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

Step version string for next patch release

.github/ISSUE_TEMPLATE/generic.md

@@ -0,0 +1,21 @@
+---
+name: Generic Issue
+about: For issues that do not fit any of the other categories
+title: "_Replace With a Descriptive Title_"
+labels: 
+assignees: ''
+
+---
+
+**Summary**
+
+_Please provide a clear and concise description of what this issue report is about._
+
+**LAMMPS Version and Platform**
+
+_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_
+
+**Details**
+
+_Please explain the issue in detail here_
+

.github/ISSUE_TEMPLATE/help_request.md

@@ -0,0 +1,15 @@
+---
+name: Request for Help
+about: "Don't post help requests here, email the lammps-users mailing list"
+title: ""
+labels: invalid
+assignees: ''
+
+---
+
+Please **do not** post requests for help (e.g. with installing or using LAMMPS) here.
+Instead send an e-mail to the lammps-users mailing list.
+
+This issue tracker is for tracking LAMMPS development related issues only.
+
+Thanks for your cooperation.

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,22 +4,19 @@ _Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in
 
 **Related Issues**
 
-__If this addresses an open GitHub Issue, mention the issue number here. Use the phrases `fixes #221` or `closes #135`, when you want those issues to be automatically closed when the pull request is merged_
+_If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_
 
 **Author(s)**
 
-_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future_
+_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (ideally something that can outlive your institution's e-mail, in case you change jobs) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this contributed code._
 
 **Licensing**
 
-By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under the GNU General Public License version 2.
-
-_Please complete the following statement by adding "yes" or "no":_
-My contribution may be re-licensed as LGPL (for use of LAMMPS as a library linked to proprietary software):
+By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
 
 **Backward Compatibility**
 
-_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+_Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why_
 
 **Implementation Notes**
 
@@ -27,7 +24,7 @@ _Provide any relevant details about how the changes are implemented, how correct
 
 **Post Submission Checklist**
 
-_Please check the fields below as they are completed **after** the pull request has been submitted_
+_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_
 
 - [ ] The feature or features in this pull request is complete
 - [ ] Licensing information is complete

cmake/CMakeLists.txt

@@ -11,6 +11,8 @@ get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
 
+find_package(Git)
+
 # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
 if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
   set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
@@ -85,7 +87,7 @@ string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
 # this is fast, so check for it all the time
 message(STATUS "Running check for auto-generated files from make-based build system")
 file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
-list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h)
+list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h ${LAMMPS_SOURCE_DIR}/lmpgitversion.h)
 foreach(_SRC ${SRC_AUTOGEN_FILES})
   get_filename_component(FILENAME "${_SRC}" NAME)
   if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME})
@@ -178,7 +180,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
   USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
   USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
   USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK
-  USER-QUIP USER-QMMM USER-YAFF)
+  USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 set(OTHER_PACKAGES CORESHELL QEQ)
 foreach(PKG ${DEFAULT_PACKAGES})
@@ -201,6 +203,17 @@ endif()
 
 include_directories(${LAMMPS_SOURCE_DIR})
 
+
+if(PKG_USER-ADIOS)
+  # The search for ADIOS2 must come before MPI because
+  # it includes its own MPI search with the latest FindMPI.cmake
+  # script that defines the MPI::MPI_C target
+  enable_language(C)
+  find_package(ADIOS2 REQUIRED)
+  list(APPEND LAMMPS_LINK_LIBS adios2::adios2)
+endif()
+
+
 # do MPI detection after language activation, if MPI for these language is required
 find_package(MPI QUIET)
 option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
@@ -307,10 +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()
@@ -354,7 +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)
@@ -368,19 +386,10 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
 endif()
 
 if(PKG_PYTHON)
-  find_package(PythonInterp REQUIRED)
   find_package(PythonLibs REQUIRED)
   add_definitions(-DLMP_PYTHON)
   include_directories(${PYTHON_INCLUDE_DIR})
   list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
-  if(BUILD_LIB AND BUILD_SHARED_LIBS)
-    if(NOT PYTHON_INSTDIR)
-      execute_process(COMMAND ${PYTHON_EXECUTABLE}
-        -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
-        OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
-    endif()
-    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
-  endif()
 endif()
 
 find_package(JPEG QUIET)
@@ -439,7 +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" ${DOWNLOAD_VORO_DEFAULT})
   if(DOWNLOAD_VORO)
     message(STATUS "Voro++ download requested - we will build our own")
     include(ExternalProject)
@@ -453,7 +468,7 @@ if(PKG_VORONOI)
     set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
 
     ExternalProject_Add(voro_build
-      URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
+      URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
       URL_MD5 2338b824c3b7b25590e18e8df5d68af9
       CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
       )
@@ -472,7 +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")
@@ -484,6 +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)
@@ -499,7 +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)
@@ -539,8 +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})
@@ -554,29 +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 ${CMAKE_DL_LIBS})
@@ -584,7 +640,7 @@ if(PKG_USER-PLUMED)
     set(PLUMED_INCLUDE_DIRS "${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)
@@ -600,9 +656,13 @@ if(PKG_USER-PLUMED)
 endif()
 
 if(PKG_USER-MOLFILE)
+  set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
   add_library(molfile INTERFACE)
-  target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
-  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+  target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
+  # no need to link with -ldl on windows
+  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+  endif()
   list(APPEND LAMMPS_LINK_LIBS molfile)
 endif()
 
