Merge pull request #1522 from akohlmey/next_version

Step version string for next patch release

cmake/Modules/CodeCoverage.cmake

@@ -0,0 +1,28 @@
+###############################################################################
+# Coverage
+#
+# Requires latest gcovr (for GCC 8.1 support):#
+# pip install git+https://github.com/gcovr/gcovr.git
+###############################################################################
+if(ENABLE_COVERAGE)
+    find_program(GCOVR_BINARY gcovr)
+    find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
+
+    if(GCOVR_FOUND)
+        get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
+
+        add_custom_target(
+            gen_coverage_xml
+            COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Generating XML Coverage Report..."
+        )
+
+        add_custom_target(
+            gen_coverage_html
+            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Generating HTML Coverage Report..."
+        )
+    endif()
+endif()

cmake/Modules/Documentation.cmake

@@ -0,0 +1,59 @@
+###############################################################################
+# Build documentation
+###############################################################################
+option(BUILD_DOC "Build LAMMPS documentation" OFF)
+if(BUILD_DOC)
+  include(ProcessorCount)
+  ProcessorCount(NPROCS)
+  find_package(PythonInterp 3 REQUIRED)
+
+  set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
+
+  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
+  file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
+  list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
+
+  add_custom_command(
+    OUTPUT docenv
+    COMMAND ${VIRTUALENV} docenv
+  )
+
+  set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
+
+  add_custom_command(
+    OUTPUT requirements.txt
+    DEPENDS docenv
+    COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
+    COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade
+    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+  )
+
+  set(RST_FILES "")
+  set(RST_DIR ${CMAKE_BINARY_DIR}/rst)
+  file(MAKE_DIRECTORY ${RST_DIR})
+  foreach(TXT_FILE ${DOC_SOURCES})
+    get_filename_component(FILENAME ${TXT_FILE} NAME_WE)
+    set(RST_FILE ${RST_DIR}/${FILENAME}.rst)
+    list(APPEND RST_FILES ${RST_FILE})
+    add_custom_command(
+      OUTPUT ${RST_FILE}
+      DEPENDS requirements.txt docenv ${TXT_FILE}
+      COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}
+    )
+  endforeach()
+
+  add_custom_command(
+    OUTPUT html
+    DEPENDS ${RST_FILES}
+    COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}
+    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html
+  )
+
+  add_custom_target(
+    doc ALL
+    DEPENDS html
+    SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
+  )
+
+  install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})
+endif()

cmake/Modules/FindKIM-API.cmake

@@ -36,14 +36,23 @@
 # KIM-API-CMAKE_CXX_COMPILER
 # KIM-API-CMAKE_Fortran_COMPILER
 #
-find_package(PkgConfig REQUIRED)
+
+if(KIM-API_FIND_QUIETLY)
+  set(REQ_OR_QUI "QUIET")
+else()
+  set(REQ_OR_QUI "REQUIRED")
+endif()
+
+find_package(PkgConfig ${REQ_OR_QUI})
 include(FindPackageHandleStandardArgs)
 
-pkg_check_modules(KIM-API REQUIRED libkim-api>=2.0)
+pkg_check_modules(KIM-API ${REQ_OR_QUI} libkim-api>=2.0)
 
-pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)
+if(KIM-API_FOUND)
-pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)
+  pkg_get_variable(KIM-API-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)
-pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
+  pkg_get_variable(KIM-API-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)
+  pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
+endif()
 
 # handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
 # if all listed variables are TRUE

cmake/Modules/LAMMPSUtils.cmake

@@ -0,0 +1,71 @@
+# Utility functions
+function(list_to_bulletpoints result)
+    list(REMOVE_AT ARGV 0)
+    set(temp "")
+    foreach(item ${ARGV})
+        set(temp "${temp}* ${item}\n")
+    endforeach()
+    set(${result} "${temp}" PARENT_SCOPE)
+endfunction(list_to_bulletpoints)
+
+function(validate_option name values)
+    string(TOLOWER ${${name}} needle_lower)
+    string(TOUPPER ${${name}} needle_upper)
+    list(FIND ${values} ${needle_lower} IDX_LOWER)
+    list(FIND ${values} ${needle_upper} IDX_UPPER)
+    if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
+        list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
+        message(FATAL_ERROR "\n########################################################################\n"
+                            "Invalid value '${${name}}' for option ${name}\n"
+                            "\n"
+                            "Possible values are:\n"
+                            "${POSSIBLE_VALUE_LIST}"
+                            "########################################################################")
+    endif()
+endfunction(validate_option)
+
+function(get_lammps_version version_header variable)
+    file(READ ${version_header} line)
+    set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}")
+    string(STRIP ${day} day)
+    string(STRIP ${month} month)
+    string(STRIP ${year} year)
+    list(FIND MONTHS "${month}" month)
+    string(LENGTH ${day} day_length)
+    string(LENGTH ${month} month_length)
+    if(day_length EQUAL 1)
+        set(day "0${day}")
+    endif()
+    if(month_length EQUAL 1)
+        set(month "0${month}")
+    endif()
+    set(${variable} "${year}${month}${day}" PARENT_SCOPE)
+endfunction()
+
+function(check_for_autogen_files source_dir)
+    message(STATUS "Running check for auto-generated files from make-based build system")
+    file(GLOB SRC_AUTOGEN_FILES ${source_dir}/style_*.h)
+    file(GLOB SRC_AUTOGEN_PACKAGES ${source_dir}/packages_*.h)
+    list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
+    foreach(_SRC ${SRC_AUTOGEN_FILES})
+      get_filename_component(FILENAME "${_SRC}" NAME)
+      if(EXISTS ${source_dir}/${FILENAME})
+        message(FATAL_ERROR "\n########################################################################\n"
+                              "Found header file(s) generated by the make-based build system\n"
+                              "\n"
+                              "Please run\n"
+                              "make -C ${source_dir} purge\n"
+                              "to remove\n"
+                              "########################################################################")
+      endif()
+    endforeach()
+endfunction()
+
+macro(pkg_depends PKG1 PKG2)
+  if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
+    message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
+  endif()
+endmacro()

cmake/Modules/OpenCLUtils.cmake

@@ -6,7 +6,7 @@ function(GenerateOpenCLHeader varname outfile files)
     foreach(IDX RANGE 2 ${ARG_END})
         list(GET ARGV ${IDX} filename)
         file(READ ${filename} content)
-        string(REGEX REPLACE "\\s*//[^\n]*\n" "" content "${content}")
+        string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}")
         string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
         string(REGEX REPLACE "\"" "\\\\\"" content "${content}")
         string(REGEX REPLACE "([^\n]+)\n" "\"\\1\\\\n\"\n" content "${content}")

cmake/Modules/Packages/COMPRESS.cmake

@@ -0,0 +1,5 @@
+if(PKG_COMPRESS)
+  find_package(ZLIB REQUIRED)
+  include_directories(${ZLIB_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
+endif()

cmake/Modules/Packages/CORESHELL.cmake

@@ -0,0 +1,13 @@
+if(PKG_CORESHELL)
+    set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL)
+    set(CORESHELL_SOURCES)
+    set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}")
+
+    # detects styles which have a CORESHELL version
+    RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES)
+
+    get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES)
+
+    list(APPEND LIB_SOURCES ${CORESHELL_SOURCES})
+    include_directories(${CORESHELL_SOURCES_DIR})
+endif()

cmake/Modules/Packages/GPU.cmake

@@ -0,0 +1,194 @@
+if(PKG_GPU)
+    if (CMAKE_VERSION VERSION_LESS "3.1")
+      message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
+    endif()
+    set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
+    set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
+                    ${GPU_SOURCES_DIR}/fix_gpu.h
+                    ${GPU_SOURCES_DIR}/fix_gpu.cpp)
+
+    set(GPU_API "opencl" CACHE STRING "API used by GPU package")
+    set(GPU_API_VALUES opencl cuda)
+    set_property(CACHE GPU_API PROPERTY STRINGS ${GPU_API_VALUES})
+    validate_option(GPU_API GPU_API_VALUES)
+    string(TOUPPER ${GPU_API} GPU_API)
+
+    set(GPU_PREC "mixed" CACHE STRING "LAMMPS GPU precision")
+    set(GPU_PREC_VALUES double mixed single)
+    set_property(CACHE GPU_PREC PROPERTY STRINGS ${GPU_PREC_VALUES})
+    validate_option(GPU_PREC GPU_PREC_VALUES)
+    string(TOUPPER ${GPU_PREC} GPU_PREC)
+
+    if(GPU_PREC STREQUAL "DOUBLE")
+      set(GPU_PREC_SETTING "DOUBLE_DOUBLE")
+    elseif(GPU_PREC STREQUAL "MIXED")
+      set(GPU_PREC_SETTING "SINGLE_DOUBLE")
+    elseif(GPU_PREC STREQUAL "SINGLE")
+      set(GPU_PREC_SETTING "SINGLE_SINGLE")
+    endif()
+
+    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
+    file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+    if(GPU_API STREQUAL "CUDA")
+      find_package(CUDA REQUIRED)
+      find_program(BIN2C bin2c)
+      if(NOT BIN2C)
+        message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
+      endif()
+      option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+      option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
+      if(CUDA_MPS_SUPPORT)
+        set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
+      endif()
+
+      set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
+
+      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
+
+      cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+      if(CUDPP_OPT)
+        cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+        file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
+        file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
+      endif()
+
+      # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
+      # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
+      set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
+      # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
+      if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
+      endif()
+      # Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
+      if(CUDA_VERSION VERSION_GREATER "4.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
+      endif()
+      # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
+      if(CUDA_VERSION VERSION_GREATER "5.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
+      endif()
+      # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
+      if(CUDA_VERSION VERSION_GREATER "7.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
+      endif()
+      # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
+      if(CUDA_VERSION VERSION_GREATER "8.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
+      endif()
+      # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
+      if(CUDA_VERSION VERSION_GREATER "9.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
+      endif()
+
+      cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
+              -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+
+      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})
+
+      foreach(CU_OBJ ${GPU_GEN_OBJS})
+        get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
+        string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
+        add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+          COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+          DEPENDS ${CU_OBJ}
+          COMMENT "Generating ${CU_NAME}_cubin.h")
+        list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
+      endforeach()
+      set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
+
+
+      add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
+      target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+      target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
+      if(CUDPP_OPT)
+        target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+        target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
+      endif()
+
+      list(APPEND LAMMPS_LINK_LIBS gpu)
+
+      add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+      target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
+      target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+      target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
+
+
+    elseif(GPU_API STREQUAL "OPENCL")
+      find_package(OpenCL REQUIRED)
+      set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
+      set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
+      set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
+      validate_option(OCL_TUNE OCL_TUNE_VALUES)
+      string(TOUPPER ${OCL_TUNE} OCL_TUNE)
+
+      include(OpenCLUtils)
+      set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
+
+      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
+      list(REMOVE_ITEM GPU_LIB_CU
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
+      )
+
+      foreach(GPU_KERNEL ${GPU_LIB_CU})
+          get_filename_component(basename ${GPU_KERNEL} NAME_WE)
+          string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
+          GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
+          list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
+      endforeach()
+
+      GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
+      GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
+      GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu)
+      GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu)
+      GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
+      GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
+      GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
+
+      list(APPEND GPU_LIB_SOURCES
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
+      )
+
+      add_library(gpu STATIC ${GPU_LIB_SOURCES})
+      target_link_libraries(gpu ${OpenCL_LIBRARIES})
+      target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
+      target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
+
+      list(APPEND LAMMPS_LINK_LIBS gpu)
+
+      add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+      target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
+      target_link_libraries(ocl_get_devices PRIVATE ${OpenCL_LIBRARIES})
+      target_include_directories(ocl_get_devices PRIVATE ${OpenCL_INCLUDE_DIRS})
+    endif()
+
+    # GPU package
+    FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
+
+    set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
+
+    # detects styles which have GPU version
+    RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
+
+    get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
+
+    list(APPEND LIB_SOURCES ${GPU_SOURCES})
+    include_directories(${GPU_SOURCES_DIR})
+endif()

cmake/Modules/Packages/KIM.cmake

@@ -0,0 +1,42 @@
+if(PKG_KIM)
+  find_package(CURL)
+  if(CURL_FOUND)
+    include_directories(${CURL_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
+    add_definitions(-DLMP_KIM_CURL)
+  endif()
+  find_package(KIM-API QUIET)
+  if(KIM-API_FOUND)
+    set(DOWNLOAD_KIM_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_KIM_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
+  if(DOWNLOAD_KIM)
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
+    endif()
+    message(STATUS "KIM-API download requested - we will build our own")
+    enable_language(C)
+    enable_language(Fortran)
+    include(ExternalProject)
+    ExternalProject_Add(kim_build
+      URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz
+      URL_MD5 537d9c0abd30f85b875ebb584f9143fa
+      BINARY_DIR build
+      CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+                 -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                 -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
+                 -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                 -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+      )
+    ExternalProject_get_property(kim_build INSTALL_DIR)
+    set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)
+    set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
+    list(APPEND LAMMPS_DEPS kim_build)
+  else()
+    find_package(KIM-API REQUIRED)
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
+  include_directories(${KIM-API_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/KOKKOS.cmake

