whitespace

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

.github/workflows/check-cpp23.yml

@@ -1,4 +1,4 @@
-# GitHub action to build LAMMPS on Linux with gcc or clang and C++23
+# GitHub action to build LAMMPS on Linux with gcc and C++23
 name: "Check for C++23 Compatibility"
 
 on:
@@ -11,19 +11,11 @@ on:
 
   workflow_dispatch:
 
-concurrency:
-  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: ${{github.event_name == 'pull_request'}}
-
 jobs:
   build:
     name: Build with C++23 support enabled
     if: ${{ github.repository == 'lammps/lammps' }}
     runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 2
-      matrix:
-        idx: [ gcc, clang ]
     env:
       CCACHE_DIR: ${{ github.workspace }}/.ccache
 
@@ -37,11 +29,8 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get install -y ccache \
-                                clang \
-                                libcurl4-openssl-dev \
                                 libeigen3-dev \
-                                libfftw3-dev \
-                                libomp-dev \
+                                libcurl4-openssl-dev \
                                 mold \
                                 mpi-default-bin \
                                 mpi-default-dev \
@@ -55,8 +44,8 @@ jobs:
       uses: actions/cache@v4
       with:
         path: ${{ env.CCACHE_DIR }}
-        key: linux-cpp23-ccache-${{ matrix.idx }}-${{ github.sha }}
-        restore-keys: linux-cpp23-ccache-${{ matrix.idx }}
+        key: linux-cpp23-ccache-${{ github.sha }}
+        restore-keys: linux-cpp23-ccache-
 
     - name: Building LAMMPS via CMake
       shell: bash
@@ -69,14 +58,14 @@ jobs:
         cmake -S cmake -B build \
               -C cmake/presets/most.cmake \
               -C cmake/presets/kokkos-openmp.cmake \
-              -C cmake/presets/${{ matrix.idx }}.cmake \
               -D CMAKE_CXX_STANDARD=23 \
+              -D CMAKE_CXX_COMPILER=g++ \
+              -D CMAKE_C_COMPILER=gcc \
               -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
               -D CMAKE_C_COMPILER_LAUNCHER=ccache \
               -D CMAKE_BUILD_TYPE=Debug \
               -D CMAKE_CXX_FLAGS_DEBUG="-Og -g" \
               -D DOWNLOAD_POTENTIALS=off \
-              -D FFT=KISS \
               -D BUILD_MPI=on \
               -D BUILD_SHARED_LIBS=on \
               -D BUILD_TOOLS=off \

cmake/CMakeLists.txt

@@ -7,10 +7,6 @@ if(CMAKE_VERSION VERSION_LESS 3.20)
   message(WARNING "LAMMPS is planning to require at least CMake version 3.20 by Summer 2025. Please upgrade!")
 endif()
 ########################################
-# initialize version variables with project command
-if(POLICY CMP0048)
-  cmake_policy(SET CMP0048 NEW)
-endif()
 # set policy to silence warnings about ignoring <PackageName>_ROOT but use it
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
@@ -31,10 +27,7 @@ endif()
 
 ########################################
 
-project(lammps
-        DESCRIPTION "The LAMMPS Molecular Dynamics Simulator"
-        HOMEPAGE_URL "https://www.lammps.org"
-        LANGUAGES CXX C)
+project(lammps CXX)
 set(SOVERSION 0)
 get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
 
@@ -138,9 +131,7 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
 endif()
 
 # silence nvcc warnings
-if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT
-    ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
-    OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")))
+if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
 endif()
 
@@ -203,10 +194,6 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
   set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
 endif()
 
-# do not include the (obsolete) MPI C++ bindings which makes for leaner object files
-# and avoids namespace conflicts. Put this early to increase its visbility.
-set(MPI_CXX_SKIP_MPICXX TRUE CACHE BOOL "Skip MPI C++ Bindings" FORCE)
-
 ########################################################################
 # User input options                                                   #
 ########################################################################
@@ -244,6 +231,15 @@ 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})
@@ -268,7 +264,6 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 set(STANDARD_PACKAGES
   ADIOS
   AMOEBA
-  APIP
   ASPHERE
   ATC
   AWPMD
@@ -382,6 +377,7 @@ if(PKG_ADIOS)
   # The search for ADIOS2 must come before MPI because
   # it includes its own MPI search with the latest FindMPI.cmake
   # script that defines the MPI::MPI_C target
+  enable_language(C)
   find_package(ADIOS2 REQUIRED)
   if(BUILD_MPI)
     if(NOT ADIOS2_HAVE_MPI)
@@ -396,18 +392,21 @@ if(PKG_ADIOS)
 endif()
 
 if(NOT CMAKE_CROSSCOMPILING)
-  find_package(MPI QUIET COMPONENTS CXX)
+  find_package(MPI QUIET)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()
   option(BUILD_MPI "Build MPI version" OFF)
 endif()
 
 if(BUILD_MPI)
+  # do not include the (obsolete) MPI C++ bindings which makes
+  # for leaner object files and avoids namespace conflicts
+  set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
     include(MPI4WIN)
   else()
-    find_package(MPI REQUIRED COMPONENTS CXX)
+    find_package(MPI REQUIRED)
     option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
     if(LAMMPS_LONGLONG_TO_LONG)
       target_compile_definitions(lammps PRIVATE -DLAMMPS_LONGLONG_TO_LONG)
@@ -468,7 +467,6 @@ 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)
@@ -535,6 +533,7 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUA
 endif()
 
 if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR PKG_RHEO OR BUILD_TOOLS)
+  enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
     find_package(BLAS)

cmake/Modules/LAMMPSInterfacePlugin.cmake

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

cmake/Modules/LAMMPSUtils.cmake

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

cmake/Modules/MPI4WIN.cmake

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

cmake/Modules/Packages/COLVARS.cmake

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

cmake/Modules/Packages/GPU.cmake

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

cmake/Modules/Packages/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/4.6.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "c8e2854ddad96378df9e9b5467638df9" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  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")
   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 4.6.01 REQUIRED CONFIG)
+  find_package(Kokkos 4.6.00 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

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

cmake/Modules/Packages/ML-PACE.cmake

@@ -53,13 +53,7 @@ else()
       add_library(yaml-cpp::yaml-cpp ALIAS yaml-cpp)
     endif()
 
-    # 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(${lib-pace} build-pace EXCLUDE_FROM_ALL)
+    add_subdirectory(${lib-pace} build-pace)
     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

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

cmake/Modules/Testing.cmake

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

cmake/Modules/Tools.cmake

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

cmake/presets/all_off.cmake

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

cmake/presets/all_on.cmake

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

cmake/presets/hip_amd.cmake

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

cmake/presets/kokkos-cuda.cmake

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

cmake/presets/kokkos-hip.cmake

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

cmake/presets/nolib.cmake

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

doc/Makefile

@@ -99,6 +99,8 @@ 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 \
@@ -160,6 +162,8 @@ 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 ;\
 	)
@@ -179,6 +183,8 @@ 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 ;\

doc/graphviz/lammps-releases.dot

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

doc/lammps.1

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

doc/src/Build.rst

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

doc/src/Build_development.rst

@@ -28,6 +28,28 @@ 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)

doc/src/Build_extras.rst

@@ -35,7 +35,6 @@ 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>`
@@ -615,9 +614,6 @@ They must be specified in uppercase.
    *  - ZEN4
       - HOST
       - AMD Zen4 architecture
-   *  - ZEN5
-      - HOST
-      - AMD Zen5 architecture
    *  - RISCV_SG2042
       - HOST
       - SG2042 (RISC-V) CPUs
@@ -672,12 +668,6 @@ 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
@@ -726,11 +716,8 @@ 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 4.6.1 of the Kokkos library.
+This list was last updated for version 4.6.0 of the Kokkos library.
 
 .. tabs::
 
@@ -1285,34 +1272,6 @@ 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_prerequisites.rst

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

doc/src/Commands_fix.rst

@@ -22,7 +22,6 @@ 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>`
@@ -30,7 +29,6 @@ OPT.
    * :doc:`ave/grid <fix_ave_grid>`
    * :doc:`ave/histo <fix_ave_histo>`
    * :doc:`ave/histo/weight <fix_ave_histo>`
-   * :doc:`ave/moments <fix_ave_moments>`
    * :doc:`ave/time <fix_ave_time>`
    * :doc:`aveforce <fix_aveforce>`
    * :doc:`balance <fix_balance>`
@@ -79,7 +77,6 @@ OPT.
    * :doc:`flow/gauss <fix_flow_gauss>`
    * :doc:`freeze (k) <fix_freeze>`
    * :doc:`gcmc <fix_gcmc>`
-   * :doc:`gjf <fix_gjf>`
    * :doc:`gld <fix_gld>`
    * :doc:`gle <fix_gle>`
    * :doc:`gravity (ko) <fix_gravity>`
@@ -92,8 +89,6 @@ OPT.
    * :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>`
@@ -221,7 +216,6 @@ OPT.
    * :doc:`rigid/small (o) <fix_rigid>`
    * :doc:`rx (k) <fix_rx>`
    * :doc:`saed/vtk <fix_saed_vtk>`
-   * :doc:`set <fix_set>`
    * :doc:`setforce (k) <fix_setforce>`
    * :doc:`setforce/spin <fix_setforce>`
    * :doc:`sgcmc <fix_sgcmc>`

doc/src/Commands_kspace.rst

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

doc/src/Commands_pair.rst

@@ -96,9 +96,7 @@ 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>`
@@ -126,9 +124,6 @@ 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>`
@@ -242,9 +237,6 @@ 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:: \
 
 ------
 
@@ -12,21 +12,10 @@ stop LAMMPS and print a suitable error message in most cases, when a
 style/command is used that has been removed or will replace the command
 with the direct alternative (if available) and print a warning.
 