@@ -614,7 +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)
@@ -656,28 +722,43 @@ if(PKG_USER-VTK)
 endif()
 
 if(PKG_KIM)
-  option(DOWNLOAD_KIM "Download KIM-API v1 from OpenKIM instead of using an already installed one)" OFF)
+  find_package(CURL)
+  if(CURL_FOUND)
+    include_directories(${CURL_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
+    add_definitions(-DLMP_KIM_CURL)
+  endif()
+  find_package(KIM-API QUIET)
+  if(KIM-API_FOUND)
+    set(DOWNLOAD_KIM_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_KIM_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
   if(DOWNLOAD_KIM)
-    message(STATUS "KIM-API v1 download requested - we will build our own")
+    message(STATUS "KIM-API download requested - we will build our own")
+    enable_language(C)
+    enable_language(Fortran)
     include(ExternalProject)
     ExternalProject_Add(kim_build
-      URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
-      URL_MD5 9f66efc128da33039e30659f36fc6d00
-      BUILD_IN_SOURCE 1
-      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+      URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz
+      URL_MD5 537d9c0abd30f85b875ebb584f9143fa
+      BINARY_DIR build
+      CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+                 -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                 -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
+                 -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                 -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
       )
     ExternalProject_get_property(kim_build INSTALL_DIR)
-    set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
-    set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
+    set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)
+    set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
     list(APPEND LAMMPS_DEPS kim_build)
   else()
-    find_package(KIM)
-    if(NOT KIM_FOUND)
-      message(FATAL_ERROR "KIM-API v1 not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
-    endif()
+    find_package(KIM-API REQUIRED)
   endif()
-  list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
-  include_directories(${KIM_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
+  include_directories(${KIM-API_INCLUDE_DIRS})
 endif()
 
 if(PKG_MESSAGE)
@@ -692,6 +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()
 
@@ -711,7 +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)" ${DOWNLOAD_MSCG_DEFAULT})
   if(DOWNLOAD_MSCG)
     if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
       message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
@@ -760,7 +848,6 @@ endif()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
-include(CheckIncludeFileCXX)
 foreach(HEADER cmath)
   check_include_file_cxx(${HEADER} FOUND_${HEADER})
   if(NOT FOUND_${HEADER})
@@ -927,7 +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)
 
@@ -1040,37 +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()
@@ -1083,33 +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)
@@ -1151,6 +1279,10 @@ if(PKG_GPU)
         message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
       endif()
       option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+      option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
+      if(CUDA_MPS_SUPPORT)
+        set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
+      endif()
 
       set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
 
@@ -1214,7 +1346,7 @@ if(PKG_GPU)
       add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
       target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
       target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
-      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
       if(CUDPP_OPT)
         target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
         target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
@@ -1240,7 +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)
@@ -1251,7 +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 ${OpenCL_LIBRARIES})
@@ -1308,6 +1462,18 @@ message(STATUS "Generating lmpinstalledpkgs.h...")
 file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" )
 execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h")
 
+######################################
+# Generate lmpgitversion.h
+######################################
+add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
+  -DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
+  -DGIT_EXECUTABLE="${GIT_EXECUTABLE}"
+  -DGIT_FOUND="${GIT_FOUND}"
+  -DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
+  -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/generate_lmpgitversion.cmake)
+set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${LAMMPS_STYLE_HEADERS_DIR}/gitversion.h)
+list(APPEND LAMMPS_DEPS gitversion)
+
 ###########################################
 # Actually add executable and lib to build
 ############################################
@@ -1352,8 +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
 ###############################################################################
@@ -1415,11 +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(
@@ -1428,6 +1608,49 @@ install(
   DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d
 )
 
+###############################################################################
+# Install LAMMPS lib and python module into site-packages folder with
+# "install-python" target.  Behaves exactly like "make install-python" for
+# conventional build.  Only available, if a shared library is built.
+# This is primarily for people that only want to use the Python wrapper.
+###############################################################################
+if(BUILD_LIB AND BUILD_SHARED_LIBS)
+  find_package(PythonInterp)
+  if (PYTHONINTERP_FOUND)
+    add_custom_target(
+      install-python
+      ${PYTHON_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
+      -m ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py
+      -l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
+      WORKING_DIRECTORY  ${CMAKE_CURRENT_SOURCE_DIR}/../python
+      COMMENT "Installing LAMMPS Python module")
+  else()
+    add_custom_target(
+      install-python
+      ${CMAKE_COMMAND} -E echo "Must have Python installed to install the LAMMPS Python module")
+  endif()
+else()
+  add_custom_target(
+    install-python
+    ${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
+endif()
+
+###############################################################################
+# Add LAMMPS python module to "install" target. This is taylored for building
+# LAMMPS for package managers and with different prefix settings.
+# This requires either a shared library or that the PYTHON package is included.
+###############################################################################
+if((BUILD_LIB AND BUILD_SHARED_LIBS) OR (PKG_PYTHON))
+  find_package(PythonInterp)
+  if (PYTHONINTERP_FOUND)
+    execute_process(COMMAND ${PYTHON_EXECUTABLE}
+      -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
+      OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
+    set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
+  endif()
+endif()
+
 ###############################################################################
 # Testing
 #

cmake/Modules/FindKIM-API.cmake

@@ -0,0 +1,59 @@
+#
+# CDDL HEADER START
+#
+# The contents of this file are subject to the terms of the Common Development
+# and Distribution License Version 1.0 (the "License").
+#
+# You can obtain a copy of the license at
+# http://www.opensource.org/licenses/CDDL-1.0.  See the License for the
+# specific language governing permissions and limitations under the License.
+#
+# When distributing Covered Code, include this CDDL HEADER in each file and
+# include the License file in a prominent location with the name LICENSE.CDDL.
+# If applicable, add the following below this CDDL HEADER, with the fields
+# enclosed by brackets "[]" replaced with your own identifying information:
+#
+# Portions Copyright (c) [yyyy] [name of copyright owner]. All rights reserved.
+#
+# CDDL HEADER END
+#
+
+#
+# Copyright (c) 2013--2019, Regents of the University of Minnesota.
+# All rights reserved.
+#
+# Contributors:
+#    Richard Berger
+#    Christoph Junghans
+#    Ryan S. Elliott
+#
+
+# - Find KIM-API
+#
+# sets standard pkg_check_modules variables plus:
+#
+# KIM-API-CMAKE_C_COMPILER
+# KIM-API-CMAKE_CXX_COMPILER
+# KIM-API-CMAKE_Fortran_COMPILER
+#
+
+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 ${REQ_OR_QUI} libkim-api>=2.0)
+
+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
+find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES)

cmake/Modules/FindKIM.cmake

@@ -1,22 +0,0 @@
-# - Find kim
-# Find the native KIM headers and libraries.
-#
-#  KIM_INCLUDE_DIRS - where to find kim.h, etc.
-#  KIM_LIBRARIES    - List of libraries when using kim.
-#  KIM_FOUND        - True if kim found.
-#
-
-find_path(KIM_INCLUDE_DIR KIM_API.h PATH_SUFFIXES kim-api-v1)
-
-find_library(KIM_LIBRARY NAMES kim-api-v1)
-
-set(KIM_LIBRARIES ${KIM_LIBRARY})
-set(KIM_INCLUDE_DIRS ${KIM_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set KIM_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(KIM DEFAULT_MSG KIM_LIBRARY KIM_INCLUDE_DIR)
-
-mark_as_advanced(KIM_INCLUDE_DIR KIM_LIBRARY )

