Merge pull request #1480 from akohlmey/next_version

Step version string for next release

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,7 +4,7 @@ _Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in
 
 **Related Issues**
 
-__If this addresses an open GitHub Issue, mention the issue number here. Use the phrases `fixes #221` or `closes #135`, when you want those issues to be automatically closed when the pull request is merged_
+_If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_
 
 **Author(s)**
 
@@ -16,7 +16,7 @@ By submitting this pull request, I agree, that my contribution will be included
 
 **Backward Compatibility**
 
-_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+_Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why_
 
 **Implementation Notes**
 
@@ -24,7 +24,7 @@ _Provide any relevant details about how the changes are implemented, how correct
 
 **Post Submission Checklist**
 
-_Please check the fields below as they are completed **after** the pull request has been submitted_
+_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_
 
 - [ ] The feature or features in this pull request is complete
 - [ ] Licensing information is complete

cmake/CMakeLists.txt

@@ -11,6 +11,8 @@ get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
 
+find_package(Git)
+
 # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
 if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
   set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
@@ -85,7 +87,8 @@ string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
 # this is fast, so check for it all the time
 message(STATUS "Running check for auto-generated files from make-based build system")
 file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
-list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h)
+file(GLOB SRC_AUTOGEN_PACKAGES ${LAMMPS_SOURCE_DIR}/packages_*.h)
+list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h ${LAMMPS_SOURCE_DIR}/lmpgitversion.h)
 foreach(_SRC ${SRC_AUTOGEN_FILES})
   get_filename_component(FILENAME "${_SRC}" NAME)
   if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME})
@@ -170,21 +173,17 @@ set(LAMMPS_LINK_LIBS)
 set(LAMMPS_DEPS)
 set(LAMMPS_API_DEFINES)
 
-set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
-  KSPACE MANYBODY MC MESSAGE MISC MOLECULE PERI REPLICA RIGID SHOCK
-  SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
-  USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
-  USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
-  USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
-  USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
-  USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK
-  USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
+set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
+  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ
+  REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
+  USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS
+  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB
+  USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+  USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC
+  USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
+  USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
-set(OTHER_PACKAGES CORESHELL QEQ)
-foreach(PKG ${DEFAULT_PACKAGES})
-  option(PKG_${PKG} "Build ${PKG} Package" OFF)
-endforeach()
-foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
@@ -201,17 +200,15 @@ endif()
 
 include_directories(${LAMMPS_SOURCE_DIR})
 
-
 if(PKG_USER-ADIOS)
   # The search for ADIOS2 must come before MPI because
   # it includes its own MPI search with the latest FindMPI.cmake
-  # script that defines the MPI::MPI_C target 
+  # script that defines the MPI::MPI_C target
   enable_language(C)
   find_package(ADIOS2 REQUIRED)
   list(APPEND LAMMPS_LINK_LIBS adios2::adios2)
 endif()
 
-
 # do MPI detection after language activation, if MPI for these language is required
 find_package(MPI QUIET)
 option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
@@ -231,7 +228,6 @@ else()
   list(APPEND LAMMPS_LINK_LIBS mpi_stubs)
 endif()
 
-
 set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
 set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
@@ -318,10 +314,26 @@ pkg_depends(USER-LB MPI)
 pkg_depends(USER-PHONON KSPACE)
 pkg_depends(USER-SCAFACOS MPI)
 
+include(CheckIncludeFileCXX)
 find_package(OpenMP QUIET)
-option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
-if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
+
+# TODO: this is a temporary workaround until a better solution is found. AK 2019-05-30
+# GNU GCC 9.x uses settings incompatible with our use of 'default(none)' in OpenMP pragmas
+# where we assume older GCC semantics. For the time being, we disable OpenMP by default
+# for GCC 9.x and beyond. People may manually turn it on, but need to run the script
+# src/USER-OMP/hack_openmp_for_pgi_gcc9.sh on all sources to make it compatible with gcc 9.
+if ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0.0))
+  option(BUILD_OMP "Build with OpenMP support" OFF)
+else()
+  option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
+endif()
+
+if(BUILD_OMP)
   find_package(OpenMP REQUIRED)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  if(NOT HAVE_OMP_H_INCLUDE)
+    message(FATAL_ERROR "Cannot find required 'omp.h' header file")
+  endif()
   set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
 endif()
@@ -365,7 +377,7 @@ if(PKG_KSPACE)
   endif()
 endif()
 
-if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUIP OR PKG_LATTE)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@@ -379,19 +391,10 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
 endif()
 
 if(PKG_PYTHON)
-  find_package(PythonInterp REQUIRED)
   find_package(PythonLibs REQUIRED)
   add_definitions(-DLMP_PYTHON)
   include_directories(${PYTHON_INCLUDE_DIR})
   list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
-  if(BUILD_LIB AND BUILD_SHARED_LIBS)
-    if(NOT PYTHON_INSTDIR)
-      execute_process(COMMAND ${PYTHON_EXECUTABLE}
-        -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
-        OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
-    endif()
-    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
-  endif()
 endif()
 
 find_package(JPEG QUIET)
@@ -448,9 +451,14 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-
 if(PKG_VORONOI)
-  option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" OFF)
+  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)
     message(STATUS "Voro++ download requested - we will build our own")
     include(ExternalProject)
@@ -483,7 +491,13 @@ if(PKG_VORONOI)
 endif()
 
 if(PKG_LATTE)
-  option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" OFF)
+  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")
@@ -495,6 +509,9 @@ if(PKG_LATTE)
       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)
@@ -510,7 +527,15 @@ endif()
 
 if(PKG_USER-SCAFACOS)
   find_package(GSL REQUIRED)
-  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" OFF)
+  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)
     message(STATUS "ScaFaCoS download requested - we will build our own")
     include(ExternalProject)
@@ -550,8 +575,8 @@ if(PKG_USER-SCAFACOS)
     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 scafacos REQUIRED)
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(SCAFACOS REQUIRED scafacos)
     list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
   endif()
   include_directories(${SCAFACOS_INCLUDE_DIRS})
@@ -565,29 +590,53 @@ if(PKG_USER-PLUMED)
   validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
   string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
 
-  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF)
+  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(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/v2.4.4/plumed-src-2.4.4.tgz
-      URL_MD5 71ed465bdc7c2059e282dbda8d564e71
+      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>
                                                ${CONFIGURE_REQUEST_PIC}
-                                                --enable-modules=all
-                                               CXX=${CMAKE_MPI_CXX_COMPILER}
-                                               CC=${CMAKE_MPI_C_COMPILER}
+                                               --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 ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o
-        "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS})
+      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 ${CMAKE_DL_LIBS})
+      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 ${CMAKE_DL_LIBS})
@@ -595,7 +644,7 @@ if(PKG_USER-PLUMED)
     set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
   else()
     find_package(PkgConfig REQUIRED)
-    pkg_check_modules(PLUMED plumed 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)
@@ -611,9 +660,13 @@ if(PKG_USER-PLUMED)
 endif()
 
 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 ${LAMMPS_LIB_SOURCE_DIR}/molfile)
-  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+  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()
 
@@ -624,9 +677,14 @@ if(PKG_USER-NETCDF)
   add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
 endif()
 
-
 if(PKG_USER-SMD)
-  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
+  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)
@@ -668,15 +726,27 @@ if(PKG_USER-VTK)
 endif()
 
 if(PKG_KIM)
-  option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF)
+  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" ${DOWNLOAD_KIM_DEFAULT})
   if(DOWNLOAD_KIM)
-    message(STATUS "KIM-API v2 download requested - we will build our own")
+    message(STATUS "KIM-API download requested - we will build our own")
     enable_language(C)
     enable_language(Fortran)
     include(ExternalProject)
     ExternalProject_Add(kim_build
-      URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.1.txz
-      URL_MD5 289c57f0c3bc2a549662283cac1c4ef1
+      URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz
+      URL_MD5 537d9c0abd30f85b875ebb584f9143fa
       BINARY_DIR build
       CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
                  -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
@@ -685,17 +755,14 @@ if(PKG_KIM)
                  -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
       )
     ExternalProject_get_property(kim_build INSTALL_DIR)
-    set(KIM-API-V2_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v2)
-    set(KIM-API-V2_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api-v2${CMAKE_SHARED_LIBRARY_SUFFIX})
+    set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)
+    set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
     list(APPEND LAMMPS_DEPS kim_build)
   else()
-    find_package(KIM-API-V2)
-    if(NOT KIM-API-V2_FOUND)
-      message(FATAL_ERROR "KIM-API v2 not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")
-    endif()
+    find_package(KIM-API REQUIRED)
   endif()
-  list(APPEND LAMMPS_LINK_LIBS "${KIM-API-V2_LDFLAGS}")
-  include_directories(${KIM-API-V2_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
+  include_directories(${KIM-API_INCLUDE_DIRS})
 endif()
 
 if(PKG_MESSAGE)
@@ -710,6 +777,7 @@ if(PKG_MESSAGE)
     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()
 
@@ -729,7 +797,13 @@ endif()
 
 if(PKG_MSCG)
   find_package(GSL REQUIRED)
-  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" OFF)
+  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)" ${DOWNLOAD_MSCG_DEFAULT})
   if(DOWNLOAD_MSCG)
     if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
       message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
@@ -778,7 +852,6 @@ endif()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
-include(CheckIncludeFileCXX)
 foreach(HEADER cmath)
   check_include_file_cxx(${HEADER} FOUND_${HEADER})
   if(NOT FOUND_${HEADER})
@@ -826,6 +899,8 @@ foreach(PKG ${DEFAULT_PACKAGES})
     list(APPEND LIB_SOURCES ${${PKG}_SOURCES})
     include_directories(${${PKG}_SOURCES_DIR})
   endif()
+
+  RegisterPackages(${${PKG}_SOURCES_DIR})
 endforeach()
 
 # packages that need defines set
@@ -844,6 +919,8 @@ foreach(PKG ${ACCEL_PACKAGES})
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
+
+  RegisterPackages(${${PKG}_SOURCES_DIR})
 endforeach()
 
 ##############################################
@@ -892,7 +969,6 @@ if(PKG_USER-H5MD)
   include_directories(${HDF5_INCLUDE_DIRS})
 endif()
 
-
 ######################################################################
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
@@ -945,7 +1021,7 @@ if(PKG_USER-OMP)
 
     # detects styles which have USER-OMP version
     RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
-    RegisterFixStyle("${USER-OMP_SOURCES_DIR}/fix_omp.h")
+    RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
 
     get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
 
@@ -1058,37 +1134,76 @@ if(PKG_OPT)
 endif()
 
 if(PKG_USER-INTEL)
-    find_package(TBB REQUIRED)
-    find_package(MKL REQUIRED)
+  add_definitions(-DLMP_USER_INTEL)
 
-    if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-      message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler")
-    endif()
+  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)
 
-    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()
-
-    if(NOT BUILD_OMP)
-        message(FATAL_ERROR "USER-INTEL requires OpenMP")
-    endif()
-
-    if(NOT ${LAMMPS_MEMALIGN} STREQUAL "64")
-        message(FATAL_ERROR "USER-INTEL is only useful with LAMMPS_MEMALIGN=64")
-    endif()
-
-    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 ${INTEL_ARCH} INTEL_ARCH)
-
-    if(INTEL_ARCH STREQUAL "KNL")
-      set(CMAKE_EXE_LINKER_FLAGS  "${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)
+  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()
@@ -1101,33 +1216,35 @@ if(PKG_USER-INTEL)
           add_compile_options(${_FLAG})
         endif()
       endforeach()
+    else()
+      add_compile_options(-O3 -ffast-math)
     endif()
+  endif()
 
-    add_definitions(-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG)
+  # 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)
 
-    list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES} ${MKL_LIBRARIES})
+  set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
 