@@ -0,0 +1,53 @@
+if(PKG_KOKKOS)
+  set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
+  set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
+  add_definitions(-DLMP_KOKKOS)
+  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+
+  set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
+                          ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
+                          ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
+                          ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+  include_directories(${Kokkos_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS kokkos)
+
+  set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
+  set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
+
+  if(PKG_KSPACE)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp)
+  endif()
+
+  set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+
+  # detects styles which have KOKKOS version
+  RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
+
+  # register kokkos-only styles
+  RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
+  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
+
+  if(PKG_USER-DPD)
+    get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
+    RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
+    set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+  endif()
+
+  get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+
+  list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})
+  include_directories(${KOKKOS_PKG_SOURCES_DIR})
+endif()

cmake/Modules/Packages/KSPACE.cmake

@@ -0,0 +1,38 @@
+if(PKG_KSPACE)
+  option(FFT_SINGLE "Use single precision FFT instead of double" OFF)
+  set(FFTW "FFTW3")
+  if(FFT_SINGLE)
+    set(FFTW "FFTW3F")
+    add_definitions(-DFFT_SINGLE)
+  endif()
+  find_package(${FFTW} QUIET)
+  if(${FFTW}_FOUND)
+    set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package")
+  else()
+    set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
+  endif()
+  set(FFT_VALUES KISS ${FFTW} MKL)
+  set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
+  validate_option(FFT FFT_VALUES)
+  string(TOUPPER ${FFT} FFT)
+  if(NOT FFT STREQUAL "KISS")
+    find_package(${FFT} REQUIRED)
+    if(NOT FFT STREQUAL "FFTW3F")
+      add_definitions(-DFFT_FFTW)
+    else()
+      add_definitions(-DFFT_${FFT})
+    endif()
+    include_directories(${${FFT}_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
+  else()
+    add_definitions(-DFFT_KISS)
+  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})
+  validate_option(FFT_PACK FFT_PACK_VALUES)
+  if(NOT FFT_PACK STREQUAL "array")
+    string(TOUPPER ${FFT_PACK} FFT_PACK)
+    add_definitions(-DFFT_PACK_${FFT_PACK})
+  endif()
+endif()

cmake/Modules/Packages/LATTE.cmake

@@ -0,0 +1,38 @@
+if(PKG_LATTE)
+  enable_language(Fortran)
+  find_package(LATTE)
+  if(LATTE_FOUND)
+    set(DOWNLOAD_LATTE_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_LATTE_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
+  if(DOWNLOAD_LATTE)
+    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
+      message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
+    endif()
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool")
+    endif()
+    message(STATUS "LATTE download requested - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(latte_build
+      URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
+      URL_MD5 85ac414fdada2d04619c8f936344df14
+      SOURCE_SUBDIR cmake
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
+      -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
+      -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
+      -DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+    )
+    ExternalProject_get_property(latte_build INSTALL_DIR)
+    set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
+    list(APPEND LAMMPS_DEPS latte_build)
+  else()
+    find_package(LATTE)
+    if(NOT LATTE_FOUND)
+      message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
+    endif()
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
+endif()

cmake/Modules/Packages/MESSAGE.cmake

@@ -0,0 +1,29 @@
+if(PKG_MESSAGE)
+  option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
+  file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
+      ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
+      ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
+
+  add_library(cslib STATIC ${cslib_SOURCES})
+  if(BUILD_MPI)
+    target_compile_definitions(cslib PRIVATE -DMPI_YES)
+    set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
+  else()
+    target_compile_definitions(cslib PRIVATE -DMPI_NO)
+    target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
+    set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
+  endif()
+
+  if(MESSAGE_ZMQ)
+    target_compile_definitions(cslib PRIVATE -DZMQ_YES)
+    find_package(ZMQ REQUIRED)
+    target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
+    target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
+  else()
+    target_compile_definitions(cslib PRIVATE -DZMQ_NO)
+    target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
+  endif()
+
+  list(APPEND LAMMPS_LINK_LIBS cslib)
+  include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
+endif()

cmake/Modules/Packages/MSCG.cmake

@@ -0,0 +1,45 @@
+if(PKG_MSCG)
+  find_package(GSL REQUIRED)
+  find_package(MSCG QUIET)
+  if(MSGC_FOUND)
+    set(DOWNLOAD_MSCG_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_MSCG_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
+  if(DOWNLOAD_MSCG)
+    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
+      message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
+    endif()
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool")
+    endif()
+    include(ExternalProject)
+    if(NOT LAPACK_FOUND)
+      set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
+    endif()
+    ExternalProject_Add(mscg_build
+      URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
+      URL_MD5 8c45e269ee13f60b303edd7823866a91
+      SOURCE_SUBDIR src/CMake
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
+      BUILD_COMMAND make mscg INSTALL_COMMAND ""
+      )
+    ExternalProject_get_property(mscg_build BINARY_DIR)
+    set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)
+    ExternalProject_get_property(mscg_build SOURCE_DIR)
+    set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src)
+    list(APPEND LAMMPS_DEPS mscg_build)
+    if(NOT LAPACK_FOUND)
+      file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS})
+      add_dependencies(mscg_build linalg)
+    endif()
+  else()
+    find_package(MSCG)
+    if(NOT MSCG_FOUND)
+      message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
+    endif()
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
+  include_directories(${MSCG_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/OPT.cmake

@@ -0,0 +1,13 @@
+if(PKG_OPT)
+    set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
+    set(OPT_SOURCES)
+    set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
+
+    # detects styles which have OPT version
+    RegisterStylesExt(${OPT_SOURCES_DIR} opt OPT_SOURCES)
+
+    get_property(OPT_SOURCES GLOBAL PROPERTY OPT_SOURCES)
+
+    list(APPEND LIB_SOURCES ${OPT_SOURCES})
+    include_directories(${OPT_SOURCES_DIR})
+endif()

cmake/Modules/Packages/PYTHON.cmake

@@ -0,0 +1,6 @@
+if(PKG_PYTHON)
+  find_package(PythonLibs REQUIRED)
+  add_definitions(-DLMP_PYTHON)
+  include_directories(${PYTHON_INCLUDE_DIR})
+  list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
+endif()

cmake/Modules/Packages/QEQ.cmake

@@ -0,0 +1,20 @@
+# Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed
+if(PKG_QEQ)
+  set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
+  file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
+  file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
+
+  if(NOT PKG_MANYBODY)
+    list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
+    list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
+  endif()
+  set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
+
+  foreach(MY_HEADER ${QEQ_HEADERS})
+    AddStyleHeader(${MY_HEADER} FIX)
+  endforeach()
+
+  get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
+  list(APPEND LIB_SOURCES ${QEQ_SOURCES})
+  include_directories(${QEQ_SOURCES_DIR})
+endif()

cmake/Modules/Packages/USER-H5MD.cmake

@@ -0,0 +1,8 @@
+if(PKG_USER-H5MD)
+  enable_language(C)
+
+  find_package(HDF5 REQUIRED)
+  target_link_libraries(h5md ${HDF5_LIBRARIES})
+  target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
+  include_directories(${HDF5_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/USER-INTEL.cmake

@@ -0,0 +1,118 @@
+if(PKG_USER-INTEL)
+  check_include_file_cxx(immintrin.h FOUND_IMMINTRIN)
+  if(NOT FOUND_IMMINTRIN)
+    message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it")
+  endif()
+
+  add_definitions(-DLMP_USER_INTEL)
+
+  set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
+  set(INTEL_ARCH_VALUES cpu knl)
+  set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
+  validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
+  string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
+
+  find_package(Threads QUIET)
+  if(Threads_FOUND)
+    set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
+  else()
+    set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
+  endif()
+  set(INTEL_LRT_VALUES none threads c++11)
+  set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES})
+  validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES)
+  string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE)
+  if(INTEL_LRT_MODE STREQUAL "THREADS")
+    if(Threads_FOUND)
+      add_definitions(-DLMP_INTEL_USELRT)
+      list(APPEND LAMMPS_LINK_LIBS ${CMAKE_THREAD_LIBS_INIT})
+    else()
+      message(FATAL_ERROR "Must have working threads library for Long-range thread support")
+    endif()
+  endif()
+  if(INTEL_LRT_MODE STREQUAL "C++11")
+    add_definitions(-DLMP_INTEL_USERLRT -DLMP_INTEL_LRT11)
+  endif()
+
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+    if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
+      message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
+    endif()
+  else()
+    message(WARNING "USER-INTEL gives best performance with Intel compilers")
+  endif()
+
+  find_package(TBB QUIET)
+  if(TBB_FOUND)
+    list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES})
+  else()
+    add_definitions(-DLMP_INTEL_NO_TBB)
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
+    endif()
+  endif()
+
+  find_package(MKL QUIET)
+  if(MKL_FOUND)
+    add_definitions(-DLMP_USE_MKL_RNG)
+    list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
+  else()
+    message(STATUS "Pair style dpd/intel will be faster with MKL libraries")
+  endif()
+
+  if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
+    message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
+  endif()
+
+  if(INTEL_ARCH STREQUAL "KNL")
+    if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
+    endif()
+    set(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
+    set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
+    add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
+    add_definitions(-DLMP_INTEL_OFFLOAD)
+  else()
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost")
+      endif()
+      include(CheckCXXCompilerFlag)
+      foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
+        check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG})
+        if(COMPILER_SUPPORTS${_FLAG})
+          add_compile_options(${_FLAG})
+        endif()
+      endforeach()
+    else()
+      add_compile_options(-O3 -ffast-math)
+    endif()
+  endif()
+
+  # collect sources
+  set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
+  set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
+                         ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
+
+  set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
+
+  # detect styles which have a USER-INTEL version
+  RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
+  RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
+  RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
+  RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
+
+  get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
+  if(PKG_KSPACE)
+    list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
+    RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
+  endif()
+
+  list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
+  include_directories(${USER-INTEL_SOURCES_DIR})
+endif()

cmake/Modules/Packages/USER-MOLFILE.cmake

@@ -0,0 +1,10 @@
+if(PKG_USER-MOLFILE)
+  set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
+  add_library(molfile INTERFACE)
+  target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
+  # no need to link with -ldl on windows
+  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS molfile)
+endif()

cmake/Modules/Packages/USER-NETCDF.cmake

@@ -0,0 +1,6 @@
+if(PKG_USER-NETCDF)
+  find_package(NetCDF REQUIRED)
+  include_directories(${NETCDF_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
+  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
+endif()

cmake/Modules/Packages/USER-OMP.cmake

@@ -0,0 +1,42 @@
+if(PKG_USER-OMP)
+    set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
+    set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
+                         ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
+    add_definitions(-DLMP_USER_OMP)
+    set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
+
+    # detects styles which have USER-OMP version
+    RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
+    RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
+
+    get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
+
+    # manually add package dependent source files from USER-OMP that do not provide styles
+
+    if(PKG_ASPHERE)
+      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
+    endif()
+
+    if(PKG_RIGID)
+      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
+    endif()
+
+    if(PKG_USER-REAXC)
+      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
+    endif()
+
+    list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
+    include_directories(${USER-OMP_SOURCES_DIR})
+endif()

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -0,0 +1,79 @@
+if(PKG_USER-PLUMED)
+  find_package(GSL REQUIRED)
+  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
+  set(PLUMED_MODE_VALUES static shared runtime)
+  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
+  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
+  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
+
+  find_package(PkgConfig QUIET)
+  set(DOWNLOAD_PLUMED_DEFAULT ON)
+  if(PKG_CONFIG_FOUND)
+    pkg_check_modules(PLUMED QUIET plumed)
+    if(PLUMED_FOUND)
+      set(DOWNLOAD_PLUMED_DEFAULT OFF)
+    endif()
+  endif()
+
+  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
+  if(DOWNLOAD_PLUMED)
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded Plumed library with Ninja build tool")
+    endif()
+    if(BUILD_MPI)
+      set(PLUMED_CONFIG_MPI "--enable-mpi")
+      set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
+      set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})
+    else()
+      set(PLUMED_CONFIG_MPI "--disable-mpi")
+      set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})
+      set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
+    endif()
+    if(BUILD_OMP)
+      set(PLUMED_CONFIG_OMP "--enable-openmp")
+    else()
+      set(PLUMED_CONFIG_OMP "--disable-openmp")
+    endif()
+    message(STATUS "PLUMED download requested - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(plumed_build
+      URL https://github.com/plumed/plumed2/releases/download/v2.5.1/plumed-src-2.5.1.tgz
+      URL_MD5 c2a7b519e32197a120cdf47e0f194f81
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+                                               ${CONFIGURE_REQUEST_PIC}
+                                               --enable-modules=all
+                                               ${PLUMED_CONFIG_MPI}
+                                               ${PLUMED_CONFIG_OMP}
+                                               CXX=${PLUMED_CONFIG_CXX}
+                                               CC=${PLUMED_CONFIG_CC}
+    )
+    ExternalProject_get_property(plumed_build INSTALL_DIR)
+    set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
+    list(APPEND LAMMPS_DEPS plumed_build)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      add_definitions(-D__PLUMED_WRAPPER_CXX=1)
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${GSL_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_DL_LIBS})
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so ${CMAKE_DL_LIBS})
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
+    endif()
+    set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
+  else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(PLUMED REQUIRED plumed)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      add_definitions(-D__PLUMED_WRAPPER_CXX=1)
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel.so)
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
+    endif()
+    list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})
+  endif()
+  include_directories(${PLUMED_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/USER-QMMM.cmake

@@ -0,0 +1,9 @@
+if(PKG_USER-QMMM)
+  enable_language(Fortran)
+  enable_language(C)
+
+  message(WARNING "Building QMMM with CMake is still experimental")
+  find_package(QE REQUIRED)
+  include_directories(${QE_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES})
+endif()

cmake/Modules/Packages/USER-QUIP.cmake

@@ -0,0 +1,5 @@
+if(PKG_USER-QUIP)
+  enable_language(Fortran)
+  find_package(QUIP REQUIRED)
+  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES})
+endif()

cmake/Modules/Packages/USER-SCAFACOS.cmake

@@ -0,0 +1,62 @@
+if(PKG_USER-SCAFACOS)
+  enable_language(Fortran)
+  enable_language(C)
+
+  find_package(GSL REQUIRED)
+  find_package(PkgConfig QUIET)
+  set(DOWNLOAD_SCAFACOS_DEFAULT ON)
+  if(PKG_CONFIG_FOUND)
+    pkg_check_modules(SCAFACOS QUIET scafacos)
+    if(SCAFACOS_FOUND)
+      set(DOWNLOAD_SCAFACOS_DEFAULT OFF)
+    endif()
+  endif()
+  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
+  if(DOWNLOAD_SCAFACOS)
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded ScaFaCoS library with Ninja build tool")
+    endif()
+    message(STATUS "ScaFaCoS download requested - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(scafacos_build
+      URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
+      URL_MD5 bd46d74e3296bd8a444d731bb10c1738
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
+                                               --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
+                                               --with-internal-fftw --with-internal-pfft
+                                               --with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
+                                               FC=${CMAKE_MPI_Fortran_COMPILER}
+                                               CXX=${CMAKE_MPI_CXX_COMPILER}
+                                               CC=${CMAKE_MPI_C_COMPILER}
+                                               F77=
+    )
+    ExternalProject_get_property(scafacos_build INSTALL_DIR)
+    set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})
+    set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include)
+    list(APPEND LAMMPS_DEPS scafacos_build)
+    # list and order from pkg_config file of ScaFaCoS build
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a)
+    list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a)
+    list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
+    list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
+  else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(SCAFACOS REQUIRED scafacos)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
+  endif()
+  include_directories(${SCAFACOS_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/USER-SDPD.cmake