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

@@ -50,6 +50,7 @@ function(CreateStyleHeader path filename)
         list(REMOVE_AT ARGV 0 1)
         set(header_list)
         foreach(FNAME ${ARGV})
+            set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${FNAME}")
             get_filename_component(FNAME ${FNAME} NAME)
             list(APPEND header_list ${FNAME})
         endforeach()
@@ -61,6 +62,7 @@ function(CreateStyleHeader path filename)
     message(STATUS "Generating ${filename}...")
     file(WRITE "${path}/${filename}.tmp" "${temp}" )
     execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
+    set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}")
 endfunction(CreateStyleHeader)
 
 function(GenerateStyleHeader path property style)
@@ -89,6 +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/Modules/generate_lmpgitversion.cmake

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

cmake/README.md

@@ -155,11 +155,13 @@ make
 
 The CMake build exposes a lot of different options. In the old build system
 some of the package selections were possible by using special make target like
-`make yes-std` or `make no-lib`. Achieving the same result with cmake requires
+`make yes-std` or `make no-lib`. Achieving a similar result with cmake requires
 specifying all options manually. This can quickly become a very long command
 line that is hard to handle.  While these could be stored in a simple script
 file, there is another way of defining "presets" to compile LAMMPS in a certain
-way.
+way. Since the cmake build process - contrary to the conventional build system -
+includes the compilation of the bundled libraries into the standard build process,
+the grouping of those presets is somewhat different.
 
 A preset is a regular CMake script file that can use constructs such as
 variables, lists and for-loops to manipulate configuration options and create
@@ -171,10 +173,10 @@ Such a file can then be passed to cmake via the `-C` flag. Several examples of
 presets can be found in the `cmake/presets` folder.
 
 ```bash
-# build LAMMPS with all "standard" packages which don't use libraries and enable GPU package
+# build LAMMPS with all packages enabled which don't use external libraries and enable GPU package
 mkdir build
 cd build
-cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
+cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on ../cmake
 ```
 
 # Reference
@@ -209,7 +211,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
   </td>
 </tr>
 <tr>
-  <td><code><CMAKE_VERBOSE_MAKEFILE/code></td>
+  <td><code>CMAKE_VERBOSE_MAKEFILE</code></td>
   <td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
   <td>
   <dl>
@@ -1429,6 +1431,17 @@ TODO
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>INTEL_LRT_MODE</code></td>
+  <td>How to support Long-range thread mode in Verlet integration</td>
+  <td>
+  <dl>
+    <dt><code>threads</code> (default, if pthreads available)</dt>
+    <dt><code>none</code> (default, if pthreads not available)</dt>
+    <dt><code>c++11</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -1503,6 +1516,16 @@ target API.
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>CUDA_MPS_SUPPORT</code> (CUDA only)</td>
+  <td>Enable tweaks for running with Nvidia CUDA Multi-process services daemon</td>
+  <td>
+  <dl>
+    <dt><code>on</code></dt>
+    <dt><code>off</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>BIN2C</code> (CUDA only)</td>
   <td>Path to bin2c executable, will automatically pick up the first one in your $PATH.</td>

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

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

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

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

cmake/presets/all_off.cmake

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

cmake/presets/all_on.cmake

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

cmake/presets/clang.cmake

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

cmake/presets/manual_selection.cmake

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

cmake/presets/mingw-cross.cmake

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

cmake/presets/minimal.cmake

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

cmake/presets/most.cmake

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

cmake/presets/nolib.cmake

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

cmake/presets/std.cmake

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

cmake/presets/std_nolib.cmake

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

cmake/presets/user.cmake

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

doc/.gitignore

@@ -1,3 +1,4 @@
+/old
 /html
 /latex
 /spelling

doc/Makefile

@@ -39,7 +39,7 @@ help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html       create HTML doc pages in html dir"
 	@echo "  pdf        create Developer.pdf and Manual.pdf in this dir"
-	@echo "  old        create old-style HTML doc pages in old dir"
+	@echo "  old        create old-style HTML doc pages and Manual.pdf in old dir"
 	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
 	@echo "  epub       create ePUB format manual for e-book readers"
 	@echo "  mobi       convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@@ -56,7 +56,7 @@ clean-all: clean
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
 
 clean:
-	rm -rf $(RSTDIR) html old epub
+	rm -rf $(RSTDIR) html old epub latex
 	rm -rf spelling
 
 clean-spelling:
@@ -115,21 +115,44 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: utils/txt2html/txt2html.exe
+pdf: $(OBJECTS) $(ANCHORCHECK)
 	@(\
-		set -e; \
 		cd src/Developer; \
 		pdflatex developer; \
 		pdflatex developer; \
 		mv developer.pdf ../../Developer.pdf; \
-		cd ..; \
-		../utils/txt2html/txt2html.exe -b *.txt; \
-		htmldoc --batch lammps.book;          \
-		for s in `echo *.txt | sed -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
-			do grep -q ^$$s lammps.book || \
-			echo WARNING: doc file $$s missing in src/lammps.book; done; \
-		rm *.html; \
+		cd ../../; \
 	)
+	@(\
+                . $(VENV)/bin/activate ;\
+                cp -r src/* $(RSTDIR)/ ;\
+                sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+                echo "############################################" ;\
+                doc_anchor_check src/*.txt ;\
+                echo "############################################" ;\
+                deactivate ;\
+	)
+	@cd latex && \
+          sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
+	  mv temp Makefile && \
+	  sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
+	  mv tmp.tex LAMMPS.tex && \
+	  sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
+	  mv tmp.tex LAMMPS.tex && \
+	  make && \
+	  make && \
+	  mv LAMMPS.pdf ../Manual.pdf && \
+	  cd ../;
+	@rm -rf latex/_sources
+	@rm -rf latex/PDF
+	@rm -rf latex/USER
+	@cp -r src/PDF latex/PDF
+	@cp -r src/USER latex/USER
+	@rm -rf latex/PDF/.[sg]*
+	@rm -rf latex/USER/.[sg]*
+	@rm -rf latex/USER/*/.[sg]*
+	@rm -rf latex/USER/*/*.[sg]*
+	@echo "Build finished. Manual.pdf and Developer.pdf are in this directory."
 
