t status

Merge branch 'develop' into rheo

.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 \

README

@@ -34,6 +34,7 @@ lib                        additional provided or external libraries
 potentials                 interatomic potential files
 python                     Python module for LAMMPS
 src                        source files
+third_party                Copies of thirdparty software bundled with LAMMPS
 tools                      pre- and post-processing tools
 unittest                   test programs for use with CTest
 .github                    Git and GitHub related files and tools

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)
 
@@ -44,6 +51,7 @@ set(LAMMPS_DOC_DIR        ${LAMMPS_DIR}/doc)
 set(LAMMPS_TOOLS_DIR      ${LAMMPS_DIR}/tools)
 set(LAMMPS_PYTHON_DIR     ${LAMMPS_DIR}/python)
 set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials)
+set(LAMMPS_THIRDPARTY_DIR ${LAMMPS_DIR}/third_party)
 
 set(LAMMPS_DOWNLOADS_URL "https://download.lammps.org" CACHE STRING "Base URL for LAMMPS downloads")
 set(LAMMPS_POTENTIALS_URL "${LAMMPS_DOWNLOADS_URL}/potentials")
@@ -105,46 +113,35 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
       set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Qrestrict")
     endif()
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-      set(CMAKE_TUNE_DEFAULT "/QxCOMMON-AVX512")
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /QxCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "/QxHost")
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /QxHost")
     endif()
   else()
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-      set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
     endif()
   endif()
 endif()
 
 # silence excessive warnings for new Intel Compilers
 if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
-  set(CMAKE_TUNE_DEFAULT "-fp-model precise -Wno-tautological-constant-compare -Wno-unused-command-line-argument")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fp-model precise -Wno-tautological-constant-compare -Wno-unused-command-line-argument")
 endif()
 
 # silence excessive warnings for PGI/NVHPC compilers
 if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "PGI"))
-  set(CMAKE_TUNE_DEFAULT "-Minform=severe")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Minform=severe")
-endif()
-
-# this hack is required to compile fmt lib with CrayClang version 15.0.2
-# CrayClang is only directly recognized by version 3.28 and later
-if(CMAKE_VERSION VERSION_LESS 3.28)
-  get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
-  if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
-    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
-  endif()
-else()
-  if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
-    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
-  endif()
 endif()
 
 # silence nvcc warnings
-if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
+if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT
-  set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT}" "-Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
+    ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
+    OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")))
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
 endif()
 
 # we *require* C++11 without extensions but prefer C++17.
@@ -206,6 +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                                                   #
 ########################################################################
@@ -383,12 +384,12 @@ endforeach()
 # packages with special compiler needs or external libs
 ######################################################
 target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}>)
+target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_THIRDPARTY_DIR}>)
 
 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)
@@ -403,21 +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)
@@ -450,6 +448,19 @@ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
   target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 endif()
 
+# this hack is required to compile fmt lib with CrayClang version 15.0.2
+# CrayClang is only directly recognized by CMake version 3.28 and later
+if(CMAKE_VERSION VERSION_LESS 3.28)
+  get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
+    target_compile_definitions(lammps PRIVATE -DFMT_STATIC_THOUSANDS_SEPARATOR)
+  endif()
+else()
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
+    target_compile_definitions(lammps PRIVATE -DFMT_STATIC_THOUSANDS_SEPARATOR)
+  endif()
+endif()
+
 # "hard" dependencies between packages resulting
 # in an error instead of skipping over files
 pkg_depends(ML-IAP ML-SNAP)
@@ -507,13 +518,13 @@ if(BUILD_OMP)
   if(CMAKE_VERSION VERSION_LESS 3.28)
     get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
     if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
-      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
+      set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -fopenmp")
-      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
+      set(CMAKE_STATIC_LINKER_FLAGS "${CMAKE_STATIC_LINKER_FLAGS} -fopenmp")
     endif()
   else()
     if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
-      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
+      set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -fopenmp")
-      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
+      set(CMAKE_STATIC_LINKER_FLAGS "${CMAKE_STATIC_LINKER_FLAGS} -fopenmp")
     endif()
   endif()
 endif()
@@ -531,7 +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)
@@ -628,10 +638,6 @@ if(WITH_SWIG)
   add_subdirectory(${LAMMPS_SWIG_DIR} swig)
 endif()
 
-set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
-separate_arguments(CMAKE_TUNE_FLAGS)
-target_compile_options(lammps PRIVATE ${CMAKE_TUNE_FLAGS})
-target_compile_options(lmp PRIVATE ${CMAKE_TUNE_FLAGS})
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################

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

@@ -30,7 +30,7 @@ function(check_omp_h_include)
   if(OpenMP_CXX_FOUND)
     set(CMAKE_REQUIRED_FLAGS ${OpenMP_CXX_FLAGS})
     set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
-    set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
+    separate_arguments(CMAKE_REQUIRED_LINK_OPTIONS NATIVE_COMMAND ${OpenMP_CXX_FLAGS}) # needs to be a list
     set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
     # there are all kinds of problems with finding omp.h
     # for Clang and derived compilers so we pretend it is there.
@@ -75,13 +75,25 @@ function(get_lammps_version version_header variable)
     list(FIND MONTHS "${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

@@ -1,7 +1,4 @@
-# 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)
-
-if(USE_MSMPI)
 message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
 set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
 set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
@@ -25,50 +22,10 @@ if(USE_MSMPI)
 set_target_properties(MPI::MPI_CXX PROPERTIES
   IMPORTED_LOCATION "${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()
-  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

@@ -14,10 +14,6 @@ endif()
 
 add_library(colvars STATIC ${COLVARS_SOURCES})
 target_compile_definitions(colvars PRIVATE -DCOLVARS_LAMMPS)
-separate_arguments(CMAKE_TUNE_FLAGS)
-foreach(_FLAG ${CMAKE_TUNE_FLAGS})
-  target_compile_options(colvars PRIVATE ${_FLAG})
-endforeach()
 set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
 target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 # The line below is needed to locate math_eigen_impl.h
@@ -30,6 +26,10 @@ if(BUILD_OMP)
   target_link_libraries(colvars PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
+if(BUILD_MPI)
+  target_link_libraries(colvars PUBLIC MPI::MPI_CXX)
+endif()
+
 if(COLVARS_DEBUG)
   # Need to export the define publicly to be valid in interface code
   target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)

cmake/Modules/Packages/GPU.cmake

@@ -189,7 +189,7 @@ if(GPU_API STREQUAL "CUDA")
   endif()
 
   add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
-  target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
+  target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR -DLAMMPS_${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/Packages/MC.cmake

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

cmake/Modules/Packages/SCAFACOS.cmake

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

cmake/Modules/Testing.cmake

@@ -21,11 +21,11 @@ if(ENABLE_TESTING)
   # also only verified with Fedora Linux > 30 and Ubuntu 18.04 or 22.04+(Ubuntu 20.04 fails)
   if((CMAKE_SYSTEM_NAME STREQUAL "Linux")
       AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
-    if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND
+    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

@@ -1,22 +1,21 @@
-# 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)
 set(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
 
-set(CMAKE_CXX_COMPILER hipcc CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -munsafe-fp-atomics" CACHE STRING "" FORCE)
-set(CMAKE_TUNE_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"

cmake/presets/kokkos-sycl-intel.cmake

@@ -21,9 +21,10 @@ set(CMAKE_C_COMPILER icx CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
-# Silence everything
+
-set(CMAKE_CXX_FLAGS "-w" CACHE STRING "" FORCE)
+# set(_intel_sycl_flags " -w -fsycl -flink-huge-device-code -fsycl-targets=spir64_gen "
+set(_intel_sycl_flags " -w -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen ")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
+
 #set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code -fsycl-targets=spir64_gen " CACHE STRING "" FORCE)
-#set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen" CACHE STRING "" FORCE)
+set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fsycl -flink-huge-device-code " CACHE STRING "" FORCE)
-set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code " CACHE STRING "" FORCE)
-set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel " CACHE STRING "" FORCE)

cmake/presets/kokkos-sycl-nvidia.cmake

@@ -14,5 +14,7 @@ set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
 set(CMAKE_CXX_COMPILER clang++ CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
-set(CMAKE_SHARED_LINKER_FLAGS "-Xsycl-target-frontend -O3" CACHE STRING "" FORCE)
+set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -Xsycl-target-frontend -O3 " CACHE STRING "" FORCE)
-set(CMAKE_TUNE_FLAGS "-fgpu-inline-threshold=100000 -Xsycl-target-frontend -O3  -Xsycl-target-frontend -ffp-contract=on -Wno-unknown-cuda-version" CACHE STRING "" FORCE)
+
+set(_intel_sycl_flags "-fgpu-inline-threshold=100000 -Xsycl-target-frontend -O3  -Xsycl-target-frontend -ffp-contract=on -Wno-unknown-cuda-version")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_intel_sycl_flags}" CACHE STRING "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -91,7 +91,7 @@ endif()
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
 set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
-set(CMAKE_TUNE_FLAGS "-Wno-missing-include-dirs" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-missing-include-dirs" CACHE STRING "" FORCE)
 set(CMAKE_EXE_LINKER_FLAGS "-Wl,--enable-stdcall-fixup,--as-needed,-lssp" CACHE STRING "" FORCE)
 set(CMAKE_SHARED_LINKER_FLAGS "-Wl,--enable-stdcall-fixup,--as-needed,-lssp" CACHE STRING "" FORCE)
 set(BUILD_TOOLS ON CACHE BOOL "" FORCE)

cmake/presets/windows-intel-llvm.cmake

@@ -5,4 +5,4 @@ set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
 set(INTEL_LRT_MODE "C++11" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
-set(CMAKE_TUNE_FLAGS -Wno-unused-command-line-argument)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-command-line-argument" CACHE STRING "" FORCE)

doc/graphviz/lammps-releases.dot

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

doc/src/Build.rst

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

doc/src/Build_basics.rst

@@ -212,11 +212,7 @@ LAMMPS.
       You can tell CMake to look for a specific compiler with setting
       CMake variables (listed below) during configuration.  For a few
       common choices, there are also presets in the ``cmake/presets``
-      folder.  For convenience, there is a ``CMAKE_TUNE_FLAGS`` variable
+      folder.  You may also specify the corresponding ``CMAKE_*_FLAGS``
-      that can be set to apply global compiler options (applied to
-      compilation only), to be used for adding compiler or host specific
-      optimization flags in addition to the "flags" variables listed
-      below. You may also specify the corresponding ``CMAKE_*_FLAGS``
       variables individually, if you want to experiment with alternate
       optimization flags.  You should specify all 3 compilers, so that
       the (few) LAMMPS source files written in C or Fortran are built
@@ -266,10 +262,6 @@ LAMMPS.
       ``-C ../cmake/presets/pgi.cmake`` will switch the compiler to the PGI compilers,
       and ``-C ../cmake/presets/nvhpc.cmake`` will switch to the NVHPC compilers.
 