@@ -0,0 +1,13 @@
+# Fix rigid/meso requires RIGID to be installed
+if(PKG_USER-SDPD)
+  set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)
+
+  get_property(hlist GLOBAL PROPERTY FIX)
+  if(NOT PKG_RIGID)
+    list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
+    list(REMOVE_ITEM LIB_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
+  endif()
+  set_property(GLOBAL PROPERTY FIX "${hlist}")
+
+  include_directories(${USER-SDPD_SOURCES_DIR})
+endif()

cmake/Modules/Packages/USER-SMD.cmake

@@ -0,0 +1,28 @@
+if(PKG_USER-SMD)
+  find_package(Eigen3 NO_MODULE)
+  if(EIGEN3_FOUND)
+    set(DOWNLOAD_EIGEN3_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_EIGEN3_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
+  if(DOWNLOAD_EIGEN3)
+    message(STATUS "Eigen3 download requested - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(Eigen3_build
+      URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
+      URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+    )
+    ExternalProject_get_property(Eigen3_build SOURCE_DIR)
+    set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
+    list(APPEND LAMMPS_DEPS Eigen3_build)
+  else()
+    find_package(Eigen3 NO_MODULE)
+    mark_as_advanced(Eigen3_DIR)
+    if(NOT EIGEN3_FOUND)
+      message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
+    endif()
+  endif()
+  include_directories(${EIGEN3_INCLUDE_DIR})
+endif()

cmake/Modules/Packages/USER-VTK.cmake

@@ -0,0 +1,6 @@
+if(PKG_USER-VTK)
+  find_package(VTK REQUIRED NO_MODULE)
+  include(${VTK_USE_FILE})
+  add_definitions(-DLAMMPS_VTK)
+  list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
+endif()

cmake/Modules/Packages/VORONOI.cmake

@@ -0,0 +1,41 @@
+if(PKG_VORONOI)
+  find_package(VORO)
+  if(VORO_FOUND)
+    set(DOWNLOAD_VORO_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_VORO_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
+  if(DOWNLOAD_VORO)
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded Voro++ library with Ninja build tool")
+    endif()
+    message(STATUS "Voro++ download requested - we will build our own")
+    include(ExternalProject)
+
+    if(BUILD_SHARED_LIBS)
+      set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+    else()
+      set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+    endif()
+    string(APPEND VORO_BUILD_CFLAGS ${CMAKE_CXX_FLAGS})
+    set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+
+    ExternalProject_Add(voro_build
+      URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
+      URL_MD5 2338b824c3b7b25590e18e8df5d68af9
+      CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
+      )
+    ExternalProject_get_property(voro_build SOURCE_DIR)
+    set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a)
+    set(VORO_INCLUDE_DIRS ${SOURCE_DIR}/src)
+    list(APPEND LAMMPS_DEPS voro_build)
+  else()
+    find_package(VORO)
+    if(NOT VORO_FOUND)
+      message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+    endif()
+  endif()
+  include_directories(${VORO_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
+endif()

cmake/Modules/StyleHeaderUtils.cmake

@@ -91,6 +91,10 @@ function(RegisterFixStyle path)
     AddStyleHeader(${path} FIX)
 endfunction(RegisterFixStyle)
 
+function(RegisterIntegrateStyle path)
+    AddStyleHeader(${path} INTEGRATE)
+endfunction(RegisterIntegrateStyle)
+
 function(RegisterStyles search_path)
     FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
     FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
@@ -177,3 +181,88 @@ function(DetectBuildSystemConflict lammps_src_dir)
     endforeach()
   endif()
 endfunction(DetectBuildSystemConflict)
+
+
+function(FindPackagesHeaders path style_class file_pattern headers)
+    file(GLOB files "${path}/${file_pattern}*.h")
+    get_property(plist GLOBAL PROPERTY ${headers})
+
+    foreach(file_name ${files})
+        file(STRINGS ${file_name} is_style LIMIT_COUNT 1 REGEX ${style_class})
+        if(is_style)
+            list(APPEND plist ${file_name})
+        endif()
+    endforeach()
+    set_property(GLOBAL PROPERTY ${headers} "${plist}")
+endfunction(FindPackagesHeaders)
+
+function(RegisterPackages search_path)
+    FindPackagesHeaders(${search_path} ANGLE_CLASS     angle_     PKGANGLE     ) # angle     ) # force
+    FindPackagesHeaders(${search_path} ATOM_CLASS      atom_vec_  PKGATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
+    FindPackagesHeaders(${search_path} BODY_CLASS      body_      PKGBODY      ) # body      ) # atom_vec_body
+    FindPackagesHeaders(${search_path} BOND_CLASS      bond_      PKGBOND      ) # bond      ) # force
+    FindPackagesHeaders(${search_path} COMMAND_CLASS   "[^.]"     PKGCOMMAND   ) # command   ) # input
+    FindPackagesHeaders(${search_path} COMPUTE_CLASS   compute_   PKGCOMPUTE   ) # compute   ) # modify
+    FindPackagesHeaders(${search_path} DIHEDRAL_CLASS  dihedral_  PKGDIHEDRAL  ) # dihedral  ) # force
+    FindPackagesHeaders(${search_path} DUMP_CLASS      dump_      PKGDUMP      ) # dump      ) # output    write_dump
+    FindPackagesHeaders(${search_path} FIX_CLASS       fix_       PKGFIX       ) # fix       ) # modify
+    FindPackagesHeaders(${search_path} IMPROPER_CLASS  improper_  PKGIMPROPER  ) # improper  ) # force
+    FindPackagesHeaders(${search_path} INTEGRATE_CLASS "[^.]"     PKGINTEGRATE ) # integrate ) # update
+    FindPackagesHeaders(${search_path} KSPACE_CLASS    "[^.]"     PKGKSPACE    ) # kspace    ) # force
+    FindPackagesHeaders(${search_path} MINIMIZE_CLASS  min_       PKGMINIMIZE  ) # minimize  ) # update
+    FindPackagesHeaders(${search_path} NBIN_CLASS      nbin_      PKGNBIN      ) # nbin      ) # neighbor
+    FindPackagesHeaders(${search_path} NPAIR_CLASS     npair_     PKGNPAIR     ) # npair     ) # neighbor
+    FindPackagesHeaders(${search_path} NSTENCIL_CLASS  nstencil_  PKGNSTENCIL  ) # nstencil  ) # neighbor
+    FindPackagesHeaders(${search_path} NTOPO_CLASS     ntopo_     PKGNTOPO     ) # ntopo     ) # neighbor
+    FindPackagesHeaders(${search_path} PAIR_CLASS      pair_      PKGPAIR      ) # pair      ) # force
+    FindPackagesHeaders(${search_path} READER_CLASS    reader_    PKGREADER    ) # reader    ) # read_dump
+    FindPackagesHeaders(${search_path} REGION_CLASS    region_    PKGREGION    ) # region    ) # domain
+endfunction(RegisterPackages)
+
+function(CreatePackagesHeader path filename)
+  set(temp "")
+  if(ARGC GREATER 2)
+    list(REMOVE_AT ARGV 0 1)
+    foreach(FNAME ${ARGV})
+      set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${FNAME}")
+      get_filename_component(DNAME ${FNAME} DIRECTORY)
+      get_filename_component(DNAME ${DNAME} NAME)
+      get_filename_component(FNAME ${FNAME} NAME)
+      set(temp "${temp}#undef PACKAGE\n#define PACKAGE \"${DNAME}\"\n")
+      set(temp "${temp}#include \"${DNAME}/${FNAME}\"\n")
+    endforeach()
+  endif()
+  message(STATUS "Generating ${filename}...")
+  file(WRITE "${path}/${filename}.tmp" "${temp}" )
+  execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
+  set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}")
+endfunction(CreatePackagesHeader)
+
+function(GeneratePackagesHeader path property style)
+  get_property(files GLOBAL PROPERTY ${property})
+  CreatePackagesHeader("${path}" "packages_${style}.h" ${files})
+endfunction(GeneratePackagesHeader)
+
+function(GeneratePackagesHeaders output_path)
+    GeneratePackagesHeader(${output_path} PKGANGLE      angle     ) # force
+    GeneratePackagesHeader(${output_path} PKGATOM_VEC   atom      ) # atom      atom_vec_hybrid
+    GeneratePackagesHeader(${output_path} PKGBODY       body      ) # atom_vec_body
+    GeneratePackagesHeader(${output_path} PKGBOND       bond      ) # force
+    GeneratePackagesHeader(${output_path} PKGCOMMAND    command   ) # input
+    GeneratePackagesHeader(${output_path} PKGCOMPUTE    compute   ) # modify
+    GeneratePackagesHeader(${output_path} PKGDIHEDRAL   dihedral  ) # force
+    GeneratePackagesHeader(${output_path} PKGDUMP       dump      ) # output    write_dump
+    GeneratePackagesHeader(${output_path} PKGFIX        fix       ) # modify
+    GeneratePackagesHeader(${output_path} PKGIMPROPER   improper  ) # force
+    GeneratePackagesHeader(${output_path} PKGINTEGRATE  integrate ) # update
+    GeneratePackagesHeader(${output_path} PKGKSPACE     kspace    ) # force
+    GeneratePackagesHeader(${output_path} PKGMINIMIZE   minimize  ) # update
+    GeneratePackagesHeader(${output_path} PKGNBIN       nbin      ) # neighbor
+    GeneratePackagesHeader(${output_path} PKGNPAIR      npair     ) # neighbor
+    GeneratePackagesHeader(${output_path} PKGNSTENCIL   nstencil  ) # neighbor
+    GeneratePackagesHeader(${output_path} PKGNTOPO      ntopo     ) # neighbor
+    GeneratePackagesHeader(${output_path} PKGPAIR       pair      ) # force
+    GeneratePackagesHeader(${output_path} PKGREADER     reader    ) # read_dump
+    GeneratePackagesHeader(${output_path} PKGREGION     region    ) # domain
+endfunction(GeneratePackagesHeaders)
+

cmake/Modules/Testing.cmake

@@ -0,0 +1,52 @@
+###############################################################################
+# Testing
+###############################################################################
+option(ENABLE_TESTING "Enable testing" OFF)
+if(ENABLE_TESTING AND BUILD_EXE)
+  enable_testing()
+  option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
+  option(LAMMPS_TESTING_GIT_TAG    "Git tag of lammps-testing" "master")
+  mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
+
+  if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
+    include(FetchContent)
+
+    FetchContent_Declare(lammps-testing
+      GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
+      GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
+    )
+
+    FetchContent_GetProperties(lammps-testing)
+    if(NOT lammps-testing_POPULATED)
+      message(STATUS "Downloading tests...")
+      FetchContent_Populate(lammps-testing)
+    endif()
+
+    set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
+  elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
+    message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
+                    "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
+  endif()
+
+  add_test(ShowHelp ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -help)
+
+  if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
+    message(STATUS "Running test discovery...")
+
+    file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
+    foreach(script_path ${TEST_SCRIPTS})
+      get_filename_component(TEST_NAME ${script_path} EXT)
+      get_filename_component(SCRIPT_NAME ${script_path} NAME)
+      get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
+      string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
+      string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
+      string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
+      set(TEST_NAME "test_core_${TEST_NAME}_serial")
+      add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})
+      set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})
+    endforeach()
+    list(LENGTH TEST_SCRIPTS NUM_TESTS)
+
+    message(STATUS "Found ${NUM_TESTS} tests.")
+  endif()
+endif()

cmake/README.md

@@ -155,11 +155,13 @@ make
 
 The CMake build exposes a lot of different options. In the old build system
 some of the package selections were possible by using special make target like
-`make yes-std` or `make no-lib`. Achieving the same result with cmake requires
+`make yes-std` or `make no-lib`. Achieving a similar result with cmake requires
 specifying all options manually. This can quickly become a very long command
 line that is hard to handle.  While these could be stored in a simple script
 file, there is another way of defining "presets" to compile LAMMPS in a certain
-way.
+way. Since the cmake build process - contrary to the conventional build system -
+includes the compilation of the bundled libraries into the standard build process,
+the grouping of those presets is somewhat different.
 
 A preset is a regular CMake script file that can use constructs such as
 variables, lists and for-loops to manipulate configuration options and create
@@ -171,10 +173,10 @@ Such a file can then be passed to cmake via the `-C` flag. Several examples of
 presets can be found in the `cmake/presets` folder.
 
 ```bash
-# build LAMMPS with all "standard" packages which don't use libraries and enable GPU package
+# build LAMMPS with all packages enabled which don't use external libraries and enable GPU package
 mkdir build
 cd build
-cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
+cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on ../cmake
 ```
 
 # Reference
@@ -209,7 +211,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
   </td>
 </tr>
 <tr>
-  <td><code><CMAKE_VERBOSE_MAKEFILE/code></td>
+  <td><code>CMAKE_VERBOSE_MAKEFILE</code></td>
   <td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
   <td>
   <dl>
@@ -1429,6 +1431,17 @@ TODO
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>INTEL_LRT_MODE</code></td>
+  <td>How to support Long-range thread mode in Verlet integration</td>
+  <td>
+  <dl>
+    <dt><code>threads</code> (default, if pthreads available)</dt>
+    <dt><code>none</code> (default, if pthreads not available)</dt>
+    <dt><code>c++11</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 

cmake/etc/profile.d/lammps.csh.in

@@ -1,2 +1,4 @@
-# set environment for LAMMPS executables to find potential files
+# set environment for LAMMPS and msi2lmp executables
+# to find potential and force field files
 if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@
+if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@

cmake/etc/profile.d/lammps.sh.in

@@ -1,2 +1,5 @@
-# set environment for LAMMPS executables to find potential files
+# set environment for LAMMPS and msi2lmp executables
-export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
+# to find potential and force field files
+LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
+MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@}
+export LAMMPS_POTENTIALS MSI2LMP_LIBRARY

cmake/presets/all_off.cmake

@@ -1,21 +1,17 @@
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+# preset that turns on all existing packages off. can be used to reset
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
+# an existing package selection without losing any other settings
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
 
-set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
-                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+        MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
-                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+        SRD VORONOI
-                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
+        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
-                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-                  USER-UEF USER-VTK)
+        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
-
+        USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
+        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
+        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
+        USER-TALLY USER-UEF USER-VTK USER-YAFF)
-
-set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/all_on.cmake

@@ -1,21 +1,19 @@
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+# preset that turns on all existing packages. using the combination
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
+# this preset followed by the nolib.cmake preset should configure a
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
+# LAMMPS binary, with as many packages included, that can be compiled
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+# with just a working C++ compiler and an MPI library.
 