 old: utils/txt2html/txt2html.exe
 	@rm -rf old
@@ -139,6 +162,18 @@ old: utils/txt2html/txt2html.exe
 	  cp Eqs/*.jpg ../old/Eqs; \
 	  cp JPG/* ../old/JPG; \
 	  cp PDF/* ../old/PDF;
+	@(      set -e;\
+		cd src/Developer; \
+		pdflatex developer; \
+		pdflatex developer; \
+		mv developer.pdf ../../old/Developer.pdf; \
+		cd ../../old; \
+	        for s in `echo ../src/*.txt | sed -e 's,\.\./src/,,g' -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
+			do grep -q ^$$s ../src/lammps.book || \
+			echo WARNING: doc file $$s missing in src/lammps.book; done; \
+		htmldoc --batch ../src/lammps.book;          \
+	)
+
 
 fetch:
 	@rm -rf html_www Manual_www.pdf Developer_www.pdf
@@ -176,7 +211,7 @@ $(VENV):
 	@( \
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install Sphinx; \
+		pip install Sphinx==1.7.6; \
 		deactivate;\
 	)
 

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_basics.txt

@@ -116,6 +116,18 @@ enables OpenMP. For GNU compilers it is -fopenmp.  For (recent) Intel
 compilers it is -qopenmp.  If you are using a different compiler,
 please refer to its documentation.
 
+[OpenMP Compiler compatibility info]: :link(default-none-issues)
+
+Some compilers do not fully support the 'default(none)' directive
+and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
+semantics, which are incompatible with the OpenMP 3.1 directives used
+in LAMMPS (for maximal compatibility with compiler versions in use).
+In those case, all 'default(none)' directives (which aid in detecting
+incorrect and unwanted sharing) can be replaced with 'default(shared)'
+while dropping all 'shared()' directives. The script
+'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate
+this conversion.
+
 :line
 
 Choice of compiler and compile/link options :h4,link(compile)

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

@@ -37,6 +37,7 @@ This is the list of packages that may require additional steps.
 "POEMS"_#poems,
 "PYTHON"_#python,
 "VORONOI"_#voronoi,
+"USER-ADIOS"_#user-adios,
 "USER-ATC"_#user-atc,
 "USER-AWPMD"_#user-awpmd,
 "USER-COLVARS"_#user-colvars,
@@ -81,17 +82,19 @@ which GPU hardware to build for.
 
 [CMake build]:
 
--D GPU_API=value      # value = opencl (default) or cuda
--D GPU_PREC=value     # precision setting
-                      # value = double or mixed (default) or single
--D OCL_TUNE=value     # hardware choice for GPU_API=opencl
-                      # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
--D GPU_ARCH=value     # primary GPU hardware choice for GPU_API=cuda
-                      # value = sm_XX, see below
-                      # default is Cuda-compiler dependent, but typically sm_20
--D CUDPP_OPT=value    # optimization setting for GPU_API=cuda
-                      # enables CUDA Performance Primitives Optimizations
-                      # yes (default) or no :pre
+-D GPU_API=value          # value = opencl (default) or cuda
+-D GPU_PREC=value         # precision setting
+                          # value = double or mixed (default) or single
+-D OCL_TUNE=value         # hardware choice for GPU_API=opencl
+                          # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
+-D GPU_ARCH=value         # primary GPU hardware choice for GPU_API=cuda
+                          # value = sm_XX, see below
+                          # default is Cuda-compiler dependent, but typically sm_20
+-D CUDPP_OPT=value        # optimization setting for GPU_API=cuda
+                          # enables CUDA Performance Primitives Optimizations
+                          # value = yes (default) or no
+-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
+                          # value = yes or no (default) :pre
 
 GPU_ARCH settings for different GPU hardware is as follows:
 
@@ -168,39 +171,33 @@ used to build the GPU library.
 
 KIM package :h4,link(kim)
 
-To build with this package, the KIM library must be downloaded and
-built on your system.  It must include the KIM models that you want to
-use with LAMMPS.
+To build with this package, the KIM library with API v2 must be downloaded
+and built on your system.  It must include the KIM models that you want to
+use with LAMMPS. If you want to use the "kim_query"_kim_query.html
+command, you also need to have libcurl installed with the matching
+development headers and the curl-config tool.
 
 Note that in LAMMPS lingo, a KIM model driver is a pair style
 (e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
 element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file.  Also note that installing the KIM API
-library with all its models, may take around 30 min to build.  Of
-course you only need to do that once.
+specific EAM potential file.  Also note that downloading and installing
+the KIM API library with all its models, may take a long time (10s of
+minutes to hours) to build.  Of course you only need to do that once.
 
 See the list of KIM model drivers here:
-https://openkim.org/kim-items/model-drivers/alphabetical
+https://openkim.org/browse/model-drivers/alphabetical
 
 See the list of all KIM models here:
-https://openkim.org/kim-items/models/by-model-drivers
-
-See the list of example KIM models included by default here:
-https://openkim.org/kim-api on the "What is in the KIM API source
-package?" page.
+https://openkim.org/browse/models/by-model-drivers
 
 [CMake build]:
 
--D DOWNLOAD_KIM=value    # download OpenKIM API v1 for build, value = no (default) or yes
--D KIM_LIBRARY=path      # KIM library file (only needed if a custom location)
--D KIM_INCLUDE_DIR=path  # KIM include directory (only needed if a custom location) :pre
+-D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes :pre
 
 If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
 inside the CMake build directory.  If the KIM library is already on
-your system (in a location CMake cannot find it), KIM_LIBRARY is the
-filename (plus path) of the KIM library file, not the directory the
-library file is in.  KIM_INCLUDE_DIR is the directory the KIM include
-file is in.
+your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH
+environment variable so that libkim-api can be found.
 
