Merge branch 'develop' into atom-style-var-with-python

.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.sif
+wget https://download.lammps.org/static/fedora41_musl_mingw.sif
-apptainer shell fedora41_musl.sif
+apptainer shell fedora41_musl_mingw.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 for macOS
+#### Build Multi-arch App-bundle with GUI 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 on Ubuntu 20.04LTS
+#### Build Linux x86_64 binary tarball with GUI 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 and C++23
+# GitHub action to build LAMMPS on Linux with gcc or clang and C++23
 name: "Check for C++23 Compatibility"
 
 on:
@@ -11,11 +11,19 @@ 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
 
@@ -29,8 +37,11 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get install -y ccache \
-                                libeigen3-dev \
+                                clang \
                                 libcurl4-openssl-dev \
+                                libeigen3-dev \
+                                libfftw3-dev \
+                                libomp-dev \
                                 mold \
                                 mpi-default-bin \
                                 mpi-default-dev \
@@ -58,14 +69,14 @@ 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

@@ -7,6 +7,10 @@ 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)
@@ -27,7 +31,10 @@ endif()
 
 ########################################
 
-project(lammps CXX)
+project(lammps
+        DESCRIPTION "The LAMMPS Molecular Dynamics Simulator"
+        HOMEPAGE_URL "https://www.lammps.org"
+        LANGUAGES CXX C)
 set(SOVERSION 0)
 get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
 
@@ -196,6 +203,10 @@ 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                                                   #
 ########################################################################
@@ -379,7 +390,6 @@ 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)
@@ -394,21 +404,18 @@ if(PKG_ADIOS)
 endif()
 
 if(NOT CMAKE_CROSSCOMPILING)
-  find_package(MPI QUIET)
+  find_package(MPI QUIET COMPONENTS CXX)
   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)
+    find_package(MPI REQUIRED COMPONENTS CXX)
     option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
     if(LAMMPS_LONGLONG_TO_LONG)
       target_compile_definitions(lammps PRIVATE -DLAMMPS_LONGLONG_TO_LONG)
@@ -535,7 +542,6 @@ 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

@@ -62,6 +62,9 @@ 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)
@@ -128,8 +131,7 @@ endif()
 ################################################################################
 # MPI configuration
 if(NOT CMAKE_CROSSCOMPILING)
-  set(MPI_CXX_SKIP_MPICXX TRUE)
+  find_package(MPI QUIET COMPONENTS CXX)
-  find_package(MPI QUIET)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()
   option(BUILD_MPI "Build MPI version" OFF)
@@ -141,9 +143,6 @@ if(BUILD_MPI)
   set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
-    # Download and configure MinGW compatible MPICH development files for Windows
-    option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
-    if(USE_MSMPI)
     message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
     set(MPICH2_WIN64_DEVEL_URL "${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")
@@ -167,52 +166,15 @@ if(BUILD_MPI)
     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")
+      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 "${SOURCE_DIR}/include")
-      set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+    set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
     set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
   else()
-      # Download and configure custom MPICH files for Windows
+    find_package(MPI REQUIRED COMPONENTS CXX)
-      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()
-  else()
-    find_package(MPI REQUIRED)
     option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
     if(LAMMPS_LONGLONG_TO_LONG)
       target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)

cmake/Modules/LAMMPSUtils.cmake

@@ -75,13 +75,25 @@ function(get_lammps_version version_header variable)
     list(FIND MONTHS "${month}" month)
     string(LENGTH ${day} day_length)
     string(LENGTH ${month} month_length)
-    if(day_length EQUAL 1)
+    # no leading zero needed for new version string with dots
-        set(day "0${day}")
+    # 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")
     endif()
-    if(month_length EQUAL 1)
+    if(NOT tweak)
-        set(month "0${month}")
+      set(tweak "0")
     endif()
-    set(${variable} "${year}${month}${day}" PARENT_SCOPE)
+    # new version string with dots
+    set(${variable} "${year}.${month}.${day}.${tweak}" PARENT_SCOPE)
+    # old version string without dots
+    # set(${variable} "${year}${month}${day}" PARENT_SCOPE)
 endfunction()
 
 function(check_for_autogen_files source_dir)

cmake/Modules/MPI4WIN.cmake

@@ -1,74 +1,31 @@
-# Download and configure MinGW compatible MPICH development files for Windows
+# set-up MS-MPI library for Windows with MinGW compatibility
-option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
+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)
 
-if(USE_MSMPI)
+include(ExternalProject)
-  message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
+if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-  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()
+else()
   message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
-  endif()
+endif()
 
-  ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-  file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-  add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-  set_target_properties(MPI::MPI_CXX PROPERTIES
+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")
+  INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
-  add_dependencies(MPI::MPI_CXX mpi4win_build)
+add_dependencies(MPI::MPI_CXX mpi4win_build)
 
-  # set variables for status reporting at the end of CMake run
+# set variables for status reporting at the end of CMake run
-  set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
-  set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
-  set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
+set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
-else()
-  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()

cmake/Modules/Packages/COLVARS.cmake

@@ -27,7 +27,6 @@ if(BUILD_OMP)
 endif()
 
 if(BUILD_MPI)
-  target_compile_definitions(colvars PUBLIC -DCOLVARS_MPI)
   target_link_libraries(colvars PUBLIC MPI::MPI_CXX)
 endif()
 

cmake/Modules/Packages/GPU.cmake

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

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
+    if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04))
-          ((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=${CMAKE_LINKER} HAVE_LD_PATH_FLAG)
       check_cxx_compiler_flag(-fuse-ld=mold HAVE_MOLD_LINKER_FLAG)
       check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
       check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
@@ -50,6 +50,17 @@ if(ENABLE_TESTING)
       if(NOT "${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/presets/hip_amd.cmake

@@ -19,12 +19,19 @@ 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" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp=libomp -I${_libomp_root}/include" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp=libomp -I${_libomp_root}/include" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

cmake/presets/kokkos-hip.cmake

@@ -1,8 +1,8 @@
-# preset that enables KOKKOS and selects HIP compilation with OpenMP
+# preset that enables KOKKOS and selects HIP compilation withOUT OpenMP.
-# enabled as well. Also sets some performance related compiler flags.
+# Kokkos OpenMP is not compatible with the second pass of hipcc.
 set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
-set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_OPENMP OFF 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 CUFFT for FFTs
+# If KSPACE is also enabled, use HIPFFT 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/src/Commands_fix.rst

@@ -29,6 +29,7 @@ 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>`
@@ -218,6 +219,7 @@ 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/Developer_updating.rst

@@ -29,6 +29,7 @@ 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`_
 
 ----
 
@@ -610,3 +611,47 @@ 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:: TBD
+
+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/Speed_compare.rst

@@ -75,15 +75,34 @@ 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. The KOKKOS package attempts to run most of the
+  of) PPPM calculations (and runs the remaining force computations on
+  the CPU concurrently).  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 can be compiled for CUDA, HIP, or OpenCL and thus supports
+* The GPU package benefits from running multiple MPI processes (2-8) per
-  NVIDIA, AMD, and Intel GPUs well. On NVIDIA hardware, using CUDA is
+  GPU to parallelize the non-GPU accelerated styles.  The KOKKOS package
-  typically resulting in equal or better performance over OpenCL.
+  usually not, especially when all parts of the calculation have KOKKOS
-* OpenCL in the GPU package does theoretically also support Intel CPUs or
+  support.
-  Intel Xeon Phi, but the native support for those in KOKKOS (or INTEL)
+* The GPU package can be compiled for CUDA, HIP, or OpenCL and thus
-  is superior.
+  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.

doc/src/Speed_measure.rst

@@ -1,16 +1,218 @@
 Measuring performance
 =====================
 
-Before trying to make your simulation run faster, you should
+Factors that influence performance
-understand how it currently performs and where the bottlenecks are.
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The best way to do this is run the your system (actual number of
+Before trying to make your simulation run faster, you should understand
-atoms) for a modest number of timesteps (say 100 steps) on several
+how it currently performs and where the bottlenecks are.  We generally
-different processor counts, including a single processor if possible.
+distinguish between serial performance (how fast can a single process do
-Do this for an equilibrium version of your system, so that the
+the calculations?) and parallel efficiency (how much faster does a
-100-step timings are representative of a much longer run.  There is
+calculation get by using more processes?).  There are many factors
-typically no need to run for 1000s of timesteps to get accurate
+affecting either and below are some lists discussing some commonly
-timings; you can simply extrapolate from short runs.
+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.
 
 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
@@ -28,12 +230,15 @@ 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
+style, as discussed below.  Comparing how the percentages change as you
-you increase the processor count gives you a sense of how different
+increase the processor count gives you a sense of how different
-operations within the timestep are scaling.  Note that if you are
+operations within the timestep are scaling.  If you are using PPPM as
-running with a Kspace solver, there is additional output on the
+Kspace solver, you can turn on an additional output with
-breakdown of the Kspace time.  For PPPM, this includes the fraction
+:doc:`kspace_modify fftbench yes <kspace_modify>` which measures the
-spent on FFTs, which can be communication intensive.
+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.
 
 Another important detail in the timing info are the histograms of
 atoms counts and neighbor counts.  If these vary widely across

doc/src/fix.rst

@@ -208,6 +208,7 @@ 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
@@ -397,6 +398,7 @@ 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_ave_correlate_long.rst

@@ -82,10 +82,9 @@ 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.  For
+evaluation of an equal-style or vector-style variable.  The specified
-vector-style variables, the specified indices can include a wildcard
+indices can include a wildcard string.  See the
-character.  See the :doc:`fix ave/correlate <fix_ave_correlate>` page
+:doc:`fix ave/correlate <fix_ave_correlate>` page for details on that.
-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

@@ -0,0 +1,296 @@
+.. 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:: TBD
+
+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_set.rst

@@ -0,0 +1,173 @@
+.. 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
+"""""""""""
+
+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/pair_hybrid.rst

@@ -100,6 +100,56 @@ 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
@@ -374,12 +424,11 @@ selected sub-style.
 
 ----------
 
-.. note::
+Even though the command name "pair_style" would suggest that these are
-
+pair-wise interactions, several of the potentials defined via the
-   Several of the potentials defined via the pair_style command in
+pair_style command in LAMMPS are really many-body potentials, such as
-   LAMMPS are really many-body potentials, such as Tersoff, AIREBO, MEAM,
+Tersoff, AIREBO, MEAM, ReaxFF, etc.  The way to think about using these
-   ReaxFF, etc.  The way to think about using these potentials in a
+potentials in a hybrid setting is as follows.
-   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/run.rst

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

doc/src/set.rst

@@ -22,21 +22,110 @@ Syntax
        for style = *region*, ID = a region ID
 
 * one or more keyword/value pairs may be appended
-* 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
+* keyword = *angle* or *angmom* or *bond* or *cc* or *charge* or
-  *dipole* or *dipole/random* or *quat* or *spin/atom* or *spin/atom/random* or
+  *density* or *density/disc* or *diameter* or *dihedral* or *dipole*
-  *spin/electron* or *radius/electron* or
+  or *dipole/random* or *dpd/theta* or *edpd/cv* or *edpd/temp* or
-  *quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or
+  *epsilon* or *image* or *improper* or *length* or *mass* or *mol* or
-  *theta* or *theta/random* or *angmom* or *omega* or
+  *omega* or *quat* or *quat/random* or *radius/electron* or *shape* or
-  *mass* or *density* or *density/disc* or *temperature* or
+  *smd/contact/radius* or *smd/mass/density* or *sph/cv* or *sph/e* or
-  *volume* or *image* or *bond* or *angle* or *dihedral* or
+  *sph/rho* or *spin/atom* or *spin/atom/random* or *spin/electron* or
-  *improper* or *sph/e* or *sph/cv* or *sph/rho* or
+  *temperature* or *theta* or *theta/random* or *tri* or *type* or
-  *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or
+  *type/fraction* or *type/ratio* or *type/subset* or *volume* or *vx*
-  *edpd/temp* or *edpd/cv* or *cc* or *epsilon* or
+  or *vy* or *vz* or *x* or *y* or *z* or *i_name* or *d_name* or
-  *i_name* or *d_name* or *i2_name* or *d2_name*
+  *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
@@ -51,104 +140,22 @@ 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)
-       *mol* value = molecule ID
+       *volume* value = particle volume for Peridynamic particle (distance\^3 units)
-       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)
-       *charge* value = atomic charge (charge units)
+       *x*,\ *y*,\ *z* value = atom coordinate (distance 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
-       *i2_name* value = column of a custom integer array with name
+         value can be an atom-style variable (see below)
+       *i2_name* value = custom integer array with name
                          column specified as i2_name[N] where N is 1 to Ncol
-       *d2_name* value = column of a custom floating-point array with name
+         value can be an atom-style variable (see below)
+       *d2_name* value = 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
 """"""""
@@ -177,22 +184,26 @@ 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>`
+:doc:`read_restart <read_restart>` or :doc:`create_atoms
-commands, this command changes those assignments.  This can be useful
+<create_atoms>` commands, this command changes those assignments.
-for overriding the default values assigned by the
+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
+:doc:`create_atoms <create_atoms>` command (e.g. charge = 0.0).  It
-be useful for altering pairwise and molecular force interactions,
+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
+when they are output in :doc:`dump <dump>` files.  It can also be
-for debugging purposes; i.e. positioning an atom at a precise location
+useful for debugging purposes; i.e. positioning an atom at a precise
-to compute subsequent forces or energy.
+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
@@ -211,8 +222,8 @@ 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 a wildcard asterisk can be used to specify a range
+numeric value, or with a wildcard asterisk to specify a range of
-of values.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  For
+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
@@ -222,25 +233,25 @@ 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
+region.  See the :doc:`group <group>` and :doc:`region <region>`
-for details of how to specify a group or region.
+commands for details of how to specify a group or region.
 
 ----------
 
-This section describes the keyword options for which properties to
+The next 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, it should be specified as v_name, where name is the variable
-variable name.  In this case, the variable will be evaluated, and its
+name.  In this case, the variable will be evaluated, and its resulting
-resulting per-atom value used to determine the value assigned to each
+per-atom value used to determine the value assigned to each selected
-selected atom.  Note that the per-atom value from the variable will be
+atom.  Note that the per-atom value from the variable will be ignored
-ignored for atoms that are not selected via the *style* and *ID*
+for atoms that are not selected via the *style* and *ID* settings
-settings explained above.  A simple way to use per-atom values from
+explained above.  A simple way to use per-atom values from the
-the variable to reset a property for all atoms is to use style *atom*
+variable to reset a property for all atoms is to use style *atom* with
-with *ID* = "\*"; this selects all atom IDs.
+*ID* = "\*"; this selects all atom IDs.
 
 Atom-style variables can specify formulas with various mathematical
 functions, and include :doc:`thermo_style <thermo_style>` command
@@ -256,52 +267,110 @@ 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,
+   per-atom values.  If the values are assigned to an integer
-   such as the molecule ID, then the floating point value is truncated to
+   variable, such as the molecule ID, then the floating point value is
-   its integer portion, e.g. a value of 2.6 would become 2.
+   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 atom, bond, angle,
+   Support for type labels was added for setting angle types
-   dihedral, and improper types
 
-Keyword *type* sets the atom type for all selected atoms.  A specified
+Keyword *angle* sets the angle type of all angles of selected atoms to
-value can be either a numeric atom type or an atom type label. When
+the specified value.  The value can be a numeric type from 1 to
-using a numeric type, the specified value must be from 1 to ntypes,
+nangletypes.  Or it can be a angle type label.  See the :doc:`Howto
-where ntypes was set by the :doc:`create_box <create_box>` command or
+type labels <Howto_type_labels>` doc page for the allowed syntax of
-the *atom types* field in the header of the data file read by the
+type labels and a general discussion of how type labels can be used.
-:doc:`read_data <read_data>` command.  When using a type label it must
+All atoms in a particular angle must be selected atoms in order for
-have been defined previously.  See the :doc:`Howto type labels
+the change to be made.  The value of nangletypes was set by the *angle
-<Howto_type_labels>` doc page for the allowed syntax of type labels
+types* field in the header of the data file read by the
-and a general discussion of how type labels can be used.
+:doc:`read_data <read_data>` command.  This keyword does NOT allow use
+of an atom-style variable.
 
-Keyword *type/fraction* sets the atom type for a fraction of the selected
+Keyword *angmom* sets the angular momentum of selected atoms.  The
-atoms.  The actual number of atoms changed is not guaranteed
+particles must be ellipsoids as defined by the :doc:`atom_style
-to be exactly the specified fraction (0 <= *fraction* <= 1), but
+ellipsoid <atom_style>` command or triangles as defined by the
-should be statistically close.  Random numbers are used in such a way
+:doc:`atom_style tri <atom_style>` command.  The angular momentum
-that a particular atom is changed or not changed, regardless of how
+vector of the particles is set to the 3 specified components.
-many processors are being used.  This keyword does not allow use of an
-atom-style variable.
 
-Keywords *type/ratio* and *type/subset* also set the atom type for a
+.. versionchanged:: 28Mar2023
-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.
 
-Keyword *mol* sets the molecule ID for all selected atoms.  The
+   Support for type labels was added for setting bond types
-:doc:`atom style <atom_style>` being used must support the use of
-molecule IDs.
 
-Keywords *x*, *y*, *z*, and *charge* set the coordinates or
+Keyword *bond* sets the bond type of all bonds of selected atoms to
-charge of all selected atoms.  For *charge*, the :doc:`atom style
+the specified value.  The value can be a numeric type from 1 to
-<atom_style>` being used must support the use of atomic
+nbondtypes.  Or it can be a bond type label.  See the :doc:`Howto type
-charge. Keywords *vx*, *vy*, and *vz* set the velocities of all
+labels <Howto_type_labels>` doc page for the allowed syntax of type
-selected atoms.
+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.
 
 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
@@ -313,40 +382,106 @@ 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.
 
-.. versionchanged:: 15Sep2022
+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.
 
-Keyword *spin/atom* uses the specified g value to set the magnitude of the
+Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric
-magnetic spin vectors, and the x,y,z values as components of a vector
+heat capacity of an eDPD particle as defined by the DPD-MESO package.
-to set as the orientation of the magnetic spin vectors of the selected
+Currently, only :doc:`atom_style edpd <atom_style>` defines particles
-atoms.  This keyword was previously called *spin*.
+with these attributes. The values for the temperature and heat
+capacity must be positive.
 
