Merge pull request #4645 from akohlmey/improve-tests-for-set

Add or improve unit test programs to improve test coverage and specifically check recent additions

.github/release_steps.md

@@ -104,13 +104,13 @@ 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
-apptainer shell fedora41_musl.sif
+wget https://download.lammps.org/static/fedora41_musl_mingw.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
 cmake --build build-release --target install
-/usr/musl/bin/x86_64-linux-musl-strip lammps-static/bin/*
+/usr/musl/bin/x86_64-linux-musl-strip -g lammps-static/bin/*
 tar -czvvf ../lammps-linux-x86_64-4Feb2025.tar.gz lammps-static
 exit # fedora 41 container
 cd ..
@@ -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 \
@@ -44,8 +55,8 @@ jobs:
       uses: actions/cache@v4
       with:
         path: ${{ env.CCACHE_DIR }}
-        key: linux-cpp23-ccache-${{ github.sha }}
-        restore-keys: linux-cpp23-ccache-
+        key: linux-cpp23-ccache-${{ matrix.idx }}-${{ github.sha }}
+        restore-keys: linux-cpp23-ccache-${{ matrix.idx }}
 
     - name: Building LAMMPS via CMake
       shell: bash
@@ -58,14 +69,14 @@ jobs:
         cmake -S cmake -B build \
               -C cmake/presets/most.cmake \
               -C cmake/presets/kokkos-openmp.cmake \
+              -C cmake/presets/${{ matrix.idx }}.cmake \
               -D CMAKE_CXX_STANDARD=23 \
-              -D CMAKE_CXX_COMPILER=g++ \
-              -D CMAKE_C_COMPILER=gcc \
               -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
               -D CMAKE_C_COMPILER_LAUNCHER=ccache \
               -D CMAKE_BUILD_TYPE=Debug \
               -D CMAKE_CXX_FLAGS_DEBUG="-Og -g" \
               -D DOWNLOAD_POTENTIALS=off \
+              -D FFT=KISS \
               -D BUILD_MPI=on \
               -D BUILD_SHARED_LIBS=on \
               -D BUILD_TOOLS=off \

cmake/CMakeLists.txt

@@ -3,10 +3,11 @@
 # CMake build system
 # This file is part of LAMMPS
 cmake_minimum_required(VERSION 3.16)
-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 +28,10 @@ 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)
 
@@ -131,7 +135,9 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
 endif()
 
 # silence nvcc warnings
-if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
+if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT
+    ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
+    OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")))
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
 endif()
 
@@ -147,9 +153,6 @@ endif()
 if(CMAKE_CXX_STANDARD LESS 11)
   message(FATAL_ERROR "C++ standard must be set to at least 11")
 endif()
-if(CMAKE_CXX_STANDARD LESS 17)
-  message(WARNING "Selecting C++17 standard is preferred over C++${CMAKE_CXX_STANDARD}")
-endif()
 if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
   set(CMAKE_CXX_STANDARD 17)
 endif()
@@ -194,6 +197,10 @@ 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                                                   #
 ########################################################################
@@ -231,15 +238,6 @@ option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared lib
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
 option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
 
-# Support using clang-tidy for C++ files with selected options
-set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
-if(ENABLE_CLANG_TIDY)
-  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,readability-qualified-auto,misc-unused-parameters,modernize-deprecated-ios-base-aliases,modernize-loop-convert,modernize-shrink-to-fit,modernize-use-auto,modernize-use-using,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
-else()
-  unset(CMAKE_CXX_CLANG_TIDY CACHE)
-endif()
-
-
 file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
 file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
@@ -264,6 +262,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 set(STANDARD_PACKAGES
   ADIOS
   AMOEBA
+  APIP
   ASPHERE
   ATC
   AWPMD
@@ -356,17 +355,6 @@ foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
-set(DEPRECATED_PACKAGES AWPMD ATC POEMS)
-foreach(PKG ${DEPRECATED_PACKAGES})
-  if(PKG_${PKG})
-    message(WARNING
-          "The ${PKG} package will be removed from LAMMPS in Summer 2025 due to lack of "
-          "maintenance and use of code constructs that conflict with modern C++ compilers "
-          "and standards.  Please contact developers@lammps.org if you have any concerns "
-          "about this step.")
-  endif()
-endforeach()
-
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
@@ -377,7 +365,6 @@ if(PKG_ADIOS)
   # The search for ADIOS2 must come before MPI because
   # it includes its own MPI search with the latest FindMPI.cmake
   # script that defines the MPI::MPI_C target
-  enable_language(C)
   find_package(ADIOS2 REQUIRED)
   if(BUILD_MPI)
     if(NOT ADIOS2_HAVE_MPI)
@@ -392,21 +379,18 @@ 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)
@@ -467,6 +451,7 @@ pkg_depends(ELECTRODE KSPACE)
 pkg_depends(EXTRA-MOLECULE MOLECULE)
 pkg_depends(MESONT MOLECULE)
 pkg_depends(RHEO BPM)
+pkg_depends(APIP ML-PACE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -533,7 +518,6 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUA
 endif()
 
 if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR PKG_RHEO OR BUILD_TOOLS)
-  enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
     find_package(BLAS)

cmake/Modules/LAMMPSInterfacePlugin.cmake

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

cmake/Modules/LAMMPSUtils.cmake

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

cmake/Modules/MPI4WIN.cmake

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

cmake/Modules/Packages/COLVARS.cmake

@@ -26,6 +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/KOKKOS.cmake

@@ -57,8 +57,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.6.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "61b2b69ae50d83eedcc7d47a3fa3d6cb" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.6.02.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "14c02fac07bfcec48a1654f88ddee9c6" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -83,7 +83,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 4.6.00 REQUIRED CONFIG)
+  find_package(Kokkos 4.6.02 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

cmake/Modules/Packages/MC.cmake

@@ -7,3 +7,23 @@ 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 hmc may only be installed if also fix rigid/small from RIGID is installed
+if(NOT PKG_RIGID)
+  get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
+  list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MC/fix_hmc.h)
+  set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_hmc.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES "${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/ML-PACE.cmake

@@ -53,7 +53,13 @@ else()
       add_library(yaml-cpp::yaml-cpp ALIAS yaml-cpp)
     endif()
 
-    add_subdirectory(${lib-pace} build-pace)
+    # fixup yaml-cpp/emitterutils.cpp for GCC 15+ until patch is applied
+    file(READ ${lib-pace}/yaml-cpp/src/emitterutils.cpp yaml_emitterutils)
+    string(REPLACE "#include <sstream>" "#include <sstream>\n#include <cinttypes>" yaml_tmp_emitterutils "${yaml_emitterutils}")
+    string(REPLACE "#include <cinttypes>\n#include <cinttypes>" "#include <cinttypes>" yaml_emitterutils "${yaml_tmp_emitterutils}")
+    file(WRITE ${lib-pace}/yaml-cpp/src/emitterutils.cpp "${yaml_emitterutils}")
+
+    add_subdirectory(${lib-pace} build-pace EXCLUDE_FROM_ALL)
     set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
 
     if(CMAKE_PROJECT_NAME STREQUAL "lammps")

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_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of 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 "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
-          ((CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04) OR (CMAKE_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04)))
+    if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (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/Modules/Tools.cmake

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

cmake/packaging/linux_wrapper.sh

@@ -7,6 +7,11 @@ export LC_ALL=C
 BASEDIR="$(dirname "$0")"
 EXENAME="$(basename "$0")"
 
+# save old settings (for restoring them later)
+OLDPATH="${PATH}"
+OLDLDLIB="${LD_LIBRARY_PATH}"
+
+# prepend path to find our custom executables
 PATH="${BASEDIR}/bin:${PATH}"
 
 # append to LD_LIBRARY_PATH to prefer local (newer) libs
@@ -15,6 +20,8 @@ LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BASEDIR}/lib"
 # set some environment variables for LAMMPS etc.
 LAMMPS_POTENTIALS="${BASEDIR}/share/lammps/potentials"
 MSI2LMP_LIBRARY="${BASEDIR}/share/lammps/frc_files"
-export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH
+
+# export everything
+export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH OLDPATH OLDLDLIB
 
 exec "${BASEDIR}/bin/${EXENAME}" "$@"

cmake/packaging/xdg-open

@@ -33,6 +33,14 @@
 #
 #---------------------------------------------
 
+# restore previously saved environment variables, if available
+if [ -n "${OLDPATH}" ]
+then
+    PATH="${OLDPATH}"
+    LD_LIBRARY_PATH="${OLDLDLIB}"
+    export PATH LD_LIBRARY_PATH
+fi
+
 NEW_LIBRARY_PATH="/usr/local/lib64"
 for s in $(echo $LD_LIBRARY_PATH | sed -e 's/:/ /g')
 do \

cmake/presets/all_off.cmake

@@ -4,6 +4,7 @@
 set(ALL_PACKAGES
   ADIOS
   AMOEBA
+  APIP
   ASPHERE
   ATC
   AWPMD

cmake/presets/all_on.cmake

@@ -6,6 +6,7 @@
 set(ALL_PACKAGES
   ADIOS
   AMOEBA
+  APIP
   ASPHERE
   ATC
   AWPMD

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-cuda.cmake

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

cmake/presets/kokkos-hip.cmake

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

cmake/presets/nolib.cmake

@@ -3,6 +3,7 @@
 
 set(PACKAGES_WITH_LIB
   ADIOS
+  APIP
   ATC
   AWPMD
   COMPRESS

doc/Makefile

@@ -99,8 +99,6 @@ html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJ
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		ln -sf Manual.html html/index.html;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
@@ -162,8 +160,6 @@ epub: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
 	)
@@ -183,8 +179,6 @@ pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build  $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\
@@ -256,6 +250,15 @@ link_check : $(VENV) html
 		deactivate ;\
 	)
 
+upgrade: $(VENV)
+	@(\
+		. $(VENV)/bin/activate; \
+		pip $(PIP_OPTIONS) install --upgrade pip; \
+		pip $(PIP_OPTIONS) install --upgrade wheel; \
+		pip $(PIP_OPTIONS) install --upgrade -r $(BUILDDIR)/utils/requirements.txt; \
+		deactivate;\
+	)
+
 xmlgen : doxygen/xml/index.xml
 
 doxygen/Doxyfile: doxygen/Doxyfile.in

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/lammps.1

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

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_development.rst

@@ -28,28 +28,6 @@ variable VERBOSE set to 1:
 
 ----------
 
-.. _clang-tidy:
-
-Enable static code analysis with clang-tidy (CMake only)
---------------------------------------------------------
-
-The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
-static code analysis tool to diagnose (and potentially fix) typical
-programming errors or coding style violations.  It has a modular framework
-of tests that can be adjusted to help identifying problems before they
-become bugs and also assist in modernizing large code bases (like LAMMPS).
-It can be enabled for all C++ code with the following CMake flag
-
-.. code-block:: bash
-
-   -D ENABLE_CLANG_TIDY=value    # value = no (default) or yes
-
-With this flag enabled all source files will be processed twice, first to
-be compiled and then to be analyzed. Please note that the analysis can be
-significantly more time-consuming than the compilation itself.
-
-----------
-
 .. _iwyu_processing:
 
 Report missing and unneeded '#include' statements (CMake only)
@@ -523,7 +501,7 @@ to do this to install it via pip:
 
 .. code-block:: bash
 
-   pip install git+https://github.com/gcovr/gcovr.git
+   python3 -m pip install gcovr
 
 After post-processing with ``gen_coverage_html`` the results are in
 a folder ``coverage_html`` and can be viewed with a web browser.

doc/src/Build_extras.rst

@@ -35,6 +35,7 @@ This is the list of packages that may require additional steps.
    :columns: 6
 
    * :ref:`ADIOS <adios>`
+   * :ref:`APIP <apip>`
    * :ref:`ATC <atc>`
    * :ref:`AWPMD <awpmd>`
    * :ref:`COLVARS <colvar>`
@@ -614,6 +615,9 @@ They must be specified in uppercase.
    *  - ZEN4
       - HOST
       - AMD Zen4 architecture
+   *  - ZEN5
+      - HOST
+      - AMD Zen5 architecture
    *  - RISCV_SG2042
       - HOST
       - SG2042 (RISC-V) CPUs
@@ -668,6 +672,12 @@ They must be specified in uppercase.
    *  - HOPPER90
       - GPU
       - NVIDIA Hopper generation CC 9.0
+   *  - BLACKWELL100
+      - GPU
+      - NVIDIA Blackwell generation CC 10.0
+   *  - BLACKWELL120
+      - GPU
+      - NVIDIA Blackwell generation CC 12.0
    *  - AMD_GFX906
       - GPU
       - AMD GPU MI50/60
@@ -716,8 +726,11 @@ They must be specified in uppercase.
    *  - INTEL_PVC
       - GPU
       - Intel GPU Ponte Vecchio
+   *  - INTEL_DG2
+      - GPU
+      - Intel GPU DG2
 
-This list was last updated for version 4.6.0 of the Kokkos library.
+This list was last updated for version 4.6.2 of the Kokkos library.
 
 .. tabs::
 
@@ -1272,6 +1285,34 @@ systems.
 
 ----------
 
+.. _apip:
+
+APIP package
+-----------------------------
+
+The APIP package depends on the library of the
+:ref:`ML-PACE <ml-pace>` package.
+The code for the library can be found
+at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      No additional settings are needed besides ``-D PKG_APIP=yes``
+      and ``-D PKG_ML-PACE=yes``.
+      One can use a local version of the ML-PACE library instead of
+      automatically downloading the library as described :ref:`here <ml-pace>`.
+
+
+   .. tab:: Traditional make
+
+      You need to install the ML-PACE package *first* and follow
+      the instructions :ref:`here <ml-pace>` before installing
+      the APIP package.
+
+----------
+
 .. _atc:
 
 ATC package

doc/src/Build_manual.rst

@@ -57,6 +57,8 @@ Python interpreter version 3.8 or later, the ``doxygen`` tools and
 internet access to download additional files and tools are required.
 This download is usually only required once or after the documentation
 folder is returned to a pristine state with ``make clean-all``.
+You can also upgrade those packages to their latest available versions
+with ``make upgrade``.
 
 For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into
@@ -82,6 +84,7 @@ folder.  The following ``make`` commands are available:
 
    make clean         # remove intermediate RST files created by HTML build
    make clean-all     # remove entire build folder and any cached data
+   make upgrade       # upgrade the python packages in the virtual environment
 
    make anchor_check  # check for duplicate anchor labels
    make style_check   # check for complete and consistent style lists

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/Commands_fix.rst

@@ -22,6 +22,7 @@ OPT.
    * :doc:`append/atoms <fix_append_atoms>`
    * :doc:`atc <fix_atc>`
    * :doc:`atom/swap <fix_atom_swap>`
+   * :doc:`atom_weight/apip <fix_atom_weight_apip>`
    * :doc:`ave/atom <fix_ave_atom>`
    * :doc:`ave/chunk <fix_ave_chunk>`
    * :doc:`ave/correlate <fix_ave_correlate>`
@@ -29,6 +30,7 @@ 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>`
@@ -64,7 +66,7 @@ OPT.
    * :doc:`electrode/conp (i) <fix_electrode>`
    * :doc:`electrode/conq (i) <fix_electrode>`
    * :doc:`electrode/thermo (i) <fix_electrode>`
-   * :doc:`electron/stopping <fix_electron_stopping>`
+   * :doc:`electron/stopping (k) <fix_electron_stopping>`
    * :doc:`electron/stopping/fit <fix_electron_stopping>`
    * :doc:`enforce2d (k) <fix_enforce2d>`
    * :doc:`eos/cv <fix_eos_cv>`
@@ -77,6 +79,7 @@ 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>`
@@ -84,11 +87,14 @@ OPT.
    * :doc:`halt <fix_halt>`
    * :doc:`heat <fix_heat>`
    * :doc:`heat/flow <fix_heat_flow>`
+   * :doc:`hmc <fix_hmc>`
    * :doc:`hyper/global <fix_hyper_global>`
    * :doc:`hyper/local <fix_hyper_local>`
    * :doc:`imd <fix_imd>`
    * :doc:`indent <fix_indent>`
    * :doc:`ipi <fix_ipi>`
+   * :doc:`lambda/apip <fix_lambda_apip>`
+   * :doc:`lambda_thermostat/apip <fix_lambda_thermostat_apip>`
    * :doc:`langevin (k) <fix_langevin>`
    * :doc:`langevin/drude <fix_langevin_drude>`
    * :doc:`langevin/eff <fix_langevin_eff>`
@@ -111,6 +117,7 @@ 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 +223,7 @@ 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_kspace.rst