-set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
-                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+        MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
-                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+        SRD VORONOI
-                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
+        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
-                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-                  USER-UEF USER-VTK)
+        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
-
+        USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
+        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
+        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
+        USER-TALLY USER-UEF USER-VTK USER-YAFF)
-
-set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/clang.cmake

@@ -0,0 +1,17 @@
+# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBG" CACHE STRING "" FORCE)
+set(MPI_CXX "clang++" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+
+set(OpenMP_C "clang" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "/usr/lib64/libomp.so" CACHE PATH "" FORCE)
+

cmake/presets/manual_selection.cmake

@@ -1,71 +0,0 @@
-set(PKG_ASPHERE OFF CACHE BOOL "" FORCE)
-set(PKG_BODY OFF CACHE BOOL "" FORCE)
-set(PKG_CLASS2 OFF CACHE BOOL "" FORCE)
-set(PKG_COLLOID OFF CACHE BOOL "" FORCE)
-set(PKG_COMPRESS OFF CACHE BOOL "" FORCE)
-set(PKG_CORESHELL OFF CACHE BOOL "" FORCE)
-set(PKG_DIPOLE OFF CACHE BOOL "" FORCE)
-set(PKG_GPU OFF CACHE BOOL "" FORCE)
-set(PKG_GRANULAR OFF CACHE BOOL "" FORCE)
-set(PKG_KIM OFF CACHE BOOL "" FORCE)
-set(PKG_KOKKOS OFF CACHE BOOL "" FORCE)
-set(PKG_KSPACE OFF CACHE BOOL "" FORCE)
-set(PKG_LATTE OFF CACHE BOOL "" FORCE)
-set(PKG_LIB OFF CACHE BOOL "" FORCE)
-set(PKG_MANYBODY OFF CACHE BOOL "" FORCE)
-set(PKG_MC OFF CACHE BOOL "" FORCE)
-set(PKG_MEAM OFF CACHE BOOL "" FORCE)
-set(PKG_MISC OFF CACHE BOOL "" FORCE)
-set(PKG_MOLECULE OFF CACHE BOOL "" FORCE)
-set(PKG_MPIIO OFF CACHE BOOL "" FORCE)
-set(PKG_MSCG OFF CACHE BOOL "" FORCE)
-set(PKG_OPT OFF CACHE BOOL "" FORCE)
-set(PKG_PERI OFF CACHE BOOL "" FORCE)
-set(PKG_POEMS OFF CACHE BOOL "" FORCE)
-set(PKG_PYTHOFF OFF CACHE BOOL "" FORCE)
-set(PKG_QEQ OFF CACHE BOOL "" FORCE)
-set(PKG_REAX OFF CACHE BOOL "" FORCE)
-set(PKG_REPLICA OFF CACHE BOOL "" FORCE)
-set(PKG_RIGID OFF CACHE BOOL "" FORCE)
-set(PKG_SHOCK OFF CACHE BOOL "" FORCE)
-set(PKG_SNAP OFF CACHE BOOL "" FORCE)
-set(PKG_SRD OFF CACHE BOOL "" FORCE)
-set(PKG_VOROFFOI OFF CACHE BOOL "" FORCE)
-
-set(PKG_USER OFF CACHE BOOL "" FORCE)
-set(PKG_USER-ATC OFF CACHE BOOL "" FORCE)
-set(PKG_USER-AWPMD OFF CACHE BOOL "" FORCE)
-set(PKG_USER-BOCS OFF CACHE BOOL "" FORCE)
-set(PKG_USER-CGDNA OFF CACHE BOOL "" FORCE)
-set(PKG_USER-CGSDK OFF CACHE BOOL "" FORCE)
-set(PKG_USER-COLVARS OFF CACHE BOOL "" FORCE)
-set(PKG_USER-DIFFRACTIOFF OFF CACHE BOOL "" FORCE)
-set(PKG_USER-DPD OFF CACHE BOOL "" FORCE)
-set(PKG_USER-DRUDE OFF CACHE BOOL "" FORCE)
-set(PKG_USER-EFF OFF CACHE BOOL "" FORCE)
-set(PKG_USER-FEP OFF CACHE BOOL "" FORCE)
-set(PKG_USER-H5MD OFF CACHE BOOL "" FORCE)
-set(PKG_USER-INTEL OFF CACHE BOOL "" FORCE)
-set(PKG_USER-LB OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MANIFOLD OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MEAMC OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MESO OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MGPT OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MISC OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE)
-set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE)
-set(PKG_USER-OMP OFF CACHE BOOL "" FORCE)
-set(PKG_USER-PHONON OFF CACHE BOOL "" FORCE)
-set(PKG_USER-PLUMED OFF CACHE BOOL "" FORCE)
-set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
-set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
-set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)
-set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE)
-set(PKG_USER-SDPD OFF CACHE BOOL "" FORCE)
-set(PKG_USER-SMD OFF CACHE BOOL "" FORCE)
-set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE)
-set(PKG_USER-SPH OFF CACHE BOOL "" FORCE)
-set(PKG_USER-TALLY OFF CACHE BOOL "" FORCE)
-set(PKG_USER-UEF OFF CACHE BOOL "" FORCE)
-set(PKG_USER-VTK OFF CACHE BOOL "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -0,0 +1,17 @@
+set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+                 GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI POEMS QEQ
+                 REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD
+                 USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
+                 USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD
+                 USER-MEAMC USER-MESO USER-MISC USER-MOFFF USER-MOLFILE USER-OMP
+                 USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD USER-SMD
+                 USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
+
+foreach(PKG ${WIN_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()
+
+set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
+set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
+set(INTEL_LRT_MODE "none" CACHE STRING "" FORCE)

cmake/presets/minimal.cmake

@@ -0,0 +1,8 @@
+# preset that turns on just a few, frequently used packages
+# this will be compiled quickly and handle a lot of common inputs.
+
+set(ALL_PACKAGES KSPACE MANYBODY MOLECULE RIGID)
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/most.cmake

@@ -0,0 +1,15 @@
+# preset that turns on a wide range of packages, some of which require
+# external libraries. Compared to all_on.cmake some more unusual packages
+# are removed. The resulting binary should be able to run most inputs.
+
+set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
+        GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
+        PYTHON QEQ REPLICA RIGID SHOCK SRD VORONOI
+        USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
+        USER-DRUDE USER-FEP USER-MEAMC USER-MESO
+        USER-MISC USER-MOFFF USER-OMP USER-PLUMED USER-PHONON USER-REAXC
+        USER-SPH USER-SMD USER-UEF USER-YAFF)
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/nolib.cmake

@@ -1,21 +1,10 @@
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+# preset that turns off all packages that require some form of external
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
+# library or special compiler (fortran or cuda) or equivalent.
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
 
-set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
-                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+        VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
-                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+        USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
-                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+        USER-SCAFACOS USER-SMD USER-VTK)
-                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
-                  USER-UEF USER-VTK)
-
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
-                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
-
-set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 
 foreach(PKG ${PACKAGES_WITH_LIB})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/std.cmake

@@ -1,22 +0,0 @@
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
-
-set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
-                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
-                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
-                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
-                  USER-UEF USER-VTK)
-
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
-                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
-
-set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
-
-foreach(PKG ${STANDARD_PACKAGES})
-  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
-endforeach()

cmake/presets/std_nolib.cmake

@@ -1,26 +0,0 @@
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
-
-set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
-                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
-                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
-                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
-                  USER-UEF USER-VTK)
-
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
-                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
-
-set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
-
-foreach(PKG ${STANDARD_PACKAGES})
-  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
-endforeach()
-
-foreach(PKG ${PACKAGES_WITH_LIB})
-  set(PKG_${PKG} OFF CACHE BOOL "" FORCE)
-endforeach()

cmake/presets/user.cmake

@@ -1,22 +0,0 @@
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
-
-set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
-                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
-                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
-                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
-                  USER-UEF USER-VTK)
-
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
-                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
-
-set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
-
-foreach(PKG ${USER_PACKAGES})
-  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
-endforeach()

doc/Makefile

@@ -211,7 +211,7 @@ $(VENV):
 	@( \
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install Sphinx==1.7.6; \
+		pip install Sphinx; \
 		deactivate;\
 	)
 

doc/lammps.1

@@ -1,40 +1,259 @@
-.TH LAMMPS "2018-08-22"
+.TH LAMMPS "18 June 2019" "2019-06-18"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
 
 .SH SYNOPSIS
 .B lmp
--in in.file
+\-in <input file> [OPTIONS] ...
 
 or
 
 mpirun \-np 2
 .B lmp
--in in.file
+<input file> [OPTIONS] ...
+
+or
+
+.B lmp
+\-r2data file.restart file.data
 
 .SH DESCRIPTION
 .B LAMMPS
-LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale 
+is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale
-Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft 
+\fBA\fRtomic/\fBM\fRolecular \fBM\fRassively \fBP\fRarallel \fBS\fRimulator.
-materials (biomolecules, polymers) and solid-state materials (metals, 
+.B LAMMPS
+has potentials for soft
+materials (bio-molecules, polymers) and solid-state materials (metals,
 semiconductors) and coarse-grained or mesoscopic systems. It can be used to
 model atoms or, more generically, as a parallel particle simulator at the
 atomic, meso, or continuum scale.
 
-See http://lammps.sandia.gov/ for documentation.
+See https://lammps.sandia.gov/ for more information and documentation.
+
+.SH EXECUTABLE NAME
+The
+.B LAMMPS
+executable can have different names depending on how it was configured,
+compiled and installed. It will be either
+.B lmp
+or
+.B lmp_<machine name>.
+The <machine name> suffix corresponds to the (machine specific) makefile
+used to compile
+.B LAMMPS
+when using the conventional build process. When building
+.B LAMMPS
+using
+.B CMake
+this <machine name> parameter can be chosen arbitrarily at configuration
+time, but more common is to just use
+.B lmp
+without a suffix. In this manpage we will use
+.B lmp
+to represent any of those names.
 
 .SH OPTIONS
-See https://lammps.sandia.gov/doc/Run_options.html for details on
+
-command-line options.
+.TP
+\fB\-h\fR or \fB\-help\fR
+Print a brief help summary and a list of settings and options compiled
+into this executable. It also explicitly lists all LAMMPS styles
+(atom_style, fix, compute, pair_style, bond_style, etc) available in
+the specific executable. This can tell you if the command you want to
+use was included via the appropriate package at compile time.
+LAMMPS will print the info and immediately exit if this switch is used.
+.TP
+\fB\-e\fR or \fB\-echo\fR
+Set the style of command echoing. The style can be
+.B none
+or
+.B screen
+or
+.B log
+or
+.B both.
+Depending on the style, each command read from the input script will
+be echoed to the screen and/or logfile. This can be useful to figure
+out which line of your script is causing an input error.
+The default value is
+.B log.
+.TP
+\fB\-i <input file>\fR or \fB\-in <input file>\fR
+Specify a file to use as an input script. If it is not specified,
+LAMMPS reads its script from standard input. This is a required
+switch when running LAMMPS in multi-partition mode.
+.TP
+\fB\-k on/off [keyword value]\fR or \fB\-kokkos on/off [keyword value]\fR
+Enable or disable general KOKKOS support, as provided by the KOKKOS
+package.  Even if LAMMPS is built with this package, this switch must
+be set to \fBon\fR to enable running with KOKKOS-enabled styles. More
+details on this switch and its optional keyword value pairs are discussed
+at: https://lammps.sandia.gov/doc/Run_options.html
+.TP
+\fB\-l <log file>\fR or \fB\-log <log file>\fR
+Specify a log file for LAMMPS to write status information to.
+The default value is "log.lammps". If the file name "none" is used,
+\fBLAMMPS\fR will not write a log file. In multi-partition mode only
+some high-level all-partition information is written to the "<log file>"
+file, the remainder is written in a per-partition file "<log file>.N"
+with "N" being the respective partition number, unless overridden
+by the \-plog flag (see below).
+.TP
+\fB\-m <number>\fR or \fB\-mpicolor <number>\fR
+If used, this must be the first command-line argument after the
+.B LAMMPS
+executable name. It is only used when
+.B LAMMPS
+is launched by an mpirun command which also launches one or more
+other executable(s) at the same time.
+.B LAMMPS
+and the other executable(s) perform an MPI_Comm_split(), each with
+their own different colors, to split the MPI_COMM_WORLD communicator
+for each executable to the subset of processors they are supposed to
+be actually running on. Currently, this is only used in
+.B LAMMPS
+to perform client/server messaging with another application.
+.B LAMMPS
+can act as either a client or server (or both).
+.TP
+\fB\-nc\fR or \fB\-nocite\fR
+Disable writing the "log.cite" file which is normally written to
+list references for specific cite-able features used during a
+.B LAMMPS
+run.
+.TP
+\fB\-pk <style> [options]\fR or \fB\-package <style> [options]\fR
+Invoke the \fBpackage\R command with <style> and optional arguments.
+The syntax is the same as if the command appeared in an input script.
+For example "-pk gpu 2" is the same as "package gpu 2" in the input
+script. The possible styles and options are discussed in the
+.B LAMMPS
+manual for the "package" command. This switch can be used multiple
+times, e.g. to set options for the USER-INTEL and USER-OMP packages
+when used together. Along with the "-sf" or "-suffix" switch, this
+is a convenient mechanism for invoking accelerator packages and their
+options without having to edit an input script.
+.TP
+\fB\-p\fR or \fB\-partition\fR
+Invoke
+.B LAMMPS
+in multi-partition mode. Without this,
+.B LAMMPS
+uses all P processors allocated via MPI to run a single simulation.
+If this switch is used, the P processors are split into separate
+partitions and each partition runs its own simulation. The arguments
+to the switch specify the number of processors in each partition.
+Arguments of the form "MxN" mean M partitions, each with N processors.
+Arguments of the form "N" mean a single partition with N processors.
+The sum of processors in all partitions must be equal P. Thus the
+command “-partition 8x2 4 5” has 10 partitions and runs on a total
+of 25 processors.  Running with multiple partitions is required for
+multi-replica simulations, where each replica runs on on one or more
+few processors.
+.TP
+\fB\-pl <basename>\fR or \fB\-plog <basename>\fR
+Specify the base name for the per-partition log files in multi-partition
+runs, where partition N writes log information to <basename>.N.
+If basename is set to "none", then no per-partition log files are created.
+This overrides the name specified in the \-log command-line option.
+.TP
+\fB\-ps <basename>\fR or \fB\-pscreen <basename>\fR
+Specify the base name for the per-partition screen files in multi-partition
+runs, where partition N writes screen output to <basename>.N.
+If basename is set to "none", then no per-partition screen files are created.
+The default value is "screen" or whatever is set by the \-screen flag.
+.TP
+\fB\-r2data <restart file> [remap] <data file>\fR or
+\fB\-restart2data <restart file> [remap] <data file>\fR
+Convert <restart file> previously written by
+.B LAMMPS
+into a data file and immediately exit. This option has replaced the
+external restart2data executable. Following <restart file>
+argument, the optional word "remap" may be used. This has the
+same effect like adding it to a "read_restart" command.
+The syntax following the <data file> name is identical to the
+arguments of the "write_data" command. See the
+.B LAMMPS
+manual for details on either of the two commands.
+.TP
+\fB\-r2dump <restart file> [remap] <dump file>\fR or
+\fB\-restart2dump <restart file> [remap] <dump file>\fR
+Convert <restart file> previously written by
+.B LAMMPS
+into a dump file and immediately exit. Following <restart file>
+argument, the optional word "remap" may be used. This has the
+same effect like adding it to a "read_restart" command.
+The syntax following the <dump file> name is identical to the
+arguments of the "dump" command. See the
+.B LAMMPS
+manual for details on either of the two commands.
+.TP
+\fB\-sc <file name>\fR or \fB\-screen <file name>\fR
+Specify a file for
+.B LAMMPS
+to write its screen information to. By default, this will be
+the standard output. If <file name> is "none", (most) screen
+output will be suppressed.  In multi-partition mode only
+some high-level all-partition information is written to the
+screen or "<file name>" file, the remainder is written in a
+per-partition file "screen.N" or "<file name>.N" 
+with "N" being the respective partition number, and unless
+overridden by the \-pscreen flag (see above).
+.TP
+\fB\-sf <suffix>\fR or \fB\-suffix <suffix>\fR
+Use variants of various styles in the input, if they exist. This is
+achieved by transparently trying to convert a style named <my/style>
+into <my/style/suffix> if that latter style exists, but otherwise
+fall back to the former. The most useful suffixes are  "gpu",
+"intel", "kk", "omp", "opt", or "hybrid". These refer to styles from
+optional packages that LAMMPS can be built with. The hybrid suffix is
+special, as it enables, having two suffixes tried (e.g. first "intel"
+and then "omp") and thus requires two arguments. Along with the
+"-package" command-line switch, this is a convenient mechanism for
+invoking styles from accelerator packages and setting their options
+without having to edit an input script.
+
+See https://lammps.sandia.gov/doc/Run_options.html for additional
+details and discussions on command-line options.
+
+.SH LAMMPS BASICS
+LAMMPS executes by reading commands from a input script (text file),
+one line at a time.  When the input script ends, LAMMPS exits.  Each
+command causes LAMMPS to take some action.  It may set or change an
+internal, read and parse a file, or run a simulation.  Most commands
+have default settings, which means you only need to use the command
+if you wish to change the default.
+
+The ordering of commands in an input script is usually not very important
+unless a command like "run" is encountered, which starts some calculation
+using the current internal state. Also, if a "pair_style" or "bond_style"
+other similar style command is issued that has a different name from what
+was previously active, it will replace the previous style and wipe out
+all corresponding "pair_coeff" or "bond_coeff" or equivalent settings.
+Some commands are only valid when they follow other commands.  For
+example you cannot set the temperature of a group of atoms until atoms
+have been defined and a group command is used to define which atoms
+belong to the group of a given name. Sometimes command B will use values
+that can be set by command A. This means command A must precede command
+B in the input to have the desired effect. Some commands must be issued
+.B before
+the simulation box is defined and others can only be issued
+.B after.
+Many input script errors are detected by
+.B LAMMPS
+and an ERROR or WARNING message is printed.  The documentation for
+each command lists restrictions on how the command can be used, and
+the chapter on errors in the
+.B LAMMPS
+manual gives some additional information about error messages, if possible.
 