-    set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
-    set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h
-                           ${USER-INTEL_SOURCES_DIR}/intel_buffers.h
-                           ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
-                           ${USER-INTEL_SOURCES_DIR}/math_extra_intel.h
-                           ${USER-INTEL_SOURCES_DIR}/nbin_intel.h
-                           ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
-                           ${USER-INTEL_SOURCES_DIR}/npair_intel.h
-                           ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp
-                           ${USER-INTEL_SOURCES_DIR}/intel_simd.h
-                           ${USER-INTEL_SOURCES_DIR}/intel_intrinsics.h)
+  # detect styles which have a USER-INTEL version
+  RegisterStylesExt(${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)
 
-    set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
+  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()
 
-    # detects styles which have USER-INTEL version
-    RegisterStylesExt(${USER-INTEL_SOURCES_DIR} opt USER-INTEL_SOURCES)
-
-    get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
-
-    list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
-    include_directories(${USER-INTEL_SOURCES_DIR})
+  list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
+  include_directories(${USER-INTEL_SOURCES_DIR})
 endif()
 
 if(PKG_GPU)
@@ -1169,6 +1286,10 @@ if(PKG_GPU)
         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)")
 
@@ -1232,7 +1353,7 @@ if(PKG_GPU)
       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)
+      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)
@@ -1258,7 +1379,15 @@ if(PKG_GPU)
       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)
+      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)
@@ -1269,7 +1398,21 @@ if(PKG_GPU)
 
       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)
-      list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h)
+      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})
@@ -1302,10 +1445,12 @@ endif()
 ######################################################
 # Generate style headers based on global list of
 # styles registered during package selection
+# Generate packages headers from all packages
 ######################################################
 set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
 
 GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})
+GeneratePackagesHeaders(${LAMMPS_STYLE_HEADERS_DIR})
 
 include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 
@@ -1314,7 +1459,7 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 ######################################
 set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")
 set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] =  {\n")
-set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
 list(SORT temp_PKG_LIST)
 foreach(PKG ${temp_PKG_LIST})
     if(PKG_${PKG})
@@ -1326,6 +1471,18 @@ message(STATUS "Generating lmpinstalledpkgs.h...")
 file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" )
 execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h")
 
+######################################
+# Generate lmpgitversion.h
+######################################
+add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
+  -DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
+  -DGIT_EXECUTABLE="${GIT_EXECUTABLE}"
+  -DGIT_FOUND="${GIT_FOUND}"
+  -DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
+  -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/generate_lmpgitversion.cmake)
+set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${LAMMPS_STYLE_HEADERS_DIR}/gitversion.h)
+list(APPEND LAMMPS_DEPS gitversion)
+
 ###########################################
 # Actually add executable and lib to build
 ############################################
@@ -1370,8 +1527,16 @@ if(BUILD_EXE)
   if(ENABLE_TESTING)
     add_test(ShowHelp ${LAMMPS_BINARY} -help)
   endif()
-endif()
 
+  enable_language(C)
+  get_filename_component(MSI2LMP_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../tools/msi2lmp/src ABSOLUTE)
+  file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
+  add_executable(msi2lmp ${MSI2LMP_SOURCES})
+  target_link_libraries(msi2lmp m)
+  install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
+  install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
+
+endif()
 
 ###############################################################################
 # Build documentation
@@ -1434,11 +1599,14 @@ if(BUILD_DOC)
 endif()
 
 ###############################################################################
-# Install potential files in data directory
+# Install potential and force field files in data directory
 ###############################################################################
 set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
 install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials/ DESTINATION ${LAMMPS_POTENTIALS_DIR})
 
+set(LAMMPS_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files)
+install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../tools/msi2lmp/frc_files/ DESTINATION ${LAMMPS_FRC_FILES_DIR})
+
 configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
 configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)
 install(
@@ -1447,6 +1615,49 @@ install(
   DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d
 )
 
+###############################################################################
+# Install LAMMPS lib and python module into site-packages folder with
+# "install-python" target.  Behaves exactly like "make install-python" for
+# conventional build.  Only available, if a shared library is built.
+# This is primarily for people that only want to use the Python wrapper.
+###############################################################################
+if(BUILD_LIB AND BUILD_SHARED_LIBS)
+  find_package(PythonInterp)
+  if (PYTHONINTERP_FOUND)
+    add_custom_target(
+      install-python
+      ${PYTHON_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
+      -m ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py
+      -l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
+      WORKING_DIRECTORY  ${CMAKE_CURRENT_SOURCE_DIR}/../python
+      COMMENT "Installing LAMMPS Python module")
+  else()
+    add_custom_target(
+      install-python
+      ${CMAKE_COMMAND} -E echo "Must have Python installed to install the LAMMPS Python module")
+  endif()
+else()
+  add_custom_target(
+    install-python
+    ${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
+endif()
+
+###############################################################################
+# Add LAMMPS python module to "install" target. This is taylored for building
+# LAMMPS for package managers and with different prefix settings.
+# This requires either a shared library or that the PYTHON package is included.
+###############################################################################
+if((BUILD_LIB AND BUILD_SHARED_LIBS) OR (PKG_PYTHON))
+  find_package(PythonInterp)
+  if (PYTHONINTERP_FOUND)
+    execute_process(COMMAND ${PYTHON_EXECUTABLE}
+      -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
+      OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
+    set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
+  endif()
+endif()
+
 ###############################################################################
 # Testing
 #
@@ -1479,7 +1690,7 @@ endif()
 ###############################################################################
 # Print package summary
 ###############################################################################
-foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
   if(PKG_${PKG})
     message(STATUS "Building package: ${PKG}")
   endif()

cmake/Modules/FindKIM-API.cmake

@@ -19,7 +19,7 @@
 #
 
 #
-# Copyright (c) 2013--2018, Regents of the University of Minnesota.
+# Copyright (c) 2013--2019, Regents of the University of Minnesota.
 # All rights reserved.
 #
 # Contributors:
@@ -28,23 +28,32 @@
 #    Ryan S. Elliott
 #
 
-# - Find KIM-API-V2
+# - Find KIM-API
 #
 # sets standard pkg_check_modules variables plus:
 #
-# KIM-API-V2-CMAKE_C_COMPILER
-# KIM-API-V2-CMAKE_CXX_COMPILER
-# KIM-API-V2-CMAKE_Fortran_COMPILER
+# KIM-API-CMAKE_C_COMPILER
+# 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-V2 REQUIRED libkim-api-v2>=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-v2 CMAKE_C_COMPILER)
-pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api-v2 CMAKE_CXX_COMPILER)
-pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api-v2 CMAKE_Fortran_COMPILER)
+if(KIM-API_FOUND)
+  pkg_get_variable(KIM-API-CMAKE_C_COMPILER libkim-api CMAKE_C_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-V2_FOUND to TRUE
+# handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
 # if all listed variables are TRUE
-find_package_handle_standard_args(KIM-API-V2 REQUIRED_VARS KIM-API-V2_LIBRARIES)
+find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES)

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/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/generate_lmpgitversion.cmake

@@ -0,0 +1,30 @@
+set(temp "#ifndef LMP_GIT_VERSION_H\n#define LMP_GIT_VERSION_H\n")
+set(temp_git_commit "(unknown)")
+set(temp_git_branch "(unknown)")
+set(temp_git_describe "(unknown)")
+set(temp_git_info "false")
+if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
+  set(temp_git_info "true")
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD
+    OUTPUT_VARIABLE temp_git_commit
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD
+    OUTPUT_VARIABLE temp_git_branch
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified
+    OUTPUT_VARIABLE temp_git_describe
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+endif()
+
+set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n")
+set(temp "${temp}#endif\n\n")
+
+message(STATUS "Generating lmpgitversion.h...")
+file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )
+execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")

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>
 
@@ -1503,6 +1516,16 @@ target API.
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>CUDA_MPS_SUPPORT</code> (CUDA only)</td>
+  <td>Enable tweaks for running with Nvidia CUDA Multi-process services daemon</td>
+  <td>
+  <dl>
+    <dt><code>on</code></dt>
+    <dt><code>off</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>BIN2C</code> (CUDA only)</td>
   <td>Path to bin2c executable, will automatically pick up the first one in your $PATH.</td>

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
-export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
+# set environment for LAMMPS and msi2lmp executables
+# to find potential and force field files
+LAMMPS_POTENTIALS=${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
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+# preset that turns on all existing packages off. can be used to reset
+# an existing package selection without losing any other settings
 
-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})
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
+        MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+        SRD VORONOI
+        USER-ADIOS 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-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
+        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+        USER-TALLY USER-UEF USER-VTK USER-YAFF)
 
 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
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+# preset that turns on all existing packages. using the combination
+# this preset followed by the nolib.cmake preset should configure a
+# LAMMPS binary, with as many packages included, that can be compiled
+# 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
-                  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})
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
+        MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+        SRD VORONOI
+        USER-ADIOS 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-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
+        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+        USER-TALLY USER-UEF USER-VTK USER-YAFF)
 
 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
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+# preset that turns off all packages that require some form of external
+# library or special compiler (fortran or cuda) or equivalent.
 
-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})
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
+        VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
+        USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
+        USER-SCAFACOS USER-SMD USER-VTK)
 
 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

@@ -116,6 +116,13 @@ mobi: epub
 	@echo "Conversion finished. The MOBI manual file is created."
 
 pdf: $(OBJECTS) $(ANCHORCHECK)
+	@(\
+		cd src/Developer; \
+		pdflatex developer; \
+		pdflatex developer; \
+		mv developer.pdf ../../Developer.pdf; \
+		cd ../../; \
+	)
 	@(\
                 . $(VENV)/bin/activate ;\
                 cp -r src/* $(RSTDIR)/ ;\
@@ -135,14 +142,7 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
 	  make && \
 	  make && \
 	  mv LAMMPS.pdf ../Manual.pdf && \
-	  cd ../; 
-	@(\
-		cd src/Developer; \
-		pdflatex developer; \
-		pdflatex developer; \
-		mv developer.pdf ../../Developer.pdf; \
-		cd ../../; \
-	)
+	  cd ../;
 	@rm -rf latex/_sources
 	@rm -rf latex/PDF
 	@rm -rf latex/USER

doc/lammps.1

@@ -1,40 +1,259 @@
-.TH LAMMPS "2018-08-22"
+.TH LAMMPS "31 May 2019" "2019-05-31"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
 
 .SH SYNOPSIS
-.B lmp 
--in in.file
+.B lmp
+\-in <input file> [OPTIONS] ...
 
 or
 
-mpirun \-np 2 
-.B lmp 
--in in.file
+mpirun \-np 2
+.B lmp
+<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 
-Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft 
-materials (biomolecules, 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 
+.B LAMMPS
+is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale
+\fBA\fRtomic/\fBM\fRolecular \fBM\fRassively \fBP\fRarallel \fBS\fRimulator.
+.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.
 
-.SH COPYRIGHT 
-© 2003--2018 Sandia Corporation
+.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--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
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
+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

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

@@ -28,7 +28,7 @@ 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
@@ -41,7 +41,8 @@ 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 +109,8 @@ 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,
@@ -82,17 +81,19 @@ which GPU hardware to build for.
 
 [CMake build]:
 
--D GPU_API=value      # value = opencl (default) or cuda
--D GPU_PREC=value     # precision setting
-                      # value = double or mixed (default) or single
--D OCL_TUNE=value     # hardware choice for GPU_API=opencl
-                      # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
--D GPU_ARCH=value     # primary GPU hardware choice for GPU_API=cuda
-                      # value = sm_XX, see below
-                      # default is Cuda-compiler dependent, but typically sm_20
--D CUDPP_OPT=value    # optimization setting for GPU_API=cuda
-                      # enables CUDA Performance Primitives Optimizations
-                      # yes (default) or no :pre
+-D GPU_API=value          # value = opencl (default) or cuda
+-D GPU_PREC=value         # precision setting
+                          # value = double or mixed (default) or single
+-D OCL_TUNE=value         # hardware choice for GPU_API=opencl
+                          # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
+-D GPU_ARCH=value         # primary GPU hardware choice for GPU_API=cuda
+                          # value = sm_XX, see below
+                          # default is Cuda-compiler dependent, but typically sm_20
+-D CUDPP_OPT=value        # optimization setting for GPU_API=cuda
+                          # enables CUDA Performance Primitives Optimizations
+                          # value = yes (default) or no
+-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
+                          # value = yes or no (default) :pre
 
 GPU_ARCH settings for different GPU hardware is as follows:
 
@@ -169,26 +170,24 @@ used to build the GPU library.
 