-      Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
-      compiler flags to tune for optimal performance on given hosts.
-      This variable is empty by default.
-
       .. note::
 
          When the cmake command completes, it prints a summary to the

doc/src/Build_prerequisites.rst

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

doc/src/Build_settings.rst

@@ -18,7 +18,6 @@ explains how to do this for building both with CMake and make.
 * `Memory allocation alignment`_
 * `Workaround for long long integers`_
 * `Exception handling when using LAMMPS as a library`_ to capture errors
-* `Trigger selected floating-point exceptions`_
 
 ----------
 
@@ -659,40 +658,3 @@ code has to be set up to *catch* exceptions thrown from within LAMMPS.
    throw an exception and thus other MPI ranks may get stuck waiting for
    messages from the ones with errors.
 
-----------
-
-.. _trap_fpe:
-
-Trigger selected floating-point exceptions
-------------------------------------------
-
-Many kinds of CPUs have the capability to detect when a calculation
-results in an invalid math operation, like a division by zero or calling
-the square root with a negative argument.  The default behavior on
-most operating systems is to continue and have values for ``NaN`` (= not
-a number) or ``Inf`` (= infinity).  This allows software to detect and
-recover from such conditions.  This behavior can be changed, however,
-often through use of compiler flags.  On Linux systems (or more general
-on systems using the GNU C library), these so-called floating-point traps
-can also be selectively enabled through library calls.  LAMMPS supports
-that by setting the ``-DLAMMPS_TRAP_FPE`` pre-processor define.  As it is
-done in the ``main()`` function, this applies only to the standalone
-executable, not the library.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D CMAKE_TUNE_FLAGS=-DLAMMPS_TRAP_FPE
-
-   .. tab:: Traditional make
-
-      .. code-block:: make
-
-         LMP_INC = -DLAMMPS_TRAP_FPE  <other LMP_INC settings>
-
-After compilation with this flag set, the LAMMPS executable will stop
-and produce a core dump when a division by zero, overflow, illegal math
-function argument or other invalid floating point operation is encountered.

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>`
@@ -77,6 +78,7 @@ OPT.
    * :doc:`flow/gauss <fix_flow_gauss>`
    * :doc:`freeze (k) <fix_freeze>`
    * :doc:`gcmc <fix_gcmc>`
+   * :doc:`gjf <fix_gjf>`
    * :doc:`gld <fix_gld>`
    * :doc:`gle <fix_gle>`
    * :doc:`gravity (ko) <fix_gravity>`
@@ -111,6 +113,7 @@ OPT.
    * :doc:`mvv/tdpd <fix_mvv_dpd>`
    * :doc:`neb <fix_neb>`
    * :doc:`neb/spin <fix_neb_spin>`
+   * :doc:`neighbor/swap <fix_neighbor_swap>`
    * :doc:`nonaffine/displacement <fix_nonaffine_displacement>`
    * :doc:`nph (ko) <fix_nh>`
    * :doc:`nph/asphere (o) <fix_nph_asphere>`
@@ -216,6 +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/Commands_pair.rst

@@ -179,6 +179,7 @@ OPT.
    * :doc:`lj/long/dipole/long <pair_dipole>`
    * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
    * :doc:`lj/mdf <pair_mdf>`
+   * :doc:`lj/pirani (o) <pair_lj_pirani>`
    * :doc:`lj/relres (o) <pair_lj_relres>`
    * :doc:`lj/spica (gko) <pair_spica>`
    * :doc:`lj/spica/coul/long (gko) <pair_spica>`

doc/src/Commands_removed.rst

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

doc/src/Developer_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/Errors_details.rst

@@ -159,13 +159,17 @@ angle, dihedral, or improper with just one atom in the actual
 sub-domain.  Typically, this cutoff is set to the largest cutoff from
 the :doc:`pair style(s) <pair_style>` plus the :doc:`neighbor list skin
 distance <neighbor>` and will typically be sufficient for all bonded
-interactions.  But if the pair style cutoff is small, this may not be
+interactions.  But if the pair style cutoff is small (e.g. with a
-enough.  LAMMPS will print a warning in this case using some heuristic
+repulsive-only Lennard-Jones potential) this may not be enough.  It is
-based on the equilibrium bond length, but that still may not be
+even worse if there is no pair style defined (or the pair style is set
-sufficient for cases where the force constants are small and thus bonds
+to "none"), since then there will be no ghost atoms created at all.
-may be stretched very far.  The communication cutoff can be adjusted
+
-with :doc:`comm_modify cutoff \<value\> <comm_modify>`, but setting this
+The communication cutoff can be set or adjusted with :doc:`comm_modify
-too large will waste CPU time and memory.
+cutoff \<value\> <comm_modify>`, but setting this too large will waste
+CPU time and memory.  LAMMPS will print warnings in these cases.  For
+bonds it uses some heuristic based on the equilibrium bond length, but
+that still may not be sufficient for cases where the force constants are
+small and thus bonds may be stretched very far.
 
 .. _hint09:
 
@@ -982,3 +986,59 @@ order of preference there are:
 - Send an email to ``developers@lammps.org``
 - Send an email to an :doc:`individual LAMMPS developer <Intro_authors>`
   that you know and trust
+
+.. _err0036:
+
+Neighbor list overflow, boost neigh_modify one
+----------------------------------------------
+
+The neighbor list code in LAMMPS uses a special memory allocation strategy
+to speed up building and accessing neighbor lists.
+
+Instead of making a memory allocation for each list of neighbors of the atoms
+LAMMPS allocates "pages" that have room for several neighbor lists.  This has
+two main advantages:
+
+#. It is not needed to first count how many neighbors there are for an
+   atom to determine the storage required.  Since the pages are much
+   larger than individual lists, LAMMPS just "fills up" the page until
+   there is not enough space left and then allocates a new page.
+
+#. There are fewer calls to the memory allocator functions (which can be
+   time consuming for long-running jobs and fragmented memory space) and
+   the resulting neighbor lists are close to each other physically which
+   improves cache efficiency.
+
+This is controlled by the two parameters "one" and "page", respectively,
+that can be set via the :doc:`neigh_modify command <neigh_modify>`. The
+parameter "one" is the maximum number of entries in a list of neighbors
+for a single atom.  If an atom has more neighbors as the "one" parameter
+allows, the "overflow" error message is triggered.  The parameter "page"
+sets the size of the page.  The neighbor list code checks, if there are
+"one" entries left in the current page.  If not, a new page is allocated.
+
+The default settings are suitable for most systems.  They need to be
+changed, for instance, when simulating a system with a very high density
+or when setting a very long cutoff (e.g. :math:`\gtrapprox 15 \AA` with
+:doc:`units real <units>`).  The value of "page" **must** be at least
+10x the value of "one", but 50x to 100x are recommended to avoid wasting
+memory.  The neighbor list storage is typically the largest amount of
+RAM required by a LAMMPS calculation.
+
+Even though the LAMMPS error message recommends to increase the "one"
+parameter, this may not always be the correct solution.  The neighbor
+list overflow can also be a symptom for some other error that cannot be
+easily detected.  For example, a frequent reason for an (unexpected)
+high density are incorrect box boundaries (since LAMMPS wraps atoms back
+into the principal box with periodic boundaries) or coordinates provided
+as fractional coordinates.  In both cases, LAMMPS cannot easily know
+whether the input geometry has such a high density (and thus requiring
+more neighbor list storage per atom) by intention.  Rather than blindly
+increasing the "one" parameter, it is thus worth checking if this is
+justified by the combination of density and cutoff.
+
+When boosting (= increasing) the "one" parameter, it is recommended to
+also increase the value for the "page" parameter to maintain the ratio
+between "one" and "page" to reduce waste of memory.  For some more
+details, please check out the documentation for the :doc:`neigh_modify
+command <neigh_modify>`.

doc/src/Howto.rst

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

doc/src/Howto_FFgeneral.rst

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

doc/src/Howto_bioFF.rst

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

doc/src/Howto_cmake.rst

@@ -285,7 +285,7 @@ when used before the CMake directory, there may be a space between the
 can have boolean values (on/off, yes/no, or 1/0 are all valid) or are
 strings representing a choice, or a path, or are free format. If the
 string would contain whitespace, it must be put in quotes, for example
-``-D CMAKE_TUNE_FLAGS="-ftree-vectorize -ffast-math"``.
+``-D CMAKE_CXX_FLAGS="-O3 -Wall -ftree-vectorize -ffast-math"``.
 