 .SH COPYRIGHT
-© 2003--2018 Sandia Corporation
+© 2003--2019 Sandia Corporation
 
 This package is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
+it under the terms of the GNU General Public License version 2 as
-the Free Software Foundation; either version 2 of the License, or
+published by the Free Software Foundation.
-(at your option) any later version.
 
 This package is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of

doc/msi2lmp.1

@@ -0,0 +1,111 @@
+.TH MSI2LMP "v3.9.9" "2018-11-05"
+.SH NAME
+.B MSI2LMP
+\- Converter for Materials Studio files to LAMMPS
+
+.SH SYNOPSIS
+.B msi2lmp
+<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
+
+.SH DESCRIPTION
+.PP
+.B MSI2LMP
+is a tool bundled with LAMMPS to aide in the conversion of simulation
+inputs from Biovia's Materials Studio software for use with LAMMPS.
+It is a standalone program that generates a LAMMPS data file based on
+the information in an MS .car file (atom coordinates), an .mdf file
+(molecular topology and atom types) and an .frc (forcefield parameters)
+file.  The .car and .mdf files are specific to a molecular system while
+the .frc file is specific to a forcefield (variant).  The only coherency
+needed between .frc and .car/.mdf files are the atom types.
+.PP
+
+.SH OPTIONS
+.TP
+\fB\<ROOTNAME>\fR
+This has to be the first argument and is a
+.B mandatory
+argument. It defines the root of the file names; i.e. for a
+.B <ROOTNAME>
+of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf'
+in the current working directory.
+.B msi2lmp
+will then read and process those files according to its remaining settings.
+All other settins are optional and have defaults as listed.
+.TP
+\fB\-c <I,1,II,2,O,0>\fR, \fB\-class <I,1,II,2,O,0>\fR
+The \-c or \-class option selects the force field class, i.e which pair
+styles and bond styles and so on are required in the LAMMPS input file.
+Class I or class 1 uses similar combination of functional forms as Amber
+and Charmm force field and support the force fields 
+.B cvff
+and
+.B clayff.
+Class II or class 2 corresponds to the more complex force fields
+.B COMPASS
+and
+.B pcff.
+Class O or class 0 finally is an experimental and incomplete extension
+and supports generating output for
+.B OPLS-AA
+.TP
+\fB\-f <ffname>\fR, \fB\-frc <ffname>\fR
+The \-c or \-frc option allows the selection of the force field parameter
+file
+.B<ffname>.frc.
+Valid names for <ffname> with this distribution are: cvff, clayff, cvff_aug,
+pcff, compass_published, cff91, and oplsaa. If the argument is a pathname,
+i.e. it starts with a '.' or a '/', then this absolute path is used to read
+the force field, otherwise
+.B msi2lmp
+will look in the folder pointed to by the environment variable
+$MSI2LMP_LIBRARY. If the variable is not set, then it will look in the current
+directory. The extension '.frc' is appended, if missing.
+Default is to look for the cvff.frc force field file.
+.TP
+\fB\-p <loglevel>\fR, \fB\-print <loglevel>\fR,
+Selects the amount of information messages about the progress of the
+conversion printed to the screen.
+.B <loglevel>
+can be a number from 0 (silent except for errors) to 3 (very detailed).
+.TP
+\fB\-i\fR, \fB\-ignore\fR,
+Ignore errors about missing parameters and use 0.0 for the respective
+force constants making these no-ops. Is correct to be used for a few
+molecules and settings, but often an indication, that either the atom
+type assignment have errors, or the force field file is missing entries.
+.TP
+\fB\-n\fR, \fB\-nocenter\fR,
+Do not center the box around the (geometrical) center of the atoms,
+but around the origin. Default is to recenter.
+.TP
+\fB\-o\fR, \fB\-oldstyle\fR,
+Write out a data file without style hint comments to be compatible
+with old LAMMPS versions. Default is to write out those comments.
+.TP
+\fB-s <x> <y> <z>\fR, \fB-shift <x> <y> <z>\fR,
+Shift the entire system (box and coordinates) by a vector
+(default: 0.0 0.0 0.0).
+.TP
+
+.SH EXAMPLES
+
+msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc
+
+msi2lmp benzene-class1 -c I
+
+msi2lmp decane -c 0 -f oplsaa
+
+
+.SH COPYRIGHT
+© 2003--2019 Sandia Corporation
+
+This package is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License version 2 as
+published by the Free Software Foundation.
+
+This package is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+

doc/src/Build_cmake.txt

@@ -28,20 +28,29 @@ Makefile(s). Example:
 
 cd lammps                        # change to the LAMMPS distribution directory
 mkdir build; cd build            # create a new directory (folder) for build
-cmake ../cmake \[options ...\]   # configuration with (command-line) cmake
+cmake \[options ...\] ../cmake     # configuration with (command-line) cmake
 make                             # compilation :pre
 
 The cmake command will detect available features, enable selected
-packages and options, and will generate the build environment.  The make
+packages and options, and will generate the build environment.  By default
-command will then compile and link LAMMPS, producing (by default) an
+this build environment will be created for "Unix Makefiles" on most
-executable called "lmp" and a library called "liblammps.a" in the
+platforms and particularly on Linux.  However, alternate build tools
-"build" folder.
+(e.g. Ninja) and support files for Integrated Development Environments
+(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
+selected via the "-G" command line flag. For the rest of the documentation
+we will assume that the build environment is generated for makefiles
+and thus the make command will be used to compile and link LAMMPS as
+indicated above, producing (by default) an executable called "lmp" and
+a library called "liblammps.a" in the "build" folder.  When generating
+a build environment for the "Ninja" build tool, the build command would
+be "ninja" instead of "make".
 
 If your machine has multiple CPU cores (most do these days), using a
 command like "make -jN" (with N being the number of available local
 CPU cores) can be much faster.  If you plan to do development on
 LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
-ccache (= Compiler Cache) software may speed up compilation even more.
+ccache (= Compiler Cache) software may speed up repeated compilation
+even more.
 
 After compilation, you can optionally copy the LAMMPS executable and
 library into your system folders (by default under $HOME/.local) with:
@@ -108,7 +117,8 @@ command-line options.  Several useful ones are:
 -D CMAKE_BUILD_TYPE=type      # type = Release or Debug
 -G output                     # style of output CMake generates
 -DVARIABLE=value              # setting for a LAMMPS feature to enable
--D VARIABLE=value             # ditto, but cannot come after CMakeLists.txt dir :pre
+-D VARIABLE=value             # ditto, but cannot come after CMakeLists.txt dir
+-C path/to/preset/file        # load some CMake settings before configuring :pre
 
 All the LAMMPS-specific -D variables that a LAMMPS build supports are
 described on the pages linked to from the "Build"_Build.html doc page.

doc/src/Build_extras.txt

@@ -30,7 +30,6 @@ This is the list of packages that may require additional steps.
 "KIM"_#kim,
 "KOKKOS"_#kokkos,
 "LATTE"_#latte,
-"MEAM"_#meam,
 "MESSAGE"_#message,
 "MSCG"_#mscg,
 "OPT"_#opt,
@@ -247,7 +246,10 @@ Maxwell50 = NVIDIA Maxwell generation CC 5.0
 Maxwell52 = NVIDIA Maxwell generation CC 5.2
 Maxwell53 = NVIDIA Maxwell generation CC 5.3
 Pascal60 = NVIDIA Pascal generation CC 6.0
-Pascal61 = NVIDIA Pascal generation CC 6.1 :ul
+Pascal61 = NVIDIA Pascal generation CC 6.1
+Volta70 = NVIDIA Volta generation CC 7.0
+Volta72 = NVIDIA Volta generation CC 7.2
+Turing75 = NVIDIA Turing generation CC 7.5 :ul
 
 [CMake build]:
 
@@ -348,49 +350,6 @@ the compiler you use on your system to build LATTE.
 
 :line
 
-MEAM package :h4,link(meam)
-
-NOTE: the use of the MEAM package is discouraged, as it has been
-superseded by the USER-MEAMC package, which is a direct translation of
-the Fortran code in the MEAM library to C++. The code in USER-MEAMC
-should be functionally equivalent to the MEAM package, fully supports
-use of "pair_style hybrid"_pair_hybrid.html (the MEAM package does
-not), and has optimizations that make it significantly faster than the
-MEAM package.
-
-[CMake build]:
-
-No additional settings are needed besides "-D PKG_MEAM=yes".
-
-[Traditional make]:
-
-Before building LAMMPS, you must build the MEAM library in lib/meam.
-You can build the MEAM library manually if you prefer; follow the
-instructions in lib/meam/README.  You can also do it in one step from
-the lammps/src dir, using a command like these, which simply invoke
-the lib/meam/Install.py script with the specified args:
-
-make lib-meam                  # print help message
-make lib-meam args="-m mpi"    # build with default Fortran compiler compatible with your MPI library
-make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
-make lib-meam args="-m ifort"  # build with Intel Fortran compiler using Makefile.ifort :pre
-
-NOTE: You should test building the MEAM library with both the Intel
-and GNU compilers to see if a simulation runs faster with one versus
-the other on your system.
-
-The build should produce two files: lib/meam/libmeam.a and
-lib/meam/Makefile.lammps.  The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (MEAM library).  Typically the two compilers used for LAMMPS
-and the MEAM library need to be consistent (e.g. both Intel or both
-GNU compilers).  If necessary, you can edit/create a new
-lib/meam/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-:line
-
 MESSAGE package :h4,link(message)
 
 This package can optionally include support for messaging via sockets,
@@ -859,23 +818,34 @@ file.
 USER-INTEL package :h4,link(user-intel)
 
 To build with this package, you must choose which hardware you want to
-build for, either Intel CPUs or Intel KNLs.  You should also typically
+build for, either x86 CPUs or Intel KNLs in offload mode.  You should
-"install the USER-OMP package"_#user-omp, as it can be used in tandem
+also typically "install the USER-OMP package"_#user-omp, as it can be
-with the USER-INTEL package to good effect, as explained on the "Speed
+used in tandem with the USER-INTEL package to good effect, as explained
-intel"_Speed_intel.html doc page.
+on the "Speed intel"_Speed_intel.html doc page.
 
 [CMake build]:
 
 -D INTEL_ARCH=value     # value = cpu (default) or knl
--D BUILD_OMP=yes        # also required to build with the USER-INTEl package :pre
+-D INTEL_LRT_MODE=value # value = threads, none, or c++11 :pre
 
-Requires an Intel compiler as well as the Intel TBB and MKL libraries.
+In Long-range thread mode (LRT) a modified verlet style is used, that
+operates the Kspace calculation in a separate thread concurrently to
+other calculations. This has to be enabled in the "package intel"_package.html
+command at runtime. With the setting "threads" it used the pthreads
+library, while c++11 will use the built-in thread support of C++11
+compilers. The option "none" skips compilation of this feature. The
+default is to use "threads" if pthreads is available and otherwise "none".
+
+Best performance is achieved with Intel hardware, Intel compilers, as well as
+the Intel TBB and MKL libraries. However, the code also compiles, links, and
+runs with other compilers and without TBB and MKL.
 
 [Traditional make]:
 
 Choose which hardware to compile for in Makefile.machine via the
 following settings.  See src/MAKE/OPTIONS/Makefile.intel_cpu* and
-Makefile.knl files for examples.
+Makefile.knl files for examples. and src/USER-INTEL/README for
+additional information.
 
 For CPUs:
 

doc/src/Build_package.txt

@@ -41,7 +41,6 @@ packages:
 "KIM"_Build_extras.html#kim,
 "KOKKOS"_Build_extras.html#kokkos,
 "LATTE"_Build_extras.html#latte,
-"MEAM"_Build_extras.html#meam,
 "MESSAGE"_Build_extras.html#message,
 "MSCG"_Build_extras.html#mscg,
 "OPT"_Build_extras.html#opt,
@@ -149,26 +148,41 @@ system. Using these files you can enable/disable portions of the
 available packages in LAMMPS. If you need a custom preset you can take
 one of them as a starting point and customize it to your needs.
 
-cmake -C ../cmake/presets/all_on.cmake \[OPTIONS\] ../cmake | enable all packages
+cmake -C ../cmake/presets/all_on.cmake  \[OPTIONS\] ../cmake |
-cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake | disable all packages
+      enable all packages |
-cmake -C ../cmake/presets/std.cmake \[OPTIONS\] ../cmake | enable standard packages
+cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake |
-cmake -C ../cmake/presets/user.cmake \[OPTIONS\] ../cmake | enable user packages
+      disable all packages |
-cmake -C ../cmake/presets/std_nolib.cmake \[OPTIONS\] ../cmake | enable standard packages that do not require extra libraries
+cmake -C ../cmake/presets/minimal.cmake \[OPTIONS\] ../cmake |
-cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake | disable all packages that do not require extra libraries
+      enable just a few core packages |
-cmake -C ../cmake/presets/manual_selection.cmake \[OPTIONS\] ../cmake | example of how to create a manual selection of packages :tb(s=|,a=l)
+cmake -C ../cmake/presets/most.cmake    \[OPTIONS\] ../cmake |
+      enable most common packages |
+cmake -C ../cmake/presets/nolib.cmake   \[OPTIONS\] ../cmake |
+      disable packages that do require extra libraries or tools |
+cmake -C ../cmake/presets/clang.cmake   \[OPTIONS\] ../cmake |
+      change settings to use the Clang compilers by default |
+cmake -C ../cmake/presets/mingw.cmake \[OPTIONS\] ../cmake |
+      enable all packages compatible with MinGW compilers :tb(c=2,s=|,a=l)
 
 NOTE: Running cmake this way manipulates the variable cache in your
-current build directory. You can combine presets and options with
+current build directory. You can combine multiple presets and options
-multiple cmake runs.
+in a single cmake run, or change settings incrementally by running
+cmake with new flags.
 