-GJF formulation in fix langevin
--------------------------------
-
-.. deprecated:: 12Jun2025
-
-The *gjf* keyword in fix langevin is deprecated and will be removed
-soon.  The GJF functionality has been moved to its own fix style
-:doc:`fix gjf <fix_gjf>` and it is strongly recommended to use that
-fix instead.
-
-
 LAMMPS shell
 ------------
 
-.. deprecated:: 29Aug2024
+.. versionchanged:: 29Aug2024
 
 The LAMMPS shell has been removed from the LAMMPS distribution. Users
 are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
@@ -34,7 +23,7 @@ are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
 i-PI tool
 ---------
 
-.. deprecated:: 27Jun2024
+.. versionchanged:: 27Jun2024
 
 The i-PI tool has been removed from the LAMMPS distribution.  Instead,
 instructions to install i-PI from PyPI via pip are provided.

doc/src/Developer_plugins.rst

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

doc/src/Developer_updating.rst

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

doc/src/Errors_common.rst

@@ -1,149 +1,124 @@
-Common issues that are often regarded as bugs
-=============================================
+Common problems
+===============
 
-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 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.
 
-- 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.
+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.
 
-- 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.
+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 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.
+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.
 
-- 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.
+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.
 
-- 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.
+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/>`_.
 
-- 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/>`_.
+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.
 
-- 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.
+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):
 
-- 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):
+.. parsed-literal::
 
-  .. parsed-literal::
+   ERROR: Expected integer parameter instead of '1.0' in input script or data file
 
-     ERROR: Expected integer parameter instead of '1.0' in input script or data file
+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,
 
-- 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,
+.. note::
 
-  .. note::
+   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:
 
-     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:
+.. parsed-literal::
 
-  .. parsed-literal::
+   ERROR: Expected floating point parameter instead of 'v_name' in input script or data file
 
-     ERROR: Expected floating point parameter instead of 'v_name' in input script or data file
+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:
 
-- 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>`).
+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.
 
-- 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).
+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.
 
-- 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.
+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.

doc/src/Errors_details.rst

@@ -51,11 +51,8 @@ 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
-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,
+only when running in parallel.  That doesn't mean there is no problem,
+only the symptoms are not triggering an error quickly.  Correspondingly,
 errors may be triggered faster with more processors and thus smaller
 sub-domains.
 
@@ -162,17 +159,13 @@ angle, dihedral, or improper with just one atom in the actual
 sub-domain.  Typically, this cutoff is set to the largest cutoff from
 the :doc:`pair style(s) <pair_style>` plus the :doc:`neighbor list skin
 distance <neighbor>` and will typically be sufficient for all bonded
-interactions.  But if the pair style cutoff is small (e.g. with a
-repulsive-only Lennard-Jones potential) this may not be enough.  It is
-even worse if there is no pair style defined (or the pair style is set
-to "none"), since then there will be no ghost atoms created at all.
-
-The communication cutoff can be set or adjusted with :doc:`comm_modify
-cutoff \<value\> <comm_modify>`, but setting this too large will waste
-CPU time and memory.  LAMMPS will print warnings in these cases.  For
-bonds it uses some heuristic based on the equilibrium bond length, but
-that still may not be sufficient for cases where the force constants are
-small and thus bonds may be stretched very far.
+interactions.  But if the pair style cutoff is small, this may not be
+enough.  LAMMPS will print a warning in this case using some heuristic
+based on the equilibrium bond length, but that still may not be
+sufficient for cases where the force constants are small and thus bonds
+may be stretched very far.  The communication cutoff can be adjusted
+with :doc:`comm_modify cutoff \<value\> <comm_modify>`, but setting this
+too large will waste CPU time and memory.
 
 .. _hint09:
 
@@ -247,25 +240,6 @@ 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:
@@ -1051,15 +1025,13 @@ 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 dimensions (since LAMMPS wraps atoms back
+high density are incorrect box boundaries (since LAMMPS wraps atoms back
 into the principal box with periodic boundaries) or coordinates provided
-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.
+as fractional coordinates.  In both cases, LAMMPS cannot easily know
+whether the input geometry has such a high density (and thus requiring
+more neighbor list storage per atom) by intention.  Rather than blindly
+increasing the "one" parameter, it is thus worth checking if this is
+justified by the combination of density and cutoff.
 
 When boosting (= increasing) the "one" parameter, it is recommended to
 also increase the value for the "page" parameter to maintain the ratio

doc/src/Fortran.rst

@@ -69,11 +69,10 @@ statement.  Internally, it will call either
 :cpp:func:`lammps_open_fortran` or :cpp:func:`lammps_open_no_mpi` from
 the C library API to create the class instance.  All arguments are
 optional and :cpp:func:`lammps_mpi_init` will be called automatically
-if it is needed.  Similarly, optional calls to
-:cpp:func:`lammps_mpi_finalize`, :cpp:func:`lammps_kokkos_finalize`,
-:cpp:func:`lammps_python_finalize`, and :cpp:func:`lammps_plugin_finalize`
-are integrated into the :f:func:`close` function and triggered with the
-optional logical argument set to ``.TRUE.``. Here is a simple example:
+if it is needed.  Similarly, a possible call to
+:cpp:func:`lammps_mpi_finalize` is integrated into the :f:func:`close`
+function and triggered with the optional logical argument set to
+``.TRUE.``. Here is a simple example:
 
 .. code-block:: fortran
 
@@ -522,8 +521,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    This method will close down the LAMMPS instance through calling
    :cpp:func:`lammps_close`.  If the *finalize* argument is present and
    has a value of ``.TRUE.``, then this subroutine also calls
-   :cpp:func:`lammps_kokkos_finalize`, :cpp:func:`lammps_mpi_finalize`,
-   :cpp:func:`lammps_python_finalize`, and :cpp:func:`lammps_plugin_finalize`.
+   :cpp:func:`lammps_kokkos_finalize` and
+   :cpp:func:`lammps_mpi_finalize`.
 
    :o finalize: shut down the MPI environment of the LAMMPS
     library if ``.TRUE.``.
@@ -531,8 +530,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    :to: :cpp:func:`lammps_close`
    :to: :cpp:func:`lammps_mpi_finalize`
    :to: :cpp:func:`lammps_kokkos_finalize`
-   :to: :cpp:func:`lammps_python_finalize`
-   :to: :cpp:func:`lammps_plugin_finalize`
 
 --------
 
@@ -2099,7 +2096,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
 --------
 
-.. f:function:: create_atoms([id,] type, x, [v,] [image,] [bexpand])
+.. f:subroutine:: 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,
@@ -2128,8 +2125,6 @@ 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::
@@ -2154,18 +2149,6 @@ 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

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

doc/src/Howto_FFgeneral.rst

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

doc/src/Howto_apip.rst

@@ -1,225 +0,0 @@
-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

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

doc/src/Howto_lammps_gui.rst

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

doc/src/Howto_spc.rst

@@ -1,5 +1,5 @@
-SPC and SPC/E water model
-=========================
+SPC water model
+===============
 
 The SPC water model specifies a 3-site rigid water molecule with
 charges and Lennard-Jones parameters assigned to each of the three atoms.
@@ -8,18 +8,6 @@ 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.
 
@@ -51,9 +39,7 @@ 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.  For simplicity and speed the example uses a
-cutoff Coulomb.  Most production simulations require long-range Coulomb
-instead.
+SPC/E with rigid bonds.
 
 .. code-block:: LAMMPS
 

doc/src/Howto_thermostat.rst

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

doc/src/Howto_tip3p.rst

@@ -5,24 +5,17 @@ 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.
 
-One suitable pair style with cutoff Coulomb would for instance be:
+A suitable pair style with cutoff Coulomb would be:
 
 * :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
 
-These commands are examples for a long-range Coulomb model:
+or these commands 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
@@ -107,9 +100,7 @@ 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.  For simplicity and speed the example uses a
-cutoff Coulomb.  Most production simulations require long-range Coulomb
-instead.
+TIP3P with rigid bonds.
 
 .. code-block:: LAMMPS
 

doc/src/Howto_tip4p.rst

@@ -1,5 +1,5 @@
-TIP4P and OPC water models
-==========================
+TIP4P water model
+=================
 
 The four-point TIP4P rigid water model extends the traditional
 :doc:`three-point TIP3P <Howto_tip3p>` model by adding an additional
@@ -9,11 +9,9 @@ the oxygen along the bisector of the HOH bond angle.  A bond style of
 :doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
 <angle_harmonic>` or :doc:`charmm <angle_charmm>` should also be used.
 In case of rigid bonds also bond style :doc:`zero <bond_zero>` and angle
-style :doc:`zero <angle_zero>` can be used.  Very similar to the TIP4P
-model is the OPC water model.  It can be realized the same way as TIP4P
-but has different geometry and force field parameters.
+style :doc:`zero <angle_zero>` can be used.
 
-There are two ways to implement TIP4P-like water in LAMMPS:
+There are two ways to implement TIP4P water in LAMMPS:
 
 #. Use a specially written pair style that uses the :ref:`TIP3P geometry
    <tip3p_molecule>` without the point M. The point M location is then
@@ -23,10 +21,7 @@ There are two ways to implement TIP4P-like water in LAMMPS:
    computationally very efficient, but the charge distribution in space
    is only correct within the tip4p labeled styles.  So all other
    computations using charges will "see" the negative charge incorrectly
-   located on the oxygen atom unless they are specially written for using
-   the TIP4P geometry internally as well, e.g. :doc:`compute dipole/tip4p
-   <compute_dipole>`, :doc:`fix efield/tip4p <fix_efield>`, or
-   :doc:`kspace_style pppm/tip4p <kspace_style>`.
+   on the oxygen atom.
 
