Merge pull request #4077 from akohlmey/fix_ewald_const_issue

Fix compilation issue for some pair styles using ewald_const.h

.github/workflows/codeql-analysis.yml

@@ -30,12 +30,12 @@ jobs:
         fetch-depth: 2
 
     - name: Setup Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         config-file: ./.github/codeql/${{ matrix.language }}.yml
@@ -55,4 +55,4 @@ jobs:
         cmake --build . --parallel 2
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

.github/workflows/compile-msvc.yml

@@ -24,7 +24,7 @@ jobs:
         fetch-depth: 2
 
     - name: Select Python version
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
 

.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.*') }}
@@ -59,16 +59,13 @@ jobs:
         -D BUILD_SHARED_LIBS=on \
         -D LAMMPS_SIZES=SMALLBIG \
         -D LAMMPS_EXCEPTIONS=off \
-        -D PKG_MESSAGE=on \
-        -D PKG_MPIIO=on \
         -D PKG_ATC=on \
         -D PKG_AWPMD=on \
-        -D PKG_BOCS=on \
-        -D PKG_EFF=on \
         -D PKG_H5MD=on \
         -D PKG_INTEL=on \
         -D PKG_LATBOLTZ=on \
         -D PKG_MANIFOLD=on \
+        -D PKG_MDI=on \
         -D PKG_MGPT=on \
         -D PKG_ML-PACE=on \
         -D PKG_ML-RANN=on \
@@ -77,7 +74,6 @@ jobs:
         -D PKG_PTM=on \
         -D PKG_QTB=on \
         -D PKG_SMTBQ=on \
-        -D PKG_TALLY=on \
         ../cmake
 
     - name: Run Coverity Scan

.github/workflows/unittest-macos.yml

@@ -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 }}

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")
@@ -415,6 +428,7 @@ 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.
@@ -971,34 +985,37 @@ if(PKG_KOKKOS)
   endif()
 endif()
 if(PKG_KSPACE)
-  message(STATUS "<<< FFT settings >>>
+  if (FFT_USE_HEFFTE)
+    message(STATUS "<<< FFT settings >>>
+-- Primary FFT lib:  heFFTe")
+    if (FFT_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()
+      message(STATUS "Using double precision FFTs")
+    endif()
+  else()
+    message(STATUS "<<< FFT settings >>>
 -- Primary FFT lib:  ${FFT}")
-  if(FFT_SINGLE)
-    message(STATUS "Using single precision FFTs")
-  else()
-    message(STATUS "Using double precision FFTs")
-  endif()
-  if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
-    message(STATUS "Using threaded FFTs")
-  else()
-    message(STATUS "Using non-threaded FFTs")
+    if(FFT_SINGLE)
+      message(STATUS "Using single precision FFTs")
+    else()
+      message(STATUS "Using double precision FFTs")
+    endif()
+    if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
+      message(STATUS "Using threaded FFTs")
+    else()
+      message(STATUS "Using non-threaded FFTs")
+    endif()
+    message(STATUS "Using builtin distributed FFT algorithms")
   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()
+    message(STATUS "Kokkos FFT: ${FFT_KOKKOS}")
   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 "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2022.01.04.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "8d3a801e87a2c6653bf0e27707063914" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.02.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "f3573cf9daa3558ba46fd5866517f38f" 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/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
@@ -151,10 +158,10 @@ if(GPU_API STREQUAL "CUDA")
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   foreach(CU_OBJ ${GPU_GEN_OBJS})
     get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)

cmake/Modules/Packages/KOKKOS.cmake

@@ -16,11 +16,6 @@ endif()
 if(Kokkos_ENABLE_OPENMP)
   if(NOT BUILD_OMP)
     message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
-  else()
-    # NVHPC/(AMD)Clang does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
-    if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
-      message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
-    endif()
   endif()
 endif()
 ########################################################################
@@ -50,8 +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/4.1.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "a5f096bd8ad01b97fdc7a32583b17a33" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.2.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "731647b61a4233f568d583702e9cd6d1" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -76,7 +71,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 4.1.00 REQUIRED CONFIG)
+  find_package(Kokkos 4.2.00 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@@ -131,16 +126,32 @@ 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"))
-      target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
+    if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "CUFFT")))
+      message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or 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")
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
       target_link_libraries(lammps PRIVATE 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

@@ -46,6 +46,61 @@ else()
   target_compile_definitions(lammps PRIVATE -DFFT_KISS)
 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, use the heFFTe parallel engine instead of the builtin fftMPI engine
+
+  # 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")
+    set(Heffte_ENABLE_FFTW "ON" CACHE BOOL "Enables FFTW backend for heFFTe")
+  elseif(FFT_HEFFTE_BACKEND STREQUAL "MKL")
+    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)
+
+    # 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()
+
 set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
 set(FFT_PACK_VALUES array pointer memcpy)
 set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})

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_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum 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 "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-PACE.cmake

@@ -1,33 +1,40 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.10.04.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "70ff79f4e59af175e55d24f3243ad1ff" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
 
-# download library sources to build folder
-if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
-  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-endif()
-if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
-  message(STATUS "Downloading ${PACELIB_URL}")
-  file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
-  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-  if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
-    message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
-    file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
-  endif()
+# LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
+# to make it easier to check local build without going through the public github releases
+if(LOCAL_ML-PACE)
+ set(lib-pace "${LOCAL_ML-PACE}")
 else()
-  message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
-endif()
+  # download library sources to build folder
+  if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
+    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+  endif()
+  if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
+    message(STATUS "Downloading ${PACELIB_URL}")
+    file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
+    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+    if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
+      message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
+      file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
+    endif()
+  else()
+    message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+  endif()
 
-# uncompress downloaded sources
-execute_process(
-  COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
-  COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
-  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-)
-get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+
+  # uncompress downloaded sources
+  execute_process(
+    COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
+    COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+  )
+  get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+endif()
 
 add_subdirectory(${lib-pace} build-pace)
 set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})

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

@@ -21,9 +21,9 @@ 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"
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.3/plumed-src-2.8.3.tgz"
   CACHE STRING "URL for PLUMED tarball")
-set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
+set(PLUMED_MD5 "76d23cd394eba9e6530316ed1184e219" CACHE STRING "MD5 checksum of PLUMED tarball")
 
 mark_as_advanced(PLUMED_URL)
 mark_as_advanced(PLUMED_MD5)

cmake/presets/gpu-cuda.cmake

@@ -0,0 +1,11 @@
+# preset that enables GPU and selects CUDA API
+
+set(PKG_GPU ON CACHE BOOL "Build GPU package" FORCE)
+set(GPU_API "cuda" CACHE STRING "APU used by GPU package" FORCE)
+set(GPU_PREC "mixed" CACHE STRING "" FORCE)
+
+set(CUDA_NVCC_FLAGS "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_DEBUG "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_MINSIZEREL "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_RELWITHDEBINFO "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_RELEASE "-allow-unsupported-compiler" CACHE STRING "" FORCE)

cmake/presets/kokkos-cuda.cmake

@@ -6,6 +6,11 @@ set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)
 set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
+get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
+set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)
+
+# 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/oneapi.cmake

@@ -18,11 +18,11 @@ set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
 unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icx" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_Fortran_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_Fortran_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
 

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/github-development-workflow.md

@@ -36,10 +36,10 @@ requests.
 MUST be submitted as a pull request to GitHub.  All changes to the
 "develop" branch must be made exclusively through merging pull requests.
 The "release" and "stable" branches, respectively, are only to be
-updated upon feature or stable releases based on the associated
-tags.  Updates to the stable release in between stable releases
+updated upon "feature releases" or "stable releases" based on the
+associated tags.  Updates to the stable release in between stable releases
 (for example, back-ported bug fixes) are first merged into the "maintenance"
-branch and then into the "stable" branch as update releases.
+branch and then into the "stable" branch as "stable update releases".
 
 Pull requests may also be submitted to (long-running) feature branches
 created by LAMMPS developers inside the LAMMPS project, if needed. Those
@@ -131,7 +131,7 @@ testing -- that the code in the branch "develop" does not get easily
 broken.  These tests are run after every update to a pull request.  More
 extensive and time-consuming tests (including regression testing) are
 performed after code is merged to the "develop" branch.  There are feature
-releases of LAMMPS made about every 4-6 weeks at a point, when the LAMMPS
+releases of LAMMPS made about every 4-8 weeks at a point, when the LAMMPS
 developers feel, that a sufficient number of changes have been included
 and all post-merge testing has been successful.  These feature releases are
 marked with a `patch_<version date>` tag and the "release" branch

doc/graphviz/Makefile

@@ -16,8 +16,11 @@ clean:
 	rm -f $(IMGSVG) $(IMGPDF) $(IMGPNG) *~
 
 ifeq ($(HAS_DOT),YES)
-$(IMGDIR)/%.png: %.dot
+$(IMGDIR)/lammps-classes.png : lammps-classes.dot
 	dot -Tpng -Kneato -o $@ $<
+
+$(IMGDIR)/%.png: %.dot
+	dot -Tpng -Kdot -o $@ $<
 endif
 
 ifeq ($(HAS_DOT),NO)

doc/graphviz/lammps-releases.dot

@@ -0,0 +1,34 @@
+// LAMMPS branches and releases
+digraph releases {
+    rankdir="LR";
+    github [shape="box" label="Pull Requests\non GitHub" height=0.75];
+    github -> develop [label="Merge commits"];
+    {
+        rank = "same";
+        work [shape="none" label="Development branches:"]
+        develop [label="'develop' branch" height=0.75];
+        maintenance [label="'maintenance' branch" height=0.75];
+    };
+    {
+        rank = "same";
+        upload [shape="none" label="Release branches:"]
+        release [label="'release' branch" height=0.75];
+        stable [label="'stable' branch" height=0.75];
+    };
+    develop -> release [label="Feature release\n(every 4-8 weeks)"];
+    release -> stable [label="Stable release\n(once per year)"];
+    stable -> maintenance [label="Reset on stable release" style="setlinewidth(2)"];
+    develop -> maintenance [label="Backports of bugfixes" style="dashed"];
+    maintenance -> stable [label="Updates to stable release"];
+    {
+        rank = "same";
+        tag [shape="none" label="Applied tags:"];
+        patchtag [shape="box" label="patch_<date>"];
+        stabletag [shape="box" label="stable_<date>"];
+        updatetag [shape="box" label="stable_<date>_update<num>"];
+    };
+    release -> patchtag [label="feature release" style="dotted"];
+    stable -> stabletag [label="stable release" style="dotted"];
+    stable -> updatetag [label="update release" style="dotted"];
+}
+

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "21 November 2023" "2023-11-21"
+.TH LAMMPS "1" "7 February 2024" "2024-02-07"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 21 November 2023
+\- Molecular Dynamics Simulator.  Version 7 February 2024
 
 .SH SYNOPSIS
 .B lmp

doc/src/Bibliography.rst

@@ -562,6 +562,9 @@ Bibliography
 **(Kumar)**
    Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008)
 
+**(Lafourcade)**
+  Lafourcade, Maillet, Denoual, Duval, Allera, Goryaeva, and Marinica, `Comp. Mat. Science, 230, 112534 (2023) <https://doi.org/10.1016/j.commatsci.2023.112534>`_
+
 **(Lamoureux and Roux)**
    G.\  Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
 

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
-on various platforms and with a variety of settings), unit testing
-(i.e. whether certain individual parts of the code produce the expected
-results for given inputs), run testing (whether selected complete input
-decks run without crashing for multiple configurations), and 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>`_.
+during development:
+
+- Integration testing (i.e. whether the code compiles
+  on various platforms and with a variety of compilers and settings),
+- Unit testing (i.e. whether certain functions or classes of the code
+  produce the expected results for given inputs),
+- Run testing (i.e. whether selected input decks can run to completion
+  without crashing for multiple configurations),
+- 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
-of the LAMMPS source code distribution itself.  It can be enabled by
+The unit testing facility is integrated into the CMake build process of
+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
-headers (if those are not found locally a recent version will be
-downloaded and compiled along with LAMMPS and the test program) to
-compile and will download and compile a specific recent version of the
-`Googletest <https://github.com/google/googletest/>`_ C++ test framework
-for implementing the tests.
+It requires the `YAML <https://pyyaml.org/>`_ library and matching
+development headers to compile (if those are not found locally a recent
+version of that library will be downloaded and compiled along with
+LAMMPS and the test programs) and will download and compile a specific
+version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
+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
-styles) are performed with the same test executable using different
-input files in YAML format.  So to add a test for another style of the
-same kind it may be 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.
+Tests as shown by the ``ctest`` program are command lines defined in the
+``CMakeLists.txt`` files in the ``unittest`` directory tree.  A few
+tests simply execute LAMMPS with specific command line flags and check
+the output to the screen for expected content.  A large number of unit
+tests are special tests programs using the `GoogleTest framework
+<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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -255,16 +281,18 @@ A test run is then a a collection multiple individual test runs each
 with many comparisons to reference results based on template input
 files, individual command settings, relative error margins, and
 reference data stored in a YAML format file with ``.yaml``
-suffix. Currently the programs ``test_pair_style``, ``test_bond_style``, and
-``test_angle_style`` are implemented.  They will compare forces, energies and
-(global) stress for all atoms after a ``run 0`` calculation and after a
-few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
-with different settings and also for multiple accelerated styles. If a
-prerequisite style or package is missing, the individual tests are
-skipped.  All tests will be executed on a single MPI process, so using
-the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
-since this will skip the MPI initialization for each test run.
-Below is an example command and output:
+suffix. Currently the programs ``test_pair_style``, ``test_bond_style``,
+``test_angle_style``, ``test_dihedral_style``, and
+``test_improper_style`` are implemented.  They will compare forces,
+energies and (global) stress for all atoms after a ``run 0`` calculation
+and after a few steps of MD with :doc:`fix nve <fix_nve>`, each in
+multiple variants with different settings and also for multiple
+accelerated styles. If a prerequisite style or package is missing, the
+individual tests are skipped.  All force style tests will be executed on
+a single MPI process, so using the CMake option ``-D BUILD_MPI=off`` can
+significantly speed up testing, since this will skip the MPI
+initialization for each test run.  Below is an example command and
+output:
 
 .. code-block:: console
 
@@ -416,15 +444,16 @@ When compiling LAMMPS with enabled tests, most test executables will
 need to be linked against the LAMMPS library.  Since this can be a very
 large library with many C++ objects when many packages are enabled, link
 times can become very long on machines that use the GNU BFD linker (e.g.
-Linux systems).  Alternatives like the ``lld`` linker of the LLVM project
-or the ``gold`` linker available with GNU binutils can speed up this step
-substantially. CMake will by default test if any of the two can be
-enabled and use it when ``ENABLE_TESTING`` is active.  It can also be
-selected manually through the ``CMAKE_CUSTOM_LINKER`` CMake variable.
-Allowed values are ``lld``, ``gold``, ``bfd``, or ``default``.  The
-``default`` option will use the system default linker otherwise, the
-linker is chosen explicitly.  This option is only available for the
-GNU or Clang C++ compiler.
+Linux systems).  Alternatives like the ``mold`` linker, the ``lld``
+linker of the LLVM project, or the ``gold`` linker available with GNU
+binutils can speed up this step substantially (in this order).  CMake
+will by default test if any of the three can be enabled and use it when
+``ENABLE_TESTING`` is active.  It can also be selected manually through
+the ``CMAKE_CUSTOM_LINKER`` CMake variable.  Allowed values are
+``mold``, ``lld``, ``gold``, ``bfd``, or ``default``.  The ``default``
+option will use the system default linker otherwise, the linker is
+chosen explicitly.  This option is only available for the GNU or Clang
+C++ compilers.
 
 Tests for other components and utility functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -518,6 +547,8 @@ The following options are available.
    make fix-errordocs       # remove error docs in header files
    make check-permissions   # search for files with permissions issues
    make fix-permissions     # correct permissions issues in files
+   make check-docs          # search for several issues in the manual
+   make check-version       # list files with pending release version tags
    make check               # run all check targets from above
 
 These should help to make source and documentation files conforming

doc/src/Build_extras.rst

@@ -626,22 +626,22 @@ They must be specified in uppercase.
    *  - HOPPER90
       - GPU
       - NVIDIA Hopper generation CC 9.0 GPU
-   *  - VEGA900
+   *  - AMD_GFX906
       - GPU
-      - AMD GPU MI25 GFX900
-   *  - VEGA906
+      - AMD GPU MI50/MI60
+   *  - AMD_GFX908
       - GPU
-      - AMD GPU MI50/MI60 GFX906
-   *  - VEGA908
+      - AMD GPU MI100
+   *  - AMD_GFX90A
       - GPU
-      - AMD GPU MI100 GFX908
-   *  - VEGA90A
+      - AMD GPU MI200
+   *  - AMD_GFX942
       - GPU
-      - AMD GPU MI200 GFX90A
-   *  - NAVI1030
+      - AMD GPU MI300
+   *  - AMD_GFX1030
       - GPU
       - AMD GPU V620/W6800
-   *  - NAVI1100
+   *  - AMD_GFX1100
       - GPU
       - AMD GPU RX7900XTX
    *  - INTEL_GEN
@@ -666,7 +666,7 @@ They must be specified in uppercase.
       - GPU
       - Intel GPU Ponte Vecchio
 
-This list was last updated for version 4.0.1 of the Kokkos library.
+This list was last updated for version 4.2 of the Kokkos library.
 
 .. tabs::
 

doc/src/Build_settings.rst

@@ -44,6 +44,14 @@ 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:: 7Feb2024
+
+Alternatively, LAMMPS can use the `heFFTe
+<https://icl-utk-edu.github.io/heffte/>`_ library for the MPI
+communication algorithms, which comes with many optimizations for
+special cases, e.g. leveraging available 2D and 3D FFTs in the back end
+libraries and better pipelining for packing and communication.
+
 .. tabs::
 
    .. tab:: CMake build
@@ -51,14 +59,19 @@ LAMMPS can use them if they are available on your system.
       .. 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
-         an exception to the rule that all CMake variables can be specified
-         with lower-case values.
+         When the Kokkos variant of a package is compiled and selected at run time,
+         the FFT library selected by the FFT_KOKKOS variable applies. Otherwise,
+         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
@@ -76,6 +89,16 @@ LAMMPS can use them if they are available on your system.
          -D MKL_INCLUDE_DIR=path     # ditto for Intel MKL library
          -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
          -D MKL_LIBRARY=path         # path to MKL libraries
+         -D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock heFFTe back end
+         -D Heffte_ROOT=path         # path to an existing heFFTe installation
+
+      .. note::
+
+         heFFTe comes with a builtin (= stock) back end for FFTs, i.e. a
+         default internal FFT implementation; however, this stock back
+         end is intended for testing purposes only and is not optimized
+         for production runs.
+
 
    .. tab:: Traditional make
 
@@ -87,6 +110,8 @@ LAMMPS can use them if they are available on your system.
 
          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
@@ -97,6 +122,8 @@ LAMMPS can use them if they are available on your system.
 
          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
@@ -111,6 +138,24 @@ LAMMPS can use them if they are available on your system.
       files in its default search path.  You must specify ``FFT_LIB``
       with the appropriate FFT libraries to include in the link.
 
+      Traditional make can also link to heFFTe using an existing installation
+
+      .. code-block:: make
+
+         include <path-to-heffte-installation>/share/heffte/HeffteMakefile.in
+         FFT_INC = -DFFT_HEFFTE -DFFT_HEFFTE_FFTW $(heffte_include)
+         FFT_PATH =
+         FFT_LIB = $(heffte_link) $(heffte_libs)
+
+      The heFFTe install path will contain `HeffteMakefile.in`.
+      which will define the `heffte_` include variables needed to link to heFFTe from
+      an external project using traditional make.
+      The `-DFFT_HEFFTE` is required to switch to using heFFTe, while the optional `-DFFT_HEFFTE_FFTW`
+      selects the desired heFFTe back end, e.g., `-DFFT_HEFFTE_FFTW` or `-DFFT_HEFFTE_MKL`,
+      omitting the variable will default to the `stock` back end.
+      The heFFTe `stock` back end is intended to be used for testing and debugging,
+      but is not performance optimized for large scale production runs.
+
 The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
 included in the LAMMPS distribution.  It is portable across all
 platforms.  Depending on the size of the FFTs and the number of
@@ -141,6 +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
@@ -152,11 +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
-library a second time with support for single-precision.
+When using ``-DFFT_SINGLE`` with FFTW3, you may need to ensure that
+the FFTW3 installation includes support for single-precision.
 
-For FFTW3, do the following, which should produce the additional
-library ``libfftw3f.a`` or ``libfftw3f.so``\ .
+When compiler FFTW3 from source, you can do the following, which should
+produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
 
 .. code-block:: bash
 
@@ -170,6 +220,16 @@ Depending on the machine, the size of the FFT grid, the number of
 processors used, one option may be slightly faster.  The default is
 ARRAY mode.
 
+When using ``-DFFT_HEFFTE`` CMake will first look for an existing
+install with hints provided by ``-DHeffte_ROOT``, as recommended by the
+CMake standard and note that the name is case sensitive. If CMake cannot
+find a heFFTe installation with the correct back end (e.g., FFTW or
+MKL), it will attempt to download and build the library automatically.
+In this case, LAMMPS CMake will also accept all heFFTe specific
+variables listed in the `heFFTe documentation
+<https://mkstoyanov.bitbucket.io/heffte/md_doxygen_installation.html>`_
+and those variables will be passed into the heFFTe build.
+
 ----------
 
 .. _size:
@@ -463,8 +523,8 @@ Exception handling when using LAMMPS as a library
 
 LAMMPS errors do not kill the calling code, but throw an exception.  In
 the C-library interface, the call stack is unwound and control returns
-to the caller, e.g. to Python or a code that is coupled to LAMMPS and
-the error status can be queried.  When using C++ directly, the calling
+to the caller, e.g. to Python or a code that is coupled to LAMMPS. The
+error status can then be queried.  When using C++ directly, the calling
 code has to be set up to *catch* exceptions thrown from within LAMMPS.
 
 .. note::

doc/src/Commands_bond.rst

@@ -124,7 +124,7 @@ 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:`fourier (io) <dihedral_fourier>`

doc/src/Commands_compute.rst

@@ -100,6 +100,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`nbond/atom <compute_nbond_atom>`
    * :doc:`omega/chunk <compute_omega_chunk>`
    * :doc:`orientorder/atom (k) <compute_orientorder_atom>`
+   * :doc:`pace <compute_pace>`
    * :doc:`pair <compute_pair>`
    * :doc:`pair/local <compute_pair_local>`
    * :doc:`pe <compute_pe>`
@@ -115,12 +116,15 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`property/grid <compute_property_grid>`
    * :doc:`property/local <compute_property_local>`
    * :doc:`ptm/atom <compute_ptm_atom>`
+   * :doc:`rattlers/atom <compute_rattlers_atom>`
    * :doc:`rdf <compute_rdf>`
+   * :doc:`reaxff/atom (k) <compute_reaxff_atom>`
    * :doc:`reduce <compute_reduce>`
    * :doc:`reduce/chunk <compute_reduce_chunk>`
    * :doc:`reduce/region <compute_reduce>`
    * :doc:`rigid/local <compute_rigid_local>`
    * :doc:`saed <compute_saed>`
+   * :doc:`slcsa/atom <compute_slcsa_atom>`
    * :doc:`slice <compute_slice>`
    * :doc:`smd/contact/radius <compute_smd_contact_radius>`
    * :doc:`smd/damage <compute_smd_damage>`

doc/src/Commands_fix.rst

@@ -122,6 +122,7 @@ OPT.
    * :doc:`mvv/tdpd <fix_mvv_dpd>`
    * :doc:`neb <fix_neb>`
    * :doc:`neb/spin <fix_neb_spin>`
+   * :doc:`nonaffine/displacement <fix_nonaffine_displacement>`
    * :doc:`nph (ko) <fix_nh>`
    * :doc:`nph/asphere (o) <fix_nph_asphere>`
    * :doc:`nph/body <fix_nph_body>`
@@ -238,10 +239,10 @@ OPT.
    * :doc:`store/force <fix_store_force>`
    * :doc:`store/state <fix_store_state>`
    * :doc:`tdpd/source <fix_dpd_source>`
-   * :doc:`temp/berendsen <fix_temp_berendsen>`
+   * :doc:`temp/berendsen (k) <fix_temp_berendsen>`
    * :doc:`temp/csld <fix_temp_csvr>`
    * :doc:`temp/csvr <fix_temp_csvr>`
-   * :doc:`temp/rescale <fix_temp_rescale>`
+   * :doc:`temp/rescale (k) <fix_temp_rescale>`
    * :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
    * :doc:`tfmc <fix_tfmc>`
    * :doc:`tgnpt/drude <fix_tgnh_drude>`

doc/src/Commands_pair.rst

@@ -87,7 +87,7 @@ OPT.
    * :doc:`coul/long/soft (o) <pair_fep_soft>`
    * :doc:`coul/msm (o) <pair_coul>`
    * :doc:`coul/slater/cut <pair_coul_slater>`
-   * :doc:`coul/slater/long <pair_coul_slater>`
+   * :doc:`coul/slater/long (g) <pair_coul_slater>`
    * :doc:`coul/shield <pair_coul_shield>`
    * :doc:`coul/streitz <pair_coul>`
    * :doc:`coul/tt <pair_coul_tt>`
@@ -110,7 +110,7 @@ OPT.
    * :doc:`eam/he <pair_eam>`
    * :doc:`edip (o) <pair_edip>`
    * :doc:`edip/multi <pair_edip>`
-   * :doc:`edpd <pair_mesodpd>`
+   * :doc:`edpd (g) <pair_mesodpd>`
    * :doc:`eff/cut <pair_eff>`
    * :doc:`eim (o) <pair_eim>`
    * :doc:`exp6/rx (k) <pair_exp6_rx>`
@@ -146,7 +146,7 @@ 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>`
@@ -158,14 +158,14 @@ OPT.
    * :doc:`lj/cut (gikot) <pair_lj>`
    * :doc:`lj/cut/coul/cut (gko) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/cut/dielectric (o) <pair_dielectric>`
-   * :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/coul/cut/soft (go) <pair_fep_soft>`
    * :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/debye/dielectric (o) <pair_dielectric>`
    * :doc:`lj/cut/coul/dsf (gko) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/long (gikot) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/long/cs <pair_cs>`
    * :doc:`lj/cut/coul/long/dielectric (o) <pair_dielectric>`
-   * :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/coul/long/soft (go) <pair_fep_soft>`
    * :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/msm/dielectric <pair_dielectric>`
    * :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
@@ -202,7 +202,7 @@ OPT.
    * :doc:`lubricate/poly (o) <pair_lubricate>`
    * :doc:`lubricateU <pair_lubricateU>`
    * :doc:`lubricateU/poly <pair_lubricateU>`
-   * :doc:`mdpd <pair_mesodpd>`
+   * :doc:`mdpd (g) <pair_mesodpd>`
    * :doc:`mdpd/rhosum <pair_mesodpd>`
    * :doc:`meam (k) <pair_meam>`
    * :doc:`meam/ms (k) <pair_meam>`
@@ -268,11 +268,11 @@ OPT.
    * :doc:`smtbq <pair_smtbq>`
    * :doc:`snap (ik) <pair_snap>`
    * :doc:`soft (go) <pair_soft>`
-   * :doc:`sph/heatconduction <pair_sph_heatconduction>`
+   * :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
    * :doc:`sph/idealgas <pair_sph_idealgas>`
-   * :doc:`sph/lj <pair_sph_lj>`
+   * :doc:`sph/lj (g) <pair_sph_lj>`
    * :doc:`sph/rhosum <pair_sph_rhosum>`
-   * :doc:`sph/taitwater <pair_sph_taitwater>`
+   * :doc:`sph/taitwater (g) <pair_sph_taitwater>`
    * :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`
    * :doc:`spin/dipole/cut <pair_spin_dipole>`
    * :doc:`spin/dipole/long <pair_spin_dipole>`

doc/src/Commands_removed.rst

@@ -126,6 +126,17 @@ syntax compatible with the removed reax pair style, so input files will
 have to be adapted.  The REAXFF package was originally called
 USER-REAXC.
 
+USER-REAXC package
+------------------
+
+.. 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
+the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining
+backward compatibility by providing aliases for the styles.  These have
+been removed, so using "reaxff" is now *required*.
+
 USER-CUDA package
 -----------------
 

doc/src/Developer_platform.rst

@@ -70,6 +70,9 @@ File and path functions and global constants
 .. doxygenfunction:: is_console
    :project: progguide
 
+.. doxygenfunction:: disk_free
+   :project: progguide
+
 .. doxygenfunction:: path_is_directory
    :project: progguide
 

doc/src/Developer_unittest.rst

@@ -121,7 +121,7 @@ will be suppressed and only a summary printed, but adding
 the '-V' option will then produce output from the tests
 above like the following:
 
-.. code-block::
+.. code-block:: console
 
    [...]
    1: [ RUN      ] Tokenizer.empty_string
@@ -180,19 +180,11 @@ discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
 environment variable, ``TEST_ARGS=-v``) it can be printed and used to
 understand why tests fail unexpectedly.
 
-Another complexity of these tests stems from the need to capture
-situations where LAMMPS will stop with an error, i.e. handle so-called
-"death tests".  Here the LAMMPS code will operate differently depending
-on whether it was configured to throw C++ exceptions on errors or call
-either ``exit()`` or ``MPI_Abort()``.  In the latter case, the test code
-also needs to detect whether LAMMPS was compiled with the OpenMPI
-library, as OpenMPI is **only** compatible the death test options of the
-GoogleTest library when C++ exceptions are enabled; otherwise those
-"death tests" must be skipped to avoid reporting bogus failures.  The
-specifics of this step are implemented in the ``TEST_FAILURE()``
-macro. These tests operate by capturing the screen output when executing
-the failing command and then comparing that with a provided regular
-expression string pattern.  Example:
+The specifics of so-called "death tests", i.e. conditions where LAMMPS
+should fail and throw an exception, are implemented in the
+``TEST_FAILURE()`` macro. These tests operate by capturing the screen
+output when executing the failing command and then comparing that with a
+provided regular expression string pattern.  Example:
 
 .. code-block:: c++
 
@@ -282,9 +274,7 @@ Tests for using the Fortran module are in the ``unittest/fortran``
 folder.  Since they are also using the GoogleTest library, they require
 to also implement test wrappers in C++ that will call fortran functions
 which provide a C function interface through ISO_C_BINDINGS that will in
-turn call the functions in the LAMMPS Fortran module.  This part of the
-unit tests is incomplete since the Fortran module it is based on is
-incomplete as well.
+turn call the functions in the LAMMPS Fortran module.
 
 Tests for the C++-style library interface
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -405,10 +395,10 @@ compare with the reference and also start from the data file.  A final
 check will use multi-cutoff r-RESPA (if supported by the pair style) at
 a 1:1 split and compare to the Verlet results.  These sets of tests are
 run with multiple test fixtures for accelerated styles (OPT, OPENMP,
-INTEL) and for the latter two with 4 OpenMP threads enabled.  For
-these tests the relative error (epsilon) is lowered by a common factor
-due to the additional numerical noise, but the tests are still comparing
-to the same reference data.
+INTEL, KOKKOS (OpenMP only)) and for the latter three with 4 OpenMP
+threads enabled.  For these tests the relative error (epsilon) is lowered
+by a common factor due to the additional numerical noise, but the tests
+are still comparing to the same reference data.
 
 Additional tests will check whether all listed extract keywords are
 supported and have the correct dimensionality and the final set of tests
@@ -442,17 +432,19 @@ The ``test_pair_style`` tester is used with 4 categories of test inputs:
   pair style is defined, but the computation of the pair style contributions
   is disabled.
 
-The ``test_bond_style`` and ``test_angle_style`` are set up in a similar
-fashion and share support functions with the pair style tester.  The final
-group of tests in this section is for fix styles that add/manipulate forces
-and velocities, e.g. for time integration, thermostats and more.
+The ``test_bond_style``, ``test_angle_style``, ``test_dihedral_style``, and
+``test_improper_style`` tester programs are set up in a similar fashion and
+share support functions with the pair style tester.  The final group of
+tests in this section is for fix styles that add/manipulate forces and
+velocities, e.g. for time integration, thermostats and more.
 
-Adding a new test is easiest done by copying and modifying an existing test
-for a style that is similar to one to be tested.  The file name should follow
-the naming conventions described above and after copying the file, the first
-step is to replace the style names where needed.  The coefficient values
-do not have to be meaningful, just in a reasonable range for the given system.
-It does not matter if some forces are large, for as long as they do not diverge.
+Adding a new test is easiest done by copying and modifying an existing YAML
+file for a style that is similar to one to be tested.  The file name should
+follow the naming conventions described above and after copying the file,
+the first step is to replace the style names where needed.  The coefficient
+values do not have to be meaningful, just in a reasonable range for the
+given system.  It does not matter if some forces are large, for as long as
+they do not diverge.
 
 The template input files define a large number of index variables at the top
 that can be modified inside the YAML file to control the behavior.  For example,
@@ -480,7 +472,7 @@ Note that this disables computing the kspace contribution, but still will run
 the setup.  The "gewald" parameter should be set explicitly to speed up the run.
 For styles with long-range electrostatics, typically two tests are added one using
 the (slower) analytic approximation of the erfc() function and the other using
-the tabulated coulomb, to test both code paths. The reference results in the YAML
+the tabulated coulomb, to test both code paths.  The reference results in the YAML
 files then should be compared manually, if they agree well enough within the limits
 of those two approximations.
 
@@ -534,3 +526,102 @@ The ``unittest/tools`` folder contains tests for programs in the
 shell, which are implemented as a python scripts using the ``unittest``
 Python module and launching the tool commands through the ``subprocess``
 Python module.
+
+
+Troubleshooting failed unit tests
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The are by default no unit tests for newly added features (e.g. pair, fix,
+or compute styles) unless your pull request also includes tests for the
+added features.  If you are modifying some features, you may see failures
+for existing tests, if your modifications have some unexpected side effects
+or your changes render the existing text invalid.  If you are adding an
+accelerated version of an existing style, then only tests for INTEL,
+KOKKOS (with OpenMP only), OPENMP, and OPT will be run automatically.
+Tests for the GPU package are time consuming and thus are only run
+*after* a merge, or when a special label, ``gpu_unit_tests`` is added
+to the pull request.  After the test has started, it is often best to
+remove the label since every PR activity will re-trigger the test (that
+is a limitation of triggering a test with a label).  Support for unit
+tests with using KOKKOS with GPU acceleration is currently not supported.
+
+When you see a failed build on GitHub, click on ``Details`` to be taken
+to the corresponding LAMMPS Jenkins CI web page.  Click on the "Exit"
+symbol near the ``Logout`` button on the top right of that page to go to
+the "classic view".  In the classic view, there is a list of the
+individual runs that make up this test run (they are shown but cannot be
+inspected in the default view).  You can click on any of those.
+Clicking on ``Test Result`` will display the list of failed tests. Click
+on the "Status" column to sort the tests based on their Failed or Passed
+status.  Then click on the failed test to expand its output.
+
+For example, the following output snippet shows the failed unit test
+
+.. code-block:: console
+
+   [ RUN      ] PairStyle.gpu
+   /home/builder/workspace/dev/pull_requests/ubuntu_gpu/unit_tests/cmake_gpu_opencl_mixed_smallbig_clang_static/unittest/force-styles/test_main.cpp:63: Failure
+   Expected: (err) <= (epsilon)
+   Actual: 0.00018957912910606503 vs 0.0001
+   Google Test trace:
+   /home/builder/workspace/dev/pull_requests/ubuntu_gpu/unit_tests/cmake_gpu_opencl_mixed_smallbig_clang_static/unittest/force-styles/test_main.cpp:56: EXPECT_FORCES: init_forces (newton off)
+   /home/builder/workspace/dev/pull_requests/ubuntu_gpu/unit_tests/cmake_gpu_opencl_mixed_smallbig_clang_static/unittest/force-styles/test_main.cpp:64: Failure
+   Expected: (err) <= (epsilon)
+   Actual: 0.00022892713393549854 vs 0.0001
+
+The failed assertions provide line numbers in the test source
+(e.g. ``test_main.cpp:56``), from which one can understand what
+specific assertion failed.
+
+Note that the force style engine runs one of a small number of systems
+in a rather off-equilibrium configuration with a few atoms for a few
+steps, writes data and restart files, uses :doc:`the clear command
+<clear>` to reset LAMMPS, and then runs from those files with different
+settings (e.g. newton on/off) and integrators (e.g. verlet vs. respa).
+Beyond potential issues/bugs in the source code, the mismatch between
+the expected and actual values could be that force arrays are not
+properly cleared between multiple run commands or that class members are
+not correctly initialized or written to or read from a data or restart
+file.
+
+While the epsilon (relative precision) for a single, `IEEE 754 compliant
+<https://en.wikipedia.org/wiki/IEEE_754>`_, double precision floating
+point operation is at about 2.2e-16, the achievable precision for the
+tests is lower due to most numbers being sums over intermediate results
+and the non-associativity of floating point math leading to larger
+errors.  In some cases specific properties of the tested style.  As a
+rule of thumb, the test epsilon can often be in the range 5.0e-14 to
+1.0e-13.  But for "noisy" force kernels, e.g. those a larger amount of
+arithmetic operations involving `exp()`, `log()` or `sin()` functions,
+and also due to the effect of compiler optimization or differences
+between compilers or platforms, epsilon may need to be further relaxed,
+sometimes epsilon can be relaxed to 1.0e-12. If interpolation or lookup
+tables are used, epsilon may need to be set to 1.0e-10 or even higher.
+For tests of accelerated styles, the per-test epsilon is multiplied
+by empirical factors that take into account the differences in the order
+of floating point operations or that some or most intermediate operations
+may be done using approximations or with single precision floating point
+math.
+
+To rerun the failed unit test individually, change to the ``build`` directory
+and run the test with verbose output. For example,
+
+.. code-block:: bash
+
+    env TEST_ARGS=-v ctest -R ^MolPairStyle:lj_cut_coul_long -V
+
+``ctest`` with the ``-V`` flag also shows the exact command line
+of the test. One can then use ``gdb --args`` to further debug and
+catch exceptions with the test command, for example,
+
+.. code-block:: bash
+
+    gdb --args /path/to/lammps/build/test_pair_style /path/to/lammps/unittest/force-styles/tests/mol-pair-lj_cut_coul_long.yaml
+
+
+It is recommended to configure the build with ``-D
+BUILD_SHARED_LIBS=on`` and use a custom linker to shorten the build time
+during recompilation.  Installing `ccache` in your development
+environment helps speed up recompilation by caching previous
+compilations and detecting when the same compilation is being done
+again.  Please see :doc:`Build_development` for further details.

doc/src/Developer_updating.rst

@@ -20,6 +20,7 @@ Available topics in mostly chronological order are:
 - `Use ev_init() to initialize variables derived from eflag and vflag`_
 - `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`_
 - `Simplify customized error messages`_
 - `Use of "override" instead of "virtual"`_
 - `Simplified and more compact neighbor list requests`_
@@ -196,6 +197,71 @@ New:
 
    fp = utils::open_potential(filename, lmp);
 
+Use symbolic Atom and AtomVec constants instead of numerical values
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 18Sep2020
+
+Properties in LAMMPS that were represented by integer values (0, 1,
+2, 3) to indicate settings in the ``Atom`` and ``AtomVec`` classes (or
+classes derived from it) (and its derived classes) have been converted
+to use scoped enumerators instead.
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Symbolic Constant
+     - Value
+     - Symbolic Constant
+     - Value
+   * - Atom::GROW
+     - 0
+     - Atom::MAP_NONE
+     - 0
+   * - Atom::RESTART
+     - 1
+     - Atom::MAP_ARRAY
+     - 1
+   * - Atom::BORDER
+     - 2
+     - Atom::MAP_HASH
+     - 2
+   * - Atom::ATOMIC
+     - 0
+     - Atom::MAP_YES
+     - 3
+   * - Atom::MOLECULAR
+     - 1
+     - AtomVec::PER_ATOM
+     - 0
+   * - Atom::TEMPLATE
+     - 2
+     - AtomVec::PER_TYPE
+     - 1
+
+Old:
+
+.. code-block:: c++
+
+   molecular = 0;
+   mass_type = 1;
+   if (atom->molecular == 2)
+   if (atom->map_style == 2)
+   atom->add_callback(0);
+   atom->delete_callback(id,1);
+
+New:
+
+.. code-block:: c++
+
+   molecular = Atom::ATOMIC;
+   mass_type = AtomVec::PER_TYPE;
+   if (atom->molecular == Atom::TEMPLATE)
+   if (atom->map_style == Atom::MAP_HASH)
+   atom->add_callback(Atom::GROW);
+   atom->delete_callback(id,Atom::RESTART);
+
 Simplify customized error messages
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Fortran.rst

@@ -315,6 +315,10 @@ 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`
@@ -1398,7 +1402,28 @@ 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 +1431,23 @@ 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`
 
 --------
 
@@ -3038,14 +3079,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    This function can be used to query if an error inside of LAMMPS
    has thrown a :ref:`C++ exception <exceptions>`.
 
-   .. note::
-
-      This function will always report "no error" when the LAMMPS library
-      has been compiled without ``-DLAMMPS_EXCEPTIONS``, which turns fatal
-      errors aborting LAMMPS into C++ exceptions. You can use the library
-      function :cpp:func:`lammps_config_has_exceptions` to check if this is
-      the case.
-
    :to: :cpp:func:`lammps_has_error`
    :r has_error: ``.TRUE.`` if there is an error.
    :rtype has_error: logical
@@ -3068,13 +3101,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    would happen only in a single MPI rank and thus may not be recoverable, as
    other MPI ranks may be waiting on the failing MPI rank(s) to send messages.
 
-   .. note::
-
-      This function will do nothing when the LAMMPS library has been
-      compiled without ``-DLAMMPS_EXCEPTIONS``, which turns errors aborting
-      LAMMPS into C++ exceptions.  You can use the function
-      :f:func:`config_has_exceptions` to check whether this is the case.
-
    :p character(len=\*) buffer: string buffer to copy the error message into
    :o integer(c_int) status [optional]: 1 when all ranks had the error,
     2 on a single-rank error.

doc/src/Howto.rst

@@ -101,6 +101,7 @@ Tutorials howto
    Howto_cmake
    Howto_github
    Howto_lammps_gui
+   Howto_moltemplate
    Howto_pylammps
    Howto_wsl
 

doc/src/Howto_body.rst

@@ -335,7 +335,7 @@ faces are listed, so that M = 6 + 3\*N + 1.
 The integer line has three values: number of vertices (N), number of
 edges (E) and number of faces (F). The floating point line(s) list 6
 moments of inertia followed by the coordinates of the N vertices (x1
-to zN) as 3N values, followed by 2N vertex indices corresponding to
+to zN) as 3N values, followed by 2E vertex indices corresponding to
 the end points of the E edges, then 4\*F vertex indices defining F
 faces.  The last value is the diameter value = the rounded diameter of
 the sphere that surrounds each vertex. The diameter value can be

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_github.rst

@@ -480,11 +480,11 @@ Some recent changes to the workflow are not captured in this tutorial.
 For example, in addition to the *develop* branch, to which all new
 features should be submitted, there is also a *release*, a *stable*, and
 a *maintenance* branch; the *release* branch is updated from the
-*develop* as part of a feature release, and *stable* (together with
-*release*) are updated from *develop* when a stable release is made. In
-between stable releases, selected bug fixes and infrastructure updates
-are back-ported from the *develop* branch to the *maintenance* branch
-and occasionally merged to *stable* as an update release.
+*develop* branch as part of a "feature release", and *stable* (together
+with *release*) are updated from *develop* when a "stable release" is
+made. In between stable releases, selected bug fixes and infrastructure
+updates are back-ported from the *develop* branch to the *maintenance*
+branch and occasionally merged to *stable* as an update release.
 
 Furthermore, the naming of the release tags now follow the pattern
 "patch_<Day><Month><Year>" to simplify comparisons between releases.

doc/src/Howto_moltemplate.rst

@@ -0,0 +1,371 @@
+Moltemplate Tutorial
+====================
+
+In this tutorial, we are going to use the tool :ref:`Moltemplate
+<moltemplate>` to set up a classical molecular dynamic simulation using
+the :ref:`OPLS-AA force field <OPLSAA96>`. The first
+task is to describe an organic compound and create a complete input deck
+for LAMMPS. The second task is to map the OPLS-AA force field to a
+molecular sample created with an external tool, e.g. PACKMOL, and
+exported as a PDB file.  The files used in this tutorial can be found
+in the ``tools/moltemplate/tutorial-files`` folder of the LAMMPS
+source code distribution.
+
+Simulating an organic solvent
+"""""""""""""""""""""""""""""
+
+This example aims to create a cubic box of the organic solvent
+formamide.
+
+The first step is to create a molecular topology in the
+LAMMPS-template (LT) file format representing a single molecule, which
+will be stored in a Moltemplate object called ``_FAM inherits OPLSAA {}``.
+This command states that the object ``_FAM`` is based on an existing
+object called ``OPLSAA``, which contains OPLS-AA parameters, atom type
+definitions, partial charges, masses and bond-angle rules for many organic
+and biological compounds.
+
+The atomic structure is the starting point to populate the command
+``write('Data Atoms') {}``, which will write the ``Atoms`` section in the
+LAMMPS data file. The OPLS-AA force field uses the ``atom_style full``,
+therefore, this column format is used:
+``# atomID molID atomType charge coordX coordY coordZ``.
+The ``atomID``\ s are replaced with Moltemplate ``$``-type variables, which
+are then substituted with unique numerical IDs. The same logic is applied
+to the ``molID``, except that the same variable is used for the whole
+molecule. The atom types are assigned using ``@``-type variables. The
+assignment of atom types (e.g. ``@atom:177``, ``@atom:178``) is done using
+the OPLS-AA atom types defined in the "In Charges" section of the file
+``oplsaa.lt``, looking for a reasonable match with the description of the atom.
+The resulting file (``formamide.lt``) follows:
+
+.. code-block:: bash
+
+   _FAM inherits OPLSAA {
+
+     # atomID    molID  atomType  charge  coordX  coordY  coordZ
+     write('Data Atoms') {
+       $atom:C00 $mol   @atom:177  0.00    0.100   0.490   0.0
+       $atom:O01 $mol   @atom:178  0.00    1.091  -0.250   0.0
+       $atom:N02 $mol   @atom:179  0.00   -1.121  -0.181   0.0
+       $atom:H03 $mol   @atom:182  0.00   -2.013   0.272   0.0
+       $atom:H04 $mol   @atom:182  0.00   -1.056  -1.190   0.0
+       $atom:H05 $mol   @atom:221  0.00    0.144   1.570   0.0
+     }
+
+     # A list of the bonds in the molecule:
+     # BondID   AtomID1   AtomID2
+     write('Data Bond List') {
+       $bond:C1 $atom:C00 $atom:O01
+       $bond:C2 $atom:C00 $atom:H05
+       $bond:C3 $atom:C00 $atom:N02
+       $bond:C4 $atom:N02 $atom:H03
+       $bond:C5 $atom:N02 $atom:H04
+     }
+   }
+
+You don't have to specify the charge in this example because they will
+be assigned according to the atom type. Analogously, only a
+"Data Bond List" section is needed as the atom type will determine the
+bond type. The other bonded interactions (e.g. angles,
+dihedrals, and impropers) will be automatically generated by
+Moltemplate.
+
+If the simulation is non-neutral, or Moltemplate complains that you have
+missing bond, angle, or dihedral types, this means at least one of your
+atom types is incorrect.
+
+The second step is to create a master file with instructions to build a
+starting structure and the LAMMPS commands to run an NPT simulation. The
+master file (``solv_01.lt``) follows:
+
+.. code-block:: bash
+
+   # Import the force field.
+   import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
+   import formamide.lt # after oplsaa.lt, as it depends on it.
+
+   # Create the input sample.
+   solv = new _FAM [5].move( 4.6, 0, 0)
+                   [5].move( 0, 4.6, 0)
+                   [5].move( 0, 0, 4.6)
+   solv[*][*][*].move(-11.5, -11.5, -11.5)
+
+   # Set the simulation box.
+   write_once("Data Boundary") {
+    -11.5 11.5 xlo xhi
+    -11.5 11.5 ylo yhi
+    -11.5 11.5 zlo zhi
+   }
+
+   # Create an input deck for LAMMPS.
+   write_once("In Init"){
+    # Input variables.
+    variable run    string solv_01   # output name
+    variable ts     equal  1         # timestep
+    variable temp   equal  300       # equilibrium temperature
+    variable p      equal  1.        # equilibrium pressure
+    variable d      equal  1000      # output frequency
+    variable equi   equal  5000      # Equilibration steps
+    variable prod   equal  30000     # Production steps
+
+    # PBC (set them before the creation of the box).
+    boundary p p p
+   }
+
+   # Run an NPT simulation.
+   write_once("In Run"){
+    # Derived variables.
+    variable tcouple equal \$\{ts\}*100
+    variable pcouple equal \$\{ts\}*1000
+
+    # Output.
+    thermo          \$d
+    thermo_style custom step etotal evdwl ecoul elong ebond eangle &
+    edihed eimp ke pe temp press vol density cpu
+    thermo_modify flush yes
+
+    # Trajectory.
+    dump TRJ all dcd \$d \$\{run\}.dcd
+    dump_modify TRJ unwrap yes
+
+    # Thermalisation and relaxation, NPT ensemble.
+    timestep       \$\{ts\}
+    fix             NPT all npt temp \$\{temp\} \$\{temp\} \$\{tcouple\} iso \$p \$p \$\{pcouple\}
+    velocity all create \$\{temp\} 858096 dist gaussian
+    # Short runs to update the PPPM settings as the box shinks.
+    run    \$\{equi\} post no
+    run    \$\{equi\} post no
+    run    \$\{equi\} post no
+    run    \$\{equi\}
+    # From now on, the density shouldn't change too much.
+    run    \$\{prod\}
+    unfix NPT
+   }
+
+The first two commands insert the content of files ``oplsaa.lt`` and
+``formamide.lt`` into the master file. At this point, we can use the
+command ``solv = new _FAM [N]`` to create N copies of a molecule of type
+``_FAM``. In this case, we create an array of 5*5*5 molecules on a cubic
+grid using the coordinate transformation command ``.move( 4.6, 0, 0)``.
+See the Moltemplate documentation to learn more about the syntax. As
+the sample was created from scratch, we also specify the simulation box
+size in the "Data Boundary" section.
+
+The LAMMPS setting for the force field are specified in the file
+``oplsaa.lt`` and are written automatically in the input deck. We also
+specify the boundary conditions and a set of variables in
+the "In Init" section. The remaining commands to run an NPT simulation
+are written in the "In Run" section. Note that in this script, LAMMPS
+variables are protected with the escape character ``\`` to distinguish
+them from Moltemplate variables, e.g. ``\$\{run\}`` is a LAMMPS
+variable that is written in the input deck as ``${run}``.
+
+Compile the master file with:
+
+.. code-block:: bash
+
+   moltemplate.sh -overlay-all solv_01.lt
+
+And execute the simulation with the following:
+
+.. code-block:: bash
+
+   mpirun -np 4 lmp -in solv_01.in -l solv_01.log
+
+.. figure:: JPG/solv_01.png
+   :figwidth: 80%
+   :figclass: align-center
+
+   Snapshot of the sample at the beginning and end of the simulation.
+   Rendered with Ovito.
+
+Mapping an existing structure
+"""""""""""""""""""""""""""""
+
+Another helpful way to use Moltemplate is mapping an existing molecular
+sample to a force field. This is useful when a complex sample is
+assembled from different simulations or created with specialized
+software (e.g. PACKMOL). As in the previous example, all molecular
+species in the sample must be defined using single-molecule Moltemplate
+objects.  For this example, we use a short polymer in a box containing
+water molecules and ions in the PDB file ``model.pdb``.
+
+It is essential to understand that the order of atoms in the PDB file
+and in the Moltemplate master script must match, as we are using the
+coordinates from the PDB file in the order they appear. The order of
+atoms and molecules in the PDB file provided is as follows:
+
+- 500 water molecules, with atoms ordered in this sequence:
+
+  .. parsed-literal::
+
+     ATOM      1  O   MOL D   1       5.901   7.384   1.103  0.00  0.00      DUM
+     ATOM      2  H   MOL D   1       6.047   8.238   0.581  0.00  0.00      DUM
+     ATOM      3  H   MOL D   1       6.188   7.533   2.057  0.00  0.00      DUM
+
+- 1 polymer molecule.
+- 1 Ca\ :sup:`2+` ion.
+- 2 Cl\ :sup:`-` ions.
+
+In the master LT file, this sequence of molecules is matched with the
+following commands:
+
+.. code-block:: bash
+
+   # Create the sample.
+   wat=new SPC[500]
+   pol=new PolyNIPAM[1]
+   cat=new Ca[1]
+   ani=new Cl[2]
+
+Note that the first command would create 500 water molecules in the
+same position in space, and the other commands will use the coordinates
+specified in the corresponding molecular topology block. However, the
+coordinates will be overwritten by rendering an external atomic
+structure file. Note that if the same molecule species are scattered in
+the input structure, it is recommended to reorder and group together
+for molecule types to facilitate the creation of the input sample.
+
+The molecular topology for the polymer is created as in the previous
+example, with the atom types assigned as in the following schema:
+
+.. figure:: JPG/PolyNIPAM.jpg
+   :scale: 30%
+   :align: center
+
+   Atom types assigned to the polymer's repeating unit.
+
+The molecular topology of the water and ions is stated directly into
+the master file for the sake of space, but they could also be written
+in a separate file(s) and imported before the sample is created.
+
+The resulting master LT file defining short annealing at a fixed volume
+(NVT) follows:
+
+.. code-block:: bash
+
+   # Use the OPLS-AA force field for all species.
+   import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
+   import PolyNIPAM.lt
+
+   # Define the SPC water and ions as in the OPLS-AA
+   Ca inherits OPLSAA {
+     write("Data Atoms"){
+       $atom:a1  $mol:. @atom:354 0.0  0.00000 0.00000 0.000000
+     }
+   }
+   Cl inherits OPLSAA {
+     write("Data Atoms"){
+       $atom:a1  $mol:. @atom:344 0.0  0.00000 0.00000 0.000000
+     }
+   }
+   SPC inherits OPLSAA {
+     write("Data Atoms"){
+       $atom:O  $mol:. @atom:76 0.  0.0000000 0.00000 0.000000
+       $atom:H1 $mol:. @atom:77 0.  0.8164904 0.00000 0.5773590
+       $atom:H2 $mol:. @atom:77 0. -0.8164904 0.00000 0.5773590
+     }
+     write("Data Bond List") {
+       $bond:OH1 $atom:O $atom:H1
+       $bond:OH2 $atom:O $atom:H2
+     }
+   }
+
+   # Create the sample.
+   wat=new SPC[500]
+   pol=new PolyNIPAM[1]
+   cat=new Ca[1]
+   ani=new Cl[2]
+
+   # Periodic boundary conditions:
+   write_once("Data Boundary"){
+     0 26 xlo xhi
+     0 26 ylo yhi
+     0 26 zlo zhi
+   }
+
+   # Define the input variables.
+   write_once("In Init"){
+     # Input variables.
+     variable run    string sample01  # output name
+     variable ts     equal  2         # timestep
+     variable temp   equal  298.15    # equilibrium temperature
+     variable p      equal  1.        # equilibrium pressure
+     variable equi   equal  30000     # equilibration steps
+
+     # PBC (set them before the creation of the box).
+     boundary p p p
+     neighbor        3 bin
+   }
+
+   # Run an NVT simulation.
+   write_once("In Run"){
+     # Set the output.
+     thermo          1000
+     thermo_style    custom step etotal evdwl ecoul elong ebond eangle &
+     edihed eimp pe ke temp press atoms vol density cpu
+     thermo_modify flush yes
+     compute pe1 all pe/atom pair
+     dump TRJ all custom 100 \$\{run\}.dump id xu yu zu c_pe1
+
+     # Minimise the input structure, just in case.
+     minimize        .01 .001 1000 100000
+     write_data \$\{run\}.min
+
+     # Set the constrains.
+     group watergroup type @atom:76 @atom:77
+     fix 0 watergroup shake 0.0001 10 0 b @bond:042_043 a @angle:043_042_043
+
+     # Short annealing.
+     timestep        \$\{ts\}
+     fix       1 all nvt temp \$\{temp\} \$\{temp\} \$(100*dt)
+     velocity    all create \$\{temp\} 315443
+     run             \$\{equi\}
+     unfix 1
+   }
+
+
+In this example, the water model is SPC and it is defined in the
+``oplsaa.lt`` file with atom types ``@atom:76`` and ``@atom:77``.  For
+water we also use the ``group`` and ``fix shake`` commands with
+Moltemplate ``@``-type variables, to ensure consistency with the
+numerical values assigned during compilation. To identify the bond and
+angle types, look for the extended ``@atom`` IDs, which in this case
+are:
+
+.. code-block:: bash
+
+   replace{ @atom:76 @atom:76_b042_a042_d042_i042 }
+   replace{ @atom:77 @atom:77_b043_a043_d043_i043 }
+
+From which we can identify the following "Data Bonds By Type":
+``@bond:042_043 @atom:*_b042*_a*_d*_i* @atom:*_b043*_a*_d*_i*`` and
+"Data Angles By Type": ``@angle:043_042_043 @atom:*_b*_a043*_d*_i*
+@atom:*_b*_a042*_d*_i* @atom:*_b*_a043*_d*_i*``
+
+Compile the master file with:
+
+.. code-block:: bash
+
+   moltemplate.sh -overlay-all -pdb model.pdb sample01.lt
+
+And execute the simulation with the following:
+
+.. code-block:: bash
+
+   mpirun -np 4 lmp -in sample01.in -l sample01.log
+
+.. figure:: JPG/sample01.png
+   :figwidth: 50%
+   :figclass: align-center
+
+   Sample visualized with Ovito loading the trajectory into the DATA
+   file written after minimization.
+
+------------
+
+.. _OPLSAA96:
+
+**(OPLS-AA)**  Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc,
+118(45), 11225-11236 (1996).

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_tip4p.rst

@@ -193,11 +193,14 @@ file changed):
     write_data tip4p-implicit.data nocoeff
 
 Below is the code for a LAMMPS input file using the explicit method and
-a TIP4P molecule file.  Because of using :doc:`fix rigid/nvt/small
+a TIP4P molecule file.  Because of using :doc:`fix rigid/small
 <fix_rigid>` no bonds need to be defined and thus no extra storage needs
-to be reserved for them, but we need to switch to atom style full or use
-:doc:`fix property/atom mol <fix_property_atom>` so that fix
-rigid/nvt/small can identify rigid bodies by their molecule ID:
+to be reserved for them, but we need to either switch to atom style full
+or use :doc:`fix property/atom mol <fix_property_atom>` so that fix
+rigid/small can identify rigid bodies by their molecule ID.  Also a
+:doc:`neigh_modify exclude <neigh_modify>` command is added to exclude
+computing intramolecular non-bonded interactions, since those are
+removed by the rigid fix anyway:
 
 .. code-block:: LAMMPS
 
@@ -216,17 +219,17 @@ rigid/nvt/small can identify rigid bodies by their molecule ID:
     pair_coeff 2 2 0.0    1.0
     pair_coeff 3 3 0.0    1.0
 
-    fix mol all property/atom mol
+    fix mol all property/atom mol ghost yes
     molecule water tip4p.mol
     create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
+    neigh_modify exclude molecule/intra all
 
     timestep 0.5
-    fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0
-    velocity all create 300.0 5463576
+    fix integrate all rigid/small molecule langevin 300.0 300.0 100.0 2345634
 
     thermo_style custom step temp press etotal density pe ke
-    thermo 1000
-    run 20000
+    thermo 2000
+    run 40000
     write_data tip4p-explicit.data nocoeff
 
 .. _tip4p_molecule:

doc/src/Howto_tip5p.rst

@@ -81,11 +81,13 @@ long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS).
 
 Below is the code for a LAMMPS input file for setting up a simulation of
 TIP5P water with a molecule file.  Because of using :doc:`fix
-rigid/nvt/small <fix_rigid>` no bonds need to be defined and thus no
-extra storage needs to be reserved for them, but we need to switch to
+rigid/small <fix_rigid>` no bonds need to be defined and thus no extra
+storage needs to be reserved for them, but we need to either switch to
 atom style full or use :doc:`fix property/atom mol <fix_property_atom>`
-so that fix rigid/nvt/small can identify rigid bodies by their molecule
-ID:
+so that fix rigid/small can identify rigid bodies by their molecule ID.
+Also a :doc:`neigh_modify exclude <neigh_modify>` command is added to
+exclude computing intramolecular non-bonded interactions, since those
+are removed by the rigid fix anyway:
 
 .. code-block:: LAMMPS
 
@@ -107,11 +109,11 @@ ID:
     fix mol all property/atom mol
     molecule water tip5p.mol
     create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
+    neigh_modify exclude molecule/intra all
 
     timestep 0.5
-    fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0
+    fix integrate all rigid/small molecule langevin 300.0 300.0 50.0 235664
     reset_timestep 0
-    velocity all create 300.0 5463576
 
     thermo_style custom step temp press etotal density pe ke
     thermo 1000

doc/src/Install_git.rst

@@ -28,16 +28,16 @@ provides `limited support for subversion clients <svn_>`_.
 
 You can follow the LAMMPS development on 4 different git branches:
 
-* **release**  :  this branch is updated with every patch or feature release;
-  updates are always "fast-forward" merges from *develop*
-* **develop**  :  this branch follows the ongoing development and
-  is updated with every merge commit of a pull request
-* **stable**   :  this branch is updated from the *release* branch with
-  every stable release version and also has selected bug fixes with every
-  update release when the *maintenance* branch is merged into it
-* **maintenance**  :  this branch collects back-ported bug fixes from the
-  *develop* branch to the *stable* branch. It is used to update *stable*
-  for update releases and it synchronized with *stable* at each stable release.
+* **develop** : this branch follows the ongoing development and is
+  updated with every merge commit of a pull request
+* **release** : this branch is updated with every "feature release";
+   updates are always "fast-forward" merges from *develop*
+* **maintenance** : this branch collects back-ported bug fixes from the
+  *develop* branch to the *stable* branch.  It is used to update the
+  *stable* branch for "stable update releases".
+* **stable** : this branch is updated from the *release* branch with
+  every "stable release" version and also has selected bug fixes with
+  every "update release" when the *maintenance* branch is merged into it
 
 To access the git repositories on your box, use the clone command to
 create a local copy of the LAMMPS repository with a command like:

doc/src/Library.rst

@@ -80,13 +80,15 @@ run LAMMPS in serial mode.
    :class: note
 
    If the LAMMPS executable encounters an error condition, it will abort
-   after printing an error message. For a library interface this is
-   usually not desirable.  Thus LAMMPS can be compiled to to :ref:`throw
-   a C++ exception <exceptions>` instead.  If enabled, the library
-   functions will catch those exceptions and return.  The error status
-   :cpp:func:`can be queried <lammps_has_error>` and an :cpp:func:`error
-   message retrieved <lammps_get_last_error_message>`.  We thus
-   recommend enabling C++ exceptions when using the library interface,
+   after printing an error message.  It does so by catching the
+   exceptions that LAMMPS could throw.  For a C library interface this
+   is usually not desirable since the calling code might lack the
+   ability to catch such exceptions.  Thus, the library functions will
+   catch those exceptions and return from the affected functions.  The
+   error status :cpp:func:`can be queried <lammps_has_error>` and an
+   :cpp:func:`error message retrieved <lammps_get_last_error_message>`.
+   This is, for example used by the :doc:`LAMMPS python module
+   <Python_module>` and then a suitable Python exception is thrown.
 
 .. admonition:: Using the C library interface as a plugin
    :class: note

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/Manual_version.rst

@@ -3,45 +3,25 @@ What does a LAMMPS version mean
 
 The LAMMPS "version" is the date when it was released, such as 1 May
 2014.  LAMMPS is updated continuously, and we aim to keep it working
-correctly and reliably at all times.  You can follow its development
-in a public `git repository on GitHub <https://github.com/lammps/lammps>`_.
-
-Modifications of the LAMMPS source code (like bug fixes, code refactors,
-updates to existing features, or addition of new features) are organized
-into pull requests.  Pull requests will be merged into the *develop*
-branch of the git repository after they pass automated testing and code
-review by the LAMMPS developers.  When a sufficient number of changes
-have accumulated *and* the *develop* branch version passes an extended
-set of automated tests, we release it as a *feature release*, which are
-currently made every 4 to 8 weeks.  The *release* branch of the git
-repository is updated with every such release.  A summary of the most
-important changes of the patch releases are on `this website page
-<https://www.lammps.org/bug.html>`_.  More detailed release notes are
-`available on GitHub <https://github.com/lammps/lammps/releases/>`_.
-
-Once or twice a year, we have a "stabilization period" where we apply
-only bug fixes and small, non-intrusive changes to the *develop*
-branch.  At the same time, the code is subjected to more detailed and
-thorough manual testing than the default automated testing.  Also,
-several variants of static code analysis are run to improve the overall
-code quality, consistency, and compliance with programming standards,
-best practices and style conventions.
-
-The release after such a stabilization period is called a *stable*
-version and both, the *release* and the *stable* branches are updated
-with it.  Between stable releases, we collect back-ported bug fixes and
-updates from the *develop* branch in the *maintenance* branch.  From the
-*maintenance* branch we make occasional update releases and update the
-*stable* branch accordingly.
+correctly and reliably at all times.  Also, several variants of static
+code analysis are run regularly to maintain or improve the overall code
+quality, consistency, and compliance with programming standards, best
+practices and style conventions.  You can follow its development in a
+public `git repository on GitHub <https://github.com/lammps/lammps>`_.
 
 Each version of LAMMPS contains all the documented *features* up to and
 including its version date.  For recently added features, we add markers
 to the documentation at which specific LAMMPS version a feature or
 keyword was added or significantly changed.
 
-The version date is printed to the screen and log file every time you run
-LAMMPS.  It is also in the file src/version.h and in the LAMMPS
-directory name created when you unpack a tarball.  And it is on the
+Identifying the Version
+^^^^^^^^^^^^^^^^^^^^^^^
+
+The version date is printed to the screen and log file every time you
+run LAMMPS.  There also is an indication, if a LAMMPS binary was
+compiled from version with modifications **after** a release.
+It is also visible in the file src/version.h and in the LAMMPS directory
+name created when you unpack a downloaded tarball.  And it is on the
 first page of the :doc:`manual <Manual>`.
 
 * If you browse the HTML pages of the online version of the LAMMPS
@@ -53,3 +33,56 @@ first page of the :doc:`manual <Manual>`.
 * If you browse the HTML pages included in your downloaded tarball, they
   describe the version you have, which may be older than the online
   version.
+
+LAMMPS releases, branches, and tags
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. figure:: JPG/lammps-releases.png
+   :figclass: align-center
+
+   Relations between releases, main branches, and tags in the LAMMPS git repository
+
+Development
+"""""""""""
+
+Modifications of the LAMMPS source code (like bug fixes, code
+refactoring, updates to existing features, or addition of new features)
+are organized into pull requests.  Pull requests will be merged into the
+*develop* branch of the git repository after they pass automated testing
+and code review by the LAMMPS developers.
+
+Feature Releases
+""""""""""""""""
+
+When a sufficient number of new features and updates have accumulated
+*and* the LAMMPS version on the *develop* branch passes an extended set
+of automated tests, we release it as a *feature release*, which are
+currently made every 4 to 8 weeks.  The *release* branch of the git
+repository is updated with every such *feature release* and a tag in the
+format ``patch_1May2014`` is added.  A summary of the most important
+changes of these releases for the current year are posted on `this
+website page <https://www.lammps.org/bug.html>`_.  More detailed release
+notes are `available on GitHub
+<https://github.com/lammps/lammps/releases/>`_.
+
+Stable Releases
+"""""""""""""""
+
+About once a year, we release a *stable release* version of LAMMPS.
+This is done after a "stabilization period" where we apply only bug
+fixes and small, non-intrusive changes to the *develop* branch but no
+new features.  At the same time, the code is subjected to more detailed
+and thorough manual testing than the default automated testing.
+After such a *stable release*, both the *release* and the *stable*
+branches are updated and two tags are applied, a ``patch_1May2014`` format
+and a ``stable_1May2014`` format tag.
+
+Stable Release Updates
+""""""""""""""""""""""
+
+Between *stable releases*, we collect bug fixes and updates back-ported
+from the *develop* branch in a branch called *maintenance*.  From the
+*maintenance* branch we make occasional *stable update releases* and
+update the *stable* branch accordingly.  The first update to the
+``stable_1May2014`` release would be tagged as
+``stable_1May2014_update1``.  These updates contain no new features.

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

@@ -2226,7 +2226,7 @@ and third order tensor from finite differences.
 
 **Install:**
 
-The PHONON package requires that also the :ref:`KSPACE <PKG-KSPACE>`
+The fix phonon command also requires that the :ref:`KSPACE <PKG-KSPACE>`
 package is installed.
 
 

doc/src/Python_error.rst

@@ -1,11 +1,11 @@
 Handling LAMMPS errors
 **********************
 
-The shared library is compiled with :ref:`C++ exception support
-<exceptions>` to provide a better error handling experience.  C++
-exceptions allow capturing errors on the C++ side and rethrowing them on
-the Python side.  This way LAMMPS errors can be handled through the
-Python exception handling mechanism.
+LAMMPS and the LAMMPS library are compiled with :ref:`C++ exception support
+<exceptions>` to provide a better error handling experience.  LAMMPS errors
+trigger throwing a C++ exception. These exceptions allow capturing errors on
+the C++ side and rethrowing them on the Python side.  This way LAMMPS errors
+can be handled through the Python exception handling mechanism.
 
 .. code-block:: python
 
@@ -15,9 +15,7 @@ Python exception handling mechanism.
 
    try:
       # LAMMPS will normally terminate itself and the running process if an error
-      # occurs. This would kill the Python interpreter. To avoid this, make sure to
-      # compile with LAMMPS_EXCEPTIONS enabled. This ensures the library API calls
-      # will not terminate the parent process. Instead, the library wrapper will
+      # occurs. This would kill the Python interpreter.  The library wrapper will
       # detect that an error has occured and throw a Python exception
 
       lmp.command('unknown')

doc/src/Python_install.rst

@@ -5,8 +5,7 @@ The LAMMPS Python module enables calling the :ref:`LAMMPS C library API
 <lammps_c_api>` from Python by dynamically loading functions in the
 LAMMPS shared library through the Python `ctypes <ctypes_>`_
 module.  Because of the dynamic loading, it is required that LAMMPS is
-compiled in :ref:`"shared" mode <exe>`.  It is also recommended to
-compile LAMMPS with :ref:`C++ exceptions <exceptions>` enabled.
+compiled in :ref:`"shared" mode <exe>`.
 
 Two components are necessary for Python to be able to invoke LAMMPS code:
 

doc/src/Run_output.rst

@@ -49,14 +49,17 @@ simulation.  An example set of statistics is shown here:
 ----------
 
 The first section provides a global loop timing summary. The *loop time*
-is the total wall-clock time for the simulation to run.  The
-*Performance* line is provided for convenience to help predict how long
-it will take to run a desired physical simulation and to have numbers
-useful for performance comparison between different simulation settings
-or system sizes.  The *CPU use* line provides the CPU utilization per
-MPI task; it should be close to 100% times the number of OpenMP threads
-(or 1 of not using OpenMP).  Lower numbers correspond to delays due to
-file I/O or insufficient thread utilization.
+is the total wall-clock time for the MD steps of the simulation run,
+excluding the time for initialization and setup (i.e. the parts that may
+be skipped with :doc:`run N pre no <run>`).  The *Performance* line is
+provided for convenience to help predict how long it will take to run a
+desired physical simulation and to have numbers useful for performance
+comparison between different simulation settings or system sizes.  The
+*CPU use* line provides the CPU utilization per MPI task; it should be
+close to 100% times the number of OpenMP threads (or 1 if not using
+OpenMP).  Lower numbers correspond to delays due to file I/O or
+insufficient thread utilization from parts of the code that have not
+been multi-threaded.
 
 ----------
 

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_lepton.rst

@@ -11,7 +11,16 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   angle_style lepton
+   angle_style style args
+
+* style = *lepton*
+* args = optional arguments
+
+.. parsed-literal::
+
+   args = *auto_offset* or *no_offset*
+     *auto_offset* = offset the potential energy so that the value at theta0 is 0.0 (default)
+     *no_offset* = do not offset the potential energy
 
 Examples
 """"""""
@@ -19,6 +28,7 @@ Examples
 .. code-block:: LAMMPS
 
    angle_style lepton
+   angle_style lepton no_offset
 
    angle_coeff  1  120.0  "k*theta^2; k=250.0"
    angle_coeff  2   90.0  "k2*theta^2 + k3*theta^3 + k4*theta^4; k2=300.0; k3=-100.0; k4=50.0"
@@ -41,6 +51,13 @@ 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:: 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
+*auto_offset*.  When using the keyword *no_offset* instead, the
+potential energy is not shifted.
+
 The `Lepton library <https://simtk.org/projects/lepton>`_, that the
 *lepton* angle style interfaces with, evaluates this expression string
 at run time to compute the pairwise energy.  It also creates an

doc/src/atom_style.rst

@@ -49,248 +49,221 @@ Examples
 Description
 """""""""""
 
-Define what style of atoms to use in a simulation.  This determines
-what attributes are associated with the atoms.  This 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.
+The *atom_style* command selects which per-atom attributes are
+associated with atoms in a LAMMPS simulation and thus stored and
+communicated with those atoms as well as read from and stored in data
+and restart files.  Different models (e.g. :doc:`pair styles
+<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
-   LAMMPS was built with a specific package, as listed below in the
-   Restrictions section.
+   Many of the atom styles discussed here are only enabled if LAMMPS was
+   built with a specific package, as listed below in the Restrictions
+   section.
 
-Once a style is assigned, it cannot be changed, so use a style general
-enough to encompass all attributes.  E.g. with style *bond*, angular
-terms cannot be used or added later to the model.  It is OK to use a
-style more general than needed, though it may be slightly inefficient.
+Once a style is selected and the simulation box defined, it cannot be
+changed but only augmented with the :doc:`fix property/atom
+<fix_property_atom>` command.  So one should select an atom style
+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,
-what quantities are communicated between processors to enable forces
-to be computed, and what quantities are listed in the data file read
-by the :doc:`read_data <read_data>` command.
+It is OK to use a style more general than needed, though it may be
+slightly inefficient because it will allocate and communicate
+additional unused data.
 
-These are the additional attributes of each style and the typical
-kinds of physical systems they are used to model.  All styles store
-coordinates, velocities, atom IDs and types.  See the
+Atom style attributes
+"""""""""""""""""""""
+
+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
-quantities.
+:doc:`set <set>` commands for details on how to set these various
+quantities.  More information about many of the styles is provided in
+the Additional Information section below.
 
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *amoeba*     | molecular + charge + 1/5 neighbors                  | AMOEBA/HIPPO polarized force fields  |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *angle*      | bonds and angles                                    | bead-spring polymers with stiffness  |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *atomic*     | only the default values                             | coarse-grain liquids, solids, metals |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *body*       | mass, inertia moments, quaternion, angular momentum | arbitrary bodies                     |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *bond*       | bonds                                               | bead-spring polymers                 |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *charge*     | charge                                              | atomic system with charges           |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *dielectric* | normx normy normz area/patch ed em epsilon curv     | system with surface polarization     |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *dipole*     | charge and dipole moment                            | system with dipolar particles        |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *dpd*        | internal temperature and internal energies          | DPD particles                        |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *edpd*       | temperature and heat capacity                       | eDPD particles                       |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *electron*   | charge and spin and eradius                         | electronic force field               |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *ellipsoid*  | shape, quaternion, angular momentum                 | aspherical particles                 |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *full*       | molecular + charge                                  | bio-molecules                        |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *line*       | end points, angular velocity                        | rigid bodies                         |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *mdpd*       | density                                             | mDPD particles                       |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *molecular*  | bonds, angles, dihedrals, impropers                 | uncharged molecules                  |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *oxdna*      | nucleotide polarity                                 | coarse-grained DNA and RNA models    |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *peri*       | mass, volume                                        | mesoscopic Peridynamic models        |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *smd*        | volume, kernel diameter, contact radius, mass       | solid and fluid SPH particles        |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *sph*        | rho, esph, cv                                       | SPH particles                        |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *sphere*     | diameter, mass, angular velocity                    | granular models                      |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *bpm/sphere* | diameter, mass, angular velocity, quaternion        | granular bonded particle models (BPM)|
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *spin*       | magnetic moment                                     | system with magnetic particles       |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *tdpd*       | chemical concentration                              | tDPD particles                       |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *template*   | template index, template atom                       | small molecules with fixed topology  |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *tri*        | corner points, angular momentum                     | rigid bodies                         |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im           | AWPMD                                |
-+--------------+-----------------------------------------------------+--------------------------------------+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Atom style
+     - Attributes
+     - Required package
+     - Applications
+   * - *amoeba*
+     - *full* + "1-5 special neighbor data"
+     - :ref:`AMOEBA <PKG-AMOEBA>`
+     - AMOEBA/HIPPO force fields
+   * - *angle*
+     - *bond* + "angle data"
+     - :ref:`MOLECULE <PKG-MOLECULE>`
+     - bead-spring polymers with stiffness
+   * - *atomic*
+     - tag, type, x, v, f, image, mask
+     -
+     - atomic liquids, solids, metals
+   * - *body*
+     - *atomic* + radius, rmass, angmom, torque, body
+     - :ref:`BODY <PKG-BODY>`
+     - arbitrary bodies, see :doc:`body howto <Howto_body>`
+   * - *bond*
+     - *atomic* + molecule, nspecial, special + "bond data"
+     - :ref:`MOLECULE <PKG-MOLECULE>`
+     - bead-spring polymers
+   * - *bpm/sphere*
+     - *bond* + radius, rmass, omega, torque, quat
+     - :ref:`BPM <PKG-BPM>`
+     - granular bonded particle models, see :doc:`BPM howto <Howto_bpm>`
+   * - *charge*
+     - *atomic* + q
+     -
+     - atomic systems with charges
+   * - *dielectric*
+     - *full* + mu, area, ed, em, epsilon, curvature, q_scaled
+     - :ref:`DIELECTRIC <PKG-DIELECTRIC>`
+     - systems with surface polarization
+   * - *dipole*
+     - *charge* + mu
+     - :ref:`DIPOLE <PKG-DIPOLE>`
+     - atomic systems with charges and point dipoles
+   * - *dpd*
+     - *atomic* + rho + "reactive DPD data"
+     - :ref:`DPD-REACT <PKG-DPD-REACT>`
+     - reactive DPD
+   * - *edpd*
+     - *atomic* + "eDPD data"
+     - :ref:`DPD-MESO <PKG-DPD-MESO>`
+     - Energy conservative DPD (eDPD)
+   * - *electron*
+     - *charge* + espin, eradius, ervel, erforce
+     - :ref:`EFF <PKG-EFF>`
+     - Electron force field systems
+   * - *ellipsoid*
+     - *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
+   * - *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
-   atom styles that do not have them via the :doc:`fix property/atom
-   <fix_property_atom>` command.  This command also allows new custom
-   attributes consisting of extra integer or floating-point values to
-   be added to atoms.  See the :doc:`fix property/atom
-   <fix_property_atom>` page for examples of cases where this is
-   useful and details on how to initialize, access, and output the
-   custom values.
+   It is possible to add some attributes, such as a molecule ID and
+   charge, to atom styles that do not have them built in using the
+   :doc:`fix property/atom <fix_property_atom>` command.  This command
+   also allows new custom-named attributes consisting of extra integer
+   or floating-point values or vectors to be added to atoms.  See the
+   :doc:`fix property/atom <fix_property_atom>` page for examples of
+   cases where this is useful and details on how to initialize,
+   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
-per-type basis, using the :doc:`mass <mass>` command, The finite-size
-particle styles assign mass to individual particles on a per-particle
-basis.
+Particle size and mass
+""""""""""""""""""""""
 
-For the *sphere* and *bpm/sphere* styles, the particles are spheres
-and each stores a per-particle diameter and mass.  If the diameter >
-0.0, the particle is a finite-size sphere.  If the diameter = 0.0, it
-is a point particle.  Note that by use of 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 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.
+All of the atom styles define point particles unless they (1) define
+finite-size spherical particles via the *radius* attribute, or (2)
+define finite-size aspherical particles (e.g. the *body*, *ellipsoid*,
+*line*, and *tri* styles).  Most of these styles can also be used with
+mixtures of point and finite-size particles.
 
-For the *ellipsoid* style, the particles are ellipsoids and each
-stores a flag which indicates whether it is a finite-size ellipsoid or
-a point particle.  If it is an ellipsoid, it also stores a shape
-vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
-with its orientation.
+Note that the *radius* property may need to be provided as a
+*diameter* (e.g. in :doc:`molecule files <molecule>` or :doc:`data
+files <read_data>`).  See the :doc:`Howto spherical <Howto_spherical>`
+page for an overview of using finite-size spherical and aspherical
+particle models with LAMMPS.
 
-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 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.
+Unless an atom style defines the per-atom *rmass* attribute, particle
+masses are defined on a per-type basis, using the :doc:`mass <mass>`
+command.  This means each particle's mass is indexed by its atom
+*type*.
 
-For the *dipole* style, a point dipole 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 atom_style hybrid sphere dipole, which will assign both a
-diameter and dipole moment to each particle.
+A few styles define the per-atom *rmass* attribute which can also be
+added using the :doc:`fix property/atom <fix_property_atom>` command.
+In this case each particle stores its own mass.  Atom styles that have
+a per-atom rmass may define it indirectly through setting particle
+diameter and density on a per-particle basis.  If both per-type mass
+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
-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.
+Additional information about specific atom styles
+"""""""""""""""""""""""""""""""""""""""""""""""""
 
 For the *body* style, the particles are arbitrary bodies with internal
 attributes defined by the "style" of the bodies, which is specified by
@@ -309,6 +282,148 @@ 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 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 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.
@@ -326,11 +441,12 @@ 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
-styles; see the :doc:`Modify <Modify>` doc page.
+LAMMPS can be extended with new atom styles as well as new body styles;
+see the corresponding manual page on :doc:`modifying & extending LAMMPS
+<Modify_atom>`.
 
 ----------
 
@@ -346,54 +462,20 @@ 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.
-
-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>`.
+<Build_package>` page for more info.  The table above lists which package
+is required for individual atom styles.
 
 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
-default argument is 0.
+The default atom style is *atomic*.  If atom_style *sphere* or
+*bpm/sphere* is used, its default argument is 0.
 
 ----------
 

doc/src/bond_bpm_rotational.rst

@@ -147,8 +147,8 @@ By default, pair forces are not calculated between bonded particles.
 Pair forces can alternatively be overlaid on top of bond forces by setting
 the *overlay/pair* keyword to *yes*. These settings require specific
 :doc:`special_bonds <special_bonds>` settings described in the
-restrictions.  Further details can be found in the :doc:`how to
-<Howto_bpm>` page on BPMs.
+restrictions.  Further details can be found in the :doc:`how to <Howto_bpm>`
+page on BPMs.
 
 .. versionadded:: 28Mar2023
 

doc/src/bond_bpm_spring.rst

@@ -113,8 +113,8 @@ By default, pair forces are not calculated between bonded particles.
 Pair forces can alternatively be overlaid on top of bond forces by setting
 the *overlay/pair* keyword to *yes*. These settings require specific
 :doc:`special_bonds <special_bonds>` settings described in the
-restrictions.  Further details can be found in the :doc:`how to
-<Howto_bpm>` page on BPMs.
+restrictions.  Further details can be found in the :doc:`how to <Howto_bpm>`
+page on BPMs.
 
 .. versionadded:: 28Mar2023
 

doc/src/bond_lepton.rst

@@ -11,7 +11,16 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   bond_style lepton
+   bond_style style args
+
+* style = *lepton*
+* args = optional arguments
+
+.. parsed-literal::
+
+   args = *auto_offset* or *no_offset*
+     *auto_offset* = offset the potential energy so that the value at r0 is 0.0 (default)
+     *no_offset* = do not offset the potential energy
 
 Examples
 """"""""
@@ -19,6 +28,7 @@ Examples
 .. code-block:: LAMMPS
 
    bond_style lepton
+   bond_style lepton no_offset
 
    bond_coeff  1  1.5 "k*r^2; k=250.0"
    bond_coeff  2  1.1 "k2*r^2 + k3*r^3 + k4*r^4; k2=300.0; k3=-100.0; k4=50.0"
@@ -40,6 +50,13 @@ 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:: 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
+*auto_offset*.  When using the keyword *no_offset* instead, the
+potential energy is not shifted.
+
 The `Lepton library <https://simtk.org/projects/lepton>`_, that the
 *lepton* bond style interfaces with, evaluates this expression string at
 run time to compute the pairwise energy.  It also creates an analytical

doc/src/compute.rst

@@ -264,6 +264,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`nbond/atom <compute_nbond_atom>` - calculates number of bonds per atom
 * :doc:`omega/chunk <compute_omega_chunk>` - angular velocity for each chunk
 * :doc:`orientorder/atom <compute_orientorder_atom>` - Steinhardt bond orientational order parameters Ql
+* :doc:`pace <compute_pace>` - atomic cluster expansion descriptors and related quantities
 * :doc:`pair <compute_pair>` - values computed by a pair style
 * :doc:`pair/local <compute_pair_local>` - distance/energy/force of each pairwise interaction
 * :doc:`pe <compute_pe>` - potential energy
@@ -279,12 +280,15 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`property/grid <compute_property_grid>` - convert per-grid attributes to per-grid vectors/arrays
 * :doc:`property/local <compute_property_local>` - convert local attributes to local vectors/arrays
 * :doc:`ptm/atom <compute_ptm_atom>` - determines the local lattice structure based on the Polyhedral Template Matching method
+* :doc:`rattlers/atom <compute_rattlers_atom>` - identify under-coordinated rattler atoms
 * :doc:`rdf <compute_rdf>` - radial distribution function :math:`g(r)` histogram of group of atoms
+* :doc:`reaxff/atom <compute_reaxff_atom>` - extract ReaxFF bond information
 * :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
 * :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
 * :doc:`reduce/region <compute_reduce>` - same as compute reduce, within a region
 * :doc:`rigid/local <compute_rigid_local>` - extract rigid body attributes
 * :doc:`saed <compute_saed>` - electron diffraction intensity on a mesh of reciprocal lattice nodes
+* :doc:`slcsa/atom <compute_slcsa_atom>` - perform Supervised Learning Crystal Structure Analysis (SL-CSA)
 * :doc:`slice <compute_slice>` - extract values from global vector or array
 * :doc:`smd/contact/radius <compute_smd_contact_radius>` - contact radius for Smooth Mach Dynamics
 * :doc:`smd/damage <compute_smd_damage>` - damage status of SPH particles in Smooth Mach Dynamics

doc/src/compute_contact_atom.rst

@@ -36,6 +36,9 @@ sum of the radii of the two particles.
 The value of the contact number will be 0.0 for atoms not in the
 specified compute group.
 
+The optional *group2-ID* argument allows to specify from which group atoms
+contribute to the coordination number. Default setting is group 'all'.
+
 Output info
 """""""""""
 
@@ -47,9 +50,6 @@ overview of LAMMPS output options.
 The per-atom vector values will be a number :math:`\ge 0.0`, as explained
 above.
 
-The optional *group2-ID* argument allows to specify from which group atoms
-contribute to the coordination number. Default setting is group 'all.'
-
 Restrictions
 """"""""""""
 
@@ -69,6 +69,3 @@ Default
 """""""
 
 *group2-ID* = all
-
-
-none

doc/src/compute_pace.rst

@@ -0,0 +1,253 @@
+.. index:: compute pace
+
+compute pace command
+========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   compute ID group-ID pace ace_potential_filename ... keyword values ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* pace = style name of this compute command
+* ace_potential_filename = file name (in the .yace or .ace format from :doc:`pace pair_style <pair_pace>`) including ACE hyper-parameters, bonds, and generalized coupling coefficients
+* keyword = *bikflag* or *dgradflag*
+
+  .. parsed-literal::
+
+       *bikflag* value = *0* or *1*
+          *0* = descriptors are summed over atoms of each type
+          *1* = descriptors are listed separately for each atom
+       *dgradflag* value = *0* or *1*
+          *0* = descriptor gradients are summed over atoms of each type
+          *1* = descriptor gradients are listed separately for each atom pair
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute pace all pace coupling_coefficients.yace
+   compute pace all pace coupling_coefficients.yace 0 1
+   compute pace all pace coupling_coefficients.yace 1 1
+
+Description
+"""""""""""
+
+.. versionadded:: 7Feb2024
+
+This compute calculates a set of quantities related to the atomic
+cluster expansion (ACE) descriptors of the atoms in a group.  ACE
+descriptors are highly general atomic descriptors, encoding the radial
+and angular distribution of neighbor atoms, up to arbitrary bond order
+(rank).  The detailed mathematical definition is given in the paper by
+:ref:`(Drautz) <Drautz19>`.  These descriptors are used in the
+:doc:`pace pair_style <pair_pace>`.  Quantities obtained from `compute
+pace` are related to those used in :doc:`pace pair_style <pair_pace>` to
+evaluate atomic energies, forces, and stresses for linear ACE models.
+
+For example, the energy for a linear ACE model is calculated as:
+:math:`E=\sum_i^{N\_atoms} \sum_{\boldsymbol{\nu}} c_{\boldsymbol{\nu}}
+B_{i,\boldsymbol{\boldsymbol{\nu}}}`.  The ACE descriptors for atom `i`
+:math:`B_{i,\boldsymbol{\nu}}`, and :math:`c_{\nu}` are linear model
+parameters.  The detailed definition and indexing convention for ACE
+descriptors is given in :ref:`(Drautz) <Drautz19>`.  In short, body
+order :math:`N`, angular character, radial character, and chemical
+elements in the *N-body* descriptor are encoded by :math:`\nu`.  In the
+:doc:`pace pair_style <pair_pace>`, the linear model parameters and the
+ACE descriptors are combined for efficient evaluation of energies and
+forces.  The details and benefits of this efficient implementation are
+given in :ref:`(Lysogorskiy) <Lysogorskiy21>`, but the combined
+descriptors and linear model parameters for the purposes of `compute
+pace` may be expressed in terms of the ACE descriptors mentioned above.
+
+:math:`c_{\boldsymbol{\nu}} B_{i,\boldsymbol{\nu}}= \sum_{\boldsymbol{\nu}' \in \boldsymbol{\nu} } \big[ c_{\boldsymbol{\nu}} C(\boldsymbol{\nu}') \big] A_{i,\boldsymbol{\nu}'}`
+
+where the bracketed terms on the right-hand side are the combined functions
+with linear model parameters typically provided in the `<name>.yace` potential
+file for `pace pair_style`. When these bracketed terms are multiplied by the
+products of the atomic base from :ref:`(Drautz) <Drautz19>`,
+:math:`A_{i,\boldsymbol{\nu'}}`, the ACE descriptors are recovered but they
+are also scaled by linear model parameters. The generalized coupling coefficients,
+written in short-hand here as :math:`C(\boldsymbol{\nu}')`, are the generalized
+Clebsch-Gordan or generalized Wigner symbols. It may be desirable to reverse the
+combination of these descriptors and the linear model parameters so that the
+ACE descriptors themselves may be used. The ACE descriptors and their gradients
+are often used when training ACE models, performing custom data analysis,
+generalizing ACE model forms, and other tasks that involve direct computation of
+descriptors. The key utility of `compute pace` is that it can compute the ACE
+descriptors and gradients so that these tasks can be performed during a LAMMPS
+simulation or so that LAMMPS can be used as a driver for tasks like ACE model
+parameterization. To see how this command can be used within a Python workflow
+to train ACE potentials, see the examples in
+`FitSNAP <https://github.com/FitSNAP/FitSNAP>`_. Examples on using outputs from
+this compute to construct general ACE potential forms are demonstrated in
+:ref:`(Goff) <Goff23>`. The various keywords and inputs to `compute pace`
+determine what ACE descriptors and related quantities are returned in a compute
+array.
+
+The coefficient file, `<name>.yace`, ultimately defines the number of ACE
+descriptors to be computed, their maximum body-order, the degree of angular
+character they have, the degree of radial character they have, the chemical
+character (which element-element interactions are encoded by descriptors),
+and other hyper-parameters defined in :ref:`(Drautz) <Drautz19>`. These may
+be modeled after the potential files in :doc:`pace pair_style <pair_pace>`,
+and have the same format. Details on how to generate the coefficient files
+to train ACE models may be found in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_.
+
+The keyword *bikflag* determines whether or not to list the descriptors of
+each atom separately, or sum them together and list in a single row. If
+*bikflag* is set to *0* then a single descriptor row is used, which contains
+the per-atom ACE descriptors :math:`B_{i,\boldsymbol{\nu}}` summed over all
+atoms *i* to produce :math:`B_{\boldsymbol{\nu}}`. If *bikflag* is set to
+*1* this is replaced by a separate per-atom ACE descriptor row for each atom.
+In this case, the entries in the final column for these rows are set to zero.
+
+The keyword *dgradflag* determines whether to sum atom gradients or list
+them separately. If *dgradflag* is set to 0, the ACE
+descriptor gradients w.r.t. atom *j* are summed over all atoms *i'*
+of, which may be useful when training linear ACE models on atomic forces.
+If *dgradflag* is set to 1, gradients are listed separately for each pair of atoms.
+Each row corresponds
+to a single term :math:`\frac{\partial {B_{i,\boldsymbol{\nu}}}}{\partial {r}^a_j}`
+where :math:`{r}^a_j` is the *a-th* position coordinate of the atom with global
+index *j*. This also changes the number of columns to be equal to the number of
+ACE descriptors, with 3 additional columns representing the indices :math:`i`,
+:math:`j`, and :math:`a`, as explained more in the Output info section below.
+The option *dgradflag=1* requires that *bikflag=1*.
+
+.. note::
+
+    It is noted here that in contrast to :doc:`pace pair_style <pair_pace>`,
+    the *.yace* file for `compute pace` typically should not contain linear
+    parameters for an ACE potential. If :math:`c_{\nu}` are included,
+    the value of the descriptor will not be returned in the `compute` array,
+    but instead, the energy contribution from that descriptor will be returned.
+    Do not do this unless it is the desired behavior.
+    *In short, you should not plug in a '.yace' for a pace potential into this
+    compute to evaluate descriptors.*
+
+.. note::
+
+    *Generalized Clebsch-Gordan or Generalized Wigner symbols (with appropriate
+    factors) must be used to evaluate ACE descriptors with this compute.* There
+    are multiple ways to define the generalized coupling coefficients. Because
+    of this, this compute will not revert your potential file to a coupling
+    coefficient file. Instead this compute allows the user to supply coupling
+    coefficients that follow any convention.
+
+.. note::
+
+   Using *dgradflag* = 1 produces a global array with :math:`N + 3N^2 + 1` rows
+   which becomes expensive for systems with more than 1000 atoms.
+
+.. note::
+
+   If you have a bonded system, then the settings of :doc:`special_bonds
+   <special_bonds>` command can remove pairwise interactions between
+   atoms in the same bond, angle, or dihedral.  This is the default
+   setting for the :doc:`special_bonds <special_bonds>` command, and
+   means those pairwise interactions do not appear in the neighbor list.
+   Because this fix uses the neighbor list, it also means those pairs
+   will not be included in the calculation.  One way to get around this,
+   is to write a dump file, and use the :doc:`rerun <rerun>` command to
+   compute the ACE descriptors for snapshots in the dump file.
+   The rerun script can use a :doc:`special_bonds <special_bonds>`
+   command that includes all pairs in the neighbor list.
+
+----------
+
+Output info
+"""""""""""
+
+Compute *pace* evaluates a global array.  The columns are arranged into
+*ntypes* blocks, listed in order of atom type *I*\ . Each block contains
+one column for each ACE descriptor, the same as for compute
+*sna/atom*\ in :doc:`compute snap <compute_sna_atom>`. A final column contains the corresponding energy, force
+component on an atom, or virial stress component. The rows of the array
+appear in the following order:
+
+* 1 row: *pace* average descriptor values for all atoms of type *I*
+* 3\*\ *n* force rows: quantities, with derivatives w.r.t. x, y, and z coordinate of atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID and run up to the total number of atoms, *n*.
+* 6 rows: *virial* quantities summed for all atoms of type *I*
+
+For example, if :math:`\# \; B_{i, \boldsymbol{\nu}}` =30 and ntypes=1, the number of columns in the
+The number of columns in the global array generated by *pace* are 31, and
+931, respectively, while the number of rows is 1+3\*\ *n*\ +6, where *n*
+is the total number of atoms.
+
+If the *bik* keyword is set to 1, the structure of the pace array is expanded.
+The first :math:`N` rows of the pace array
+correspond to :math:`\# \; B_{i,\boldsymbol{\nu}}` instead of a single row summed over atoms :math:`i`.
+In this case, the entries in the final column for these rows
+are set to zero. Also, each row contains only non-zero entries for the
+columns corresponding to the type of that atom. This is not true in the case
+of *dgradflag* keyword = 1 (see below).
+
+If the *dgradflag* keyword is set to 1, this changes the structure of the
+global array completely.
+Here the per-atom quantities are replaced with rows corresponding to
+descriptor gradient components on single atoms:
+
+.. math::
+
+  \frac{\partial {B_{i,\boldsymbol{\nu}}  }}{\partial {r}^a_j}
+
+where :math:`{r}^a_j` is the *a-th* position coordinate of the atom with global
+index *j*. The rows are
+organized in chunks, where each chunk corresponds to an atom with global index
+:math:`j`. The rows in an atom :math:`j` chunk correspond to
+atoms with global index :math:`i`. The total number of rows for
+these descriptor gradients is therefore :math:`3N^2`.
+The number of columns is equal to the number of ACE descriptors,
+plus 3 additional left-most columns representing the global atom indices
+:math:`i`, :math:`j`,
+and Cartesian direction :math:`a`  (0, 1, 2, for x, y, z).
+The first 3 columns of the first :math:`N` rows belong to the reference
+potential force components. The remaining K columns contain the
+:math:`B_{i,\boldsymbol{\nu}}` per-atom descriptors corresponding to the non-zero entries
+obtained when *bikflag* = 1.
+The first column of the last row, after the first
+:math:`N + 3N^2` rows, contains the reference potential
+energy. The virial components are not used with this option. The total number of
+rows is therefore :math:`N + 3N^2 + 1` and the number of columns is :math:`K + 3`.
+
+These values can be accessed by any command that uses global values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
+page for an overview of LAMMPS output options.
+
+Restrictions
+""""""""""""
+
+These computes are part of the ML-PACE package.  They are only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style pace <pair_pace>`
+:doc:`pair_style snap <pair_snap>`
+:doc:`compute snap <compute_sna_atom>`
+
+Default
+"""""""
+
+The optional keyword defaults are *bikflag* = 0,
+*dgradflag* = 0
+
+----------
+
+.. _Drautz19:
+
+**(Drautz)** Drautz, Phys Rev B, 99, 014104 (2019).
+
+.. _Lysogorskiy21:
+
+**(Lysogorskiy)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
+
+.. _Goff23:
+
+**(Goff)** Goff, Zhang, Negre, Rohskopf, Niklasson, Journal of Chemical Theory and Computation 19, no. 13 (2023).

doc/src/compute_property_atom.rst

@@ -128,9 +128,9 @@ Attributes *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
 per-atom integer and floating-point vectors or arrays that have been
 added via the :doc:`fix property/atom <fix_property_atom>` command.
 When that command is used specific names are given to each attribute
-which are the "name" portion of these attributes.  For arrays *i2_name*
-and *d2_name*, the column of the array must also be included following
-the name in brackets (e.g., d2_xyz[2] or i2_mySpin[3]).
+which are the "name" portion of these attributes.  For arrays
+*i2_name* and *d2_name*, the column of the array must also be included
+following the name in brackets (e.g., d2_xyz[2] or i2_mySpin[3]).
 
 The additional quantities only accessible via this command, and not
 directly via the :doc:`dump custom <dump>` command, are as follows.

doc/src/compute_rattlers_atom.rst

@@ -0,0 +1,92 @@
+.. index:: compute rattlers/atom
+
+compute rattlers/atom command
+=============================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   compute ID group-ID rattlers/atom cutoff zmin ntries
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* rattlers/atom = style name of this compute command
+* cutoff = *type* or *radius*
+
+  .. parsed-literal::
+
+       *type* = cutoffs determined based on atom types
+       *radius* = cutoffs determined based on atom diameters (atom style sphere)
+
+* zmin = minimum coordination for a non-rattler atom
+* ntries = maximum number of iterations to remove rattlers
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute 1 all rattlers/atom type 4 10
+
+Description
+"""""""""""
+
+.. 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
+do not have the required number of contacts to constrain their translational
+degrees of freedom. Such atoms are not considered rigid and can often freely
+rattle around in the system. This compute identifies rattlers which can be
+helpful for excluding them from analysis or providing extra damping forces
+to accelerate relaxation processes.
+
+Rattlers are identified using an interactive approach. The coordination
+number of all atoms is first calculated.  The *type* and *radius* settings
+are used to select whether interaction cutoffs are determined by atom
+types or by the sum of atomic radii (atom style sphere), respectively.
+Rattlers are then identified as atoms with a coordination number less
+than *zmin* and are removed from consideration. Atomic coordination
+numbers are then recalculated, excluding previously identified rattlers,
+to identify a new set of rattlers. This process is iterated up to a maximum
+of *ntries* or until no new rattlers are identified and the remaining
+atoms form a stable network of contacts.
+
+In dense homogeneous systems where the average atom coordination number
+is expected to be larger than *zmin*, this process usually only takes a few
+iterations and a value of *ntries* around ten may be sufficient. In systems
+with significant heterogeneity or average coordination numbers less than
+*zmin*, an appropriate value of *ntries* depends heavily on the specific
+system. For instance, a linear chain of N rattler atoms with a *zmin* of 2
+would take N/2 iterations to identify that all the atoms are rattlers.
+
+Output info
+"""""""""""
+
+This compute calculates a per-atom vector and a global scalar. The vector
+designates which atoms are rattlers, indicated by a value 1. Non-rattlers
+have a value of 0. The global scalar returns the total number of rattlers
+in the system. See the :doc:`Howto output <Howto_output>` page for an
+overview of LAMMPS output options.
+
+Restrictions
+""""""""""""
+
+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.
+
+The *radius* cutoff option requires that atoms store a radius as defined by the
+:doc:`atom_style sphere <atom_style>` or similar commands.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute coord/atom <compute_coord_atom>`
+:doc:`compute contact/atom <compute_contact_atom>`
+
+Default
+"""""""
+
+none

doc/src/compute_reaxff_atom.rst

@@ -0,0 +1,97 @@
+.. index:: compute reaxff/atom
+.. index:: compute reaxff/atom/kk
+
+compute reaxff/atom command
+===========================
+
+Accelerator Variants: *reaxff/atom/kk*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   compute ID group-ID reaxff/atom attribute args ... keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* reaxff/atom = name of this compute command
+* attribute = *pair*
+
+  .. parsed-literal::
+
+       *pair* args = nsub
+         nsub = *n*-instance of a sub-style, if a pair style is used multiple times in a hybrid style
+
+* keyword = *bonds*
+
+  .. parsed-literal::
+
+       *bonds* value = *no* or *yes*
+         *no* = ignore list of local bonds
+         *yes* = include list of local bonds
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute 1 all reaxff/atom bonds yes
+
+Description
+"""""""""""
+
+.. versionadded:: 7Feb2024
+
+Define a computation that extracts bond information computed by the ReaxFF
+potential specified by :doc:`pair_style reaxff <pair_reaxff>`.
+
+By default, it produces per-atom data that includes the following columns:
+
+* abo = atom bond order (sum of all bonds)
+* nlp = number of lone pairs
+* nb = number of bonds
+
+Bonds will only be included if its atoms are in the group.
+
+In addition, if ``bonds`` is set to ``yes``, the compute will also produce a
+local array of all bonds on the current processor whose atoms are in the group.
+The columns of each entry of this local array are:
+
+* id_i = atom i id of bond
+* id_j = atom j id of bond
+* bo = bond order of bond
+
+Output info
+"""""""""""
+
+This compute calculates a per-atom array and local array depending on the
+number of keywords. The number of rows in the local array is the number of
+bonds as described above. Both per-atom and local array have 3 columns.
+
+The arrays can be accessed by any command that uses local and per-atom values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` page for
+an overview of LAMMPS output options.
+
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
+Restrictions
+""""""""""""
+
+The compute reaxff/atom command requires that the :doc:`pair_style reaxff
+<pair_reaxff>` is invoked.  This fix is part of the REAXFF package.  It is only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style reaxff <pair_reaxff>`
+
+Default
+"""""""
+
+The option defaults are *bonds* = *no*.

doc/src/compute_saed.rst

@@ -68,7 +68,7 @@ reciprocal lattice nodes. The mesh spacing is defined either (a)  by
 the entire simulation domain or (b) manually using selected values as
 shown in the 2D diagram below.
 
-.. image:: img/saed_mesh.jpg
+.. image:: img/saed_mesh.png
    :scale: 75%
    :align: center
 

doc/src/compute_slcsa_atom.rst

@@ -0,0 +1,162 @@
+.. index:: compute slcsa/atom
+
+compute slcsa/atom command
+============================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   compute ID group-ID slcsa/atom twojmax nclasses db_mean_descriptor_file lda_file lr_decision_file lr_bias_file maha_file value
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* slcsa/atom = style name of this compute command
+* twojmax = band limit for bispectrum components (non-negative integer)
+* nclasses = number of crystal structures used in the database for the classifier SL-CSA
+* db_mean_descriptor_file = file name of file containing the database mean descriptor
+* lda_file = file name of file containing the linear discriminant analysis matrix for dimension reduction
+* lr_decision_file = file name of file containing the scaling matrix for logistic regression classification
+* lr_bias_file = file name of file containing the bias vector for logistic regression classification
+* maha_file = file name of file containing for each crystal structure: the Mahalanobis distance threshold for sanity check purposes, the average reduced descriptor and the inverse of the corresponding covariance matrix
+* c_ID[*] = compute ID of previously required *compute sna/atom* command
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute b1 all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.3
+   compute b2 all slcsa/atom 8 4 mean_descriptors.dat lda_scalings.dat lr_decision.dat lr_bias.dat maha_thresholds.dat c_b1[*]
+
+Description
+"""""""""""
+
+.. versionadded:: 7Feb2024
+
+Define a computation that performs the Supervised Learning Crystal
+Structure Analysis (SL-CSA) from :ref:`(Lafourcade) <Lafourcade2023_1>`
+for each atom in the group. The SL-CSA tool takes as an input a per-atom
+descriptor (bispectrum) that is computed through the *compute sna/atom*
+command and then proceeds to a dimension reduction step followed by a
+logistic regression in order to assign a probable crystal structure to
+each atom in the group. The SL-CSA tool is pre-trained on a database
+containing :math:`C` distinct crystal structures from which a crystal
+structure classifier is derived and a tutorial to build such a tool is
+available at `SL-CSA <https://github.com/lafourcadep/SL-CSA>`_.
+
+The first step of the SL-CSA tool consists in performing a dimension
+reduction of the per-atom descriptor :math:`\mathbf{B}^i \in
+\mathbb{R}^{D}` through the Linear Discriminant Analysis (LDA) method,
+leading to a new projected descriptor
+:math:`\mathbf{x}^i=\mathrm{P}_\mathrm{LDA}(\mathbf{B}^i):\mathbb{R}^D
+\rightarrow \mathbb{R}^{d=C-1}`:
+
+.. math::
+
+   \mathbf{x}^i = \mathbf{C}^T_\mathrm{LDA} \cdot (\mathbf{B}^i - \mu^\mathbf{B}_\mathrm{db})
+
+where :math:`\mathbf{C}^T_\mathrm{LDA} \in \mathbb{R}^{D \times d}` is
+the reduction coefficients matrix of the LDA model read in file
+*lda_file*, :math:`\mathbf{B}^i \in \mathbb{R}^{D}` is the bispectrum of
+atom :math:`i` and :math:`\mu^\mathbf{B}_\mathrm{db} \in \mathbb{R}^{D}`
+is the average descriptor of the entire database. The latter is computed
+from the average descriptors of each crystal structure read from the
+file *mean_descriptors_file*.
+
+The new projected descriptor with dimension :math:`d=C-1` allows for a
+good separation of different crystal structures fingerprints in the
+latent space.
+
+Once the dimension reduction step is performed by means of LDA, the new
+descriptor :math:`\mathbf{x}^i \in \mathbb{R}^{d=C-1}` is taken as an
+input for performing a multinomial logistic regression (LR) which
+provides a score vector
+:math:`\mathbf{s}^i=\mathrm{P}_\mathrm{LR}(\mathbf{x}^i):\mathbb{R}^d
+\rightarrow \mathbb{R}^C` defined as:
+
+.. math::
+
+   \mathbf{s}^i = \mathbf{b}_\mathrm{LR} + \mathbf{D}_\mathrm{LR} \cdot {\mathbf{x}^i}^T
+
+with :math:`\mathbf{b}_\mathrm{LR} \in \mathbb{R}^C` and
+:math:`\mathbf{D}_\mathrm{LR} \in \mathbb{R}^{C \times d}` the bias
+vector and decision matrix of the LR model after training both read in
+files *lr_fil1* and *lr_file2* respectively.
+
+Finally, a probability vector
+:math:`\mathbf{p}^i=\mathrm{P}_\mathrm{LR}(\mathbf{x}^i):\mathbb{R}^d
+\rightarrow \mathbb{R}^C` is defined as:
+
+.. math::
+
+   \mathbf{p}^i = \frac{\mathrm{exp}(\mathbf{s}^i)}{\sum\limits_{j} \mathrm{exp}(s^i_j) }
+
+from which the crystal structure assigned to each atom with descriptor
+:math:`\mathbf{B}^i` and projected descriptor :math:`\mathbf{x}^i` is
+computed as the *argmax* of the probability vector
+:math:`\mathbf{p}^i`. Since the logistic regression step systematically
+attributes a crystal structure to each atom, a sanity check is needed to
+avoid misclassification. To this end, a per-atom Mahalanobis distance to
+each crystal structure *CS* present in the database is computed:
+
+.. math::
+
+   d_\mathrm{Mahalanobis}^{i \rightarrow \mathrm{CS}} = \sqrt{(\mathbf{x}^i - \mathbf{\mu}^\mathbf{x}_\mathrm{CS})^\mathrm{T} \cdot \mathbf{\Sigma}^{-1}_\mathrm{CS} \cdot (\mathbf{x}^i - \mathbf{\mu}^\mathbf{x}_\mathrm{CS}) }
+
+where :math:`\mathbf{\mu}^\mathbf{x}_\mathrm{CS} \in \mathbb{R}^{d}` is
+the average projected descriptor of crystal structure *CS* in the
+database and where :math:`\mathbf{\Sigma}_\mathrm{CS} \in \mathbb{R}^{d
+\times d}` is the corresponding covariance matrix. Finally, if the
+Mahalanobis distance to crystal structure *CS* for atom *i* is greater
+than the pre-determined threshold, no crystal structure is assigned to
+atom *i*. The Mahalanobis distance thresholds are read in file
+*maha_file* while the covariance matrices are read in file
+*covmat_file*.
+
+The `SL-CSA <https://github.com/lafourcadep/SL-CSA>`_ framework provides
+an automatic computation of the different matrices and thresholds
+required for a proper classification and writes down all the required
+files for calling the *compute slcsa/atom* command.
+
+The *compute slcsa/atom* command requires that the :doc:`compute
+sna/atom <compute_sna_atom>` command is called before as it takes the
+resulting per-atom bispectrum as an input. In addition, it is crucial
+that the value *twojmax* is set to the same value of the value *twojmax*
+used in the *compute sna/atom* command, as well as that the value
+*nclasses* is set to the number of crystal structures used in the
+database to train the SL-CSA tool.
+
+Output info
+"""""""""""
+
+By default, this compute computes the Mahalanobis distances to the
+different crystal structures present in the database in addition to
+assigning a crystal structure for each atom as a per-atom vector, which
+can be accessed by any command that uses per-atom values from a compute
+as input.  See the :doc:`Howto output <Howto_output>` page for an
+overview of LAMMPS output options.
+
+Restrictions
+""""""""""""
+
+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.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute sna/atom <compute_sna_atom>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Lafourcade2023_1:
+
+**(Lafourcade)** Lafourcade, Maillet, Denoual, Duval, Allera, Goryaeva, and Marinica,
+`Comp. Mat. Science, 230, 112534 (2023) <https://doi.org/10.1016/j.commatsci.2023.112534>`_

doc/src/compute_sna_atom.rst

@@ -45,7 +45,7 @@ Syntax
 * w_1, w_2,... = list of neighbor weights, one for each type
 * nx, ny, nz = number of grid points in x, y, and z directions (positive integer)
 * zero or more keyword/value pairs may be appended
-* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner* or *dgradflag*
+* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner* or *dgradflag* or *nnn* or *wmode* or *delta*
 
   .. parsed-literal::
 
@@ -82,6 +82,16 @@ Syntax
           *0* = descriptor gradients are summed over atoms of each type
           *1* = descriptor gradients are listed separately for each atom pair
 
+* additional keyword = *nnn* or *wmode* or *delta*
+
+  .. parsed-literal::
+
+       *nnn* value = number of considered nearest neighbors to compute the bispectrum over a target specific number of neighbors (only implemented for compute sna/atom)
+       *wmode* value = weight function for finding optimal cutoff to match the target number of neighbors (required if nnn used, only implemented for compute sna/atom)
+          *0* = heavyside weight function
+          *1* = hyperbolic tangent weight function
+       *delta* value = transition interval centered at cutoff distance for hyperbolic tangent weight function (ignored if wmode=0, required if wmode=1, only implemented for compute sna/atom)
+
 Examples
 """"""""
 
@@ -94,6 +104,7 @@ Examples
    compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1
    compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1 sinner 1.35 1.6 dinner 0.25 0.3
    compute bgrid all sna/grid/local 200 200 200 1.4 0.95 6 2.0 1.0
+   compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.2
 
 Description
 """""""""""
@@ -433,6 +444,25 @@ requires that *bikflag=1*.
    The rerun script can use a :doc:`special_bonds <special_bonds>`
    command that includes all pairs in the neighbor list.
 
+The keyword *nnn* allows for the calculation of the bispectrum over a
+specific target number of neighbors. This option is only implemented for
+the compute *sna/atom*\ .  An optimal cutoff radius for defining the
+neighborhood of the central atom is calculated by means of a dichotomy
+algorithm.  This iterative process allows to assign weights to
+neighboring atoms in order to match the total sum of weights with the
+target number of neighbors.  Depending on the radial weight function
+used in that process, the cutoff radius can fluctuate a lot in the
+presence of thermal noise.  Therefore, in addition to the *nnn* keyword,
+the keyword *wmode* allows to choose whether a Heaviside (*wmode* = 0)
+function or a Hyperbolic tangent function (*wmode* = 1) should be used.
+If the Heaviside function is used, the cutoff radius exactly matches the
+distance between the central atom an its *nnn*'th neighbor.  However, in
+the case of the hyperbolic tangent function, the dichotomy algorithm
+allows to span the weights over a distance *delta* in order to reduce
+fluctuations in the resulting local atomic environment fingerprint.  The
+detailed formalism is given in the paper by Lafourcade et
+al. :ref:`(Lafourcade) <Lafourcade2023_2>`.
+
 ----------
 
 Output info
@@ -585,6 +615,7 @@ Related commands
 """"""""""""""""
 
 :doc:`pair_style snap <pair_snap>`
+:doc:`compute slcsa/atom <compute_slcsa_atom>`
 
 Default
 """""""
@@ -592,6 +623,7 @@ Default
 The optional keyword defaults are *rmin0* = 0,
 *switchflag* = 1, *bzeroflag* = 1, *quadraticflag* = 0,
 *bnormflag* = 0, *wselfallflag* = 0, *switchinnerflag* = 0,
+*nnn* = -1, *wmode* = 0, *delta* = 1.e-3
 
 ----------
 
@@ -623,3 +655,8 @@ of Angular Momentum, World Scientific, Singapore (1987).
 .. _Ellis2021:
 
 **(Ellis)** Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam,  Phys Rev B, 104, 035120, (2021)
+
+.. _Lafourcade2023_2:
+
+**(Lafourcade)** Lafourcade, Maillet, Denoual, Duval, Allera, Goryaeva, and Marinica,
+`Comp. Mat. Science, 230, 112534 (2023) <https://doi.org/10.1016/j.commatsci.2023.112534>`_

doc/src/compute_stress_atom.rst

@@ -127,11 +127,11 @@ result in more consistent heat flux values for angle, dihedrals,
 improper and constraint force contributions
 when computed via :doc:`compute heat/flux <compute_heat_flux>`.
 
-If no extra keywords are listed, the kinetic contribution all of the
-virial contribution terms are included in the per-atom stress tensor.
-If any extra keywords are listed, only those terms are summed to
-compute the tensor.  The *virial* keyword means include all terms
-except the kinetic energy *ke*\ .
+If no extra keywords are listed, the kinetic contribution *and* all
+of the virial contribution terms are included in the per-atom stress
+tensor.  If any extra keywords are listed, only those terms are
+summed to compute the tensor.  The *virial* keyword means include all
+terms except the kinetic energy *ke*\ .
 
 Note that the stress for each atom is due to its interaction with all
 other atoms in the simulation, not just with other atoms in the group.

doc/src/compute_stress_mop.rst

@@ -18,7 +18,7 @@ Syntax
 * style = *stress/mop* or *stress/mop/profile*
 * dir = *x* or *y* or *z* is the direction normal to the plane
 * args = argument specific to the compute style
-* keywords = *kin* or *conf* or *total* or *pair* or *bond* or *angle* (one or more can be specified)
+* keywords = *kin* or *conf* or *total* or *pair* or *bond* or *angle* or *dihedral* (one or more can be specified)
 
 .. parsed-literal::
 
@@ -68,15 +68,13 @@ Verlet algorithm.
 
 .. versionadded:: 15Jun2023
 
-   contributions from bond and angle potentials
+   contributions from bond, angle and dihedral potentials
 
-Between one and six keywords can be used to indicate which contributions
+Between one and seven keywords can be used to indicate which contributions
 to the stress must be computed: total stress (total), kinetic stress
 (kin), configurational stress (conf), stress due to bond stretching
-(bond), stress due to angle bending (angle) and/or due to pairwise
-non-bonded interactions (pair).  The angle keyword is currently
-available only for the *stress/mop* command and **not** the
-*stress/mop/profile* command.
+(bond), stress due to angle bending (angle), stress due to dihedral terms (dihedral)
+and/or due to pairwise non-bonded interactions (pair).
 
 NOTE 1: The configurational stress is computed considering all pairs of
 atoms where at least one atom belongs to group group-ID.
@@ -134,14 +132,9 @@ 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* does not work with more than two-body pair
+*stress/mop/profile* and *stress/mop* do not work with more than two-body pair
 interactions, long range (kspace) interactions and
-angle/dihedral/improper intramolecular interactions. Similarly, compute
-*stress/mop* does not work with more than two-body pair interactions,
-long range (kspace) interactions and dihedral/improper intramolecular
-interactions but works with all bond interactions with the class method
-single() implemented and all angle interactions with the class method
-born_matrix() implemented.
+improper intramolecular interactions.
 
 Related commands
 """"""""""""""""

doc/src/compute_xrd.rst

@@ -62,28 +62,29 @@ equations:
    \frac{\sin(\theta)}{\lambda} &= \frac{\left\lVert\mathbf{k}\right\rVert}{2}
 
 Here, :math:`\mathbf{k}` is the location of the reciprocal lattice node,
-:math:`r_j` is the position of each atom, :math:`f_j` are atomic scattering
-factors, *Lp* is the Lorentz-polarization factor, and :math:`\theta` is the
-scattering angle of diffraction.  The Lorentz-polarization factor can be turned
-off using the optional *LP* keyword.
+:math:`r_j` is the position of each atom, :math:`f_j` are atomic
+scattering factors, *Lp* is the Lorentz-polarization factor, and
+:math:`\theta` is the scattering angle of diffraction.  The
+Lorentz-polarization factor can be turned off using the optional *LP*
+keyword.
 
 Diffraction intensities are calculated on a three-dimensional mesh of
-reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire
-simulation domain or (b) manually using selected values as
-shown in the 2D diagram below.
+reciprocal lattice nodes. The mesh spacing is defined either (a) by the
+entire simulation domain or (b) manually using selected values as shown
+in the 2D diagram below.
 
-.. image:: img/xrd_mesh.jpg
+.. image:: img/xrd_mesh.png
    :scale: 75%
    :align: center
 
 For a mesh defined by the simulation domain, a rectilinear grid is
 constructed with spacing :math:`c A^{-1}` along each reciprocal lattice
-axis, where :math:`A` is a matrix containing the vectors corresponding to the
-edges of the simulation cell. If one or two directions has non-periodic
-boundary conditions, then the spacing in these directions is defined from the
-average of the (inversed) box lengths with periodic boundary conditions.
-Meshes defined by the simulation domain must contain at least one periodic
-boundary.
+axis, where :math:`A` is a matrix containing the vectors corresponding
+to the edges of the simulation cell. If one or two directions has
+non-periodic boundary conditions, then the spacing in these directions
+is defined from the average of the (inversed) box lengths with periodic
+boundary conditions.  Meshes defined by the simulation domain must
+contain at least one periodic boundary.
 
 If the *manual* flag is included, the mesh of reciprocal lattice nodes
 will be defined using the *c* values for the spacing along each

doc/src/create_atoms.rst

@@ -536,6 +536,11 @@ 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/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/dump.rst

@@ -805,16 +805,16 @@ computes, fixes, or variables when they are evaluated, so this is a very
 general means of creating quantities to output to a dump file.
 
 The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to
-per-atom integer and floating-point vectors or arrays that have been
-added via the :doc:`fix property/atom <fix_property_atom>` command.
-When that command is used specific names are given to each attribute
-which are the "name" portion of these keywords.  For arrays *i2_name*
-and *d2_name*, the column of the array must also be included following
-the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is
-in the range from 1 to :math:`M`, where :math:`M` is the number of
-columns in the custom array). See the discussion above for how :math:`i`
-can be specified with a wildcard asterisk to effectively specify
-multiple values.
+custom per-atom integer and floating-point vectors or arrays that have
+been added via the :doc:`fix property/atom <fix_property_atom>`
+command.  When that command is used specific names are given to each
+attribute which are the "name" portion of these keywords.  For arrays
+*i2_name* and *d2_name*, the column of the array must also be included
+following the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where
+:math:`i` is in the range from 1 to :math:`M`, where :math:`M` is the
+number of columns in the custom array).  See the discussion above for
+how :math:`i` can be specified with a wildcard asterisk to effectively
+specify multiple values.
 
 See the :doc:`Modify <Modify>` page for information on how to add
 new compute and fix styles to LAMMPS to calculate per-atom quantities

doc/src/fix.rst

@@ -287,6 +287,7 @@ accelerated styles exist.
 * :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
 * :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
 * :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
+* :doc:`nonaffine/displacement <fix_nonaffine_displacement>` - calculate nonaffine displacement of atoms
 * :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
 * :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
 * :doc:`nph/body <fix_nph_body>` - NPH for body particles

doc/src/fix_adapt.rst

@@ -205,6 +205,8 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`pace, pace/extrapolation <pair_pace>`                                  | scale                                            | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`quip <pair_quip>`                                                      | scale                                            | type global |
++------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`snap <pair_snap>`                                                      | scale                                            | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`spin/dmi <pair_spin_dmi>`                                              | coulombic_cutoff                                 | type global |
@@ -219,7 +221,7 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`table <pair_table>`                                                    | table_cutoff                                     | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
-| :doc:`ufm <pair_ufm>`                                                        | epsilon,sigma                                    | type pairs  |
+| :doc:`ufm <pair_ufm>`                                                        | epsilon,sigma,scale                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`wf/cut <pair_wf_cut>`                                                  | epsilon,sigma,nu,mu                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
@@ -315,21 +317,21 @@ Currently *bond* does not support bond_style hybrid nor bond_style
 hybrid/overlay as bond styles. The bond styles that currently work
 with fix_adapt are
 
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`class2 <bond_class2>`        | r0         | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`fene <bond_fene>`            | k,r0       | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`fene/nm <bond_fene>`         | k,r0       | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`gromos <bond_gromos>`        | k,r0       | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`harmonic <bond_harmonic>`    | k,r0       | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`morse <bond_morse>`          | r0         | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`nonlinear <bond_nonlinear>`  | epsilon,r0 | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 
 ----------
 
@@ -353,11 +355,11 @@ Currently *angle* does not support angle_style hybrid nor angle_style
 hybrid/overlay as angle styles. The angle styles that currently work
 with fix_adapt are
 
-+------------------------------------+-------+-----------------+
-| :doc:`harmonic <angle_harmonic>`    | k,theta0 | type angles |
-+------------------------------------+-------+-----------------+
-| :doc:`cosine <angle_cosine>`        | k        | type angles |
-+------------------------------------+-------+-----------------+
++------------------------------------+----------+-------------+
+| :doc:`harmonic <angle_harmonic>`   | k,theta0 | type angles |
++------------------------------------+----------+-------------+
+| :doc:`cosine <angle_cosine>`       | k        | type angles |
++------------------------------------+----------+-------------+
 
 Note that internally, theta0 is stored in radians, so the variable
 this fix uses to reset theta0 needs to generate values in radians.
@@ -482,7 +484,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute ti <compute_ti>`
+:doc:`compute ti <compute_ti>`, :doc:`fix adapt/fep <fix_adapt_fep>`
 
 Default
 """""""

doc/src/fix_adapt_fep.rst

@@ -123,19 +123,29 @@ styles and their energy formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`born <pair_born>`                                                      | a,b,c                   | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
+| :doc:`born/gauss <pair_born_gauss>`                                          | biga0,biga1,r0          | type pairs |
++------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm  <pair_buck>`       | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`buck/mdf <pair_mdf>`                                                   | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
-| :doc:`coul/cut <pair_coul>`                                                  | scale                   | type pairs |
+| :doc:`coul/cut, coul/cut/global <pair_coul>`                                 | scale                   | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`coul/cut/soft <pair_fep_soft>`                                         | lambda                  | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
+| :doc:`coul/debye <pair_coul>`                                                | scale                   | type pairs |
++------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`coul/long, coul/msm <pair_coul>`                                       | scale                   | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`coul/long/soft <pair_fep_soft>`                                        | scale, lambda           | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
-| :doc:`eam <pair_eam>`                                                        | scale                   | type pairs |
+| :doc:`coul/slater/long <pair_coul_slater>`                                   | scale                   | type pairs |
++------------------------------------------------------------------------------+-------------------------+------------+
+| :doc:`coul/streitz <pair_coul>`                                              | scale                   | type pairs |
++------------------------------------------------------------------------------+-------------------------+------------+
+| :doc:`eam, eam/alloy, eam/fs <pair_eam>`                                     | scale                   | type pairs |
++------------------------------------------------------------------------------+-------------------------+------------+
+| :doc:`harmonic/cut <pair_harmonic_cut>`                                      | k                       | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`gauss <pair_gauss>`                                                    | a                       | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
@@ -163,6 +173,8 @@ styles and their energy formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`lj/sf/dipole/sf <pair_dipole>`                                         | epsilon,sigma,scale     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
+| :doc:`meam <pair_meam>`                                                      | scale                   | type pairs |
++------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`mie/cut <pair_mie>`                                                    | epsilon,sigma,gamR,gamA | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`morse, morse/smooth/linear <pair_morse>`                               | d0,r0,alpha             | type pairs |
@@ -173,12 +185,16 @@ styles and their energy formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>`                           | e0,r0,nn,mm             | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
+| :doc:`pace, pace/extrapolation <pair_pace>`                                  | scale                   | type pairs |
++------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`snap <pair_snap>`                                                      | scale                   | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`soft <pair_soft>`                                                      | a                       | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`ufm <pair_ufm>`                                                        | epsilon,sigma,scale     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
+| :doc:`wf/cut <pair_wf_cut>`                                                  | epsilon,sigma,nu,mu     | type pairs |
++------------------------------------------------------------------------------+-------------------------+------------+
 
 .. note::
 
@@ -307,7 +323,9 @@ the :doc:`run <run>` command.  This fix is not invoked during
 
 Restrictions
 """"""""""""
- none
+
+The keyword "scale yes" is not supported for scaling per-atom parameters
+diameter and change. You can use :doc:`fix adapt <fix_adapt>` for those.
 
 Related commands
 """"""""""""""""

doc/src/fix_atom_swap.rst

@@ -181,6 +181,12 @@ This fix is part of the MC package.  It is only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 doc page for more info.
 
+This fix cannot be used with systems that do not have per-type masses
+(e.g. atom style sphere) since the implemented algorithm pre-computes
+velocity rescaling factors from per-type masses and ignores any per-atom
+masses, if present.  In case both, per-type and per-atom masses are
+present, a warning is printed.
+
 Related commands
 """"""""""""""""
 

doc/src/fix_halt.rst

@@ -183,4 +183,4 @@ Related commands
 Default
 """""""
 
-The option defaults are error = hard, message = yes, and path = ".".
+The option defaults are error = soft, message = yes, and path = ".".

doc/src/fix_neb.rst

@@ -109,7 +109,7 @@ Note that in this case the specified *Kspring* is in
 force/distance units.
 
 With a value of *ideal*, the spring force is computed as suggested in
-ref`(WeinanE) <WeinanE>`
+:ref:`(WeinanE) <WeinanE>`
 
 .. math::
 
@@ -120,18 +120,18 @@ and :math:`RD_{ideal}` is the ideal *RD* for which all the images are
 equally spaced.  I.e. :math:`RD_{ideal} = (i-1) \cdot meanDist` when the
 climbing replica is off, where *i* is the replica number).  The
 *meanDist* is the average distance between replicas.  Note that in this
-case the specified *Kspring* is in force units. When the climbing replica
-is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated separately
-each side of the climbing image. Note that the *ideal* form of nudging
-can often be more effective at keeping the replicas equally spaced before
-climbing, then equally spaced either side of the climbing image whilst
-climbing.
+case the specified *Kspring* is in force units. When the climbing
+replica is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated
+separately each side of the climbing image. Note that the *ideal* form
+of nudging can often be more effective at keeping the replicas equally
+spaced before climbing, then equally spaced either side of the climbing
+image whilst climbing.
 
-With a value of *equal* the spring force is computed as for *ideal*
-when the climbing replica is off, promoting equidistance. When the climbing
+With a value of *equal* the spring force is computed as for *ideal* when
+the climbing replica is off, promoting equidistance. When the climbing
 replica is on, the spring force is computed to promote equidistant
-absolute differences in energy, rather than distance, each side of
-the climbing image:
+absolute differences in energy, rather than distance, each side of the
+climbing image:
 
 .. math::
 
@@ -143,23 +143,22 @@ where *ED* is the cumulative sum of absolute energy differences:
 
    ED = \sum_{i<N} \left|E(R_{i+1}) - E(R_i)\right|,
 
-*meanEdist* is the average absolute energy difference between
-replicas up to the climbing image or from the climbing image
-to the final image, for images before or after the climbing
-image respectively. :math:`ED_{ideal}` is the corresponding
-cumulative sum of average absolute energy differences in
-each case, in close analogy to *ideal*. This form of nudging
-is to aid schemes which integrate forces along, or near to,
-NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
+*meanEdist* is the average absolute energy difference between replicas
+up to the climbing image or from the climbing image to the final image,
+for images before or after the climbing image
+respectively. :math:`ED_{ideal}` is the corresponding cumulative sum of
+average absolute energy differences in each case, in close analogy to
+*ideal*. This form of nudging is to aid schemes which integrate forces
+along, or near to, NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
 
 ----------
 
-The keyword *perp* specifies if and how a perpendicular nudging force
-is computed.  It adds a spring force perpendicular to the path in
-order to prevent the path from becoming too strongly kinked.  It can
+The keyword *perp* specifies if and how a perpendicular nudging force is
+computed.  It adds a spring force perpendicular to the path in order to
+prevent the path from becoming too strongly kinked.  It can
 significantly improve the convergence of the NEB calculation when the
-resolution is poor.  I.e. when few replicas are used; see
-:ref:`(Maras) <Maras1>` for details.
+resolution is poor.  I.e. when few replicas are used; see :ref:`(Maras)
+<Maras1>` for details.
 
 The perpendicular spring force is given by
 
@@ -181,10 +180,10 @@ force is added.
 
 By default, no additional forces act on the first and last replicas
 during the NEB relaxation, so these replicas simply relax toward their
-respective local minima.  By using the key word *end*, additional
-forces can be applied to the first and/or last replicas, to enable
-them to relax toward a MEP while constraining their energy E to the
-target energy ETarget.
+respective local minima.  By using the key word *end*, additional forces
+can be applied to the first and/or last replicas, to enable them to
+relax toward a MEP while constraining their energy E to the target
+energy ETarget.
 
 If :math:`E_{Target} > E`, the interatomic force :math:`F_i` for the
 specified replica becomes:
@@ -197,33 +196,33 @@ specified replica becomes:
 The "spring" constant on the difference in energies is the specified
 *Kspring3* value.
 
-When *estyle* is specified as *first*, the force is applied to the
-first replica.  When *estyle* is specified as *last*, the force is
-applied to the last replica.  Note that the *end* keyword can be used
-twice to add forces to both the first and last replicas.
+When *estyle* is specified as *first*, the force is applied to the first
+replica.  When *estyle* is specified as *last*, the force is applied to
+the last replica.  Note that the *end* keyword can be used twice to add
+forces to both the first and last replicas.
 
 For both these *estyle* settings, the target energy *ETarget* is set
 to the initial energy of the replica (at the start of the NEB
 calculation).
 
 If the *estyle* is specified as *last/efirst* or *last/efirst/middle*,
-force is applied to the last replica, but the target energy *ETarget*
-is continuously set to the energy of the first replica, as it evolves
+force is applied to the last replica, but the target energy *ETarget* is
+continuously set to the energy of the first replica, as it evolves
 during the NEB relaxation.
 
 The difference between these two *estyle* options is as follows.  When
 *estyle* is specified as *last/efirst*, no change is made to the
-inter-replica force applied to the intermediate replicas (neither
-first or last).  If the initial path is too far from the MEP, an
-intermediate replica may relax "faster" and reach a lower energy than
-the last replica.  In this case the intermediate replica will be
-relaxing toward its own local minima.  This behavior can be prevented
-by specifying *estyle* as *last/efirst/middle* which will alter the
-inter-replica force applied to intermediate replicas by removing the
-contribution of the gradient to the inter-replica force.  This will
-only be done if a particular intermediate replica has a lower energy
-than the first replica.  This should effectively prevent the
-intermediate replicas from over-relaxing.
+inter-replica force applied to the intermediate replicas (neither first
+or last).  If the initial path is too far from the MEP, an intermediate
+replica may relax "faster" and reach a lower energy than the last
+replica.  In this case the intermediate replica will be relaxing toward
+its own local minima.  This behavior can be prevented by specifying
+*estyle* as *last/efirst/middle* which will alter the inter-replica
+force applied to intermediate replicas by removing the contribution of
+the gradient to the inter-replica force.  This will only be done if a
+particular intermediate replica has a lower energy than the first
+replica.  This should effectively prevent the intermediate replicas from
+over-relaxing.
 
 After converging a NEB calculation using an *estyle* of
 *last/efirst/middle*, you should check that all intermediate replicas
@@ -237,9 +236,10 @@ target energy.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
-are relevant to this fix.  No global or per-atom quantities are stored
-by this fix for access by various :doc:`output commands <Howto_output>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
+relevant to this fix.  No global or per-atom quantities are stored by
+this fix for access by various :doc:`output commands <Howto_output>`.
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
 

doc/src/fix_nh_uef.rst

@@ -23,7 +23,7 @@ Syntax
   .. parsed-literal::
 
      keyword = *erate* or *ext* or *strain* or *temp* or *iso* or *x* or *y* or *z* or *tchain* or *pchain* or *tloop* or *ploop* or *mtk*
-       *erate* values = e_x e_y = engineering strain rates (required)
+       *erate* values = e_x e_y = true strain rates (required)
        *ext* value = *x* or *y* or *z* or *xy* or *yz* or *xz* = external dimensions
          sets the external dimensions used to calculate the scalar pressure
        *strain* values = e_x e_y = initial strain
@@ -62,7 +62,7 @@ performed using the :doc:`fix deform <fix_deform>`, :doc:`fix nvt/sllod
 <fix_nvt_sllod>`, and :doc:`compute temp/deform <compute_temp_deform>`
 commands.
 
-The applied flow field is set by the *eps* keyword. The values
+The applied flow field is set by the *erate* keyword. The values
 *edot_x* and *edot_y* correspond to the strain rates in the xx and yy
 directions.  It is implicitly assumed that the flow field is
 traceless, and therefore the strain rate in the zz direction is eqal

doc/src/fix_nonaffine_displacement.rst

@@ -0,0 +1,133 @@
+.. index:: fix nonaffine/displacement
+
+fix nonaffine/displacement command
+==================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group nonaffine/displacement style args reference/style nstep
+
+* ID, group are documented in :doc:`fix <fix>` command
+* nonaffine/displacement = style name of this fix command
+* nevery = calculate nonaffine displacement every this many timesteps
+* style = *d2min* or *integrated*
+
+  .. parsed-literal::
+
+       *d2min* args = cutoff args
+         cutoff = *type* or *radius* or *custom*
+           *type* args = none, cutoffs determined by atom types
+           *radius* args = none, cutoffs determined based on atom diameters (atom style sphere)
+           *custom* args = *rmax*, cutoff set by a constant numeric value *rmax* (distance units)
+       *integrated* args = none
+
+* reference/style = *fixed* or *update* or *offset*
+
+  .. parsed-literal::
+
+       *fixed* = use a fixed reference frame at *nstep*
+       *update* = update the reference frame every *nstep* timesteps
+       *offset* = update the reference frame *nstep* timesteps before calculating the nonaffine displacement
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all nonaffine/displacement 100 integrated update 100
+   fix 1 all nonaffine/displacement 1000 d2min type fixed 0
+   fix 1 all nonaffine/displacement 1000 d2min custom 2.0 offset 100
+
+Description
+"""""""""""
+
+.. versionadded:: 7Feb2024
+
+This fix computes different metrics of the nonaffine displacement of
+particles. The first metric, *d2min* calculates the :math:`D^2_\mathrm{min}`
+nonaffine displacement by Falk and Langer in :ref:`(Falk) <d2min-Falk>`.
+For each atom, the fix computes the two tensors
+
+.. math::
+
+   X = \sum_{\mathrm{neighbors}} \vec{r} \left(\vec{r}_{0} \right)^T
+
+and
+
+.. math::
+
+   Y = \sum_{\mathrm{neighbors}} \vec{r}_0 \left(\vec{r}_{0} \right)^T
+
+where the neighbors include all other atoms within the distance criterion
+set by the cutoff option, discussed below, :math:`\vec{r}` is the current
+displacement between particles, and :math:`\vec{r}_0` is the reference
+displacement. A deformation gradient tensor is then calculated as
+:math:`F = X Y^{-1}` from which
+
+.. math::
+
+    D^2_\mathrm{min} = \sum_{\mathrm{neighbors}} \left| \vec{r} - F \vec{r}_0 \right|^2
+
+and a strain tensor is calculated :math:`E = F F^{T} - I` where :math:`I`
+is the identity tensor. This calculation is only performed on timesteps that
+are a multiple of *nevery* (including timestep zero). Data accessed before
+this occurs will simply be zeroed.
+
+The *integrated* style simply integrates the velocity of particles
+every timestep to calculate a displacement. This style only works if
+used in conjunction with another fix that deforms the box and displaces
+atom positions such as :doc:`fix deform <fix_deform>` with remap x,
+:doc:`fix press/berendsen <fix_press_berendsen>`, or :doc:`fix nh <fix_nh>`.
+
+Both of these methods require defining a reference state. With the *fixed* reference
+style, the user picks a specific timestep *nstep* at which particle positions are saved.
+If peratom data is accessed from this compute prior to this timestep, it will simply be
+zeroed. The *update* reference style implies the reference state will be updated every
+*nstep* timesteps. The *offset* reference only applies to the *d2min* metric and will
+update the reference state *nstep* timesteps before a multiple of *nevery* timesteps.
+
+
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+The reference state is saved to :doc:`binary restart files <restart>`.
+
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this
+fix.
+
+This fix computes a peratom array with 3 columns, which can be accessed
+by indices 1-3 using any command that uses per-atom values from a fix
+as input.
+
+For the *integrated* style, the three columns are the nonaffine
+displacements in the x, y, and z directions. For the *d2min* style,
+the three columns are the calculated :math:`\sqrt{D^2_\mathrm{min}}`, the
+volumetric strain, and the deviatoric strain.
+
+Restrictions
+""""""""""""
+
+This compute is part of the EXTRA-FIX package.  It is only enabled if
+LAMMPS was built with that package.  See the
+:doc:`Build package <Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+none
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _d2min-Falk:
+
+**(Falk)** Falk and Langer PRE, 57, 7192 (1998).

doc/src/fix_phonon.rst

@@ -181,10 +181,10 @@ This fix assumes a crystalline system with periodical lattice. The
 temperature of the system should not exceed the melting temperature to
 keep the system in its solid state.
 
-This fix is part of the PHONON package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
-
-This fix requires LAMMPS be built with an FFT library.  See the :doc:`Build settings <Build_settings>` page for details.
+This fix is part of the PHONON package.  It is only enabled if LAMMPS
+was built with that package.  This fix also requires LAMMPS to be built
+with 3d-FFT support which is included in the KSPACE package.  See the
+:doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/fix_qeq.rst

@@ -232,8 +232,6 @@ These fixes are part of the QEQ package.  They are only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
-These qeq fixes are not compatible with the GPU and USER-INTEL packages.
-
 These qeq fixes will ignore electric field contributions from
 :doc:`fix efield <fix_efield>`.
 

doc/src/fix_rigid.rst

@@ -80,7 +80,7 @@ Syntax
          groupID1, groupID2, ... = list of N group IDs
 
 * zero or more keyword/value pairs may be appended
-* keyword = *langevin* or *reinit* or *temp* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile* or *gravity*
+* keyword = *langevin* or *reinit* or *temp*  or *mol* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile* or *gravity*
 
   .. parsed-literal::
 
@@ -92,6 +92,8 @@ Syntax
        *temp* values = Tstart Tstop Tdamp
          Tstart,Tstop = desired temperature at start/stop of run (temperature units)
          Tdamp = temperature damping parameter (time units)
+       *mol* value = template-ID
+         template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
        *iso* or *aniso* values = Pstart Pstop Pdamp
          Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
          Pdamp = pressure damping parameter (time units)

doc/src/fix_temp_berendsen.rst

@@ -1,8 +1,11 @@
 .. index:: fix temp/berendsen
+.. index:: fix temp/berendsen/kk
 
 fix temp/berendsen command
 ==========================
 
+Accelerator Variants: *temp/berendsen/kk*
+
 Syntax
 """"""
 
@@ -118,6 +121,10 @@ remaining thermal degrees of freedom, and the bias is added back in.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_temp_rescale.rst

@@ -1,8 +1,11 @@
 .. index:: fix temp/rescale
+.. index:: fix temp/rescale/kk
 
 fix temp/rescale command
 ========================
 
+Accelerator Variants: *temp/rescale/kk*
+
 Syntax
 """"""
 
@@ -125,6 +128,10 @@ remaining thermal degrees of freedom, and the bias is added back in.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""