 CMake variables fall into two categories: 1) common CMake variables that
 are used by default for any CMake configuration setup and 2) project
@@ -341,8 +341,6 @@ Some common LAMMPS specific variables
      - compile some additional executables from the ``tools`` folder (default: ``off``)
    * - ``BUILD_DOC``
      - include building the HTML format documentation for packaging/installing (default: ``off``)
-   * - ``CMAKE_TUNE_FLAGS``
-     - common compiler flags, for optimization or instrumentation (default:)
    * - ``LAMMPS_MACHINE``
      - when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a``
    * - ``FFT``

doc/src/Howto_github.rst

@@ -498,3 +498,7 @@ systems.  Some unit and regression testing is applied as well.
 A detailed discussion of the LAMMPS developer GitHub workflow can be
 found in the file `doc/github-development-workflow.md
 <https://github.com/lammps/lammps/blob/develop/doc/github-development-workflow.md>`_
+
+.. raw:: latex
+
+   \clearpage

doc/src/Howto_lammps_gui.rst

@@ -1,36 +1,25 @@
 Using LAMMPS-GUI
 ================
 
+LAMMPS-GUI is a graphical text editor programmed using the `Qt Framework
+<https://www.qt.io/>`_ and customized for editing LAMMPS input files.  It
+is linked to the :ref:`LAMMPS library <lammps_c_api>` and thus can run
+LAMMPS directly using the contents of the editor's text buffer as input.
+
+It *differs* from other known interfaces to LAMMPS in that it can
+retrieve and display information from LAMMPS *while it is running*,
+display visualizations created with the :doc:`dump image command
+<dump_image>`, can launch the online LAMMPS documentation for known
+LAMMPS commands and styles, and directly integrates with a collection
+of LAMMPS tutorials (:ref:`Gravelle1 <Gravelle1>`).
+
 This document describes **LAMMPS-GUI version 1.6**.
 
 -----
 
-LAMMPS-GUI is a graphical text editor customized for editing LAMMPS
+.. contents::
-input files that is linked to the :ref:`LAMMPS library <lammps_c_api>`
-and thus can run LAMMPS directly using the contents of the editor's text
-buffer as input.  It can retrieve and display information from LAMMPS
-while it is running, display visualizations created with the :doc:`dump
-image command <dump_image>`, and is adapted specifically for editing
-LAMMPS input files through text completion and reformatting, and linking
-to the online LAMMPS documentation for known LAMMPS commands and styles.
 
-.. note::
+----
-
-   Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux x86\_64
-   (Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big
-   Sur or later), and Windows (version 10 or later) :ref:`are available
-   <lammps_gui_install>` for download.  Non-MPI LAMMPS executables (as
-   ``lmp``) for running LAMMPS from the command-line and :doc:`some
-   LAMMPS tools <Tools>` compiled executables are also included.  Also,
-   the pre-compiled LAMMPS-GUI packages include the WHAM executables
-   from http://membrane.urmc.rochester.edu/content/wham/ for use with
-   LAMMPS tutorials documented in this paper (:ref:`Gravelle1
-   <Gravelle1>`).
-
-   The source code for LAMMPS-GUI is included in the LAMMPS source code
-   distribution and can be found in the ``tools/lammps-gui`` folder.  It
-   can be compiled alongside LAMMPS when :doc:`compiling with CMake
-   <Build_cmake>`.
 
 LAMMPS-GUI tries to provide an experience similar to what people
 traditionally would have running LAMMPS using a command-line window and
@@ -65,8 +54,8 @@ simple LAMMPS simulations.  It is very suitable for tutorials on LAMMPS
 since you only need to learn how to use a single program for most tasks
 and thus time can be saved and people can focus on learning LAMMPS.
 The tutorials at https://lammpstutorials.github.io/ are specifically
-updated for use with LAMMPS-GUI and can their tutorial materials can
+updated for use with LAMMPS-GUI and their tutorial materials can
-be downloaded and loaded directly from the GUI.
+be downloaded and edited directly from the GUI.
 
 Another design goal is to keep the barrier low when replacing part of
 the functionality of LAMMPS-GUI with external tools.  That said, LAMMPS-GUI
@@ -79,10 +68,31 @@ has some unique functionality that is not found elsewhere:
 - monitoring of simulation progress
 - interactive visualization using the :doc:`dump image <dump_image>`
   command with the option to copy-paste the resulting settings
-- automatic slide show generation from dump image out at runtime
+- automatic slide show generation from dump image output at runtime
-- automatic plotting of thermodynamics data at runtime
+- automatic plotting of thermodynamic data at runtime
 - inspection of binary restart files
 
+.. admonition:: Download LAMMPS-GUI for your platform
+   :class: Hint
+
+   Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux x86\_64
+   (Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big
+   Sur or later), and Windows (version 10 or later) :ref:`are available
+   <lammps_gui_install>` for download.  Non-MPI LAMMPS executables (as
+   ``lmp``) for running LAMMPS from the command-line and :doc:`some
+   LAMMPS tools <Tools>` compiled executables are also included.  Also,
+   the pre-compiled LAMMPS-GUI packages include the WHAM executables
+   from http://membrane.urmc.rochester.edu/content/wham/ for use with
+   LAMMPS tutorials documented in this paper (:ref:`Gravelle1
+   <Gravelle1>`).
+
+   The source code for LAMMPS-GUI is included in the LAMMPS source code
+   distribution and can be found in the ``tools/lammps-gui`` folder.  It
+   can be compiled alongside LAMMPS when :doc:`compiling with CMake
+   <Build_cmake>`.
+
+-----
+
 The following text provides a detailed tour of the features and
 functionality of LAMMPS-GUI.  Suggestions for new features and
 reports of bugs are always welcome.  You can use the :doc:`the same
@@ -93,9 +103,12 @@ channels as for LAMMPS itself <Errors_bugs>` for that purpose.
 Installing Pre-compiled LAMMPS-GUI Packages
 -------------------------------------------
 
-LAMMPS-GUI is available as pre-compiled binary packages for Linux
+LAMMPS-GUI is available for download as pre-compiled binary packages for
-x86\_64, macOS 11 and later, and Windows 10 and later.  Alternately, it
+Linux x86\_64 (Ubuntu 20.04LTS or later and compatible), macOS (version
-can be compiled from source.
+11 aka Big Sur or later), and Windows (version 10 or later) from the
+`LAMMPS release pages on GitHub <https://github.com/lammps/lammps/releases/>`_.
+A backup download location is at https://download.lammps.org/static/
+Alternately, LAMMPS-GUI can be compiled from source when building LAMMPS.
 
 Windows 10 and later
 ^^^^^^^^^^^^^^^^^^^^
@@ -295,7 +308,10 @@ of the *Output* window showing how many warnings and errors were
 detected and how many lines the entire output has.  By clicking on the
 button on the right with the warning symbol or by using the keyboard
 shortcut `Ctrl-N` (`Command-N` on macOS), you can jump to the next
-line with a warning or error.
+line with a warning or error.  If there is a URL pointing to additional
+explanations in the online manual, that URL will be highlighted and
+double-clicking on it shall open the corresponding manual page in
+the web browser.  The option is also available from the context menu.
 
 By default, the *Output* window is replaced each time a run is started.
 The runs are counted and the run number for the current run is displayed
@@ -350,8 +366,13 @@ data or both.  The smoothing uses a `Savitzky-Golay convolution filter
 window width (left) and order (right) parameters can be set in the boxes
 next to the drop down menu.  Default settings are 10 and 4 which means
 that the smoothing window includes 10 points each to the left and the
-right of the current data point and a fourth order polynomial is fit to
+right of the current data point for a total of 21 points and a fourth
-the data in the window.
+order polynomial is fitted to the data in the window.
+
+The "Title:" and "Y:" input boxes allow to edit the text shown as the
+plot title and the y-axis label, respectively.  The text entered in the
+"Title:" box is applied to *all* charts, while the "Y:" text changes
+only the y-axis label of the currently *selected* plot.
 
 You can use the mouse to zoom into the graph (hold the left button and
 drag to mark an area) or zoom out (right click) and you can reset the
@@ -383,6 +404,11 @@ here you get the compounded data set starting with the last change of
 output fields or timestep setting, while the export from the log will
 contain *all* YAML output but *segmented* into individual runs.
 
+The *Preferences* dialog has a *Charts* tab, where you can configure
+multiple chart-related settings, like the default title, colors for the
+graphs, default choice of the raw / smooth graph selection, and the
+default chart graph size.
+
 Image Slide Show
 ----------------
 
@@ -462,11 +488,11 @@ correspond to (via their mass) and then colorize them in the image and
 set their atom diameters accordingly.  If this is not possible, for
 instance when using reduced (= 'lj') :doc:`units <units>`, then
 LAMMPS-GUI will check the current pair style and if it is a
-Lennard-Jones type potential, it will extract the *sigma* parameter
+Lennard-Jones type potential, it will extract the *sigma* parameter for
-for each atom type and assign atom diameters from those numbers.
+each atom type and assign atom diameters from those numbers.  For cases
-For cases where atom diameters are not auto-detected, the *Atom size* field
+where atom diameters are not auto-detected, the *Atom size* field can be
-can be edited and a suitable value set manually. The default value
+edited and a suitable value set manually. The default value is inferred
-is inferred from the x-direction lattice spacing.
+from the x-direction lattice spacing.
 