    This can be done with the following pair styles for Coulomb with a cutoff:
 
@@ -73,90 +68,77 @@ TIP4P/2005 model :ref:`(Abascal2) <Abascal2>` and a version of TIP4P
 parameters adjusted for use with a long-range Coulombic solver
 (e.g. Ewald or PPPM in LAMMPS).  Note that for implicit TIP4P models the
 OM distance is specified in the :doc:`pair_style <pair_style>` command,
-not as part of the pair coefficients. Also parameters for the OPC
-model (:ref:`Izadi <Izadi>`) are provided.
+not as part of the pair coefficients.
 
 .. list-table::
       :header-rows: 1
-      :widths: 40 12 12 14 11 11
+      :widths: 36 19 13 15 17
 
       * - Parameter
         - TIP4P (original)
         - TIP4P/Ice
         - TIP4P/2005
         - TIP4P (Ewald)
-        - OPC
       * - O mass (amu)
         - 15.9994
         - 15.9994
         - 15.9994
         - 15.9994
-        - 15.9994
       * - H mass (amu)
         - 1.008
         - 1.008
         - 1.008
         - 1.008
-        - 1.008
       * - O or M charge (:math:`e`)
         - -1.040
         - -1.1794
         - -1.1128
         - -1.04844
-        - -1.3582
       * - H charge (:math:`e`)
         - 0.520
         - 0.5897
         - 0.5564
         - 0.52422
-        - 0.6791
       * - LJ :math:`\epsilon` of OO (kcal/mole)
         - 0.1550
         - 0.21084
         - 0.1852
         - 0.16275
-        - 0.21280
       * - LJ :math:`\sigma` of OO (:math:`\AA`)
         - 3.1536
         - 3.1668
         - 3.1589
         - 3.16435
-        - 3.1660
       * - LJ :math:`\epsilon` of HH, MM, OH, OM, HM (kcal/mole)
         - 0.0
         - 0.0
         - 0.0
         - 0.0
-        - 0.0
       * - LJ :math:`\sigma` of HH, MM, OH, OM, HM (:math:`\AA`)
         - 1.0
         - 1.0
         - 1.0
         - 1.0
-        - 1.0
       * - :math:`r_0` of OH bond (:math:`\AA`)
         - 0.9572
         - 0.9572
         - 0.9572
         - 0.9572
-        - 0.8724
       * - :math:`\theta_0` of HOH angle
         - 104.52\ :math:`^{\circ}`
         - 104.52\ :math:`^{\circ}`
         - 104.52\ :math:`^{\circ}`
         - 104.52\ :math:`^{\circ}`
-        - 103.60\ :math:`^{\circ}`
       * - OM distance (:math:`\AA`)
         - 0.15
         - 0.1577
         - 0.1546
         - 0.1250
-        - 0.1594
 
-Note that the when using a TIP4P pair style, the neighbor list cutoff
+Note that the when using the TIP4P pair style, the neighbor list cutoff
 for Coulomb interactions is effectively extended by a distance 2 \* (OM
 distance), to account for the offset distance of the fictitious charges
-on O atoms in water molecules.  Thus, it is typically best in an
+on O atoms in water molecules.  Thus it is typically best in an
 efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2\*(OM
 distance), to shrink the size of the neighbor list.  This leads to
 slightly larger cost for the long-range calculation, so you can test the
@@ -167,9 +149,7 @@ 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).  For simplicity and speed the example uses a cutoff
-Coulomb.  Most production simulations require long-range Coulomb
-instead.
+file changed):
 
 .. code-block:: LAMMPS
 
@@ -212,94 +192,6 @@ instead.
     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
@@ -387,8 +279,3 @@ Phys, 79, 926 (1983).
 
 **(Abascal2)** Abascal, J Chem Phys, 123, 234505 (2005)
    https://doi.org/10.1063/1.2121687
-
-.. _Izadi:
-
-**(Izadi)** Izadi, Anandakrishnan, Onufriev, J. Phys. Chem. Lett., 5, 21, 3863 (2014)
-   https://doi.org/10.1021/jz501780a

doc/src/Howto_tip5p.rst

@@ -87,9 +87,7 @@ 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.  For simplicity and speed the
-example uses a cutoff Coulomb.  Most production simulations require
-long-range Coulomb instead.
+are removed by the rigid fix anyway:
 
 .. 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"
-  and updates are always "fast-forward" merges from *develop*
+* **release** : this branch is updated with every "feature release";
+   updates are always "fast-forward" merges from *develop*
 * **maintenance** : this branch collects back-ported bug fixes from the
   *develop* branch to the *stable* branch.  It is used to update the
   *stable* branch for "stable update releases".

doc/src/Intro_authors.rst

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

doc/src/Intro_portability.rst

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

doc/src/Library_create.rst

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

doc/src/Library_scatter.rst

@@ -27,7 +27,6 @@ It documents the following functions:
 - :cpp:func:`lammps_scatter`
 - :cpp:func:`lammps_scatter_subset`
 - :cpp:func:`lammps_create_atoms`
-- :cpp:func:`lammps_create_molecule`
 
 -----------------------
 
@@ -104,8 +103,4 @@ 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

@@ -28,7 +28,6 @@ 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>`
@@ -187,60 +186,6 @@ 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

@@ -38,11 +38,6 @@ 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

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

doc/src/Speed_compare.rst

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

doc/src/Speed_measure.rst

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

doc/src/Tools.rst

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

doc/src/atom_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    atom_style style args
 
-* 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*
+* 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*
 
   .. parsed-literal::
 
@@ -117,10 +117,6 @@ 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

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

doc/src/compute_bond_local.rst

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

doc/src/compute_dihedral_local.rst

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

doc/src/compute_msd.rst

@@ -49,6 +49,8 @@ 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
@@ -109,10 +111,7 @@ distance\ :math:`^2` :doc:`units <units>`.
 Restrictions
 """"""""""""
 
-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>`.
+Compute *msd* cannot be used with a dynamic group.
 
 Related commands
 """"""""""""""""

doc/src/compute_pair_local.rst

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

doc/src/compute_property_atom.rst

@@ -34,8 +34,6 @@ 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::
 
@@ -72,13 +70,6 @@ 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:
@@ -171,22 +162,6 @@ 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/create_atoms.rst

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

doc/src/dump_image.rst

@@ -783,109 +783,134 @@ x-component of velocity if the atom-attribute "vx" was specified.
 The basic idea of a color map is that the atom-attribute will be
 within a range of values, and that range is associated with a series
 of colors (e.g. red, blue, green).  An atom's specific value (vx =
--3.2) can then mapped to the series of colors (e.g. halfway between
-red and blue), and a specific color is determined via an interpolation
-procedure.
+-3.2) can then be mapped to a specific color.  The details of the
+mapping procedure depend on the *style* of the color map, as explained
+below.
 
-There are many possible options for the color map, enabled by the
-*amap* keyword.  Here are the details.
+There are many possible options for defining a color map, enabled by
+the *amap* keyword.  Here are the details.
 
 The *lo* and *hi* settings determine the range of values allowed for
 the atom attribute.  If numeric values are used for *lo* and/or *hi*,
-then values that are lower/higher than that value are set to the
-value.  I.e. the range is static.  If *lo* is specified as *min* or
-*hi* as *max* then the range is dynamic, and the lower and/or
-upper bound will be calculated each time an image is drawn, based
-on the set of atoms being visualized.
+then individual atom values which are lower/higher than lo/hi are set
+to lo/hi for purposes of determining the atom's color.  I.e. the range
+is static.  If *lo* is specified as *min* or *hi* as *max* then the
+range is dynamic.  The lower and/or upper bound will be calculated
+each time an image is drawn, based on the current atom values of all
+the atoms being visualized.
 
 The *style* setting is two letters, such as "ca".  The first letter is
 either "c" for continuous, "d" for discrete, or "s" for sequential.
 The second letter is either "a" for absolute, or "f" for fractional.
 
-A continuous color map is one in which the color changes continuously
-from value to value within the range.  A discrete color map is one in
-which discrete colors are assigned to sub-ranges of values within the
-range.  A sequential color map is one in which discrete colors are
-assigned to a sequence of sub-ranges of values covering the entire
-range.
+A *continuous* color map is one in which the color of an atom changes
+continuously as its attribute value increases within the range.
+Colors are assigned to specific values within the range; an atom with
+an attribue value between two adjacent specific values is assigned a
+color interpolated between the two adjacent colors.
 
-An absolute color map is one in which the values to which colors are
-assigned are specified explicitly as values within the range.  A
-fractional color map is one in which the values to which colors are
-assigned are specified as a fractional portion of the range.  For
-example if the range is from -10.0 to 10.0, and the color red is to be
-assigned to atoms with a value of 5.0, then for an absolute color map
-the number 5.0 would be used.  But for a fractional map, the number
-0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.
+A *discrete* color map is one in which discrete colors are assigned to
+sub-ranges of values within the overall range.  Each sub-range can be
+of variable width and overlap with other sub-ranges.  An atom with an
+attribute value is mapped to one of the sub-ranges and assigned that
+color.
+
+A *sequential* color map is similar to a discrete color map except that
+all sub-ranges are of equal width and discrete colors are assigned to
+each sub-range in a round-robin fashion until the overall range is
+covered from *lo* to *hi*.
+
+An *absolute* color map is one in which the numeric settings
+associated with assigned colors are specified explicitly as values
+within the range.
+
+A *fractional* color map is one in which the numeric settings
+associated with assigned colors are specified as a fractional position
+within the range.
+
+For a continuous color map, the numeric settings are the specific
+values each color is assigned to.  For a discrete color map, the
+numeric settings are the bounds of each sub-range.  For a sequential
+color map, the numeric settings is the width of all the sub-ranges.
+For example if the overall range is from -10.0 to 10.0, and the color
+red is to be assigned to atoms with an attribute value of 5.0, then
+for an absolute color map the numeric value of 5.0 should map to red.
+But for a fractional map, the numeric value of 0.75 should map to red,
+since 5.0 is 3/4 of the way from -10.0 to 10.0.
 