 KIM package :h4,link(kim)
 
-To build with this package, the KIM library must be downloaded and
-built on your system.  It must include the KIM models that you want to
-use with LAMMPS.
+To build with this package, the KIM library with API v2 must be downloaded
+and built on your system.  It must include the KIM models that you want to
+use with LAMMPS. If you want to use the "kim_query"_kim_query.html
+command, you also need to have libcurl installed with the matching
+development headers and the curl-config tool.
 
 Note that in LAMMPS lingo, a KIM model driver is a pair style
 (e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
 element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file.  Also note that installing the KIM API
-library with all its models, may take around 30 min to build.  Of
-course you only need to do that once.
+specific EAM potential file.  Also note that downloading and installing
+the KIM API library with all its models, may take a long time (10s of
+minutes to hours) to build.  Of course you only need to do that once.
 
 See the list of KIM model drivers here:
-https://openkim.org/kim-items/model-drivers/alphabetical
+https://openkim.org/browse/model-drivers/alphabetical
 
 See the list of all KIM models here:
-https://openkim.org/kim-items/models/by-model-drivers
-
-See the list of example KIM models included by default here:
-https://openkim.org/kim-api on the "What is in the KIM API source
-package?" page.
+https://openkim.org/browse/models/by-model-drivers
 
 [CMake build]:
 
@@ -197,7 +196,7 @@ package?" page.
 If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
 inside the CMake build directory.  If the KIM library is already on
 your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH
-environment variable so that libkim-api-v2 can be found.
+environment variable so that libkim-api can be found.
 
 [Traditional make]:
 
@@ -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
-"install the USER-OMP package"_#user-omp, as it can be used in tandem
-with the USER-INTEL package to good effect, as explained on the "Speed
-intel"_Speed_intel.html doc page.
+build for, either x86 CPUs or Intel KNLs in offload mode.  You should
+also typically "install the USER-OMP package"_#user-omp, as it can be
+used in tandem with the USER-INTEL package to good effect, as explained
+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:
 
@@ -897,7 +867,17 @@ USER-MOLFILE package :h4,link(user-molfile)
 
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_USER-MOLFILE=yes".
+-D MOLFILE_INCLUDE_DIRS=path   # (optional) path where VMD molfile plugin headers are installed
+-D PKG_USER-MOLFILE=yes     :pre
+
+
+Using "-D PKG_USER-MOLFILE=yes" enables the package, and setting
+"-D MOLFILE_INCLUDE DIRS" allows to provide a custom location for
+the molfile plugin header files. These should match the ABI of the
+plugin files used, and thus one typically sets them to include
+folder of the local VMD installation in use. LAMMPS ships with a
+couple of default header files that correspond to a popular VMD
+version, usually the latest release.
 
 [Traditional make]:
 
@@ -906,7 +886,11 @@ loading library libdl.a that is typically present on all systems.  It
 is required for LAMMPS to link with this package.  If the setting is
 not valid for your system, you will need to edit the Makefile.lammps
 file.  See lib/molfile/README and lib/molfile/Makefile.lammps for
-details.
+details. It is also possible to configure a different folder with
+the VMD molfile plugin header files. LAMMPS ships with a couple of
+default headers, but these are not compatible with all VMD versions,
+so it is often best to change this setting to the location of the
+same include files of the local VMD installation in use.
 
 :line
 

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_off.cmake \[OPTIONS\] ../cmake | disable all packages
-cmake -C ../cmake/presets/std.cmake \[OPTIONS\] ../cmake | enable standard packages
-cmake -C ../cmake/presets/user.cmake \[OPTIONS\] ../cmake | enable user packages
-cmake -C ../cmake/presets/std_nolib.cmake \[OPTIONS\] ../cmake | enable standard packages that do not require extra libraries
-cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake | disable all packages that do not require extra libraries
-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/all_on.cmake  \[OPTIONS\] ../cmake |
+      enable all packages |
+cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake |
+      disable all packages |
+cmake -C ../cmake/presets/minimal.cmake \[OPTIONS\] ../cmake |
+      enable just a few core packages |
+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
-multiple cmake runs.
+current build directory. You can combine multiple presets and options
+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
-# use libraries and enable GPU package
+# build LAMMPS with most commonly used packages, but then remove
+# 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

@@ -57,10 +57,10 @@ FFT_INC = -DFFT_SINGLE        # do not specify for double precision
 FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY :pre
                               # default is FFT_PACK_ARRAY if not specified
 
-FFT_INC =    	-I/usr/local/include
+FFT_INC =       -I/usr/local/include
 FFT_PATH =      -L/usr/local/lib
-FFT_LIB =	-lfftw3             # FFTW3 double precision
-FFT_LIB =	-lfftw3 -lfftw3f    # FFTW3 single precision
+FFT_LIB =       -lfftw3             # FFTW3 double precision
+FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
 FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core  # MKL with Intel compiler
 FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core     # MKL with GNU compier :pre
 
@@ -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
-"bigbig" setting.
+Note that the USER-ATC package and the USER-INTEL package are currently
+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
-for this; you will have to request that makefiles are generated and
-manually set the compiler.
+the old build system is provided. Using CMake for this mode of compilation
+is untested and not likely to work.
 
-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_all.txt

@@ -68,6 +68,7 @@ An alphabetic list of all general LAMMPS commands.
 "improper_style"_improper_style.html,
 "include"_include.html,
 "jump"_jump.html,
+"kim_query"_kim_query.html,
 "kspace_modify"_kspace_modify.html,
 "kspace_style"_kspace_style.html,
 "label"_label.html,
@@ -78,9 +79,11 @@ An alphabetic list of all general LAMMPS commands.
 "minimize"_minimize.html,
 "min_modify"_min_modify.html,
 "min_style"_min_style.html,
+"min_style spin"_min_spin.html,
 "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_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,
@@ -224,7 +226,7 @@ OPT.
 "wall/body/polyhedron"_fix_wall_body_polyhedron.html,
 "wall/colloid"_fix_wall.html,
 "wall/ees"_fix_wall_ees.html,
-"wall/gran (o)"_fix_wall_gran.html,
+"wall/gran"_fix_wall_gran.html,
 "wall/gran/region"_fix_wall_gran_region.html,
 "wall/harmonic"_fix_wall.html,
 "wall/lj1043"_fix_wall.html,

doc/src/Commands_pair.txt

@@ -80,6 +80,8 @@ 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 +100,7 @@ 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/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/min_spin_damping.tex

@@ -0,0 +1,13 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \frac{d \vec{s}_{i}}{dt} = \lambda\, \vec{s}_{i} \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right)
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/min_spin_timestep.tex

@@ -0,0 +1,14 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    {\Delta t}_{\rm max} = \frac{2\pi}{\kappa
+    \left|\vec{\omega}_{\rm max} \right|} 
+    \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/Errors_messages.txt

@@ -5828,6 +5828,12 @@ 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
@@ -7448,6 +7454,11 @@ 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 +10001,25 @@ 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 +10060,19 @@ 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 +10088,23 @@ 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 +10112,7 @@ 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 +10120,7 @@ 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 +10128,7 @@ 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 +10144,7 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Unknown pair style} :dt
+{Unrecognized pair style} :dt
 
 The choice of pair style is unknown. :dd
 
@@ -10141,7 +10152,7 @@ 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/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
-coefficients is done in the input data file via the
-"read_data"_read_data.html command or in the input script with
+used in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
+coefficients is done either from special sections in an input data file
+via the "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
-additional tools that can use CHARMM or AMBER to assign force field
-coefficients and convert their output into LAMMPS input.
+"bond_coeff"_bond_coeff.html and so on.  See the "Tools"_Tools.html doc
+page for additional tools that can use CHARMM, AMBER, or Materials
+Studio generated files to assign force field coefficients and convert
+their output into LAMMPS input.
 
 See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
-field.  See "(Cornell)"_#howto-Cornell for a description of the AMBER force
-field.
+field.  See "(Cornell)"_#howto-Cornell for a description of the AMBER
+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
-with common options in CHARMM or AMBER.  See each command's
-documentation for the formula it computes.
+The interaction styles listed below compute force field formulas that
+are consistent with common options in CHARMM or AMBER.  See each
+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
-released in March 2017.  We recommend they be used instead of the
-older {charmm} styles.  See discussion of the differences on the "pair
-charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
-doc pages.
+NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were released
+in March 2017.  We recommend they be used instead of the older {charmm}
+styles.  See discussion of the differences on the "pair
+charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html doc
+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
-main-group inorganic molecules. The philosophy in DREIDING is to use
-general force constants and geometry parameters based on simple
-hybridization considerations, rather than individual force constants
-and geometric parameters that depend on the particular combinations of
-atoms involved in the bond, angle, or torsion terms. DREIDING has an
-"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
-interactions involving a hydrogen atom on very electronegative atoms
-(N, O, F).
+predicting structures and dynamics of organic, biological and main-group
+inorganic molecules. The philosophy in DREIDING is to use general force
+constants and geometry parameters based on simple hybridization
+considerations, rather than individual force constants and geometric
+parameters that depend on the particular combinations of atoms involved
+in the bond, angle, or torsion terms. DREIDING has an "explicit hydrogen
+bond term"_pair_hbond_dreiding.html to describe interactions involving a
+hydrogen atom on very electronegative atoms (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
-with the DREIDING force field.  See each command's
+The interaction styles listed below compute force field formulas that
+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_pylammps.txt

@@ -57,6 +57,17 @@ library is then loaded by the Python interface. In this example we enable the
 MOLECULE package and compile LAMMPS with C++ exceptions, PNG, JPEG and FFMPEG
 output support enabled.
 
+Step 1a: For the CMake based build system, the steps are:
+
+mkdir $LAMMPS_DIR/build-shared
+cd  $LAMMPS_DIR/build-shared :pre
+
+# MPI, PNG, Jpeg, FFMPEG are auto-detected
+cmake ../cmake -DPKG_MOLECULE=yes -DLAMMPS_EXCEPTIONS=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
+make :pre
+
+Step 1b: For the legacy, make based build system, the steps are:
+
 cd $LAMMPS_DIR/src :pre
 
 # add packages if necessary
@@ -68,10 +79,9 @@ make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS
 Step 2: Installing the LAMMPS Python package :h6
 
 PyLammps is part of the lammps Python package. To install it simply install
-that package into your current Python installation.
+that package into your current Python installation with:
 
-cd $LAMMPS_DIR/python
-python install.py :pre
+make install-python :pre
 
 NOTE: Recompiling the shared library requires re-installing the Python package
 
@@ -94,14 +104,21 @@ apt-get install python-virtualenv :pre
 
 Creating a virtualenv with lammps installed :h6
 
-# create virtualenv name 'testing' :pre
+# create virtualenv named 'testing'
+virtualenv $HOME/python/testing :pre
 
 # activate 'testing' environment
-source testing/bin/activate :pre
+source $HOME/python/testing/bin/activate :pre
+
+Now configure and compile the LAMMPS shared library as outlined above.
+When using CMake and the shared library has already been build, you
+need to re-run CMake to update the location of the python executable
+to the location in the virtual environment with:
+
+cmake . -DPYTHON_EXECUTABLE=$(which python) :pre
 
 # install LAMMPS package in virtualenv
-(testing) cd $LAMMPS_DIR/python
-(testing) python install.py :pre
+(testing) make install-python :pre
 
 # install other useful packages
 (testing) pip install matplotlib jupyter mpi4py :pre

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="28 Feb 2019 version">
+<META NAME="docnumber" CONTENT="31 May 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
-28 Feb 2019 version :c,h2
+31 May 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:]
@@ -341,6 +341,8 @@ KIM package :link(PKG-KIM),h4
 A "pair_style kim"_pair_kim.html command which is a wrapper on the
 Knowledge Base for Interatomic Models (KIM) repository of interatomic
 potentials, enabling any of them to be used in LAMMPS simulations.
+Also a "kim_query"_kim_query.html command, which allows to query
+the OpenKIM database for stored properties.
 