 If elements cannot be detected the default sequence of colors of the
 :doc:`dump image <dump_image>` command is assigned to the different atom
@@ -481,22 +507,31 @@ types.
 |gui-image1|  |gui-image2|
 
 The default image size, some default image quality settings, the view
-style and some colors can be changed in the *Preferences* dialog
+style and some colors can be changed in the *Preferences* dialog window.
-window.  From the image viewer window further adjustments can be made:
+From the image viewer window further adjustments can be made: actual
-actual image size, high-quality (SSAO) rendering, anti-aliasing, view
+image size, high-quality (SSAO) rendering, anti-aliasing, view style,
-style, display of box or axes, zoom factor.  The view of the system can
+display of box or axes, zoom factor.  The view of the system can be
-be rotated horizontally and vertically.  It is also possible to only
+rotated horizontally and vertically.
-display the atoms within a group defined in the input script (default is
+
-"all").  The image can also be re-centered on the center of mass of the
+It is also possible to display only the atoms within a :doc:`group
-selected group.  After each change, the image is rendered again and the
+defined in the input script <group>` (default is "all").  The available
-display updated.  The small palette icon on the top left is colored
+groups can be selected from the drop down list next to the "Group:"
-while LAMMPS is running to render the new image; it is grayed out when
+label.  Similarly, if there are :doc:`molecules defined in the input
-LAMMPS is finished.  When there are many atoms to render and high
+<molecule>`, it is possible to select one of them (default is "none")
-quality images with anti-aliasing are requested, re-rendering may take
+and visualize it (it will be shown at the center of the simulation box).
-several seconds.  From the *File* menu of the image window, the
+While a molecule is selected, the group selection is disabled.  It can
-current image can be saved to a file (keyboard shortcut `Ctrl-S`) or
+be restored by selecting the molecule "none".
-copied to the clipboard (keyboard shortcut `Ctrl-C`) for pasting the
+
-image into another application.
+The image can also be re-centered on the center of mass of the selected
+group.  After each change, the image is rendered again and the display
+updated.  The small palette icon on the top left is colored while LAMMPS
+is running to render the new image; it is grayed out when LAMMPS is
+finished.  When there are many atoms to render and high quality images
+with anti-aliasing are requested, re-rendering may take several seconds.
+From the *File* menu of the image window, the current image can be saved
+to a file (keyboard shortcut `Ctrl-S`) or copied to the clipboard
+(keyboard shortcut `Ctrl-C`) for pasting the image into another
+application.
 
 From the *File* menu it is also possible to copy the current
 :doc:`dump image <dump_image>` and :doc:`dump_modify <dump_image>`
@@ -726,13 +761,16 @@ Tutorials
 
 The *Tutorials* menu is to support the set of LAMMPS tutorials for
 beginners and intermediate LAMMPS users documented in (:ref:`Gravelle1
-<Gravelle1>`).  From the drop down menu you can select which of the eight
+<Gravelle1>`).  From the drop down menu you can select which of the
-currently available tutorial sessions you want to start and then will be
+eight currently available tutorial sessions you want to begin.  This
-taken to a 'wizard' dialog where you can choose in which folder you want
+opens a 'wizard' dialog where you can choose in which folder you want to
-to work, whether you want that folder to be cleared, and also whether
+work, whether you want that folder to be wiped from *any* files, whether
-you want to download the solutions files (can be large).  The dialog
+you want to download the solutions files (which can be large) to a
-will then start downloading the files requested and load the first input
+``solution`` sub-folder, and whether you want the corresponding
-file for the selected session into LAMMPS-GUI.
+tutorial's online version opened in your web browser.  The dialog will
+then start downloading the files requested (download progress is
+reported in the status line) and load the first input file for the
+selected session into LAMMPS-GUI.
 
 About
 ^^^^^
@@ -797,18 +835,21 @@ look of LAMMPS-GUI.  The settings are grouped and each group is
 displayed within a tab.
 
 .. |guiprefs1| image:: JPG/lammps-gui-prefs-general.png
-   :width: 24%
+   :width: 19%
 
 .. |guiprefs2| image:: JPG/lammps-gui-prefs-accel.png
-   :width: 24%
+   :width: 19%
 
 .. |guiprefs3| image:: JPG/lammps-gui-prefs-image.png
-   :width: 24%
+   :width: 19%
 
 .. |guiprefs4| image:: JPG/lammps-gui-prefs-editor.png
-   :width: 24%
+   :width: 19%
 
-|guiprefs1|  |guiprefs2|  |guiprefs3|  |guiprefs4|
+.. |guiprefs5| image:: JPG/lammps-gui-prefs-charts.png
+   :width: 19%
+
+|guiprefs1|  |guiprefs2|  |guiprefs3|  |guiprefs4|  |guiprefs5|
 
 General Settings:
 ^^^^^^^^^^^^^^^^^
@@ -903,7 +944,7 @@ lists to select the background and box colors.
 Editor Settings:
 ^^^^^^^^^^^^^^^^
 
-This tab allows tweaking settings of the editor window.  Specifically
+This tab allows tweaking settings of the editor window.  Specifically,
 the amount of padding to be added to LAMMPS commands, types or type
 ranges, IDs (e.g. for fixes), and names (e.g. for groups).  The value
 set is the minimum width for the text element and it can be chosen in
@@ -915,6 +956,16 @@ the completion pop-up window, and whether auto-save mode is enabled.
 In auto-save mode the editor buffer is saved before a run or before
 exiting LAMMPS-GUI.
 
+Charts Settings:
+----------------
+
+This tab allows tweaking settings of the *Charts* window.  Specifically,
+one can set the default chart title (if the title contains '%f' it will
+be replaced with the name of the current input file), one can select
+whether by default the raw data, the smoothed data or both will be
+plotted, one can set the colors for the two lines, the default smoothing
+parameters, and the default size of the chart graph in pixels.
+
 -----------
 
 Keyboard Shortcuts
@@ -1013,3 +1064,7 @@ Window), and `Ctrl-Q` (Quit Application) are supported.
 .. _Gravelle2:
 
 **(Gravelle2)** Gravelle https://lammpstutorials.github.io/
+
+.. raw:: latex
+
+   \clearpage

doc/src/Howto_spc.rst

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

doc/src/Howto_thermostat.rst

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

doc/src/Howto_tip4p.rst

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

doc/src/Install_git.rst

@@ -12,19 +12,10 @@ several advantages:
   LAMMPS.  For that, you should first create your own :doc:`fork on
   GitHub <Howto_github>`, though.
 
-You must have `git <git_>`_ installed on your system to use the
+You must have `git <git_>`_ installed on your system to use the commands
-commands explained below to communicate with the git servers on
+explained below to communicate with the git servers on GitHub.
-GitHub.  For people still using subversion (svn), GitHub also
-provides `limited support for subversion clients <svn_>`_.
-
-.. note::
-
-   As of October 2016, the official home of public LAMMPS development is
-   on GitHub.  The previously advertised LAMMPS git repositories on
-   git.lammps.org and bitbucket.org are now offline or deprecated.
 
 .. _git: https://git-scm.com
-.. _svn: https://help.github.com/en/github/importing-your-projects-to-github/working-with-subversion-on-github
 
 You can follow the LAMMPS development on 4 different git branches:
 

doc/src/Intro_authors.rst

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

doc/src/Intro_portability.rst

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

doc/src/Modify_pair.rst

@@ -46,6 +46,8 @@ Here is a brief list of some the class methods in the Pair class that
 +---------------------------------+------------------------------------------------------------------------+
 | compute_inner/middle/outer      | versions of compute used by rRESPA                                     |
 +---------------------------------+------------------------------------------------------------------------+
+| compute_atomic_energy           | energy of one atom, equivalent to per-atom energy                      |
++---------------------------------+------------------------------------------------------------------------+
 | memory_usage                    | return estimated amount of memory used by the pair style               |
 +---------------------------------+------------------------------------------------------------------------+
 | modify_params                   | process arguments to pair_modify command                               |
@@ -122,3 +124,5 @@ setting.
 +---------------------------------+-------------------------------------------------------------+---------+
 | spinflag                        | 1 if compatible with spin kspace_style                      | 0       |
 +---------------------------------+-------------------------------------------------------------+---------+
+| atomic_energy_enable            | 1 if compute_atomic_energy() routine exists                 | 0       |
++---------------------------------+-------------------------------------------------------------+---------+

doc/src/Python_launch.rst

@@ -1,7 +1,7 @@
 Running LAMMPS and Python in serial
 -----------------------------------
 
-To run a LAMMPS in serial, type these lines into Python
+To run a LAMMPS input in serial, type these lines into Python
 interactively from the ``bench`` directory:
 
 .. code-block:: python

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/Tools.rst

@@ -475,9 +475,13 @@ beginners to start with LAMMPS, it is also the expectation that
 LAMMPS-GUI users will eventually transition to workflows that most
 experienced LAMMPS users employ.
 
-All features have been extensively exposed to keyboard shortcuts, so
+.. image:: JPG/lammps-gui-screen.png
-that there is also appeal for experienced LAMMPS users for prototyping
+   :align: center
-and testing simulation setups.
+   :scale: 50%
+
+Features have been extensively exposed to keyboard shortcuts, so that
+there is also appeal for experienced LAMMPS users for prototyping and
+testing simulation setups.
 
 Features
 ^^^^^^^^
@@ -502,7 +506,7 @@ Here are a few highlights of LAMMPS-GUI
 - Visualization of current state in Image Viewer (via calling :doc:`write_dump image <dump_image>`)
 - Capture of images created via :doc:`dump image <dump_image>` in Slide show window
 - Dialog to set variables, similar to the LAMMPS command-line flag '-v' / '-var'
-- Support for GPU, INTEL, KOKKOS/OpenMP, OPENMAP, and OPT and accelerator packages
+- Support for GPU, INTEL, KOKKOS/OpenMP, OPENMP, and OPT accelerator packages
 
 Parallelization
 ^^^^^^^^^^^^^^^
@@ -523,8 +527,8 @@ with CMake is required.
 The LAMMPS-GUI has been successfully compiled and tested on:
 
 - Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
-- Fedora Linux 40 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS
+- Fedora Linux 41 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS
-- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.7
+- Fedora Linux 41 x86\_64 using GCC 14, Qt version 6.8
 - Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
 - Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
 - Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.40, Qt version 6.7
@@ -1250,10 +1254,10 @@ tabulate tool
 
 .. versionadded:: 22Dec2022
 
-The ``tabulate`` folder contains Python scripts scripts to generate tabulated
+The ``tabulate`` folder contains Python scripts scripts to generate and
-potential files for LAMMPS.  The bulk of the code is in the ``tabulate`` module
+visualize tabulated potential files for LAMMPS.  The bulk of the code is in the
-in the ``tabulate.py`` file.  Some example files demonstrating its use are
+``tabulate`` module in the ``tabulate.py`` file.  Some example files
-included.  See the README file for more information.
+demonstrating its use are included.  See the README file for more information.
 