 [Example:]
 
-# build LAMMPS with all "standard" packages which don't
+# build LAMMPS with most commonly used packages, but then remove
-# use libraries and enable GPU package
+# those requiring additional library or tools, but still enable
+# GPU package and configure it for using CUDA. You can run.
 mkdir build
 cd build
-cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake :pre
+cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake :pre
 
+# to add another package, say BODY to the previous configuration you can run:
+cmake -D PKG_BODY=on . :pre
+
+# to reset the package selection from above to the default of no packages
+# but leaving all other settings untouched. You can run:
+cmake -C ../cmake/presets/no_all.cmake . :pre
 :line
 
 [Make shortcuts for installing many packages]:

doc/src/Build_settings.txt

@@ -179,8 +179,11 @@ e.g. from 511 to -512, which can cause diagnostics like the
 mean-squared displacement, as calculated by the "compute
 msd"_compute_msd.html command, to be faulty.
 
-Note that the USER-ATC package is not currently compatible with the
+Note that the USER-ATC package and the USER-INTEL package are currently
-"bigbig" setting.
+not compatible with the "bigbig" setting. Also, there are limitations
+when using the library interface. Some functions with known issues
+have been replaced by dummy calls printing a corresponding error rather
+than crashing randomly or corrupting data.
 
 Also note that the GPU package requires its lib/gpu library to be
 compiled with the same size setting, or the link will fail.  A CMake

doc/src/Build_windows.txt

@@ -51,11 +51,10 @@ provides a unix/linux interface to low-level Windows functions, so LAMMPS
 can be compiled on Windows. The necessary (minor) modifications to LAMMPS
 are included, but may not always up-to-date for recently added functionality
 and the corresponding new code. A machine makefile for using cygwin for
-the old build system is provided. The CMake build system is untested
+the old build system is provided. Using CMake for this mode of compilation
-for this; you will have to request that makefiles are generated and
+is untested and not likely to work.
-manually set the compiler.
 
-When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
+When compiling for Windows do [not] set the -DLAMMPS_MEMALIGN define
 in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
 flags in LIB makefile variable. Try adding -static-libgcc or -static or
 both to the linker flags when your resulting LAMMPS Windows executable
@@ -79,7 +78,13 @@ probably the currently best tested and supported way to build LAMMPS
 executables for Windows.  There are makefiles provided for the
 traditional build system, but CMake has also been successfully tested
 using the mingw32-cmake and mingw64-cmake wrappers that are bundled
-with the cross-compiler environment on Fedora machines.
+with the cross-compiler environment on Fedora machines. A CMake preset
+selecting all packages compatible with this cross-compilation build
+is provided. You likely need to disable the GPU package unless you
+download and install the contents of the pre-compiled "OpenCL ICD loader
+library"_https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz
+into your MinGW64 cross-compiler environment. The cross-compilation
+currently will only produce non-MPI serial binaries.
 
 Please keep in mind, though, that this only applies to compiling LAMMPS.
 Whether the resulting binaries do work correctly is no tested by the

doc/src/Commands.txt

@@ -33,6 +33,11 @@ commands in it are used to define a LAMMPS simulation.
    Commands_bond
    Commands_kspace
 
+.. toctree::
+   :maxdepth: 1
+
+   Commands_removed
+
 END_RST -->
 
 <!-- HTML_ONLY -->
@@ -49,5 +54,7 @@ END_RST -->
 "Bond, angle, dihedral, improper commands"_Commands_bond.html
 "KSpace solvers"_Commands_kspace.html  :all(b)
 
+"Removed commands and packages"_Commands_removed.html  :all(b)
+
 <!-- END_HTML_ONLY -->
 

doc/src/Commands_all.txt

@@ -83,6 +83,7 @@ An alphabetic list of all general LAMMPS commands.
 "molecule"_molecule.html,
 "ndx2group"_group2ndx.html,
 "neb"_neb.html,
+"neb/spin"_neb_spin.html,
 "neigh_modify"_neigh_modify.html,
 "neighbor"_neighbor.html,
 "newton"_newton.html,

doc/src/Commands_bond.txt

@@ -28,8 +28,12 @@ OPT.
 
 "none"_bond_none.html,
 "zero"_bond_zero.html,
-"hybrid"_bond_hybrid.html :tb(c=3,ea=c)
+"hybrid"_bond_hybrid.html,
-
+,
+,
+,
+,
+,
 "class2 (ko)"_bond_class2.html,
 "fene (iko)"_bond_fene.html,
 "fene/expand (o)"_bond_fene_expand.html,
@@ -56,8 +60,12 @@ OPT.
 
 "none"_angle_none.html,
 "zero"_angle_zero.html,
-"hybrid"_angle_hybrid.html :tb(c=3,ea=c)
+"hybrid"_angle_hybrid.html,
-
+,
+,
+,
+,
+,
 "charmm (iko)"_angle_charmm.html,
 "class2 (ko)"_angle_class2.html,
 "class2/p6"_angle_class2.html,
@@ -89,8 +97,12 @@ OPT.
 
 "none"_dihedral_none.html,
 "zero"_dihedral_zero.html,
-"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c)
+"hybrid"_dihedral_hybrid.html,
-
+,
+,
+,
+,
+,
 "charmm (iko)"_dihedral_charmm.html,
 "charmmfsw"_dihedral_charmm.html,
 "class2 (ko)"_dihedral_class2.html,
@@ -117,8 +129,12 @@ OPT.
 
 "none"_improper_none.html,
 "zero"_improper_zero.html,
-"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
+"hybrid"_improper_hybrid.html,
-
+,
+,
+,
+,
+,
 "class2 (ko)"_improper_class2.html,
 "cossq (o)"_improper_cossq.html,
 "cvff (io)"_improper_cvff.html,

doc/src/Commands_category.txt

@@ -116,6 +116,7 @@ Actions:
 
 "minimize"_minimize.html,
 "neb"_neb.html,
+"neb_spin"_neb_spin.html,
 "prd"_prd.html,
 "rerun"_rerun.html,
 "run"_run.html,

doc/src/Commands_fix.txt

@@ -61,6 +61,7 @@ OPT.
 "edpd/source"_fix_dpd_source.html,
 "efield"_fix_efield.html,
 "ehex"_fix_ehex.html,
+"electron/stopping"_fix_electron_stopping.html,
 "enforce2d (k)"_fix_enforce2d.html,
 "eos/cv"_fix_eos_cv.html,
 "eos/table"_fix_eos_table.html,
@@ -106,6 +107,7 @@ OPT.
 "mvv/edpd"_fix_mvv_dpd.html,
 "mvv/tdpd"_fix_mvv_dpd.html,
 "neb"_fix_neb.html,
+"neb_spin"_fix_neb_spin.html,
 "nph (ko)"_fix_nh.html,
 "nph/asphere (o)"_fix_nph_asphere.html,
 "nph/body"_fix_nph_body.html,

doc/src/Commands_pair.txt

@@ -27,8 +27,11 @@ OPT.
 "none"_pair_none.html,
 "zero"_pair_zero.html,
 "hybrid (k)"_pair_hybrid.html,
-"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
+"hybrid/overlay (k)"_pair_hybrid.html,
-
+,
+,
+,
+,
 "adp (o)"_pair_adp.html,
 "agni (o)"_pair_agni.html,
 "airebo (io)"_pair_airebo.html,
@@ -80,6 +83,8 @@ OPT.
 "dpd/fdt/energy (k)"_pair_dpd_fdt.html,
 "dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
+"e3b"_pair_e3b.html,
+"drip"_pair_drip.html,
 "eam (gikot)"_pair_eam.html,
 "eam/alloy (gikot)"_pair_eam.html,
 "eam/cd (o)"_pair_eam.html,
@@ -98,6 +103,7 @@ OPT.
 "gran/hertz/history (o)"_pair_gran.html,
 "gran/hooke (o)"_pair_gran.html,
 "gran/hooke/history (ko)"_pair_gran.html,
+"granular"_pair_granular.html,
 "gw"_pair_gw.html,
 "gw/zbl"_pair_gw.html,
 "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,

doc/src/Commands_removed.txt

@@ -0,0 +1,66 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html)
+
+:line
+
+Removed commands and packages :h3
+
+This page lists LAMMPS commands and packages that have been removed from
+the distribution and provides suggestions for alternatives or replacements.
+LAMMPS has special dummy styles implemented, that will stop LAMMPS and
+print a suitable error message in most cases, when a style/command is used
+that has been removed.
+
+Fix ave/spatial and fix ave/spatial/sphere :h4
+
+The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
+since they were superseded by the more general and extensible "chunk
+infrastructure".  Here the system is partitioned in one of many possible
+ways through the "compute chunk/atom"_compute_chunk_atom.html command
+and then averaging is done using "fix ave/chunk"_fix_ave_chunk.html.
+Please refer to the "chunk HOWTO"_Howto_chunk.html section for an overview.
+
+MEAM package :h4
+
+The MEAM package has been removed since it was superseded by the
+"USER-MEAMC package"_Package_details.html#PKG-USER-MEAMC. The code in
+the USER-MEAMC package is a translation of the Fortran code of MEAM into C++,
+which removes several restrictions (e.g. there can be multiple instances
+in hybrid pair styles) and allows for some optimizations leading
+to better performance.  The new pair style "meam/c"_pair_meamc.html has
+the exact same syntax as the old "meam" pair style and thus pair style
+"meam"_pair_meamc.html is an alias to the new style and backward
+compatibility of old inputs is preserved.
+
+REAX package :h4
+
+The REAX package has been removed since it was superseded by the
+"USER-REAXC package"_Package_details.html#PKG-USER-REAXC.  The USER-REAXC
+package has been tested to yield equivalent results to the REAX package,
+offers better performance, supports OpenMP multi-threading via USER-OMP,
+and GPU and threading parallelization through KOKKOS.  The new pair styles
+are not syntax compatible with the removed reax pair style, so input
+files will have to be adapted.
+
+USER-CUDA package :h4
+
+The USER-CUDA package had been removed, since it had been unmaintained
+for a long time and had known bugs and problems.  Significant parts of
+the design were transferred to the
+"KOKKOS package"_Package_details.html#PKG-KOKKOS, which has similar
+performance characteristics on Nvidia GPUs. Both, the KOKKOS
+and the "GPU package"_Package_details.html#PKG-GPU are maintained
+and allow running LAMMPS with GPU acceleration.
+
+restart2data tool :h4
+
+The functionality of the restart2data tool has been folded into the
+LAMMPS executable directly instead of having a separate tool.  A
+combination of the commands "read_restart"_read_restart.html and
+"write_data"_write_data.html can be used to the same effect.  For added
+convenience this conversion can also be triggered by "command line
+flags"_Run_options.html

doc/src/Eqs/e3b.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+\usepackage{amsmath}
+\begin{document}
+
+\begin{align*}
+E =& E_2 \sum_{i,j}e^{-k_2 r_{ij}} + E_A \sum_{\substack{i,j,k,\ell \\\in \textrm{type A}}} f(r_{ij})f(r_{k\ell}) + E_B \sum_{\substack{i,j,k,\ell \\\in \textrm{type B}}} f(r_{ij})f(r_{k\ell}) + E_C \sum_{\substack{i,j,k,\ell \\\in \textrm{type C}}} f(r_{ij})f(r_{k\ell}) \\
+f(r) =& e^{-k_3 r}s(r) \\
+s(r) =& \begin{cases}
+  1 & r<R_s \\
+  \displaystyle\frac{(R_f-r)^2(R_f-3R_s+2r)}{(R_f-R_s)^3} & R_s\leq r\leq R_f \\
+  0 & r>R_f\\
+\end{cases}
+\end{align*}
+
+\end{document}

doc/src/Eqs/fix_spin_cubic.tex

@@ -0,0 +1,21 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{H}_{cubic} = -\sum_{{ i}=1}^{N} K_{1}
+    \Big[
+    \left(\vec{s}_{i} \cdot \vec{n1} \right)^2
+    \left(\vec{s}_{i} \cdot \vec{n2} \right)^2 +
+    \left(\vec{s}_{i} \cdot \vec{n2} \right)^2
+    \left(\vec{s}_{i} \cdot \vec{n3} \right)^2 +
+    \left(\vec{s}_{i} \cdot \vec{n1} \right)^2
+    \left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \Big]
+    +K_{2}^{(c)} \left(\vec{s}_{i} \cdot \vec{n1} \right)^2
+    \left(\vec{s}_{i} \cdot \vec{n2} \right)^2
+    \left(\vec{s}_{i} \cdot \vec{n3} \right)^2 \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/neb_spin_angle.tex

@@ -0,0 +1,15 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \omega_i^{\nu} = 
+    (\nu - 1) \Delta \omega_i
+    {\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
+  , \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/neb_spin_k.tex

@@ -0,0 +1,16 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{k}_i =  
+    \frac{\vec{m}_i^I \times \vec{m}_i^F}{\left|\vec{m}_i^I 
+    \times \vec{m}_i^F\right|} 
+    %&{\rm ~if~}& \vec{m}_i^I \times \vec{m}_i^F  
+  , \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/neb_spin_rodrigues_formula.tex

@@ -0,0 +1,16 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{m}_i^{\nu} = \vec{m}_i^{I} \cos(\omega_i^{\nu})
+    + (\vec{k}_i \times \vec{m}_i^{I}) \sin(\omega_i^{\nu})
+    + (1.0-\cos(\omega_i^{\nu})) \vec{k}_i (\vec{k}_i\cdot
+    \vec{m}_i^{I})
+  , \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_drip.tex

@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+\usepackage{amsmath}
+\usepackage{bm}
+
+\begin{document}
+
+\begin{eqnarray*}
+E &=& \frac{1}{2} \sum_{i} \sum_{j\notin\text{layer}\,i} \phi_{ij} \\\phi_{ij} &=& f_\text{c}(x_r) \left[ e^{-\lambda(r_{ij} - z_0 )} \left[C+f(\rho_{ij})+  g(\rho_{ij}, \{\alpha_{ij}^{(m)}\}) \right]- A\left (\frac{z_0}{r_{ij}} \right)^6 \right] \\
+\end{eqnarray*}  
+
+
+
+                        
+\end{document}

doc/src/Eqs/pair_mdf-6.tex

@@ -1,9 +1,9 @@
 \documentclass[12pt]{article}
-
+\pagestyle{empty}
 \begin{document}
 
 $$
-   E(r) = \frac{A}{r^{12}} - \frac{A}{r^{6}}
+   E(r) = \frac{A}{r^{12}} - \frac{B}{r^{6}}
 $$
 
