax of
-type labels and a general discussion of how type labels can be used.
-All atoms in a particular angle must be selected atoms in order for
-the change to be made.  The value of nangletypes was set by the *angle
-types* field in the header of the data file read by the
-:doc:`read_data <read_data>` command.  This keyword does NOT allow use
-of an atom-style variable.
+Keyword *type* sets the atom type for all selected atoms.  A specified
+value can be either a numeric atom type or an atom type label. When
+using a numeric type, the specified value must be from 1 to ntypes,
+where ntypes was set by the :doc:`create_box <create_box>` command or
+the *atom types* field in the header of the data file read by the
+:doc:`read_data <read_data>` command.  When using a type label it must
+have been defined previously.  See the :doc:`Howto type labels
+<Howto_type_labels>` doc page for the allowed syntax of type labels
+and a general discussion of how type labels can be used.
 
-Keyword *angmom* sets the angular momentum of selected atoms.  The
-particles must be ellipsoids as defined by the :doc:`atom_style
-ellipsoid <atom_style>` command or triangles as defined by the
-:doc:`atom_style tri <atom_style>` command.  The angular momentum
-vector of the particles is set to the 3 specified components.
+Keyword *type/fraction* sets the atom type for a fraction of the selected
+atoms.  The actual number of atoms changed is not guaranteed
+to be exactly the specified fraction (0 <= *fraction* <= 1), but
+should be statistically close.  Random numbers are used in such a way
+that a particular atom is changed or not changed, regardless of how
+many processors are being used.  This keyword does not allow use of an
+atom-style variable.
 
-.. versionchanged:: 28Mar2023
+Keywords *type/ratio* and *type/subset* also set the atom type for a
+fraction of the selected atoms.  The actual number of atoms changed
+will be exactly the requested number.  For *type/ratio* the specified
+fraction (0 <= *fraction* <= 1) determines the number.  For
+*type/subset*, the specified *Nsubset* is the number.  An iterative
+algorithm is used which ensures the correct number of atoms are
+selected, in a perfectly random fashion.  Which atoms are selected
+will change with the number of processors used.  These keywords do not
+allow use of an atom-style variable.
 
-   Support for type labels was added for setting bond types
+Keyword *mol* sets the molecule ID for all selected atoms.  The
+:doc:`atom style <atom_style>` being used must support the use of
+molecule IDs.
 
-Keyword *bond* sets the bond type of all bonds of selected atoms to
-the specified value.  The value can be a numeric type from 1 to
-nbondtypes.  Or it can be a bond type label.  See the :doc:`Howto type
-labels <Howto_type_labels>` doc page for the allowed syntax of type
-labels and a general discussion of how type labels can be used.  All
-atoms in a particular bond must be selected atoms in order for the
-change to be made.  The value of nbondtypes was set by the *bond
-types* field in the header of the data file read by the
-:doc:`read_data <read_data>` command.  This keyword does NOT allow use
-of an atom-style variable.
-
-Keyword *cc* sets the chemical concentration of a tDPD particle for a
-specified species as defined by the DPD-MESO package. Currently, only
-:doc:`atom_style tdpd <atom_style>` defines particles with this
-attribute. An integer for "index" selects a chemical species (1 to
-Nspecies) where Nspecies is set by the atom_style command. The value
-for the chemical concentration must be >= 0.0.
-
-Keyword *charge* set the charge of all selected atoms.  The :doc:`atom
-style <atom_style>` being used must support the use of atomic charge.
-
-Keyword *density* or *density/disc* also sets the mass of all selected
-particles, but in a different way.  The particles must have a per-atom
-mass attribute, as defined by the :doc:`atom_style <atom_style>`
-command.  If the atom has a radius attribute (see :doc:`atom_style
-sphere <atom_style>`) and its radius is non-zero, its mass is set from
-the density and particle volume for 3d systems (the input density is
-assumed to be in mass/distance\^3 units).  For 2d, the default is for
-LAMMPS to model particles with a radius attribute as spheres.
-However, if the *density/disc* keyword is used, then they can be
-modeled as 2d discs (circles).  Their mass is set from the density and
-particle area (the input density is assumed to be in mass/distance\^2
-units).
-
-If the atom has a shape attribute (see :doc:`atom_style ellipsoid
-<atom_style>`) and its 3 shape parameters are non-zero, then its mass
-is set from the density and particle volume (the input density is
-assumed to be in mass/distance\^3 units).  The *density/disc* keyword
-has no effect; it does not (yet) treat 3d ellipsoids as 2d ellipses.
-
-If the atom has a length attribute (see :doc:`atom_style line
-<atom_style>`) and its length is non-zero, then its mass is set from
-the density and line segment length (the input density is assumed to
-be in mass/distance units).  If the atom has an area attribute (see
-:doc:`atom_style tri <atom_style>`) and its area is non-zero, then its
-mass is set from the density and triangle area (the input density is
-assumed to be in mass/distance\^2 units).
-
-If none of these cases are valid, then the mass is set to the density
-value directly (the input density is assumed to be in mass units).
-
-Keyword *diameter* sets the size of the selected atoms.  The particles
-must be finite-size spheres as defined by the :doc:`atom_style sphere
-<atom_style>` command.  The diameter of a particle can be set to 0.0,
-which means they will be treated as point particles.  Note that this
-command does not adjust the particle mass, even if it was defined with
-a density, e.g. via the :doc:`read_data <read_data>` command.
-
-.. versionchanged:: 28Mar2023
-
-   Support for type labels was added for setting dihedral types
-
-Keyword *dihedral* sets the dihedral type of all dihedrals of selected
-atoms to the specified value.  The value can be a numeric type from 1
-to ndihedraltypes.  Or it can be a dihedral type label.  See the
-:doc:`Howto type labels <Howto_type_labels>` doc page for the allowed
-syntax of type labels and a general discussion of how type labels can
-be used.  All atoms in a particular dihedral must be selected atoms in
-order for the change to be made.  The value of ndihedraltypes was set
-by the *dihedral types* field in the header of the data file read by
-the :doc:`read_data <read_data>` command.  This keyword does NOT allow
-use of an atom-style variable.
+Keywords *x*, *y*, *z*, and *charge* set the coordinates or
+charge of all selected atoms.  For *charge*, the :doc:`atom style
+<atom_style>` being used must support the use of atomic
+charge. Keywords *vx*, *vy*, and *vz* set the velocities of all
+selected atoms.
 
 Keyword *dipole* uses the specified x,y,z values as components of a
 vector to set as the orientation of the dipole moment vectors of the
@@ -382,106 +313,40 @@ moment vectors for the selected atoms and sets the magnitude of each
 to the specified *Dlen* value.  For 2d systems, the z component of the
 orientation is set to 0.0.  Random numbers are used in such a way that
 the orientation of a particular atom is the same, regardless of how
-many processors are being used.  This keyword does NOT allow use of an
+many processors are being used.  This keyword does not allow use of an
 atom-style variable.
 
-Keyword *dpd/theta* sets the internal temperature of a DPD particle as
-defined by the DPD-REACT package.  If the specified value is a number
-it must be >= 0.0.  If the specified value is NULL, then the kinetic
-temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2
-m v\^2 = 1/2 m (vx\*vx+vy\*vy+vz\*vz).  Each particle's internal
-temperature is set to Tkin.  If the specified value is an atom-style
-variable, then the variable is evaluated for each particle.  If a
-value >= 0.0, the internal temperature is set to that value.  If it is
-< 0.0, the computation of Tkin is performed and the internal
-temperature is set to that value.
+.. versionchanged:: 15Sep2022
 
-Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric
-heat capacity of an eDPD particle as defined by the DPD-MESO package.
-Currently, only :doc:`atom_style edpd <atom_style>` defines particles
-with these attributes. The values for the temperature and heat
-capacity must be positive.
+Keyword *spin/atom* uses the specified g value to set the magnitude of the
+magnetic spin vectors, and the x,y,z values as components of a vector
+to set as the orientation of the magnetic spin vectors of the selected
+atoms.  This keyword was previously called *spin*.
 
-Keyword *epsilon* sets the dielectric constant of a particle to be
-that of the medium where the particle resides as defined by the
-DIELECTRIC package. Currently, only :doc:`atom_style dielectric
-<atom_style>` defines particles with this attribute. The value for the
-dielectric constant must be >= 0.0.  Note that the set command with
-this keyword will rescale the particle charge accordingly so that the
-real charge (e.g., as read from a data file) stays intact. To change
-the real charges, one needs to use the set command with the *charge*
-keyword. Care must be taken to ensure that the real and scaled charges
-and the dielectric constants are consistent.
+.. versionchanged:: 15Sep2022
 
-Keyword *image* sets which image of the simulation box the atom is
-considered to be in.  An image of 0 means it is inside the box as
-defined.  A value of 2 means add 2 box lengths to get the true value.
-A value of -1 means subtract 1 box length to get the true value.
-LAMMPS updates these flags as atoms cross periodic boundaries during
-the simulation.  The flags can be output with atom snapshots via the
-:doc:`dump <dump>` command.  If a value of NULL is specified for any
-of nx,ny,nz, then the current image value for that dimension is
-unchanged.  For non-periodic dimensions only a value of 0 can be
-specified.  This command can be useful after a system has been
-equilibrated and atoms have diffused one or more box lengths in
-various directions.  This command can then reset the image values for
-atoms so that they are effectively inside the simulation box, e.g if a
-diffusion coefficient is about to be measured via the :doc:`compute
-msd <compute_msd>` command.  Care should be taken not to reset the
-image flags of two atoms in a bond to the same value if the bond
-straddles a periodic boundary (rather they should be different by +/-
-1).  This will not affect the dynamics of a simulation, but may mess
-up analysis of the trajectories if a LAMMPS diagnostic or your own
-analysis relies on the image flags to unwrap a molecule which
-straddles the periodic box.
+Keyword *spin/atom/random* randomizes the orientation of the magnetic spin
+vectors for the selected atoms and sets the magnitude of each to the
+specified *Dlen* value.  This keyword was previously called *spin/random*.
 
-.. versionchanged:: 28Mar2023
+.. versionadded:: 15Sep2022
 
-   Support for type labels was added for setting improper types
+Keyword *radius/electron* uses the specified value to set the radius of
+electrons or fixed cores.
 
-Keyword *improper* sets the improper type of all impropers of selected
-atoms to the specified value.  The value can be a numeric type from 1
-to nimpropertypes.  Or it can be a improper type label.  See the
-:doc:`Howto type labels <Howto_type_labels>` doc page for the allowed
-syntax of type labels and a general discussion of how type labels can
-be used.  All atoms in a particular improper must be selected atoms in
-order for the change to be made.  The value of nimpropertypes was set
-by the *improper types* field in the header of the data file read by
-the :doc:`read_data <read_data>` command.  This keyword does NOT allow
-use of an atom-style variable.
+.. versionadded:: 15Sep2022
 
-Keyword *length* sets the length of selected atoms.  The particles
-must be line segments as defined by the :doc:`atom_style line
-<atom_style>` command.  If the specified value is non-zero the line
-segment is (re)set to a length = the specified value, centered around
-the particle position, with an orientation along the x-axis.  If the
-specified value is 0.0, the particle will become a point particle.
-Note that this command does not adjust the particle mass, even if it
-was defined with a density, e.g. via the :doc:`read_data <read_data>`
-command.
-
-Keyword *mass* sets the mass of all selected particles.  The particles
-must have a per-atom mass attribute, as defined by the
-:doc:`atom_style <atom_style>` command.  See the "mass" command for
-how to set mass values on a per-type basis.
-
-Keyword *mol* sets the molecule ID for all selected atoms.  The
-:doc:`atom style <atom_style>` being used must support the use of
-molecule IDs.
-
-Keyword *omega* sets the angular velocity of selected atoms.  The
-particles must be spheres as defined by the :doc:`atom_style sphere
-<atom_style>` command.  The angular velocity vector of the particles
-is set to the 3 specified components.
+Keyword *spin/electron* sets the spin of an electron (+/- 1) or indicates
+nuclei (=0), fixed-cores (=2), or pseudo-cores (= 3).
 
 Keyword *quat* uses the specified values to create a quaternion
 (4-vector) that represents the orientation of the selected atoms.  The
 particles must define a quaternion for their orientation
 (e.g. ellipsoids, triangles, body particles) as defined by the
-:doc:`atom_style <atom_style>` command.  Note that particles defined
-by :doc:`atom_style ellipsoid <atom_style>` have 3 shape parameters.
-The 3 values must be non-zero for each particle set by this command.
-They are used to specify the aspect ratios of an ellipsoidal particle,
+:doc:`atom_style <atom_style>` command.  Note that particles defined by
+:doc:`atom_style ellipsoid <atom_style>` have 3 shape parameters.  The 3
+values must be non-zero for each particle set by this command.  They
+are used to specify the aspect ratios of an ellipsoidal particle,
 which is oriented by default with its x-axis along the simulation
 box's x-axis, and similarly for y and z.  If this body is rotated (via
 the right-hand rule) by an angle theta around a unit rotation vector
@@ -495,77 +360,51 @@ ignored, since a rotation vector of (0,0,1) is the only valid choice.
 Keyword *quat/random* randomizes the orientation of the quaternion for
 the selected atoms.  The particles must define a quaternion for their
 orientation (e.g. ellipsoids, triangles, body particles) as defined by
-the :doc:`atom_style <atom_style>` command.  Random numbers are used
-in such a way that the orientation of a particular atom is the same,
+the :doc:`atom_style <atom_style>` command.  Random numbers are used in
+such a way that the orientation of a particular atom is the same,
 regardless of how many processors are being used.  For 2d systems,
 only orientations in the xy plane are generated.  As with keyword
 *quat*, for ellipsoidal particles, the 3 shape values must be non-zero
-for each particle set by this command.  This keyword does NOT allow
+for each particle set by this command.  This keyword does not allow
 use of an atom-style variable.
 
-.. versionadded:: 15Sep2022
-
-Keyword *radius/electron* uses the specified value to set the radius
-of electrons or fixed cores.
+Keyword *diameter* sets the size of the selected atoms.  The particles
+must be finite-size spheres as defined by the :doc:`atom_style sphere
+<atom_style>` command.  The diameter of a particle can be set to 0.0,
+which means they will be treated as point particles.  Note that this
+command does not adjust the particle mass, even if it was defined with
+a density, e.g. via the :doc:`read_data <read_data>` command.
 
 Keyword *shape* sets the size and shape of the selected atoms.  The
 particles must be ellipsoids as defined by the :doc:`atom_style
-ellipsoid <atom_style>` command.  The *Sx*, *Sy*, *Sz* settings are
-the 3 diameters of the ellipsoid in each direction.  All 3 can be set
-to the same value, which means the ellipsoid is effectively a sphere.
-They can also all be set to 0.0 which means the particle will be
-treated as a point particle.  Note that this command does not adjust
-the particle mass, even if it was defined with a density, e.g. via the
-:doc:`read_data <read_data>` command.
+ellipsoid <atom_style>` command.  The *Sx*, *Sy*, *Sz* settings
+are the 3 diameters of the ellipsoid in each direction.  All 3 can be
+set to the same value, which means the ellipsoid is effectively a
+sphere.  They can also all be set to 0.0 which means the particle will
+be treated as a point particle.  Note that this command does not
+adjust the particle mass, even if it was defined with a density,
+e.g. via the :doc:`read_data <read_data>` command.
 
-Keyword *smd/contact/radius* only applies to simulations with the
-Smooth Mach Dynamics package MACHDYN.  Itsets an interaction radius
-for computing short-range interactions, e.g. repulsive forces to
-prevent different individual physical bodies from penetrating each
-other. Note that the SPH smoothing kernel diameter used for computing
-long range, nonlocal interactions, is set using the *diameter*
-keyword.
+Keyword *length* sets the length of selected atoms.  The particles
+must be line segments as defined by the :doc:`atom_style line
+<atom_style>` command.  If the specified value is non-zero the line
+segment is (re)set to a length = the specified value, centered around
+the particle position, with an orientation along the x-axis.  If the
+specified value is 0.0, the particle will become a point particle.
+Note that this command does not adjust the particle mass, even if it
+was defined with a density, e.g. via the :doc:`read_data <read_data>`
+command.
 
-Keyword *smd/mass/density* sets the mass of all selected particles,
-but it is only applicable to the Smooth Mach Dynamics package MACHDYN.
-It assumes that the particle volume has already been correctly set and
-calculates particle mass from the provided mass density value.
-
-Keywords *sph/cv*, *sph/e*, and *sph/rho* set the heat capacity,
-energy, and density of smoothed particle hydrodynamics (SPH)
-particles.  See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to
-using SPH in LAMMPS.
-
-.. note::
-
-   Note that the SPH PDF guide file has not been updated for many
-   years and thus does not reflect the current *syntax* of the SPH
-   package commands. For that, please refer to the LAMMPS manual.
-
-.. versionchanged:: 15Sep2022
-
-Keyword *spin/atom* uses the specified g value to set the magnitude of
-the magnetic spin vectors, and the x,y,z values as components of a
-vector to set as the orientation of the magnetic spin vectors of the
-selected atoms.  This keyword was previously called *spin*.
-
-.. versionchanged:: 15Sep2022
-
-Keyword *spin/atom/random* randomizes the orientation of the magnetic
-spin vectors for the selected atoms and sets the magnitude of each to
-the specified *Dlen* value.  This keyword does NOT allow use of an
-atom-style variable.  This keyword was previously called
-*spin/random*.
-
-.. versionadded:: 15Sep2022
-
-Keyword *spin/electron* sets the spin of an electron (+/- 1) or
-indicates nuclei (=0), fixed-cores (=2), or pseudo-cores (= 3).
-
-Keyword *temperature* sets the temperature of a finite-size particle.
-Currently, only the GRANULAR package supports this attribute. The
-temperature must be added using an instance of :doc:`fix property/atom
-<fix_property_atom>` The values for the temperature must be positive.
+Keyword *tri* sets the size of selected atoms.  The particles must be
+triangles as defined by the :doc:`atom_style tri <atom_style>` command.
+If the specified value is non-zero the triangle is (re)set to be an
+equilateral triangle in the xy plane with side length = the specified
+value, with a centroid at the particle position, with its base
+parallel to the x axis, and the y-axis running from the center of the
+base to the top point of the triangle.  If the specified value is 0.0,
+the particle will become a point particle.  Note that this command
+does not adjust the particle mass, even if it was defined with a
+density, e.g. via the :doc:`read_data <read_data>` command.
 
 Keyword *theta* sets the orientation of selected atoms.  The particles
 must be line segments as defined by the :doc:`atom_style line
@@ -574,71 +413,169 @@ orientation angle of the line segments with respect to the x axis.
 
 Keyword *theta/random* randomizes the orientation of theta for the
 selected atoms.  The particles must be line segments as defined by the
-:doc:`atom_style line <atom_style>` command.  Random numbers are used
-in such a way that the orientation of a particular atom is the same,
+:doc:`atom_style line <atom_style>` command.  Random numbers are used in
+such a way that the orientation of a particular atom is the same,
 regardless of how many processors are being used.  This keyword does
-NOT allow use of an atom-style variable.
+not allow use of an atom-style variable.
 
-Keyword *tri* sets the size of selected atoms.  The particles must be
-triangles as defined by the :doc:`atom_style tri <atom_style>`
-command.  If the specified value is non-zero the triangle is (re)set
-to be an equilateral triangle in the xy plane with side length = the
-specified value, with a centroid at the particle position, with its
-base parallel to the x axis, and the y-axis running from the center of
-the base to the top point of the triangle.  If the specified value is
-0.0, the particle will become a point particle.  Note that this
-command does not adjust the particle mass, even if it was defined with
-a density, e.g. via the :doc:`read_data <read_data>` command.
+Keyword *angmom* sets the angular momentum of selected atoms.  The
+particles must be ellipsoids as defined by the :doc:`atom_style
+ellipsoid <atom_style>` command or triangles as defined by the
+:doc:`atom_style tri <atom_style>` command.  The angular momentum
+vector of the particles is set to the 3 specified components.
 
-.. versionchanged:: 28Mar2023
+Keyword *omega* sets the angular velocity of selected atoms.  The
+particles must be spheres as defined by the :doc:`atom_style sphere
+<atom_style>` command.  The angular velocity vector of the particles is
+set to the 3 specified components.
 
-   Support for type labels was added for setting atom types
+Keyword *mass* sets the mass of all selected particles.  The particles
+must have a per-atom mass attribute, as defined by the :doc:`atom_style
+<atom_style>` command.  See the "mass" command for how to set mass
+values on a per-type basis.
 
-Keyword *type* sets the atom type for all selected atoms.  A specified
-value can be either a numeric atom type or an atom type label. When
-using a numeric type, the specified value must be from 1 to ntypes,
-where ntypes was set by the :doc:`create_box <create_box>` command or
-the *atom types* field in the header of the data file read by the
-:doc:`read_data <read_data>` command.  When using a type label it must
-have been defined previously.  See the :doc:`Howto type labels
+Keyword *density* or *density/disc* also sets the mass of all selected
+particles, but in a different way.  The particles must have a per-atom
+mass attribute, as defined by the :doc:`atom_style <atom_style>`
+command.  If the atom has a radius attribute (see :doc:`atom_style
+sphere <atom_style>`) and its radius is non-zero, its mass is set from
+the density and particle volume for 3d systems (the input density is
+assumed to be in mass/distance\^3 units).  For 2d, the default is for
+LAMMPS to model particles with a radius attribute as spheres.  However,
+if the *density/disc* keyword is used, then they can be modeled as 2d
+discs (circles).  Their mass is set from the density and particle area
+(the input density is assumed to be in mass/distance\^2 units).
+
+If the atom has a shape attribute (see :doc:`atom_style ellipsoid
+<atom_style>`) and its 3 shape parameters are non-zero, then its mass is
+set from the density and particle volume (the input density is assumed
+to be in mass/distance\^3 units).  The *density/disc* keyword has no
+effect; it does not (yet) treat 3d ellipsoids as 2d ellipses.
+
+If the atom has a length attribute (see :doc:`atom_style line
+<atom_style>`) and its length is non-zero, then its mass is set from the
+density and line segment length (the input density is assumed to be in
+mass/distance units).  If the atom has an area attribute (see
+:doc:`atom_style tri <atom_style>`) and its area is non-zero, then its
+mass is set from the density and triangle area (the input density is
+assumed to be in mass/distance\^2 units).
+
+If none of these cases are valid, then the mass is set to the density
+value directly (the input density is assumed to be in mass units).
+
+Keyword *temperature* sets the temperature of a finite-size particle.
+Currently, only the GRANULAR package supports this attribute. The
+temperature must be added using an instance of
+:doc:`fix property/atom <fix_property_atom>` The values for the
+temperature must be positive.
+
+Keyword *volume* sets the volume of all selected particles.  Currently,
+only the :doc:`atom_style peri <atom_style>` command defines particles
+with a volume attribute.  Note that this command does not adjust the
+particle mass.
+
+Keyword *image* sets which image of the simulation box the atom is
+considered to be in.  An image of 0 means it is inside the box as
+defined.  A value of 2 means add 2 box lengths to get the true value.  A
+value of -1 means subtract 1 box length to get the true value.  LAMMPS
+updates these flags as atoms cross periodic boundaries during the
+simulation.  The flags can be output with atom snapshots via the
+:doc:`dump <dump>` command.  If a value of NULL is specified for any of
+nx,ny,nz, then the current image value for that dimension is unchanged.
+For non-periodic dimensions only a value of 0 can be specified.  This
+command can be useful after a system has been equilibrated and atoms
+have diffused one or more box lengths in various directions.  This
+command can then reset the image values for atoms so that they are
+effectively inside the simulation box, e.g if a diffusion coefficient is
+about to be measured via the :doc:`compute msd <compute_msd>` command.
+Care should be taken not to reset the image flags of two atoms in a bond
+to the same value if the bond straddles a periodic boundary (rather they
+should be different by +/- 1).  This will not affect the dynamics of a
+simulation, but may mess up analysis of the trajectories if a LAMMPS
+diagnostic or your own analysis relies on the image flags to unwrap a
+molecule which straddles the periodic box.
+
+Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond
+type (angle type, etc) of all bonds (angles, etc) of selected atoms to
+the specified value.  The value can be a numeric type from 1 to
+nbondtypes (nangletypes, etc).  Or it can be a type label (bond type
+label, angle type label, etc).  See the :doc:`Howto type labels
 <Howto_type_labels>` doc page for the allowed syntax of type labels
-and a general discussion of how type labels can be used.
+and a general discussion of how type labels can be used.  All atoms in
+a particular bond (angle, etc) must be selected atoms in order for the
+change to be made.  The value of nbondtypes (nangletypes, etc) was set
+by the *bond types* (\ *angle types*, etc) field in the header of the
+data file read by the :doc:`read_data <read_data>` command.  These
+keywords do not allow use of an atom-style variable.
 
-Keyword *type/fraction* sets the atom type for a fraction of the
-selected atoms.  The actual number of atoms changed is not guaranteed
-to be exactly the specified fraction (0 <= *fraction* <= 1), but
-should be statistically close.  Random numbers are used in such a way
-that a particular atom is changed or not changed, regardless of how
-many processors are being used.  This keyword does NOT allow use of an
-atom-style variable.
+Keywords *rheo/rho* and *rheo/status* set the density and the status of
+rheo particles. In particular, one can only set the phase in the status
+as described by the :doc:`RHEO howto page <Howto_rheo>`.
 