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

doc/src/Commands_pair.rst

@@ -96,7 +96,9 @@ OPT.
    * :doc:`eam/cd <pair_eam>`
    * :doc:`eam/cd/old <pair_eam>`
    * :doc:`eam/fs (gikot) <pair_eam>`
+   * :doc:`eam/fs/apip <pair_eam_apip>`
    * :doc:`eam/he <pair_eam>`
+   * :doc:`eam/apip <pair_eam_apip>`
    * :doc:`edip (o) <pair_edip>`
    * :doc:`edip/multi <pair_edip>`
    * :doc:`edpd (g) <pair_mesodpd>`
@@ -124,6 +126,9 @@ OPT.
    * :doc:`ilp/tmd (t) <pair_ilp_tmd>`
    * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
    * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
+   * :doc:`lambda/input/apip <pair_lambda_input_apip>`
+   * :doc:`lambda/input/csp/apip <pair_lambda_input_apip>`
+   * :doc:`lambda/zone/apip <pair_lambda_zone_apip>`
    * :doc:`lcbop <pair_lcbop>`
    * :doc:`lebedeva/z <pair_lebedeva_z>`
    * :doc:`lennard/mdf <pair_mdf>`
@@ -237,6 +242,9 @@ OPT.
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`pace (k) <pair_pace>`
    * :doc:`pace/extrapolation (k) <pair_pace>`
+   * :doc:`pace/apip <pair_pace_apip>`
+   * :doc:`pace/fast/apip <pair_pace_apip>`
+   * :doc:`pace/precise/apip <pair_pace_apip>`
    * :doc:`pedone (o) <pair_pedone>`
    * :doc:`pod (k) <pair_pod>`
    * :doc:`peri/eps <pair_peri>`

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:: 12Jun2025
+
+The *gjf* keyword in fix langevin is deprecated and will be removed
+soon.  The GJF functionality has been moved to its own fix style
+:doc:`fix gjf <fix_gjf>` and it is strongly recommended to use that
+fix instead.
+
+
 LAMMPS shell
 ------------
 
-.. 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_plugins.rst

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

doc/src/Developer_updating.rst

@@ -29,6 +29,8 @@ 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`_
+- `Use utils::logmesg() instead of error->warning()`_
 
 ----
 
@@ -610,3 +612,71 @@ KSpace solvers which use distributed FFT grids:
 - ``src/KSPACE/pppm.cpp``
 
 This change is **required** or else the code will not compile.
+
+FLERR as first argument to minimum image functions in Domain class
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 12Jun2025
+
+The ``Domain::minimum_image()`` and ``Domain::minimum_image_big()``
+functions were changed to take the ``FLERR`` macros as first argument.
+This way the error message indicates *where* the function was called
+instead of pointing to the implementation of the function.  Example:
+
+Old:
+
+.. code-block:: c++
+
+   double delx1 = x[i1][0] - x[i2][0];
+   double dely1 = x[i1][1] - x[i2][1];
+   double delz1 = x[i1][2] - x[i2][2];
+   domain->minimum_image(delx1, dely1, delz1);
+   double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
+
+   double delx2 = x[i3][0] - x[i2][0];
+   double dely2 = x[i3][1] - x[i2][1];
+   double delz2 = x[i3][2] - x[i2][2];
+   domain->minimum_image_big(delx2, dely2, delz2);
+   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
+
+New:
+
+.. code-block:: c++
+
+   double delx1 = x[i1][0] - x[i2][0];
+   double dely1 = x[i1][1] - x[i2][1];
+   double delz1 = x[i1][2] - x[i2][2];
+   domain->minimum_image(FLERR, delx1, dely1, delz1);
+   double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
+
+   double delx2 = x[i3][0] - x[i2][0];
+   double dely2 = x[i3][1] - x[i2][1];
+   double delz2 = x[i3][2] - x[i2][2];
+   domain->minimum_image_big(FLERR, delx2, dely2, delz2);
+   double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
+
+This change is **required** or else the code will not compile.
+
+Use utils::logmesg() instead of error->warning()
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: TBD
+
+The ``Error::message()`` method has been removed since its functionality
+has been superseded by the :cpp:func:`utils::logmesg` function.
+
+Old:
+
+.. code-block:: c++
+
+   if (comm->me == 0) {
+     error->message(FLERR, "INFO: About to read data file: {}", filename);
+  }
+
+New:
+
+.. code-block:: c++
+
+   if (comm->me == 0) utils::logmesg(lmp, "INFO: About to read data file: {}\n", filename);
+
+This change is **required** or else the code will not compile.

doc/src/Errors_common.rst

@@ -1,124 +1,149 @@
-Common problems
-===============
+Common issues that are often regarded as bugs
+=============================================
 
-If two LAMMPS runs do not produce the exact same answer on different
-machines or different numbers of processors, this is typically not a
-bug.  In theory you should get identical answers on any number of
-processors and on any machine.  In practice, numerical round-off can
-cause slight differences and eventual divergence of molecular dynamics
-phase space trajectories within a few 100s or few 1000s of timesteps.
-However, the statistical properties of the two runs (e.g. average
-energy or temperature) should still be the same.
+The list below are some random notes on behavior of LAMMPS that is
+sometimes unexpected or even considered a bug.  Most of the time, these
+are just issues of understanding how LAMMPS is implemented and
+parallelized.  Please also have a look at the :doc:`Error details
+discussions page <Errors_details>` that contains recommendations for
+tracking down issues and explanations for error messages that may
+sometimes be confusing or need additional explanations.
 
-If the :doc:`velocity <velocity>` command is used to set initial atom
-velocities, a particular atom can be assigned a different velocity
-when the problem is run on a different number of processors or on
-different machines.  If this happens, the phase space trajectories of
-the two simulations will rapidly diverge.  See the discussion of the
-*loop* option in the :doc:`velocity <velocity>` command for details and
-options that avoid this issue.
+- A LAMMPS simulation typically has two stages, 1) issuing commands
+  and 2) run or minimize.  Most LAMMPS errors are detected in stage 1),
+  others at the beginning of stage 2), and finally others like a bond
+  stretching too far may or lost atoms or bonds may not occur until the
+  middle of a run.
 
-Similarly, the :doc:`create_atoms <create_atoms>` command generates a
-lattice of atoms.  For the same physical system, the ordering and
-numbering of atoms by atom ID may be different depending on the number
-of processors.
+- If two LAMMPS runs do not produce the exact same answer on different
+  machines or different numbers of processors, this is typically not a
+  bug.  In theory you should get identical answers on any number of
+  processors and on any machine.  In practice, numerical round-off can
+  cause slight differences and eventual divergence of molecular dynamics
+  phase space trajectories within a few 100s or few 1000s of timesteps.
+  This can be triggered by different ordering of atoms due to different
+  domain decompositions, but also through different CPU architectures,
+  different operating systems, different compilers or compiler versions,
+  different compiler optimization levels, different FFT libraries.
+  However, the statistical properties of the two runs (e.g. average
+  energy or temperature) should still be the same.
 
-Some commands use random number generators which may be setup to
-produce different random number streams on each processor and hence
-will produce different effects when run on different numbers of
-processors.  A commonly-used example is the :doc:`fix langevin <fix_langevin>` command for thermostatting.
+- If the :doc:`velocity <velocity>` command is used to set initial atom
+  velocities, a particular atom can be assigned a different velocity
+  when the problem is run on a different number of processors or on
+  different machines.  If this happens, the phase space trajectories of
+  the two simulations will rapidly diverge.  See the discussion of the
+  *loop* option in the :doc:`velocity <velocity>` command for details
+  and options that avoid this issue.
 
-A LAMMPS simulation typically has two stages, setup and run.  Most
-LAMMPS errors are detected at setup time; others like a bond
-stretching too far may not occur until the middle of a run.
+- Similarly, the :doc:`create_atoms <create_atoms>` command generates a
+  lattice of atoms.  For the same physical system, the ordering and
+  numbering of atoms by atom ID may be different depending on the number
+  of processors.
 
-LAMMPS tries to flag errors and print informative error messages so
-you can fix the problem.  For most errors it will also print the last
-input script command that it was processing.  Of course, LAMMPS cannot
-figure out your physics or numerical mistakes, like choosing too big a
-timestep, specifying erroneous force field coefficients, or putting 2
-atoms on top of each other!  If you run into errors that LAMMPS
-does not catch that you think it should flag, please send an email to
-the `developers <https://www.lammps.org/authors.html>`_ or create an new
-topic on the dedicated `MatSci forum section <https://matsci.org/lammps/>`_.
+- Some commands use random number generators which may be setup to
+  produce different random number streams on each processor and hence
+  will produce different effects when run on different numbers of
+  processors.  A commonly-used example is the :doc:`fix langevin
+  <fix_langevin>` command for thermostatting.
 
-If you get an error message about an invalid command in your input
-script, you can determine what command is causing the problem by
-looking in the log.lammps file or using the :doc:`echo command <echo>`
-to see it on the screen.  If you get an error like "Invalid ...
-style", with ... being fix, compute, pair, etc, it means that you
-mistyped the style name or that the command is part of an optional
-package which was not compiled into your executable.  The list of
-available styles in your executable can be listed by using
-:doc:`the -h command-line switch <Run_options>`.  The installation and
-compilation of optional packages is explained on the
-:doc:`Build packages <Build_package>` doc page.
+- LAMMPS tries to flag errors and print informative error messages so
+  you can fix the problem.  For most errors it will also print the last
+  input script command that it was processing or even point to the
+  keyword that is causing troubles.  Of course, LAMMPS cannot figure out
+  your physics or numerical mistakes, like choosing too big a timestep,
+  specifying erroneous force field coefficients, or putting 2 atoms on
+  top of each other!  Also, LAMMPS does not know what you *intend* to
+  do, but very strictly applies the syntax as described in the
+  documentation.  If you run into errors that LAMMPS does not catch that
+  you think it should flag, please send an email to the `developers
+  <https://www.lammps.org/authors.html>`_ or create an new topic on the
+  dedicated `MatSci forum section <https://matsci.org/lammps/>`_.
 
-For a given command, LAMMPS expects certain arguments in a specified
-order.  If you mess this up, LAMMPS will often flag the error, but it
-may also simply read a bogus argument and assign a value that is
-valid, but not what you wanted.  E.g. trying to read the string "abc"
-as an integer value of 0.  Careful reading of the associated doc page
-for the command should allow you to fix these problems. In most cases,
-where LAMMPS expects to read a number, either integer or floating point,
-it performs a stringent test on whether the provided input actually
-is an integer or floating-point number, respectively, and reject the
-input with an error message (for instance, when an integer is required,
-but a floating-point number 1.0 is provided):
+- If you get an error message about an invalid command in your input
+  script, you can determine what command is causing the problem by
+  looking in the log.lammps file or using the :doc:`echo command <echo>`
+  to see it on the screen.  If you get an error like "Invalid ...
+  style", with ... being fix, compute, pair, etc, it means that you
+  mistyped the style name or that the command is part of an optional
+  package which was not compiled into your executable.  The list of
+  available styles in your executable can be listed by using
+  :doc:`the -h command-line switch <Run_options>`.  The installation and
+  compilation of optional packages is explained on the :doc:`Build
+  packages <Build_package>` doc page.
 
-.. parsed-literal::
+- For a given command, LAMMPS expects certain arguments in a specified
+  order.  If you mess this up, LAMMPS will often flag the error, but it
+  may also simply read a bogus argument and assign a value that is
+  valid, but not what you wanted.  E.g. trying to read the string "abc"
+  as an integer value of 0.  Careful reading of the associated doc page
+  for the command should allow you to fix these problems. In most cases,
+  where LAMMPS expects to read a number, either integer or floating
+  point, it performs a stringent test on whether the provided input
+  actually is an integer or floating-point number, respectively, and
+  reject the input with an error message (for instance, when an integer
+  is required, but a floating-point number 1.0 is provided):
 
-   ERROR: Expected integer parameter instead of '1.0' in input script or data file
+  .. parsed-literal::
 
-Some commands allow for using variable references in place of numeric
-constants so that the value can be evaluated and may change over the
-course of a run.  This is typically done with the syntax *v_name* for a
-parameter, where name is the name of the variable. On the other hand,
-immediate variable expansion with the syntax ${name} is performed while
-reading the input and before parsing commands,
+     ERROR: Expected integer parameter instead of '1.0' in input script or data file
 
-.. note::
+- Some commands allow for using variable references in place of numeric
+  constants so that the value can be evaluated and may change over the
+  course of a run.  This is typically done with the syntax *v_name* for
+  a parameter, where name is the name of the variable. On the other
+  hand, immediate variable expansion with the syntax ${name} is
+  performed while reading the input and before parsing commands,
 
-   Using a variable reference (i.e. *v_name*) is only allowed if
-   the documentation of the corresponding command explicitly says it is.
-   Otherwise, you will receive an error message of this kind:
+  .. note::
 
-.. parsed-literal::
+     Using a variable reference (i.e. *v_name*) is only allowed if
+     the documentation of the corresponding command explicitly says it is.
+     Otherwise, you will receive an error message of this kind:
 
-   ERROR: Expected floating point parameter instead of 'v_name' in input script or data file
+  .. parsed-literal::
 
-Generally, LAMMPS will print a message to the screen and logfile and
-exit gracefully when it encounters a fatal error.  Sometimes it will
-print a WARNING to the screen and logfile and continue on; you can
-decide if the WARNING is important or not.  A WARNING message that is
-generated in the middle of a run is only printed to the screen, not to
-the logfile, to avoid cluttering up thermodynamic output.  If LAMMPS
-crashes or hangs without spitting out an error message first then it
-could be a bug (see :doc:`this section <Errors_bugs>`) or one of the following
-cases:
+     ERROR: Expected floating point parameter instead of 'v_name' in input script or data file
 
-LAMMPS runs in the available memory a processor allows to be
-allocated.  Most reasonable MD runs are compute limited, not memory
-limited, so this should not be a bottleneck on most platforms.  Almost
-all large memory allocations in the code are done via C-style malloc's
-which will generate an error message if you run out of memory.
-Smaller chunks of memory are allocated via C++ "new" statements.  If
-you are unlucky you could run out of memory just when one of these
-small requests is made, in which case the code will crash or hang (in
-parallel), since LAMMPS does not trap on those errors.
+- Generally, LAMMPS will print a message to the screen and logfile and
+  exit gracefully when it encounters a fatal error.  When running in
+  parallel this message may be stuck in an I/O buffer and LAMMPS will be
+  terminated before that buffer is printed.  In that case you can try
+  adding the ``-nonblock`` or ``-nb`` command-line flag to turn off that
+  buffering.  Please note that this should not be used for production
+  runs, since turning off buffering usually has a significant negative
+  impact on performance (even worse than :doc:`thermo_modify flush yes
+  <thermo_modify>`).  Sometimes LAMMPS will print a WARNING to the
+  screen and logfile and continue on; you can decide if the WARNING is
+  important or not, but as a general rule do not ignore warnings that
+  you not understand.  A WARNING message that is generated in the middle
+  of a run is only printed to the screen, not to the logfile, to avoid
+  cluttering up thermodynamic output.  If LAMMPS crashes or hangs
+  without generating an error message first then it could be a bug
+  (see :doc:`this section <Errors_bugs>`).
 
-Illegal arithmetic can cause LAMMPS to run slow or crash.  This is
-typically due to invalid physics and numerics that your simulation is
-computing.  If you see wild thermodynamic values or NaN values in your
-LAMMPS output, something is wrong with your simulation.  If you
-suspect this is happening, it is a good idea to print out
-thermodynamic info frequently (e.g. every timestep) via the
-:doc:`thermo <thermo>` so you can monitor what is happening.
-Visualizing the atom movement is also a good idea to ensure your model
-is behaving as you expect.
+- LAMMPS runs in the available memory a processor allows to be
+  allocated.  Most reasonable MD runs are compute limited, not memory
+  limited, so this should not be a bottleneck on most platforms.  Almost
+  all large memory allocations in the code are done via C-style malloc's
+  which will generate an error message if you run out of memory.
+  Smaller chunks of memory are allocated via C++ "new" statements.  If
+  you are unlucky you could run out of memory just when one of these
+  small requests is made, in which case the code will crash or hang (in
+  parallel).
 
-In parallel, one way LAMMPS can hang is due to how different MPI
-implementations handle buffering of messages.  If the code hangs
-without an error message, it may be that you need to specify an MPI
-setting or two (usually via an environment variable) to enable
-buffering or boost the sizes of messages that can be buffered.
+- Illegal arithmetic can cause LAMMPS to run slow or crash.  This is
+  typically due to invalid physics and numerics that your simulation is
+  computing.  If you see wild thermodynamic values or NaN values in your
+  LAMMPS output, something is wrong with your simulation.  If you
+  suspect this is happening, it is a good idea to print out
+  thermodynamic info frequently (e.g. every timestep) via the
+  :doc:`thermo <thermo>` so you can monitor what is happening.
+  Visualizing the atom movement is also a good idea to ensure your model
+  is behaving as you expect.
+
+- When running in parallel with MPI, one way LAMMPS can hang is because
+  LAMMPS has come across an error condition, but only on one or a few
+  MPI processes and not all of them.  LAMMPS has two different "stop
+  with an error message" functions and the correct one has to be called
+  or else it will hang.

doc/src/Errors_details.rst

@@ -51,8 +51,11 @@ Parallel versus serial
 ^^^^^^^^^^^^^^^^^^^^^^
 
 Issues where something is "lost" or "missing" often exhibit that issue
-only when running in parallel.  That doesn't mean there is no problem,
-only the symptoms are not triggering an error quickly.  Correspondingly,
+*only* when running in parallel.  That doesn't mean there is no problem
+when running in serial, only the symptoms are not triggering an error.
+This may be because there is no domain decomposition with just one
+processor and thus all atoms are accessible, or it may be because the
+problem will manifest faster with smaller subdomains.  Correspondingly,
 errors may be triggered faster with more processors and thus smaller
 sub-domains.
 