 \end{document}

doc/src/Eqs/pair_spin_dipole.tex

@@ -0,0 +1,42 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,graphics,bm,setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \mathcal{H}_{\rm long}= 
+    -\frac{\mu_{0} \left( \mu_B\right)^2}{4\pi} 
+    \sum_{i,j,i\neq j}^{N}
+    \frac{g_i g_j}{r_{ij}^3}
+    \Big(3 
+    \left(\bm{e}_{ij}\cdot \bm{s}_{i}\right) 
+    \left(\bm{e}_{ij}\cdot \bm{s}_{j}\right) 
+    -\bm{s}_i\cdot\bm{s}_j \Big)
+    \nonumber
+  \end{equation}
+  \begin{equation}
+    \bm{\omega}_i = 
+    \frac{\mu_0 (\mu_B)^2}{4\pi\hbar}\sum_{j}
+    \frac{g_i g_j}{r_{ij}^3}
+    \, \Big(
+    3\,(\bm{e}_{ij}\cdot\bm{s}_{j})\bm{e}_{ij}
+    -\bm{s}_{j} \Big) \nonumber
+  \end{equation}
+  \begin{equation}
+    \bm{F}_i =
+    \frac{3\, \mu_0 (\mu_B)^2}{4\pi} \sum_j
+    \frac{g_i g_j}{r_{ij}^4}
+    \Big[\big( (\bm{s}_i\cdot\bm{s}_j) 
+    -5(\bm{e}_{ij}\cdot\bm{s}_i)
+    (\bm{e}_{ij}\cdot\bm{s}_j)\big) \bm{e}_{ij}+
+    \big(
+    (\bm{e}_{ij}\cdot\bm{s}_i)\bm{s}_j+
+    (\bm{e}_{ij}\cdot\bm{s}_j)\bm{s}_i
+    \big)
+    \Big]
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_long_range.tex

@@ -0,0 +1,20 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,graphics,bm,setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \mathcal{H}_{\rm long}= 
+    -\frac{\mu_{0} \left( \mu_B\right)^2}{4\pi} 
+    \sum_{i,j,i\neq j}^{N}
+    \frac{g_i g_j}{r_{ij}^3}
+    \Big(3 
+    \left(\bm{e}_{ij}\cdot \bm{s}_{i}\right) 
+    \left(\bm{e}_{ij}\cdot \bm{s}_{j}\right) 
+    -\bm{s}_i\cdot\bm{s}_j \Big)
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_long_range_force.tex

@@ -0,0 +1,23 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,graphics,bm,setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{F}_i =
+    \frac{\mu_0 (\mu_B)^2}{4\pi} \sum_j
+    \frac{g_i g_j}{r_{ij}^4}
+    \Big[\big( (\bm{s}_i\cdot\bm{s}_j) 
+    -5(\bm{e}_{ij}\cdot\bm{s}_i)
+    (\bm{e}_{ij}\cdot\bm{s}_j)\big) \bm{e}_{ij}+
+    \big(
+    (\bm{e}_{ij}\cdot\bm{s}_i)\bm{s}_j+
+    (\bm{e}_{ij}\cdot\bm{s}_j)\bm{s}_i
+    \big)
+    \Big]
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_long_range_magforce.tex

@@ -0,0 +1,17 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,graphics,bm,setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{\omega}_i = 
+    \frac{\mu_0 (\mu_B)^2}{4\pi\hbar}\sum_{j}
+    \frac{g_i g_j}{r_{ij}^3}
+    \, \Big(
+    3\,(\bm{e}_{ij}\cdot\bm{s}_{j})\bm{e}_{ij}
+    -\bm{s}_{j} \Big) \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Errors_messages.txt

@@ -610,6 +610,62 @@ This means there is something invalid about the topology definitions. :dd
 
 The data file header lists bonds but no bond types. :dd
 
+{Bond/react: Cannot use fix bond/react with non-molecular systems} :dt
+
+Only systems with bonds that can be changed can be used. Atom_style
+template does not qualify. :dd
+
+{Bond/react: Rmax cutoff is longer than pairwise cutoff} :dt
+
+This is not allowed because bond creation is done using the pairwise
+neighbor list. :dd
+
+{Bond/react: Molecule template ID for fix bond/react does not exist} :dt
+
+A valid molecule template must have been created with the molecule
+command. :dd
+
+{Bond/react: Reaction templates must contain the same number of atoms} :dt
+
+There should be a one-to-one correspondence between atoms in the
+pre-reacted and post-reacted templates, as specified by the map file. :dd
+
+{Bond/react: Unknown section in map file} :dt
+
+Please ensure reaction map files are properly formatted. :dd
+
+{Bond/react: Atom affected by reaction too close to template edge} :dt
+
+This means an atom which changes type or connectivity during the
+reaction is too close to an 'edge' atom defined in the superimpose
+file. This could cause incorrect assignment of bonds, angle, etc.
+Generally, this means you must include more atoms in your templates,
+such that there are at least two atoms between each atom involved in
+the reaction and an edge atom. :dd
+
+{Bond/react: Fix bond/react needs ghost atoms from farther away} :dt
+
+This is because a processor needs to superimpose the entire unreacted
+molecule template onto simulation atoms it knows about. The
+comm_modify cutoff command can be used to extend the communication
+range. :dd
+
+{Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted} :dt
+
+Self-explanatory. :dd
+
+{Bond/react special bond generation overflow} :dt
+
+The number of special bonds per-atom created by a reaction exceeds the
+system setting. See the read_data or create_box command for how to
+specify this value. :dd
+
+{Bond/react topology/atom exceed system topology/atom} :dt
+
+The number of bonds, angles etc per-atom created by a reaction exceeds
+the system setting. See the read_data or create_box command for how to
+specify this value. :dd
+
 {Both restart files must use % or neither} :dt
 
 Self-explanatory. :dd
@@ -2146,10 +2202,6 @@ Self-explanatory. :dd
 
 This is a current restriction in LAMMPS. :dd
 
-{Cannot use pair hybrid with GPU neighbor list builds} :dt
-
-Neighbor list builds must be done on the CPU for this pair style. :dd
-
 {Cannot use pair tail corrections with 2d simulations} :dt
 
 The correction factors are only currently defined for 3d systems. :dd
@@ -5467,10 +5519,6 @@ Self-explanatory. :dd
 For this pair style, you cannot run part of the force calculation on
 the host.  See the package command. :dd
 
-{GPU split param must be positive for hybrid pair styles} :dt
-
-See the package gpu command. :dd
-
 {GPUs are requested but Kokkos has not been compiled for CUDA} :dt
 
 Re-compile Kokkos with CUDA support to use GPUs. :dd
@@ -5828,6 +5876,12 @@ Must have periodic x,y dimensions and non-periodic z dimension to use
 Must have periodic x,y dimensions and non-periodic z dimension to use
 2d slab option with pppm/disp. :dd
 
+{Incorrect conversion in format string} :dt
+
+A format style variable was not using either a %f, a %g, or a %e conversion.
+Or an immediate variable with format suffix was not using either
+a %f, a %g or a %e conversion in the format suffix. :dd
+
 {Incorrect element names in ADP potential file} :dt
 
 The element names in the ADP file do not match those requested. :dd
@@ -7035,6 +7089,18 @@ Self-explanatory. :dd
 
 One or more GPUs must be used when Kokkos is compiled for CUDA. :dd
 
+{Kspace_modify mesh parameter must be all zero or all positive} :dt
+
+Valid kspace mesh parameters are >0. The code will try to auto-detect
+suitable values when all three mesh sizes are set to zero (the default). :dd
+
+{Kspace_modify mesh/disp parameter must be all zero or all positive} :dt
+
+Valid kspace mesh/disp parameters are >0. The code will try to auto-detect
+suitable values when all three mesh sizes are set to zero [and]
+the required accuracy via {force/disp/real} as well as
+{force/disp/kspace} is set. :dd
+
 {Kspace style does not support compute group/group} :dt
 
 Self-explanatory. :dd
@@ -7448,6 +7514,11 @@ The Atoms section of a data file must come before a Triangles section. :dd
 The Atoms section of a data file must come before a Velocities
 section. :dd
 
+{Must re-specify non-restarted pair style (xxx) after read_restart} :dt
+
+For pair styles, that do not store their settings in a restart file,
+it must be defined with a new 'pair_style' command after read_restart. :dd
+
 {Must set both respa inner and outer} :dt
 
 Cannot use just the inner or outer option with respa without using the
@@ -9990,25 +10061,25 @@ quote. :dd
 
 Self-explanatory. :dd
 
-{Unexpected end of AngleCoeffs section} :dt
+{Unexpected empty line in AngleCoeffs section} :dt
 
-Read a blank line. :dd
+Read a blank line where there should be coefficient data. :dd
 
-{Unexpected end of BondCoeffs section} :dt
+{Unexpected empty line in BondCoeffs section} :dt
 
-Read a blank line. :dd
+Read a blank line where there should be coefficient data. :dd
 
-{Unexpected end of DihedralCoeffs section} :dt
+{Unexpected empty line in DihedralCoeffs section} :dt
 
-Read a blank line. :dd
+Read a blank line where there should be coefficient data. :dd
 
-{Unexpected end of ImproperCoeffs section} :dt
+{Unexpected empty line in ImproperCoeffs section} :dt
 
-Read a blank line. :dd
+Read a blank line where there should be coefficient data. :dd
 
-{Unexpected end of PairCoeffs section} :dt
+{Unexpected empty line in PairCoeffs section} :dt
 
-Read a blank line. :dd
+Read a blank line where there should be coefficient data. :dd
 
 {Unexpected end of custom file} :dt
 
@@ -10049,19 +10120,19 @@ create_box command. :dd
 A universe or uloop style variable must specify a number of values >= to the
 number of processor partitions. :dd
 
-{Unknown angle style} :dt
+{Unrecognized angle style} :dt
 
 The choice of angle style is unknown. :dd
 
-{Unknown atom style} :dt
+{Unrecognized atom style} :dt
 
 The choice of atom style is unknown. :dd
 
-{Unknown body style} :dt
+{Unrecognized body style} :dt
 
 The choice of body style is unknown. :dd
 
-{Unknown bond style} :dt
+{Unrecognized bond style} :dt
 
 The choice of bond style is unknown. :dd
 
@@ -10077,23 +10148,23 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Unknown command: %s} :dt
+{Unrecognized command: %s} :dt
 
 The command is not known to LAMMPS.  Check the input script. :dd
 
-{Unknown compute style} :dt
+{Unrecognized compute style} :dt
 
 The choice of compute style is unknown. :dd
 
-{Unknown dihedral style} :dt
+{Unrecognized dihedral style} :dt
 
 The choice of dihedral style is unknown. :dd
 
-{Unknown dump reader style} :dt
+{Unrecognized dump reader style} :dt
 
 The choice of dump reader style via the format keyword is unknown. :dd
 
-{Unknown dump style} :dt
+{Unrecognized dump style} :dt
 
 The choice of dump style is unknown. :dd
 
@@ -10101,7 +10172,7 @@ The choice of dump style is unknown. :dd
 
 Self-explanatory. :dd
 
-{Unknown fix style} :dt
+{Unrecognized fix style} :dt
 
 The choice of fix style is unknown. :dd
 
@@ -10109,7 +10180,7 @@ The choice of fix style is unknown. :dd
 
 A section of the data file cannot be read by LAMMPS. :dd
 
-{Unknown improper style} :dt
+{Unrecognized improper style} :dt
 
 The choice of improper style is unknown. :dd
 
@@ -10117,7 +10188,7 @@ The choice of improper style is unknown. :dd
 
 One or more specified keywords are not recognized. :dd
 
-{Unknown kspace style} :dt
+{Unrecognized kspace style} :dt
 
 The choice of kspace style is unknown. :dd
 
@@ -10133,7 +10204,7 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Unknown pair style} :dt
+{Unrecognized pair style} :dt
 
 The choice of pair style is unknown. :dd
 
@@ -10141,7 +10212,7 @@ The choice of pair style is unknown. :dd
 
 The choice of sub-style is unknown. :dd
 
-{Unknown region style} :dt
+{Unrecognized region style} :dt
 
 The choice of region style is unknown. :dd
 

doc/src/Errors_warnings.txt

@@ -82,6 +82,15 @@ bond/angle/dihedral.  LAMMPS computes this by taking the maximum bond
 length, multiplying by the number of bonds in the interaction (e.g. 3
 for a dihedral) and adding a small amount of stretch. :dd
 
+{Bond/react: Atom affected by reaction too close to template edge} :dt
+
+This means an atom which changes type or connectivity during the
+reaction is too close to an 'edge' atom defined in the superimpose
+file. This could cause incorrect assignment of bonds, angle, etc.
+Generally, this means you must include more atoms in your templates,
+such that there are at least two atoms between each atom involved in
+the reaction and an edge atom. :dd
+
 {Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt
 
 Self-explanatory. :dd

doc/src/Examples.txt

@@ -11,7 +11,7 @@ Section"_Tools.html :c
 Example scripts :h3
 
 The LAMMPS distribution includes an examples sub-directory with many
-sample problems.  Many are 2d models that run quickly are are
+sample problems.  Many are 2d models that run quickly and are
 straightforward to visualize, requiring at most a couple of minutes to
 run on a desktop machine.  Each problem has an input script (in.*) and
 produces a log file (log.*) when it runs.  Some use a data file
@@ -52,13 +52,14 @@ Lowercase directories :h4
 
 accelerate: run with various acceleration options (OpenMP, GPU, Phi)
 airebo:   polyethylene with AIREBO potential
+atm:      Axilrod-Teller-Muto potential example
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
 cmap:     CMAP 5-body contributions to CHARMM force field
 colloid:  big colloid particles in a small particle solvent, 2d system
 comb:     models using the COMB potential
-coreshell: core/shell model using CORESHELL package
 controller: use of fix controller as a thermostat
+coreshell: core/shell model using CORESHELL package
 crack:    crack propagation in a 2d solid
 deposit:  deposit atoms and molecules on a surface
 dipole:   point dipolar particles, 2d system
@@ -70,10 +71,13 @@ friction: frictional contact of spherical asperities between 2d surfaces
 gcmc:     Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
 granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
+hyper:    global and local hyperdynamics of diffusion on Pt surface
 indent:   spherical indenter into a 2d solid
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
+latte:    examples for using fix latte for DFTB via the LATTE library
 meam:     MEAM test for SiC and shear (same as shear examples)
 melt:     rapid melt of 3d LJ system
+message:  demos for LAMMPS client/server coupling with the MESSAGE package
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
 min:      energy minimization of 2d LJ melt
 mscg:     parameterize a multi-scale coarse-graining (MSCG) model
@@ -88,6 +92,7 @@ pour:     pouring of granular particles into a 3d box, then chute flow
 prd:      parallel replica dynamics of vacancy diffusion in bulk Si
 python:   using embedded Python in a LAMMPS input script
 qeq:      use of the QEQ package for charge equilibration
+rdf-adf:  computing radial and angle distribution functions for water
 reax:     RDX and TATB models using the ReaxFF
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void
@@ -95,6 +100,7 @@ snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
 srd:      stochastic rotation dynamics (SRD) particles as solvent
 streitz:  use of Streitz/Mintmire potential with charge equilibration
 tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
+threebody: regression test input for a variety of manybody potentials
 vashishta: use of the Vashishta potential
 voronoi:  Voronoi tesselation via compute voronoi/atom command :tb(s=:)
 
@@ -131,8 +137,10 @@ COUPLE: examples of how to use LAMMPS as a library
 DIFFUSE: compute diffusion coefficients via several methods
 ELASTIC: compute elastic constants at zero temperature
 ELASTIC_T: compute elastic constants at finite temperature
+HEAT: compute thermal conductivity for LJ and water via fix ehex
 KAPPA: compute thermal conductivity via several methods
 MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system
+SPIN: examples for features of the SPIN package
 USER: examples for USER packages and USER-contributed commands
 VISCOSITY: compute viscosity via several methods :tb(s=:)
 

doc/src/Howto.txt

@@ -148,7 +148,7 @@ END_RST -->
 
 <!-- HTML_ONLY -->
 
-"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
+"CHARMM, AMBER, COMPASS, and DREIDING force fields"_Howto_bioFF.html
 "TIP3P water model"_Howto_tip3p.html
 "TIP4P water model"_Howto_tip4p.html
 "SPC water model"_Howto_spc.html :all(b)

doc/src/Howto_bioFF.txt

@@ -7,29 +7,31 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-CHARMM, AMBER, and DREIDING force fields :h3
+CHARMM, AMBER, COMPASS, and DREIDING force fields :h3
 
 A force field has 2 parts: the formulas that define it and the
 coefficients used for a particular system.  Here we only discuss
 formulas implemented in LAMMPS that correspond to formulas commonly
-used in the CHARMM, AMBER, and DREIDING force fields.  Setting
+used in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
-coefficients is done in the input data file via the
+coefficients is done either from special sections in an input data file
-"read_data"_read_data.html command or in the input script with
+via the "read_data"_read_data.html command or in the input script with
 commands like "pair_coeff"_pair_coeff.html or
-"bond_coeff"_bond_coeff.html.  See the "Tools"_Tools.html doc page for
+"bond_coeff"_bond_coeff.html and so on.  See the "Tools"_Tools.html doc
-additional tools that can use CHARMM or AMBER to assign force field
+page for additional tools that can use CHARMM, AMBER, or Materials
-coefficients and convert their output into LAMMPS input.
+Studio generated files to assign force field coefficients and convert
+their output into LAMMPS input.
 