 To use this package you must have the KIM library available on your
 system.
@@ -356,7 +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:]
@@ -402,7 +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:]
@@ -475,7 +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:]
@@ -652,7 +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:]
@@ -684,7 +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:]
@@ -704,7 +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).
@@ -741,7 +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:]
@@ -773,7 +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:]
@@ -903,7 +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:]
 
@@ -916,6 +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
@@ -962,7 +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:]
@@ -1014,7 +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:]
@@ -1041,7 +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:]
@@ -1181,7 +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:]
@@ -1226,7 +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:]
@@ -1359,7 +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:]
@@ -1397,7 +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:]
@@ -1534,7 +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
@@ -1617,7 +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:]
@@ -1657,7 +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:]
@@ -1701,7 +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:]
@@ -1785,7 +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:]
@@ -1843,7 +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:]
@@ -1961,7 +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:]
@@ -2087,7 +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:]

doc/src/Python_install.txt

@@ -12,16 +12,23 @@ Installing LAMMPS in Python :h3
 For Python to invoke LAMMPS, there are 2 files it needs to know about:
 
 python/lammps.py
-src/liblammps.so :ul
+liblammps.so or liblammps.dylib :ul
 
-Lammps.py is the Python wrapper on the LAMMPS library interface.
-Liblammps.so is the shared LAMMPS library that Python loads, as
-described above.
+The python source code in lammps.py is the Python wrapper on the
+LAMMPS library interface. The liblammps.so or liblammps.dylib file
+is the shared LAMMPS library that Python loads dynamically.
 
-You can insure Python can find these files in one of two ways:
+You can achieve that Python can find these files in one of two ways:
 
-set two environment variables
-run the python/install.py script :ul
+set two environment variables pointing to the location in the source tree
+run "make install-python" or run the python/install.py script explicitly :ul
+
+When calling "make install-python" LAMMPS will try to install the
+python module and the shared library into the python site-packages folders;
+either the system-wide ones, or the local users ones (in case of insufficient
+permissions for the global install). Python will then find the module
+and shared library file automatically. The exact location of these folders
+depends on your python version and your operating system.
 
 If you set the paths to these files as environment variables, you only
 have to do it once.  For the csh or tcsh shells, add something like
@@ -30,42 +37,28 @@ this to your ~/.cshrc file, one line for each of the two files:
 setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python
 setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
 
-If you use the python/install.py script, you need to invoke it every
-time you rebuild LAMMPS (as a shared library) or make changes to the
-python/lammps.py file.
+On MacOSX you may also need to set DYLD_LIBRARY_PATH accordingly.
+For Bourne/Korn shells accordingly into the corresponding files using
+the "export" shell builtin.
 
-You can invoke install.py from the python directory as
+If you use "make install-python" or the python/install.py script, you need
+to invoke it every time you rebuild LAMMPS (as a shared library) or
+make changes to the python/lammps.py file, so that the site-packages
+files are updated with the new version.
 
-% python install.py \[libdir\] \[pydir\] :pre
+If the default settings of "make install-python" are not what you want,
+you can invoke install.py from the python directory manually as
 
-The optional libdir is where to copy the LAMMPS shared library to; the
-default is /usr/local/lib.  The optional pydir is where to copy the
-lammps.py file to; the default is the site-packages directory of the
-version of Python that is running the install script.
+% python install.py -m \<python module\> -l <shared library> -v <version.h file> \[-d \<pydir\>\] :pre
 
-Note that libdir must be a location that is in your default
-LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib.  And pydir must be a
-location that Python looks in by default for imported modules, like
-its site-packages dir.  If you want to copy these files to
-non-standard locations, such as within your own user space, you will
-need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
-accordingly, as above.
+The -m flag points to the lammps.py python module file to be installed,
+the -l flag points to the LAMMPS shared library file to be installed,
+the -v flag points to the version.h file in the LAMMPS source
+and the optional -d flag to a custom (legacy) installation folder :ul
 
-If the install.py script does not allow you to copy files into system
-directories, prefix the python command with "sudo".  If you do this,
-make sure that the Python that root runs is the same as the Python you
-run.  E.g. you may need to do something like
-
-% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre
-
-You can also invoke install.py from the make command in the src
-directory as
-
-% make install-python :pre
-
-In this mode you cannot append optional arguments.  Again, you may
-need to prefix this with "sudo".  In this mode you cannot control
-which Python is invoked by root.
+If you use a legacy installation folder, you will need to set your
+PYTHONPATH and LD_LIBRARY_PATH (and/or DYLD_LIBRARY_PATH) environment
+variables accordingly, as described above.
 
 Note that if you want Python to be able to load different versions of
 the LAMMPS shared library (see "this section"_Python_shlib.html), you will

doc/src/Python_library.txt

@@ -180,7 +180,7 @@ doubles is returned, one value per atom, which you can use via normal
 Python subscripting. The values will be zero for atoms not in the
 specified group.
 
-The get_thermo() method returns returns the current value of a thermo
+The get_thermo() method returns the current value of a thermo
 keyword as a float.
 
 The get_natoms() method returns the total number of atoms in the

doc/src/Python_overview.txt

@@ -13,11 +13,11 @@ Overview of Python and LAMMPS :h3
 LAMMPS can work together with Python in three ways.  First, Python can
 wrap LAMMPS through the its "library interface"_Howto_library.html, so
 that a Python script can create one or more instances of LAMMPS and
-launch one or more simulations.  In Python lingo, this is "extending"
-Python with LAMMPS.
+launch one or more simulations.  In Python lingo, this is called
+"extending" Python with a LAMMPS module.
 
 Second, a lower-level Python interface can be used indirectly through
-provided PyLammps and IPyLammps wrapper classes, written in Python.
+the provided PyLammps and IPyLammps wrapper classes, written in Python.
 These wrappers try to simplify the usage of LAMMPS in Python by
 providing an object-based interface to common LAMMPS functionality.
 They also reduces the amount of code necessary to parameterize LAMMPS
@@ -25,11 +25,12 @@ scripts through Python and make variables and computes directly
 accessible.
 
 Third, LAMMPS can use the Python interpreter, so that a LAMMPS
-input script can invoke Python code directly, and pass information
-back-and-forth between the input script and Python functions you
-write.  This Python code can also callback to LAMMPS to query or change
-its attributes.  In Python lingo, this is "embedding" Python in
-LAMMPS.  When used in this mode, Python can perform operations that
-the simple LAMMPS input script syntax cannot.
+input script or styles can invoke Python code directly, and pass
+information back-and-forth between the input script and Python
+functions you write.  This Python code can also callback to LAMMPS
+to query or change its attributes through the LAMMPS Python module
+mentioned above.  In Python lingo, this is "embedding" Python in
+LAMMPS.  When used in this mode, Python can perform script operations
+that the simple LAMMPS input script syntax can not.
 
 

doc/src/Run_options.txt

@@ -79,7 +79,7 @@ stdin.
 Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
 package.  Even if LAMMPS is built with this package, as described
 in "Speed kokkos"_Speed_kokkos.html, this switch must be set to enable
-running with the KOKKOS-enabled styles the package provides.  If the
+running with KOKKOS-enabled styles the package provides.  If the
 switch is not set (the default), LAMMPS will operate as if the KOKKOS
 package were not installed; i.e. you can run standard LAMMPS or with
 the GPU or USER-OMP packages, for testing or benchmarking purposes.
@@ -242,7 +242,7 @@ processors.
 
 Running with multiple partitions can be useful for running
 "multi-replica simulations"_Howto_replica.html, where each replica
-runs on on one or a few processors.  Note that with MPI installed on a
+runs on one or a few processors.  Note that with MPI installed on a
 machine (e.g. your desktop), you can run on more (virtual) processors
 than you have physical processors.
 
@@ -448,7 +448,7 @@ partition screen files file.N.
 [-suffix style args] :link(suffix)
 
 Use variants of various styles if they exist.  The specified style can
-be {cuda}, {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}.  These
+be {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}.  These
 refer to optional packages that LAMMPS can be built with, as described
 in "Accelerate performance"_Speed.html.  The "gpu" style corresponds to the
 GPU package, the "intel" style to the USER-INTEL package, the "kk"

doc/src/Run_output.txt

@@ -93,7 +93,7 @@ monitor thread utilization and load balance is provided. A new {Thread
 timings} section is also added, which lists the time spent in reducing
 the per-thread data elements to the storage for non-threaded
 computation. These thread timings are measured for the first MPI rank
-only and and thus, because the breakdown for MPI tasks can change from
+only and thus, because the breakdown for MPI tasks can change from
 MPI rank to MPI rank, this breakdown can be very different for
 individual ranks. Here is an example output for this section:
 

doc/src/Speed_intel.txt

@@ -24,7 +24,7 @@ LAMMPS to run on the CPU cores and co-processor cores simultaneously.
 
 Angle Styles: charmm, harmonic :ulb,l
 Bond Styles: fene, fourier, harmonic :l
-Dihedral Styles: charmm, harmonic, opls :l
+Dihedral Styles: charmm, fourier, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l
 Improper Styles: cvff, harmonic :l
 Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long,
@@ -34,6 +34,10 @@ rebo, sw, tersoff :l
 K-Space Styles: pppm, pppm/disp :l
 :ule
 
+IMPORTANT NOTE: None of the styles in the USER-INTEL package currently
+support computing per-atom stress.  If any compute or fix in your
+input requires it, LAMMPS will abort with an error message.
+
 [Speed-ups to expect:]
 
 The speedups will depend on your simulation, the hardware, which

doc/src/Speed_kokkos.txt

@@ -111,16 +111,10 @@ Makefile.kokkos_mpi_only) will give better performance than the OpenMP
 back end (i.e. Makefile.kokkos_omp) because some of the overhead to make
 the code thread-safe is removed.
 
-NOTE: The default for the "package kokkos"_package.html command is to
-use "full" neighbor lists and set the Newton flag to "off" for both
-pairwise and bonded interactions. However, when running on CPUs, it
-will typically be faster to use "half" neighbor lists and set the
-Newton flag to "on", just as is the case for non-accelerated pair
-styles. It can also be faster to use non-threaded communication.  Use
-the "-pk kokkos" "command-line switch"_Run_options.html to change the
-default "package kokkos"_package.html options. See its doc page for
-details and default settings. Experimenting with its options can
-provide a speed-up for specific calculations. For example:
+NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html to 
+change the default "package kokkos"_package.html options. See its doc 
+page for details and default settings. Experimenting with its options 
+can provide a speed-up for specific calculations. For example: 
 
 mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj       # Newton on, Half neighbor list, non-threaded comm :pre
 
@@ -190,19 +184,18 @@ tasks/node. The "-k on t Nt" command-line switch sets the number of
 threads/task as Nt. The product of these two values should be N, i.e.
 256 or 264.
 