-.. versionchanged:: 15Sep2022
+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.
 
-Keyword *spin/atom/random* randomizes the orientation of the magnetic spin
+Keyword *image* sets which image of the simulation box the atom is
-vectors for the selected atoms and sets the magnitude of each to the
+considered to be in.  An image of 0 means it is inside the box as
-specified *Dlen* value.  This keyword was previously called *spin/random*.
+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.
 
-.. versionadded:: 15Sep2022
+.. versionchanged:: 28Mar2023
 
-Keyword *radius/electron* uses the specified value to set the radius of
+   Support for type labels was added for setting improper types
-electrons or fixed cores.
 
-.. versionadded:: 15Sep2022
+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.
 
-Keyword *spin/electron* sets the spin of an electron (+/- 1) or indicates
+Keyword *length* sets the length of selected atoms.  The particles
-nuclei (=0), fixed-cores (=2), or pseudo-cores (= 3).
+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 *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 <atom_style>` command.  Note that particles defined
-:doc:`atom_style ellipsoid <atom_style>` have 3 shape parameters.  The 3
+by :doc:`atom_style ellipsoid <atom_style>` have 3 shape parameters.
-values must be non-zero for each particle set by this command.  They
+The 3 values must be non-zero for each particle set by this command.
-are used to specify the aspect ratios of an ellipsoidal particle,
+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
@@ -360,51 +495,77 @@ 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
+the :doc:`atom_style <atom_style>` command.  Random numbers are used
-such a way that the orientation of a particular atom is the same,
+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.
 
-Keyword *diameter* sets the size of the selected atoms.  The particles
+.. versionadded:: 15Sep2022
-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,
+Keyword *radius/electron* uses the specified value to set the radius
-which means they will be treated as point particles.  Note that this
+of electrons or fixed cores.
-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
+ellipsoid <atom_style>` command.  The *Sx*, *Sy*, *Sz* settings are
-are the 3 diameters of the ellipsoid in each direction.  All 3 can be
+the 3 diameters of the ellipsoid in each direction.  All 3 can be set
-set to the same value, which means the ellipsoid is effectively a
+to the same value, which means the ellipsoid is effectively a sphere.
-sphere.  They can also all be set to 0.0 which means the particle will
+They can also all be set to 0.0 which means the particle will be
-be treated as a point particle.  Note that this command does not
+treated as a point particle.  Note that this command does not adjust
-adjust the particle mass, even if it was defined with a density,
+the particle mass, even if it was defined with a density, e.g. via the
-e.g. via the :doc:`read_data <read_data>` command.
+:doc:`read_data <read_data>` command.
 
-Keyword *length* sets the length of selected atoms.  The particles
+Keyword *smd/contact/radius* only applies to simulations with the
-must be line segments as defined by the :doc:`atom_style line
+Smooth Mach Dynamics package MACHDYN.  Itsets an interaction radius
-<atom_style>` command.  If the specified value is non-zero the line
+for computing short-range interactions, e.g. repulsive forces to
-segment is (re)set to a length = the specified value, centered around
+prevent different individual physical bodies from penetrating each
-the particle position, with an orientation along the x-axis.  If the
+other. Note that the SPH smoothing kernel diameter used for computing
-specified value is 0.0, the particle will become a point particle.
+long range, nonlocal interactions, is set using the *diameter*
-Note that this command does not adjust the particle mass, even if it
+keyword.
-was defined with a density, e.g. via the :doc:`read_data <read_data>`
-command.
 
-Keyword *tri* sets the size of selected atoms.  The particles must be
+Keyword *smd/mass/density* sets the mass of all selected particles,
-triangles as defined by the :doc:`atom_style tri <atom_style>` command.
+but it is only applicable to the Smooth Mach Dynamics package MACHDYN.
-If the specified value is non-zero the triangle is (re)set to be an
+It assumes that the particle volume has already been correctly set and
-equilateral triangle in the xy plane with side length = the specified
+calculates particle mass from the provided mass density value.
-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
+Keywords *sph/cv*, *sph/e*, and *sph/rho* set the heat capacity,
-base to the top point of the triangle.  If the specified value is 0.0,
+energy, and density of smoothed particle hydrodynamics (SPH)
-the particle will become a point particle.  Note that this command
+particles.  See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to
-does not adjust the particle mass, even if it was defined with a
+using SPH in LAMMPS.
-density, e.g. via the :doc:`read_data <read_data>` command.
+
+.. 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 *theta* sets the orientation of selected atoms.  The particles
 must be line segments as defined by the :doc:`atom_style line
@@ -413,169 +574,71 @@ 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
+:doc:`atom_style line <atom_style>` command.  Random numbers are used
-such a way that the orientation of a particular atom is the same,
+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 *angmom* sets the angular momentum of selected atoms.  The
+Keyword *tri* sets the size of selected atoms.  The particles must be
-particles must be ellipsoids as defined by the :doc:`atom_style
+triangles as defined by the :doc:`atom_style tri <atom_style>`
-ellipsoid <atom_style>` command or triangles as defined by the
+command.  If the specified value is non-zero the triangle is (re)set
-:doc:`atom_style tri <atom_style>` command.  The angular momentum
+to be an equilateral triangle in the xy plane with side length = the
-vector of the particles is set to the 3 specified components.
+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 *omega* sets the angular velocity of selected atoms.  The
+.. versionchanged:: 28Mar2023
-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 *mass* sets the mass of all selected particles.  The particles
+   Support for type labels was added for setting atom types
-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 *density* or *density/disc* also sets the mass of all selected
+Keyword *type* sets the atom type for all selected atoms.  A specified
-particles, but in a different way.  The particles must have a per-atom
+value can be either a numeric atom type or an atom type label. When
-mass attribute, as defined by the :doc:`atom_style <atom_style>`
+using a numeric type, the specified value must be from 1 to ntypes,
-command.  If the atom has a radius attribute (see :doc:`atom_style
+where ntypes was set by the :doc:`create_box <create_box>` command or
-sphere <atom_style>`) and its radius is non-zero, its mass is set from
+the *atom types* field in the header of the data file read by the
-the density and particle volume for 3d systems (the input density is
+:doc:`read_data <read_data>` command.  When using a type label it must
-assumed to be in mass/distance\^3 units).  For 2d, the default is for
+have been defined previously.  See the :doc:`Howto type labels
-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.  All atoms in
+and a general discussion of how type labels can be used.
-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.
 
-Keywords *rheo/rho* and *rheo/status* set the density and the status of
+Keyword *type/fraction* sets the atom type for a fraction of the
-rheo particles. In particular, one can only set the phase in the status
+selected atoms.  The actual number of atoms changed is not guaranteed
-as described by the :doc:`RHEO howto page <Howto_rheo>`.
+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 *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
+Keywords *type/ratio* and *type/subset* also set the atom type for a
-and density of smoothed particle hydrodynamics (SPH) particles.  See
+fraction of the selected atoms.  The actual number of atoms changed
-`this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
+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.
 
-.. note::
+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.
 
-   Please note that the SPH PDF guide file has not been updated for
+Keywords *vx*, *vy*, and *vz* set the velocities of all selected
-   many years and thus does not reflect the current *syntax* of the
+atoms.
-   SPH package commands. For that please refer to the LAMMPS manual.
 
-Keyword *smd/mass/density* sets the mass of all selected particles, but
+Keywords *x*, *y*, *z* set the coordinates of all selected atoms.
-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 must also be included following
+and *d2_name*, the column of the array to set must also be included
-the name in brackets: e.g. d2_xyz[2], i2_mySpin[3].
+following the name in brackets: e.g. d2_xyz[2] or i2_mySpin[3].
 
 Restrictions
 """"""""""""
@@ -584,7 +647,7 @@ 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 your system
+setting of bond types (angle types, etc).  This means that the 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.
@@ -599,7 +662,7 @@ Related commands
 """"""""""""""""
 
 :doc:`create_box <create_box>`, :doc:`create_atoms <create_atoms>`,
-:doc:`read_data <read_data>`
+:doc:`read_data <read_data>`, :doc:`fix set <fix_set>`
 
 Default
 """""""

doc/utils/sphinx-config/false_positives.txt

@@ -82,6 +82,7 @@ Alessandro
 Alexey
 ali
 aliceblue
+aliphatic
 Allera
 Allinger
 allocatable
@@ -630,6 +631,7 @@ cp
 cpp
 cpu
 cradius
+Cramer
 createatoms
 createAtoms
 CreateIDs
@@ -670,6 +672,7 @@ cuFFT
 CuH
 Cui
 Cummins
+cumulants
 Cundall
 cundall
 Curk
@@ -1174,6 +1177,7 @@ Fermionic
 Ferrand
 fexternal
 Fexternal
+ffast
 ffield
 ffl
 fflush
@@ -1770,6 +1774,7 @@ jik
 JIK
 jku
 jN
+Joanes
 Joannopoulos
 Jochim
 Jonsson
@@ -1814,6 +1819,7 @@ Karniadakis
 Karplus
 Karttunen
 kate
+katom
 Katsnelson
 Katsura
 Kaufmann
@@ -2192,6 +2198,7 @@ Materias
 mathbf
 mathjax
 matlab
+Matom
 Matous
 matplotlib
 Matsubara
@@ -2701,6 +2708,7 @@ Nprocs
 npt
 nr
 Nr
+Nrecent
 Nrecompute
 Nrepeat
 nreset
@@ -2779,6 +2787,7 @@ ocl
 octahedral
 octants
 Odegard
+Og
 Ohara
 O'Hearn
 ohenrich
@@ -3361,6 +3370,7 @@ Rmin
 RMS
 rmsd
 rnage
+rnflag
 rng
 rNEMD
 ro
@@ -3416,6 +3426,7 @@ ry
 Ryckaert
 Rycroft
 Rydbergs
+Ryzen
 rz
 Rz
 Sabry
@@ -3835,6 +3846,7 @@ Thiaville
 Thibaudeau
 Thijsse
 Thirumalai
+Threadripper
 threebody
 thrid
 ThunderX

examples/COUPLE/plugin/CMakeLists.txt

@@ -27,10 +27,7 @@ if(MSVC)
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
-find_package(MPI REQUIRED)
+find_package(MPI REQUIRED COMPONENTS C)
-# 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/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/moments/in.converge

@@ -0,0 +1,35 @@
+# 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

@@ -0,0 +1,27 @@
+# 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

@@ -0,0 +1,28 @@
+# 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

@@ -0,0 +1,171 @@
+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

@@ -0,0 +1,171 @@
+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

@@ -0,0 +1,177 @@
+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

@@ -0,0 +1,177 @@
+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

@@ -0,0 +1,178 @@
+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

@@ -0,0 +1,178 @@
+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/neighbor-swap/MoCoNiVFeAlCr_2nn.meam

@@ -0,0 +1 @@
+../../../potentials/MoCoNiVFeAlCr_2nn.meam

examples/PACKAGES/neighbor-swap/in.KMC_pulse_center

@@ -0,0 +1,46 @@
+# May 2025
+# Test script for MD-KMC accelerated diffusion testing in LAMMPS
+# Created by Jacob Tavenner, Baylor University
+
+# Initiation -------------------------------------
+units           metal
+dimension       3
+boundary        p p p
+atom_style      atomic
+
+# Atom Definition --------------------------------
+lattice fcc 3.762
+region          whole block 0 1 0 1 0 1
+create_box      2 whole
+create_atoms    1 region whole
+
+replicate 6 16 6
+
+region      puck block INF INF 7 9 INF INF 
+set         region puck type 2
+
+# Force Fields -----------------------------------
+pair_style      meam
+pair_coeff      * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
+
+# Settings ---------------------------------------
+timestep        0.002
+thermo          100
+
+# Computations -----------------------------------
+compute         voroN all voronoi/atom neighbors yes
+
+run             0
+thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe
+
+# Execution --------------------------------------
+
+velocity    all create 2400 908124 loop geom
+fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
+fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
+thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
+#dump           dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
+
+run 1000
+
+#write_data     pulse_center.data

examples/PACKAGES/neighbor-swap/in.KMC_pulse_edge

@@ -0,0 +1,47 @@
+# May 2025
+# Test script for MD-KMC accelerated diffusion testing in LAMMPS
+# Created by Jacob Tavenner, Baylor University
+
+# Initiation -------------------------------------
+units           metal
+dimension       3
+boundary        p p p
+atom_style      atomic
+
+
+# Atom Definition --------------------------------
+lattice fcc 3.762
+region          whole block 0 1 0 1 0 1
+create_box      2 whole
+create_atoms    1 region whole
+
+replicate 6 16 6
+
+region      puck block INF INF INF 2 INF INF 
+set         region puck type 2
+
+# Force Fields -----------------------------------
+pair_style      meam
+pair_coeff      * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
+
+# Settings ---------------------------------------
+timestep        0.002
+thermo          100
+
+# Computations -----------------------------------
+compute         voroN all voronoi/atom neighbors yes
+
+run             0
+thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe
+
+# Execution --------------------------------------
+
+velocity    all create 2400 908124 loop geom
+fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
+fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
+thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
+#dump           dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
+
+run 1000
+
+#write_data     pulse_end.data

examples/PACKAGES/neighbor-swap/library_2nn.meam

@@ -0,0 +1 @@
+../../../potentials/library_2nn.meam

examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_center.g++.1

@@ -0,0 +1,154 @@
+LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
+  using 1 OpenMP thread(s) per MPI task
+# May 2025
+# Test script for MD-KMC accelerated diffusion testing in LAMMPS
+# Created by Jacob Tavenner, Baylor University
+
+# Initiation -------------------------------------
+units		metal
+dimension	3
+boundary	p p p
+atom_style	atomic
+
+# Atom Definition --------------------------------
+lattice	fcc 3.762
+Lattice spacing in x,y,z = 3.762 3.762 3.762
+region		whole block 0 1 0 1 0 1
+create_box	2 whole
+Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 region whole
+Created 4 atoms
+  using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
+  create_atoms CPU = 0.000 seconds
+
+replicate 6 16 6
+Replication is creating a 6x16x6 = 576 times larger system...
+  orthogonal box = (0 0 0) to (22.572 60.192 22.572)
+  1 by 1 by 1 MPI processor grid
+  2304 atoms
+  replicate CPU = 0.000 seconds
+
+region      puck block INF INF 7 9 INF INF
+set         region puck type 2
+Setting atom values ...
+  360 settings made for type
+
+# Force Fields -----------------------------------
+pair_style	meam
+pair_coeff	* * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
+Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
+Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
+
+# Settings ---------------------------------------
+timestep	0.002
+thermo		100
+
+# Computations -----------------------------------
+compute		voroN all voronoi/atom neighbors yes
+
+run		0
+WARNING: No fixes with time integration, atoms won't move
+For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 7 18 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   0             -9674.3728      0             -9674.3728     -212400.94    
+Loop time of 1.202e-06 on 1 procs for 0 steps with 2304 atoms
+
+0.0% 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          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 1.202e-06  |            |       |100.00
+
+Nlocal:           2304 ave        2304 max        2304 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           4735 ave        4735 max        4735 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          99072 ave       99072 max       99072 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:       198144 ave      198144 max      198144 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 198144
+Ave neighs/atom = 86
+Neighbor list builds = 0
+Dangerous builds = 0
+thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe
+
+# Execution --------------------------------------
+
+velocity    all create 2400 908124
+fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
+fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
+thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
+#dump		dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
+
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
+   Step          Temp          Press           Pxx            Pyy            Pzz             Lx             Ly             Lz           Volume         PotEng        f_mc[1]        f_mc[2]    
+         0   2400          -187517.52     -187403.07     -187750.14     -187399.35      22.572         60.192         22.572         30667.534     -9674.3728      0              0            
+       100   1664.9956      14000          14280.682      15095.077      12624.241      21.635315      57.726568      21.64791       27036.778     -9592.8978      24             22           
+       200   1560.0093     -5452.2434     -5749.5816     -2957.4228     -7649.7258      21.734212      58.085959      21.724853      27426.596     -9562.8822      48             45           
+       300   1586.4553      2030.9253      2776.4677      775.50538      2540.803       21.678654      58.101753      21.654423      27275.215     -9571.1308      72             66           
+       400   1603.6896     -223.16773      156.17673     -478.47929     -347.20061      21.701021      58.098904      21.657752      27306.213     -9576.4456      96             90           
+       500   1618.236      -925.51874     -1640.9078      451.6228      -1587.2713      21.718334      58.042685      21.666081      27312.054     -9581.2045      120            110          
+       600   1581.9995      290.10126      1359.1314      1407.5434     -1896.371       21.679813      58.086147      21.692118      27316.815     -9570.4803      144            132          
+       700   1568.3261      1387.3472      938.81523      2159.3686      1063.8577      21.685928      58.075626      21.67273       27295.153     -9566.2914      168            155          
+       800   1607.1531      46.792964     -453.90265     -1533.3908      2127.6723      21.685188      58.202356      21.628338      27297.753     -9577.7848      192            177          
+       900   1573.4747     -84.225488      548.90935     -1356.7479      555.16208      21.69634       58.150052      21.651847      27316.908     -9567.7039      216            196          
+      1000   1609.2136      1215.0833      764.08936      3301.0811     -419.92053      21.683731      58.000401      21.68726       27275.31      -9578.2843      240            219          
+Loop time of 31.6263 on 1 procs for 1000 steps with 2304 atoms
+
+Performance: 5.464 ns/day, 4.393 hours/ns, 31.619 timesteps/s, 72.851 katom-step/s
+99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 28.487     | 28.487     | 28.487     |   0.0 | 90.07
+Neigh   | 0.22789    | 0.22789    | 0.22789    |   0.0 |  0.72
+Comm    | 0.010808   | 0.010808   | 0.010808   |   0.0 |  0.03
+Output  | 0.00033526 | 0.00033526 | 0.00033526 |   0.0 |  0.00
+Modify  | 2.8963     | 2.8963     | 2.8963     |   0.0 |  9.16
+Other   |            | 0.003905   |            |       |  0.01
+
+Nlocal:           2304 ave        2304 max        2304 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           4750 ave        4750 max        4750 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:         130023 ave      130023 max      130023 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:       260046 ave      260046 max      260046 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 260046
+Ave neighs/atom = 112.86719
+Neighbor list builds = 65
+Dangerous builds = 0
+
+#write_data	pulse_center.data
+Total wall time: 0:00:31

examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_center.g++.4

@@ -0,0 +1,154 @@
+LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
+  using 1 OpenMP thread(s) per MPI task
+# May 2025
+# Test script for MD-KMC accelerated diffusion testing in LAMMPS
+# Created by Jacob Tavenner, Baylor University
+
+# Initiation -------------------------------------
+units		metal
+dimension	3
+boundary	p p p
+atom_style	atomic
+
+# Atom Definition --------------------------------
+lattice	fcc 3.762
+Lattice spacing in x,y,z = 3.762 3.762 3.762
+region		whole block 0 1 0 1 0 1
+create_box	2 whole
+Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 region whole
+Created 4 atoms
+  using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
+  create_atoms CPU = 0.000 seconds
+
+replicate 6 16 6
+Replication is creating a 6x16x6 = 576 times larger system...
+  orthogonal box = (0 0 0) to (22.572 60.192 22.572)
+  1 by 4 by 1 MPI processor grid
+  2304 atoms
+  replicate CPU = 0.000 seconds
+
+region      puck block INF INF 7 9 INF INF
+set         region puck type 2
+Setting atom values ...
+  360 settings made for type
+
+# Force Fields -----------------------------------
+pair_style	meam
+pair_coeff	* * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
+Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
+Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
+
+# Settings ---------------------------------------
+timestep	0.002
+thermo		100
+
+# Computations -----------------------------------
+compute		voroN all voronoi/atom neighbors yes
+
+run		0
+WARNING: No fixes with time integration, atoms won't move
+For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 7 18 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   0             -9674.3728      0             -9674.3728     -212400.94    
+Loop time of 1.422e-06 on 4 procs for 0 steps with 2304 atoms
+
+35.2% 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          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 1.422e-06  |            |       |100.00
+
+Nlocal:            576 ave         576 max         576 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:           2131 ave        2131 max        2131 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:          24768 ave       24768 max       24768 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:        49536 ave       49536 max       49536 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 198144
+Ave neighs/atom = 86
+Neighbor list builds = 0
+Dangerous builds = 0
+thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe
+
+# Execution --------------------------------------
+
+velocity    all create 2400 908124
+fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
+fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
+thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
+#dump		dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
+
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
+   Step          Temp          Press           Pxx            Pyy            Pzz             Lx             Ly             Lz           Volume         PotEng        f_mc[1]        f_mc[2]    
+         0   2400          -187517.52     -187403.09     -187750.05     -187399.42      22.572         60.192         22.572         30667.534     -9674.3728      0              0            
+       100   1668.8754      13300.763      12419.304      15568.772      11914.212      21.636248      57.724775      21.647685      27036.823     -9594.7526      24             23           
+       200   1584.9699     -5686.0414     -4741.8496     -5914.7681     -6401.5064      21.729384      58.060532      21.730736      27415.923     -9571.0639      48             46           
+       300   1582.0473      2806.2983      3413.4122      2716.0124      2289.4702      21.6679        58.033587      21.694744      27280.402     -9570.5549      72             69           
+       400   1582.5825      845.29268     -849.61221      2123.5339      1261.9563      21.676298      58.14253       21.656418      27293.905     -9570.7948      96             93           
+       500   1591.7285     -501.17955      1151.9743     -1719.3712     -936.14174      21.696367      58.157211      21.648308      27315.839     -9573.5089      120            116          
+       600   1610.708      -821.74669     -1002.4957      291.88502     -1754.6294      21.730338      58.008213      21.661226      27304.8       -9579.5573      144            138          
+       700   1598.5176     -590.00633     -1844.42        408.97706     -334.57602      21.712908      57.96131       21.698129      27307.281     -9575.8973      168            162          
+       800   1584.3478      330.16711      666.88818      74.698331      248.91482      21.650908      58.045055      21.719838      27295.933     -9571.9268      192            186          
+       900   1557.9946      1471.1207      2124.6512      1526.9937      761.71731      21.645578      58.156083      21.681637      27293.323     -9564.4385      216            207          
+      1000   1582.5312      379.57005     -602.96446      2696.737      -955.06238      21.655418      58.231248      21.649581      27300.598     -9571.9879      240            227          
+Loop time of 9.1632 on 4 procs for 1000 steps with 2304 atoms
+
+Performance: 18.858 ns/day, 1.273 hours/ns, 109.132 timesteps/s, 251.440 katom-step/s
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.867      | 7.9923     | 8.1311     |   4.3 | 87.22
+Neigh   | 0.054997   | 0.057518   | 0.060145   |   1.0 |  0.63
+Comm    | 0.017529   | 0.14801    | 0.27408    |  29.5 |  1.62
+Output  | 0.00015963 | 0.00017216 | 0.00020869 |   0.0 |  0.00
+Modify  | 0.95227    | 0.96325    | 0.9917     |   1.7 | 10.51
+Other   |            | 0.001983   |            |       |  0.02
+
+Nlocal:            576 ave         609 max         540 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:         2161.5 ave        2173 max        2151 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:        32450.2 ave       35422 max       29271 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+FullNghs:      64900.5 ave       70800 max       58684 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 259602
+Ave neighs/atom = 112.67448
+Neighbor list builds = 62
+Dangerous builds = 0
+
+#write_data	pulse_center.data
+Total wall time: 0:00:09

examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_edge.g++.1

@@ -0,0 +1,155 @@
+LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
+  using 1 OpenMP thread(s) per MPI task
+# May 2025
+# Test script for MD-KMC accelerated diffusion testing in LAMMPS
+# Created by Jacob Tavenner, Baylor University
+
+# Initiation -------------------------------------
+units		metal
+dimension	3
+boundary	p p p
+atom_style	atomic
+
+
+# Atom Definition --------------------------------
+lattice	fcc 3.762
+Lattice spacing in x,y,z = 3.762 3.762 3.762
+region		whole block 0 1 0 1 0 1
+create_box	2 whole
+Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 region whole
+Created 4 atoms
+  using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
+  create_atoms CPU = 0.000 seconds
+
+replicate 6 16 6
+Replication is creating a 6x16x6 = 576 times larger system...
+  orthogonal box = (0 0 0) to (22.572 60.192 22.572)
+  1 by 1 by 1 MPI processor grid
+  2304 atoms
+  replicate CPU = 0.000 seconds
+
+region      puck block INF INF INF 2 INF INF
+set         region puck type 2
+Setting atom values ...
+  360 settings made for type
+
+# Force Fields -----------------------------------
+pair_style	meam
+pair_coeff	* * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
+Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
+Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
+
+# Settings ---------------------------------------
+timestep	0.002
+thermo		100
+
+# Computations -----------------------------------
+compute		voroN all voronoi/atom neighbors yes
+
+run		0
+WARNING: No fixes with time integration, atoms won't move
+For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 7 18 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   0             -9674.3728      0             -9674.3728     -212400.94    
+Loop time of 1.232e-06 on 1 procs for 0 steps with 2304 atoms
+
+81.2% 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          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 1.232e-06  |            |       |100.00
+
+Nlocal:           2304 ave        2304 max        2304 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           4735 ave        4735 max        4735 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          99072 ave       99072 max       99072 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:       198144 ave      198144 max      198144 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 198144
+Ave neighs/atom = 86
+Neighbor list builds = 0
+Dangerous builds = 0
+thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe
+
+# Execution --------------------------------------
+
+velocity    all create 2400 908124 loop geom
+fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
+fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
+thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
+#dump		dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
+
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
+   Step          Temp          Press           Pxx            Pyy            Pzz             Lx             Ly             Lz           Volume         PotEng        f_mc[1]        f_mc[2]    
+         0   2400          -187517.52     -187464.47     -188202.62     -186885.48      22.572         60.192         22.572         30667.534     -9674.3728      0              0            
+       100   1665.6154      14281.316      14426.547      14555.867      13861.534      21.637238      57.719793      21.637281      27022.733     -9594.4303      24             24           
+       200   1603.3309     -7325.7341     -8878.1524     -5333.0485     -7766.0015      21.710246      58.122827      21.725933      27415.106     -9577.4545      48             48           
+       300   1603.2974      207.19165      1983.4565     -1841.9518      480.07024      21.678227      58.079126      21.674033      27288.745     -9577.6391      72             69           
+       400   1600.1515      810.95054      1087.969       802.04946      542.83316      21.683731      58.045848      21.678505      27285.662     -9576.6508      96             92           
+       500   1629.8313     -2808.1005     -3197.9357      310.89931     -5537.265       21.683924      58.090375      21.697076      27330.229     -9585.5435      120            113          
+       600   1598.8232     -67.845623     -1573.0718     -1526.7607      2896.2957      21.70213       58.12191       21.653853      27313.504     -9576.4147      144            137          
+       700   1607.2185      154.66718     -1777.2469      2566.4705     -325.22208      21.712408      57.971553      21.678708      27287.033     -9579.1772      168            158          
+       800   1582.559      -891.23631     -632.46037     -636.88203     -1404.3665      21.671936      58.127004      21.678224      27308.594     -9571.6663      192            180          
+       900   1586.7172     -617.17083     -2495.5378     -2302.8766      2946.9018      21.658489      58.181921      21.668968      27305.771     -9572.9641      216            204          
+      1000   1607.563      -389.8113       810.4908       298.84287     -2278.7676      21.624573      58.076745      21.724272      27283.183     -9579.5034      240            227          
+Loop time of 31.7733 on 1 procs for 1000 steps with 2304 atoms
+
+Performance: 5.439 ns/day, 4.413 hours/ns, 31.473 timesteps/s, 72.514 katom-step/s
+99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 28.604     | 28.604     | 28.604     |   0.0 | 90.02
+Neigh   | 0.21293    | 0.21293    | 0.21293    |   0.0 |  0.67
+Comm    | 0.010645   | 0.010645   | 0.010645   |   0.0 |  0.03
+Output  | 0.00033194 | 0.00033194 | 0.00033194 |   0.0 |  0.00
+Modify  | 2.9411     | 2.9411     | 2.9411     |   0.0 |  9.26
+Other   |            | 0.00448    |            |       |  0.01
+
+Nlocal:           2304 ave        2304 max        2304 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           4748 ave        4748 max        4748 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:         130301 ave      130301 max      130301 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:       260602 ave      260602 max      260602 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 260602
+Ave neighs/atom = 113.10851
+Neighbor list builds = 62
+Dangerous builds = 0
+
+#write_data	pulse_end.data
+Total wall time: 0:00:31

examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_edge.g++.4

@@ -0,0 +1,155 @@
+LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
+  using 1 OpenMP thread(s) per MPI task
+# May 2025
+# Test script for MD-KMC accelerated diffusion testing in LAMMPS
+# Created by Jacob Tavenner, Baylor University
+
+# Initiation -------------------------------------
+units		metal
+dimension	3
+boundary	p p p
+atom_style	atomic
+
+
+# Atom Definition --------------------------------
+lattice	fcc 3.762
+Lattice spacing in x,y,z = 3.762 3.762 3.762
+region		whole block 0 1 0 1 0 1
+create_box	2 whole
+Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 region whole
+Created 4 atoms
+  using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
+  create_atoms CPU = 0.000 seconds
+
+replicate 6 16 6
+Replication is creating a 6x16x6 = 576 times larger system...
+  orthogonal box = (0 0 0) to (22.572 60.192 22.572)
+  1 by 4 by 1 MPI processor grid
+  2304 atoms
+  replicate CPU = 0.000 seconds
+
+region      puck block INF INF INF 2 INF INF
+set         region puck type 2
+Setting atom values ...
+  360 settings made for type
+
+# Force Fields -----------------------------------
+pair_style	meam
+pair_coeff	* * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
+Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
+Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
+
+# Settings ---------------------------------------
+timestep	0.002
+thermo		100
+
+# Computations -----------------------------------
+compute		voroN all voronoi/atom neighbors yes
+
+run		0
+WARNING: No fixes with time integration, atoms won't move
+For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 7 18 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   0             -9674.3728      0             -9674.3728     -212400.94    
+Loop time of 1.53e-06 on 4 procs for 0 steps with 2304 atoms
+
+65.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 1.53e-06   |            |       |100.00
+
+Nlocal:            576 ave         576 max         576 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:           2131 ave        2131 max        2131 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:          24768 ave       24768 max       24768 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:        49536 ave       49536 max       49536 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 198144
+Ave neighs/atom = 86
+Neighbor list builds = 0
+Dangerous builds = 0
+thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe
+
+# Execution --------------------------------------
+
+velocity    all create 2400 908124 loop geom
+fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
+fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
+thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
+#dump		dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
+
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
+   Step          Temp          Press           Pxx            Pyy            Pzz             Lx             Ly             Lz           Volume         PotEng        f_mc[1]        f_mc[2]    
+         0   2400          -187517.52     -187464.47     -188202.62     -186885.48      22.572         60.192         22.572         30667.534     -9674.3728      0              0            
+       100   1665.569       14271.813      14638.855      14316.569      13860.016      21.63675       57.721065      21.637799      27023.366     -9594.291       24             24           
+       200   1598.6479     -6990.8349     -8574.1986     -5033.6147     -7364.6916      21.708963      58.123129      21.724821      27412.223     -9575.7322      48             47           
+       300   1604.388       456.43285      1926.408      -1214.1721      657.0626       21.673369      58.090421      21.671716      27285.018     -9577.698       72             70           
+       400   1601.1591      1303.6721      703.88473      1137.6607      2069.471       21.684004      58.049595      21.671161      27278.522     -9576.4811      96             94           
+       500   1623.6044     -2243.2478     -2084.532       320.87709     -4966.0885      21.686171      58.097101      21.695911      27334.758     -9583.1878      120            118          
+       600   1587.2041      421.60034      190.88741     -328.76599      1402.6796      21.712439      58.086039      21.655927      27312.229     -9572.559       144            141          
+       700   1591.2923      32.327829     -2893.2353      1839.7574      1150.4614      21.719102      57.999862      21.666164      27292.974     -9573.9009      168            165          
+       800   1580.8587     -105.51079      654.26389     -160.04168     -810.75457      21.670225      58.109245      21.684683      27306.229     -9570.6482      192            186          
+       900   1570.7648      1290.088       1252.3689      255.62548      2362.2695      21.68101       58.100507      21.658755      27283.051     -9567.9864      216            209          
+      1000   1598.1483     -125.35291     -3626.5479      3404.789      -154.29983      21.720146      57.952942      21.686111      27297.313     -9576.2975      240            231          
+Loop time of 9.17241 on 4 procs for 1000 steps with 2304 atoms
+
+Performance: 18.839 ns/day, 1.274 hours/ns, 109.023 timesteps/s, 251.188 katom-step/s
+98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.7477     | 8.0143     | 8.1344     |   5.5 | 87.37
+Neigh   | 0.050543   | 0.056882   | 0.05986    |   1.6 |  0.62
+Comm    | 0.069784   | 0.16898    | 0.40996    |  34.2 |  1.84
+Output  | 0.00015612 | 0.0001707  | 0.00021249 |   0.0 |  0.00
+Modify  | 0.90628    | 0.93003    | 0.96157    |   2.2 | 10.14
+Other   |            | 0.002053   |            |       |  0.02
+
+Nlocal:            576 ave         614 max         505 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost:        2165.75 ave        2204 max        2132 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+Neighs:        32430.8 ave       35552 max       26564 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+FullNghs:      64861.5 ave       71111 max       53164 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+
+Total # of neighbors = 259446
+Ave neighs/atom = 112.60677
+Neighbor list builds = 62
+Dangerous builds = 0
+
+#write_data	pulse_end.data
+Total wall time: 0:00:09

examples/plugins/LAMMPSInterfaceCXX.cmake

@@ -33,23 +33,19 @@ endif()
 
 ################################################################################
 # MPI configuration
+# do not include the (obsolete) MPI C++ bindings which makes
+# for leaner object files and avoids namespace conflicts
+set(MPI_CXX_SKIP_MPICXX TRUE)
 if(NOT CMAKE_CROSSCOMPILING)
-  set(MPI_CXX_SKIP_MPICXX TRUE)
+  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)
-    # 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 "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
     set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
@@ -73,50 +69,13 @@ if(BUILD_MPI)
     set_target_properties(MPI::MPI_CXX PROPERTIES
       IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
       INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
-        INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      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 "${SOURCE_DIR}/include")
-      set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+    set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
     set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
-    else()
-      # 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()
   else()
     find_package(MPI REQUIRED)
     option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)

lib/atc/LammpsInterface.cpp

@@ -561,7 +561,7 @@ bool LammpsInterface::region_bounds(const char * regionName,
 }
 
 void LammpsInterface::minimum_image(double & dx, double & dy, double & dz) const {
-  lammps_->domain->minimum_image(dx,dy,dz);
+  lammps_->domain->minimum_image(FLERR,dx,dy,dz);
 }
 
 void LammpsInterface::closest_image(const double * const xi, const double * const xj, double * const xjImage) const {

lib/gpu/lal_eam.cpp

@@ -61,7 +61,7 @@ int EAMT::init(const int ntypes, double host_cutforcesq, int **host_type2rhor,
       if (onetype>0)
         onetype=-1;
       else if (onetype==0)
-        onetype=i*max_shared_types+i;
+        onetype=i;
     }
   if (onetype<0) onetype=0;
   #endif
@@ -109,7 +109,7 @@ int EAMT::init(const int ntypes, double host_cutforcesq, int **host_type2rhor,
   int lj_types=ntypes;
   shared_types=false;
 