 See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
-field.  See "(Cornell)"_#howto-Cornell for a description of the AMBER force
+field.  See "(Cornell)"_#howto-Cornell for a description of the AMBER
-field.
+force field.  See "(Sun)"_#howto-Sun for a description of the COMPASS
+force field.
 
 :link(charmm,http://www.scripps.edu/brooks)
 :link(amber,http://amber.scripps.edu)
 
-These style choices compute force field formulas that are consistent
+The interaction styles listed below compute force field formulas that
-with common options in CHARMM or AMBER.  See each command's
+are consistent with common options in CHARMM or AMBER.  See each
-documentation for the formula it computes.
+command's documentation for the formula it computes.
 
 "bond_style"_bond_harmonic.html harmonic
 "angle_style"_angle_charmm.html charmm
@@ -44,28 +46,54 @@ documentation for the formula it computes.
 "special_bonds"_special_bonds.html charmm
 "special_bonds"_special_bonds.html amber :ul
 
-NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
+NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were released
-released in March 2017.  We recommend they be used instead of the
+in March 2017.  We recommend they be used instead of the older {charmm}
-older {charmm} styles.  See discussion of the differences on the "pair
+styles.  See discussion of the differences on the "pair
-charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
+charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html doc
-doc pages.
+pages.
+
+COMPASS is a general force field for atomistic simulation of common
+organic molecules, inorganic small molecules, and polymers which was
+developed using ab initio and empirical parameterization techniques.
+See the "Tools"_Tools.html doc page for the msi2lmp tool for creating
+LAMMPS template input and data files from BIOVIA's Materials Studio
+files.  Please note that the msi2lmp tool is very old and largely
+unmaintained, so it does not support all features of Materials Studio
+provided force field files, especially additions during the last decade.
+You should watch the output carefully and compare results, where
+possible.  See "(Sun)"_#howto-Sun for a description of the COMPASS force
+field.
+
+These interaction styles listed below compute force field formulas that
+are consistent with the COMPASS force field.  See each command's
+documentation for the formula it computes.
+
+"bond_style"_bond_class2.html class2
+"angle_style"_angle_class2.html class2
+"dihedral_style"_dihedral_class2.html class2
+"improper_style"_improper_class2.html class2 :ul
+
+"pair_style"_pair_class2.html lj/class2
+"pair_style"_pair_class2.html lj/class2/coul/cut
+"pair_style"_pair_class2.html lj/class2/coul/long :ul
+
+"special_bonds"_special_bonds.html lj/coul 0 0 1 :ul
 
 DREIDING is a generic force field developed by the "Goddard
 group"_http://www.wag.caltech.edu at Caltech and is useful for
-predicting structures and dynamics of organic, biological and
+predicting structures and dynamics of organic, biological and main-group
-main-group inorganic molecules. The philosophy in DREIDING is to use
+inorganic molecules. The philosophy in DREIDING is to use general force
-general force constants and geometry parameters based on simple
+constants and geometry parameters based on simple hybridization
-hybridization considerations, rather than individual force constants
+considerations, rather than individual force constants and geometric
-and geometric parameters that depend on the particular combinations of
+parameters that depend on the particular combinations of atoms involved
-atoms involved in the bond, angle, or torsion terms. DREIDING has an
+in the bond, angle, or torsion terms. DREIDING has an "explicit hydrogen
-"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
+bond term"_pair_hbond_dreiding.html to describe interactions involving a
-interactions involving a hydrogen atom on very electronegative atoms
+hydrogen atom on very electronegative atoms (N, O, F).
-(N, O, F).
 
 See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field
 
-These style choices compute force field formulas that are consistent
+The interaction styles listed below compute force field formulas that
-with the DREIDING force field.  See each command's
+are consistent with the DREIDING force field.  See each command's
 documentation for the formula it computes.
 
 "bond_style"_bond_harmonic.html harmonic
@@ -100,6 +128,9 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
 [(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
 Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
 
+:link(howto-Sun)
+[(Sun)] Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
+
 :link(howto-Mayo)
 [(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
 (1990).

doc/src/Howto_diffusion.txt

@@ -29,3 +29,5 @@ diffusion coefficient.  The instantaneous VACF values can be
 accumulated in a vector via the "fix vector"_fix_vector.html command,
 and time integrated via the "variable trap"_variable.html function,
 and thus extract D.
+
+:line

doc/src/Howto_drude2.txt

@@ -274,7 +274,7 @@ crash. Even without reaching this extreme case, the correlation
 between nearby dipoles on the same molecule may be exaggerated.  Often,
 special bond relations prevent bonded neighboring atoms to see the
 charge of each other's DP, so that the problem does not always appear.
-It is possible to use screened dipole dipole interactions by using the
+It is possible to use screened dipole-dipole interactions by using the
 "{pair_style thole}"_pair_thole.html.  This is implemented as a
 correction to the Coulomb pair_styles, which dampens at short distance
 the interactions between the charges representing the induced dipoles.

doc/src/Howto_library.txt

@@ -166,9 +166,6 @@ void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *)
 void lammps_scatter_atoms(void *, char *, int, int, void *)
 void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre
 
-void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
-                         imageint *, int) :pre
-
 The gather functions collect peratom info of the requested type (atom
 coords, atom types, forces, etc) from all processors, and returns the
 same vector of values to each calling processor.  The scatter
@@ -176,6 +173,11 @@ functions do the inverse.  They distribute a vector of peratom values,
 passed by all calling processors, to individual atoms, which may be
 owned by different processors.
 
+IMPORTANT NOTE: These functions are not compatible with the
+-DLAMMPS_BIGBIG setting when compiling LAMMPS.  Dummy functions
+that result in an error message and abort will be substituted
+instead of resulting in random crashes and memory corruption.
+
 The lammps_gather_atoms() function does this for all N atoms in the
 system, ordered by atom ID, from 1 to N.  The
 lammps_gather_atoms_concat() function does it for all N atoms, but
@@ -196,6 +198,9 @@ those values to each atom in the system.  The
 lammps_scatter_atoms_subset() function takes a subset of IDs as an
 argument and only scatters those values to the owning atoms.
 
+void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
+                         imageint *, int) :pre
+
 The lammps_create_atoms() function takes a list of N atoms as input
 with atom types and coords (required), an optionally atom IDs and
 velocities and image flags.  It uses the coords of each atom to assign

doc/src/Howto_replica.txt

@@ -17,6 +17,7 @@ periodically.
 These are the relevant commands:
 
 "neb"_neb.html for nudged elastic band calculations
+"neb_spin"_neb_spin.html for magnetic nudged elastic band calculations
 "prd"_prd.html for parallel replica dynamics
 "tad"_tad.html for temperature accelerated dynamics
 "temper"_temper.html for parallel tempering

doc/src/Howto_spins.txt

@@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 Magnetic spins :h3
 
 The magnetic spin simulations are enabled by the SPIN package, whose
-implementation is detailed in "Tranchida"_#Tranchida7.
+implementation is detailed in "Tranchida"_#Tranchida.
 
 The model represents the simulation of atomic magnetic spins coupled
 to lattice vibrations. The dynamics of those magnetic spins can be used
@@ -36,13 +36,28 @@ A Langevin thermostat can be applied to those magnetic spins using
 "fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
 can be coupled to another Langevin thermostat applied to the atoms
 using "fix langevin"_fix_langevin.html in order to simulate
-thermostatted spin-lattice system.
+thermostatted spin-lattice systems.
 
 The magnetic Gilbert damping can also be applied using "fix
 langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
 the thermal energy of the Langevin thermostat, or to perform a
 relaxation of the magnetic configuration toward an equilibrium state.
 
+The command "fix setforce/spin"_fix_setforce.html allows to set the 
+components of the magnetic precession vectors (while erasing and 
+replacing the previously computed magnetic precession vectors on 
+the atom). 
+This command can be used to freeze the magnetic moment of certain 
+atoms in the simulation by zeroing their precession vector. 
+
+The command "fix nve/spin"_fix_nve_spin.html can be used to
+perform a symplectic integration of the combined dynamics of spins 
+and atomic motions.
+
+The minimization style "min/spin"_min_spin.html can be applied
+to the spins to perform a minimization of the spin configuration. 
+
+
 All the computed magnetic properties can be output by two main
 commands. The first one is "compute spin"_compute_spin.html, that
 enables to evaluate magnetic averaged quantities, such as the total
@@ -54,6 +69,6 @@ magnetic spin, or the magnetic force acting on this spin.
 
 :line
 
-:link(Tranchida7)
+:link(Tranchida)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/Howto_tip3p.txt

@@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 TIP3P water model :h3
 
 The TIP3P water model as implemented in CHARMM
-"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with
+"(MacKerell)"_#howto-tip3p specifies a 3-site rigid water molecule with
 charges and Lennard-Jones parameters assigned to each of the 3 atoms.
 In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
 the two O-H bonds and the H-O-H angle rigid.  A bond style of
@@ -60,6 +60,10 @@ models"_http://en.wikipedia.org/wiki/Water_model.
 
 :line
 
+:link(howto-tip3p)
+[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+
 :link(Jorgensen1)
 [(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
 Phys, 79, 926 (1983).

doc/src/Install_git.txt

@@ -52,7 +52,7 @@ as if you unpacked a current LAMMPS tarball, with the exception, that
 the HTML documentation files are not included.  They can be fetched
 from the LAMMPS website by typing "make fetch" in the doc directory.
 Or they can be generated from the content provided in doc/src by
-typing "make html" from the the doc directory.
+typing "make html" from the doc directory.
 
 After initial cloning, as bug fixes and new features are added to
 LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay

doc/src/Install_svn.txt

@@ -40,7 +40,7 @@ as if you unpacked a current LAMMPS tarball, with the exception, that
 the HTML documentation files are not included.  They can be fetched
 from the LAMMPS website by typing "make fetch" in the doc directory.
 Or they can be generated from the content provided in doc/src by
-typing "make html" from the the doc directory.
+typing "make html" from the doc directory.
 
 After initial checkout, as bug fixes and new features are added to
 LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="29 Mar 2019 version">
+<META NAME="docnumber" CONTENT="18 Jun 2019 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-29 Mar 2019 version :c,h2
+18 Jun 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -208,7 +208,7 @@ available on your system.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#compress on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -358,7 +358,7 @@ developed the pair style.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#kim on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -404,7 +404,7 @@ lib/kokkos.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#kokkos on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -477,7 +477,7 @@ Cawkwell, Anders Niklasson, and Christian Negre.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#latte on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -654,7 +654,7 @@ University of Chicago.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#mscg on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -686,7 +686,7 @@ and Vincent Natoli (Stone Ridge Technolgy).
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#opt on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -706,7 +706,7 @@ PERI package :link(PKG-PERI),h4
 
 An atom style, several pair styles which implement different
 Peridynamics materials models, and several computes which calculate
-diagnostics.  Peridynamics is a a particle-based meshless continuum
+diagnostics.  Peridynamics is a particle-based meshless continuum
 model.
 
 [Authors:] The original package was created by Mike Parks (Sandia).
@@ -743,7 +743,7 @@ connections at hinge points.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#poems on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -775,7 +775,7 @@ lib/python/README for more details.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#python on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -905,7 +905,7 @@ SPIN package :link(PKG-SPIN),h4
 Model atomic magnetic spins classically, coupled to atoms moving in
 the usual manner via MD.  Various pair, fix, and compute styles.
 
-[Author:] Julian Tranchida (Sandia).
+[Author:] Julien Tranchida (Sandia).
 
 [Supporting info:]
 
@@ -918,6 +918,7 @@ src/SPIN: filenames -> commands
 "fix nve/spin"_fix_nve_spin.html
 "fix precession/spin"_fix_precession_spin.html
 "compute spin"_compute_spin.html
+"neb/spin"_neb_spin.html
 examples/SPIN :ul
 
 :line
@@ -964,7 +965,7 @@ and LBNL.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#voronoi on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1016,7 +1017,7 @@ atomic information to continuum fields.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-atc on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1043,7 +1044,7 @@ model.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-awpmd on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1183,7 +1184,7 @@ Tribello.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-plumed on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1228,7 +1229,7 @@ isothermal, isoenergetic, isobaric and isenthalpic conditions are
 included.  These enable long timesteps via the Shardlow splitting
 algorithm.
 
-[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John
+[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John
 Brennan (ARL).
 
 [Supporting info:]
@@ -1361,7 +1362,7 @@ H5MD format.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-h5md on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1399,7 +1400,7 @@ NOTE: the USER-INTEL package contains styles that require using the
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-intel on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1536,7 +1537,7 @@ USER-MESO package :link(PKG-USER-MESO),h4
 
 [Contents:]
 
-Several extensions of the the dissipative particle dynamics (DPD)
+Several extensions of the dissipative particle dynamics (DPD)
 method.  Specifically, energy-conserving DPD (eDPD) that can model
 non-isothermal processes, many-body DPD (mDPD) for simulating
 vapor-liquid coexistence, and transport DPD (tDPD) for modeling
@@ -1619,7 +1620,7 @@ at
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-molfile on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1659,7 +1660,7 @@ tools:
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-netcdf on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1703,7 +1704,7 @@ install/un-install the package and build LAMMPS in the usual manner:
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-omp on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1787,7 +1788,7 @@ without changes to LAMMPS itself.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-qmmm on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1845,7 +1846,7 @@ on your system.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-quip on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1963,7 +1964,7 @@ Dynamics, Ernst Mach Institute, Germany).
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-smd on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -2089,7 +2090,7 @@ system.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-vtk on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]