-NOTE: The default for the "package kokkos"_package.html command is to
-use "full" neighbor lists and set the Newton flag to "off" for both
-pairwise and bonded interactions. When running on KNL, this will
-typically be best for pair-wise potentials. For many-body potentials,
-using "half" neighbor lists and setting the Newton flag to "on" may be
-faster. It can also be faster to use non-threaded communication.  Use
-the "-pk kokkos" "command-line switch"_Run_options.html to change the
-default "package kokkos"_package.html options. See its doc page for
-details and default settings. Experimenting with its options can
-provide a speed-up for specific calculations. For example:
+NOTE: The default for the "package kokkos"_package.html command when 
+running on KNL is to use "half" neighbor lists and set the Newton flag 
+to "on" for both pairwise and bonded interactions. This will typically 
+be best for many-body potentials. For simpler pair-wise potentials, it 
+may be faster to use a "full" neighbor list with Newton flag to "off". 
+Use the "-pk kokkos" "command-line switch"_Run_options.html to change 
+the default "package kokkos"_package.html options. See its doc page for 
+details and default settings. Experimenting with its options can provide 
+a speed-up for specific calculations. For example: 
 
-mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj      #  Newton off, full neighbor list, non-threaded comm
-mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax      # Newton on, half neighbor list, non-threaded comm :pre
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax      #  Newton on, half neighbor list, threaded comm
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj      # Newton off, full neighbor list, non-threaded comm :pre
 
 NOTE: MPI tasks and threads should be bound to cores as described
 above for CPUs.
@@ -236,19 +229,19 @@ one or more nodes, each with two GPUs:
 mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj          # 1 node,   2 MPI tasks/node, 2 GPUs/node
 mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj  # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre
 
-NOTE: The default for the "package kokkos"_package.html command is to
-use "full" neighbor lists and set the Newton flag to "off" for both
-pairwise and bonded interactions, along with threaded communication.
-When running on Maxwell or Kepler GPUs, this will typically be
-best. For Pascal GPUs, using "half" neighbor lists and setting the
-Newton flag to "on" may be faster. For many pair styles, setting the
-neighbor binsize equal to the ghost atom cutoff will give speedup.
-Use the "-pk kokkos" "command-line switch"_Run_options.html to change
-the default "package kokkos"_package.html options. See its doc page
-for details and default settings. Experimenting with its options can
-provide a speed-up for specific calculations. For example:
+NOTE: The default for the "package kokkos"_package.html command when 
+running on GPUs is to use "full" neighbor lists and set the Newton flag 
+to "off" for both pairwise and bonded interactions, along with threaded 
+communication. When running on Maxwell or Kepler GPUs, this will 
+typically be best. For Pascal GPUs, using "half" neighbor lists and 
+setting the Newton flag to "on" may be faster. For many pair styles, 
+setting the neighbor binsize equal to twice the CPU default value will 
+give speedup, which is the default when running on GPUs. Use the "-pk 
+kokkos" "command-line switch"_Run_options.html to change the default 
+"package kokkos"_package.html options. See its doc page for details and 
+default settings. Experimenting with its options can provide a speed-up 
+for specific calculations. For example: 
 
-mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj      # Set binsize = neighbor ghost cutoff
 mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre
 
 NOTE: For good performance of the KOKKOS package on GPUs, you must

doc/src/Tools.txt

@@ -77,6 +77,7 @@ Post-processing tools :h3
 "python"_#pythontools,
 "reax"_#reax_tool,
 "smd"_#smd,
+"spin"_#spin,
 "xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
 
 Miscellaneous tools :h3
@@ -511,6 +512,20 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
 
 :line
 
+spin tool :h4,link(spin)
+
+The spin sub-directory contains a C file interpolate.c which can
+be compiled and used to perform a cubic polynomial interpolation of 
+the MEP following a GNEB calculation.
+
+See the README file in tools/spin/interpolate_gneb for more details.
+
+This tool was written by the SPIN package author, Julien
+Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei 
+Ivanov, at University of Iceland (ali5 at hi.is).
+
+:line
+
 vim tool :h4,link(vim)
 
 The files in the tools/vim directory are add-ons to the VIM editor

doc/src/commands_list.txt

@@ -53,6 +53,7 @@ Commands :h1
    include
    info
    jump
+   kim_query
    kspace_modify
    kspace_style
    label
@@ -61,10 +62,12 @@ Commands :h1
    mass
    message
    min_modify
+   min_spin
    min_style
    minimize
    molecule
    neb
+   neb_spin
    neigh_modify
    neighbor
    newton

doc/src/compute.txt

@@ -54,9 +54,10 @@ local quantities have the word "local" in their style,
 e.g. {bond/local}.  Styles with neither "atom" or "local" in their
 style produce global quantities.
 
-Note that a single compute produces either global or per-atom or local
-quantities, but never more than one of these (with only a few
-exceptions, as documented by individual compute commands).
+Note that a single compute can produce either global or per-atom or
+local quantities, but not both global and per-atom.  It can produce
+local quantities in tandem with global or per-atom quantities.  The
+compute doc page will explain.
 
 Global, per-atom, and local quantities each come in three kinds: a
 single scalar value, a vector of values, or a 2d array of values.  The

doc/src/compute_chunk_atom.txt

@@ -468,7 +468,7 @@ property/chunk"_compute_property_chunk.html command.
 NOTE: The compression operation requires global communication across
 all processors to share their chunk ID values.  It can require large
 memory on every processor to store them, even after they are
-compressed, if there are are a large number of unique chunk IDs with
+compressed, if there are a large number of unique chunk IDs with
 atoms assigned to them.  It uses a STL map to find unique chunk IDs
 and store them in sorted order.  Each time an atom is assigned a
 compressed chunk ID, it must access the STL map.  All of this means

doc/src/compute_chunk_spread_atom.txt

@@ -49,7 +49,7 @@ For inputs that are computes, they must be a compute that calculates
 per-chunk values.  These are computes whose style names end in
 "/chunk".
 
-For inputs that are fixes, they should be a a fix that calculates
+For inputs that are fixes, they should be a fix that calculates
 per-chunk values.  For example, "fix ave/chunk"_fix_ave_chunk.html or
 "fix ave/time"_fix_ave_time.html (assuming it is time-averaging
 per-chunk data).

doc/src/compute_coord_atom.txt

@@ -15,8 +15,9 @@ compute ID group-ID coord/atom cstyle args ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 coord/atom = style name of this compute command :l
 cstyle = {cutoff} or {orientorder} :l
-  {cutoff} args = cutoff typeN
+  {cutoff} args = cutoff \[group group2-ID\] typeN
     cutoff = distance within which to count coordination neighbors (distance units)
+    group {group2-ID} = select group-ID to restrict which atoms to consider for coordination number (optional)
     typeN = atom type for Nth coordination count (see asterisk form below)
   {orientorder} args = orientorderID threshold
     orientorderID = ID of an orientorder/atom compute
@@ -28,6 +29,7 @@ cstyle = {cutoff} or {orientorder} :l
 compute 1 all coord/atom cutoff 2.0
 compute 1 all coord/atom cutoff 6.0 1 2
 compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
+compute 1 solute coord/atom cutoff 2.0 group solvent
 compute 1 all coord/atom orientorder 2 0.5 :pre
 
 [Description:]
@@ -38,9 +40,14 @@ meaning of the resulting value depend on the {cstyle} keyword used.
 
 The {cutoff} cstyle calculates one or more traditional coordination
 numbers for each atom.  A coordination number is defined as the number
-of neighbor atoms with specified atom type(s) that are within the
-specified cutoff distance from the central atom.  Atoms not in the
-specified group are included in the coordination number tally.
+of neighbor atoms with specified atom type(s), and optionally within
+the specified group, that are within the specified cutoff distance from
+the central atom. The compute group selects only the central atoms; all
+neighboring atoms, unless selected by type, type range, or group option,
+are included in the coordination number tally.
+
+The optional {group} keyword allows to specify from which group atoms
+contribute to the coordination number. Default setting is group 'all'. 
 
 The {typeN} keywords allow specification of which atom types
 contribute to each coordination number.  One coordination number is
@@ -122,7 +129,9 @@ explained above.
 "compute cluster/atom"_compute_cluster_atom.html
 "compute orientorder/atom"_compute_orientorder_atom.html
 
-[Default:] none
+[Default:]
+
+group = all
 
 :line
 

doc/src/compute_voronoi_atom.txt

@@ -96,7 +96,7 @@ group. The argument {maxedge} of the this keyword is the largest number
 of edges on a single Voronoi cell face expected to occur in the
 sample. This keyword adds the generation of a global vector with
 {maxedge}+1 entries. The last entry in the vector contains the number of
-faces with with more than {maxedge} edges. Since the polygon with the
+faces with more than {maxedge} edges. Since the polygon with the
 smallest amount of edges is a triangle, entries 1 and 2 of the vector
 will always be zero.
 

doc/src/dihedral_spherical.txt

@@ -47,7 +47,7 @@ division by sin(74.4)*sin(48.1) (the minima positions for theta1 and theta2).
 
 The following coefficients must be defined for each dihedral type via the
 "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
-the Dihedral Coeffs section of a data file file read by the
+the Dihedral Coeffs section of a data file read by the
 "read_data"_read_data.html command:
 
 n (integer >= 1)

doc/src/dihedral_table_cut.txt

@@ -174,7 +174,7 @@ radians instead of degrees.  (Note: This changes the way the forces
 are scaled in the 4th column of the data file.)
 
 The optional "CHECKU" keyword is followed by a filename.  This allows
-the user to save all of the the {Ntable} different entries in the
+the user to save all of the {Ntable} different entries in the
 interpolated energy table to a file to make sure that the interpolated
 function agrees with the user's expectations.  (Note: You can
 temporarily increase the {Ntable} parameter to a high value for this

doc/src/dump.txt

@@ -21,7 +21,7 @@ dump ID group-ID style N file args :pre
 
 ID = user-assigned name for the dump :ulb,l
 group-ID = ID of the group of atoms to be dumped :l
-style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
+style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
 N = dump every this many timesteps :l
 file = name of file to write dump info to :l
 args = list of arguments for a particular style :l
@@ -196,7 +196,7 @@ For post-processing purposes the {atom}, {local}, and {custom} text
 files are self-describing in the following sense.
 
 The dimensions of the simulation box are included in each snapshot.
-For an orthogonal simulation box this information is is formatted as:
+For an orthogonal simulation box this information is formatted as:
 
 ITEM: BOX BOUNDS xx yy zz
 xlo xhi
@@ -619,7 +619,7 @@ should be replaced by the actual name of the variable that has been
 defined previously in the input script.  Only an atom-style variable
 can be referenced, since it is the only style that generates per-atom
 values.  Variables of style {atom} can reference individual atom
-attributes, per-atom atom attributes, thermodynamic keywords, or
+attributes, per-atom attributes, thermodynamic keywords, or
 invoke other computes, fixes, or variables when they are evaluated, so
 this is a very general means of creating quantities to output to a
 dump file.

doc/src/dump_modify.txt

@@ -310,7 +310,7 @@ NOTE: Atom and molecule IDs are stored internally as 4-byte or 8-byte
 signed integers, depending on how LAMMPS was compiled.  When
 specifying the {format int} option you can use a "%d"-style format
 identifier in the format string and LAMMPS will convert this to the
-corresponding 8-byte form it it is needed when outputting those
+corresponding 8-byte form if it is needed when outputting those
 values.  However, when specifying the {line} option or {format M
 string} option for those values, you should specify a format string
 appropriate for an 8-byte signed integer, e.g. one with "%ld", if

doc/src/fix.txt

@@ -83,8 +83,10 @@ not in the specified fix group.  Local quantities are calculated by
 each processor based on the atoms it owns, but there may be zero or
 more per atoms.
 
-Note that a single fix may produces either global or per-atom or local
-quantities (or none at all), but never more than one of these.
+Note that a single fix can produce either global or per-atom or local
+quantities (or none at all), but not both global and per-atom.  It can
+produce local quantities in tandem with global or per-atom quantities.
+The fix doc page will explain.
 
 Global, per-atom, and local quantities each come in three kinds: a
 single scalar value, a vector of values, or a 2d array of values.  The
@@ -199,6 +201,7 @@ accelerated styles exist.
 "edpd/source"_fix_dpd_source.html -
 "efield"_fix_efield.html - impose electric field on system
 "ehex"_fix_ehex.html - enhanced heat exchange algorithm
+"electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force
 "enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
 "eos/cv"_fix_eos_cv.html -
 "eos/table"_fix_eos_table.html -
@@ -318,20 +321,16 @@ accelerated styles exist.
 "restrain"_fix_restrain.html - constrain a bond, angle, dihedral
 "rhok"_fix_rhok.html -
 "rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration
-"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
-"rigid/nph/small"_fix_rigid.html -
-"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration
-"rigid/npt/small"_fix_rigid.html -
-"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
-"rigid/nve/small"_fix_rigid.html -
-"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration
-"rigid/nvt/small"_fix_rigid.html -
-"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
-"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration
-"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration
-"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
-"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
 "rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
+"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
+"rigid/nph/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration
+"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration
+"rigid/npt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration
+"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
+"rigid/nve/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
+"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration
+"rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
+"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
 "rx"_fix_rx.html -
 "saed/vtk"_fix_saed_vtk.html -
 "setforce"_fix_setforce.html - set the force on each atom

doc/src/fix_atom_swap.txt

@@ -141,11 +141,16 @@ specify if this should be done.
 