 ----------
 
@@ -1276,7 +1280,7 @@ Those scripts were written by Steve Plimpton sjplimp at gmail.com
 valgrind tool
 -------------
 
-The ``valgrind`` folder contains additional suppressions fur LAMMPS when
+The ``valgrind`` folder contains additional suppressions for LAMMPS when
 using `valgrind's <https://valgrind.org/>`_ ` `memcheck tool
 <https://valgrind.org/info/tools.html#memcheck>`_ to search for memory
 access violation and memory leaks.  These suppressions are automatically

doc/src/compute_bond_local.rst

@@ -64,20 +64,32 @@ All these properties are computed for the pair of atoms in a bond,
 whether the two atoms represent a simple diatomic molecule, or are part
 of some larger molecule.
 
-The value *dist* is the current length of the bond.
+.. versionchanged:: TBD
-The values *dx*, *dy*, and *dz* are the xyz components of the
+
-*distance* between the pair of atoms. This value is always the
+   The sign of *dx*, *dy*, *dz* is no longer determined by the atom IDs
-distance from the atom of lower to the one with the higher id.
+   of the bonded atoms but by their order in the bond list to be
+   consistent with *fx*, *fy*, and *fz*.
+
+The value *dist* is the current length of the bond.  The values *dx*,
+*dy*, and *dz* are the :math:`(x,y,z)` components of the distance vector
+:math:`\vec{x_i} - \vec{x_j}` between the atoms in the bond.  The order
+of the atoms is determined by the bond list and the respective atom-IDs
+can be output with :doc:`compute property/local
+<compute_property_local>`.
 
 The value *engpot* is the potential energy for the bond,
 based on the current separation of the pair of atoms in the bond.
 
-The value *force* is the magnitude of the force acting between the
+The value *force* is the magnitude of the force acting between the pair
-pair of atoms in the bond.
+of atoms in the bond, which is positive for a repulsive force and
+negative for an attractive force.
 
-The values *fx*, *fy*, and *fz* are the xyz components of
+The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
-*force* between the pair of atoms in the bond. For bond styles that apply
+the force on the first atom *i* in the bond due to the second atom *j*.
-non-central forces, such as :doc:`bond_style bpm/rotational
+Mathematically, they are obtained by multiplying the value of *force*
+from above with a unit vector created from the *dx*, *dy*, and *dz*
+components of the distance vector also described above.  For bond styles
+that apply non-central forces, such as :doc:`bond_style bpm/rotational
 <bond_bpm_rotational>`, these values only include the :math:`(x,y,z)`
 components of the normal force component.
 

doc/src/compute_pair_local.rst

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

doc/src/create_atoms.rst

@@ -28,7 +28,7 @@ Syntax
          region-ID = create atoms within this region, use NULL for entire simulation box
 
 * zero or more keyword/value pairs may be appended
-* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *radscale* or *meshmode* or *rotate* or *overlap* or *maxtry* or *units*
+* keyword = *mol* or *basis* or *ratio* or *subset* or *group* or *remap* or *var* or *set* or *radscale* or *meshmode* or *rotate* or *overlap* or *maxtry* or *units*
 
   .. parsed-literal::
 
@@ -44,6 +44,7 @@ Syntax
        *subset* values = Nsubset seed
          Nsubset = # of lattice sites to populate randomly
          seed = random # seed (positive integer)
+       *group* value = group name
        *remap* value = *yes* or *no*
        *var* value = name = variable name to evaluate for test of atom creation
        *set* values = dim name
@@ -83,7 +84,7 @@ Examples
 
    create_atoms 3 region regsphere basis 2 3
    create_atoms 3 region regsphere basis 2 3 ratio 0.5 74637
-   create_atoms 3 single 0 0 5
+   create_atoms 3 single 0 0 5 group newatom
    create_atoms 1 box var v set x xpos set y ypos
    create_atoms 2 random 50 12345 NULL overlap 2.0 maxtry 50
    create_atoms 1 mesh open_box.stl meshmode qrand 0.1 units box
@@ -395,6 +396,14 @@ correct number of particles are inserted, in a perfectly random
 fashion.  Which lattice sites are selected will change with the number
 of processors used.
 
+.. versionadded:: TBD
+
+The *group* keyword adds the newly created atoms to the named
+:doc:`group <group>`.  If the group does not yet exist it will be
+created.  There can be only one such group, thus if the *group* keyword
+is used multiple times, only the last one will be used.  All created
+atoms are always added to the group "all".
+
 The *remap* keyword only applies to the *single* style.  If it is set
 to *yes*, then if the specified position is outside the simulation
 box, it will mapped back into the box, assuming the relevant

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
@@ -256,6 +257,7 @@ accelerated styles exist.
 * :doc:`flow/gauss <fix_flow_gauss>` - Gaussian dynamics for constant mass flux
 * :doc:`freeze <fix_freeze>` - freeze atoms in a granular simulation
 * :doc:`gcmc <fix_gcmc>` - grand canonical insertions/deletions
+* :doc:`gjf <fix_gjf>` - statistically correct Langevin temperature control using the GJ methods
 * :doc:`gld <fix_gld>` - generalized Langevin dynamics integrator
 * :doc:`gle <fix_gle>` - generalized Langevin equation thermostat
 * :doc:`gravity <fix_gravity>` - add gravity to atoms in a granular simulation
@@ -290,6 +292,7 @@ accelerated styles exist.
 * :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
 * :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
 * :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
+* :doc:`neighbor/swap <fix_neighbor_swap>` - kinetic Monte Carlo (kMC) atom swapping
 * :doc:`nonaffine/displacement <fix_nonaffine_displacement>` - calculate nonaffine displacement of atoms
 * :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
 * :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
@@ -395,6 +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_adapt.rst

@@ -14,7 +14,7 @@ Syntax
 * adapt = style name of this fix command
 * N = adapt simulation settings every this many timesteps
 * one or more attribute/arg pairs may be appended
-* attribute = *pair* or *bond* or *angle* or *improper* or *kspace* or *atom*
+* attribute = *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *atom*
 
   .. parsed-literal::
 
@@ -33,6 +33,11 @@ Syntax
          aparam = parameter to adapt over time
          I = type angle to set parameter for (integer or type label)
          v_name = variable with name that calculates value of aparam
+       *dihedral* args = dstyle dparam I v_name
+         dstyle = dihedral style name (e.g., quadratic)
+         dparam = parameter to adapt over time
+         I = type dihedral to set parameter for (integer or type label)
+         v_name = variable with name that calculates value of iparam
        *improper* args = istyle iparam I v_name
          istyle = improper style name (e.g., cvff)
          iparam = parameter to adapt over time
@@ -209,6 +214,8 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`lj/mdf <pair_mdf>`                                                     | epsilon,sigma                                    | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`lj/pirani <pair_lj_pirani>`                                            | alpha, beta, gamma, rm, epsilon                  | type pairs  |
++------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`lj/sf/dipole/sf <pair_dipole>`                                         | epsilon,sigma,scale                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`lubricate <pair_lubricate>`                                            | mu                                               | global      |
@@ -433,6 +440,48 @@ this fix uses to reset theta0 needs to generate values in radians.
 
 ----------
 
+.. versionadded:: TBD
+
+The *dihedral* keyword uses the specified variable to change the value of
+a dihedral coefficient over time, very similar to how the *angle* keyword
+operates. The only difference is that now a dihedral coefficient for a
+given dihedral type is adapted.
+
+A wild-card asterisk can be used in place of or in conjunction with the
+dihedral type argument to set the coefficients for multiple dihedral types.
+This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is
+the number of dihedral types, then an asterisk with no numeric values means
+all types from 1 to :math:`N`.  A leading asterisk means all types from
+1 to n (inclusive).  A trailing asterisk means all types from m to
+:math:`N` (inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+If :doc:`dihedral_style hybrid <dihedral_hybrid>` is used, *dstyle* should be a
+sub-style name. The dihedral styles that currently work with fix adapt are:
+
++------------------------------------------------------------------------+-------------------------+----------------+
+| :doc:`charmm  <dihedral_charmm>`                                       | k,n,d                   | type dihedrals |
++------------------------------------------------------------------------+-------------------------+----------------+
+| :doc:`charmmfsw <dihedral_charmm>`                                     | k,n,d                   | type dihedrals |
++------------------------------------------------------------------------+-------------------------+----------------+
+| :doc:`class2 <dihedral_class2>`                                        | k1,k2,k3,phi1,phi2,phi3 | type dihedrals |
++------------------------------------------------------------------------+-------------------------+----------------+
+| :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>`  | k,phi0                  | type dihedrals |
++------------------------------------------------------------------------+-------------------------+----------------+
+| :doc:`helix <dihedral_helix>`                                          | a,b,c                   | type dihedrals |
++------------------------------------------------------------------------+-------------------------+----------------+
+| :doc:`multi/harmonic <dihedral_multi_harmonic>`                        | a1,a2,a3,a4,a5          | type dihedrals |
++------------------------------------------------------------------------+-------------------------+----------------+
+| :doc:`opls <dihedral_opls>`                                            | k1,k2,k3,k4             | type dihedrals |
++------------------------------------------------------------------------+-------------------------+----------------+
+| :doc:`quadratic <dihedral_quadratic>`                                  | k,phi0                  | type dihedrals |
++------------------------------------------------------------------------+-------------------------+----------------+
+
+Note that internally, phi0 is stored in radians, so the variable
+this fix use to reset phi0 needs to generate values in radians.
+
+----------
+
 .. versionadded:: 2Apr2025
 
 The *improper* keyword uses the specified variable to change the value of

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_gjf.rst

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

doc/src/fix_langevin.rst

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

doc/src/fix_neighbor_swap.rst

@@ -0,0 +1,264 @@
+.. index:: fix neighbor/swap
+
+fix neighbor/swap command
+=========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID neighbor/swap N X seed T R0 voro-ID keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* neighbor/swap = style name of this fix command
+* N = invoke this fix every N steps
+* X = number of swaps to attempt every N steps
+* seed = random # seed (positive integer)
+* T = scaling temperature of the MC swaps (temperature units)
+* R0 = scaling swap probability of the MC swaps (distance units)
+* voro-ID = valid voronoi compute id (compute voronoi/atom)
+* one or more keyword/value pairs may be appended to args
+* keywords *types* and *diff* are mutually exclusive, but one must be specified
+* keyword = *types* or *diff* or *ke* or *region* or *rates*
+
+  .. parsed-literal::
+
+       *types* values = two or more atom types (Integers in range [1,Ntypes] or type labels)
+       *diff* values = one atom type
+       *ke* value = *yes* or *no*
+         *yes* = kinetic energy is conserved after atom swaps
+         *no* = no conservation of kinetic energy after atom swaps
+       *region* value = region-ID
+         region-ID = ID of region to use as an exchange/move volume
+       *rates* values = V1 V2 . . . Vntypes values to conduct variable diffusion for different atom types (unitless)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute voroN all voronoi/atom neighbors yes
+   fix mc all neighbor/swap 10 160 15238 1000.0 3.0 voroN diff 2
+   fix myFix all neighbor/swap 100 1 12345 298.0 3.0 voroN region my_swap_region types 5 6
+   fix kmc all neighbor/swap 1 100 345 1.0 3.0 voroN diff 3 rates 3 1 6
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This fix performs Monte-Carlo (MC) evaluations to enable kinetic
+Monte Carlo (kMC)-type behavior during MD simulation by allowing
+neighboring atoms to swap their positions. In contrast to the :doc:`fix
+atom/swap <fix_atom_swap>` command which swaps pairs of atoms anywhere
+in the simulation domain, the restriction of the MC swapping to
+neighbors enables a hybrid MD/kMC-like simulation.
+
+Neighboring atoms are defined by using a Voronoi tesselation performed
+by the :doc:`compute voronoi/atom <compute_voronoi_atom>` command.
+Two atoms are neighbors if their Voronoi cells share a common face
+(3d) or edge (2d).
+
+The selection of a swap neighbor is made using a distance-based
+criterion for weighting the selection probability of each swap, in the
+same manner as kMC selects a next event using relative probabilities.
+The acceptance or rejection of each swap is determined via the
+Metropolis criterion after evaluating the change in system energy due
+to the swap.
+
+A detailed explanation of the original implementation of this
+algorithm can be found in :ref:`(Tavenner 2023) <TavennerMDkMC>`
+where it was used to simulated accelerated diffusion in an MD context.
+
+Simulating inherently kinetically-limited behaviors which rely on rare
+events (such as atomic diffusion in a solid) is challenging for
+traditional MD since its relatively short timescale will not naturally
+sample many events. This fix addresses this challenge by allowing rare
+neighbor hopping events to be sampled in a kMC-like fashion at a much
+faster rate (set by the specified *N* and *X* parameters).  This enables
+the processes of atomic diffusion to be approximated during an MD
+simulation, effectively decoupling the MD atomic vibrational timescale
+and the atomic hopping (kMC event) timescale.
+
+The algorithm implemented by this fix is as follows:
+
+   - The MD simulation is paused every *N* steps
+   - A Voronoi tesselation is performed for the current atom configuration.
+   - Then *X* atom swaps are attempted, one after the other.
+   - For each swap, an atom *I* is selected randomly from the list of
+     atom types specified by either the *types* or *diff* keywords.
+   - One of *I*'s Voronoi neighbors *J* is selected using the
+     distance-weighted probability for each neighbor detailed below.
+   - The *I,J* atom IDs are communicated to all processors so that a
+     global energy evaluation can be performed for the post-swap state
+     of the system.
+   - The swap is accepted or rejected based on the Metropolis criterion
+     using the energy change of the system and the specified temperature
+     *T*.
+
+Here are a few comments on the computational cost of the swapping
+algorithm.
+
+   1. The cost of a global energy evaluation is similar to that of an MD
+      timestep.
+
+   2. Similar to other MC algorithms in LAMMPS, improved parallel
+      efficiency is achieved with a smaller number of atoms per
+      processor than would typically be used in an standard MD
+      simulation. This is because the per-energy evaluation cost
+      increases relative to the balance of MD/MC steps as indicated by
+      1., but the communication cost remains relatively constant for a
+      given number of MD steps.
+
+   3. The MC portion of the simulation will run dramatically slower if
+      the pair style uses different cutoffs for different atom types (or
+      type pairs).  This is because each atom swap then requires a
+      rebuild of the neighbor list to ensure the post-swap global energy
+      can be computed correctly.
+
+Limitations are imposed on selection of *I,J* atom pairs to avoid
+swapping of atoms which are outside of a reasonable cutoff (e.g. due to
+a Voronoi tesselation near free surfaces) though the use of a
+distance-weighted probability scaling.
+
+----------
+
+This section gives more details on other arguments and keywords.
+
+The random number generator (RNG) used by all the processors for MC
+operations is initialized with the specified *seed*.
+
+The distance-based probability is weighted by the specified *R0* which
+sets the radius :math:`r_0` in this formula
+
+.. math::
+
+    p_{ij} = e^{(\frac{r_{ij}}{r_0})^2}
+
+where :math:`p_{ij}` is the probability of selecting atom :math:`j` to
+swap with atom :math:`i`.  Typically, a value for *R0* around the
+average nearest-neighbor spacing is appropriate.  Since this is simply a
+probability weighting, the swapping behavior is not very sensitive to
+the exact value of *R0*.
+
+The required *voro-ID* value is the compute-ID of a
+:doc:`compute voronoi/atom <compute_voronoi_atom>` command like
+this:
+
+.. code-block:: LAMMPS
+
+    compute compute-ID group-ID voronoi/atom neighbors yes
+
+It must return per-atom list of valid neighbor IDs as in the
+:doc:`compute voronoi/atom <compute_voronoi_atom>` command.
+
+The keyword *types* takes two or more atom types as its values.  Only
+atoms *I* of the first atom type will be selected.  Only atoms *J* of the
+remaining atom types will be considered as potential swap partners.
+
+The keyword *diff* take a single atom type as its value.  Only atoms
+*I* of the that atom type will be selected.  Atoms *J* of all
+remaining atom types will be considered as potential swap partners.
+This includes the atom type specified with the *diff* keyword to
+account for self-diffusive hops between two atoms of the same type.
+
+Note that the *neighbors yes* option must be enabled for use with this
+fix. The group-ID should include all the atoms which this fix will
+potentially select. I.e. the group-ID used in the voronoi compute should
+include the same atoms as that indicated by the *types* keyword. If the
+*diff* keyword is used, the group-ID should include atoms of all types
+in the simulation.
+
+The keyword *ke* takes *yes* (default) or *no* as its value.  It two
+atoms are swapped with different masses, then a value of *yes* will
+rescale their respective velocities to conserve the kinetic energy of
+the system.  A value of *no* will perform no rescaling, so that
+kinetic energy is not conserved.  See the restriction on this keyword
+below.
+
+The *region* keyword takes a *region-ID* as its value.  If specified,
+then only atoms *I* and *J* within the geometric region will be
+considered as swap partners.  See the :doc:`region <region>` command
+for details.  This means the group-ID for the :doc:`compute
+voronoi/atom <compute_voronoi_atom>` command also need only contain
+atoms within the region.
+
+The keyword *rates* can modify the swap rate based on the type of atom
+*J*.  Ntype values must be specified, where Ntype = the number of atom
+types in the system.  Each value is used to scale the probability
+weighting given by the equation above.  In the third example command
+above, a simulation has 3 atoms types.  Atom *I*s of type 1 are
+eligible for swapping.  Swaps may occur with atom *J*s of all 3 types.
+Assuming all *J* atoms are equidistant from an atom *I*, *J* atoms of
+type 1 will be 3x more likely to be selected as a swap partner than
+atoms of type 2.  And *J* atoms of type 3 will be 6.5x more likely to
+be selected than atoms of type 2.  If the *rates* keyword is not used,
+all atom types will be treated with the same probability during selection
+of swap attempts.
+
+
+Restart, fix_modify, output, run start/stop, minimize info
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This fix writes the state of the fix to :doc:`binary restart files
+<restart>`.  This includes information about the random number generator
+seed, the next timestep for MC exchanges, and the number of exchange
+attempts and successes.  See the :doc:`read_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this
+fix.
+
+This fix computes a global vector of length 2, which can be accessed
+by various :doc:`output commands <Howto_output>`.  The vector values are
+the following global cumulative quantities:
+
+  #. swap attempts
+  #. swap accepts
+
+The vector values calculated by this fix are "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 fix is part of the MC package.  It is only enabled if LAMMPS was
+built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.  Also this fix requires that the :ref:`VORONOI
+package <PKG-VORONOI>` is installed, otherwise the fix will not be
+compiled.
+
+The :doc:`compute voronoi/atom <compute_voronoi_atom>` command
+referenced by the required voro-ID must return neighboring atoms as
+illustrated in the examples above.
+
+If this fix is used with systems that do not have per-type masses
+(e.g. atom style sphere), the *ke* keyword must be set to *off* since
+the implemented algorithm will not be able to re-scale velocities
+properly.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt <fix_nh>`, :doc:`compute voronoi/atom <compute_voronoi_atom>`
+:doc:`delete_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`,
+:doc:`fix atom/swap <fix_atom_swap>`, :doc:`fix mol/swap <fix_mol_swap>`,
+:doc:`fix sgcmc <fix_sgcmc>`
+
+Default
+"""""""
+
+The option defaults are *ke* = yes and *rates* = 1 for all atom types.
+
+----------
+
+.. _TavennerMDkMC:
+
+**(Tavenner 2023)** J Tavenner, M Mendelev, J Lawson, Computational
+ Materials Science, 218, 111929 (2023).

doc/src/fix_qeq_rel_reaxff.rst

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

doc/src/fix_qtpie_reaxff.rst

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

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/fix_sgcmc.rst

@@ -30,7 +30,9 @@ Syntax
          N = number of times sampling window is moved during one MC cycle
        *window_size* frac
          frac = size of sampling window (must be between 0.5 and 1.0)
-
+       *atomic/energy* yes/no
+         yes = use the atomic energy method to calculate energy changes
+         no = use the default method to calculate energy changes
 
 Examples
 """"""""
@@ -127,6 +129,14 @@ The number of times the window is moved during a MC cycle is set using
 the parameter *window_moves* (see Sect. III.B in :ref:`Sadigh1
 <Sadigh1>` for details).
 
