Merge pull request #1459 from akohlmey/next-patch-release

Step version string for next patch release

cmake/CMakeLists.txt

@@ -320,10 +320,15 @@ 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" ${OpenMP_FOUND})
-if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
+if(BUILD_OMP)
   find_package(OpenMP REQUIRED)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  if(NOT HAVE_OMP_H_INCLUDE)
+    message(FATAL_ERROR "Cannot find required 'omp.h' header file")
+  endif()
   set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
 endif()
@@ -367,7 +372,7 @@ 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)
@@ -443,7 +448,13 @@ 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)
@@ -476,7 +487,13 @@ 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")
@@ -488,6 +505,9 @@ 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)
@@ -503,7 +523,15 @@ 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)
@@ -543,8 +571,8 @@ 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})
@@ -558,29 +586,53 @@ 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 ${CMAKE_DL_LIBS})
@@ -588,7 +640,7 @@ if(PKG_USER-PLUMED)
     set(PLUMED_INCLUDE_DIRS "${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(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
@@ -607,7 +659,10 @@ if(PKG_USER-MOLFILE)
   set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
   add_library(molfile INTERFACE)
   target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
-  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+  # 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()
 
@@ -619,7 +674,13 @@ if(PKG_USER-NETCDF)
 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)
@@ -667,7 +728,13 @@ if(PKG_KIM)
     list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
     add_definitions(-DLMP_KIM_CURL)
   endif()
-  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" OFF)
+  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 download requested - we will build our own")
     enable_language(C)
@@ -688,10 +755,7 @@ if(PKG_KIM)
     set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
     list(APPEND LAMMPS_DEPS kim_build)
   else()
-    find_package(KIM-API)
-    if(NOT KIM-API_FOUND)
-      message(FATAL_ERROR "KIM-API not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")
-    endif()
+    find_package(KIM-API REQUIRED)
   endif()
   list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
   include_directories(${KIM-API_INCLUDE_DIRS})
@@ -709,6 +773,7 @@ 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()
 
@@ -728,7 +793,13 @@ 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)" ${DOWNLOAD_MSCG_DEFAULT})
   if(DOWNLOAD_MSCG)
     if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
       message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
@@ -777,7 +848,6 @@ endif()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
-include(CheckIncludeFileCXX)
 foreach(HEADER cmath)
   check_include_file_cxx(${HEADER} FOUND_${HEADER})
   if(NOT FOUND_${HEADER})
@@ -944,7 +1014,7 @@ 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)
 
@@ -1057,37 +1127,76 @@ 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()
@@ -1100,33 +1209,35 @@ 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)
@@ -1261,7 +1372,15 @@ 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)
@@ -1272,7 +1391,21 @@ 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})
@@ -1385,9 +1518,19 @@ if(BUILD_EXE)
   if(ENABLE_TESTING)
     add_test(ShowHelp ${LAMMPS_BINARY} -help)
   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
 ###############################################################################
@@ -1449,11 +1592,14 @@ 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(

cmake/Modules/FindKIM-API.cmake

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

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

cmake/README.md

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

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

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

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

@@ -1,2 +1,5 @@
-# set environment for LAMMPS executables to find potential files
-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/lammps.1

@@ -1,40 +1,259 @@
-.TH LAMMPS "2018-08-22"
+.TH LAMMPS "15 May 2019" "2019-05-15"
 .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

@@ -247,7 +247,10 @@ 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]:
 
@@ -859,23 +862,34 @@ 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:
 

doc/src/Build_package.txt

@@ -149,26 +149,41 @@ 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

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

doc/src/Commands_category.txt

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

doc/src/Commands_fix.txt

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

doc/src/Commands_pair.txt

@@ -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/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/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

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_replica.txt

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

doc/src/Howto_spins.txt

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

doc/src/Howto_tip3p.txt

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

doc/src/Install_git.txt

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

doc/src/Install_svn.txt

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

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="29 Mar 2019 version">
+<META NAME="docnumber" CONTENT="15 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
-29 Mar 2019 version :c,h2
+15 May 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -706,7 +706,7 @@ PERI package :link(PKG-PERI),h4
 
 An atom style, several pair styles which implement different
 Peridynamics materials models, and several computes which calculate
-diagnostics.  Peridynamics is a a particle-based meshless continuum
+diagnostics.  Peridynamics is a particle-based meshless continuum
 model.
 
 [Authors:] The original package was created by Mike Parks (Sandia).
@@ -905,7 +905,7 @@ SPIN package :link(PKG-SPIN),h4
 Model atomic magnetic spins classically, coupled to atoms moving in
 the usual manner via MD.  Various pair, fix, and compute styles.
 
-[Author:] Julian Tranchida (Sandia).
+[Author:] Julien Tranchida (Sandia).
 
 [Supporting info:]
 
@@ -918,6 +918,7 @@ src/SPIN: filenames -> commands
 "fix nve/spin"_fix_nve_spin.html
 "fix precession/spin"_fix_precession_spin.html
 "compute spin"_compute_spin.html
+"neb/spin"_neb_spin.html
 examples/SPIN :ul
 
 :line
@@ -1228,7 +1229,7 @@ isothermal, isoenergetic, isobaric and isenthalpic conditions are
 included.  These enable long timesteps via the Shardlow splitting
 algorithm.
 
-[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John
+[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John
 Brennan (ARL).
 
 [Supporting info:]
@@ -1536,7 +1537,7 @@ USER-MESO package :link(PKG-USER-MESO),h4
 
 [Contents:]
 
-Several extensions of the the dissipative particle dynamics (DPD)
+Several extensions of the dissipative particle dynamics (DPD)
 method.  Specifically, energy-conserving DPD (eDPD) that can model
 non-isothermal processes, many-body DPD (mDPD) for simulating
 vapor-liquid coexistence, and transport DPD (tDPD) for modeling

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/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,

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

@@ -67,6 +67,7 @@ Commands :h1
    minimize
    molecule
    neb
+   neb_spin
    neigh_modify
    neighbor
    newton

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_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

@@ -201,6 +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 -
@@ -320,20 +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_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_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_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_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

@@ -188,7 +188,7 @@ 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 12, which

doc/src/fix_hyper_local.txt

@@ -301,7 +301,7 @@ 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 21,
@@ -322,13 +322,13 @@ vector stores the following quantities:
 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)
+12 = max bias coeff for any bond during this run (unitless) :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
+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

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).

doc/src/fix_precession_spin.txt

@@ -14,24 +14,28 @@ fix ID group precession/spin style args :pre
 
 ID, group are documented in "fix"_fix.html command :ulb,l
 precession/spin = style name of this fix command :l
-style = {zeeman} or {anisotropy} :l
+style = {zeeman} or {anisotropy} or {cubic} :l
   {zeeman} args = H x y z
     H = intensity of the magnetic field (in Tesla)
     x y z = vector direction of the field
   {anisotropy} args = K x y z
     K = intensity of the magnetic anisotropy (in eV)
     x y z = vector direction of the anisotropy :pre
+  {cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z 
+    K1 and K2c = intensity of the magnetic anisotropy (in eV)
+    n1x to n3z = three direction vectors of the cubic anisotropy :pre
 :ule
 
 [Examples:]
 
 fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0
-fix 1 all precession/spin anisotropy 0.001 0.0 0.0 1.0
+fix 1 3 precession/spin anisotropy 0.001 0.0 0.0 1.0
+fix 1 iron precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
 fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre
 
 [Description:]
 
-Impose a force torque to each magnetic spin in the group.
+This fix applies a precession torque to each magnetic spin in the group.
 