 This fix writes the state of the fix to "binary restart
 files"_restart.html.  This includes information about the random
-number generator seed, the next timestep for MC exchanges, etc.  See
+number generator seed, the next timestep for MC exchanges, the number
+of exchange attempts and successes etc.  See
 the "read_restart"_read_restart.html command for info on how to
 re-specify a fix in an input script that reads a restart file, so that
 the operation of the fix continues in an uninterrupted fashion.
 
+NOTE: For this to work correctly, the timestep must [not] be changed
+after reading the restart with "reset_timestep"_reset_timestep.html.
+The fix will try to detect it and stop with an error.
+
 None of the "fix_modify"_fix_modify.html options are relevant to this
 fix.
 

doc/src/fix_ave_chunk.txt

@@ -361,7 +361,7 @@ computes that calculate a temperature to see which ones implement a
 bias.
 
 The {adof} and {cdof} keywords define the values used in the degree of
-freedom (DOF) formula described above for for temperature calculation
+freedom (DOF) formula described above for temperature calculation
 for each chunk.  They are only used when the {temp} value is
 calculated.  They can be used to calculate a more appropriate
 temperature for some kinds of chunks.  Here are 3 examples:

doc/src/fix_ave_histo.txt

@@ -35,6 +35,7 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti
   {mode} arg = {scalar} or {vector}
     scalar = all input values are scalars
     vector = all input values are vectors
+  {kind} arg = {global} or {peratom} or {local}
   {file} arg = filename
     filename = name of file to output histogram(s) to
   {ave} args = {one} or {running} or {window}
@@ -92,7 +93,8 @@ either all global, all per-atom, or all local quantities.  Inputs of
 different kinds (e.g. global and per-atom) cannot be mixed.  Atom
 attributes are per-atom vector values.  See the doc page for
 individual "compute" and "fix" commands to see what kinds of
-quantities they generate.
+quantities they generate.  See the optional {kind} keyword below for
+how to force the fix ave/histo command to disambiguate if necessary.
 
 Note that the output of this command is a single histogram for all
 input values combined together, not one histogram per input value.
@@ -231,6 +233,14 @@ keyword is set to {vector}, then all input values must be global or
 per-atom or local vectors, or columns of global or per-atom or local
 arrays.
 
+The {kind} keyword only needs to be set if a compute or fix produces
+more than one kind of output (global, per-atom, local).  If this is
+not the case, then LAMMPS will determine what kind of input is
+provided and whether all the input arguments are consistent.  If a
+compute or fix produces more than one kind of output, the {kind}
+keyword should be used to specify which output will be used.  The
+remaining input arguments must still be consistent.
+
 The {beyond} keyword determines how input values that fall outside the
 {lo} to {hi} bounds are treated.  Values such that {lo} <= value <=
 {hi} are assigned to one bin.  Values on a bin boundary are assigned
@@ -240,7 +250,7 @@ If {beyond} is set to {end} then values < {lo} are counted in the
 first bin and values > {hi} are counted in the last bin.  If {beyond}
 is set to {extend} then two extra bins are created, so that there are
 Nbins+2 total bins.  Values < {lo} are counted in the first bin and
-values > {hi} are counted in the last bin (Nbins+1).  Values between
+values > {hi} are counted in the last bin (Nbins+2).  Values between
 {lo} and {hi} (inclusive) are counted in bins 2 through Nbins+1.  The
 "coordinate" stored and printed for these two extra bins is {lo} and
 {hi}.
@@ -354,5 +364,6 @@ ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html,
 
 [Default:] none
 
-The option defaults are mode = scalar, ave = one, start = 0, no file
-output, beyond = ignore, and title 1,2,3 = strings as described above.
+The option defaults are mode = scalar, kind = figured out from input
+arguments, ave = one, start = 0, no file output, beyond = ignore, and
+title 1,2,3 = strings as described above.

doc/src/fix_bond_react.txt

@@ -385,6 +385,10 @@ No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.
 
+When fix bond/react is 'unfixed,' all internally-created groups are
+deleted. Therefore, fix bond/react can only be unfixed after unfixing
+all other fixes that use any group created by fix bond/react.
+
 [Restrictions:]
 
 This fix is part of the USER-MISC package.  It is only enabled if

doc/src/fix_colvars.txt

@@ -98,6 +98,16 @@ fix to add the energy change from the biasing force added by the fix
 to the system's potential energy as part of "thermodynamic
 output"_thermo_style.html.
 
+The {fix_modify configfile <config file>} option allows to add settings
+from an additional config file to the colvars module. This option can
+only be used, after the system has been initialized with a "run"_run.html
+command.
+
+The {fix_modify config <quoted string>} option allows to add settings
+from inline strings. Those have to fit on a single line when enclosed
+in a pair of double quotes ("), or can span multiple lines when bracketed
+by a pair of triple double quotes (""", like python embedded documentation).
+
 This fix computes a global scalar which can be accessed by various
 "output commands"_Howto_output.html.  The scalar is the cumulative
 energy change due to this fix.  The scalar value calculated by this

doc/src/fix_deposit.txt

@@ -261,6 +261,10 @@ next timestep for deposition, etc.  See the
 a fix in an input script that reads a restart file, so that the
 operation of the fix continues in an uninterrupted fashion.
 
+NOTE: For this to work correctly, the timestep must [not] be changed
+after reading the restart with "reset_timestep"_reset_timestep.html.
+The fix will try to detect it and stop with an error.
+
 None of the "fix_modify"_fix_modify.html options are relevant to this
 fix.  No global or per-atom quantities are stored by this fix for
 access by various "output commands"_Howto_output.html.  No parameter

doc/src/fix_electron_stopping.txt

@@ -0,0 +1,165 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+fix electron/stopping command :h3
+
+[Syntax:]
+
+fix ID group-ID electron/stopping Ecut file keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+electron/stopping = style name of this fix command :l
+Ecut = minimum kinetic energy for electronic stopping (energy units) :l
+file = name of the file containing the electronic stopping power table :l
+zero or more keyword/value pairs may be appended to args :l
+keyword = {region} or {minneigh} :l
+  {region} value = region-ID
+    region-ID = region, whose atoms will be affected by this fix
+  {minneigh} value = minneigh
+    minneigh = minimum number of neighbors an atom to have stopping applied :pre
+:ule
+
+[Examples:]
+
+fix el all electron/stopping 10.0 elstop-table.txt
+fix el all electron/stopping 10.0 elstop-table.txt minneigh 3
+fix el mygroup electron/stopping 1.0 elstop-table.txt region bulk :pre
+
+[Description:]
+
+This fix implements inelastic energy loss for fast projectiles in solids. It
+applies a friction force to fast moving atoms to slow them down due to
+"electronic stopping"_#elstopping (energy lost via electronic collisions per
+unit of distance). This fix should be used for simulation of irradiation
+damage or ion implantation, where the ions can lose noticeable amounts of
+energy from electron excitations. If the electronic stopping power is not
+considered, the simulated range of the ions can be severely overestimated
+("Nordlund98"_#Nordlund98, "Nordlund95"_#Nordlund95).
+
+The electronic stopping is implemented by applying a friction force
+to each atom as:
+
+\begin\{equation\}
+\vec\{F\}_i = \vec\{F\}^0_i - \frac\{\vec\{v\}_i\}\{\|\vec\{v\}_i\|\} \cdot S_e
+\end\{equation\}
+
+where \(\vec\{F\}_i\) is the resulting total force on the atom.
+\(\vec\{F\}^0_i\) is the original force applied to the atom, \(\vec\{v\}_i\) is
+its velocity and \(S_e\) is the stopping power of the ion.
+
+NOTE: In addition to electronic stopping, atomic cascades and irradiation
+simulations require the use of an adaptive timestep (see
+"fix dt/reset"_fix_dt_reset.html) and the repulsive ZBL potential (see
+"ZBL"_pair_zbl.html potential) or similar. Without these settings the
+interaction between the ion and the target atoms will be faulty. It is also
+common to use in such simulations a thermostat ("fix_nvt"_fix_nh.html) in
+the borders of the simulation cell.
+
+NOTE: This fix removes energy from fast projectiles without depositing it as a
+heat to the simulation cell. Such implementation might lead to the unphysical
+results when the amount of energy deposited to the electronic system is large,
+e.g. simulations of Swift Heavy Ions (energy per nucleon of 100 keV/amu or
+higher) or multiple projectiles. You could compensate energy loss by coupling
+bulk atoms with some thermostat or control heat transfer between electronic and
+atomic subsystems with the two-temperature model ("fix_ttm"_fix_ttm.html).
+
+At low velocities the electronic stopping is negligible. The electronic
+friction is not applied to atoms whose kinetic energy is smaller than {Ecut},
+or smaller than the lowest energy value given in the table in {file}.
+Electronic stopping should be applied only when a projectile reaches bulk
+material. This fix scans neighbor list and excludes atoms with fewer than
+{minneigh} neighbors (by default one). If the pair potential cutoff is large,
+minneigh should be increased, though not above the number of nearest neighbors
+in bulk material. An alternative is to disable the check for neighbors by
+setting {minneigh} to zero and using the {region} keyword. This is necessary
+when running simulations of cluster bombardment.
+
+If the {region} keyword is used, the atom must also be in the specified
+geometric "region"_region.html in order to have electronic stopping applied to
+it. This is useful if the position of the bulk material is fixed. By default
+the electronic stopping is applied everywhere in the simulation cell.
+
+:line
+
+The energy ranges and stopping powers are read from the file {file}.
+Lines starting with {#} and empty lines are ignored. Otherwise each
+line must contain exactly [N+1] numbers, where [N] is the number of atom
+types in the simulation.
+
+The first column is the energy for which the stopping powers on that
+line apply. The energies must be sorted from the smallest to the largest.
+The other columns are the stopping powers \(S_e\) for each atom type,
+in ascending order, in force "units"_units.html. The stopping powers for
+intermediate energy values are calculated with linear interpolation between
+2 nearest points.
+
+For example:
+
+# This is a comment
+#       atom-1    atom-2
+# eV    eV/Ang    eV/Ang  # units metal
+ 10        0        0
+250       60       80
+750      100      150 :pre
+
+
+If an atom which would have electronic stopping applied to it has a
+kinetic energy higher than the largest energy given in {file}, LAMMPS
+will exit with an error message.
+
+The stopping power depends on the energy of the ion and the target
+material. The electronic stopping table can be obtained from
+scientific publications, experimental databases or by using
+"SRIM"_#SRIM software. Other programs such as "CasP"_#CasP or
+"PASS"_#PASS can calculate the energy deposited as a function
+of the impact parameter of the ion; these results can be used
+to derive the stopping power.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html options are not supported.
+
+This fix computes a global scalar, which can be accessed by various
+"output commands"_Howto_output.html. The scalar is the total energy
+loss from electronic stopping applied by this fix since the start of
+the latest run. It is considered "intensive".
+
+The {start/stop} keywords of the "run"_run.html command have no effect
+on this fix.
+
+[Restrictions:]
+
+This pair style is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build package"_Build_package.html
+doc page for more info.
+
+[Default:]
+
+The default is no limitation by region, and minneigh = 1.
+
+:line
+:link(elstopping)
+[(electronic stopping)] Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29
+
+:link(Nordlund98)
+[(Nordlund98)] Nordlund, Kai, et al.  Physical Review B 57.13 (1998): 7556.
+
+:link(Nordlund95)
+[(Nordlund95)] Nordlund, Kai. Computational materials science 3.4 (1995): 448-456.
+
+:link(SRIM)
+[(SRIM)] SRIM webpage: http://www.srim.org/
+
+:link(CasP)
+[(CasP)] CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html
+
+:link(PASS)
+[(PASS)] PASS webpage: https://www.sdu.dk/en/DPASS

doc/src/fix_gcmc.txt

@@ -373,11 +373,16 @@ adds all inserted atoms of the specified type to the
 
 This fix writes the state of the fix to "binary restart
 files"_restart.html.  This includes information about the random
-number generator seed, the next timestep for MC exchanges, etc.  See
+number generator seed, the next timestep for MC exchanges,  the number
+of MC step attempts and successes etc.  See
 the "read_restart"_read_restart.html command for info on how to
 re-specify a fix in an input script that reads a restart file, so that
 the operation of the fix continues in an uninterrupted fashion.
 