-Keywords *type/ratio* and *type/subset* also set the atom type for a
-fraction of the selected atoms.  The actual number of atoms changed
-will be exactly the requested number.  For *type/ratio* the specified
-fraction (0 <= *fraction* <= 1) determines the number.  For
-*type/subset*, the specified *Nsubset* is the number.  An iterative
-algorithm is used which ensures the correct number of atoms are
-selected, in a perfectly random fashion.  Which atoms are selected
-will change with the number of processors used.  These keywords do not
-allow use of an atom-style variable.
+Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
+and density of smoothed particle hydrodynamics (SPH) particles.  See
+`this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
 
-Keyword *volume* sets the volume of all selected particles.
-Currently, only the :doc:`atom_style peri <atom_style>` command
-defines particles with a volume attribute.  Note that this command
-does not adjust the particle mass.
+.. note::
 
-Keywords *vx*, *vy*, and *vz* set the velocities of all selected
-atoms.
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
 
-Keywords *x*, *y*, *z* set the coordinates of all selected atoms.
+Keyword *smd/mass/density* sets the mass of all selected particles, but
+it is only applicable to the Smooth Mach Dynamics package MACHDYN.  It
+assumes that the particle volume has already been correctly set and
+calculates particle mass from the provided mass density value.
+
+Keyword *smd/contact/radius* only applies to simulations with the Smooth
+Mach Dynamics package MACHDYN.  Itsets an interaction radius for
+computing short-range interactions, e.g. repulsive forces to prevent
+different individual physical bodies from penetrating each other. Note
+that the SPH smoothing kernel diameter used for computing long range,
+nonlocal interactions, is set using the *diameter* keyword.
+
+Keyword *dpd/theta* sets the internal temperature of a DPD particle as
+defined by the DPD-REACT package.  If the specified value is a number it
+must be >= 0.0.  If the specified value is NULL, then the kinetic
+temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2 m
+v\^2 = 1/2 m (vx\*vx+vy\*vy+vz\*vz).  Each particle's internal
+temperature is set to Tkin.  If the specified value is an atom-style
+variable, then the variable is evaluated for each particle.  If a value
+>= 0.0, the internal temperature is set to that value.  If it is < 0.0,
+the computation of Tkin is performed and the internal temperature is set
+to that value.
+
+Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric
+heat capacity of an eDPD particle as defined by the DPD-MESO package.
+Currently, only :doc:`atom_style edpd <atom_style>` defines particles
+with these attributes. The values for the temperature and heat capacity
+must be positive.
+
+Keyword *cc* sets the chemical concentration of a tDPD particle for a
+specified species as defined by the DPD-MESO package. Currently, only
+:doc:`atom_style tdpd <atom_style>` defines particles with this
+attribute. An integer for "index" selects a chemical species (1 to
+Nspecies) where Nspecies is set by the atom_style command. The value for
+the chemical concentration must be >= 0.0.
+
+Keyword *epsilon* sets the dielectric constant of a particle, precisely
+of the medium where the particle resides as defined by the DIELECTRIC
+package. Currently, only :doc:`atom_style dielectric <atom_style>`
+defines particles with this attribute. The value for the dielectric
+constant must be >= 0.0.  Note that the set command with this keyword
+will rescale the particle charge accordingly so that the real charge
+(e.g., as read from a data file) stays intact. To change the real
+charges, one needs to use the set command with the *charge*
+keyword. Care must be taken to ensure that the real and scaled charges,
+and dielectric constants are consistent.
 
 Keywords *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
 per-atom integer and floating-point vectors or arrays that have been
 added via the :doc:`fix property/atom <fix_property_atom>` command.
 When that command is used specific names are given to each attribute
 which are the "name" portion of these keywords.  For arrays *i2_name*
-and *d2_name*, the column of the array to set must also be included
-following the name in brackets: e.g. d2_xyz[2] or i2_mySpin[3].
+and *d2_name*, the column of the array must also be included following
+the name in brackets: e.g. d2_xyz[2], i2_mySpin[3].
 
 Restrictions
 """"""""""""
@@ -647,7 +584,7 @@ You cannot set an atom attribute (e.g. *mol* or *q* or *volume*\ ) if
 the :doc:`atom_style <atom_style>` does not have that attribute.
 
 This command requires inter-processor communication to coordinate the
-setting of bond types (angle types, etc).  This means that the system
+setting of bond types (angle types, etc).  This means that your system
 must be ready to perform a simulation before using one of these
 keywords (force fields set, atom mass set, etc).  This is not
 necessary for other keywords.
@@ -662,7 +599,7 @@ Related commands
 """"""""""""""""
 
 :doc:`create_box <create_box>`, :doc:`create_atoms <create_atoms>`,
-:doc:`read_data <read_data>`, :doc:`fix set <fix_set>`
+:doc:`read_data <read_data>`
 
 Default
 """""""

doc/src/variable.rst

@@ -45,8 +45,7 @@ Syntax
        *universe* args = one or more strings
        *world* args = one string for each partition of processors
 
-       *equal* or *vector* or *atom* args = one formula containing numbers, thermo keywords,
-           math operations, built-in functions, atom values and vectors, compute/fix/variable references
+       *equal* or *vector* or *atom* args = one formula containing numbers, thermo keywords, math operations, built-in functions, atom values and vectors, compute/fix/variable references
          numbers = 0.0, 100, -5.4, 2.8e-4, etc
          constants = PI, version, on, off, true, false, yes, no
          thermo keywords = vol, ke, press, etc from :doc:`thermo_style <thermo_style>`
@@ -68,12 +67,8 @@ Syntax
                            bound(group,dir,region), gyration(group,region), ke(group,reigon),
                            angmom(group,dim,region), torque(group,dim,region),
                            inertia(group,dimdim,region), omega(group,dim,region)
-         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), \                                  gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name),
-                             extract_setting(name), label2type(kind,label),
-                             is_typelabel(kind,label), is_timeout()
-         feature functions = is_available(category,feature), is_active(category,feature),
-                             is_defined(category,id)
-         python function wrapper = py_varname(x,y,z,...)
+         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout()
+         feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
          atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
          atom vector = id, mass, type, mol, radius, q, x, y, z, vx, vy, vz, fx, fy, fz
          custom atom property = i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d2_name[i][j]
@@ -132,21 +127,18 @@ command), or used as input to an averaging fix (see the :doc:`fix
 ave/time <fix_ave_time>` command).  Variables of style *vector* store
 a formula which produces a vector of such values which can be used as
 input to various averaging fixes, or elements of which can be part of
-thermodynamic output.
-
-Variables of style *atom* store a formula which when evaluated
-produces one numeric value per atom which can be output to a dump file
-(see the :doc:`dump custom <dump>` command) or used as input to an
-averaging fix (see the :doc:`fix ave/chunk <fix_ave_chunk>` and
-:doc:`fix ave/atom <fix_ave_atom>` commands).  Variables of style
-*atomfile* can be used anywhere in an input script that atom-style
-variables are used; they get their per-atom values from a file rather
-than from a formula.
-
-Variables of style *python* can be hooked to Python functions using
-Python code you provide, so that the variable gets its value from the
-evaluation of the Python code.  Variables of style *internal* are used
-by a few commands which set their value directly.
+thermodynamic output.  Variables of style *atom* store a formula which
+when evaluated produces one numeric value per atom which can be output
+to a dump file (see the :doc:`dump custom <dump>` command) or used as
+input to an averaging fix (see the :doc:`fix ave/chunk
+<fix_ave_chunk>` and :doc:`fix ave/atom <fix_ave_atom>` commands).
+Variables of style *atomfile* can be used anywhere in an input script
+that atom-style variables are used; they get their per-atom values
+from a file rather than from a formula.  Variables of style *python*
+can be hooked to Python functions using code you provide, so that the
+variable gets its value from the evaluation of the Python code.
+Variables of style *internal* are used by a few commands which set
+their value directly.
 
 .. note::
 
@@ -174,16 +166,15 @@ simulation.
 
 .. note::
 
-   When an input script line is encountered that defines a variable of
-   style *equal* or *vector* or *atom* or *python* that contains a
-   formula or links to Python code, the formula or Python code is NOT
-   immediately evaluated.  Instead, it is evaluated each time the
-   variable is **used**.  If you simply want to evaluate a formula in
-   place you can use a so-called immediate variable. as described in
-   the preceding note.  Or see the section below about "Immediate
-   Evaluation of Variables" for more details on the topic.  This is
-   also true of a *format* style variable since it evaluates another
-   variable when it is invoked.
+   When an input script line is encountered that defines a variable
+   of style *equal* or *vector* or *atom* or *python* that contains a
+   formula or Python code, the formula is NOT immediately evaluated.  It
+   will be evaluated every time when the variable is **used** instead.  If
+   you simply want to evaluate a formula in place you can use as
+   so-called. See the section below about "Immediate Evaluation of
+   Variables" for more details on the topic.  This is also true of a
+   *format* style variable since it evaluates another variable when it is
+   invoked.
 
 Variables of style *equal* and *vector* and *atom* can be used as
 inputs to various other commands which evaluate their formulas as
@@ -192,12 +183,12 @@ this context, variables of style *timer* or *internal* or *python* can
 be used in place of an equal-style variable, with the following two
 caveats.
 
-First, internal-style variables require their values be set by code
-elsewhere in LAMMPS.  When a LAMMPS input script or command evaluates
-an internal-style variable, it must have a current value set
-(internally) via that mechanism.  Second, python-style variables can
-be used so long as the associated Python function, as defined by the
-:doc:`python <python>` command, returns a numeric value.  When the
+First, internal-style variables can be used except by commands that
+set the value stored by the internal variable.  When the LAMMPS
+command evaluates the internal-style variable, it will use the value
+set (internally) by another command.  Second, python-style variables
+can be used so long as the associated Python function, as defined by
+the :doc:`python <python>` command, returns a numeric value.  When the
 LAMMPS command evaluates the python-style variable, the Python
 function will be executed.
 
@@ -397,24 +388,13 @@ using the :doc:`command-line switch -var <Run_options>`.
 
 For the *internal* style a numeric value is provided.  This value will
 be assigned to the variable until a LAMMPS command sets it to a new
-value.
-
-Note however, that most commands which use internal-style variables do
-not require them to be defined in the input script.  They create one or
-more internal-style variables if they do not already exist.  Examples
-are these commands:
-
-* :doc:`create_atoms <create_atoms>`
-* :doc:`fix deposit <fix_deposit>`
-* :doc:`compute bond/local <compute_bond_local>`
-* :doc:`compute angle/local <compute_angle_local>`
-* :doc:`compute dihedral/local <compute_dihedral_local>`
-* :doc:`python <python>` command in conjunction with Python function wrappers used in equal- and atom-style variable formulas
-
-A command which does require an internal-style variable to be defined in
-the input script is the :doc:`fix controller <fix_controller>` command,
-because another (arbitrary) command typically also references the
-variable.
+value.  There are currently only two LAMMPS commands that require
+*internal* variables as inputs, because they reset them:
+:doc:`create_atoms <create_atoms>` and :doc:`fix controller
+<fix_controller>`.  As mentioned above, an internal-style variable can
+be used in place of an equal-style variable anywhere else in an input
+script, e.g. as an argument to another command that allows for
+equal-style variables.
 
 ----------
 
@@ -459,15 +439,6 @@ python-style variable can be used in place of an equal-style variable
 anywhere in an input script, e.g. as an argument to another command
 that allows for equal-style variables.
 
-A python-style variable can also be used within the formula for an
-equal-style or atom-style formula in a Python function wrapper, as
-explained below for variable formulas.  In this context, the usage
-syntax is py_varname(arg1,arg2,...), where varname is the name of the
-python-style variable.  When a Python wrapper function is used in an
-atom-style formula, it can be invoked once per atom using arguments
-specific to each atom.  The resulting values in the atom-style
-variable can thus be calculated by Python code.
-
 ----------
 
 For the *string* style, a single string is assigned to the variable.
@@ -557,9 +528,9 @@ is a valid (though strange) variable formula:
 
 Specifically, a formula can contain numbers, constants, thermo
 keywords, math operators, math functions, group functions, region
-functions, special functions, feature functions, Python function
-wrappers, atom values, atom vectors, custom atom properties, compute
-references, fix references, and references to other variables.
+functions, special functions, feature functions, atom values, atom
+vectors, custom atom properties, compute references, fix references, and references to other
+variables.
 
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Number                 | 0.2, 100, 1.0e20, -15.4, etc                                                                                                                                                                                                                                                                                                                               |
@@ -580,8 +551,6 @@ references, fix references, and references to other variables.
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Feature functions      | is_available(category,feature), is_active(category,feature), is_defined(category,id)                                                                                                                                                                                                                                                                       |
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| Python func wrapper    | py_varname(x,y,z,...)                                                                                                                                                                                                                                                                                                                                      |
-+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Atom values            | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]                                                                                                                                                                                                                                                          |
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Atom vectors           | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q                                                                                                                                                                                                                                                                                                    |
@@ -1192,84 +1161,6 @@ variable name.
 
 ----------
 
-Python Function wrapper
-------------------------
-
-A Python function wrapper enables the formula for an equal-style or
-atom-style variable to invoke functions coded in Python.  In the case
-of an equal-style variable, the Python-coded function will be invoked
-once.  In the case of an atom-style variable, it can be invoked once
-per atom, if one or more of its arguments include a per-atom quantity,
-e.g. the position of an atom.  As illustrated below, the reason to use
-a Python function wrapper is to make it easy to pass LAMMPS-related
-arguments to the Python-coded function associated with a python-style
-variable.
-
-The syntax for defining a Python function wrapper is
-
-.. code-block:: LAMMPS
-
-   py_varname(arg1,arg2,...argN)
-
-where *varname* is the name of a python-style variable which couples
-to a Python-coded function.  The function will be passed the zero or
-more arguments listed in parentheses: *arg1*, *arg2*, ... *argN*.  As
-with Math Functions, each argument can itself be an arbitrarily
-complex formula.
-
-A Python function wrapper can be used in the following manner by an
-input script:
-
-.. code-block:: LAMMPS
-
-   variable        foo python truncate
-   python          truncate return v_foo input 1 v_arg format fi here """
-   def truncate(x):
-    return int(x)
-   """
-   variable        xtrunc atom py_foo(x)
-   variable        ytrunc atom py_foo(y)
-   variable        ztrunc atom py_foo(z)
-   dump            1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
-
-The first two commands define a python-style variable *foo* and couple
-it to the Python-coded function *truncate()* which takes a single
-floating point argument, and returns its truncated integer value.  In
-this case, the Python code for truncate() is included in the *python*
-command; it could also be contained in a file.  See the :doc:`python
-<python>` command doc page for details.
-
-The next three commands define atom-style variables *xtrunc*,
-*ytrunc*, and *ztrunc*.  Each of them include the same Python function
-wrapper in their formula, with a different argument.  The atom-style
-variable *xtrunc* will invoke the python-style variable *foo*, which
-will in turn invoke the Python-coded *truncate()* method.  Because
-*xtrunc* is an atom-style variable, and the argument *x* in the Python
-function wrapper is a per-atom quantity (the x-coord of each atom),
-each processor will invoke the *truncate()* method once per atom, for
-the atoms it owns.
-
-When invoked for the Ith atom, the value of the *arg* internal-style
-variable, defined by the *python* command, is set to the x-coord of
-the Ith atom.  The call via python-style variable *foo* to the Python
-*truncate()* function passes the value of the *arg* variable as the
-function's first (and only) argument.  Likewise, the return value of
-the Python function is stored by the python-style variable *foo* and
-used in the *xtrunc* atom-style variable formula for the Ith atom.
-
-The resulting per-atom vector for *xtrunc* will thus contain the
-truncated x-coord of every atom in the system.  The dump command
-includes the truncated xyz coords for each atom in its output.
-
-See the :doc:`python <python>` command for more details on options the
-*python* command can specify as well as examples of more complex Python
-functions which can be wrapped in this manner.  In particular, the
-Python function can take a variety of arguments, some generated by the
-*python* command, and others by the arguments of the Python function
-wrapper.
-
-----------
-
 Atom Values and Vectors
 -----------------------
 

doc/utils/sphinx-config/conf.py.in

@@ -370,17 +370,6 @@ latex_elements = {
 {%
   \hypersetup{pageanchor=false}% avoid duplicate destination warnings
   \begin{titlepage}%
-    \sffamily\Large
-    The LAMMPS developers are thinking about dropping the PDF format version of
-    the LAMMPS manual.  This would allow us to focus on the HTML version, use
-    HTML-only features, and skip checking if the documentation source files,
-    especially the embedded mathematical expressions, are compatible with \LaTeX{} output.
-
-    Please let us know how you feel about this change by sending an email to
-    \texttt{developers@lammps.org} stating whether you agree or disagree with
-    removing support for the PDF format version of the  manual and optionally
-    provide arguments for your preference.
-    \clearpage
     \sffamily\bfseries
     \begingroup % for PDF information dictionary
       \def\endgraf{ }\def\and{\& }%

doc/utils/sphinx-config/false_positives.txt

@@ -82,7 +82,6 @@ Alessandro
 Alexey
 ali
 aliceblue
-aliphatic
 Allera
 Allinger
 allocatable
@@ -104,7 +103,6 @@ Amit
 amsmath
 amu
 Amzallag
-Anandakrishnan
 analytical
 Anders
 Andric
@@ -112,7 +110,6 @@ Andrienko
 Andzelm
 Ang
 anglegrad
-anglelist
 angleoffset
 angletangrad
 angmom
@@ -230,7 +227,6 @@ Bagi
 Bagnold
 Baig
 Bajaj
-bak
 Bal
 balancer
 Balankura
@@ -351,7 +347,6 @@ Bomont
 BondAngle
 BondBond
 bondchk
-bondlist
 bondmax
 bondscreened
 bondscreenedspin
@@ -400,7 +395,6 @@ Broglie
 brownian
 brownw
 Broyden
-Bruenger
 Bruskin
 Brusselle
 Bryantsev
@@ -632,7 +626,6 @@ cp
 cpp
 cpu
 cradius
-Cramer
 createatoms
 createAtoms
 CreateIDs
@@ -673,7 +666,6 @@ cuFFT
 CuH
 Cui
 Cummins
-cumulants
 Cundall
 cundall
 Curk
@@ -827,7 +819,6 @@ diffusively
 diffusivities
 diffusivity
 dihedral
-dihedrallist
 dihedrals
 Dihedrals
 dihydride
@@ -1178,7 +1169,6 @@ Fermionic
 Ferrand
 fexternal
 Fexternal
-ffast
 ffield
 ffl
 fflush
@@ -1207,7 +1197,6 @@ filesystem
 filesystems
 Fily
 Fincham
-Finkelstein
 Fint
 fingerprintconstants
 fingerprintsperelement
@@ -1334,6 +1323,7 @@ Geocomputing
 georg
 Georg
 Geotechnica
+Gergs
 germain
 Germann
 Germano
@@ -1361,8 +1351,6 @@ Gillan
 Gingold
 Gissinger
 github
-Giusti
-GJ
 gjf
 gjwagne
 gl
@@ -1621,7 +1609,6 @@ imagename
 imd
 Impey
 impl
-improperlist
 impropers
 Impropers
 imulator
@@ -1738,7 +1725,6 @@ Iyz
 iz
 izcm
 ized
-Izadi
 Izrailev
 Izumi
 Izvekov
@@ -1775,7 +1761,6 @@ jik
 JIK
 jku
 jN
-Joanes
 Joannopoulos
 Jochim
 Jonsson
@@ -1820,7 +1805,6 @@ Karniadakis
 Karplus
 Karttunen
 kate
-katom
 Katsnelson
 Katsura
 Kaufmann
@@ -1869,7 +1853,6 @@ Kloss
 Kloza
 kmax
 Kmax
-kMC
 KMP
 kmu
 Knizhnik
@@ -1934,7 +1917,6 @@ Lachet
 Lackmann
 Ladd
 lagrangian
-Lalli
 lambdai
 LambdaLanczos
 Lambrecht
@@ -1997,7 +1979,6 @@ lennard
 Lennard
 Lenosky
 Lenz
-Leoni
 Lett
 Leuven
 Leven
@@ -2199,7 +2180,6 @@ Materias
 mathbf
 mathjax
 matlab
-Matom
 Matous
 matplotlib
 Matsubara
@@ -2497,7 +2477,6 @@ namespaces
 nan
 NaN
 Nandor
-nanglelist
 nangles
 Nangletype
 nangletypes
@@ -2534,7 +2513,6 @@ nbodies
 nbody
 Nbody
 nbond
-nbondlist
 nbonds
 nbondtype
 Nbondtype
@@ -2556,7 +2534,6 @@ ncount
 nd
 ndactrung
 ndescriptors
-ndihedrallist
 ndihedrals
 Ndihedraltype
 ndihedraltypes
@@ -2614,7 +2591,6 @@ NiAlH
 Nicklas
 Niklasson
 Nikolskiy
-nimproperlist
 nimpropers
 Nimpropertype
 nimpropertypes
@@ -2709,7 +2685,6 @@ Nprocs
 npt
 nr
 Nr
-Nrecent
 Nrecompute
 Nrepeat
 nreset
@@ -2788,7 +2763,6 @@ ocl
 octahedral
 octants
 Odegard
-Og
 Ohara
 O'Hearn
 ohenrich
@@ -2821,7 +2795,6 @@ oneMKL
 oneway
 onlysalt
 ons
-Onufriev
 OO
 Oord
 opencl
@@ -3130,7 +3103,6 @@ Pxy
 pxz
 py
 Py
-pyargs
 pydir
 pylammps
 PyLammps
@@ -3371,7 +3343,6 @@ Rmin
 RMS
 rmsd
 rnage
-rnflag
 rng
 rNEMD
 ro
@@ -3427,7 +3398,6 @@ ry
 Ryckaert
 Rycroft
 Rydbergs
-Ryzen
 rz
 Rz
 Sabry
@@ -3493,7 +3463,6 @@ sectoring
 sed
 Seddon
 segmental
-Seibold
 Seifert
 Seleson
 sellerio
@@ -3847,7 +3816,6 @@ Thiaville
 Thibaudeau
 Thijsse
 Thirumalai
-Threadripper
 threebody
 thrid
 ThunderX
@@ -4073,7 +4041,6 @@ Vaiwala
 valent
 Valeriu
 valgrind
-validator
 Valone
 valuev
 Valuev
@@ -4083,7 +4050,6 @@ Vanduyfhuys
 varargs
 varavg
 variational
-varname
 Varshalovich
 Varshney
 vashishta
@@ -4116,11 +4082,9 @@ versa
 Verstraelen
 ves
 vf
-vfull
 vflag
 vflow
 vfrac
-vhalf
 vhi
 vibrational
 Vij
@@ -4152,7 +4116,6 @@ volpress
 volumetric
 von
 Voro
-voro
 Vorobyov
 voronoi
 Voronoi

examples/COUPLE/plugin/CMakeLists.txt

@@ -27,7 +27,10 @@ if(MSVC)
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
-find_package(MPI REQUIRED COMPONENTS C)
+find_package(MPI REQUIRED)
+# do not include the (obsolete) MPI C++ bindings which makes
+# for leaner object files and avoids namespace conflicts
+set(MPI_CXX_SKIP_MPICXX TRUE)
 
 ##########################
 

examples/COUPLE/plugin/liblammpsplugin.c

@@ -79,7 +79,6 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
   ADDSYM(mpi_finalize);
   ADDSYM(kokkos_finalize);
   ADDSYM(python_finalize);
-  ADDSYM(plugin_finalize);
 
   ADDSYM(error);
   ADDSYM(expand);
@@ -145,7 +144,6 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
   ADDSYM(find_pair_neighlist);
   ADDSYM(find_fix_neighlist);
   ADDSYM(find_compute_neighlist);
-  ADDSYM(request_single_neighlist);
   ADDSYM(neighlist_num_elements);
   ADDSYM(neighlist_element_neighbors);
 

examples/COUPLE/plugin/liblammpsplugin.h

@@ -94,17 +94,6 @@ enum _LMP_VAR_CONST {
   LMP_VAR_STRING = 3  /*!< return value will be a string (catch-all) */
 };
 
-/** Neighbor list settings constants
- *
- * Must be kept in sync with the equivalent constants in ``python/lammps/constants.py``,
- * ``fortran/lammps.f90``, ``tools/swig/lammps.i``, and
- * ``examples/COUPLE/plugin/liblammpsplugin.h`` */
-
-enum _LMP_NEIGH_CONST {
-  LMP_NEIGH_HALF = 0,  /*!< request (default) half neighbor list */
-  LMP_NEIGH_FULL = 1,  /*!< request full neighbor list */
-};
-
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -134,7 +123,6 @@ struct _liblammpsplugin {
   void (*mpi_finalize)();
   void (*kokkos_finalize)();
   void (*python_finalize)();
-  void (*plugin_finalize)();
 
   void (*error)(void *, int, const char *);
   char *(*expand)(void *, const char *);
@@ -201,17 +189,14 @@ struct _liblammpsplugin {
  * caller must match to how LAMMPS library is built */
 
 #if !defined(LAMMPS_BIGBIG)
- int (*create_atoms)(void *, int, const int *, const int *, const double *, const double *,
-                     const int *, int);
+ int (*create_atoms)(void *, int, int *, int *, double *, double *, int *, int);
 #else
-  int (*create_atoms)(void *, int, const int64_t *, const int *, const double *, const double *,
-                      const int64_t *, int);
+  int (*create_atoms)(void *, int, int64_t *, int *, double *, double *, int64_t *, int);
 #endif
 
   int (*find_pair_neighlist)(void *, const char *, int, int, int);
   int (*find_fix_neighlist)(void *, const char *, int);
   int (*find_compute_neighlist)(void *, const char *, int);
-  int (*request_single_neighlist)(void *, const char *, int, double);
   int (*neighlist_num_elements)(void *, int);
   void (*neighlist_element_neighbors)(void *, int, int, int *, int *, int **);
 

examples/COUPLE/simple/CMakeLists.txt

@@ -25,10 +25,10 @@ if(MSVC)
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
+find_package(MPI QUIET)
 # do not include the (obsolete) MPI C++ bindings which makes
 # for leaner object files and avoids namespace conflicts
 set(MPI_CXX_SKIP_MPICXX TRUE)
-find_package(MPI QUIET COMPONENTS C CXX)
 
 ##########################
 

examples/PACKAGES/imd/in.bucky-plus-cnt

@@ -46,8 +46,8 @@ fix     integrate   mobile nve
 fix     thermostat  mobile langevin 300.0 300.0 2000.0 234624
 
 # IMD setup.
-#fix  comm       all imd 6789 unwrap on trate 10
-fix  comm       all imd 6789 unwrap on trate 10 nowait on
+fix  comm       all imd 6789 unwrap on trate 10
+#fix  comm       all imd 6789 unwrap on trate 10 nowait on
 
 # temperature is based on mobile atoms only
 compute mobtemp mobile temp

examples/PACKAGES/imd/in.bucky-plus-cnt-gpu

@@ -1,20 +1,16 @@
 # stick a buckyball into a nanotube
-
-# enable GPU package from within the input:
-package gpu 0 pair/only on
-suffix gpu
-
 units           real
 dimension       3
 boundary       f f f
 atom_style      molecular
+newton          off
 
 processors * * 1
 
 # read topology 
 read_data       data.bucky-plus-cnt
 
-pair_style  lj/cut  10.0
+pair_style  lj/cut/gpu  10.0
 bond_style  harmonic
 angle_style charmm
 dihedral_style charmm
@@ -33,6 +29,9 @@ neigh_modify    delay 0 every 1 check yes
 
 timestep        2.0
 
+# required for GPU acceleration
+fix   gpu  all      gpu  force 0 0 1.0
+
 # we only move some atoms.
 group mobile type 1
 
@@ -50,8 +49,8 @@ fix     integrate   mobile nve
 fix     thermostat  mobile langevin 300.0 300.0 2000.0 234624
 
 # IMD setup.
-#fix  comm       all imd 6789 unwrap on trate 10
-fix  comm       all imd 6789 unwrap on trate 10 nowait on
+fix  comm       all imd 6789 unwrap on trate 10
+#fix  comm       all imd 6789 unwrap on trate 10 nowait on
 