 Style {zeeman} is used for the simulation of the interaction
 between the magnetic spins in the defined group and an external
@@ -50,10 +54,29 @@ for the magnetic spins in the defined group:
 with n defining the direction of the anisotropy, and K (in eV) its intensity.
 If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
 
-In both cases, the choice of (x y z) imposes the vector direction for the force.
-Only the direction of the vector is important; it's length is ignored.
+Style {cubic} is used to simulate a cubic anisotropy, with three
+possible easy axis for the magnetic spins in the defined group: 
 
-Both styles can be combined within one single command line.
+:c,image(Eqs/fix_spin_cubic.jpg)
+
+with K1 and K2c (in eV) the intensity coefficients and 
+n1, n2 and n3 defining the three anisotropic directions
+defined by the command (from n1x to n3z). 
+For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an 
+iron type anisotropy (easy axis along the (001)-type cube
+edges), and K1 > 0 defines a nickel type anisotropy (easy axis
+along the (111)-type cube diagonals). 
+K2^c > 0 also defines easy axis along the (111)-type cube
+diagonals.
+See chapter 2 of "(Skomski)"_#Skomski1 for more details on cubic
+anisotropies.
+
+In all cases, the choice of (x y z) only imposes the vector
+directions for the forces. Only the direction of the vector is 
+important; it's length is ignored (the entered vectors are
+normalized).
+
+Those styles can be combined within one single command line.
 
 :line
 
@@ -85,3 +108,9 @@ package"_Build_package.html doc page for more info.
 "atom_style spin"_atom_style.html
 
 [Default:] none
+
+:line
+
+:link(Skomski1)
+[(Skomski)] Skomski, R. (2008). Simple models of magnetism.
+Oxford University Press.

doc/src/fix_print.txt

@@ -14,7 +14,7 @@ fix ID group-ID print N string keyword value ... :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 print = style name of this fix command :l
-N = print every N steps :l
+N = print every N steps; N can be a variable (see below) :l
 string = text string to print with optional variable names :l
 zero or more keyword/value pairs may be appended :l
 keyword = {file} or {append} or {screen} or {title} :l
@@ -40,6 +40,21 @@ If it contains variables it must be enclosed in double quotes to
 insure they are not evaluated when the input script line is read, but
 will instead be evaluated each time the string is printed.
 
+Instead of a numeric value, N can be specified as an "equal-style
+variable"_variable.html, which should be specified as v_name, where
+name is the variable name.  In this case, the variable is evaluated at
+the beginning of a run to determine the [next] timestep at which the
+string will be written out.  On that timestep, the variable will be
+evaluated again to determine the next timestep, etc.
+Thus the variable should return timestep values.  See the stagger()
+and logfreq() and stride() math functions for "equal-style
+variables"_variable.html, as examples of useful functions to use in
+this context. For example, the following commands will print output at
+timesteps 10,20,30,100,200,300,1000,2000,etc:
+
+variable        s equal logfreq(10,3,10)
+fix extra all print v_s "Coords of marker atom = $x $y $z" :pre
+
 The specified group-ID is ignored by this fix.
 
 See the "variable"_variable.html command for a description of {equal}

doc/src/fix_setforce.txt

@@ -8,6 +8,7 @@
 
 fix setforce command :h3
 fix setforce/kk command :h3
+fix setforce/spin command :h3
 
 [Syntax:]
 
@@ -27,6 +28,7 @@ keyword = {region}  :l
 
 fix freeze indenter setforce 0.0 0.0 0.0
 fix 2 edge setforce NULL 0.0 0.0
+fix 1 edge setforce/spin 0.0 0.0 0.0
 fix 2 edge setforce NULL 0.0 v_oscillate :pre
 
 [Description:]
@@ -65,6 +67,19 @@ to it.
 
 :line
 
+Style {spin} suffix sets the components of the magnetic precession 
+vectors instead of the mechanical forces. This also erases all 
+previously computed magnetic precession vectors on the atom, though 
+additional magnetic fixes could add new forces.
+
+This command can be used to freeze the magnetic moment of certain 
+atoms in the simulation by zeroing their precession vector. 
+
+All options defined above remain valid, they just apply to the magnetic 
+precession vectors instead of the forces.
+
+:line
+
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
@@ -117,7 +132,10 @@ forces to any value besides zero when performing a minimization.  Use
 the "fix addforce"_fix_addforce.html command if you want to apply a
 non-zero force to atoms during a minimization.
 
-[Restrictions:] none
+[Restrictions:] 
+
+The fix {setforce/spin} only makes sense when LAMMPS was built with the
+SPIN package.
 
 [Related commands:]
 

doc/src/fix_wall_gran.txt

@@ -17,13 +17,13 @@ wall/gran = style name of this fix command :l
 fstyle = style of force interactions between particles and wall :l
   possible choices: hooke, hooke/history, hertz/history, granular :pre
 fstyle_params = parameters associated with force interaction style :l
-  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 
-	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 
-	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 
-	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 
-	gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)  
-	xmu = static yield criterion (unitless value between 0.0 and 1.0e4) 
-	dampflag = 0 or 1 if tangential damping force is excluded or included :pre
+  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
+        Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
+        Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
+        gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
+        gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
+        xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
+        dampflag = 0 or 1 if tangential damping force is excluded or included :pre
   For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
 wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l
 args = list of arguments for a particular style :l
@@ -46,10 +46,10 @@ keyword = {wiggle} or {shear} :l
 
 fix 1 all wall/gran hooke  200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0
 fix 1 all wall/gran hooke/history 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL
-fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 
-fix 3 all wall/gran granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 zplane 0.0 NULL
-fix 4 all wall/gran granular jkr 1000.0 50.0 0.3 5.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall zcylinder 15.0 wiggle z 3.0 2.0
-fix 5 all wall/gran granular dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall zplane 0.0 NULL :pre
+fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
+fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
+fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
+fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre
 
 [Description:]
 

doc/src/fix_wall_gran_region.txt

@@ -17,23 +17,23 @@ wall/region = style name of this fix command :l
 fstyle = style of force interactions between particles and wall :l
   possible choices: hooke, hooke/history, hertz/history, granular :pre
 fstyle_params = parameters associated with force interaction style :l
-  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 
-	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 
-	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 
-	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 
-	gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)  
-	xmu = static yield criterion (unitless value between 0.0 and 1.0e4) 
-	dampflag = 0 or 1 if tangential damping force is excluded or included :pre
+  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
+        Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
+        Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
+        gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
+        gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
+        xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
+        dampflag = 0 or 1 if tangential damping force is excluded or included :pre
   For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
 wallstyle = region (see "fix wall/gran"_fix_wall_gran.html for options for other kinds of walls) :l
 region-ID = region whose boundary will act as wall :l,ule
 
 [Examples:]
 
-fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone 
-fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 region myBox
-fix 4 all wall/gran/region granular jkr 1000.0 50.0 tangential linear_history 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
-fix 5 all wall/gran/region granular dmt 1000.0 50.0 0.3 10.0 tangential linear_history 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall region myCone :pre
+fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone
+fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
+fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
+fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre
 
 [Description:]
 

doc/src/fixes.txt

@@ -40,6 +40,7 @@ Fixes :h1
    fix_dt_reset
    fix_efield
    fix_ehex
+   fix_electron_stopping
    fix_enforce2d
    fix_eos_cv
    fix_eos_table
@@ -83,6 +84,7 @@ Fixes :h1
    fix_msst
    fix_mvv_dpd
    fix_neb
+   fix_neb_spin
    fix_nh
    fix_nh_eff
    fix_nh_uef

doc/src/kim_query.txt

@@ -26,12 +26,13 @@ kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 &
 The kim_query command allows to retrieve properties from the OpenKIM
 through a web query. The result is stored in a string style
 "variable"_variable.html, the name of which must be given as the first
-argument of the kim_query command. The second required argument is the
-name of the actual query function (e.g. {get_test_result}). All following
+argument of the kim_query command.  The second required argument is the
+name of the actual query function (e.g. {get_test_result}).  All following
 arguments are parameters handed over to the web query in the format
-{keyword=value}. This list of supported keywords and the type of how
-the value has to be encoded depends on the query function used.
-For more details on this, please refer to the OpenKIM homepage.
+{keyword=value}.  The list of supported keywords and the type of how
+the value has to be encoded depends on the query function used.  This
+mirrors the functionality available on the OpenKIM webpage at
+"https://query.openkim.org"_https://query.openkim.org/
 