@@ -159,13 +162,17 @@ 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
-enough.  LAMMPS will print a warning in this case using some heuristic
-based on the equilibrium bond length, but that still may not be
-sufficient for cases where the force constants are small and thus bonds
-may be stretched very far.  The communication cutoff can be adjusted
-with :doc:`comm_modify cutoff \<value\> <comm_modify>`, but setting this
-too large will waste CPU time and memory.
+interactions.  But if the pair style cutoff is small (e.g. with a
+repulsive-only Lennard-Jones potential) this may not be enough.  It is
+even worse if there is no pair style defined (or the pair style is set
+to "none"), since then there will be no ghost atoms created at all.
+
+The communication cutoff can be set or adjusted with :doc:`comm_modify
+cutoff \<value\> <comm_modify>`, but setting this too large will waste
+CPU time and memory.  LAMMPS will print warnings in these cases.  For
+bonds it uses some heuristic based on the equilibrium bond length, but
+that still may not be sufficient for cases where the force constants are
+small and thus bonds may be stretched very far.
 
 .. _hint09:
 
@@ -240,6 +247,25 @@ equal style (or similar) variables can only be expanded before the box
 is defined if they do not reference anything that cannot be defined
 before the box (e.g. a compute or fix reference or a thermo keyword).
 
+.. _hint13:
+
+Illegal ... command
+^^^^^^^^^^^^^^^^^^^
+
+These are a catchall error messages that used to be used a lot in LAMMPS
+(also programmers are sometimes lazy).  They usually include the name of
+the source file and the line where the error happened.  This can be used
+to track down what caused the error (most often some form of syntax error)
+by looking at the source code.  However, this has two disadvantages: 1. one
+has to check the source file from the exact same LAMMPS version, or else
+the line number would be different or the core may have been rewritten and
+that specific error does not exist anymore.
+
+The LAMMPS developers are committed to replace these too generic error
+messages with more descriptive errors, e.g. listing *which* keyword was
+causing the error, so that it will be much simpler to look up the
+correct syntax in the manual (and without referring to the source code).
+
 ------
 
 .. _err0001:
@@ -1025,13 +1051,15 @@ 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
+high density are incorrect box dimensions (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.
+as fractional coordinates (LAMMPS does not support this for data files).
+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) on purpose or by accident.  Rather than blindly increasing the
+"one" parameter, it is thus worth checking if this is justified by the
+combination of density and cutoff.  This is particularly recommended
+when using some tool(s) to convert input or data files.
 
 When boosting (= increasing) the "one" parameter, it is recommended to
 also increase the value for the "page" parameter to maintain the ratio

doc/src/Fortran.rst

@@ -69,10 +69,11 @@ statement.  Internally, it will call either
 :cpp:func:`lammps_open_fortran` or :cpp:func:`lammps_open_no_mpi` from
 the C library API to create the class instance.  All arguments are
 optional and :cpp:func:`lammps_mpi_init` will be called automatically
-if it is needed.  Similarly, a possible call to
-:cpp:func:`lammps_mpi_finalize` is integrated into the :f:func:`close`
-function and triggered with the optional logical argument set to
-``.TRUE.``. Here is a simple example:
+if it is needed.  Similarly, optional calls to
+:cpp:func:`lammps_mpi_finalize`, :cpp:func:`lammps_kokkos_finalize`,
+:cpp:func:`lammps_python_finalize`, and :cpp:func:`lammps_plugin_finalize`
+are integrated into the :f:func:`close` function and triggered with the
+optional logical argument set to ``.TRUE.``. Here is a simple example:
 
 .. code-block:: fortran
 
@@ -521,8 +522,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    This method will close down the LAMMPS instance through calling
    :cpp:func:`lammps_close`.  If the *finalize* argument is present and
    has a value of ``.TRUE.``, then this subroutine also calls
-   :cpp:func:`lammps_kokkos_finalize` and
-   :cpp:func:`lammps_mpi_finalize`.
+   :cpp:func:`lammps_kokkos_finalize`, :cpp:func:`lammps_mpi_finalize`,
+   :cpp:func:`lammps_python_finalize`, and :cpp:func:`lammps_plugin_finalize`.
 
    :o finalize: shut down the MPI environment of the LAMMPS
     library if ``.TRUE.``.
@@ -530,6 +531,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    :to: :cpp:func:`lammps_close`
    :to: :cpp:func:`lammps_mpi_finalize`
    :to: :cpp:func:`lammps_kokkos_finalize`
+   :to: :cpp:func:`lammps_python_finalize`
+   :to: :cpp:func:`lammps_plugin_finalize`
 
 --------
 
@@ -2096,7 +2099,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
 --------
 
-.. f:subroutine:: create_atoms([id,] type, x, [v,] [image,] [bexpand])
+.. f:function:: create_atoms([id,] type, x, [v,] [image,] [bexpand])
 
    This method calls :cpp:func:`lammps_create_atoms` to create additional atoms
    from a given list of coordinates and a list of atom types. Additionally,
@@ -2125,6 +2128,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
     will be created, not dropped, and the box dimensions will be extended.
     Default is ``.FALSE.``
    :otype bexpand: logical,optional
+   :r atoms: number of created atoms
+   :rtype atoms: integer(c_int)
    :to: :cpp:func:`lammps_create_atoms`
 
    .. note::
@@ -2149,6 +2154,18 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
 --------
 
+.. f:subroutine:: create_molecule(id, jsonstr)
+
+   Add molecule template from string with JSON data
+
+   .. versionadded:: TBD
+
+   :p character(len=\*) id: desired molecule-ID
+   :p character(len=\*) jsonstr: string with JSON data defining the molecule template
+   :to: :cpp:func:`lammps_create_molecule`
+
+--------
+
 .. f:function:: find_pair_neighlist(style[, exact][, nsub][, reqid])
 
    Find index of a neighbor list requested by a pair style.

doc/src/Howto.rst

@@ -66,6 +66,7 @@ Force fields howto
    :name: force_howto
    :maxdepth: 1
 
+   Howto_FFgeneral
    Howto_bioFF
    Howto_amoeba
    Howto_tip3p
@@ -92,6 +93,7 @@ Packages howto
    Howto_manifold
    Howto_rheo
    Howto_spins
+   Howto_apip
 
 Tutorials howto
 ===============

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_apip.rst

@@ -0,0 +1,225 @@
+Adaptive-precision interatomic potentials (APIP)
+================================================
+
+The :ref:`PKG-APIP <PKG-APIP>` enables use of adaptive-precision potentials
+as described in :ref:`(Immel) <Immel2025_1>`.
+In the context of this package, precision refers to the accuracy of an interatomic
+potential.
+
+Modern machine-learning (ML) potentials translate the accuracy of DFT
+simulations into MD simulations, i.e., ML potentials are more accurate
+compared to traditional empirical potentials.
+However, this accuracy comes at a cost: there is a considerable performance
+gap between the evaluation of classical and ML potentials, e.g., the force
+calculation of a classical EAM potential is 100-1000 times faster compared
+to the ML-based ACE method.
+The evaluation time difference results in a conflict between large time and
+length scales on the one hand and accuracy on the other.
+This conflict is resolved by an APIP model for simulations, in which the highest precision
+is required only locally but not globally.
+
+An APIP model uses a precise but
+expensive ML potential only for a subset of atoms, while a fast
+potential is used for the remaining atoms.
+Whether the precise or the fast potential is used is determined
+by a continuous switching parameter :math:`\lambda_i` that can be defined for each
+atom :math:`i`.
+The switching parameter can be adjusted dynamically during a simulation or
+kept constant as explained below.
+
+The potential energy :math:`E_i` of an atom :math:`i` described by an
+adaptive-precision
+interatomic potential is given by :ref:`(Immel) <Immel2025_1>`
+
+.. math::
+
+   E_i = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)},
+
+whereas :math:`E_i^\text{(fast)}` is the potential energy of atom :math:`i`
+according to a fast interatomic potential,
+:math:`E_i^\text{(precise)}` is the potential energy according to a precise
+interatomic potential and :math:`\lambda_i\in[0,1]` is the
+switching parameter that decides how the potential energies are weighted.
+
+Adaptive-precision saves computation time when the computation of the
+precise potential is not required for many atoms, i.e., when
+:math:`\lambda_i=1` applies for many atoms.
+
+The currently implemented potentials are:
+
+.. list-table::
+   :header-rows: 1
+
+   * - Fast potential
+     - Precise potential
+   * - :doc:`ACE <pair_pace_apip>`
+     - :doc:`ACE <pair_pace_apip>`
+   * - :doc:`EAM <pair_eam_apip>`
+     -
+
+In theory, any short-range potential can be used for an adaptive-precision
+interatomic potential. How to implement a new (fast or precise)
+adaptive-precision
+potential is explained in :ref:`here <implementing_new_apip_styles>`.
+
+The switching parameter :math:`\lambda_i` that combines the two potentials
+can be dynamically calculated during a
+simulation.
+Alternatively, one can set a constant switching parameter before the start
+of a simulation.
+To run a simulation with an adaptive-precision potential, one needs the
+following components:
+
+.. tabs::
+
+   .. tab:: dynamic switching parameter
+
+        #. :doc:`atom_style apip <atom_style>` so that the switching parameter :math:`\lambda_i` can be stored.
+        #. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/fast/apip <pair_pace_apip>`.
+        #. A precise potential: :doc:`pace/precise/apip <pair_pace_apip>`.
+        #. :doc:`pair_style lambda/input/apip  <pair_lambda_input_apip>` to calculate :math:`\lambda_i^\text{input}`, from which :math:`\lambda_i` is calculated.
+        #. :doc:`fix lambda/apip <fix_lambda_apip>` to calculate the switching parameter :math:`\lambda_i`.
+        #. :doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>` to calculate the spatial transition zone of the switching parameter.
+        #. :doc:`pair_style hybrid/overlay <pair_hybrid>` to combine the previously mentioned pair_styles.
+        #. :doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>` to conserve the energy when switching parameters change.
+        #. :doc:`fix atom_weight/apip <fix_atom_weight_apip>` to approximate the load caused by every atom, as the computations of the pair_styles are only required for a subset of atoms.
+        #. :doc:`fix balance <fix_balance>` to perform dynamic load balancing with the calculated load.
+
+   .. tab:: constant switching parameter
+
+        #. :doc:`atom_style apip <atom_style>` so that the switching parameter :math:`\lambda_i` can be stored.
+        #. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/fast/apip <pair_pace_apip>`.
+        #. A precise potential: :doc:`pace/precise/apip <pair_pace_apip>`.
+        #. :doc:`set <set>` command to set the switching parameter :math:`\lambda_i`.
+        #. :doc:`pair_style hybrid/overlay <pair_hybrid>` to combine the previously mentioned pair_styles.
+        #. :doc:`fix atom_weight/apip <fix_atom_weight_apip>` to approximate the load caused by every atom, as the computations of the pair_styles are only required for a subset of atoms.
+        #. :doc:`fix balance <fix_balance>` to perform dynamic load balancing with the calculated load.
+
+----------
+
+Example
+"""""""
+.. note::
+
+   How to select the values of the parameters of an adaptive-precision
+   interatomic potential is discussed in detail in :ref:`(Immel) <Immel2025_1>`.
+
+
+.. tabs::
+
+   .. tab:: dynamic switching parameter
+
+      Lines like these would appear in the input script:
+
+
+      .. code-block:: LAMMPS
+
+         atom_style apip
+         comm_style tiled
+
+         pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
+         pair_coeff * * eam/fs/apip Cu.eam.fs Cu
+         pair_coeff * * pace/precise/apip Cu.yace Cu
+         pair_coeff * * lambda/input/csp/apip
+         pair_coeff * * lambda/zone/apip
+
+         fix 2 all lambda/apip 2.5 3.0 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
+         fix 3 all lambda_thermostat/apip N_rescaling 200
+         fix 4 all atom_weight/apip 100 eam ace lambda/input lambda/zone all
+
+         variable myweight atom f_4
+
+         fix 5 all balance 100 1.1 rcb weight var myweight
+
+      First, the :doc:`atom_style apip <atom_style>` and the communication style are set.
+
+      .. note::
+         Note, that :doc:`comm_style <comm_style>` *tiled* is required for the style *rcb* of
+         :doc:`fix balance <fix_balance>`, but not for APIP.
+         However, the flexibility offered by the balancing style *rcb*, compared to the
+         balancing style *shift*, is advantageous for APIP.
+
+      An adaptive-precision EAM-ACE potential, for which the switching parameter
+      :math:`\lambda` is calculated from the CSP, is defined via
+      :doc:`pair_style hybrid/overlay <pair_hybrid>`.
+      The fixes ensure that the switching parameter is calculated, the energy conserved,
+      the weight for the load balancing calculated and the load-balancing itself is done.
+
+   .. tab:: constant switching parameter
+
+      Lines like these would appear in the input script:
+
+      .. code-block:: LAMMPS
+
+         atom_style apip
+         comm_style tiled
+
+         pair_style hybrid/overlay eam/fs/apip pace/precise/apip
+         pair_coeff * * eam/fs/apip Cu.eam.fs Cu
+         pair_coeff * * pace/precise/apip Cu.yace Cu
+
+         # calculate lambda somehow
+         variable lambda atom ...
+         set group all apip/lambda v_lambda
+
+         fix 4 all atom_weight/apip 100 eam ace lambda/input lambda/zone all
+
+         variable myweight atom f_4
+
+         fix 5 all balance 100 1.1 rcb weight var myweight
+
+      First, the :doc:`atom_style apip <atom_style>` and the communication style are set.
+
+      .. note::
+         Note, that :doc:`comm_style <comm_style>` *tiled* is required for the style *rcb* of
+         :doc:`fix balance <fix_balance>`, but not for APIP.
+         However, the flexibility offered by the balancing style *rcb*, compared to the
+         balancing style *shift*, is advantageous for APIP.
+
+      An adaptive-precision EAM-ACE potential is defined via
+      :doc:`pair_style hybrid/overlay <pair_hybrid>`.
+      The switching parameter :math:`\lambda_i` of the adaptive-precision
+      EAM-ACE potential is set via the :doc:`set command <set>`.
+      The parameter is not updated during the simulation.
+      Therefore, the potential is conservative.
+      The fixes ensure that the weight for the load balancing is calculated
+      and the load-balancing itself is done.
+
+----------
+
+.. _implementing_new_apip_styles:
+
+Implementing new APIP pair styles
+"""""""""""""""""""""""""""""""""
+
+One can introduce adaptive-precision to an existing pair style by modifying
+the original pair style.
+One should calculate the force
+:math:`F_i = - \nabla_i \sum_j E_j^\text{original}` for a fast potential or
+:math:`F_i = - (1-\nabla_i) \sum_j E_j^\text{original}` for a precise
+potential from the original potential
+energy :math:`E_j^\text{original}` to see where the switching parameter
+:math:`\lambda_i` needs to be introduced in the force calculation.
+The switching parameter :math:`\lambda_i` is known for all atoms :math:`i`
+in force calculation routine.
+One needs to introduce an abortion criterion based on :math:`\lambda_i` to
+ensure that all not required calculations are skipped and compute time can
+be saved.
+Furthermore, one needs to provide the number of calculations and measure the
+computation time.
+Communication within the force calculation needs to be prevented to allow
+effective load-balancing.
+With communication, the load balancer cannot balance few calculations of the
+precise potential on one processor with many computations of the fast
+potential on another processor.
+
+All changes in the pair_style pace/apip compared to the pair_style pace
+are annotated and commented.
+Thus, the pair_style pace/apip can serve as an example for the implementation
+of new adaptive-precision potentials.
+
+----------
+
+.. _Immel2025_1:
+
+**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

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
-force fields with explicit bonded interactions (like the ones discussed
-in this HowTo) is given in :ref:`(Gissinger) <Typelabel2>`.
-
-A force field has 2 parts: the formulas that define it and the
-coefficients used for a particular system.  Here we only discuss
-formulas implemented in LAMMPS that correspond to formulas commonly used
-in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
-coefficients is done either from special sections in an input data file
-via the :doc:`read_data <read_data>` command or in the input script with
-commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
-<bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc page for
-additional tools that can use CHARMM, AMBER, or Materials Studio
-generated files to assign force field coefficients and convert their
-output into LAMMPS input. LAMMPS input scripts can also be generated by
-`charmm-gui.org <https://charmm-gui.org/>`_.
+Here we only discuss formulas implemented in LAMMPS that correspond to
+formulas commonly used in the CHARMM, AMBER, COMPASS, and DREIDING force
+fields.  Setting coefficients is done either from special sections in an
+input data file via the :doc:`read_data <read_data>` command or in the
+input script with commands like :doc:`pair_coeff <pair_coeff>` or
+:doc:`bond_coeff <bond_coeff>` and so on.  See the :doc:`Tools <Tools>`
+doc page for additional tools that can use CHARMM, AMBER, or Materials
+Studio generated files to assign force field coefficients and convert
+their output into LAMMPS input. LAMMPS input scripts can also be
+generated by `charmm-gui.org <https://charmm-gui.org/>`_.
 
 CHARMM and AMBER
 ----------------
@@ -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
-or AMBER, the DREIDING force field has not been parameterized for
-considering solvents (like water).
+hydrogen atom on very electronegative atoms (N, O, F).  Unlike CHARMM or
+AMBER, the DREIDING force field has not been parameterized for
+considering solvents (like water) and has no rules for assigning
+(partial) charges.  That will seriously limit its accuracy when used for
+simulating systems where those matter.
 