+NOTE: For this to work correctly, the timestep must [not] be changed
+after reading the restart with "reset_timestep"_reset_timestep.html.
+The fix will try to detect it and stop with an error.
+
 None of the "fix_modify"_fix_modify.html options are relevant to this
 fix.
 

doc/src/fix_halt.txt

@@ -113,12 +113,11 @@ state of the system, e.g. via a "write_dump"_write_dump.html or
 "write_restart"_write_restart.html command.
 
 If its value is {continue}, the behavior is the same as for {soft},
-except subsequent subsequent "run"_run.html or
-"minimize"_minimize.html commands are executed.  This allows your
-script to remedy the condition that triggered the halt, if necessary.
-Note that you may wish use the "unfix"_unfix.html command on the fix
-halt ID, so that the same condition is not immediately triggered in a
-subsequent run.
+except subsequent "run"_run.html or "minimize"_minimize.html commands
+are executed.  This allows your script to remedy the condition that
+triggered the halt, if necessary.  Note that you may wish use the
+"unfix"_unfix.html command on the fix halt ID, so that the same
+condition is not immediately triggered in a subsequent run.
 
 The optional {message} keyword determines whether a message is printed
 to the screen and logfile when the halt condition is triggered.  If

doc/src/fix_hyper_global.txt

@@ -102,7 +102,7 @@ Bi = exp(beta * Vij(max)) :pre
 where beta = 1/kTequil, and {Tequil} is the temperature of the system
 and an argument to this fix.  Note that Bi >= 1 at every step.
 
-NOTE: To run GHD, the input script must also use the "fix
+NOTE: To run a GHD simulation, the input script must also use the "fix
 langevin"_fix_langevin.html command to thermostat the atoms at the
 same {Tequil} as specified by this fix, so that the system is running
 constant-temperature (NVT) dynamics.  LAMMPS does not check that this
@@ -166,9 +166,9 @@ correctly.  There will just be fewer events because the hyper time
 
 NOTE: If you have no physical intuition as to the smallest barrier
 height in your system, a reasonable strategy to determine the largest
-{Vmax} you can use for an LHD model, is to run a sequence of
+{Vmax} you can use for a GHD model, is to run a sequence of
 simulations with smaller and smaller {Vmax} values, until the event
-rate does not change.
+rate does not change (as a function of hyper time).
 
 The {Tequil} argument is the temperature at which the system is
 simulated; see the comment above about the "fix
@@ -177,7 +177,8 @@ beta term in the exponential factor that determines how much boost is
 achieved as a function of the bias potential.
 
 In general, the lower the value of {Tequil} and the higher the value
-of {Vmax}, the more boost will be achievable by the GHD algorithm.
+of {Vmax}, the more time boost will be achievable by the GHD
+algorithm.
 
 :line
 
@@ -187,44 +188,46 @@ No information about this fix is written to "binary restart
 files"_restart.html.
 
 The "fix_modify"_fix_modify.html {energy} option is supported by this
-fix to add the energy of the bias potential to the the system's
+fix to add the energy of the bias potential to the system's
 potential energy as part of "thermodynamic output"_thermo_style.html.
 
-This fix computes a global scalar and global vector of length 11, which
+This fix computes a global scalar and global vector of length 12, which
 can be accessed by various "output commands"_Howto_output.html.  The
 scalar is the magnitude of the bias potential (energy units) applied on
 the current timestep.  The vector stores the following quantities:
 
 1 = boost factor on this step (unitless)
-2 = max strain Eij of any bond on this step (unitless)
+2 = max strain Eij of any bond on this step (absolute value, unitless)
 3 = ID of first atom in the max-strain bond
 4 = ID of second atom in the max-strain bond
 5 = average # of bonds/atom on this step :ul
 
-6 = fraction of timesteps with bias = 0.0 during this run
-7 = max drift distance of any atom during this run (distance units)
-8 = max bond length during this run (distance units) :ul
+6 = fraction of timesteps where the biased bond has bias = 0.0 during this run
+7 = fraction of timesteps where the biased bond has negative strain during this run
+8 = max drift distance of any atom during this run (distance units)
+9 = max bond length during this run (distance units) :ul
 
-9 = cumulative hyper time since fix was defined (time units)
-10 = cumulative count of event timesteps since fix was defined
-11 = cumulative count of atoms in events since fix was defined :ul
+10 = cumulative hyper time since fix was defined (time units)
+11 = cumulative count of event timesteps since fix was defined
+12 = cumulative count of atoms in events since fix was defined :ul
 
-The first 5 quantities are for the current timestep.  Quantities 6-8
-are for the current hyper run.  Quantities 9-11 are cumulative across
-multiple runs (since the fix was defined in the input script).
+The first 5 quantities are for the current timestep.  Quantities 6-9
+are for the current hyper run.  They are reset each time a new hyper
+run is performed.  Quantities 19-12 are cumulative across multiple
+runs (since the point in the input script the fix was defined).
 
-For value 7, drift is the distance an atom moves between timesteps
-when the bond list is reset, i.e. between events.  Atoms involved in
-an event will typically move the greatest distance since others are
-typically oscillating around their lattice site.
+For value 8, drift is the distance an atom moves between two quenched
+states when the second quench determines an event has occurred.  Atoms
+involved in an event will typically move the greatest distance since
+others typically remain near their original quenched position.
 
-For value 10, events are checked for by the "hyper"_hyper.html command
+For value 11, events are checked for by the "hyper"_hyper.html command
 once every {Nevent} timesteps.  This value is the count of those
 timesteps on which one (or more) events was detected.  It is NOT the
 number of distinct events, since more than one event may occur in the
 same {Nevent} time window.
 
-For value 11, each time the "hyper"_hyper.html command checks for an
+For value 12, each time the "hyper"_hyper.html command checks for an
 event, it invokes a compute to flag zero or more atoms as
 participating in one or more events.  E.g. atoms that have displaced
 more than some distance from the previous quench state.  Value 11 is

doc/src/fix_hyper_local.txt

@@ -22,10 +22,9 @@ Dcut = minimum distance between boosted bonds (distance units) :l
 alpha = boostostat relaxation time (time units) :l
 Btarget = desired time boost factor (unitless) :l
 zero or more keyword/value pairs may be appended :l
-keyword = {lost} or {check/bias} or {check/coeff}
-  {lostbond} value = error/warn/ignore
-  {check/bias} values = Nevery error/warn/ignore
-  {check/coeff} values = Nevery error/warn/ignore :pre
+keyword = {check/ghost} or {check/bias} :l
+  {check/ghost} values = none
+  {check/bias} values = Nevery error/warn/ignore :pre
 :ule
 
 [Examples:]
@@ -65,8 +64,8 @@ To understand this description, you should first read the description
 of the GHD algorithm on the "fix hyper/global"_fix_hyper_global.html
 doc page.  This description of LHD builds on the GHD description.
 
-The definition of bonds, Eij, and Emax are the same for GHD and LHD.
-The formulas for Vij(max) and Fij(max) are also the same except for a
+The definition of bonds and Eij are the same for GHD and LHD.  The
+formulas for Vij(max) and Fij(max) are also the same except for a
 pre-factor Cij, explained below.
 
 The bias energy Vij applied to a bond IJ with maximum strain is
@@ -117,11 +116,11 @@ where Vkl(max) is the bias energy of the maxstrain bond KL within bond
 IJ's neighborhood, beta = 1/kTequil, and {Tequil} is the temperature
 of the system and an argument to this fix.
 
-NOTE: To run LHD, the input script must also use the "fix
-langevin"_fix_langevin.html command to thermostat the atoms at the
-same {Tequil} as specified by this fix, so that the system is running
-constant-temperature (NVT) dynamics.  LAMMPS does not check that this
-is done.
+NOTE: To run an LHD simulation, the input script must also use the
+"fix langevin"_fix_langevin.html command to thermostat the atoms at
+the same {Tequil} as specified by this fix, so that the system is
+running constant-temperature (NVT) dynamics.  LAMMPS does not check
+that this is done.
 
 Note that if IJ = KL, then bond IJ is a biased bond on that timestep,
 otherwise it is not.  But regardless, the boost factor Bij can be
@@ -216,20 +215,20 @@ each pair.  E.g. something like 2x the cutoff of the interatomic
 potential.  In practice a {Dcut} value of ~10 Angstroms seems to work
 well for many solid-state systems.
 
-NOTE: You must also insure that ghost atom communication is performed
-for a distance of at least {Dcut} + {cutevent} where {cutevent} = the
-distance one or more atoms move (between quenched states) to be
-considered an "event".  It is an argument to the "compute
-event/displace" command used to detect events.  By default the ghost
-communication distance is set by the pair_style cutoff, which will
-typically be < {Dcut}.  The "comm_modify cutoff"_comm_modify.html
-command can be used to set the ghost cutoff explicitly, e.g.
+NOTE: You should insure that ghost atom communication is performed for
+a distance of at least {Dcut} + {cutevent} = the distance one or more
+atoms move (between quenched states) to be considered an "event".  It
+is an argument to the "compute event/displace" command used to detect
+events.  By default the ghost communication distance is set by the
+pair_style cutoff, which will typically be < {Dcut}.  The "comm_modify
+cutoff"_comm_modify.html command should be used to override the ghost
+cutoff explicitly, e.g.
 
 comm_modify cutoff 12.0 :pre
 
-This fix does not know the {cutevent} parameter, but uses half the
-bond length as an estimate to warn if the ghost cutoff is not long
-enough.
+Note that this fix does not know the {cutevent} parameter, but uses
+half the {cutbond} parameter as an estimate to warn if the ghost
+cutoff is not long enough.
 
 As described above the {alpha} argument is a pre-factor in the
 boostostat update equation for each bond's Cij prefactor.  {Alpha} is
@@ -269,7 +268,30 @@ NOTE: If you have no physical intuition as to the smallest barrier
 height in your system, a reasonable strategy to determine the largest
 {Btarget} you can use for an LHD model, is to run a sequence of
 simulations with smaller and smaller {Btarget} values, until the event
-rate does not change.
+rate does not change (as a function of hyper time).
+
+:line
+
+Here is additional information on the optional keywords for this fix.
+
+The {check/ghost} keyword turns on extra computation each timestep to
+compute statistics about ghost atoms used to determine which bonds to
+bias.  The output of these stats are the vector values 14 and 15,
+described below.  If this keyword is not enabled, the output
+of the stats will be zero.
+
+The {check/bias} keyword turns on extra computation and communication
+to check if any biased bonds are closer than {Dcut} to each other,
+which should not be the case if LHD is operating correctly.  Thus it
+is a debugging check.  The {Nevery} setting determines how often the
+check is made.  The {error}, {warn}, or {ignore} setting determines
+what is done if the count of too-close bonds is not zero.  Either the
+code will exit, or issue a warning, or silently tally the count.  The
+count can be output as vector value 17, as described below.  If this
+keyword is not enabled, the output of that statistic will be 0.
+
+Note that both of these computations are costly, hence they are only
+enabled by these keywords.
 
 :line
 
@@ -279,98 +301,123 @@ No information about this fix is written to "binary restart
 files"_restart.html.
 