 [Traditional make]:
 
@@ -214,8 +211,8 @@ make lib-kim args="-b "   # (re-)install KIM API lib with only example models
 make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
 make lib-kim args="-b -a everything"     # install KIM API lib with all models
 make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
-make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
-make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
+make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
+make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
 
 :line
 
@@ -250,7 +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]:
 
@@ -576,6 +576,32 @@ the lib/voronoi/Makefile.lammps file.
 
 :line
 
+USER-ADIOS package :h4,link(user-adios)
+
+The USER-ADIOS package requires the "ADIOS I/O library"_https://github.com/ornladios/ADIOS2,
+version 2.3.1 or newer. Make sure that you have ADIOS built either with or
+without MPI to match if you build LAMMPS with or without MPI.
+ADIOS compilation settings for LAMMPS are automatically detected, if the PATH
+and LD_LIBRARY_PATH environment variables have been updated for the local ADIOS
+installation and the instructions below are followed for the respective build systems.
+
+[CMake build]:
+
+-D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed
+-D PKG_USER-ADIOS=yes     :pre
+
+[Traditional make]:
+
+Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:
+
+make yes-user-adios                       :pre
+
+otherwise, set ADIOS2_DIR environment variable when turning on the package:
+
+ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed :pre
+
+:line
+
 USER-ATC package :h4,link(user-atc)
 
 The USER-ATC package requires the MANYBODY package also be installed.
@@ -836,23 +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:
 
@@ -874,7 +911,17 @@ USER-MOLFILE package :h4,link(user-molfile)
 
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_USER-MOLFILE=yes".
+-D MOLFILE_INCLUDE_DIRS=path   # (optional) path where VMD molfile plugin headers are installed
+-D PKG_USER-MOLFILE=yes     :pre
+
+
+Using "-D PKG_USER-MOLFILE=yes" enables the package, and setting
+"-D MOLFILE_INCLUDE DIRS" allows to provide a custom location for
+the molfile plugin header files. These should match the ABI of the
+plugin files used, and thus one typically sets them to include
+folder of the local VMD installation in use. LAMMPS ships with a
+couple of default header files that correspond to a popular VMD
+version, usually the latest release.
 
 [Traditional make]:
 
@@ -883,7 +930,11 @@ loading library libdl.a that is typically present on all systems.  It
 is required for LAMMPS to link with this package.  If the setting is
 not valid for your system, you will need to edit the Makefile.lammps
 file.  See lib/molfile/README and lib/molfile/Makefile.lammps for
-details.
+details. It is also possible to configure a different folder with
+the VMD molfile plugin header files. LAMMPS ships with a couple of
+default headers, but these are not compatible with all VMD versions,
+so it is often best to change this setting to the location of the
+same include files of the local VMD installation in use.
 
 :line
 
@@ -932,7 +983,9 @@ LINKFLAGS: -fopenmp             # for GNU Compilers
 LINKFLAGS: -qopenmp             # for Intel compilers on Linux :pre
 
 For other platforms and compilers, please consult the documentation
-about OpenMP support for your compiler.
+about OpenMP support for your compiler. Please see the note about
+how to address compatibility "issues with the 'default(none)'
+directive"_Build_basics.html#default-none-issues of some compilers.
 
 :line
 

doc/src/Build_package.txt

@@ -48,6 +48,7 @@ packages:
 "POEMS"_Build_extras.html#poems,
 "PYTHON"_Build_extras.html#python,
 "VORONOI"_Build_extras.html#voronoi,
+"USER-ADIOS"_Build_extras.html#user-adios,
 "USER-ATC"_Build_extras.html#user-atc,
 "USER-AWPMD"_Build_extras.html#user-awpmd,
 "USER-COLVARS"_Build_extras.html#user-colvars,
@@ -148,26 +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

@@ -48,12 +48,14 @@ An alphabetic list of all general LAMMPS commands.
 "dimension"_dimension.html,
 "displace_atoms"_displace_atoms.html,
 "dump"_dump.html,
+"dump adios"_dump_adios.html,
 "dump image"_dump_image.html,
 "dump_modify"_dump_modify.html,
 "dump movie"_dump_image.html,
 "dump netcdf"_dump_netcdf.html,
 "dump netcdf/mpiio"_dump_netcdf.html,
 "dump vtk"_dump_vtk.html,
+"dynamical_matrix"_dynamical_matrix.html,
 "echo"_echo.html,
 "fix"_fix.html,
 "fix_modify"_fix_modify.html,
@@ -66,6 +68,7 @@ An alphabetic list of all general LAMMPS commands.
 "improper_style"_improper_style.html,
 "include"_include.html,
 "jump"_jump.html,
+"kim_query"_kim_query.html,
 "kspace_modify"_kspace_modify.html,
 "kspace_style"_kspace_style.html,
 "label"_label.html,
@@ -76,9 +79,11 @@ An alphabetic list of all general LAMMPS commands.
 "minimize"_minimize.html,
 "min_modify"_min_modify.html,
 "min_style"_min_style.html,
+"min_style spin"_min_spin.html,
 "molecule"_molecule.html,
 "ndx2group"_group2ndx.html,
 "neb"_neb.html,
+"neb/spin"_neb_spin.html,
 "neigh_modify"_neigh_modify.html,
 "neighbor"_neighbor.html,
 "newton"_newton.html,