 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_lammps_gui.rst

@@ -1,10 +1,15 @@
 Using LAMMPS-GUI
 ================
 
+.. image:: JPG/lammps-gui-banner.png
+   :align: center
+   :scale: 75%
+
 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.
+<https://www.qt.io/>`_ and customized for editing and running 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 and without having to launch the LAMMPS executable.
 
 It *differs* from other known interfaces to LAMMPS in that it can
 retrieve and display information from LAMMPS *while it is running*,
@@ -13,7 +18,7 @@ display visualizations created with the :doc:`dump image command
 LAMMPS commands and styles, and directly integrates with a collection
 of LAMMPS tutorials (:ref:`Gravelle1 <Gravelle1>`).
 
-This document describes **LAMMPS-GUI version 1.6**.
+This document describes **LAMMPS-GUI version 1.7**.
 
 -----
 
@@ -21,17 +26,20 @@ This document describes **LAMMPS-GUI version 1.6**.
 
 ----
 
-LAMMPS-GUI tries to provide an experience similar to what people
-traditionally would have running LAMMPS using a command-line window and
-the console LAMMPS executable but just rolled into a single executable:
+LAMMPS-GUI aims to provide the traditional experience of running LAMMPS
+using a text editor, a command-line window, and launching the LAMMPS
+text-mode executable printing output to the screen, but just integrated
+into a single application:
 
-- writing & editing LAMMPS input files with a text editor
-- run LAMMPS on those input file with selected command-line flags
-- extract data from the created files and visualize it with and
-  external software
+- Write and edit LAMMPS input files using the built-in text editor.
+- Run LAMMPS on those input file with command-line flags to enable a
+  specific accelerator package (or none).
+- Extract data from the created files (like trajectory files, log files
+  with thermodynamic data, or images) and visualize it using external
+  software.
 
-That procedure is quite effective for people proficient in using the
-command-line, as that allows them to use tools for the individual steps
+That traditional procedure is effective for people proficient in using the
+command-line, as it allows them to use the tools for the individual steps
 that they are most comfortable with.  In fact, it is often *required* to
 adopt this workflow when running LAMMPS simulations on high-performance
 computing facilities.
@@ -42,35 +50,46 @@ window or using external programs, let alone writing scripts to extract
 data from the generated output.  It also integrates well with graphical
 desktop environments where the `.lmp` filename extension can be
 registered with LAMMPS-GUI as the executable to launch when double
-clicking on such files.  Also, LAMMPS-GUI has support for drag-n-drop,
-i.e.  an input file can be selected and then moved and dropped on the
-LAMMPS-GUI executable, and LAMMPS-GUI will launch and read the file into
-its buffer.  In many cases LAMMPS-GUI will be integrated into the
-graphical desktop environment and can be launched like other
-applications.
+clicking on such files using a file manager.  LAMMPS-GUI also has
+support for 'drag and drop' for opening inputs: an input file can
+be selected and then moved and dropped on the LAMMPS-GUI executable;
+LAMMPS-GUI will launch and read the file into its buffer.  Input files
+also can be dropped into the editor window of the running LAMMPS-GUI
+application, which will close the current file and open the new file.
+In many cases LAMMPS-GUI will be integrated into the graphical desktop
+environment and can be launched just like any other applications from
+the graphical interface.
 
 LAMMPS-GUI thus makes it easier for beginners to get started running
-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 their tutorial materials can
-be downloaded and edited directly from the GUI.
+LAMMPS and is well-suited for LAMMPS tutorials, since you only need to
+work with a single, ready-to-use program for most of the tasks.  Plus it
+is available for download as pre-compiled package for popular operating
+systems (Linux, macOS, Windows).  This saves time and allows users to
+focus on learning LAMMPS itself, without the need to learn how to
+compile LAMMPS, learn how to use the command line, or learn how to use a
+separate text editor.
 
-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
-has some unique functionality that is not found elsewhere:
+The tutorials at https://lammpstutorials.github.io/ are specifically
+updated for use with LAMMPS-GUI and their tutorial materials can be
+downloaded and edited directly from within the GUI while automatically
+loading the matching tutorial instructions into a webbrowser.
+
+Yet the basic control flow remains similar to running LAMMPS from the
+command line, so the barrier for replacing parts of the functionality of
+LAMMPS-GUI with external tools is low.  That said, LAMMPS-GUI offer some
+unique features that are not easily found elsewhere:
 
 - auto-adapting to features available in the integrated LAMMPS library
-- auto-completion for LAMMPS commands and options
-- context-sensitive online help
+- auto-completion for available LAMMPS commands and options only
+- context-sensitive online help for known LAMMPS commands
 - start and stop of simulations via mouse or keyboard
-- monitoring of simulation progress
-- interactive visualization using the :doc:`dump image <dump_image>`
+- monitoring of simulation progress and CPU use
+- interactive visualization using the LAMMPS :doc:`dump image feature <dump_image>`
   command with the option to copy-paste the resulting settings
 - automatic slide show generation from dump image output at runtime
 - automatic plotting of thermodynamic data at runtime
 - inspection of binary restart files
+- integration will a set of LAMMPS tutorials
 
 .. admonition:: Download LAMMPS-GUI for your platform
    :class: Hint
@@ -93,7 +112,7 @@ has some unique functionality that is not found elsewhere:
 
 -----
 
-The following text provides a detailed tour of the features and
+The following text provides a documentation 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
 channels as for LAMMPS itself <Errors_bugs>` for that purpose.
@@ -230,8 +249,8 @@ editor buffer, which may contain multiple :doc:`run <run>` or
 
 LAMMPS runs in a separate thread, so the GUI stays responsive and is
 able to interact with the running calculation and access data it
-produces.  It is important to note that running LAMMPS this way is
-using the contents of the input buffer for the run (via the
+produces.  It is important to note that running LAMMPS this way is using
+the contents of the input buffer for the run (via the
 :cpp:func:`lammps_commands_string()` function of the LAMMPS C-library
 interface), and **not** the original file it was read from.  Thus, if
 there are unsaved changes in the buffer, they *will* be used.  As an
@@ -240,28 +259,55 @@ of a file from the *Run LAMMPS from File* menu entry or with
 `Ctrl-Shift-Enter`.  This option may be required in some rare cases
 where the input uses some functionality that is not compatible with
 running LAMMPS from a string buffer.  For consistency, any unsaved
-changes in the buffer must be either saved to the file or undone
-before LAMMPS can be run from a file.
+changes in the buffer must be either saved to the file or undone before
+LAMMPS can be run from a file.
+
+The line number of the currently executed command is highlighted in
+green in the line number display for the *Editor* Window.
 
 .. image:: JPG/lammps-gui-running.png
    :align: center
    :scale: 75%
 
-While LAMMPS is running, the contents of the status bar change.  On
-the left side there is a text indicating that LAMMPS is running, which
-also indicates the number of active threads, when thread-parallel
-acceleration was selected in the *Preferences* dialog.  On the right
+While LAMMPS is running, the contents of the status bar change.  The
+text fields that normally show "Ready." and the current working
+directory, change into an area showing the CPU utilization in percent.
+Nest to it is a text indicating that LAMMPS is running, which also
+indicates the number of active threads (in case thread-parallel
+acceleration was selected in the *Preferences* dialog).  On the right
 side, a progress bar is shown that displays the estimated progress for
 the current :doc:`run <run>` or :doc:`minimize <minimize>` command.
 
-Also, the line number of the currently executed command is highlighted
-in green.
+.. admonition:: CPU Utilization
+   :class: note
+
+   The CPU Utilization should ideally be close to 100% times the number
+   of threads like in the screenshot image above.  Since the GUI is
+   running as a separate thread, the CPU utilization can be higher, for
+   example when the GUI needs to work hard to keep up with the
+   simulation.  This can be caused by having frequent thermo output or
+   running a simulation of a small system.  In the *Preferences* dialog,
+   the polling interval for updating the the *Output* and *Charts*
+   windows can be set. The intervals may need to be lowered to not miss
+   data between *Charts* data updates or to avoid stalling when the
+   thermo output is not transferred to the *Output* window fast enough.
+   It is also possible to reduce the amount of data by increasing the
+   :doc:`thermo interval <thermo>`.  LAMMPS-GUI detects, if the
+   associated I/O buffer is by a significant percentage and will print a
+   warning after the run with suggested adjustments.  The utilization
+   can also be lower, e.g.  when the simulation is slowed down by the
+   GUI or other processes also running on the host computer and
+   competing with LAMMPS-GUI for GPU resources.
+
+   .. image:: JPG/lammps-gui-buffer-warn.png
+      :align: center
+      :scale: 75%
 
 If an error occurs (in the example below the command :doc:`label
 <label>` was incorrectly capitalized as "Label"), an error message
 dialog is shown and the line of the input which triggered the error is
-highlighted.  The state of LAMMPS in the status bar is set to "Failed."
-instead of "Ready."
+highlighted in red.  The state of LAMMPS in the status bar is set to
+"Failed."  instead of "Ready."
 
 .. image:: JPG/lammps-gui-run-error.png
    :align: center
@@ -308,7 +354,10 @@ 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
@@ -348,33 +397,29 @@ plot of thermodynamic output of the LAMMPS calculation as shown below.
    :align: center
    :scale: 33%
 
-The drop down menu on the top right allows selection of different
-properties that are computed and written to thermo output.  Only one
-property can be shown at a time.  The plots are updated regularly with
-new data as the run progresses, so they can be used to visually monitor
-the evolution of available properties.  The update interval can be set
-in the *Preferences* dialog.  By default, the raw data for the selected
-property is plotted as a blue graph. As soon as there are a sufficient
-number of data points, there will be a second graph shown in red with a
-smoothed version of the data.  From the drop down menu on the top left,
-you can select whether to plot only the raw data, only the smoothed
-data or both.  The smoothing uses a `Savitzky-Golay convolution filter
-<https://en.wikipedia.org/wiki/Savitzky%E2%80%93Golay_filter>`_ The
-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 for a total of 21 points and a fourth
-order polynomial is fitted to the data in the window.
+The "Data:" drop down menu on the top right allows selection of
+different properties that are computed and written as thermodynamic
+output to the output window.  Only one property can be shown at a time.
+The plots are updated regularly with new data as the run progresses, so
+they can be used to visually monitor the evolution of available
+properties.  The update interval can be set in the *Preferences* dialog.
+By default, the raw data for the selected property is plotted as a blue
+graph.  From the "Plot:" drop menu on the second row and on the left,
+you can select whether to plot only raw data graph, only a smoothed data
+graph, or both graphs on top of each other.  The smoothing process uses
+a `Savitzky-Golay convolution filter
+<https://en.wikipedia.org/wiki/Savitzky%E2%80%93Golay_filter>`_.  The
+convolution 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 for a total of 21 points
+and a fourth 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
-view with a click to the "lens" button next to the data drop down menu.
-
 The window title shows the current run number that this chart window
 corresponds to.  Same as for the *Output* window, the chart window is
 replaced on each new run, but the behavior can be changed in the
@@ -406,6 +451,35 @@ 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.
 
+
+
+.. admonition:: Slowdown of Simulations from Charts Data Processing
+   :class: warning
+
+   Using frequent thermo output during long simulations can result in a
+   significant slowdown of that simulation since it is accumulating many
+   data points for each of the thermo properties in the chart window to
+   be redrawn with every update.  The updates are consuming additional
+   CPU time when smoothing enabled.  This slowdown can be confirmed when
+   an increasing percentage of the total run time is spent in the
+   "Output" or "Other" sections of the :doc:`MPI task timing breakdown
+   <Run_output>`.  It is thus recommended to use a large enough value as
+   argument `N` for the :doc:`thermo command <thermo>` and to select
+   plotting only the "Raw" data in the *Charts Window* during such
+   simulations.  It is always possible to switch between the different
+   display styles for charts during the simulation and after it has
+   finished.
+
+   .. versionchanged:: 1.7
+
+      As of LAMMPS-GUI version 1.7 the chart data processing is
+      significantly optimized compared to older versions of LAMMPS-GUI.
+      The general problem of accumulating excessive amounts of data
+      and the overhead of too frequently polling LAMMPS for new data
+      cannot be optimized away, though.  If necessary, the command
+      line LAMMPS executable needs to be used and the output accumulated
+      of a very fast disk (e.g. a high-performance SSD).
+
 Image Slide Show
 ----------------
 
@@ -637,13 +711,27 @@ generated with a :doc:`write_data command <write_data>`.  The third
 window is a :ref:`Snapshot Image Viewer <snapshot_viewer>` containing a
 visualization of the system in the restart.
 
-If the restart file is larger than 250 MBytes, a dialog will ask
-for confirmation before continuing, since large restart files
-may require large amounts of RAM since the entire system must
-be read into RAM.  Thus restart file for large simulations that
-have been run on an HPC cluster may overload a laptop or local
-workstation. The *Show Details...* button will display a rough
-estimate of the additional memory required.
+.. |inspect1| image:: JPG/lammps-gui-inspect-data.png
+   :width: 32%
+
+.. |inspect2| image:: JPG/lammps-gui-inspect-info.png
+   :width: 32%
+
+.. |inspect3| image:: JPG/lammps-gui-inspect-image.png
+   :width: 32%
+
+|inspect1|  |inspect2|  |inspect3|
+
+.. admonition:: Large Restart Files
+   :class: warning
+
+   If the restart file is larger than 250 MBytes, a dialog will ask for
+   confirmation before continuing, since large restart files may require
+   large amounts of RAM since the entire system must be read into RAM.
+   Thus restart file for large simulations that have been run on an HPC
+   cluster may overload a laptop or local workstation. The *Show
+   Details...* button will display a rough estimate of the additional
+   memory required.
 
 Menu
 ----
@@ -715,6 +803,12 @@ timestep.  The *Stop LAMMPS* entry will do this by calling the
 :cpp:func:`lammps_force_timeout` library function, which is equivalent
 to a :doc:`timer timeout 0 <timer>` command.
 
+The *Relaunch LAMMPS Instance* will destroy the current LAMMPS thread
+and free its data and then create a new thread with a new LAMMPS
+instance.  This is usually not needed, since LAMMPS-GUI tries to detect
+when this is needed and does it automatically.  This is available
+in case it missed something and LAMMPS behaves in unexpected ways.
+
 The *Set Variables...* entry opens a dialog box where
 :doc:`index style variables <variable>` can be set. Those variables
 are passed to the LAMMPS instance when it is created and are thus
@@ -769,6 +863,10 @@ 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.
 
+.. image:: JPG/lammps-gui-tutorials.png
+   :align: center
+   :scale: 50%
+
 About
 ^^^^^
 
@@ -875,13 +973,12 @@ General Settings:
 - *Replace image window on new render:* when checked, an existing
   chart window will be replaced when a new snapshot image is requested,
   otherwise each command will create a new image window.
-- *Path to LAMMPS Shared Library File:* this option is only visible
-  when LAMMPS-GUI was compiled to load the LAMMPS library at run time
-  instead of being linked to it directly.  With the *Browse..* button
-  or by changing the text, a different shared library file with a
-  different compilation of LAMMPS with different settings or from a
-  different version can be loaded.  After this setting was changed,
-  LAMMPS-GUI needs to be re-launched.
+- *Download tutorial solutions enabled* this controls whether the
+  "Download solutions" option is enabled by default when setting up
+  a tutorial.
+- *Open tutorial webpage enabled* this controls whether the "Open
+  tutorial webpage in web browser" option is enabled by default when
+  setting up a tutorial.
 - *Select Default Font:* Opens a font selection dialog where the type
   and size for the default font (used for everything but the editor and
   log) of the application can be set.
@@ -905,16 +1002,31 @@ General Settings:
   or for downloading tutorial files from the *Tutorials* menu.  If the
   ``https_proxy`` environment variable was set externally, its value is
   displayed but cannot be changed.
+- *Path to LAMMPS Shared Library File:* this option is only visible
+  when LAMMPS-GUI was compiled to load the LAMMPS library at run time
+  instead of being linked to it directly.  With the *Browse..* button
+  or by changing the text, a different shared library file with a
+  different compilation of LAMMPS with different settings or from a
+  different version can be loaded.  After this setting was changed,
+  LAMMPS-GUI needs to be re-launched.
 
 Accelerators:
 ^^^^^^^^^^^^^
 
-This tab enables selection of an accelerator package for LAMMPS to use
-and is equivalent to using the `-suffix` and `-package` flags on the
-command-line.  Only settings supported by the LAMMPS library and local
-hardware are available.  The `Number of threads` field allows setting
-the maximum number of threads for the accelerator packages that use
-threads.
+This tab enables selection of an accelerator package and modify some of
+its settings to use for running LAMMPS and is equivalent to using the
+:doc:`-sf <suffix>` and :doc:`-pk <package>` flags :doc:`on the
+command-line <Run_options>`.  Only settings supported by the LAMMPS
+library and local hardware are available.  The `Number of threads` field
+allows setting the number of threads for the accelerator packages that
+support using threads (OPENMP, INTEL, KOKKOS, and GPU).  Furthermore,
+the choice of precision mode (double, mixed, or single) for the INTEL
+package can be selected and for the GPU package, whether the neighbor
+lists are built on the GPU or the host (required for :doc:`pair style
+hybrid <pair_hybrid>`) and whether only pair styles should be
+accelerated (i.e. run PPPM entirely on the CPU, which sometimes leads
+to better overall performance).  Whether settings can be changed depends
+on which accelerator package is chosen (or "None").
 