 The "fix_modify"_fix_modify.html {energy} option is supported by this
-fix to add the energy of the bias potential to the the system's
+fix to add the energy of the bias potential to the system's
 potential energy as part of "thermodynamic output"_thermo_style.html.
 
-This fix computes a global scalar and global vector of length 23,
-which can be accessed by various "output
-commands"_Howto_output.html.  The scalar is the magnitude of
-the bias potential (energy units) applied on the current timestep,
-summed over all biased bonds.  The vector stores the following
-quantities:
+This fix computes a global scalar and global vector of length 21,
+which can be accessed by various "output commands"_Howto_output.html.
+The scalar is the magnitude of the bias potential (energy units)
+applied on the current timestep, summed over all biased bonds.  The
+vector stores the following quantities:
 
 1 = # of biased bonds on this step
-2 = max strain Eij of any bond on this step (unitless)
-3 = average bias potential for all biased bonds on this step (energy units)
+2 = max strain Eij of any bond on this step (absolute value, unitless)
+3 = average bias coeff for all bonds on this step (unitless)
 4 = average # of bonds/atom on this step
 5 = average neighbor bonds/bond on this step within {Dcut} :ul
 
-6 = fraction of steps and bonds with no bias during this run
-7 = max drift distance of any atom during this run (distance units)
-8 = max bond length during this run (distance units)
-9 = average # of biased bonds/step during this run
-10 = average bias potential for all biased bonds during this run (energy units)
-11 = max bias potential for any biased bond during this run (energy units)
-12 = min bias potential for any biased bond during this run (energy units)
-13 = max distance from my sub-box of any ghost atom with maxstrain < qfactor during this run (distance units)
-14 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
-15 = count of ghost neighbor atoms not found on reneighbor steps during this run
-16 = count of lost bond partners during this run
-17 = average bias coeff for lost bond partners during this run
-18 = count of bias overlaps found during this run
-19 = count of non-matching bias coefficients found during this run :ul
+6 = max bond length during this run (distance units)
+7 = average # of biased bonds/step during this run
+8 = fraction of biased bonds with no bias during this run
+9 = fraction of biased bonds with negative strain during this run
+10 = average bias coeff for all bonds during this run (unitless)
+11 = min bias coeff for any bond during this run (unitless)
+12 = max bias coeff for any bond during this run (unitless) :ul
 
-20 = cumulative hyper time since fix created (time units)
-21 = cumulative count of event timesteps since fix created
-22 = cumulative count of atoms in events since fix created
-23 = cumulative # of new bonds since fix created :ul
+13 = max drift distance of any bond atom during this run (distance units)
+14 = max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units)
+15 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
+16 = count of ghost atoms that could not be found on reneighbor steps during this run
+17 = count of bias overlaps (< Dcut) found during this run :ul
+
+18 = cumulative hyper time since fix created (time units)
+19 = cumulative count of event timesteps since fix created
+20 = cumulative count of atoms in events since fix created
+21 = cumulative # of new bonds formed since fix created :ul
 
 The first quantities (1-5) are for the current timestep.  Quantities
-6-19 are for the current hyper run.  They are reset each time a new
-hyper run is performed.  Quantities 20-23 are cumulative across
-multiple runs (since the fix was defined in the input script).
+6-17 are for the current hyper run.  They are reset each time a new
+hyper run is performed.  Quantities 18-21 are cumulative across
+multiple runs (since the point in the input script the fix was
+defined).
 
-For value 6, the numerator is a count of all biased bonds on every
+For value 8, the numerator is a count of all biased bonds on each
 timestep whose bias energy = 0.0 due to Eij >= {qfactor}.  The
 denominator is the count of all biased bonds on all timesteps.
 
-For value 7, drift is the distance an atom moves between timesteps
-when the bond list is reset, i.e. between events.  Atoms involved in
-an event will typically move the greatest distance since others are
-typically oscillating around their lattice site.
+For value 9, the numerator is a count of all biased bonds on each
+timestep with negative strain.  The denominator is the count of all
+biased bonds on all timesteps.
 
-For values 13 and 14, the maxstrain of a ghost atom is the maxstrain
-of any bond it is part of, and it is checked for ghost atoms within
-the bond neighbor cutoff.
+Values 13-17 are mostly useful for debugging and diagnostic purposes.
 
-Values 15-19 are mostly useful for debugging and diagnostic purposes.
+For value 13, drift is the distance an atom moves between two quenched
+states when the second quench determines an event has occurred.  Atoms
+involved in an event will typically move the greatest distance since
+others typically remain near their original quenched position.
 
-For values 15-17, it is possible that a ghost atom owned by another
-processor will move far enough (e.g. as part of an event-in-progress)
-that it will no longer be within the communication cutoff distance for
-acquiring ghost atoms.  Likewise it may be a ghost atom bond partner
-that cannot be found because it has moved too far.  These values count
-those occurrences.  Because they typically involve atoms that are part
-of events, they do not usually indicate bad dynamics.  Value 16 is the
-average bias coefficient for bonds where a partner atom was lost.
+For values 14-16, neighbor atoms in the full neighbor list with cutoff
+{Dcut} may be ghost atoms outside a processor's sub-box.  Before the
+next event occurs they may move further than {Dcut} away from the
+sub-box boundary.  Value 14 is the furthest (from the sub-box) any
+ghost atom in the neighbor list with maxstrain < {qfactor} was
+accessed during the run.  Value 15 is the same except that the ghost
+atom's maxstrain may be >= {qfactor}, which may mean it is about to
+participate in an event.  Value 16 is a count of how many ghost atoms
+could not be found on reneighbor steps, presumably because they moved
+too far away due to their participation in an event (which will likely
+be detected at the next quench).
 
-For value 18, no two bonds should be biased if they are within a
+Typical values for 14 and 15 should be slightly larger than {Dcut},
+which accounts for ghost atoms initially at a {Dcut} distance moving
+thermally before the next event takes place.
+
+Note that for values 14 and 15 to be computed, the optional keyword
+{check/ghost} must be specified.  Otherwise these values will be zero.
+This is because computing them incurs overhead, so the values are only
+computed if requested.
+
+Value 16 should be zero or small.  As explained above a small count
+likely means some ghost atoms were participating in their own events
+and moved a longer distance.  If the value is large, it likely means
+the communication cutoff for ghosts is too close to {Dcut} leading to
+many not-found ghost atoms before the next event.  This may lead to a
+reduced number of bonds being selected for biasing, since the code
+assumes those atoms are part of highly strained bonds.  As explained
+above, the "comm_modify cutoff"_comm_modify.html command can be used
+to set a longer cutoff.
+
+For value 17, no two bonds should be biased if they are within a
 {Dcut} distance of each other.  This value should be zero, indicating
-that no pair of bonds "overlap", meaning they are closer than {Dcut}
-from each other.
+that no pair of biased bonds are closer than {Dcut} from each other.
 
-For value 19, the same bias coefficient is stored by both atoms in an
-IJ bond.  This value should be zero, indicating that for all bonds,
-each atom in the bond stores the a bias coefficient with the same
-value.
+Note that for values 17 to be computed, the optional keyword
+{check/bias} must be specified and it determines how often this check
+is performed.  This is because performing the check incurs overhead,
+so if only computed as often as requested.
 
-Value 20 is simply the specified {boost} factor times the number of
-timestep times the timestep size.
+The result at the end of the run is the cumulative total from every
+timestep the check was made.  Note that the value is a count of atoms
+in bonds which found other atoms in bonds too close, so it is almost
+always an over-count of the number of too-close bonds.
 
-For value 21, events are checked for by the "hyper"_hyper.html command
+Value 18 is simply the specified {boost} factor times the number of
+timesteps times the timestep size.
+
+For value 19, events are checked for by the "hyper"_hyper.html command
 once every {Nevent} timesteps.  This value is the count of those
 timesteps on which one (or more) events was detected.  It is NOT the
 number of distinct events, since more than one event may occur in the
 same {Nevent} time window.
 
-For value 22, each time the "hyper"_hyper.html command checks for an
+For value 20, each time the "hyper"_hyper.html command checks for an
 event, it invokes a compute to flag zero or more atoms as
 participating in one or more events.  E.g. atoms that have displaced
-more than some distance from the previous quench state.  Value 22 is
+more than some distance from the previous quench state.  Value 20 is
 the cumulative count of the number of atoms participating in any of
 the events that were found.
 
-Value 23 tallies the number of new bonds created by the bond reset
+Value 21 tallies the number of new bonds created by the bond reset
 operation.  Bonds between a specific I,J pair of atoms may persist for
 the entire hyperdynamics simulation if neither I or J are involved in
 an event.
@@ -378,6 +425,16 @@ an event.
 The scalar and vector values calculated by this fix are all
 "intensive".
 
+This fix also computes a local vector of length the number of bonds
+currently in the system.  The value for each bond is its Cij prefactor
+(bias coefficient).  These values can be can be accessed by various
+"output commands"_Howto_output.html.  A particularly useful one is the
+"fix ave/histo"_fix_ave_histo.html command which can be used to
+histogram the Cij values to see if they are distributed reasonably
+close to 1.0, which indicates a good choice of {Vmax}.
+
+The local values calculated by this fix are unitless.
+
 No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.
@@ -392,7 +449,9 @@ doc page for more info.
 
 "hyper"_hyper.html, "fix hyper/global"_fix_hyper_global.html
 
-[Default:] None
+[Default:]
+
+The check/ghost and check/bias keywords are not enabled by default.
 
 :line
 

doc/src/fix_langevin_spin.txt

@@ -99,4 +99,4 @@ integration fix (e.g. {fix nve/spin}).
 
 :link(Tranchida2)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/fix_neb.txt

@@ -97,7 +97,7 @@ Note that in this case the specified {Kspring} is in force/distance
 units.
 
 With a value of {ideal}, the spring force is computed as suggested in
-"(WeinenE)"_#WeinenE :
+"(WeinanE)"_#WeinanE :
 
 Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre
 
@@ -224,8 +224,8 @@ specified (no inter-replica force on the end replicas).
 [(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
 9901-9904 (2000).
 
-:link(WeinenE)
-[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
+:link(WeinanE)
+[(WeinanE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
 
 :link(Jonsson)
 [(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum

doc/src/fix_neb_spin.txt

@@ -0,0 +1,76 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+fix neb/spin command :h3
+
+[Syntax:]
+
+fix ID group-ID neb/spin Kspring :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+neb/spin = style name of this fix command :l
+Kspring = spring constant for parallel nudging force
+(force/distance units or force units, see parallel keyword) :pre,ule
+
+[Examples:]
+
+fix 1 active neb/spin 1.0
+
+[Description:]
+
+Add nudging forces to spins in the group for a multi-replica
+simulation run via the "neb/spin"_neb_spin.html command to perform a 
+geodesic nudged elastic band (GNEB) calculation for finding the 
+transition state.
+Hi-level explanations of GNEB are given with the 
+"neb/spin"_neb_spin.html command and on the 
+"Howto replica"_Howto_replica.html doc page.  
+The fix neb/spin command must be used with the "neb/spin" command and 
+defines how inter-replica nudging forces are computed.  A GNEB 
+calculation is divided in two stages. In the first stage n replicas 
+are relaxed toward a MEP until convergence.  In the second stage, the 
+climbing image scheme is enabled, so that the replica having the highest 
+energy relaxes toward the saddle point (i.e. the point of highest energy 
+along the MEP), and a second relaxation is performed.
+
+The nudging forces are calculated as explained in
+"(BessarabB)"_#BessarabB).
+See this reference for more explanation about their expression.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+as invoked by the "minimize"_minimize.html command via the
+"neb/spin"_neb_spin.html command.
+
+[Restrictions:]
+
+This command can only be used if LAMMPS was built with the SPIN
+package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"neb_spin"_neb_spin.html
+
+[Default:]
+
+none
+
+:line
+
+:link(BessarabB)
+[(BessarabB)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
+335-347 (2015).

doc/src/fix_nve_spin.txt

@@ -73,4 +73,4 @@ instead of "array" is also valid.
 
 :link(Tranchida1)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).