 # temperature is based on mobile atoms only
 compute mobtemp mobile temp

examples/PACKAGES/imd/in.deca-ala_imd-gpu

@@ -1,12 +1,8 @@
-#
-
-# enable GPU package from within the input:
-package gpu 0 pair/only on
-suffix gpu
-
+# 
 units           real
 neighbor        2.5 bin
 neigh_modify    delay 1 every 1 
+newton          off
 
 atom_style      full
 bond_style      harmonic
@@ -14,18 +10,20 @@ angle_style     charmm
 dihedral_style  charmm
 improper_style  harmonic
 
-pair_style      lj/charmm/coul/long 8 10
+pair_style      lj/charmm/coul/long/gpu 8 10
 pair_modify     mix arithmetic
 special_bonds   charmm
 read_data       data.deca-ala-solv
 
+fix             0 all gpu force/neigh 0 0 1.0    
+
 group peptide   id <= 103
 fix             rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
 
 thermo          100
 thermo_style    multi
 timestep        2.0
-kspace_style    pppm 1e-5
+kspace_style    pppm/gpu 1e-5
 
 fix             ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
 

examples/PACKAGES/imd/in.melt_imd-gpu

@@ -1,32 +1,30 @@
-# 3d Lennard-Jones melt with GPU package acceleration
+# 3d Lennard-Jones melt
 
-# enable GPU package from within the input:
-package gpu 0
-suffix gpu
+units		lj
+atom_style	atomic
+newton      off
 
-units           lj
-atom_style      atomic
+lattice		fcc 0.8442
+region		box block 0 10 0 10 0 10
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
 
-lattice         fcc 0.8442
-region          box block 0 10 0 10 0 10
-create_box      1 box
-create_atoms    1 box
-mass            1 1.0
+velocity	all create 3.0 87287
 
-velocity        all create 3.0 87287
+pair_style	lj/cut/gpu 2.5
+pair_coeff	1 1 1.0 1.0 2.5
 
-pair_style      lj/cut 2.5
-pair_coeff      1 1 1.0 1.0 2.5
-
-neighbor        0.3 bin
-neigh_modify    every 5 delay 10 check yes
+neighbor	0.3 bin
+neigh_modify	every 5 delay 10 check yes
 
 thermo_style    custom step pe ke spcpu
 
-fix             1 all nve
+fix     0 all gpu force/neigh 0 0 1.0
+fix		1 all nve
 
 # IMD setup.
 fix  comm       all imd 5678 unwrap off fscale 20.0 trate 20 nowait on
 
-thermo          500
-run             5000000
+thermo		500
+run		5000000

examples/PACKAGES/moments/in.converge

@@ -1,35 +0,0 @@
-# Detect convergence in a simulation using the relative change in
-# moments. This demonstrates the "history" option.
-# ---------------------------------------------------------------------
-
-# create pure copper system
-units metal
-lattice fcc 3.75
-region box block 0 6 0 6 0 6
-create_box 2 box
-
-timestep 0.002
-create_atoms 1 box
-
-pair_style eam/alloy
-pair_coeff * * AlCu.eam.alloy Cu Al
-
-# Initialize to a high temperature, then cool in npt ensemble
-velocity all create 1000.0 6567345
-fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
-
-# compute mean and stddev over the preceding 5000 steps, every 20 steps
-variable toteng equal "etotal"
-fix 2 all ave/moments 10 500 200 v_toteng mean stddev history 5
-
-# Convergence criterion: stddev is smaller than threshold and was previously larger
-# This avoids issues with system oscillations in the order of the averaging window
-# that would otherwise lead to "nodes" in the stddev.
-variable conv equal "(f_2[2] < 2.0) && (f_2[2][1] < f_2[2][5])"
-fix 3 all halt 100 v_conv == 1
-
-thermo_style custom step temp press etotal f_2[*][1] f_2[*][5] v_conv
-
-thermo 100
-run 10000
-

examples/PACKAGES/moments/in.simple

@@ -1,27 +0,0 @@
-# Perform a simple simulation and output the moments of the total energy
-# ---------------------------------------------------------------------
-
-# create pure copper system
-units metal
-lattice fcc 3.75
-region box block 0 6 0 6 0 6
-create_box 2 box
-
-timestep 0.002
-create_atoms 1 box
-
-pair_style eam/alloy
-pair_coeff * * AlCu.eam.alloy Cu Al
-
-# Initialize to a high temperature, then cool in npt ensemble
-velocity all create 1000.0 6567345
-fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
-
-variable toteng equal "etotal"
-fix 2 all ave/moments 5 200 100 v_toteng mean stddev variance skew kurtosis
-
-thermo_style custom step temp press etotal f_2[*]
-
-thermo 100
-run 10000
-

examples/PACKAGES/moments/in.valtest

@@ -1,28 +0,0 @@
-# Output raw and computed data. This can be used to perform the moment
-# calculation in some external tool and validate our results
-# ---------------------------------------------------------------------
-
-# create pure copper system
-units metal
-lattice fcc 3.75
-region box block 0 6 0 6 0 6
-create_box 2 box
-
-timestep 0.002
-create_atoms 1 box
-
-pair_style eam/alloy
-pair_coeff * * AlCu.eam.alloy Cu Al
-
-# Initialize to a high temperature, then cool in npt ensemble
-velocity all create 1000.0 6567345
-fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
-
-variable toteng equal "etotal"
-fix 2 all ave/moments 1 10 10 v_toteng mean variance skew kurtosis
-
-thermo_style custom step etotal f_2[*]
-thermo_modify format float %14.8f
-
-thermo 1
-run 100

examples/PACKAGES/moments/log.02May2025.converge.g++.1

@@ -1,171 +0,0 @@
-LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
-  using 1 OpenMP thread(s) per MPI task
-# create pure copper system
-units metal
-lattice fcc 3.75
-Lattice spacing in x,y,z = 3.75 3.75 3.75
-region box block 0 6 0 6 0 6
-create_box 2 box
-Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
-  1 by 1 by 1 MPI processor grid
-
-timestep 0.002
-create_atoms 1 box
-Created 864 atoms
-  using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
-  create_atoms CPU = 0.001 seconds
-
-pair_style eam/alloy
-pair_coeff * * AlCu.eam.alloy Cu Al
-
-# Initialize to a high temperature, then cool in npt ensemble
-velocity all create 1000.0 6567345
-fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
-fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
-fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
-
-variable toteng equal "etotal"
-fix 2 all ave/moments 10 500 200 v_toteng mean stddev history 5
-
-variable conv equal "(f_2[2] < 2) && (f_2[2][1] < f_2[2][5])"
-fix 3 all halt 1000 v_conv == 1
-
-thermo_style custom step temp press etotal f_2[*][1] f_2[*][5] v_conv
-
-thermo 100
-run 10000
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.6825
-  ghost atom cutoff = 8.6825
-  binsize = 4.34125, bins = 6 6 6
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair eam/alloy, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.484 | 3.484 | 3.484 Mbytes
-   Step          Temp          Press          TotEng       f_2[1][1]      f_2[2][1]      f_2[1][5]      f_2[2][5]        v_conv    
-         0   1000          -107410.22     -2884.9159      0              0              0              0              0            
-       100   512.04214     -124.66263     -2928.6         0              0              0              0              0            
-       200   479.34328     -136.26635     -2931.3905     -2928.6251      2.1584834      0              0              0            
-       300   480.05298      128.92946     -2933.9233     -2928.6251      2.1584834      0              0              0            
-       400   471.83641     -29.253334     -2936.8631     -2931.3742      3.3668783      0              0              0            
-       500   456.96309     -274.69336     -2939.9081     -2931.3742      3.3668783      0              0              0            
-       600   450.32413      14.606227     -2942.973      -2934.277       5.0681849      0              0              0            
-       700   431.71192     -45.641261     -2946.006      -2934.277       5.0681849      0              0              0            
-       800   436.4217       589.91981     -2948.8885     -2937.2386      6.823233       0              0              0            
-       900   407.84688     -3728.1499     -2951.6643     -2937.2386      6.823233       0              0              0            
-      1000   401.69178      6695.3653     -2954.2959     -2940.1463      8.4728269     -2928.6251      2.1584834      0            
-      1100   370.87469     -2294.843      -2956.9413     -2940.1463      8.4728269     -2928.6251      2.1584834      0            
-      1200   375.15562      704.6568      -2959.3841     -2942.9613      10.001542     -2931.3742      3.3668783      0            
-      1300   371.09077     -493.04016     -2961.6803     -2942.9613      10.001542     -2931.3742      3.3668783      0            
-      1400   365.88512      490.98174     -2963.8365     -2945.6475      11.378724     -2934.277       5.0681849      0            
-      1500   358.42655     -218.94911     -2965.8652     -2945.6475      11.378724     -2934.277       5.0681849      0            
-      1600   329.08402      56.411923     -2967.7662     -2948.1844      12.597017     -2937.2386      6.823233       0            
-      1700   317.74207      1192.918      -2969.557      -2948.1844      12.597017     -2937.2386      6.823233       0            
-      1800   331.98966     -2205.7213     -2971.1465     -2950.559       13.653575     -2940.1463      8.4728269      0            
-      1900   330.96814      1401.3066     -2972.6923     -2950.559       13.653575     -2940.1463      8.4728269      0            
-      2000   315.41816     -909.41909     -2974.0785     -2952.7764      14.568194     -2942.9613      10.001542      0            
-      2100   320.4269       1226.2006     -2975.3676     -2952.7764      14.568194     -2942.9613      10.001542      0            
-      2200   302.88235     -1238.8052     -2976.5099     -2954.8327      15.341787     -2945.6475      11.378724      0            
-      2300   300.4349       2667.202      -2977.5329     -2954.8327      15.341787     -2945.6475      11.378724      0            
-      2400   292.94691     -5532.1854     -2978.3724     -2956.7266      15.978754     -2948.1844      12.597017      0            
-      2500   286.12064      4647.3841     -2979.2217     -2956.7266      15.978754     -2948.1844      12.597017      0            
-      2600   290.74305     -1950.526      -2979.9142     -2958.4592      16.485773     -2950.559       13.653575      0            
-      2700   281.51347      937.60472     -2980.4808     -2958.4592      16.485773     -2950.559       13.653575      0            
-      2800   279.71836     -801.62498     -2980.8899     -2960.032       16.869365     -2952.7764      14.568194      0            
-      2900   277.41241      609.21495     -2981.1721     -2960.032       16.869365     -2952.7764      14.568194      0            
-      3000   281.31161     -760.27203     -2981.3003     -2961.4399      17.128547     -2954.8327      15.341787      0            
-      3100   284.72904      315.53038     -2981.297      -2961.4399      17.128547     -2954.8327      15.341787      0            
-      3200   278.39445      516.25074     -2981.1224     -2962.6768      17.263037     -2956.7266      15.978754      0            
-      3300   294.46998     -655.06212     -2980.8266     -2962.6768      17.263037     -2956.7266      15.978754      0            
-      3400   290.04647      788.30424     -2980.3963     -2963.7417      17.280979     -2958.4592      16.485773      0            
-      3500   283.218       -844.33188     -2979.8504     -2963.7417      17.280979     -2958.4592      16.485773      0            
-      3600   288.76031      1339.2734     -2979.2382     -2964.6345      17.192698     -2960.032       16.869365      0            
-      3700   289.44519     -3015.7161     -2978.5394     -2964.6345      17.192698     -2960.032       16.869365      0            
-      3800   309.04206      5579.3265     -2977.8282     -2965.3649      17.01845      -2961.4399      17.128547      0            
-      3900   309.34588     -4255.5213     -2977.1281     -2965.3649      17.01845      -2961.4399      17.128547      0            
-      4000   305.79444      2358.1383     -2976.5251     -2965.9537      16.784519     -2962.6768      17.263037      0            
-      4100   309.12957     -1401.6484     -2975.9173     -2965.9537      16.784519     -2962.6768      17.263037      0            
-      4200   309.41928      1180.4111     -2975.3857     -2966.4277      16.516135     -2963.7417      17.280979      0            
-      4300   299.88949     -1549.6591     -2974.927      -2966.4277      16.516135     -2963.7417      17.280979      0            
-      4400   319.09918      1937.7006     -2974.5598     -2966.8138      16.232551     -2964.6345      17.192698      0            
-      4500   326.48719     -1489.2073     -2974.311      -2966.8138      16.232551     -2964.6345      17.192698      0            
-      4600   310.93392      37.586899     -2974.1959     -2967.1394      15.948448     -2965.3649      17.01845       0            
-      4700   314.28994      317.12347     -2974.1763     -2967.1394      15.948448     -2965.3649      17.01845       0            
-      4800   309.88756     -698.72705     -2974.2892     -2967.4334      15.675606     -2965.9537      16.784519      0            
-      4900   309.53444      962.42921     -2974.5261     -2967.4334      15.675606     -2965.9537      16.784519      0            
-      5000   316.06666     -1869.3275     -2974.8492     -2967.7182      15.421633     -2966.4277      16.516135      0            
-      5100   304.82485      4042.6797     -2975.2715     -2967.7182      15.421633     -2966.4277      16.516135      0            
-      5200   307.75342     -5058.4814     -2975.7195     -2969.5853      13.236776     -2966.8138      16.232551      0            
-      5300   298.83511      3096.4566     -2976.3329     -2969.5853      13.236776     -2966.8138      16.232551      0            
-      5400   296.85413     -1929.1654     -2976.8797     -2971.2747      11.121537     -2967.1394      15.948448      0            
-      5500   295.88343      1449.3005     -2977.4488     -2971.2747      11.121537     -2967.1394      15.948448      0            
-      5600   305.59328     -1504.0321     -2977.9573     -2972.77        9.1579616     -2967.4334      15.675606      0            
-      5700   293.40683      2579.0134     -2978.4364     -2972.77        9.1579616     -2967.4334      15.675606      0            
-      5800   297.93644     -2742.705      -2978.8276     -2974.0625      7.4101102     -2967.7182      15.421633      0            
-      5900   290.39408      1189.4042     -2979.2224     -2974.0625      7.4101102     -2967.7182      15.421633      0            
-      6000   293.73148     -232.54292     -2979.503      -2975.1594      5.8959922     -2969.5853      13.236776      0            
-      6100   292.04933     -168.30971     -2979.6898     -2975.1594      5.8959922     -2969.5853      13.236776      0            
-      6200   299.23747      839.17828     -2979.7883     -2976.0647      4.6378408     -2971.2747      11.121537      0            
-      6300   294.92201     -1597.9426     -2979.7975     -2976.0647      4.6378408     -2971.2747      11.121537      0            
-      6400   291.7185       3411.2916     -2979.6978     -2976.7848      3.643826      -2972.77        9.1579616      0            
-      6500   285.34227     -4280.7968     -2979.4874     -2976.7848      3.643826      -2972.77        9.1579616      0            
-      6600   295.53838      2138.7496     -2979.2799     -2977.3265      2.9178925     -2974.0625      7.4101102      0            
-      6700   288.54718     -1818.7662     -2978.9379     -2977.3265      2.9178925     -2974.0625      7.4101102      0            
-      6800   290.41342      2175.3559     -2978.543      -2977.7009      2.4532223     -2975.1594      5.8959922      0            
-      6900   296.34456     -4782.08       -2978.0362     -2977.7009      2.4532223     -2975.1594      5.8959922      0            
-      7000   303.74314      5905.219      -2977.577      -2977.9137      2.2279716     -2976.0647      4.6378408      0            
-      7100   303.90284     -3291.7627     -2977.1308     -2977.9137      2.2279716     -2976.0647      4.6378408      0            
-      7200   296.13966      2209.574      -2976.7001     -2977.9829      2.1708943     -2976.7848      3.643826       0            
-      7300   295.79694     -1609.1898     -2976.2816     -2977.9829      2.1708943     -2976.7848      3.643826       0            
-      7400   306.53289      988.50902     -2975.8992     -2977.931       2.1935882     -2977.3265      2.9178925      0            
-      7500   303.89992     -631.22838     -2975.5597     -2977.931       2.1935882     -2977.3265      2.9178925      0            
-      7600   303.83684     -348.48744     -2975.3074     -2977.7831      2.2226664     -2977.7009      2.4532223      0            
-      7700   309.67313      1350.9414     -2975.1279     -2977.7831      2.2226664     -2977.7009      2.4532223      0            
-      7800   309.74314     -1182.8905     -2975.0174     -2977.5683      2.2106484     -2977.9137      2.2279716      0            
-      7900   309.42429      999.08033     -2975.0089     -2977.5683      2.2106484     -2977.9137      2.2279716      0            
-      8000   315.51872     -1337.8894     -2975.0791     -2977.3233      2.1379295     -2977.9829      2.1708943      0            
-      8100   314.80533      2392.3424     -2975.25       -2977.3233      2.1379295     -2977.9829      2.1708943      0            
-      8200   303.80236     -3224.5976     -2975.4744     -2977.0851      2.0176342     -2977.931       2.1935882      0            
-      8300   295.0505       3296.6912     -2975.8196     -2977.0851      2.0176342     -2977.931       2.1935882      0            
-      8400   302.4154      -3314.5096     -2976.1586     -2976.8877      1.883051      -2977.7831      2.2226664      1            
-      8500   300.95491      2971.1291     -2976.5859     -2976.8877      1.883051      -2977.7831      2.2226664      1            
-      8600   301.68919     -2297.6673     -2976.9953     -2976.7596      1.785401      -2977.5683      2.2106484      1            
-      8700   291.21002      1477.5703     -2977.4323     -2976.7596      1.785401      -2977.5683      2.2106484      1            
-      8800   305.87126     -1085.459      -2977.8247     -2976.7169      1.7541517     -2977.3233      2.1379295      1            
-      8900   296.17567      777.95805     -2978.2081     -2976.7169      1.7541517     -2977.3233      2.1379295      1            
-Fix halt condition for fix-id 3 met on step 9000 with value 1 (src/fix_halt.cpp:310)
-      9000   295.71917     -425.00708     -2978.5264     -2976.7595      1.7755885     -2977.0851      2.0176342      1            
-Loop time of 42.1758 on 1 procs for 9000 steps with 864 atoms
-
-Performance: 36.874 ns/day, 0.651 hours/ns, 213.393 timesteps/s, 184.371 katom-step/s
-99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 41.126     | 41.126     | 41.126     |   0.0 | 97.51
-Neigh   | 0.0078787  | 0.0078787  | 0.0078787  |   0.0 |  0.02
-Comm    | 0.26508    | 0.26508    | 0.26508    |   0.0 |  0.63
-Output  | 0.0096224  | 0.0096224  | 0.0096224  |   0.0 |  0.02
-Modify  | 0.65597    | 0.65597    | 0.65597    |   0.0 |  1.56
-Other   |            | 0.1108     |            |       |  0.26
-
-Nlocal:            864 ave         864 max         864 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:           3767 ave        3767 max        3767 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:          96746 ave       96746 max       96746 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 96746
-Ave neighs/atom = 111.97454
-Neighbor list builds = 1
-Dangerous builds = 0
-
-Total wall time: 0:00:42

examples/PACKAGES/moments/log.02May2025.converge.g++.4

@@ -1,171 +0,0 @@
-LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
-  using 1 OpenMP thread(s) per MPI task
-# create pure copper system
-units metal
-lattice fcc 3.75
-Lattice spacing in x,y,z = 3.75 3.75 3.75
-region box block 0 6 0 6 0 6
-create_box 2 box
-Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
-  1 by 2 by 2 MPI processor grid
-
-timestep 0.002
-create_atoms 1 box
-Created 864 atoms
-  using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
-  create_atoms CPU = 0.001 seconds
-
-pair_style eam/alloy
-pair_coeff * * AlCu.eam.alloy Cu Al
-
-# Initialize to a high temperature, then cool in npt ensemble
-velocity all create 1000.0 6567345
-fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
-fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
-fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
-
-variable toteng equal "etotal"
-fix 2 all ave/moments 10 500 200 v_toteng mean stddev history 5
-
-variable conv equal "(f_2[2] < 2) && (f_2[2][1] < f_2[2][5])"
-fix 3 all halt 1000 v_conv == 1
-
-thermo_style custom step temp press etotal f_2[*][1] f_2[*][5] v_conv
-
-thermo 100
-run 10000
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.6825
-  ghost atom cutoff = 8.6825
-  binsize = 4.34125, bins = 6 6 6
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair eam/alloy, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.42 | 3.42 | 3.42 Mbytes
-   Step          Temp          Press          TotEng       f_2[1][1]      f_2[2][1]      f_2[1][5]      f_2[2][5]        v_conv    
-         0   1000          -107410.22     -2884.9159      0              0              0              0              0            
-       100   492.38014     -134.33622     -2928.6874      0              0              0              0              0            
-       200   484.82396     -214.26318     -2931.4603     -2928.6979      2.1805063      0              0              0            
-       300   476.69743      15.78678      -2934.0022     -2928.6979      2.1805063      0              0              0            
-       400   482.51415      141.67184     -2936.9347     -2931.4437      3.3715811      0              0              0            
-       500   455.45411      2.4424602     -2939.9649     -2931.4437      3.3715811      0              0              0            
-       600   455.20054     -6.8170934     -2943.0454     -2934.339       5.0598781      0              0              0            
-       700   429.81168     -75.812923     -2946.0438     -2934.339       5.0598781      0              0              0            
-       800   428.22097      604.18705     -2948.9285     -2937.2965      6.813037       0              0              0            
-       900   399.10914     -3622.6904     -2951.7252     -2937.2965      6.813037       0              0              0            
-      1000   394.62543      7905.9041     -2954.2925     -2940.2044      8.4668749     -2928.6979      2.1805063      0            
-      1100   404.27007     -2565.5508     -2956.9736     -2940.2044      8.4668749     -2928.6979      2.1805063      0            
-      1200   368.47178      741.43707     -2959.4264     -2943.0151      9.9914785     -2931.4437      3.3715811      0            
-      1300   360.91266     -267.08372     -2961.69       -2943.0151      9.9914785     -2931.4437      3.3715811      0            
-      1400   356.74405      158.09093     -2963.8501     -2945.696       11.36357      -2934.339       5.0598781      0            
-      1500   335.45696     -71.007783     -2965.8817     -2945.696       11.36357      -2934.339       5.0598781      0            
-      1600   331.01199     -454.90004     -2967.7708     -2948.2278      12.577884     -2937.2965      6.813037       0            
-      1700   329.223        2428.4284     -2969.5452     -2948.2278      12.577884     -2937.2965      6.813037       0            
-      1800   327.61481     -4757.648      -2971.1105     -2950.5985      13.632251     -2940.2044      8.4668749      0            
-      1900   318.18741      2226.7765     -2972.6906     -2950.5985      13.632251     -2940.2044      8.4668749      0            
-      2000   308.79313     -1089.8603     -2974.0899     -2952.8123      14.545164     -2943.0151      9.9914785      0            
-      2100   303.32047      757.53534     -2975.3597     -2952.8123      14.545164     -2943.0151      9.9914785      0            
-      2200   307.41102     -837.97246     -2976.4966     -2954.8654      15.317558     -2945.696       11.36357       0            
-      2300   303.01088      1618.29       -2977.5454     -2954.8654      15.317558     -2945.696       11.36357       0            
-      2400   297.59385     -3233.8282     -2978.4064     -2956.7565      15.953758     -2948.2278      12.577884      0            
-      2500   288.72232      5209.2099     -2979.1999     -2956.7565      15.953758     -2948.2278      12.577884      0            
-      2600   298.92201     -2193.618      -2979.8873     -2958.4845      16.457635     -2950.5985      13.632251      0            
-      2700   282.61818      765.88178     -2980.4563     -2958.4845      16.457635     -2950.5985      13.632251      0            
-      2800   273.63104     -389.49749     -2980.8636     -2960.0533      16.839029     -2952.8123      14.545164      0            
-      2900   274.12166     -9.2552992     -2981.1421     -2960.0533      16.839029     -2952.8123      14.545164      0            
-      3000   279.43592      212.25445     -2981.2716     -2961.4578      17.096628     -2954.8654      15.317558      0            
-      3100   291.10071     -1139.205      -2981.2475     -2961.4578      17.096628     -2954.8654      15.317558      0            
-      3200   281.53171      3124.6411     -2981.0818     -2962.6921      17.230604     -2956.7565      15.953758      0            
-      3300   277.0223      -2795.9494     -2980.7825     -2962.6921      17.230604     -2956.7565      15.953758      0            
-      3400   284.8443       1587.8876     -2980.3701     -2963.754       17.247489     -2958.4845      16.457635      0            
-      3500   281.19        -1143.0785     -2979.8374     -2963.754       17.247489     -2958.4845      16.457635      0            
-      3600   296.58287      1156.4706     -2979.2182     -2964.645       17.159411     -2960.0533      16.839029      0            
-      3700   297.24517     -1888.4993     -2978.5352     -2964.645       17.159411     -2960.0533      16.839029      0            
-      3800   290.81586      3843.3483     -2977.8509     -2965.3746      16.985916     -2961.4578      17.096628      0            
-      3900   300.39456     -5584.8386     -2977.0837     -2965.3746      16.985916     -2961.4578      17.096628      0            
-      4000   306.15811      3310.0105     -2976.5086     -2965.9619      16.752214     -2962.6921      17.230604      0            
-      4100   295.907       -1475.0458     -2975.9096     -2965.9619      16.752214     -2962.6921      17.230604      0            
-      4200   322.70162      933.76586     -2975.3867     -2966.4348      16.484219     -2963.754       17.247489      0            
-      4300   306.69631     -512.7048      -2974.9324     -2966.4348      16.484219     -2963.754       17.247489      0            
-      4400   309.23776      226.77219     -2974.5791     -2966.8208      16.201471     -2964.645       17.159411      0            
-      4500   313.15783      508.29785     -2974.3263     -2966.8208      16.201471     -2964.645       17.159411      0            
-      4600   316.26151     -2043.7571     -2974.1697     -2967.1463      15.918137     -2965.3746      16.985916      0            
-      4700   312.27329      1831.682      -2974.1732     -2967.1463      15.918137     -2965.3746      16.985916      0            
-      4800   307.61066     -1476.0019     -2974.2885     -2967.4397      15.645834     -2965.9619      16.752214      0            
-      4900   305.73489      1303.4848     -2974.5506     -2967.4397      15.645834     -2965.9619      16.752214      0            
-      5000   309.3774      -1574.6812     -2974.8687     -2967.7249      15.392787     -2966.4348      16.484219      0            
-      5100   304.8602       2679.7476     -2975.3082     -2967.7249      15.392787     -2966.4348      16.484219      0            
-      5200   297.54226     -5008.0905     -2975.7443     -2969.5904      13.211657     -2966.8208      16.201471      0            
-      5300   306.18872      4840.4175     -2976.324      -2969.5904      13.211657     -2966.8208      16.201471      0            
-      5400   299.57661     -2513.1706     -2976.8842     -2971.2774      11.099846     -2967.1463      15.918137      0            
-      5500   302.30844      1301.3525     -2977.4539     -2971.2774      11.099846     -2967.1463      15.918137      0            
-      5600   302.11038     -760.79712     -2977.9764     -2972.7712      9.1381778     -2967.4397      15.645834      0            
-      5700   294.49825      718.67318     -2978.4584     -2972.7712      9.1381778     -2967.4397      15.645834      0            
-      5800   305.97636     -478.64224     -2978.8638     -2974.0628      7.3929182     -2967.7249      15.392787      0            
-      5900   291.93868     -419.74179     -2979.2292     -2974.0628      7.3929182     -2967.7249      15.392787      0            
-      6000   289.50667      859.85085     -2979.5018     -2975.1575      5.8837236     -2969.5904      13.211657      0            
-      6100   305.70118     -933.35917     -2979.6877     -2975.1575      5.8837236     -2969.5904      13.211657      0            
-      6200   284.37805      1526.0707     -2979.806      -2976.062       4.6281363     -2971.2774      11.099846      0            
-      6300   291.08863     -2156.6708     -2979.8064     -2976.062       4.6281363     -2971.2774      11.099846      0            
-      6400   295.99073      2819.8245     -2979.7378     -2976.7827      3.6358684     -2972.7712      9.1381778      0            
-      6500   298.06769     -3396.3504     -2979.5428     -2976.7827      3.6358684     -2972.7712      9.1381778      0            
-      6600   301.78514      5496.6525     -2979.2768     -2977.3261      2.9112079     -2974.0628      7.3929182      0            
-      6700   290.80665     -5229.4989     -2978.9177     -2977.3261      2.9112079     -2974.0628      7.3929182      0            
-      6800   296.75761      2401.7807     -2978.5996     -2977.7014      2.4473856     -2975.1575      5.8837236      0            
-      6900   295.77553     -1521.6269     -2978.1619     -2977.7014      2.4473856     -2975.1575      5.8837236      0            
-      7000   303.59015      1530.7255     -2977.7097     -2977.9176      2.2219164     -2976.062       4.6281363      0            
-      7100   297.51038     -3016.4426     -2977.2025     -2977.9176      2.2219164     -2976.062       4.6281363      0            
-      7200   293.53789      2705.9808     -2976.7651     -2977.9894      2.1638143     -2976.7827      3.6358684      0            
-      7300   301.78809     -1042.1076     -2976.3388     -2977.9894      2.1638143     -2976.7827      3.6358684      0            
-      7400   307.50053      214.56923     -2975.9581     -2977.9394      2.1852009     -2977.3261      2.9112079      0            
-      7500   301.98985      281.86495     -2975.6146     -2977.9394      2.1852009     -2977.3261      2.9112079      0            
-      7600   318.37347     -1145.7795     -2975.3473     -2977.7949      2.2136707     -2977.7014      2.4473856      0            
-      7700   314.94512      4536.9887     -2975.1351     -2977.7949      2.2136707     -2977.7014      2.4473856      0            
-      7800   312.91485     -2980.6408     -2975.0156     -2977.5818      2.2038198     -2977.9176      2.2219164      0            
-      7900   310.06854      2244.3877     -2975.0094     -2977.5818      2.2038198     -2977.9176      2.2219164      0            
-      8000   308.55007     -2427.1464     -2975.0491     -2977.3378      2.1348358     -2977.9894      2.1638143      0            
-      8100   323.02796      3187.4728     -2975.2081     -2977.3378      2.1348358     -2977.9894      2.1638143      0            
-      8200   327.05029     -6447.7875     -2975.3162     -2977.0986      2.0196599     -2977.9394      2.1852009      0            
-      8300   311.194        4273.1174     -2975.7217     -2977.0986      2.0196599     -2977.9394      2.1852009      0            
-      8400   290.61931     -2301.019      -2976.0963     -2976.8989      1.8918948     -2977.7949      2.2136707      1            
-      8500   314.00559      1966.1297     -2976.5206     -2976.8989      1.8918948     -2977.7949      2.2136707      1            
-      8600   288.26541     -1608.4524     -2976.9304     -2976.7685      1.7971228     -2977.5818      2.2038198      1            
-      8700   298.92083      1353.9988     -2977.355      -2976.7685      1.7971228     -2977.5818      2.2038198      1            
-      8800   299.97274     -638.68301     -2977.766      -2976.722       1.7650747     -2977.3378      2.1348358      1            
-      8900   300.66443     -279.62514     -2978.1476     -2976.722       1.7650747     -2977.3378      2.1348358      1            
-Fix halt condition for fix-id 3 met on step 9000 with value 1 (src/fix_halt.cpp:310)
-      9000   290.44715      489.06352     -2978.4892     -2976.7631      1.7846181     -2977.0986      2.0196599      1            
-Loop time of 14.7347 on 4 procs for 9000 steps with 864 atoms
-
-Performance: 105.547 ns/day, 0.227 hours/ns, 610.804 timesteps/s, 527.735 katom-step/s
-92.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 10.565     | 11.474     | 12.015     |  16.1 | 77.87
-Neigh   | 0.0020313  | 0.0020966  | 0.002163   |   0.1 |  0.01
-Comm    | 2.008      | 2.5374     | 3.4278     |  33.5 | 17.22
-Output  | 0.0030284  | 0.0036299  | 0.0051776  |   1.5 |  0.02
-Modify  | 0.42442    | 0.43307    | 0.44329    |   1.0 |  2.94
-Other   |            | 0.2849     |            |       |  1.93
-
-Nlocal:            216 ave         224 max         204 min
-Histogram: 1 0 0 0 0 0 0 2 0 1
-Nghost:           2147 ave        2159 max        2139 min
-Histogram: 1 0 0 2 0 0 0 0 0 1
-Neighs:        24185.8 ave       26045 max       21309 min
-Histogram: 1 0 0 0 0 1 0 0 0 2
-
-Total # of neighbors = 96743
-Ave neighs/atom = 111.97106
-Neighbor list builds = 1
-Dangerous builds = 0
-
-Total wall time: 0:00:14

examples/PACKAGES/moments/log.02May2025.simple.g++.1

@@ -1,177 +0,0 @@
-LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
-  using 1 OpenMP thread(s) per MPI task
-# create pure copper system
-units metal
-lattice fcc 3.75
-Lattice spacing in x,y,z = 3.75 3.75 3.75
-region box block 0 6 0 6 0 6
-create_box 2 box
-Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
-  1 by 1 by 1 MPI processor grid
-
-timestep 0.002
-create_atoms 1 box
-Created 864 atoms
-  using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
-  create_atoms CPU = 0.001 seconds
-
-pair_style eam/alloy
-pair_coeff * * AlCu.eam.alloy Cu Al
-
-# Initialize to a high temperature, then cool in npt ensemble
-velocity all create 1000.0 6567345
-fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
-fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
-fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
-
-variable toteng equal "etotal"
-fix 2 all ave/moments 5 200 100 v_toteng mean stddev variance skew kurtosis
-
-thermo_style custom step temp press etotal f_2[*]
-
-thermo 100
-run 10000
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.6825
-  ghost atom cutoff = 8.6825
-  binsize = 4.34125, bins = 6 6 6
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair eam/alloy, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.484 | 3.484 | 3.484 Mbytes
-   Step          Temp          Press          TotEng         f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]    
-         0   1000          -107410.22     -2884.9159      0              0              0              0              0            
-       100   512.04214     -124.66263     -2928.6        -2927.1688      1.6797138      2.8214386      2.5218138      6.164012     
-       200   479.34328     -136.26635     -2931.3905     -2928.6374      1.9791406      3.9169976      1.3377745      3.2426285    
-       300   480.05298      128.92946     -2933.9233     -2929.9825      2.5401119      6.4521682      0.66415393     0.77130236   
-       400   471.83641     -29.253334     -2936.8631     -2931.346       3.2640831      10.654239      0.29075579    -0.26904542   
-       500   456.96309     -274.69336     -2939.9081     -2932.7721      4.1077082      16.873267      0.094954709   -0.72240572   
-       600   450.32413      14.606227     -2942.973      -2934.2328      4.9928765      24.928816      0.0090731063  -0.93757177   
-       700   431.71192     -45.641261     -2946.006      -2935.7111      5.8871117      34.658084     -0.024573652   -1.0540107    
-       800   436.4217       589.91981     -2948.8885     -2937.1871      6.762411       45.730202     -0.028553126   -1.1275153    
-       900   407.84688     -3728.1499     -2951.6643     -2938.652       7.6129868      57.957569     -0.020186137   -1.172618     
-      1000   401.69178      6695.3653     -2954.2959     -2940.0921      8.423174       70.949861     -0.0018224075  -1.2051609    
-      1100   370.87469     -2294.843      -2956.9413     -2942.9469      8.384346       70.297257      0.016964628   -1.2643199    
-      1200   375.15562      704.6568      -2959.3841     -2945.7589      8.3201293      69.224551      0.070500644   -1.2400262    
-      1300   371.09077     -493.04016     -2961.6803     -2948.5516      8.1425118      66.300499      0.11183042    -1.2099873    
-      1400   365.88512      490.98174     -2963.8365     -2951.2897      7.8673969      61.895934      0.13639588    -1.198071     
-      1500   358.42655     -218.94911     -2965.8652     -2953.9337      7.5491659      56.989906      0.15564307    -1.1896984    
-      1600   329.08402      56.411923     -2967.7662     -2956.467       7.2016413      51.863637      0.17198437    -1.186472     
-      1700   317.74207      1192.918      -2969.557      -2958.8765      6.8379658      46.757776      0.19041811    -1.1812241    
-      1800   331.98966     -2205.7213     -2971.1465     -2961.1601      6.4614065      41.749774      0.20925197    -1.1714131    
-      1900   330.96814      1401.3066     -2972.6923     -2963.3191      6.0867317      37.048302      0.22552163    -1.1523125    
-      2000   315.41816     -909.41909     -2974.0785     -2965.3567      5.7020261      32.513101      0.2328316     -1.1454375    
-      2100   320.4269       1226.2006     -2975.3676     -2967.2609      5.3260556      28.366869      0.24130517    -1.1432352    
-      2200   302.88235     -1238.8052     -2976.5099     -2969.0355      4.9584282      24.58601       0.25200271    -1.141699     
-      2300   300.4349       2667.202      -2977.5329     -2970.6815      4.5986371      21.147463      0.26764984    -1.1380521    
-      2400   292.94691     -5532.1854     -2978.3724     -2972.201       4.2403749      17.980779      0.28797864    -1.1357902    
-      2500   286.12064      4647.3841     -2979.2217     -2973.5946      3.8875889      15.113348      0.31556585    -1.1249025    
-      2600   290.74305     -1950.526      -2979.9142     -2974.8686      3.5422986      12.547879      0.34719546    -1.0987558    
-      2700   281.51347      937.60472     -2980.4808     -2976.0235      3.1955646      10.211633      0.38268676    -1.0664838    
-      2800   279.71836     -801.62498     -2980.8899     -2977.0588      2.844105       8.0889331      0.41930147    -1.0460672    
-      2900   277.41241      609.21495     -2981.1721     -2977.9673      2.4956133      6.2280855      0.47337432    -1.0140054    
-      3000   281.31161     -760.27203     -2981.3003     -2978.7489      2.1466012      4.6078967      0.55325134    -0.95161956   
-      3100   284.72904      315.53038     -2981.297      -2979.4023      1.7929581      3.2146986      0.66481771    -0.84726207   
-      3200   278.39445      516.25074     -2981.1224     -2979.9226      1.4369984      2.0649644      0.82583409    -0.63830994   
-      3300   294.46998     -655.06212     -2980.8266     -2980.3134      1.0905211      1.1892364      1.0357766     -0.22841943   
-      3400   290.04647      788.30424     -2980.3963     -2980.5732      0.77030961     0.59337689     1.1867647      0.34447355   
-      3500   283.218       -844.33188     -2979.8504     -2980.6995      0.54590076     0.29800764     0.78163948    -0.42619888   
-      3600   288.76031      1339.2734     -2979.2382     -2980.6921      0.56032295     0.31396181     0.83603869    -0.30853278   
-      3700   289.44519     -3015.7161     -2978.5394     -2980.5581      0.77708069     0.60385439     1.0796997     -0.022962365  
-      3800   309.04206      5579.3265     -2977.8282     -2980.3052      1.0531468      1.1091181      0.890018      -0.56034495   
-      3900   309.34588     -4255.5213     -2977.1281     -2979.9487      1.3153981      1.7302721      0.65242676    -0.95498589   
-      4000   305.79444      2358.1383     -2976.5251     -2979.5068      1.5325477      2.3487025      0.44420123    -1.1839975    
-      4100   309.12957     -1401.6484     -2975.9173     -2978.9985      1.6923829      2.86416        0.26850538    -1.3006942    
-      4200   309.41928      1180.4111     -2975.3857     -2978.4446      1.7941259      3.2188877      0.11443933    -1.3365167    
-      4300   299.88949     -1549.6591     -2974.927      -2977.8616      1.8268192      3.3372683     -0.018659059   -1.3293426    
-      4400   319.09918      1937.7006     -2974.5598     -2977.273       1.7942266      3.219249      -0.13743367    -1.2958767    
-      4500   326.48719     -1489.2073     -2974.311      -2976.7017      1.7042328      2.9044096     -0.25309558    -1.2385503    
-      4600   310.93392      37.586899     -2974.1959     -2976.1697      1.5590672      2.4306905     -0.3757949     -1.1641151    
-      4700   314.28994      317.12347     -2974.1763     -2975.6978      1.3661244      1.8662958     -0.51792367    -1.0609001    
-      4800   309.88756     -698.72705     -2974.2892     -2975.3021      1.1422822      1.3048085     -0.69587053    -0.87319738   
-      4900   309.53444      962.42921     -2974.5261     -2974.9944      0.89961859     0.80931361    -0.91892105    -0.49661907   
-      5000   316.06666     -1869.3275     -2974.8492     -2974.7804      0.65817496     0.43319428    -1.0974595      0.048447651  
-      5100   304.82485      4042.6797     -2975.2715     -2974.6661      0.47073268     0.22158926    -0.82059377    -0.31531887   
-      5200   307.75342     -5058.4814     -2975.7195     -2974.6547      0.44733518     0.20010876    -0.68956594    -0.65171579   
-      5300   298.83511      3096.4566     -2976.3329     -2974.7467      0.60599527     0.36723026    -1.0652601      0.032591262  
-      5400   296.85413     -1929.1654     -2976.8797     -2974.9367      0.82832935     0.68612952    -0.91576774    -0.50322222   
-      5500   295.88343      1449.3005     -2977.4488     -2975.215       1.044317       1.090598      -0.67574925    -0.92510515   
-      5600   305.59328     -1504.0321     -2977.9573     -2975.5653      1.2243609      1.4990595     -0.46160433    -1.1708115    
-      5700   293.40683      2579.0134     -2978.4364     -2975.97        1.3577316      1.843435      -0.27746111    -1.2993802    
-      5800   297.93644     -2742.705      -2978.8276     -2976.411       1.4332742      2.054275      -0.11245859    -1.3584974    
-      5900   290.39408      1189.4042     -2979.2224     -2976.8733      1.4576633      2.1247823      0.030209056   -1.3466833    
-      6000   293.73148     -232.54292     -2979.503      -2977.3408      1.4300816      2.0451335      0.15663025    -1.2965878    
-      6100   292.04933     -168.30971     -2979.6898     -2977.7936      1.3523929      1.8289665      0.28027258    -1.2214523    
-      6200   299.23747      839.17828     -2979.7883     -2978.2154      1.2284868      1.5091798      0.40149929    -1.1382373    
-      6300   294.92201     -1597.9426     -2979.7975     -2978.589       1.072002       1.1491883      0.53769821    -1.0262094    
-      6400   291.7185       3411.2916     -2979.6978     -2978.9013      0.89165749     0.79505308     0.70748196    -0.83601078   
-      6500   285.34227     -4280.7968     -2979.4874     -2979.1407      0.69727552     0.48619315     0.91500724    -0.4890805    
-      6600   295.53838      2138.7496     -2979.2799     -2979.3084      0.50938648     0.25947459     1.0827149     -0.0043801382 
-      6700   288.54718     -1818.7662     -2978.9379     -2979.3979      0.3658125      0.13381879     0.85573626    -0.20104653   
-      6800   290.41342      2175.3559     -2978.543      -2979.4085      0.34439248     0.11860618     0.70989241    -0.55138716   
-      6900   296.34456     -4782.08       -2978.0362     -2979.3362      0.47081063     0.22166265     1.1051059      0.16381282   
-      7000   303.74314      5905.219      -2977.577      -2979.182       0.65635739     0.43080502     0.97456755    -0.34269231   
-      7100   303.90284     -3291.7627     -2977.1308     -2978.9595      0.83412944     0.69577192     0.71973637    -0.85687335   
-      7200   296.13966      2209.574      -2976.7001     -2978.6767      0.98885368     0.97783159     0.50554418    -1.124705     
-      7300   295.79694     -1609.1898     -2976.2816     -2978.3446      1.1093729      1.2307082      0.32952142    -1.2657581    
-      7400   306.53289      988.50902     -2975.8992     -2977.977       1.1910167      1.4185209      0.17936365    -1.331845     
-      7500   303.89992     -631.22838     -2975.5597     -2977.5901      1.2352698      1.5258915      0.033110856   -1.3362459    
-      7600   303.83684     -348.48744     -2975.3074     -2977.1915      1.2312686      1.5160224     -0.094817417   -1.3063491    
-      7700   309.67313      1350.9414     -2975.1279     -2976.7984      1.1829266      1.3993154     -0.21343083    -1.2573517    
-      7800   309.74314     -1182.8905     -2975.0174     -2976.4294      1.0913021      1.1909402     -0.3401118     -1.198459     
-      7900   309.42429      999.08033     -2975.0089     -2976.0995      0.96393318     0.92916717    -0.48456322    -1.1149956    
-      8000   315.51872     -1337.8894     -2975.0791     -2975.822       0.81535467     0.66480324    -0.67906685    -0.90499956   
-      8100   314.80533      2392.3424     -2975.25       -2975.6019      0.64582022     0.41708376    -0.90521871    -0.5328796    
-      8200   303.80236     -3224.5976     -2975.4744     -2975.4481      0.47449379     0.22514436    -1.0884377     -0.00018150871
-      8300   295.0505       3296.6912     -2975.8196     -2975.3667      0.34164698     0.11672266    -0.83269043    -0.31809119   
-      8400   302.4154      -3314.5096     -2976.1586     -2975.3606      0.32904826     0.10827276    -0.73500255    -0.57861735   
-      8500   300.95491      2971.1291     -2976.5859     -2975.4288      0.44584452     0.19877734    -1.0760301      0.014924509  
-      8600   301.68919     -2297.6673     -2976.9953     -2975.5682      0.60852433     0.37030186    -0.91802963    -0.5143582    
-      8700   291.21002      1477.5703     -2977.4323     -2975.7733      0.76843347     0.59048999    -0.68059043    -0.92051715   
-      8800   305.87126     -1085.459      -2977.8247     -2976.0327      0.90672273     0.82214612    -0.47413162    -1.1492716    
-      8900   296.17567      777.95805     -2978.2081     -2976.3349      1.0129061      1.0259789     -0.29734681    -1.271416     
-      9000   295.71917     -425.00708     -2978.5264     -2976.6672      1.0786137      1.1634075     -0.14055755    -1.3302079    
-      9100   296.85578     -533.46289     -2978.8197     -2977.0152      1.1000855      1.2101882      0.0045950751  -1.3434868    
-      9200   293.949        605.27065     -2979.0349     -2977.3702      1.0854405      1.1781811      0.123965      -1.3093197    
-      9300   289.11704     -896.44753     -2979.1981     -2977.7166      1.0353526      1.071955       0.23898813    -1.2558296    
-      9400   285.34521      1181.7542     -2979.2879     -2978.0404      0.95298596     0.90818224     0.36461645    -1.1736585    
-      9500   296.17714     -2503.9848     -2979.2668     -2978.3301      0.8407037      0.70678272     0.50841734    -1.0540275    
-      9600   296.43744      4912.6395     -2979.1829     -2978.5736      0.70352404     0.49494608     0.68312042    -0.86335848   
-      9700   288.63317     -3935.8902     -2979.0381     -2978.7635      0.55322477     0.30605764     0.88509388    -0.54108379   
-      9800   296.27133      1365.4106     -2978.8723     -2978.8969      0.40665162     0.16536554     1.0460992     -0.092552905  
-      9900   299.37628     -1267.2668     -2978.5934     -2978.9673      0.29467695     0.086834506    0.80391757    -0.38307943   
-     10000   296.60645      1950.1018     -2978.2725     -2978.9739      0.28169006     0.079349287    0.70171659    -0.62026504   
-Loop time of 47.4814 on 1 procs for 10000 steps with 864 atoms
-
-Performance: 36.393 ns/day, 0.659 hours/ns, 210.609 timesteps/s, 181.966 katom-step/s
-99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 46.299     | 46.299     | 46.299     |   0.0 | 97.51
-Neigh   | 0.010908   | 0.010908   | 0.010908   |   0.0 |  0.02
-Comm    | 0.29643    | 0.29643    | 0.29643    |   0.0 |  0.62
-Output  | 0.0090682  | 0.0090682  | 0.0090682  |   0.0 |  0.02
-Modify  | 0.7406     | 0.7406     | 0.7406     |   0.0 |  1.56
-Other   |            | 0.1254     |            |       |  0.26
-
-Nlocal:            864 ave         864 max         864 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:           3767 ave        3767 max        3767 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:          96746 ave       96746 max       96746 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 96746
-Ave neighs/atom = 111.97454
-Neighbor list builds = 1
-Dangerous builds = 0
-
-Total wall time: 0:00:47

examples/PACKAGES/moments/log.02May2025.simple.g++.4

@@ -1,177 +0,0 @@
-LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
-  using 1 OpenMP thread(s) per MPI task
-# create pure copper system
-units metal
-lattice fcc 3.75
-Lattice spacing in x,y,z = 3.75 3.75 3.75
-region box block 0 6 0 6 0 6
-create_box 2 box
-Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
-  1 by 2 by 2 MPI processor grid
-
-timestep 0.002
-create_atoms 1 box
-Created 864 atoms
-  using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
-  create_atoms CPU = 0.010 seconds
-
-pair_style eam/alloy
-pair_coeff * * AlCu.eam.alloy Cu Al
-
-# Initialize to a high temperature, then cool in npt ensemble
-velocity all create 1000.0 6567345
-fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
-fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
-fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
-
-variable toteng equal "etotal"
-fix 2 all ave/moments 5 200 100 v_toteng mean stddev variance skew kurtosis
-
-thermo_style custom step temp press etotal f_2[*]
-
-thermo 100
-run 10000
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.6825
-  ghost atom cutoff = 8.6825
-  binsize = 4.34125, bins = 6 6 6
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair eam/alloy, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.42 | 3.42 | 3.42 Mbytes
-   Step          Temp          Press          TotEng         f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]    
-         0   1000          -107410.22     -2884.9159      0              0              0              0              0            
-       100   492.38014     -134.33622     -2928.6874     -2927.2291      1.7092959      2.9216925      2.5081594      6.099781     
-       200   484.82396     -214.26318     -2931.4603     -2928.71        2.0003214      4.0012857      1.3645049      3.3103886    
-       300   476.69743      15.78678      -2934.0022     -2930.0515      2.5470901      6.4876682      0.6954232      0.86102766   
-       400   482.51415      141.67184     -2936.9347     -2931.4152      3.2681043      10.680505      0.30641098    -0.22337036   
-       500   455.45411      2.4424602     -2939.9649     -2932.8397      4.1076295      16.87262       0.10483325    -0.6997127    
-       600   455.20054     -6.8170934     -2943.0454     -2934.2947      4.9842257      24.842506      0.018003661   -0.92490336   
-       700   429.81168     -75.812923     -2946.0438     -2935.7704      5.8766819      34.53539      -0.019539731   -1.0444564    
-       800   428.22097      604.18705     -2948.9285     -2937.2449      6.7522047      45.592268     -0.026384526   -1.1194924    
-       900   399.10914     -3622.6904     -2951.7252     -2938.7094      7.6043904      57.826753     -0.019997758   -1.1658244    
-      1000   394.62543      7905.9041     -2954.2925     -2940.15        8.4168551      70.84345      -0.0026187371  -1.2004009    
-      1100   404.27007     -2565.5508     -2956.9736     -2943.0009      8.3722389      70.094384      0.015852037   -1.2665587    
-      1200   368.47178      741.43707     -2959.4264     -2945.8091      8.3127243      69.101386      0.069744698   -1.2412651    
-      1300   360.91266     -267.08372     -2961.69       -2948.5981      8.1334656      66.153263      0.1116445     -1.2129213    
-      1400   356.74405      158.09093     -2963.8501     -2951.3302      7.8574973      61.740264      0.13825232    -1.1999727    
-      1500   335.45696     -71.007783     -2965.8817     -2953.9689      7.5384846      56.82875       0.15915227    -1.1877331    
-      1600   331.01199     -454.90004     -2967.7708     -2956.5         7.1862592      51.642321      0.17403957    -1.1840985    
-      1700   329.223        2428.4284     -2969.5452     -2958.9073      6.8228029      46.55064       0.19027454    -1.1778276    
-      1800   327.61481     -4757.648      -2971.1105     -2961.1863      6.4445074      41.531675      0.20819854    -1.1712539    
-      1900   318.18741      2226.7765     -2972.6906     -2963.3396      6.0703365      36.848986      0.22378928    -1.1556732    
-      2000   308.79313     -1089.8603     -2974.0899     -2965.3712      5.6913723      32.391718      0.23279863    -1.1445916    
-      2100   303.32047      757.53534     -2975.3597     -2967.2741      5.3153102      28.252523      0.23857925    -1.1465858    
-      2200   307.41102     -837.97246     -2976.4966     -2969.0433      4.9515105      24.517456      0.25216298    -1.1426077    
-      2300   303.01088      1618.29       -2977.5454     -2970.6862      4.593227       21.097734      0.26914071    -1.1356519    
-      2400   297.59385     -3233.8282     -2978.4064     -2972.2049      4.235209       17.936995      0.28804295    -1.1332908    
-      2500   288.72232      5209.2099     -2979.1999     -2973.5963      3.8804647      15.058006      0.31533205    -1.1258312    
-      2600   298.92201     -2193.618      -2979.8873     -2974.8649      3.5301507      12.461964      0.34927897    -1.1048024    
-      2700   282.61818      765.88178     -2980.4563     -2976.0148      3.1852407      10.145758      0.3879755     -1.0655899    
-      2800   273.63104     -389.49749     -2980.8636     -2977.0468      2.8322558      8.021673       0.4259426     -1.0370247    
-      2900   274.12166     -9.2552992     -2981.1421     -2977.9525      2.4816703      6.1586877      0.47721359    -1.0061337    
-      3000   279.43592      212.25445     -2981.2716     -2978.7309      2.1328425      4.5490171      0.5532015     -0.94983292   
-      3100   291.10071     -1139.205      -2981.2475     -2979.3812      1.7828537      3.1785674      0.66452451    -0.83906914   
-      3200   281.53171      3124.6411     -2981.0818     -2979.9003      1.4287164      2.0412304      0.81952022    -0.6386061    
-      3300   277.0223      -2795.9494     -2980.7825     -2980.287       1.0830229      1.1729385      1.0186688     -0.26502454   
-      3400   284.8443       1587.8876     -2980.3701     -2980.5435      0.76893619     0.59126286     1.1646672      0.27529682   
-      3500   281.19        -1143.0785     -2979.8374     -2980.6693      0.54860209     0.30096426     0.79069857    -0.36626891   
-      3600   296.58287      1156.4706     -2979.2182     -2980.6646      0.55745952     0.31076112     0.81914175    -0.31895116   
-      3700   297.24517     -1888.4993     -2978.5352     -2980.5318      0.77195451     0.59591377     1.0713124     -0.027796216  
-      3800   290.81586      3843.3483     -2977.8509     -2980.2819      1.0444771      1.0909324      0.88270245    -0.57339499   
-      3900   300.39456     -5584.8386     -2977.0837     -2979.9273      1.3073719      1.7092212      0.65444496    -0.94023014   
-      4000   306.15811      3310.0105     -2976.5086     -2979.4859      1.5269967      2.3317191      0.45120199    -1.1665402    
-      4100   295.907       -1475.0458     -2975.9096     -2978.9779      1.6878413      2.8488082      0.27738537    -1.2909517    
-      4200   322.70162      933.76586     -2975.3867     -2978.425       1.7872637      3.1943116      0.12322364    -1.3421568    
-      4300   306.69631     -512.7048      -2974.9324     -2977.8465      1.8221493      3.3202281     -0.016769435   -1.3380921    
-      4400   309.23776      226.77219     -2974.5791     -2977.2621      1.788532       3.1988469     -0.14279249    -1.3044784    
-      4500   313.15783      508.29785     -2974.3263     -2976.6947      1.6959722      2.8763217     -0.26351575    -1.2425552    
-      4600   316.26151     -2043.7571     -2974.1697     -2976.1635      1.5525328      2.4103582     -0.38443906    -1.156175     
-      4700   312.27329      1831.682      -2974.1732     -2975.6917      1.3614048      1.8534231     -0.52504872    -1.0383081    
-      4800   307.61066     -1476.0019     -2974.2885     -2975.296       1.1354139      1.2891647     -0.69734331    -0.84719677   
-      4900   305.73489      1303.4848     -2974.5506     -2974.9905      0.8913743      0.79454814    -0.90609876    -0.50216921   
-      5000   309.3774      -1574.6812     -2974.8687     -2974.7812      0.65272109     0.42604482    -1.0613188      0.00291608   
-      5100   304.8602       2679.7476     -2975.3082     -2974.6718      0.4727141      0.22345862    -0.75321909    -0.42028824   
-      5200   297.54226     -5008.0905     -2975.7443     -2974.6646      0.45797515     0.20974124    -0.66557441    -0.64583954   
-      5300   306.18872      4840.4175     -2976.324      -2974.7575      0.61348896     0.3763687     -1.0084709     -0.10258503   
-      5400   299.57661     -2513.1706     -2976.8842     -2974.9472      0.83376011     0.69515592    -0.88189118    -0.55222188   
-      5500   302.30844      1301.3525     -2977.4539     -2975.2244      1.0486412      1.0996484     -0.65075151    -0.94687541   
-      5600   302.11038     -760.79712     -2977.9764     -2975.5765      1.2259535      1.502962      -0.44510538    -1.1709493    
-      5700   294.49825      718.67318     -2978.4584     -2975.9844      1.357155       1.8418697     -0.27309672    -1.2848748    
-      5800   305.97636     -478.64224     -2978.8638     -2976.429       1.4331646      2.0539608     -0.1197893     -1.3417863    
-      5900   291.93868     -419.74179     -2979.2292     -2976.8905      1.4535887      2.1129201      0.024018983   -1.349863     
-      6000   289.50667      859.85085     -2979.5018     -2977.3557      1.4249736      2.0305497      0.15271261    -1.3095465    
-      6100   305.70118     -933.35917     -2979.6877     -2977.8064      1.3480601      1.8172659      0.27785119    -1.2402584    
-      6200   284.37805      1526.0707     -2979.806      -2978.2265      1.2296781      1.5121082      0.40681415    -1.1355005    
-      6300   291.08863     -2156.6708     -2979.8064     -2978.6017      1.0733214      1.1520189      0.54137333    -1.0156432    
-      6400   295.99073      2819.8245     -2979.7378     -2978.9165      0.8941904      0.79957647     0.7073501     -0.82385123   
-      6500   298.06769     -3396.3504     -2979.5428     -2979.1626      0.70228297     0.49320137     0.91043588    -0.48653641   
-      6600   301.78514      5496.6525     -2979.2768     -2979.3329      0.51276653     0.26292952     1.0681056     -0.036293782  
-      6700   290.80665     -5229.4989     -2978.9177     -2979.4217      0.36990055     0.13682642     0.81466085    -0.37332419   
-      6800   296.75761      2401.7807     -2978.5996     -2979.4338      0.34589164     0.11964103     0.65253856    -0.7737558    
-      6900   295.77553     -1521.6269     -2978.1619     -2979.3685      0.46007271     0.21166689     1.0427138     -0.013014477  
-      7000   303.59015      1530.7255     -2977.7097     -2979.225       0.63320287     0.40094588     0.93012255    -0.45527217   
-      7100   297.51038     -3016.4426     -2977.2025     -2979.0103      0.81101521     0.65774567     0.7114444     -0.84465178   
-      7200   293.53789      2705.9808     -2976.7651     -2978.7294      0.97512025     0.95085951     0.52979295    -1.0479526    
-      7300   301.78809     -1042.1076     -2976.3388     -2978.3998      1.1024575      1.2154126      0.35564664    -1.2137023    
-      7400   307.50053      214.56923     -2975.9581     -2978.0341      1.188001       1.4113463      0.20025025    -1.3077784    
-      7500   301.98985      281.86495     -2975.6146     -2977.6451      1.2301918      1.5133718      0.063886193   -1.3465506    
-      7600   318.37347     -1145.7795     -2975.3473     -2977.2486      1.2295055      1.5116837     -0.066939137   -1.3475567    
-      7700   314.94512      4536.9887     -2975.1351     -2976.8564      1.1948121      1.427576      -0.19450637    -1.2864658    
-      7800   312.91485     -2980.6408     -2975.0156     -2976.4828      1.1134406      1.2397499     -0.32749726    -1.207718     
-      7900   310.06854      2244.3877     -2975.0094     -2976.1462      0.99080702     0.98169854    -0.48336959    -1.0840695    
-      8000   308.55007     -2427.1464     -2975.0491     -2975.8566      0.83800849     0.70225823    -0.65822117    -0.89212512   
-      8100   323.02796      3187.4728     -2975.2081     -2975.6251      0.66510054     0.44235872    -0.84857729    -0.62984027   
-      8200   327.05029     -6447.7875     -2975.3162     -2975.4608      0.49730291     0.24731018    -1.0534735     -0.14095413   
-      8300   311.194        4273.1174     -2975.7217     -2975.3642      0.35491458     0.12596436    -0.95967595    -0.04445204   
-      8400   290.61931     -2301.019      -2976.0963     -2975.3446      0.31530296     0.09941596    -0.69056625    -0.72257435   
-      8500   314.00559      1966.1297     -2976.5206     -2975.3995      0.41659574     0.17355201    -1.1134124      0.18107632   
-      8600   288.26541     -1608.4524     -2976.9304     -2975.526       0.57968749     0.33603759    -1.0014591     -0.34698354   
-      8700   298.92083      1353.9988     -2977.355      -2975.7203      0.74176087     0.55020919    -0.74109062    -0.86227705   
-      8800   299.97274     -638.68301     -2977.766      -2975.9682      0.87950613     0.77353104    -0.50839929    -1.1555064    
-      8900   300.66443     -279.62514     -2978.1476     -2976.262       0.99526406     0.99055054    -0.33059914    -1.261881     
-      9000   290.44715      489.06352     -2978.4892     -2976.5918      1.0763797      1.1585932     -0.17871557    -1.3082755    
-      9100   289.06733     -1063.4482     -2978.784      -2976.943       1.1174524      1.2486999     -0.037767225   -1.3120851    
-      9200   297.63931      2664.6535     -2979.0202     -2977.3033      1.1127042      1.2381106      0.090936095   -1.2913777    
-      9300   297.9983      -4684.428      -2979.1316     -2977.6563      1.0596342      1.1228247      0.20756305    -1.2867214    
-      9400   285.14009      2779.1548     -2979.2804     -2977.9868      0.98034602     0.96107833     0.33668495    -1.2294268    
-      9500   284.11569     -2437.5003     -2979.2918     -2978.2852      0.87286876     0.76189987     0.48407552    -1.1274969    
-      9600   291.97193      2772.1396     -2979.2473     -2978.5402      0.74294711     0.55197041     0.67450455    -0.91152584   
-      9700   292.59563     -3615.4496     -2979.0801     -2978.7442      0.59448857     0.35341666     0.91630006    -0.47180257   
-      9800   296.1785       4869.2744     -2978.8849     -2978.891       0.43463281     0.18890568     1.1020846      0.093881572  
-      9900   298.44745     -3587.7391     -2978.5978     -2978.9712      0.30680426     0.094128854    0.8532075     -0.19634913   
-     10000   297.99863      1312.5643     -2978.3205     -2978.9854      0.27829395     0.077447522    0.60818263    -0.79004935   
-Loop time of 15.3108 on 4 procs for 10000 steps with 864 atoms
-
-Performance: 112.862 ns/day, 0.213 hours/ns, 653.136 timesteps/s, 564.309 katom-step/s
-92.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 11.428     | 12.158     | 12.621     |  13.0 | 79.41
-Neigh   | 0.0019158  | 0.0020708  | 0.002163   |   0.2 |  0.01
-Comm    | 1.936      | 2.3948     | 3.0967     |  28.3 | 15.64
-Output  | 0.0026067  | 0.0037308  | 0.0066123  |   2.7 |  0.02
-Modify  | 0.44688    | 0.45929    | 0.47131    |   1.6 |  3.00
-Other   |            | 0.2928     |            |       |  1.91
-
-Nlocal:            216 ave         224 max         204 min
-Histogram: 1 0 0 0 0 0 0 2 0 1
-Nghost:           2147 ave        2159 max        2139 min
-Histogram: 1 0 0 2 0 0 0 0 0 1
-Neighs:        24185.8 ave       26045 max       21309 min
-Histogram: 1 0 0 0 0 1 0 0 0 2
-
-Total # of neighbors = 96743
-Ave neighs/atom = 111.97106
-Neighbor list builds = 1
-Dangerous builds = 0
-
-Total wall time: 0:00:15

examples/PACKAGES/moments/log.02May2025.valtest.g++.1

@@ -1,178 +0,0 @@
-LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
-  using 1 OpenMP thread(s) per MPI task
-# create pure copper system
-units metal
-lattice fcc 3.75
-Lattice spacing in x,y,z = 3.75 3.75 3.75
-region box block 0 6 0 6 0 6
-create_box 2 box
-Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
-  1 by 1 by 1 MPI processor grid
-
-timestep 0.002
-create_atoms 1 box
-Created 864 atoms
-  using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
-  create_atoms CPU = 0.001 seconds
-
-pair_style eam/alloy
-pair_coeff * * AlCu.eam.alloy Cu Al
-
-# Initialize to a high temperature, then cool in npt ensemble
-velocity all create 1000.0 6567345
-fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
-fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
-fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
-
-variable toteng equal "etotal"
-fix 2 all ave/moments 1 10 10 v_toteng mean variance skew kurtosis
-
-thermo_style custom step etotal f_2[*]
-thermo_modify format float %14.8f
-
-thermo 1
-run 100
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.6825
-  ghost atom cutoff = 8.6825
-  binsize = 4.34125, bins = 6 6 6
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair eam/alloy, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.484 | 3.484 | 3.484 Mbytes
-   Step         TotEng         f_2[1]         f_2[2]         f_2[3]         f_2[4]    
-         0  -2884.91592826     0.00000000     0.00000000     0.00000000     0.00000000
-         1  -2888.74461907     0.00000000     0.00000000     0.00000000     0.00000000
-         2  -2898.78491936     0.00000000     0.00000000     0.00000000     0.00000000
-         3  -2910.70619667     0.00000000     0.00000000     0.00000000     0.00000000
-         4  -2919.41734302     0.00000000     0.00000000     0.00000000     0.00000000
-         5  -2923.24980175     0.00000000     0.00000000     0.00000000     0.00000000
-         6  -2923.79800148     0.00000000     0.00000000     0.00000000     0.00000000
-         7  -2922.97580252     0.00000000     0.00000000     0.00000000     0.00000000
-         8  -2921.95601941     0.00000000     0.00000000     0.00000000     0.00000000
-         9  -2921.45319499     0.00000000     0.00000000     0.00000000     0.00000000
-        10  -2921.81460149 -2915.29004998   148.32538381     1.60272422     1.50844200
-        11  -2923.00059466 -2915.29004998   148.32538381     1.60272422     1.50844200
-        12  -2924.63075671 -2915.29004998   148.32538381     1.60272422     1.50844200
-        13  -2926.18037946 -2915.29004998   148.32538381     1.60272422     1.50844200
-        14  -2927.22356281 -2915.29004998   148.32538381     1.60272422     1.50844200
-        15  -2927.62053073 -2915.29004998   148.32538381     1.60272422     1.50844200
-        16  -2927.49949128 -2915.29004998   148.32538381     1.60272422     1.50844200
-        17  -2927.12292174 -2915.29004998   148.32538381     1.60272422     1.50844200
-        18  -2926.73637250 -2915.29004998   148.32538381     1.60272422     1.50844200
-        19  -2926.49482990 -2915.29004998   148.32538381     1.60272422     1.50844200
-        20  -2926.44714720 -2926.29565870     2.07215006     1.62317861     2.37019300
-        21  -2926.56102718 -2926.29565870     2.07215006     1.62317861     2.37019300
-        22  -2926.76734347 -2926.29565870     2.07215006     1.62317861     2.37019300
-        23  -2926.98403044 -2926.29565870     2.07215006     1.62317861     2.37019300
-        24  -2927.15193693 -2926.29565870     2.07215006     1.62317861     2.37019300
-        25  -2927.24498540 -2926.29565870     2.07215006     1.62317861     2.37019300
-        26  -2927.26914121 -2926.29565870     2.07215006     1.62317861     2.37019300
-        27  -2927.25021402 -2926.29565870     2.07215006     1.62317861     2.37019300
-        28  -2927.21637817 -2926.29565870     2.07215006     1.62317861     2.37019300
-        29  -2927.19085616 -2926.29565870     2.07215006     1.62317861     2.37019300
-        30  -2927.18360687 -2927.08195198     0.05722486     1.54894969     1.44984748
-        31  -2927.19243579 -2927.08195198     0.05722486     1.54894969     1.44984748
-        32  -2927.20805612 -2927.08195198     0.05722486     1.54894969     1.44984748
-        33  -2927.22285606 -2927.08195198     0.05722486     1.54894969     1.44984748
-        34  -2927.23274852 -2927.08195198     0.05722486     1.54894969     1.44984748
-        35  -2927.23953263 -2927.08195198     0.05722486     1.54894969     1.44984748
-        36  -2927.24805761 -2927.08195198     0.05722486     1.54894969     1.44984748
-        37  -2927.26215638 -2927.08195198     0.05722486     1.54894969     1.44984748
-        38  -2927.28298252 -2927.08195198     0.05722486     1.54894969     1.44984748
-        39  -2927.31025065 -2927.08195198     0.05722486     1.54894969     1.44984748
-        40  -2927.33874897 -2927.25378252     0.00209108    -0.65432756    -0.21113798
-        41  -2927.36224413 -2927.25378252     0.00209108    -0.65432756    -0.21113798
-        42  -2927.37729800 -2927.25378252     0.00209108    -0.65432756    -0.21113798
-        43  -2927.38671916 -2927.25378252     0.00209108    -0.65432756    -0.21113798
-        44  -2927.39115082 -2927.25378252     0.00209108    -0.65432756    -0.21113798
-        45  -2927.39614318 -2927.25378252     0.00209108    -0.65432756    -0.21113798
-        46  -2927.40444730 -2927.25378252     0.00209108    -0.65432756    -0.21113798
-        47  -2927.41888601 -2927.25378252     0.00209108    -0.65432756    -0.21113798
-        48  -2927.43954388 -2927.25378252     0.00209108    -0.65432756    -0.21113798
-        49  -2927.46210058 -2927.25378252     0.00209108    -0.65432756    -0.21113798
-        50  -2927.48270024 -2927.41212333     0.00148630    -0.72914987    -0.39161968
-        51  -2927.49822500 -2927.41212333     0.00148630    -0.72914987    -0.39161968
-        52  -2927.50765361 -2927.41212333     0.00148630    -0.72914987    -0.39161968
-        53  -2927.51223225 -2927.41212333     0.00148630    -0.72914987    -0.39161968
-        54  -2927.51510653 -2927.41212333     0.00148630    -0.72914987    -0.39161968
-        55  -2927.52035921 -2927.41212333     0.00148630    -0.72914987    -0.39161968
-        56  -2927.53170012 -2927.41212333     0.00148630    -0.72914987    -0.39161968
-        57  -2927.54910408 -2927.41212333     0.00148630    -0.72914987    -0.39161968
-        58  -2927.57357292 -2927.41212333     0.00148630    -0.72914987    -0.39161968
-        59  -2927.60356966 -2927.41212333     0.00148630    -0.72914987    -0.39161968
-        60  -2927.63344447 -2927.54449679     0.00204640    -1.06571776     0.04430271
-        61  -2927.66186165 -2927.54449679     0.00204640    -1.06571776     0.04430271
-        62  -2927.68810360 -2927.54449679     0.00204640    -1.06571776     0.04430271
-        63  -2927.71163480 -2927.54449679     0.00204640    -1.06571776     0.04430271
-        64  -2927.73036225 -2927.54449679     0.00204640    -1.06571776     0.04430271
-        65  -2927.74726656 -2927.54449679     0.00204640    -1.06571776     0.04430271
-        66  -2927.76525638 -2927.54449679     0.00204640    -1.06571776     0.04430271
-        67  -2927.78432762 -2927.54449679     0.00204640    -1.06571776     0.04430271
-        68  -2927.80305095 -2927.54449679     0.00204640    -1.06571776     0.04430271
-        69  -2927.82406714 -2927.54449679     0.00204640    -1.06571776     0.04430271
-        70  -2927.84622122 -2927.75621522     0.00356092     0.06232090    -0.94076248
-        71  -2927.86886493 -2927.75621522     0.00356092     0.06232090    -0.94076248
-        72  -2927.89150302 -2927.75621522     0.00356092     0.06232090    -0.94076248
-        73  -2927.91480122 -2927.75621522     0.00356092     0.06232090    -0.94076248
-        74  -2927.93739399 -2927.75621522     0.00356092     0.06232090    -0.94076248
-        75  -2927.96075707 -2927.75621522     0.00356092     0.06232090    -0.94076248
-        76  -2927.98525702 -2927.75621522     0.00356092     0.06232090    -0.94076248
-        77  -2928.00918972 -2927.75621522     0.00356092     0.06232090    -0.94076248
-        78  -2928.03266453 -2927.75621522     0.00356092     0.06232090    -0.94076248
-        79  -2928.05673430 -2927.75621522     0.00356092     0.06232090    -0.94076248
-        80  -2928.08120268 -2927.97383685     0.00511363    -0.03242365    -1.20956903
-        81  -2928.10618717 -2927.97383685     0.00511363    -0.03242365    -1.20956903
-        82  -2928.13191751 -2927.97383685     0.00511363    -0.03242365    -1.20956903
-        83  -2928.15675025 -2927.97383685     0.00511363    -0.03242365    -1.20956903
-        84  -2928.18178044 -2927.97383685     0.00511363    -0.03242365    -1.20956903
-        85  -2928.20538210 -2927.97383685     0.00511363    -0.03242365    -1.20956903
-        86  -2928.22991006 -2927.97383685     0.00511363    -0.03242365    -1.20956903
-        87  -2928.25238345 -2927.97383685     0.00511363    -0.03242365    -1.20956903
-        88  -2928.27490378 -2927.97383685     0.00511363    -0.03242365    -1.20956903
-        89  -2928.29697980 -2927.97383685     0.00511363    -0.03242365    -1.20956903
-        90  -2928.31902032 -2928.21552149     0.00511983     0.08421866    -1.19120544
-        91  -2928.34079951 -2928.21552149     0.00511983     0.08421866    -1.19120544
-        92  -2928.36448072 -2928.21552149     0.00511983     0.08421866    -1.19120544
-        93  -2928.38918869 -2928.21552149     0.00511983     0.08421866    -1.19120544
-        94  -2928.41578734 -2928.21552149     0.00511983     0.08421866    -1.19120544
-        95  -2928.44466633 -2928.21552149     0.00511983     0.08421866    -1.19120544
-        96  -2928.47414034 -2928.21552149     0.00511983     0.08421866    -1.19120544
-        97  -2928.50507273 -2928.21552149     0.00511983     0.08421866    -1.19120544
-        98  -2928.53751007 -2928.21552149     0.00511983     0.08421866    -1.19120544
-        99  -2928.56947939 -2928.21552149     0.00511983     0.08421866    -1.19120544
-       100  -2928.60000318 -2928.46411283     0.00779929    -0.14908790    -1.24292534
-Loop time of 0.579661 on 1 procs for 100 steps with 864 atoms
-
-Performance: 29.811 ns/day, 0.805 hours/ns, 172.515 timesteps/s, 149.053 katom-step/s
-96.3% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.54316    | 0.54316    | 0.54316    |   0.0 | 93.70
-Neigh   | 0.0041212  | 0.0041212  | 0.0041212  |   0.0 |  0.71
-Comm    | 0.0034702  | 0.0034702  | 0.0034702  |   0.0 |  0.60
-Output  | 0.014085   | 0.014085   | 0.014085   |   0.0 |  2.43
-Modify  | 0.01321    | 0.01321    | 0.01321    |   0.0 |  2.28
-Other   |            | 0.001612   |            |       |  0.28
-
-Nlocal:            864 ave         864 max         864 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:           3767 ave        3767 max        3767 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:          96746 ave       96746 max       96746 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 96746
-Ave neighs/atom = 111.97454
-Neighbor list builds = 1
-Dangerous builds = 0
-
-Total wall time: 0:00:00