+The *atomic/energy* keyword controls which method is used for calculating
+the energy change when atom types are swapped. A value of *no*
+uses the default method, see discussion below in Restrictions section.
+A value of *yes* uses the atomic energy method,
+if the method has been implemented for the LAMMPS energy model,
+otherwise LAMMPS will exit with an error message.
+So far this has only been implemented for EAM type potentials.
+
 ------------
 
 Restart, fix_modify, output, run start/stop, minimize info
@@ -159,16 +169,26 @@ page for more info.
 This fix style requires an :doc:`atom style <atom_style>` with per atom
 type masses.
 
-At present the fix provides optimized subroutines for EAM type
+The fix provides three methods for calculating the potential energy
-potentials (see above) that calculate potential energy changes due to
+change due to atom type swaps. For EAM type potentials, the default
-*local* atom type swaps very efficiently.  Other potentials are
+method is a carefully optimized local energy change calculation that
-supported by using the generic potential functions. This, however, will
+is part of the source code for this fix. It takes advantage of the
-lead to exceedingly slow simulations since it implies that the
+specific computational and communication requirements of EAM. Customizing
-energy of the *entire* system is recomputed at each MC trial step.  If
+the local method to handle other energy models such as Tersoff has been done,
-other potentials are to be used it is strongly recommended to modify and
+but these cases are not supported in the public LAMMPS code.
-optimize the existing generic potential functions for this purpose.
+For all other LAMMPS energy models, the default method calculates
-Also, the generic energy calculation can not be used for parallel
+the *total* potential energy of the system before and after each
-execution i.e. it only works with a single MPI process.
+atom type swap.  This method does not depend on the details of the
+energy model and so is guaranteed to be correct.  It is also
+orders of magnitude slower than the custom EAM calculation.
+In addition, it can not be used with parallel execution i.e. only
+a single MPI process is allowed.
+The third method uses the *atomic/energy* keyword described above.
+This allows parallel execution and it is also a local calculation,
+making it only a bit slower than a fully-optimized local calculation.
+So far, this has been implemented for EAM type potentials.
+It is straightforward to extend this to other potentials,
+requiring adding an atomic energy method to the pair style.
 
 ------------
 
@@ -180,6 +200,7 @@ The optional parameters default to the following values:
 * *randseed* = 324234
 * *window_moves* = 8
 * *window_size* = automatic
+* *atomic/energy* = no
 
 ------------
 

doc/src/pair_granular.rst

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

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/pair_lj_pirani.rst

@@ -0,0 +1,163 @@
+.. index:: pair_style lj/pirani
+.. index:: pair_style lj/pirani/omp
+
+pair_style lj/pirani command
+============================
+
+Accelerator Variants: *lj/pirani/omp*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style lj/pirani cutoff
+
+* lj/pirani = name of the pair style
+* cutoff = global cutoff (distance units)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style lj/pirani 10.0
+   pair_coeff 1 1 4.0 7.0 6.0 3.5 0.0045
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Pair style *lj/pirani* computes pairwise interactions from an Improved
+Lennard-Jones (ILJ) potential according to :ref:`(Pirani) <Pirani>`.
+The ILJ force field is adequate to model both equilibrium and
+non-equilibrium properties of matter, in gaseous and condensed phases,
+and at gas-surface interfaces. In particular, its use improves the
+description of elementary process dynamics where the traditional
+Lennard-Jones (LJ) formulation is usually applied.
+
+
+.. math::
+
+   x = r/R_m   \\
+   n_x = \alpha*x^2 + \beta   \\
+   \gamma \equiv m  \\
+
+  V(x) = \varepsilon \cdot \left( \frac{\gamma}{ n_x - \gamma}  \left(\frac{1}{x} \right)^{n_x}
+          -  \frac{n_x}{n_x - \gamma}  \left(\frac{1}{x} \right)^{\gamma} \right) \qquad r < r_c
+
+:math:`r_c` is the cutoff.
+
+
+An additional parameter, :math:`\alpha`, has been introduced in order to
+be able to recover the traditional Lennard-Jones 12-6 with a specific
+choice of parameters. With :math:`R_m \equiv r_0 = \sigma \cdot 2^{1 /
+6}`, :math:`\alpha = 0`, :math:`\beta = 12` and :math:`\gamma = 6` it is
+straightforward to prove that LJ 12-6 is obtained. Also, it can be
+verified that using :math:`\alpha= 4`, :math:`\beta= 8` and
+:math:`\gamma = 6`, at the equilibrium distance, the first and second
+derivatives of ILJ match those of LJ 12-6. The parameter :math:`R_m`
+corresponds to the equilibrium distance and :math:`\epsilon` to the well
+depth.
+
+
+This potential provides some advantages with respect to the standard LJ
+potential, as explained in :ref:`(Pirani) <Pirani>`: it provides a more
+realistic description of the long range behavior and an attenuation of
+the hardness of the repulsive wall.
+
+This force field can be used for neutral-neutral (:math:`\gamma = 6`),
+ion-neutral (:math:`\gamma = 4`) or ion-ion systems (:math:`\gamma =
+1`).  Notice that this implementation does not include explicit
+electrostatic interactions.  If these are desired, this pair style
+should be used along with a Coulomb pair style like
+:doc:`pair styles coul/cut or coul/long <pair_coul>` by using
+:doc:`pair style hybrid/overlay <pair_hybrid>` and a suitable
+:doc:`kspace style <kspace_style>`, if needed.
+
+As discussed in :ref:`(Pirani) <Pirani>`, analysis of a variety of
+systems showed that :math:`\alpha= 4` generally works very well.  In
+some special cases (e.g. those involving very small multiple charged
+ions) this factor may take a slightly different value. The parameter
+:math:`\beta` codifies the hardness (polarizability) of the interacting
+partners, and for neutral-neutral systems it usually ranges from 6
+to 11.  Moreover, the modulation of :math:`\beta` can model additional
+interaction effects, such as charge transfer in the perturbative limit,
+and can mitigate the effect of some uncertainty in the data used to
+build up the potential function.
+
+The following coefficients must be defined for each pair of atoms
+types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
+above, or in the data file or restart files read by the
+:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
+commands:
+
+* :math:`\alpha` (dimensionless)
+* :math:`\beta` (dimensionless)
+* :math:`\gamma` (dimensionless)
+* :math:`R_m` (distance units)
+* :math:`\epsilon` (energy units)
+* cutoff (distance units)
+
+The last coefficient is optional. If not specified, the global cutoff is used.
+
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This pair style does not support mixing.  Thus, coefficients for all I,J
+pairs must be specified explicitly.
+
+This pair style supports the :doc:`pair_modify <pair_modify>` shift
+option for the energy of the pair interaction.
+
+The :doc:`pair_modify <pair_modify>` table options are not relevant for
+this pair style.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files
+<restart>`, so pair_style and pair_coeff commands do not need to be
+specified in an input script that reads a restart file.
+
+This pair style supports the use of the *inner*, *middle*, and
+*outer* keywords of the :doc:`run_style respa <run_style>` command,
+meaning the pairwise forces can be partitioned by distance at different
+levels of the rRESPA hierarchy. See the :doc:`run_style <run_style>`
+command for details.
+
+
+----------
+
+Restrictions
+""""""""""""
+
+This pair style is only enabled if LAMMPS was built with the EXTRA-PAIR
+package.  See the :doc:`Build package <Build_package>` page for more
+info.
+
+Related commands
+""""""""""""""""
+
+* :doc:`pair_coeff <pair_coeff>`
+* :doc:`pair_style lj/cut <pair_lj>`
+
+Default
+"""""""
+
+none
+
+--------------
+
+.. _Pirani:
+
+**(Pirani)** F. Pirani, S. Brizi, L. Roncaratti, P. Casavecchia, D. Cappelletti and F. Vecchiocattivi,
+Phys. Chem. Chem. Phys., 2008, 10, 5489-5503.

doc/src/pair_lj_smooth.rst

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

doc/src/pair_style.rst

@@ -272,6 +272,7 @@ accelerated styles exist.
 * :doc:`lj/long/dipole/long <pair_dipole>` - long-range LJ and long-range point dipoles
 * :doc:`lj/long/tip4p/long <pair_lj_long>` - long-range LJ and long-range Coulomb for TIP4P water
 * :doc:`lj/mdf <pair_mdf>` - LJ potential with a taper function
+* :doc:`lj/pirani <pair_lj_pirani>` - Improved LJ potential
 * :doc:`lj/relres <pair_lj_relres>` - LJ using multiscale Relative Resolution (RelRes) methodology :ref:`(Chaimovich) <Chaimovich2>`.
 * :doc:`lj/spica <pair_spica>` - LJ for SPICA coarse-graining
 * :doc:`lj/spica/coul/long <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb

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
@@ -103,6 +104,7 @@ Amit
 amsmath
 amu
 Amzallag
+Anandakrishnan
 analytical
 Anders
 Andric
@@ -110,6 +112,7 @@ Andrienko
 Andzelm
 Ang
 anglegrad
+anglelist
 angleoffset
 angletangrad
 angmom
@@ -347,6 +350,7 @@ Bomont
 BondAngle
 BondBond
 bondchk
+bondlist
 bondmax
 bondscreened
 bondscreenedspin
@@ -389,11 +393,13 @@ Bretonnet
 Briels
 Brien
 Brilliantov
+Brizi
 Broadwell
 Broglie
 brownian
 brownw
 Broyden
+Bruenger
 Bruskin
 Brusselle
 Bryantsev
@@ -431,10 +437,12 @@ Camiloni
 Campana
 Cangi
 Cao
+Cappelletti
 Capolungo
 Caro
 cartesian
 Cas
+Casavecchia
 CasP
 Caswell
 Cates
@@ -623,6 +631,7 @@ cp
 cpp
 cpu
 cradius
+Cramer
 createatoms
 createAtoms
 CreateIDs
@@ -663,6 +672,7 @@ cuFFT
 CuH
 Cui
 Cummins
+cumulants
 Cundall
 cundall
 Curk
@@ -816,6 +826,7 @@ diffusively
 diffusivities
 diffusivity
 dihedral
+dihedrallist
 dihedrals
 Dihedrals
 dihydride
@@ -1166,6 +1177,7 @@ Fermionic
 Ferrand
 fexternal
 Fexternal
+ffast
 ffield
 ffl
 fflush
@@ -1194,6 +1206,7 @@ filesystem
 filesystems
 Fily
 Fincham
+Finkelstein
 Fint
 fingerprintconstants
 fingerprintsperelement
@@ -1320,7 +1333,6 @@ Geocomputing
 georg
 Georg
 Geotechnica
-Gergs
 germain
 Germann
 Germano
@@ -1348,6 +1360,8 @@ Gillan
 Gingold
 Gissinger
 github
+Giusti
+GJ
 gjf
 gjwagne
 gl
@@ -1606,6 +1620,7 @@ imagename
 imd
 Impey
 impl
+improperlist
 impropers
 Impropers
 imulator
@@ -1722,6 +1737,7 @@ Iyz
 iz
 izcm
 ized
+Izadi
 Izrailev
 Izumi
 Izvekov
@@ -1758,6 +1774,7 @@ jik
 JIK
 jku
 jN
+Joanes
 Joannopoulos
 Jochim
 Jonsson
@@ -1802,6 +1819,7 @@ Karniadakis
 Karplus
 Karttunen
 kate
+katom
 Katsnelson
 Katsura
 Kaufmann
@@ -1850,6 +1868,7 @@ Kloss
 Kloza
 kmax
 Kmax
+kMC
 KMP
 kmu
 Knizhnik
@@ -1914,6 +1933,7 @@ Lachet
 Lackmann
 Ladd
 lagrangian
+Lalli
 lambdai
 LambdaLanczos
 Lambrecht
@@ -1976,6 +1996,7 @@ lennard
 Lennard
 Lenosky
 Lenz
+Leoni
 Lett
 Leuven
 Leven
@@ -2177,6 +2198,7 @@ Materias
 mathbf
 mathjax
 matlab
+Matom
 Matous
 matplotlib
 Matsubara
@@ -2474,6 +2496,7 @@ namespaces
 nan
 NaN
 Nandor
+nanglelist
 nangles
 Nangletype
 nangletypes
@@ -2510,6 +2533,7 @@ nbodies
 nbody
 Nbody
 nbond
+nbondlist
 nbonds
 nbondtype
 Nbondtype
@@ -2531,6 +2555,7 @@ ncount
 nd
 ndactrung
 ndescriptors
+ndihedrallist
 ndihedrals
 Ndihedraltype
 ndihedraltypes
@@ -2588,6 +2613,7 @@ NiAlH
 Nicklas
 Niklasson
 Nikolskiy
+nimproperlist
 nimpropers
 Nimpropertype
 nimpropertypes
@@ -2682,6 +2708,7 @@ Nprocs
 npt
 nr
 Nr
+Nrecent
 Nrecompute
 Nrepeat
 nreset
@@ -2760,6 +2787,7 @@ ocl
 octahedral
 octants
 Odegard
+Og
 Ohara
 O'Hearn
 ohenrich
@@ -2792,6 +2820,7 @@ oneMKL
 oneway
 onlysalt
 ons
+Onufriev
 OO
 Oord
 opencl
@@ -2922,6 +2951,7 @@ perp
 Perram
 persp
 Persp
+perturbative
 peru
 Peskin
 Pettifor
@@ -2960,6 +2990,8 @@ pimdb
 Piola
 pIp
 pipelining
+Pirani
+pirani
 Pisarev
 Pishevar
 Pitera
@@ -3337,6 +3369,7 @@ Rmin
 RMS
 rmsd
 rnage
+rnflag
 rng
 rNEMD
 ro
@@ -3346,6 +3379,7 @@ Rockett
 rocksalt
 Rodrigues
 Rohart
+Roncaratti
 Ronchetti
 Ronevich
 Rosati
@@ -3391,6 +3425,7 @@ ry
 Ryckaert
 Rycroft
 Rydbergs
+Ryzen
 rz
 Rz
 Sabry
@@ -3456,6 +3491,7 @@ sectoring
 sed
 Seddon
 segmental
+Seibold
 Seifert
 Seleson
 sellerio
@@ -3809,6 +3845,7 @@ Thiaville
 Thibaudeau
 Thijsse
 Thirumalai
+Threadripper
 threebody
 thrid
 ThunderX
@@ -4058,6 +4095,7 @@ vdW
 vdwl
 vec
 Vecchio
+Vecchiocattivi
 vectorial
 vectorization
 Vectorization
@@ -4074,9 +4112,11 @@ versa
 Verstraelen
 ves
 vf
+vfull
 vflag
 vflow
 vfrac
+vhalf
 vhi
 vibrational
 Vij
@@ -4108,6 +4148,7 @@ volpress
 volumetric
 von
 Voro
+voro
 Vorobyov
 voronoi
 Voronoi

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/plugin/liblammpsplugin.c

@@ -144,6 +144,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
   ADDSYM(find_pair_neighlist);
   ADDSYM(find_fix_neighlist);
   ADDSYM(find_compute_neighlist);
+  ADDSYM(request_single_neighlist);
   ADDSYM(neighlist_num_elements);
   ADDSYM(neighlist_element_neighbors);
 

examples/COUPLE/plugin/liblammpsplugin.h

@@ -94,6 +94,17 @@ enum _LMP_VAR_CONST {
   LMP_VAR_STRING = 3  /*!< return value will be a string (catch-all) */
 };
 
+/** Neighbor list settings constants
+ *
+ * Must be kept in sync with the equivalent constants in ``python/lammps/constants.py``,
+ * ``fortran/lammps.f90``, ``tools/swig/lammps.i``, and
+ * ``examples/COUPLE/plugin/liblammpsplugin.h`` */
+
+enum _LMP_NEIGH_CONST {
+  LMP_NEIGH_HALF = 0,  /*!< request (default) half neighbor list */
+  LMP_NEIGH_FULL = 1,  /*!< request full neighbor list */
+};
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -189,14 +200,17 @@ struct _liblammpsplugin {
  * caller must match to how LAMMPS library is built */
 
 #if !defined(LAMMPS_BIGBIG)
- int (*create_atoms)(void *, int, int *, int *, double *, double *, int *, int);
+ int (*create_atoms)(void *, int, const int *, const int *, const double *, const double *,
+                     const int *, int);
 #else
-  int (*create_atoms)(void *, int, int64_t *, int *, double *, double *, int64_t *, int);
+  int (*create_atoms)(void *, int, const int64_t *, const int *, const double *, const double *,
+                      const int64_t *, int);
 #endif
 
   int (*find_pair_neighlist)(void *, const char *, int, int, int);
   int (*find_fix_neighlist)(void *, const char *, int);
   int (*find_compute_neighlist)(void *, const char *, int);
+  int (*request_single_neighlist)(void *, const char *, int, double);
   int (*neighlist_num_elements)(void *, int);
   void (*neighlist_element_neighbors)(void *, int, int, int *, int *, int **);
 

examples/COUPLE/simple/CMakeLists.txt

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

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

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

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

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

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

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

examples/PACKAGES/imd/in.melt_imd-gpu

@@ -1,8 +1,11 @@
-# 3d Lennard-Jones melt
+# 3d Lennard-Jones melt with GPU package acceleration
+
+# enable GPU package from within the input:
+package gpu 0
+suffix gpu
 
 units           lj
 atom_style      atomic
-newton      off
 
 lattice         fcc 0.8442
 region          box block 0 10 0 10 0 10
@@ -12,7 +15,7 @@ mass		1 1.0
 
 velocity        all create 3.0 87287
 
-pair_style	lj/cut/gpu 2.5
+pair_style      lj/cut 2.5
 pair_coeff      1 1 1.0 1.0 2.5
 
 neighbor        0.3 bin
@@ -20,7 +23,6 @@ neigh_modify	every 5 delay 10 check yes
 
 thermo_style    custom step pe ke spcpu
 
-fix     0 all gpu force/neigh 0 0 1.0
 fix             1 all nve
 
 # IMD setup.

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