 [Restrictions:]
 

doc/src/lammps.book

@@ -179,6 +179,7 @@ min_spin.html
 minimize.html
 molecule.html
 neb.html
+neb_spin.html
 neigh_modify.html
 neighbor.html
 newton.html
@@ -265,6 +266,7 @@ fix_drude_transform.html
 fix_dt_reset.html
 fix_efield.html
 fix_ehex.html
+fix_electron_stopping.html
 fix_enforce2d.html
 fix_eos_cv.html
 fix_eos_table.html
@@ -308,6 +310,7 @@ fix_mscg.html
 fix_msst.html
 fix_mvv_dpd.html
 fix_neb.html
+fix_neb_spin.html
 fix_nh.html
 fix_nh_eff.html
 fix_nph_asphere.html
@@ -571,6 +574,8 @@ pair_dipole.html
 pair_dpd.html
 pair_dpd_fdt.html
 pair_dsmc.html
+pair_e3b.html
+pair_drip.html
 pair_eam.html
 pair_edip.html
 pair_eff.html

doc/src/lattice.txt

@@ -124,7 +124,7 @@ so that they describe a tilted parallelepiped.  Via the {basis}
 keyword you add atoms, one at a time, to the unit cell.  Its arguments
 are fractional coordinates (0.0 <= x,y,z < 1.0).  The position vector
 x of a basis atom within the unit cell is thus a linear combination of
-the the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3,
+the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3,
 where bx,by,bz are the 3 values specified for the {basis} keyword.
 
 :line

doc/src/molecule.txt

@@ -396,7 +396,7 @@ If flag = 0, no a,b,c,d values are listed on the line, just the
 If flag = 1, a,b,c are listed, where a = ID of central atom in the
 angle, and b,c the other two atoms in the angle.
 
-If flag = 2, a,b are listed, where a = ID of atom in bond with the the
+If flag = 2, a,b are listed, where a = ID of atom in bond with the
 lowest ID, and b = ID of atom in bond with the highest ID.
 
 If flag = 3, a,b,c are listed, where a = ID of central atom,

doc/src/neb_spin.txt

@@ -0,0 +1,375 @@
+"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
+
+neb/spin command :h3
+
+[Syntax:]
+
+neb/spin etol ttol N1 N2 Nevery file-style arg keyword :pre
+
+etol = stopping tolerance for energy (energy units) :ulb,l
+ttol = stopping tolerance for torque ( units) :l
+N1 = max # of iterations (timesteps) to run initial NEB :l
+N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l
+Nevery = print replica energies and reaction coordinates every this many timesteps :l
+file-style = {final} or {each} or {none} :l
+  {final} arg = filename
+    filename = file with initial coords for final replica
+      coords for intermediate replicas are linearly interpolated
+      between first and last replica
+  {each} arg = filename
+    filename = unique filename for each replica (except first)
+      with its initial coords
+  {none} arg = no argument all replicas assumed to already have
+      their initial coords :pre
+keyword = {verbose}
+:ule
+
+[Examples:]
+
+neb/spin 0.1 0.0 1000 500 50 final coords.final
+neb/spin 0.0 0.001 1000 500 50 each coords.initial.$i
+neb/spin 0.0 0.001 1000 500 50 none verbose :pre
+
+[Description:]
+
+Perform a geodesic nudged elastic band (GNEB) calculation using multiple
+replicas of a system.  Two or more replicas must be used; the first
+and last are the end points of the transition path.
+
+GNEB is a method for finding both the spin configurations and height
+of the energy barrier associated with a transition state, e.g.
+spins to perform a collective rotation from one energy basin to
+another. 
+The implementation in LAMMPS follows the discussion in the
+following paper: "(BessarabA)"_#BessarabA.
+
+Each replica runs on a partition of one or more processors.  Processor
+partitions are defined at run-time using the "-partition command-line
+switch"_Run_options.html.  Note that if you have MPI installed, you
+can run a multi-replica simulation with more replicas (partitions)
+than you have physical processors, e.g you can run a 10-replica
+simulation on just one or two processors.  You will simply not get the
+performance speed-up you would see with one or more physical
+processors per replica.  See the "Howto replica"_Howto_replica.html
+doc page for further discussion.
+
+NOTE: As explained below, a GNEB calculation performs a damped dynamics
+minimization across all the replicas.  The "spin"_min_spin.html
+style minimizer has to be defined in your input script. 
+
+When a GNEB calculation is performed, it is assumed that each replica
+is running the same system, though LAMMPS does not check for this.
+I.e. the simulation domain, the number of magnetic atoms, the 
+interaction potentials, and the starting configuration when the neb 
+command is issued should be the same for every replica.
+
+In a GNEB calculation each replica is connected to other replicas by
+inter-replica nudging forces.  These forces are imposed by the "fix
+neb/spin"_fix_neb_spin.html command, which must be used in conjunction 
+with the neb command.  
+The group used to define the fix neb/spin command defines the
+GNEB magnetic atoms which are the only ones that inter-replica springs 
+are applied to.  
+If the group does not include all magnetic atoms, then non-GNEB
+magnetic atoms have no inter-replica springs and the torques they feel 
+and their precession motion is computed in the usual way due only 
+to other magnetic atoms within their replica.  
+Conceptually, the non-GNEB atoms provide a background force field for 
+the GNEB atoms.  
+Their magnetic spins can be allowed to evolve during the GNEB 
+minimization procedure.
+
+The initial spin configuration for each of the replicas can be
+specified in different manners via the {file-style} setting, as
+discussed below.  Only atomic spins whose initial coordinates should 
+differ from the current configuration need to be specified.
+
+Conceptually, the initial and final configurations for the first
+replica should be states on either side of an energy barrier.
+
+As explained below, the initial configurations of intermediate
+replicas can be spin coordinates interpolated in a linear fashion
+between the first and last replicas.  This is often adequate for
+simple transitions.  For more complex transitions, it may lead to slow
+convergence or even bad results if the minimum energy path (MEP, see
+below) of states over the barrier cannot be correctly converged to
+from such an initial path.  In this case, you will want to generate
+initial states for the intermediate replicas that are geometrically
+closer to the MEP and read them in.
+
+:line
+
+For a {file-style} setting of {final}, a filename is specified which
+contains atomic and spin coordinates for zero or more atoms, in the 
+format described below.  
+For each atom that appears in the file, the new coordinates are 
+assigned to that atom in the final replica.  Each intermediate replica 
+also assigns a new spin to that atom in an interpolated manner.  
+This is done by using the current direction of the spin at the starting 
+point and the read-in direction as the final point.  
+The "angular distance" between them is calculated, and the new direction 
+is assigned to be a fraction of the angular distance.
+
+NOTE: The "angular distance" between the starting and final point is 
+evaluated in the geodesic sense, as described in 
+"(BessarabA)"_#BessarabA. 
+
+NOTE: The angular interpolation between the starting and final point 
+is achieved using Rodrigues formula:
+
+:c,image(Eqs/neb_spin_rodrigues_formula.jpg)
+
+where m_i^I is the initial spin configuration for the spin i,
+omega_i^nu is a rotation angle defined as:
+
+:c,image(Eqs/neb_spin_angle.jpg)
+
+with nu the image number, Q the total number of images, and 
+omega_i the total rotation between the initial and final spins.
+k_i defines a rotation axis such as:
+
+:c,image(Eqs/neb_spin_k.jpg)
+
+if the initial and final spins are not aligned.
+If the initial and final spins are aligned, then their cross
+product is null, and the expression above does not apply.
+If they point toward the same direction, the intermediate images 
+conserve the same orientation.
+If the initial and final spins are aligned, but point toward
+opposite directions, an arbitrary rotation vector belonging to
+the plane perpendicular to initial and final spins is chosen. 
+In this case, a warning message is displayed.
+
+For a {file-style} setting of {each}, a filename is specified which is
+assumed to be unique to each replica. 
+See the "neb"_neb.html documentation page for more information about this 
+option.
+
+For a {file-style} setting of {none}, no filename is specified.  Each
+replica is assumed to already be in its initial configuration at the
+time the neb command is issued.  This allows each replica to define
+its own configuration by reading a replica-specific data or restart or
+dump file, via the "read_data"_read_data.html,
+"read_restart"_read_restart.html, or "read_dump"_read_dump.html
+commands.  The replica-specific names of these files can be specified
+as in the discussion above for the {each} file-style.  Also see the
+section below for how a NEB calculation can produce restart files, so
+that a long calculation can be restarted if needed.
+
+NOTE: None of the {file-style} settings change the initial
+configuration of any atom in the first replica.  The first replica
+must thus be in the correct initial configuration at the time the neb
+command is issued.
+
+:line
+
+A NEB calculation proceeds in two stages, each of which is a
+minimization procedure, performed via damped dynamics.  To enable
+this, you must first define a damped spin dynamics
+"min_style"_min_style.html, using the {spin} style (see
+"min_spin"_min_spin.html for more information).  
+The other styles cannot be used, since they relax the lattice
+degrees of freedom instead of the spins.
+
+The minimizer tolerances for energy and force are set by {etol} and
+{ttol}, the same as for the "minimize"_minimize.html command.
+
+A non-zero {etol} means that the GNEB calculation will terminate if the
+energy criterion is met by every replica.  The energies being compared
+to {etol} do not include any contribution from the inter-replica
+nudging forces, since these are non-conservative.  A non-zero {ttol}
+means that the GNEB calculation will terminate if the torque criterion
+is met by every replica.  The torques being compared to {ttol} include
+the inter-replica nudging forces.
+
+The maximum number of iterations in each stage is set by {N1} and
+{N2}.  These are effectively timestep counts since each iteration of
+damped dynamics is like a single timestep in a dynamics
+"run"_run.html.  During both stages, the potential energy of each
+replica and its normalized distance along the reaction path (reaction
+coordinate RD) will be printed to the screen and log file every
+{Nevery} timesteps.  The RD is 0 and 1 for the first and last replica.
+For intermediate replicas, it is the cumulative angular distance 
+(normalized by the total cumulative angular distance) between adjacent 
+replicas, where "distance" is defined as the length of the 3N-vector of 
+the geodesic distances in spin coordinates, with N the number of
+GNEB spins involved (see equation (13) in "(BessarabA)"_#BessarabA).
+These outputs allow you to monitor NEB's progress in
+finding a good energy barrier.  {N1} and {N2} must both be multiples
+of {Nevery}.
+
+In the first stage of GNEB, the set of replicas should converge toward
+a minimum energy path (MEP) of conformational states that transition
+over a barrier.  The MEP for a transition is defined as a sequence of
+3N-dimensional spin states, each of which has a potential energy 
+gradient parallel to the MEP itself.  
+The configuration of highest energy along a MEP corresponds to a saddle 
+point.  The replica states will also be roughly equally spaced along 
+the MEP due to the inter-replica nudging force added by the 
+"fix neb"_fix_neb.html command.
+
+In the second stage of GNEB, the replica with the highest energy is
+selected and the inter-replica forces on it are converted to a force
+that drives its spin coordinates to the top or saddle point of the
+barrier, via the barrier-climbing calculation described in
+"(BessarabA)"_#BessarabA.  As before, the other replicas rearrange
+themselves along the MEP so as to be roughly equally spaced.
+
+When both stages are complete, if the GNEB calculation was successful,
+the configurations of the replicas should be along (close to) the MEP
+and the replica with the highest energy should be a spin
+configuration at (close to) the saddle point of the transition. The
+potential energies for the set of replicas represents the energy
+profile of the transition along the MEP.
+
+:line
+
+An atom map must be defined which it is not by default for "atom_style
+atomic"_atom_style.html problems.  The "atom_modify
+map"_atom_modify.html command can be used to do this.
+
+An initial value can be defined for the timestep. Although, the {spin} 
+minimization algorithm is an adaptive timestep methodology, so that 
+this timestep is likely to evolve during the calculation.  
+
+The minimizers in LAMMPS operate on all spins in your system, even
+non-GNEB atoms, as defined above.  
+
+:line
+
+Each file read by the neb/spin command containing spin coordinates used
+to initialize one or more replicas must be formatted as follows.
+
+The file can be ASCII text or a gzipped text file (detected by a .gz
+suffix).  The file can contain initial blank lines or comment lines
+starting with "#" which are ignored.  The first non-blank, non-comment
+line should list N = the number of lines to follow.  The N successive
+lines contain the following information:
+
+ID1 g1 x1 y1 z1 sx1 sy1 sz1
+ID2 g2 x2 y2 z2 sx2 sy2 sz2
+...
+IDN gN yN zN sxN syN szN :pre
+
+The fields are the atom ID, the norm of the associated magnetic spin, 
+followed by the {x,y,z} coordinates and the {sx,sy,sz} spin coordinates.
+The lines can be listed in any order.  Additional trailing information on
+the line is OK, such as a comment.
+
+Note that for a typical GNEB calculation you do not need to specify
+initial spin coordinates for very many atoms to produce differing starting
+and final replicas whose intermediate replicas will converge to the
+energy barrier.  Typically only new spin coordinates for atoms
+geometrically near the barrier need be specified.
+
+Also note there is no requirement that the atoms in the file
+correspond to the GNEB atoms in the group defined by the "fix
+neb"_fix_neb.html command.  Not every GNEB atom need be in the file,
+and non-GNEB atoms can be listed in the file.
+
+:line
+
+Four kinds of output can be generated during a GNEB calculation: energy
+barrier statistics, thermodynamic output by each replica, dump files,
+and restart files.
+
+When running with multiple partitions (each of which is a replica in
+this case), the print-out to the screen and master log.lammps file
+contains a line of output, printed once every {Nevery} timesteps.  It
+contains the timestep, the maximum torque per replica, the maximum
+torque per atom (in any replica), potential gradients in the initial,
+final, and climbing replicas, the forward and backward energy
+barriers, the total reaction coordinate (RDT), and the normalized
+reaction coordinate and potential energy of each replica.
+
+The "maximum torque per replica" is the two-norm of the
+3N-length vector given by the cross product of a spin by its
+precession vector omega, in each replica, maximized across replicas, 
+which is what the {ttol} setting is checking against.  In this case, N is
+all the atoms in each replica.  The "maximum torque per atom" is the
+maximum torque component of any atom in any replica.  The potential
+gradients are the two-norm of the 3N-length magnetic precession vector 
+solely due to the interaction potential i.e. without adding in 
+inter-replica forces, and projected along the path tangent (as detailed 
+in Appendix D of "(BessarabA)"_#BessarabA).
+
+The "reaction coordinate" (RD) for each replica is the two-norm of the
+3N-length vector of geodesic distances between its spins and the preceding
+replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), added to 
+the RD of the preceding replica. The RD of the first replica RD1 = 0.0; 
+the RD of the final replica RDN = RDT, the total reaction coordinate.  
+The normalized RDs are divided by RDT, so that they form a monotonically 
+increasing sequence from zero to one. When computing RD, N only includes 
+the spins being operated on by the fix neb/spin command.
+
+The forward (reverse) energy barrier is the potential energy of the
+highest replica minus the energy of the first (last) replica.
+
+Supplementary information for all replicas can be printed out to the
+screen and master log.lammps file by adding the verbose keyword. This
+information include the following. 
+The "GradVidottan" are the projections of the potential gradient for 
+the replica i on its tangent vector (as detailed in Appendix D of 
+"(BessarabA)"_#BessarabA).
+The "DNi" are the non normalized geodesic distances (see equation (13) 
+of "(BessarabA)"_#BessarabA), between a replica i and the next replica 
+i+1. For the last replica, this distance is not defined and a "NAN"
+value is the corresponding output. 
+
+When a NEB calculation does not converge properly, the supplementary
+information can help understanding what is going wrong. 
+
+When running on multiple partitions, LAMMPS produces additional log
+files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a
+GNEB calculation, these contain the thermodynamic output for each
+replica.
+
+If "dump"_dump.html commands in the input script define a filename
+that includes a {universe} or {uloop} style "variable"_variable.html,
+then one dump file (per dump command) will be created for each
+replica.  At the end of the GNEB calculation, the final snapshot in
+each file will contain the sequence of snapshots that transition the
+system over the energy barrier.  Earlier snapshots will show the
+convergence of the replicas to the MEP.
+
+Likewise, "restart"_restart.html filenames can be specified with a
+{universe} or {uloop} style "variable"_variable.html, to generate
+restart files for each replica.  These may be useful if the GNEB
+calculation fails to converge properly to the MEP, and you wish to
+restart the calculation from an intermediate point with altered
+parameters.
+
+A c file script in provided in the tool/spin/interpolate_gneb
+directory, that interpolates the MEP given the information provided 
+by the verbose output option (as detailed in Appendix D of
+"(BessarabA)"_#BessarabA). 
+
+:line
+
+[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.
+
+:line
+
+[Related commands:]
+
+"min/spin"_min_spin.html, "fix neb/spin"_fix_neb_spin.html
+
+[Default:]
+
+none
+
+:line
+
+:link(BessarabA)
+[(BessarabA)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
+335-347 (2015).

doc/src/neigh_modify.txt

@@ -187,9 +187,9 @@ used in neighbor list construction to sort and find neighboring atoms.
 By default, for "neighbor style bin"_neighbor.html, LAMMPS uses bins
 that are 1/2 the size of the maximum pair cutoff.  For "neighbor style
 multi"_neighbor.html, the bins are 1/2 the size of the minimum pair
-cutoff.  Typically these are good values values for minimizing the
-time for neighbor list construction.  This setting overrides the
-default.  If you make it too big, there is little overhead due to
+cutoff.  Typically these are good values for minimizing the time for
+neighbor list construction.  This setting overrides the default.
+If you make it too big, there is little overhead due to
 looping over bins, but more atoms are checked.  If you make it too
 small, the optimal number of atoms is checked, but bin overhead goes
 up.  If you set the binsize to 0.0, LAMMPS will use the default

doc/src/neighbor.txt

@@ -56,7 +56,7 @@ bin size is set to 1/2 of the shortest cutoff distance and multiple
 sets of bins are defined to search over for different atom types.
 This imposes some extra setup overhead, but the searches themselves
 may be much faster for the short-cutoff cases.  See the "comm_modify
-mode multi"_comm_modify.html command for a communication option option
+mode multi"_comm_modify.html command for a communication option
 that may also be beneficial for simulations of this kind.
 
 The "neigh_modify"_neigh_modify.html command has additional options

doc/src/package.txt

@@ -64,7 +64,7 @@ args = arguments specific to the style :l
       {no_affinity} values = none
   {kokkos} args = keyword value ...
     zero or more keyword/value pairs may be appended
-    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse}
+    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {gpu/direct}
       {neigh} value = {full} or {half}
         full = full neighbor list
         half = half neighbor list built in thread-safe manner
@@ -72,7 +72,7 @@ args = arguments specific to the style :l
         full = full neighbor list
         half = half neighbor list built in thread-safe manner
       {newton} = {off} or {on}
-        off = set Newton pairwise and bonded flags off (default)
+        off = set Newton pairwise and bonded flags off
         on = set Newton pairwise and bonded flags on
       {binsize} value = size
         size = bin size for neighbor list construction (distance units)
@@ -422,101 +422,103 @@ processes/threads used for LAMMPS.
 
 :line
 
-The {kokkos} style invokes settings associated with the use of the
-KOKKOS package.
+The {kokkos} style invokes settings associated with the use of the 
+KOKKOS package. 
 
-All of the settings are optional keyword/value pairs.  Each has a
-default value as listed below.
+All of the settings are optional keyword/value pairs. Each has a default 
+value as listed below. 
 
-The {neigh} keyword determines how neighbor lists are built.  A value
-of {half} uses a thread-safe variant of half-neighbor lists,
-the same as used by most pair styles in LAMMPS.
+The {neigh} keyword determines how neighbor lists are built. A value of 
+{half} uses a thread-safe variant of half-neighbor lists, the same as 
+used by most pair styles in LAMMPS, which is the default when running on 
+CPUs (i.e. the Kokkos CUDA back end is not enabled). 
 
-A value of {full} uses a full neighbor lists and is the default.  This
-performs twice as much computation as the {half} option, however that
-is often a win because it is thread-safe and doesn't require atomic
-operations in the calculation of pair forces.  For that reason, {full}
-is the default setting.  However, when running in MPI-only mode with 1
-thread per MPI task, {half} neighbor lists will typically be faster,
-just as it is for non-accelerated pair styles. Similarly, the {neigh/qeq}
-keyword determines how neighbor lists are built for "fix qeq/reax/kk"_fix_qeq_reax.html.
-If not explicitly set, the value of {neigh/qeq} will match {neigh}.
+A value of {full} uses a full neighbor lists and is the default when 
+running on GPUs. This performs twice as much computation as the {half} 
+option, however that is often a win because it is thread-safe and 
+doesn't require atomic operations in the calculation of pair forces. For 
+that reason, {full} is the default setting for GPUs. However, when 
+running on CPUs, a {half} neighbor list is the default because it are 
+often faster, just as it is for non-accelerated pair styles. Similarly, 
+the {neigh/qeq} keyword determines how neighbor lists are built for "fix 
+qeq/reax/kk"_fix_qeq_reax.html. If not explicitly set, the value of 
+{neigh/qeq} will match {neigh}. 
 
-The {newton} keyword sets the Newton flags for pairwise and bonded
-interactions to {off} or {on}, the same as the "newton"_newton.html
-command allows.  The default is {off} because this will almost always
-give better performance for the KOKKOS package.  This means more
-computation is done, but less communication.  However, when running in
-MPI-only mode with 1 thread per MPI task, a value of {on} will
-typically be faster, just as it is for non-accelerated pair styles.
+The {newton} keyword sets the Newton flags for pairwise and bonded 
+interactions to {off} or {on}, the same as the "newton"_newton.html 
+command allows. The default for GPUs is {off} because this will almost 
+always give better performance for the KOKKOS package. This means more 
+computation is done, but less communication. However, when running on 
+CPUs a value of {on} is the default since it can often be faster, just 
+as it is for non-accelerated pair styles 
 
-The {binsize} keyword sets the size of bins used to bin atoms in
-neighbor list builds.  The same value can be set by the "neigh_modify
-binsize"_neigh_modify.html command.  Making it an option in the
-package kokkos command allows it to be set from the command line.  The
-default value is 0.0, which means the LAMMPS default will be used,
-which is bins = 1/2 the size of the pairwise cutoff + neighbor skin
-distance.  This is fine when neighbor lists are built on the CPU.  For
-GPU builds, a 2x larger binsize equal to the pairwise cutoff +
-neighbor skin, is often faster, which can be set by this keyword.
-Note that if you use a longer-than-usual pairwise cutoff, e.g. to
-allow for a smaller fraction of KSpace work with a "long-range
-Coulombic solver"_kspace_style.html because the GPU is faster at
-performing pairwise interactions, then this rule of thumb may give too
-large a binsize.
+The {binsize} keyword sets the size of bins used to bin atoms in 
+neighbor list builds. The same value can be set by the "neigh_modify 
+binsize"_neigh_modify.html command. Making it an option in the package 
+kokkos command allows it to be set from the command line. The default 
+value for CPUs is 0.0, which means the LAMMPS default will be used, 
+which is bins = 1/2 the size of the pairwise cutoff + neighbor skin 
+distance. This is fine when neighbor lists are built on the CPU. For GPU 
+builds, a 2x larger binsize equal to the pairwise cutoff + neighbor skin 
+is often faster, which is the default. Note that if you use a 
+longer-than-usual pairwise cutoff, e.g. to allow for a smaller fraction 
+of KSpace work with a "long-range Coulombic solver"_kspace_style.html 
+because the GPU is faster at performing pairwise interactions, then this 
+rule of thumb may give too large a binsize and the default should be 
+overridden with a smaller value. 
 
-The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse} keywords determine
-whether the host or device performs the packing and unpacking of data
-when communicating per-atom data between processors.  "Exchange"
-communication happens only on timesteps that neighbor lists are
-rebuilt.  The data is only for atoms that migrate to new processors.
-"Forward" communication happens every timestep. "Reverse" communication
-happens every timestep if the {newton} option is on.  The data is for atom
-coordinates and any other atom properties that needs to be updated for
-ghost atoms owned by each processor.
+The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse} 
+keywords determine whether the host or device performs the packing and 
+unpacking of data when communicating per-atom data between processors. 
+"Exchange" communication happens only on timesteps that neighbor lists 
+are rebuilt. The data is only for atoms that migrate to new processors. 
+"Forward" communication happens every timestep. "Reverse" communication 
+happens every timestep if the {newton} option is on. The data is for 
+atom coordinates and any other atom properties that needs to be updated 
+for ghost atoms owned by each processor. 
 
-The {comm} keyword is simply a short-cut to set the same value
-for both the {comm/exchange} and {comm/forward} and {comm/reverse} keywords.
+The {comm} keyword is simply a short-cut to set the same value for both 
+the {comm/exchange} and {comm/forward} and {comm/reverse} keywords. 
 
-The value options for all 3 keywords are {no} or {host} or {device}.
-A value of {no} means to use the standard non-KOKKOS method of
-packing/unpacking data for the communication.  A value of {host} means
-to use the host, typically a multi-core CPU, and perform the
-packing/unpacking in parallel with threads.  A value of {device}
-means to use the device, typically a GPU, to perform the
-packing/unpacking operation.
+The value options for all 3 keywords are {no} or {host} or {device}. A 
+value of {no} means to use the standard non-KOKKOS method of 
+packing/unpacking data for the communication. A value of {host} means to 
+use the host, typically a multi-core CPU, and perform the 
+packing/unpacking in parallel with threads. A value of {device} means to 
+use the device, typically a GPU, to perform the packing/unpacking 
+operation. 
 
-The optimal choice for these keywords depends on the input script and
-the hardware used.  The {no} value is useful for verifying that the
-Kokkos-based {host} and {device} values are working correctly.
-It may also be the fastest choice when using Kokkos styles in
-MPI-only mode (i.e. with a thread count of 1).
+The optimal choice for these keywords depends on the input script and 
+the hardware used. The {no} value is useful for verifying that the 
+Kokkos-based {host} and {device} values are working correctly. It is the 
+default when running on CPUs since it is usually the fastest. 
 
-When running on CPUs or Xeon Phi, the {host} and {device} values work
-identically.  When using GPUs, the {device} value will typically be
-optimal if all of your styles used in your input script are supported
-by the KOKKOS package.  In this case data can stay on the GPU for many
-timesteps without being moved between the host and GPU, if you use the
-{device} value.  This requires that your MPI is able to access GPU
-memory directly.  Currently that is true for OpenMPI 1.8 (or later
-versions), Mvapich2 1.9 (or later), and CrayMPI.  If your script uses
-styles (e.g. fixes) which are not yet supported by the KOKKOS package,
-then data has to be move between the host and device anyway, so it is
-typically faster to let the host handle communication, by using the
-{host} value.  Using {host} instead of {no} will enable use of
-multiple threads to pack/unpack communicated data.
+When running on CPUs or Xeon Phi, the {host} and {device} values work 
+identically. When using GPUs, the {device} value is the default since it 
+will typically be optimal if all of your styles used in your input 
+script are supported by the KOKKOS package. In this case data can stay 
+on the GPU for many timesteps without being moved between the host and 
+GPU, if you use the {device} value. This requires that your MPI is able 
+to access GPU memory directly. Currently that is true for OpenMPI 1.8 
+(or later versions), Mvapich2 1.9 (or later), and CrayMPI. If your 
+script uses styles (e.g. fixes) which are not yet supported by the 
+KOKKOS package, then data has to be move between the host and device 
+anyway, so it is typically faster to let the host handle communication, 
+by using the {host} value. Using {host} instead of {no} will enable use 
+of multiple threads to pack/unpack communicated data. 
 
-The {gpu/direct} keyword chooses whether GPU-direct will be used. When
-this keyword is set to {on}, buffers in GPU memory are passed directly
-through MPI send/receive calls. This reduces overhead of first copying
-the data to the host CPU. However GPU-direct is not supported on all
-systems, which can lead to segmentation faults and would require
-using a value of {off}. If LAMMPS can safely detect that GPU-direct is
-not available (currently only possible with OpenMPI v2.0.0 or later),
-then the {gpu/direct} keyword is automatically set to {off} by default.
-When the {gpu/direct} keyword is set to {off} while any of the {comm}
-keywords are set to {device}, the value for these {comm} keywords will
-be automatically changed to {host}.
+The {gpu/direct} keyword chooses whether GPU-direct will be used. When 
+this keyword is set to {on}, buffers in GPU memory are passed directly 
+through MPI send/receive calls. This reduces overhead of first copying 
+the data to the host CPU. However GPU-direct is not supported on all 
+systems, which can lead to segmentation faults and would require using a 
+value of {off}. If LAMMPS can safely detect that GPU-direct is not 
+available (currently only possible with OpenMPI v2.0.0 or later), then 
+the {gpu/direct} keyword is automatically set to {off} by default. When 
+the {gpu/direct} keyword is set to {off} while any of the {comm} 
+keywords are set to {device}, the value for these {comm} keywords will 
+be automatically changed to {host}. This setting has no effect if not 
+running on GPUs.
 
 :line
 
@@ -620,17 +622,19 @@ except "omp" and "mode", are ignored if LAMMPS was not built with Xeon
 Phi co-processor support.  These settings are made automatically if the
 "-sf intel" "command-line switch"_Run_options.html is used.  If it is
 not used, you must invoke the package intel command in your input
-script or or via the "-pk intel" "command-line
+script or via the "-pk intel" "command-line
 switch"_Run_options.html.
 
-For the KOKKOS package, the option defaults neigh = full, neigh/qeq =
-full, newton = off, binsize = 0.0, and comm = device, gpu/direct = on.
-When LAMMPS can safely detect, that GPU-direct is not available, the
-default value of gpu/direct becomes "off".
-These settings are made automatically by the required "-k on"
-"command-line switch"_Run_options.html. You can change them by
-using the package kokkos command in your input script or via the
-"-pk kokkos command-line switch"_Run_options.html.
+For the KOKKOS package, the option defaults for GPUs are neigh = full, 
+neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default 
+value, comm = device, gpu/direct = on. When LAMMPS can safely detect 
+that GPU-direct is not available, the default value of gpu/direct 
+becomes "off". For CPUs or Xeon Phis, the option defaults are neigh = 
+half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. These 
+settings are made automatically by the required "-k on" "command-line 
+switch"_Run_options.html. You can change them by using the package 
+kokkos command in your input script or via the "-pk kokkos command-line 
+switch"_Run_options.html.
 
 For the OMP package, the default is Nthreads = 0 and the option
 defaults are neigh = yes.  These settings are made automatically if

doc/src/pair_airebo.txt

@@ -36,7 +36,7 @@ pair_style airebo/morse 3.0
 pair_coeff * * ../potentials/CH.airebo-m H C :pre
 
 pair_style rebo
-pair_coeff * * ../potentials/CH.airebo H C :pre
+pair_coeff * * ../potentials/CH.rebo H C :pre
 
 [Description:]
 
@@ -57,7 +57,8 @@ The {rebo} pair style computes the Reactive Empirical Bond Order (REBO)
 Potential of "(Brenner)"_#Brenner. Note that this is the so-called
 2nd generation REBO from 2002, not the original REBO from 1990.
 As discussed below, 2nd generation REBO is closely related to the
-initial AIREBO; it is just a subset of the potential energy terms.
+initial AIREBO; it is just a subset of the potential energy terms
+with a few slightly different parameters
 
 The AIREBO potential consists of three terms:
 
@@ -113,12 +114,12 @@ various dihedral angle preferences in hydrocarbon configurations.
 :line
 
 Only a single pair_coeff command is used with the {airebo}, {airebo}
-or {rebo} style which specifies an AIREBO or AIREBO-M potential file
-with parameters for C and H.  Note that the {rebo} style in LAMMPS
-uses the same AIREBO-formatted potential file.  These are mapped to
-LAMMPS atom types by specifying N additional arguments after the
-filename in the pair_coeff command, where N is the number of LAMMPS
-atom types:
+or {rebo} style which specifies an AIREBO, REBO, or AIREBO-M potential
+file with parameters for C and H.  Note that as of LAMMPS version
+15 May 2019 the {rebo} style in LAMMPS uses its own potential
+file (CH.rebo).  These are mapped to LAMMPS atom types by specifying
+N additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
 
 filename
 N element names = mapping of AIREBO elements to atom types :ul

doc/src/pair_drip.txt

@@ -0,0 +1,141 @@
+"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
+
+pair_style drip command :h3
+
+[Syntax:]
+
+pair_style hybrid/overlay drip \[styles ...\] :pre
+
+styles = other styles to be overlayed with drip (optional) :ul
+
+[Examples:]
+
+pair_style hybrid/overlay drip
+pair_coeff * * none
+pair_coeff * * drip  C.drip  C :pre
+
+pair_style hybrid/overlay drip rebo
+pair_coeff * * drip  C.drip     C
+pair_coeff * * rebo  CH.airebo  C :pre
+
+pair_style hybrid/overlay drip rebo
+pair_coeff * * drip  C.drip     C NULL
+pair_coeff * * rebo  CH.airebo  C H :pre
+
+
+[Description:]
+
+Style {drip} computes the interlayer interactions of layered materials using
+the dihedral-angle-corrected registry-dependent (DRIP) potential as described
+in "(Wen)"_#Wen2018, which is based on the "(Kolmogorov)"_#Kolmogorov2005
+potential and provides an improved prediction for forces.
+The total potential energy of a system is
+
+:c,image(Eqs/pair_drip.jpg)
+
+where the {r^-6} term models the attractive London dispersion,
+the exponential term is designed to capture the registry effect due to
+overlapping {pi} bonds, and {fc} is a cutoff function.
+
+
+This potential (DRIP) only provides the interlayer interactions between
+graphene layers. So, to perform a realistic simulation, it should be used in
+combination with an intralayer potential such as "REBO"_pair_airebo.html and
+"Tersoff"_pair_tersoff.html.
+To keep the intralayer interactions unaffected, we should avoid applying DRIP
+to contribute energy to intralayer interactions. This can be achieved by
+assigning different molecular IDs to atoms in different layers, and DRIP is
+implemented such that only atoms with different molecular ID can interact with
+each other. For this purpose, "atom style"_atom_style.html "molecular" or
+"full" has to be used.
+
+On the other way around, "REBO"_pair_airebo.html ("Tersoff"_pair_tersoff.html
+or any other potential used to provide the intralayer interactions) should not
+interfere with the interlayer interactions described by DRIP. This is typically
+automatically achieved using the commands provided in the {Examples} section
+above, since the cutoff distance for carbon-carbon interaction in the intralayer
+potentials (e.g. 2 Angstrom for "REBO"_pair_airebo.html) is much smaller than
+the equilibrium layer distance of graphene layers (about 3.4 Angstrom).
+If you want, you can enforce this by assigning different atom types to atoms in
+different layers, and apply an intralayer potential to one atom type.
+See "pair_hybrid"_pair_hybrid.html for details.
+
+:line
+
+The "pair_coeff"_pair_coeff.html command for DRIP takes {4+N} arguments, where
+{N} is the number of LAMMPS atom types. The fist three arguments must be fixed
+to be {* * drip}, the fourth argument is the path to the DRIP parameter file,
+and the remaining N arguments specifying the mapping between element in the
+parameter file and atom types. For example, if your LAMMPS simulation has 3 atom
+types and you want all of them to be C, you would use the following pair_coeff
+command:
+
+pair_coeff * * drip  C.drip  C C C :pre
+
+If a mapping value is specified as NULL, the mapping is not performed. This
+could be useful when DRIP is used to model part of the system where other
+element exists. Suppose you have a hydrocarbon system, with C of atom type 1
+and H of atom type 2, you can use the following command to inform DRIP not to
+model H atoms:
+
+pair_style hybrid/overlay drip rebo
+pair_coeff * * drip  C.drip     C NULL
+pair_coeff * * rebo  CH.airebo  C H :pre
+
+NOTE: The potential parameters developed in "(Wen)"_#Wen2018 are provided with
+LAMMPS (see the "potentials" directory). Besides those in "Wen"_#Wen2018, an
+additional parameter "normal_cutoff", specific to the LAMMPS implementation, is
+used to find the three nearest neighbors of an atom to construct the normal.
+
+
+:line
+
+[Mixing, shift, table, tail correction, and restart info]:
+
+This pair style does not support the pair_modify mix, shift, table,
+and tail options.
+
+This pair style does not write their information to binary restart files, since
+it is stored in potential files. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+
+[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.
+
+This pair potential requires the "newton"_newton.html setting to be "on" for
+pair interactions.
+
+
+The {C.drip} parameter file provided with LAMMPS (see the "potentials"
+directory) is parameterized for metal "units"_units.html. You can use the DRIP
+potential with any LAMMPS units, but you would need to create your own custom
+parameter file with coefficients listed in the appropriate units, if your
+simulation doesn't use "metal" units.
+
+
+[Related commands:]
+
+"pair_style lebedeva_z"_pair_lebedeva_z.html,
+"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
+"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
+"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
+
+
+:line
+
+:link(Wen2018)
+[(Wen)] M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B,
+98, 235404 (2018)
+
+:link(Kolmogorov2005)
+[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
+