 Snapshot Image:
 ^^^^^^^^^^^^^^^

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.
@@ -8,6 +8,18 @@ the two O-H bonds and the H-O-H angle rigid.  A bond style of
 *harmonic* and an angle style of *harmonic* or *charmm* should also be
 used.
 
+One suitable pair style with cutoff Coulomb would for instance be:
+
+* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
+
+These commands are examples for a long-range Coulomb model:
+
+* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
+* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
+* :doc:`kspace_style pppm <kspace_style>`
+* :doc:`pair_style lj/long/coul/long <pair_lj_long>`
+* :doc:`kspace_style pppm/disp <kspace_style>`
+
 These are the additional parameters (in real units) to set for O and H
 atoms and the water molecule to run a rigid SPC model.
 
@@ -39,7 +51,9 @@ the SPC and SPC/E models.
 Below is the code for a LAMMPS input file and a molecule file
 (``spce.mol``) of SPC/E water for use with the :doc:`molecule command
 <molecule>` demonstrating how to set up a small bulk water system for
-SPC/E with rigid bonds.
+SPC/E with rigid bonds.  For simplicity and speed the example uses a
+cutoff Coulomb.  Most production simulations require long-range Coulomb
+instead.
 
 .. code-block:: LAMMPS
 

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_tip3p.rst

@@ -5,17 +5,24 @@ The TIP3P water model as implemented in CHARMM :ref:`(MacKerell)
 <howto-tip3p>` specifies a 3-site rigid water molecule with charges and
 Lennard-Jones parameters assigned to each of the three atoms.
 
-A suitable pair style with cutoff Coulomb would be:
+One suitable pair style with cutoff Coulomb would for instance be:
 
 * :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
 
-or these commands for a long-range Coulomb model:
+These commands are examples for a long-range Coulomb model:
 
 * :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
 * :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
 * :doc:`kspace_style pppm <kspace_style>`
+* :doc:`pair_style lj/long/coul/long <pair_lj_long>`
 * :doc:`kspace_style pppm/disp <kspace_style>`
 
+And these pair styles are compatible with the CHARMM force field:
+
+* :doc:`pair_style lj/charmm/coul/charmm <pair_charmm>`
+* :doc:`pair_style lj/charmm/coul/long <pair_charmm>`
+* :doc:`pair_style lj/charmmfsw/coul/long <pair_charmm>`
+
 In LAMMPS the :doc:`fix shake or fix rattle <fix_shake>` command can be
 used to hold the two O-H bonds and the H-O-H angle rigid.  A bond style
 of :doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
@@ -100,7 +107,9 @@ ignored.
 Below is the code for a LAMMPS input file and a molecule file
 (``tip3p.mol``) of TIP3P water for use with the :doc:`molecule command
 <molecule>` demonstrating how to set up a small bulk water system for
-TIP3P with rigid bonds.
+TIP3P with rigid bonds.  For simplicity and speed the example uses a
+cutoff Coulomb.  Most production simulations require long-range Coulomb
+instead.
 
 .. code-block:: LAMMPS
 

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
@@ -149,7 +167,9 @@ cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long
 Below is the code for a LAMMPS input file using the implicit method and
 the :ref:`TIP3P molecule file <tip3p_molecule>`.  Because the TIP4P
 charges are different from TIP3P they need to be reset (or the molecule
-file changed):
+file changed).  For simplicity and speed the example uses a cutoff
+Coulomb.  Most production simulations require long-range Coulomb
+instead.
 
 .. code-block:: LAMMPS
 
@@ -192,6 +212,94 @@ 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 +387,8 @@ 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/Howto_tip5p.rst

@@ -87,7 +87,9 @@ atom style full or use :doc:`fix property/atom mol <fix_property_atom>`
 so that fix rigid/small can identify rigid bodies by their molecule ID.
 Also a :doc:`neigh_modify exclude <neigh_modify>` command is added to
 exclude computing intramolecular non-bonded interactions, since those
-are removed by the rigid fix anyway:
+are removed by the rigid fix anyway.  For simplicity and speed the
+example uses a cutoff Coulomb.  Most production simulations require
+long-range Coulomb instead.
 
 .. code-block:: LAMMPS
 

doc/src/Install_git.rst

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

doc/src/Intro_authors.rst

@@ -84,8 +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,
-and Ray Shan, now at Materials Design.
+Past core developers include Paul Crozier and Mark Stevens, both at SNL,
+and Ray Shan while at SNL and later at Materials Design, now at Thermo
+Fisher Scientific.
 
 ----------
 

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
-ends can be created using CMake.  CMake must be at least version 3.16.
+shell (``/bin/sh`` or ``/bin/bash``).  Alternatively, a build system
+with different back ends can be created using CMake.  CMake must be
+at least version 3.16.
 
 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
-build system of required external libraries or packages.
+LAMMPS source code or through incompatibilities or build system
+limitations of required external libraries or packages.
 
-Executables for Windows may be created natively using either Cygwin or
-Visual Studio or with a Linux to Windows MinGW cross-compiler.
+Executables for Windows may be created either natively using Cygwin,
+MinGW, Intel, Clang, or Microsoft Visual C++ compilers, or with a Linux
+to Windows MinGW cross-compiler.  Native compilation is supported using
+Microsoft Visual Studio or a terminal window (using the CMake build
+system).
+
+Executables for macOS may be created either using Xcode or GNU compilers
+installed with Homebrew.  In the latter case, building of LAMMPS through
+Homebrew instead of a manual compile is also possible.
 
 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
-regularly tested.
+64-bit ARM and PowerPC (64-bit, Little Endian) are currently regularly
+tested.  Further architectures are tested by Linux distributions that
+bundle LAMMPS.
 
 Portability compliance
 ^^^^^^^^^^^^^^^^^^^^^^

doc/src/Library.rst

@@ -93,14 +93,19 @@ run LAMMPS in serial mode.
 .. admonition:: Using the C library interface as a plugin
    :class: note
 
-   Rather than including the C library directly and link to the LAMMPS
+   Rather than including the C library interface directly using the
+   ``library.h`` header file and link to the LAMMPS (static or shared)
    library at compile time, you can use the ``liblammpsplugin.h`` header
    file and the ``liblammpsplugin.c`` C code in the
    ``examples/COUPLE/plugin`` folder for an interface to LAMMPS that is
    largely identical to the regular library interface, only that it will
    load a LAMMPS shared library file at runtime.  This can be useful for
    applications where the interface to LAMMPS would be an optional
-   feature.
+   feature or where you would like to load different version of the
+   LAMMPS library (e.g. an updated one) without replacing the executable.
+   The :ref:`LAMMPS-GUI <lammps_gui>` is an example for such a program.
+   It has its own wrapper that supports both modes and they can be
+   changed at compile time.
 
 .. warning::
 

doc/src/Library_create.rst

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

doc/src/Library_scatter.rst

@@ -27,6 +27,7 @@ It documents the following functions:
 - :cpp:func:`lammps_scatter`
 - :cpp:func:`lammps_scatter_subset`
 - :cpp:func:`lammps_create_atoms`
+- :cpp:func:`lammps_create_molecule`
 
 -----------------------
 
@@ -103,4 +104,8 @@ It documents the following functions:
 .. doxygenfunction:: lammps_create_atoms(void *handle, int n, const int *id, const int *type, const double *x, const double *v, const int *image, int bexpand)
    :project: progguide
 
+-----------------------
+
+.. doxygenfunction:: lammps_create_molecule
+   :project: progguide
 

doc/src/Packages_details.rst

@@ -28,6 +28,7 @@ gives those details.
 
    * :ref:`ADIOS <PKG-ADIOS>`
    * :ref:`AMOEBA <PKG-AMOEBA>`
+   * :ref:`APIP <PKG-APIP>`
    * :ref:`ASPHERE <PKG-ASPHERE>`
    * :ref:`ATC <PKG-ATC>`
    * :ref:`AWPMD <PKG-AWPMD>`
@@ -186,6 +187,60 @@ provided by the Ponder group in their
 
 ----------
 
+.. _PKG-APIP:
+
+APIP package
+------------
+
+**Contents:**
+
+This package provides adaptive-precision interatomic potentials (APIP) as
+described in:
+
+D. Immel, R. Drautz and G. Sutmann, "Adaptive-precision potentials for
+large-scale atomistic simulations", J. Chem. Phys. 162, 114119 (2025)
+`link <immel2025_doi_>`_
+
+Adaptive-precision means, that a fast interatomic potential, such as EAM,
+is coupled to a precise interatomic potential, such as ACE.
+This package provides the required pair_styles and fixes to run an efficient,
+energy-conserving adaptive-precision simulation.
+
+In the context of this package, precision refers to the accuracy of an interatomic
+potential.
+
+.. _immel2025_doi: https://doi.org/10.1063/5.0245877
+
+**Authors:**
+
+This package was written by David Immel^1,
+Ralf Drautz^2 and Godehard Sutmann^1^2.
+
+ ^1: Forschungszentrum Juelich, Juelich, Germany
+
+ ^2: Ruhr-University Bochum, Bochum, Germany
+
+**Install:**
+
+The APIP package requires also the installation of ML-PACE, which has
+:ref:`specific installation instructions <ml-pace>` on the
+:doc:`Build extras <Build_extras>` page.
+
+**Supporting info:**
+
+* ``src/APIP``: filenames -> commands
+* :doc:`Howto APIP <Howto_apip>`
+* ``examples/PACKAGES/apip``
+* :doc:`fix atom_weight/apip <fix_atom_weight_apip>`
+* :doc:`fix lambda/apip <fix_lambda_apip>`
+* :doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`
+* :doc:`pair_style eam/apip <pair_eam_apip>`
+* :doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`
+* :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`
+* :doc:`pair_style pace/apip <pair_pace_apip>`
+
+----------
+
 .. _PKG-ASPHERE:
 
 ASPHERE package

doc/src/Packages_list.rst

@@ -38,6 +38,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
      - amoeba
      - no
+   * - :ref:`APIP <PKG-APIP>`
+     - adaptive-precision interatomic potentials
+     - :doc:`Howto APIP <Howto_apip>`
+     - ``PACKAGES/apip``
+     - ext
    * - :ref:`ASPHERE <PKG-ASPHERE>`
      - aspherical particle models
      - :doc:`Howto spherical <Howto_spherical>`

doc/src/Python_call.rst

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

doc/src/Python_install.rst

@@ -106,20 +106,37 @@ folder that the dynamic loader searches or inside of the installed
       has to be made during the CMake configuration step.
 
       If the default settings of ``make install-python`` are not what you want,
-      you can invoke ``install.py`` from the python directory manually as
+      you can invoke ``install.py`` from the ``python`` directory manually as
 
       .. code-block:: bash
 
-         python install.py -p <python package> -l <shared library> -v <version.h file> [-n] [-f]
+         python3 install.py -p <python package> -l <shared library> -v <version.h file> [-n] [-f]
+
+      * The ``-p`` flag argument is the full path to the
+        ``python/lammps`` folder to be installed,
+      * the ``-l`` flag argument is the full path to the LAMMPS shared
+        library file to be installed,
+      * the ``-v`` flag argument is the full path to the ``src/version.h`` file
+      * the optional ``-n`` flag instructs the script to only build a
+        wheel file but not attempt to install it (default is to try installing),
+      * the optional ``-w`` flag argument is the path to a folder where
+        to store the resulting wheel file (default is the current folder)
+      * and the optional ``-f`` argument instructs the script to force
+        installation even if pip would otherwise refuse installation
+        with an :ref:`error about externally managed environments
+        <externally_managed>`. The Python developers recommend to not
+        augment a Python installation with custom packages, both at the
+        user and the system level, and advise to use virtual
+        environments instead.  Some recent Linux distributions enforce
+        that recommendation by default.
+
+      Example command line for building only the wheel after building
+      LAMMPS with ``cmake`` in the folder ``build``:
+
+      .. code-block:: bash
+
+         python3 python/install.py -n -p python/lammps -l build/liblammps.so -v src/version.h -w build
 
-      * The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
-      * the ``-l`` flag points to the LAMMPS shared library file to be installed,
-      * the ``-v`` flag points to the LAMMPS version header file to extract the version date,
-      * the optional ``-n`` instructs the script to only build a wheel file but not attempt
-        to install it,
-      * and the optional ``-f`` argument instructs the script to force installation even if
-        pip would otherwise refuse installation with an
-        :ref:`error about externally managed environments <externally_managed>`.
 
    .. tab:: Virtual environment
 
@@ -335,4 +352,3 @@ that the order of the lines is not deterministic
    Proc 1 out of 4 procs
    Proc 2 out of 4 procs
    Proc 3 out of 4 procs
-

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
-  NVIDIA, AMD, and Intel GPUs well. On NVIDIA hardware, using CUDA is
-  typically resulting in equal or better performance over OpenCL.
-* OpenCL in the GPU package does theoretically also support Intel CPUs or
-  Intel Xeon Phi, but the native support for those in KOKKOS (or INTEL)
-  is superior.
+* The GPU package benefits from running multiple MPI processes (2-8) per
+  GPU to parallelize the non-GPU accelerated styles.  The KOKKOS package
+  usually not, especially when all parts of the calculation have KOKKOS
+  support.
+* The GPU package can be compiled for CUDA, HIP, or OpenCL and thus
+  supports NVIDIA, AMD, and Intel GPUs well. On NVIDIA or AMD hardware,
+  using native CUDA or HIP compilation, respectively, with either GPU or
+  KOKKOS results in equal or better performance over OpenCL.
+* OpenCL in the GPU package supports NVIDIA, AMD, and Intel GPUs at the
+  *same time* and with the *same executable*.  KOKKOS currently does not
+  support OpenCL.
+* The GPU package supports single precision floating point, mixed
+  precision floating point, and double precision floating point math on
+  the GPU.  This must be chosen at compile time.  KOKKOS currently only
+  supports double precision floating point math.  Using single or mixed
+  precision (recommended) results in significantly improved performance
+  on consumer GPUs for some loss in accuracy (which is rather small with
+  mixed precision).  Single and mixed precision support for KOKKOS is in
+  development (no ETA yet).
+* Some pair styles (for example :doc:`snap <pair_snap>`, :doc:`mliap
+  <pair_mliap>` or :doc:`reaxff <pair_reaxff>` in the KOKKOS package have
+  seen extensive optimizations and specializations for GPUs and CPUs.

doc/src/Speed_measure.rst

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

doc/src/Tools.rst

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

doc/src/atom_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    atom_style style args
 
-* style = *amoeba* or *angle* or *atomic* or *body* or *bond* or *charge* or *dielectric* or *dipole* or  *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *wavepacket* or *hybrid*
+* style = *amoeba* or *angle* or *apip* or *atomic* or *body* or *bond* or *charge* or *dielectric* or *dipole* or  *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *wavepacket* or *hybrid*
 
   .. parsed-literal::
 
@@ -117,6 +117,10 @@ the Additional Information section below.
      - *bond* + "angle data"
      - :ref:`MOLECULE <PKG-MOLECULE>`
      - bead-spring polymers with stiffness
+   * - *apip*
+     - *atomic* + apip_lambda, apip_lambda_required, apip_lambda_input, apip_lambda_const, apip_lambda_input_ta, apip_e_fast, apip_e_precise, apip_f_const_lambda, apip_f_dyn_lambda
+     - :ref:`APIP <PKG-APIP>`
+     - adaptive-precision interatomic potentials(APIP), see :doc:`APIP howto <Howto_apip>`
    * - *atomic*
      - tag, type, x, v, f, image, mask
      -

doc/src/compute_angle_local.rst

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

doc/src/compute_bond_local.rst

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

doc/src/compute_dihedral_local.rst

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

doc/src/compute_msd.rst

@@ -49,8 +49,6 @@ proportional to the diffusion coefficient of the diffusing atoms.
 The displacement of an atom is from its reference position. This is
 normally the original position at the time
 the compute command was issued, unless the *average* keyword is set to *yes*\ .
-The value of the displacement will be
-0.0 for atoms not in the specified compute group.
 
 If the *com* option is set to *yes* then the effect of any drift in
 the center-of-mass of the group of atoms is subtracted out before the
@@ -111,7 +109,10 @@ distance\ :math:`^2` :doc:`units <units>`.
 Restrictions
 """"""""""""
 
-Compute *msd* cannot be used with a dynamic group.
+Compute *msd* cannot be used with a dynamic group and the number of
+atoms in the compute group must not be changed by some fixes like,
+for example, :doc:`fix deposit <fix_deposit>` or
+:doc:`fix evaporate <fix_evaporate>`.
 
 Related commands
 """"""""""""""""

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.
-The values *dx*, *dy*, and *dz* are the :math:`(x,y,z)` components of the
-*distance* between the pair of atoms. This value is always the
-distance from the atom of higher to the one with the lower atom ID.
+.. versionchanged:: 12Jun2025
+
+   The sign of *dx*, *dy*, *dz* is no longer determined by the value of
+   their atom-IDs but by their order in the neighbor list to be
+   consistent with *fx*, *fy*, and *fz*.
+
+The value *dist* is the distance between the pair of atoms.  The values
+*dx*, *dy*, and *dz* are the :math:`(x,y,z)` components of the distance
+vector :math:`\vec{x_i} - \vec{x_j}` between the pair of atoms.  The
+order of the atoms is determined by the neighbor list and the respective
+atom-IDs can be output with :doc:`compute property/local
+<compute_property_local>`.
 
 The value *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* on atom I. For pair styles that apply non-central forces,
-such as :doc:`granular pair styles <pair_gran>`, these values only include
-the :math:`(x,y,z)` components of the normal force component.
+force.
+
+The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
+the force vector on the first atom *i* of a pair in the neighbor list
+due to the second atom *j*.  Mathematically, they are obtained by
+multiplying the value of *force* from above with a unit vector created
+from the *dx*, *dy*, and *dz* components of the distance vector also
+described above.  For pair styles that apply non-central forces, such as
+:doc:`granular pair styles <pair_gran>`, these values only include the
+:math:`(x,y,z)` components of the normal force component.
 
 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/compute_property_atom.rst

@@ -34,6 +34,8 @@ Syntax
                              i_name, d_name, i2_name[I], d2_name[I],
                              vfrac, s0, espin, eradius, ervel, erforce,
                              rho, drho, e, de, cv, buckling,
+                             apip_lambda, apip_lambda_input, apip_e_fast,
+                             apip_e_precise
 
   .. parsed-literal::
 
@@ -70,6 +72,13 @@ Syntax
            *i2_name[I]* = Ith column of custom integer array with name
            *d2_name[I]* = Ith column of custom floating-point array with name
 
+  .. parsed-literal::
+
+           APIP package per-atom properties:
+           *apip_lambda* = switching parameter
+           *apip_lambda_input* = input used to calculate the switching parameter
+           *apip_e_fast,apip_e_precise* = potential energies mixed by the adaptive-precision potential
+
   .. parsed-literal::
 
            PERI package per-atom properties:
@@ -162,6 +171,22 @@ segment particles and define the end points of each line segment.
 *corner2z*, *corner3x*, *corner3y*, *corner3z*, are defined for
 triangular particles and define the corner points of each triangle.
 
+The accessible quantities from the :doc:`APIP package <Howto_apip>` are
+explained in the doc pages of this package in detail.
+In short: *apip_lambda* is the switching parameter :math:`\lambda\in[0,1]`,
+that is calculated from *apip_lambda_input* and that mixes the energies
+of a fast (*apip_e_fast*) and a precise (*apip_e_precise*) potential
+into an adaptive-precision energy.
+
+.. note::
+
+   The energy according to the fast and the precise potential are only
+   computed for the subset of atoms, for which it is required, i.e.,
+   for an atom :math:`i` with :math:`\lambda_i=1` one does not need
+   :math:`E_i^\text{precise}` and with :math:`\lambda_i=0` one does
+   not need :math:`E_i^\text{fast}`.
+
+
 In addition, the various per-atom quantities listed above for specific
 packages are only accessible by this command.
 

doc/src/compute_stress_mop.rst

@@ -45,13 +45,13 @@ Examples
 Description
 """""""""""
 
-Compute *stress/mop* and compute *stress/mop/profile* define
-computations that calculate components of the local stress tensor using
-the method of planes :ref:`(Todd) <mop-todd>`.  Specifically in compute
-*stress/mop* calculates 3 components are computed in directions *dir*,\
-*x*\ ; *dir*,\ *y*\ ; and *dir*,\ *z*\ ; where *dir* is the direction
-normal to the plane, while in compute *stress/mop/profile* the profile
-of the stress is computed.
+Compute *stress/mop* and compute *stress/mop/profile*
+calculate components of the local stress tensor using
+the method of planes :ref:`(Todd) <mop-todd>`.  Specifically, compute
+*stress/mop* calculates 3 components in directions :math:`ix`,
+:math:`iy`, and :math:`iz` where :math:`i` is the direction
+normal to the plane, while compute *stress/mop/profile* calculates the profile
+of the local stress along the :math:`i` direction.
 
 Contrary to methods based on histograms of atomic stress (i.e., using
 :doc:`compute stress/atom <compute_stress_atom>`), the method of planes
@@ -103,14 +103,15 @@ Output info
 Compute *stress/mop* calculates a global vector (indices starting at 1),
 with 3 values for each declared keyword (in the order the keywords have
 been declared). For each keyword, the stress tensor components are
-ordered as follows: stress_dir,x, stress_dir,y, and stress_dir,z.
+ordered as follows: :math:`P_{ix}`, :math:`P_{iy}`, and :math:`P_{iz}`,
+where :math:`i` is the direction normal to the plane.
 
 Compute *stress/mop/profile* instead calculates a global array, with 1
 column giving the position of the planes where the stress tensor was
 computed, and with 3 columns of values for each declared keyword (in the
 order the keywords have been declared). For each keyword, the profiles
-of stress tensor components are ordered as follows: stress_dir,x;
-stress_dir,y; and stress_dir,z.
+of stress tensor components are ordered as follows: :math:`P_{ix}`,
+:math:`P_{iy}`, and :math:`P_{iz}`.
 
 The values are in pressure :doc:`units <units>`.
 
@@ -129,15 +130,11 @@ package <Build_package>` doc page on for more info.
 The method is implemented for orthogonal simulation boxes whose
 size does not change in time, and axis-aligned planes.
 
-Contributions from bonds, angles, and dihedrals are not compatible
-with MPI parallel runs.
-
-The method only works with two-body pair interactions, because it
-requires the class method ``Pair::single()`` to be implemented, which is
-not possible for manybody potentials.  In particular, compute
-*stress/mop/profile* and *stress/mop* do not work with more than two-body
-pair interactions, long range (kspace) interactions and
-improper intramolecular interactions.
+Compute *stress/mop* and *stress/mop/profile* do not work with manybody
+non-bonded interactions, long range (kspace) interactions and
+improper intramolecular interactions. The reason is that the current
+implementation requires the class method ``Pair::single()`` to be implemented,
+which is not possible for manybody potentials.
 
 The impact of fixes that affect the stress (e.g. fix langevin) is
 also not included in the stress computed here.

doc/src/create_atoms.rst

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

doc/src/fix.rst

@@ -201,6 +201,7 @@ accelerated styles exist.
 * :doc:`append/atoms <fix_append_atoms>` - append atoms to a running simulation
 * :doc:`atc <fix_atc>` - initiates a coupled MD/FE simulation
 * :doc:`atom/swap <fix_atom_swap>` - Monte Carlo atom type swapping
+* :doc:`atom_weight/apip <fix_atom_weight_apip>` - compute atomic load of an :doc:`APIP potential <Howto_apip>` for load balancing
 * :doc:`ave/atom <fix_ave_atom>` - compute per-atom time-averaged quantities
 * :doc:`ave/chunk <fix_ave_chunk>` - compute per-chunk time-averaged quantities
 * :doc:`ave/correlate <fix_ave_correlate>` - compute/output time correlations
@@ -208,6 +209,7 @@ 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 +258,7 @@ 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
@@ -263,11 +266,13 @@ accelerated styles exist.
 * :doc:`halt <fix_halt>` - terminate a dynamics run or minimization
 * :doc:`heat <fix_heat>` - add/subtract momentum-conserving heat
 * :doc:`heat/flow <fix_heat_flow>` - plain time integration of heat flow with per-atom temperature updates
+* :doc:`hmc <fix_hmc>` -  Hybrid/Hamiltonian Monte Carlo (HMC) particle propagation
 * :doc:`hyper/global <fix_hyper_global>` - global hyperdynamics
 * :doc:`hyper/local <fix_hyper_local>` - local hyperdynamics
 * :doc:`imd <fix_imd>` - implements the "Interactive MD" (IMD) protocol
 * :doc:`indent <fix_indent>` - impose force due to an indenter
 * :doc:`ipi <fix_ipi>` - enable LAMMPS to run as a client for i-PI path-integral simulations
+* :doc:`lambda/apip <fix_lambda_apip>` - compute switching parameter, that controls the precision of an :doc:`APIP potential <Howto_apip>`
 * :doc:`langevin <fix_langevin>` - Langevin temperature control
 * :doc:`langevin/drude <fix_langevin_drude>` - Langevin temperature control of Drude oscillators
 * :doc:`langevin/eff <fix_langevin_eff>` - Langevin temperature control for the electron force field model
@@ -276,6 +281,7 @@ accelerated styles exist.
 * :doc:`lb/momentum <fix_lb_momentum>` - :doc:`fix momentum <fix_momentum>` replacement for use with a lattice-Boltzmann fluid
 * :doc:`lb/viscous <fix_lb_viscous>` - :doc:`fix viscous <fix_viscous>` replacement for use with a lattice-Boltzmann fluid
 * :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
+* :doc:`lambda_thermostat/apip <fix_lambda_thermostat_apip>` - apply energy conserving correction for an :doc:`APIP potential <Howto_apip>`
 * :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
 * :doc:`mdi/qm <fix_mdi_qm>` - LAMMPS operates as a client for a quantum code via the MolSSI Driver Interface (MDI)
 * :doc:`mdi/qmmm <fix_mdi_qmmm>` - LAMMPS operates as client for QM/MM simulation with a quantum code via the MolSSI Driver Interface (MDI)
@@ -290,6 +296,7 @@ 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 +402,7 @@ 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

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

doc/src/fix_atom_swap.rst

@@ -116,7 +116,10 @@ charge would not be conserved. As a consequence, no checks on atomic
 charges are performed, and successful switches update the atom type but
 not the atom charge. While it is possible to use *semi-grand* with
 groups of atoms that have different charges, these charges will not be
-changed when the atom types change.
+changed when the atom types change.  The same applies for systems
+with per-atom masses: non *semi-grand* will swap atom masses, but
+the masses have to be the same each for the atom types.  When using
+*semi-grand* no per-atom masses are changed.
 
 Since this fix computes total potential energies before and after
 proposed swaps, even complicated potential energy calculations are
@@ -184,11 +187,10 @@ When this fix is used with a :doc:`hybrid pair style <pair_hybrid>`
 system, only swaps between atom types of the same sub-style (or
 combination of sub-styles) are permitted.
 
-This fix cannot be used with systems that do not have per-type masses
-(e.g. atom style sphere) since the implemented algorithm pre-computes
-velocity rescaling factors from per-type masses and ignores any per-atom
-masses, if present.  In case both, per-type and per-atom masses are
-present, a warning is printed.
+This fix can be used with systems that have per-atom masses
+(e.g. atom style sphere) provided all atoms of the types handled
+by this fix have the same mass per type. The fix will check for that.
+In case both, per-type and per-atom masses are present, a warning is printed.
 
 Related commands
 """"""""""""""""

doc/src/fix_atom_weight_apip.rst

@@ -0,0 +1,143 @@
+.. index:: fix atom_weight/apip
+
+fix atom_weight/apip command
+============================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID atom_weight/apip nevery fast_potential precise_potential lambda_input lambda_zone group_lambda_input [no_rescale]
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* atom_weight/apip = style name of this fix command
+* nevery = perform load calculation every this many steps
+* fast_potential = *eam* or *ace* for time measurements of the corresponding pair_style or float for constant time
+* precise_potential = *ace* for a time measurement of the pair_style pace/apip or float for constant time
+* lambda_input = *lambda/input* for a time measurement of pair_style lambda/input/apip or float for constant time
+* lambda_zone = *lambda/zone* for a time measurement of pair_style lambda/zone/apip or float for constant time
+* group_lambda_input = group-ID of the group for which lambda_input is computed
+* no_rescale = do not rescale the work per processor to the measured total force-computation time
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 2 all atom_weight/apip 50 eam ace lambda/input lambda/zone all
+   fix 2 all atom_weight/apip 50 1e-05 0.0004 4e-06 4e-06 all
+   fix 2 all atom_weight/apip 50 ace ace 4e-06 4e-06 all no_rescale
+
+Description
+"""""""""""
+
+This command approximates the load every atom causes when an
+adaptive-precision interatomic potential (APIP) according to
+:ref:`(Immel) <Immel2025_2>` is used.
+This approximated load can be saved as atomic variable and
+used as input for the dynamic load balancing via the
+:doc:`fix balance <fix_balance>` command.
+
+An adaptive-precision potential like :doc:`eam/apip <pair_eam_apip>`
+and :doc:`pace/apip <pair_pace_apip>` is calculated only
+for a subset of atoms.
+The switching parameter that determines per atom, which potential energy is
+used, can be also calculated by
+:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`.
+A spatial switching zone, that ensures a smooth transition between two
+different interatomic potentials, can be calculated by
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`.
+Thus, there are up to four force-subroutines, that are computed only for a
+subset of atoms and combined via the pair_style :doc:`hybrid/overlay <pair_hybrid>`.
+For all four force-subroutines, the average work per atom is be measured
+per processor by the corresponding pair_style.
+This fix extracts these measurements of the pair styles every *nevery*
+steps. The average compute times are used to calculates a per-atom vector with
+the approximated atomic weight, whereas the average compute time of the four
+subroutines contributes only to the load of atoms, for which the corresponding
+subroutine was calculated.
+If not disabled via *no_rescale*, the so calculated load is
+rescaled per processor so that the total atomic compute time matches the
+also measured total compute time of the whole pair_style.
+This atomic weight is intended to be used
+as input for :doc:`fix balance <fix_balance>`:
+
+.. code-block:: LAMMPS
+
+   variable nevery equal 10
+   fix weight_atom all atom_weight/apip ${nevery} eam ace lambda/input lambda/zone all
+   variable myweight atom f_weight_atom
+   fix balance all balance ${nevery} 1.1 rcb weight var myweight
+
+Furthermore, this fix provides the over the processors averaged compute time of the
+four pair_styles, which are used to approximate the atomic weight, as vector.
+
+----------
+
+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.
+
+This fix produces a per-atom vector that contains the atomic
+weight of each atom.
+The per-atom vector can only be accessed on timesteps that are multiples
+of *nevery*.
+
+Furthermore, this fix computes a global vector of length 4 with
+statistical information about the four different (possibly)
+measured compute times per force subroutine. The four
+values in the vector are as follows:
+
+  #. average compute time for one atom using the fast pair_style
+  #. average compute time for one atom using the precise pair_style
+  #. average compute time of lambda/input/apip for one atom
+  #. average compute time of lambda/zone/apip for one atom
+
+The compute times are computed as average of all processors that
+measured at least one computation of the corresponding style.
+The vector values calculated by this fix are "intensive" and
+updated whenever the per-atom vector is computed, i.e., in
+timesteps that are multiples of *nevery*.
+
+The vector and the per-atom vector can be accessed 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
+""""""""""""
+
+This fix is part of the APIP 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 balance <fix_balance>`,
+:doc:`fix lambda/apip <fix_lambda_apip>`,
+:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
+:doc:`pair_style lambda/input/apip  <pair_lambda_input_apip>`,
+:doc:`pair_style eam/apip <pair_eam_apip>`,
+:doc:`pair_style pace/apip  <pair_pace_apip>`,
+
+Default
+"""""""
+
+*no_rescale* is not used by default.
+
+----------
+
+.. _Immel2025_2:
+
+**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

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

doc/src/fix_bond_create.rst

@@ -21,7 +21,7 @@ Syntax
 * Rmin = two atoms separated by less than Rmin can bond (distance units)
 * bondtype = type of created bonds (integer or type label)
 * zero or more keyword/value pairs may be appended to args
-* keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype* or *aconstrain*
+* keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype* or *aconstrain* or *molecule*
 
   .. parsed-literal::
 
@@ -43,6 +43,10 @@ Syntax
        *aconstrain* value = amin amax
          amin = minimal angle at which new bonds can be created
          amax = maximal angle at which new bonds can be created
+       *molecule* value = *off* or *inter* or *intra*
+         *off* = allow both inter- and intramolecular reactions (default)
+         *inter* = search for reactions between molecules with different IDs
+         *intra* = search for reactions within the same molecule
 
 Examples
 """"""""
@@ -52,6 +56,7 @@ Examples
    fix 5 all bond/create 10 1 2 0.8 1
    fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3
    fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2
+   fix 5 all bond/create 10 13 25 7 28 iparam 1 15 jparam 1 27 prob 0.2 91322 molecule inter
    fix 5 all bond/create/angle 10 1 2 1.122 1 aconstrain 120 180 prob 1 4928459 iparam 2 1 jparam 2 2
 
    labelmap atom 1 c1 2 n2
@@ -123,6 +128,8 @@ actually created.  The *fraction* setting must be a value between 0.0
 and 1.0.  A uniform random number between 0.0 and 1.0 is generated and
 the eligible bond is only created if the random number is less than *fraction*.
 
+The *molecule* keyword can be used to force the reaction to be intermolecular, intramolecular or either. When the value is set to *off*, molecule IDs are not considered when searching for reactions (default). When the value is set to *inter*, atoms must have different molecule IDs in order to be considered for the reaction. When the value is set to *intra*, only atoms with the same molecule ID are considered for the reaction.
+
 The *aconstrain* keyword is only available with the fix
 bond/create/angle command.  It allows one to specify minimum and maximum
 angles *amin* and *amax*, respectively, between the two prospective bonding

doc/src/fix_controller.rst

@@ -98,52 +98,53 @@ the following dynamic equation:
 
    \frac{dc}{dt}  = -\alpha (K_p e + K_i \int_0^t e \, dt + K_d \frac{de}{dt} )
 
-where *c* is the continuous time analog of the control variable,
-*e* =\ *pvar*\ -\ *setpoint* is the error in the process variable, and
-:math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are constants
-set by the corresponding
-keywords described above. The discretized version of this equation is:
+where *c* is the continuous time analog of the control variable, *e*
+=\ *pvar*\ -\ *setpoint* is the error in the process variable, and
+:math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are
+constants set by the corresponding keywords described above. The
+discretized version of this equation is:
 
 .. math::
 
    c_n  = c_{n-1} -\alpha \left( K_p \tau e_n + K_i \tau^2 \sum_{i=1}^n e_i + K_d (e_n - e_{n-1}) \right)
 
-where :math:`\tau = \mathtt{Nevery} \cdot \mathtt{timestep}` is the time
-interval between updates,
-and the subscripted variables indicate the values of *c* and *e* at
-successive updates.
+where :math:`\tau = \mathtt{Nevery} \cdot \mathtt{timestep}` is the
+time interval between updates, and the subscripted variables indicate
+the values of *c* and *e* at successive updates.
 
 From the first equation, it is clear that if the three gain values
 :math:`K_p`, :math:`K_i`, :math:`K_d` are dimensionless constants,
-then :math:`\alpha` must have
-units of [unit *cvar*\ ]/[unit *pvar*\ ]/[unit time] e.g. [ eV/K/ps
-]. The advantage of this unit scheme is that the value of the
-constants should be invariant under a change of either the MD timestep
-size or the value of *Nevery*\ . Similarly, if the LAMMPS :doc:`unit style <units>` is changed, it should only be necessary to change
-the value of :math:`\alpha` to reflect this, while leaving :math:`K_p`,
-:math:`K_i`, and :math:`K_d` unaltered.
+then :math:`\alpha` must have units of [unit *cvar*\ ]/[unit *pvar*\
+]/[unit time] e.g. [ eV/K/ps ]. The advantage of this unit scheme is
+that the value of the constants should be invariant under a change of
+either the MD timestep size or the value of *Nevery*\ . Similarly, if
+the LAMMPS :doc:`unit style <units>` is changed, it should only be
+necessary to change the value of :math:`\alpha` to reflect this, while
+leaving :math:`K_p`, :math:`K_i`, and :math:`K_d` unaltered.
 
 When choosing the values of the four constants, it is best to first
 pick a value and sign for :math:`\alpha` that is consistent with the
-magnitudes and signs of *pvar* and *cvar*\ .  The magnitude of :math:`K_p`
-should then be tested over a large positive range keeping :math:`K_i = K_d =0`.
-A good value for :math:`K_p` will produce a fast response in *pvar*,
-without overshooting the *setpoint*\ .  For many applications, proportional
-feedback is sufficient, and so :math:`K_i = K_d =0` can be used. In cases
-where there is a substantial lag time in the response of *pvar* to a change
-in *cvar*, this can be counteracted by increasing :math:`K_d`. In situations
+magnitudes and signs of *pvar* and *cvar*\ .  The magnitude of
+:math:`K_p` should then be tested over a large positive range keeping
+:math:`K_i = K_d =0`.  A good value for :math:`K_p` will produce a
+fast response in *pvar*, without overshooting the *setpoint*\ .  For
+many applications, proportional feedback is sufficient, and so
+:math:`K_i = K_d =0` can be used. In cases where there is a
+substantial lag time in the response of *pvar* to a change in *cvar*,
+this can be counteracted by increasing :math:`K_d`. In situations
 where *pvar* plateaus without reaching *setpoint*, this can be
-counteracted by increasing :math:`K_i`.  In the language of Charles Dickens,
-:math:`K_p` represents the error of the present, :math:`K_i` the error of
-the past, and :math:`K_d` the error yet to come.
+counteracted by increasing :math:`K_i`.  In the language of Charles
+Dickens, :math:`K_p` represents the error of the present, :math:`K_i`
+the error of the past, and :math:`K_d` the error yet to come.
 
 Because this fix updates *cvar*, but does not initialize its value,
-the initial value :math:`c_0` is that assigned by the user in the input script via
-the :doc:`internal-style variable <variable>` command.  This value is
-used (by every other LAMMPS command that uses the variable) until this
-fix performs its first update of *cvar* after *Nevery* timesteps.  On
-the first update, the value of the derivative term is set to zero,
-because the value of :math:`e_{n-1}` is not yet defined.
+the initial value :math:`c_0` is that assigned by the user in the
+input script via the :doc:`internal-style variable <variable>`
+command.  This value is used (by every other LAMMPS command that uses
+the variable) until this fix performs its first update of *cvar* after
+*Nevery* timesteps.  On the first update, the value of the derivative
+term is set to zero, because the value of :math:`e_{n-1}` is not yet
+defined.
 
 ----------
 
@@ -154,21 +155,23 @@ must produce a global quantity, not a per-atom or local quantity.
 
 If *pvar* begins with "c\_", a compute ID must follow which has been
 previously defined in the input script and which generates a global
-scalar or vector.  See the individual :doc:`compute <compute>` doc page
-for details.  If no bracketed integer is appended, the scalar
+scalar or vector.  See the individual :doc:`compute <compute>` doc
+page for details.  If no bracketed integer is appended, the scalar
 calculated by the compute is used.  If a bracketed integer is
 appended, the Ith value of the vector calculated by the compute is
-used.  Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
+used.  Users can also write code for their own compute styles and
+:doc:`add them to LAMMPS <Modify>`.
 
 If *pvar* begins with "f\_", a fix ID must follow which has been
 previously defined in the input script and which generates a global
 scalar or vector.  See the individual :doc:`fix <fix>` page for
 details.  Note that some fixes only produce their values on certain
 timesteps, which must be compatible with when fix controller
-references the values, or else an error results.  If no bracketed integer
-is appended, the scalar calculated by the fix is used.  If a bracketed
-integer is appended, the Ith value of the vector calculated by the fix
-is used.  Users can also write code for their own fix style and :doc:`add them to LAMMPS <Modify>`.
+references the values, or else an error results.  If no bracketed
+integer is appended, the scalar calculated by the fix is used.  If a
+bracketed integer is appended, the Ith value of the vector calculated
+by the fix is used.  Users can also write code for their own fix style
+and :doc:`add them to LAMMPS <Modify>`.
 
 If *pvar* begins with "v\_", a variable name must follow which has been
 previously defined in the input script.  Only equal-style variables
@@ -182,19 +185,21 @@ variable.
 The target value *setpoint* for the process variable must be a numeric
 value, in whatever units *pvar* is defined for.
 
-The control variable *cvar* must be the name of an :doc:`internal-style variable <variable>` previously defined in the input script.  Note
-that it is not specified with a "v\_" prefix, just the name of the
-variable.  It must be an internal-style variable, because this fix
-updates its value directly.  Note that other commands can use an
-equal-style versus internal-style variable interchangeably.
+The control variable *cvar* must be the name of an
+:doc:`internal-style variable <variable>` previously defined in the
+input script.  Note that it is not specified with a "v\_" prefix, just
+the name of the variable.  It must be an internal-style variable,
+because this fix updates its value directly.  Note that other commands
+can use an equal-style versus internal-style variable interchangeably.
 
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-Currently, no information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
-are relevant to this fix.
+Currently, no information about this fix is written to :doc:`binary
+restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>`
+options are relevant to this fix.
 
 This fix produces a global vector with 3 values which can be accessed
 by various :doc:`output commands <Howto_output>`.  The values can be
@@ -211,7 +216,8 @@ variable is in.  The vector values calculated by this fix are
 "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_deform.rst

@@ -298,7 +298,8 @@ Note that it should return the "change" in box length, not the
 absolute box length.  This means it should evaluate to 0.0 when
 invoked on the initial timestep of the run following the definition of
 fix deform.  It should evaluate to a value > 0.0 to dilate the box at
-future times, or a value < 0.0 to compress the box.
+future times, or a value < 0.0 to compress the box. The exception
+would be if the run command uses the *pre no* option.
 
 The variable *name2* must also be an :doc:`equal-style variable
 <variable>` and should calculate the rate of box length change, in

doc/src/fix_deposit.rst

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

doc/src/fix_electron_stopping.rst

@@ -1,9 +1,12 @@
 .. index:: fix electron/stopping
+.. index:: fix electron/stopping/kk
 .. index:: fix electron/stopping/fit
 
 fix electron/stopping command
 =============================
 
+Accelerator Variants: *electron/stopping/kk*
+
 fix electron/stopping/fit command
 =================================
 
@@ -157,6 +160,18 @@ of the atom types. There is an examples/PACKAGES/electron_stopping/ directory,
 which illustrates uses of this command. Details of this implementation are
 further described in :ref:`Stewart2018 <Stewart2018>` and :ref:`Lee2020 <Lee2020>`.
 
+----------
+
+.. include:: accel_styles.rst
+
+.. note::
+
+  The region keyword is supported by Kokkos, but a Kokkos-enabled
+  region must be used. See the region :doc:`region <region>` command for
+  more information.
+
+----------
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

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

doc/src/fix_hmc.rst

@@ -0,0 +1,250 @@
+.. index:: fix hmc
+
+fix hmc command
+===============
+
+Syntax
+""""""
+.. code-block:: LAMMPS
+
+   fix ID group-ID hmc N seed T keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* hmc = style name of this fix command
+* N = invoke a Monte Carlo step every N steps
+* seed = random # seed (positive integer)
+* T = temperature for assigning velocities and acceptance criterion
+* one or more keyword/value pairs may be appended
+
+  .. parsed-literal::
+
+     keyword = *rigid* or *resample* or *mom*
+       *rigid* value = rigidID
+          rigidID = ID of :doc:`fix rigid/small <fix_rigid>` command
+       *resample* value = *yes* or *no*
+       *mom* value = *yes* or *no*
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all hmc 10 123 500
+   fix hmc_water all hmc 100 123 298.15 rigid 1
+   fix 2 all hmc 10 12345 300 mom no resample yes
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This fix implements the hybrid or Hamiltonian Monte Carlo (HMC)
+algorithm.  The basic idea is to use molecular dynamics (MD) to
+generate trial MC "moves" which are then accepted or rejected via the
+Metropolis criterion.  In this context, an MC "move" is the new
+configuration of particles after *N* MD steps, i.e. all the particles
+in the system have moved to new positions. HMC generates a canonical
+distribution in configuration space. More details on the theory behind
+HMC can be found in the references, :ref:`(Mehlig) <Mehlig1>` and
+:ref:`(Mehlig) <Mehlig2>`.
+
+The details of the HMC algorithm for a repeating series of $N$ MD
+steps are as follows:
+
+(1) The configuration of the system is stored along with its current
+total energy.  This includes all particle positions and velocities and other
+per-atom properties (e.g. dipole orientation vector for particles with
+dipole moments).
+
+(2) The system is time integrated in the NVE ensemble for the
+specified *N* MD steps and the new energy is calculated.  The new
+configuration is the trial "move" to accept or reject.
+
+(3) The energy change :math:`\Delta{H}` in the Hamiltonian of the
+system due to the "move" is calculated by the following equation:
+
+.. math::
+
+   \Delta{H} = H(q',p') -  H(q,p)
+
+The new configuration is then accepted/rejected according to the
+Metropolis criterion with probability:
+
+.. math::
+
+   p^{acc} = min(1,e^{\frac{-\Delta{H}}{k_B T}})
+
+where *T* is the specified temperature.
+
+The idea of HMC is to use a timestep large enough that total energy is
+*not* conserved. The change in total energy (the Hamiltonian) is what
+the Metropolis criterion is based on, not the change in potential
+energy.
+
+(4) If accepted, the new configuration becomes the starting point for
+the next trial MC "move". If *resample* is *yes* then the velocities are
+resampled at this point as well.
+
+(5) If rejected, the old configuration (from *N* steps ago) is
+restored and new momenta (velocities) are assigned to each particle
+in the fix group by randomly resampling from a normal distribution
+at the specified temperature $T$ using the following equation:
+
+.. math::
+
+   p_{x,y,z} = \textbf{N}(0,1) \sqrt{\frac{k_B T}{2 m^2}}
+
+The velocity-modified "old" configuration becomes the starting point
+for the next trial MC "move".
+
+.. note::
+
+   HMC should be run with a larger timestep than would be used for
+   traditional MD, which enables total energy fluctuations and
+   generation of new conformations which MD would not normally generate
+   as quickly.  The timestep size may also affect the acceptance ratio
+   as a larger timestep will lead to larger and more extreme MC moves
+   which are less likely to be accepted.  The timestep size must strike
+   a balance between allowing the total energy to change and generating
+   errors such as lost atoms due to atomic overlap.  This means that
+   during the MD portion of the algorithm, unphysical dynamics will take
+   place, such as large temperature fluctuations and large forces
+   between atoms.  This is expected and is part of the HMC algorithm, as
+   the MD step is not intended to produce a physically realistic
+   trajectory, but rather to generate a new configuration of particles
+   that can be accepted or rejected based on the Metropolis criterion.
+
+.. note::
+
+   High acceptance ratios indicate that the MC algorithm is inefficient,
+   as it is not generating new configurations of particles any faster
+   than MD would on its own. In the limit of an acceptance ratio of 1.0,
+   the algorithm is equivalent to MD (with momentum resampling every *N*
+   timesteps if *resample* = *yes*), and no benefit is gained from MC.
+   A good rule of thumb is to aim for an acceptance ratio of 0.5 to 0.8,
+   which can be monitored via the output of this fix.  This can be
+   achieved by adjusting the *N* parameter and the timestep size.
+   Increasing either of these values will increase the size of the total
+   energy fluctuations, which can decrease acceptance ratio.  Increasing
+   *N* will also increase the computation time for each MC step, as more
+   MD steps are performed before each acceptance/rejection decision.  As
+   noted above, increasing the timestep too much can lead to LAMMPS
+   errors due to lost atoms or bonds, so both of these parameters should
+   be chosen carefully.
+
+.. note::
+
+   This fix is designed to be used only for constant NVE simulations.
+   No thermostat or barostat should be used, though LAMMPS does not
+   check for this.  A :doc:`fix nve <fix_nve>` command must be defined
+   to perform time integration for the MD portion of the algorithm.  See
+   the explanation of the *rigid* keyword below for an exception when
+   rigid bodies are defined.  Also note that only per-atom data is
+   restored on MC move rejection, so anything which adds or remove
+   particles, changes the box size, or has some external state not
+   dependent on per-atom data will have undefined behavior.
+
+----------
+
+The keyword/value options are as follows:
+
+The *rigid* keyword enables use of HMC for systems containing a
+collection of small rigid bodies, with or without solvent (atomic
+fluid or non-rigid molecular fluid).
+
+The *rigidID* value should be the ID of a :doc:`fix rigid/small
+<fix_rigid>` or :doc:`fix rigid/nve/small <fix_rigid>` command which
+defines the rigid bodies.  Its integrator will be used during the MD
+timesteps.  If there are additional particles in the system,
+e.g. solvent, they should be time-integrated by a :doc:`fix nve
+<fix_nve>` command as explained above.
+
+The *resample* keyword determines whether velocities are also
+resampled upon acceptance in step (4) above, in addition to step (5).
+If *resample* = *yes*, velocities are resampled upon acceptance.  If
+*resample* = *no* (default), velocities are not resampled upon
+acceptance.
+
+The *mom* keyword sets the linear momentum of the ensemble of
+particles each time velocities are reset in steps (4 or 5) above.  If
+*mom* = *yes* (default), the linear momentum of the ensemble of
+velocities is zeroed. If *mom* = *no*, the linear momentum of the
+ensemble of velocities is not zeroed.
+
+----------
+
+This fix creates several additional computes for monitoring the energy
+and virial of the system and storing/restoring the system state.  This
+is done internally, as if these commands had been issued, where ID is
+the ID of this fix:
+
+.. code-block:: LAMMPS
+
+   compute hmc_ke_ID all ke
+   compute hmc_pe_ID all pe
+   compute hmc_peatom_ID all pe/atom
+   compute hmc_press_ID all pressure NULL virial
+   compute hmc_pressatom_ID all stress/atom NULL virial
+
+The output of these computes can be accessed by the input script,
+along with the other outputs described in the next section.
+
+----------
+
+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.
+
+This fix calculates a global scalar and global vector of length 5,
+which can be accessed by various :doc:`output commands
+<Howto_output>`.  The scalar is the fraction (0-1) of attempted MC
+moves which have been accepted.  The vector stores the following
+quantities:
+
+* 1 = cumulative number of accepted moves
+* 2 = cumulative number of rejected moves
+* 3 = change in potential energy for last trial move
+* 4 = change in kinetic energy for last trial move
+* 5 = change in total energy (kinetic + potential energy) for last trial move
+
+These values are updated once every *N* timesteps.  The scalar and
+cumulative counts are "intensive"; the three energies are "extensive"
+and are in energy :doc:`units <units>`.
+
+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 and requires the RIGID package to
+be installed. It is only enabled if LAMMPS was built with both
+packages.  See the :doc:`Build package <Build_package>` doc page for
+more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix nvt <fix_nh>`, :doc:`fix gcmc <fix_gcmc>`,
+:doc:`fix tfmc <fix_tfmc>`
+
+Default
+"""""""
+
+The option defaults are resample = no and mom = yes.
+
+----------
+
+.. _Mehlig1:
+
+**(Mehlig1)** Mehlig, B., Heermann, D. W., & Forrest, B. M. (1992).
+Hybrid Monte Carlo method for condensed-matter systems. Physical Review B, 45(2), 679.
+
+.. _Mehlig2:
+
+**(Mehlig2)** Mehlig, B., Heermann, D. W., & Forrest, B. M. (1992).
+Exact langevin algorithms. Molecular Physics, 76(6), 1347-1357.

doc/src/fix_lambda_apip.rst

@@ -0,0 +1,262 @@
+.. index:: fix lambda/apip
+
+fix lambda/apip command
+=======================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID lambda/apip thr_lo thr_hi keyword args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* lambda/apip = style name of this fix command
+* thr_lo = value below which :math:`\lambda_i^\text{input}` results in a switching parameter of 1
+* thr_hi = value above which :math:`\lambda_i^\text{input}` results in a switching parameter of 0
+* zero or one keyword/args pairs may be appended
+* keyword = *time_averaged_zone* or *min_delta_lambda* or *lambda_non_group* or *store_atomic_stats* or *dump_atomic_history* or *group_fast* or *group_precise* or *group_ignore_lambda_input*
+
+  .. parsed-literal::
+
+       *time_averaged_zone* args = cut_lo cut_hi history_len_lambda_input history_len_lambda
+         cut_lo = distance at which the radial function decreases from 1
+         cut_hi = distance from which on the radial function is 0
+         history_len_lambda_input = number of time steps for which lambda_input is averaged
+         history_len_lambda = number of time steps for which the switching parameter is averaged
+       *min_delta_lambda* args = delta
+         delta = value below which changes of the switching parameter are neglected (>= 0)
+       *lambda_non_group* args = lambda_ng
+         lambda_ng = *precise* or *fast* or float
+           *precise* = assign a constant switching parameter of 0 to atoms, that are not in the group specified by group-ID
+           *fast* = assign a constant switching parameter of 1 to atoms, that are not in the group specified by group-ID
+           float = assign this constant switching parameter to atoms, that are not in the group specified by group-ID (0 <= float <= 1)
+       *group_fast* args = group-ID-fast
+         group-ID-fast = the switching parameter of 1 is used instead of the one computed by lambda_input for atoms in the group specified by group-ID-fast
+       *group_precise* args = group-ID-precise
+         group-ID-precise = the switching parameter of 0 is used instead of the one computed by lambda_input for atoms in the group specified by group-ID-precise
+       *group_ignore_lambda_input* args = group-ID-ignore-lambda-input
+         group-ID-ignore-lambda-input = the switching parameter of lambda_ng is used instead of the one computed by lambda_input for atoms in the group specified by group-ID-ignore-lambda-input
+       *store_atomic_stats* args = none
+       *dump_atomic_history* args = none
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
+   fix 2 mobile lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01 group_ignore_lambda_input immobile lambda_non_group fast
+
+Description
+"""""""""""
+The potential energy :math:`E_i` of an atom :math:`i` of an adaptive-precision
+potential according to :ref:`(Immel) <Immel2025_3>` is given by
+
+.. math::
+
+   E_i = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)},
+
+whereas :math:`E_i^\text{(fast)}` is the potential energy of atom :math:`i`
+according to a fast interatomic potential like EAM,
+:math:`E_i^\text{(precise)}` is the potential energy according to a precise
+interatomic potential such as ACE and :math:`\lambda_i\in[0,1]` is the
+switching parameter that decides which potential energy is used.
+This fix calculates the switching parameter :math:`\lambda_i` based on the
+input provided from :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`.
+
+The calculation of the switching parameter is described in detail in
+:ref:`(Immel) <Immel2025_3>`.
+This fix calculates the switching parameter for all atoms in the
+:doc:`group <group>`
+described by group-ID, while the value of *lambda_non_group* is used
+as switching parameter for all other atoms.
+
+First, this fix calculates per atom :math:`i` the time averaged input
+:math:`\lambda^\text{input}_{\text{avg},i}` from
+:math:`\lambda^\text{input}_{i}`, whereas the number of averaged timesteps
+can be set via *time_averaged_zone*.
+
+.. note::
+
+   :math:`\lambda^\text{input}_{i}` is calculated by
+   :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`, which needs to be included
+   in the input script as well.
+
+The time averaged input :math:`\lambda^\text{input}_{\text{avg},i}` is then
+used to calculate the switching parameter
+
+.. math::
+
+   \lambda_{0,i}(t) = f^\text{(cut)} \left(\frac{\lambda_{\text{avg},i}^\text{input}(t) - \lambda_\text{lo}^\text{input}}{\lambda_\text{hi}^\text{input} - \lambda_\text{lo}^\text{input}} \right)\,,
+
+whereas the thresholds :math:`\lambda_\text{hi}^\text{input}`
+and  :math:`\lambda_\text{lo}^\text{input}` are set by the
+values provided as *thr_lo* and *thr_hi* and :math:`f^\text{(cut)}(x)` is a cutoff function
+that is 1 for :math:`x\leq 0`, decays from 1 to 0 for :math:`x\in[0,1]`, and
+is 0 for :math:`x\geq 1`.
+If the *group_precise* argument is used, :math:`\lambda_{0,i}=0` is used for all
+atoms :math:`i` assigned to the corresponding :doc:`group <group>`.
+If the *group_fast* argument is used, :math:`\lambda_{0,i}=1` is used for all
+atoms :math:`i` assigned to the corresponding :doc:`group <group>`.
+If an atom is in the groups *group_fast* and *group_precise*,
+:math:`\lambda_{0,i}=0` is used.
+If the *group_ignore_lambda_input* argument is used,
+:math:`\lambda_i^\text{input}` is not computed for all atoms :math:`i` assigned
+to the corresponding :doc:`group <group>`; instead, if the value is not already
+set by *group_fast* or *group_precise*, the value of *lambda_non_group* is
+used.
+
+.. note::
+
+   The computation of :math:`\lambda_i^\text{input}` is not required for
+   atoms that are in the groups *group_fast* and *group_precise*.
+   Thus, one should use *group_ignore_lambda_input* and prevent the
+   computation of :math:`\lambda_i^\text{input}` for all atoms, for
+   which a constant input is used.
+
+A spatial transition zone between the fast and the precise potential is
+introduced via
+
+.. math::
+
+   \lambda_{\text{min},i}(t) = \text{min}\left(\left\{1 - (1 -\lambda_{0,j}(t)) f^\text{(cut)}\left(\frac{r_{ij}(t)-r_{\lambda,\text{lo}}}{r_{\lambda,\text{hi}} - r_{\lambda,\text{lo}}}\right) : j \in \Omega_{\lambda,i} \right\}\right)\,,
+
+whereas the thresholds :math:`r_{\lambda,\text{lo}}` and
+:math:`r_{\lambda,\text{hi}}`
+of the cutoff function are set via *time_averaged_zone* and
+:math:`\Omega_{\lambda,i}` is the set of
+neighboring atoms of atom :math:`i`.
+
+.. note::
+
+   :math:`\lambda_{\text{min},i}` is calculated by
+   :doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`, which needs to be included
+   in the input script as well.
+
+The switching parameter is smoothed by the calculation of the time average
+
+.. math::
+
+   \lambda_{\text{avg},i}(t) = \frac{1}{N_{\lambda,\text{avg}}} \sum_{n=1}^{N_{\lambda,\text{avg}}} \lambda_{\text{min},i}(t - n \Delta t)\,,
+
+whereas :math:`\Delta t` is the :doc:`timestep <timestep>` and
+:math:`N_{\lambda,\text{avg}}` is the number of averaged timesteps, that
+can be set via *time_averaged_zone*.
+
+Finally, numerical fluctuations of the switching parameter are suppressed by the usage of
+
+.. math::
+
+   \lambda_{i}(t) = \left\{
+   \begin{array}{ll}
+   \lambda_{\text{avg},i}(t) & \text{ for } \left|\lambda_{\text{avg},i}(t) - \lambda_{i}(t-\Delta t)\right|\geq \Delta\lambda_\text{min} \text{ or } \lambda_{\text{avg},i}(t)\in\{0,1\}, \\
+   \lambda_{i}(t-\Delta t) & \text{ otherwise}\,,
+   \end{array}
+   \right.
+
+whereas the minimum change :math:`\Delta\lambda_\text{min}` is set by the
+*min_delta_lambda* argument.
+
+.. note::
+
+   *group_fast* affects only :math:`\lambda_{0,i}(t)`. The switching parameter
+   of atoms in this :doc:`group <group>` may change due to the calculation of the
+   spatial switching zone.
+   A switching parameter of 1 can be enforced by excluding the corresponding
+   atoms from the :doc:`group <group>` described by group-ID and using *lambda_non_group* 1
+   as argument.
+
+----------
+
+A code example for the calculation of the switching parameter for an
+adaptive-precision potential is given in the following:
+The adaptive-precision potential is created
+by combining :doc:`pair_style eam/fs/apip <pair_eam_apip>`
+and :doc:`pair_style pace/precise/apip <pair_pace_apip>`.
+The input, from which the switching parameter is calculated, is provided
+by :doc:`pair lambda/input/csp/apip <pair_lambda_input_apip>`.
+The switching parameter is calculated by this fix, whereas the spatial
+transition zone of the switching parameter is calculated by
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`.
+
+.. code-block:: LAMMPS
+
+   pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
+   pair_coeff * * eam/fs/apip Cu.eam.fs Cu
+   pair_coeff * * pace/precise/apip Cu_precise.yace Cu
+   pair_coeff * * lambda/input/csp/apip
+   pair_coeff * * lambda/zone/apip
+   fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
+
+
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+The saved history of the switching parameter :math:`\lambda_i`
+and the saved history of
+:math:`\lambda_i^\text{input}` are written to
+:doc:`binary restart files <restart>` allow a smooth restart of a simulation.
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
+
+If the *store_atomic_stats* argument is used, basic statistics is provided as
+per-atom array:
+
+  #. :math:`\lambda_i^\text{input}(t)`
+  #. :math:`\lambda_{\text{avg},i}^\text{input}(t)`
+  #. :math:`\lambda_{0,i}(t)`
+  #. :math:`\lambda_{\text{min},i}(t)`
+  #. :math:`\lambda_{i}(t)`
+
+If the *dump_atomic_history* argument is used, the whole saved history
+of :math:`\lambda_i^\text{input}(t)` is appended to the previously
+mentioned array per atom.
+
+The per-atom vector can be accessed 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
+""""""""""""
+
+This fix is part of the APIP 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:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
+:doc:`pair_style lambda/input/apip  <pair_lambda_input_apip>`,
+:doc:`pair_style eam/apip <pair_eam_apip>`,
+:doc:`pair_style pace/apip  <pair_pace_apip>`,
+:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
+:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
+
+Default
+"""""""
+
+*min_delta_lambda* = 0,
+*lambda_non_group* = 1,
+*cut_lo* = 4.0,
+*cut_hi* = 12.0,
+*history_len_lambda_input* = 100,
+*history_len_lambda* = 100,
+*store_atomic_stats* is not used,
+*dump_atomic_history* is not used,
+*group_fast* is not used,
+*group_precise* is not used,
+*group_ignore_lambda_input* is not used
+
+----------
+
+.. _Immel2025_3:
+
+**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

doc/src/fix_lambda_thermostat_apip.rst

@@ -0,0 +1,176 @@
+.. index:: fix lambda_thermostat/apip
+
+fix lambda_thermostat/apip command
+==================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID lambda_thermostat/apip keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* lambda_thermostat/apip = style name of this fix command
+* zero or more keyword/value pairs may be appended
+* keyword = *seed* or *store_atomic_forces* or *N_rescaling*
+
+  .. parsed-literal::
+
+       *seed* value = integer
+         integer = integer that is used as seed for the random number generator (> 0)
+       *store_atomic_forces* value = nevery
+         nevery = provide per-atom output every this many steps
+       *N_rescaling* value = groupsize
+         groupsize = rescale this many neighboring atoms (> 1)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 2 all lambda_thermostat/apip
+   fix 2 all lambda_thermostat/apip N_rescaling 100
+   fix 2 all lambda_thermostat/apip seed 42
+   fix 2 all lambda_thermostat/apip seed 42 store_atomic_forces 1000
+
+Description
+"""""""""""
+
+This command applies the local thermostat described in
+:ref:`(Immel) <Immel2025_4>`
+to conserve the energy when the switching parameters of an
+:doc:`adaptive-precision interatomic potential <Howto_apip>` (APIP)
+are updated while the gradient
+of the switching parameter is neglected in the force calculation.
+
+.. warning::
+
+   The temperature change caused by this fix is only the means to the end of
+   conserving the energy. Thus, this fix is not a classical thermostat, that
+   ensures a given temperature in the system.
+   All available thermostats are listed :doc:`here <Howto_thermostat>`.
+
+The potential energy :math:`E_i` of an atom :math:`i` is given by the formula from
+:ref:`(Immel) <Immel2025_4>`
+
+.. math::
+
+   E_i = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)},
+
+whereas :math:`E_i^\text{(fast)}` is the potential energy of atom :math:`i`
+according to a fast interatomic potential like EAM,
+:math:`E_i^\text{(precise)}` is the potential energy according to a precise
+interatomic potential such as ACE and :math:`\lambda_i\in[0,1]` is the
+switching parameter that decides which potential energy is used.
+This potential energy and the corresponding forces are conservative when
+the switching parameter :math:`\lambda_i` is constant in time for all atoms
+:math:`i`.
+
+For a conservative force calculation and dynamic switching parameters,
+the atomic force on an atom is given by
+:math:`F_i = -\nabla_i \sum_j E_j` and includes the derivative of the switching
+parameter :math:`\lambda_i`.
+The force contribution of this gradient of the switching function can cause
+large forces which are not similar to the forces of the fast or the precise
+interatomic potential as discussed in :ref:`(Immel) <Immel2025_4>`.
+Thus, one can neglect the gradient of the switching parameter in the force
+calculation and compensate for the violation of energy conservation by
+the application of the local thermostat implemented in this fix.
+One can compute the violation of the energy conservation :math:`\Delta H_i`
+for all atoms :math:`i` as discussed in :ref:`(Immel) <Immel2025_4>`.
+To locally correct this energy violation :math:`\Delta H_i`, one
+can rescale the velocity of atom :math:`i`  and of neighboring atoms.
+The rescaling is done relative to the center-of-mass velocity of the
+group and, thus, conserves the momentum.
+
+.. note::
+
+   This local thermostat provides the NVE ensemble rather than the NVT
+   ensemble as
+   the energy :math:`\Delta H_i` determines the rescaling factor rather than
+   a temperature.
+
+Velocities :math:`v` are updated by the integrator according to
+:math:`\Delta v_i = (F_i/m_i)\Delta t`, whereas `m` denotes the mass of atom
+:math:`i` and :math:`\Delta t` is the time step.
+One can interpret the velocity difference :math:`\Delta v` caused by the
+rescaling as the application of an additional force which is given by
+:math:`F^\text{lt}_i = (v^\text{unscaled}_i - v^\text{rescaled}_i) m_i
+/ \Delta t` :ref:`(Immel) <Immel2025_4>`.
+This additional force is computed when the *store_atomic_forces* option
+is used.
+
+The local thermostat is not appropriate for simulations at a temperature of 0K.
+
+.. note::
+
+   The maximum decrease of the kinetic energy is achieved with a rescaling
+   factor of 0, i.e., the relative velocity of the group of rescaled atoms
+   is set to zero. One cannot decrease the energy further. Thus, the
+   local thermostat can fail, which is, however, reported by the returned
+   vector.
+
+----------
+
+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.
+
+If the *store_atomic_forces* option is used, this fix produces every
+*nevery* time steps a per-atom array that contains the theoretical force
+applied by the local thermostat in all three spatial dimensions in the first
+three components. :math:`\Delta H_i` is the fourth component of the per-atom
+array.
+The per-atom array can only be accessed on timesteps that are multiples
+of *nevery*.
+
+Furthermore, this fix computes a global vector of length 6 with
+information about the rescaling:
+
+  #. number of atoms whose energy changed due to the last :math:`\lambda` update
+  #. contribution of the potential energy to the last computed :math:`\Delta H`
+  #. contribution of the kinetic energy to the last computed :math:`\Delta H`
+  #. sum over all atoms of the absolute energy change caused by the last rescaling step
+  #. energy change that could not be compensated accumulated over all timesteps
+  #. number of atoms whose energy change could not be compensated accumulated over all timesteps
+
+The vector and the per-atom vector can be accessed 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
+""""""""""""
+
+This fix is part of the APIP 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 lambda/apip <fix_lambda_apip>`,
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
+:doc:`pair_style lambda/input/apip  <pair_lambda_input_apip>`,
+:doc:`pair_style eam/apip <pair_eam_apip>`,
+:doc:`pair_style pace/apip  <pair_pace_apip>`,
+:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
+
+Default
+"""""""
+
+seed = 42, N_rescaling = 200, *store_atomic_forces* is not used
+
+----------
+
+.. _Immel2025_4:
+
+**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

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