-  if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
+  if (lj_types<=max_shared_types && this->_block_size>=max_shared_types*max_shared_types) {
     lj_types=max_shared_types;
     shared_types=true;
   }

lib/voronoi/voro-make.patch

@@ -1,5 +1,35 @@
---- src/Makefile.orig	2020-05-03 03:50:23.501557199 -0400
+--- Makefile.orig	2025-06-04 12:16:01.056286325 -0400
-+++ src/Makefile	2020-05-03 03:53:32.147681674 -0400
++++ Makefile	2025-06-04 12:18:47.454879006 -0400
+@@ -11,8 +11,7 @@
+ 
+ # Build all of the executable files
+ all:
+-	$(MAKE) -C src
+-	$(MAKE) -C examples
++	$(MAKE) -C src depend libvoro++.a
+ 
+ # Build the help files (with Doxygen)
+ help:
+@@ -24,16 +23,12 @@
+ 	$(MAKE) -C examples clean
+ 
+ # Install the executable, man page, and shared library
+-install:
+-	$(MAKE) -C src
+-	$(INSTALL) -d $(IFLAGS_EXEC) $(PREFIX)/bin
++install: all
+ 	$(INSTALL) -d $(IFLAGS_EXEC) $(PREFIX)/lib
+ 	$(INSTALL) -d $(IFLAGS_EXEC) $(PREFIX)/man
+ 	$(INSTALL) -d $(IFLAGS_EXEC) $(PREFIX)/man/man1
+ 	$(INSTALL) -d $(IFLAGS_EXEC) $(PREFIX)/include
+ 	$(INSTALL) -d $(IFLAGS_EXEC) $(PREFIX)/include/voro++
+-	$(INSTALL) $(IFLAGS_EXEC) src/voro++ $(PREFIX)/bin
+-	$(INSTALL) $(IFLAGS) man/voro++.1 $(PREFIX)/man/man1
+ 	$(INSTALL) $(IFLAGS) src/libvoro++.a $(PREFIX)/lib
+ 	$(INSTALL) $(IFLAGS) src/voro++.hh $(PREFIX)/include/voro++
+ 	$(INSTALL) $(IFLAGS) src/c_loops.hh $(PREFIX)/include/voro++
+--- src/Makefile.orig	2013-10-17 13:54:13.000000000 -0400
++++ src/Makefile	2025-06-04 12:16:47.293104880 -0400
 @@ -10,10 +10,10 @@
  # List of the common source files
  objs=cell.o common.o container.o unitcell.o v_compute.o c_loops.o \

src/AMOEBA/angle_amoeba.cpp

@@ -834,13 +834,13 @@ double AngleAmoeba::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;

src/BPM/bond_bpm.cpp

@@ -352,7 +352,7 @@ double BondBPM::equilibrium_distance(int /*i*/)
           delx = x[i][0] - x[j][0];
           dely = x[i][1] - x[j][1];
           delz = x[i][2] - x[j][2];
-          domain->minimum_image(delx, dely, delz);
+          domain->minimum_image(FLERR, delx, dely, delz);
 
           r = sqrt(delx * delx + dely * dely + delz * delz);
           if (r > r0_max_estimate) r0_max_estimate = r;

src/BPM/bond_bpm_rotational.cpp

@@ -177,7 +177,7 @@ void BondBPMRotational::store_data()
       }
 
       // Get closest image in case bonded with ghost
-      domain->minimum_image(delx, dely, delz);
+      domain->minimum_image(FLERR, delx, dely, delz);
       r = sqrt(delx * delx + dely * dely + delz * delz);
       rinv = 1.0 / r;
 

src/BPM/bond_bpm_spring.cpp

@@ -140,7 +140,7 @@ void BondBPMSpring::store_data()
       delz = x[i][2] - x[j][2];
 
       // Get closest image in case bonded with ghost
-      domain->minimum_image(delx, dely, delz);
+      domain->minimum_image(FLERR, delx, dely, delz);
       r = sqrt(delx * delx + dely * dely + delz * delz);
 
       fix_bond_history->update_atom_value(i, m, 0, r);

src/BPM/bond_bpm_spring_plastic.cpp

@@ -148,7 +148,7 @@ void BondBPMSpringPlastic::store_data()
       delz = x[i][2] - x[j][2];
 
       // Get closest image in case bonded with ghost
-      domain->minimum_image(delx, dely, delz);
+      domain->minimum_image(FLERR, delx, dely, delz);
       r = sqrt(delx * delx + dely * dely + delz * delz);
 
       fix_bond_history->update_atom_value(i, m, 0, r);

src/CG-SPICA/angle_spica.cpp

@@ -458,13 +458,13 @@ double AngleSPICA::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
@@ -479,7 +479,7 @@ double AngleSPICA::single(int type, int i1, int i2, int i3)
     double delx3 = x[i1][0] - x[i3][0];
     double dely3 = x[i1][1] - x[i3][1];
     double delz3 = x[i1][2] - x[i3][2];
-    domain->minimum_image(delx3,dely3,delz3);
+    domain->minimum_image(FLERR, delx3,dely3,delz3);
 
     const int type1 = atom->type[i1];
     const int type3 = atom->type[i3];

src/CLASS2/angle_class2.cpp

@@ -436,13 +436,13 @@ double AngleClass2::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;

src/COLVARS/colvarproxy_lammps.cpp

@@ -188,7 +188,7 @@ cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1,
   double xtmp = pos2.x - pos1.x;
   double ytmp = pos2.y - pos1.y;
   double ztmp = pos2.z - pos1.z;
-  _lmp->domain->minimum_image_big(xtmp,ytmp,ztmp);
+  _lmp->domain->minimum_image_big(FLERR, xtmp,ytmp,ztmp);
   return {xtmp, ytmp, ztmp};
 }
 

src/DIELECTRIC/fix_polarize_functional.cpp

@@ -652,7 +652,7 @@ void FixPolarizeFunctional::calculate_Rww_cutoff()
           double delx = xtmp - x[k][0];
           double dely = ytmp - x[k][1];
           double delz = ztmp - x[k][2];
-          domain->minimum_image(delx, dely, delz);
+          domain->minimum_image(FLERR, delx, dely, delz);
           int mk = tag2mat[tag[k]];
 
           // G1ww[mi][mk] = calculate_greens_ewald(delx, dely, delz);
@@ -861,7 +861,7 @@ void FixPolarizeFunctional::calculate_qiRqw_cutoff()
           delx = xtmp - x[k][0];
           dely = ytmp - x[k][1];
           delz = ztmp - x[k][2];
-          domain->minimum_image(delx, dely, delz);
+          domain->minimum_image(FLERR, delx, dely, delz);
           r = sqrt(delx * delx + dely * dely + delz * delz);
 
           int mk = tag2mat[tag[k]];
@@ -902,7 +902,7 @@ void FixPolarizeFunctional::calculate_qiRqw_cutoff()
           delx = x[i][0] - xtmp;
           dely = x[i][1] - ytmp;
           delz = x[i][2] - ztmp;
-          domain->minimum_image(delx, dely, delz);
+          domain->minimum_image(FLERR, delx, dely, delz);
 
           int mi = tag2mat_ions[tag[i]];    //ion_idx[i];
 

src/DIPOLE/angle_dipole.cpp

@@ -251,7 +251,7 @@ double AngleDipole::single(int type, int iRef, int iDip, int /*iDummy*/)
   double dely = x[iRef][1] - x[iDip][1];
   double delz = x[iRef][2] - x[iDip][2];
 
-  domain->minimum_image(delx, dely, delz);
+  domain->minimum_image(FLERR, delx, dely, delz);
 
   double r = sqrt(delx * delx + dely * dely + delz * delz);
   if (r < SMALL) return 0.0;

src/EXTRA-COMPUTE/compute_born_matrix.cpp

@@ -764,7 +764,7 @@ void ComputeBornMatrix::compute_bonds()
       dx = x[atom2][0] - x[atom1][0];
       dy = x[atom2][1] - x[atom1][1];
       dz = x[atom2][2] - x[atom1][2];
-      domain->minimum_image(dx, dy, dz);
+      domain->minimum_image(FLERR, dx, dy, dz);
       rsq = dx * dx + dy * dy + dz * dz;
       rij[0] = dx;
       rij[1] = dy;
@@ -870,7 +870,7 @@ void ComputeBornMatrix::compute_angles()
       delx1 = x[atom1][0] - x[atom2][0];
       dely1 = x[atom1][1] - x[atom2][1];
       delz1 = x[atom1][2] - x[atom2][2];
-      domain->minimum_image(delx1, dely1, delz1);
+      domain->minimum_image(FLERR, delx1, dely1, delz1);
       del1[0] = delx1;
       del1[1] = dely1;
       del1[2] = delz1;
@@ -882,7 +882,7 @@ void ComputeBornMatrix::compute_angles()
       delx2 = x[atom3][0] - x[atom2][0];
       dely2 = x[atom3][1] - x[atom2][1];
       delz2 = x[atom3][2] - x[atom2][2];
-      domain->minimum_image(delx2, dely2, delz2);
+      domain->minimum_image(FLERR, delx2, dely2, delz2);
       del2[0] = delx2;
       del2[1] = dely2;
       del2[2] = delz2;
@@ -1046,7 +1046,7 @@ void ComputeBornMatrix::compute_dihedrals()
       vb1x = x[atom2][0] - x[atom1][0];
       vb1y = x[atom2][1] - x[atom1][1];
       vb1z = x[atom2][2] - x[atom1][2];
-      domain->minimum_image(vb1x, vb1y, vb1z);
+      domain->minimum_image(FLERR, vb1x, vb1y, vb1z);
       b1[0] = vb1x;
       b1[1] = vb1y;
       b1[2] = vb1z;
@@ -1055,7 +1055,7 @@ void ComputeBornMatrix::compute_dihedrals()
       vb2x = x[atom3][0] - x[atom2][0];
       vb2y = x[atom3][1] - x[atom2][1];
       vb2z = x[atom3][2] - x[atom2][2];
-      domain->minimum_image(vb2x, vb2y, vb2z);
+      domain->minimum_image(FLERR, vb2x, vb2y, vb2z);
       b2[0] = vb2x;
       b2[1] = vb2y;
       b2[2] = vb2z;
@@ -1064,7 +1064,7 @@ void ComputeBornMatrix::compute_dihedrals()
       vb3x = x[atom4][0] - x[atom3][0];
       vb3y = x[atom4][1] - x[atom3][1];
       vb3z = x[atom4][2] - x[atom3][2];
-      domain->minimum_image(vb3x, vb3y, vb3z);
+      domain->minimum_image(FLERR, vb3x, vb3y, vb3z);
       b3[0] = vb3x;
       b3[1] = vb3y;
       b3[2] = vb3z;

src/EXTRA-COMPUTE/compute_stress_cartesian.cpp

@@ -480,7 +480,7 @@ void ComputeStressCartesian::compute_pressure(double fpair, double xi, double yi
       tmp1[dir1] = (bin1 + 1) * bin_width1 - xi;
     else
       tmp1[dir1] = bin1 * bin_width1 - xi;
-    domain->minimum_image(tmp1[0],tmp1[1],tmp1[2]);
+    domain->minimum_image(FLERR, tmp1[0],tmp1[1],tmp1[2]);
     l1 = tmp1[dir1] / rij1;
 
     double l2;
@@ -489,7 +489,7 @@ void ComputeStressCartesian::compute_pressure(double fpair, double xi, double yi
       tmp2[dir2] = (bin2 + 1) * bin_width2 - yi;
     else
       tmp2[dir2] = bin2 * bin_width2 - yi;
-    domain->minimum_image(tmp2[0],tmp2[1],tmp2[2]);
+    domain->minimum_image(FLERR, tmp2[0],tmp2[1],tmp2[2]);
     l2 = tmp2[dir2] / rij2;
 
     if ((dims == 1 || l1 < l2 || l2 < lb + SMALL) && l1 <= 1.0 && l1 > lb) {

src/EXTRA-COMPUTE/compute_stress_mop.cpp

@@ -82,7 +82,7 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) : Compute(
     error->warning(FLERR, "The specified initial plane lies outside of the simulation box");
     double dx[3] = {0.0, 0.0, 0.0};
     dx[dir] = pos - 0.5 * (domain->boxhi[dir] + domain->boxlo[dir]);
-    domain->minimum_image(dx[0], dx[1], dx[2]);
+    domain->minimum_image(FLERR, dx[0], dx[1], dx[2]);
     pos = 0.5 * (domain->boxhi[dir] + domain->boxlo[dir]) + dx[dir];
 
     if ((pos > domain->boxhi[dir]) || (pos < domain->boxlo[dir]))
@@ -478,7 +478,7 @@ void ComputeStressMop::compute_pairs()
 
           // minimum image of xi with respect to the plane
           xi[dir] -= pos;
-          domain->minimum_image(xi[0], xi[1], xi[2]);
+          domain->minimum_image(FLERR, xi[0], xi[1], xi[2]);
           xi[dir] += pos;
 
           //velocities at t
@@ -601,7 +601,7 @@ void ComputeStressMop::compute_bonds()
       dx[1] = x[atom1][1];
       dx[2] = x[atom1][2];
       dx[dir] -= pos;
-      domain->minimum_image(dx[0], dx[1], dx[2]);
+      domain->minimum_image(FLERR, dx[0], dx[1], dx[2]);
       x_bond_1[0] = dx[0];
       x_bond_1[1] = dx[1];
       x_bond_1[2] = dx[2];
@@ -612,7 +612,7 @@ void ComputeStressMop::compute_bonds()
       dx[0] = x[atom2][0] - x_bond_1[0];
       dx[1] = x[atom2][1] - x_bond_1[1];
       dx[2] = x[atom2][2] - x_bond_1[2];
-      domain->minimum_image(dx[0], dx[1], dx[2]);
+      domain->minimum_image(FLERR, dx[0], dx[1], dx[2]);
       x_bond_2[0] = x_bond_1[0] + dx[0];
       x_bond_2[1] = x_bond_1[1] + dx[1];
       x_bond_2[2] = x_bond_1[2] + dx[2];
@@ -728,7 +728,7 @@ void ComputeStressMop::compute_angles()
       dx[1] = x[atom1][1];
       dx[2] = x[atom1][2];
       dx[dir] -= pos;
-      domain->minimum_image(dx[0], dx[1], dx[2]);
+      domain->minimum_image(FLERR, dx[0], dx[1], dx[2]);
       x_angle_left[0] = dx[0];
       x_angle_left[1] = dx[1];
       x_angle_left[2] = dx[2];
@@ -739,7 +739,7 @@ void ComputeStressMop::compute_angles()
       dx_left[0] = x[atom2][0] - x_angle_left[0];
       dx_left[1] = x[atom2][1] - x_angle_left[1];
       dx_left[2] = x[atom2][2] - x_angle_left[2];
-      domain->minimum_image(dx_left[0], dx_left[1], dx_left[2]);
+      domain->minimum_image(FLERR, dx_left[0], dx_left[1], dx_left[2]);
       x_angle_middle[0] = x_angle_left[0] + dx_left[0];
       x_angle_middle[1] = x_angle_left[1] + dx_left[1];
       x_angle_middle[2] = x_angle_left[2] + dx_left[2];
@@ -749,7 +749,7 @@ void ComputeStressMop::compute_angles()
       dx_right[0] = x[atom3][0] - x_angle_middle[0];
       dx_right[1] = x[atom3][1] - x_angle_middle[1];
       dx_right[2] = x[atom3][2] - x_angle_middle[2];
-      domain->minimum_image(dx_right[0], dx_right[1], dx_right[2]);
+      domain->minimum_image(FLERR, dx_right[0], dx_right[1], dx_right[2]);
       x_angle_right[0] = x_angle_middle[0] + dx_right[0];
       x_angle_right[1] = x_angle_middle[1] + dx_right[1];
       x_angle_right[2] = x_angle_middle[2] + dx_right[2];
@@ -920,14 +920,14 @@ void ComputeStressMop::compute_dihedrals()
       x_atom_1[1] = x[atom1][1];
       x_atom_1[2] = x[atom1][2];
       x_atom_1[dir] -= pos;
-      domain->minimum_image(x_atom_1[0], x_atom_1[1], x_atom_1[2]);
+      domain->minimum_image(FLERR, x_atom_1[0], x_atom_1[1], x_atom_1[2]);
       x_atom_1[dir] += pos;
 
       // minimum image of atom2 with respect to atom1
       diffx[0] = x[atom2][0] - x_atom_1[0];
       diffx[1] = x[atom2][1] - x_atom_1[1];
       diffx[2] = x[atom2][2] - x_atom_1[2];
-      domain->minimum_image(diffx[0], diffx[1], diffx[2]);
+      domain->minimum_image(FLERR, diffx[0], diffx[1], diffx[2]);
       x_atom_2[0] = x_atom_1[0] + diffx[0];
       x_atom_2[1] = x_atom_1[1] + diffx[1];
       x_atom_2[2] = x_atom_1[2] + diffx[2];
@@ -936,7 +936,7 @@ void ComputeStressMop::compute_dihedrals()
       diffx[0] = x[atom3][0] - x_atom_2[0];
       diffx[1] = x[atom3][1] - x_atom_2[1];
       diffx[2] = x[atom3][2] - x_atom_2[2];
-      domain->minimum_image(diffx[0], diffx[1], diffx[2]);
+      domain->minimum_image(FLERR, diffx[0], diffx[1], diffx[2]);
       x_atom_3[0] = x_atom_2[0] + diffx[0];
       x_atom_3[1] = x_atom_2[1] + diffx[1];
       x_atom_3[2] = x_atom_2[2] + diffx[2];
@@ -945,7 +945,7 @@ void ComputeStressMop::compute_dihedrals()
       diffx[0] = x[atom4][0] - x_atom_3[0];
       diffx[1] = x[atom4][1] - x_atom_3[1];
       diffx[2] = x[atom4][2] - x_atom_3[2];
-      domain->minimum_image(diffx[0], diffx[1], diffx[2]);
+      domain->minimum_image(FLERR, diffx[0], diffx[1], diffx[2]);
       x_atom_4[0] = x_atom_3[0] + diffx[0];
       x_atom_4[1] = x_atom_3[1] + diffx[1];
       x_atom_4[2] = x_atom_3[2] + diffx[2];

src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp

@@ -537,14 +537,14 @@ void ComputeStressMopProfile::compute_pairs()
 
             // minimum image of xi with respect to the plane
             xi[dir] -= pos;
-            domain->minimum_image(xi[0], xi[1], xi[2]);
+            domain->minimum_image(FLERR, xi[0], xi[1], xi[2]);
             xi[dir] += pos;
 
