Merge conflicts

.github/CODEOWNERS

@@ -37,7 +37,8 @@ src/MESONT/*          @iafoss
 src/ML-HDNNP/*        @singraber
 src/ML-IAP/*          @athomps
 src/ML-PACE/*         @yury-lysogorskiy
-src/ML-POD/*          @exapde @rohskopf
+src/ML-POD/*          @exapde
+src/ML-UF3/*          @monk-04
 src/MOFFF/*           @hheenen
 src/MOLFILE/*         @akohlmey
 src/NETCDF/*          @pastewka
@@ -65,10 +66,15 @@ src/MANYBODY/pair_nb3b_screened.*   @flodesani
 src/REPLICA/*_grem.*                @dstelter92
 src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
 src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
+src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
 src/MISC/*_tracker.*                @jtclemm
 src/MC/fix_gcmc.*                   @athomps
 src/MC/fix_sgcmc.*                  @athomps
+src/REAXFF/compute_reaxff_atom.*    @rbberger
+src/KOKKOS/compute_reaxff_atom_kokkos.*    @rbberger
 src/REPLICA/fix_pimd_langevin.*     @Yi-FanLi
+src/DPD-BASIC/pair_dpd_coul_slater_long.* @Eddy-Barraud
+src/GPU/pair_dpd_coul_slater_long.* @Eddy-Barraud
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp
@@ -80,7 +86,7 @@ src/bond.*                @sjplimp
 src/comm*.*               @sjplimp
 src/compute.*             @sjplimp
 src/dihedral.*            @sjplimp
-src/domain.*              @sjplimp
+src/domain.*              @sjplimp @stanmoore1
 src/dump*.*               @sjplimp
 src/error.*               @sjplimp
 src/finish.*              @sjplimp

.github/workflows/coverity.yml

@@ -25,7 +25,7 @@ jobs:
 
     - name: Cache Coverity
       id: cache-coverity
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ./download/
         key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}

.github/workflows/unittest-macos.yml

@@ -15,7 +15,7 @@ jobs:
   build:
     name: MacOS Unit Test
     if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: macos-latest
+    runs-on: macos-13
     env:
       CCACHE_DIR: ${{ github.workspace }}/.ccache
 
@@ -32,7 +32,7 @@ jobs:
       run: mkdir build
 
     - name: Set up ccache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.CCACHE_DIR }}
         key: macos-ccache-${{ github.sha }}
@@ -43,6 +43,8 @@ jobs:
       working-directory: build
       run: |
         ccache -z
+        python3 -m venv macosenv
+        source macosenv/bin/activate
         python3 -m pip install numpy
         python3 -m pip install pyyaml
         cmake -C ../cmake/presets/clang.cmake \

cmake/CMakeLists.txt

@@ -120,6 +120,19 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
   set(CMAKE_TUNE_DEFAULT "-Minform=severe")
 endif()
 
+# this hack is required to compile fmt lib with CrayClang version 15.0.2
+# CrayClang is only directly recognized by version 3.28 and later
+if(CMAKE_VERSION VERSION_LESS 3.28)
+  get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
+    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
+  endif()
+else()
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
+    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
+  endif()
+endif()
+
 # silence nvcc warnings
 if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
   set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
@@ -209,6 +222,10 @@ endif()
 add_executable(lmp ${MAIN_SOURCES})
 target_link_libraries(lmp PRIVATE lammps)
 set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
+# re-export all symbols for plugins
+if(PKG_PLUGIN AND (NOT ((CMAKE_SYSTEM_NAME STREQUAL "Windows"))))
+  set_target_properties(lmp PROPERTIES ENABLE_EXPORTS TRUE)
+endif()
 install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
@@ -239,6 +256,7 @@ set(STANDARD_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -268,6 +286,7 @@ set(STANDARD_PACKAGES
   ML-RANN
   ML-SNAP
   ML-POD
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
@@ -416,6 +435,7 @@ if(BUILD_OMP)
       (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
     # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
     # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
@@ -426,6 +446,21 @@ if(BUILD_OMP)
   target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=${LAMMPS_OMP_COMPAT_LEVEL})
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
   target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
+
+  # this hack is required to correctly link with OpenMP support when using CrayClang version 15.0.2
+  # CrayClang is only directly recognized by version 3.28 and later
+  if(CMAKE_VERSION VERSION_LESS 3.28)
+    get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
+    if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
+      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
+      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
+    endif()
+  else()
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
+      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
+      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
+    endif()
+  endif()
 endif()
 
 # lower C++ standard for fmtlib sources when using Intel classic compiler
@@ -540,12 +575,12 @@ endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
-foreach(HEADER cmath)
+if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")))
-  check_include_file_cxx(${HEADER} FOUND_${HEADER})
+  check_include_file_cxx(cmath FOUND_CMATH)
-  if(NOT FOUND_${HEADER})
+  if(NOT FOUND_CMATH)
-    message(FATAL_ERROR "Could not find needed header - ${HEADER}")
+    message(FATAL_ERROR "Could not find the required 'cmath' header")
-  endif(NOT FOUND_${HEADER})
+  endif(NOT FOUND_CMATH)
-endforeach(HEADER)
+endif()
 
 # make the standard math library overrideable and autodetected (for systems that don't have it)
 find_library(STANDARD_MATH_LIB m DOC "Standard Math library")
@@ -657,7 +692,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-BASIC DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -972,14 +1007,15 @@ if(PKG_KOKKOS)
   endif()
 endif()
 if(PKG_KSPACE)
-  if (LMP_HEFFTE)
+  if (FFT_USE_HEFFTE)
     message(STATUS "<<< FFT settings >>>
 -- Primary FFT lib:  heFFTe")
-    if (HEFFTE_BACKEND)
+    if (FFT_HEFFTE_BACKEND)
-      message(STATUS "heFFTe backend:  ${HEFFTE_BACKEND}")
+      message(STATUS "heFFTe backend:  ${FFT_HEFFTE_BACKEND}")
     else()
       message(STATUS "heFFTe backend:  stock (builtin FFT implementation, tested for corrected but not optimized for production)")
     endif()
+    message(STATUS "Using distributed FFT algorithms from heFTTe")
     if(FFT_SINGLE)
       message(STATUS "Using single precision FFTs")
     else()
@@ -998,28 +1034,10 @@ if(PKG_KSPACE)
     else()
       message(STATUS "Using non-threaded FFTs")
     endif()
-    if (FFT_HEFFTE)
+    message(STATUS "Using builtin distributed FFT algorithms")
-      message(STATUS "Using distributed algorithms from heFTTe")
+  endif()
-    else()
+  if(PKG_KOKKOS)
-      message(STATUS "Using builtin distributed algorithms")
+    message(STATUS "Kokkos FFT: ${FFT_KOKKOS}")
-    endif()
-    if(PKG_KOKKOS)
-      if(Kokkos_ENABLE_CUDA)
-        if(FFT STREQUAL "KISS")
-          message(STATUS "Kokkos FFT: KISS")
-        else()
-          message(STATUS "Kokkos FFT: cuFFT")
-        endif()
-      elseif(Kokkos_ENABLE_HIP)
-        if(FFT STREQUAL "KISS")
-          message(STATUS "Kokkos FFT: KISS")
-        else()
-          message(STATUS "Kokkos FFT: hipFFT")
-        endif()
-      else()
-        message(STATUS "Kokkos FFT: ${FFT}")
-      endif()
-    endif()
   endif()
 endif()
 if(BUILD_DOC)

cmake/Modules/DetectHIPInstallation.cmake

@@ -1,11 +1,3 @@
-if(NOT DEFINED HIP_PATH)
-    if(NOT DEFINED ENV{HIP_PATH})
-        message(FATAL_ERROR "HIP support requires HIP_PATH to be defined.\n"
-        "Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
-    else()
-        set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
-    endif()
-endif()
 if(NOT DEFINED ROCM_PATH)
     if(NOT DEFINED ENV{ROCM_PATH})
         set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
@@ -13,4 +5,4 @@ if(NOT DEFINED ROCM_PATH)
         set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
     endif()
 endif()
-list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})
+list(APPEND CMAKE_PREFIX_PATH ${ROCM_PATH})

cmake/Modules/ExternalCMakeProject.cmake

@@ -43,5 +43,5 @@ function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
       "${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/CMakeLists.txt")
   endif()
   add_subdirectory("${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}"
-    "${CMAKE_BINARY_DIR}/_deps/${target}-build")
+    "${CMAKE_BINARY_DIR}/_deps/${target}-build" EXCLUDE_FROM_ALL)
 endfunction(ExternalCMakeProject)

cmake/Modules/OpenCLLoader.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building OpenCL loader library")
-set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2022.01.04.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.05.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "8d3a801e87a2c6653bf0e27707063914" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "e7796826b21c059224fabe997e0f2075" CACHE STRING "MD5 checksum of OpenCL loader tarball")
 mark_as_advanced(OPENCL_LOADER_URL)
 mark_as_advanced(OPENCL_LOADER_MD5)
 
@@ -8,4 +8,3 @@ set(INSTALL_LIBOPENCL OFF CACHE BOOL "" FORCE)
 include(ExternalCMakeProject)
 ExternalCMakeProject(opencl_loader ${OPENCL_LOADER_URL} ${OPENCL_LOADER_MD5} opencl-loader . "")
 
-add_library(OpenCL::OpenCL ALIAS OpenCL)

cmake/Modules/Packages/DPD-BASIC.cmake

@@ -0,0 +1,9 @@
+# pair style dpd/coul/slater/long may only be installed if also KSPACE is installed
+if(NOT PKG_KSPACE)
+  get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
+  list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.h)
+  set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
+endif()

cmake/Modules/Packages/GPU.cmake

@@ -1,3 +1,10 @@
+
+# Silence CMake warnings about FindCUDA being obsolete.
+# We may need to eventually rewrite this section to use enable_language(CUDA)
+if(POLICY CMP0146)
+  cmake_policy(SET CMP0146 OLD)
+endif()
+
 set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
 set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
                 ${GPU_SOURCES_DIR}/fix_gpu.h

cmake/Modules/Packages/INTEL.cmake

@@ -111,6 +111,9 @@ if(PKG_KSPACE)
   list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
   RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
 endif()
+if(PKG_ML-SNAP)
+  list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/sna_intel.cpp)
+endif()
 
 target_sources(lammps PRIVATE ${INTEL_SOURCES})
 target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

cmake/Modules/Packages/KOKKOS.cmake

@@ -45,8 +45,8 @@ 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/4.2.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "731647b61a4233f568d583702e9cd6d1" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_MD5 "243de871b3dc2cf3990c1c404032df83" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -71,7 +71,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 4.2.00 REQUIRED CONFIG)
+  find_package(Kokkos 4.3.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@@ -126,16 +126,33 @@ if(PKG_KSPACE)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
+  set(FFT_KOKKOS "KISS" CACHE STRING "FFT library for Kokkos-enabled KSPACE package")
+  set(FFT_KOKKOS_VALUES KISS FFTW3 MKL HIPFFT CUFFT)
+  set_property(CACHE FFT_KOKKOS PROPERTY STRINGS ${FFT_KOKKOS_VALUES})
+  validate_option(FFT_KOKKOS FFT_KOKKOS_VALUES)
+  string(TOUPPER ${FFT_KOKKOS} FFT_KOKKOS)
+
   if(Kokkos_ENABLE_CUDA)
-    if(NOT (FFT STREQUAL "KISS"))
+    if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "CUFFT")))
-      target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
+      message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.")
-      target_link_libraries(lammps PRIVATE cufft)
+    elseif(FFT_KOKKOS STREQUAL "KISS")
+      message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.")
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
+    elseif(FFT_KOKKOS STREQUAL "CUFFT")
+      find_package(CUDAToolkit REQUIRED)
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
+      target_link_libraries(lammps PRIVATE CUDA::cufft)
     endif()
   elseif(Kokkos_ENABLE_HIP)
-    if(NOT (FFT STREQUAL "KISS"))
+    if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "HIPFFT")))
+      message(FATAL_ERROR "The HIP backend of Kokkos requires either KISS FFT or HIPFFT.")
+    elseif(FFT_KOKKOS STREQUAL "KISS")
+      message(WARNING "Using KISS FFT with the HIP backend of Kokkos may be sub-optimal.")
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
+    elseif(FFT_KOKKOS STREQUAL "HIPFFT")
       include(DetectHIPInstallation)
       find_package(hipfft REQUIRED)
-      target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT)
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_HIPFFT)
       target_link_libraries(lammps PRIVATE hip::hipfft)
     endif()
   endif()

cmake/Modules/Packages/KSPACE.cmake

@@ -48,10 +48,15 @@ endif()
 
 option(FFT_USE_HEFFTE  "Use heFFTe as the distributed FFT engine, overrides the FFT option."  OFF)
 if(FFT_USE_HEFFTE)
-  # if FFT_HEFFTE is enabled, switch the builtin FFT engine with Heffte
+  # if FFT_HEFFTE is enabled, use the heFFTe parallel engine instead of the builtin fftMPI engine
-  set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL)
+
-  set(FFT_HEFFTE_BACKEND "" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
+  # map standard FFT choices to available heFFTe backends: FFTW3 -> FFTW, KISS -> BUILTIN
+  set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL BUILTIN)
+  string(REPLACE FFTW3 FFTW FFT_HEFFTE_BACKEND_DEFAULT ${FFT})
+  string(REPLACE KISS BUILTIN FFT_HEFFTE_BACKEND_DEFAULT ${FFT_HEFFTE_BACKEND_DEFAULT})
+  set(FFT_HEFFTE_BACKEND "${FFT_HEFFTE_BACKEND_DEFAULT}" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
   set_property(CACHE FFT_HEFFTE_BACKEND PROPERTY STRINGS ${FFT_HEFFTE_BACKEND_VALUES})
+  validate_option(FFT_HEFFTE_BACKEND FFT_HEFFTE_BACKEND_VALUES)
 
   if(FFT_HEFFTE_BACKEND STREQUAL "FFTW") # respect the backend choice, FFTW or MKL
     set(HEFFTE_COMPONENTS "FFTW")
@@ -60,24 +65,38 @@ if(FFT_USE_HEFFTE)
     set(HEFFTE_COMPONENTS "MKL")
     set(Heffte_ENABLE_MKL "ON" CACHE BOOL "Enables MKL backend for heFFTe")
   else()
+    set(HEFFTE_COMPONENTS "BUILTIN")
     message(WARNING "FFT_HEFFTE_BACKEND not selected, defaulting to the builtin 'stock' backend, which is intended for testing and is not optimized for production runs")
   endif()
 
   find_package(Heffte 2.4.0 QUIET COMPONENTS ${HEFFTE_COMPONENTS})
   if (NOT Heffte_FOUND) # download and build
+    if(BUILD_SHARED_LIBS)
+      set(BUILD_SHARED_LIBS_WAS_ON YES)
+      set(BUILD_SHARED_LIBS OFF)
+    endif()
+    if(CMAKE_REQUEST_PIC)
+      set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+    endif()
+    set(Heffte_ENABLE_${FFT_HEFFTE_BACKEND} ON)
     include(FetchContent)
     FetchContent_Declare(HEFFTE_PROJECT # using v2.4.0
       URL  "https://github.com/icl-utk-edu/heffte/archive/refs/tags/v2.4.0.tar.gz"
       URL_HASH SHA256=02310fb4f9688df02f7181667e61c3adb7e38baf79611d80919d47452ff7881d
       )
     FetchContent_Populate(HEFFTE_PROJECT)
-    add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR})
-    set_target_properties(lmp PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-    set_target_properties(lammps PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-    add_library(Heffte::Heffte INTERFACE IMPORTED GLOBAL)
-    target_link_libraries(Heffte::Heffte INTERFACE Heffte)
-  endif()
 
+    # fixup git hash to show "(unknown)" to avoid compilation failures.
+    file(READ ${heffte_project_SOURCE_DIR}/include/heffte_config.cmake.h HEFFTE_CFG_FILE_TEXT)
+    string(REPLACE "@Heffte_GIT_HASH@" "(unknown)" HEFFTE_CFG_FILE_TEXT "${HEFFTE_CFG_FILE_TEXT}")
+    file(WRITE ${heffte_project_SOURCE_DIR}/include/heffte_config.cmake.h "${HEFFTE_CFG_FILE_TEXT}")
+
+    add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR} EXCLUDE_FROM_ALL)
+    add_library(Heffte::Heffte ALIAS Heffte)
+    if(BUILD_SHARED_LIBS_WAS_ON)
+      set(BUILD_SHARED_LIBS ON)
+    endif()
+  endif()
   target_compile_definitions(lammps PRIVATE -DFFT_HEFFTE "-DFFT_HEFFTE_${FFT_HEFFTE_BACKEND}")
   target_link_libraries(lammps PRIVATE Heffte::Heffte)
 endif()

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_MD5 "3124bb85259471e2a53a891f04bf697a" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   GetFallbackURL(MDI_URL MDI_FALLBACK)

cmake/Modules/Packages/ML-IAP.cmake

@@ -10,6 +10,14 @@ endif()
 
 option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
 
+# if ML-PACE package *and* MLIAP with Python is enabled is included we may also include ML-PACE support in ML-IAP
+set(MLIAP_ENABLE_ACE_DEFAULT OFF)
+if(PKG_ML-PACE)
+  set(MLIAP_ENABLE_ACE_DEFAULT ON)
+endif()
+
+option(MLIAP_ENABLE_ACE "Build ML-IAP package with ACE support" ${MLIAP_ENABLE_ACE_DEFAULT})
+
 if(MLIAP_ENABLE_PYTHON)
   find_package(Cythonize REQUIRED)
   find_package(Python COMPONENTS NumPy REQUIRED)
@@ -36,3 +44,10 @@ if(MLIAP_ENABLE_PYTHON)
   target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
   target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
 endif()
+
+if(MLIAP_ENABLE_ACE)
+  if(NOT PKG_ML-PACE)
+    message(FATAL_ERROR "Must enable ML-PACE package for including ACE support in ML-IAP")
+  endif()
+  target_compile_definitions(lammps PRIVATE -DMLIAP_ACE)
+endif()

cmake/Modules/Packages/ML-QUIP.cmake

@@ -18,7 +18,9 @@ if(DOWNLOAD_QUIP)
     set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
     set(temp "${temp}F95_PRE_FILENAME_FLAG = -Tf\n")
   elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
-    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
+    # quip library uses GNU fortran extensions. If any more restrictive standards are set, reset them
+    string(REGEX REPLACE -std=f[0-9]+ -std=gnu _fopt "${CMAKE_Fortran_FLAGS_${BTYPE}}")
+    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${_fopt} -fmax-stack-var-size=6553600\n")
     set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
     set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
     set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
@@ -56,7 +58,7 @@ if(DOWNLOAD_QUIP)
     GIT_SUBMODULES "src/fox;src/GAP"
     PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
     CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
-    BUILD_COMMAND env QUIP_ARCH=lammps make libquip
+    BUILD_COMMAND env QUIP_ARCH=lammps make -j1 libquip
     INSTALL_COMMAND ""
     BUILD_IN_SOURCE YES
     BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}

cmake/Modules/Packages/PLUMED.cmake

@@ -1,5 +1,9 @@
 # Plumed2 support for PLUMED package
 
+# for supporting multiple concurrent plumed2 installations for debugging and testing
+set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
+mark_as_advanced(PLUMED_SUFFIX)
+
 if(BUILD_MPI)
   set(PLUMED_CONFIG_MPI "--enable-mpi")
   set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
@@ -21,9 +25,11 @@ else()
   set(PLUMED_CONFIG_OMP "--disable-openmp")
 endif()
 
-set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz"
+# Note: must also adjust check for supported API versions in
+# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.1/plumed-src-2.9.1.tgz"
   CACHE STRING "URL for PLUMED tarball")
-set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
+set(PLUMED_MD5 "c3b2d31479c1e9ce211719d40e9efbd7" CACHE STRING "MD5 checksum of PLUMED tarball")
 
 mark_as_advanced(PLUMED_URL)
 mark_as_advanced(PLUMED_MD5)
@@ -151,15 +157,15 @@ else()
     file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
   else()
     find_package(PkgConfig REQUIRED)
-    pkg_check_modules(PLUMED REQUIRED plumed)
+    pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
     add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
     if(PLUMED_MODE STREQUAL "STATIC")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.static)
     elseif(PLUMED_MODE STREQUAL "SHARED")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
+      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.shared)
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
-      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${PLUMED_SUFFIX}Kernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
+      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.runtime)
     endif()
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")

cmake/packaging/build_linux_tgz.sh

@@ -59,12 +59,14 @@ done
 
 echo "Set up wrapper script"
 MYDIR=$(dirname "$0")
+cp ${MYDIR}/xdg-open ${DESTDIR}/bin
 cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin
 for s in ${DESTDIR}/bin/*
 do \
         EXE=$(basename $s)
         test ${EXE} = linux_wrapper.sh && continue
         test ${EXE} = qt.conf && continue
+        test ${EXE} = xdg-open && continue
         ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE}
 done
 

cmake/packaging/linux_wrapper.sh

@@ -4,15 +4,17 @@
 # reset locale to avoid problems with decimal numbers
 export LC_ALL=C
 
-BASEDIR=$(dirname "$0")
+BASEDIR="$(dirname "$0")"
-EXENAME=$(basename "$0")
+EXENAME="$(basename "$0")"
+
+PATH="${BASEDIR}/bin:${PATH}"
 
 # append to LD_LIBRARY_PATH to prefer local (newer) libs
-LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BASEDIR}/lib
+LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BASEDIR}/lib"
 
 # set some environment variables for LAMMPS etc.
-LAMMPS_POTENTIALS=${BASEDIR}/share/lammps/potentials
+LAMMPS_POTENTIALS="${BASEDIR}/share/lammps/potentials"
-MSI2LMP_LIBRARY=${BASEDIR}/share/lammps/frc_files
+MSI2LMP_LIBRARY="${BASEDIR}/share/lammps/frc_files"
-export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY
+export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH
 
 exec "${BASEDIR}/bin/${EXENAME}" "$@"

cmake/presets/all_off.cmake

@@ -28,6 +28,7 @@ set(ALL_PACKAGES
   DRUDE
   ELECTRODE
   EFF
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -60,6 +61,7 @@ set(ALL_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE

cmake/presets/all_on.cmake

@@ -30,6 +30,7 @@ set(ALL_PACKAGES
   DRUDE
   ELECTRODE
   EFF
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -62,6 +63,7 @@ set(ALL_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE

cmake/presets/kokkos-cuda.cmake

@@ -9,5 +9,8 @@ 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)
 
+# If KSPACE is also enabled, use CUFFT for FFTs
+set(FFT_KOKKOS "CUFFT" CACHE STRING "" FORCE)
+
 # hide deprecation warnings temporarily for stable release
 set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

cmake/presets/kokkos-hip.cmake

@@ -12,6 +12,9 @@ set(BUILD_OMP ON CACHE BOOL "" FORCE)
 set(CMAKE_CXX_COMPILER hipcc CACHE STRING "" FORCE)
 set(CMAKE_TUNE_FLAGS "-munsafe-fp-atomics" CACHE STRING "" FORCE)
 
+# 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)
 

cmake/presets/mingw-cross.cmake

@@ -24,6 +24,7 @@ set(WIN_PACKAGES
   DRUDE
   ELECTRODE
   EFF
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -50,6 +51,7 @@ set(WIN_PACKAGES
   ML-POD
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE

cmake/presets/most.cmake

@@ -26,6 +26,7 @@ set(ALL_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -45,6 +46,7 @@ set(ALL_PACKAGES
   ML-IAP
   ML-POD
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   OPENMP

cmake/presets/windows.cmake

@@ -22,6 +22,7 @@ set(WIN_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -42,6 +43,7 @@ set(WIN_PACKAGES
   ML-IAP
   ML-POD
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE

doc/Makefile

@@ -100,6 +100,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -182,6 +183,7 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -231,6 +233,7 @@ role_check :
 	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst && exit 1 || : )
 
 link_check : $(VENV) html
 	@(\

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "21 November 2023" "2023-11-21"
+.TH LAMMPS "1" "17 April 2024" "2024-04-17"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 21 November 2023
+\- Molecular Dynamics Simulator.  Version 17 April 2024
 
 .SH SYNOPSIS
 .B lmp
@@ -297,7 +297,7 @@ the chapter on errors in the
 manual gives some additional information about error messages, if possible.
 
 .SH COPYRIGHT
-© 2003--2022 Sandia Corporation
+© 2003--2024 Sandia Corporation
 
 This package is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License version 2 as

doc/src/Bibliography.rst

@@ -877,6 +877,9 @@ Bibliography
 **(PLUMED)**
    G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
 
+**(Pavlov)**
+D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
+
 **(Paquay)**
    Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
 

doc/src/Build_development.rst

@@ -122,32 +122,39 @@ Code Coverage and Unit Testing (CMake only)
 -------------------------------------------
 
 The LAMMPS code is subject to multiple levels of automated testing
-during development: integration testing (i.e. whether the code compiles
+during development:
-on various platforms and with a variety of settings), unit testing
+
-(i.e. whether certain individual parts of the code produce the expected
+- Integration testing (i.e. whether the code compiles
-results for given inputs), run testing (whether selected complete input
+  on various platforms and with a variety of compilers and settings),
-decks run without crashing for multiple configurations), and regression
+- Unit testing (i.e. whether certain functions or classes of the code
-testing (i.e. whether selected input examples reproduce the same
+  produce the expected results for given inputs),
-results over a given number of steps and operations within a given
+- Run testing (i.e. whether selected input decks can run to completion
-error margin).  The status of this automated testing can be viewed on
+  without crashing for multiple configurations),
-`https://ci.lammps.org <https://ci.lammps.org>`_.
+- Regression testing (i.e. whether selected input examples reproduce the
+  same results over a given number of steps and operations within a
+  given error margin).
+
+The status of this automated testing can be viewed on `https://ci.lammps.org
+<https://ci.lammps.org>`_.
 
 The scripts and inputs for integration, run, and regression testing
 are maintained in a
 `separate repository <https://github.com/lammps/lammps-testing>`_
-of the LAMMPS project on GitHub.
+of the LAMMPS project on GitHub.  A few tests are also run as GitHub
+Actions and their configuration files are in the ``.github/workflows/``
+folder of the LAMMPS git tree.
 
-The unit testing facility is integrated into the CMake build process
+The unit testing facility is integrated into the CMake build process of
-of the LAMMPS source code distribution itself.  It can be enabled by
+the LAMMPS source code distribution itself.  It can be enabled by
 setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
-It requires the `YAML <https://pyyaml.org/>`_ library and development
+It requires the `YAML <https://pyyaml.org/>`_ library and matching
-headers (if those are not found locally a recent version will be
+development headers to compile (if those are not found locally a recent
-downloaded and compiled along with LAMMPS and the test program) to
+version of that library will be downloaded and compiled along with
-compile and will download and compile a specific recent version of the
+LAMMPS and the test programs) and will download and compile a specific
-`Googletest <https://github.com/google/googletest/>`_ C++ test framework
+version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
-for implementing the tests.
+test framework that is used to implement the tests.
 
-.. admonition:: Software version requirements for testing
+.. admonition:: Software version and LAMMPS configuration requirements
    :class: note
 
    The compiler and library version requirements for the testing
@@ -155,7 +162,7 @@ for implementing the tests.
    example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
    (version 4.8.x) are not sufficient.  The CMake configuration will try
    to detect incompatible versions and either skip incompatible tests or
-   stop with an error.  Also the number of tests will depend on
+   stop with an error.  Also the number of available tests will depend on
    installed LAMMPS packages, development environment, operating system,
    and configuration settings.
 
@@ -234,12 +241,31 @@ will be skipped if prerequisite features are not available in LAMMPS.
    time.  Preference is given to parts of the code base that are easy to
    test or commonly used.
 
-Tests for styles of the same kind of style (e.g. pair styles or bond
+Tests as shown by the ``ctest`` program are command lines defined in the
-styles) are performed with the same test executable using different
+``CMakeLists.txt`` files in the ``unittest`` directory tree.  A few
-input files in YAML format.  So to add a test for another style of the
+tests simply execute LAMMPS with specific command line flags and check
-same kind it may be sufficient to add a suitable YAML file.
+the output to the screen for expected content.  A large number of unit
-:doc:`Detailed instructions for adding tests <Developer_unittest>` are
+tests are special tests programs using the `GoogleTest framework
-provided in the Programmer Guide part of the manual.
+<https://github.com/google/googletest/>`_ and linked to the LAMMPS
+library that test individual functions or create a LAMMPS class
+instance, execute one or more commands and check data inside the LAMMPS
+class hierarchy.  There are also tests for the C-library, Fortran, and
+Python module interfaces to LAMMPS.  The Python tests use the Python
+"unittest" module in a similar fashion than the others use `GoogleTest`.
+These special test programs are structured to perform multiple
+individual tests internally and each of those contains several checks
+(aka assertions) for internal data being changed as expected.
+
+Tests for force computing or modifying styles (e.g. styles for non-bonded
+and bonded interactions and selected fixes) are run by using a more generic
+test program that reads its input from files in YAML format. The YAML file
+provides the information on how to customized the test program to test
+a specific style and - if needed - with specific settings.
+To add a test for another, similar style (e.g. a new pair style) it is
+usually sufficient to add a suitable YAML file.  :doc:`Detailed
+instructions for adding tests <Developer_unittest>` are provided in the
+Programmer Guide part of the manual.  A description of what happens
+during the tests is given below.
 
 Unit tests for force styles
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/src/Build_extras.rst

@@ -533,9 +533,6 @@ They must be specified in uppercase.
    *  - A64FX
       - HOST
       - ARMv8.2 with SVE Support
-   *  - WSM
-      - HOST
-      - Intel Westmere CPU (SSE 4.2)
    *  - SNB
       - HOST
       - Intel Sandy/Ivy Bridge CPU (AVX 1)
@@ -566,18 +563,15 @@ They must be specified in uppercase.
    *  - KNL
       - HOST
       - Intel Knights Landing Xeon Phi
-   *  - BGQ
-      - HOST
-      - IBM Blue Gene/Q CPU
-   *  - POWER7
-      - HOST
-      - IBM POWER7 CPU
    *  - POWER8
       - HOST
       - IBM POWER8 CPU
    *  - POWER9
       - HOST
       - IBM POWER9 CPU
+   *  - RISCV_SG2042
+      - HOST
+      - SG2042 (RISC-V) CPU
    *  - KEPLER30
       - GPU
       - NVIDIA Kepler generation CC 3.0 GPU
@@ -666,7 +660,7 @@ They must be specified in uppercase.
       - GPU
       - Intel GPU Ponte Vecchio
 
-This list was last updated for version 4.2 of the Kokkos library.
+This list was last updated for version 4.3.0 of the Kokkos library.
 
 .. tabs::
 

doc/src/Build_settings.rst

@@ -44,7 +44,7 @@ require use of an FFT library to compute 1d FFTs.  The KISS FFT
 library is included with LAMMPS, but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 Alternatively, LAMMPS can use the `heFFTe
 <https://icl-utk-edu.github.io/heffte/>`_ library for the MPI
@@ -59,15 +59,19 @@ libraries and better pipelining for packing and communication.
       .. code-block:: bash
 
          -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
+         -D FFT_KOKKOS=value       # FFTW3 or MKL or KISS or CUFFT or HIPFFT, default is KISS
          -D FFT_SINGLE=value       # yes or no (default), no = double precision
          -D FFT_PACK=value         # array (default) or pointer or memcpy
          -D FFT_USE_HEFFTE=value   # yes or no (default), yes links to heFFTe
 
       .. note::
 
-         The values for the FFT variable must be in upper-case.  This is
+         When the Kokkos variant of a package is compiled and selected at run time,
-         an exception to the rule that all CMake variables can be specified
+         the FFT library selected by the FFT_KOKKOS variable applies. Otherwise,
-         with lower-case values.
+         the FFT library selected by the FFT variable applies.
+         The same FFT settings apply to both. FFT_KOKKOS must be compatible with the
+         Kokkos back end - for example, when using the CUDA back end of Kokkos,
+         you must use either CUFFT or KISS.
 
       Usually these settings are all that is needed.  If FFTW3 is
       selected, then CMake will try to detect, if threaded FFTW
@@ -106,6 +110,8 @@ libraries and better pipelining for packing and communication.
 
          FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
                                        # default is KISS if not specified
+         FFT_INC = -DFFT_KOKKOS_CUFFT  # -DFFT_KOKKOS_{FFTW,FFTW3,MKL,CUFFT,HIPFFT,KISS}
+                                       # default is KISS if not specified
          FFT_INC = -DFFT_SINGLE        # do not specify for double precision
          FFT_INC = -DFFT_FFTW_THREADS  # enable using threaded FFTW3 libraries
          FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
@@ -116,6 +122,8 @@ libraries and better pipelining for packing and communication.
 
          FFT_INC =       -I/usr/local/include
          FFT_PATH =      -L/usr/local/lib
+         FFT_LIB =       -lhipfft            # hipFFT either precision
+         FFT_LIB =       -lcufft             # cuFFT either precision
          FFT_LIB =       -lfftw3             # FFTW3 double precision
          FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
          FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
@@ -178,6 +186,11 @@ The Intel MKL math library is part of the Intel compiler suite.  It
 can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
 above).
 
+The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and
+AMD's HIP installations, respectively. These FFT libraries require the
+Kokkos acceleration package to be enabled and the Kokkos back end to be
+GPU-resident (i.e., HIP or CUDA).
+
 Performing 3d FFTs in parallel can be time-consuming due to data access
 and required communication.  This cost can be reduced by performing
 single-precision FFTs instead of double precision.  Single precision
@@ -189,11 +202,11 @@ generally less than the difference in precision. Using the
 ``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory
 use and parallel communication costs for transposing 3d FFT data.
 
-When using ``-DFFT_SINGLE`` with FFTW3, you may need to build the FFTW
+When using ``-DFFT_SINGLE`` with FFTW3, you may need to ensure that
-library a second time with support for single-precision.
+the FFTW3 installation includes support for single-precision.
 
-For FFTW3, do the following, which should produce the additional
+When compiler FFTW3 from source, you can do the following, which should
-library ``libfftw3f.a`` or ``libfftw3f.so``\ .
+produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
 
 .. code-block:: bash
 

doc/src/Commands_bond.rst

@@ -27,7 +27,7 @@ OPT.
 
    * :doc:`none <bond_none>`
    * :doc:`zero <bond_zero>`
-   * :doc:`hybrid <bond_hybrid>`
+   * :doc:`hybrid (k) <bond_hybrid>`
    *
    *
    *
@@ -90,6 +90,7 @@ OPT.
    * :doc:`cosine/shift (o) <angle_cosine_shift>`
    * :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
    * :doc:`cosine/squared (o) <angle_cosine_squared>`
+   * :doc:`cosine/squared/restricted (o) <angle_cosine_squared_restricted>`
    * :doc:`cross <angle_cross>`
    * :doc:`dipole (o) <angle_dipole>`
    * :doc:`fourier (o) <angle_fourier>`
@@ -125,9 +126,10 @@ OPT.
    *
    *
    * :doc:`charmm (iko) <dihedral_charmm>`
-   * :doc:`charmmfsw <dihedral_charmm>`
+   * :doc:`charmmfsw (k) <dihedral_charmm>`
    * :doc:`class2 (ko) <dihedral_class2>`
    * :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
+   * :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>`
    * :doc:`fourier (io) <dihedral_fourier>`
    * :doc:`harmonic (iko) <dihedral_harmonic>`
    * :doc:`helix (o) <dihedral_helix>`

doc/src/Commands_fix.rst

@@ -61,6 +61,7 @@ OPT.
    * :doc:`controller <fix_controller>`
    * :doc:`damping/cundall <fix_damping_cundall>`
    * :doc:`deform (k) <fix_deform>`
+   * :doc:`deform/pressure <fix_deform_pressure>`
    * :doc:`deposit <fix_deposit>`
    * :doc:`dpd/energy (k) <fix_dpd_energy>`
    * :doc:`drag <fix_drag>`
@@ -267,6 +268,7 @@ OPT.
    * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
    * :doc:`wall/colloid <fix_wall>`
    * :doc:`wall/ees <fix_wall_ees>`
+   * :doc:`wall/flow (k) <fix_wall_flow>`
    * :doc:`wall/gran (k) <fix_wall_gran>`
    * :doc:`wall/gran/region <fix_wall_gran_region>`
    * :doc:`wall/harmonic <fix_wall>`

doc/src/Commands_pair.rst

@@ -25,16 +25,16 @@ OPT.
 
    * :doc:`none <pair_none>`
    * :doc:`zero <pair_zero>`
-   * :doc:`hybrid (k) <pair_hybrid>`
+   * :doc:`hybrid (ko) <pair_hybrid>`
-   * :doc:`hybrid/overlay (k) <pair_hybrid>`
+   * :doc:`hybrid/molecular (o) <pair_hybrid>`
-   * :doc:`hybrid/scaled <pair_hybrid>`
+   * :doc:`hybrid/overlay (ko) <pair_hybrid>`
+   * :doc:`hybrid/scaled (o) <pair_hybrid>`
    * :doc:`kim <pair_kim>`
    * :doc:`list <pair_list>`
    * :doc:`tracker <pair_tracker>`
    *
    *
    *
-   *
    * :doc:`adp (ko) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
    * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@@ -94,9 +94,10 @@ OPT.
    * :doc:`coul/wolf (ko) <pair_coul>`
    * :doc:`coul/wolf/cs <pair_cs>`
    * :doc:`dpd (giko) <pair_dpd>`
-   * :doc:`dpd/fdt <pair_dpd_fdt>`
+   * :doc:`dpd/coul/slater/long (g) <pair_dpd_coul_slater_long>`
    * :doc:`dpd/ext (ko) <pair_dpd_ext>`
    * :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
+   * :doc:`dpd/fdt <pair_dpd_fdt>`
    * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
    * :doc:`dpd/tstat (gko) <pair_dpd>`
    * :doc:`dsmc <pair_dsmc>`
@@ -146,7 +147,7 @@ OPT.
    * :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
    * :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
    * :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
-   * :doc:`lj/charmmfsw/coul/long <pair_charmm>`
+   * :doc:`lj/charmmfsw/coul/long (k) <pair_charmm>`
    * :doc:`lj/class2 (gko) <pair_class2>`
    * :doc:`lj/class2/coul/cut (ko) <pair_class2>`
    * :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`
@@ -245,6 +246,7 @@ OPT.
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`pace (k) <pair_pace>`
    * :doc:`pace/extrapolation (k) <pair_pace>`
+   * :doc:`pedone (o) <pair_pedone>`
    * :doc:`pod <pair_pod>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
@@ -256,6 +258,7 @@ OPT.
    * :doc:`rann <pair_rann>`
    * :doc:`reaxff (ko) <pair_reaxff>`
    * :doc:`rebo (io) <pair_airebo>`
+   * :doc:`rebomos (o) <pair_rebomos>`
    * :doc:`resquared (go) <pair_resquared>`
    * :doc:`rheo <pair_rheo>`
    * :doc:`rheo/solid <pair_rheo_solid>`
@@ -269,7 +272,7 @@ OPT.
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
    * :doc:`snap (ik) <pair_snap>`
-   * :doc:`soft (go) <pair_soft>`
+   * :doc:`soft (gko) <pair_soft>`
    * :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
    * :doc:`sph/idealgas <pair_sph_idealgas>`
    * :doc:`sph/lj (g) <pair_sph_lj>`
@@ -303,6 +306,7 @@ OPT.
    * :doc:`tip4p/long/soft (o) <pair_fep_soft>`
    * :doc:`tri/lj <pair_tri_lj>`
    * :doc:`ufm (got) <pair_ufm>`
+   * :doc:`uf3 (k) <pair_uf3>`
    * :doc:`vashishta (gko) <pair_vashishta>`
    * :doc:`vashishta/table (o) <pair_vashishta>`
    * :doc:`wf/cut <pair_wf_cut>`

doc/src/Commands_removed.rst

@@ -129,7 +129,7 @@ USER-REAXC.
 USER-REAXC package
 ------------------
 
-.. deprecated:: TBD
+.. deprecated:: 7Feb2024
 
 The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
 In the process also the pair style and related fixes were renamed to use
@@ -148,6 +148,14 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS
 and the :ref:`GPU package <PKG-GPU>` are maintained
 and allow running LAMMPS with GPU acceleration.
 
+i-PI tool
+---------
+
+.. versionchanged:: TBD
+
+The i-PI tool has been removed from the LAMMPS distribution.  Instead,
+instructions to install i-PI from PyPi via pip are provided.
+
 restart2data tool
 -----------------
 

doc/src/Developer_updating.rst

@@ -18,6 +18,7 @@ Available topics in mostly chronological order are:
 - `Setting flags in the constructor`_
 - `Rename of pack/unpack_comm() to pack/unpack_forward_comm()`_
 - `Use ev_init() to initialize variables derived from eflag and vflag`_
+- `Use utils::count_words() functions instead of atom->count_words()`_
 - `Use utils::numeric() functions instead of force->numeric()`_
 - `Use utils::open_potential() function to open potential files`_
 - `Use symbolic Atom and AtomVec constants instead of numerical values`_
@@ -130,6 +131,41 @@ Not applying this change will not cause a compilation error, but
 can lead to inconsistent behavior and incorrect tallying of
 energy or virial.
 
+Use utils::count_words() functions instead of atom->count_words()
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 2Jun2020
+
+The "count_words()" functions for parsing text have been moved from the
+Atom class to the :doc:`utils namespace <Developer_utils>`.  The
+"count_words()" function in "utils" uses the Tokenizer class internally
+to split a line into words and count them, thus it will not modify the
+argument string as the function in the Atoms class did and thus had a
+variant using a copy buffer.  Unlike the old version, the new version
+does not remove comments. For that you can use the
+:cpp:func:`utils::trim_comment() function
+<LAMMPS_NS::utils::trim_comment>` as shown in the example below.
+
+Old:
+
+.. code-block:: c++
+
+   nwords = atom->count_words(line);
+   int nwords = atom->count_words(buf);
+
+New:
+
+.. code-block:: c++
+
+   nwords = utils::count_words(line);
+   int nwords = utils::count_words(utils::trim_comment(buf));
+
+.. seealso::
+
+   :cpp:func:`utils::count_words() <LAMMPS_NS::utils::count_words>`,
+   :cpp:func:`utils::trim_comments() <LAMMPS_NS::utils::trim_comments>`
+
+
 Use utils::numeric() functions instead of force->numeric()
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -137,11 +173,12 @@ Use utils::numeric() functions instead of force->numeric()
 
 The "numeric()" conversion functions (including "inumeric()",
 "bnumeric()", and "tnumeric()") have been moved from the Force class to
-the utils namespace.  Also they take an additional argument that selects
+the :doc:`utils namespace <Developer_utils>`.  Also they take an
-whether the ``Error::all()`` or ``Error::one()`` function should be
+additional argument that selects whether the ``Error::all()`` or
-called in case of an error.  The former should be used when *all* MPI
+``Error::one()`` function should be called in case of an error.  The
-processes call the conversion function and the latter *must* be used
+former should be used when *all* MPI processes call the conversion
-when they are called from only one or a subset of the MPI processes.
+function and the latter *must* be used when they are called from only
+one or a subset of the MPI processes.
 
 Old:
 

doc/src/Developer_utils.rst

@@ -635,10 +635,10 @@ Tohoku University (under MIT license)
 
 ----------
 
-.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec)
+.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec, int sort)
    :project: progguide
 
-.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3])
+.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3], int sort)
    :project: progguide
 
 ---------------------------

doc/src/Errors_details.rst

@@ -13,15 +13,44 @@ discussions of such cases.
 Unknown identifier in data file
 -------------------------------
 
-This error happens when LAMMPS encounters a line of text in an unexpected format
+This error happens when LAMMPS encounters a line of text with an
-while reading a data file. This is most commonly cause by inconsistent header and
+unexpected keyword while :doc:`reading a data file <read_data>`.  This
-section data.  The header section informs LAMMPS how many entries or lines are expected in the
+would be either header keywords or section header keywords.  This is
-various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of the data file.
+most commonly due to a mistyped keyword or due to a keyword that is
-If there is a mismatch, LAMMPS will either keep reading beyond the end of a section
+inconsistent with the :doc:`atom style <atom_style>` used.
-or stop reading before the section has ended.
 
-Such a mismatch can happen unexpectedly when the first line of the data
+The header section informs LAMMPS how many entries or lines are expected
-is *not* a comment as required by the format.  That would result in
+in the various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of
-LAMMPS expecting, for instance, 0 atoms because the "atoms" header line
+the data file.  If there is a mismatch, LAMMPS will either keep reading
-is treated as a comment.
+beyond the end of a section or stop reading before the section has
+ended.  In that case the next line will not contain a recognized keyword.
 
+Such a mismatch can also happen when the first line of the data
+is *not* a comment as required by the format, but a line with a valid
+header keyword.  That would result in LAMMPS expecting, for instance,
+0 atoms because the "atoms" header line is the first line and thus
+treated as a comment.
+
+Another possibility to trigger this error is to have a keyword in the
+data file that corresponds to a fix (e.g. :doc:`fix cmap <fix_cmap>`)
+but the :doc:`read_data <read_data>` command is missing the (optional)
+arguments that identify the fix and the header keyword and section
+keyword or those arguments are inconsistent with the keywords in the
+data file.
+
+.. _err0002:
+
+Incorrect format in ... section of data file
+--------------------------------------------
+
+This error happens when LAMMPS reads the contents of a section of a
+:doc:`data file <read_data>` and the number of parameters in the line
+differs from what is expected.  This most commonly happens, when the
+atom style is different from what is expected for a specific data file
+since changing the atom style usually changes the format of the line.
+
+This error can also happen when the number of entries indicated in the
+header of a data file (e.g. the number of atoms) is larger than the
+number of lines provided (e.g. in the corresponding Atoms section)
+and then LAMMPS will continue reading into the next section and that
+would have a completely different format.

doc/src/Errors_messages.rst

@@ -7883,12 +7883,6 @@ keyword to allow for additional bonds to be formed
    Fix poems cannot (yet) work with coupled bodies whose joints connect
    the bodies in a tree structure.
 
-*Triclinic box skew is too large*
-   The displacement in a skewed direction must be less than half the box
-   length in that dimension.  E.g. the xy tilt must be between -half and
-   +half of the x box length.  This constraint can be relaxed by using
-   the box tilt command.
-
 *Tried to convert a double to int, but input_double > INT_MAX*
    Self-explanatory.
 

doc/src/Errors_warnings.rst

@@ -752,13 +752,6 @@ This will most likely cause errors in kinetic fluctuations.
    More than the maximum # of neighbors was found multiple times.  This
    was unexpected.
 
-*Triclinic box skew is large*
-   The displacement in a skewed direction is normally required to be less
-   than half the box length in that dimension.  E.g. the xy tilt must be
-   between -half and +half of the x box length.  You have relaxed the
-   constraint using the box tilt command, but the warning means that a
-   LAMMPS simulation may be inefficient as a result.
-
 *Use special bonds = 0,1,1 with bond style fene*
    Most FENE models need this setting for the special_bonds command.
 

doc/src/Fortran.rst

@@ -305,6 +305,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype extract_setting: function
    :f extract_global: :f:func:`extract_global`
    :ftype extract_global: function
+   :f map_atom: :f:func:`map_atom`
+   :ftype map_atom: function
    :f extract_atom: :f:func:`extract_atom`
    :ftype extract_atom: function
    :f extract_compute: :f:func:`extract_compute`
@@ -315,6 +317,10 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype extract_variable: function
    :f set_variable: :f:subr:`set_variable`
    :ftype set_variable: subroutine
+   :f set_string_variable: :f:subr:`set_set_string_variable`
+   :ftype set_string_variable: subroutine
+   :f set_internal_variable: :f:subr:`set_internal_variable`
+   :ftype set_internal_variable: subroutine
    :f gather_atoms: :f:subr:`gather_atoms`
    :ftype gather_atoms: subroutine
    :f gather_atoms_concat: :f:subr:`gather_atoms_concat`
@@ -1251,8 +1257,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    three elements of the global vector calculated by fix recenter into the
    variables *dx*, *dy*, and *dz*, respectively.
 
-   If asked for per-atom or local data, :f:func:`extract_compute` returns a
+   If asked for per-atom or local data, :f:func:`extract_fix` returns a
-   pointer to actual LAMMPS data. The pointer so returned will have the
+   pointer to actual LAMMPS data.  The pointer returned will have the
    appropriate size to match the internal data, and will be
    type/kind/rank-checked at the time of the assignment. For example,
 
@@ -1398,7 +1404,28 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    Set the value of a string-style variable.
 
-   .. versionadded:: 3Nov2022
+   .. deprecated:: 7Feb2024
+
+   This function assigns a new value from the string *str* to the string-style
+   variable *name*\ . If *name* does not exist or is not a string-style
+   variable, an error is generated.
+
+   .. warning::
+
+      This subroutine is deprecated and :f:subr:`set_string_variable`
+      should be used instead.
+
+   :p character(len=*) name: name of the variable
+   :p character(len=*) str:  new value to assign to the variable
+   :to: :cpp:func:`lammps_set_variable`
+
+--------
+
+.. f:subroutine:: set_string_variable(name, str)
+
+   Set the value of a string-style variable.
+
+   .. versionadded:: 7Feb2024
 
    This function assigns a new value from the string *str* to the string-style
    variable *name*\ . If *name* does not exist or is not a string-style
@@ -1406,7 +1433,23 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    :p character(len=*) name: name of the variable
    :p character(len=*) str:  new value to assign to the variable
-   :to: :cpp:func:`lammps_set_variable`
+   :to: :cpp:func:`lammps_set_string_variable`
+
+--------
+
+.. f:subroutine:: set_internal_variable(name, val)
+
+   Set the value of a internal-style variable.
+
+   .. versionadded:: 7Feb2024
+
+   This function assigns a new value from the floating-point number *val* to
+   the internal-style variable *name*\ . If *name* does not exist or is not
+   an internal-style variable, an error is generated.
+
+   :p character(len=*) name: name of the variable
+   :p read(c_double) val:  new value to assign to the variable
+   :to: :cpp:func:`lammps_set_internal_variable`
 
 --------
 

doc/src/Howto_2d.rst

@@ -1,42 +1,112 @@
-2d simulations
+================
-==============
+ 2d simulations
+================
 
-Use the :doc:`dimension <dimension>` command to specify a 2d simulation.
+You must use the :doc:`dimension <dimension>` command to specify a 2d
+simulation.  The default is 3d.
 
-Make the simulation box periodic in z via the :doc:`boundary <boundary>`
+A 2d simulation box must be periodic in z as set by the :doc:`boundary
-command.  This is the default.
+<boundary>` command.  This is the default.
 
-If using the :doc:`create_box <create_box>` command to define a
+Simulation boxes in LAMMPS can be either orthogonal or triclinic in
-simulation box, set the z dimensions narrow, but finite, so that the
+shape.  Orthogonal boxes in 2d are a rectangle with 4 edges that are
-:doc:`create_atoms <create_atoms>` command will fill the 3d simulation
+each perpendicular to either the x or y coordinate axes.  Triclinic
-box with a single z plane of atoms - e.g.
+boxes in 2d are a parallelogram with opposite pairs of faces parallel
+to each other.  LAMMPS supports two forms of triclinic boxes,
+restricted and general, which for 2d differ in how the box is oriented
+with respect to the xy coordinate axes.  See the :doc:`Howto triclinic
+<Howto_triclinic>` for a detailed description of all 3 kinds of
+simulation boxes.
+
+Here are examples of using the :doc:`create_box <create_box>` command
+to define the simulation box for a 2d system.
 
 .. code-block:: LAMMPS
 
-   create_box 1 -10 10 -10 10 -0.25 0.25
+   # 2d orthogonal box using a block-style region
+   region mybox block -10 10 0 10 -0.5 0.5
+   create_box 1 mybox
 
-If using the :doc:`read_data <read_data>` command to read in a file of
+   # 2d restricted triclinic box using a prism-style region with only xy tilt
-atom coordinates, set the "zlo zhi" values to be finite but narrow,
+   region mybox prism 0 10 0 10 -0.5 0.5 2.0 0.0 0.0
-similar to the create_box command settings just described.  For each
+   create_box 1 mybox
-atom in the file, assign a z coordinate so it falls inside the
-z-boundaries of the box - e.g. 0.0.
 
-Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last
+   # 2d general triclinic box using a primitive cell for a 2d hex lattice
-defined fix to ensure that the z-components of velocities and forces
+   lattice       custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 &
-are zeroed out every timestep.  The reason to make it the last fix is
+                 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
-so that any forces induced by other fixes will be zeroed out.
+   create_box    1 NULL 0 5 0 5 -0.5 0.5
 
-Many of the example input scripts included in the LAMMPS distribution
+Note that for 2d orthogonal or restricted triclinic boxes, the box has
+a 3rd dimension which must straddle z = 0.0 in the z dimension.
+Typically the width of box in the z dimension should be narrow,
+e.g. -0.5 to 0.5, but that is not required.  For a 2d general
+triclinic box, the *a3* vector defined by the :doc:`lattice <lattice>`
+command must be (0.0,0.0,1.0), which is its default value.  Also the
+*clo* and *chi* arguments of the :doc:`create_box <create_box>`
+command must be -0.5 and 0.5.
+
+Here are examples of using the :doc:`read_data <read_data>` command
+to define the simulation box for a 2d system via keywords in the
+header section of the data file.  These are the same boxes as the examples
+for the :doc:`create_box <create_box>` command
+
+.. code-block:: LAMMPS
+
+   # 2d orthogonal box
+   -10 10   xlo xhi
+   0 10     ylo yhi
+   -0.5 0.5 zlo zhi       # this is the default, so no need to specify
+
+   # 2d restricted triclinic box with only xy tilt
+   -10 10   xlo xhi
+   0 10     ylo yhi
+   -0.5 0.5 zlo zhi       # this is the default, so no need to specify
+   2.0 0.0 0.0 xy xz yz
+
+   # 3d general triclinic box using a primitive cell for a 2d hex lattice
+   5 0 0              avec
+   2.5 4.3301270189 0 bvec
+   0 0 1              cvec           # this is the default, so no need to specify
+   0 0 -0.5           abc origin     # this is the default for 2d, so no need to specify
+
+Note that for 2d orthogonal or restricted triclinic boxes, the box has
+a 3rd dimension specified by the *zlo zhi* values, which must straddle
+z = 0.0.  Typically the width of box in the z dimension should be
+narrow, e.g. -0.5 to 0.5, but that is not required.  For a 2d general
+triclinic box, the z component of *avec* and *bvec* must be zero, and
+*cvec* must be (0,0,1), which is the default.  The z component of *abc
+origin* must also be -0.5, which is the default.
+
+If using the :doc:`create_atoms <create_atoms>` command to create
+atoms in the 2d simulation box, all the z coordinates of created atoms
+will be zero.
+
+If using the :doc:`read_data <read_data>` command to read in a data
+file of atom coordinates for a 2d system, the z coordinates of all
+atoms should be zero.  A value within epsilon of zero is also allowed
+in case the data file was generated by another program with finite
+numeric precision, in which case the z coord for the atom will be set
+to zero.
+
+Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last fix
+defined in the input script.  It ensures that the z-components of
+velocities and forces are zeroed out every timestep.  The reason to
+make it the last fix is so that any forces added by other fixes will
+also be zeroed out.
+
+Many of the example input scripts included in the examples directory
 are for 2d models.
 
 .. note::
 
    Some models in LAMMPS treat particles as finite-size spheres, as
-   opposed to point particles.  See the :doc:`atom_style sphere <atom_style>` and :doc:`fix nve/sphere <fix_nve_sphere>`
+   opposed to point particles.  See the :doc:`atom_style sphere
-   commands for details.  By default, for 2d simulations, such particles
+   <atom_style>` and :doc:`fix nve/sphere <fix_nve_sphere>` commands
-   will still be modeled as 3d spheres, not 2d discs (circles), meaning
+   for details.  By default, for 2d simulations, such particles will
+   still be modeled as 3d spheres, not 2d discs (circles), meaning
    their moment of inertia will be that of a sphere.  If you wish to
-   model them as 2d discs, see the :doc:`set density/disc <set>` command
+   model them as 2d discs, see the :doc:`set density/disc <set>`
-   and the *disc* option for the :doc:`fix nve/sphere <fix_nve_sphere>`,
+   command and the *disc* option for the :doc:`fix nve/sphere
-   :doc:`fix nvt/sphere <fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere <fix_npt_sphere>`
+   <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
-   commands.
+   :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
+   <fix_npt_sphere>` commands.

doc/src/Howto_body.rst

@@ -102,8 +102,19 @@ particles of different styles
 | :doc:`dump image <dump_image>`                 | output body particle attributes as an image         |
 +------------------------------------------------+-----------------------------------------------------+
 
-The pair styles defined for use with specific body styles are listed
+The pair styles currently defined for use with specific body styles
-in the sections below.
+are listed in the sections below.
+
+Note that for all the body styles, if the data file defines a general
+triclinic box, then the orientation of the body particle and its
+corresponding 6 moments of inertia and other orientation-dependent
+values should reflect the fact the body is defined withing a general
+triclinic box with edge vectors **A**,**B**,**C**.  LAMMPS will rotate
+the box to convert it to a restricted triclinic box.  This operation
+will also rotate the orientation of the body particles.  See the
+:doc:`Howto triclinic <Howto_triclinic>` doc page for more details.
+The sections below highlight the orientation-dependent values specific
+to each body style.
 
 ----------
 
@@ -154,12 +165,18 @@ values consistent with the current orientation of the rigid body
 around its center of mass.  The values are with respect to the
 simulation box XYZ axes, not with respect to the principal axes of the
 rigid body itself.  LAMMPS performs the latter calculation internally.
+
 The coordinates of each sub-particle are specified as its x,y,z
 displacement from the center-of-mass of the body particle.  The
 center-of-mass position of the particle is specified by the x,y,z
 values in the *Atoms* section of the data file, as is the total mass
 of the body particle.
 
+Note that if the data file defines a general triclinic simulation box,
+these sub-particle displacements are orientation-dependent and, as
+mentioned above, should reflect the body particle's orientation within
+the general triclinic box.
+
 The :doc:`pair_style body/nparticle <pair_body_nparticle>` command can be used
 with this body style to compute body/body and body/non-body interactions.
 
@@ -226,6 +243,7 @@ values consistent with the current orientation of the rigid body
 around its center of mass.  The values are with respect to the
 simulation box XYZ axes, not with respect to the principal axes of the
 rigid body itself.  LAMMPS performs the latter calculation internally.
+
 The coordinates of each vertex are specified as its x,y,z displacement
 from the center-of-mass of the body particle.  The center-of-mass
 position of the particle is specified by the x,y,z values in the
@@ -270,6 +288,11 @@ A disk, whose diameter is 3.0, mass 1.0, is specified as follows:
    0 0 0
    3.0
 
+Note that if the data file defines a general triclinic simulation box,
+these polygon vertex displacements are orientation-dependent and, as
+mentioned above, should reflect the body particle's orientation within
+the general triclinic box.
+
 The :doc:`pair_style body/rounded/polygon <pair_body_rounded_polygon>`
 command can be used with this body style to compute body/body
 interactions.  The :doc:`fix wall/body/polygon <fix_wall_body_polygon>`
@@ -366,6 +389,7 @@ values consistent with the current orientation of the rigid body
 around its center of mass.  The values are with respect to the
 simulation box XYZ axes, not with respect to the principal axes of the
 rigid body itself.  LAMMPS performs the latter calculation internally.
+
 The coordinates of each vertex are specified as its x,y,z displacement
 from the center-of-mass of the body particle.  The center-of-mass
 position of the particle is specified by the x,y,z values in the
@@ -435,6 +459,11 @@ A sphere whose diameter is 3.0 and mass 1.0, is specified as follows:
 The number of edges and faces for a rod or sphere must be listed,
 but is ignored.
 
+Note that if the data file defines a general triclinic simulation box,
+these polyhedron vertex displacements are orientation-dependent and,
+as mentioned above, should reflect the body particle's orientation
+within the general triclinic box.
+
 The :doc:`pair_style body/rounded/polhedron
 <pair_body_rounded_polyhedron>` command can be used with this body
 style to compute body/body interactions.  The :doc:`fix

doc/src/Howto_bpm.rst

@@ -15,7 +15,8 @@ orientation for rotational models. This produces a stress-free initial
 state. Furthermore, bonds are allowed to break under large strains,
 producing fracture. The examples/bpm directory has sample input scripts
 for simulations of the fragmentation of an impacted plate and the
-pouring of extended, elastic bodies.
+pouring of extended, elastic bodies. See :ref:`(Clemmer) <howto-Clemmer>`
+for more general information on the approach and the LAMMPS implementation.
 
 ----------
 
@@ -150,3 +151,9 @@ the following are currently compatible with BPM bond styles:
    interactions, one will need to switch between different *special_bonds*
    settings in the input script. An example is found in
    ``examples/bpm/impact``.
+
+----------
+
+.. _howto-Clemmer:
+
+**(Clemmer)** Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).

doc/src/Howto_cmake.rst

@@ -349,6 +349,8 @@ Some common LAMMPS specific variables
      - when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a``
    * - ``FFT``
      - select which FFT library to use: ``FFTW3``, ``MKL``, ``KISS`` (default, unless FFTW3 is found)
+   * - ``FFT_KOKKOS``
+     - select which FFT library to use in Kokkos-enabled styles: ``FFTW3``, ``MKL``, ``HIPFFT``, ``CUFFT``, ``KISS`` (default)
    * - ``FFT_SINGLE``
      - select whether to use single precision FFTs (default: ``off``)
    * - ``WITH_JPEG``

doc/src/Howto_granular.rst

@@ -45,10 +45,15 @@ atoms, and should be used for granular system instead of the fix style
 
 To model heat conduction, one must add the temperature and heatflow
 atom variables with:
+
 * :doc:`fix property/atom <fix_property_atom>`
+
 a temperature integration fix
+
 * :doc:`fix heat/flow <fix_heat_flow>`
+
 and a heat conduction option defined in both
+
 * :doc:`pair_style granular <pair_granular>`
 * :doc:`fix wall/gran <fix_wall_gran>`
 

doc/src/Howto_structured_data.rst

@@ -52,8 +52,8 @@ JSON
      "ke": 2.4962152903997174569
    }
 
-YAML format thermo_style output
+YAML format thermo_style or dump_style output
-===============================
+=============================================
 
 Extracting data from log file
 -----------------------------
@@ -112,6 +112,9 @@ of that run:
    Number of runs:  2
    TotEng  =  -4.62140097780047
 
+Extracting data from dump file
+------------------------------
+
 .. versionadded:: 4May2022
 
 YAML format output has been added to multiple commands in LAMMPS,

doc/src/Howto_triclinic.rst

@@ -2,43 +2,195 @@ Triclinic (non-orthogonal) simulation boxes
 ===========================================
 
 By default, LAMMPS uses an orthogonal simulation box to encompass the
-particles.  The :doc:`boundary <boundary>` command sets the boundary
+particles.  The orthogonal box has its "origin" at (xlo,ylo,zlo) and
-conditions of the box (periodic, non-periodic, etc).  The orthogonal
+extends to (xhi,yhi,zhi).  Conceptually it is defined by 3 edge
-box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
+vectors starting from the origin given by **A** = (xhi-xlo,0,0); **B**
-starting from the origin given by **a** = (xhi-xlo,0,0); **b** =
+= (0,yhi-ylo,0); **C** = (0,0,zhi-zlo).  The :doc:`boundary
-(0,yhi-ylo,0); **c** = (0,0,zhi-zlo).  The 6 parameters
+<boundary>` command sets the boundary conditions for the 6 faces of
+the box (periodic, non-periodic, etc).  The 6 parameters
 (xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
-is created, e.g. by the :doc:`create_box <create_box>` or
+is created by one of these commands:
-:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
-commands.  Additionally, LAMMPS defines box size parameters lx,ly,lz
-where lx = xhi-xlo, and similarly in the y and z dimensions.  The 6
-parameters, as well as lx,ly,lz, can be output via the
-:doc:`thermo_style custom <thermo_style>` command.
 
-LAMMPS also allows simulations to be performed in triclinic
+* :doc:`create_box <create_box>`
-(non-orthogonal) simulation boxes shaped as a parallelepiped with
+* :doc:`read_data <read_data>`
-triclinic symmetry.  The parallelepiped has its "origin" at
+* :doc:`read_restart <read_restart>`
-(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
+* :doc:`read_dump <read_dump>`
-origin given by **a** = (xhi-xlo,0,0); **b** = (xy,yhi-ylo,0); **c** =
-(xz,yz,zhi-zlo).  *xy,xz,yz* can be 0.0 or positive or negative values
-and are called "tilt factors" because they are the amount of
-displacement applied to faces of an originally orthogonal box to
-transform it into the parallelepiped.  In LAMMPS the triclinic
-simulation box edge vectors **a**, **b**, and **c** cannot be arbitrary
-vectors.  As indicated, **a** must lie on the positive x axis.  **b** must
-lie in the xy plane, with strictly positive y component. **c** may have
-any orientation with strictly positive z component.  The requirement
-that **a**, **b**, and **c** have strictly positive x, y, and z components,
-respectively, ensures that **a**, **b**, and **c** form a complete
-right-handed basis.  These restrictions impose no loss of generality,
-since it is possible to rotate/invert any set of 3 crystal basis
-vectors so that they conform to the restrictions.
 
-For example, assume that the 3 vectors **A**,\ **B**,\ **C** are the edge
+Internally, LAMMPS defines box size parameters lx,ly,lz where lx =
-vectors of a general parallelepiped, where there is no restriction on
+xhi-xlo, and similarly in the y and z dimensions.  The 6 parameters, as
-**A**,\ **B**,\ **C** other than they form a complete right-handed basis i.e.
+well as lx,ly,lz, can be output via the :doc:`thermo_style custom
-**A** x **B** . **C** > 0.  The equivalent LAMMPS **a**,\ **b**,\ **c** are a linear
+<thermo_style>` command.  See the :doc:`Howto 2d <Howto_2d>` doc page
-rotation of **A**, **B**, and **C** and can be computed as follows:
+for info on how zlo and zhi are defined for 2d simulations.
+
+----------
+
+Triclinic simulation boxes
+""""""""""""""""""""""""""
+
+LAMMPS also allows simulations to be performed using triclinic
+(non-orthogonal) simulation boxes shaped as a 3d parallelepiped with
+triclinic symmetry.  For 2d simulations a triclinic simulation box is
+effectively a parallelogram; see the :doc:`Howto 2d <Howto_2d>` doc
+page for details.
+
+One use of triclinic simulation boxes is to model solid-state crystals
+with triclinic symmetry.  The :doc:`lattice <lattice>` command can be
+used with non-orthogonal basis vectors to define a lattice that will
+tile a triclinic simulation box via the :doc:`create_atoms
+<create_atoms>` command.
+
+A second use is to run Parrinello-Rahman dynamics via the :doc:`fix
+npt <fix_nh>` command, which will adjust the xy, xz, yz tilt factors
+to compensate for off-diagonal components of the pressure tensor.  The
+analog for an :doc:`energy minimization <minimize>` is the :doc:`fix
+box/relax <fix_box_relax>` command.
+
+A third use is to shear a bulk solid to study the response of the
+material.  The :doc:`fix deform <fix_deform>` command can be used for
+this purpose.  It allows dynamic control of the xy, xz, yz tilt
+factors as a simulation runs.  This is discussed in the :doc:`Howto
+NEMD <Howto_nemd>` doc page on non-equilibrium MD (NEMD) simulations.
+
+Conceptually, a triclinic parallelepiped is defined with an "origin"
+at (xlo,ylo,zhi) and 3 edge vectors **A** = (ax,ay,az), **B** =
+(bx,by,bz), **C** = (cx,cy,cz) which can be arbitrary vectors, so long
+as they are non-zero, distinct, and not co-planar.  In addition, they
+must define a right-handed system, such that (**A** cross **B**)
+points in the direction of **C**.  Note that a left-handed system can
+be converted to a right-handed system by simply swapping the order of
+any pair of the **A**, **B**, **C** vectors.
+
+The 4 commands listed above for defining orthogonal simulation boxes
+have triclinic options which allow for specification of the origin and
+edge vectors **A**, **B**, **C**.  For each command, this can be done
+in one of two ways, for what LAMMPS calls a *general* triclinic box or
+a *restricted* triclinic box.
+
+A *general* triclinic box is specified by an origin (xlo, ylo, zlo)
+and arbitrary edge vectors **A** = (ax,ay,az), **B** = (bx,by,bz), and
+**C** = (cx,cy,cz).  So there are 12 parameters in total.
+
+A *restricted* triclinic box also has an origin (xlo,ylo,zlo), but its
+edge vectors are of the following restricted form: **A** =
+(xhi-xlo,0,0), **B** = (xy,yhi-ylo,0), **C** = (xz,yz,zhi-zlo).  So
+there are 9 parameters in total.  Note that the restricted form
+requires **A** to be along the x-axis, **B** to be in the xy plane
+with a y-component in the +y direction, and **C** to have its
+z-component in the +z direction.  Note that a restricted triclinic box
+is *right-handed* by construction since (**A** cross **B**) points in
+the direction of **C**.
+
+The *xy,xz,yz* values can be zero or positive or negative.  They are
+called "tilt factors" because they are the amount of displacement
+applied to edges of faces of an orthogonal box to change it into a
+restricted triclinic parallelepiped.
+
+.. note::
+
+   Any right-handed general triclinic box (i.e. solid-state crystal
+   basis vectors) can be rotated in 3d around its origin in order to
+   conform to the LAMMPS definition of a restricted triclinic box.
+   See the discussion in the next sub-section about general triclinic
+   simulation boxes in LAMMPS.
+
+Note that the :doc:`thermo_style custom <thermo_style>` command has
+keywords for outputting the various parameters that define the size
+and shape of orthogonal, restricted triclinic, and general triclinic
+simulation boxes.
+
+For orthogonal boxes there 6 thermo keywords (xlo,ylo,zlo) and
+(xhi,yhi,zhi).
+
+For restricted triclinic boxes there are 9 thermo keywords for
+(xlo,ylo,zlo), (xhi,yhi,zhi), and the (xy,xz,yz) tilt factors.
+
+For general triclinic boxes there are 12 thermo keywords for
+(xlo,ylo,zhi) and the components of the **A**, **B**, **C** edge
+vectors, namely (avecx,avecy,avecz), (bvecx,bvecy,bvecz), and
+(cvecx,cvecy,cvecz),
+
+The remainder of this doc page explains (a) how LAMMPS operates with
+general triclinic simulation boxes, (b) mathematical transformations
+between general and restricted triclinic boxes which may be useful
+when creating LAMMPS inputs or interpreting outputs for triclinic
+simulations, and (c) how LAMMPS uses tilt factors for restricted
+triclinic simulation boxes.
+
+----------
+
+General triclinic simulation boxes in LAMMPS
+""""""""""""""""""""""""""""""""""""""""""""
+
+LAMMPS allows specification of general triclinic simulation boxes with
+their atoms as a convenience for users who may be converting data from
+solid-state crystallographic representations or from DFT codes for
+input to LAMMPS.  Likewise it allows output of dump files, data files,
+and thermodynamic data (e.g. pressure tensor) in a general triclinic
+format.
+
+However internally, LAMMPS only uses restricted triclinic simulation
+boxes.  This is for parallel efficiency and to formulate partitioning
+of the simulation box across processors, neighbor list building, and
+inter-processor communication of per-atom data with methods similar to
+those used for orthogonal boxes.
+
+This means 4 things which are important to understand:
+
+* Input of a general triclinic system is immediately converted to a
+  restricted triclinic system.
+* If output of per-atom data for a general triclinic system is
+  requested (e.g. for atom coordinates in a dump file),
+  conversion from a restricted to general triclinic system is done at
+  the time of output.
+* The conversion of the simulation box and per-atom data from general
+  triclinic to restricted triclinic (and vice versa) is a 3d rotation
+  operation around an origin, which is the lower left corner of the
+  simulation box.  This means an input data file for a general
+  triclinic system should specify all per-atom quantities consistent
+  with the general triclinic box and its orientation relative to the
+  standard x,y,z coordinate axes.  For example, atom coordinates
+  should be inside the general triclinic simulation box defined by the
+  edge vectors **A**, **B**, **C** and its origin.  Likewise per-atom
+  velocities should be in directions consistent with the general
+  triclinic box orientation.  E.g. a velocity vector which will be in
+  the +x direction once LAMMPS converts from a general to restricted
+  triclinic box, should be specified in the data file in the direction
+  of the **A** edge vector.  See the :doc:`read_data <read_data>` doc
+  page for info on all the per-atom vector quantities to which this
+  rule applies when a data file for a general triclinic box is input.
+* If commands such as :doc:`write_data <write_data>` or :doc:`dump
+  custom <dump>` are used to output general triclinic information, it
+  is effectively the inverse of the operation described in the
+  preceding bullet.
+* Other LAMMPS commands such as :doc:`region <region>` or
+  :doc:`velocity <velocity>` or :doc:`set <set>`, operate on a
+  restricted triclinic system even if a general triclinic system was
+  defined initially.
+
+This is the list of commands which have general triclinic options:
+
+* :doc:`create_box <create_box>` - define a general triclinic box
+* :doc:`create_atoms <create_atoms>` - add atoms to a general triclinic box
+* :doc:`lattice <lattice>` - define a custom lattice consistent with the **A**, **B**, **C** edge vectors of a general triclinic box
+* :doc:`read_data <read_data>` - read a data file for a general triclinic system
+* :doc:`write_data <write_data>` - write a data file for a general triclinic system
+* :doc:`dump atom, dump custom <dump>` - output dump snapshots in general triclinic format
+* :doc:`dump_modify triclinic/general <dump_modify>` - select general triclinic format for dump output
+* :doc:`thermo_style <thermo_style>` - output the pressure tensor in
+  general triclinic format
+* :doc:`thermo_modify triclinic/general <thermo_modify>` - select general triclinic format for thermo output
+* :doc:`read_restart <read_restart>` - read a restart file for a general triclinic system
+* :doc:`write_restart <read_restart>` - write a restart file for a general triclinic system
+
+----------
+
+Transformation from general to restricted triclinic boxes
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Let **A**,\ **B**,\ **C** be the right-handed edge vectors of a
+general triclinic simulation box.  The equivalent LAMMPS **a**,\
+**b**,\ **c** for a restricted triclinic box are a 3d rotation of
+**A**, **B**, and **C** and can be computed as follows:
 
 .. math::
 
@@ -55,23 +207,17 @@ rotation of **A**, **B**, and **C** and can be computed as follows:
   c_y = & \mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})} \times \mathbf{\hat{A}} \quad = \quad \frac{\mathbf{B} \cdot \mathbf{C} - b_x c_x}{b_y} \\
   c_z = & |\mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})}|\quad = \quad \sqrt{C^2 - {c_x}^2 - {c_y}^2}
 
-where A = \| **A** \| indicates the scalar length of **A**\ . The hat symbol (\^)
+where A = \| **A** \| indicates the scalar length of **A**\ . The hat
-indicates the corresponding unit vector. :math:`\beta` and :math:`\gamma` are angles
+symbol (\^) indicates the corresponding unit vector. :math:`\beta` and
-between the vectors described below. Note that by construction,
+:math:`\gamma` are angles between the **A**, **B**, **C** vectors
-**a**, **b**, and **c** have strictly positive x, y, and z components, respectively.
+as described below.
-If it should happen that
-**A**, **B**, and **C** form a left-handed basis, then the above equations
-are not valid for **c**\ . In this case, it is necessary
-to first apply an inversion. This can be achieved
-by interchanging two basis vectors or by changing the sign of one of them.
 
-For consistency, the same rotation/inversion applied to the basis vectors
+For consistency, the same rotation applied to the triclinic box edge
-must also be applied to atom positions, velocities,
+vectors can also be applied to atom positions, velocities, and other
-and any other vector quantities.
+vector quantities.  This can be conveniently achieved by first
-This can be conveniently achieved by first converting to
+converting to fractional coordinates in the general triclinic
-fractional coordinates in the
+coordinates and then converting to coordinates in the restricted
-old basis and then converting to distance coordinates in the new basis.
+triclinic basis.  The transformation is given by the following equation:
-The transformation is given by the following equation:
 
 .. math::
 
@@ -82,87 +228,24 @@ The transformation is given by the following equation:
       \mathbf{A \times B}
     \end{pmatrix} \cdot \mathbf{X}
 
-where *V* is the volume of the box, **X** is the original vector quantity and
+where *V* is the volume of the box (same in either basis), **X** is
-**x** is the vector in the LAMMPS basis.
+the fractional vector in the general triclinic basis and **x** is the
+resulting vector in the restricted triclinic basis.
 
-There is no requirement that a triclinic box be periodic in any
+----------
-dimension, though it typically should be in at least the second dimension
-of the tilt (y in xy) if you want to enforce a shift in periodic
-boundary conditions across that boundary.  Some commands that work
-with triclinic boxes, e.g. the :doc:`fix deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require periodicity or non-shrink-wrap
-boundary conditions in specific dimensions.  See the command doc pages
-for details.
 
-The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
+Crystallographic general triclinic representation of a simulation box
-time the simulation box is created.  This happens in one of 3 ways.
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-If the :doc:`create_box <create_box>` command is used with a region of
-style *prism*, then a triclinic box is setup.  See the
-:doc:`region <region>` command for details.  If the
-:doc:`read_data <read_data>` command is used to define the simulation
-box, and the header of the data file contains a line with the "xy xz
-yz" keyword, then a triclinic box is setup.  See the
-:doc:`read_data <read_data>` command for details.  Finally, if the
-:doc:`read_restart <read_restart>` command reads a restart file which
-was written from a simulation using a triclinic box, then a triclinic
-box will be setup for the restarted simulation.
 
-Note that you can define a triclinic box with all 3 tilt factors =
+General triclinic crystal structures are often defined using three
-0.0, so that it is initially orthogonal.  This is necessary if the box
+lattice constants *a*, *b*, and *c*, and three angles :math:`\alpha`,
-will become non-orthogonal, e.g. due to the :doc:`fix npt <fix_nh>` or
+:math:`\beta`, and :math:`\gamma`. Note that in this nomenclature, the
-:doc:`fix deform <fix_deform>` commands.  Alternatively, you can use the
+a, b, and c lattice constants are the scalar lengths of the edge
-:doc:`change_box <change_box>` command to convert a simulation box from
-orthogonal to triclinic and vice versa.
-
-As with orthogonal boxes, LAMMPS defines triclinic box size parameters
-lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
-The 9 parameters, as well as lx,ly,lz, can be output via the
-:doc:`thermo_style custom <thermo_style>` command.
-
-To avoid extremely tilted boxes (which would be computationally
-inefficient), LAMMPS normally requires that no tilt factor can skew
-the box more than half the distance of the parallel box length, which
-is the first dimension in the tilt factor (x for xz).  This is required
-both when the simulation box is created, e.g. via the
-:doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands,
-as well as when the box shape changes dynamically during a simulation,
-e.g. via the :doc:`fix deform <fix_deform>` or :doc:`fix npt <fix_nh>`
-commands.
-
-For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
-the xy tilt factor must be between -5 and 5.  Similarly, both xz and
-yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2.  Note that this is
-not a limitation, since if the maximum tilt factor is 5 (as in this
-example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
-... are geometrically all equivalent.  If the box tilt exceeds this
-limit during a dynamics run (e.g. via the :doc:`fix deform <fix_deform>`
-command), then the box is "flipped" to an equivalent shape with a tilt
-factor within the bounds, so the run can continue.  See the :doc:`fix deform <fix_deform>` page for further details.
-
-One exception to this rule is if the first dimension in the tilt
-factor (x for xy) is non-periodic.  In that case, the limits on the
-tilt factor are not enforced, since flipping the box in that dimension
-does not change the atom positions due to non-periodicity.  In this
-mode, if you tilt the system to extreme angles, the simulation will
-simply become inefficient, due to the highly skewed simulation box.
-
-Box flips that may occur using the :doc:`fix deform <fix_deform>` or
-:doc:`fix npt <fix_nh>` commands can be turned off using the *flip no*
-option with either of the commands.
-
-Note that if a simulation box has a large tilt factor, LAMMPS will run
-less efficiently, due to the large volume of communication needed to
-acquire ghost atoms around a processor's irregular-shaped subdomain.
-For extreme values of tilt, LAMMPS may also lose atoms and generate an
-error.
-
-Triclinic crystal structures are often defined using three lattice
-constants *a*, *b*, and *c*, and three angles :math:`\alpha`,
-:math:`\beta`, and :math:`\gamma`. Note that in this nomenclature,
-the a, b, and c lattice constants are the scalar lengths of the edge
 vectors **a**, **b**, and **c** defined above.  The relationship
 between these 6 quantities (a, b, c, :math:`\alpha`, :math:`\beta`,
-:math:`\gamma`) and the LAMMPS box sizes (lx,ly,lz) =
+:math:`\gamma`) and the LAMMPS restricted triclinic box sizes
-(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
+(lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is
+as follows:
 
 .. math::
 
@@ -186,15 +269,19 @@ The inverse relationship can be written as follows:
 
 The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and
 :math:`\gamma` can be printed out or accessed by computes using the
-:doc:`thermo_style custom <thermo_style>` keywords
+:doc:`thermo_style custom <thermo_style>` keywords *cella*, *cellb*,
-*cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*, *cellgamma*,
+*cellc*, *cellalpha*, *cellbeta*, *cellgamma*, respectively.
-respectively.
+
+----------
+
+Output of restricted and general triclinic boxes in a dump file
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 As discussed on the :doc:`dump <dump>` command doc page, when the BOX
-BOUNDS for a snapshot is written to a dump file for a triclinic box,
+BOUNDS for a snapshot is written to a dump file for a restricted
-an orthogonal bounding box which encloses the triclinic simulation box
+triclinic box, an orthogonal bounding box which encloses the triclinic
-is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
+simulation box is output, along with the 3 tilt factors (xy, xz, yz) of
-box, formatted as follows:
+the restricted triclinic box, formatted as follows:
 
 .. parsed-literal::
 
@@ -204,7 +291,7 @@ box, formatted as follows:
    zlo_bound zhi_bound yz
 
 This bounding box is convenient for many visualization programs and is
-calculated from the 9 triclinic box parameters
+calculated from the 9 restricted triclinic box parameters
 (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
 
 .. parsed-literal::
@@ -217,22 +304,66 @@ calculated from the 9 triclinic box parameters
    zhi_bound = zhi
 
 These formulas can be inverted if you need to convert the bounding box
-back into the triclinic box parameters, e.g. xlo = xlo_bound -
+back into the restricted triclinic box parameters, e.g. xlo =
-MIN(0.0,xy,xz,xy+xz).
+xlo_bound - MIN(0.0,xy,xz,xy+xz).
 
-One use of triclinic simulation boxes is to model solid-state crystals
+----------
-with triclinic symmetry.  The :doc:`lattice <lattice>` command can be
-used with non-orthogonal basis vectors to define a lattice that will
-tile a triclinic simulation box via the
-:doc:`create_atoms <create_atoms>` command.
 
-A second use is to run Parrinello-Rahman dynamics via the :doc:`fix npt <fix_nh>` command, which will adjust the xy, xz, yz tilt
+Periodicity and tilt factors for triclinic simulation boxes
-factors to compensate for off-diagonal components of the pressure
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-tensor.  The analog for an :doc:`energy minimization <minimize>` is
-the :doc:`fix box/relax <fix_box_relax>` command.
 
-A third use is to shear a bulk solid to study the response of the
+There is no requirement that a triclinic box be periodic in any
-material.  The :doc:`fix deform <fix_deform>` command can be used for
+dimension, though it typically should be in y or z if you wish to
-this purpose.  It allows dynamic control of the xy, xz, yz tilt
+enforce a shift in coordinates due to periodic boundary conditions
-factors as a simulation runs.  This is discussed in the next section
+across the y or z boundaries.  See the doc page for the :doc:`boundary
-on non-equilibrium MD (NEMD) simulations.
+<boundary>` command for an explanation of shifted coordinates for
+restricted triclinic boxes which are periodic.
+
+Some commands that work with triclinic boxes, e.g. the :doc:`fix
+deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require
+periodicity or non-shrink-wrap boundary conditions in specific
+dimensions.  See the command doc pages for details.
+
+A restricted triclinic box can be defined with all 3 tilt factors =
+0.0, so that it is initially orthogonal.  This is necessary if the box
+will become non-orthogonal, e.g. due to use of the :doc:`fix npt
+<fix_nh>` or :doc:`fix deform <fix_deform>` commands.  Alternatively,
+you can use the :doc:`change_box <change_box>` command to convert a
+simulation box from orthogonal to restricted triclinic and vice versa.
+
+.. note::
+
+   Highly tilted restricted triclinic simulation boxes can be
+   computationally inefficient.  This is due to the large volume of
+   communication needed to acquire ghost atoms around a processor's
+   irregular-shaped subdomain.  For extreme values of tilt, LAMMPS may
+   also lose atoms and generate an error.
+
+LAMMPS will issue a warning if you define a restricted triclinic box
+with a tilt factor which skews the box more than half the distance of
+the parallel box length, which is the first dimension in the tilt
+factor (e.g. x for xz).
+
+For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
+the xy tilt factor should be between -5 and 5 to avoid the warning.
+Similarly, both xz and yz should be between -(xhi-xlo)/2 and
++(yhi-ylo)/2.  Note that these are not limitations, since if the
+maximum tilt factor is 5 (as in this example), then simulations boxes
+and atom configurations with tilt = ..., -15, -5, 5, 15, 25, ... are
+all geometrically equivalent.
+
+If the box tilt exceeds this limit during a dynamics run (e.g. due to
+the :doc:`fix deform <fix_deform>` command), then by default the box
+is "flipped" to an equivalent shape with a tilt factor within the
+warning bounds, and the run continues.  See the :doc:`fix deform
+<fix_deform>` page for further details.  Box flips that would normally
+occur using the :doc:`fix deform <fix_deform>` or :doc:`fix npt
+<fix_nh>` commands can be suppressed using the *flip no* option with
+either of the commands.
+
+One exception to box flipping is if the first dimension in the tilt
+factor (e.g. x for xy) is non-periodic.  In that case, the limits on
+the tilt factor are not enforced, since flipping the box in that
+dimension would not change the atom positions due to non-periodicity.
+In this mode, if the system tilts to large angles, the simulation will
+simply become inefficient, due to the highly skewed simulation box.

doc/src/Howto_type_labels.rst

@@ -14,16 +14,17 @@ wherever they appear in LAMMPS input or output files.  The total number
 Ntypes for each interaction is "locked in" when the simulation box
 is created.
 
-A recent addition to LAMMPS is the option to use strings - referred
+A recent addition to LAMMPS is the option to use strings - referred to
-to as type labels - as an alternative.  Using type labels instead of
+as type labels - as an alternative.  Using type labels instead of
 numeric types can be advantageous in various scenarios.  For example,
-type labels can make inputs more readable and generic (i.e. usable through
+type labels can make inputs more readable and generic (i.e. usable
-the :doc:`include command <include>` for different systems with different
+through the :doc:`include command <include>` for different systems with
-numerical values assigned to types.  This generality also applies to
+different numerical values assigned to types.  This generality also
-other inputs like data files read by :doc:`read_data <read_data>` or
+applies to other inputs like data files read by :doc:`read_data
-molecule template files read by the :doc:`molecule <molecule>`
+<read_data>` or molecule template files read by the :doc:`molecule
-command.  See below for a list of other commands that can use
+<molecule>` command.  A discussion of the current type label support can
-type labels in different ways.
+be found in :ref:`(Gissinger) <Typelabel24>`.  See below for a list of
+other commands that can use type labels in different ways.
 
 LAMMPS will *internally* continue to use numeric types, which means
 that many previous restrictions still apply.  For example, the total
@@ -124,3 +125,9 @@ between the files.  The creation of simulation-ready reaction templates
 for :doc:`fix bond/react <fix_bond_react>` is much simpler when using
 type labels, and results in templates that can be used without
 modification in multiple simulations or different systems.
+
+-----------
+
+.. _Typelabel24:
+
+**(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/Intro_citing.rst

@@ -47,6 +47,8 @@ In addition there are DOIs generated for individual stable releases:
 - 3 March 2020 version: `DOI:10.5281/zenodo.3726417 <https://dx.doi.org/10.5281/zenodo.3726417>`_
 - 29 October 2020 version: `DOI:10.5281/zenodo.4157471 <https://dx.doi.org/10.5281/zenodo.4157471>`_
 - 29 September 2021 version: `DOI:10.5281/zenodo.6386596 <https://dx.doi.org/10.5281/zenodo.6386596>`_
+- 23 June 2022 version: `DOI:10.5281/zenodo.10806836 <https://doi.org/10.5281/zenodo.10806836>`_
+- 2 August 2023 version: `DOI:10.5281/zenodo.10806852 <https://doi.org/10.5281/zenodo.10806852>`_
 
 Home page
 ^^^^^^^^^

doc/src/Intro_features.rst

@@ -29,7 +29,7 @@ General features
 * spatial decomposition of simulation domain for MPI parallelism
 * particle decomposition inside spatial decomposition for OpenMP and GPU parallelism
 * GPLv2 licensed open-source distribution
-* highly portable C++-11
+* highly portable C++-11 (optional packages may require C++17)
 * modular code with most functionality in optional packages
 * only depends on MPI library for basic parallel functionality, MPI stub for serial compilation
 * other libraries are optional and only required for specific packages
@@ -81,7 +81,7 @@ commands)
 * pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, Class II (COMPASS), hydrogen bond, harmonic, gaussian, tabulated, scripted
 * charged pairwise potentials: Coulombic, point-dipole
 * many-body potentials: EAM, Finnis/Sinclair, MEAM, MEAM+SW, EIM, EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, Streitz-Mintmire, 3-body polymorphic, BOP, Vashishta
-* machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN
+* machine learning potentials: ACE, AGNI, GAP, Behler-Parrinello (N2P2), POD, RANN, SNAP
 * interfaces to ML potentials distributed by external groups: ANI, ChIMES, DeepPot, HIPNN, MTP
 * long-range interactions for charge, point-dipoles, and LJ dispersion:  Ewald, Wolf, PPPM (similar to particle-mesh Ewald), MSM, ScaFaCoS
 * polarization models: :doc:`QEq <fix_qeq>`, :doc:`core/shell model <Howto_coreshell>`, :doc:`Drude dipole model <Howto_drude>`

doc/src/Library_objects.rst

@@ -9,6 +9,8 @@ fixes, or variables in LAMMPS using the following functions:
 - :cpp:func:`lammps_extract_variable_datatype`
 - :cpp:func:`lammps_extract_variable`
 - :cpp:func:`lammps_set_variable`
+- :cpp:func:`lammps_set_string_variable`
+- :cpp:func:`lammps_set_internal_variable`
 - :cpp:func:`lammps_variable_info`
 
 -----------------------
@@ -38,6 +40,16 @@ fixes, or variables in LAMMPS using the following functions:
 
 -----------------------
 
+.. doxygenfunction:: lammps_set_string_variable
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_set_internal_variable
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_variable_info
    :project: progguide
 

doc/src/Library_properties.rst

@@ -13,6 +13,7 @@ This section documents the following functions:
 - :cpp:func:`lammps_extract_setting`
 - :cpp:func:`lammps_extract_global_datatype`
 - :cpp:func:`lammps_extract_global`
+- :cpp:func:`lammps_map_atom`
 
 --------------------
 
@@ -120,3 +121,8 @@ subdomains and processors.
 .. doxygenfunction:: lammps_extract_global
    :project: progguide
 
+-----------------------
+
+.. doxygenfunction:: lammps_map_atom
+   :project: progguide
+

doc/src/Modify_style.rst

@@ -96,6 +96,39 @@ list all non-conforming lines.  By adding the `-f` flag to the command
 line, they will modify the flagged files to try to remove the detected
 issues.
 
+Constants (strongly preferred)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Global or per-file constants should be declared as `static constexpr`
+variables rather than via the pre-processor with `#define`.  The name of
+constants should be all uppercase.  This has multiple advantages:
+
+- constants are easily identified as such by their all upper case name
+- rather than a pure text substitution during pre-processing, `constexpr
+  variables` have a type associated with them and are processed later in
+  the parsing process where the syntax checks and type specific
+  processing (e.g. via overloads) can be applied to them.
+- compilers can emit a warning if the constant is not used and thus can
+  be removed (we regularly check for and remove dead code like this)
+- there are no unexpected substitutions and thus confusing syntax errors
+  when compiling leading to, for instance, conflicts so that LAMMPS
+  cannot be compiled with certain combinations of packages (this *has*
+  happened multiple times in the past).
+
+Pre-processor defines should be limited to macros (but consider C++
+templates) and conditional compilation.  If a per-processor define must
+be used, it should be defined at the top of the .cpp file after the
+include statements and at all cost it should be avoided to put them into
+header files.
+
+Some sets of commonly used constants are provided in the ``MathConst``
+and ``EwaldConst`` namespaces and implemented in the files
+``math_const.h`` and ``ewald_const.h``, respectively.
+
+There are always exceptions, special cases, and legacy code in LAMMPS,
+so please contact the LAMMPS developers if you are not sure.
+
+
 Placement of braces (strongly preferred)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Packages_details.rst

@@ -52,6 +52,7 @@ page gives those details.
    * :ref:`DRUDE <PKG-DRUDE>`
    * :ref:`EFF <PKG-EFF>`
    * :ref:`ELECTRODE <PKG-ELECTRODE>`
+   * :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
    * :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
    * :ref:`EXTRA-DUMP <PKG-EXTRA-DUMP>`
    * :ref:`EXTRA-FIX <PKG-EXTRA-FIX>`
@@ -84,6 +85,7 @@ page gives those details.
    * :ref:`ML-QUIP <PKG-ML-QUIP>`
    * :ref:`ML-RANN <PKG-ML-RANN>`
    * :ref:`ML-SNAP <PKG-ML-SNAP>`
+   * :ref:`ML-UF3 <PKG-ML-UF3>`
    * :ref:`MOFFF <PKG-MOFFF>`
    * :ref:`MOLECULE <PKG-MOLECULE>`
    * :ref:`MOLFILE <PKG-MOLFILE>`
@@ -404,6 +406,7 @@ and :ref:`ASPHERE <PKG-ASPHERE>` packages are installed.
 * :doc:`bond_style oxdna2/\* <bond_oxdna>`
 * :doc:`bond_style oxrna2/\* <bond_oxdna>`
 * :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+* examples/PACKAGES/cgdna
 
 ----------
 
@@ -677,7 +680,12 @@ DPD-BASIC package
 Pair styles for the basic dissipative particle dynamics (DPD) method
 and DPD thermostatting.
 
-**Author:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP)
+Pair style :doc:`dpd/coul/slater/long <pair_dpd_coul_slater_long>` also
+includes smeared charges for coulomb interactions and thus requires the
+:ref:`KSPACE <PKG-KSPACE>` package to be installed to handle the long-range
+Coulomb part of the interactions.
+
+**Authors:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP), Eddy Barraud (IFPEN)
 
 **Supporting info:**
 
@@ -686,6 +694,7 @@ and DPD thermostatting.
 * :doc:`pair_style dpd/tstat <pair_dpd>`
 * :doc:`pair_style dpd/ext <pair_dpd_ext>`
 * :doc:`pair_style dpd/ext/tstat <pair_dpd_ext>`
+* :doc:`pair_style dpd/coul/slater/long <pair_dpd_coul_slater_long>`
 * examples/PACKAGES/dpd-basic
 
 ----------
@@ -887,6 +896,22 @@ This package has :ref:`specific installation instructions <electrode>` on the
 
 ----------
 
+.. _PKG-EXTRA-COMMAND:
+
+EXTRA-COMMAND package
+---------------------
+
+**Contents:**
+
+Additional command styles that are less commonly used.
+
+**Supporting info:**
+
+* src/EXTRA-COMMAND: filenames -> commands
+* :doc:`general commands <Commands_all>`
+
+----------
+
 .. _PKG-EXTRA-COMPUTE:
 
 EXTRA-COMPUTE package
@@ -1926,6 +1951,31 @@ computes which analyze attributes of the potential.
 
 ----------
 
+.. _PKG-ML-UF3:
+
+ML-UF3 package
+--------------
+
+**Contents:**
+
+A pair style for the ultra-fast force field potentials (UF3). UF3 is a
+methodology for deriving a highly accurate classical potential which is
+fast to evaluate and is fitted to a large archives of quantum mechanical
+(DFT) data.  The use of b-spline basis set in UF3 enables the rapid
+evaluation of 2-body and 3-body interactions.
+
+**Authors:** Ajinkya C Hire (University of Florida),
+Hendrik Krass (University of Constance),
+Matthias Rupp (Luxembourg Institute of Science and Technology),
+Richard Hennig (University of Florida)
+
+**Supporting info:**
+
+* src/ML-UF3: filenames -> commands
+* :doc:`pair_style uf3 <pair_uf3>`
+* examples/uf3
+* https://github.com/uf3/uf3
+
 .. _PKG-MOFFF:
 
 MOFFF package

doc/src/Packages_list.rst

@@ -158,6 +158,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`fix electrode/conp <fix_electrode>`
      - PACKAGES/electrode
      - no
+   * - :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
+     - additional command styles
+     - :doc:`general commands <Commands_all>`
+     - n/a
+     - no
    * - :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
      - additional compute styles
      - :doc:`compute <compute>`
@@ -318,6 +323,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`pair_style snap <pair_snap>`
      - snap
      - no
+   * - :ref:`ML-UF3 <PKG-ML-UF3>`
+     - quantum-fitted ultra fast potentials
+     - :doc:`pair_style uf3 <pair_uf3>`
+     - PACKAGES/uf3
+     - no
    * - :ref:`MOFFF <PKG-MOFFF>`
      - styles for `MOF-FF <MOFplus_>`_ force field
      - :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>`

doc/src/Python_scatter.rst

@@ -54,8 +54,21 @@ like this:
    x[3] = x coord of atom with ID 2
    ...
    x[n3-1] = z coord of atom with ID natoms
-   lmp.scatter_atoms("x",1,3,x)
+   lmp.scatter_atoms("x", 1, 3, x)
+
+The coordinates can also be provided as arguments to the initializer of x:
+
+.. code-block:: python
+
+   from ctypes import c_double
+   natoms = 2
+   n3 = 3*natoms
+   # init in constructor
+   x = (n3*c_double)(0.0, 0.0, 0.0, 1.0, 1.0, 1.0)
+   lmp.scatter_atoms("x", 1, 3, x)
+   # or using a list
+   coords = [1.0, 2.0, 3.0, -3.0, -2.0, -1.0]
+   x = (c_double*len(coords))(*coords)
 
 Alternatively, you can just change values in the vector returned by
 the gather methods, since they are also ctypes vectors.
-

doc/src/Speed_kokkos.rst

@@ -20,11 +20,28 @@ including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
 (Sandia). For more information on developing using Kokkos abstractions
 see the `Kokkos Wiki <https://github.com/kokkos/kokkos/wiki>`_.
 
-Kokkos currently provides support for 4 modes of execution (per MPI
+.. note::
+
+   The Kokkos library is under active development and tracking the
+   availability of accelerator hardware, so is the KOKKOS package in
+   LAMMPS.  This means that only a certain range of versions of the
+   Kokkos library are compatible with the KOKKOS package of a certain
+   range of LAMMPS versions.  For that reason LAMMPS comes with a
+   bundled version of the Kokkos library that has been validated on
+   multiple platforms and may contain selected back-ported bug fixes
+   from upstream Kokkos versions.  While it is possible to build LAMMPS
+   with an external version of Kokkos, it is untested and may result in
+   incorrect execution or crashes.
+
+Kokkos currently provides full support for 4 modes of execution (per MPI
 task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
-(threading for many-core CPUs and Intel Phi), CUDA (for NVIDIA
+(threading for many-core CPUs and Intel Phi), CUDA (for NVIDIA GPUs) and
-GPUs) and HIP (for AMD GPUs). You choose the mode at build time to
+HIP (for AMD GPUs).  Additional modes (e.g. OpenMP target, Intel data
-produce an executable compatible with a specific hardware.
+center GPUs) are under development.  You choose the mode at build time
+to produce an executable compatible with a specific hardware.
+
+The following compatibility notes have been last updated for LAMMPS
+version 23 November 2023 and Kokkos version 4.2.
 
 .. admonition:: C++17 support
    :class: note
@@ -54,22 +71,22 @@ produce an executable compatible with a specific hardware.
    :class: note
 
    Kokkos with CUDA currently implicitly assumes that the MPI library is
-   GPU-aware. This is not always the case, especially when using
+   GPU-aware.  This is not always the case, especially when using
    pre-compiled MPI libraries provided by a Linux distribution. This is
    not a problem when using only a single GPU with a single MPI
-   rank. When running with multiple MPI ranks, you may see segmentation
+   rank.  When running with multiple MPI ranks, you may see segmentation
    faults without GPU-aware MPI support. These can be avoided by adding
    the flags :doc:`-pk kokkos gpu/aware off <Run_options>` to the
    LAMMPS command line or by using the command :doc:`package kokkos
    gpu/aware off <package>` in the input file.
 
-.. admonition:: AMD GPU support
+.. admonition:: Intel Data Center GPU support
    :class: note
 
-   To build with Kokkos the HIPCC compiler from the AMD ROCm software
+   Support for Kokkos with Intel Data Center GPU accelerators (formerly
-   version 3.5 or later is required.  Supporting this Kokkos mode in
+   known under the code name "Ponte Vecchio") in LAMMPS is still a work
-   LAMMPS is still work in progress.  Please contact the LAMMPS developers
+   in progress.  Only a subset of the functionality works correctly.
-   if you run into problems.
+   Please contact the LAMMPS developers if you run into problems.
 
 Building LAMMPS with the KOKKOS package
 """""""""""""""""""""""""""""""""""""""
@@ -292,6 +309,10 @@ one or more nodes, each with two GPUs:
    settings. Experimenting with its options can provide a speed-up for
    specific calculations. For example:
 
+.. code-block:: bash
+
+   mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
+
 .. note::
 
    The default binsize for :doc:`atom sorting <atom_modify>` on GPUs
@@ -302,9 +323,15 @@ one or more nodes, each with two GPUs:
    frequent sorting than default (e.g. sorting every 100 time steps
    instead of 1000) may improve performance.
 
-.. code-block:: bash
+.. note::
 
-   mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
+   When running on GPUs with many MPI ranks (tens of thousands and
+   more), the creation of the atom map (required for molecular systems)
+   on the GPU can slow down significantly or run out of GPU memory and
+   thus slow down the whole calculation or cause a crash.  You can use
+   the "-pk kokkos atom/map no" :doc:`command-line switch <Run_options>`
+   of the :doc:`package kokkos atom/map no <package>` command to create
+   the atom map on the CPU instead.
 
 .. note::
 
@@ -416,15 +443,22 @@ Generally speaking, the following rules of thumb apply:
   performance of a KOKKOS style is a bit slower than the OPENMP
   package.
 * When running large number of atoms per GPU, KOKKOS is typically faster
-  than the GPU package when compiled for double precision. The benefit
+  than the GPU package when compiled for double precision.  The benefit
   of using single or mixed precision with the GPU package depends
   significantly on the hardware in use and the simulated system and pair
   style.
-* When running on Intel hardware, KOKKOS is not as fast as
+* When running on Intel Phi hardware, KOKKOS is not as fast as
   the INTEL package, which is optimized for x86 hardware (not just
   from Intel) and compilation with the Intel compilers.  The INTEL
   package also can increase the vector length of vector instructions
   by switching to single or mixed precision mode.
+* The KOKKOS package by default assumes that you are using exactly one
+  MPI rank per GPU. When trying to use multiple MPI ranks per GPU it is
+  mandatory to enable `CUDA Multi-Process Service (MPS)
+  <https://docs.nvidia.com/deploy/mps/index.html>`_ to get good
+  performance.  In this case it is better to not use all available
+  MPI ranks in order to avoid competing with the MPS daemon for
+  CPU resources.
 
 See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
 LAMMPS website for performance of the KOKKOS package on different

doc/src/Tools.rst

@@ -90,7 +90,7 @@ Miscellaneous tools
 
    * :ref:`LAMMPS coding standards <coding_standard>`
    * :ref:`emacs <emacs>`
-   * :ref:`i-pi <ipi>`
+   * :ref:`i-PI <ipi>`
    * :ref:`kate <kate>`
    * :ref:`LAMMPS shell <lammps_shell>`
    * :ref:`LAMMPS GUI <lammps_gui>`
@@ -376,21 +376,40 @@ See README file in the tools/fep directory.
 
 .. _ipi:
 
-i-pi tool
+i-PI tool
 -------------------
 
-The tools/i-pi directory contains a version of the i-PI package, with
+.. versionchanged:: TBD
-all the LAMMPS-unrelated files removed.  It is provided so that it can
+
-be used with the :doc:`fix ipi <fix_ipi>` command to perform
+The tools/i-pi directory used to contain a bundled version of the i-PI
-path-integral molecular dynamics (PIMD).
+software package for use with LAMMPS.  This version, however, was
+removed in 06/2024.
 
 The i-PI package was created and is maintained by Michele Ceriotti,
 michele.ceriotti at gmail.com, to interface to a variety of molecular
 dynamics codes.
 
-See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
+i-PI is now available via PyPi using the pip package manager at:
-:doc:`fix ipi <fix_ipi>` page for further details on running PIMD
+https://pypi.org/project/ipi/
-calculations with LAMMPS.
+
+Here are the commands to set up a virtual environment and install
+i-PI into it with all its dependencies.
+
+.. code-block:: sh
+
+   python -m venv ipienv
+   source ipienv/bin/activate
+   pip install --upgrade pip
+   pip install ipi
+
+To install the development version from GitHub, please use:
+
+.. code-block:: sh
+
+   pip install git+https://github.com/i-pi/i-pi.git
+
+For further information, please consult the [i-PI home
+page](https://ipi-code.org).
 
 ----------
 
@@ -709,8 +728,8 @@ 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 38 x86\_64 using GCC 13 and Clang 16, Qt version 5.15LTS
+- Fedora Linux 40 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS
-- Fedora Linux 38 x86\_64 using GCC 13, Qt version 6.5LTS
+- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.5LTS
 - 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 MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
@@ -752,22 +771,23 @@ if necessary.  When both, Qt5 and Qt6 are available, Qt6 will be preferred
 unless ``-D LAMMPS_GUI_USE_QT5=yes`` is set.
 
 It should be possible to build the LAMMPS GUI as a standalone
-compilation (e.g. when LAMMPS has been compiled with traditional make),
+compilation (e.g. when LAMMPS has been compiled with traditional make).
-then the CMake configuration needs to be told where to find the LAMMPS
+Then the CMake configuration needs to be told where to find the LAMMPS
 headers and the LAMMPS library, via ``-D
 LAMMPS_SOURCE_DIR=/path/to/lammps/src``.  CMake will try to guess a
 build folder with the LAMMPS library from that path, but it can also be
 set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
 
 Rather than linking to the LAMMPS library during compilation, it is also
-possible to compile the GUI with a plugin loader library that will load
+possible to compile the GUI with a plugin loader that will load
 the LAMMPS library dynamically at runtime during the start of the GUI
 from a shared library; e.g. ``liblammps.so`` or ``liblammps.dylib`` or
 ``liblammps.dll`` (depending on the operating system).  This has the
-advantage that the LAMMPS library can be updated LAMMPS without having
+advantage that the LAMMPS library can be built from updated or modified
-to recompile the GUI.  The ABI of the LAMMPS C-library interface is very
+LAMMPS source without having to recompile the GUI.  The ABI of the
-stable and generally backward compatible.  This feature is enabled by
+LAMMPS C-library interface is very stable and generally backward
-setting ``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
+compatible.  This feature is enabled by setting
+``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
 LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
 would be the ``examples/COUPLE/plugin`` folder of the LAMMPS
 distribution.
@@ -779,8 +799,8 @@ macOS
 """""
 
 When building on macOS, the build procedure will try to manufacture a
-drag-n-drop installer, LAMMPS-macOS-multiarch.dmg, when using the 'dmg'
+drag-n-drop installer, ``LAMMPS-macOS-multiarch.dmg``, when using the
-target (i.e. ``cmake --build <build dir> --target dmg`` or ``make dmg``.
+'dmg' target (i.e. ``cmake --build <build dir> --target dmg`` or ``make dmg``.
 
 To build multi-arch executables that will run on both, arm64 and x86_64
 architectures natively, it is necessary to set the CMake variable ``-D
@@ -820,11 +840,11 @@ and LAMMPS GUI can be launched from anywhere from the command line.
 The standard CMake build procedure can be applied and the
 ``mingw-cross.cmake`` preset used. By using ``mingw64-cmake`` the CMake
 command will automatically include a suitable CMake toolset file (the
-regular cmake command can be used after that).  After building the
+regular cmake command can be used after that to modify the configuration
-libraries and executables, you can build the target 'zip'
+settings, if needed).  After building the libraries and executables,
-(i.e. ``cmake --build <build dir> --target zip`` or ``make zip``
+you can build the target 'zip' (i.e. ``cmake --build <build dir> --target zip``
-to stage all installed files into a LAMMPS_GUI folder and then
+or ``make zip`` to stage all installed files into a LAMMPS_GUI folder
-run a script to copy all required dependencies, some other files,
+and then run a script to copy all required dependencies, some other files,
 and create a zip file from it.
 
 Linux

doc/src/angle_charmm.rst

@@ -70,7 +70,9 @@ for more info.
 Related commands
 """"""""""""""""
 
-:doc:`angle_coeff <angle_coeff>`
+:doc:`angle_coeff <angle_coeff>`, :doc:`pair_style lj/charmm variants <pair_charmm>`,
+:doc:`dihedral_style charmm <dihedral_charmm>`,
+:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
 
 Default
 """""""

doc/src/angle_cosine_squared_restricted.rst

@@ -0,0 +1,80 @@
+.. index:: angle_style cosine/squared/restricted
+.. index:: angle_style cosine/squared/restricted/omp
+
+angle_style cosine/squared/restricted command
+=============================================
+
+Accelerator Variants: *cosine/squared/restricted/omp*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/squared/restricted
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   angle_style cosine/squared/restricted
+   angle_coeff 2*4 75.0 100.0
+
+Description
+"""""""""""
+
+.. versionadded:: 17Apr2024
+
+The *cosine/squared/restricted* angle style uses the potential
+
+.. math::
+
+   E = K [\cos(\theta) - \cos(\theta_0)]^2 / \sin^2(\theta)
+
+, which is commonly used in the MARTINI force field,
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K`
+is a prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
+
+See :ref:`(Bulacu) <restricted-Bulacu>` for a description of the restricted angle for the MARTINI force field.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read_data <read_data>`
+or :doc:`read_restart <read_restart>` commands:
+
+* :math:`K` (energy)
+* :math:`\theta_0` (degrees)
+
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+internally.
+
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
+Restrictions
+""""""""""""
+
+This angle style can only be used if LAMMPS was built with the
+EXTRA-MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle_coeff <angle_coeff>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _restricted-Bulacu:
+
+**(Bulacu)** Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292
+(2013).

doc/src/angle_lepton.rst

@@ -51,7 +51,7 @@ angle coefficient.  For example `"200.0*theta^2"` represents a
 
    U_{angle,i} = K (\theta_i - \theta_0)^2 = K \theta^2 \qquad \theta = \theta_i - \theta_0
 
-.. versionchanged:: TBD
+.. versionchanged:: 7Feb2024
 
 By default the potential energy U is shifted so that the value U is 0.0
 for $theta = theta_0$.  This is equivalent to using the optional keyword

doc/src/angle_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    angle_style style
 
-* style = *none* or *zero* or *hybrid* or *amoeba* or *charmm* or *class2* or *class2/p6* or *cosine* or *cosine/buck6d* or *cosine/delta* or *cosine/periodic* or *cosine/shift* or *cosine/shift/exp* or *cosine/squared* or *cross* or *dipole* or *fourier* or *fourier/simple* or *gaussian* or *harmonic* or *lepton* or *mm3* or *quartic* or *spica* or *table*
+* style = *none* or *zero* or *hybrid* or *amoeba* or *charmm* or *class2* or *class2/p6* or *cosine* or *cosine/buck6d* or *cosine/delta* or *cosine/periodic* or *cosine/shift* or *cosine/shift/exp* or *cosine/squared* or *cosine/squared/restricted* or *cross* or *dipole* or *fourier* or *fourier/simple* or *gaussian* or *harmonic* or *lepton* or *mm3* or *quartic* or *spica* or *table*
 
 Examples
 """"""""
@@ -84,6 +84,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 * :doc:`cosine/shift <angle_cosine_shift>` - angle cosine with a shift
 * :doc:`cosine/shift/exp <angle_cosine_shift_exp>` - cosine with shift and exponential term in spring constant
 * :doc:`cosine/squared <angle_cosine_squared>` - angle with cosine squared term
+* :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` - angle with restricted cosine squared term
 * :doc:`cross <angle_cross>` - cross term coupling angle and bond lengths
 * :doc:`dipole <angle_dipole>` - angle that controls orientation of a point dipole
 * :doc:`fourier <angle_fourier>` - angle with multiple cosine terms

doc/src/atom_style.rst

@@ -49,252 +49,229 @@ Examples
 Description
 """""""""""
 
-Define what style of atoms to use in a simulation.  This determines
+The *atom_style* command selects which per-atom attributes are
-what attributes are associated with the atoms.  This command must be
+associated with atoms in a LAMMPS simulation and thus stored and
-used before a simulation is setup via a :doc:`read_data <read_data>`,
+communicated with those atoms as well as read from and stored in data
-:doc:`read_restart <read_restart>`, or :doc:`create_box <create_box>`
+and restart files.  Different models (e.g. :doc:`pair styles
-command.
+<pair_style>`) require access to specific per-atom attributes and thus
+require a specific atom style.  For example, to compute Coulomb
+interactions, the atom must have a "charge" (aka "q") attribute.
+
+A number of distinct atom styles exist that combine attributes.  Some
+atom styles are a superset of other atom styles.  Further attributes
+may be added to atoms either via using a hybrid style which provides a
+union of the attributes of the sub-styles, or via the :doc:`fix
+property/atom <fix_property_atom>` command.  The *atom_style* command
+must be used before a simulation is setup via a :doc:`read_data
+<read_data>`, :doc:`read_restart <read_restart>`, or :doc:`create_box
+<create_box>` command.
 
 .. note::
 
-   Many of the atom styles discussed here are only enabled if
+   Many of the atom styles discussed here are only enabled if LAMMPS was
-   LAMMPS was built with a specific package, as listed below in the
+   built with a specific package, as listed below in the Restrictions
-   Restrictions section.
+   section.
 
-Once a style is assigned, it cannot be changed, so use a style general
+Once a style is selected and the simulation box defined, it cannot be
-enough to encompass all attributes.  E.g. with style *bond*, angular
+changed but only augmented with the :doc:`fix property/atom
-terms cannot be used or added later to the model.  It is OK to use a
+<fix_property_atom>` command.  So one should select an atom style
-style more general than needed, though it may be slightly inefficient.
+general enough to encompass all attributes required.  E.g. with atom
+style *bond*, it is not possible to define angles and use angle styles.
 
-The choice of style affects what quantities are stored by each atom,
+It is OK to use a style more general than needed, though it may be
-what quantities are communicated between processors to enable forces
+slightly inefficient because it will allocate and communicate
-to be computed, and what quantities are listed in the data file read
+additional unused data.
-by the :doc:`read_data <read_data>` command.
 
-These are the additional attributes of each style and the typical
+Atom style attributes
-kinds of physical systems they are used to model.  All styles store
+"""""""""""""""""""""
-coordinates, velocities, atom IDs and types.  See the
+
+The atom style *atomic* has the minimum subset of per-atom attributes
+and is also the default setting.  It encompasses the following per-atom
+attributes (name of the vector or array in the :doc:`Atom class
+<Classes_atom>` is given in parenthesis): atom-ID (tag), type (type),
+position (x), velocities (v), forces (f), image flags (image), group
+membership (mask).  Since all atom styles are a superset of atom style
+*atomic*\ , they all include these attributes.
+
+This table lists all the available atom styles, which attributes they
+provide, which :doc:`package <Packages>` is required to use them, and
+what the typical applications are that use them.  See the
 :doc:`read_data <read_data>`, :doc:`create_atoms <create_atoms>`, and
-:doc:`set <set>` commands for info on how to set these various
+:doc:`set <set>` commands for details on how to set these various
-quantities.
+quantities.  More information about many of the styles is provided in
+the Additional Information section below.
 
-+----------------+-----------------------------------------------------+--------------------------------------+
+.. list-table::
-| *amoeba*       | molecular + charge + 1/5 neighbors                  | AMOEBA/HIPPO polarized force fields  |
+   :header-rows: 1
-+----------------+-----------------------------------------------------+--------------------------------------+
+   :widths: auto
-| *angle*        | bonds and angles                                    | bead-spring polymers with stiffness  |
+
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - Atom style
-| *atomic*       | only the default values                             | coarse-grain liquids, solids, metals |
+     - Attributes
-+----------------+-----------------------------------------------------+--------------------------------------+
+     - Required package
-| *body*         | mass, inertia moments, quaternion, angular momentum | arbitrary bodies                     |
+     - Applications
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *amoeba*
-| *bond*         | bonds                                               | bead-spring polymers                 |
+     - *full* + "1-5 special neighbor data"
-+----------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`AMOEBA <PKG-AMOEBA>`
-| *charge*       | charge                                              | atomic system with charges           |
+     - AMOEBA/HIPPO force fields
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *angle*
-| *dielectric*   | normx normy normz area/patch ed em epsilon curv     | system with surface polarization     |
+     - *bond* + "angle data"
-+----------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`MOLECULE <PKG-MOLECULE>`
-| *dipole*       | charge and dipole moment                            | system with dipolar particles        |
+     - bead-spring polymers with stiffness
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *atomic*
-| *dpd*          | internal temperature and internal energies          | DPD particles                        |
+     - tag, type, x, v, f, image, mask
-+----------------+-----------------------------------------------------+--------------------------------------+
+     -
-| *edpd*         | temperature and heat capacity                       | eDPD particles                       |
+     - atomic liquids, solids, metals
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *body*
-| *electron*     | charge and spin and eradius                         | electronic force field               |
+     - *atomic* + radius, rmass, angmom, torque, body
-+----------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`BODY <PKG-BODY>`
-| *ellipsoid*    | shape, quaternion, angular momentum                 | aspherical particles                 |
+     - arbitrary bodies, see :doc:`body howto <Howto_body>`
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *bond*
-| *full*         | molecular + charge                                  | bio-molecules                        |
+     - *atomic* + molecule, nspecial, special + "bond data"
-+----------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`MOLECULE <PKG-MOLECULE>`
-| *line*         | end points, angular velocity                        | rigid bodies                         |
+     - bead-spring polymers
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *bpm/sphere*
-| *mdpd*         | density                                             | mDPD particles                       |
+     - *bond* + radius, rmass, omega, torque, quat
-+----------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`BPM <PKG-BPM>`
-| *molecular*    | bonds, angles, dihedrals, impropers                 | uncharged molecules                  |
+     - granular bonded particle models, see :doc:`BPM howto <Howto_bpm>`
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *charge*
-| *oxdna*        | nucleotide polarity                                 | coarse-grained DNA and RNA models    |
+     - *atomic* + q
-+----------------+-----------------------------------------------------+--------------------------------------+
+     -
-| *peri*         | mass, volume                                        | mesoscopic Peridynamic models        |
+     - atomic systems with charges
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *dielectric*
-| *rheo*         | rho, status                                         | solid and fluid RHEO particles       |
+     - *full* + mu, area, ed, em, epsilon, curvature, q_scaled
-+----------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`DIELECTRIC <PKG-DIELECTRIC>`
-| *rheo/thermal* | rho, status, temperature                            | RHEO particles with temperature      |
+     - systems with surface polarization
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *dipole*
-| *smd*          | volume, kernel diameter, contact radius, mass       | solid and fluid SPH particles        |
+     - *charge* + mu
-+----------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`DIPOLE <PKG-DIPOLE>`
-| *sph*          | rho, esph, cv                                       | SPH particles                        |
+     - atomic systems with charges and point dipoles
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *dpd*
-| *sphere*       | diameter, mass, angular velocity                    | granular models                      |
+     - *atomic* + rho + "reactive DPD data"
-+----------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`DPD-REACT <PKG-DPD-REACT>`
-| *bpm/sphere*   | diameter, mass, angular velocity, quaternion        | granular bonded particle models (BPM)|
+     - reactive DPD
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *edpd*
-| *spin*         | magnetic moment                                     | system with magnetic particles       |
+     - *atomic* + "eDPD data"
-+----------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`DPD-MESO <PKG-DPD-MESO>`
-| *tdpd*         | chemical concentration                              | tDPD particles                       |
+     - Energy conservative DPD (eDPD)
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *electron*
-| *template*     | template index, template atom                       | small molecules with fixed topology  |
+     - *charge* + espin, eradius, ervel, erforce
-+----------------+-----------------------------------------------------+--------------------------------------+
+     - :ref:`EFF <PKG-EFF>`
-| *tri*          | corner points, angular momentum                     | rigid bodies                         |
+     - Electron force field systems
-+----------------+-----------------------------------------------------+--------------------------------------+
+   * - *ellipsoid*
-| *wavepacket*   | charge, spin, eradius, etag, cs_re, cs_im           | AWPMD                                |
+     - *atomic* + rmass, angmom, torque, ellipsoid
-+----------------+-----------------------------------------------------+--------------------------------------+
+     -
+     - aspherical particles
+   * - *full*
+     - *molecular* + q
+     - :ref:`MOLECULE <PKG-MOLECULE>`
+     - molecular force fields
+   * - *line*
+     - *atomic* + molecule, radius, rmass, omega, torque, line
+     -
+     - 2-d rigid body particles
+   * - *mdpd*
+     - *atomic* + rho, drho, vest
+     - :ref:`DPD-MESO <PKG-DPD-MESO>`
+     - Many-body DPD (mDPD)
+   * - *molecular*
+     - *angle* + "dihedral and improper data"
+     - :ref:`MOLECULE <PKG-MOLECULE>`
+     - apolar and uncharged molecules
+   * - *oxdna*
+     - *atomic* + id5p
+     - :ref:`CG-DNA <PKG-CG-DNA>`
+     - coarse-grained DNA and RNA models
+   * - *peri*
+     - *atomic* + rmass, vfrac, s0, x0
+     - :ref:`PERI <PKG-PERI>`
+     - mesoscopic Peridynamics models
+   * - *smd*
+     - *atomic* + molecule, radius, rmass + "smd data"
+     - :ref:`MACHDYN <PKG-MACHDYN>`
+     - Smooth Mach Dynamics models
+   * - *rheo*
+     - *atomic* + rho, status
+     - :ref:`RHEO <PKG-RHEO>`
+     - solid and fluid RHEO particles
+   * - *rheo/thermal*
+     - *atomic* + rho, status, temperature
+     - :ref:`RHEO <PKG-RHEO>`
+     - RHEO particles with temperature
+   * - *sph*
+     - *atomic* + "sph data"
+     - :ref:`SPH <PKG-SPH>`
+     - Smoothed particle hydrodynamics models
+   * - *sphere*
+     - *atomic* + radius, rmass, omega, torque
+     -
+     - finite size spherical particles, e.g. granular models
+   * - *spin*
+     - *atomic* + "magnetic moment data"
+     - :ref:`SPIN <PKG-SPIN>`
+     - magnetic particles
+   * - *tdpd*
+     - *atomic* + cc, cc_flux, vest
+     - :ref:`DPD-MESO <PKG-DPD-MESO>`
+     - Transport DPD (tDPD)
+   * - *template*
+     - *atomic* + molecule, molindex, molatom
+     - :ref:`MOLECULE <PKG-MOLECULE>`
+     - molecular systems where attributes are taken from :doc:`molecule files <molecule>`
+   * - *tri*
+     - *sphere* + molecule, angmom, tri
+     -
+     - 3-d triangulated rigid body LJ particles
+   * - *wavepacket*
+     - *charge* + "wavepacket data"
+     - :ref:`AWPMD <PKG-AWPMD>`
+     - Antisymmetrized wave packet MD
 
 .. note::
 
-   It is possible to add some attributes, such as a molecule ID, to
+   It is possible to add some attributes, such as a molecule ID and
-   atom styles that do not have them via the :doc:`fix property/atom
+   charge, to atom styles that do not have them built in using the
-   <fix_property_atom>` command.  This command also allows new custom
+   :doc:`fix property/atom <fix_property_atom>` command.  This command
-   attributes consisting of extra integer or floating-point values to
+   also allows new custom-named attributes consisting of extra integer
-   be added to atoms.  See the :doc:`fix property/atom
+   or floating-point values or vectors to be added to atoms.  See the
-   <fix_property_atom>` page for examples of cases where this is
+   :doc:`fix property/atom <fix_property_atom>` page for examples of
-   useful and details on how to initialize, access, and output the
+   cases where this is useful and details on how to initialize,
-   custom values.
+   access, and output these custom values.
 
-All of the above styles define point particles, except the *sphere*,
+----------
-*bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*,
-*tri*, and *body* styles, which define finite-size particles.  See the
-:doc:`Howto spherical <Howto_spherical>` page for an overview of using
-finite-size particle models with LAMMPS.
 
-All of the point-particle styles assign mass to particles on a
+Particle size and mass
-per-type basis, using the :doc:`mass <mass>` command, The finite-size
+""""""""""""""""""""""
-particle styles assign mass to individual particles on a per-particle
-basis.
 
-For the *sphere* and *bpm/sphere* styles, the particles are spheres
+All of the atom styles define point particles unless they (1) define
-and each stores a per-particle diameter and mass.  If the diameter >
+finite-size spherical particles via the *radius* attribute, or (2)
-0.0, the particle is a finite-size sphere.  If the diameter = 0.0, it
+define finite-size aspherical particles (e.g. the *body*, *ellipsoid*,
-is a point particle.  Note that by use of the *disc* keyword with the
+*line*, and *tri* styles).  Most of these styles can also be used with
-:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
+mixtures of point and finite-size particles.
-<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`,
-:doc:`fix npt/sphere <fix_npt_sphere>` commands for the *sphere* style,
-spheres can be effectively treated as 2d discs for a 2d simulation if
-desired.  See also the :doc:`set density/disc <set>` command.  These
-styles take an optional 0 or 1 argument.  A value of 0 means the
-radius of each sphere is constant for the duration of the simulation.
-A value of 1 means the radii may vary dynamically during the simulation,
-e.g. due to use of the :doc:`fix adapt <fix_adapt>` command.
 
-For the *ellipsoid* style, the particles are ellipsoids and each
+Note that the *radius* property may need to be provided as a
-stores a flag which indicates whether it is a finite-size ellipsoid or
+*diameter* (e.g. in :doc:`molecule files <molecule>` or :doc:`data
-a point particle.  If it is an ellipsoid, it also stores a shape
+files <read_data>`).  See the :doc:`Howto spherical <Howto_spherical>`
-vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
+page for an overview of using finite-size spherical and aspherical
-with its orientation.
+particle models with LAMMPS.
 
-For the *dielectric* style, each particle can be either a physical
+Unless an atom style defines the per-atom *rmass* attribute, particle
-particle (e.g. an ion), or an interface particle representing a boundary
+masses are defined on a per-type basis, using the :doc:`mass <mass>`
-element between two regions of different dielectric constant. For
+command.  This means each particle's mass is indexed by its atom
-interface particles, in addition to the properties associated with
+*type*.
-atom_style full, each particle also should be assigned a normal unit
-vector (defined by normx, normy, normz), an area (area/patch), the
-difference and mean of the dielectric constants of two sides of the
-interface along the direction of the normal vector (ed and em), the
-local dielectric constant at the boundary element (epsilon), and a mean
-local curvature (curv).  Physical particles must be assigned these
-values, as well, but only their local dielectric constants will be used;
-see documentation for associated :doc:`pair styles <pair_dielectric>`
-and :doc:`fixes <fix_polarize>`.  The distinction between the physical
-and interface particles is only meaningful when :doc:`fix polarize
-<fix_polarize>` commands are applied to the interface particles. This
-style is part of the DIELECTRIC package.
 
-For the *dipole* style, a point dipole is defined for each point
+A few styles define the per-atom *rmass* attribute which can also be
-particle.  Note that if you wish the particles to be finite-size
+added using the :doc:`fix property/atom <fix_property_atom>` command.
-spheres as in a Stockmayer potential for a dipolar fluid, so that the
+In this case each particle stores its own mass.  Atom styles that have
-particles can rotate due to dipole-dipole interactions, then you need
+a per-atom rmass may define it indirectly through setting particle
-to use atom_style hybrid sphere dipole, which will assign both a
+diameter and density on a per-particle basis.  If both per-type mass
-diameter and dipole moment to each particle.
+and per-atom *rmass* are defined (e.g. in a hybrid style), the
+per-atom mass will take precedence in any operation which which works
+with both flavors of mass.
 
-For the *electron* style, the particles representing electrons are 3d
+----------
-Gaussians with a specified position and bandwidth or uncertainty in
-position, which is represented by the eradius = electron size.
 
-For the *peri* style, the particles are spherical and each stores a
+Additional information about specific atom styles
-per-particle mass and volume.
+"""""""""""""""""""""""""""""""""""""""""""""""""
-
-The *bpm/sphere* style is part of the BPM package.
-
-The *oxdna* style is for coarse-grained nucleotides and stores the
-3'-to-5' polarity of the nucleotide strand, which is set through
-the bond topology in the data file. The first (second) atom in a
-bond definition is understood to point towards the 3'-end (5'-end)
-of the strand. Note that this style is part of the CG-DNA package.
-
-The *dpd* style is for dissipative particle dynamics (DPD) particles.
-Note that it is part of the DPD-REACT package, and is not for use with
-the :doc:`pair_style dpd or dpd/stat <pair_dpd>` commands, which can
-simply use atom_style atomic.  Atom_style dpd extends DPD particle
-properties with internal temperature (dpdTheta), internal conductive
-energy (uCond), internal mechanical energy (uMech), and internal
-chemical energy (uChem).
-
-The *edpd* style is for energy-conserving dissipative particle
-dynamics (eDPD) particles which store a temperature (edpd_temp), and
-heat capacity(edpd_cv).
-
-The *mdpd* style is for many-body dissipative particle dynamics (mDPD)
-particles which store a density (rho) for considering
-density-dependent many-body interactions.
-
-The *tdpd* style is for transport dissipative particle dynamics (tDPD)
-particles which store a set of chemical concentration. An integer
-"cc_species" is required to specify the number of chemical species
-involved in a tDPD system.
-
-The *sph* style is for smoothed particle hydrodynamics (SPH)
-particles which store a density (rho), energy (esph), and heat capacity
-(cv).
-
-The *smd* style is for a general formulation of Smooth Particle
-Hydrodynamics.  Both fluids and solids can be modeled.  Particles
-store the mass and volume of an integration point, a kernel diameter
-used for calculating the field variables (e.g. stress and deformation)
-and a contact radius for calculating repulsive forces which prevent
-individual physical bodies from penetrating each other.
-
-For the *spin* style, a magnetic spin is associated to each atom.
-Those spins have a norm (their magnetic moment) and a direction.
-
-The *wavepacket* style is similar to *electron*, but the electrons may
-consist of several Gaussian wave packets, summed up with coefficients
-cs= (cs_re,cs_im).  Each of the wave packets is treated as a separate
-particle in LAMMPS, wave packets belonging to the same electron must
-have identical *etag* values.
-
-For the *line* style, the particles are idealized line segments and
-each stores a per-particle mass and length and orientation (i.e. the
-end points of the line segment).
-
-For the *tri* style, the particles are planar triangles and each
-stores a per-particle mass and size and orientation (i.e. the corner
-points of the triangle).
-
-The *template* style allows molecular topology (bonds,angles,etc) to be
-defined via a molecule template using the :doc:`molecule <molecule>`
-command.  The template stores one or more molecules with a single copy
-of the topology info (bonds,angles,etc) of each.  Individual atoms
-only store a template index and template atom to identify which
-molecule and which atom-within-the-molecule they represent.  Using the
-*template* style instead of the *bond*, *angle*, *molecular* styles
-can save memory for systems comprised of a large number of small
-molecules, all of a single type (or small number of types).  See the
-paper by Grime and Voth, in :ref:`(Grime) <Grime>`, for examples of how this
-can be advantageous for large-scale coarse-grained systems.
-The ``examples/template`` directory has a few demo inputs and examples
-showing the use of the *template* atom style versus *molecular*.
-
-.. note::
-
-   When using the *template* style with a :doc:`molecule template
-   <molecule>` that contains multiple molecules, you should ensure the
-   atom types, bond types, angle_types, etc in all the molecules are
-   consistent.  E.g. if one molecule represents H2O and another CO2,
-   then you probably do not want each molecule file to define 2 atom
-   types and a single bond type, because they will conflict with each
-   other when a mixture system of H2O and CO2 molecules is defined,
-   e.g. by the :doc:`read_data <read_data>` command.  Rather the H2O
-   molecule should define atom types 1 and 2, and bond type 1.  And
-   the CO2 molecule should define atom types 3 and 4 (or atom types 3
-   and 2 if a single oxygen type is desired), and bond type 2.
 
 For the *body* style, the particles are arbitrary bodies with internal
 attributes defined by the "style" of the bodies, which is specified by
@@ -313,6 +290,149 @@ Note that there may be additional arguments required along with the
 *bstyle* specification, in the atom_style body command.  These
 arguments are described on the :doc:`Howto body <Howto_body>` doc page.
 
+For the *dielectric* style, each particle can be either a physical
+particle (e.g. an ion), or an interface particle representing a
+boundary element between two regions of different dielectric
+constant. For interface particles, in addition to the properties
+associated with atom_style full, each particle also should be assigned
+a unit dipole vector (mu) representing the direction of the induced
+dipole moment at each interface particle, an area (area/patch), the
+difference and mean of the dielectric constants of two sides of the
+interface along the direction of the normal vector (ed and em), the
+local dielectric constant at the boundary element (epsilon), and a
+mean local curvature (curv).  Physical particles must be assigned
+these values, as well, but only their local dielectric constants will
+be used; see documentation for associated :doc:`pair styles
+<pair_dielectric>` and :doc:`fixes <fix_polarize>`.  The distinction
+between the physical and interface particles is only meaningful when
+:doc:`fix polarize <fix_polarize>` commands are applied to the
+interface particles. This style is part of the DIELECTRIC package.
+
+For the *dipole* style, a point dipole vector mu is defined for each
+point particle.  Note that if you wish the particles to be finite-size
+spheres as in a Stockmayer potential for a dipolar fluid, so that the
+particles can rotate due to dipole-dipole interactions, then you need
+to use the command `atom_style hybrid sphere dipole`, which will
+assign both a diameter and dipole moment to each particle.  This also
+requires using an integrator with a "/sphere" suffix like :doc:`fix
+nve/sphere <fix_nve_sphere>` or :doc:`fix nvt/sphere <fix_nvt_sphere>`
+and the "update dipole" or "update dlm" parameters to the fix
+commands.
+
+The *dpd* style is for reactive dissipative particle dynamics (DPD)
+particles.  Note that it is part of the DPD-REACT package, and is not
+required for use with the :doc:`pair_style dpd or dpd/stat <pair_dpd>`
+commands, which only require the attributes from atom_style *atomic*.
+Atom_style *dpd* extends DPD particle properties with internal
+temperature (dpdTheta), internal conductive energy (uCond), internal
+mechanical energy (uMech), and internal chemical energy (uChem).
+
+The *edpd* style is for energy-conserving dissipative particle
+dynamics (eDPD) particles which store a temperature (edpd_temp), and
+heat capacity (edpd_cv).
+
+For the *electron* style, the particles representing electrons are 3d
+Gaussians with a specified position and bandwidth or uncertainty in
+position, which is represented by the eradius = electron size.
+
+For the *ellipsoid* style, particles can be ellipsoids which each
+stores a shape vector with the 3 diameters of the ellipsoid and a
+quaternion 4-vector with its orientation.  Each particle stores a flag
+in the ellipsoid vector which indicates whether it is an ellipsoid (1)
+or a point particle (0).
+
+For the *line* style, particles can be are idealized line segments
+which store a per-particle mass and length and orientation (i.e. the
+end points of the line segment).  Each particle stores a flag in the
+line vector which indicates whether it is a line segment (1) or a
+point particle (0).
+
+The *mdpd* style is for many-body dissipative particle dynamics (mDPD)
+particles which store a density (rho) for considering density-dependent
+many-body interactions.
+
+The *oxdna* style is for coarse-grained nucleotides and stores the
+3'-to-5' polarity of the nucleotide strand, which is set through
+the bond topology in the data file. The first (second) atom in a
+bond definition is understood to point towards the 3'-end (5'-end)
+of the strand.
+
+For the *peri* style, the particles are spherical and each stores a
+per-particle mass and volume.
+
+The *smd* style is for Smooth Particle Mach dynamics.  Both fluids and
+solids can be modeled.  Particles store the mass and volume of an
+integration point, a kernel diameter used for calculating the field
+variables (e.g. stress and deformation) and a contact radius for
+calculating repulsive forces which prevent individual physical bodies
+from penetrating each other.
+
+The *sph* style is for smoothed particle hydrodynamics (SPH) particles
+which store a density (rho), energy (esph), and heat capacity (cv).
+
+For the *spin* style, a magnetic spin is associated with each atom.
+Those spins have a norm (their magnetic moment) and a direction.
+
+The *tdpd* style is for transport dissipative particle dynamics (tDPD)
+particles which store a set of chemical concentration. An integer
+"cc_species" is required to specify the number of chemical species
+involved in a tDPD system.
+
+The *wavepacket* style is similar to the *electron* style, but the
+electrons may consist of several Gaussian wave packets, summed up with
+coefficients cs= (cs_re,cs_im).  Each of the wave packets is treated
+as a separate particle in LAMMPS, wave packets belonging to the same
+electron must have identical *etag* values.
+
+The *sphere* and *bpm/sphere* styles allow particles to be either point
+particles or finite-size particles.  If the *radius* attribute is >
+0.0, the particle is a finite-size sphere.  If the diameter = 0.0, it
+is a point particle.  Note that by using the *disc* keyword with the
+:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
+<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix
+npt/sphere <fix_npt_sphere>` commands for the *sphere* style, spheres
+can be effectively treated as 2d discs for a 2d simulation if desired.
+See also the :doc:`set density/disc <set>` command.  These styles also
+take an optional 0 or 1 argument.  A value of 0 means the radius of
+each sphere is constant for the duration of the simulation (this is
+the default).  A value of 1 means the radii may vary dynamically
+during the simulation, e.g. due to use of the :doc:`fix adapt
+<fix_adapt>` command.
+
+The *template* style allows molecular topology (bonds,angles,etc) to be
+defined via a molecule template using the :doc:`molecule <molecule>`
+command.  The template stores one or more molecules with a single copy
+of the topology info (bonds,angles,etc) of each.  Individual atoms only
+store a template index and template atom to identify which molecule and
+which atom-within-the-molecule they represent.  Using the *template*
+style instead of the *bond*, *angle*, *molecular* styles can save memory
+for systems comprised of a large number of small molecules, all of a
+single type (or small number of types).  See the paper by Grime and
+Voth, in :ref:`(Grime) <Grime>`, for examples of how this can be
+advantageous for large-scale coarse-grained systems.  The
+``examples/template`` directory has a few demo inputs and examples
+showing the use of the *template* atom style versus *molecular*.
+
+.. note::
+
+   When using the *template* style with a :doc:`molecule template
+   <molecule>` that contains multiple molecules, you should ensure the
+   atom types, bond types, angle_types, etc in all the molecules are
+   consistent.  E.g. if one molecule represents H2O and another CO2,
+   then you probably do not want each molecule file to define 2 atom
+   types and a single bond type, because they will conflict with each
+   other when a mixture system of H2O and CO2 molecules is defined,
+   e.g. by the :doc:`read_data <read_data>` command.  Rather the H2O
+   molecule should define atom types 1 and 2, and bond type 1.  And
+   the CO2 molecule should define atom types 3 and 4 (or atom types 3
+   and 2 if a single oxygen type is desired), and bond type 2.
+
+For the *tri* style, particles can be planar triangles which each
+stores a per-particle mass and size and orientation (i.e. the corner
+points of the triangle).  Each particle stores a flag in the tri
+vector which indicates whether it is a triangle (1) or a point
+particle (0).
+
 ----------
 
 Typically, simulations require only a single (non-hybrid) atom style.
@@ -330,11 +450,12 @@ dipole".  When a hybrid style is used, atoms store and communicate the
 union of all quantities implied by the individual styles.
 
 When using the *hybrid* style, you cannot combine the *template* style
-with another molecular style that stores bond,angle,etc info on a
+with another molecular style that stores bond, angle, etc info on a
 per-atom basis.
 
-LAMMPS can be extended with new atom styles as well as new body
+LAMMPS can be extended with new atom styles as well as new body styles;
-styles; see the :doc:`Modify <Modify>` doc page.
+see the corresponding manual page on :doc:`modifying & extending LAMMPS
+<Modify_atom>`.
 
 ----------
 
@@ -350,54 +471,20 @@ This command cannot be used after the simulation box is defined by a
 
 Many of the styles listed above are only enabled if LAMMPS was built
 with a specific package, as listed below.  See the :doc:`Build package
-<Build_package>` page for more info.
+<Build_package>` page for more info.  The table above lists which package
-
+is required for individual atom styles.
-The *amoeba* style is part of the AMOEBA package.
-
-The *angle*, *bond*, *full*, *molecular*, and *template* styles are
-part of the MOLECULE package.
-
-The *line* and *tri* styles are part of the ASPHERE package.
-
-The *body* style is part of the BODY package.
-
-The *dipole* style is part of the DIPOLE package.
-
-The *peri* style is part of the PERI package for Peridynamics.
-
-The *oxdna* style is part of the CG-DNA package for coarse-grained
-simulation of DNA and RNA.
-
-The *electron* style is part of the EFF package for :doc:`electronic
-force fields <pair_eff>`.
-
-The *dpd* style is part of the DPD-REACT package for dissipative
-particle dynamics (DPD).
-
-The *edpd*, *mdpd*, and *tdpd* styles are part of the DPD-MESO package
-for energy-conserving dissipative particle dynamics (eDPD), many-body
-dissipative particle dynamics (mDPD), and transport dissipative particle
-dynamics (tDPD), respectively.
-
-The *sph* style is part of the SPH package for smoothed particle
-hydrodynamics (SPH).  See `this PDF guide
-<PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
-
-The *spin* style is part of the SPIN package.
-
-The *wavepacket* style is part of the AWPMD package for the
-:doc:`antisymmetrized wave packet MD method <pair_awpmd>`.
 
 Related commands
 """"""""""""""""
 
-:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`
+:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`,
+:doc:`fix property/atom <fix_property_atom>`, :doc:`set <set>`
 
 Default
 """""""
 
-The default atom style is atomic.  If atom_style sphere is used its
+The default atom style is *atomic*.  If atom_style *sphere* or
-default argument is 0.
+*bpm/sphere* is used, its default argument is 0.
 
 ----------
 

doc/src/bond_hybrid.rst

@@ -1,8 +1,11 @@
 .. index:: bond_style hybrid
+.. index:: bond_style hybrid/kk
 
 bond_style hybrid command
 =========================
 
+Accelerator Variants: *hybrid/kk*
+
 Syntax
 """"""
 
@@ -15,7 +18,7 @@ Syntax
 Examples
 """"""""
 
-.. code-block: LAMMPS
+.. code-block:: LAMMPS
 
    bond_style hybrid harmonic fene
    bond_coeff 1 harmonic 80.0 1.2
@@ -60,6 +63,10 @@ bond types.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Restrictions
 """"""""""""
 

doc/src/bond_lepton.rst

@@ -50,7 +50,7 @@ constant *K* of 200.0 energy units:
 
    U_{bond,i} = K (r_i - r_0)^2 = K r^2 \qquad r = r_i - r_0
 
-.. versionchanged:: TBD
+.. versionchanged:: 7Feb2024
 
 By default the potential energy U is shifted so that he value U is 0.0
 for $r = r_0$.  This is equivalent to using the optional keyword

doc/src/bond_oxdna.rst

@@ -27,6 +27,7 @@ Examples
 
 .. code-block:: LAMMPS
 
+   # LJ units
    bond_style oxdna/fene
    bond_coeff * 2.0 0.25 0.7525
 
@@ -36,6 +37,32 @@ Examples
    bond_style oxrna2/fene
    bond_coeff * 2.0 0.25 0.76107
 
+   bond_style oxdna/fene
+   bond_coeff * oxdna_lj.cgdna
+
+   # Real units
+   bond_style oxdna/fene
+   bond_coeff * 11.92337812042065 2.1295 6.409795
+
+   bond_style oxdna2/fene
+   bond_coeff * 11.92337812042065 2.1295 6.4430152
+
+   bond_style oxrna2/fene
+   bond_coeff * 11.92337812042065 2.1295 6.482800913
+
+   bond_style oxrna2/fene
+   bond_coeff * oxrna2_real.cgdna
+
+.. note::
+
+   The coefficients in the above examples have to be kept fixed and
+   cannot be changed without reparameterizing the entire model. They are
+   provided in forms compatible with both *units lj* and *units real*
+   (see documentation of :doc:`units <units>`).  These can also be read
+   from a potential file with correct unit style by specifying the name
+   of the file. Several potential files for each unit style are included
+   in the ``potentials`` directory of the LAMMPS distribution.
+
 Description
 """""""""""
 
@@ -46,15 +73,14 @@ The *oxdna/fene*, *oxdna2/fene*, and *oxrna2/fene* bond styles use the potential
    E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r_0}{\Delta}\right)^2\right]
 
 to define a modified finite extensible nonlinear elastic (FENE)
-potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of the
+potential :ref:`(Ouldridge) <Ouldridge0>` to model the connectivity of
-phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
+the phosphate backbone in the oxDNA/oxRNA force field for coarse-grained
 modelling of DNA/RNA.
 
 The following coefficients must be defined for the bond type via the
 :doc:`bond_coeff <bond_coeff>` command as given in the above example, or
-in the data file or restart files read by the
+in the data file or restart files read by the :doc:`read_data
-:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
+<read_data>` or :doc:`read_restart <read_restart>` commands:
-commands:
 
 * :math:`\epsilon` (energy)
 * :math:`\Delta` (distance)
@@ -62,41 +88,40 @@ commands:
 
 .. note::
 
-   The oxDNA bond style has to be used together with the
+   The oxDNA bond style has to be used together with the corresponding
-   corresponding oxDNA pair styles for excluded volume interaction
+   oxDNA pair styles for excluded volume interaction *oxdna/excv* ,
-   *oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and
+   stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and coaxial
-   coaxial stacking interaction *oxdna/coaxstk* as well as
+   stacking interaction *oxdna/coaxstk* as well as hydrogen-bonding
-   hydrogen-bonding interaction *oxdna/hbond* (see also documentation of
+   interaction *oxdna/hbond* (see also documentation of :doc:`pair_style
-   :doc:`pair_style oxdna/excv <pair_oxdna>`). For the oxDNA2
+   oxdna/excv <pair_oxdna>`). For the oxDNA2 :ref:`(Snodin) <Snodin0>`
-   :ref:`(Snodin) <Snodin0>` bond style the analogous pair styles
+   bond style the analogous pair styles *oxdna2/excv* , *oxdna2/stk* ,
-   *oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* ,
+   *oxdna2/xstk* , *oxdna2/coaxstk* , *oxdna2/hbond* and an additional
-   *oxdna2/hbond* and an additional Debye-Hueckel pair style
+   Debye-Hueckel pair style *oxdna2/dh* have to be defined. The same
-   *oxdna2/dh* have to be defined. The same applies to the oxRNA2
+   applies to the oxRNA2 :ref:`(Sulc1) <Sulc01>` styles.
-   :ref:`(Sulc1) <Sulc01>` styles.
-   The coefficients in the above example have to be kept fixed and cannot
-   be changed without reparameterizing the entire model.
 
 .. note::
 
-   This bond style has to be used with the *atom_style hybrid bond ellipsoid oxdna*
+   This bond style has to be used with the *atom_style hybrid bond
-   (see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
+   ellipsoid oxdna* (see documentation of :doc:`atom_style
-   stores the 3'-to-5' polarity of the nucleotide strand, which is set through
+   <atom_style>`). The *atom_style oxdna* stores the 3'-to-5' polarity
-   the bond topology in the data file. The first (second) atom in a bond definition
+   of the nucleotide strand, which is set through the bond topology in
-   is understood to point towards the 3'-end (5'-end) of the strand.
+   the data file. The first (second) atom in a bond definition is
+   understood to point towards the 3'-end (5'-end) of the strand.
 
 .. warning::
 
-   If data files are produced with :doc:`write_data <write_data>`, then the
+   If data files are produced with :doc:`write_data <write_data>`, then
-   :doc:`newton <newton>` command should be set to *newton on* or *newton off on*.
+   the :doc:`newton <newton>` command should be set to *newton on* or
-   Otherwise the data files will not have the same 3'-to-5' polarity as the
+   *newton off on*.  Otherwise the data files will not have the same
-   initial data file. This limitation does not apply to binary restart files
+   3'-to-5' polarity as the initial data file. This limitation does not
-   produced with :doc:`write_restart <write_restart>`.
+   apply to binary restart files produced with :doc:`write_restart
+   <write_restart>`.
 
 Example input and data files for DNA and RNA duplexes can be found in
-examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/.  A simple python
+``examples/PACKAGES/cgdna/examples/oxDNA/`, `.../oxDNA2/`` and
-setup tool which creates single straight or helical DNA strands, DNA/RNA
+``.../oxRNA2/``.  A simple python setup tool which creates single
-duplexes or arrays of DNA/RNA duplexes can be found in
+straight or helical DNA strands, DNA/RNA duplexes or arrays of DNA/RNA
-examples/PACKAGES/cgdna/util/.
+duplexes can be found in ``examples/PACKAGES/cgdna/util/``.
 
 Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses
 this implementation. An updated documentation that contains general information
@@ -113,6 +138,39 @@ and for sequence-specific hydrogen-bonding and stacking interactions
 
 ----------
 
+Potential file reading
+""""""""""""""""""""""
+
+For each style oxdna, oxdna2 and oxrna2, the first parameter argument
+can be a filename, and if it is, no further arguments should be
+supplied. Therefore the following command:
+
+.. code-block:: LAMMPS
+
+   bond_style oxdna/fene
+   bond_coeff * oxdna_lj.cgdna
+
+will be interpreted as a request to read the (FENE) potential
+:ref:`(Ouldridge) <Ouldridge0>` parameters from the file with the given
+name.  The file can define multiple potential parameters for both bonded
+and pair interactions, but for the above bonded interactions there must
+exist in the file a line of the form:
+
+.. code-block:: LAMMPS
+
+   *   fene    epsilon delta r0
+
+There are sample potential files for each unit style in the
+``potentials`` directory of the LAMMPS distribution. The potential file
+unit system must align with the units defined via the :doc:`units
+<units>` command. For conversion between different *LJ* and *real* unit
+systems for oxDNA, the python tool *lj2real.py* located in the
+``examples/PACKAGES/cgdna/util/`` directory can be used. This tool
+assumes similar file structure to the examples found in
+``examples/PACKAGES/cgdna/examples/``.
+
+----------
+
 Restrictions
 """"""""""""
 

doc/src/boundary.rst

@@ -42,8 +42,10 @@ commands.
 The style *p* means the box is periodic, so that particles interact
 across the boundary, and they can exit one end of the box and re-enter
 the other end.  A periodic dimension can change in size due to
-constant pressure boundary conditions or box deformation (see the :doc:`fix npt <fix_nh>` and :doc:`fix deform <fix_deform>` commands).  The *p*
+constant pressure boundary conditions or box deformation (see the
-style must be applied to both faces of a dimension.
+:doc:`fix npt <fix_nh>` and :doc:`fix deform <fix_deform>` commands).
+The *p* style must be applied to both faces of a dimension.  For 2d
+simulations the z dimension must be periodic (which is the default).
 
 The styles *f*, *s*, and *m* mean the box is non-periodic, so that
 particles do not interact across the boundary and do not move from one
@@ -76,28 +78,44 @@ atoms becomes less than 50.0.  This can be useful if you start a
 simulation with an empty box or if you wish to leave room on one side
 of the box, e.g. for atoms to evaporate from a surface.
 
-For triclinic (non-orthogonal) simulation boxes, if the second dimension
+LAMMPS also allows use of triclinic (non-orthogonal) simulation boxes.
-of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
-enforced with the tilt factor offset.  If the first dimension is
-shrink-wrapped, then the shrink wrapping is applied to the tilted box
-face, to encompass the atoms.  E.g. for a positive xy tilt, the xlo
-and xhi faces of the box are planes tilting in the +y direction as y
-increases.  These tilted planes are shrink-wrapped around the atoms to
-determine the x extent of the box.
-
 See the :doc:`Howto triclinic <Howto_triclinic>` page for a
-geometric description of triclinic boxes, as defined by LAMMPS, and
+description of both general and restricted triclinic boxes and how to
-how to transform these parameters to and from other commonly used
+define them.  General triclinic boxes (arbitrary edge vectors **A**,
-triclinic representations.
+**B**, and **C**) are converted internally to restricted triclinic
+boxes with tilt factors (xy,xz,yz) which skew an otherwise orthogonal
+box.
+
+The boundary <boundary> command settings explained above for the 6
+faces of an orthogonal box also apply in similar manner to the 6 faces
+of a restricted triclinic box (and thus to the corresponding 6 faces
+of a general triclinic box), with the following context.
+
+if the second dimension of a tilt factor (e.g. y for xy) is periodic,
+then the periodicity is enforced with the tilt factor offset.  This
+means that for y periodicity a particle which exits the lower y
+boundary is displaced in the x-direction by xy before it re-enters the
+upper y boundary.  And vice versa if a particle exits the upper y
+boundary.  Likewise the ghost atoms surrounding a particle near the
+lower y boundary include images of particles near the upper y-boundary
+which are displaced in the x-direction by xy.  Similar rules apply for
+z-periodicity and the xz and/or yz tilt factors.
+
+If the first dimension of a tilt factor is shrink-wrapped, then the
+shrink wrapping is applied to the tilted box face, to encompass the
+atoms.  E.g. for a positive xy tilt, the xlo and xhi faces of the box
+are planes tilting in the +y direction as y increases.  The position
+of these tilted planes are adjusted dynamically to shrink-wrap around
+the atoms to determine the xlo and xhi extents of the box.
 
 Restrictions
 """"""""""""
 
 This command cannot be used after the simulation box is defined by a
-:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command or
+:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command
-:doc:`read_restart <read_restart>` command.  See the
+or :doc:`read_restart <read_restart>` command.  See the
-:doc:`change_box <change_box>` command for how to change the simulation
+:doc:`change_box <change_box>` command for how to change the
-box boundaries after it has been defined.
+simulation box boundaries after it has been defined.
 
 For 2d simulations, the z dimension must be periodic.
 

doc/src/compute_adf.rst

@@ -204,8 +204,23 @@ angles per atom satisfying the ADF criteria.
 Restrictions
 """"""""""""
 
-This compute is part of the EXTRA-COMPUTE package.  It is only enabled if
+This compute is part of the EXTRA-COMPUTE package.  It is only enabled
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+By default, the ADF is not computed for distances longer than the
+largest force cutoff, since the neighbor list creation will only contain
+pairs up to that distance (plus neighbor list skin).  If you use outer
+cutoffs larger than that, you must use :doc:`neighbor style 'bin' or
+'nsq' <neighbor>`.
+
+If you want an ADF for a larger outer cutoff, you can also use the
+:doc:`rerun <rerun>` command to post-process a dump file, use :doc:`pair
+style zero <pair_zero>` and set the force cutoff to be larger in the
+rerun script.  Note that in the rerun context, the force cutoff is
+arbitrary and with pair style zero you are not computing any forces, and
+since you are not running dynamics you are not changing the model that
+generated the trajectory.
 
 The ADF is not computed for neighbors outside the force cutoff,
 since processors (in parallel) don't know about atom coordinates for

doc/src/compute_ave_sphere_atom.rst

@@ -102,6 +102,8 @@ This compute is part of the EXTRA-COMPUTE package.  It is only enabled
 if LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
+This compute requires :doc:`neighbor styles 'bin' or 'nsq' <neighbor>`.
+
 Related commands
 """"""""""""""""
 

doc/src/compute_composition_atom.rst

@@ -107,6 +107,8 @@ This compute is part of the EXTRA-COMPUTE package.  It is only enabled
 if LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
+This compute requires :doc:`neighbor styles 'bin' or 'nsq' <neighbor>`.
+
 Related commands
 """"""""""""""""
 

doc/src/compute_count_type.rst

@@ -12,7 +12,7 @@ Syntax
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * count/type = style name of this compute command
-* mode = {atom} or {bond} or {angle} or {dihedral} or {improper}
+* mode = *atom* or *bond* or *angle* or *dihedral* or *improper*
 
 Examples
 """"""""
@@ -69,29 +69,42 @@ for each type:
 
 ----------
 
-If the {mode} setting is {atom} then the count of atoms for each atom
+If the *mode* setting is *atom* then the count of atoms for each atom
 type is tallied.  Only atoms in the specified group are counted.
 
-If the {mode} setting is {bond} then the count of bonds for each bond
+The atom count for each type can be normalized by the total number of
+atoms like so:
+
+.. code-block:: LAMMPS
+
+   compute typevec all count/type atom # number of atoms of each type
+   variable normtypes vector c_typevec/atoms # divide by total number of atoms
+   variable ntypes equal extract_setting(ntypes) # number of atom types
+   thermo_style custom step v_normtypes[*${ntypes}] # vector variable needs upper limit
+
+Similarly, bond counts can be normalized by the total number of bonds.
+The same goes for angles, dihedrals, and impropers (see below).
+
+If the *mode* setting is *bond* then the count of bonds for each bond
 type is tallied.  Only bonds with both atoms in the specified group
 are counted.
 
-For {mode} = {bond}, broken bonds with a bond type of zero are also
+For *mode* = *bond*, broken bonds with a bond type of zero are also
 counted.  The :doc:`bond_style quartic <bond_quartic>` and :doc:`BPM
-bond styles <Howto_bpm>` break bonds by doing this.  See the :doc:`
+bond styles <Howto_bpm>` break bonds by doing this.  See the
-Howto broken bonds <Howto_broken_bonds>` doc page for more details.
+:doc:`Howto broken bonds <Howto_broken_bonds>` doc page for more details.
 Note that the group setting is ignored for broken bonds; all broken
 bonds in the system are counted.
 
-If the {mode} setting is {angle} then the count of angles for each
+If the *mode* setting is *angle* then the count of angles for each
 angle type is tallied.  Only angles with all 3 atoms in the specified
 group are counted.
 
-If the {mode} setting is {dihedral} then the count of dihedrals for
+If the *mode* setting is *dihedral* then the count of dihedrals for
 each dihedral type is tallied.  Only dihedrals with all 4 atoms in the
 specified group are counted.
 
-If the {mode} setting is {improper} then the count of impropers for
+If the *mode* setting is *improper* then the count of impropers for
 each improper type is tallied.  Only impropers with all 4 atoms in the
 specified group are counted.
 
@@ -101,18 +114,19 @@ Output info
 """""""""""
 
 This compute calculates a global vector of counts.  If the mode is
-{atom} or {bond} or {angle} or {dihedral} or {improper}, then the
+*atom* or *bond* or *angle* or *dihedral* or *improper*, then the
 vector length is the number of atom types or bond types or angle types
 or dihedral types or improper types, respectively.
 
-If the mode is {bond} this compute also calculates a global scalar
+If the mode is *bond* this compute also calculates a global scalar
 which is the number of broken bonds with type = 0, as explained above.
 
 These values can be used by any command that uses global scalar or
 vector values from a compute as input.  See the :doc:`Howto output
 <Howto_output>` page for an overview of LAMMPS output options.
 
-The scalar and vector values calculated by this compute are "extensive".
+The scalar and vector values calculated by this compute are both
+"intensive".
 
 Restrictions
 """"""""""""

doc/src/compute_efield_wolf_atom.rst

@@ -106,6 +106,8 @@ Restrictions
 This compute is part of the EXTRA-COMPUTE package. It is only enabled if
 LAMMPS was built with that package.
 
+This compute requires :doc:`neighbor styles 'bin' or 'nsq' <neighbor>`.
+
 Related commands
 """"""""""""""""
 

doc/src/compute_fabric.rst

@@ -64,7 +64,7 @@ tangential force tensor. The contact tensor is calculated as
 
 .. math::
 
-   C_{ab}  =  \frac{15}{2} (\phi_{ab} - \mathrm{Tr}(\phi) \delta_{ab})
+   C_{ab}  =  \frac{15}{2} (\phi_{ab} - \frac{1}{3} \mathrm{Tr}(\phi) \delta_{ab})
 
 where :math:`a` and :math:`b` are the :math:`x`, :math:`y`, :math:`z`
 directions, :math:`\delta_{ab}` is the Kronecker delta function, and
@@ -83,7 +83,7 @@ The branch tensor is calculated as
 
 .. math::
 
-   B_{ab}  =  \frac{15}{6 \mathrm{Tr}(D)} (D_{ab} - \mathrm{Tr}(D) \delta_{ab})
+   B_{ab}  =  \frac{15}{2\, \mathrm{Tr}(D)} (D_{ab} - \frac{1}{3} \mathrm{Tr}(D) \delta_{ab})
 
 where the tensor :math:`D` is defined as
 
@@ -101,7 +101,7 @@ The normal force fabric tensor is calculated as
 
 .. math::
 
-   F^n_{ab}  =  \frac{15}{6\, \mathrm{Tr}(N)} (N_{ab} - \mathrm{Tr}(N) \delta_{ab})
+   F^n_{ab}  =  \frac{15}{2\, \mathrm{Tr}(N)} (N_{ab} - \frac{1}{3} \mathrm{Tr}(N) \delta_{ab})
 
 where the tensor :math:`N` is defined as
 
@@ -119,7 +119,7 @@ as
 
 .. math::
 
-   F^t_{ab}  =  \frac{15}{9\, \mathrm{Tr}(N)} (T_{ab} - \mathrm{Tr}(T) \delta_{ab})
+   F^t_{ab}  =  \frac{5}{\mathrm{Tr}(N)} (T_{ab} - \frac{1}{3} \mathrm{Tr}(T) \delta_{ab})
 
 where the tensor :math:`T` is defined as
 

doc/src/compute_mliap.rst

@@ -20,7 +20,7 @@ Syntax
        *model* values = style
          style = *linear* or *quadratic* or *mliappy*
        *descriptor* values = style filename
-         style = *sna*
+         style = *sna* or *ace*
          filename = name of file containing descriptor definitions
        *gradgradflag* value = 0/1
          toggle gradgrad method for force gradient
@@ -31,6 +31,7 @@ Examples
 .. code-block:: LAMMPS
 
    compute mliap model linear descriptor sna Ta06A.mliap.descriptor
+   compute mliap model linear descriptor ace H_N_O_ccs.yace gradgradflag 1
 
 Description
 """""""""""
@@ -40,18 +41,15 @@ of machine-learning interatomic potentials with respect to model parameters.
 It is used primarily for calculating the gradient of energy, force, and
 stress components with respect to model parameters, which is useful when
 training :doc:`mliap pair_style <pair_mliap>` models to match target data.
-It provides separate
+It provides separate definitions of the interatomic potential functional
-definitions of the interatomic potential functional form (*model*)
+form (*model*) and the geometric quantities that characterize the atomic
-and the geometric quantities that characterize the atomic positions
+positions (*descriptor*). By defining *model* and *descriptor* separately,
-(*descriptor*). By defining *model* and *descriptor* separately,
 it is possible to use many different models with a given descriptor,
-or many different descriptors with a given model. Currently, the
+or many different descriptors with a given model. Currently, the compute
-compute supports just two models, *linear* and *quadratic*,
+supports *linear* and *quadratic* SNAP descriptor computes used in
-and one descriptor, *sna*, the SNAP descriptor used by
+:doc:`pair_style snap <pair_snap>`, *linear* SO3 descriptor computes, and
-:doc:`pair_style snap <pair_snap>`, including the linear, quadratic,
+*linear* ACE descriptor computes used in :doc:`pair_style pace <pair_pace>`,
-and chem variants. Work is currently underway to extend
+and it is straightforward to add new descriptor styles.
-the interface to handle neural network energy models,
-and it is also straightforward to add new descriptor styles.
 
 The compute *mliap* command must be followed by two keywords
 *model* and *descriptor* in either order.
@@ -60,19 +58,31 @@ The *model* keyword is followed by the model style (*linear*,
 *quadratic* or *mliappy*).  The *mliappy* model is only available if
 LAMMPS is built with the *mliappy* Python module. There are
 :ref:`specific installation instructions <mliap>` for that module.
+For the *mliap* compute, specifying a *linear* model will compute the
+specified descriptors and gradients with respect to linear model parameters
+whereas *quadratic* will do the same, but for the quadratic products of
+descriptors.
 
 The *descriptor* keyword is followed by a descriptor style, and
-additional arguments.  The compute currently supports two descriptor
+additional arguments.  The compute currently supports three descriptor
-styles *sna* and *so3*, but it is is straightforward to add additional
+styles: *sna*, *so3*, and *ace*, but it is is straightforward to add
-descriptor styles.  The SNAP descriptor style *sna* is the same as that
+additional descriptor styles.  The SNAP descriptor style *sna* is the
-used by :doc:`pair_style snap <pair_snap>`, including the linear,
+same as that used by :doc:`pair_style snap <pair_snap>`, including the
-quadratic, and chem variants.  A single additional argument specifies
+linear, quadratic, and chem variants.  A single additional argument
-the descriptor filename containing the parameters and setting used by
+specifies the descriptor filename containing the parameters and setting used
-the SNAP descriptor.  The descriptor filename usually ends in the
+by the SNAP descriptor.  The descriptor filename usually ends in the
 *.mliap.descriptor* extension.  The format of this file is identical to
 the descriptor file in the :doc:`pair_style mliap <pair_mliap>`, and is
 described in detail there.
 
+The ACE descriptor style *ace* is the same as :doc:`pair_style pace <pair_pace>`.
+A single additional argument specifies the *ace* descriptor filename
+that contains parameters and settings for the ACE descriptors. This file
+format differs from the SNAP or SO3 descriptor files, and has a *.yace* or
+*.ace* extension. However, as with other mliap descriptor styles, this file
+is identical to the ace descriptor file in :doc:`pair_style mliap <pair_mliap>`,
+where it is described in further detail.
+
 .. note::
 
    The number of LAMMPS atom types (and the value of *nelems* in the model)
@@ -172,8 +182,10 @@ This compute is part of the ML-IAP package.  It is only enabled if
 LAMMPS was built with that package. In addition, building LAMMPS with
 the ML-IAP package requires building LAMMPS with the ML-SNAP package.
 The *mliappy* model also requires building LAMMPS with the PYTHON
-package.  See the :doc:`Build package <Build_package>` page for more
+package. The *ace* descriptor also requires building LAMMPS with the
-info.
+ML-PACE package. See the :doc:`Build package <Build_package>` page for
+more info. Note that `kk` (KOKKOS) accelerated variants of SNAP and
+ACE descriptors are not compatible with `mliap descriptor`.
 
 Related commands
 """"""""""""""""

doc/src/compute_pace.rst

@@ -36,7 +36,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 This compute calculates a set of quantities related to the atomic
 cluster expansion (ACE) descriptors of the atoms in a group.  ACE

doc/src/compute_pressure.rst

@@ -153,7 +153,8 @@ Related commands
 Default
 """""""
 
-none
+By default the compute includes contributions from the keywords:
+``ke pair bond angle dihedral improper kspace fix``
 
 ----------
 

doc/src/compute_property_atom.rst

@@ -23,8 +23,9 @@ Syntax
                              spx, spy, spz, sp, fmx, fmy, fmz,
                              nbonds,
                              radius, diameter, omegax, omegay, omegaz,
+                             temperature, heatflow,
                              angmomx, angmomy, angmomz,
-                             shapex,shapey, shapez,
+                             shapex, shapey, shapez,
                              quatw, quati, quatj, quatk, tqx, tqy, tqz,
                              end1x, end1y, end1z, end2x, end2y, end2z,
                              corner1x, corner1y, corner1z,
@@ -56,6 +57,8 @@ Syntax
            *nbonds* = number of bonds assigned to an atom
            *radius,diameter* = radius,diameter of spherical particle
            *omegax,omegay,omegaz* = angular velocity of spherical particle
+           *temperature* = internal temperature of spherical particle
+           *heatflow* = internal heat flow of spherical particle
            *angmomx,angmomy,angmomz* = angular momentum of aspherical particle
            *shapex,shapey,shapez* = 3 diameters of aspherical particle
            *quatw,quati,quatj,quatk* = quaternion components for aspherical or body particles

doc/src/compute_rattlers_atom.rst

@@ -32,7 +32,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 Define a compute that identifies rattlers in a system. Rattlers are often
 identified in granular or glassy packings as under-coordinated atoms that

doc/src/compute_rdf.rst

@@ -13,8 +13,8 @@ Syntax
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * rdf = style name of this compute command
 * Nbin = number of RDF bins
-* itypeN = central atom type for Nth RDF histogram (see asterisk form below)
+* itypeN = central atom type for Nth RDF histogram (integer, type label, or asterisk form)
-* jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below)
+* jtypeN = distribution atom type for Nth RDF histogram (integer, type label, or asterisk form)
 * zero or more keyword/value pairs may be appended
 * keyword = *cutoff*
 
@@ -96,14 +96,16 @@ is computed for :math:`g(r)` between all atom types.  If one or more pairs are
 listed, then a separate histogram is generated for each
 *itype*,\ *jtype* pair.
 
-The *itypeN* and *jtypeN* settings can be specified in one of two
+The *itypeN* and *jtypeN* settings can be specified in one of three
-ways.  An explicit numeric value can be used, as in the fourth example
+ways.  One or both of the types in the I,J pair can be a
-above.  Or a wild-card asterisk can be used to specify a range of atom
+:doc:`type label <Howto_type_labels>`.  Or an explicit numeric value can be
-types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If
+used, as in the fourth example above. Or a wild-card asterisk can be used
-:math:`N` is the number of atom types, then an asterisk with no numeric values
+to specify a range of atom types.  This takes the form "\*" or "\*n" or
-means all types from 1 to :math:`N`. A leading asterisk means all types from 1
+"m\*" or "m\*n". If :math:`N` is the number of atom types, then an asterisk
-to n (inclusive).  A trailing asterisk means all types from m to :math:`N`
+with no numeric values means all types from 1 to :math:`N`. A leading
-(inclusive).  A middle asterisk means all types from m to n (inclusive).
+asterisk means all types from 1 to n (inclusive).  A trailing asterisk
+means all types from m to :math:`N` (inclusive).  A middle asterisk means
+all types from m to n (inclusive).
 
 If both *itypeN* and *jtypeN* are single values, as in the fourth example
 above, this means that a :math:`g(r)` is computed where atoms of type *itypeN*
@@ -176,22 +178,29 @@ also numbers :math:`\ge 0.0`.
 Restrictions
 """"""""""""
 
-The RDF is not computed for distances longer than the force cutoff,
+By default, the RDF is not computed for distances longer than the
-since processors (in parallel) do not know about atom coordinates for
+largest force cutoff, since the neighbor list creation will only contain
-atoms further away than that distance.  If you want an RDF for larger
+pairs up to that distance (plus neighbor list skin).  This distance can
-distances, you can use the :doc:`rerun <rerun>` command to post-process
+be increased using the *cutoff* keyword but this keyword is only valid
-a dump file and set the cutoff for the potential to be longer in the
+with :doc:`neighbor styles 'bin' and 'nsq' <neighbor>`.
+
+If you want an RDF for larger distances, you can also use the
+:doc:`rerun <rerun>` command to post-process a dump file, use :doc:`pair
+style zero <pair_zero>` and set the force cutoff to be longer in the
 rerun script.  Note that in the rerun context, the force cutoff is
-arbitrary, since you are not running dynamics and thus are not changing
+arbitrary and with pair style zero you are not computing any forces, and
-your model.  The definition of :math:`g(r)` used by LAMMPS is only appropriate
+you are not running dynamics you are not changing the model that
-for characterizing atoms that are uniformly distributed throughout the
+generated the trajectory.
-simulation cell. In such cases, the coordination number is still
+
-correct and meaningful.  As an example, if a large simulation cell
+The definition of :math:`g(r)` used by LAMMPS is only appropriate for
-contains only one atom of type *itypeN* and one of *jtypeN*, then :math:`g(r)`
+characterizing atoms that are uniformly distributed throughout the
-will register an arbitrarily large spike at whatever distance they
+simulation cell. In such cases, the coordination number is still correct
-happen to be at, and zero everywhere else.
+and meaningful.  As an example, if a large simulation cell contains only
-The function :math:`\text{coord}(r)` will show a step
+one atom of type *itypeN* and one of *jtypeN*, then :math:`g(r)` will
-change from zero to one at the location of the spike in :math:`g(r)`.
+register an arbitrarily large spike at whatever distance they happen to
+be at, and zero everywhere else.  The function :math:`\text{coord}(r)`
+will show a step change from zero to one at the location of the spike in
+:math:`g(r)`.
 
 .. note::
 

doc/src/compute_reaxff_atom.rst

@@ -40,7 +40,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 Define a computation that extracts bond information computed by the ReaxFF
 potential specified by :doc:`pair_style reaxff <pair_reaxff>`.

doc/src/compute_reduce.rst

@@ -56,8 +56,9 @@ Examples
    compute 1 all reduce sum c_force
    compute 1 all reduce/region subbox sum c_force
    compute 2 all reduce min c_press[2] f_ave v_myKE
-   compute 2 all reduce min c_press[*] f_ave v_myKE
+   compute 2 all reduce min c_press[*] f_ave v_myKE inputs peratom
    compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
+   compute 4 all reduce max c_bond inputs local
 
 Description
 """""""""""

doc/src/compute_slcsa_atom.rst

@@ -32,7 +32,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 7Feb2024
 
 Define a computation that performs the Supervised Learning Crystal
 Structure Analysis (SL-CSA) from :ref:`(Lafourcade) <Lafourcade2023_1>`

doc/src/compute_stress_atom.rst

@@ -289,7 +289,8 @@ Related commands
 Default
 """""""
 
-none
+By default the compute includes contributions from the keywords:
+``ke pair bond angle dihedral improper kspace fix``
 
 ----------
 

doc/src/compute_stress_mop.rst

@@ -126,16 +126,19 @@ These styles are part of the EXTRA-COMPUTE package. They are only
 enabled if LAMMPS is built with that package. See the :doc:`Build
 package <Build_package>` doc page on for more info.
 
-The method is only implemented for 3d orthogonal simulation boxes whose
+The method is implemented for orthogonal simulation boxes whose
 size does not change in time, and axis-aligned planes.
 
 The method only works with two-body pair interactions, because it
 requires the class method ``Pair::single()`` to be implemented, which is
 not possible for manybody potentials.  In particular, compute
-*stress/mop/profile* and *stress/mop* do not work with more than two-body pair
+*stress/mop/profile* and *stress/mop* do not work with more than two-body
-interactions, long range (kspace) interactions and
+pair interactions, long range (kspace) interactions and
 improper intramolecular interactions.
 
+The impact of fixes that affect the stress (e.g. fix langevin) is
+also not included in the stress computed here.
+
 Related commands
 """"""""""""""""
 

doc/src/create_atoms.rst

@@ -10,7 +10,7 @@ Syntax
 
    create_atoms type style args keyword values ...
 
-* type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)
+* type = atom type (1-Ntypes or type label) of atoms to create (offset for molecule creation)
 * style = *box* or *region* or *single* or *mesh* or *random*
 
   .. parsed-literal::
@@ -37,7 +37,7 @@ Syntax
          seed = random # seed (positive integer)
        *basis* values = M itype
          M = which basis atom
-         itype = atom type (1-N) to assign to this basis atom
+         itype = atom type (1-Ntypes or type label) to assign to this basis atom
        *ratio* values = frac seed
          frac = fraction of lattice sites (0 to 1) to populate randomly
          seed = random # seed (positive integer)
@@ -74,6 +74,13 @@ Examples
 .. code-block:: LAMMPS
 
    create_atoms 1 box
+
+   labelmap atom 1 Pt
+   create_atoms Pt box
+
+   labelmap atom 1 C 2 Si
+   create_atoms C region regsphere basis Si C
+
    create_atoms 3 region regsphere basis 2 3
    create_atoms 3 region regsphere basis 2 3 ratio 0.5 74637
    create_atoms 3 single 0 0 5
@@ -86,25 +93,46 @@ Description
 """""""""""
 
 This command creates atoms (or molecules) within the simulation box,
-either on a lattice, or a single atom (or molecule), or on a surface
+either on a lattice, or at random points, or on a surface defined by a
-defined by a triangulated mesh, or a random collection of atoms (or
+triangulated mesh.  Or it creates a single atom (or molecule) at a
-molecules).  It is an alternative to reading in atom coordinates
+specified point.  It is an alternative to reading in atom coordinates
 explicitly via a :doc:`read_data <read_data>` or :doc:`read_restart
-<read_restart>` command.  A simulation box must already exist, which is
+<read_restart>` command.
+
+To use this command a simulation box must already exist, which is
 typically created via the :doc:`create_box <create_box>` command.
-Before using this command, a lattice must also be defined using the
+Before using this command, a lattice must typically also be defined
-:doc:`lattice <lattice>` command, unless you specify the *single* style
+using the :doc:`lattice <lattice>` command, unless you specify the
-with units = box or the *random* style.  For the remainder of this doc
+*single* or *mesh* style with units = box or the *random* style.  To
-page, a created atom or molecule is referred to as a "particle".
+create atoms on a lattice for general triclinic boxes, see the
+discussion below.
+
+For the remainder of this doc page, a created atom or molecule is
+referred to as a "particle".
 
 If created particles are individual atoms, they are assigned the
 specified atom *type*, though this can be altered via the *basis*
 keyword as discussed below.  If molecules are being created, the type
-of each atom in the created molecule is specified in the file read by
+of each atom in the created molecule is specified in a specified file
-the :doc:`molecule <molecule>` command, and those values are added to
+read by the :doc:`molecule <molecule>` command, and those values are
-the specified atom *type* (e.g., if *type* = 2 and the file specifies
+added to the specified atom *type* (e.g., if *type* = 2 and the file
-atom types 1, 2, and 3, then each created molecule will have atom types
+specifies atom types 1, 2, and 3, then each created molecule will have
-3, 4, and 5).
+atom types 3, 4, and 5).
+
+.. note::
+
+   You cannot use this command to create atoms that are outside the
+   simulation box; they will just be ignored by LAMMPS.  This is true
+   even if you are using shrink-wrapped box boundaries, as specified
+   by the :doc:`boundary <boundary>` command.  However, you can first
+   use the :doc:`change_box <change_box>` command to temporarily
+   expand the box, then add atoms via create_atoms, then finally use
+   change_box command again if needed to re-shrink-wrap the new atoms.
+   See the :doc:`change_box <change_box>` doc page for an example of
+   how to do this, using the create_atoms *single* style to insert a
+   new atom outside the current simulation box.
+
+----------
 
 For the *box* style, the create_atoms command fills the entire
 simulation box with particles on the lattice.  If your simulation box
@@ -126,10 +154,117 @@ periodic boundaries.  If this is desired, you should either use the
 *box* style, or tweak the region size to get precisely the particles
 you want.
 
+----------
+
+If the simulation box is formulated as a general triclinic box defined
+by arbitrary edge vectors **A**, **B**, **C**, then the *box* and
+*region* styles will create atoms on a lattice commensurate with those
+edge vectors.  See the :doc:`Howto_triclinic <Howto_triclinic>` doc
+page for a detailed explanation of orthogonal, restricted triclinic,
+and general triclinic simulation boxes.  As with the :doc:`create_box
+<create_box>` command, the :doc:`lattice <lattice>` command used by
+this command must be of style *custom* and use its *triclinic/general*
+option.  The *a1, *a2*, *a3* settings of the :doc:`lattice <lattice>`
+command define the edge vectors of a unit cell of the general
+triclinic lattice. The :doc:`create_box <create_box>` command creates
+a simulation box which replicates that unit cell along each of the
+**A**, **B**, **C** edge vectors.
+
+.. note::
+
+   LAMMPS allows specification of general triclinic simulation boxes
+   as a convenience for users who may be converting data from
+   solid-state crystallographic representations or from DFT codes for
+   input to LAMMPS.  However, as explained on the
+   :doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
+   LAMMPS only uses restricted triclinic simulation boxes.  This means
+   the box created by the :doc:`create_box <create_box>` command as
+   well as the atoms created by this command with their per-atom
+   information (e.g. coordinates, velocities) are converted (rotated)
+   from general to restricted triclinic form when the two commands are
+   invoked.  The <Howto_triclinic>` doc page also discusses other
+   LAMMPS commands which can input/output general triclinic
+   representations of the simulation box and per-atom data.
+
+The *box* style will fill the entire general triclinic box with
+particles on the lattice, as explained above.
+
+.. note::
+
+    The *region* style also operates as explained above, but the check
+    for particles inside the region is performed *after* the particle
+    coordinates have been converted to the restricted triclinic box.
+    This means the region must also be defined with respect to the
+    restricted triclinic box, not the general triclinic box.
+
+If the simulation box is general triclinic, the *single*, *random*,
+and *mesh* styles described next operate on the box *after* it has
+been converted to restricted triclinic.  So all the settings for those
+styles should be made in that context.
+
+----------
+
 For the *single* style, a single particle is added to the system at
 the specified coordinates.  This can be useful for debugging purposes
 or to create a tiny system with a handful of particles at specified
-positions.
+positions.  For a 2d simulation the specified z coordinate must be
+0.0.
+
+.. versionchanged:: 2Jun2022
+
+The *porosity* style has been renamed to *random* with added functionality.
+
+For the *random* style, *N* particles are added to the system at
+randomly generated coordinates, which can be useful for generating an
+amorphous system.  For 2d simulations, the z coordinates of all added
+atoms will be 0.0.
+
+The particles are created one by one using the specified random number
+*seed*, resulting in the same set of particle coordinates, independent
+of how many processors are being used in the simulation.  Unless the
+*overlap* keyword is specified, particles created by the *random*
+style will typically be highly overlapped.  Various additional
+criteria can be used to accept or reject a random particle insertion;
+see the keyword discussion below.  Multiple attempts per particle are
+made (see the *maxtry* keyword) until the insertion is either
+successful or fails.  If this command fails to add all requested *N*
+particles, a warning will be output.
+
+If the *region-ID* argument is specified as NULL, then the randomly
+created particles will be anywhere in the simulation box.  If a
+*region-ID* is specified, a geometric volume is filled that is both
+inside the simulation box and is also consistent with the region
+volume.  See the :doc:`region <region>` command for details.  Note
+that a region can be specified so that its "volume" is either inside
+or outside its geometric boundary.
+
+Note that the create_atoms command adds particles to those that
+already exist.  This means it can be used to add particles to a system
+previously read in from a data or restart file.  Or the create_atoms
+command can be used multiple times, to add multiple sets of particles
+to the simulation.  For example, grain boundaries can be created, by
+interleaving the create_atoms command with :doc:`lattice <lattice>`
+commands specifying different orientations.
+
+When this command is used, care should be taken to ensure the
+resulting system does not contain particles that are highly
+overlapped.  Such overlaps will cause many interatomic potentials to
+compute huge energies and forces, leading to bad dynamics.  There are
+several strategies to avoid this problem:
+
+* Use the :doc:`delete_atoms overlap <delete_atoms>` command after
+  create_atoms.  For example, this strategy can be used to overlay and
+  surround a large protein molecule with a volume of water molecules,
+  then delete water molecules that overlap with the protein atoms.
+
+* For the *random* style, use the optional *overlap* keyword to avoid
+  overlaps when each new particle is created.
+
+* Before running dynamics on an overlapped system, perform an
+  :doc:`energy minimization <minimize>`.  Or run initial dynamics with
+  :doc:`pair_style soft <pair_soft>` or with :doc:`fix nve/limit
+  <fix_nve_limit>` to un-overlap the particles, before running normal
+  dynamics.
 
 .. figure:: img/marble_race.jpg
             :figwidth: 33%
@@ -189,73 +324,6 @@ to the area of that triangle.
    beneficial to exclude computing interactions between the created
    particles using :doc:`neigh_modify exclude <neigh_modify>`.
 
-.. versionchanged:: 2Jun2022
-
-The *porosity* style has been renamed to *random* with added functionality.
-
-For the *random* style, *N* particles are added to the system at
-randomly generated coordinates, which can be useful for generating an
-amorphous system.  The particles are created one by one using the
-specified random number *seed*, resulting in the same set of particle
-coordinates, independent of how many processors are being used in the
-simulation.  Unless the *overlap* keyword is specified, particles
-created by the *random* style will typically be highly overlapped.
-Various additional criteria can be used to accept or reject a random
-particle insertion; see the keyword discussion below.  Multiple
-attempts per particle are made (see the *maxtry* keyword) until the
-insertion is either successful or fails.  If this command fails to add
-all requested *N* particles, a warning will be output.
-
-If the *region-ID* argument is specified as NULL, then the randomly
-created particles will be anywhere in the simulation box.  If a
-*region-ID* is specified, a geometric volume is filled that is both
-inside the simulation box and is also consistent with the region
-volume.  See the :doc:`region <region>` command for details.  Note
-that a region can be specified so that its "volume" is either inside
-or outside its geometric boundary.
-
-Note that the create_atoms command adds particles to those that
-already exist.  This means it can be used to add particles to a system
-previously read in from a data or restart file.  Or the create_atoms
-command can be used multiple times, to add multiple sets of particles
-to the simulation.  For example, grain boundaries can be created, by
-interleaving the create_atoms command with :doc:`lattice <lattice>`
-commands specifying different orientations.
-
-When this command is used, care should be taken to ensure the
-resulting system does not contain particles that are highly
-overlapped.  Such overlaps will cause many interatomic potentials to
-compute huge energies and forces, leading to bad dynamics.  There are
-several strategies to avoid this problem:
-
-* Use the :doc:`delete_atoms overlap <delete_atoms>` command after
-  create_atoms.  For example, this strategy can be used to overlay and
-  surround a large protein molecule with a volume of water molecules,
-  then delete water molecules that overlap with the protein atoms.
-
-* For the *random* style, use the optional *overlap* keyword to avoid
-  overlaps when each new particle is created.
-
-* Before running dynamics on an overlapped system, perform an
-  :doc:`energy minimization <minimize>`.  Or run initial dynamics with
-  :doc:`pair_style soft <pair_soft>` or with :doc:`fix nve/limit
-  <fix_nve_limit>` to un-overlap the particles, before running normal
-  dynamics.
-
-.. note::
-
-   You cannot use any of the styles explained above to create atoms
-   that are outside the simulation box; they will just be ignored by
-   LAMMPS.  This is true even if you are using shrink-wrapped box
-   boundaries, as specified by the :doc:`boundary <boundary>` command.
-   However, you can first use the :doc:`change_box <change_box>`
-   command to temporarily expand the box, then add atoms via
-   create_atoms, then finally use change_box command again if needed
-   to re-shrink-wrap the new atoms.  See the :doc:`change_box
-   <change_box>` doc page for an example of how to do this, using the
-   create_atoms *single* style to insert a new atom outside the
-   current simulation box.
-
 ----------
 
 Individual atoms are inserted by this command, unless the *mol*
@@ -268,6 +336,12 @@ molecule can be specified in the molecule file.  See the
 required to be in this file are the coordinates and types of atoms in
 the molecule.
 
+.. note::
+
+  If you are using the *mol* keyword in combination with the
+  :doc:`atom style template <atom_style>` command, they must use
+  the same molecule template-ID.
+
 Using a lattice to add molecules, e.g. via the *box* or *region* or
 *single* styles, is exactly the same as adding atoms on lattice
 points, except that entire molecules are added at each point, i.e. on
@@ -401,12 +475,13 @@ to.
 
 The *overlap* keyword only applies to the *random* style.  It prevents
 newly created particles from being created closer than the specified
-*Doverlap* distance from any other particle.  When the particles being
+*Doverlap* distance from any other particle.  If particles have finite
-created are molecules, the radius of the molecule (from its geometric
+size (see :doc:`atom_style sphere <atom_style>` for example) *Doverlap*
-center) is added to *Doverlap*.  If particles have finite size (see
+should be specified large enough to include the particle size in the
-:doc:`atom_style sphere <atom_style>` for example) *Doverlap* should
+non-overlapping criterion.  If molecules are being randomly inserted, then
-be specified large enough to include the particle size in the
+an insertion is only accepted if each particle in the molecule meets the
-non-overlapping criterion.
+overlap criterion with respect to other particles (not including particles
+in the molecule itself).
 
 .. note::
 
@@ -463,12 +538,19 @@ on a single CPU core.
 -----
 
 The *units* keyword determines the meaning of the distance units used
-to specify the coordinates of the one particle created by the *single*
+by parameters for various styles.  A *box* value selects standard
-style, or the overlap distance *Doverlap* by the *overlap* keyword.  A
+distance units as defined by the :doc:`units <units>` command (e.g.,
-*box* value selects standard distance units as defined by the
+:math:`\AA` for units = *real* or *metal*\ .  A *lattice* value means
-:doc:`units <units>` command (e.g., :math:`\AA` for
+the distance units are in lattice spacings.  These are affected settings:
-units = *real* or *metal*\ .  A *lattice* value means the distance units are in
+
-lattice spacings.
+* for *single* style: coordinates of the particle created
+* for *random* style: overlap distance *Doverlap* by the *overlap* keyword
+* for *mesh* style: *bisect* threshold value for *meshmode* = *bisect*
+* for *mesh* style: *radthresh* value for *meshmode* = *bisect*
+* for *mesh* style: *density* value for *meshmode* = *qrand*
+
+Since *density* represents an area (distance ^2), the lattice spacing
+factor is also squared.
 
 ----------
 
@@ -536,6 +618,11 @@ command.
 A rotation vector specified for a single molecule must be in
 the z-direction for a 2d model.
 
+For :doc:`molecule templates <molecule>` that are created from multiple
+files, i.e. contain multiple molecule *sets*, only the first set is
+used.  To create multiple molecules the files currently need to be
+merged and different molecule IDs assigned with a Molecules section.
+
 Related commands
 """"""""""""""""
 

doc/src/create_box.rst

@@ -9,9 +9,11 @@ Syntax
 .. code-block:: LAMMPS
 
    create_box N region-ID keyword value ...
+   create_box N NULL alo ahi blo bhi clo chi keyword value ...
 
 * N = # of atom types to use in this simulation
-* region-ID = ID of region to use as simulation domain
+* region-ID = ID of region to use as simulation domain or NULL for general triclinic box
+* alo,ahi,blo,bhi,clo,chi = multipliers on a1,a2,a3 vectors defined by :doc"`lattice <lattice>` command (only when region-ID = NULL)
 * zero or more keyword/value pairs may be appended
 * keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom*
 
@@ -32,121 +34,204 @@ Examples
 
 .. code-block:: LAMMPS
 
+   # orthogonal or restricted triclinic box using regionID = mybox
    create_box 2 mybox
    create_box 2 mybox bond/types 2 extra/bond/per/atom 1
 
+.. code-block:: LAMMPS
+
+   # 2d general triclinic box using primitive cell for 2d hex lattice
+   lattice       custom 1.0 a1 1.0 0.0 0.0 a2 0.5 0.86602540378 0.0 &
+                 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 triclinic/general
+   create_box    1 NULL 0 5 0 5 -0.5 0.5
+
+.. code-block:: LAMMPS
+
+   # 3d general triclinic box using primitive cell for 3d fcc lattice
+   lattice custom 1.0 a2 0.0 0.5 0.5 a1 0.5 0.0 0.5 a3 0.5 0.5 0.0 basis 0.0 0.0 0.0 triclinic/general
+   create box 1 NULL -5 5 -10 10 0 20
+
 Description
 """""""""""
 
-This command creates a simulation box based on the specified region.
+This command creates a simulation box. It also partitions the box into
-Thus a :doc:`region <region>` command must first be used to define a
+a regular 3d grid of smaller sub-boxes, one per processor (MPI task).
-geometric domain.  It also partitions the simulation box into a
+The geometry of the partitioning is based on the size and shape of the
-regular 3d grid of rectangular bricks, one per processor, based on the
+simulation box, the number of processors being used and the settings
-number of processors being used and the settings of the
+of the :doc:`processors <processors>` command.  The partitioning can
-:doc:`processors <processors>` command.  The partitioning can later be
+later be changed by the :doc:`balance <balance>` or :doc:`fix balance
-changed by the :doc:`balance <balance>` or :doc:`fix balance <fix_balance>` commands.
+<fix_balance>` commands.
 
-The argument N is the number of atom types that will be used in the
+Simulation boxes in LAMMPS can be either orthogonal or triclinic in
+shape.  Orthogonal boxes are a brick in 3d (rectangle in 2d) with 6
+faces that are each perpendicular to one of the standard xyz
+coordinate axes.  Triclinic boxes are a parallelepiped in 3d
+(parallelogram in 2d) with opposite pairs of faces parallel to each
+other.  LAMMPS supports two forms of triclinic boxes, restricted and
+general, which differ in how the box is oriented with respect to the
+xyz coordinate axes.  See the :doc:`Howto triclinic <Howto_triclinic>`
+for a detailed description of all 3 kinds of simulation boxes.
+
+The argument *N* is the number of atom types that will be used in the
 simulation.
 
+Orthogonal and restricted triclinic boxes are created by specifying a
+region ID previously defined by the :doc:`region <region>` command.
+General triclinic boxes are discussed below.
+
 If the region is not of style *prism*, then LAMMPS encloses the region
 (block, sphere, etc.) with an axis-aligned orthogonal bounding box
-which becomes the simulation domain.
+which becomes the simulation domain.  For a 2d simulation, the zlo and
+zhi values of the simulation box must straddle zero.
 
 If the region is of style *prism*, LAMMPS creates a non-orthogonal
 simulation domain shaped as a parallelepiped with triclinic symmetry.
 As defined by the :doc:`region prism <region>` command, the
-parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by three
+parallelepiped has an "origin" at (xlo,ylo,zlo) and three edge vectors
-edge vectors starting from the origin given by
+starting from the origin given by :math:`\vec a =
-:math:`\vec a = (x_\text{hi}-x_\text{lo},0,0)`;
+(x_\text{hi}-x_\text{lo},0,0)`; :math:`\vec b =
-:math:`\vec b = (xy,y_\text{hi}-y_\text{lo},0)`; and
+(xy,y_\text{hi}-y_\text{lo},0)`; and :math:`\vec c =
-:math:`\vec c = (xz,yz,z_\text{hi}-z_\text{lo})`.
+(xz,yz,z_\text{hi}-z_\text{lo})`.  In LAMMPS lingo, this is a
-The parameters *xy*\ , *xz*\ , and *yz* can be 0.0 or
+restricted triclinic box because the three edge vectors cannot be
-positive or negative values and are called "tilt factors" because they
+defined in arbitrary (general) directions.  The parameters *xy*\ ,
-are the amount of displacement applied to faces of an originally
+*xz*\ , and *yz* can be 0.0 or positive or negative values and are
-orthogonal box to transform it into the parallelepiped.
+called "tilt factors" because they are the amount of displacement
+applied to faces of an originally orthogonal box to transform it into
+the parallelepiped.  For a 2d simulation, the zlo and zhi values of
+the simulation box must straddle zero.
 
-By default, a *prism* region used with the create_box command must have
+Typically a *prism* region used with the create_box command should
-tilt factors :math:`(xy,xz,yz)` that do not skew the box more than half
+have tilt factors :math:`(xy,xz,yz)` that do not skew the box more
-the distance of the parallel box length.  For example, if
+than half the distance of the parallel box length.  For example, if
-:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x`
+:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the
-box length is 10 and the :math:`xy` tilt factor must be between
+:math:`x` box length is 10 and the :math:`xy` tilt factor must be
-:math:`-5` and :math:`5`.  Similarly, both :math:`xz` and :math:`yz`
+between :math:`-5` and :math:`5`.  Similarly, both :math:`xz` and
-must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and
+:math:`yz` must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and
 :math:`+(y_\text{hi}-y_\text{lo})/2`.  Note that this is not a
-limitation, since if the maximum tilt factor is 5 (as in this example),
+limitation, since if the maximum tilt factor is 5 (as in this
-then configurations with tilt :math:`= \dots, -15`, :math:`-5`,
+example), then configurations with tilt :math:`= \dots, -15`,
-:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically
+:math:`-5`, :math:`5`, :math:`15`, :math:`25, \dots` are all
-equivalent.  Simulations with large tilt factors will run inefficiently,
+geometrically equivalent.
-since they require more ghost atoms and thus more communication.  With
-very large tilt factors, LAMMPS will eventually produce incorrect
-trajectories and stop with errors due to lost atoms or similar.
 
-See the :doc:`Howto triclinic <Howto_triclinic>` page for a
+LAMMPS will issue a warning if the tilt factors of the created box do
-geometric description of triclinic boxes, as defined by LAMMPS, and
+not meet this criterion.  This is because simulations with large tilt
-how to transform these parameters to and from other commonly used
+factors may run inefficiently, since they require more ghost atoms and
-triclinic representations.
+thus more communication.  With very large tilt factors, LAMMPS may
+eventually produce incorrect trajectories and stop with errors due to
+lost atoms or similar issues.
 
-When a prism region is used, the simulation domain should normally be periodic
+See the :doc:`Howto triclinic <Howto_triclinic>` page for geometric
-in the dimension that the tilt is applied to, which is given by the second
+descriptions of triclinic boxes and tilt factors, as well as how to
-dimension of the tilt factor (e.g., :math:`y` for :math:`xy` tilt).  This is so
+transform the restricted triclinic parameters to and from other
-that pairs of atoms interacting across that boundary will have one of them
+commonly used triclinic representations.
-shifted by the tilt factor.  Periodicity is set by the
+
-:doc:`boundary <boundary>` command.  For example, if the :math:`xy` tilt factor
+When a prism region is used, the simulation domain should normally be
-is non-zero, then the :math:`y` dimension should be periodic.  Similarly, the
+periodic in the dimension that the tilt is applied to, which is given
-:math:`z` dimension should be periodic if :math:`xz` or :math:`yz` is non-zero.
+by the second dimension of the tilt factor (e.g., :math:`y` for
-LAMMPS does not require this periodicity, but you may lose atoms if this is not
+:math:`xy` tilt).  This is so that pairs of atoms interacting across
-the case.
+that boundary will have one of them shifted by the tilt factor.
+Periodicity is set by the :doc:`boundary <boundary>` command.  For
+example, if the :math:`xy` tilt factor is non-zero, then the :math:`y`
+dimension should be periodic.  Similarly, the :math:`z` dimension
+should be periodic if :math:`xz` or :math:`yz` is non-zero.  LAMMPS
+does not require this periodicity, but you may lose atoms if this is
+not the case.
 
 Note that if your simulation will tilt the box (e.g., via the
-:doc:`fix deform <fix_deform>` command), the simulation box must be set up to
+:doc:`fix deform <fix_deform>` command), the simulation box must be
-be triclinic, even if the tilt factors are initially 0.0.  You can
+created as triclinic, even if the tilt factors are initially 0.0.  You
-also change an orthogonal box to a triclinic box or vice versa by
+can also change an orthogonal box to a triclinic box or vice versa by
 using the :doc:`change box <change_box>` command with its *ortho* and
 *triclinic* options.
 
 .. note::
 
-   If the system is non-periodic (in a dimension), then you should
+   If the system is non-periodic (in a dimension), then you should not
-   not make the lo/hi box dimensions (as defined in your
+   make the lo/hi box dimensions (as defined in your :doc:`region
-   :doc:`region <region>` command) radically smaller/larger than the extent
+   <region>` command) radically smaller/larger than the extent of the
-   of the atoms you eventually plan to create (e.g., via the
+   atoms you eventually plan to create (e.g., via the
-   :doc:`create_atoms <create_atoms>` command).  For example, if your atoms
+   :doc:`create_atoms <create_atoms>` command).  For example, if your
-   extend from 0 to 50, you should not specify the box bounds as :math:`-10000`
+   atoms extend from 0 to 50, you should not specify the box bounds as
-   and :math:`10000`. This is because as described above, LAMMPS uses the
+   :math:`-10000` and :math:`10000`. This is because as described
-   specified box size to lay out the 3d grid of processors.  A huge
+   above, LAMMPS uses the specified box size to lay out the 3d grid of
-   (mostly empty) box will be sub-optimal for performance when using
+   processors.  A huge (mostly empty) box will be sub-optimal for
-   "fixed" boundary conditions (see the :doc:`boundary <boundary>`
+   performance when using "fixed" boundary conditions (see the
-   command).  When using "shrink-wrap" boundary conditions (see the
+   :doc:`boundary <boundary>` command).  When using "shrink-wrap"
-   :doc:`boundary <boundary>` command), a huge (mostly empty) box may cause
+   boundary conditions (see the :doc:`boundary <boundary>` command), a
-   a parallel simulation to lose atoms the first time that LAMMPS
+   huge (mostly empty) box may cause a parallel simulation to lose
-   shrink-wraps the box around the atoms.
+   atoms the first time that LAMMPS shrink-wraps the box around the
+   atoms.
+
+----------
+
+As noted above, general triclinic boxes in LAMMPS allow the box to
+have arbitrary edge vectors **A**, **B**, **C**.  The only
+restrictions are that the three vectors be distinct, non-zero, and not
+co-planar.  They must also define a right-handed system such that
+(**A** x **B**) points in the direction of **C**.  Note that a
+left-handed system can be converted to a right-handed system by simply
+swapping the order of any pair of the **A**, **B**, **C** vectors.
+
+To create a general triclinic boxes, the region is specified as NULL
+and the next 6 parameters (alo,ahi,blo,bhi,clo,chi) define the three
+edge vectors **A**, **B**, **C** using additional information
+previously defined by the :doc:`lattice <lattice>` command.
+
+The lattice must be of style *custom* and use its *triclinic/general*
+option.  This insures the lattice satisfies the restrictions listed
+above.  The *a1, *a2*, *a3* settings of the :doc:`lattice <lattice>`
+command define the edge vectors of a unit cell of the general
+triclinic lattice.  This command uses them to define the three edge
+vectors and origin of the general triclinic box as:
+
+* **A** = (ahi-alo) * *a1*
+* **B** = (bhi-blo) * *a2*
+* **C** = (chi-clo) * *a3*
+* origin = (alo*a1 + blo*a2 + clo*a3)
+
+For 2d general triclinic boxes, clo = -0.5 and chi = 0.5 is required.
+
+.. note::
+
+   LAMMPS allows specification of general triclinic simulation boxes
+   as a convenience for users who may be converting data from
+   solid-state crystallographic representations or from DFT codes for
+   input to LAMMPS.  However, as explained on the
+   :doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
+   LAMMPS only uses restricted triclinic simulation boxes.  This means
+   the box defined by this command and per-atom information
+   (e.g. coordinates, velocities) defined by the :doc:`create_atoms
+   <create_atoms>` command are converted (rotated) from general to
+   restricted triclinic form when the two commands are invoked.  The
+   <Howto_triclinic>` doc page also discusses other LAMMPS commands
+   which can input/output general triclinic representations of the
+   simulation box and per-atom data.
 
 ----------
 
 The optional keywords can be used to create a system that allows for
 bond (angle, dihedral, improper) interactions, or for molecules with
-special 1--2, 1--3, or 1--4 neighbors to be added later.  These optional
+special 1--2, 1--3, or 1--4 neighbors to be added later.  These
-keywords serve the same purpose as the analogous keywords that can be
+optional keywords serve the same purpose as the analogous keywords
-used in a data file which are recognized by the
+that can be used in a data file which are recognized by the
 :doc:`read_data <read_data>` command when it sets up a system.
 
 Note that if these keywords are not used, then the create_box command
 creates an atomic (non-molecular) simulation that does not allow bonds
-between pairs of atoms to be defined, or a
+between pairs of atoms to be defined, or a :doc:`bond potential
-:doc:`bond potential <bond_style>` to be specified, or for molecules with
+<bond_style>` to be specified, or for molecules with special neighbors
-special neighbors to be added to the system by commands such as
+to be added to the system by commands such as :doc:`create_atoms mol
-:doc:`create_atoms mol <create_atoms>`, :doc:`fix deposit <fix_deposit>`
+<create_atoms>`, :doc:`fix deposit <fix_deposit>` or :doc:`fix pour
-or :doc:`fix pour <fix_pour>`.
+<fix_pour>`.
 
 As an example, see the examples/deposit/in.deposit.molecule script,
 which deposits molecules onto a substrate.  Initially there are no
-molecules in the system, but they are added later by the
+molecules in the system, but they are added later by the :doc:`fix
-:doc:`fix deposit <fix_deposit>` command.  The create_box command in the
+deposit <fix_deposit>` command.  The create_box command in the script
-script uses the bond/types and extra/bond/per/atom keywords to allow
+uses the bond/types and extra/bond/per/atom keywords to allow this.
-this.  If the added molecule contained more than one special bond
+If the added molecule contained more than one special bond (allowed by
-(allowed by default), an extra/special/per/atom keyword would also
+default), an extra/special/per/atom keyword would also need to be
-need to be specified.
+specified.
 
 ----------
 

doc/src/delete_bonds.rst

@@ -43,6 +43,9 @@ Examples
    delete_bonds all bond 0*3 special
    delete_bonds all stats
 
+   labelmap atom 4 hc
+   delete_bonds all atom hc special
+
 Description
 """""""""""
 
@@ -59,19 +62,20 @@ For all styles, by default, an interaction is only turned off (or on)
 if all the atoms involved are in the specified group.  See the *any*
 keyword to change the behavior.
 
-Several of the styles (\ *atom*, *bond*, *angle*, *dihedral*,
+Several of the styles (\ *atom*, *bond*, *angle*, *dihedral*, *improper*\ )
-*improper*\ ) take a *type* as an argument.  The specified *type* should
+take a *type* as an argument.  The specified *type* can be a
-be an integer from 0 to :math:`N`, where :math:`N` is the number of relevant
+:doc:`type label <Howto_type_labels>`.  Otherwise, the type should be an
+integer from 0 to :math:`N`, where :math:`N` is the number of relevant
 types (atom types, bond types, etc.).  A value of 0 is only relevant for
-style *bond*\ ; see details below.  In all cases, a wildcard asterisk
+style *bond*\ ; see details below.  For numeric types, a wildcard asterisk
 can be used in place of or in conjunction with the *type* argument to
 specify a range of types.  This takes the form "\*" or "\*n" or "m\*" or
-"m\*n".  If :math:`N` is the number of types, then an asterisk with no numeric
+"m\*n".  If :math:`N` is the number of types, then an asterisk with no
-values means all types from 0 to :math:`N`.  A leading asterisk means all
+numeric values means all types from 0 to :math:`N`.  A leading asterisk
-types from 0 to n (inclusive).  A trailing asterisk means all types
+means all types from 0 to n (inclusive).  A trailing asterisk means all
-from m to N (inclusive).  A middle asterisk means all types from m to
+types from m to N (inclusive).  A middle asterisk means all types from m to
-n (inclusive).  Note that it is fine to include a type of 0 for
+n (inclusive).  Note that it is fine to include a type of 0 for non-bond
-non-bond styles; it will simply be ignored.
+styles; it will simply be ignored.
 
 For style *multi* all bond, angle, dihedral, and improper interactions
 of any type, involving atoms in the group, are turned off.

doc/src/dihedral_charmm.rst

@@ -3,6 +3,7 @@
 .. index:: dihedral_style charmm/kk
 .. index:: dihedral_style charmm/omp
 .. index:: dihedral_style charmmfsw
+.. index:: dihedral_style charmmfsw/kk
 
 dihedral_style charmm command
 =============================
@@ -12,6 +13,8 @@ Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
 dihedral_style charmmfsw command
 ================================
 
+Accelerator Variants: *charmmfsw/kk*
+
 Syntax
 """"""
 
@@ -144,7 +147,9 @@ for more info.
 Related commands
 """"""""""""""""
 
-:doc:`dihedral_coeff <dihedral_coeff>`
+:doc:`dihedral_coeff <dihedral_coeff>`,
+:doc:`pair_style lj/charmm variants <pair_charmm>`,
+:doc:`angle_style charmm <angle_charmm>`, :doc:`fix cmap <fix_cmap>`
 
 Default
 """""""

doc/src/dihedral_cosine_squared_restricted.rst

@@ -0,0 +1,71 @@
+.. index:: dihedral_style cosine/squared/restricted
+
+dihedral_style cosine/squared/restricted command
+================================================
+
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   dihedral_style cosine/squared/restricted
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   dihedral_style cosine/squared/restricted
+   dihedral_coeff 1 10.0 120
+
+Description
+"""""""""""
+
+.. versionadded:: 17Apr2024
+
+The *cosine/squared/restricted* dihedral style uses the potential
+
+.. math::
+
+   E = K [\cos(\phi) - \cos(\phi_0)]^2 / \sin^2(\phi)
+
+, which is commonly used in the MARTINI force field.
+
+See :ref:`(Bulacu) <restricted-Bul>` for a description of the restricted dihedral for the MARTINI force field.
+
+The following coefficients must be defined for each dihedral type via the
+:doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read_data <read_data>`
+or :doc:`read_restart <read_restart>` commands:
+
+* :math:`K` (energy)
+* :math:`\phi_0` (degrees)
+
+:math:`\phi_0` is specified in degrees, but LAMMPS converts it to radians internally.
+
+----------
+
+Restrictions
+""""""""""""
+
+This dihedral style can only be used if LAMMPS was built with the
+EXTRA-MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral_coeff <dihedral_coeff>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _restricted-Bul:
+
+**(Bulacu)** Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292
+(2013).

doc/src/dihedral_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    dihedral_style style
 
-* style = *none* or *zero* or *hybrid* or *charmm* or *charmmfsw* or *class2* or *cosine/shift/exp* or *fourier* or *harmonic* or *helix* or *lepton* or *multi/harmonic* or *nharmonic* or *opls* or *spherical* or *table* or *table/cut*
+* style = *none* or *zero* or *hybrid* or *charmm* or *charmmfsw* or *class2* or *cosine/shift/exp* or *cosine/squared/restricted* or *fourier* or *harmonic* or *helix* or *lepton* or *multi/harmonic* or *nharmonic* or *opls* or *spherical* or *table* or *table/cut*
 
 Examples
 """"""""
@@ -105,6 +105,7 @@ exist.
 * :doc:`charmmfsw <dihedral_charmm>` - CHARMM dihedral with force switching
 * :doc:`class2 <dihedral_class2>` - COMPASS (class 2) dihedral
 * :doc:`cosine/shift/exp <dihedral_cosine_shift_exp>` - dihedral with exponential in spring constant
+* :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>` - squared cosine dihedral with restricted term
 * :doc:`fourier <dihedral_fourier>` - dihedral with multiple cosine terms
 * :doc:`harmonic <dihedral_harmonic>` - harmonic dihedral
 * :doc:`helix <dihedral_helix>` - helix dihedral

doc/src/dump.rst

@@ -104,7 +104,6 @@ Syntax
                                q, mux, muy, muz, mu,
                                radius, diameter, omegax, omegay, omegaz,
                                angmomx, angmomy, angmomz, tqx, tqy, tqz,
-                               heatflow, temperature,
                                c_ID, c_ID[I], f_ID, f_ID[I], v_name,
                                i_name, d_name, i2_name[I], d2_name[I]
 
@@ -115,6 +114,7 @@ Syntax
            proc = ID of processor that owns atom
            procp1 = ID+1 of processor that owns atom
            type = atom type
+           typelabel = atom :doc:`type label <Howto_type_labels>`
            element = name of atom element, as defined by :doc:`dump_modify <dump_modify>` command
            mass = atom mass
            x,y,z = unscaled atom coordinates
@@ -131,8 +131,6 @@ Syntax
            omegax,omegay,omegaz = angular velocity of spherical particle
            angmomx,angmomy,angmomz = angular momentum of aspherical particle
            tqx,tqy,tqz = torque on finite-size particles
-           heatflow = rate of heat flow into particle
-           temperature = temperature of particle
            c_ID = per-atom vector calculated by a compute with ID
            c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
            f_ID = per-atom vector calculated by a fix with ID
@@ -278,16 +276,20 @@ format <dump_modify>` command and its options.
 Format of native LAMMPS format dump files:
 
 The *atom*, *custom*, *grid*, and *local* styles create files in a
-simple LAMMPS-specific text format that is self-explanatory when
+simple LAMMPS-specific text format that is mostly self-explanatory
-viewing a dump file.  Many post-processing tools either included with
+when viewing a dump file.  Many post-processing tools either included
-LAMMPS or third-party tools can read this format, as does the
+with LAMMPS or third-party tools can read this format, as does the
 :doc:`rerun <rerun>` command.  See tools described on the :doc:`Tools
 <Tools>` doc page for examples, including `Pizza.py
 <https://lammps.github.io/pizza>`_.
 
 For all these styles, the dimensions of the simulation box are
-included in each snapshot.  For an orthogonal simulation box this
+included in each snapshot.  The simulation box in LAMMPS can be
-information is formatted as:
+defined in one of 3 ways: orthogonal, restricted triclinic, and
+general triclinic.  See the :doc:`Howto triclinic <Howto_triclinic>`
+doc page for a detailed description of all 3 options.
+
+For an orthogonal simulation box the box information is formatted as:
 
 .. parsed-literal::
 
@@ -304,10 +306,10 @@ the six characters is one of *p* (periodic), *f* (fixed), *s* (shrink wrap),
 or *m* (shrink wrapped with a minimum value).  See the
 :doc:`boundary <boundary>` command for details.
 
-For triclinic simulation boxes (non-orthogonal), an orthogonal
+For a restricted triclinic simulation box, an orthogonal bounding box
-bounding box which encloses the triclinic simulation box is output,
+which encloses the restricted triclinic simulation box is output,
-along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic box,
+along with the three tilt factors (*xy*, *xz*, *yz*) of the triclinic
-formatted as follows:
+box, formatted as follows:
 
 .. parsed-literal::
 
@@ -329,6 +331,10 @@ bounding box extents (xlo_bound, xhi_bound, etc.) are calculated from the
 triclinic parameters, and how to transform those parameters to and
 from other commonly used triclinic representations.
 
+For a general triclinic simulation box, see the "General triclinic"
+section below for a description of the ITEM: BOX BOUNDS format as well
+as how per-atom coordinates and per-atom vector quantities are output.
+
 The *atom* and *custom* styles output a "ITEM: NUMBER OF ATOMS" line
 with the count of atoms in the snapshot.  Likewise they output an
 "ITEM: ATOMS" line which includes column descriptors for the per-atom
@@ -400,7 +406,6 @@ command.
 
 Dump files in other popular formats:
 
-
 .. note::
 
    This section only discusses file formats relevant to this doc page.
@@ -466,8 +471,9 @@ followed by one line per atom with the atom type and the :math:`x`-,
 :math:`y`-, and :math:`z`-coordinate of that atom.  You can use the
 :doc:`dump_modify element <dump_modify>` option to change the output
 from using the (numerical) atom type to an element name (or some other
-label). This will help many visualization programs to guess bonds and
+label). This option will help many visualization programs to guess bonds
-colors.
+and colors. You can use the :doc:`dump_modify types labels <dump_modify>`
+option to replace numeric atom types with :doc:`type labels <Howto_type_labels>`.
 
 .. versionadded:: 22Dec2022
 
@@ -656,6 +662,87 @@ how to control the compression level in both variants.
 
 ----------
 
+General triclinic simulation box output for the *atom* and *custom* styles:
+
+As mentioned above, the simulation box can be defined as a general
+triclinic box, which means that 3 arbitrary box edge vectors **A**,
+**B**, **C** can be specified.  See the :doc:`Howto triclinic
+<Howto_triclinic>` doc page for a detailed description of general
+triclinic boxes.
+
+This option is provided as a convenience for users who may be
+converting data from solid-state crystallographic representations or
+from DFT codes for input to LAMMPS.  However, as explained on the
+:doc:`Howto_triclinic <Howto_triclinic>` doc page, internally, LAMMPS
+only uses restricted triclinic simulation boxes.  This means the box
+and per-atom information (e.g. coordinates, velocities) LAMMPS stores
+are converted (rotated) from general to restricted triclinic form when
+the system is created.
+
+For dump output, if the :doc:`dump_modify triclinic/general
+<dump_modify>` command is used, the box description and per-atom
+coordinates and other per-atom vectors will be converted (rotated)
+from restricted to general form when each dump file snapshots is
+output.  This option can only be used if the simulation box was
+initially created as general triclinic.  If the option is not used,
+and the simulation box is general triclinic, then the dump file
+snapshots will reflect the internal restricted triclinic geometry.
+
+The dump_modify triclinic/general option affects 3 aspects of the dump
+file output.
+
+First, the format for the BOX BOUNDS is as follows
+
+.. parsed-literal::
+
+   ITEM: BOX BOUNDS abc origin
+   ax ay az originx
+   bx by bz originy
+   cx cy cz originz
+
+where the **A** edge vector of the box is (ax,ay,az) and similarly
+for **B** and **C**.  The origin of all 3 edge vectors is (originx,
+originy, originz).
+
+Second, the coordinates of each atom are converted (rotated) so that
+the atom is inside (or near) the general triclinic box defined by the
+**A**, **B**, **C** edge vectors.  For style *atom*, this only alters
+output for unscaled atom coords, via the :doc:`dump_modify scaled no
+<dump_modify>` setting. For style *custom*, this alters output for
+either unscaled or unwrapped output of atom coords, via the *x,y,z* or
+*xu,yu,zu* attributes.  For output of scaled atom coords by both
+styles, there is no difference between restricted and general
+triclinic values.
+
+Third, the output for any attribute of the *custom* style which
+represents a per-atom vector quantity will be converted (rotated) to
+be oriented consistent with the general triclinic box and its
+orientation relative to the standard xyz coordinate axes.
+
+This applies to the following *custom* style attributes:
+
+* vx,vy,vz = atom velocities
+* fx,fy,fz = forces on atoms
+* mux,muy,muz = orientation of dipole moment of atom
+* omegax,omegay,omegaz = angular velocity of spherical particle
+* angmomx,angmomy,angmomz = angular momentum of aspherical particle
+* tqx,tqy,tqz = torque on finite-size particles
+
+For example, if the velocity of an atom in a restricted triclinic box
+is along the x-axis, then it will be output for a general triclinic
+box as a vector along the **A** edge vector of the box.
+
+.. note::
+
+   For style *custom*, the :doc:`dump_modify thresh <dump_modify>`
+   command may access per-atom attributes either directly or
+   indirectly through a compute or variable.  If the attribute is an
+   atom coordinate or one of the vectors mentioned above, its value
+   will *NOT* be a general triclinic (rotated) value.  Rather it will
+   be a restricted triclinic value.
+
+----------
+
 Arguments for different styles:
 
 The sections below describe per-atom, local, and per grid cell
@@ -689,21 +776,21 @@ command creates a per-atom array with six columns:
 
 Per-atom attributes used as arguments to the *custom* and *cfg* styles:
 
-The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*,
+The *id*, *mol*, *proc*, *procp1*, *type*, *typelabel*, *element*, *mass*,
-*vy*, *vz*, *fx*, *fy*, *fz*, *q* attributes are self-explanatory.
+*vx*, *vy*, *vz*, *fx*, *fy*, *fz*, *q* attributes are self-explanatory.
 
-*Id* is the atom ID.  *Mol* is the molecule ID, included in the data
+*Id* is the atom ID.  *Mol* is the molecule ID, included in the data file
-file for molecular systems.  *Proc* is the ID of the processor (0 to
+for molecular systems.  *Proc* is the ID of the processor (0 to
 :math:`N_\text{procs}-1`) that currently owns the atom.  *Procp1* is the
 proc ID+1, which can be convenient in place of a *type* attribute (1 to
 :math:`N_\text{types}`) for coloring atoms in a visualization program.
-*Type* is the atom type (1 to :math:`N_\text{types}`).  *Element* is
+*Type* is the atom type (1 to :math:`N_\text{types}`).  *Typelabel* is the
-typically the chemical name of an element, which you must assign to each
+atom :doc:`type label <Howto_type_labels>`.  *Element* is typically the
-type via the :doc:`dump_modify element <dump_modify>` command.  More
+chemical name of an element, which you must assign to each type via the
-generally, it can be any string you wish to associated with an atom
+:doc:`dump_modify element <dump_modify>` command.  More generally, it can
-type.  *Mass* is the atom mass. The quantities *vx*, *vy*, *vz*, *fx*,
+be any string you wish to associated with an atom type.  *Mass* is the atom
-*fy*, *fz*, and *q* are components of atom velocity and force and atomic
+mass.  The quantities *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are
-charge.
+components of atom velocity and force and atomic charge.
 
 There are several options for outputting atom coordinates.  The *x*,
 *y*, and *z* attributes write atom coordinates "unscaled", in the

doc/src/dump_modify.rst

@@ -17,7 +17,7 @@ Syntax
 * one or more keyword/value pairs may be appended
 
 * these keywords apply to various dump styles
-* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
+* keyword = *append* or *at* or *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *triclinic/general* or *types* or *units* or *unwrap*
 
   .. parsed-literal::
 
@@ -74,12 +74,14 @@ Syntax
           -N = sort per-atom lines in descending order by the Nth column
        *tfactor* arg = time scaling factor (> 0.0)
        *thermo* arg = *yes* or *no*
-       *time* arg = *yes* or *no*
        *thresh* args = attribute operator value
          attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
          operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|\^"
          value = numeric value to compare to, or LAST
          these 3 args can be replaced by the word "none" to turn off thresholding
+       *time* arg = *yes* or *no*
+       *triclinic/general* arg = *yes* or *no*
+       *types* value = *numeric* or *labels*
        *units* arg = *yes* or *no*
        *unwrap* arg = *yes* or *no*
 
@@ -802,8 +804,9 @@ region since the last dump.
    dump_modify ... thresh v_charge |^ LAST
 
 This will dump atoms whose charge has changed from an absolute value
-less than :math:`\frac12` to greater than :math:`\frac12` (or vice versa) since the last dump (e.g., due to reactions and subsequent charge equilibration in a
+less than :math:`\frac12` to greater than :math:`\frac12` (or vice
-reactive force field).
+versa) since the last dump (e.g., due to reactions and subsequent
+charge equilibration in a reactive force field).
 
 The choice of operators listed above are the usual comparison
 operators.  The XOR operation (exclusive or) is also included as "\|\^".
@@ -811,6 +814,18 @@ In this context, XOR means that if either the attribute or value is
 0.0 and the other is non-zero, then the result is "true" and the
 threshold criterion is met.  Otherwise it is not met.
 
+.. note::
+
+   For style *custom*, the *triclinic/general* keyword can alter dump
+   output for general triclinic simulation boxes and their atoms.  See
+   the :doc:`dump <dump>` command for details of how this changes the
+   format of dump file snapshots.  The thresh keyword may access
+   per-atom attributes either directly or indirectly through a compute
+   or variable.  If the attribute is an atom coordinate or a per-atom
+   vector (such as velocity, force, or dipole moment), its value will
+   *NOT* be a general triclinic (rotated) value.  Rather it will be a
+   restricted triclinic value.
+
 ----------
 
 The *time* keyword only applies to the dump *atom*, *custom*, *local*,
@@ -835,6 +850,36 @@ The default setting is *no*\ .
 
 ----------
 
+The *types* keyword applies only to the dump xyz style. If this keyword is
+used with a value of *numeric*, then numeric atom types are printed in the
+xyz file (default). If the value *labels* is specified, then
+:doc:`type labels <Howto_type_labels>` are printed for atom types.
+
+----------
+
+The *triclinic/general* keyword only applies to the dump *atom* and
+*custom* styles.  It can only be used with a value of *yes* if the
+simulation box was created as a general triclinic box.  See the
+:doc:`Howto_triclinic <Howto_triclinic>` doc page for a detailed
+explanation of orthogonal, restricted triclinic, and general triclinic
+simulation boxes.
+
+If this keyword is used with a value of *yes*, the box information at
+the beginning of each snapshot will include information about the 3
+arbitrary edge vectors **A**, **B**, **C** that define the general
+triclinic box as well as their origin.  The format is described on the
+:doc:`dump <dump>` doc page.
+
+The coordinates of each atom will likewise be output as values in (or
+near) the general triclinic box.  Likewise, per-atom vector quantities
+such as velocity, omega, dipole moment, etc will have orientations
+consistent with the general triclinic box, meaning they will be
+rotated relative to the standard xyz coordinate axes.  See the
+:doc:`dump <dump>` doc page for a full list of which dump attributes
+this affects.
+
+----------
+
 The *units* keyword only applies to the dump *atom*, *custom*, and
 *local* styles (and their COMPRESS package versions *atom/gz*,
 *custom/gz* and *local/gz*\ ). If set to *yes*, each individual dump
@@ -922,10 +967,12 @@ The option defaults are
 * sort = off for dump styles *atom*, *custom*, *cfg*, and *local*
 * sort = id for dump styles *dcd*, *xtc*, and *xyz*
 * thresh = none
+* time = no
+* triclinic/general = no
+* types = numeric
 * units = no
 * unwrap = no
 
 * compression_level = 9 (gz variants)
 * compression_level = 0 (zstd variants)
 * checksum = yes (zstd variants)
-

doc/src/fix.rst

@@ -226,6 +226,7 @@ accelerated styles exist.
 * :doc:`controller <fix_controller>` - apply control loop feedback mechanism
 * :doc:`damping/cundall <fix_damping_cundall>` - Cundall non-viscous damping for granular simulations
 * :doc:`deform <fix_deform>` - change the simulation box size/shape
+* :doc:`deform/pressure <fix_deform_pressure>` - change the simulation box size/shape with additional loading conditions
 * :doc:`deposit <fix_deposit>` - add new atoms above a surface
 * :doc:`dpd/energy <fix_dpd_energy>` - constant energy dissipative particle dynamics
 * :doc:`drag <fix_drag>` - drag atoms towards a defined coordinate
@@ -431,6 +432,7 @@ accelerated styles exist.
 * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>` - time integration for body particles of style :doc:`rounded/polyhedron <Howto_body>`
 * :doc:`wall/colloid <fix_wall>` - Lennard-Jones wall interacting with finite-size particles
 * :doc:`wall/ees <fix_wall_ees>` - wall for ellipsoidal particles
+* :doc:`wall/flow <fix_wall_flow>` - flow boundary conditions
 * :doc:`wall/gran <fix_wall_gran>` - frictional wall(s) for granular simulations
 * :doc:`wall/gran/region <fix_wall_gran_region>` - :doc:`fix wall/region <fix_wall_region>` equivalent for use with granular particles
 * :doc:`wall/harmonic <fix_wall>` - harmonic spring wall

doc/src/fix_adapt.rst

@@ -21,17 +21,17 @@ Syntax
        *pair* args = pstyle pparam I J v_name
          pstyle = pair style name (e.g., lj/cut)
          pparam = parameter to adapt over time
-         I,J = type pair(s) to set parameter for
+         I,J = type pair(s) to set parameter for (integer or type label)
          v_name = variable with name that calculates value of pparam
        *bond* args = bstyle bparam I v_name
          bstyle = bond style name (e.g., harmonic)
          bparam = parameter to adapt over time
-         I = type bond to set parameter for
+         I = type bond to set parameter for (integer or type label)
          v_name = variable with name that calculates value of bparam
        *angle* args = astyle aparam I v_name
          astyle = angle style name (e.g., harmonic)
          aparam = parameter to adapt over time
-         I = type angle to set parameter for
+         I = type angle to set parameter for (integer or type label)
          v_name = variable with name that calculates value of aparam
        *kspace* arg = v_name
          v_name = variable with name that calculates scale factor on :math:`k`-space terms
@@ -67,6 +67,9 @@ Examples
    variable ramp_up equal "ramp(0.01,0.5)"
    fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up
 
+   labelmap atom 1 c1
+   fix 1 all adapt 1 pair soft a c1 c1 v_prefactor
+
 Description
 """""""""""
 
@@ -254,10 +257,12 @@ should be specified to indicate which type pairs to apply it to.  If a global
 parameter is specified, the :math:`I` and :math:`J` settings still need to be
 specified, but are ignored.
 
-Similar to the :doc:`pair_coeff command <pair_coeff>`, :math:`I` and :math:`J`
+Similar to the :doc:`pair_coeff command <pair_coeff>`, :math:`I` and
-can be specified in one of two ways.  Explicit numeric values can be used for
+:math:`J` can be specified in one of several ways.  Explicit numeric values
-each, as in the first example above.  :math:`I \le J` is required.  LAMMPS sets
+can be used for each, as in the first example above.  Or, one or both of
-the coefficients for the symmetric :math:`J,I` interaction to the same values.
+the types in the I,J pair can be a :doc:`type label <Howto_type_labels>`.
+LAMMPS sets the coefficients for the symmetric :math:`J,I` interaction to
+the same values.
 
 A wild-card asterisk can be used in place of or in conjunction with
 the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
@@ -266,8 +271,9 @@ is the number of atom types, then an asterisk with no numeric values
 means all types from 1 to :math:`N`.  A leading asterisk means all types from
 1 to n (inclusive).  A trailing asterisk means all types from m to :math:`N`
 (inclusive).  A middle asterisk means all types from m to n
-(inclusive).  Note that only type pairs with :math:`I \le J` are considered; if
+(inclusive).  For the asterisk syntax, note that only type pairs with
-asterisks imply type pairs where :math:`J < I`, they are ignored.
+:math:`I \le J` are considered; if asterisks imply type pairs where
+:math:`J < I`, they are ignored.
 
 IMPORTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay
 <pair_hybrid>` is being used, then the *pstyle* will be a sub-style

doc/src/fix_adapt_fep.rst

@@ -21,13 +21,13 @@ Syntax
        *pair* args = pstyle pparam I J v_name
          pstyle = pair style name (e.g., lj/cut)
          pparam = parameter to adapt over time
-         I,J = type pair(s) to set parameter for
+         I,J = type pair(s) to set parameter for (integer or type label)
          v_name = variable with name that calculates value of pparam
        *kspace* arg = v_name
          v_name = variable with name that calculates scale factor on K-space terms
        *atom* args = aparam v_name
          aparam = parameter to adapt over time
-         I = type(s) to set parameter for
+         I = type(s) to set parameter for (integer or type label)
          v_name = variable with name that calculates value of aparam
 
 * zero or more keyword/value pairs may be appended
@@ -56,6 +56,9 @@ Examples
    fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
    fix 1 all adapt/fep 10 atom diameter 1 v_size
 
+   labelmap atom 1 c1
+   fix 1 all adapt/fep 1 pair soft a c1 c1 v_prefactor
+
 
 Example input scripts available: examples/PACKAGES/fep
 
@@ -218,10 +221,12 @@ be specified to indicate which type pairs to apply it to.  If a global
 parameter is specified, the *I* and *J* settings still need to be
 specified, but are ignored.
 
-Similar to the :doc:`pair_coeff command <pair_coeff>`, I and J can be
+Similar to the :doc:`pair_coeff command <pair_coeff>`, :math:`I` and
-specified in one of two ways.  Explicit numeric values can be used for
+:math:`J` can be specified in one of several ways.  Explicit numeric values
-each, as in the first example above.  :math:`I \le J` is required.  LAMMPS sets
+can be used for each, as in the first example above.  Or, one or both of
-the coefficients for the symmetric J,I interaction to the same values.
+the types in the I,J pair can be a :doc:`type label <Howto_type_labels>`.
+LAMMPS sets the coefficients for the symmetric :math:`J,I` interaction to
+the same values.
 
 A wild-card asterisk can be used in place of or in conjunction with
 the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
@@ -230,8 +235,9 @@ the number of atom types, then an asterisk with no numeric values means
 all types from 1 to :math:`N`.  A leading asterisk means all types from 1 to n
 (inclusive).  A trailing asterisk means all types from m to :math:`N`
 (inclusive).  A middle asterisk means all types from m to n
-(inclusive).  Note that only type pairs with :math:`I \le J` are considered; if
+(inclusive).  For the asterisk syntax, note that only type pairs with
-asterisks imply type pairs where :math:`J < I`, they are ignored.
+:math:`I \le J` are considered; if asterisks imply type pairs where
+:math:`J < I`, they are ignored.
 
 IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is
 being used, then the *pstyle* will be a sub-style name.  You must specify

doc/src/fix_amoeba_bitorsion.rst

@@ -35,7 +35,11 @@ the implementation of AMOEBA and HIPPO in LAMMPS.
 
 Bitorsion interactions add additional potential energy contributions
 to pairs of overlapping phi-psi dihedrals of amino-acids, which are
-important to properly represent their conformational behavior.
+important to properly represent their conformational behavior.  Each
+bitorsion interaction is thus defined for a 5-tuple of atoms
+:math:`IJKLM` with bonds between successive atoms in the list,
+i.e. two overlapping dihedral interactions for atoms :math:`IJKL` and
+:math:`JKLM`.
 
 The examples/amoeba directory has a sample input script and data file
 for ubiquitin, which illustrates use of the fix amoeba/bitorsion
@@ -68,14 +72,15 @@ lines:
           [...]
           N       3     314     315     317      318    330
 
-The first column is an index from 1 to :math:`N` to enumerate the bitorsion
+The first column is an index from 1 to :math:`N` to enumerate the
-5-atom tuples; it is ignored by LAMMPS.  The second column is the
+bitorsion 5-atom tuples; it is ignored by LAMMPS.  The second column
-*type* of the interaction; it is an index into the bitorsion force
+is the *type* of the interaction; it is an index into the bitorsion
-field file.  The remaining 5 columns are the atom IDs of the atoms in
+force field file.  The remaining 5 columns are the atom IDs of the
-the two 4-atom dihedrals that overlap to create the bitorsion 5-body
+atoms (in order) for the 5-tuple :math:`IJKLM`, as described above.
-interaction.  Note that the *bitorsions* and *BiTorsions* keywords for
+
-the header and body sections match those specified in the
+Note that the *bitorsions* and *BiTorsions* keywords for the header
-:doc:`read_data <read_data>` command following the data file name.
+and body sections match those specified in the :doc:`read_data
+<read_data>` command following the data file name.
 
 The data file should be generated by using the
 tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS

doc/src/fix_amoeba_pitorsion.rst

@@ -57,7 +57,7 @@ should have two lines like these in its header section:
    M pitorsion types
    N pitorsions
 
-where :math:`N` is the number of pitorsion 5-body interactions and :math:`M` is
+where :math:`N` is the number of pitorsion 6-body interactions and :math:`M` is
 the number of pitorsion types.  It should also have two sections in the body
 of the data file like these with :math:`M` and :math:`N` lines each:
 
@@ -74,21 +74,20 @@ of the data file like these with :math:`M` and :math:`N` lines each:
 
    PiTorsions
 
-          1       1       8      10      12      18      20
+          1       1       2      4      3      20      21      24
-          2       5      18      20      22      25      27
+          2       5      21     23     22      37      38      41
           [...]
-          N       3     314     315     317      318    330
+          N       7      27     29     28      30      35      36
 
-For PiTorsion Coeffs, the first column is an index from 1 to :math:`M` to
+For PiTorsion Coeffs, the first column is an index from 1 to :math:`M`
-enumerate the pitorsion types.  The second column is the single
+to enumerate the pitorsion types.  The second column is the single
 prefactor coefficient needed for each type.
 
-For PiTorsions, the first column is an index from 1 to :math:`N` to enumerate
+For PiTorsions, the first column is an index from 1 to :math:`N` to
-the pitorsion 5-atom tuples; it is ignored by LAMMPS.  The second
+enumerate the pitorsion 6-atom tuples; it is ignored by LAMMPS.  The
-column is the "type" of the interaction; it is an index into the
+second column is the "type" of the interaction; it is an index into
-PiTorsion Coeffs.  The remaining 5 columns are the atom IDs of the
+the PiTorsion Coeffs.  The remaining 6 columns are the atom IDs of the
-atoms in the two 4-atom dihedrals that overlap to create the pitorsion
+atoms (in order) for the 6-tuple :math:`IJKLMN`, as described above.
-5-body interaction.
 
 Note that the *pitorsion types* and *pitorsions* and *PiTorsion
 Coeffs* and *PiTorsions* keywords for the header and body sections of

doc/src/fix_atom_swap.rst

@@ -21,7 +21,7 @@ Syntax
 
   .. parsed-literal::
 
-       *types* values = two or more atom types
+       *types* values = two or more atom types (1-Ntypes or type label)
        *mu* values = chemical potential of swap types (energy units)
        *ke* value = *no* or *yes*
          *no* = no conservation of kinetic energy after atom swaps
@@ -168,7 +168,7 @@ the following global cumulative quantities:
 * 1 = swap attempts
 * 2 = swap accepts
 
-The vector values calculated by this fix are "extensive".
+The vector values calculated by this fix are "intensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.  This fix is not invoked during