doc/src/pair_e3b.txt

@@ -0,0 +1,140 @@
+"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
+
+pair_style e3b command :h3
+
+[Syntax:]
+
+pair_style e3b Otype :pre
+Otype = atom type for oxygen :l
+
+pair_coeff * * keyword :pre
+one or more keyword/value pairs must be appended. :l
+keyword = {preset} or {Ea} or {Eb} or {Ec} or {E2} or {K3} or {K2} or {Rs} or {Rc3} or {Rc2} or {bondL} or {neigh} :l
+If the {preset} keyword is given, no others are needed.
+Otherwise, all are mandatory except for {neigh}.
+The {neigh} keyword is always optional. :l
+  {preset} arg = {2011} or {2015} = which set of predefined parameters to use
+  	   2011 = use the potential parameters from "(Tainter 2011)"_#Tainter2011
+  	   2015 = use the potential parameters from "(Tainter 2015)"_#Tainter2015
+  {Ea} arg = three-body energy for type A hydrogen bonding interactions (energy units)
+  {Eb} arg = three-body energy for type B hydrogen bonding interactions (energy units)
+  {Ec} arg = three-body energy for type C hydrogen bonding interactions (energy units)
+  {E2} arg = two-body energy correction (energy units)
+  {K3} arg = three-body exponential constant (inverse distance units)
+  {K2} arg = two-body exponential constant (inverse distance units)
+  {Rc3} arg = three-body cutoff (distance units)
+  {Rc2} arg = two-body cutoff (distance units)
+  {Rs} arg = three-body switching function cutoff (distance units)
+  {bondL} arg = intramolecular OH bond length (distance units)
+  {neigh} arg = approximate integer number of molecules within Rc3 of an oxygen atom :pre
+
+[Examples:]
+
+pair_style e3b 1
+pair_coeff * * Ea 35.85 Eb -240.2 Ec 449.3 E2 108269.9 K3 1.907 K2 4.872 Rc3 5.2 Rc2 5.2 Rs 5.0 bondL 0.9572 :pre
+
+pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5
+pair_coeff * * e3b preset 2011 :pre
+
+[Description:]
+
+The {e3b} style computes an \"explicit three-body\" (E3B) potential for water "(Kumar 2008)"_#Kumar.
+
+:c,image(Eqs/e3b.jpg)
+
+This potential was developed as a water model that includes the three-body cooperativity of hydrogen bonding explicitly.
+To use it in this way, it must be applied in conjunction with a conventional two-body water model, through {pair_style hybrid/overlay}.
+The three body interactions are split into three types: A, B, and C.
+Type A corresponds to anti-cooperative double hydrogen bond donor interactions.
+Type B corresponds to the cooperative interaction of molecules that both donate and accept a hydrogen bond.
+Type C corresponds to anti-cooperative double hydrogen bond acceptor interactions.
+The three-body interactions are smoothly cutoff by the switching function s(r) between Rs and Rc3.
+The two-body interactions are designed to correct for the effective many-body interactions implicitly included in the conventional two-body potential.
+The two-body interactions are cut off sharply at Rc2, because K3 is typically significantly smaller than K2.
+See "(Kumar 2008)"_#Kumar for more details.
+
+Only a single {pair_coeff} command is used with the {e3b} style.
+The 1st two arguments must be * *.
+The oxygen atom type for the pair style is passed as the only argument to the {pair_style} command, not in the {pair_coeff} command.
+The hydrogen atom type is inferred by the ordering of the atoms.
+
+NOTE: Every atom of type Otype must be part of a water molecule.
+Each water molecule must have consecutive IDs with the oxygen first.
+This pair style does not test that this criteria is met.
+
+The {pair_coeff} command must have at least one keyword/value pair, as described above.
+The {preset} keyword sets the potential parameters to the values used in "(Tainter 2011)"_#Tainter2011 or "(Tainter 2015)"_#Tainter2015.
+To use the water models defined in those references, the {e3b} style should always be used in conjunction with an {lj/cut/tip4p/long} style through {pair_style hybrid/overlay}, as demonstrated in the second example above.
+The {preset 2011} option should be used with the "TIP4P water model"_Howto_tip4p.html.
+The {preset 2015} option should be used with the "TIP4P/2005 water model"_Howto_tip4p.html.
+If the {preset} keyword is used, no other keyword is needed.
+Changes to the preset parameters can be made by specifying the {preset} keyword followed by the specific parameter to change, like {Ea}.
+Note that the other keywords must come after {preset} in the pair_style command.
+The {e3b} style can also be used to implement any three-body potential of the same form by specifying all the keywords except {neigh}: {Ea}, {Eb}, {Ec}, {E2}, {K3}, {K2}, {Rc3}, {Rc2}, {Rs}, and {bondL}.
+The keyword {bondL} specifies the intramolecular OH bond length of the water model being used.
+This is needed to include H atoms that are within the cutoff even when the attached oxygen atom is not.
+
+This pair style allocates arrays sized according to the number of pairwise interactions within Rc3.
+To do this it needs an estimate for the number of water molecules within Rc3 of an oxygen atom.
+This estimate defaults to 10 and can be changed using the {neigh} keyword, which takes an integer as an argument.
+If the neigh setting is too small, the simulation will fail with the error "neigh is too small".
+If the neigh setting is too large, the pair style will use more memory than necessary.
+
+This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the "compute pair"_compute_pair.html command as a vector of values of length 4.
+The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term.
+
+See the examples/USER/e3b directory for a complete example script.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This pair style is incompatible with "respa"_run_style.html.
+
+:line
+
+[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.
+
+This pair style requires the "newton"_newton.html setting to be "on"
+for pair interactions.
+
+This pair style requires a fixed number of atoms in the simulation, so it is incompatible with fixes like "fix deposit"_fix_deposit.html.
+If the number of atoms changes between runs, this pair style must be re-initialized by calling the {pair_style} and {pair_coeffs} commands.
+This is not a fundamental limitation of the pair style, but the code currently does not support a variable number of atoms.
+
+The {preset} keyword currently only works with real, metal, si, and cgs "units"_units.html.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html, "compute pair"_compute_pair.html
+
+[Default:]
+
+The option default for the {neigh} keyword is 10.
+
+:line
+
+:link(Kumar)
+[(Kumar)] Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008)
+:link(Tainter2011)
+[(Tainter 2011)] Tainter, Pieniazek, Lin, and Skinner, J. Chem. Phys., 134, 184501 (2011)
+:link(Tainter2015)
+[(Tainter 2015)] Tainter, Shi, and Skinner, 11, 2268 (2015)

doc/src/pair_fep_soft.txt

@@ -201,7 +201,7 @@ model. The usage of the TIP4P pair style is documented in the
 "pair_lj"_pair_lj.html styles. In the soft version the parameters n, alpha_LJ
 and alpha_C are set in the "pair_style"_pair_style.html command, after the
 specific parameters of the TIP4P water model and before the cutoffs. The
-activation parameter lambda is supplied as an argument of the the
+activation parameter lambda is supplied as an argument of the
 "pair_coeff"_pair_coeff.html command, after epsilon and sigma and before the
 optional cutoffs.
 
@@ -210,7 +210,7 @@ Style {lj/charmm/coul/long/soft} implements a soft-core version of the modified
 "pair_lj_charmm"_pair_charmm.html style. In the soft version the parameters n,
 alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before
 the global cutoffs. The activation parameter lambda is introduced as an argument
-of the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and
+of the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and
 before the optional eps14 and sigma14.
 
 Style {lj/class2/soft} implements a soft-core version of the 9-6 potential in