             // minimum image of xj with respect to xi
             xj[0] -= xi[0];
             xj[1] -= xi[1];
             xj[2] -= xi[2];
-            domain->minimum_image(xi[0], xi[1], xi[2]);
+            domain->minimum_image(FLERR, xj[0], xj[1], xj[2]);
             xj[0] += xi[0];
             xj[1] += xi[1];
             xj[2] += xi[2];
@@ -649,7 +649,7 @@ void ComputeStressMopProfile::compute_bonds()
         dx[1] = x[atom1][1];
         dx[2] = x[atom1][2];
         dx[dir] -= pos;
-        domain->minimum_image(dx[0], dx[1], dx[2]);
+        domain->minimum_image(FLERR, dx[0], dx[1], dx[2]);
         x_bond_1[0] = dx[0];
         x_bond_1[1] = dx[1];
         x_bond_1[2] = dx[2];
@@ -660,7 +660,7 @@ void ComputeStressMopProfile::compute_bonds()
         dx[0] = x[atom2][0] - x_bond_1[0];
         dx[1] = x[atom2][1] - x_bond_1[1];
         dx[2] = x[atom2][2] - x_bond_1[2];
-        domain->minimum_image(dx[0], dx[1], dx[2]);
+        domain->minimum_image(FLERR, dx[0], dx[1], dx[2]);
         x_bond_2[0] = x_bond_1[0] + dx[0];
         x_bond_2[1] = x_bond_1[1] + dx[1];
         x_bond_2[2] = x_bond_1[2] + dx[2];
@@ -783,7 +783,7 @@ void ComputeStressMopProfile::compute_angles()
         dx[1] = x[atom1][1];
         dx[2] = x[atom1][2];
         dx[dir] -= pos;
-        domain->minimum_image(dx[0], dx[1], dx[2]);
+        domain->minimum_image(FLERR, dx[0], dx[1], dx[2]);
         x_angle_left[0] = dx[0];
         x_angle_left[1] = dx[1];
         x_angle_left[2] = dx[2];
@@ -793,7 +793,7 @@ void ComputeStressMopProfile::compute_angles()
         dx_left[0] = x[atom2][0] - x_angle_left[0];
         dx_left[1] = x[atom2][1] - x_angle_left[1];
         dx_left[2] = x[atom2][2] - x_angle_left[2];
-        domain->minimum_image(dx_left[0], dx_left[1], dx_left[2]);
+        domain->minimum_image(FLERR, dx_left[0], dx_left[1], dx_left[2]);
         x_angle_middle[0] = x_angle_left[0] + dx_left[0];
         x_angle_middle[1] = x_angle_left[1] + dx_left[1];
         x_angle_middle[2] = x_angle_left[2] + dx_left[2];
@@ -802,7 +802,7 @@ void ComputeStressMopProfile::compute_angles()
         dx_right[0] = x[atom3][0] - x_angle_middle[0];
         dx_right[1] = x[atom3][1] - x_angle_middle[1];
         dx_right[2] = x[atom3][2] - x_angle_middle[2];
-        domain->minimum_image(dx_right[0], dx_right[1], dx_right[2]);
+        domain->minimum_image(FLERR, dx_right[0], dx_right[1], dx_right[2]);
         x_angle_right[0] = x_angle_middle[0] + dx_right[0];
         x_angle_right[1] = x_angle_middle[1] + dx_right[1];
         x_angle_right[2] = x_angle_middle[2] + dx_right[2];
@@ -971,14 +971,14 @@ void ComputeStressMopProfile::compute_dihedrals()
         x_atom_1[1] = x[atom1][1];
         x_atom_1[2] = x[atom1][2];
         x_atom_1[dir] -= pos;
-        domain->minimum_image(x_atom_1[0], x_atom_1[1], x_atom_1[2]);
+        domain->minimum_image(FLERR, x_atom_1[0], x_atom_1[1], x_atom_1[2]);
         x_atom_1[dir] += pos;
 
         // minimum image of atom2 with respect to atom1
         diffx[0] = x[atom2][0] - x_atom_1[0];
         diffx[1] = x[atom2][1] - x_atom_1[1];
         diffx[2] = x[atom2][2] - x_atom_1[2];
-        domain->minimum_image(diffx[0], diffx[1], diffx[2]);
+        domain->minimum_image(FLERR, diffx[0], diffx[1], diffx[2]);
         x_atom_2[0] = x_atom_1[0] + diffx[0];
         x_atom_2[1] = x_atom_1[1] + diffx[1];
         x_atom_2[2] = x_atom_1[2] + diffx[2];
@@ -987,7 +987,7 @@ void ComputeStressMopProfile::compute_dihedrals()
         diffx[0] = x[atom3][0] - x_atom_2[0];
         diffx[1] = x[atom3][1] - x_atom_2[1];
         diffx[2] = x[atom3][2] - x_atom_2[2];
-        domain->minimum_image(diffx[0], diffx[1], diffx[2]);
+        domain->minimum_image(FLERR, diffx[0], diffx[1], diffx[2]);
         x_atom_3[0] = x_atom_2[0] + diffx[0];
         x_atom_3[1] = x_atom_2[1] + diffx[1];
         x_atom_3[2] = x_atom_2[2] + diffx[2];
@@ -996,7 +996,7 @@ void ComputeStressMopProfile::compute_dihedrals()
         diffx[0] = x[atom4][0] - x_atom_3[0];
         diffx[1] = x[atom4][1] - x_atom_3[1];
         diffx[2] = x[atom4][2] - x_atom_3[2];
-        domain->minimum_image(diffx[0], diffx[1], diffx[2]);
+        domain->minimum_image(FLERR, diffx[0], diffx[1], diffx[2]);
         x_atom_4[0] = x_atom_3[0] + diffx[0];
         x_atom_4[1] = x_atom_3[1] + diffx[1];
         x_atom_4[2] = x_atom_3[2] + diffx[2];

src/EXTRA-FIX/fix_ave_moments.cpp

@@ -0,0 +1,636 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Sebastian Huetter (OvGU)
+------------------------------------------------------------------------- */
+
+#include "fix_ave_moments.h"
+
+#include "arg_info.h"
+#include "compute.h"
+#include "error.h"
+#include "input.h"
+#include "math_special.h"
+#include "memory.h"
+#include "modify.h"
+#include "update.h"
+#include "variable.h"
+
+#include <algorithm>
+#include <utility>
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+using MathSpecial::square;
+using MathSpecial::cube;
+
+enum { MEAN, STDDEV, VARIANCE, SKEW, KURTOSIS };
+
+/* ---------------------------------------------------------------------- */
+
+FixAveMoments::FixAveMoments(LAMMPS *lmp, int narg, char **arg) :
+    Fix(lmp, narg, arg), nvalues(0), result_list(nullptr), window_list(nullptr)
+{
+  // this fix's data is always accessible (but might be meaningless)
+  global_freq = 1;
+  dynamic_group_allow = 1;
+  time_depend = 1;
+
+  // EXAMPLE:
+  //    fix ID group-ID ave/moments Nevery Nrepeat Nfreq value1 ... valueN moment1 ... momentM keyword value ...
+
+  // the first six arguments are fixed & need at least one input and moment
+  const int nfixedargs = 6;
+  if (narg < nfixedargs + 2) utils::missing_cmd_args(FLERR, "fix ave/moments", error);
+
+  nevery = utils::inumeric(FLERR,arg[3],false,lmp);
+  nrepeat = utils::inumeric(FLERR,arg[4],false,lmp);
+  nfreq = utils::inumeric(FLERR,arg[5],false,lmp);
+
+  // scan values to count them
+
+  nvalues = 0;
+  // first input name is position after the fixed args
+  int iarg = nfixedargs;
+  while (iarg < narg) {
+    if (utils::strmatch(arg[iarg],"^[cfv]_")) {
+      nvalues++;
+      iarg++;
+    } else break;
+  }
+  if (nvalues == 0)
+    error->all(FLERR, nfixedargs,
+               "No values from computes, fixes, or variables used in fix ave/moments command");
+
+  // next, the moments
+  iarg = consume_moments(iarg, narg, arg);
+  if (moments.empty())
+    error->all(FLERR, nfixedargs,
+               "No values from computes, fixes, or variables used in fix ave/moments command");
+
+  // parse optional keywords which must follow the data
+
+  options(iarg,narg,arg);
+
+  // expand args if any have wildcard character "*"
+  // this can reset nvalues
+
+  int expand = 0;
+  char **earg;
+  int *amap = nullptr;
+  nvalues = utils::expand_args(FLERR, nvalues, &arg[nfixedargs], /* mode=scalar */ 0, earg, lmp, &amap);
+
+  if (earg != &arg[nfixedargs]) expand = 1;
+  arg = earg;
+
+  // parse values
+
+  values.clear();
+  for (int i = 0; i < nvalues; i++) {
+    ArgInfo argi(arg[i]);
+
+    value_t val;
+    val.keyword = arg[i];
+    val.which = argi.get_type();
+
+    val.argindex = argi.get_index1();
+    val.iarg = (expand ? amap[i] : i) + nfixedargs;
+    val.varlen = 0;
+    val.id = argi.get_name();
+    val.val.c = nullptr;
+
+    if ((val.which == ArgInfo::NONE) || (val.which == ArgInfo::UNKNOWN) || (argi.get_dim() > 1))
+      error->all(FLERR, val.iarg, "Invalid fix ave/moments argument: {}", arg[i]);
+
+    values.push_back(std::move(val));
+  }
+  if (nvalues != (int)values.size())
+    error->all(FLERR, Error::NOPOINTER,
+               "Could not parse value data consistently for fix ave/moments");
+
+  // setup and error check
+  // for fix inputs, check that fix frequency is acceptable
+
+  if (nevery <= 0) error->all(FLERR, 3, "Illegal fix ave/moments nevery value: {}", nevery);
+  if (nrepeat <= 0) error->all(FLERR, 4, "Illegal fix ave/moments nrepeat value: {}", nrepeat);
+  if (nfreq <= 0) error->all(FLERR, 5, "Illegal fix ave/moments nfreq value: {}", nfreq);
+
+  for (auto &val : values) {
+    switch (val.which) {
+      case ArgInfo::COMPUTE:
+        val.val.c = modify->get_compute_by_id(val.id);
+        if (!val.val.c)
+          error->all(FLERR, val.iarg, "Compute ID {} for fix ave/moments does not exist", val.id);
+        if (val.argindex == 0 && (val.val.c->scalar_flag == 0))
+          error->all(FLERR, val.iarg, "Fix ave/moments compute {} does not calculate a scalar", val.id);
+        if (val.argindex && (val.val.c->vector_flag == 0))
+          error->all(FLERR, val.iarg, "Fix ave/moments compute {} does not calculate a vector", val.id);
+        if (val.argindex && (val.argindex > val.val.c->size_vector) &&
+            (val.val.c->size_vector_variable == 0))
+          error->all(FLERR, val.iarg, "Fix ave/moments compute {} vector is accessed out-of-range{}",
+                     val.id, utils::errorurl(20));
+        if (val.argindex && val.val.c->size_vector_variable) val.varlen = 1;
+        break;
+
+      case ArgInfo::FIX:
+        val.val.f = modify->get_fix_by_id(val.id);
+        if (!val.val.f) error->all(FLERR,"Fix ID {} for fix ave/moments does not exist", val.id);
+        if ((val.argindex == 0) && (val.val.f->scalar_flag == 0))
+          error->all(FLERR, val.iarg, "Fix ave/moments fix {} does not calculate a scalar", val.id);
+        if (val.argindex && (val.val.f->vector_flag == 0))
+          error->all(FLERR, val.iarg, "Fix ave/moments fix {} does not calculate a vector", val.id);
+        if (val.argindex && (val.val.f->size_vector_variable))
+          error->all(FLERR, val.iarg, "Fix ave/moments fix {} vector cannot be variable length", val.id);
+        if (val.argindex && (val.argindex > val.val.f->size_vector))
+          error->all(FLERR, val.iarg, "Fix ave/moments fix {} vector is accessed out-of-range{}",
+                     val.id, utils::errorurl(20));
+        if (nevery % val.val.f->global_freq)
+          error->all(FLERR, val.iarg, "Fix {} for fix ave/moments not computed at compatible time{}",
+                     val.id, utils::errorurl(7));
+        break;
+
+      case ArgInfo::VARIABLE:
+        int ivariable = input->variable->find(val.id.c_str());
+        if (ivariable < 0)
+          error->all(FLERR, val.iarg, "Variable name {} for fix ave/moments does not exist", val.id);
+        if ((val.argindex == 0) && (input->variable->equalstyle(ivariable) == 0))
+          error->all(FLERR, val.iarg, "Fix ave/moments variable {} is not equal-style variable", val.id);
+        if ((val.argindex) && (input->variable->vectorstyle(ivariable) == 0))
+          error->all(FLERR, val.iarg, "Fix ave/moments variable {} is not vector-style variable",
+                     val.id);
+        break;
+    }
+  }
+
+  // if wildcard expansion occurred, free earg memory from expand_args()
+  // wait to do this until after file comment lines are printed
+
+  if (expand) {
+    for (int i = 0; i < nvalues; i++) delete[] earg[i];
+    memory->sfree(earg);
+    memory->sfree(amap);
+  }
+
+  // allocate memory for averaging
+
+  window_list = nullptr;
+  result_list = nullptr;
+
+  // one window of nvalues columns and nrepeat rows (=all scalars of one value are consecutive)
+  memory->create(window_list, nvalues, nrepeat, "ave/moments:window_list");
+  for (int i = 0; i < nvalues; i++)
+    for (int j = 0; j < nrepeat; j++)
+      window_list[i][j] = 0.0;
+
+  // this fix produces a global vector and array
+
+  vector_flag = 1;
+  size_vector = nvalues * moments.size();
+  array_flag = 1;
+  size_array_rows = size_vector;
+  size_array_cols = nhistory;
+
+  // produce nmoments outputs per value with nhistory depth
+  memory->create(result_list, nhistory, size_vector, "ave/moments:result_list");
+  for (int i = 0; i < nhistory; i++)
+    for (int j = 0; j < size_vector; j++)
+      result_list[i][j] = 0.0;
+
+  // intensive/extensive flags set by compute,fix,variable that produces value
+
+  extvector = -1;
+  extarray = -2;
+  extlist = new int[size_vector];
+  int extvalue = 0;
+  int i = 0;
+  for (auto &val : values) {
+    switch (val.which) {
+      case ArgInfo::COMPUTE:
+        if (val.argindex == 0) extvalue = val.val.c->extscalar;
+        else if (val.val.f->extvector >= 0) extvalue = val.val.c->extvector;
+        else extvalue = val.val.c->extlist[val.argindex-1];
+        break;
+
+      case ArgInfo::FIX:
+        if (val.argindex == 0) extvalue = val.val.f->extscalar;
+        else if (val.val.f->extvector >= 0) extvalue = val.val.f->extvector;
+        else extvalue = val.val.f->extlist[val.argindex-1];
+        break;
+
+      case ArgInfo::VARIABLE:
+        extvalue = 0;
+        break;
+    }
+    if (extvalue == -1)
+      error->all(FLERR, Error::NOLASTLINE, "Fix ave/moments cannot set output array "
+                 "intensive/extensive from these inputs");
+    if (extarray < -1) extarray = extvalue;
+    else if (extvalue != extarray)
+      error->all(FLERR, Error::NOLASTLINE, "Fix ave/moments cannot set output array "
+                 "intensive/extensive from these inputs");
+    for (int j=0; j < (int)moments.size(); j++)
+      extlist[i + j] = extvalue;
+    i += moments.size();
+  }
+
+  // initializations
+
+  iwindow = window_filled = 0;
+  iresult = 0;
+
+  // nvalid = next step on which end_of_step does something
+  // add nvalid to all computes that store invocation times
+  // since don't know a priori which are invoked by this fix
+  // once in end_of_step() can set timestep for ones actually invoked
+
+  nvalid_comp_next = -1;
+  nvalid = -1;
+  setnextvalid();
+  modify->addstep_compute_all(nvalid);
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixAveMoments::~FixAveMoments()
+{
+  values.clear();
+  moments.clear();
+  delete[] extlist;
+
+  memory->destroy(window_list);
+  memory->destroy(result_list);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixAveMoments::setmask()
+{
+  int mask = 0;
+  mask |= END_OF_STEP;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixAveMoments::init()
+{
+  // update indices/pointers for all computes,fixes,variables
+
+  for (auto &val : values) {
+    switch (val.which) {
+      case ArgInfo::COMPUTE:
+        val.val.c = modify->get_compute_by_id(val.id);
+        if (!val.val.c)
+          error->all(FLERR, Error::NOLASTLINE, "Compute ID {} for fix ave/moments does not exist",
+                     val.id);
+        break;
+
+      case ArgInfo::FIX:
+        val.val.f = modify->get_fix_by_id(val.id);
+        if (!val.val.f)
+          error->all(FLERR, Error::NOLASTLINE, "Fix ID {} for fix ave/moments does not exist", val.id);
+        break;
+
+      case ArgInfo::VARIABLE:
+        val.val.v = input->variable->find(val.id.c_str());
+        if (val.val.v < 0)
+          error->all(FLERR, Error::NOLASTLINE, "Variable name {} for fix ave/moments does not exist",
+                     val.id);
+        break;
+    }
+  }
+
+  // need to reset nvalid if nvalid < ntimestep b/c minimize was performed
+
+  if (nvalid < update->ntimestep) {
+    setnextvalid();
+    modify->addstep_compute_all(nvalid);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   only does something if nvalid = current timestep
+------------------------------------------------------------------------- */
+
+void FixAveMoments::setup(int /*vflag*/)
+{
+  end_of_step();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixAveMoments::end_of_step()
+{
+  // skip if not step which requires doing something
+
+  bigint ntimestep = update->ntimestep;
+  if (ntimestep != nvalid) return;
+
+  // always take new values
+  append_values();
+
+  // if window boundary reached, do a compute, otherwise just schedule next take
+  if (ntimestep == nvalid_comp_next) {
+    update_results();
+    setnextvalid();
+  } else {
+    nvalid += nevery;
+  }
+
+  modify->addstep_compute(nvalid);
+}
+
+/* ----------------------------------------------------------------------
+   return scalar value
+------------------------------------------------------------------------- */
+
+double FixAveMoments::compute_scalar()
+{
+  return 0.0;
+}
+
+/* ----------------------------------------------------------------------
+   return Ith vector value
+------------------------------------------------------------------------- */
+
+double FixAveMoments::compute_vector(int i)
+{
+  return compute_array(i, 0);
+}
+
+/* ----------------------------------------------------------------------
+   return I,J array value
+------------------------------------------------------------------------- */
+
+double FixAveMoments::compute_array(int i, int j)
+{
+  if (i >= size_vector) return 0.0;
+  if (j >= nhistory) return 0.0;
+  // locate the j'th previous result in the ring buffer, relative to the
+  // row before iresult (the current insert cursor)
+  int row = (iresult - 1 - j + nhistory) % nhistory;
+  return result_list[row][i];
+}
+
+/* ----------------------------------------------------------------------
+   parse moment names
+------------------------------------------------------------------------- */
+
+int FixAveMoments::consume_moments(int iarg, int narg, char **arg)
+{
+  moments.clear();
+
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"mean") == 0)
+      moments.push_back(MEAN);
+    else if (strcmp(arg[iarg],"stddev") == 0)
+      moments.push_back(STDDEV);
+    else if (strcmp(arg[iarg],"variance") == 0)
+      moments.push_back(VARIANCE);
+    else if (strcmp(arg[iarg],"skew") == 0)
+      moments.push_back(SKEW);
+    else if (strcmp(arg[iarg],"kurtosis") == 0)
+      moments.push_back(KURTOSIS);
+    else
+      break;
+    iarg++;
+  }
+  return iarg;
+}
+
+/* ----------------------------------------------------------------------
+   parse optional args
+------------------------------------------------------------------------- */
+
+void FixAveMoments::options(int iarg, int narg, char **arg)
+{
+  // option defaults
+
+  nhistory = 1;
+  startstep = 0;
+
+  // optional args
+
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"history") == 0) {
+      if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/moments history", error);
+      nhistory = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      if (nhistory <= 0)
+        error->all(FLERR, iarg+2, "Illegal ave/moments history argument {}; must be > 0",
+                   nhistory);
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"start") == 0) {
+      if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/moments start", error);
+      startstep = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      iarg += 2;
+    } else error->all(FLERR,"Unknown fix ave/moments keyword {}", arg[iarg]);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   return next timestep no earlier than `after`, rounded to next
+   multiple of freq
+------------------------------------------------------------------------- */
+
+bigint next_after(const bigint ts, const bigint after, const int freq)
+{
+  if (ts >= after) return ts;
+  return ts + ((after - ts) / freq + 1) * freq;
+}
+
+/* ----------------------------------------------------------------------
+   calculate nvalid = next step on which end_of_step does something
+   this is either a step to take data
+    or a step to take and compute the values (nfreq multiple)
+   startstep is lower bound on nfreq multiple
+------------------------------------------------------------------------- */
+
+void FixAveMoments::setnextvalid()
+{
+  bigint ntimestep = update->ntimestep;
+
+  if (nvalid_comp_next > ntimestep) {
+    // next window end boundary is still in the future, just increment
+    nvalid = ntimestep + nevery;
+    return;
+  }
+
+  // get next window end first
+  bigint next_comp = (ntimestep/nfreq)*nfreq + nfreq;
+  nvalid_comp_next = next_after(next_comp, startstep, nfreq);
+
+  // from there, calculate the first time we have to take a value
+  bigint ntake = nvalid_comp_next - static_cast<bigint>(nrepeat-1)*nevery;
+  nvalid = next_after(ntake, ntimestep, nevery);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixAveMoments::get_values(std::vector<double>& scalars)
+{
+  // accumulate results of computes,fixes,variables to local copy
+  int i = 0;
+  double scalar = 0.0;
+  for (auto &val : values) {
+    switch (val.which) {
+      case ArgInfo::COMPUTE:
+        // invoke compute if not previously invoked
+        // ensure no out-of-range access to variable-length compute vector
+        if (val.argindex == 0) {
+          if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) {
+            val.val.c->compute_scalar();
+            val.val.c->invoked_flag |= Compute::INVOKED_SCALAR;
+          }
+          scalar = val.val.c->scalar;
+        } else {
+          if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) {
+            val.val.c->compute_vector();
+            val.val.c->invoked_flag |= Compute::INVOKED_VECTOR;
+          }
+          if (val.varlen && (val.val.c->size_vector < val.argindex)) scalar = 0.0;
+          else scalar = val.val.c->vector[val.argindex-1];
+        }
+        break;
+
+      case ArgInfo::FIX:
+        // access fix fields, guaranteed to be ready
+        if (val.argindex == 0)
+          scalar = val.val.f->compute_scalar();
+        else
+          scalar = val.val.f->compute_vector(val.argindex-1);
+        break;
+
+      case ArgInfo::VARIABLE:
+        // evaluate equal-style or vector-style variable
+        // if index exceeds vector length, use a zero value
+        //   this can be useful if vector length is not known a priori
+        if (val.argindex == 0)
+          scalar = input->variable->compute_equal(val.val.v);
+        else {
+          double *varvec;
+          int nvec = input->variable->compute_vector(val.val.v,&varvec);
+          if (val.argindex > nvec) scalar = 0.0;
+          else scalar = varvec[val.argindex-1];
+        }
+        break;
+    }
+
+    scalars[i] = scalar;
+    ++i;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixAveMoments::append_values()
+{
+  // accumulate results of computes,fixes,variables to local copy
+  // compute/fix/variable may invoke computes so wrap with clear/add
+
+  modify->clearstep_compute();
+
+  std::vector<double> scalars(nvalues);
+  get_values(scalars);
+
+  // transpose for faster access later
+  for (int i=0; i<nvalues; i++) {
+    window_list[i][iwindow] = scalars[i];
+  }
+
+  if (++iwindow >= nrepeat) {
+    window_filled = 1;
+    iwindow = 0;
+  }
+}
+
+void FixAveMoments::update_results()
+{
+  const int count = window_filled ? nrepeat : iwindow;
+  // Delay until we can safely do all moments. Avoids branching in the hot loop.
+  if (count<3) return;
+
+  double *result = result_list[iresult];
+
+  // zero out previous values
+
+  for (int i = 0; i < size_vector; i++)
+    result[i] = 0.0;
+
+  const double inv_n = 1.0 / count;
+  const double fk2 = (double)count / (count - 1);
+  const double fk3 = square((double)count) / ((count - 1) * (count - 2));
+  const double np1_nm3 = (count+1.0)/(count-3.0);
+  const double _3_nm1_nm3 = 3.0 * (count-1.0)/(count-3.0);
+
+  // Each value is a series that can be processed individually
+  for (int i = 0; i < nvalues; i++) {
+    const double* series = window_list[i];
+
+    // first pass: mean
+    double mean = 0.0;
+    for (int j = 0; j<count; j++)
+      mean += series[j] * inv_n;
+
+    // second pass: calculate biased sample moments
+    double m2 = 0.0;
+    double m3 = 0.0;
+    double m4 = 0.0;
+    for (int j = 0; j<count; j++) {
+      const double dx = series[j] - mean;
+      double y = square(dx) * inv_n;
+      m2 += y;
+      y *= dx;
+      m3 += y;
+      y *= dx;
+      m4 += y;
+    }
+    // obtain unbiased cumulants as defined by Cramér and
+    // reported i.e. in https://doi.org/10.1111/1467-9884.00122
+    const double k2 = fk2 * m2;
+    const double k3 = fk3 * m3;
+    const double k4 = fk3 * (np1_nm3 * m4 - _3_nm1_nm3 * square(m2));
+    // corrected sample standard deviation
+    const double stddev = sqrt(k2);
+    // adjusted Fisher-Pearson standardized moment coefficient G1
+    const double G1 = k3 / cube(stddev);
+    // adjusted Fisher-Pearson standardized moment coefficient G2 (from unbiased cumulant)
+    const double G2 = k4 / square(k2);
+
+    // map to result array, starting at value interleave offset
+    double* rfirst = &result[i * moments.size()];
+    for (int j = 0; j < (int)moments.size(); j++) {
+      switch(moments[j]) {
+        case MEAN:
+          rfirst[j] = mean;
+          break;
+        case STDDEV:
+          rfirst[j] = stddev;
+          break;
+        case VARIANCE:
+          rfirst[j] = k2;
+          break;
+        case SKEW:
+          rfirst[j] = G1;
+          break;
+        case KURTOSIS:
+          rfirst[j] = G2;
+          break;
+      }
+    }
+  }
+
+  if (++iresult >= nhistory)
+    iresult = 0;
+}

src/EXTRA-FIX/fix_ave_moments.h

@@ -0,0 +1,78 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+// clang-format off
+FixStyle(ave/moments,FixAveMoments);
+// clang-format on
+#else
+
+#ifndef LMP_FIX_AVE_MOMENTS_H
+#define LMP_FIX_AVE_MOMENTS_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixAveMoments : public Fix {
+ public:
+  FixAveMoments(class LAMMPS *, int, char **);
+  ~FixAveMoments() override;
+  int setmask() override;
+  void init() override;
+  void setup(int) override;
+  void end_of_step() override;
+  double compute_scalar() override;
+  double compute_vector(int) override;
+  double compute_array(int, int) override;
+
+ private:
+  struct value_t {
+    int which;       // type of data: COMPUTE, FIX, VARIABLE
+    int argindex;    // 1-based index if data is vector, else 0
+    int iarg;        // argument index in original argument list
+    int varlen;      // 1 if value is from variable-length compute
+    std::string id;         // compute/fix/variable ID
+    std::string keyword;    // column keyword in output
+    union {
+      class Compute *c;
+      class Fix *f;
+      int v;
+    } val;
+  };
+  std::vector<value_t> values;
+  std::vector<int> moments;
+
+  int nrepeat, nfreq;
+  int nvalues;
+  bigint nvalid, nvalid_comp_next;
+
+  int startstep;
+
+  int nhistory, iresult;
+  double **result_list;
+
+  int iwindow, window_filled;
+  double **window_list;
+
+  int consume_moments(int iarg, int narg, char **arg);
+  void options(int, int, char **);
+  void setnextvalid();
+
+  void get_values(std::vector<double>& scalars);
+  void append_values();
+  void update_results();
+};
+}    // namespace LAMMPS_NS
+#endif
+#endif

src/EXTRA-FIX/fix_drag.cpp

@@ -114,7 +114,7 @@ void FixDrag::post_force(int /*vflag*/)
       if (!xflag) dx = 0.0;
       if (!yflag) dy = 0.0;
       if (!zflag) dz = 0.0;
-      domain->minimum_image(dx,dy,dz);
+      domain->minimum_image(FLERR, dx,dy,dz);
       r = sqrt(dx*dx + dy*dy + dz*dz);
       if (r > delta) {
         prefactor = f_mag/r;

src/EXTRA-FIX/fix_filter_corotate.cpp

@@ -547,17 +547,17 @@ void FixFilterCorotate::pre_neighbor()
           del1[0] = x[atom1][0]-x[oxy][0];
           del1[1] = x[atom1][1]-x[oxy][1];
           del1[2] = x[atom1][2]-x[oxy][2];
-          domain->minimum_image(del1);
+          domain->minimum_image(FLERR, del1);
 
           del2[0] = x[atom2][0]-x[atom1][0];
           del2[1] = x[atom2][1]-x[atom1][1];
           del2[2] = x[atom2][2]-x[atom1][2];
-          domain->minimum_image(del2);
+          domain->minimum_image(FLERR, del2);
 
           del3[0] = x[atom3][0]-x[atom1][0];
           del3[1] = x[atom3][1]-x[atom1][1];
           del3[2] = x[atom3][2]-x[atom1][2];
-          domain->minimum_image(del3);
+          domain->minimum_image(FLERR, del3);
 
           double a = (del2[1])*(del3[2]) - (del2[2])*(del3[1]);
           double b = (del2[2])*(del3[0]) - (del2[0])*(del3[2]);
@@ -620,17 +620,17 @@ void FixFilterCorotate::pre_neighbor()
         del1[0] = x[atom1][0]-x[oxy][0];
         del1[1] = x[atom1][1]-x[oxy][1];
         del1[2] = x[atom1][2]-x[oxy][2];
-        domain->minimum_image(del1);
+        domain->minimum_image(FLERR, del1);
 
         del2[0] = x[atom2][0]-x[atom1][0];
         del2[1] = x[atom2][1]-x[atom1][1];
         del2[2] = x[atom2][2]-x[atom1][2];
-        domain->minimum_image(del2);
+        domain->minimum_image(FLERR, del2);
 
         del3[0] = x[atom3][0]-x[atom1][0];
         del3[1] = x[atom3][1]-x[atom1][1];
         del3[2] = x[atom3][2]-x[atom1][2];
-        domain->minimum_image(del3);
+        domain->minimum_image(FLERR, del3);
 
         double a = (del2[1])*(del3[2]) - (del2[2])*(del3[1]);
         double b = (del2[2])*(del3[0]) - (del2[0])*(del3[2]);
@@ -1414,7 +1414,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
     del[i][0] = x[list_cluster[i]][0] - x[list_cluster[0]][0];
     del[i][1] = x[list_cluster[i]][1] - x[list_cluster[0]][1];
     del[i][2] = x[list_cluster[i]][2] - x[list_cluster[0]][2];
-    domain->minimum_image(del[i]);
+    domain->minimum_image(FLERR, del[i]);
     r[i] = 1.0/sqrt(del[i][0]*del[i][0]+del[i][1]*del[i][1]+
       del[i][2]*del[i][2]);
   }

src/EXTRA-FIX/fix_pafi.cpp

@@ -261,7 +261,7 @@ void FixPAFI::post_force(int /*vflag*/)
       deviation[0] = x[i][0]-path[i][0]; // x-path
       deviation[1] = x[i][1]-path[i][1]; // x-path
       deviation[2] = x[i][2]-path[i][2]; // x-path
-      domain->minimum_image(deviation);
+      domain->minimum_image(FLERR, deviation);
 
       proj[3] += path[i][6]*deviation[0]; // (x-path).dn/nn = psi
       proj[3] += path[i][7]*deviation[1]; // (x-path).dn/nn = psi
@@ -424,7 +424,7 @@ void FixPAFI::min_post_force(int /*vflag*/)
       deviation[0] = x[i][0]-path[i][0]; // x-path
       deviation[1] = x[i][1]-path[i][1]; // x-path
       deviation[2] = x[i][2]-path[i][2]; // x-path
-      domain->minimum_image(deviation);
+      domain->minimum_image(FLERR, deviation);
 
       proj[3] += path[i][6]*deviation[0]; // (x-path).dn/nn = psi
       proj[3] += path[i][7]*deviation[1]; // (x-path).dn/nn = psi

src/EXTRA-MOLECULE/angle_cosine_delta.cpp

@@ -155,13 +155,13 @@ double AngleCosineDelta::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
@@ -185,13 +185,13 @@ void AngleCosineDelta::born_matrix(int type, int i1, int i2, int i3, double &du,
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;

src/EXTRA-MOLECULE/angle_cosine_periodic.cpp

@@ -284,13 +284,13 @@ double AngleCosinePeriodic::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
@@ -311,13 +311,13 @@ void AngleCosinePeriodic::born_matrix(int type, int i1, int i2, int i3, double &
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;

src/EXTRA-MOLECULE/angle_cosine_shift.cpp

@@ -258,13 +258,13 @@ double AngleCosineShift::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;

src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp

@@ -297,13 +297,13 @@ double AngleCosineShiftExp::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;

src/EXTRA-MOLECULE/angle_cosine_squared_restricted.cpp

@@ -242,13 +242,13 @@ double AngleCosineSquaredRestricted::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
@@ -272,13 +272,13 @@ void AngleCosineSquaredRestricted::born_matrix(int type, int i1, int i2, int i3,
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;

src/EXTRA-MOLECULE/angle_fourier.cpp

@@ -263,13 +263,13 @@ double AngleFourier::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
@@ -291,13 +291,13 @@ void AngleFourier::born_matrix(int type, int i1, int i2, int i3, double &du, dou
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;

src/EXTRA-MOLECULE/angle_fourier_simple.cpp

@@ -269,13 +269,13 @@ double AngleFourierSimple::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
@@ -297,13 +297,13 @@ void AngleFourierSimple::born_matrix(int type, int i1, int i2, int i3, double &d
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;

src/EXTRA-MOLECULE/angle_gaussian.cpp

@@ -325,13 +325,13 @@ double AngleGaussian::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;

src/EXTRA-MOLECULE/angle_mwlc.cpp

@@ -260,13 +260,13 @@ double AngleMWLC::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
@@ -289,12 +289,12 @@ void AngleMWLC::born_matrix(int type, int i1, int i2, int i3, double &du, double
   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);
+  domain->minimum_image(FLERR, delx1, dely1, 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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
   c /= sqrt((delx1 * delx1 + dely1 * dely1 + delz1 * delz1) *

src/EXTRA-MOLECULE/angle_quartic.cpp

@@ -269,13 +269,13 @@ double AngleQuartic::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
@@ -299,13 +299,13 @@ void AngleQuartic::born_matrix(int type, int i1, int i2, int i3, double &du, dou
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;

src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp

@@ -74,7 +74,7 @@ void BondHarmonicRestrain::compute(int eflag, int vflag)
     delx = x0[i1][0] - x0[i2][0];
     dely = x0[i1][1] - x0[i2][1];
     delz = x0[i1][2] - x0[i2][2];
-    domain->minimum_image(delx, dely, delz);
+    domain->minimum_image(FLERR, delx, dely, delz);
     rsq = delx * delx + dely * dely + delz * delz;
     r0 = sqrt(rsq);
 
@@ -235,7 +235,7 @@ double BondHarmonicRestrain::single(int type, double rsq, int i, int j, double &
   double delx = x0[i][0] - x0[j][0];
   double dely = x0[i][1] - x0[j][1];
   double delz = x0[i][2] - x0[j][2];
-  domain->minimum_image(delx, dely, delz);
+  domain->minimum_image(FLERR, delx, dely, delz);
   double r0 = sqrt(delx * delx + dely * dely + delz * delz);
 
   double r = sqrt(rsq);

src/EXTRA-MOLECULE/dihedral_spherical.cpp

@@ -110,9 +110,9 @@ static double Phi(double const *x1,    //array holding x,y,z coords atom 1
   }
 
   //Consider periodic boundary conditions:
-  domain->minimum_image(vb12[0], vb12[1], vb12[2]);
+  domain->minimum_image(FLERR, vb12[0], vb12[1], vb12[2]);
-  domain->minimum_image(vb23[0], vb23[1], vb23[2]);
+  domain->minimum_image(FLERR, vb23[0], vb23[1], vb23[2]);
-  domain->minimum_image(vb34[0], vb34[1], vb34[2]);
+  domain->minimum_image(FLERR, vb34[0], vb34[1], vb34[2]);
 
   //--- Compute the normal to the planes formed by atoms 1,2,3 and 2,3,4 ---
 

src/EXTRA-MOLECULE/improper_distance.cpp

@@ -94,31 +94,31 @@ void ImproperDistance::compute(int eflag, int vflag)
     xab = x[i2][0] - x[i1][0];
     yab = x[i2][1] - x[i1][1];
     zab = x[i2][2] - x[i1][2];
-    domain->minimum_image(xab,yab,zab);
+    domain->minimum_image(FLERR, xab,yab,zab);
 
     // bond 1->3
     xac = x[i3][0] - x[i1][0];
     yac = x[i3][1] - x[i1][1];
     zac = x[i3][2] - x[i1][2];
-    domain->minimum_image(xac,yac,zac);
+    domain->minimum_image(FLERR, xac,yac,zac);
 
     // bond 1->4
     xad = x[i4][0] - x[i1][0];
     yad = x[i4][1] - x[i1][1];
     zad = x[i4][2] - x[i1][2];
-    domain->minimum_image(xad,yad,zad);
+    domain->minimum_image(FLERR, xad,yad,zad);
 
     // bond 2-3
     xbc = x[i3][0] - x[i2][0];
     ybc = x[i3][1] - x[i2][1];
     zbc = x[i3][2] - x[i2][2];
-    domain->minimum_image(xbc,ybc,zbc);
+    domain->minimum_image(FLERR, xbc,ybc,zbc);
 
     // bond 2-4
     xbd = x[i4][0] - x[i2][0];
     ybd = x[i4][1] - x[i2][1];
     zbd = x[i4][2] - x[i2][2];
-    domain->minimum_image(xbd,ybd,zbd);
+    domain->minimum_image(FLERR, xbd,ybd,zbd);
 
     xna =   ybc*zbd - zbc*ybd;
     yna = -(xbc*zbd - zbc*xbd);

src/GRANULAR/fix_pour.cpp

@@ -540,7 +540,7 @@ void FixPour::pre_exchange()
           delx = coords[m][0] - xnear[i][0];
           dely = coords[m][1] - xnear[i][1];
           delz = coords[m][2] - xnear[i][2];
-          domain->minimum_image(delx, dely, delz);
+          domain->minimum_image(FLERR, delx, dely, delz);
           rsq = delx * delx + dely * dely + delz * delz;
           radsum = coords[m][3] + xnear[i][3];
           if (rsq <= radsum * radsum) break;
@@ -781,7 +781,7 @@ int FixPour::overlap(int i)
       double delx = x[0] - xc;
       double dely = x[1] - yc;
       double delz = 0.0;
-      domain->minimum_image(delx, dely, delz);
+      domain->minimum_image(FLERR, delx, dely, delz);
       double rsq = delx * delx + dely * dely;
       double r = rc + delta;
       if (rsq > r * r) return 0;

src/KOKKOS/fix_minimize_kokkos.cpp

@@ -121,7 +121,7 @@ void FixMinimizeKokkos::reset_coords()
       double dx = dx0;
       double dy = dy0;
       double dz = dz0;
-      // domain->minimum_image(dx,dy,dz);
+      // domain->minimum_image(FLERR, dx,dy,dz);
       {
         if (triclinic == 0) {
           if (xperiodic) {
@@ -175,7 +175,7 @@ void FixMinimizeKokkos::reset_coords()
             }
           }
         }
-      } // end domain->minimum_image(dx,dy,dz);
+      } // end domain->minimum_image(FLERR, dx,dy,dz);
       if (dx != dx0) l_x0[n] = l_x(i,0) - dx;
       if (dy != dy0) l_x0[n+1] = l_x(i,1) - dy;
       if (dz != dz0) l_x0[n+2] = l_x(i,2) - dz;

src/KOKKOS/mliap_model_python_kokkos.h

@@ -29,7 +29,7 @@ class MLIAPModelPythonKokkos : public MLIAPModelPython, public MLIAPModelKokkos<
  public:
   MLIAPModelPythonKokkos(LAMMPS *, char * = nullptr);
   ~MLIAPModelPythonKokkos();
-  void read_coeffs(char *fname);
+  void read_coeffs(char *fname) override;
 
   void compute_gradients(class MLIAPData *) override;
   void compute_gradgrads(class MLIAPData *) override;

src/KOKKOS/pair_pace_extrapolation_kokkos.cpp

@@ -37,15 +37,9 @@
 
 #include <cstring>
 
+// prototype repeated from base class implementation
 namespace LAMMPS_NS {
   struct ACEALImpl {
-    ACEALImpl() : basis_set(nullptr), ace(nullptr) {}
-
-    ~ACEALImpl() {
-      delete basis_set;
-      delete ace;
-    }
-
     ACEBBasisSet *basis_set;
     ACEBEvaluator *ace;
   };

src/KOKKOS/pair_pace_kokkos.cpp

@@ -38,14 +38,9 @@
 
 #include <cstring>
 
+// prototype repeated from base class implementation
 namespace LAMMPS_NS {
 struct ACEImpl {
-  ACEImpl() : basis_set(nullptr), ace(nullptr) {}
-  ~ACEImpl()
-  {
-    delete basis_set;
-    delete ace;
-  }
   ACECTildeBasisSet *basis_set;
   ACERecursiveEvaluator *ace;
 };

src/LEPTON/angle_lepton.cpp

@@ -395,13 +395,13 @@ double AngleLepton::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;

src/LEPTON/dihedral_lepton.cpp

@@ -508,9 +508,9 @@ double DihedralLepton::get_phi(double const *x1,    //array holding x,y,z coords
   }
 
   //Consider periodic boundary conditions:
-  domain->minimum_image(vb12[0], vb12[1], vb12[2]);
+  domain->minimum_image(FLERR, vb12[0], vb12[1], vb12[2]);
-  domain->minimum_image(vb23[0], vb23[1], vb23[2]);
+  domain->minimum_image(FLERR, vb23[0], vb23[1], vb23[2]);
-  domain->minimum_image(vb34[0], vb34[1], vb34[2]);
+  domain->minimum_image(FLERR, vb34[0], vb34[1], vb34[2]);
 
   //--- Compute the normal to the planes formed by atoms 1,2,3 and 2,3,4 ---
 

src/MACHDYN/pair_smd_hertz.cpp

@@ -145,7 +145,7 @@ void PairHertz::compute(int eflag, int vflag) {
                                         dely0 = x0[j][1] - x0[i][1];
                                         delz0 = x0[j][2] - x0[i][2];
                                         if (periodic) {
-                                                domain->minimum_image(delx0, dely0, delz0);
+                                                domain->minimum_image(FLERR, delx0, dely0, delz0);
                                         }
                                         rSq0 = delx0 * delx0 + dely0 * dely0 + delz0 * delz0; // initial distance
                                         sphCut = sph_radius[i] + sph_radius[j];

src/MACHDYN/pair_smd_tlsph.cpp

@@ -220,7 +220,7 @@ void PairTlsph::PreCompute() {
         dx = xj - xi;
 
         if (periodic)
-          domain->minimum_image(dx0(0), dx0(1), dx0(2));
+          domain->minimum_image(FLERR, dx0(0), dx0(1), dx0(2));
 
         r0Sq = dx0.squaredNorm();
         h = irad + radius[j];
@@ -488,7 +488,7 @@ void PairTlsph::ComputeForces(int eflag, int vflag) {
       }
 
       if (periodic)
-        domain->minimum_image(dx0(0), dx0(1), dx0(2));
+        domain->minimum_image(FLERR, dx0(0), dx0(1), dx0(2));
 
       // check that distance between i and j (in the reference config) is less than cutoff
       dx0 = x0j - x0i;

src/MACHDYN/pair_smd_triangulated_surface.cpp

@@ -154,7 +154,7 @@ void PairTriSurf::compute(int eflag, int vflag) {
                         x4(2) = x[particle][2];
                         dx = x_center - x4; //
                         if (periodic) {
-                                domain->minimum_image(dx(0), dx(1), dx(2));
+                                domain->minimum_image(FLERR, dx(0), dx(1), dx(2));
                         }
                         rsq = dx.squaredNorm();
 

src/MC/fix_bond_swap.cpp

@@ -723,7 +723,7 @@ double FixBondSwap::dist_rsq(int i, int j)
   double delx = x[i][0] - x[j][0];
   double dely = x[i][1] - x[j][1];
   double delz = x[i][2] - x[j][2];
-  domain->minimum_image(delx,dely,delz);
+  domain->minimum_image(FLERR, delx,dely,delz);
   return (delx*delx + dely*dely + delz*delz);
 }
 

src/MC/fix_neighbor_swap.cpp

@@ -20,6 +20,7 @@
 #include "angle.h"
 #include "atom.h"
 #include "bond.h"
+#include "citeme.h"
 #include "comm.h"
 #include "compute.h"
 #include "compute_voronoi_atom.h"
@@ -31,6 +32,7 @@
 #include "group.h"
 #include "improper.h"
 #include "kspace.h"
+#include "math_extra.h"
 #include "math_special.h"
 #include "memory.h"
 #include "modify.h"
@@ -40,15 +42,17 @@
 #include "region.h"
 #include "update.h"
 
-#include <cctype>
 #include <cfloat>
 #include <cmath>
 #include <cstring>
+#include <unordered_set>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
+using MathExtra::distsq3;
+using MathSpecial::square;
 
-static const char cite_fix_neighbor_swap_c[] =
+static const char cite_fix_neighbor_swap[] =
     "fix neighbor/swap command: doi:10.1016/j.commatsci.2022.111929\n\n"
     "@Article{Tavenner2023111929,\n"
     " author = {Jacob P. Tavenner and Mikhail I. Mendelev and John W. Lawson},\n"
@@ -58,15 +62,17 @@ static const char cite_fix_neighbor_swap_c[] =
     " year = {2023},\n"
     " volume = {218},\n"
     " pages = {111929}\n"
-    " url = {https://www.sciencedirect.com/science/article/pii/S0927025622006401}\n"
+    " url = {https://dx.doi.org/10.1016/j.commatsci.2022.111929}\n"
     "}\n\n";
 
 /* ---------------------------------------------------------------------- */
 
 FixNeighborSwap::FixNeighborSwap(LAMMPS *lmp, int narg, char **arg) :
-    Fix(lmp, narg, arg), region(nullptr), idregion(nullptr), type_list(nullptr), qtype(nullptr),
+    Fix(lmp, narg, arg), region(nullptr), idregion(nullptr), type_list(nullptr), rate_list(nullptr),
-    c_voro(nullptr), voro_neighbor_list(nullptr), sqrt_mass_ratio(nullptr),
+    qtype(nullptr), sqrt_mass_ratio(nullptr), voro_neighbor_list(nullptr),
-    local_swap_iatom_list(nullptr), random_equal(nullptr), c_pe(nullptr)
+    local_swap_iatom_list(nullptr), local_swap_neighbor_list(nullptr),
+    local_swap_type_list(nullptr), local_swap_probability(nullptr), random_equal(nullptr),
+    id_voro(nullptr), c_voro(nullptr), c_pe(nullptr)
 {
   if (narg < 10) utils::missing_cmd_args(FLERR, "fix neighbor/swap", error);
 
@@ -79,37 +85,49 @@ FixNeighborSwap::FixNeighborSwap(LAMMPS *lmp, int narg, char **arg) :
   restart_global = 1;
   time_depend = 1;
 
+  ke_flag = 1;
+  diff_flag = 0;
+  rates_flag = 0;
+  nswaptypes = 0;
+
+  if (lmp->citeme) lmp->citeme->add(cite_fix_neighbor_swap);
+
   // required args
 
   nevery = utils::inumeric(FLERR, arg[3], false, lmp);
   ncycles = utils::inumeric(FLERR, arg[4], false, lmp);
   seed = utils::inumeric(FLERR, arg[5], false, lmp);
   double temperature = utils::numeric(FLERR, arg[6], false, lmp);
-  r_0 = utils::inumeric(FLERR, arg[7], false, lmp);
+  double r_0 = utils::inumeric(FLERR, arg[7], false, lmp);
+
+  if (nevery <= 0)
+    error->all(FLERR, 3, "Illegal fix neighbor/swap command nevery value: {}", nevery);
+  if (ncycles < 0)
+    error->all(FLERR, 4, "Illegal fix neighbor/swap command ncycles value: {}", ncycles);
+  if (seed <= 0) error->all(FLERR, 5, "Illegal fix neighbor/swap command seed value: {}", seed);
+  if (temperature <= 0.0)
+    error->all(FLERR, 6, "Illegal fix neighbor/swap command temperature value: {}", temperature);
+  if (r_0 <= 0.0) error->all(FLERR, 7, "Illegal fix neighbor/swap command R0 value: {}", r_0);
 
   // Voro compute check
 
-  int icompute = modify->find_compute(utils::strdup(arg[8]));
+  id_voro = utils::strdup(arg[8]);
-  if (icompute < 0) error->all(FLERR, "Could not find neighbor compute ID");
+  c_voro = modify->get_compute_by_id(id_voro);
-  c_voro = modify->compute[icompute];
+  if (!c_voro) error->all(FLERR, 8, "Could not find compute voronoi ID {}", id_voro);
   if (c_voro->local_flag == 0)
-    error->all(FLERR, "Neighbor compute does not compute local info");
+    error->all(FLERR, 8, "Voronoi compute {} does not compute local info", id_voro);
   if (c_voro->size_local_cols != 3)
-    error->all(FLERR, "Neighbor compute does not give i, j, size as expected");
+    error->all(FLERR, 8, "Voronoi compute {} does not compute i, j, sizes as expected", id_voro);
-
-  if (nevery <= 0) error->all(FLERR, "Illegal fix neighbor/swap command nevery value");
-  if (ncycles < 0) error->all(FLERR, "Illegal fix neighbor/swap command ncycles value");
-  if (seed <= 0) error->all(FLERR, "Illegal fix neighbor/swap command seed value");
-  if (temperature <= 0.0) error->all(FLERR, "Illegal fix neighbor/swap command temperature value");
 
   beta = 1.0 / (force->boltz * temperature);
+  inv_r_0 = 1.0 / r_0;
 
   memory->create(type_list, atom->ntypes, "neighbor/swap:type_list");
   memory->create(rate_list, atom->ntypes, "neighbor/swap:rate_list");
 
   // read options from end of input line
 
-  options(narg - 8, &arg[8]);
+  options(narg - 9, &arg[9]);
 
   // random number generator, same for all procs
 
@@ -126,11 +144,6 @@ FixNeighborSwap::FixNeighborSwap(LAMMPS *lmp, int narg, char **arg) :
   nswap_successes = 0.0;
 
   atom_swap_nmax = 0;
-  voro_neighbor_list = nullptr;
-  local_swap_iatom_list = nullptr;
-  local_swap_neighbor_list = nullptr;
-  local_swap_probability = nullptr;
-  local_swap_type_list = nullptr;
 
   // set comm size needed by this Fix
 
@@ -153,6 +166,7 @@ FixNeighborSwap::~FixNeighborSwap()
   memory->destroy(local_swap_probability);
   memory->destroy(local_swap_type_list);
   delete[] idregion;
+  delete[] id_voro;
   delete random_equal;
 }
 
@@ -160,62 +174,85 @@ FixNeighborSwap::~FixNeighborSwap()
    parse optional parameters at end of input line
 ------------------------------------------------------------------------- */
 
+static const std::unordered_set<std::string> known_keywords = {"region", "ke", "types", "diff",
+                                                               "rates"};
+static bool is_keyword(const std::string &arg)
+{
+  return known_keywords.find(arg) != known_keywords.end();
+}
+
 void FixNeighborSwap::options(int narg, char **arg)
 {
-  if (narg < 0) error->all(FLERR, "Illegal fix neighbor/swap command\n");
+  if (narg < 0) utils::missing_cmd_args(FLERR, "fix neighbor/swap", error);
-
-  ke_flag = 1;
-  diff_flag = 0;
-  rates_flag = 0;
-  nswaptypes = 0;
 
+  int ioffset = 9;    // first 9 arguments are fixed and handled in constructor
   int iarg = 0;
   while (iarg < narg) {
     if (strcmp(arg[iarg], "region") == 0) {
-      if (iarg + 2 > narg) error->all(FLERR, "Illegal fix neighbor/swap command");
+      if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix neighbor/swap region", error);
-      region = domain->get_region_by_id(arg[iarg + 1]);
+      delete[] idregion;
-      if (!region) error->all(FLERR, "Region ID for fix neighbor/swap does not exist");
       idregion = utils::strdup(arg[iarg + 1]);
+      region = domain->get_region_by_id(idregion);
+      if (!region)
+        error->all(FLERR, iarg + 1 + ioffset, "Region ID {} for fix neighbor/swap does not exist",
+                   idregion);
       iarg += 2;
     } else if (strcmp(arg[iarg], "ke") == 0) {
-      if (iarg + 2 > narg) error->all(FLERR, "Illegal fix neighbor/swap command");
+      if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix neighbor/swap ke", error);
       ke_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
       iarg += 2;
     } else if (strcmp(arg[iarg], "types") == 0) {
-      if (iarg + 3 > narg) error->all(FLERR, "Illegal fix neighbor/swap command");
+      if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "fix neighbor/swap types", error);
-      if (diff_flag != 0) error->all(FLERR, "Illegal fix neighbor/swap command");
+      if (diff_flag)
+        error->all(FLERR, iarg + ioffset, "Cannot use 'diff' and 'types' keywords together");
       iarg++;
       nswaptypes = 0;
       while (iarg < narg) {
-        if (isalpha(arg[iarg][0])) break;
+        if (is_keyword(arg[iarg])) break;
-        if (nswaptypes >= atom->ntypes) error->all(FLERR, "Illegal fix neighbor/swap command");
+        if (nswaptypes >= atom->ntypes)
-        type_list[nswaptypes] = utils::numeric(FLERR, arg[iarg], false, lmp);
+          error->all(FLERR, iarg + ioffset, "Too many arguments to fix neighbor/swap types");
+        type_list[nswaptypes] = utils::expand_type_int(FLERR, arg[iarg], Atom::ATOM, lmp);
         nswaptypes++;
         iarg++;
       }
     } else if (strcmp(arg[iarg], "diff") == 0) {
-      if (iarg + 2 > narg) error->all(FLERR, "Illegal fix neighbor/swap command");
+      if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix neighbor/swap diff", error);
-      if (nswaptypes != 0) error->all(FLERR, "Illegal fix neighbor/swap command");
+      if (diff_flag) error->all(FLERR, iarg + ioffset, "Cannot use 'diff' keyword multiple times");
+      if (nswaptypes != 0)
+        error->all(FLERR, iarg + ioffset, "Cannot use 'diff' and 'types' keywords together");
       type_list[nswaptypes] = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
       diff_flag = 1;
       nswaptypes++;
       iarg += 2;
     } else if (strcmp(arg[iarg], "rates") == 0) {
-      if (iarg + atom->ntypes >= narg) error->all(FLERR, "Illegal fix neighbor/swap command");
+      if (iarg + atom->ntypes >= narg)
+        utils::missing_cmd_args(FLERR, "fix neighbor/swap rates", error);
       iarg++;
       int i = 0;
       while (iarg < narg) {
-        if (isalpha(arg[iarg][0])) break;
+        if (is_keyword(arg[iarg])) break;
-        if (i >= atom->ntypes) error->all(FLERR, "Illegal fix neighbor/swap command");
+        if (i >= atom->ntypes) error->all(FLERR, "Too many values for fix neighbor/swap rates");
         rate_list[i] = utils::numeric(FLERR, arg[iarg], false, lmp);
         i++;
         iarg++;
       }
       rates_flag = 1;
-      if (i != atom->ntypes) error->all(FLERR, "Illegal fix neighbor/swap command");
+      if (i != atom->ntypes)
-    } else
+        error->all(FLERR, "Fix neighbor/swap rates keyword must have exactly {} arguments",
-      error->all(FLERR, "Illegal fix neighbor/swap command");
+                   atom->ntypes);
+    } else {
+      error->all(FLERR, "Unknown fix neighbor/swap keyword: {}", arg[iarg]);
     }
+  }
+
+  // checks
+  if (!nswaptypes && !diff_flag)
+    error->all(FLERR, Error::NOLASTLINE,
+               "Must specify at either 'types' or 'diff' keyword with fix neighbor/swap");
+
+  if (nswaptypes < 2 && !diff_flag)
+    error->all(FLERR, Error::NOLASTLINE,
+               "Must specify at least 2 atom types in fix neighbor/swap 'types' keyword");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -232,23 +269,26 @@ int FixNeighborSwap::setmask()
 void FixNeighborSwap::init()
 {
   c_pe = modify->get_compute_by_id("thermo_pe");
+  if (!c_pe) error->all(FLERR, Error::NOLASTLINE, "Could not find 'thermo_pe' compute");
 