doc/src/Commands_category.txt

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

doc/src/Commands_fix.txt

@@ -61,6 +61,7 @@ OPT.
 "edpd/source"_fix_dpd_source.html,
 "efield"_fix_efield.html,
 "ehex"_fix_ehex.html,
+"electron/stopping"_fix_electron_stopping.html,
 "enforce2d (k)"_fix_enforce2d.html,
 "eos/cv"_fix_eos_cv.html,
 "eos/table"_fix_eos_table.html,
@@ -106,6 +107,7 @@ OPT.
 "mvv/edpd"_fix_mvv_dpd.html,
 "mvv/tdpd"_fix_mvv_dpd.html,
 "neb"_fix_neb.html,
+"neb_spin"_fix_neb_spin.html,
 "nph (ko)"_fix_nh.html,
 "nph/asphere (o)"_fix_nph_asphere.html,
 "nph/body"_fix_nph_body.html,
@@ -224,7 +226,7 @@ OPT.
 "wall/body/polyhedron"_fix_wall_body_polyhedron.html,
 "wall/colloid"_fix_wall.html,
 "wall/ees"_fix_wall_ees.html,
-"wall/gran (o)"_fix_wall_gran.html,
+"wall/gran"_fix_wall_gran.html,
 "wall/gran/region"_fix_wall_gran_region.html,
 "wall/harmonic"_fix_wall.html,
 "wall/lj1043"_fix_wall.html,

doc/src/Commands_pair.txt

@@ -80,6 +80,8 @@ OPT.
 "dpd/fdt/energy (k)"_pair_dpd_fdt.html,
 "dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
+"e3b"_pair_e3b.html,
+"drip"_pair_drip.html,
 "eam (gikot)"_pair_eam.html,
 "eam/alloy (gikot)"_pair_eam.html,
 "eam/cd (o)"_pair_eam.html,
@@ -98,6 +100,7 @@ OPT.
 "gran/hertz/history (o)"_pair_gran.html,
 "gran/hooke (o)"_pair_gran.html,
 "gran/hooke/history (ko)"_pair_gran.html,
+"granular"_pair_granular.html,
 "gw"_pair_gw.html,
 "gw/zbl"_pair_gw.html,
 "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,

doc/src/Eqs/e3b.tex

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

doc/src/Eqs/fix_spin_cubic.tex

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

doc/src/Eqs/min_spin_damping.tex

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

doc/src/Eqs/min_spin_timestep.tex

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

doc/src/Eqs/neb_spin_angle.tex

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

doc/src/Eqs/neb_spin_k.tex

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

doc/src/Eqs/neb_spin_rodrigues_formula.tex

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

doc/src/Eqs/pair_drip.tex

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

doc/src/Eqs/pair_mdf-6.tex

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

doc/src/Errors_messages.txt

@@ -6988,12 +6988,6 @@ The atom style defined does not have this attribute. :dd
 
 The atom style defined does not have these attributes. :dd
 
-{KIM neighbor iterator exceeded range} :dt
-
-This should not happen.  It likely indicates a bug
-in the KIM implementation of the interatomic potential
-where it is requesting neighbors incorrectly. :dd
-
 {KOKKOS package does not yet support comm_style tiled} :dt
 
 Self-explanatory. :dd
@@ -10185,10 +10179,6 @@ valid. :dd
 
 Self-explanatory. :dd
 
-{Unrecognized virial argument in pair_style command} :dt
-
-Only two options are supported: LAMMPSvirial and KIMvirial :dd
-
 {Unsupported mixing rule in kspace_style ewald/disp} :dt
 
 Only geometric mixing is supported. :dd

doc/src/Errors_warnings.txt

@@ -178,12 +178,6 @@ When using fixes like box/relax, the potential energy used by the minimizer
 is augmented by an additional energy provided by the fix. Thus the printed
 converged energy may be different from the total potential energy. :dd
 
-{Energy tally does not account for 'zero yes'} :dt
-
-The energy removed by using the 'zero yes' flag is not accounted
-for in the energy tally and thus energy conservation cannot be
-monitored in this case. :dd
-
 {Estimated error in splitting of dispersion coeffs is %g} :dt
 
 Error is greater than 0.0001 percent. :dd

doc/src/Examples.txt

@@ -11,7 +11,7 @@ Section"_Tools.html :c
 Example scripts :h3
 
 The LAMMPS distribution includes an examples sub-directory with many
-sample problems.  Many are 2d models that run quickly are are
+sample problems.  Many are 2d models that run quickly and are
 straightforward to visualize, requiring at most a couple of minutes to
 run on a desktop machine.  Each problem has an input script (in.*) and
 produces a log file (log.*) when it runs.  Some use a data file

doc/src/Howto.txt

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

doc/src/Howto_bioFF.txt

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

doc/src/Howto_diffusion.txt

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

doc/src/Howto_drude2.txt

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

doc/src/Howto_library.txt

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

doc/src/Howto_pylammps.txt

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

doc/src/Howto_replica.txt

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

doc/src/Howto_spins.txt

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

doc/src/Howto_tip3p.txt

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

doc/src/Install_git.txt

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

doc/src/Install_svn.txt

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

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="8 Feb 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
-8 Feb 2019 version :c,h2
+15 May 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -63,6 +63,7 @@ as contained in the file name.
 "SRD"_#PKG-SRD,
 "VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
 
+"USER-ADIOS"_#PKG-USER-ADIOS,
 "USER-ATC"_#PKG-USER-ATC,
 "USER-AWPMD"_#PKG-USER-AWPMD,
 "USER-BOCS"_#PKG-USER-BOCS,
@@ -340,18 +341,19 @@ KIM package :link(PKG-KIM),h4
 A "pair_style kim"_pair_kim.html command which is a wrapper on the
 Knowledge Base for Interatomic Models (KIM) repository of interatomic
 potentials, enabling any of them to be used in LAMMPS simulations.
+Also a "kim_query"_kim_query.html command, which allows to query
+the OpenKIM database for stored properties.
 
 To use this package you must have the KIM library available on your
 system.
 
 Information about the KIM project can be found at its website:
 https://openkim.org.  The KIM project is led by Ellad Tadmor and Ryan
-Elliott (U Minnesota) and James Sethna (Cornell U).
+Elliott (U Minnesota).
 
 [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
 API which the "pair_style kim"_pair_kim.html command uses.  He
-developed the pair style in collaboration with Valeriu Smirichinski (U
-Minnesota).
+developed the pair style.
 
 [Install:]
 
@@ -704,7 +706,7 @@ PERI package :link(PKG-PERI),h4
 
 An atom style, several pair styles which implement different
 Peridynamics materials models, and several computes which calculate
-diagnostics.  Peridynamics is a a particle-based meshless continuum
+diagnostics.  Peridynamics is a particle-based meshless continuum
 model.
 