 The *delta* setting must be specified for all styles, but is only used
-for the sequential style; otherwise the value is ignored.  It
-specifies the bin size to use within the range for assigning
-consecutive colors to.  For example, if the range is from :math:`-10.0` to
-:math:`10.0` and a *delta* of :math:`1.0` is used, then 20 colors will be
-assigned to the range.  The first will be from
-:math:`-10.0 \le \text{color1} < -9.0`, then second from
+for the *sequential* style; otherwise the setting is ignored.  It
+specifies the bin size of the sub-ranges of values described above,
+For example, if the overall range is from :math:`-10.0` to
+:math:`10.0` and a *delta* of :math:`1.0` is used, then 20 colors will
+be assigned to a series of sub-ranges.  The first sub-range will be
+from :math:`-10.0 \le \text{color1} < -9.0`, the second from
 :math:`-9.0 \le color2 < -8.0`, etc.
 
-The *N* setting is how many entries follow.  The format of the entries
-depends on whether the color map style is continuous, discrete or
-sequential.  In all cases the *color* setting can be any of the 140
-pre-defined colors (see below) or a color name defined by the
-dump_modify color option.
+The *N* setting is how many color entries follow.  The format of each
+color entry depends on whether the color map style is continuous,
+discrete, or sequential.  For each entry, the specified *color* can be
+any of the 140 pre-defined colors (see below) or a color name defined
+by the dump_modify color option.
 
-For continuous color maps, each entry has a *value* and a *color*\ .
-The *value* is either a number within the range of values or *min* or
-*max*\ .  The *value* of the first entry must be *min* and the *value*
-of the last entry must be *max*\ .  Any entries in between must have
-increasing values.  Note that numeric values can be specified either
-as absolute numbers or as fractions (0.0 to 1.0) of the range,
-depending on the "a" or "f" in the style setting for the color map.
+For *continuous* color maps, each entry has a *value* and a *color*\ .
+The *value* is either a number within the *lo/hi* range of values or
+*min* or *max*\ .  The *value* for the first entry must be *min* and
+the *value* for the last entry must be *max*\ .  In-between entries
+must have increasing numeric values.  There must be 2 or more entries.
+Note that numeric values are specified either as absolute numbers or
+as fractions (0.0 to 1.0) of the range, depending on the "a" or "f" in
+the style setting for the color map.
 
-Here is how the entries are used to determine the color of an individual
-atom, given the value :math:`X` of its atom attribute.  :math:`X` will
-fall between 2 of the entry values.  The color of the atom is linearly
-interpolated (in each of the RGB values) between the 2 colors associated
-with those entries.  For example, if :math:`X = -5.0` and the two
-surrounding entries are "red" at :math:`-10.0` and "blue" at
-:math:`0.0`, then the atom's color will be halfway between "red" and
-"blue", which happens to be "purple".
+Here is how the *N* entries are used to determine the color of an
+individual atom, based on the value :math:`X` of its atom attribute.
+:math:`X` will fall between 2 of the entry values.  The color of the
+atom is linearly interpolated (in each of the RGB values) between the
+2 colors associated with those entries.  For example, if :math:`X =
+-5.0` and the two surrounding entries are "red" at :math:`-10.0` and
+"blue" at :math:`0.0`, then the atom's color will be halfway between
+"red" and "blue", which in this case is "purple".
 
-For discrete color maps, each entry has a *lo* and *hi* value and a
+For *discrete* color maps, each entry has a *lo* and *hi* value and a
 *color*\ .  The *lo* and *hi* settings are either numbers within the
-range of values or *lo* can be *min* or *hi* can be *max*\ .  The *lo*
-and *hi* settings of the last entry must be *min* and *max*\ .  Other
+range of values or *min* (for *lo) or *max* (for *hi*).  The *lo* and
+*hi* settings of the last entry must be *min* and *max*\ .  Other
 entries can have any *lo* and *hi* values and the sub-ranges of
-different values can overlap.  Note that numeric *lo* and *hi* values
-can be specified either as absolute numbers or as fractions (0.0 to 1.0)
-of the range, depending on the "a" or "f" in the style setting for the
-color map.
+different entries can overlap.  There must be one or more entries.
+Note that numeric *lo* and *hi* values are specified either as
+absolute numbers or as fractions (0.0 to 1.0) of the range, depending
+on the "a" or "f" in the style setting for the color map.  The lo/hi
+values in each sub-range must satisfy lo < hi.
 
-Here is how the entries are used to determine the color of an individual
-atom, given the value X of its atom attribute.  The entries are scanned
-from first to last.  The first time that *lo* <= X <= *hi*, X is
-assigned the color associated with that entry.  You can think of the
-last entry as assigning a default color (since it will always be matched
-by X), and the earlier entries as colors that override the default.
-Also note that no interpolation of a color RGB is done.  All atoms will
-be drawn with one of the colors in the list of entries.
+Here is how the *N* entries are used to determine the color of an
+individual atom, based on the value :math:`X` of its atom attribute.
+The entries are scanned from first to last.  The first time that *lo*
+<= X <= *hi*, X is assigned the color associated with that entry.
+This means can the last entry can be thought of as a default color
+(since it will always be matched by X); the earlier entries override
+the default.  Note that for a *discrete* map, no interpolation of a
+color RGB values is done.  All atoms will be drawn with one of the
+colors in the list of entries.
 
-For sequential color maps, each entry has only a *color*\ .  Here is how
-the entries are used to determine the color of an individual atom,
-given the value X of its atom attribute.  The range is partitioned
-into N bins of width *binsize*\ .  Thus X will fall in a specific bin
-from 1 to N, say the Mth bin.  If it falls on a boundary between 2
-bins, it is considered to be in the higher of the 2 bins.  Each bin is
-assigned a color from the E entries.  If E < N, then the colors are
-repeated.  For example if 2 entries with colors red and green are
-specified, then the odd numbered bins will be red and the even bins
-green.  The color of the atom is the color of its bin.  Note that the
-sequential color map is really a shorthand way of defining a discrete
-color map without having to specify where all the bin boundaries are.
+For *sequential* color maps, each entry has only a *color*\ .  There
+must be 1 or more entries.  Here is how the *N* entries are used to
+determine the color of an individual atom, given the value X of its
+atom attribute.  The range is overlaid with M bins of width *delta*\ ,
+the last of which may extend beyond the *hi* boundary of the range.
+Thus X will fall in a specific bin from 1 to M.  If it falls on a
+boundary between 2 bins, it is considered to be in the higher of the 2
+bins (except in the case of 2 bins whose boundary is the *hi*
+boundary, it is considered to be in the lower of the 2 bins).  Each of
+the M bins is assigned a color from the *N* entries.  If M < *N*, then
+the colors are repeated in a round-robin fashion.  For example if 2
+entries with colors red and green are specified, then the odd numbered
+bins will be red and the even bins green.  An atom's color is the
+color of its bin.
 
 Here is an example of using a sequential color map to color all the
-atoms in individual molecules with a different color.  See the
-examples/pour/in.pour.2d.molecule input script for an example of how
-this is used.
+atoms in individual molecules with a different color based on its
+molecule ID.  See the examples/pour/in.pour.2d.molecule input script
+for an example of how this is used.
 
 .. code-block:: LAMMPS
 
@@ -897,8 +922,9 @@ this is used.
                    zoom 1.6 adiam 1.5
    dump_modify     1 pad 5 amap 0 10 sa 1 10 ${colors}
 
-In this case, 10 colors are defined, and molecule IDs are
-mapped to one of the colors, even if there are 1000s of molecules.
+In this case, the sequential color map has 10 color entries, and
+molecule IDs are mapped to one of the colors, even if there are 1000s
+of molecules.
 
 ----------
 

doc/src/fix.rst

@@ -201,7 +201,6 @@ 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
@@ -209,7 +208,6 @@ accelerated styles exist.
 * :doc:`ave/grid <fix_ave_grid>` - compute per-grid time-averaged quantities
 * :doc:`ave/histo <fix_ave_histo>` - compute/output time-averaged histograms
 * :doc:`ave/histo/weight <fix_ave_histo>` - weighted version of fix ave/histo
-* :doc:`ave/moments <fix_ave_moments>` - compute moments of scalar quantities
 * :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
 * :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
 * :doc:`balance <fix_balance>` - perform dynamic load-balancing
@@ -258,7 +256,6 @@ accelerated styles exist.
 * :doc:`flow/gauss <fix_flow_gauss>` - Gaussian dynamics for constant mass flux
 * :doc:`freeze <fix_freeze>` - freeze atoms in a granular simulation
 * :doc:`gcmc <fix_gcmc>` - grand canonical insertions/deletions
-* :doc:`gjf <fix_gjf>` - statistically correct Langevin temperature control using the GJ methods
 * :doc:`gld <fix_gld>` - generalized Langevin dynamics integrator
 * :doc:`gle <fix_gle>` - generalized Langevin equation thermostat
 * :doc:`gravity <fix_gravity>` - add gravity to atoms in a granular simulation
@@ -271,7 +268,6 @@ accelerated styles exist.
 * :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
@@ -280,7 +276,6 @@ 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)
@@ -400,7 +395,6 @@ accelerated styles exist.
 * :doc:`rigid/small <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NVE integration
 * :doc:`rx <fix_rx>` - solve reaction kinetic ODEs for a defined reaction set
 * :doc:`saed/vtk <fix_saed_vtk>` - time-average the intensities from :doc:`compute saed <compute_saed>`
-* :doc:`set <fix_set>` - reset an atom property via an atom-style variable every N steps
 * :doc:`setforce <fix_setforce>` - set the force on each atom
 * :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
 * :doc:`sgcmc <fix_sgcmc>` - fix for hybrid semi-grand canonical MD/MC simulations

doc/src/fix_adapt.rst

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

doc/src/fix_atom_weight_apip.rst

@@ -1,143 +0,0 @@
-.. 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

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

doc/src/fix_ave_moments.rst

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

doc/src/fix_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* or *molecule*
+* keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype* or *aconstrain*
 
   .. parsed-literal::
 
@@ -43,10 +43,6 @@ 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
 """"""""
@@ -56,7 +52,6 @@ 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
@@ -128,8 +123,6 @@ 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

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

doc/src/fix_deform.rst

@@ -298,8 +298,7 @@ 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. The exception
-would be if the run command uses the *pre no* option.
+future times, or a value < 0.0 to compress the box.
 
 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

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

doc/src/fix_gjf.rst

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

doc/src/fix_lambda_apip.rst

@@ -1,262 +0,0 @@
-.. 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

@@ -1,176 +0,0 @@
-.. 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:`(Bruenger) <Bruenger1>`
+Apply a Langevin thermostat as described in :ref:`(Schneider) <Schneider1>`
 to a group of atoms which models an interaction with a background
 implicit solvent.  Used with :doc:`fix nve <fix_nve>`, this command
 performs Brownian dynamics (BD), since the total force on each atom
@@ -241,13 +241,6 @@ to zero by subtracting off an equal part of it from each atom in the
 group.  As a result, the center-of-mass of a system with zero initial
 momentum will not drift over time.
 
-.. deprecated:: TDB
-
-The *gjf* keyword in fix langevin is deprecated and will be removed
-soon.  The GJF functionality has been moved to its own fix style
-:doc:`fix gjf <fix_gjf>` and it is strongly recommended to use that
-fix instead.
-
 The keyword *gjf* can be used to run the :ref:`Gronbech-Jensen/Farago
 <Gronbech-Jensen>` time-discretization of the Langevin model.  As
 described in the papers cited below, the purpose of this method is to
@@ -331,16 +324,14 @@ types, tally = no, zero = no, gjf = no.
 
 ----------
 
-.. _Bruenger1:
-
-**(Bruenger)** Bruenger, Brooks, and Karplus, Chem. Phys. Lett. 105, 495 (1982).
-[Previously attributed to Schneider and Stoll, Phys. Rev. B 17, 1302 (1978).
-Implementation remains unchanged.]
-
 .. _Dunweg1:
 
 **(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
 
+.. _Schneider1:
+
+**(Schneider)** Schneider and Stoll, Phys Rev B, 17, 1302 (1978).
+
 .. _Gronbech-Jensen:
 
 **(Gronbech-Jensen)** Gronbech-Jensen and Farago, Mol Phys, 111, 983

doc/src/fix_qeq_rel_reaxff.rst

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

doc/src/fix_qtpie_reaxff.rst

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

doc/src/fix_set.rst

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

doc/src/kspace_style.rst

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

doc/src/molecule.rst

@@ -34,7 +34,7 @@ Syntax
        *ioff* value = Ioff
          Ioff = offset to add to improper types
        *scale* value = sfactor
-         sfactor = scale factor to apply to the size, mass, and dipole of the molecule
+         sfactor = scale factor to apply to the size and mass of the molecule
 
 Examples
 """"""""
@@ -42,7 +42,6 @@ Examples
 .. code-block:: LAMMPS
 
    molecule 1 mymol.txt
-   molecule water tip3p.json
    molecule 1 co2.txt h2o.txt
    molecule CO2 co2.txt boff 3 aoff 2
    molecule 1 mymol.txt offset 6 9 18 23 14
@@ -66,7 +65,7 @@ templates include:
 * :doc:`atom_style template <atom_style>`
 
 The ID of a molecule template can only contain alphanumeric characters
-and underscores, same as other IDs in LAMMPS.
+and underscores.
 
 A single template can contain multiple molecules, listed one per file.
 Some of the commands listed above currently use only the first
@@ -75,13 +74,6 @@ contains multiple molecules.  The :doc:`atom_style template
 <atom_style>` command allows multiple-molecule templates to define a
 system with more than one templated molecule.
 
-The molecule file can be either in a *native* format or in `JSON format
-<https://www.json.org/>`_.  JSON formal filenames **must** have the
-extension ".json".  Files with any other name will be assumed to be in
-the "native" format.  The details of the two formats are described
-below.  When referencing multiple molecule files in a single *molecule*
-command, each of those files may be either format.
-
 Each filename can be followed by optional keywords which are applied
 only to the molecule in the file as used in this template.  This is to
 make it easy to use the same molecule file in different molecule
@@ -103,45 +95,40 @@ use that attribute (e.g. no bonds).
    labels will determine the actual types directly depending on the
    current :doc:`labelmap <labelmap>` settings.
 
-The *scale* keyword scales the size of the molecule.  This can be useful
-for modeling polydisperse granular rigid bodies.  The scale factor is
-applied to each of these properties in the molecule file, if they are
-defined: the individual particle coordinates (Coords or "coords"
-section), the individual mass of each particle (Masses or "masses"
-section), the individual diameters of each particle (Diameters or
-"diameters" section), the per-atom dipoles (Dipoles or "dipoles"
-section) the total mass of the molecule (header keyword = mass), the
-center-of-mass of the molecule (header keyword = com), and the moments
-of inertia of the molecule (header keyword = inertia).
+The *scale* keyword scales the size of the molecule.  This can be
+useful for modeling polydisperse granular rigid bodies.  The scale
+factor is applied to each of these properties in the molecule file, if
+they are defined: the individual particle coordinates (Coords
+section), the individual mass of each particle (Masses section), the
+individual diameters of each particle (Diameters section), the total
+mass of the molecule (header keyword = mass), the center-of-mass of
+the molecule (header keyword = com), and the moments of inertia of the
+molecule (header keyword = inertia).
 
 .. note::
 
    The molecule command can be used to define molecules with bonds,
-   angles, dihedrals, impropers, and special bond lists of neighbors
+   angles, dihedrals, impropers, or special bond lists of neighbors
    within a molecular topology, so that you can later add the molecules
    to your simulation, via one or more of the commands listed above.
-   Since this topology-related information requires that suitable
-   storage is reserved when LAMMPS creates the simulation box (e.g. when
-   using the :doc:`create_box <create_box>` command or the
-   :doc:`read_data <read_data>` command) suitable space has to be
-   reserved at that step so you do not overflow those pre-allocated data
-   structures when adding molecules later.  Both the :doc:`create_box
-   <create_box>` command and the :doc:`read_data <read_data>` command
-   have "extra" options which ensure extra space is allocated for
-   storing topology info for molecules that are added later.  This
-   feature is *not* available for the :doc:`read_restart command
-   <read_restart>`, thus binary restart files need to be converted
-   to data files first.
+   Since this topology-related information requires that suitable storage
+   is reserved when LAMMPS creates the simulation box (e.g. when using
+   the :doc:`create_box <create_box>` command or the
+   :doc:`read_data <read_data>` command) suitable space has to be reserved
+   so you do not overflow those pre-allocated data structures when adding
+   molecules later.  Both the :doc:`create_box <create_box>` command and
+   the :doc:`read_data <read_data>` command have "extra" options which
+   ensure space is allocated for storing topology info for molecules that
+   are added later.
 
 ----------
 
-Format of a native molecule file
-""""""""""""""""""""""""""""""""
+Format of a molecule file
+"""""""""""""""""""""""""
 
-The format of an "native" individual molecule file looks similar but is
-*different* from that of a data file read by the :doc:`read_data
-<read_data>` commands.  Here is a simple example for a TIP3P water
-molecule:
+The format of an individual molecule file looks similar but is
+different than that of a data file read by the :doc:`read_data <read_data>`
+commands.  Here is a simple example for a TIP3P water molecule:
 
 .. code-block::
 
@@ -209,7 +196,7 @@ defining a *body* particle, which requires setting the number of
 
 .. list-table::
       :header-rows: 1
-      :widths: 21 12 47 20
+      :widths: 20 13 42 15
 
       * - Number(s)
         - Keyword
@@ -218,7 +205,7 @@ defining a *body* particle, which requires setting the number of
       * - N
         - atoms
         - # of atoms N in molecule
-        - keyword is *required*
+        - 0
       * - Nb
         - bonds
         - # of bonds Nb in molecule
@@ -241,8 +228,8 @@ defining a *body* particle, which requires setting the number of
         - 0
       * - Ninteger Ndouble
         - body
-        - # of integer and floating-point values in :doc:`body particle <Howto_body>`
-        - 0 0
+        - # of integer and floating-point values in body particle
+        - 0
       * - Mtotal
         - mass
         - total mass of molecule
@@ -682,343 +669,6 @@ the file format.
 
 ----------
 
-Format of a JSON molecule file
-""""""""""""""""""""""""""""""
-
-.. versionadded:: 12Jun2025
-
-The format of a JSON format individual molecule file must follow the
-`JSON format <https://www.json.org/>`_, which evolved from the
-JavaScript programming language as a programming-language-neutral data
-interchange language.  The JSON syntax is independent of its content,
-and thus the data in the file must follow suitable conventions to be
-correctly processed.  LAMMPS provides a `JSON schema file
-<https://json-schema.org/>`_ for JSON format molecule files in the
-:ref:`tools/json folder <json>` to represent those conventions.  Using
-the schema file any JSON format molecule files can be validated.  Please
-note that the format requirement for JSON are very strict and the JSON
-reader in LAMMPS does not accept files with extensions like comments.
-Validating a particular JSON format molecule file against this schema
-ensures that both, the JSON syntax requirement *and* the LAMMPS
-conventions for molecule template files are followed.  LAMMPS should be
-able to read and parse any JSON file that passes the schema check.  This
-is a formal check only and thus it **cannot** check whether the file
-contents are consistent or physically meaningful.
-
-Here is a simple example for the same TIP3P water molecule from above in
-JSON format and also using :doc:`type labels <labelmap>` instead of
-numeric types:
-
-.. code-block:: json
-
-   {
-       "application": "LAMMPS",
-       "format": "molecule",
-       "revision": 1,
-       "title": "Water molecule. TIP3P geometry",
-       "schema": "https://download.lammps.org/json/molecule-schema.json",
-       "units": "real",
-       "coords": {
-           "format": ["atom-id", "x", "y", "z"],
-           "data": [
-               [1,  0.00000, -0.06556,  0.00000],
-               [2,  0.75695,  0.52032,  0.00000],
-               [3, -0.75695,  0.52032,  0.00000]
-           ]
-       },
-       "types": {
-           "format": ["atom-id", "type"],
-           "data": [
-               [1,  "OW"],
-               [2,  "HO1"],
-               [3,  "HO1"]
-           ]
-       },
-       "charges": {
-           "format": ["atom-id", "charge"],
-           "data": [
-               [1, -0.834],
-               [2,  0.417],
-               [3,  0.417]
-           ]
-       },
-       "bonds": {
-           "format": ["bond-type", "atom1", "atom2"],
-           "data": [
-               ["OW-HO1",  1,  2],
-               ["OW-HO1",  1,  3]
-           ]
-       },
-       "angles": {
-           "format": ["angle-type", "atom1", "atom2", "atom3"],
-           "data": [
-               ["HO1-OW-HO1",  2,  1,  3]
-           ]
-       }
-   }
-
-Unlike with the native molecule file format, there are no header or body
-sections, just a list of keywords with associated data.  JSON format
-data is read, parsed, and stored in an internal dictionary data
-structure in one step and thus the order of keywords is not relevant.
-
-Data for keywords is either provided directly following the keyword or
-as a *data block*.  A *data block* is a list that has to include two
-keywords, "format" and "data", where the former lists keywords of the
-properties that are stored in the columns of the "data" lists.  The
-names and order of entries in the "format" list (and thus how the data
-is interpreted) are currently fixed.
-
-Since the length of the various lists can be easily obtained from the
-internal data structure, several header keywords of the "native" molecule
-file are not needed.  On the other hand, some additional keywords are
-required to identify the conventions applied to the generic JSON file
-format.  The structure of the data itself mostly follows what is used
-for the "native" molecule file format.
-
-.. list-table::
-   :header-rows: 1
-
-   * - Keyword
-     - Argument(s)
-     - Required
-     - Description
-   * - application
-     - "LAMMPS"
-     - yes
-     - indicates a LAMMPS JSON file; files from other applications may be accepted in the future
-   * - format
-     - "molecule"
-     - yes
-     - indicates a molecule template file
-   * - revision
-     - an integer
-     - yes
-     - currently 1, to facility backward compatibility on changes to the conventions
-   * - title
-     - a string
-     - no
-     - information about the template which will echoed to the screen and log
-   * - schema
-     - URL as string
-     - no
-     - location of a JSON schema file for validating the molecule file format
-   * - units
-     - a string
-     - no
-     - indicates :doc:`units settings <units>` for this molecule template
-   * - com
-     - list with 3 doubles
-     - no
-     - overrides the auto-computed center-of-mass for the template
-   * - masstotal
-     - double
-     - no
-     - overrides the auto-computed total mass for the template
-   * - inertia
-     - list with 6 doubles
-     - no
-     - overrides the auto-computed moments of inertia
-   * - coords
-     - a data block
-     - no
-     - contains atom positions with the format "atom-id", "x", "y", "z" (same as Coords)
-   * - types
-     - a data block
-     - yes
-     - assigns atom types to atoms with the format "atom-id", "type" (same as Types)
-   * - molecule
-     - a data block
-     - no
-     - assigns molecule-IDs to atoms with the format "atom-id", "molecule-id" (same as Molecules)
-   * - fragments
-     - a data block
-     - no
-     - assigns atom-ids to fragment-IDs with the format "fragment-id", "atom-id-list" (same as Fragments)
-   * - charges
-     - a data block
-     - no
-     - assigns charges to atoms with the format "atom-id", "charge" (same as Charges)
-   * - dipoles
-     - a data block
-     - no
-     - assigns point dipoles to atoms with the format "atom-id", "mux", "muy", "muz" (same as Dipoles)
-   * - diameters
-     - a data block
-     - no
-     - assigns diameters to atoms with the format "atom-id", "diameter" (same as Diameters)
-   * - masses
-     - a data block
-     - no
-     - assigns per-atom masses to atoms with the format "atom-id", "mass" (same as Masses)
-   * - bonds
-     - a data block
-     - no
-     - defines bonds in the molecule template with the format "bond-type", "atom1", "atom2" (same as Bonds without bond-ID)
-   * - angles
-     - a data block
-     - no
-     - defines angles in the molecule template with the format "angle-type", "atom1", "atom2", "atom3" (same as Angles without angle-ID)
-   * - dihedrals
-     - a data block
-     - no
-     - defines dihedrals in the molecule template with the format "dihedral-type", "atom1", "atom2", "atom3", "atom4" (same as Dihedrals without dihedral-ID)
-   * - impropers
-     - a data block
-     - no
-     - defines impropers in the molecule template with the format "improper-type", "atom1", "atom2", "atom3", "atom4" (same as Impropers without improper-ID)
-   * - shake
-     - 3 JSON objects
-     - no
-     - contains the sub-sections "flags", "atoms", "bonds" described below
-   * - special
-     - 2 JSON objects
-     - no
-     - contains the sub-sections "counts" and "bonds" described below
-   * - body
-     - 2 JSON objects
-     - no
-     - contains the "integers" and "doubles" sub-sections with arrays with the same data as Body Integers and Body Doubles, respectively
-
-The following table describes the sub-sections for the "special" entry from above:
-
-.. list-table::
-   :header-rows: 1
-
-   * - Subsection
-     - Argument(s)
-     - Required
-     - Description
-   * - counts
-     - a data block
-     - yes
-     - contains the counts of 1-2, 1-3, and 1-4 special neighbors with the format "atom-id", "n12", "n13", "n14" (same as Special Bond Counts)
-   * - bonds
-     - a data block
-     - yes
-     - contains the lists of special neighbors to atoms with the format "atom-id", "atom-id-list" (same as Special Bonds)
-
-The following table describes the sub-sections for the "shake" entry from above:
-
-.. list-table::
-   :header-rows: 1
-
-   * - Subsection
-     - Argument(s)
-     - Required
-     - Description
-   * - flags
-     - a data block
-     - yes
-     - contains the counts shake flags for atoms with the format "atom-id", "flag" (same as Shake Flags)
-   * - atoms
-     - a data block
-     - yes
-     - contains the lists of shake cluster atom-ids for atoms with the format "atom-id", "atom-id-list" (same as Shake Atoms)
-   * - bonds
-     - a data block
-     - yes
-     - contains the lists of shake bond or angle types for atoms with the format "atom-id", "type-list" (same as Shake Bonds)
-
-The "special" and "shake" sections are usually not needed, since the
-data can be auto-generated as soon as the simulation box is defined.
-Below is an example for what would have to be *added* to the example
-JSON file above in case the molecule command needs to be issued earlier.
-
-.. code-block:: json
-
-   "special": {
-       "counts": {
-           "format": ["atom-id", "n12", "n13", "n14"],
-           "data": [
-               [1, 2, 0, 0],
-               [2, 1, 1, 0],
-               [3, 1, 1, 0]
-           ]
-       },
-       "bonds": {
-           "format": ["atom-id", "atom-id-list"],
-           "data": [
-               [1,  [2, 3]],
-               [2,  [1, 3]],
-               [3,  [1, 2]]
-           ]
-       }
-   },
-   "shake": {
-       "flags": {
-           "format": ["atom-id", "flag"],
-           "data": [
-               [1, 1],
-               [2, 1],
-               [3, 1]
-           ]
-       },
-       "atoms": {
-           "format": ["atom-id", "atom-id-list"],
-           "data": [
-               [1,  [1, 2, 3]],
-               [2,  [1, 2, 3]],
-               [3,  [1, 2, 3]]
-           ]
-       },
-       "types": {
-           "format": ["atom-id", "type-list"],
-           "data": [
-               [1,  ["OW-HO1",  "OW-HO1", "HO1-OW-HO1"]],
-               [2,  ["OW-HO1",  "OW-HO1", "HO1-OW-HO1"]],
-               [3,  ["OW-HO1",  "OW-HO1", "HO1-OW-HO1"]]
-           ]
-       }
-   }
-
-
-Below is a minimal example of a JSON format molecule template for a body
-particle for :doc:`pair style body/nparticle
-<pair_body_nparticle>`. Molecule templates for body particles must
-contain only one atom:
-
-.. code-block:: json
-
-   {
-       "application": "LAMMPS",
-       "format": "molecule",
-       "revision": 1,
-       "title": "Square body for body/nparticles",
-       "schema": "https://download.lammps.org/json/molecule-schema.json",
-       "units": "real",
-       "coords": {
-           "format": ["atom-id", "x", "y", "z"],
-           "data": [
-               [1,  0.00000,  0.00000,  0.00000]
-           ]
-       },
-       "types": {
-           "format": ["atom-id", "type"],
-           "data": [
-               [1,  1]
-           ]
-       },
-       "masses": {
-           "format": ["atom-id", "mass"],
-           "data": [
-               [1,  1.0]
-           ]
-       },
-       "body": {
-           "integers": [4],
-           "doubles": [
-               1.0, 1.0, 4.0, 0.0, 0.0, 0.0,
-               -0.70710678118654752440, -0.70710678118654752440, 0.0,
-               -0.70710678118654752440,  0.70710678118654752440, 0.0,
-               0.70710678118654752440,  0.70710678118654752440, 0.0,
-               0.70710678118654752440, -0.70710678118654752440, 0.0
-           ]
-       }
-   }
-
-----------
-
 Restrictions
 """"""""""""
 

doc/src/pair_eam_apip.rst

@@ -1,127 +0,0 @@
-.. index:: pair_style eam/apip
-.. index:: pair_style eam/fs/apip
-
-pair_style eam/apip command
-=============================
-
-Constant precision variant: *eam*
-
-pair_style eam/fs/apip command
-================================
-
-Constant precision variant: *eam/fs*
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   pair_style eam/apip
-   pair_style eam/fs/apip
-
-Examples
-""""""""
-
-.. 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
-
-
-Description
-"""""""""""
-Style *eam* computes pairwise interactions for metals and metal alloys
-using embedded-atom method (EAM) potentials :ref:`(Daw) <Daw2>`.  The total
-energy :math:`E_i` of an atom :math:`i` is given by
-
-.. math::
-
-   E_i^\text{EAM} = F_\alpha \left(\sum_{j \neq i}\ \rho_\beta (r_{ij})\right) +
-         \frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij})
-
-where :math:`F` is the embedding energy which is a function of the atomic
-electron density :math:`\rho`, :math:`\phi` is a pair potential interaction,
-and :math:`\alpha` and :math:`\beta` are the element types of atoms
-:math:`i` and :math:`j`.  The multi-body nature of the EAM potential is a
-result of the embedding energy term. Both summations in the formula are over
-all neighbors :math:`j` of atom :math:`i` within the cutoff distance.
-EAM is documented in detail in :doc:`pair_style eam <pair_eam>`.
-
-The potential energy :math:`E_i` of an atom :math:`i` of an adaptive-precision
-interatomic potential (APIP) according to :ref:`(Immel) <Immel2025_5>` is given by
-
-.. math::
-
-   E_i^\text{APIP} = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)}\,,
-
-whereas the switching parameter :math:`\lambda_i` is computed
-dynamically during a simulation by :doc:`fix lambda/apip <fix_lambda_apip>`
-or set prior to a simulation via :doc:`set <set>`.
-
-The pair style *eam/fs/apip* computes the potential energy
-:math:`\lambda_i E_i^\text{EAM}` and the
-corresponding force and should be combined
-with a precise potential like
-:doc:`pair_style pace/precise/apip <pair_pace_apip>` that computes the
-potential energy :math:`(1-\lambda_i) E_i^\text{(precise)}` and the
-corresponding force via :doc:`pair_style hybrid/overlay <pair_hybrid>`.
-
-Mixing, shift, table, tail correction, restart, rRESPA info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-For atom type pairs I,J and I != J, where types I and J correspond to
-two different element types, mixing is performed by LAMMPS as
-described above with the individual styles.  You never need to specify
-a pair_coeff command with I != J arguments for the eam/apip styles.
-
-This pair style does not support the :doc:`pair_modify <pair_modify>`
-shift, table, and tail options.
-
-The eam/apip pair styles do not write their information to :doc:`binary
-restart files <restart>`, since it is stored in tabulated potential
-files.  Thus, you need to re-specify the pair_style and pair_coeff
-commands in an input script that reads a restart file.
-
-The eam/apip pair styles can only be used via the *pair* keyword of the
-:doc:`run_style respa <run_style>` command.  They do not support the
-*inner*, *middle*, *outer* keywords.
-
-----------
-
-Restrictions
-""""""""""""
-
-This pair styles are 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 eam  <pair_eam>`,
-:doc:`pair_style hybrid/overlay <pair_hybrid>`,
-: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 pace/apip <pair_pace_apip>`,
-:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
-
-Default
-"""""""
-
-none
-
-----------
-
-.. _Immel2025_5:
-
-**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)
-
-.. _Daw2:
-
-**(Daw)** Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
-Daw, Baskes, Phys Rev B, 29, 6443 (1984).

doc/src/pair_granular.rst

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

doc/src/pair_hybrid.rst

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

doc/src/pair_lambda_input_apip.rst

@@ -1,151 +0,0 @@
-.. index:: pair_style lambda/input/apip
-.. index:: pair_style lambda/input/csp/apip
-
-pair_style lambda/input/apip command
-====================================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   pair_style lambda/input/apip cutoff
-
-* lambda/input/apip = style name of this pair style
-* cutoff = global cutoff (distance units)
-
-pair_style lambda/input/csp/apip command
-========================================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   pair_style lambda/input/csp/apip lattice keyword args
-
-* lambda/input/csp/apip = style name of this pair style
-* lattice = *fcc* or *bcc* or integer
-
-  .. parsed-literal::
-
-       *fcc* = use 12 nearest neighbors to calculate the CSP like in a perfect fcc lattice
-       *bcc* = use 8 nearest neighbors to calculate the CSP like in a perfect bcc lattice
-       integer = use N nearest neighbors to calculate the CSP
-
-* zero or more keyword/args pairs may be appended
-* keyword = *cutoff* or *N_buffer*
-
-  .. parsed-literal::
-
-       *cutoff* args = cutoff
-         cutoff = distance in which neighboring atoms are considered (> 0)
-       *N_buffer* args = N_buffer
-         N_buffer = number of additional neighbors, which are included in the j-j+N/2 calculation
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   pair_style lambda/input/csp/apip fcc
-   pair_style lambda/input/csp/apip fcc cutoff 5.0
-   pair_style lambda/input/csp/apip bcc cutoff 5.0 N_buffer 2
-   pair_style lambda/input/csp/apip 14
-
-Description
-"""""""""""
-
-This pair_styles calculates :math:`\lambda_i^\text{input}(t)`, which
-is required for :doc:`fix lambda/apip <fix_lambda_apip>`.
-
-The pair_style lambda_input sets :math:`\lambda_i^\text{input}(t) = 0`.
-
-The pair_style lambda_input/csp calculates
-:math:`\lambda_i^\text{input}(t) = \text{CSP}_i(t)`.
-The centro-symmetry parameter (CSP) :ref:`(Kelchner) <Kelchner_2>` is described
-in :doc:`compute centro/atom <compute_centro_atom>`.
-
-The lattice argument is described in
-:doc:`compute centro/atom <compute_centro_atom>` and determines
-the number of neighboring atoms that are used to compute the CSP.
-The *N_buffer* argument allows to include more neighboring atoms in
-the calculation of the contributions from the pair j,j+N/2 to the CSP as
-discussed in :ref:`(Immel) <Immel2025_6>`.
-
-The computation of :math:`\lambda_i^\text{input}(t)` is done by this
-pair_style instead of by :doc:`fix lambda/apip <fix_lambda_apip>`, as this computation
-takes time and this pair_style can be included in the load-balancing via
-:doc:`fix atom_weight/apip <fix_atom_weight_apip>`.
-
-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 this pair_style.
-The switching parameter is calculated by :doc:`fix lambda/apip <fix_lambda_apip>`,
-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
-
-----------
-
-Mixing, shift, table, tail correction, restart, rRESPA info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-The cutoff distance for this pair style can be mixed.  The default mix
-value is *geometric*\ .  See the "pair_modify" command for details.
-
-This pair style does not support the :doc:`pair_modify <pair_modify>`
-shift, table, and tail options.
-
-This pair style writes no information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands need
-to be specified in an input script that reads a restart file.
-
-This pair style does not support the use of the *inner*, *middle*,
-and *outer* keywords of the :doc:`run_style respa <run_style>` command.
-
-----------
-
-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:`compute centro/atom <compute_centro_atom>`,
-: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 eam/apip <pair_eam_apip>`,
-:doc:`pair_style pace/apip  <pair_pace_apip>`,
-:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
-
-Default
-"""""""
-
-N_buffer=0, cutoff=5.0
-
-----------
-
-.. _Kelchner_2:
-
-**(Kelchner)** Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).
-
-.. _Immel2025_6:
-
-**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

doc/src/pair_lambda_zone_apip.rst

@@ -1,106 +0,0 @@
-.. index:: pair_style lambda/zone/apip
-
-pair_style lambda/zone/apip command
-===================================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   pair_style lambda/zone/apip cutoff
-
-* lambda/zone/apip = style name of this pair style
-* cutoff = global cutoff (distance units)
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   pair_style lambda/zone/apip 12.0
-
-Description
-"""""""""""
-
-This pair_style calculates :math:`\lambda_{\text{min},i}`, which
-is required for :doc:`fix lambda/apip <fix_lambda_apip>`.
-The meaning of :math:`\lambda_{\text{min},i}` is documented in
-:doc:`fix lambda/apip <fix_lambda_apip>`, as this pair_style is for use with
-:doc:`fix lambda/apip <fix_lambda_apip>` only.
-
-This pair_style requires only the global cutoff as argument.
-The remaining quantities, that are required to calculate
-:math:`\lambda_{\text{min},i}` are extracted from
-:doc:`fix lambda/apip <fix_lambda_apip>` and, thus,
-do not need to be passed to this pair_style as arguments.
-
-.. warning::
-
-   The cutoff given as argument to this pair style is only relevant for the
-   neighbor list creation. The radii, which define :math:`r_{\lambda,\text{hi}}` and :math:`r_{\lambda,\text{lo}}` are defined by :doc:`fix lambda/apip <fix_lambda_apip>`.
-
-The computation of :math:`\lambda_{\text{min},i}` is done by this
-pair_style instead of by :doc:`fix lambda/apip <fix_lambda_apip>`, as this computation
-takes time and this pair_style can be included in the load-balancing via
-:doc:`fix atom_weight/apip <fix_atom_weight_apip>`.
-
-A code example for the calculation of the switching parameter for an
-adaptive-precision interatomic potential (APIP) 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 :doc:`fix lambda/apip <fix_lambda_apip>`,
-whereas the spatial transition zone of the switching parameter is calculated
-by this pair style.
-
-.. 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
-
-----------
-
-Mixing, shift, table, tail correction, restart, rRESPA info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-The cutoff distance for this pair style can be mixed.  The default mix
-value is *geometric*\ .  See the "pair_modify" command for details.
-
-This pair style does not support the :doc:`pair_modify <pair_modify>`
-shift, table, and tail options.
-
-This pair style writes no information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands need
-to be specified in an input script that reads a restart file.
-
-This pair style does not support the use of the *inner*, *middle*,
-and *outer* keywords of the :doc:`run_style respa <run_style>` command.
-
-----------
-
-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:`fix atom_weight/apip <fix_atom_weight_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 lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
-
-Default
-"""""""
-
-none

doc/src/pair_lj_pirani.rst

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

doc/src/pair_lj_smooth.rst

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

doc/src/pair_pace_apip.rst

@@ -1,147 +0,0 @@
-.. index:: pair_style pace/apip
-.. index:: pair_style pace/fast/apip
-.. index:: pair_style pace/precise/apip
-
-pair_style pace/apip command
-============================
-
-pair_style pace/fast/apip command
-=================================
-
-pair_style pace/precise/apip command
-====================================
-
-Constant precision variant: *pace*
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   pair_style pace/apip ... keyword values ...
-   pair_style pace/fast/apip ... keyword values ...
-   pair_style pace/precise/apip ... keyword values ...
-
-* one or more keyword/value pairs may be appended
-
-  .. parsed-literal::
-
-     keyword = keywords of :doc:`pair pace <pair_pace>`
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   pair_style hybrid/overlay pace/fast/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
-   pair_coeff * * pace/fast/apip Cu_fast.yace Cu
-   pair_coeff * * pace/precise/apip Cu_precise.yace Cu
-   pair_coeff * * lambda/input/csp/apip
-   pair_coeff * * lambda/zone/apip
-
-   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
-
-
-Description
-"""""""""""
-
-Pair style :doc:`pace <pair_pace>` computes interactions using the Atomic
-Cluster Expansion (ACE), which is a general expansion of the atomic energy in
-multi-body basis functions :ref:`(Drautz19) <Drautz2019_2>`.  The *pace*
-pair style provides an efficient implementation that is described in
-this paper :ref:`(Lysogorskiy21) <Lysogorskiy20211_2>`.
-
-The potential energy :math:`E_i` of an atom :math:`i` of an adaptive-precision
-interatomic potential (APIP) according to
-:ref:`(Immel25) <Immel2025_7>` is given by
-
-.. math::
-
-   E_i^\text{APIP} = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)}\,,
-
-whereas the switching parameter :math:`\lambda_i` is computed
-dynamically during a simulation by :doc:`fix lambda/apip <fix_lambda_apip>`
-or set prior to a simulation via :doc:`set <set>`.
-
-The pair style *pace/precise/apip* computes the potential energy
-:math:`(1-\lambda_i) E_i^\text{(pace)}` and the
-corresponding force and should be combined
-with a fast potential that computes the potential energy
-:math:`\lambda_i E_i^\text{(fast)}` and the corresponding force
-via :doc:`pair_style hybrid/overlay <pair_hybrid>`.
-
-The pair style *pace/fast/apip* computes the potential energy
-:math:`\lambda_i E_i^\text{(pace)}` and the
-corresponding force and should be combined
-with a precise potential that computes the potential energy
-:math:`(1-\lambda_i) E_i^\text{(precise)}` and the corresponding force
-via :doc:`pair_style hybrid/overlay <pair_hybrid>`.
-
-The pair_styles *pace/fast/apip* and *pace/precise/apip*
-commands may be followed by the optional keywords of
-:doc:`pair_style pace <pair_pace>`, which are described
-:doc:`here <pair_pace>`.
-
-Mixing, shift, table, tail correction, restart, rRESPA info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-For atom type pairs I,J and I != J, where types I and J correspond to
-two different element types, mixing is performed by LAMMPS with
-user-specifiable parameters as described above.  You never need to
-specify a pair_coeff command with I != J arguments for this style.
-
-This pair styles does not support the :doc:`pair_modify <pair_modify>`
-shift, table, and tail options.
-
-This pair styles does not write its information to :doc:`binary restart
-files <restart>`, since it is stored in potential files.  Thus, you need
-to re-specify the pair_style and pair_coeff commands in an input script
-that reads a restart file.
-
-This pair styles can only be used via the *pair* keyword of the
-:doc:`run_style respa <run_style>` command.  It does not support the
-*inner*, *middle*, *outer* keywords.
-
-----------
-
-Restrictions
-""""""""""""
-
-This pair styles are 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 pace  <pair_pace>`,
-:doc:`pair_style hybrid/overlay <pair_hybrid>`,
-: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:`fix atom_weight/apip <fix_atom_weight_apip>`
-
-Default
-"""""""
-
-See :doc:`pair_style pace <pair_pace>`.
-
-----------
-
-.. _Drautz2019_2:
-
-**(Drautz19)** Drautz, Phys Rev B, 99, 014104 (2019).
-
-.. _Lysogorskiy20211_2:
-
-**(Lysogorskiy21)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
-
-.. _Immel2025_7:
-
-**(Immel25)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

doc/src/pair_style.rst

@@ -188,9 +188,7 @@ accelerated styles exist.
 * :doc:`eam/cd <pair_eam>` - concentration-dependent EAM
 * :doc:`eam/cd/old <pair_eam>` - older two-site model for concentration-dependent EAM
 * :doc:`eam/fs <pair_eam>` - Finnis-Sinclair EAM
-* :doc:`eam/fs/apip <pair_eam_apip>` - :doc:`adaptive precision <Howto_apip>` version of FS EAM, used as fast potential
 * :doc:`eam/he <pair_eam>` - Finnis-Sinclair EAM modified for Helium in metals
-* :doc:`eam/apip <pair_eam_apip>` - :doc:`adaptive-precision <Howto_apip>` version of EAM, used as fast potential
 * :doc:`edip <pair_edip>` - three-body EDIP potential
 * :doc:`edip/multi <pair_edip>` - multi-element EDIP potential
 * :doc:`edpd <pair_mesodpd>` - eDPD particle interactions
@@ -219,9 +217,6 @@ accelerated styles exist.
 * :doc:`kim <pair_kim>` - interface to potentials provided by KIM project
 * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` - Kolmogorov-Crespi (KC) potential with no simplifications
 * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>` - Kolmogorov-Crespi (KC) potential with normals along z-axis
-* :doc:`lambda/input/apip <pair_lambda_input_apip>` - constant as input for the precision calculation of an :doc:`adaptive-precision interatomic potential (APIP) <Howto_apip>`
-* :doc:`lambda/input/csp/apip <pair_lambda_input_apip>` - CSP as input for the precision calculation of an :doc:`adaptive-precision interatomic potential (APIP) <Howto_apip>`
-* :doc:`lambda/zone/apip <pair_lambda_zone_apip>` - transition zone of an :doc:`adaptive-precision interatomic potential <Howto_apip>`
 * :doc:`lcbop <pair_lcbop>` - long-range bond-order potential (LCBOP)
 * :doc:`lebedeva/z <pair_lebedeva_z>` - Lebedeva interlayer potential for graphene with normals along z-axis
 * :doc:`lennard/mdf <pair_mdf>` - LJ potential in A/B form with a taper function
@@ -335,9 +330,6 @@ accelerated styles exist.
 * :doc:`oxrna2/xstk <pair_oxrna2>` -
 * :doc:`pace <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential
 * :doc:`pace/extrapolation <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential with extrapolation grades
-* :doc:`pace/apip <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as precise potential
-* :doc:`pace/fast/apip <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as fast potential
-* :doc:`pace/precise/apip <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as precise potential
 * :doc:`pedone <pair_pedone>` - Pedone (PMMCS) potential (non-Coulomb part)
 * :doc:`pod <pair_pod>` - Proper orthogonal decomposition (POD) machine-learning potential
 * :doc:`peri/eps <pair_peri>` - Peridynamic EPS potential

doc/src/plugin.rst

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

doc/src/python.rst

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

doc/src/read_dump.rst

@@ -16,13 +16,12 @@ Syntax
 
   .. parsed-literal::
 
-     field = *x* or *y* or *z* or *vx* or *vy* or *vz* or *q* or *ix* or *iy* or *iz* or *fx* or *fy* or *fz* or *apip_lambda*
+     field = *x* or *y* or *z* or *vx* or *vy* or *vz* or *q* or *ix* or *iy* or *iz* or *fx* or *fy* or *fz*
        *x*,\ *y*,\ *z* = atom coordinates
        *vx*,\ *vy*,\ *vz* = velocity components
        *q* = charge
        *ix*,\ *iy*,\ *iz* = image flags in each dimension
        *fx*,\ *fy*,\ *fz* = force components
-       *apip_lambda* = switching parameter of an :doc:`adaptive-precision interatomic potential <Howto_apip>`
 
 * zero or more keyword/value pairs may be appended
 * keyword = *nfile* or *box* or *timestep* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format*

doc/src/run.rst

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