-  int *type = atom->type;
+  c_voro = modify->get_compute_by_id(id_voro);
-
+  if (!c_voro)
-  if (nswaptypes < 2 && !diff_flag)
+    error->all(FLERR, Error::NOLASTLINE, "Could not find compute voronoi ID {}", id_voro);
-    error->all(FLERR, "Must specify at least 2 types in fix neighbor/swap command");
 
   // set index and check validity of region
 
   if (idregion) {
     region = domain->get_region_by_id(idregion);
-    if (!region) error->all(FLERR, "Region {} for fix setforce does not exist", idregion);
+    if (!region)
+      error->all(FLERR, Error::NOLASTLINE, "Region {} for fix neighbor/swap does not exist",
+                 idregion);
   }
 
   for (int iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
     if (type_list[iswaptype] <= 0 || type_list[iswaptype] > atom->ntypes)
-      error->all(FLERR, "Invalid atom type in fix neighbor/swap command");
+      error->all(FLERR, Error::NOLASTLINE, "Invalid atom type in fix neighbor/swap command");
 
+  int *type = atom->type;
   if (atom->q_flag) {
     double qmax, qmin;
     int firstall, first;
@@ -258,23 +298,27 @@ void FixNeighborSwap::init()
       for (int i = 0; i < atom->nlocal; i++) {
         if (atom->mask[i] & groupbit) {
           if (type[i] == type_list[iswaptype]) {
-            if (first) {
+            if (first > 0) {
               qtype[iswaptype] = atom->q[i];
               first = 0;
             } else if (qtype[iswaptype] != atom->q[i])
-              error->one(FLERR, "All atoms of a swapped type must have the same charge.");
+              first = -1;
           }
         }
       }
       MPI_Allreduce(&first, &firstall, 1, MPI_INT, MPI_MIN, world);
-      if (firstall)
+      if (firstall < 0)
-        error->all(FLERR,
+        error->all(FLERR, Error::NOLASTLINE,
-                   "At least one atom of each swapped type must be present to define charges.");
+                   "All atoms of a swapped type must have the same charge");
+      if (firstall > 0)
+        error->all(FLERR, Error::NOLASTLINE,
+                   "At least one atom of each swapped type must be present to define charges");
       if (first) qtype[iswaptype] = -DBL_MAX;
       MPI_Allreduce(&qtype[iswaptype], &qmax, 1, MPI_DOUBLE, MPI_MAX, world);
       if (first) qtype[iswaptype] = DBL_MAX;
       MPI_Allreduce(&qtype[iswaptype], &qmin, 1, MPI_DOUBLE, MPI_MIN, world);
-      if (qmax != qmin) error->all(FLERR, "All atoms of a swapped type must have same charge.");
+      if (qmax != qmin)
+        error->all(FLERR, Error::NOLASTLINE, "All atoms of a swapped type must have same charge.");
     }
   }
 
@@ -308,8 +352,9 @@ void FixNeighborSwap::init()
 
     int flagall;
     MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world);
-
+    if (flagall)
-    if (flagall) error->all(FLERR, "Cannot do neighbor/swap on atoms in atom_modify first group");
+      error->all(FLERR, Error::NOLASTLINE,
+                 "Cannot use fix neighbor/swap on atoms in atom_modify first group");
   }
 }
 
@@ -359,9 +404,6 @@ void FixNeighborSwap::pre_exchange()
 
 int FixNeighborSwap::attempt_swap()
 {
-  // int nlocal = atom->nlocal;
-  tagint *id = atom->tag;
-
   if (niswap == 0) return 0;
 
   // pre-swap energy
@@ -372,9 +414,6 @@ int FixNeighborSwap::attempt_swap()
 
   int i = pick_i_swap_atom();
 
-  // get global id and position of atom i
-  // get_global_i(i);
-
   // build nearest-neighbor list based on atom i
 
   build_i_neighbor_list(i);
@@ -382,7 +421,7 @@ int FixNeighborSwap::attempt_swap()
 
   // pick a neighbor atom j based on i neighbor list
   jtype_selected = -1;
-  int j = pick_j_swap_neighbor(i);
+  int j = pick_j_swap_neighbor();
 
   int itype = type_list[0];
   int jtype = jtype_selected;
@@ -494,26 +533,23 @@ double FixNeighborSwap::energy_full()
 int FixNeighborSwap::pick_i_swap_atom()
 {
   tagint *id = atom->tag;
-  int id_center_local = -1;
   int i = -1;
 
   int iwhichglobal = static_cast<int>(niswap * random_equal->uniform());
   if ((iwhichglobal >= niswap_before) && (iwhichglobal < niswap_before + niswap_local)) {
     int iwhichlocal = iwhichglobal - niswap_before;
     i = local_swap_iatom_list[iwhichlocal];
-    id_center_local = id[i];
     MPI_Allreduce(&id[i], &id_center, 1, MPI_INT, MPI_MAX, world);
   } else {
-    MPI_Allreduce(&id[i], &id_center, 1, MPI_INT, MPI_MAX, world);
+    id_center = -1;
   }
-
   return i;
 }
 
 /* ----------------------------------------------------------------------
 ------------------------------------------------------------------------- */
 
-int FixNeighborSwap::pick_j_swap_neighbor(int i)
+int FixNeighborSwap::pick_j_swap_neighbor()
 {
   int j = -1;
   int jtype_selected_local = -1;
@@ -535,7 +571,7 @@ int FixNeighborSwap::pick_j_swap_neighbor(int i)
         return j;
       }
     }
-    error->all(FLERR, "Did not select local neighbor swap atom");
+    error->all(FLERR, Error::NOLASTLINE, "Did not select local neighbor swap atom");
   }
 
   MPI_Allreduce(&jtype_selected_local, &jtype_selected, 1, MPI_INT, MPI_MAX, world);
@@ -545,16 +581,6 @@ int FixNeighborSwap::pick_j_swap_neighbor(int i)
 /* ----------------------------------------------------------------------
 ------------------------------------------------------------------------- */
 
-double FixNeighborSwap::get_distance(double *i, double *j)
-{
-  double r = sqrt(MathSpecial::square((i[0] - j[0])) + MathSpecial::square((i[1] - j[1])) +
-                  MathSpecial::square((i[2] - j[2])));
-  return r;
-}
-
-/* ----------------------------------------------------------------------
-------------------------------------------------------------------------- */
-
 void FixNeighborSwap::build_i_neighbor_list(int i_center)
 {
   int nghost = atom->nghost;
@@ -621,20 +647,18 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
 
             // Get distance if own center atom
             double r = INFINITY;
-            if (i_center >= 0) { double r = get_distance(x[temp_j], x[i_center]); }
 
             // Get local id of ghost center atom when ghost
             for (int i = nlocal; i < nlocal + nghost; i++) {
-              if ((id[i] == id_center) && (get_distance(x[temp_j], x[i]) < r)) {
+              double rtmp = sqrt(distsq3(x[temp_j], x[i]));
-                r = get_distance(x[temp_j], x[i]);
+              if ((id[i] == id_center) && (rtmp < r)) r = rtmp;
-              }
             }
 
             if (rates_flag) {
               local_swap_probability[njswap_local] =
-                  rate_list[type[temp_j] - 1] * exp(-MathSpecial::square(r / r_0));
+                  rate_list[type[temp_j] - 1] * exp(-square(r * inv_r_0));
             } else {
-              local_swap_probability[njswap_local] = exp(-MathSpecial::square(r / r_0));
+              local_swap_probability[njswap_local] = exp(-square(r * inv_r_0));
             }
             local_probability += local_swap_probability[njswap_local];
             local_swap_type_list[njswap_local] = type[temp_j];
@@ -646,20 +670,18 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
                 // Calculate distance from i to each j, adjust probability of selection
                 // Get distance if own center atom
                 double r = INFINITY;
-                if (i_center >= 0) { double r = get_distance(x[temp_j], x[i_center]); }
 
                 // Get local id of ghost center atom when ghost
                 for (int i = nlocal; i < nlocal + nghost; i++) {
-                  if ((id[i] == id_center) && (get_distance(x[temp_j], x[i]) < r)) {
+                  double rtmp = sqrt(distsq3(x[temp_j], x[i]));
-                    r = get_distance(x[temp_j], x[i]);
+                  if ((id[i] == id_center) && (rtmp < r)) r = rtmp;
-                  }
                 }
 
                 if (rates_flag) {
                   local_swap_probability[njswap_local] =
-                      rate_list[type[temp_j] - 1] * exp(-MathSpecial::square(r / r_0));
+                      rate_list[type[temp_j] - 1] * exp(-square(r * inv_r_0));
                 } else {
-                  local_swap_probability[njswap_local] = exp(-MathSpecial::square(r / r_0));
+                  local_swap_probability[njswap_local] = exp(-square(r * inv_r_0));
                 }
                 local_probability += local_swap_probability[njswap_local];
 
@@ -677,19 +699,18 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
           // Calculate distance from i to each j, adjust probability of selection
           // Get distance if own center atom
           double r = INFINITY;
-          if (i_center >= 0) { r = get_distance(x[temp_j], x[i_center]); }
 
           // Get local id of ghost center atoms
           for (int i = nlocal; i < nlocal + nghost; i++) {
-            if ((id[i] == id_center) && (get_distance(x[temp_j], x[i]) < r))
+            double rtmp = sqrt(distsq3(x[temp_j], x[i]));
-              r = get_distance(x[temp_j], x[i]);
+            if ((id[i] == id_center) && (rtmp < r)) r = rtmp;
           }
 
           if (rates_flag) {
             local_swap_probability[njswap_local] =
-                rate_list[type[temp_j] - 1] * exp(-MathSpecial::square(r / r_0));
+                rate_list[type[temp_j] - 1] * exp(-square(r * inv_r_0));
           } else {
-            local_swap_probability[njswap_local] = exp(-MathSpecial::square(r / r_0));
+            local_swap_probability[njswap_local] = exp(-square(r * inv_r_0));
           }
           local_probability += local_swap_probability[njswap_local];
 
@@ -702,20 +723,18 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
               // Calculate distance from i to each j, adjust probability of selection
               // Get distance if own center atom
               double r = INFINITY;
-              if (i_center >= 0) { double r = get_distance(x[temp_j], x[i_center]); }
 
               // Get local id of ghost center atom when ghost
               for (int i = nlocal; i < nlocal + nghost; i++) {
-                if ((id[i] == id_center) && (get_distance(x[temp_j], x[i]) < r)) {
+                double rtmp = sqrt(distsq3(x[temp_j], x[i]));
-                  r = get_distance(x[temp_j], x[i]);
+                if ((id[i] == id_center) && (rtmp < r)) r = rtmp;
-                }
               }
 
               if (rates_flag) {
                 local_swap_probability[njswap_local] =
-                    rate_list[type[temp_j] - 1] * exp(-MathSpecial::square(r / r_0));
+                    rate_list[type[temp_j] - 1] * exp(-square(r * inv_r_0));
               } else {
-                local_swap_probability[njswap_local] = exp(-MathSpecial::square(r / r_0));
+                local_swap_probability[njswap_local] = exp(-square(r * inv_r_0));
               }
               local_probability += local_swap_probability[njswap_local];
 
@@ -897,5 +916,6 @@ void FixNeighborSwap::restart(char *buf)
 
   bigint ntimestep_restart = (bigint) ubuf(list[n++]).i;
   if (ntimestep_restart != update->ntimestep)
-    error->all(FLERR, "Must not reset timestep when restarting fix neighbor/swap");
+    error->all(FLERR, Error::NOLASTLINE,
+               "Must not reset timestep when restarting fix neighbor/swap");
 }

src/MC/fix_neighbor_swap.h

@@ -47,7 +47,6 @@ class FixNeighborSwap : public Fix {
   int niswap, njswap;                  // # of i,j swap atoms on all procs
   int niswap_local, njswap_local;      // # of swap atoms on this proc
   int niswap_before, njswap_before;    // # of swap atoms on procs < this proc
-  // int global_i_ID;                     // global id of selected i atom
   class Region *region;    // swap region
   char *idregion;          // swap region id
 
@@ -66,7 +65,7 @@ class FixNeighborSwap : public Fix {
   bool unequal_cutoffs;
 
   int atom_swap_nmax;
-  double beta, r_0;
+  double beta, inv_r_0;
   double local_probability;     // Total swap probability stored on this proc
   double global_probability;    // Total swap probability across all proc
   double prev_probability;      // Swap probability on proc < this proc
@@ -81,15 +80,14 @@ class FixNeighborSwap : public Fix {
 
   class RanPark *random_equal;
 
-  class Compute *c_voro;
+  char *id_voro;
-  class Compute *c_pe;
+  class Compute *c_voro, *c_pe;
 
   void options(int, char **);
   int attempt_swap();
   double energy_full();
   int pick_i_swap_atom();
-  int pick_j_swap_neighbor(int);
+  int pick_j_swap_neighbor();
-  double get_distance(double[3], double[3]);
   void build_i_neighbor_list(int);
   void update_iswap_atoms_list();
 };

src/MDI/fix_mdi_qmmm.cpp

@@ -687,7 +687,7 @@ void FixMDIQMMM::pre_force(int vflag)
         double delx = xqm[i][0] - xqm[j][0];
         double dely = xqm[i][1] - xqm[j][1];
         double delz = xqm[i][2] - xqm[j][2];
-        domain->minimum_image(delx, dely, delz);
+        domain->minimum_image(FLERR, delx, dely, delz);
         rsq = delx * delx + dely * dely + delz * delz;
         qpotential_mine[i] -= qqrd2e * qqm[j] / sqrt(rsq);
       }

src/MESONT/angle_mesocnt.cpp

@@ -371,13 +371,13 @@ double AngleMesoCNT::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;

src/MISC/fix_ipi.cpp

@@ -399,7 +399,7 @@ void FixIPI::initial_integrate(int /*vflag*/)
         auto dely = x[i][1] - xhold[i][1];
         auto delz = x[i][2] - xhold[i][2];
 
-        domain->minimum_image(delx, dely, delz);
+        domain->minimum_image(FLERR, delx, dely, delz);
 
         x[i][0] = xhold[i][0] + delx;
         x[i][1] = xhold[i][1] + dely;

src/MOFFF/angle_class2_p6.cpp

@@ -453,13 +453,13 @@ double AngleClass2P6::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;

src/MOFFF/angle_cosine_buck6d.cpp

@@ -365,13 +365,13 @@ double AngleCosineBuck6d::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2,dely2,delz2);
+  domain->minimum_image(FLERR, delx2,dely2,delz2);
   double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
 
   double c = delx1*delx2 + dely1*dely2 + delz1*delz2;

src/MOLECULE/angle_charmm.cpp

@@ -282,19 +282,19 @@ double AngleCharmm::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double delxUB = x[i3][0] - x[i1][0];
   double delyUB = x[i3][1] - x[i1][1];
   double delzUB = x[i3][2] - x[i1][2];
-  domain->minimum_image(delxUB, delyUB, delzUB);
+  domain->minimum_image(FLERR, delxUB, delyUB, delzUB);
   double rUB = sqrt(delxUB * delxUB + delyUB * delyUB + delzUB * delzUB);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;

src/MOLECULE/angle_cosine.cpp

@@ -222,13 +222,13 @@ double AngleCosine::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;

src/MOLECULE/angle_cosine_squared.cpp

@@ -245,13 +245,13 @@ double AngleCosineSquared::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
@@ -273,13 +273,13 @@ void AngleCosineSquared::born_matrix(int type, int i1, int i2, int i3, double &d
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;

src/MOLECULE/angle_harmonic.cpp

@@ -248,13 +248,13 @@ double AngleHarmonic::single(int type, int i1, int i2, int i3)
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
@@ -276,13 +276,13 @@ void AngleHarmonic::born_matrix(int type, int i1, int i2, int i3, double &du, do
   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);
+  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(delx2, dely2, delz2);
+  domain->minimum_image(FLERR, delx2, dely2, delz2);
   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
 
   double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;