 [Authors:] The original package was created by Mike Parks (Sandia).
@@ -903,7 +905,7 @@ SPIN package :link(PKG-SPIN),h4
 Model atomic magnetic spins classically, coupled to atoms moving in
 the usual manner via MD.  Various pair, fix, and compute styles.
 
-[Author:] Julian Tranchida (Sandia).
+[Author:] Julien Tranchida (Sandia).
 
 [Supporting info:]
 
@@ -916,6 +918,7 @@ src/SPIN: filenames -> commands
 "fix nve/spin"_fix_nve_spin.html
 "fix precession/spin"_fix_precession_spin.html
 "compute spin"_compute_spin.html
+"neb/spin"_neb_spin.html
 examples/SPIN :ul
 
 :line
@@ -975,6 +978,31 @@ examples/voronoi :ul
 
 :line
 
+USER-ADIOS package :link(PKG-USER-ADIOS),h4
+
+[Contents:]
+
+ADIOS is a high-performance I/O library. This package implements the 
+dump "atom/adios" and dump "custom/adios" commands to write data using
+the ADIOS library. 
+
+[Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#user-adios on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-ADIOS: filenames -> commands
+src/USER-ADIOS/README
+examples/USER/adios
+https://github.com/ornladios/ADIOS2 :ul
+
+:line
+
 USER-ATC package :link(PKG-USER-ATC),h4
 
 [Contents:]
@@ -1201,7 +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:]
@@ -1509,7 +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
@@ -1700,14 +1728,19 @@ USER-PHONON package :link(PKG-USER-PHONON),h4
 A "fix phonon"_fix_phonon.html command that calculates dynamical
 matrices, which can then be used to compute phonon dispersion
 relations, directly from molecular dynamics simulations.
+And a "dynamical_matrix" command to compute the dynamical matrix
+from finite differences.
+
+[Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
+and Charlie Sievers (UC Davis) for "dynamical_matrix"
 
-[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
 
 [Supporting info:]
 
 src/USER-PHONON: filenames -> commands
 src/USER-PHONON/README
 "fix phonon"_fix_phonon.html
+"dynamical_matrix"_dynamical_matrix.html
 examples/USER/phonon :ul
 
 :line
@@ -2102,5 +2135,3 @@ src/USER-YAFF/README
 "pair_style mm3/switch3/coulgauss/long"_pair_mm3_switch3_coulgauss.html
 "pair_style lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html
 examples/USER/yaff :ul
-
-

doc/src/Packages_user.txt

@@ -38,6 +38,7 @@ int = internal library: provided with LAMMPS, but you may need to build it
 ext = external library: you will need to download and install it on your machine :ul
 
 Package, Description, Doc page, Example, Library
+"USER-ADIOS"_Packages_details.html#PKG-USER-ADIOS, dump output via ADIOS, "dump adios"_dump_adios.html, USER/adios, ext
 "USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
 "USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
 "USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no

doc/src/Python_install.txt

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

doc/src/Python_library.txt

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

doc/src/Python_overview.txt

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

doc/src/Run_options.txt

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

doc/src/Run_output.txt

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

doc/src/Speed_intel.txt

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

doc/src/Speed_kokkos.txt

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

doc/src/Tools.txt

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

doc/src/commands_list.txt

@@ -32,6 +32,7 @@ Commands :h1
    dimension
    displace_atoms
    dump
+   dump_adios
    dump_cfg_uef
    dump_h5md
    dump_image
@@ -39,6 +40,7 @@ Commands :h1
    dump_molfile
    dump_netcdf
    dump_vtk
+   dynamical_matrix
    echo
    fix
    fix_modify
@@ -51,6 +53,7 @@ Commands :h1
    include
    info
    jump
+   kim_query
    kspace_modify
    kspace_style
    label
@@ -59,10 +62,12 @@ Commands :h1
    mass
    message
    min_modify
+   min_spin
    min_style
    minimize
    molecule
    neb
+   neb_spin
    neigh_modify
    neighbor
    newton

doc/src/compute.txt

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

doc/src/compute_chunk_atom.txt

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

doc/src/compute_chunk_spread_atom.txt

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

doc/src/compute_group_group.txt

@@ -137,11 +137,12 @@ Not all pair styles can be evaluated in a pairwise mode as required by
 this compute.  For example, 3-body and other many-body potentials,
 such as "Tersoff"_pair_tersoff.html and
 "Stillinger-Weber"_pair_sw.html cannot be used.  "EAM"_pair_eam.html
-potentials only include the pair potential portion of the EAM
-interaction when used by this compute, not the embedding term.
+potentials will re-use previously computed embedding term contributions,
+so the computed pairwise forces and energies are based on the whole
+system and not valid if particles have been moved since.
 
-Not all Kspace styles support calculation of group/group interactions.
-The {ewald} and {pppm} styles do.
+Not all "Kspace styles"_kspace_style.html support the calculation of
+group/group interactions. The regular {ewald} and {pppm} styles do.
 
 [Related commands:] none
 

doc/src/compute_ptm_atom.txt

@@ -38,20 +38,20 @@ ico (icosahedral) = 4
 sc (simple cubic) = 5
 dcub (diamond cubic) = 6
 dhex (diamond hexagonal) = 7
-other = 8 :ul
+graphene = 8 :ul
 
-The value of the PTM structure will be 0 for atoms not in the specified
+The value of the PTM structure will be 0 for unknown types and -1 for atoms not in the specified
 compute group.  The choice of structures to search for can be specified using the "structures"
 argument, which is a hyphen-separated list of structure keywords.
 Two convenient pre-set options are provided:
 
 default: fcc-hcp-bcc-ico
-all: fcc-hcp-bcc-ico-sc-dcub-dhex :ul
+all: fcc-hcp-bcc-ico-sc-dcub-dhex-graphene :ul
 
 The 'default' setting detects the same structures as the Common Neighbor Analysis method.
-The 'all' setting searches for all structure types.  A small performance penalty is
-incurred for the diamond structures, so it is not recommended to use this option if
-it is known that the simulation does not contain diamond structures.
+The 'all' setting searches for all structure types.  A performance penalty is
+incurred for the diamond and graphene structures, so it is not recommended to use this option if
+it is known that the simulation does not contain these structures.
 