examples/PACKAGES/moments/log.02May2025.valtest.g++.4

@@ -1,178 +0,0 @@
-LAMMPS (2 Apr 2025 - Development - patch_4Feb2025-645-gba166d42e1-modified)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
-  using 1 OpenMP thread(s) per MPI task
-# create pure copper system
-units metal
-lattice fcc 3.75
-Lattice spacing in x,y,z = 3.75 3.75 3.75
-region box block 0 6 0 6 0 6
-create_box 2 box
-Created orthogonal box = (0 0 0) to (22.5 22.5 22.5)
-  1 by 2 by 2 MPI processor grid
-
-timestep 0.002
-create_atoms 1 box
-Created 864 atoms
-  using lattice units in orthogonal box = (0 0 0) to (22.5 22.5 22.5)
-  create_atoms CPU = 0.001 seconds
-
-pair_style eam/alloy
-pair_coeff * * AlCu.eam.alloy Cu Al
-
-# Initialize to a high temperature, then cool in npt ensemble
-velocity all create 1000.0 6567345
-fix 1 all npt temp 300.0 300.0 $(500*dt) iso 0.0 0.0 $(100*dt)
-fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 $(100*dt)
-fix 1 all npt temp 300.0 300.0 1 iso 0.0 0.0 0.2000000000000000111
-
-variable toteng equal "etotal"
-fix 2 all ave/moments 1 10 10 v_toteng mean variance skew kurtosis
-
-thermo_style custom step etotal f_2[*]
-thermo_modify format float %14.8f
-
-thermo 1
-run 100
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 8.6825
-  ghost atom cutoff = 8.6825
-  binsize = 4.34125, bins = 6 6 6
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair eam/alloy, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.42 | 3.42 | 3.42 Mbytes
-   Step         TotEng         f_2[1]         f_2[2]         f_2[3]         f_2[4]    
-         0  -2884.91592826     0.00000000     0.00000000     0.00000000     0.00000000
-         1  -2888.74473521     0.00000000     0.00000000     0.00000000     0.00000000
-         2  -2898.78463435     0.00000000     0.00000000     0.00000000     0.00000000
-         3  -2910.70366466     0.00000000     0.00000000     0.00000000     0.00000000
-         4  -2919.40999553     0.00000000     0.00000000     0.00000000     0.00000000
-         5  -2923.23570887     0.00000000     0.00000000     0.00000000     0.00000000
-         6  -2923.77707961     0.00000000     0.00000000     0.00000000     0.00000000
-         7  -2922.94386730     0.00000000     0.00000000     0.00000000     0.00000000
-         8  -2921.92251474     0.00000000     0.00000000     0.00000000     0.00000000
-         9  -2921.42476103     0.00000000     0.00000000     0.00000000     0.00000000
-        10  -2921.79501042 -2915.27419717   148.08574615     1.60354430     1.51194865
-        11  -2922.99498349 -2915.27419717   148.08574615     1.60354430     1.51194865
-        12  -2924.64023395 -2915.27419717   148.08574615     1.60354430     1.51194865
-        13  -2926.19980790 -2915.27419717   148.08574615     1.60354430     1.51194865
-        14  -2927.25022454 -2915.27419717   148.08574615     1.60354430     1.51194865
-        15  -2927.64953875 -2915.27419717   148.08574615     1.60354430     1.51194865
-        16  -2927.52804735 -2915.27419717   148.08574615     1.60354430     1.51194865
-        17  -2927.14916045 -2915.27419717   148.08574615     1.60354430     1.51194865
-        18  -2926.76078244 -2915.27419717   148.08574615     1.60354430     1.51194865
-        19  -2926.51878380 -2915.27419717   148.08574615     1.60354430     1.51194865
-        20  -2926.47129883 -2926.31628615     2.10313655     1.62594474     2.38000930
-        21  -2926.59030835 -2926.31628615     2.10313655     1.62594474     2.38000930
-        22  -2926.80121221 -2926.31628615     2.10313655     1.62594474     2.38000930
-        23  -2927.02526150 -2926.31628615     2.10313655     1.62594474     2.38000930
-        24  -2927.20079704 -2926.31628615     2.10313655     1.62594474     2.38000930
-        25  -2927.30192483 -2926.31628615     2.10313655     1.62594474     2.38000930
-        26  -2927.33194351 -2926.31628615     2.10313655     1.62594474     2.38000930
-        27  -2927.31647527 -2926.31628615     2.10313655     1.62594474     2.38000930
-        28  -2927.28391864 -2926.31628615     2.10313655     1.62594474     2.38000930
-        29  -2927.25821953 -2926.31628615     2.10313655     1.62594474     2.38000930
-        30  -2927.25085808 -2927.13609190     0.06387000     1.52055179     1.31247839
-        31  -2927.25723201 -2927.13609190     0.06387000     1.52055179     1.31247839
-        32  -2927.27197789 -2927.13609190     0.06387000     1.52055179     1.31247839
-        33  -2927.28667044 -2927.13609190     0.06387000     1.52055179     1.31247839
-        34  -2927.29879455 -2927.13609190     0.06387000     1.52055179     1.31247839
-        35  -2927.30701891 -2927.13609190     0.06387000     1.52055179     1.31247839
-        36  -2927.31785921 -2927.13609190     0.06387000     1.52055179     1.31247839
-        37  -2927.33272014 -2927.13609190     0.06387000     1.52055179     1.31247839
-        38  -2927.35282056 -2927.13609190     0.06387000     1.52055179     1.31247839
-        39  -2927.37849130 -2927.13609190     0.06387000     1.52055179     1.31247839
-        40  -2927.40448350 -2927.32080685     0.00219675    -0.52051260    -0.50322958
-        41  -2927.42423249 -2927.32080685     0.00219675    -0.52051260    -0.50322958
-        42  -2927.43769919 -2927.32080685     0.00219675    -0.52051260    -0.50322958
-        43  -2927.44493813 -2927.32080685     0.00219675    -0.52051260    -0.50322958
-        44  -2927.44923137 -2927.32080685     0.00219675    -0.52051260    -0.50322958
-        45  -2927.45439729 -2927.32080685     0.00219675    -0.52051260    -0.50322958
-        46  -2927.46365674 -2927.32080685     0.00219675    -0.52051260    -0.50322958
-        47  -2927.48173952 -2927.32080685     0.00219675    -0.52051260    -0.50322958
-        48  -2927.50371663 -2927.32080685     0.00219675    -0.52051260    -0.50322958
-        49  -2927.52750629 -2927.32080685     0.00219675    -0.52051260    -0.50322958
-        50  -2927.54872274 -2927.47358404     0.00168128    -0.79883601    -0.48497973
-        51  -2927.56277664 -2927.47358404     0.00168128    -0.79883601    -0.48497973
-        52  -2927.57050508 -2927.47358404     0.00168128    -0.79883601    -0.48497973
-        53  -2927.57241043 -2927.47358404     0.00168128    -0.79883601    -0.48497973
-        54  -2927.57517748 -2927.47358404     0.00168128    -0.79883601    -0.48497973
-        55  -2927.58161786 -2927.47358404     0.00168128    -0.79883601    -0.48497973
-        56  -2927.59393740 -2927.47358404     0.00168128    -0.79883601    -0.48497973
-        57  -2927.61367876 -2927.47358404     0.00168128    -0.79883601    -0.48497973
-        58  -2927.64096296 -2927.47358404     0.00168128    -0.79883601    -0.48497973
-        59  -2927.67356621 -2927.47358404     0.00168128    -0.79883601    -0.48497973
-        60  -2927.70625176 -2927.60908846     0.00241645    -1.10903745     0.07175615
-        61  -2927.73673853 -2927.60908846     0.00241645    -1.10903745     0.07175615
-        62  -2927.76292153 -2927.60908846     0.00241645    -1.10903745     0.07175615
-        63  -2927.78541405 -2927.60908846     0.00241645    -1.10903745     0.07175615
-        64  -2927.80292853 -2927.60908846     0.00241645    -1.10903745     0.07175615
-        65  -2927.81988675 -2927.60908846     0.00241645    -1.10903745     0.07175615
-        66  -2927.83680256 -2927.60908846     0.00241645    -1.10903745     0.07175615
-        67  -2927.85379296 -2927.60908846     0.00241645    -1.10903745     0.07175615
-        68  -2927.87418119 -2927.60908846     0.00241645    -1.10903745     0.07175615
-        69  -2927.89451588 -2927.60908846     0.00241645    -1.10903745     0.07175615
-        70  -2927.91602570 -2927.82832077     0.00334657     0.04700770    -0.91589129
-        71  -2927.93874793 -2927.82832077     0.00334657     0.04700770    -0.91589129
-        72  -2927.96195498 -2927.82832077     0.00334657     0.04700770    -0.91589129
-        73  -2927.98521535 -2927.82832077     0.00334657     0.04700770    -0.91589129
-        74  -2928.01060565 -2927.82832077     0.00334657     0.04700770    -0.91589129
-        75  -2928.03584561 -2927.82832077     0.00334657     0.04700770    -0.91589129
-        76  -2928.06090892 -2927.82832077     0.00334657     0.04700770    -0.91589129
-        77  -2928.08509438 -2927.82832077     0.00334657     0.04700770    -0.91589129
-        78  -2928.11095399 -2927.82832077     0.00334657     0.04700770    -0.91589129
-        79  -2928.13711339 -2927.82832077     0.00334657     0.04700770    -0.91589129
-        80  -2928.16413424 -2928.04905744     0.00575008    -0.05409710    -1.19501222
-        81  -2928.19005959 -2928.04905744     0.00575008    -0.05409710    -1.19501222
-        82  -2928.21654649 -2928.04905744     0.00575008    -0.05409710    -1.19501222
-        83  -2928.24249986 -2928.04905744     0.00575008    -0.05409710    -1.19501222
-        84  -2928.26861892 -2928.04905744     0.00575008    -0.05409710    -1.19501222
-        85  -2928.29480718 -2928.04905744     0.00575008    -0.05409710    -1.19501222
-        86  -2928.32144325 -2928.04905744     0.00575008    -0.05409710    -1.19501222
-        87  -2928.34727619 -2928.04905744     0.00575008    -0.05409710    -1.19501222
-        88  -2928.37131285 -2928.04905744     0.00575008    -0.05409710    -1.19501222
-        89  -2928.39531126 -2928.04905744     0.00575008    -0.05409710    -1.19501222
-        90  -2928.41739503 -2928.30652706     0.00595440     0.06693205    -1.24851322
-        91  -2928.43978811 -2928.30652706     0.00595440     0.06693205    -1.24851322
-        92  -2928.46316822 -2928.30652706     0.00595440     0.06693205    -1.24851322
-        93  -2928.48654219 -2928.30652706     0.00595440     0.06693205    -1.24851322
-        94  -2928.51132482 -2928.30652706     0.00595440     0.06693205    -1.24851322
-        95  -2928.53938009 -2928.30652706     0.00595440     0.06693205    -1.24851322
-        96  -2928.56852408 -2928.30652706     0.00595440     0.06693205    -1.24851322
-        97  -2928.59814410 -2928.30652706     0.00595440     0.06693205    -1.24851322
-        98  -2928.62787940 -2928.30652706     0.00595440     0.06693205    -1.24851322
-        99  -2928.65853178 -2928.30652706     0.00595440     0.06693205    -1.24851322
-       100  -2928.68735978 -2928.55806426     0.00711607    -0.13829819    -1.25519738
-Loop time of 0.327437 on 4 procs for 100 steps with 864 atoms
-
-Performance: 52.774 ns/day, 0.455 hours/ns, 305.402 timesteps/s, 263.868 katom-step/s
-91.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.27213    | 0.27259    | 0.27312    |   0.1 | 83.25
-Neigh   | 0.00096945 | 0.0015991  | 0.0022533  |   1.5 |  0.49
-Comm    | 0.026726   | 0.027088   | 0.027516   |   0.2 |  8.27
-Output  | 0.0029839  | 0.0048706  | 0.0097487  |   4.0 |  1.49
-Modify  | 0.012374   | 0.016834   | 0.018623   |   2.0 |  5.14
-Other   |            | 0.004455   |            |       |  1.36
-
-Nlocal:            216 ave         224 max         204 min
-Histogram: 1 0 0 0 0 0 0 2 0 1
-Nghost:           2147 ave        2159 max        2139 min
-Histogram: 1 0 0 2 0 0 0 0 0 1
-Neighs:        24185.8 ave       26045 max       21309 min
-Histogram: 1 0 0 0 0 1 0 0 0 2
-
-Total # of neighbors = 96743
-Ave neighs/atom = 111.97106
-Neighbor list builds = 1
-Dangerous builds = 0
-
-Total wall time: 0:00:00

examples/PACKAGES/reaction/tiny_nylon_json/in.tiny_nylon.stabilized

@@ -1,61 +0,0 @@
-# two monomer nylon example
-# reaction produces a condensed water molecule
-
-units real
-
-boundary p p p
-
-atom_style full
-
-kspace_style pppm 1.0e-4
-
-pair_style lj/class2/coul/long 8.5
-
-angle_style class2
-
-bond_style class2
-
-dihedral_style class2
-
-improper_style class2
-
-special_bonds lj/coul 0 0 1
-pair_modify tail yes mix sixthpower
-
-read_data tiny_nylon.data &
-  extra/bond/per/atom 5  &
-  extra/angle/per/atom 15 &
-  extra/dihedral/per/atom 15 &
-  extra/improper/per/atom 25 &
-  extra/special/per/atom 25
-
-velocity all create 300.0 4928459 dist gaussian
-
-molecule mol1 rxn1_stp1_unreacted.json
-molecule mol2 rxn1_stp1_reacted.json
-molecule mol3 rxn1_stp2_unreacted.json
-molecule mol4 rxn1_stp2_reacted.json
-
-thermo 50
-
-# dump 1 all xyz 1 test_vis.xyz
-# dump_modify 1 types labels
-
-fix myrxns all bond/react stabilization yes statted_grp .03 &
-  react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
-  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
-
-fix 1 statted_grp_REACT nvt temp 300 300 100
-
-# optionally, you can customize behavior of reacting atoms,
-# by using the internally-created 'bond_react_MASTER_group', like so:
-fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
-
-thermo_style custom step temp press density f_myrxns[*]
-
-# restart 100 restart1 restart2
-
-run 10000
-
-# write_restart restart_longrun
-# write_data restart_longrun.data

examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.1

@@ -1,444 +0,0 @@
-LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-583-g5868aa095d-modified)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
-  using 1 OpenMP thread(s) per MPI task
-# two monomer nylon example
-# reaction produces a condensed water molecule
-
-units real
-
-boundary p p p
-
-atom_style full
-
-kspace_style pppm 1.0e-4
-
-pair_style lj/class2/coul/long 8.5
-
-angle_style class2
-
-bond_style class2
-
-dihedral_style class2
-
-improper_style class2
-
-special_bonds lj/coul 0 0 1
-pair_modify tail yes mix sixthpower
-
-read_data tiny_nylon.data   extra/bond/per/atom 5    extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
-Reading data file ...
-  orthogonal box = (-25 -25 -25) to (25 25 25)
-  1 by 1 by 1 MPI processor grid
-  reading atom labelmap ...
-  reading bond labelmap ...
-  reading angle labelmap ...
-  reading dihedral labelmap ...
-  reading improper labelmap ...
-  reading atoms ...
-  44 atoms
-  reading velocities ...
-  44 velocities
-  scanning bonds ...
-  9 = max bonds/atom
-  scanning angles ...
-  21 = max angles/atom
-  scanning dihedrals ...
-  29 = max dihedrals/atom
-  scanning impropers ...
-  29 = max impropers/atom
-  orthogonal box = (-25 -25 -25) to (25 25 25)
-  1 by 1 by 1 MPI processor grid
-  reading bonds ...
-  42 bonds
-  reading angles ...
-  74 angles
-  reading dihedrals ...
-  100 dihedrals
-  reading impropers ...
-  16 impropers
-Finding 1-2 1-3 1-4 neighbors ...
-  special bond factors lj:    0        0        1       
-  special bond factors coul:  0        0        1       
-     4 = max # of 1-2 neighbors
-     6 = max # of 1-3 neighbors
-    35 = max # of special neighbors
-  special bonds CPU = 0.000 seconds
-  read_data CPU = 0.005 seconds
-
-velocity all create 300.0 4928459 dist gaussian
-
-molecule mol1 rxn1_stp1_unreacted.json
-Read molecule template mol1:
-(no title)
-  1 molecules
-  0 fragments
-  18 atoms with max type 0
-  16 bonds with max type 8
-  25 angles with max type 25
-  23 dihedrals with max type 33
-  2 impropers with max type 3
-molecule mol2 rxn1_stp1_reacted.json
-Read molecule template mol2:
-(no title)
-  1 molecules
-  0 fragments
-  18 atoms with max type 0
-  17 bonds with max type 11
-  31 angles with max type 24
-  39 dihedrals with max type 30
-  0 impropers with max type 0
-molecule mol3 rxn1_stp2_unreacted.json
-Read molecule template mol3:
-(no title)
-  1 molecules
-  0 fragments
-  15 atoms with max type 0
-  14 bonds with max type 11
-  25 angles with max type 24
-  30 dihedrals with max type 30
-  0 impropers with max type 0
-molecule mol4 rxn1_stp2_reacted.json
-Read molecule template mol4:
-(no title)
-  1 molecules
-  0 fragments
-  15 atoms with max type 0
-  13 bonds with max type 13
-  19 angles with max type 26
-  16 dihedrals with max type 29
-  2 impropers with max type 5
-
-thermo 50
-
-# dump 1 all xyz 1 test_vis.xyz
-# dump_modify 1 types labels
-
-fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
-WARNING: Fix bond/react: Atom affected by reaction rxn1 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
-WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
-dynamic group bond_react_MASTER_group defined
-dynamic group statted_grp_REACT defined
-
-fix 1 statted_grp_REACT nvt temp 300 300 100
-
-# optionally, you can customize behavior of reacting atoms,
-# by using the internally-created 'bond_react_MASTER_group', like so:
-fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
-
-thermo_style custom step temp press density f_myrxns[*]
-
-# restart 100 restart1 restart2
-
-run 10000
-
-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
-
-Your simulation uses code contributions which should be cited:
-
-- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
-
-@Article{Gissinger24,
- author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
- title = {Type Label Framework for Bonded Force Fields in LAMMPS},
- journal = {J. Phys. Chem. B},
- year =    2024,
- volume =  128,
- number =  13,
- pages =   {3282--3297}
-}
-
-- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012, doi:10.1016/j.cpc.2024.109287
-
-@Article{Gissinger17,
- author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
- title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
- journal = {Polymer},
- year =    2017,
- volume =  128,
- pages =   {211--217}
-}
-
-@Article{Gissinger20,
- author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
- title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
- journal = {Macromolecules},
- year =    2020,
- volume =  53,
- number =  22,
- pages =   {9953--9961}
-}
-
-@Article{Gissinger24,
- author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
- title = {Molecular Modeling of Reactive Systems with REACTER},
- journal = {Computer Physics Communications},
- year =    2024,
- volume =  304,
- number =  109287
-}
-
-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
-
-PPPM initialization ...
-  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
-  G vector (1/distance) = 0.23408048
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.018627396
-  estimated relative force accuracy = 5.6095851e-05
-  using double precision FFTW3
-  3d grid and FFT values/proc = 8000 3375
-Generated 55 of 55 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 10.5
-  ghost atom cutoff = 10.5
-  binsize = 5.25, bins = 10 10 10
-  2 neighbor lists, perpetual/occasional/extra = 1 1 0
-  (1) pair lj/class2/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d
-      bin: standard
-  (2) fix bond/react, occasional, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 34 | 34 | 34 Mbytes
-   Step          Temp          Press         Density      f_myrxns[1]    f_myrxns[2]  
-         0   300            357.25588      0.0034851739   0              0            
-        50   328.952       -39.291672      0.0034851739   1              0            
-       100   311.59495      29.741131      0.0034851739   1              1            
-       150   325.04965     -19.624049      0.0034851739   1              1            
-       200   313.15254      15.730975      0.0034851739   1              1            
-       250   307.88805     -22.944869      0.0034851739   1              1            
-       300   287.9343       6.7916738      0.0034851739   1              1            
-       350   314.40601      12.913246      0.0034851739   1              1            
-       400   304.58587      6.9804459      0.0034851739   1              1            
-       450   300.97668      14.68689       0.0034851739   1              1            
-       500   345.19498     -29.961085      0.0034851739   1              1            
-       550   229.37329      12.88087       0.0034851739   1              1            
-       600   239.75504     -3.575567       0.0034851739   1              1            
-       650   257.58951     -5.0844118      0.0034851739   1              1            
-       700   249.84121      22.825491      0.0034851739   1              1            
-       750   287.62022      28.059197      0.0034851739   1              1            
-       800   352.31339     -50.233738      0.0034851739   1              1            
-       850   316.12821      22.493396      0.0034851739   1              1            
-       900   283.85252      26.129698      0.0034851739   1              1            
-       950   290.30591     -25.743121      0.0034851739   1              1            
-      1000   346.57856     -2.1188627      0.0034851739   1              1            
-      1050   251.23391      20.636107      0.0034851739   1              1            
-      1100   267.48303     -15.912571      0.0034851739   1              1            
-      1150   282.66256      14.019753      0.0034851739   1              1            
-      1200   227.56518     -27.076623      0.0034851739   1              1            
-      1250   232.7204      -1.0387593      0.0034851739   1              1            
-      1300   277.28783      32.449571      0.0034851739   1              1            
-      1350   308.5732      -11.129035      0.0034851739   1              1            
-      1400   264.96641     -20.93416       0.0034851739   1              1            
-      1450   262.83931      30.82366       0.0034851739   1              1            
-      1500   276.23182     -24.480049      0.0034851739   1              1            
-      1550   319.00599     -9.8372065      0.0034851739   1              1            
-      1600   316.48228     -15.940319      0.0034851739   1              1            
-      1650   277.213        1.3856424      0.0034851739   1              1            
-      1700   302.34736     -27.623644      0.0034851739   1              1            
-      1750   312.06738     -52.786773      0.0034851739   1              1            
-      1800   232.82457     -8.2208725      0.0034851739   1              1            
-      1850   219.66312      0.0019676295   0.0034851739   1              1            
-      1900   245.49515     -24.208901      0.0034851739   1              1            
-      1950   262.40648     -1.8634047      0.0034851739   1              1            
-      2000   307.5184       10.588572      0.0034851739   1              1            
-      2050   316.54878      8.3925575      0.0034851739   1              1            
-      2100   318.99324      29.042199      0.0034851739   1              1            
-      2150   352.69886      18.443891      0.0034851739   1              1            
-      2200   326.32556     -38.670826      0.0034851739   1              1            
-      2250   333.73083      15.388091      0.0034851739   1              1            
-      2300   258.51644     -42.524581      0.0034851739   1              1            
-      2350   259.55019     -23.484535      0.0034851739   1              1            
-      2400   289.75114      28.367986      0.0034851739   1              1            
-      2450   312.34376      10.345659      0.0034851739   1              1            
-      2500   298.65847     -14.077573      0.0034851739   1              1            
-      2550   237.48617     -55.545493      0.0034851739   1              1            
-      2600   266.79718     -17.165884      0.0034851739   1              1            
-      2650   297.32794     -30.336059      0.0034851739   1              1            
-      2700   258.77594     -1.3622741      0.0034851739   1              1            
-      2750   240.05564     -0.4418629      0.0034851739   1              1            
-      2800   189.88737     -13.20747       0.0034851739   1              1            
-      2850   260.84014     -18.597276      0.0034851739   1              1            
-      2900   299.99473     -7.3249394      0.0034851739   1              1            
-      2950   377.90497      18.041664      0.0034851739   1              1            
-      3000   263.92156     -54.260856      0.0034851739   1              1            
-      3050   273.64003      26.973976      0.0034851739   1              1            
-      3100   276.52232     -3.8583179      0.0034851739   1              1            
-      3150   351.27802      84.899229      0.0034851739   1              1            
-      3200   327.48822     -10.339189      0.0034851739   1              1            
-      3250   356.11987      16.719201      0.0034851739   1              1            
-      3300   263.01966     -18.033913      0.0034851739   1              1            
-      3350   285.41196     -24.466282      0.0034851739   1              1            
-      3400   233.65271     -39.293739      0.0034851739   1              1            
-      3450   276.32895      44.300639      0.0034851739   1              1            
-      3500   300.42687      28.489275      0.0034851739   1              1            
-      3550   254.03142     -24.335427      0.0034851739   1              1            
-      3600   304.6963       4.5827938      0.0034851739   1              1            
-      3650   321.1785      -15.477109      0.0034851739   1              1            
-      3700   256.00258      25.354176      0.0034851739   1              1            
-      3750   356.60667     -5.4004451      0.0034851739   1              1            
-      3800   361.31092     -1.481153       0.0034851739   1              1            
-      3850   253.80196     -1.2120222      0.0034851739   1              1            
-      3900   258.01895      19.280499      0.0034851739   1              1            
-      3950   261.55352     -47.57161       0.0034851739   1              1            
-      4000   254.54757     -8.6460339      0.0034851739   1              1            
-      4050   301.56201      22.484551      0.0034851739   1              1            
-      4100   304.73035     -31.321217      0.0034851739   1              1            
-      4150   307.14343      0.5455717      0.0034851739   1              1            
-      4200   291.05765      51.79974       0.0034851739   1              1            
-      4250   333.73864     -24.668278      0.0034851739   1              1            
-      4300   370.55562     -11.922425      0.0034851739   1              1            
-      4350   408.03441      8.5963114      0.0034851739   1              1            
-      4400   329.13138     -25.679871      0.0034851739   1              1            
-      4450   366.98033      26.287047      0.0034851739   1              1            
-      4500   311.80954      31.766893      0.0034851739   1              1            
-      4550   292.28765      13.064974      0.0034851739   1              1            
-      4600   320.72746     -49.078838      0.0034851739   1              1            
-      4650   271.7173      -3.6846681      0.0034851739   1              1            
-      4700   305.69502      37.947369      0.0034851739   1              1            
-      4750   304.57521      52.411498      0.0034851739   1              1            
-      4800   299.22173      12.555443      0.0034851739   1              1            
-      4850   317.1756      -14.332118      0.0034851739   1              1            
-      4900   330.62798      23.762097      0.0034851739   1              1            
-      4950   342.34292     -21.428049      0.0034851739   1              1            
-      5000   415.76656      10.136854      0.0034851739   1              1            
-      5050   381.90086      18.17029       0.0034851739   1              1            
-      5100   380.63709      28.042746      0.0034851739   1              1            
-      5150   321.578        31.648896      0.0034851739   1              1            
-      5200   301.22258     -29.246031      0.0034851739   1              1            
-      5250   277.39891     -33.660526      0.0034851739   1              1            
-      5300   259.34417     -47.78529       0.0034851739   1              1            
-      5350   254.36079      10.616064      0.0034851739   1              1            
-      5400   242.39213      29.468553      0.0034851739   1              1            
-      5450   273.79403     -21.736668      0.0034851739   1              1            
-      5500   367.30713     -6.0185517      0.0034851739   1              1            
-      5550   309.52317      20.860119      0.0034851739   1              1            
-      5600   316.82746     -10.339826      0.0034851739   1              1            
-      5650   248.8707       33.659016      0.0034851739   1              1            
-      5700   314.30152      19.05817       0.0034851739   1              1            
-      5750   307.09966      14.458312      0.0034851739   1              1            
-      5800   313.07936      15.825371      0.0034851739   1              1            
-      5850   255.76382      23.890796      0.0034851739   1              1            
-      5900   274.57947     -0.19520339     0.0034851739   1              1            
-      5950   286.72486     -0.92397306     0.0034851739   1              1            
-      6000   304.60873     -4.3983652      0.0034851739   1              1            
-      6050   271.84784     -60.940602      0.0034851739   1              1            
-      6100   283.48258     -8.2903551      0.0034851739   1              1            
-      6150   336.07933     -8.2576526      0.0034851739   1              1            
-      6200   363.09919     -17.309847      0.0034851739   1              1            
-      6250   305.63822      14.475989      0.0034851739   1              1            
-      6300   274.59195      49.13711       0.0034851739   1              1            
-      6350   302.91015     -21.034604      0.0034851739   1              1            
-      6400   293.87945      0.74647589     0.0034851739   1              1            
-      6450   320.03843      47.624624      0.0034851739   1              1            
-      6500   329.4551      -52.788127      0.0034851739   1              1            
-      6550   320.74765      7.9598838      0.0034851739   1              1            
-      6600   290.63144     -19.66089       0.0034851739   1              1            
-      6650   266.9576       18.962642      0.0034851739   1              1            
-      6700   274.61389     -9.823603       0.0034851739   1              1            
-      6750   210.31417     -4.5767817      0.0034851739   1              1            
-      6800   258.23732      44.233497      0.0034851739   1              1            
-      6850   269.33119     -41.097429      0.0034851739   1              1            
-      6900   318.88077     -21.601871      0.0034851739   1              1            
-      6950   333.85796      26.067522      0.0034851739   1              1            
-      7000   320.59631     -44.226656      0.0034851739   1              1            
-      7050   348.15593      56.564077      0.0034851739   1              1            
-      7100   291.30894      7.6597589      0.0034851739   1              1            
-      7150   261.87574     -1.926724       0.0034851739   1              1            
-      7200   318.17418      61.577301      0.0034851739   1              1            
-      7250   269.73912     -41.921242      0.0034851739   1              1            
-      7300   235.40776     -7.8606915      0.0034851739   1              1            
-      7350   344.03017      73.910798      0.0034851739   1              1            
-      7400   335.03212      13.288114      0.0034851739   1              1            
-      7450   350.0822      -22.899498      0.0034851739   1              1            
-      7500   360.69025     -78.556242      0.0034851739   1              1            
-      7550   316.85895     -26.533434      0.0034851739   1              1            
-      7600   271.65568      32.425371      0.0034851739   1              1            
-      7650   264.7899      -40.230568      0.0034851739   1              1            
-      7700   281.36612      8.9888402      0.0034851739   1              1            
-      7750   276.96176      1.8256977      0.0034851739   1              1            
-      7800   330.1516      -19.751957      0.0034851739   1              1            
-      7850   325.80791     -12.52799       0.0034851739   1              1            
-      7900   322.07086      35.21732       0.0034851739   1              1            
-      7950   310.09493     -37.779071      0.0034851739   1              1            
-      8000   309.87152      40.561377      0.0034851739   1              1            
-      8050   252.91862     -27.545616      0.0034851739   1              1            
-      8100   308.23471     -25.313089      0.0034851739   1              1            
-      8150   278.69561      19.299388      0.0034851739   1              1            
-      8200   270.81879      33.341696      0.0034851739   1              1            
-      8250   312.58182      19.404863      0.0034851739   1              1            
-      8300   302.20303      19.388391      0.0034851739   1              1            
-      8350   299.55144     -12.952851      0.0034851739   1              1            
-      8400   330.13129     -34.998178      0.0034851739   1              1            
-      8450   281.66968      24.865214      0.0034851739   1              1            
-      8500   262.4416       1.0196786      0.0034851739   1              1            
-      8550   268.47784      44.761905      0.0034851739   1              1            
-      8600   274.80898      8.6257741      0.0034851739   1              1            
-      8650   264.82423     -3.9236534      0.0034851739   1              1            
-      8700   268.88205      3.7102664      0.0034851739   1              1            
-      8750   315.78315     -44.215318      0.0034851739   1              1            
-      8800   280.19362     -4.2172962      0.0034851739   1              1            
-      8850   331.88665      58.274571      0.0034851739   1              1            
-      8900   314.70472      36.746006      0.0034851739   1              1            
-      8950   395.82228      53.308443      0.0034851739   1              1            
-      9000   351.95636      29.133084      0.0034851739   1              1            
-      9050   369.74695     -37.487774      0.0034851739   1              1            
-      9100   259.4453      -2.1826545      0.0034851739   1              1            
-      9150   294.9952      -44.357151      0.0034851739   1              1            
-      9200   273.94092      12.07438       0.0034851739   1              1            
-      9250   257.18809     -29.792606      0.0034851739   1              1            
-      9300   269.54343     -19.617554      0.0034851739   1              1            
-      9350   301.09849     -26.979046      0.0034851739   1              1            
-      9400   316.93675     -46.890327      0.0034851739   1              1            
-      9450   304.52185     -8.8525101      0.0034851739   1              1            
-      9500   371.73494      11.979311      0.0034851739   1              1            
-      9550   291.23417      8.1900851      0.0034851739   1              1            
-      9600   359.20912      38.693544      0.0034851739   1              1            
-      9650   321.73443      33.448943      0.0034851739   1              1            
-      9700   362.4237       36.54429       0.0034851739   1              1            
-      9750   296.19875     -11.425255      0.0034851739   1              1            
-      9800   329.9426       16.039783      0.0034851739   1              1            
-      9850   296.79216      40.176303      0.0034851739   1              1            
-      9900   345.63868      43.479483      0.0034851739   1              1            
-      9950   282.27772     -49.08352       0.0034851739   1              1            
-     10000   286.24393     -12.060687      0.0034851739   1              1            
-Loop time of 1.29509 on 1 procs for 10000 steps with 44 atoms
-
-Performance: 667.133 ns/day, 0.036 hours/ns, 7721.451 timesteps/s, 339.744 katom-step/s
-99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.065326   | 0.065326   | 0.065326   |   0.0 |  5.04
-Bond    | 0.23111    | 0.23111    | 0.23111    |   0.0 | 17.84
-Kspace  | 0.94073    | 0.94073    | 0.94073    |   0.0 | 72.64
-Neigh   | 0.0032599  | 0.0032599  | 0.0032599  |   0.0 |  0.25
-Comm    | 0.0013719  | 0.0013719  | 0.0013719  |   0.0 |  0.11
-Output  | 0.00093869 | 0.00093869 | 0.00093869 |   0.0 |  0.07
-Modify  | 0.049692   | 0.049692   | 0.049692   |   0.0 |  3.84
-Other   |            | 0.002667   |            |       |  0.21
-
-Nlocal:             44 ave          44 max          44 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:             14 ave          14 max          14 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:            869 ave         869 max         869 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 869
-Ave neighs/atom = 19.75
-Ave special neighs/atom = 6.4090909
-Neighbor list builds = 209
-Dangerous builds = 0
-
-# write_restart restart_longrun
-# write_data restart_longrun.data
-Total wall time: 0:00:01

examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.4

@@ -1,444 +0,0 @@
-LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-583-g5868aa095d-modified)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
-  using 1 OpenMP thread(s) per MPI task
-# two monomer nylon example
-# reaction produces a condensed water molecule
-
-units real
-
-boundary p p p
-
-atom_style full
-
-kspace_style pppm 1.0e-4
-
-pair_style lj/class2/coul/long 8.5
-
-angle_style class2
-
-bond_style class2
-
-dihedral_style class2
-
-improper_style class2
-
-special_bonds lj/coul 0 0 1
-pair_modify tail yes mix sixthpower
-
-read_data tiny_nylon.data   extra/bond/per/atom 5    extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
-Reading data file ...
-  orthogonal box = (-25 -25 -25) to (25 25 25)
-  1 by 2 by 2 MPI processor grid
-  reading atom labelmap ...
-  reading bond labelmap ...
-  reading angle labelmap ...
-  reading dihedral labelmap ...
-  reading improper labelmap ...
-  reading atoms ...
-  44 atoms
-  reading velocities ...
-  44 velocities
-  scanning bonds ...
-  9 = max bonds/atom
-  scanning angles ...
-  21 = max angles/atom
-  scanning dihedrals ...
-  29 = max dihedrals/atom
-  scanning impropers ...
-  29 = max impropers/atom
-  orthogonal box = (-25 -25 -25) to (25 25 25)
-  1 by 2 by 2 MPI processor grid
-  reading bonds ...
-  42 bonds
-  reading angles ...
-  74 angles
-  reading dihedrals ...
-  100 dihedrals
-  reading impropers ...
-  16 impropers
-Finding 1-2 1-3 1-4 neighbors ...
-  special bond factors lj:    0        0        1       
-  special bond factors coul:  0        0        1       
-     4 = max # of 1-2 neighbors
-     6 = max # of 1-3 neighbors
-    35 = max # of special neighbors
-  special bonds CPU = 0.000 seconds
-  read_data CPU = 0.006 seconds
-
-velocity all create 300.0 4928459 dist gaussian
-
-molecule mol1 rxn1_stp1_unreacted.json
-Read molecule template mol1:
-(no title)
-  1 molecules
-  0 fragments
-  18 atoms with max type 0
-  16 bonds with max type 8
-  25 angles with max type 25
-  23 dihedrals with max type 33
-  2 impropers with max type 3
-molecule mol2 rxn1_stp1_reacted.json
-Read molecule template mol2:
-(no title)
-  1 molecules
-  0 fragments
-  18 atoms with max type 0
-  17 bonds with max type 11
-  31 angles with max type 24
-  39 dihedrals with max type 30
-  0 impropers with max type 0
-molecule mol3 rxn1_stp2_unreacted.json
-Read molecule template mol3:
-(no title)
-  1 molecules
-  0 fragments
-  15 atoms with max type 0
-  14 bonds with max type 11
-  25 angles with max type 24
-  30 dihedrals with max type 30
-  0 impropers with max type 0
-molecule mol4 rxn1_stp2_reacted.json
-Read molecule template mol4:
-(no title)
-  1 molecules
-  0 fragments
-  15 atoms with max type 0
-  13 bonds with max type 13
-  19 angles with max type 26
-  16 dihedrals with max type 29
-  2 impropers with max type 5
-
-thermo 50
-
-# dump 1 all xyz 1 test_vis.xyz
-# dump_modify 1 types labels
-
-fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
-WARNING: Fix bond/react: Atom affected by reaction rxn1 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
-WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
-dynamic group bond_react_MASTER_group defined
-dynamic group statted_grp_REACT defined
-
-fix 1 statted_grp_REACT nvt temp 300 300 100
-
-# optionally, you can customize behavior of reacting atoms,
-# by using the internally-created 'bond_react_MASTER_group', like so:
-fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
-
-thermo_style custom step temp press density f_myrxns[*]
-
-# restart 100 restart1 restart2
-
-run 10000
-
-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
-
-Your simulation uses code contributions which should be cited:
-
-- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
-
-@Article{Gissinger24,
- author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
- title = {Type Label Framework for Bonded Force Fields in LAMMPS},
- journal = {J. Phys. Chem. B},
- year =    2024,
- volume =  128,
- number =  13,
- pages =   {3282--3297}
-}
-
-- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012, doi:10.1016/j.cpc.2024.109287
-
-@Article{Gissinger17,
- author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
- title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
- journal = {Polymer},
- year =    2017,
- volume =  128,
- pages =   {211--217}
-}
-
-@Article{Gissinger20,
- author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
- title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
- journal = {Macromolecules},
- year =    2020,
- volume =  53,
- number =  22,
- pages =   {9953--9961}
-}
-
-@Article{Gissinger24,
- author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
- title = {Molecular Modeling of Reactive Systems with REACTER},
- journal = {Computer Physics Communications},
- year =    2024,
- volume =  304,
- number =  109287
-}
-
-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
-
-PPPM initialization ...
-  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
-  G vector (1/distance) = 0.23408048
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.018627396
-  estimated relative force accuracy = 5.6095851e-05
-  using double precision FFTW3
-  3d grid and FFT values/proc = 3380 960
-Generated 55 of 55 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 10.5
-  ghost atom cutoff = 10.5
-  binsize = 5.25, bins = 10 10 10
-  2 neighbor lists, perpetual/occasional/extra = 1 1 0
-  (1) pair lj/class2/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d
-      bin: standard
-  (2) fix bond/react, occasional, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 33.49 | 33.72 | 34.28 Mbytes
-   Step          Temp          Press         Density      f_myrxns[1]    f_myrxns[2]  
-         0   300            357.25588      0.0034851739   0              0            
-        50   328.952       -39.291672      0.0034851739   1              0            
-       100   311.59495      29.741131      0.0034851739   1              1            
-       150   325.04965     -19.624049      0.0034851739   1              1            
-       200   313.15254      15.730975      0.0034851739   1              1            
-       250   307.88805     -22.944869      0.0034851739   1              1            
-       300   287.9343       6.7916738      0.0034851739   1              1            
-       350   314.40601      12.913246      0.0034851739   1              1            
-       400   304.58587      6.9804459      0.0034851739   1              1            
-       450   300.97668      14.68689       0.0034851739   1              1            
-       500   345.19498     -29.961085      0.0034851739   1              1            
-       550   229.37329      12.88087       0.0034851739   1              1            
-       600   239.75504     -3.575567       0.0034851739   1              1            
-       650   257.58951     -5.0844118      0.0034851739   1              1            
-       700   249.84121      22.825491      0.0034851739   1              1            
-       750   287.62022      28.059197      0.0034851739   1              1            
-       800   352.31339     -50.233738      0.0034851739   1              1            
-       850   316.12821      22.493396      0.0034851739   1              1            
-       900   283.85252      26.129698      0.0034851739   1              1            
-       950   290.30591     -25.743121      0.0034851739   1              1            
-      1000   346.57856     -2.1188627      0.0034851739   1              1            
-      1050   251.23391      20.636107      0.0034851739   1              1            
-      1100   267.48303     -15.912571      0.0034851739   1              1            
-      1150   282.66256      14.019753      0.0034851739   1              1            
-      1200   227.56518     -27.076623      0.0034851739   1              1            
-      1250   232.7204      -1.0387593      0.0034851739   1              1            
-      1300   277.28783      32.449571      0.0034851739   1              1            
-      1350   308.5732      -11.129035      0.0034851739   1              1            
-      1400   264.96641     -20.93416       0.0034851739   1              1            
-      1450   262.83931      30.82366       0.0034851739   1              1            
-      1500   276.23182     -24.480049      0.0034851739   1              1            
-      1550   319.00599     -9.8372065      0.0034851739   1              1            
-      1600   316.48228     -15.940319      0.0034851739   1              1            
-      1650   277.213        1.3856424      0.0034851739   1              1            
-      1700   302.34736     -27.623644      0.0034851739   1              1            
-      1750   312.06738     -52.786773      0.0034851739   1              1            
-      1800   232.82457     -8.2208725      0.0034851739   1              1            
-      1850   219.66312      0.0019675712   0.0034851739   1              1            
-      1900   245.49515     -24.2089        0.0034851739   1              1            
-      1950   262.40648     -1.8634053      0.0034851739   1              1            
-      2000   307.5184       10.588572      0.0034851739   1              1            
-      2050   316.54878      8.3925573      0.0034851739   1              1            
-      2100   318.99324      29.042199      0.0034851739   1              1            
-      2150   352.69886      18.443891      0.0034851739   1              1            
-      2200   326.32556     -38.670827      0.0034851739   1              1            
-      2250   333.73083      15.388091      0.0034851739   1              1            
-      2300   258.51644     -42.524579      0.0034851739   1              1            
-      2350   259.55019     -23.484534      0.0034851739   1              1            
-      2400   289.75114      28.367991      0.0034851739   1              1            
-      2450   312.34376      10.34566       0.0034851739   1              1            
-      2500   298.65847     -14.077574      0.0034851739   1              1            
-      2550   237.48617     -55.545492      0.0034851739   1              1            
-      2600   266.79719     -17.165888      0.0034851739   1              1            
-      2650   297.32793     -30.336065      0.0034851739   1              1            
-      2700   258.77594     -1.3622773      0.0034851739   1              1            
-      2750   240.05564     -0.44186476     0.0034851739   1              1            
-      2800   189.88736     -13.20747       0.0034851739   1              1            
-      2850   260.84014     -18.597268      0.0034851739   1              1            
-      2900   299.99469     -7.3249657      0.0034851739   1              1            
-      2950   377.90515      18.041562      0.0034851739   1              1            
-      3000   263.92164     -54.260872      0.0034851739   1              1            
-      3050   273.63965      26.974167      0.0034851739   1              1            
-      3100   276.52188     -3.8587984      0.0034851739   1              1            
-      3150   351.27821      84.898762      0.0034851739   1              1            
-      3200   327.48898     -10.338223      0.0034851739   1              1            
-      3250   356.1212       16.719521      0.0034851739   1              1            
-      3300   263.02135     -18.034405      0.0034851739   1              1            
-      3350   285.4132      -24.466598      0.0034851739   1              1            
-      3400   233.65385     -39.293822      0.0034851739   1              1            
-      3450   276.32817      44.300742      0.0034851739   1              1            
-      3500   300.43096      28.490491      0.0034851739   1              1            
-      3550   254.03694     -24.336803      0.0034851739   1              1            
-      3600   304.68561      4.5774591      0.0034851739   1              1            
-      3650   321.19694     -15.472971      0.0034851739   1              1            
-      3700   256.01801      25.355422      0.0034851739   1              1            
-      3750   356.6048      -5.4033701      0.0034851739   1              1            
-      3800   361.31685     -1.4920086      0.0034851739   1              1            
-      3850   253.81335     -1.20491        0.0034851739   1              1            
-      3900   257.99176      19.272863      0.0034851739   1              1            
-      3950   261.56599     -47.578625      0.0034851739   1              1            
-      4000   254.55501     -8.6462427      0.0034851739   1              1            
-      4050   301.57465      22.466646      0.0034851739   1              1            
-      4100   304.71812     -31.337506      0.0034851739   1              1            
-      4150   307.05688      0.54710967     0.0034851739   1              1            
-      4200   291.11678      51.789059      0.0034851739   1              1            
-      4250   333.71702     -24.64525       0.0034851739   1              1            
-      4300   370.53725     -11.852814      0.0034851739   1              1            
-      4350   407.98596      8.5128018      0.0034851739   1              1            
-      4400   329.43106     -25.637208      0.0034851739   1              1            
-      4450   366.91557      26.250029      0.0034851739   1              1            
-      4500   311.63134      31.61568       0.0034851739   1              1            
-      4550   292.18008      13.020734      0.0034851739   1              1            
-      4600   320.76549     -49.324846      0.0034851739   1              1            
-      4650   271.72115     -3.6666938      0.0034851739   1              1            
-      4700   305.52974      38.114013      0.0034851739   1              1            
-      4750   304.37057      52.050863      0.0034851739   1              1            
-      4800   300.50548      13.158616      0.0034851739   1              1            
-      4850   317.66606     -14.951608      0.0034851739   1              1            
-      4900   331.39591      23.823575      0.0034851739   1              1            
-      4950   340.899       -19.557136      0.0034851739   1              1            
-      5000   414.45112      8.7124515      0.0034851739   1              1            
-      5050   382.95479      18.555744      0.0034851739   1              1            
-      5100   381.26344      22.674486      0.0034851739   1              1            
-      5150   309.88477      36.184971      0.0034851739   1              1            
-      5200   312.4976      -31.403643      0.0034851739   1              1            
-      5250   285.1896      -36.180241      0.0034851739   1              1            
-      5300   249.68604     -55.078779      0.0034851739   1              1            
-      5350   251.76542      12.156887      0.0034851739   1              1            
-      5400   278.40908      15.846527      0.0034851739   1              1            
-      5450   281.22116     -12.005198      0.0034851739   1              1            
-      5500   362.38064     -14.608206      0.0034851739   1              1            
-      5550   287.39255      38.446058      0.0034851739   1              1            
-      5600   264.87699     -20.21112       0.0034851739   1              1            
-      5650   300.31424     -15.899086      0.0034851739   1              1            
-      5700   318.6444       18.688317      0.0034851739   1              1            
-      5750   321.74224     -7.5355749      0.0034851739   1              1            
-      5800   314.65871      33.512178      0.0034851739   1              1            
-      5850   307.11597     -16.492491      0.0034851739   1              1            
-      5900   259.10441     -49.668159      0.0034851739   1              1            
-      5950   292.09045     -22.04962       0.0034851739   1              1            
-      6000   243.99229     -15.110485      0.0034851739   1              1            
-      6050   276.66494     -21.052012      0.0034851739   1              1            
-      6100   328.39444      64.522811      0.0034851739   1              1            
-      6150   289.49991     -18.518616      0.0034851739   1              1            
-      6200   358.50076     -9.3115021      0.0034851739   1              1            
-      6250   303.15143     -42.618735      0.0034851739   1              1            
-      6300   297.17364      18.116143      0.0034851739   1              1            
-      6350   254.2382       2.4963759      0.0034851739   1              1            
-      6400   227.56255      23.535315      0.0034851739   1              1            
-      6450   280.70805      13.243012      0.0034851739   1              1            
-      6500   251.14485     -18.466759      0.0034851739   1              1            
-      6550   284.32321      9.0351234      0.0034851739   1              1            
-      6600   284.03779     -10.683306      0.0034851739   1              1            
-      6650   315.1569      -39.736019      0.0034851739   1              1            
-      6700   302.50424      5.9013011      0.0034851739   1              1            
-      6750   368.279        44.343503      0.0034851739   1              1            
-      6800   279.67266     -35.967233      0.0034851739   1              1            
-      6850   298.98045      3.0539699      0.0034851739   1              1            
-      6900   236.94852      0.55971293     0.0034851739   1              1            
-      6950   303.38382     -9.1880246      0.0034851739   1              1            
-      7000   264.56096      3.904024       0.0034851739   1              1            
-      7050   272.26968     -44.608801      0.0034851739   1              1            
-      7100   235.38132      13.141913      0.0034851739   1              1            
-      7150   272.0985       26.601686      0.0034851739   1              1            
-      7200   314.41177     -7.6236617      0.0034851739   1              1            
-      7250   313.29915     -45.214663      0.0034851739   1              1            
-      7300   309.20548     -11.691744      0.0034851739   1              1            
-      7350   342.22769      18.805899      0.0034851739   1              1            
-      7400   301.02701      32.830071      0.0034851739   1              1            
-      7450   318.19524      48.620851      0.0034851739   1              1            
-      7500   290.00663     -9.1444424      0.0034851739   1              1            
-      7550   238.07666      32.654941      0.0034851739   1              1            
-      7600   275.95317     -23.982336      0.0034851739   1              1            
-      7650   274.54472     -29.183684      0.0034851739   1              1            
-      7700   307.25317      11.981268      0.0034851739   1              1            
-      7750   299.40271     -19.390542      0.0034851739   1              1            
-      7800   314.18813     -6.0794802      0.0034851739   1              1            
-      7850   271.14043      40.491364      0.0034851739   1              1            
-      7900   266.43792      37.250574      0.0034851739   1              1            
-      7950   330.21996      31.783381      0.0034851739   1              1            
-      8000   313.80294      44.878972      0.0034851739   1              1            
-      8050   331.1094       1.9597746      0.0034851739   1              1            
-      8100   267.80448      26.159121      0.0034851739   1              1            
-      8150   267.17305      16.135234      0.0034851739   1              1            
-      8200   290.248       -13.058622      0.0034851739   1              1            
-      8250   231.77635     -42.850795      0.0034851739   1              1            
-      8300   233.58288      29.137765      0.0034851739   1              1            
-      8350   270.2913      -11.177011      0.0034851739   1              1            
-      8400   254.69873      3.1775639      0.0034851739   1              1            
-      8450   334.88277     -27.336924      0.0034851739   1              1            
-      8500   354.95137     -9.751911       0.0034851739   1              1            
-      8550   327.78998      8.2348621      0.0034851739   1              1            
-      8600   306.15772      1.3756734      0.0034851739   1              1            
-      8650   325.68699      6.5939205      0.0034851739   1              1            
-      8700   302.84804      13.912169      0.0034851739   1              1            
-      8750   299.34988      10.311212      0.0034851739   1              1            
-      8800   258.77684     -8.0783535      0.0034851739   1              1            
-      8850   299.8835      -9.61362        0.0034851739   1              1            
-      8900   350.28205     -34.897861      0.0034851739   1              1            
-      8950   316.90133     -52.845562      0.0034851739   1              1            
-      9000   337.50548      18.172556      0.0034851739   1              1            
-      9050   306.67254      37.062973      0.0034851739   1              1            
-      9100   310.74844      58.178538      0.0034851739   1              1            
-      9150   301.53463      5.9650738      0.0034851739   1              1            
-      9200   284.61384      10.677528      0.0034851739   1              1            
-      9250   247.86475     -15.325203      0.0034851739   1              1            
-      9300   309.74481     -60.070902      0.0034851739   1              1            
-      9350   290.17111      5.6049467      0.0034851739   1              1            
-      9400   268.79925     -9.2423032      0.0034851739   1              1            
-      9450   315.80445      18.124612      0.0034851739   1              1            
-      9500   351.58161     -14.465115      0.0034851739   1              1            
-      9550   344.93028      43.161438      0.0034851739   1              1            
-      9600   265.92273      0.3396608      0.0034851739   1              1            
-      9650   261.1649      -20.46043       0.0034851739   1              1            
-      9700   262.05627      27.187613      0.0034851739   1              1            
-      9750   249.12463      15.911339      0.0034851739   1              1            
-      9800   262.40626     -16.159153      0.0034851739   1              1            
-      9850   267.48677      0.32143902     0.0034851739   1              1            
-      9900   316.15674      40.664589      0.0034851739   1              1            
-      9950   323.94181      20.356291      0.0034851739   1              1            
-     10000   307.90841      4.8392456      0.0034851739   1              1            
-Loop time of 0.937214 on 4 procs for 10000 steps with 44 atoms
-
-Performance: 921.881 ns/day, 0.026 hours/ns, 10669.916 timesteps/s, 469.476 katom-step/s
-96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.00042896 | 0.01827    | 0.04944    |  14.9 |  1.95
-Bond    | 0.00067626 | 0.061292   | 0.18867    |  31.0 |  6.54
-Kspace  | 0.50738    | 0.64527    | 0.7136     |  10.4 | 68.85
-Neigh   | 0.0031476  | 0.0031815  | 0.0032165  |   0.0 |  0.34
-Comm    | 0.01335    | 0.020817   | 0.035424   |   6.1 |  2.22
-Output  | 0.0010449  | 0.0012202  | 0.0016969  |   0.8 |  0.13
-Modify  | 0.16314    | 0.18266    | 0.20201    |   4.3 | 19.49
-Other   |            | 0.004499   |            |       |  0.48
-
-Nlocal:             11 ave          40 max           0 min
-Histogram: 2 1 0 0 0 0 0 0 0 1
-Nghost:             22 ave          40 max           4 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs:          216.5 ave         845 max           0 min
-Histogram: 3 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 866
-Ave neighs/atom = 19.681818
-Ave special neighs/atom = 6.4090909
-Neighbor list builds = 212
-Dangerous builds = 0
-
-# write_restart restart_longrun
-# write_data restart_longrun.data
-Total wall time: 0:00:00

examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_map

@@ -1,35 +0,0 @@
-this is a nominal superimpose file
-
-2 edgeIDs
-18 equivalences
-
-InitiatorIDs
-
-10
-1
-
-EdgeIDs
-
-16
-8
-
-Equivalences
-
-1	1
-2	2
-3	3
-4	4
-5	5
-6	6
-7	7
-8	8
-9	9
-10	10
-11	11
-12	12
-13	13
-14	14
-15	15
-16	16
-17	17
-18	18

examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_reacted.json

@@ -1,177 +0,0 @@
-{
-    "application": "LAMMPS",
-    "format": "molecule",
-    "revision": 1,
-    "schema": "https://download.lammps.org/json/molecule-schema.json",
-    "coords": {
-        "format": ["atom-id", "x", "y", "z"],
-        "data": [
-            [1, -5.522237178, -0.752722499, 1.631158408],
-            [2, -5.170398325, -0.545733378, 0.178129978],
-            [3, -6.469694974, -0.553071841, -0.648889109],
-            [4, -6.052075697, -1.721152483, 1.744647858],
-            [5, -6.183058842, 0.071386755, 1.971497329],
-            [6, -4.489339595, -1.389196844, -0.173156276],
-            [7, -4.637590712, 0.453703382, 0.051251954],
-            [8, -5.618657658, 0.13891881, 4.386106928],
-            [9, -4.669491736, -0.989818781, 3.943591338],
-            [10, -4.270193542, -0.766405234, 2.474102239],
-            [11, -3.348470373, -1.875393291, 2.024289246],
-            [12, -3.569793683, 0.564183226, 2.345995471],
-            [13, -5.201078949, -1.993301389, 4.044218837],
-            [14, -3.736681607, -0.984819193, 4.598304847],
-            [15, -4.255401979, 1.370923174, 2.679069013],
-            [16, -6.136393628, -0.339866195, -2.13677499],
-            [17, -6.996331494, -1.555519161, -0.517408063],
-            [18, -7.153308038, 0.284949373, -0.289930394]
-        ]
-    },
-    "types": {
-        "format": ["atom-id", "type"],
-        "data": [
-            [1, "n"],
-            [2, "c2"],
-            [3, "c2"],
-            [4, "hn"],
-            [5, "hn"],
-            [6, "hc"],
-            [7, "hc"],
-            [8, "c2"],
-            [9, "c2"],
-            [10, "c_1"],
-            [11, "o_1"],
-            [12, "o"],
-            [13, "hc"],
-            [14, "hc"],
-            [15, "ho"],
-            [16, "c2"],
-            [17, "hc"],
-            [18, "hc"]
-        ]
-    },
-    "molecules": {
-        "format": ["atom-id", "molecule-id"],
-        "data": [
-            [1, 1],
-            [2, 1],
-            [3, 1],
-            [4, 1],
-            [5, 1],
-            [6, 1],
-            [7, 1],
-            [8, 1],
-            [9, 1],
-            [10, 1],
-            [11, 1],
-            [12, 1],
-            [13, 1],
-            [14, 1],
-            [15, 1],
-            [16, 1],
-            [17, 1],
-            [18, 1]
-        ]
-    },
-    "bonds": {
-        "format": ["bond-type", "atom1", "atom2"],
-        "data": [
-            ["n-c2", 1, 2],
-            ["n-hn", 1, 4],
-            ["n-hn", 1, 5],
-            ["n-c_1", 1, 10],
-            ["c2-c2", 2, 3],
-            ["c2-hc", 2, 6],
-            ["c2-hc", 2, 7],
-            ["c2-c2", 3, 16],
-            ["c2-hc", 3, 17],
-            [ "c2-hc", 3, 18],
-            [ "c2-c2", 8, 9],
-            [ "c2-c_1", 9, 10],
-            [ "c2-hc", 9, 13],
-            [ "c2-hc", 9, 14],
-            [ "c_1-o_1", 10, 11],
-            [ "c_1-o", 10, 12],
-            [ "o-ho", 12, 15]
-        ]
-    },
-    "angles": {
-        "format": ["angle-type", "atom1", "atom2", "atom3"],
-        "data": [
-            ["c2-n-hn", 2, 1, 4],
-            ["c2-n-hn", 2, 1, 5],
-            ["c2-n-c_1", 2, 1, 10],
-            ["hn-n-hn", 4, 1, 5],
-            ["hn-n-c_1", 4, 1, 10],
-            ["hn-n-c_1", 5, 1, 10],
-            ["n-c2-c2", 1, 2, 3],
-            ["n-c2-hc", 1, 2, 6],
-            ["n-c2-hc", 1, 2, 7],
-            [ "c2-c2-hc", 3, 2, 6],
-            [ "c2-c2-hc", 3, 2, 7],
-            [ "hc-c2-hc", 6, 2, 7],
-            [ "c2-c2-c2", 2, 3, 16],
-            [ "c2-c2-hc", 2, 3, 17],
-            [ "c2-c2-hc", 2, 3, 18],
-            [ "c2-c2-hc", 16, 3, 17],
-            [ "c2-c2-hc", 16, 3, 18],
-            [ "hc-c2-hc", 17, 3, 18],
-            [ "c2-c2-c_1", 8, 9, 10],
-            [ "c2-c2-hc", 8, 9, 13],
-            [ "c2-c2-hc", 8, 9, 14],
-            [ "hc-c2-c_1", 13, 9, 10],
-            [ "hc-c2-c_1", 14, 9, 10],
-            [ "hc-c2-hc", 13, 9, 14],
-            [ "c2-c_1-o_1", 9, 10, 11],
-            [ "c2-c_1-o", 9, 10, 12],
-            [ "n-c_1-c2", 1, 10, 9],
-            [ "o_1-c_1-o", 11, 10, 12],
-            [ "n-c_1-o_1", 1, 10, 11],
-            [ "n-c_1-o", 1, 10, 12],
-            [ "c_1-o-ho", 10, 12, 15]
-        ]
-    },
-    "dihedrals": {
-        "format": ["dihedral-type", "atom1", "atom2", "atom3", "atom4"],
-        "data": [
-            ["hn-n-c2-c2", 4, 1, 2, 3],
-            ["hn-n-c2-hc", 4, 1, 2, 6],
-            ["hn-n-c2-hc", 4, 1, 2, 7],
-            ["hn-n-c2-c2", 5, 1, 2, 3],
-            ["hn-n-c2-hc", 5, 1, 2, 6],
-            ["hn-n-c2-hc", 5, 1, 2, 7],
-            ["c_1-n-c2-c2", 10, 1, 2, 3],
-            ["c_1-n-c2-hc", 10, 1, 2, 6],
-            ["c_1-n-c2-hc", 10, 1, 2, 7],
-            [ "c2-n-c_1-c2", 2, 1, 10, 9],
-            [ "c2-n-c_1-o_1", 2, 1, 10, 11],
-            [ "c2-n-c_1-o", 2, 1, 10, 12],
-            [ "hn-n-c_1-c2", 4, 1, 10, 9],
-            [ "hn-n-c_1-o_1", 4, 1, 10, 11],
-            [ "hn-n-c_1-o", 4, 1, 10, 12],
-            [ "hn-n-c_1-c2", 5, 1, 10, 9],
-            [ "hn-n-c_1-o_1", 5, 1, 10, 11],
-            [ "hn-n-c_1-o", 5, 1, 10, 12],
-            [ "n-c2-c2-c2", 1, 2, 3, 16],
-            [ "n-c2-c2-hc", 1, 2, 3, 17],
-            [ "n-c2-c2-hc", 1, 2, 3, 18],
-            [ "c2-c2-c2-hc", 16, 3, 2, 6],
-            [ "hc-c2-c2-hc", 6, 2, 3, 17],
-            [ "hc-c2-c2-hc", 6, 2, 3, 18],
-            [ "c2-c2-c2-hc", 16, 3, 2, 7],
-            [ "hc-c2-c2-hc", 7, 2, 3, 17],
-            [ "hc-c2-c2-hc", 7, 2, 3, 18],
-            [ "c2-c2-c_1-o_1", 8, 9, 10, 11],
-            [ "c2-c2-c_1-o", 8, 9, 10, 12],
-            [ "c2-c2-c_1-n", 8, 9, 10, 1],
-            [ "hc-c2-c_1-o_1", 13, 9, 10, 11],
-            [ "hc-c2-c_1-o", 13, 9, 10, 12],
-            [ "hc-c2-c_1-n", 13, 9, 10, 1],
-            [ "hc-c2-c_1-o_1", 14, 9, 10, 11],
-            [ "hc-c2-c_1-o", 14, 9, 10, 12],
-            [ "hc-c2-c_1-n", 14, 9, 10, 1],
-            [ "c2-c_1-o-ho", 9, 10, 12, 15],
-            [ "o_1-c_1-o-ho", 11, 10, 12, 15],
-            [ "n-c_1-o-ho", 1, 10, 12, 15]
-        ]
-    }
-}

examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_unreacted.json

@@ -1,184 +0,0 @@
-{
-    "application": "LAMMPS",
-    "format": "molecule",
-    "revision": 1,
-    "schema": "https://download.lammps.org/json/molecule-schema.json",
-    "coords": {
-        "format": ["atom-id", "x", "y", "z"],
-        "data": [
-            [1, -4.922858499, -0.946981747, 1.146055346],
-            [2, -5.047194816, -0.935266843, -0.358172771],
-            [3, -6.526281447, -0.755365854, -0.743523227],
-            [4, -5.282604074, 0.020446894, 1.552710361],
-            [5, -3.860696509, -1.09585019, 1.428304925],
-            [6, -4.662381862, -1.920899862, -0.781524026],
-            [7, -4.43397654, -0.072765142, -0.784070641],
-            [8, -5.506279186, 0.202610302, 4.825815562],
-            [9, -4.449176624, -0.844592213, 4.423366146],
-            [10, -4.103915981, -0.749628655, 2.925195217],
-            [11, -3.376248536, -1.886171498, 2.245643443],
-            [12, -4.49323543, 0.477213651, 2.137199034],
-            [13, -4.849052953, -1.888876753, 4.66399375],
-            [14, -3.49182295, -0.66291331, 5.018510248],
-            [15, -5.020776528, 1.189745133, 2.805427194],
-            [16, -3.964987378, 2.900602044, -1.55134117],
-            [17, -4.460693773, 2.836101897, 0.668881952],
-            [18, -4.828494, 3.219655862, -0.122111278]
-        ]
-    },
-    "types": {
-        "format": ["atom-id", "type"],
-        "data": [
-            [1, "na"],
-            [2, "c2"],
-            [3, "c2"],
-            [4, "hn"],
-            [5, "hn"],
-            [6, "hc"],
-            [7, "hc"],
-            [8, "c2"],
-            [9, "c2"],
-            [10, "c_1"],
-            [11, "o_1"],
-            [12, "o"],
-            [13, "hc"],
-            [14, "hc"],
-            [15, "ho"],
-            [16, "c2"],
-            [17, "hc"],
-            [18, "hc"]
-        ]
-    },
-    "molecules": {
-        "format": ["atom-id", "molecule-id"],
-        "data": [
-            [1, 1],
-            [2, 1],
-            [3, 1],
-            [4, 1],
-            [5, 1],
-            [6, 1],
-            [7, 1],
-            [8, 1],
-            [9, 1],
-            [10, 1],
-            [11, 1],
-            [12, 1],
-            [13, 1],
-            [14, 1],
-            [15, 1],
-            [16, 1],
-            [17, 1],
-            [18, 1]
-        ]
-    },
-    "bonds": {
-        "format": ["bond-type", "atom1", "atom2"],
-        "data": [
-            ["na-c2", 1, 2],
-            ["na-hn", 1, 4],
-            ["na-hn", 1, 5],
-            ["c2-c2", 2, 3],
-            ["c2-hc", 2, 6],
-            ["c2-hc", 2, 7],
-            ["c2-c2", 3, 16],
-            ["c2-hc", 3, 17],
-            ["c2-hc", 3, 18],
-            [ "c2-c2", 8, 9],
-            [ "c2-c_1", 9, 10],
-            [ "c2-hc", 9, 13],
-            [ "c2-hc", 9, 14],
-            [ "c_1-o_1", 10, 11],
-            [ "c_1-o", 10, 12],
-            [ "o-ho", 12, 15]
-        ]
-    },
-    "angles": {
-        "format": ["angle-type", "atom1", "atom2", "atom3"],
-        "data": [
-            ["c2-na-hn", 2, 1, 4],
-            ["c2-na-hn", 2, 1, 5],
-            ["hn-na-hn", 4, 1, 5],
-            ["na-c2-c2", 1, 2, 3],
-            ["na-c2-hc", 1, 2, 6],
-            ["na-c2-hc", 1, 2, 7],
-            ["c2-c2-hc", 3, 2, 6],
-            ["c2-c2-hc", 3, 2, 7],
-            ["hc-c2-hc", 6, 2, 7],
-            [ "c2-c2-c2", 2, 3, 16],
-            [ "c2-c2-hc", 2, 3, 17],
-            [ "c2-c2-hc", 2, 3, 18],
-            [ "c2-c2-hc", 16, 3, 17],
-            [ "c2-c2-hc", 16, 3, 18],
-            [ "hc-c2-hc", 17, 3, 18],
-            [ "c2-c2-c_1", 8, 9, 10],
-            [ "c2-c2-hc", 8, 9, 13],
-            [ "c2-c2-hc", 8, 9, 14],
-            [ "hc-c2-c_1", 13, 9, 10],
-            [ "hc-c2-c_1", 14, 9, 10],
-            [ "hc-c2-hc", 13, 9, 14],
-            [ "c2-c_1-o_1", 9, 10, 11],
-            [ "c2-c_1-o", 9, 10, 12],
-            [ "o_1-c_1-o", 11, 10, 12],
-            [ "c_1-o-ho", 10, 12, 15]
-        ]
-    },
-    "dihedrals": {
-        "format": ["dihedral-type", "atom1", "atom2", "atom3", "atom4"],
-        "data": [
-            ["hn-na-c2-c2", 4, 1, 2, 3],
-            ["hn-na-c2-hc", 4, 1, 2, 6],
-            ["hn-na-c2-hc", 4, 1, 2, 7],
-            ["hn-na-c2-c2", 5, 1, 2, 3],
-            ["hn-na-c2-hc", 5, 1, 2, 6],
-            ["hn-na-c2-hc", 5, 1, 2, 7],
-            ["na-c2-c2-c2", 1, 2, 3, 16],
-            ["na-c2-c2-hc", 1, 2, 3, 17],
-            ["na-c2-c2-hc", 1, 2, 3, 18],
-            [ "c2-c2-c2-hc", 16, 3, 2, 6],
-            [ "hc-c2-c2-hc", 6, 2, 3, 17],
-            [ "hc-c2-c2-hc", 6, 2, 3, 18],
-            [ "c2-c2-c2-hc", 16, 3, 2, 7],
-            [ "hc-c2-c2-hc", 7, 2, 3, 17],
-            [ "hc-c2-c2-hc", 7, 2, 3, 18],
-            [ "c2-c2-c_1-o_1", 8, 9, 10, 11],
-            [ "c2-c2-c_1-o", 8, 9, 10, 12],
-            [ "hc-c2-c_1-o_1", 13, 9, 10, 11],
-            [ "hc-c2-c_1-o", 13, 9, 10, 12],
-            [ "hc-c2-c_1-o_1", 14, 9, 10, 11],
-            [ "hc-c2-c_1-o", 14, 9, 10, 12],
-            [ "c2-c_1-o-ho", 9, 10, 12, 15],
-            [ "o_1-c_1-o-ho", 11, 10, 12, 15]
-        ]
-    },
-    "charges": {
-        "format": ["atom-id", "charge"],
-        "data": [
-            [1, -0.3],
-            [2, 0.0],
-            [3, 0.0],
-            [4, 0.0],
-            [5, 0.0],
-            [6, 0.0],
-            [7, 0.0],
-            [8, 0.0],
-            [9, 0.0],
-            [10, 0.3],
-            [11, 0.0],
-            [12, 0.0],
-            [13, 0.0],
-            [14, 0.0],
-            [15, 0.0],
-            [16, 0.0],
-            [17, 0.0],
-            [18, 0.0]
-        ]
-    },
-    "impropers": {
-        "format": [ "improper-type", "atom1", "atom2", "atom3", "atom4"],
-        "data": [
-            [ "c2-na-hn-hn", 2, 1, 4, 5],
-            [ "c2-c_1-o_1-o", 9, 10, 11, 12]
-        ]
-    }
-}

examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp2_map

@@ -1,32 +0,0 @@
-this is a nominal superimpose file
-
-2 edgeIDs
-15 equivalences
-
-InitiatorIDs
-
-4
-12
-
-EdgeIDs
-
-8
-3
-
-Equivalences
-
-1	1
-2	2
-3	3
-4	4
-5	5
-6	6
-7	7
-8	8
-9	9
-10	10
-11	11
-12	12
-13	13
-14	14
-15	15

examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp2_reacted.json

@@ -1,156 +0,0 @@
-{
-    "application": "LAMMPS",
-    "format": "molecule",
-    "revision": 1,
-    "schema": "https://download.lammps.org/json/molecule-schema.json",
-    "coords": {
-        "format": ["atom-id", "x", "y", "z"],
-        "data": [
-            [1, -4.856280281, -1.050467974, 1.432625159],
-            [2, -5.047194816, -0.935266843, -0.358172771],
-            [3, -6.526281447, -0.755365854, -0.743523227],
-            [4, -5.282604074, 0.020446894, 1.552710361],
-            [5, -3.860696509, -1.09585019, 1.428304925],
-            [6, -4.662381862, -1.920899862, -0.781524026],
-            [7, -4.43397654, -0.072765142, -0.784070641],
-            [8, -5.506279186, 0.202610302, 4.825815562],
-            [9, -4.449176624, -0.844592213, 4.423366146],
-            [10, -4.103915981, -0.749628655, 2.925195217],
-            [11, -3.376248536, -1.886171498, 2.245643443],
-            [12, -4.49323543, 0.477213651, 2.137199034],
-            [13, -4.849052953, -1.888876753, 4.66399375],
-            [14, -3.49182295, -0.66291331, 5.018510248],
-            [15, -5.020776528, 1.189745133, 2.805427194]
-        ]
-    },
-    "types": {
-        "format": ["atom-id", "type"],
-        "data": [
-            [1, "n"],
-            [2, "c2"],
-            [3, "c2"],
-            [4, "hw"],
-            [5, "hn"],
-            [6, "hc"],
-            [7, "hc"],
-            [8, "c2"],
-            [9, "c2"],
-            [10, "c_1"],
-            [11, "o_1"],
-            [12, "o*"],
-            [13, "hc"],
-            [14, "hc"],
-            [15, "hw"]
-        ]
-    },
-    "molecules": {
-        "format": ["atom-id", "molecule-id"],
-        "data": [
-            [1, 1],
-            [2, 1],
-            [3, 1],
-            [4, 1],
-            [5, 1],
-            [6, 1],
-            [7, 1],
-            [8, 1],
-            [9, 1],
-            [10, 1],
-            [11, 1],
-            [12, 1],
-            [13, 1],
-            [14, 1],
-            [15, 1]
-        ]
-    },
-    "bonds": {
-        "format": ["bond-type", "atom1", "atom2"],
-        "data": [
-            ["n-c2", 1, 2],
-            ["n-hn", 1, 5],
-            ["n-c_1", 1, 10],
-            ["c2-c2", 2, 3],
-            ["c2-hc", 2, 6],
-            ["c2-hc", 2, 7],
-            ["hw-o*", 4, 12],
-            ["c2-c2", 8, 9],
-            ["c2-c_1", 9, 10],
-            [ "c2-hc", 9, 13],
-            [ "c2-hc", 9, 14],
-            [ "c_1-o_1", 10, 11],
-            [ "hw-o*", 15, 12]
-        ]
-    },
-    "angles": {
-        "format": ["angle-type", "atom1", "atom2", "atom3"],
-        "data": [
-            ["c2-n-hn", 2, 1, 5],
-            ["c2-n-c_1", 2, 1, 10],
-            ["hn-n-c_1", 5, 1, 10],
-            ["n-c2-c2", 1, 2, 3],
-            ["n-c2-hc", 1, 2, 6],
-            ["n-c2-hc", 1, 2, 7],
-            ["c2-c2-hc", 3, 2, 6],
-            ["c2-c2-hc", 3, 2, 7],
-            ["hc-c2-hc", 6, 2, 7],
-            [ "c2-c2-c_1", 8, 9, 10],
-            [ "c2-c2-hc", 8, 9, 13],
-            [ "c2-c2-hc", 8, 9, 14],
-            [ "hc-c2-c_1", 13, 9, 10],
-            [ "hc-c2-c_1", 14, 9, 10],
-            [ "hc-c2-hc", 13, 9, 14],
-            [ "c2-c_1-o_1", 9, 10, 11],
-            [ "n-c_1-c2", 1, 10, 9],
-            [ "n-c_1-o_1", 1, 10, 11],
-            [ "hw-o*-hw", 15, 12, 4]
-        ]
-    },
-    "dihedrals": {
-        "format": ["dihedral-type", "atom1", "atom2", "atom3", "atom4"],
-        "data": [
-            ["hn-n-c2-c2", 5, 1, 2, 3],
-            ["hn-n-c2-hc", 5, 1, 2, 6],
-            ["hn-n-c2-hc", 5, 1, 2, 7],
-            ["c_1-n-c2-c2", 10, 1, 2, 3],
-            ["c_1-n-c2-hc", 10, 1, 2, 6],
-            ["c_1-n-c2-hc", 10, 1, 2, 7],
-            ["c2-n-c_1-c2", 2, 1, 10, 9],
-            ["c2-n-c_1-o_1", 2, 1, 10, 11],
-            ["hn-n-c_1-c2", 5, 1, 10, 9],
-            [ "hn-n-c_1-o_1", 5, 1, 10, 11],
-            [ "c2-c2-c_1-o_1", 8, 9, 10, 11],
-            [ "c2-c2-c_1-n", 8, 9, 10, 1],
-            [ "hc-c2-c_1-o_1", 13, 9, 10, 11],
-            [ "hc-c2-c_1-n", 13, 9, 10, 1],
-            [ "hc-c2-c_1-o_1", 14, 9, 10, 11],
-            [ "hc-c2-c_1-n", 14, 9, 10, 1]
-        ]
-    },
-    "charges": {
-        "format": ["atom-id", "charge"],
-        "data": [
-            [1, -0.60533],
-            [2, -0.01149],
-            [3, -0.76306],
-            [4, 0.38],
-            [5, 0.29346],
-            [6, 0.1836],
-            [7, 0.15396],
-            [8, -0.72636],
-            [9, -0.27437],
-            [10, 0.40603],
-            [11, -0.6553],
-            [12, -0.76],
-            [13, 0.21423],
-            [14, 0.18949],
-            [15, 0.38]
-        ]
-    },
-    "impropers": {
-        "format": ["improper-type", "atom1", "atom2", "atom3", "atom4"],
-        "data": [
-            ["c2-n-hn-c_1", 2, 1, 5, 10],
-            ["n-c_1-c2-o_1", 1, 10, 9, 11]
-        ]
-    }
-}

examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp2_unreacted.json

@@ -1,170 +0,0 @@
-{
-    "application": "LAMMPS",
-    "format": "molecule",
-    "revision": 1,
-    "schema": "https://download.lammps.org/json/molecule-schema.json",
-    "coords": {
-        "format": ["atom-id", "x", "y", "z"],
-        "data": [
-            [1, -4.922858499, -0.946981747, 1.146055346],
-            [2, -5.047194816, -0.935266843, -0.358172771],
-            [3, -6.526281447, -0.755365854, -0.743523227],
-            [4, -5.282604074, 0.020446894, 1.552710361],
-            [5, -3.860696509, -1.09585019, 1.428304925],
-            [6, -4.662381862, -1.920899862, -0.781524026],
-            [7, -4.43397654, -0.072765142, -0.784070641],
-            [8, -5.506279186, 0.202610302, 4.825815562],
-            [9, -4.449176624, -0.844592213, 4.423366146],
-            [10, -4.103915981, -0.749628655, 2.925195217],
-            [11, -3.376248536, -1.886171498, 2.245643443],
-            [12, -4.49323543, 0.477213651, 2.137199034],
-            [13, -4.849052953, -1.888876753, 4.66399375],
-            [14, -3.49182295, -0.66291331, 5.018510248],
-            [15, -5.020776528, 1.189745133, 2.805427194]
-        ]
-    },
-    "types": {
-        "format": ["atom-id", "type"],
-        "data": [
-            [1, "n"],
-            [2, "c2"],
-            [3, "c2"],
-            [4, "hn"],
-            [5, "hn"],
-            [6, "hc"],
-            [7, "hc"],
-            [8, "c2"],
-            [9, "c2"],
-            [10, "c_1"],
-            [11, "o_1"],
-            [12, "o"],
-            [13, "hc"],
-            [14, "hc"],
-            [15, "ho"]
-        ]
-    },
-    "molecules": {
-        "format": ["atom-id", "molecule-id"],
-        "data": [
-            [1, 1],
-            [2, 1],
-            [3, 1],
-            [4, 1],
-            [5, 1],
-            [6, 1],
-            [7, 1],
-            [8, 1],
-            [9, 1],
-            [10, 1],
-            [11, 1],
-            [12, 1],
-            [13, 1],
-            [14, 1],
-            [15, 1]
-        ]
-    },
-    "bonds": {
-        "format": ["bond-type", "atom1", "atom2"],
-        "data": [
-            ["n-c2",     1,  2],
-            ["n-hn",     1,  4],
-            ["n-hn",     1,  5],
-            ["n-c_1",    1, 10],
-            ["c2-c2",    2,  3],
-            ["c2-hc",    2,  6],
-            ["c2-hc",    2,  7],
-            ["c2-c2",    8,  9],
-            ["c2-c_1",   9, 10],
-            ["c2-hc",    9, 13],
-            ["c2-hc",    9, 14],
-            ["c_1-o_1", 10, 11],
-            ["c_1-o",   10, 12],
-            ["o-ho",    12, 15]
-        ]
-    },
-    "angles": {
-        "format": ["angle-type", "atom1", "atom2", "atom3"],
-        "data": [
-            ["c2-n-hn",    2,  1,  4],
-            ["c2-n-hn",    2,  1,  5],
-            ["c2-n-c_1",   2,  1, 10],
-            ["hn-n-hn",    4,  1,  5],
-            ["hn-n-c_1",   4,  1, 10],
-            ["hn-n-c_1",   5,  1, 10],
-            ["n-c2-c2",    1,  2,  3],
-            ["n-c2-hc",    1,  2,  6],
-            ["n-c2-hc",    1,  2,  7],
-            ["c2-c2-hc",   3,  2,  6],
-            ["c2-c2-hc",   3,  2,  7],
-            ["hc-c2-hc",   6,  2,  7],
-            ["c2-c2-c_1",  8,  9, 10],
-            ["c2-c2-hc",   8,  9, 13],
-            ["c2-c2-hc",   8,  9, 14],
-            ["hc-c2-c_1", 13,  9, 10],
-            ["hc-c2-c_1", 14,  9, 10],
-            ["hc-c2-hc",  13,  9, 14],
-            ["c2-c_1-o_1", 9, 10, 11],
-            ["c2-c_1-o",   9, 10, 12],
-            ["n-c_1-c2",   1, 10,  9],
-            ["o_1-c_1-o", 11, 10, 12],
-            ["n-c_1-o_1",  1, 10, 11],
-            ["n-c_1-o",    1, 10, 12],
-            ["c_1-o-ho",  10, 12, 15]
-        ]
-    },
-    "dihedrals": {
-        "format": ["dihedral-type", "atom1", "atom2", "atom3", "atom4"],
-        "data": [
-            ["hn-n-c2-c2", 4, 1, 2, 3],
-            ["hn-n-c2-hc", 4, 1, 2, 6],
-            ["hn-n-c2-hc", 4, 1, 2, 7],
-            ["hn-n-c2-c2", 5, 1, 2, 3],
-            ["hn-n-c2-hc", 5, 1, 2, 6],
-            ["hn-n-c2-hc", 5, 1, 2, 7],
-            ["c_1-n-c2-c2", 10, 1, 2, 3],
-            ["c_1-n-c2-hc", 10, 1, 2, 6],
-            ["c_1-n-c2-hc", 10, 1, 2, 7],
-            ["c2-n-c_1-c2", 2, 1, 10, 9],
-            ["c2-n-c_1-o_1", 2, 1, 10, 11],
-            ["c2-n-c_1-o", 2, 1, 10, 12],
-            ["hn-n-c_1-c2", 4, 1, 10, 9],
-            ["hn-n-c_1-o_1", 4, 1, 10, 11],
-            ["hn-n-c_1-o", 4, 1, 10, 12],
-            ["hn-n-c_1-c2", 5, 1, 10, 9],
-            ["hn-n-c_1-o_1", 5, 1, 10, 11],
-            ["hn-n-c_1-o", 5, 1, 10, 12],
-            ["c2-c2-c_1-o_1", 8, 9, 10, 11],
-            ["c2-c2-c_1-o", 8, 9, 10, 12],
-            ["c2-c2-c_1-n", 8, 9, 10, 1],
-            ["hc-c2-c_1-o_1", 13, 9, 10, 11],
-            ["hc-c2-c_1-o", 13, 9, 10, 12],
-            ["hc-c2-c_1-n", 13, 9, 10, 1],
-            ["hc-c2-c_1-o_1", 14, 9, 10, 11],
-            ["hc-c2-c_1-o", 14, 9, 10, 12],
-            ["hc-c2-c_1-n", 14, 9, 10, 1],
-            ["c2-c_1-o-ho", 9, 10, 12, 15],
-            ["o_1-c_1-o-ho", 11, 10, 12, 15],
-            ["n-c_1-o-ho", 1, 10, 12, 15]
-        ]
-    },
-    "charges": {
-        "format": ["atom-id", "charge"],
-        "data": [
-            [1, -0.3],
-            [2, 0.0],
-            [3, 0.0],
-            [4, 0.0],
-            [5, 0.0],
-            [6, 0.0],
-            [7, 0.0],
-            [8, 0.0],
-            [9, 0.0],
-            [10, 0.3],
-            [11, 0.0],
-            [12, 0.0],
-            [13, 0.0],
-            [14, 0.0],
-            [15, 0.0]
-        ]
-    }
-}