 
 PTM identifies structures using two steps.  First, a graph isomorphism test is used
@@ -93,9 +93,9 @@ interatomic distance
 qw
 qx
 qy
-qw :ul
+qz :ul
 
-The type is a number from 0 to 8.  The rmsd is a positive real number.
+The type is a number from -1 to 8.  The rmsd is a positive real number.
 The interatomic distance is computed from the scale factor in the RMSD equation.
 The (qw,qx,qy,qz) parameters represent the orientation of the local structure
 in quaternion form.  The reference coordinates for each template (from which the

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

@@ -13,6 +13,7 @@ dump command :h3
 "dump netcdf"_dump_netcdf.html command :h3
 "dump image"_dump_image.html command :h3
 "dump movie"_dump_image.html command :h3
+"dump adios"_dump_adios.html command :h3
 
 [Syntax:]
 
@@ -20,17 +21,19 @@ 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
   {atom} args = none
   {atom/gz} args = none
   {atom/mpiio} args = none
+  {atom/adios} args = none,  discussed on "dump adios"_dump_adios.html doc page
   {cfg} args = same as {custom} args, see below
   {cfg/gz} args = same as {custom} args, see below
   {cfg/mpiio} args = same as {custom} args, see below
   {custom}, {custom/gz}, {custom/mpiio} args = see below
+  {custom/adios} args = same as {custom} args, discussed on "dump adios"_dump_adios.html doc page
   {dcd} args = none
   {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page
   {image} args = discussed on "dump image"_dump_image.html doc page
@@ -193,7 +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
@@ -616,7 +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.
@@ -653,7 +656,7 @@ package"_Build_package.html doc page for more info.
 
 [Related commands:]
 
-"dump h5md"_dump_h5md.html, "dump image"_dump_image.html,
+"dump adios"_dump_adios.html "dump h5md"_dump_h5md.html, "dump image"_dump_image.html,
 "dump molfile"_dump_molfile.html, "dump_modify"_dump_modify.html,
 "undump"_undump.html
 

doc/src/dump_adios.txt

@@ -0,0 +1,73 @@
+"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
+
+dump atoms/adios  command :h3
+dump custom/adios command :h3
+
+[Syntax:]
+
+dump ID group-ID atoms/adios N file.bp :pre
+dump ID group-ID custom/adios N file.bp args :pre
+
+ID = user-assigned name for the dump :ulb,l
+group-ID = ID of the group of atoms to be imaged :l
+adios = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
+N = dump every this many timesteps :l
+file.bp = name of file/stream to write to :l
+args = same options as in "{dump custom}"_dump.html command :l
+:ule
+
+
+[Examples:]
+
+dump adios1 all atom/adios   100 atoms.bp
+dump 4a     all custom/adios 100 dump_adios.bp id v_p x y z
+dump 2 subgroup custom/adios 100 dump_adios.bp mass type xs ys zs vx vy vz :pre
+
+[Description:]
+
+Dump a snapshot of atom coordinates every N timesteps in the
+"ADIOS"_adios based "BP" file format, or using different I/O solutions in ADIOS,
+to a stream that can be read on-line by another program.
+ADIOS-BP files are binary, portable and self-describing.
+
+:link(adios,https://github.com/ornladios/ADIOS2)
+
+
+[Use from write_dump:]
+
+It is possible to use these dump styles with the
+"write_dump"_write_dump.html command.  In this case, the sub-intervals
+must not be set at all.  The write_dump command can be used to
+create a new file at each individual dump.
+
+dump 4     all atom/adios 100 dump.bp
+write_dump all atom/adios singledump.bp :pre
+
+:line
+
+[Restrictions:]
+
+The number of atoms per snapshot CAN change with the adios style.
+When using the ADIOS tool 'bpls' to list the content of a .bp file,
+bpls will print {__} for the size of the output table indicating that
+its size is changing every step.
+
+The {atom/adios} and {custom/adios} dump styles are part of the USER-ADIOS
+package.  They are only enabled if LAMMPS was built with that package.
+See the "Build package"_Build_package.html doc page for more info.
+
+
+:line
+
+[Related commands:]
+
+"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
+
+:line
+

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/dynamical_matrix.txt

@@ -0,0 +1,52 @@
+"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
+
+dynamical_matrix command :h3
+
+[Syntax:]
+
+dynamical_matrix group-ID style gamma args keyword value ... :pre
+
+group-ID = ID of group of atoms to displace :ulb,l
+style = {regular} or {eskm} :l
+gamma = finite different displacement length (distance units) :l
+one or more keyword/arg pairs may be appended :l
+  keyword = {file} or {binary}
+    {file} name = name of output file for the dynamical matrix
+    {binary} arg = {yes} or {no} or {gzip} :pre
+:ule
+
+[Examples:]
+
+dynamical_matrix 1 regular 0.000001
+dynamical_matrix 1 eskm 0.000001
+dynamical_matrix 3 regular 0.00004 file dynmat.dat
+dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes :pre
+
+[Description:]
+
+Calculate the dynamical matrix of the selected group.
+
+[Restrictions:]
+
+The command collects the entire dynamical matrix a single MPI rank,
+so the memory requirements can be very significant for large systems.
+
+This command assumes a periodic system.
+
+This command is part of the USER-PHONON package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"fix phonon"_fix_phonon.html
+
+[Default:]
+
+The default settings are file = "dynmat.dyn", binary = no  

doc/src/fix.txt

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

doc/src/fix_adapt.txt

@@ -158,12 +158,6 @@ the pair_*.cpp file associated with the potential.
 
 Some parameters are global settings for the pair style, e.g. the
 viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html.
-For "pair_kim"_pair_kim.html, all free parameters supported by the
-KIM Model are available (e.g., PARAM_FREE_sigmas provided by the
-LennardJones612_Universal__MO_826355984548_001 Model).  If the free
-parameter corresponds to an array, then the particular array element
-to be adapted must be specified (e.g., "PARAM_FREE_sigmas:10", to
-adapt the tenth entry of the sigmas array).
 Other parameters apply to atom type pairs within the pair style,
 e.g. the prefactor "a" for "pair_style soft"_pair_soft.html.
 

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: