patch 23Oct17

Updated neighbor list history processing for USER-OMP

.github/CODEOWNERS

@@ -0,0 +1,21 @@
+# This file contains file patterns that triggers automatic
+# code review requests from users that are owners of these files
+# Order matters, the last match has the highest precedence
+
+# library folders
+lib/colvars/*         @giacomofiorin
+lib/compress/*        @akohlmey
+lib/kokkos/*          @stanmoore1
+lib/molfile/*         @akohlmey
+lib/qmmm/*            @akohlmey
+lib/vtk/*             @rbberger
+
+# packages
+src/KOKKOS            @stanmoore1
+src/USER-CGSDK        @akohlmey
+src/USER-COLVARS      @giacomofiorin
+src/USER-OMP          @akohlmey
+src/USER-QMMM         @akohlmey
+
+# tools
+tools/msi2lmp/*       @akohlmey

.gitignore

@@ -32,3 +32,11 @@ log.cite
 .Trashes
 ehthumbs.db
 Thumbs.db
+
+#cmake
+/build*
+/CMakeCache.txt
+/CMakeFiles/
+/Makefile
+/cmake_install.cmake
+/lmp

cmake/CMakeLists.txt

@@ -0,0 +1,723 @@
+########################################
+# CMake build system
+# This file is part of LAMMPS
+# Created by Christoph Junghans and Richard Berger
+cmake_minimum_required(VERSION 3.1)
+
+project(lammps)
+set(SOVERSION 0)
+set(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src)
+set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib)
+set(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib)
+
+#To not conflict with old Makefile build system, we build everything here
+file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp)
+file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
+list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})
+
+# Cmake modules/macros are in a subdirectory to keep this file cleaner
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
+  #release comes with -O3 by default
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
+endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
+
+# remove any style headers in the src dir
+file(GLOB SRC_STYLE_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
+if(SRC_STYLE_FILES)
+  file(REMOVE ${SRC_STYLE_FILES})
+endif()
+
+enable_language(CXX)
+
+######################################################################
+# compiler tests
+# these need ot be done early (before further tests).
+#####################################################################
+include(CheckCCompilerFlag)
+
+if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+endif()
+
+########################################################################
+# User input options                                                   #
+########################################################################
+option(BUILD_SHARED_LIBS "Build shared libs" OFF)
+if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
+  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+endif()
+include(GNUInstallDirs)
+
+set(LAMMPS_LINK_LIBS)
+set(LAMMPS_DEPS)
+set(LAMMPS_API_DEFINES)
+option(ENABLE_MPI "Build MPI version" OFF)
+if(ENABLE_MPI)
+  find_package(MPI REQUIRED)
+  include_directories(${MPI_C_INCLUDE_PATH})
+  list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
+  option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
+  if(LAMMPS_LONGLONG_TO_LONG)
+    add_definitions(-DLAMMPS_LONGLONG_TO_LONG)
+  endif()
+else()
+  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
+  add_library(mpi_stubs STATIC ${MPI_SOURCES})
+  include_directories(${LAMMPS_SOURCE_DIR}/STUBS)
+  list(APPEND LAMMPS_LINK_LIBS mpi_stubs)
+endif()
+
+set(LAMMPS_SIZE_LIMIT "LAMMPS_SMALLBIG" CACHE STRING "Lammps size limit")
+set_property(CACHE LAMMPS_SIZE_LIMIT PROPERTY STRINGS LAMMPS_SMALLBIG LAMMPS_BIGBIG LAMMPS_SMALLSMALL)
+add_definitions(-D${LAMMPS_SIZE_LIMIT})
+set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${LAMMPS_SIZE_LIMIT}")
+
+set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
+add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
+
+option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
+if(LAMMPS_EXCEPTIONS)
+  add_definitions(-DLAMMPS_EXCEPTIONS)
+  set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS")
+endif()
+
+set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary and liblammps (WON'T enable any features automatically")
+mark_as_advanced(LAMMPS_MACHINE)
+if(LAMMPS_MACHINE)
+  set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
+endif()
+
+option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)
+
+option(ENABLE_TESTING "Enable testing" OFF)
+if(ENABLE_TESTING)
+  enable_testing()
+endif(ENABLE_TESTING)
+
+option(ENABLE_ALL "Build all default packages" OFF)
+set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
+  KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
+  REAX REPLICA RIGID SHOCK SNAP SRD)
+set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
+  USER-ATC USER-AWPMD USER-CGDNA USER-MESO
+  USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
+  USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
+  USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
+  USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
+set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
+foreach(PKG ${DEFAULT_PACKAGES})
+  option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
+endforeach()
+foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+  option(ENABLE_${PKG} "Build ${PKG} Package" OFF)
+endforeach()
+
+macro(pkg_depends PKG1 PKG2)
+  if(ENABLE_${PKG1} AND NOT ENABLE_${PKG2})
+    message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
+  endif()
+endmacro()
+
+pkg_depends(MPIIO MPI)
+pkg_depends(QEQ MANYBODY)
+pkg_depends(USER-ATC MANYBODY)
+pkg_depends(USER-H5MD MPI)
+pkg_depends(USER-LB MPI)
+pkg_depends(USER-MISC MANYBODY)
+pkg_depends(USER-PHONON KSPACE)
+
+if(ENABLE_BODY AND ENABLE_POEMS)
+  message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time")
+endif()
+
+######################################################
+# packages with special compiler needs or external libs
+######################################################
+if(ENABLE_REAX OR ENABLE_MEAM OR ENABLE_USER-QUIP OR ENABLE_USER-QMMM OR ENABLE_LATTE)
+  enable_language(Fortran)
+  include(CheckFortranCompilerFlag)
+  check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
+endif()
+
+if(ENABLE_KOKKOS OR ENABLE_MSCG)
+  # starting with CMake 3.1 this is all you have to do to enforce C++11
+  set(CMAKE_CXX_STANDARD 11) # C++11...
+  set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required...
+  set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11
+endif()
+
+if(ENABLE_USER-OMP OR ENABLE_KOKKOS OR ENABLE_USER-INTEL)
+  find_package(OpenMP REQUIRED)
+  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+endif()
+
+if(ENABLE_KSPACE)
+  set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package")
+  set_property(CACHE FFT PROPERTY STRINGS KISSFFT FFTW3 MKL FFTW2)
+  if(NOT FFT STREQUAL "KISSFFT")
+    find_package(${FFT} REQUIRED)
+    add_definitions(-DFFT_${FFT})
+    include_directories(${${FFT}_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
+  endif()
+  set(PACK_OPTIMIZATION "PACK_ARRAY" CACHE STRING "Optimization for FFT")
+  set_property(CACHE PACK_OPTIMIZATION PROPERTY STRINGS PACK_ARRAY PACK_POINTER PACK_MEMCPY)
+  if(NOT PACK_OPTIMIZATION STREQUAL "PACK_ARRAY")
+    add_definitions(-D${PACK_OPTIMIZATION})
+  endif()
+endif()
+
+if(ENABLE_MISC)
+  option(LAMMPS_XDR "include XDR compatibility files for doing particle dumps in XTC format" OFF)
+  if(LAMMPS_XDR)
+    add_definitions(-DLAMMPS_XDR) # for liblammps
+  endif()
+endif()
+
+if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP OR ENABLE_LATTE)
+  find_package(LAPACK)
+  if(NOT LAPACK_FOUND)
+    enable_language(Fortran)
+    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)
+    add_library(linalg STATIC ${LAPACK_SOURCES})
+    include(CheckFortranCompilerFlag)
+    check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
+    if(FC_HAS_NO_SECOND_UNDERSCORE)
+      target_compile_options(linalg PRIVATE -fno-second-underscore)
+    endif()
+    set(LAPACK_LIBRARIES linalg)
+  endif()
+endif()
+
+if(ENABLE_PYTHON)
+  find_package(PythonInterp REQUIRED)
+  find_package(PythonLibs REQUIRED)
+  add_definitions(-DLMP_PYTHON)
+  include_directories(${PYTHON_INCLUDE_DIR})
+  list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
+  if(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 ${PYTHON_INSTDIR})
+  if(NOT BUILD_SHARED_LIBS)
+    message(FATAL_ERROR "Python package need lammps to be build shared, use -DBUILD_SHARED_LIBS=ON")
+  endif()
+endif()
+
+find_package(JPEG)
+if(JPEG_FOUND)
+  add_definitions(-DLAMMPS_JPEG)
+  include_directories(${JPEG_INCLUDE_DIR})
+  list(APPEND LAMMPS_LINK_LIBS ${JPEG_LIBRARIES})
+endif()
+
+find_package(PNG)
+find_package(ZLIB)
+if(PNG_FOUND AND ZLIB_FOUND)
+  include_directories(${PNG_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${PNG_LIBRARIES} ${ZLIB_LIBRARIES})
+  add_definitions(-DLAMMPS_PNG)
+endif()
+
+find_program(GZIP_EXECUTABLE gzip)
+find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
+if(GZIP_FOUND)
+  add_definitions(-DLAMMPS_GZIP)
+endif()
+
+find_program(FFMPEG_EXECUTABLE ffmpeg)
+find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
+if(FFMPEG_FOUND)
+  add_definitions(-DLAMMPS_FFMPEG)
+endif()
+
+if(ENABLE_VORONOI)
+  find_package(VORO REQUIRED) #some distros
+  include_directories(${VORO_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
+endif()
+
+if(ENABLE_LATTE)
+  find_package(LATTE QUIET)
+  if(NOT LATTE_FOUND)
+    message(STATUS "LATTE not found - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(latte_build
+      URL https://github.com/lanl/LATTE/archive/v1.0.1.tar.gz
+      URL_MD5 5137e28cb1a64444bd571c98c98a6eee
+      SOURCE_SUBDIR cmake
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}
+      )
+    ExternalProject_get_property(latte_build INSTALL_DIR)
+    set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
+    list(APPEND LAMMPS_DEPS latte_build)
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-MOLFILE)
+  add_library(molfile INTERFACE)
+  target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
+  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+  list(APPEND LAMMPS_LINK_LIBS molfile)
+endif()
+
+if(ENABLE_USER-NETCDF)
+  find_package(NetCDF REQUIRED)
+  include_directories(NETCDF_INCLUDE_DIR)
+  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})
+  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
+endif()
+
+if(ENABLE_USER-SMD)
+  find_package(Eigen3 REQUIRED)
+  include_directories(${EIGEN3_INCLUDE_DIR})
+endif()
+
+if(ENABLE_USER-QUIP)
+  find_package(QUIP REQUIRED)
+  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-QMMM)
+  find_package(QE REQUIRED)
+  include_directories(${QE_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-VTK)
+  find_package(VTK REQUIRED NO_MODULE)
+  include(${VTK_USE_FILE})
+  add_definitions(-DLAMMPS_VTK)
+  list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
+endif()
+
+if(ENABLE_KIM)
+  find_package(KIM REQUIRED)
+  list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
+  include_directories(${KIM_INCLUDE_DIRS})
+endif()
+
+if(ENABLE_MSCG)
+  find_package(GSL REQUIRED)
+  set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mscg)
+  set(MSCG_TARBALL ${LAMMPS_LIB_MSCG_BIN_DIR}/MS-CG-master.zip)
+  set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_MSCG_BIN_DIR}/MSCG-release-master/src)
+  if(NOT EXISTS ${LAMMPS_LIB_MSCG_BIN_DIR})
+    if(NOT EXISTS ${MSCG_TARBALL})
+      message(STATUS "Downloading ${MSCG_TARBALL}")
+      file(DOWNLOAD
+        https://github.com/uchicago-voth/MSCG-release/archive/master.zip
+        ${MSCG_TARBALL} SHOW_PROGRESS) #EXPECTED_MD5 cannot be due due to master
+    endif()
+    message(STATUS "Unpacking ${MSCG_TARBALL}")
+    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xvf ${MSCG_TARBALL}
+      WORKING_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/mscg)
+  endif()
+  file(GLOB MSCG_SOURCES ${LAMMPS_LIB_MSCG_BIN_DIR}/*.cpp)
+  add_library(mscg STATIC ${MSCG_SOURCES})
+  list(APPEND LAMMPS_LINK_LIBS mscg)
+  target_compile_options(mscg PRIVATE -DDIMENSION=3 -D_exclude_gromacs=1)
+  target_include_directories(mscg PUBLIC ${LAMMPS_LIB_MSCG_BIN_DIR})
+  target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
+endif()
+
+########################################################################
+# Basic system tests (standard libraries, headers, functions, types)   #
+########################################################################
+include(CheckIncludeFile)
+foreach(HEADER math.h)
+  check_include_file(${HEADER} FOUND_${HEADER})
+  if(NOT FOUND_${HEADER})
+    message(FATAL_ERROR "Could not find needed header - ${HEADER}")
+  endif(NOT FOUND_${HEADER})
+endforeach(HEADER)
+
+set(MATH_LIBRARIES "m" CACHE STRING "math library")
+mark_as_advanced( MATH_LIBRARIES )
+include(CheckLibraryExists)
+foreach(FUNC sin cos)
+  check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
+  if(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
+    message(FATAL_ERROR "Could not find needed math function - ${FUNC}")
+  endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
+endforeach(FUNC)
+list(APPEND LAMMPS_LINK_LIBS ${MATH_LIBRARIES})
+
+######################################
+# Generate Basic Style files
+######################################
+include(StyleHeaderUtils)
+RegisterStyles(${LAMMPS_SOURCE_DIR})
+
+##############################################
+# add sources of enabled packages
+############################################
+foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES})
+  set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
+
+  # ignore PKG files which were manually installed in src folder
+  # headers are ignored during RegisterStyles
+  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
+  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
+
+  foreach(PKG_FILE in ${${PKG}_SOURCES})
+      get_filename_component(FNAME ${PKG_FILE} NAME)
+      list(REMOVE_ITEM LIB_SOURCES ${LAMMPS_SOURCE_DIR}/${FNAME})
+  endforeach()
+
+  foreach(PKG_FILE in ${${PKG}_HEADERS})
+      get_filename_component(FNAME ${PKG_FILE} NAME)
+      DetectAndRemovePackageHeader(${LAMMPS_SOURCE_DIR}/${FNAME})
+  endforeach()
+
+  if(ENABLE_${PKG})
+    # detects styles in package and adds them to global list
+    RegisterStyles(${${PKG}_SOURCES_DIR})
+
+    list(APPEND LIB_SOURCES ${${PKG}_SOURCES})
+    include_directories(${${PKG}_SOURCES_DIR})
+  endif()
+endforeach()
+
+##############################################
+# add lib sources of (simple) enabled packages
+############################################
+foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
+  USER-QMMM)
+  if(ENABLE_${SIMPLE_LIB})
+    string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
+    string(TOLOWER "${PKG_LIB}" PKG_LIB)
+    file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F
+      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp)
+    add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
+    list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
+    if(PKG_LIB STREQUAL awpmd)
+      target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
+    elseif(PKG_LIB STREQUAL h5md)
+      target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
+    else()
+      target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
+    endif()
+  endif()
+endforeach()
+
+if(ENABLE_USER-AWPMD)
+  target_link_libraries(awpmd ${LAPACK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-ATC)
+  target_link_libraries(atc ${LAPACK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-H5MD)
+  find_package(HDF5 REQUIRED)
+  target_link_libraries(h5md ${HDF5_LIBRARIES})
+  target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
+endif()
+
+if(ENABLE_MEAM AND FC_HAS_NO_SECOND_UNDERSCORE)
+  foreach(FSRC ${meam_SOURCES})
+    string(REGEX REPLACE "^.*\\." "" FEXT "${FSRC}")
+    list(FIND CMAKE_Fortran_SOURCE_FILE_EXTENSIONS "${FEXT}" FINDEX)
+    if(FINDEX GREATER -1)
+      set_property(SOURCE ${FSRC} APPEND PROPERTY COMPILE_FLAGS "-fno-second-underscore")
+    endif()
+  endforeach()
+endif()
+
+if(ENABLE_REAX AND FC_HAS_NO_SECOND_UNDERSCORE)
+  target_compile_options(reax PRIVATE -fno-second-underscore)
+endif()
+
+
+######################################################################
+# packages which selectively include variants based on enabled styles
+# e.g. accelerator packages
+######################################################################
+if(ENABLE_USER-OMP)
+    set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
+    set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
+                         ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp)
+    set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
+
+    # detects styles which have USER-OMP version
+    RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
+
+    get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
+
+    list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
+    include_directories(${USER-OMP_SOURCES_DIR})
+endif()
+
+if(ENABLE_KOKKOS)
+  set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
+  set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
+  add_definitions(-DLMP_KOKKOS)
+  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+
+  set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
+                          ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
+                          ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
+                          ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+  include_directories(${Kokkos_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS kokkos)
+
+  set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
+  set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
+  set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+
+  # detects styles which have KOKKOS version
+  RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
+
+  get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+
+  list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})
+  include_directories(${KOKKOS_PKG_SOURCES_DIR})
+endif()
+
+if(ENABLE_OPT)
+    set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
+    set(OPT_SOURCES)
+    set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
+
+    # detects styles which have OPT version
+    RegisterStylesExt(${OPT_SOURCES_DIR} opt OPT_SOURCES)
+
+    get_property(OPT_SOURCES GLOBAL PROPERTY OPT_SOURCES)
+
+    list(APPEND LIB_SOURCES ${OPT_SOURCES})
+    include_directories(${OPT_SOURCES_DIR})
+endif()
+
+if(ENABLE_USER-INTEL)
+    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
+                           ${USER-INTEL_SOURCES_DIR}/intel_intrinsics.h)
+
+    set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
+
+    # 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})
+endif()
+
+if(ENABLE_GPU)
+    set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
+    set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
+                    ${GPU_SOURCES_DIR}/fix_gpu.h
+                    ${GPU_SOURCES_DIR}/fix_gpu.cpp)
+
+    set(GPU_API "OpenCL" CACHE STRING "API used by GPU package")
+    set_property(CACHE GPU_API PROPERTY STRINGS OpenCL CUDA)
+
+    set(GPU_PREC "SINGLE_DOUBLE" CACHE STRING "LAMMPS GPU precision size")
+    set_property(CACHE GPU_PREC PROPERTY STRINGS SINGLE_DOUBLE SINGLE_SINGLE DOUBLE_DOUBLE)
+
+    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
+    file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+    if(GPU_API STREQUAL "CUDA")
+      find_package(CUDA REQUIRED)
+      find_program(BIN2C bin2c)
+      if(NOT BIN2C)
+        message(FATAL_ERROR "Couldn't find bin2c, use -DBIN2C helping cmake to find it.")
+      endif()
+      option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+
+      set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture")
+      set_property(CACHE GPU_ARCH PROPERTY STRINGS sm_10 sm_20 sm_30 sm_60)
+
+      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu)
+      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
+
+      cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+      if(CUDPP_OPT)
+        cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+        file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp)
+        file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu)
+      endif()
+
+      cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
+                   -DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC})
+
+      cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>
+                   -DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC})
+
+      foreach(CU_OBJ ${GPU_GEN_OBJS})
+        get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
+        string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
+        add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+          COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+          DEPENDS ${CU_OBJ}
+          COMMENT "Generating ${CU_NAME}_cubin.h")
+        list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
+      endforeach()
+      set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
+
+
+      add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
+      target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+      target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
+      if(CUDPP_OPT)
+        target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+        target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
+      endif()
+
+      list(APPEND LAMMPS_LINK_LIBS gpu)
+
+      add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+      target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
+      target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+      target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
+
+
+    elseif(GPU_API STREQUAL "OpenCL")
+      find_package(OpenCL REQUIRED)
+      set(OCL_TUNE "GENERIC" CACHE STRING "OpenCL Device Tuning")
+      set_property(CACHE OCL_TUNE PROPERTY STRINGS INTEL FERMI KEPLER CYPRESS GENERIC)
+
+      include(OpenCLUtils)
+      set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
+
+      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu)
+      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
+
+      foreach(GPU_KERNEL ${GPU_LIB_CU})
+          get_filename_component(basename ${GPU_KERNEL} NAME_WE)
+          string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
+          GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
+          list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
+      endforeach()
+
+      GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
+      GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
+      list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h)
+
+      add_library(gpu STATIC ${GPU_LIB_SOURCES})
+      target_link_libraries(gpu ${OpenCL_LIBRARIES})
+      target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
+      target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
+
+      list(APPEND LAMMPS_LINK_LIBS gpu)
+
+      add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+      target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
+      target_link_libraries(ocl_get_devices PRIVATE ${OpenCL_LIBRARIES})
+      target_include_directories(ocl_get_devices PRIVATE ${OpenCL_INCLUDE_DIRS})
+    endif()
+
+    # GPU package
+    FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
+
+    set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
+
+    # detects styles which have GPU version
+    RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
+
+    get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
+
+    list(APPEND LIB_SOURCES ${GPU_SOURCES})
+    include_directories(${GPU_SOURCES_DIR})
+endif()
+
+######################################################
+# Generate style headers based on global list of
+# styles registered during package selection
+######################################################
+set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
+
+GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})
+
+include_directories(${LAMMPS_SOURCE_DIR})
+include_directories(${LAMMPS_STYLE_HEADERS_DIR})
+
+###########################################
+# Actually add executable and lib to build
+############################################
+add_library(lammps ${LIB_SOURCES})
+target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
+if(LAMMPS_DEPS)
+  add_dependencies(lammps ${LAMMPS_DEPS})
+endif()
+set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
+if(BUILD_SHARED_LIBS)
+  set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
+  install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+  install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+  configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
+  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+endif()
+
+add_executable(lmp ${LMP_SOURCES})
+target_link_libraries(lmp lammps)
+set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
+install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
+if(ENABLE_TESTING)
+  add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
+endif()
+
+##################################
+# Print package summary
+##################################
+foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
+  if(ENABLE_${PKG})
+    message(STATUS "Building package: ${PKG}")
+  endif()
+endforeach()
+
+string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
+message(STATUS "<<< Build configuration >>>
+   Build type       ${CMAKE_BUILD_TYPE}
+   Install path     ${CMAKE_INSTALL_PREFIX}
+   Compilers and Flags:
+   C++ Compiler     ${CMAKE_CXX_COMPILER}
+       Type         ${CMAKE_CXX_COMPILER_ID}
+   C++ Flags        ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
+if(LANGUAGES MATCHES ".*Fortran.*")
+  message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER} 
+           Type     ${CMAKE_Fortran_COMPILER_ID}
+   Fortran Flags    ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
+endif()
+message(STATUS "Linker flags:
+   Executable      ${CMAKE_EXE_LINKER_FLAGS}")
+if(BUILD_SHARED_LIBS)
+  message(STATUS "Shared libries  ${CMAKE_SHARED_LINKER_FLAGS}")
+else()
+  message(STATUS "Static libries  ${CMAKE_STATIC_LINKER_FLAGS}")
+endif()
+message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
+

cmake/Modules/FindFFTW2.cmake

@@ -0,0 +1,22 @@
+# - Find fftw2
+# Find the native FFTW2 headers and libraries.
+#
+#  FFTW2_INCLUDE_DIRS - where to find fftw2.h, etc.
+#  FFTW2_LIBRARIES    - List of libraries when using fftw2.
+#  FFTW2_FOUND        - True if fftw2 found.
+#
+
+find_path(FFTW2_INCLUDE_DIR fftw.h)
+
+find_library(FFTW2_LIBRARY NAMES fftw)
+
+set(FFTW2_LIBRARIES ${FFTW2_LIBRARY})
+set(FFTW2_INCLUDE_DIRS ${FFTW2_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set FFTW2_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(FFTW2 DEFAULT_MSG FFTW2_LIBRARY FFTW2_INCLUDE_DIR)
+
+mark_as_advanced(FFTW2_INCLUDE_DIR FFTW2_LIBRARY )

cmake/Modules/FindFFTW3.cmake

@@ -0,0 +1,25 @@
+# - Find fftw3
+# Find the native FFTW3 headers and libraries.
+#
+#  FFTW3_INCLUDE_DIRS - where to find fftw3.h, etc.
+#  FFTW3_LIBRARIES    - List of libraries when using fftw3.
+#  FFTW3_FOUND        - True if fftw3 found.
+#
+
+find_package(PkgConfig)
+
+pkg_check_modules(PC_FFTW3 fftw3)
+find_path(FFTW3_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3_INCLUDE_DIRS})
+
+find_library(FFTW3_LIBRARY NAMES fftw3 HINTS ${PC_FFTW3_LIBRARY_DIRS})
+
+set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
+set(FFTW3_INCLUDE_DIRS ${FFTW3_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set FFTW3_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(FFTW3 DEFAULT_MSG FFTW3_LIBRARY FFTW3_INCLUDE_DIR)
+
+mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY )

cmake/Modules/FindKIM.cmake

@@ -0,0 +1,22 @@
+# - 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/FindLATTE.cmake

@@ -0,0 +1,18 @@
+# - Find latte
+# Find the native LATTE libraries.
+#
+#  LATTE_LIBRARIES    - List of libraries when using latte.
+#  LATTE_FOUND        - True if latte found.
+#
+
+find_library(LATTE_LIBRARY NAMES latte)
+
+set(LATTE_LIBRARIES ${LATTE_LIBRARY})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set LATTE_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(LATTE DEFAULT_MSG LATTE_LIBRARY)
+
+mark_as_advanced(LATTE_LIBRARY)

cmake/Modules/FindMKL.cmake

@@ -0,0 +1,22 @@
+# - Find mkl
+# Find the native MKL headers and libraries.
+#
+#  MKL_INCLUDE_DIRS - where to find mkl.h, etc.
+#  MKL_LIBRARIES    - List of libraries when using mkl.
+#  MKL_FOUND        - True if mkl found.
+#
+
+find_path(MKL_INCLUDE_DIR mkl_dfti.h HINTS $ENV{MKLROOT}/include)
+
+find_library(MKL_LIBRARY NAMES mkl_rt HINTS $ENV{MKLROOT}/lib $ENV{MKLROOT}/lib/intel64)
+
+set(MKL_LIBRARIES ${MKL_LIBRARY})
+set(MKL_INCLUDE_DIRS ${MKL_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set MKL_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(MKL DEFAULT_MSG MKL_LIBRARY MKL_INCLUDE_DIR)
+
+mark_as_advanced(MKL_INCLUDE_DIR MKL_LIBRARY )

cmake/Modules/FindNetCDF.cmake

@@ -0,0 +1,118 @@
+# - Find NetCDF
+# Find the native NetCDF includes and library
+#
+#  NETCDF_INCLUDE_DIR  - user modifiable choice of where netcdf headers are
+#  NETCDF_LIBRARY      - user modifiable choice of where netcdf libraries are
+#
+# Your package can require certain interfaces to be FOUND by setting these
+#
+#  NETCDF_CXX         - require the C++ interface and link the C++ library
+#  NETCDF_F77         - require the F77 interface and link the fortran library
+#  NETCDF_F90         - require the F90 interface and link the fortran library
+#
+# Or equivalently by calling FindNetCDF with a COMPONENTS argument containing one or
+# more of "CXX;F77;F90".
+#
+# When interfaces are requested the user has access to interface specific hints:
+#
+#  NETCDF_${LANG}_INCLUDE_DIR - where to search for interface header files
+#  NETCDF_${LANG}_LIBRARY     - where to search for interface libraries
+#
+# This module returns these variables for the rest of the project to use.
+#
+#  NETCDF_FOUND          - True if NetCDF found including required interfaces (see below)
+#  NETCDF_LIBRARIES      - All netcdf related libraries.
+#  NETCDF_INCLUDE_DIRS   - All directories to include.
+#  NETCDF_HAS_INTERFACES - Whether requested interfaces were found or not.
+#  NETCDF_${LANG}_INCLUDE_DIRS/NETCDF_${LANG}_LIBRARIES - C/C++/F70/F90 only interface
+#
+# Normal usage would be:
+#  set (NETCDF_F90 "YES")
+#  find_package (NetCDF REQUIRED)
+#  target_link_libraries (uses_everthing ${NETCDF_LIBRARIES})
+#  target_link_libraries (only_uses_f90 ${NETCDF_F90_LIBRARIES})
+
+#search starting from user editable cache var
+if (NETCDF_INCLUDE_DIR AND NETCDF_LIBRARY)
+  # Already in cache, be silent
+  set (NETCDF_FIND_QUIETLY TRUE)
+endif ()
+
+set(USE_DEFAULT_PATHS "NO_DEFAULT_PATH")
+if(NETCDF_USE_DEFAULT_PATHS)
+  set(USE_DEFAULT_PATHS "")
+endif()
+
+find_path (NETCDF_INCLUDE_DIR netcdf.h
+  HINTS "${NETCDF_DIR}/include")
+mark_as_advanced (NETCDF_INCLUDE_DIR)
+set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
+
+find_library (NETCDF_LIBRARY NAMES netcdf
+  HINTS "${NETCDF_DIR}/lib")
+mark_as_advanced (NETCDF_LIBRARY)
+
+set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
+
+#start finding requested language components
+set (NetCDF_libs "")
+set (NetCDF_includes "${NETCDF_INCLUDE_DIR}")
+
+get_filename_component (NetCDF_lib_dirs "${NETCDF_LIBRARY}" PATH)
+set (NETCDF_HAS_INTERFACES "YES") # will be set to NO if we're missing any interfaces
+
+macro (NetCDF_check_interface lang header libs)
+  if (NETCDF_${lang})
+    #search starting from user modifiable cache var
+    find_path (NETCDF_${lang}_INCLUDE_DIR NAMES ${header}
+      HINTS "${NETCDF_INCLUDE_DIR}"
+      HINTS "${NETCDF_${lang}_ROOT}/include"
+      ${USE_DEFAULT_PATHS})
+
+    find_library (NETCDF_${lang}_LIBRARY NAMES ${libs}
+      HINTS "${NetCDF_lib_dirs}"
+      HINTS "${NETCDF_${lang}_ROOT}/lib"
+      ${USE_DEFAULT_PATHS})
+
+    mark_as_advanced (NETCDF_${lang}_INCLUDE_DIR NETCDF_${lang}_LIBRARY)
+
+    #export to internal varS that rest of project can use directly
+    set (NETCDF_${lang}_LIBRARIES ${NETCDF_${lang}_LIBRARY})
+    set (NETCDF_${lang}_INCLUDE_DIRS ${NETCDF_${lang}_INCLUDE_DIR})
+
+    if (NETCDF_${lang}_INCLUDE_DIR AND NETCDF_${lang}_LIBRARY)
+      list (APPEND NetCDF_libs ${NETCDF_${lang}_LIBRARY})
+      list (APPEND NetCDF_includes ${NETCDF_${lang}_INCLUDE_DIR})
+    else ()
+      set (NETCDF_HAS_INTERFACES "NO")
+      message (STATUS "Failed to find NetCDF interface for ${lang}")
+    endif ()
+  endif ()
+endmacro ()
+
+list (FIND NetCDF_FIND_COMPONENTS "CXX" _nextcomp)
+if (_nextcomp GREATER -1)
+  set (NETCDF_CXX 1)
+endif ()
+list (FIND NetCDF_FIND_COMPONENTS "F77" _nextcomp)
+if (_nextcomp GREATER -1)
+  set (NETCDF_F77 1)
+endif ()
+list (FIND NetCDF_FIND_COMPONENTS "F90" _nextcomp)
+if (_nextcomp GREATER -1)
+  set (NETCDF_F90 1)
+endif ()
+NetCDF_check_interface (CXX netcdfcpp.h netcdf_c++)
+NetCDF_check_interface (F77 netcdf.inc  netcdff)
+NetCDF_check_interface (F90 netcdf.mod  netcdff)
+
+#export accumulated results to internal varS that rest of project can depend on
+list (APPEND NetCDF_libs "${NETCDF_C_LIBRARIES}")
+set (NETCDF_LIBRARIES ${NetCDF_libs})
+set (NETCDF_INCLUDE_DIRS ${NetCDF_includes})
+
+# handle the QUIETLY and REQUIRED arguments and set NETCDF_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (NetCDF
+  DEFAULT_MSG NETCDF_LIBRARIES NETCDF_INCLUDE_DIRS NETCDF_HAS_INTERFACES)

cmake/Modules/FindQE.cmake

@@ -0,0 +1,29 @@
+# - Find quantum-espresso
+# Find the native QE headers and libraries.
+#
+#  QE_INCLUDE_DIRS - where to find quantum-espresso.h, etc.
+#  QE_LIBRARIES    - List of libraries when using quantum-espresso.
+#  QE_FOUND        - True if quantum-espresso found.
+#
+
+find_path(QE_INCLUDE_DIR libqecouple.h PATH_SUFFIXES COUPLE/include)
+
+find_library(QECOUPLE_LIBRARY NAMES qecouple)
+find_library(PW_LIBRARY NAMES pw)
+find_library(QEMOD_LIBRARY NAMES qemod)
+find_library(QEFFT_LIBRARY NAMES qefft)
+find_library(QELA_LIBRARY NAMES qela)
+find_library(CLIB_LIBRARY NAMES clib)
+find_library(IOTK_LIBRARY NAMES iotk)
+
+
+set(QE_LIBRARIES ${QECOUPLE_LIBRARY} ${PW_LIBRARY} ${QEMOD_LIBRARY} ${QEFFT_LIBRARY} ${QELA_LIBRARY} ${CLIB_LIBRARY} ${IOTK_LIBRARY})
+set(QE_INCLUDE_DIRS ${QE_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set QE_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(QE DEFAULT_MSG QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY QE_INCLUDE_DIR)
+
+mark_as_advanced(QE_INCLUDE_DIR QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY)

cmake/Modules/FindQUIP.cmake

@@ -0,0 +1,18 @@
+# - Find quip
+# Find the native QUIP libraries.
+#
+#  QUIP_LIBRARIES    - List of libraries when using fftw3.
+#  QUIP_FOUND        - True if fftw3 found.
+#
+
+find_library(QUIP_LIBRARY NAMES quip)
+
+set(QUIP_LIBRARIES ${QUIP_LIBRARY})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set QUIP_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(QUIP DEFAULT_MSG QUIP_LIBRARY)
+
+mark_as_advanced(QUIP_LIBRARY)

cmake/Modules/FindVORO.cmake

@@ -0,0 +1,22 @@
+# - Find voro++
+# Find the native VORO headers and libraries.
+#
+#  VORO_INCLUDE_DIRS - where to find voro++.hh, etc.
+#  VORO_LIBRARIES    - List of libraries when using voro++.
+#  VORO_FOUND        - True if voro++ found.
+#
+
+find_path(VORO_INCLUDE_DIR voro++.hh PATH_SUFFIXES voro++)
+
+find_library(VORO_LIBRARY NAMES voro++)
+
+set(VORO_LIBRARIES ${VORO_LIBRARY})
+set(VORO_INCLUDE_DIRS ${VORO_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set VORO_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(VORO DEFAULT_MSG VORO_LIBRARY VORO_INCLUDE_DIR)
+
+mark_as_advanced(VORO_INCLUDE_DIR VORO_LIBRARY )

cmake/Modules/OpenCLUtils.cmake

@@ -0,0 +1,18 @@
+function(GenerateOpenCLHeader varname outfile files)
+    message("Creating ${outfile}...")
+    file(WRITE ${outfile} "const char * ${varname} = \n")
+    math(EXPR ARG_END   "${ARGC}-1")
+
+    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 "\\\\" "\\\\\\\\" content "${content}")
+        string(REGEX REPLACE "\"" "\\\\\"" content "${content}")
+        string(REGEX REPLACE "([^\n]+)\n" "\"\\1\\\\n\"\n" content "${content}")
+        string(REGEX REPLACE "\n+" "\n" content "${content}")
+        file(APPEND ${outfile} "${content}")
+    endforeach()
+
+    file(APPEND ${outfile} ";\n")
+endfunction(GenerateOpenCLHeader)

cmake/Modules/StyleHeaderUtils.cmake

@@ -0,0 +1,161 @@
+function(FindStyleHeaders path style_class file_pattern headers)
+    file(GLOB files "${path}/${file_pattern}*.h")
+    get_property(hlist GLOBAL PROPERTY ${headers})
+
+    foreach(file_name ${files})
+        file(STRINGS ${file_name} is_style LIMIT_COUNT 1 REGEX ${style_class})
+        if(is_style)
+            list(APPEND hlist ${file_name})
+        endif()
+    endforeach()
+    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
+endfunction(FindStyleHeaders)
+
+function(FindStyleHeadersExt path style_class extension headers sources)
+    get_property(hlist GLOBAL PROPERTY ${headers})
+    get_property(slist GLOBAL PROPERTY ${sources})
+    set(ext_list)
+    get_filename_component(abs_path "${path}" ABSOLUTE)
+
+    foreach(file_name ${hlist})
+        get_filename_component(basename ${file_name} NAME_WE)
+        set(ext_file_name "${abs_path}/${basename}_${extension}.h")
+        if(EXISTS "${ext_file_name}")
+            file(STRINGS ${ext_file_name} is_style LIMIT_COUNT 1 REGEX ${style_class})
+            if(is_style)
+                list(APPEND ext_list ${ext_file_name})
+
+                set(source_file_name "${abs_path}/${basename}_${extension}.cpp")
+                if(EXISTS "${source_file_name}")
+                    list(APPEND slist ${source_file_name})
+                endif()
+            endif()
+        endif()
+    endforeach()
+
+    list(APPEND hlist ${ext_list})
+    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
+    set_property(GLOBAL PROPERTY ${sources} "${slist}")
+endfunction(FindStyleHeadersExt)
+
+function(CreateStyleHeader path filename)
+    math(EXPR N "${ARGC}-2")
+
+    set(temp "")
+    if(N GREATER 0)
+        math(EXPR ARG_END   "${ARGC}-1")
+ 
+        foreach(IDX RANGE 2 ${ARG_END})
+            list(GET ARGV ${IDX} FNAME)
+            get_filename_component(FNAME ${FNAME} NAME)
+            set(temp "${temp}#include \"${FNAME}\"\n")
+        endforeach()
+    endif()
+    message(STATUS "Generating ${filename}...")
+    file(WRITE "${path}/${filename}.tmp" "${temp}" )
+    execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
+endfunction(CreateStyleHeader)
+
+function(GenerateStyleHeader path property style)
+    get_property(files GLOBAL PROPERTY ${property})
+    #message("${property} = ${files}")
+    CreateStyleHeader("${path}" "style_${style}.h" ${files})
+endfunction(GenerateStyleHeader)
+
+function(RegisterStyles search_path)
+    FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
+    FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
+    FindStyleHeaders(${search_path} BODY_CLASS      body_      BODY      ) # body      ) # atom_vec_body
+    FindStyleHeaders(${search_path} BOND_CLASS      bond_      BOND      ) # bond      ) # force
+    FindStyleHeaders(${search_path} COMMAND_CLASS   ""         COMMAND   ) # command   ) # input
+    FindStyleHeaders(${search_path} COMPUTE_CLASS   compute_   COMPUTE   ) # compute   ) # modify
+    FindStyleHeaders(${search_path} DIHEDRAL_CLASS  dihedral_  DIHEDRAL  ) # dihedral  ) # force
+    FindStyleHeaders(${search_path} DUMP_CLASS      dump_      DUMP      ) # dump      ) # output    write_dump
+    FindStyleHeaders(${search_path} FIX_CLASS       fix_       FIX       ) # fix       ) # modify
+    FindStyleHeaders(${search_path} IMPROPER_CLASS  improper_  IMPROPER  ) # improper  ) # force
+    FindStyleHeaders(${search_path} INTEGRATE_CLASS ""         INTEGRATE ) # integrate ) # update
+    FindStyleHeaders(${search_path} KSPACE_CLASS    ""         KSPACE    ) # kspace    ) # force
+    FindStyleHeaders(${search_path} MINIMIZE_CLASS  min_       MINIMIZE  ) # minimize  ) # update
+    FindStyleHeaders(${search_path} NBIN_CLASS      nbin_      NBIN      ) # nbin      ) # neighbor
+    FindStyleHeaders(${search_path} NPAIR_CLASS     npair_     NPAIR     ) # npair     ) # neighbor
+    FindStyleHeaders(${search_path} NSTENCIL_CLASS  nstencil_  NSTENCIL  ) # nstencil  ) # neighbor
+    FindStyleHeaders(${search_path} NTOPO_CLASS     ntopo_     NTOPO     ) # ntopo     ) # neighbor
+    FindStyleHeaders(${search_path} PAIR_CLASS      pair_      PAIR      ) # pair      ) # force
+    FindStyleHeaders(${search_path} READER_CLASS    reader_    READER    ) # reader    ) # read_dump
+    FindStyleHeaders(${search_path} REGION_CLASS    region_    REGION    ) # region    ) # domain
+endfunction(RegisterStyles)
+
+function(RemovePackageHeader headers pkg_header)
+    get_property(hlist GLOBAL PROPERTY ${headers})
+    list(REMOVE_ITEM hlist ${pkg_header})
+    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
+endfunction(RemovePackageHeader)
+
+function(DetectAndRemovePackageHeader fname)
+    RemovePackageHeader(ANGLE     ${fname})
+    RemovePackageHeader(ATOM_VEC  ${fname})
+    RemovePackageHeader(BODY      ${fname})
+    RemovePackageHeader(BOND      ${fname})
+    RemovePackageHeader(COMMAND   ${fname})
+    RemovePackageHeader(COMPUTE   ${fname})
+    RemovePackageHeader(DIHEDRAL  ${fname})
+    RemovePackageHeader(DUMP      ${fname})
+    RemovePackageHeader(FIX       ${fname})
+    RemovePackageHeader(IMPROPER  ${fname})
+    RemovePackageHeader(INTEGRATE ${fname})
+    RemovePackageHeader(KSPACE    ${fname})
+    RemovePackageHeader(MINIMIZE  ${fname})
+    RemovePackageHeader(NBIN      ${fname})
+    RemovePackageHeader(NPAIR     ${fname})
+    RemovePackageHeader(NSTENCIL  ${fname})
+    RemovePackageHeader(NTOPO     ${fname})
+    RemovePackageHeader(PAIR      ${fname})
+    RemovePackageHeader(READER    ${fname})
+    RemovePackageHeader(REGION    ${fname})
+endfunction(DetectAndRemovePackageHeader)
+
+function(RegisterStylesExt search_path extension sources)
+    FindStyleHeadersExt(${search_path} ANGLE_CLASS     ${extension}  ANGLE     ${sources})
+    FindStyleHeadersExt(${search_path} ATOM_CLASS      ${extension}  ATOM_VEC  ${sources})
+    FindStyleHeadersExt(${search_path} BODY_CLASS      ${extension}  BODY      ${sources})
+    FindStyleHeadersExt(${search_path} BOND_CLASS      ${extension}  BOND      ${sources})
+    FindStyleHeadersExt(${search_path} COMMAND_CLASS   ${extension}  COMMAND   ${sources})
+    FindStyleHeadersExt(${search_path} COMPUTE_CLASS   ${extension}  COMPUTE   ${sources})
+    FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS  ${extension}  DIHEDRAL  ${sources})
+    FindStyleHeadersExt(${search_path} DUMP_CLASS      ${extension}  DUMP      ${sources})
+    FindStyleHeadersExt(${search_path} FIX_CLASS       ${extension}  FIX       ${sources})
+    FindStyleHeadersExt(${search_path} IMPROPER_CLASS  ${extension}  IMPROPER  ${sources})
+    FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension}  INTEGRATE ${sources})
+    FindStyleHeadersExt(${search_path} KSPACE_CLASS    ${extension}  KSPACE    ${sources})
+    FindStyleHeadersExt(${search_path} MINIMIZE_CLASS  ${extension}  MINIMIZE  ${sources})
+    FindStyleHeadersExt(${search_path} NBIN_CLASS      ${extension}  NBIN      ${sources})
+    FindStyleHeadersExt(${search_path} NPAIR_CLASS     ${extension}  NPAIR     ${sources})
+    FindStyleHeadersExt(${search_path} NSTENCIL_CLASS  ${extension}  NSTENCIL  ${sources})
+    FindStyleHeadersExt(${search_path} NTOPO_CLASS     ${extension}  NTOPO     ${sources})
+    FindStyleHeadersExt(${search_path} PAIR_CLASS      ${extension}  PAIR      ${sources})
+    FindStyleHeadersExt(${search_path} READER_CLASS    ${extension}  READER    ${sources})
+    FindStyleHeadersExt(${search_path} REGION_CLASS    ${extension}  REGION    ${sources})
+endfunction(RegisterStylesExt)
+
+function(GenerateStyleHeaders output_path)
+    GenerateStyleHeader(${output_path} ANGLE      angle     ) # force
+    GenerateStyleHeader(${output_path} ATOM_VEC   atom      ) # atom      atom_vec_hybrid
+    GenerateStyleHeader(${output_path} BODY       body      ) # atom_vec_body
+    GenerateStyleHeader(${output_path} BOND       bond      ) # force
+    GenerateStyleHeader(${output_path} COMMAND    command   ) # input
+    GenerateStyleHeader(${output_path} COMPUTE    compute   ) # modify
+    GenerateStyleHeader(${output_path} DIHEDRAL   dihedral  ) # force
+    GenerateStyleHeader(${output_path} DUMP       dump      ) # output    write_dump
+    GenerateStyleHeader(${output_path} FIX        fix       ) # modify
+    GenerateStyleHeader(${output_path} IMPROPER   improper  ) # force
+    GenerateStyleHeader(${output_path} INTEGRATE  integrate ) # update
+    GenerateStyleHeader(${output_path} KSPACE     kspace    ) # force
+    GenerateStyleHeader(${output_path} MINIMIZE   minimize  ) # update
+    GenerateStyleHeader(${output_path} NBIN       nbin      ) # neighbor
+    GenerateStyleHeader(${output_path} NPAIR      npair     ) # neighbor
+    GenerateStyleHeader(${output_path} NSTENCIL   nstencil  ) # neighbor
+    GenerateStyleHeader(${output_path} NTOPO      ntopo     ) # neighbor
+    GenerateStyleHeader(${output_path} PAIR       pair      ) # force
+    GenerateStyleHeader(${output_path} READER     reader    ) # read_dump
+    GenerateStyleHeader(${output_path} REGION     region    ) # domain
+endfunction(GenerateStyleHeaders)

cmake/README.md

@@ -0,0 +1,19 @@
+cmake-buildsystem
+-----------------
+
+To use the cmake build system instead of the make-driven one, do:
+```
+cmake /path/to/lammps/source/cmake
+```
+(please note the cmake directory as the very end)
+
+To enable package, e.g. GPU do
+```
+cmake /path/to/lammps/source/cmake -DENABLE_GPU=ON
+```
+
+cmake has many many options, do get an overview use the curses-based cmake interface, ccmake:
+```
+ccmake /path/to/lammps/source/cmake
+```
+(Don't forget to press "g" for generate once you are done with configuring)

cmake/gpu/lal_pppm_d.cu

@@ -0,0 +1,4 @@
+#define grdtyp double
+#define grdtyp4 double4
+
+#include "lal_pppm.cu"

cmake/gpu/lal_pppm_f.cu

@@ -0,0 +1,4 @@
+#define grdtyp float
+#define grdtyp4 float4
+
+#include "lal_pppm.cu"

cmake/pkgconfig/liblammps.pc.in

@@ -0,0 +1,18 @@
+# pkg-config file for lammps
+# https://people.freedesktop.org/~dbn/pkg-config-guide.html
+# Usage: cc `pkg-config --cflags --libs liblammps` -o myapp myapp.c
+# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
+# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
+
+prefix=@CMAKE_INSTALL_FULL_PREFIX@
+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
+includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
+
+Name: liblammps@LAMMPS_MACHINE@
+Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
+URL: http://lammps.sandia.gov
+Version:
+Requires:
+Libs: -L${libdir} -llammps@LAMMPS_MACHINE@
+Libs.private: -lm
+Cflags: -I${includedir} @LAMMPS_API_DEFINES@

doc/src/Eqs/bond_gromos.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+
+\begin{document}
+
+$$
+   E = K (r^2 - r_0^2)^2
+$$
+
+\end{document}

doc/src/Eqs/fix_mvv_dpd.tex

@@ -0,0 +1,21 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  v(t+\frac{\Delta t}{2}) = v(t) + \frac{\Delta t}{2}\cdot a(t),
+$$
+
+$$
+  r(t+\Delta t) = r(t) + \Delta t\cdot v(t+\frac{\Delta t}{2}),
+$$
+
+$$
+  a(t+\Delta t) = \frac{1}{m}\cdot F\left[ r(t+\Delta t), v(t) +\lambda \cdot \Delta t\cdot a(t)\right],
+$$
+
+$$
+  v(t+\Delta t) = v(t+\frac{\Delta t}{2}) + \frac{\Delta t}{2}\cdot a(t+\Delta t)
+$$
+
+\end{document}

doc/src/Eqs/fix_rhok.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ U &=&  \frac{1}{2} K (|\rho_{\vec{k}}| - a)^2 \\
+ \rho_{\vec{k}} &=& \sum_j^N \exp(-i\vec{k} \cdot \vec{r}_j )/\sqrt{N} \\
+ \vec{k} &=& (2\pi n_x /L_x , 2\pi n_y  /L_y , 2\pi n_z/L_z ) 
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_edpd_force.tex

@@ -0,0 +1,33 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \mathbf{F}_{ij}^{C} = \alpha_{ij}{\omega_{C}}(r_{ij})\mathbf{e}_{ij},
+$$
+
+$$
+  \mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij},
+$$
+
+$$
+  \mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij},
+$$
+
+$$
+  \omega_{C}(r) = 1 - r/r_c,
+$$
+
+$$
+  \alpha_{ij} = A\cdot k_B(T_i + T_j)/2,
+$$
+
+$$  
+  \omega_{D}(r) = \omega^2_{R}(r) = (1-r/r_c)^s,
+$$
+
+$$  
+  \sigma_{ij}^2 = 4\gamma k_B T_i T_j/(T_i + T_j),
+$$
+
+\end{document}

doc/src/Eqs/pair_edpd_gov.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \frac{\mathrm{d}^2 \mathbf{r}_i}{\mathrm{d} t^2}=
+  \frac{\mathrm{d} \mathbf{v}_i}{\mathrm{d} t}
+  =\mathbf{F}_{i}=\sum_{i\neq j}(\mathbf{F}_{ij}^{C}+\mathbf{F}_{ij}^{D}+\mathbf{F}_{ij}^{R}),
+$$
+
+$$
+  C_v\frac{\mathrm{d} T_i}{\mathrm{d} t}= q_{i} = \sum_{i\neq j}(q_{ij}^{C}+q_{ij}^{V}+q_{ij}^{R}),
+$$
+
+\end{document}

doc/src/Eqs/pair_edpd_heat.tex

@@ -0,0 +1,29 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  q_i^C = \sum_{j \ne i} k_{ij} \omega_{CT}(r_{ij}) \left( \frac{1}{T_i} - \frac{1}{T_j} \right),
+$$  
+  
+$$
+  q_i^V = \frac{1}{2 C_v}\sum_{j \ne i}{ \left\{ \omega_D(r_{ij})\left[\gamma_{ij} \left( \mathbf{e}_{ij} \cdot \mathbf{v}_{ij} \right)^2 - \frac{\left( \sigma _{ij} \right)^2}{m}\right] - \sigma _{ij} \omega_R(r_{ij})\left( \mathbf{e}_{ij} \cdot \mathbf{v}_{ij} \right){\xi_{ij}} \right\} },
+$$  
+
+$$
+  q_i^R = \sum_{j \ne i} \beta _{ij} \omega_{RT}(r_{ij}) d {t^{ - 1/2}} \xi_{ij}^e,
+$$
+
+$$
+  \omega_{CT}(r)=\omega_{RT}^2(r)=\left(1-r/r_{ct}\right)^{s_T},
+$$
+
+$$
+  k_{ij}=C_v^2\kappa(T_i + T_j)^2/4k_B,
+$$
+
+$$
+  \beta_{ij}^2=2k_Bk_{ij},
+$$
+
+\end{document}

doc/src/Eqs/pair_edpd_kappa.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \kappa  = \frac{315k_B\upsilon }{2\pi \rho C_v r_{ct}^5}\frac{1}{Pr},
+$$
+
+\end{document}

doc/src/Eqs/pair_mdpd_force.tex

@@ -0,0 +1,17 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \mathbf{F}_{ij}^C = Aw_c(r_{ij})\mathbf{e}_{ij} + B(\rho_i+\rho_j)w_d(r_{ij})\mathbf{e}_{ij},
+$$
+
+$$
+  \mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij},
+$$
+
+$$
+  \mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij},
+$$
+
+\end{document}

doc/src/Eqs/pair_tdpd_flux.tex

@@ -0,0 +1,21 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  Q_{ij}^D = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right),
+$$  
+  
+$$  
+  Q_{ij}^R = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij},
+$$
+
+$$
+  w_{DC}(r_{ij})=w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power\_{cc}},
+$$
+
+$$
+  \epsilon_{ij}^2 = m_s^2\kappa_{ij}\rho,
+$$
+
+\end{document}

doc/src/Eqs/pair_tdpd_force.tex

@@ -0,0 +1,29 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \mathbf{F}_{ij}^{C} = A{\omega_{C}}(r_{ij})\mathbf{e}_{ij},
+$$
+
+$$
+  \mathbf{F}_{ij}^{D} = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij},
+$$
+
+$$
+  \mathbf{F}_{ij}^{R} = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij},
+$$
+
+$$
+  \omega_{C}(r) = 1 - r/r_c,
+$$
+
+$$
+  \omega_{D}(r) = \omega^2_{R}(r) = (1-r/r_c)^{\rm power\_f},
+$$
+
+$$
+  \sigma^2 = 2\gamma k_B T,
+$$
+
+\end{document}

doc/src/Eqs/pair_tdpd_gov.tex

@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  \frac{\mathrm{d}^2 \mathbf{r}_i}{\mathrm{d} t^2} = \frac{\mathrm{d} \mathbf{v}_i}{\mathrm{d} t}=\mathbf{F}_{i}=\sum_{i\neq j}(\mathbf{F}_{ij}^{C}+\mathbf{F}_{ij}^{D}+\mathbf{F}_{ij}^{R}),
+$$
+
+$$
+  \frac{\mathrm{d} C_{i}}{\mathrm{d} t}= Q_{i} = \sum_{i\neq j}(Q_{ij}^{D}+Q_{ij}^{R}) + Q_{i}^{S}, 
+$$
+
+\end{document}

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="24 Jul 2017 version">
+<META NAME="docnumber" CONTENT="23 Oct 2017 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 @@
 <H1></H1>
 
 LAMMPS Documentation :c,h3
-24 Jul 2017 version :c,h4
+23 Oct 2017 version :c,h4
 
 Version info: :h4
 
@@ -79,7 +79,7 @@ bug reports and feature requests are mainly coordinated through the
 "LAMMPS project on GitHub."_https://github.com/lammps/lammps
 The lammps.org domain, currently hosting "public continuous integration
 testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux
-RPM and Windows installer packages"_http://rpm.lammps.org is located
+RPM and Windows installer packages"_http://packages.lammps.org is located
 at Temple University and managed by Richard Berger,
 richard.berger at temple.edu.
 

doc/src/Section_accelerate.txt

@@ -233,8 +233,8 @@ set any needed options for the package via "-pk" "command-line switch"_Section_s
 use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
 :tb(c=2,s=|)
 
-Note that the first 4 steps can be done as a single command, using the
-src/Make.py tool.  This tool is discussed in "Section
+Note that the first 4 steps can be done as a single command with
+suitable make command invocations. This is discussed in "Section
 4"_Section_packages.html of the manual, and its use is
 illustrated in the individual accelerator sections.  Typically these
 steps only need to be done once, to create an executable that uses one

doc/src/Section_commands.txt

@@ -532,7 +532,8 @@ package"_Section_start.html#start_3.
 "dump vtk"_dump_vtk.html,
 "group2ndx"_group2ndx.html,
 "ndx2group"_group2ndx.html,
-"temper/grem"_temper_grem.html :tb(c=3,ea=c)
+"temper/grem"_temper_grem.html,
+"temper/npt"_temper_npt.html :tb(c=3,ea=c)
 
 :line
 
@@ -579,6 +580,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "halt"_fix_halt.html,
 "heat"_fix_heat.html,
 "indent"_fix_indent.html,
+"latte"_fix_latte.html,
 "langevin (k)"_fix_langevin.html,
 "lineforce"_fix_lineforce.html,
 "momentum (k)"_fix_momentum.html,
@@ -685,6 +687,7 @@ package"_Section_start.html#start_3.
 "drude"_fix_drude.html,
 "drude/transform/direct"_fix_drude_transform.html,
 "drude/transform/reverse"_fix_drude_transform.html,
+"edpd/source"_fix_dpd_source.html,
 "eos/cv"_fix_eos_cv.html,
 "eos/table"_fix_eos_table.html,
 "eos/table/rx"_fix_eos_table_rx.html,
@@ -704,6 +707,9 @@ package"_Section_start.html#start_3.
 "meso"_fix_meso.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso/stationary"_fix_meso_stationary.html,
+"mvv/dpd"_fix_mvv_dpd.html,
+"mvv/edpd"_fix_mvv_dpd.html,
+"mvv/tdpd"_fix_mvv_dpd.html,
 "nve/dot"_fix_nve_dot.html,
 "nve/dotc/langevin"_fix_nve_dotc_langevin.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
@@ -714,6 +720,8 @@ package"_Section_start.html#start_3.
 "nve/eff"_fix_nve_eff.html,
 "nvt/eff"_fix_nh_eff.html,
 "nvt/sllod/eff"_fix_nvt_sllod_eff.html,
+"npt/uef"_fix_nh_uef.html,
+"nvt/uef"_fix_nh_uef.html,
 "phonon"_fix_phonon.html,
 "pimd"_fix_pimd.html,
 "qbmsst"_fix_qbmsst.html,
@@ -722,6 +730,7 @@ package"_Section_start.html#start_3.
 "qtb"_fix_qtb.html,
 "reax/c/bonds"_fix_reax_bonds.html,
 "reax/c/species"_fix_reaxc_species.html,
+"rhok"_fix_rhok.html,
 "rx"_fix_rx.html,
 "saed/vtk"_fix_saed_vtk.html,
 "shardlow"_fix_shardlow.html,
@@ -732,10 +741,11 @@ package"_Section_start.html#start_3.
 "smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
 "smd/setvel"_fix_smd_setvel.html,
 "smd/wall/surface"_fix_smd_wall_surface.html,
+"tdpd/source"_fix_dpd_source.html,
 "temp/rescale/eff"_fix_temp_rescale_eff.html,
 "ti/spring"_fix_ti_spring.html,
-"ttm/mod"_fix_ttm.html
-"wall/ees"_fix_wall_ees.html
+"ttm/mod"_fix_ttm.html,
+"wall/ees"_fix_wall_ees.html,
 "wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c)
 
 :line
@@ -750,6 +760,7 @@ package"_Section_accelerate.html.  This is indicated by additional
 letters in parenthesis: g = GPU, i = USER-INTEL, k =
 KOKKOS, o = USER-OMP, t = OPT.
 
+"aggregate/atom"_compute_cluster_atom.html,
 "angle"_compute_angle.html,
 "angle/local"_compute_angle_local.html,
 "angmom/chunk"_compute_angmom_chunk.html,
@@ -775,6 +786,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "erotate/sphere"_compute_erotate_sphere.html,
 "erotate/sphere/atom"_compute_erotate_sphere_atom.html,
 "event/displace"_compute_event_displace.html,
+"fragment/atom"_compute_cluster_atom.html,
 "global/atom"_compute_global_atom.html,
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
@@ -836,6 +848,7 @@ package"_Section_start.html#start_3.
 "cnp/atom"_compute_cnp_atom.html,
 "dpd"_compute_dpd.html,
 "dpd/atom"_compute_dpd_atom.html,
+"edpd/temp/atom"_compute_edpd_temp_atom.html,
 "fep"_compute_fep.html,
 "force/tally"_compute_tally.html,
 "heat/flux/tally"_compute_tally.html,
@@ -846,6 +859,7 @@ package"_Section_start.html#start_3.
 "meso/t/atom"_compute_meso_t_atom.html,
 "pe/tally"_compute_tally.html,
 "pe/mol/tally"_compute_tally.html,
+"pressure/uef"_compute_pressure_uef.html,
 "saed"_compute_saed.html,
 "smd/contact/radius"_compute_smd_contact_radius.html,
 "smd/damage"_compute_smd_damage.html,
@@ -868,11 +882,13 @@ package"_Section_start.html#start_3.
 "smd/ulsph/stress"_compute_smd_ulsph_stress.html,
 "smd/vol"_compute_smd_vol.html,
 "stress/tally"_compute_tally.html,
+"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
 "temp/drude"_compute_temp_drude.html,
 "temp/eff"_compute_temp_eff.html,
 "temp/deform/eff"_compute_temp_deform_eff.html,
 "temp/region/eff"_compute_temp_region_eff.html,
 "temp/rotate"_compute_temp_rotate.html,
+"temp/uef"_compute_temp_uef.html,
 "xrd"_compute_xrd.html :tb(c=6,ea=c)
 
 :line
@@ -892,8 +908,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "hybrid"_pair_hybrid.html,
 "hybrid/overlay"_pair_hybrid.html,
 "adp (o)"_pair_adp.html,
-"airebo (o)"_pair_airebo.html,
-"airebo/morse (o)"_pair_airebo.html,
+"airebo (oi)"_pair_airebo.html,
+"airebo/morse (oi)"_pair_airebo.html,
 "beck (go)"_pair_beck.html,
 "body"_pair_body.html,
 "bop"_pair_bop.html,
@@ -904,11 +920,12 @@ KOKKOS, o = USER-OMP, t = OPT.
 "born/coul/long/cs"_pair_born.html,
 "born/coul/msm (o)"_pair_born.html,
 "born/coul/wolf (go)"_pair_born.html,
+"born/coul/wolf/cs"_pair_born.html,
 "brownian (o)"_pair_brownian.html,
 "brownian/poly (o)"_pair_brownian.html,
-"buck (gkio)"_pair_buck.html,
-"buck/coul/cut (gkio)"_pair_buck.html,
-"buck/coul/long (gkio)"_pair_buck.html,
+"buck (giko)"_pair_buck.html,
+"buck/coul/cut (giko)"_pair_buck.html,
+"buck/coul/long (giko)"_pair_buck.html,
 "buck/coul/long/cs"_pair_buck.html,
 "buck/coul/msm (o)"_pair_buck.html,
 "buck/long/coul/long (o)"_pair_buck_long.html,
@@ -923,12 +940,13 @@ KOKKOS, o = USER-OMP, t = OPT.
 "coul/msm"_pair_coul.html,
 "coul/streitz"_pair_coul.html,
 "coul/wolf (ko)"_pair_coul.html,
-"dpd (go)"_pair_dpd.html,
+"coul/wolf/cs"_pair_coul.html,
+"dpd (gio)"_pair_dpd.html,
 "dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
-"eam (gkiot)"_pair_eam.html,
-"eam/alloy (gkot)"_pair_eam.html,
-"eam/fs (gkot)"_pair_eam.html,
+"eam (gikot)"_pair_eam.html,
+"eam/alloy (gikot)"_pair_eam.html,
+"eam/fs (gikot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
 "gauss (go)"_pair_gauss.html,
 "gayberne (gio)"_pair_gayberne.html,
@@ -942,7 +960,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "kim"_pair_kim.html,
 "lcbop"_pair_lcbop.html,
 "line/lj"_pair_line_lj.html,
-"lj/charmm/coul/charmm (ko)"_pair_charmm.html,
+"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
 "lj/charmm/coul/long (giko)"_pair_charmm.html,
 "lj/charmm/coul/msm"_pair_charmm.html,
@@ -990,13 +1008,13 @@ KOKKOS, o = USER-OMP, t = OPT.
 "polymorphic"_pair_polymorphic.html,
 "python"_pair_python.html,
 "reax"_pair_reax.html,
-"rebo (o)"_pair_airebo.html,
+"rebo (oi)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
 "snap"_pair_snap.html,
 "soft (go)"_pair_soft.html,
-"sw (gkio)"_pair_sw.html,
+"sw (giko)"_pair_sw.html,
 "table (gko)"_pair_table.html,
-"tersoff (gkio)"_pair_tersoff.html,
+"tersoff (giko)"_pair_tersoff.html,
 "tersoff/mod (gko)"_pair_tersoff_mod.html,
 "tersoff/mod/c (o)"_pair_tersoff_mod.html,
 "tersoff/zbl (gko)"_pair_tersoff_zbl.html,
@@ -1024,6 +1042,7 @@ package"_Section_start.html#start_3.
 "eam/cd (o)"_pair_eam.html,
 "edip (o)"_pair_edip.html,
 "edip/multi"_pair_edip.html,
+"edpd"_pair_meso.html,
 "eff/cut"_pair_eff.html,
 "exp6/rx"_pair_exp6_rx.html,
 "gauss/cut"_pair_gauss.html,
@@ -1041,6 +1060,8 @@ package"_Section_start.html#start_3.
 "lj/sdk (gko)"_pair_sdk.html,
 "lj/sdk/coul/long (go)"_pair_sdk.html,
 "lj/sdk/coul/msm (o)"_pair_sdk.html,
+"mdpd"_pair_meso.html,
+"mdpd/rhosum"_pair_meso.html,
 "meam/c"_pair_meam.html,
 "meam/spline (o)"_pair_meam_spline.html,
 "meam/sw/spline"_pair_meam_sw_spline.html,
@@ -1074,6 +1095,7 @@ package"_Section_start.html#start_3.
 "sph/taitwater/morris"_pair_sph_taitwater_morris.html,
 "srp"_pair_srp.html,
 "table/rx"_pair_table_rx.html,
+"tdpd"_pair_meso.html,
 "tersoff/table (o)"_pair_tersoff.html,
 "thole"_pair_thole.html,
 "tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
@@ -1096,6 +1118,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "class2 (ko)"_bond_class2.html,
 "fene (iko)"_bond_fene.html,
 "fene/expand (o)"_bond_fene_expand.html,
+"gromos (o)"_bond_gromos.html,
 "harmonic (ko)"_bond_harmonic.html,
 "morse (o)"_bond_morse.html,
 "nonlinear (o)"_bond_nonlinear.html,
@@ -1162,7 +1185,7 @@ USER-OMP, t = OPT.
 "none"_dihedral_none.html,
 "zero"_dihedral_zero.html,
 "hybrid"_dihedral_hybrid.html,
-"charmm (ko)"_dihedral_charmm.html,
+"charmm (iko)"_dihedral_charmm.html,
 "charmmfsw"_dihedral_charmm.html,
 "class2 (ko)"_dihedral_class2.html,
 "harmonic (io)"_dihedral_harmonic.html,
@@ -1175,7 +1198,7 @@ used if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.
 
 "cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
-"fourier (o)"_dihedral_fourier.html,
+"fourier (io)"_dihedral_fourier.html,
 "nharmonic (o)"_dihedral_nharmonic.html,
 "quadratic (o)"_dihedral_quadratic.html,
 "spherical (o)"_dihedral_spherical.html,
@@ -1198,7 +1221,7 @@ USER-OMP, t = OPT.
 "hybrid"_improper_hybrid.html,
 "class2 (ko)"_improper_class2.html,
 "cvff (io)"_improper_cvff.html,
-"harmonic (ko)"_improper_harmonic.html,
+"harmonic (iko)"_improper_harmonic.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
 
 These are additional improper styles in USER packages, which can be

doc/src/Section_errors.txt

@@ -7886,8 +7886,8 @@ keyword to allow for additional bonds to be formed :dd
 
 {New bond exceeded special list size in fix bond/create} :dt
 
-See the "special_bonds extra" command
-(or the "read_data extra/special/per/atom" command)
+See the "read_data extra/special/per/atom" command
+(or the "create_box extra/special/per/atom" command)
 for info on how to leave space in the special bonds
 list to allow for additional bonds to be formed. :dd
 
@@ -9666,8 +9666,8 @@ you are running. :dd
 
 {Special list size exceeded in fix bond/create} :dt
 
-See the special_bonds extra command
-(or the read_data extra/special/per/atom command)
+See the "read_data extra/special/per/atom" command
+(or the "create_box extra/special/per/atom" command)
 for info on how to leave space in the special bonds
 list to allow for additional bonds to be formed. :dd
 

doc/src/Section_example.txt

@@ -49,6 +49,7 @@ Lists of both kinds of directories are given below.
 Lowercase directories :h4
 
 accelerate: run with various acceleration options (OpenMP, GPU, Phi)
+airebo:   polyethylene with AIREBO potential
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
 cmap:     CMAP 5-body contributions to CHARMM force field

doc/src/Section_howto.txt

@@ -2859,8 +2859,8 @@ The nature of the atoms (core, Drude particle or non-polarizable) is
 specified via the "fix drude"_fix_drude.html command.  The special
 list of neighbors is automatically refactored to account for the
 equivalence of core and Drude particles as regards special 1-2 to 1-4
-screening. It may be necessary to use the {extra} keyword of the
-"special_bonds"_special_bonds.html command. If using "fix
+screening. It may be necessary to use the {extra/special/per/atom}
+keyword of the "read_data"_read_data.html command. If using "fix
 shake"_fix_shake.html, make sure no Drude particle is in this fix
 group.
 

doc/src/Section_packages.txt

@@ -25,6 +25,17 @@ There are two kinds of packages in LAMMPS, standard and user packages:
 "Table of standard packages"_#table_standard
 "Table of user packages"_#table_user :ul
 
+Either of these kinds of packages may work as is, may require some
+additional code compiled located in the lib folder, or may require
+an external library to be downloaded, compiled, installed, and LAMMPS
+configured to know about its location and additional compiler flags.
+You can often do the build of the internal or external libraries
+in one step by typing "make lib-name args='...'" from the src dir,
+with appropriate arguments included in args='...'. If you just type
+"make lib-name" you should see a help message about supported flags
+and some examples. For more details about this, please study the
+tables below and the sections about the individual packages.
+
 Standard packages are supported by the LAMMPS developers and are
 written in a syntax and style consistent with the rest of LAMMPS.
 This means the developers will answer questions about them, debug and
@@ -34,7 +45,9 @@ LAMMPS.
 User packages have been contributed by users, and begin with the
 "user" prefix.  If they are a single command (single file), they are
 typically in the user-misc package.  User packages don't necessarily
-meet the requirements of the standard packages.  If you have problems
+meet the requirements of the standard packages. This means the
+developers will try to keep things working and usually can answer
+technical questions about compiling the package. If you have problems
 using a feature provided in a user package, you may need to contact
 the contributor directly to get help.  Information on how to submit
 additions you make to LAMMPS as single files or as a standard or user
@@ -78,11 +91,12 @@ Package, Description, Doc page, Example, Library
 "COMPRESS"_#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
 "CORESHELL"_#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -
 "DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
-"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, WWW bench, int
+"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
 "GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
-"KIM"_#KIM, openKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
-"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, WWW bench, -
+"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
+"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
+"LATTE"_#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
 "MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
 "MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
 "MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
@@ -90,7 +104,7 @@ Package, Description, Doc page, Example, Library
 "MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
 "MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
 "MSCG"_#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
-"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, WWW bench, -
+"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "PERI"_#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
 "POEMS"_#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
 "PYTHON"_#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
@@ -99,10 +113,9 @@ Package, Description, Doc page, Example, Library
 "REPLICA"_#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
 "RIGID"_#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
 "SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
-"SNAP"_#SNAP, quantum-fitted potential, "pair snap"_pair_snap.html, snap, -
+"SNAP"_#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
 "SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
-"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext
-:tb(ea=c,ca1=l)
+"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
 
 [USER packages] :link(table_user),p
 
@@ -118,15 +131,16 @@ Package, Description, Doc page, Example, Library
 "USER-EFF"_#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
 "USER-FEP"_#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
 "USER-H5MD"_#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
-"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, WWW bench, -
+"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
 "USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
+"USER-MESO"_#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
 "USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
 "USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
-"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, WWW bench, -
+"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
 "USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
@@ -136,8 +150,8 @@ Package, Description, Doc page, Example, Library
 "USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
 "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
 "USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
-"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext
-:tb(ea=c,ca1=l)
+"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
+"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
 
 :line
 :line
@@ -364,9 +378,12 @@ GPU package :link(GPU),h4
 [Contents:]
 
 Dozens of pair styles and a version of the PPPM long-range Coulombic
-solver optimized for NVIDIA GPUs.  All such styles have a "gpu" as a
-suffix in their style name.  "Section 5.3.1"_accelerate_gpu.html gives
-details of what hardware and Cuda software is required on your system,
+solver optimized for GPUs.  All such styles have a "gpu" as a
+suffix in their style name. The GPU code can be compiled with either
+CUDA or OpenCL, however the OpenCL variants are no longer actively
+maintained and only the CUDA versions are regularly tested.
+"Section 5.3.1"_accelerate_gpu.html gives details of what
+hardware and GPU software is required on your system,
 and details on how to build and use this package.  Its styles can be
 invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line
 switches"_Section_start.html#start_6.  See also the "KOKKOS"_#KOKKOS
@@ -378,32 +395,41 @@ package, which has GPU-enabled styles.
 [Install or un-install:]
 
 Before building LAMMPS with this package, you must first build the GPU
-library in lib/gpu from a set of provided C and Cuda files.  You can
+library in lib/gpu from a set of provided C and CUDA files.  You can
 do this manually if you prefer; follow the instructions in
-lib/gpu/README.  You can also do it in one step from the lammps/src
+lib/gpu/README. Please note, that the GPU library uses MPI calls, so
+you have to make certain to use the same MPI library (or the STUBS
+library) settings as the main LAMMPS code. That same applies to the
+-DLAMMPS_BIGBIG, -DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL define.
+
+You can also do it in one step from the lammps/src
 dir, using a command like these, which simply invoke the
 lib/gpu/Install.py script with the specified args:
 
-make lib-gpu                                # print help message
-make lib-gpu args="-m"                      # build GPU library with default Makefile.linux
-make lib-gpu args="-i xk7 -p single -o xk7.single"      # create new Makefile.xk7.single, altered for single-precision
-make lib-gpu args="-i xk7 -p single -o xk7.single -m"   # ditto, also build GPU library
+make lib-gpu               # print help message
+make lib-gpu args="-b"     # build GPU library with default Makefile.linux
+make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
+make lib-gpu args="-m mpi -p mixed -b" # build GPU library with mixed precision using settings in Makefile.mpi :pre
 
-Note that this procedure starts with one of the existing
-Makefile.machine files in lib/gpu.  It allows you to alter 4 important
-settings in that Makefile, via the -h, -a, -p, -e switches,
-and save the new Makefile, if desired:
+Note that this procedure through the '-m machine' flag starts with one of
+the existing Makefile.machine files in lib/gpu. For your convenience,
+machine makefiles for "mpi" and "serial" are provided, which have the
+same settings as the corresponding machine makefiles in the main LAMMPS
+source folder. In addition you can alter 4 important settings in that
+Makefile, via the -h, -a, -p, -e switches, and also save a copy of the
+new Makefile, if desired:
 
-CUDA_HOME = where NVIDIA Cuda software is installed on your system
+CUDA_HOME = where NVIDIA CUDA software is installed on your system
 CUDA_ARCH = what GPU hardware you have (see help message for details)
 CUDA_PRECISION = precision (double, mixed, single)
 EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
 
-If the library build is successful, 2 files should be created:
-lib/gpu/libgpu.a and lib/gpu/Makefile.lammps.  The latter has settings
-that enable LAMMPS to link with Cuda libraries.  If the settings in
-Makefile.lammps for your machine are not correct, the LAMMPS build
-will fail.
+If the library build is successful, at least 3 files should be created:
+lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps.
+The latter has settings that enable LAMMPS to link with CUDA libraries.
+If the settings in Makefile.lammps for your machine are not correct,
+the LAMMPS build will fail, and lib/gpu/Makefile.lammps may need to
+be edited.
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -492,14 +518,40 @@ Minnesota).
 
 [Install or un-install:]
 
-Using this package requires the KIM library and its models
-(interatomic potentials) to be downloaded and installed on your
-system.  The library can be downloaded and built in lib/kim or
-elsewhere on your system.  Details of the download, build, and install
-process for KIM are given in the lib/kim/README file.
+Before building LAMMPS with this package, you must first download and
+build the KIM library and include the KIM models that you want to
+use. You can do this manually if you prefer; follow the instructions
+in lib/kim/README.  You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/kim/Install.py script with the specified args.
 
-Once that process is complete, you can then install/un-install the
-package and build LAMMPS in the usual manner:
+make lib-kim              # print help message
+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
+
+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.
+
+See the list of KIM model drivers here:
+https://openkim.org/kim-items/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 in the "What is in the KIM API source
+package?" section
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
 
 make yes-kim
 make machine :pre
@@ -523,7 +575,7 @@ KOKKOS package :link(KOKKOS),h4
 
 Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
 styles adapted to compile using the Kokkos library which can convert
-them to OpenMP or Cuda code so that they run efficiently on multicore
+them to OpenMP or CUDA code so that they run efficiently on multicore
 CPUs, KNLs, or GPUs.  All the styles have a "kk" as a suffix in their
 style name.  "Section 5.3.3"_accelerate_kokkos.html gives details of
 what hardware and software is required on your system, and how to
@@ -553,28 +605,28 @@ files for examples.
 For multicore CPUs using OpenMP:
 
 KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = HSW           # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc
+KOKKOS_ARCH = HSW           # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc :pre
 
 For Intel KNLs using OpenMP:
 
 KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = KNL
+KOKKOS_ARCH = KNL :pre
 
-For NVIDIA GPUs using Cuda:
+For NVIDIA GPUs using CUDA:
 
 KOKKOS_DEVICES = Cuda
 KOKKOS_ARCH = Pascal60,Power8     # P100 hosted by an IBM Power8, etc
-KOKKOS_ARCH = Kepler37,Power8     # K80 hosted by an IBM Power8, etc
+KOKKOS_ARCH = Kepler37,Power8     # K80 hosted by an IBM Power8, etc :pre
 
 For GPUs, you also need these 2 lines in your Makefile.machine before
 the CC line is defined, in this case for use with OpenMPI mpicxx.  The
 2 lines define a nvcc wrapper compiler, which will use nvcc for
-compiling Cuda files or use a C++ compiler for non-Kokkos, non-Cuda
+compiling CUDA files or use a C++ compiler for non-Kokkos, non-CUDA
 files.
 
 KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
 export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
-CC =		mpicxx
+CC =		mpicxx :pre
 
 Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner.
@@ -645,6 +697,66 @@ bench/in.rhodo :ul
 
 :line
 
+LATTE package :link(LATTE),h4
+
+[Contents:]
+
+A fix command which wraps the LATTE DFTB code, so that molecular
+dynamics can be run with LAMMPS using density-functional tight-binding
+quantum forces calculated by LATTE.
+
+More information on LATTE can be found at this web site:
+"https://github.com/lanl/LATTE"_latte_home.  A brief technical
+description is given with the "fix latte"_fix_latte.html command.
+
+:link(latte_home,https://github.com/lanl/LATTE)
+
+[Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia).  LATTE
+itself is developed at Los Alamos National Laboratory by Marc
+Cawkwell, Anders Niklasson, and Christian Negre.
+
+[Install or un-install:]
+
+Before building LAMMPS with this package, you must first download and
+build the LATTE library.  You can do this manually if you prefer;
+follow the instructions in lib/latte/README.  You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invokes the lib/latte/Install.py script with the specified
+args:
+
+make lib-latte                          # print help message
+make lib-latte args="-b"                # download and build in lib/latte/LATTE-master
+make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
+make lib-latte args="-b -m gfortran"    # download and build in lib/latte and 
+                                        #   copy Makefile.lammps.gfortran to Makefile.lammps
+:pre
+
+Note that 3 symbolic (soft) links, "includelink" and "liblink" and
+"filelink", are created in lib/latte to point into the LATTE home dir.
+When LAMMPS builds in src it will use these links.  You should 
+also check that the Makefile.lammps file you create is apporpriate
+for the compiler you use on your system to build LATTE.
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-latte
+make machine :pre
+
+make no-latte
+make machine :pre
+
+[Supporting info:]
+
+src/LATTE: filenames -> commands
+src/LATTE/README
+lib/latte/README
+"fix latte"_fix_latte.html
+examples/latte
+"LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS :ul
+
+:line
+
 MANYBODY package :link(MANYBODY),h4
 
 [Contents:]
@@ -710,6 +822,12 @@ MEAM package :link(MEAM),h4
 
 A pair style for the modified embedded atom (MEAM) potential.
 
+Please note that the MEAM package has been superseded by the
+"USER-MEAMC"_#USER-MEAMC package, which is a direct translation
+of the MEAM package to C++. USER-MEAMC contains additional
+optimizations making it run faster than MEAM on most machines,
+while providing the identical features and USER interface.
+
 [Author:] Greg Wagner (Northwestern U) while at Sandia.
 
 [Install or un-install:]
@@ -720,9 +838,10 @@ follow the instructions in lib/meam/README.  You can also do it in one
 step from the lammps/src dir, using a command like these, which simply
 invoke the lib/meam/Install.py script with the specified args:
 
-make lib-meam                      # print help message
-make lib-meam args="-m gfortran"   # build with GNU Fortran compiler
-make lib-meam args="-m ifort"      # build with Intel ifort compiler :pre
+make lib-meam                  # print help message
+make lib-meam args="-m mpi"    # build with default Fortran compiler compatible with your MPI library
+make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
+make lib-meam args="-m ifort"  # build with Intel Fortran compiler using Makefile.ifort :pre
 
 The build should produce two files: lib/meam/libmeam.a and
 lib/meam/Makefile.lammps.  The latter is copied from an existing
@@ -765,6 +884,9 @@ A variety of compute, fix, pair, dump styles with specialized
 capabilities that don't align with other packages.  Do a directory
 listing, "ls src/MISC", to see the list of commands.
 
+NOTE: the MISC package contains styles that require using the
+-restrict flag, when compiling with Intel compilers.
+
 [Install or un-install:]
 
 make yes-misc
@@ -878,9 +1000,9 @@ University of Chicago.
 
 Before building LAMMPS with this package, you must first download and
 build the MS-CG library.  Building the MS-CG library and using it from
-LAMMPS requires a C++11 compatible compiler, and that LAPACK and GSL
-(GNU Scientific Library) libraries be installed on your machine.  See
-the lib/mscg/README and MSCG/Install files for more details.
+LAMMPS requires a C++11 compatible compiler and that the GSL
+(GNU Scientific Library) headers and libraries are installed on your
+machine.  See the lib/mscg/README and MSCG/Install files for more details.
 
 Assuming these libraries are in place, you can do the download and
 build of MS-CG manually if you prefer; follow the instructions in
@@ -888,15 +1010,16 @@ lib/mscg/README.  You can also do it in one step from the lammps/src
 dir, using a command like these, which simply invoke the
 lib/mscg/Install.py script with the specified args:
 
-make lib-mscg                                # print help message
-make lib-mscg args="-g -b -l"                # download and build in default lib/mscg/MSCG-release-master
-make lib-mscg args="-h . MSCG -g -b -l"      # download and build in lib/mscg/MSCG
-make lib-mscg args="-h ~ MSCG -g -b -l"      # download and build in ~/mscg :pre
+make lib-mscg             # print help message
+make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
+                                    # with the settings compatible with "make serial"
+make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
+                                    # with the settings compatible with "make mpi"
+make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre
 
-Note that the final -l switch is to create 2 symbolic (soft) links,
-"includelink" and "liblink", in lib/mscg to point to the MS-CG src
-dir.  When LAMMPS builds it will use these links.  You should not need
-to edit the lib/mscg/Makefile.lammps file.
+Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg
+to point to the MS-CG src/installation dir.  When LAMMPS is built in src it will use these links.
+You should not need to edit the lib/mscg/Makefile.lammps file.
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -942,11 +1065,11 @@ make no-opt
 make machine :pre
 
 NOTE: The compile flag "-restrict" must be used to build LAMMPS with
-the OPT package.  It should be added to the CCFLAGS line of your
-Makefile.machine.  See Makefile.opt in src/MAKE/OPTIONS for an
-example.
+the OPT package when using Intel compilers.  It should be added to
+the CCFLAGS line of your Makefile.machine.  See Makefile.opt in
+src/MAKE/OPTIONS for an example.
 
-CCFLAGS: add -restrict :ul
+CCFLAGS: add -restrict for Intel compilers :ul
 
 [Supporting info:]
 
@@ -1015,9 +1138,10 @@ follow the instructions in lib/poems/README.  You can also do it in
 one step from the lammps/src dir, using a command like these, which
 simply invoke the lib/poems/Install.py script with the specified args:
 
-make lib-poems                      # print help message
-make lib-poems args="-m g++"        # build with GNU g++ compiler
-make lib-poems args="-m icc"        # build with Intel icc compiler :pre
+make lib-poems                   # print help message
+make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
+make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+make lib-poems args="-m icc"     # build with Intel icc compiler :pre
 
 The build should produce two files: lib/poems/libpoems.a and
 lib/poems/Makefile.lammps.  The latter is copied from an existing
@@ -1127,9 +1251,10 @@ follow the instructions in lib/reax/README.  You can also do it in one
 step from the lammps/src dir, using a command like these, which simply
 invoke the lib/reax/Install.py script with the specified args:
 
-make lib-reax                      # print help message
-make lib-reax args="-m gfortran"   # build with GNU Fortran compiler
-make lib-reax args="-m ifort"      # build with Intel ifort compiler :pre
+make lib-reax                    # print help message
+make lib-reax args="-m serial"   # build with GNU Fortran compiler (settings as with "make serial")
+make lib-reax args="-m mpi"      # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-reax args="-m ifort"    # build with Intel ifort compiler :pre
 
 The build should produce two files: lib/reax/libreax.a and
 lib/reax/Makefile.lammps.  The latter is copied from an existing
@@ -1280,7 +1405,7 @@ make machine :pre
 [Supporting info:]
 
 src/SNAP: filenames -> commands
-"pair snap"_pair_snap.html
+"pair_style snap"_pair_snap.html
 "compute sna/atom"_compute_sna_atom.html
 "compute snad/atom"_compute_sna_atom.html
 "compute snav/atom"_compute_sna_atom.html
@@ -1346,15 +1471,15 @@ one step from the lammps/src dir, using a command like these, which
 simply invoke the lib/voronoi/Install.py script with the specified
 args:
 
-make lib-voronoi                                # print help message
-make lib-voronoi args="-g -b -l"                # download and build in default lib/voronoi/voro++-0.4.6
-make lib-voronoi args="-h . voro++ -g -b -l"    # download and build in lib/voronoi/voro++
-make lib-voronoi args="-h ~ voro++ -g -b -l"    # download and build in ~/voro++ :pre
+make lib-voronoi                          # print help message
+make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
+make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
+make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre
 
-Note that the final -l switch is to create 2 symbolic (soft) links,
-"includelink" and "liblink", in lib/voronoi to point to the Voro++ src
-dir.  When LAMMPS builds it will use these links.  You should not need
-to edit the lib/voronoi/Makefile.lammps file.
+Note that 2 symbolic (soft) links, "includelink" and "liblink", are
+created in lib/voronoi to point to the Voro++ src dir.  When LAMMPS
+builds in src it will use these links.  You should not need to edit
+the lib/voronoi/Makefile.lammps file.
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -1396,7 +1521,8 @@ from the lammps/src dir, using a command like these, which simply
 invoke the lib/atc/Install.py script with the specified args:
 
 make lib-atc                      # print help message
-make lib-atc args="-m g++"        # build with GNU g++ compiler
+make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
 make lib-atc args="-m icc"        # build with Intel icc compiler :pre
 
 The build should produce two files: lib/atc/libatc.a and
@@ -1413,8 +1539,10 @@ can either exist on your system, or you can use the files provided in
 lib/linalg.  In the latter case you also need to build the library
 in lib/linalg with a command like these:
 
-make lib-linalg                      # print help message
-make lib-atc args="-m gfortran"      # build with GNU Fortran compiler
+make lib-linalg                     # print help message
+make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -1454,9 +1582,10 @@ follow the instructions in lib/awpmd/README.  You can also do it in
 one step from the lammps/src dir, using a command like these, which
 simply invoke the lib/awpmd/Install.py script with the specified args:
 
-make lib-awpmd                      # print help message
-make lib-awpmd args="-m g++"        # build with GNU g++ compiler
-make lib-awpmd args="-m icc"        # build with Intel icc compiler :pre
+make lib-awpmd                   # print help message
+make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+make lib-awpmd args="-m icc"     # build with Intel icc compiler :pre
 
 The build should produce two files: lib/awpmd/libawpmd.a and
 lib/awpmd/Makefile.lammps.  The latter is copied from an existing
@@ -1472,8 +1601,10 @@ these can either exist on your system, or you can use the files
 provided in lib/linalg.  In the latter case you also need to build the
 library in lib/linalg with a command like these:
 
-make lib-linalg                      # print help message
-make lib-atc args="-m gfortran"      # build with GNU Fortran compiler
+make lib-linalg                     # print help message
+make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -1488,7 +1619,7 @@ make machine :pre
 
 src/USER-AWPMD: filenames -> commands
 src/USER-AWPMD/README
-"pair awpmd/cut"_pair_awpmd.html
+"pair_style awpmd/cut"_pair_awpmd.html
 examples/USER/awpmd :ul
 
 :line
@@ -1566,9 +1697,11 @@ Restraints.  A "fix colvars"_fix_colvars.html command is implemented
 which wraps a COLVARS library, which implements these methods.
 simulations.
 
-[Authors:] Axel Kohlmeyer (Temple U).  The COLVARS library was written
-by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
-Jerome Henin (LISM, CNRS, Marseille, France).
+[Authors:] The COLVARS library is written and maintained by
+Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA)
+and Jerome Henin (LISM, CNRS, Marseille, France), originally for
+the NAMD MD code, but with portability in mind.  Axel Kohlmeyer
+(Temple U) provided the interface to LAMMPS.
 
 [Install or un-install:]
 
@@ -1580,7 +1713,9 @@ which simply invoke the lib/colvars/Install.py script with the
 specified args:
 
 make lib-colvars                      # print help message
-make lib-colvars args="-m g++"        # build with GNU g++ compiler :pre
+make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
+make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled :pre
 
 The build should produce two files: lib/colvars/libcolvars.a and
 lib/colvars/Makefile.lammps.  The latter is copied from an existing
@@ -1673,12 +1808,12 @@ src/USER-DPD: filenames -> commands
 "fix eos/table/rx"_fix_eos_table_rx.html
 "fix shardlow"_fix_shardlow.html
 "fix rx"_fix_rx.html
-"pair table/rx"_pair_table_rx.html
-"pair dpd/fdt"_pair_dpd_fdt.html
-"pair dpd/fdt/energy"_pair_dpd_fdt.html
-"pair exp6/rx"_pair_exp6_rx.html
-"pair multi/lucy"_pair_multi_lucy.html
-"pair multi/lucy/rx"_pair_multi_lucy_rx.html
+"pair_style table/rx"_pair_table_rx.html
+"pair_style dpd/fdt"_pair_dpd_fdt.html
+"pair_style dpd/fdt/energy"_pair_dpd_fdt.html
+"pair_style exp6/rx"_pair_exp6_rx.html
+"pair_style multi/lucy"_pair_multi_lucy.html
+"pair_style multi/lucy/rx"_pair_multi_lucy_rx.html
 examples/USER/dpd :ul
 
 :line
@@ -1713,8 +1848,8 @@ src/USER-DRUDE/README
 "fix drude"_fix_drude.html
 "fix drude/transform/*"_fix_drude_transform.html
 "compute temp/drude"_compute_temp_drude.html
-"pair thole"_pair_thole.html
-"pair lj/cut/thole/long"_pair_thole.html
+"pair_style thole"_pair_thole.html
+"pair_style lj/cut/thole/long"_pair_thole.html
 examples/USER/drude
 tools/drude :ul
 
@@ -1752,8 +1887,8 @@ src/USER-EFF/README
 "fix npt/eff"_fix_nh_eff.html
 "fix langevin/eff"_fix_langevin_eff.html
 "compute temp/eff"_compute_temp_eff.html
-"pair eff/cut"_pair_eff.html
-"pair eff/inline"_pair_eff.html
+"pair_style eff/cut"_pair_eff.html
+"pair_style eff/inline"_pair_eff.html
 examples/USER/eff
 tools/eff/README
 tools/eff
@@ -1868,7 +2003,12 @@ Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP
 packages, which have styles optimized for CPUs and KNLs.
 
 You need to have an Intel compiler, version 14 or higher to take full
-advantage of this package.
+advantage of this package. While compilation with GNU compilers is
+supported, performance will be suboptimal.
+
+NOTE: the USER-INTEL package contains styles that require using the
+-restrict flag, when compiling with Intel compilers.
+
 
 [Author:] Mike Brown (Intel).
 
@@ -1885,17 +2025,17 @@ For CPUs:
 
 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
 CCFLAGS =	-g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
-                -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+-fno-alias -ansi-alias -restrict $(OPTFLAGS)
 LINKFLAGS =	-g -qopenmp $(OPTFLAGS)
-LIB =           -ltbbmalloc -ltbbmalloc_proxy
+LIB =           -ltbbmalloc -ltbbmalloc_proxy :pre
 
 For KNLs:
 
 OPTFLAGS =      -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
 CCFLAGS =	-g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
-                -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+-fno-alias -ansi-alias -restrict $(OPTFLAGS)
 LINKFLAGS =	-g -qopenmp $(OPTFLAGS)
-LIB =           -ltbbmalloc
+LIB =           -ltbbmalloc :pre
 
 Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner.
@@ -2078,11 +2218,47 @@ make machine :pre
 
 src/USER-MEAMC: filenames -> commands
 src/USER-MEAMC/README
-"pair meam/c"_pair_meam.html
+"pair_style meam/c"_pair_meam.html
 examples/meam :ul
 
 :line
 
+USER-MESO package :link(USER-MESO),h4
+
+[Contents:]
+
+Several extensions of the 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
+advection-diffuion-reaction systems. The equations of motion of these
+DPD extensions are integrated through a modified velocity-Verlet (MVV)
+algorithm.
+
+[Author:] Zhen Li (Division of Applied Mathematics, Brown University)
+
+[Install or un-install:]
+  
+make yes-user-meso
+make machine :pre
+ 
+make no-user-meso
+make machine :pre
+ 
+[Supporting info:]
+
+src/USER-MESO: filenames -> commands
+src/USER-MESO/README
+"atom_style edpd"_atom_style.html
+"pair_style edpd"_pair_meso.html
+"pair_style mdpd"_pair_meso.html
+"pair_style tdpd"_pair_meso.html
+"fix mvv/dpd"_fix_mvv_dpd.html
+examples/USER/meso
+http://lammps.sandia.gov/movies.html#mesodpd :ul
+
+:line
+
 USER-MOLFILE package :link(USER-MOLFILE),h4
 
 [Contents:]
@@ -2200,11 +2376,15 @@ CPUs.
 
 [Author:] Axel Kohlmeyer (Temple U).
 
-NOTE: The compile flags "-restrict" and "-fopenmp" must be used to
-build LAMMPS with the USER-OMP package, as well as the link flag
-"-fopenmp".  They should be added to the CCFLAGS and LINKFLAGS lines
-of your Makefile.machine.  See src/MAKE/OPTIONS/Makefile.omp for an
-example.
+NOTE: To enable multi-threading support the compile flag "-fopenmp"
+and the link flag "-fopenmp" (for GNU compilers, you have to look up
+the equivalent flags for other compilers) must be used to build LAMMPS.
+When using Intel compilers, also the "-restrict" flag is required.
+The USER-OMP package can be compiled without enabling OpenMP; then
+all code will be compiled as serial and the only improvement over the
+regular styles are some data access optimization. These flags should
+be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine.
+See src/MAKE/OPTIONS/Makefile.omp for an example.
 
 Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner:
@@ -2217,7 +2397,7 @@ make machine :pre
 make no-user-omp
 make machine :pre
 
-CCFLAGS: add -fopenmp and -restrict
+CCFLAGS: add -fopenmp (and -restrict when using Intel compilers)
 LINKFLAGS: add -fopenmp :ul
 
 [Supporting info:]
@@ -2286,12 +2466,14 @@ without changes to LAMMPS itself.
 
 Before building LAMMPS with this package, you must first build the
 QMMM library in lib/qmmm.  You can do this manually if you prefer;
-follow the first two steps explained in lib/colvars/README.  You can
+follow the first two steps explained in lib/qmmm/README.  You can
 also do it in one step from the lammps/src dir, using a command like
-these, which simply invoke the lib/colvars/Install.py script with the
+these, which simply invoke the lib/qmmm/Install.py script with the
 specified args:
 
 make lib-qmmm                      # print help message
+make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
+make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
 make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler :pre
 
 The build should produce two files: lib/qmmm/libqmmm.a and
@@ -2468,15 +2650,13 @@ follow the instructions in lib/smd/README.  You can also do it in one
 step from the lammps/src dir, using a command like these, which simply
 invoke the lib/smd/Install.py script with the specified args:
 
-make lib-smd                            # print help message
-make lib-smd args="-g -l"               # download in default lib/smd/eigen-eigen-*
-make lib-smd args="-h . eigen -g -l"    # download in lib/smd/eigen
-make lib-smd args="-h ~ eigen -g -l"    # download and build in ~/eigen :pre
+make lib-smd                         # print help message
+make lib-smd args="-b"               # download and build in default lib/smd/eigen-eigen-...
+make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3 :pre
 
-Note that the final -l switch is to create a symbolic (soft) link
-named "includelink" in lib/smd to point to the Eigen dir.  When LAMMPS
-builds it will use this link.  You should not need to edit the
-lib/smd/Makefile.lammps file.
+Note that a symbolic (soft) link named "includelink" is created in
+lib/smd to point to the Eigen dir.  When LAMMPS builds it will use
+this link.  You should not need to edit the lib/smd/Makefile.lammps file.
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -2592,13 +2772,44 @@ examples/USER/tally :ul
 
 :line
 
+USER-UEF package :link(USER-UEF),h4
+
+[Contents:]
+
+A fix style for the integration of the equations of motion under
+extensional flow with proper boundary conditions, as well as several
+supporting compute styles and an output option.
+
+[Author:] David Nicholson (MIT).
+
+[Install or un-install:]
+
+make yes-user-uef
+make machine :pre
+
+make no-user-uef
+make machine :pre
+
+[Supporting info:]
+
+src/USER-UEF: filenames -> commands
+src/USER-UEF/README
+"fix nvt/uef"_fix_nh_uef.html
+"fix npt/uef"_fix_nh_uef.html
+"compute pressure/uef"_compute_pressure_uef.html
+"compute temp/uef"_compute_temp_uef.html
+"dump cfg/uef"_dump_cfg_uef.html
+examples/uef :ul
+
+:line
+
 USER-VTK package :link(USER-VTK),h4
 
 [Contents:]
 
-A "dump vtk"_dump_vtk.html command which outputs
-snapshot info in the "VTK format"_vtk, enabling visualization by
-"Paraview"_paraview or other visuzlization packages.
+A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
+"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
+other visuzlization packages.
 
 :link(vtk,http://www.vtk.org)
 :link(paraview,http://www.paraview.org)

doc/src/Section_start.txt

@@ -536,7 +536,7 @@ You should get the executable lmp_foo when the build is complete.
 
 :line
 
-Errors that can occur when making LAMMPS: h5 :link(start_2_3)
+Errors that can occur when making LAMMPS :h5 :link(start_2_3)
 
 If an error occurs when building LAMMPS, the compiler or linker will
 state very explicitly what the problem is.  The error message should
@@ -587,8 +587,7 @@ Typing "make clean-all" or "make clean-machine" will delete *.o object
 files created when LAMMPS is built, for either all builds or for a
 particular machine.
 
-Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
--DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
+Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
 
 As explained above, any of these 3 settings can be specified on the
 LMP_INC line in your low-level src/MAKE/Makefile.foo.
@@ -659,22 +658,29 @@ utilities.
 For Cygwin and the MinGW cross-compilers, suitable makefiles are
 provided in src/MAKE/MACHINES. When using other compilers, like
 Visual C++ or Intel compilers for Windows, you may have to implement
-your own build system. Since none of the current LAMMPS core developers
-has significant experience building executables on Windows, we are
-happy to distribute contributed instructions and modifications, but
-we cannot provide support for those.
+your own build system. Due to differences between the Windows OS
+and Windows system libraries to Unix-like environments like Linux
+or MacOS, when compiling for Windows a few adjustments may be needed:
+
+Do [not] set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable)
+Add -lwsock32 -lpsapi to the linker flags (see LIB makefile variable)
+Try adding -static-libgcc or -static or both to the linker flags when your LAMMPS executable complains about missing .dll files  :ul
+
+Since none of the current LAMMPS core developers has significant
+experience building executables on Windows, we are happy to distribute
+contributed instructions and modifications to improve the situation,
+but we cannot provide support for those.
 
 With the so-called "Anniversary Update" to Windows 10, there is a
 Ubuntu Linux subsystem available for Windows, that can be installed
 and then used to compile/install LAMMPS as if you are running on a
 Ubuntu Linux system instead of Windows.
 
-As an alternative, you can download "daily builds" (and some older
-versions) of the installer packages from
-"rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html.
-These executables are built with most optional packages and the
-download includes documentation, potential files, some tools and
-many examples, but no source code.
+As an alternative, you can download pre-compiled installer packages from
+"packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html.
+These executables are built with most optional packages included and the
+download includes documentation, potential files, some tools and many
+examples, but no source code.
 
 :line
 
@@ -909,12 +915,12 @@ src/MAKE/OPTIONS, which include the settings.  Note that the
 USER-INTEL and KOKKOS packages can use settings that build LAMMPS for
 different hardware.  The USER-INTEL package can be compiled for Intel
 CPUs and KNLs; the KOKKOS package builds for CPUs (OpenMP), GPUs
-(Cuda), and Intel KNLs.
+(CUDA), and Intel KNLs.
 
 Makefile.intel_cpu
 Makefile.intel_phi
 Makefile.kokkos_omp
-Makefile.kokkos_cuda
+Makefile.kokkos_cuda_mpi
 Makefile.kokkos_phi
 Makefile.omp
 Makefile.opt :ul
@@ -1087,7 +1093,7 @@ LAMMPS to be built with one or more of its optional packages.
 :line
 
 On a Windows box, you can skip making LAMMPS and simply download an
-installer package from "here"_http://rpm.lammps.org/windows.html
+installer package from "here"_http://packages.lammps.org/windows.html
 
 For running the non-MPI executable, follow these steps:
 
@@ -1099,18 +1105,27 @@ the [in.lj] input from the bench folder. (e.g. by typing: cd "Documents"). :l
 
 At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj]
 with the name of your LAMMPS input script. :l
+
+The serial executable includes support for multi-threading
+parallelization from the styles in the USER-OMP packages.
+
+To run with, e.g. 4 threads, type "lmp_serial -in in.lj -pk omp 4 -sf omp"
 :ule
 
-For the MPI version, which allows you to run LAMMPS under Windows on
-multiple processors, follow these steps:
+For the MPI version, which allows you to run LAMMPS under Windows with
+the more general message passing parallel library (LAMMPS has been
+designed from ground up to use MPI efficiently), follow these steps:
 
-Download and install
-"MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads
-for Windows. :ulb,l
+Download and install a compatible MPI library binary package:
+for 32-bit Windows
+"mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
+and for 64-bit Windows
+"mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi
+:ulb,l
 
 The LAMMPS Windows installer packages will automatically adjust your
 path for the default location of this MPI package. After the installation
-of the MPICH software, it needs to be integrated into the system.
+of the MPICH2 software, it needs to be integrated into the system.
 For this you need to start a Command Prompt in {Administrator Mode}
 (right click on the icon and select it). Change into the MPICH2
 installation directory, then into the subdirectory [bin] and execute
@@ -1129,7 +1144,7 @@ or
 
 mpiexec -np 4 lmp_mpi -in in.lj :pre
 
-replacing in.lj with the name of your LAMMPS input script. For the latter
+replacing [in.lj] with the name of your LAMMPS input script. For the latter
 case, you may be prompted to enter your password. :l
 
 In this mode, output may not immediately show up on the screen, so if
@@ -1141,6 +1156,11 @@ something like:
 
 lmp_mpi -in in.lj :pre
 
+And the parallel executable also includes OpenMP multi-threading, which
+can be combined with MPI using something like:
+
+mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp :pre
+
 :ule
 
 :line

doc/src/accelerate_gpu.txt

@@ -62,7 +62,7 @@ respectively to your input script.
 [Required hardware/software:]
 
 To use this package, you currently need to have an NVIDIA GPU and
-install the NVIDIA Cuda software on your system:
+install the NVIDIA CUDA software on your system:
 
 Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information
 Go to http://www.nvidia.com/object/cuda_get.html
@@ -74,13 +74,8 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t
 This requires two steps (a,b): build the GPU library, then build
 LAMMPS with the GPU package.
 
-You can do both these steps in one line, using the src/Make.py script,
-described in "Section 4"_Section_packages.html of the manual.
-Type "Make.py -h" for help.  If run from the src directory, this
-command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
-starting Makefile.machine:
-
-Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi :pre
+You can do both these steps in one line as described in
+"Section 4"_Section_packages.html of the manual.
 
 Or you can follow these two (a,b) steps:
 
@@ -90,7 +85,7 @@ The GPU library is in lammps/lib/gpu.  Select a Makefile.machine (in
 lib/gpu) appropriate for your system.  You should pay special
 attention to 3 settings in this makefile.
 
-CUDA_HOME = needs to be where NVIDIA Cuda software is installed on your system
+CUDA_HOME = needs to be where NVIDIA CUDA software is installed on your system
 CUDA_ARCH = needs to be appropriate to your GPUs
 CUDA_PREC = precision (double, mixed, single) you desire :ul
 

doc/src/accelerate_intel.txt

@@ -25,12 +25,14 @@ LAMMPS to run on the CPU cores and coprocessor cores simultaneously.
 [Currently Available USER-INTEL Styles:]
 
 Angle Styles: charmm, harmonic :ulb,l
-Bond Styles: fene, harmonic :l
+Bond Styles: fene, fourier, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
-Fixes: nve, npt, nvt, nvt/sllod :l
+Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l
 Improper Styles: cvff, harmonic :l
-Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
-charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, sw, tersoff :l
+Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long, 
+buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, 
+lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, 
+rebo, sw, tersoff :l
 K-Space Styles: pppm, pppm/disp :l
 :ule
 
@@ -52,11 +54,12 @@ warmup run (for use with offload benchmarks).
 :c,image(JPG/user_intel.png)
 
 Results are speedups obtained on Intel Xeon E5-2697v4 processors
-(code-named Broadwell) and Intel Xeon Phi 7250 processors
-(code-named Knights Landing) with "June 2017" LAMMPS built with
-Intel Parallel Studio 2017 update 2. Results are with 1 MPI task
-per physical core. See {src/USER-INTEL/TEST/README} for the raw
-simulation rates and instructions to reproduce.
+(code-named Broadwell), Intel Xeon Phi 7250 processors (code-named
+Knights Landing), and Intel Xeon Gold 6148 processors (code-named
+Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio
+2017 update 2. Results are with 1 MPI task per physical core. See
+{src/USER-INTEL/TEST/README} for the raw simulation rates and
+instructions to reproduce.
 
 :line
 
@@ -80,6 +83,11 @@ this order :l
 The {newton} setting applies to all atoms, not just atoms shared
 between MPI tasks :l
 Vectorization can change the order for adding pairwise forces :l
+When using the -DLMP_USE_MKL_RNG define (all included intel optimized
+makefiles do) at build time, the random number generator for
+dissipative particle dynamics (pair style dpd/intel) uses the Mersenne
+Twister generator included in the Intel MKL library (that should be
+more robust than the default Masaglia random number generator) :l
 :ule
 
 The precision mode (described below) used with the USER-INTEL
@@ -106,7 +114,7 @@ $t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
 For some of the simple 2-body potentials without long-range
 electrostatics, performance and scalability can be better with
 the "newton off" setting added to the input script :l
-For simulations on higher node counts, add "processors * * * grid 
+For simulations on higher node counts, add "processors * * * grid
 numa" to the beginning of the input script for better scalability :l
 If using {kspace_style pppm} in the input script, add
 "kspace_modify diff ad" for better performance :l
@@ -117,8 +125,8 @@ For Intel Xeon Phi CPUs:
 Runs should be performed using MCDRAM. :ulb,l
 :ule
 
-For simulations using {kspace_style pppm} on Intel CPUs
-supporting AVX-512:
+For simulations using {kspace_style pppm} on Intel CPUs supporting
+AVX-512:
 
 Add "kspace_modify diff ad" to the input script :ulb,l
 The command-line option should be changed to
@@ -225,11 +233,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
 # or psxevars.csh for C-shell
 make intel_cpu_intelmpi :pre
 
-Alternatively, the build can be accomplished with the src/Make.py
-script, described in "Section 4"_Section_packages.html of the
-manual. Type "Make.py -h" for help. For an example:
-
-Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi :pre
+Alternatively this can be done as a single command with
+suitable make command invocations. This is discussed in "Section
+4"_Section_packages.html of the manual.
 
 Note that if you build with support for a Phi coprocessor, the same
 binary can be used on nodes with or without coprocessors installed.
@@ -237,15 +243,17 @@ However, if you do not have coprocessors on your system, building
 without offload support will produce a smaller binary.
 
 The general requirements for Makefiles with the USER-INTEL package
-are as follows. "-DLAMMPS_MEMALIGN=64" is required for CCFLAGS. When
-using Intel compilers, "-restrict" is required and "-qopenmp" is
-highly recommended for CCFLAGS and LINKFLAGS. LIB should include
-"-ltbbmalloc". For builds supporting offload, "-DLMP_INTEL_OFFLOAD"
-is required for CCFLAGS and "-qoffload" is required for LINKFLAGS.
-Other recommended CCFLAG options for best performance are
-"-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2
--no-prec-div". The Make.py command will add all of these
-automatically.
+are as follows. When using Intel compilers, "-restrict" is required 
+and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS. 
+CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads
+are not supported in the build environment) and "-DLMP_USE_MKL_RNG"
+(unless Intel Math Kernel Library (MKL) is not available in the build
+environment). For Intel compilers, LIB should include "-ltbbmalloc" 
+or if the library is not available, "-DLMP_INTEL_NO_TBB" can be added
+to CCFLAGS. For builds supporting offload, "-DLMP_INTEL_OFFLOAD" is
+required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other
+recommended CCFLAG options for best performance are "-O2 -fno-alias
+-ansi-alias -qoverride-limits fp-model fast=2 -no-prec-div".
 
 NOTE: The vectorization and math capabilities can differ depending on
 the CPU. For Intel compilers, the "-x" flag specifies the type of
@@ -362,10 +370,14 @@ intel"_package.html command that can improve performance when using
 "PPPM"_kspace_style.html for long-range electrostatics on processors
 with SMT. It generates an extra pthread for each MPI task. The thread
 is dedicated to performing some of the PPPM calculations and MPI
-communications. On Intel Xeon Phi x200 series CPUs, this will likely
-always improve performance, even on a single node. On Intel Xeon
-processors, using this mode might result in better performance when
-using multiple nodes, depending on the machine. To use this mode,
+communications. This feature requires setting the preprocessor flag
+-DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset
+in the default makefiles ({Makefile.mpi} and {Makefile.serial}) but
+it is set in all makefiles tuned for the USER-INTEL package.  On Intel
+Xeon Phi x200 series CPUs, the LRT feature will likely improve
+performance, even on a single node. On Intel Xeon processors, using
+this mode might result in better performance when using multiple nodes,
+depending on the specific machine configuration. To enable LRT mode,
 specify that the number of OpenMP threads is one less than would
 normally be used for the run and add the "lrt yes" option to the "-pk"
 command-line suffix or "package intel" command. For example, if a run

doc/src/accelerate_kokkos.txt

@@ -60,8 +60,7 @@ More details follow.
 use a C++11 compatible compiler
 make yes-kokkos
 make mpi KOKKOS_DEVICES=OpenMP                 # build with the KOKKOS package
-make kokkos_omp                                # or Makefile.kokkos_omp already has variable set
-Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi   # or one-line build via Make.py :pre
+make kokkos_omp                                # or Makefile.kokkos_omp already has variable set :pre
 
 mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj              # 1 node, 16 MPI tasks/node, no threads
 mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj   # 2 nodes, 1 MPI task/node, 16 threads/task
@@ -82,8 +81,7 @@ use a C++11 compatible compiler
 KOKKOS_DEVICES = Cuda, OpenMP
 KOKKOS_ARCH = Kepler35
 make yes-kokkos
-make machine
-Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda :pre
+make machine :pre
 
 mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj          # one MPI task, 6 threads on CPU
 mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj   # ditto on 4 nodes :pre
@@ -98,8 +96,7 @@ use a C++11 compatible compiler
 KOKKOS_DEVICES = OpenMP
 KOKKOS_ARCH = KNC
 make yes-kokkos
-make machine
-Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi :pre
+make machine :pre
 
 host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
 mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj           # 1 MPI task on 1 Phi, 1*240 = 240
@@ -116,7 +113,7 @@ To build with Kokkos support for CPUs, your compiler must support the
 OpenMP interface.  You should have one or more multi-core CPUs so that
 multiple threads can be launched by each MPI task running on a CPU.
 
-To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
+To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software
 version 7.5 or later must be installed on your system.  See the
 discussion for the "GPU"_accelerate_gpu.html package for details of
 how to check and do this.
@@ -135,13 +132,13 @@ mode like the USER-INTEL package supports.
 You must choose at build time whether to build for CPUs (OpenMP),
 GPUs, or Phi.
 
-You can do any of these in one line, using the src/Make.py script,
-described in "Section 4"_Section_packages.html of the manual.
-Type "Make.py -h" for help.  If run from the src directory, these
-commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
+You can do any of these in one line, using the suitable make command
+line flags as described in "Section 4"_Section_packages.html of the
+manual. If run from the src directory, these
+commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda_mpi, and
 lmp_kokkos_phi.  Note that the OMP and PHI options use
 src/MAKE/Makefile.mpi as the starting Makefile.machine.  The CUDA
-option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.
+option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi.
 
 The latter two steps can be done using the "-k on", "-pk kokkos" and
 "-sf kk" "command-line switches"_Section_start.html#start_6
@@ -162,7 +159,7 @@ CPU-only (only MPI, no threading):
 
 cd lammps/src
 make yes-kokkos
-make kokkos_mpi :pre
+make kokkos_mpi_only :pre
 
 Intel Xeon Phi (Intel Compiler, Intel MPI):
 
@@ -170,11 +167,11 @@ cd lammps/src
 make yes-kokkos
 make kokkos_phi :pre
 
-CPUs and GPUs (with MPICH):
+CPUs and GPUs (with MPICH or OpenMPI):
 
 cd lammps/src
 make yes-kokkos
-make kokkos_cuda_mpich :pre
+make kokkos_cuda_mpi :pre
 
 These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
 make command line which requires a GNU-compatible make command.  Try

doc/src/accelerate_omp.txt

@@ -23,8 +23,7 @@ one or more 16-core nodes.  More details follow.
 use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine
 make yes-user-omp
 make mpi                                   # build with USER-OMP package, if settings added to Makefile.mpi
-make omp                                   # or Makefile.omp already has settings
-Make.py -v -p omp -o mpi -a file mpi       # or one-line build via Make.py :pre
+make omp                                   # or Makefile.omp already has settings :pre
 
 lmp_mpi -sf omp -pk omp 16 < in.script                         # 1 MPI task, 16 threads
 mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task
@@ -40,14 +39,11 @@ each MPI task running on a CPU.
 
 The lines above illustrate how to include/build with the USER-OMP
 package in two steps, using the "make" command.  Or how to do it with
-one command via the src/Make.py script, described in "Section
-4"_Section_packages.html of the manual.  Type "Make.py -h" for
-help.
+one command as described in "Section 4"_Section_packages.html of the manual.
 
 Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
 include "-fopenmp".  Likewise, if you use an Intel compiler, the
-CCFLAGS setting must include "-restrict".  The Make.py command will
-add these automatically.
+CCFLAGS setting must include "-restrict".
 
 [Run with the USER-OMP package from the command line:]
 

doc/src/accelerate_opt.txt

@@ -21,8 +21,7 @@ Here is a quick overview of how to use the OPT package.  More details
 follow.
 
 make yes-opt
-make mpi                               # build with the OPT package
-Make.py -v -p opt -o mpi -a file mpi   # or one-line build via Make.py :pre
+make mpi                               # build with the OPT package :pre
 
 lmp_mpi -sf opt -in in.script                # run in serial
 mpirun -np 4 lmp_mpi -sf opt -in in.script   # run in parallel :pre
@@ -35,13 +34,10 @@ None.
 
 The lines above illustrate how to build LAMMPS with the OPT package in
 two steps, using the "make" command.  Or how to do it with one command
-via the src/Make.py script, described in "Section
-4"_Section_packages.html of the manual.  Type "Make.py -h" for
-help.
+as described in "Section 4"_Section_packages.html of the manual.
 
 Note that if you use an Intel compiler to build with the OPT package,
 the CCFLAGS setting in your Makefile.machine must include "-restrict".
-The Make.py command will add this automatically.
 
 [Run with the OPT package from the command line:]
 

doc/src/atom_modify.txt

@@ -16,7 +16,7 @@ atom_modify keyword values ... :pre
 one or more keyword/value pairs may be appended :ulb,l
 keyword = {id} or {map} or {first} or {sort} :l
    {id} value = {yes} or {no}
-   {map} value = {array} or {hash}
+   {map} value = {yes} or {array} or {hash}
    {first} value = group-ID = group whose atoms will appear first in internal atom lists
    {sort} values = Nfreq binsize
      Nfreq = sort atoms spatially every this many time steps
@@ -25,8 +25,8 @@ keyword = {id} or {map} or {first} or {sort} :l
 
 [Examples:]
 
-atom_modify map hash
-atom_modify map array sort 10000 2.0
+atom_modify map yes
+atom_modify map hash sort 10000 2.0
 atom_modify first colloid :pre
 
 [Description:]
@@ -62,29 +62,33 @@ switch.  This is described in "Section 2.2"_Section_start.html#start_2
 of the manual.  If atom IDs are not used, they must be specified as 0
 for all atoms, e.g. in a data or restart file.
 
-The {map} keyword determines how atom ID lookup is done for molecular
-atom styles.  Lookups are performed by bond (angle, etc) routines in
-LAMMPS to find the local atom index associated with a global atom ID.
+The {map} keyword determines how atoms with specific IDs are found
+when required.  An example are the bond (angle, etc) methods which
+need to find the local index of an atom with a specific global ID
+which is a bond (angle, etc) partner.  LAMMPS performs this operation
+efficiently by creating a "map", which is either an {array} or {hash}
+table, as descibed below.
 
-When the {array} value is used, each processor stores a lookup table
-of length N, where N is the largest atom ID in the system.  This is a
+When the {map} keyword is not specified in your input script, LAMMPS
+only creates a map for "atom_styles"_atom_style.html for molecular
+systems which have permanent bonds (angles, etc).  No map is created
+for atomic systems, since it is normally not needed.  However some
+LAMMPS commands require a map, even for atomic systems, and will
+generate an error if one does not exist.  The {map} keyword thus
+allows you to force the creation of a map.  The {yes} value will
+create either an {array} or {hash} style map, as explained in the next
+paragraph.  The {array} and {hash} values create an atom-style or
+hash-style map respectively.
+
+For an {array}-style map, each processor stores a lookup table of
+length N, where N is the largest atom ID in the system.  This is a
 fast, simple method for many simulations, but requires too much memory
-for large simulations.  The {hash} value uses a hash table to perform
-the lookups.  This can be slightly slower than the {array} method, but
-its memory cost is proportional to the number of atoms owned by a
-processor, i.e. N/P when N is the total number of atoms in the system
-and P is the number of processors.
-
-When this setting is not specified in your input script, LAMMPS
-creates a map, if one is needed, as an array or hash.  See the
-discussion of default values below for how LAMMPS chooses which kind
-of map to build.  Note that atomic systems do not normally need to
-create a map.  However, even in this case some LAMMPS commands will
-create a map to find atoms (and then destroy it), or require a
-permanent map.  An example of the former is the "velocity loop
-all"_velocity.html command, which uses a map when looping over all
-atoms and insuring the same velocity values are assigned to an atom
-ID, no matter which processor owns it.
+for large simulations.  For a {hash}-style map, a hash table is
+created on each processor, which finds an atom ID in constant time
+(independent of the global number of atom IDs).  It can be slightly
+slower than the {array} map, but its memory cost is proportional to
+the number of atoms owned by a processor, i.e. N/P when N is the total
+number of atoms in the system and P is the number of processors.
 
 The {first} keyword allows a "group"_group.html to be specified whose
 atoms will be maintained as the first atoms in each processor's list

doc/src/atom_style.txt

@@ -13,17 +13,19 @@ atom_style command :h3
 atom_style style args :pre
 
 style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
-        {dpd} or {electron} or {ellipsoid} or {full} or {line} or {meso} or \
-        {molecular} or {peri} or {smd} or {sphere} or {tri} or \
-        {template} or {hybrid} :ulb,l
+        {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \
+        {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \
+        {sphere} or {tri} or {template} or {hybrid} :ulb,l
   args = none for any style except the following
-  {body} args = bstyle bstyle-args
-    bstyle = style of body particles
-    bstyle-args = additional arguments specific to the bstyle
-                  see the "body"_body.html doc page for details
-  {template} args = template-ID
-    template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
-  {hybrid} args = list of one or more sub-styles, each with their args :pre
+    {body} args = bstyle bstyle-args
+      bstyle = style of body particles
+      bstyle-args = additional arguments specific to the bstyle
+                    see the "body"_body.html doc page for details
+    {tdpd} arg = Nspecies
+      Nspecies = # of chemical species
+    {template} arg = template-ID
+      template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
+    {hybrid} args = list of one or more sub-styles, each with their args :pre
 
 accelerated styles (with same args) = {angle/kk} or {atomic/kk} or {bond/kk} or {charge/kk} or {full/kk} or {molecular/kk} :l
 :ule
@@ -36,7 +38,8 @@ atom_style full
 atom_style body nparticle 2 10
 atom_style hybrid charge bond
 atom_style hybrid charge body nparticle 2 5
-atom_style template myMols :pre
+atom_style template myMols 
+atom_style tdpd 2 :pre
 
 [Description:]
 
@@ -74,6 +77,9 @@ quantities.
 {charge} | charge | atomic system with charges |
 {dipole} | charge and dipole moment | system with dipolar particles |
 {dpd} | internal temperature and internal energies | DPD particles |
+{edpd} | temperature and heat capacity | eDPD particles |
+{mdpd} | density | mDPD particles |
+{tdpd} | chemical concentration | tDPD particles |
 {electron} | charge and spin and eradius | electronic force field |
 {ellipsoid} | shape, quaternion, angular momentum | aspherical particles |
 {full} | molecular + charge | bio-molecules |
@@ -145,6 +151,19 @@ properties with internal temperature (dpdTheta), internal conductive
 energy (uCond), internal mechanical energy (uMech), and internal
 chemical energy (uChem).
 
+The {edpd} style is for energy-conserving dissipative particle
+dynamics (eDPD) particles which store a temperature (edpd_temp), and
+heat capacity(edpd_cv).
+
+The {mdpd} style is for many-body dissipative particle dynamics (mDPD)
+particles which store a density (rho) for considering
+density-dependent many-body interactions.
+
+The {tdpd} style is for transport dissipative particle dynamics (tDPD)
+particles which store a set of chemical concentration. An integer
+"cc_species" is required to specify the number of chemical species
+involved in a tDPD system.
+
 The {meso} style is for smoothed particle hydrodynamics (SPH)
 particles which store a density (rho), energy (e), and heat capacity
 (cv).
@@ -284,6 +303,11 @@ force fields"_pair_eff.html.
 The {dpd} style is part of the USER-DPD package for dissipative
 particle dynamics (DPD).
 
+The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package 
+for energy-conserving dissipative particle dynamics (eDPD), many-body 
+dissipative particle dynamics (mDPD), and transport dissipative particle 
+dynamics (tDPD), respectively.
+
 The {meso} style is part of the USER-SPH package for smoothed particle
 hydrodynamics (SPH).  See "this PDF
 guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.

doc/src/bond_gromos.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,Section_commands.html#comm)
+
+:line
+
+bond_style gromos command :h3
+bond_style gromos/omp command :h3
+
+[Syntax:]
+
+bond_style gromos :pre
+
+[Examples:]
+
+bond_style gromos
+bond_coeff 5 80.0 1.2 :pre
+
+[Description:]
+
+The {gromos} bond style uses the potential
+
+:c,image(Eqs/bond_gromos.jpg)
+
+where r0 is the equilibrium bond distance.  Note that the usual 1/4
+factor is included in K.
+
+The following coefficients must be defined for each bond type via the
+"bond_coeff"_bond_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+K (energy/distance^4)
+r0 (distance) :ul
+
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+MOLECULE package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
+
+[Related commands:]
+
+"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
+
+[Default:] none

doc/src/bonds.txt

@@ -8,6 +8,7 @@ Bond Styles :h1
    bond_class2
    bond_fene
    bond_fene_expand
+   bond_gromos
    bond_harmonic
    bond_harmonic_shift
    bond_harmonic_shift_cut

doc/src/commands.txt

@@ -32,6 +32,7 @@ Commands :h1
    dimension
    displace_atoms
    dump
+   dump_cfg_uef
    dump_h5md
    dump_image
    dump_modify
@@ -92,6 +93,7 @@ Commands :h1
    tad
    temper
    temper_grem
+   temper_npt
    thermo
    thermo_modify
    thermo_style

doc/src/compute.txt

@@ -169,6 +169,7 @@ by users which are included in the LAMMPS distribution.  The list of
 these with links to the individual styles are given in the compute
 section of "this page"_Section_commands.html#cmd_5.
 
+"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
 "angle/local"_compute_bond_local.html - theta and energy of each angle
 "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
 "body/local"_compute_body_local.html - attributes of body sub-particles
@@ -191,6 +192,7 @@ section of "this page"_Section_commands.html#cmd_5.
 "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
 "erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
 "event/displace"_compute_event_displace.html - detect event on atom displacement
+"fragment/atom"_compute_cluster_atom.html - fragment ID for each atom
 "group/group"_compute_group_group.html - energy/force between two groups of atoms
 "gyration"_compute_gyration.html - radius of gyration of group of atoms
 "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk

doc/src/compute_cluster_atom.txt

@@ -7,37 +7,62 @@
 :line
 
 compute cluster/atom command :h3
+compute fragment/atom command :h3
+compute aggregate/atom command :h3
 
 [Syntax:]
 
-compute ID group-ID cluster/atom cutoff :pre
+compute ID group-ID cluster/atom cutoff
+compute ID group-ID fragment/atom
+compute ID group-ID aggregate/atom cutoff :pre
 
 ID, group-ID are documented in "compute"_compute.html command
-cluster/atom = style name of this compute command
+{cluster/atom} or {fragment/atom} or {aggregate/atom} = style name of this compute command
 cutoff = distance within which to label atoms as part of same cluster (distance units) :ul
 
 [Examples:]
 
-compute 1 all cluster/atom 1.0 :pre
+compute 1 all cluster/atom 3.5
+compute 1 all fragment/atom :pre
+compute 1 all aggregate/atom 3.5 :pre
 
 [Description:]
 
-Define a computation that assigns each atom a cluster ID.
+Define a computation that assigns each atom a cluster, fragement,
+or aggregate ID.
 
 A cluster is defined as a set of atoms, each of which is within the
 cutoff distance from one or more other atoms in the cluster.  If an
 atom has no neighbors within the cutoff distance, then it is a 1-atom
-cluster.  The ID of every atom in the cluster will be the smallest
-atom ID of any atom in the cluster.
+cluster.
+
+A fragment is similarly defined as a set of atoms, each of
+which has an explicit bond (i.e. defined via a "data file"_read_data.html,
+the "create_bonds"_create_bonds.html command, or through fixes like
+"fix bond/create"_fix_bond_create.html, "fix bond/swap"_fix_bond_swap.html,
+or "fix bond/break"_fix_bond_break.html).  The cluster ID or fragment ID
+of every atom in the cluster will be set to the smallest atom ID of any atom
+in the cluster or fragment, respectively.
+
+An aggregate is defined by combining the rules for clusters and
+fragments, i.e. a set of atoms, where each of it is within the cutoff
+distance from one or more atoms within a fragment that is part of
+the same cluster. This measure can be used to track molecular assemblies
+like micelles.
 
 Only atoms in the compute group are clustered and assigned cluster
-IDs.  Atoms not in the compute group are assigned a cluster ID = 0.
+IDs. Atoms not in the compute group are assigned a cluster ID = 0.
+For fragments, only bonds where [both] atoms of the bond are included
+in the compute group are assigned to fragments, so that only fragmets
+are detected where [all] atoms are in the compute group. Thus atoms
+may be included in the compute group, yes still have a fragment ID of 0.
 
-The neighbor list needed to compute this quantity is constructed each
-time the calculation is performed (i.e. each time a snapshot of atoms
-is dumped).  Thus it can be inefficient to compute/dump this quantity
-too frequently or to have multiple compute/dump commands, each of a
-{cluster/atom} style.
+For computes {cluster/atom} and {aggregate/atom} the neighbor list needed
+to compute this quantity is constructed each time the calculation is
+performed (i.e. each time a snapshot of atoms is dumped).  Thus it can be
+inefficient to compute/dump this quantity too frequently or to have
+multiple compute/dump commands, each of a {cluster/atom} or
+{aggregate/atom} style.
 
 NOTE: If you have a bonded system, then the settings of
 "special_bonds"_special_bonds.html command can remove pairwise

doc/src/compute_edpd_temp_atom.txt

@@ -0,0 +1,62 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute edpd/temp/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID edpd/temp/atom :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+edpd/temp/atom = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all edpd/temp/atom :pre
+
+[Description:]
+
+Define a computation that calculates the per-atom temperature
+for each eDPD particle in a group.
+
+The temperature is a local temperature derived from the internal energy 
+of each eDPD particle based on the local equilibrium hypothesis.
+For more details please see "(Espanol1997)"_#Espanol1997 and
+"(Li2014)"_#Li2014a.
+
+[Output info:]
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+"Section 6.15"_Section_howto.html#howto_15 for an overview of
+LAMMPS output options.
+
+The per-atom vector values will be in temperature "units"_units.html.
+
+[Restrictions:]
+
+This compute is part of the USER-MESO package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"pair_style edpd"_pair_meso.html
+
+[Default:] none
+
+:line
+
+:link(Espanol1997)
+[(Espanol1997)] Espanol, Europhys Lett, 40(6): 631-636 (1997).  DOI:
+10.1209/epl/i1997-00515-8
+
+:link(Li2014a)
+[(Li2014)] Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265:
+113-127 (2014).  DOI: 10.1016/j.jcp.2014.02.003.
+

doc/src/compute_pressure_uef.txt

@@ -0,0 +1,61 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute pressure/uef command :h3
+
+[Syntax:]
+
+compute ID group-ID pressure/uef temp-ID keyword ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+pressure/uef = style name of this compute command
+temp-ID = ID of compute that calculates temperature, can be NULL if not needed
+zero or more keywords may be appended
+keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
+
+[Examples:]
+
+compute 1 all pressure/uef my_temp_uef
+compute 2 all pressure/uef my_temp_uef virial :pre
+
+[Description:]
+
+This command is used to compute the pressure tensor in  
+the reference frame of the applied flow field when
+"fix nvt/uef"_fix_nh_uef.html" or 
+"fix npt/uef"_fix_nh_uef.html" is used. 
+It is not necessary to use this command to compute the scalar
+value of the pressure. A "compute pressure"_compute_pressure.html
+may be used for that purpose.
+
+The keywords and output information are documented in 
+"compute_pressure"_compute_pressure.html.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF package. It is only enabled if
+LAMMPS was built with that package. See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+This command can only be used when "fix nvt/uef"_fix_nh_uef.html
+or "fix npt/uef"_fix_nh_uef.html is active.
+
+The kinetic contribution to the pressure tensor
+will be accurate only when 
+the compute specificed by {temp-ID} is a 
+"compute temp/uef"_compute_temp_uef.html.
+
+[Related commands:]
+
+"compute pressure"_compute_pressure.html,
+"fix nvt/uef"_fix_nh_uef.html,
+"compute temp/uef"_compute_temp_uef.html
+
+[Default:] none
+
+

doc/src/compute_tdpd_cc_atom.txt

@@ -0,0 +1,60 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute tdpd/cc/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID tdpd/cc/atom index :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+tdpd/cc/atom = style name of this compute command 
+index = index of chemical species (1 to Nspecies) :ul
+
+[Examples:]
+
+compute 1 all tdpd/cc/atom 2 :pre
+
+[Description:]
+
+Define a computation that calculates the per-atom chemical
+concentration of a specified species for each tDPD particle in a
+group.
+
+The chemical concentration of each species is defined as the number of
+molecules carried by a tDPD particle for dilute solution.  For more
+details see "(Li2015)"_#Li2015a.
+
+[Output info:]
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+"Section 6.15"_Section_howto.html#howto_15 for an overview of
+LAMMPS output options.
+
+The per-atom vector values will be in the units of chemical species 
+per unit mass.
+
+[Restrictions:]
+
+This compute is part of the USER-MESO package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"pair_style tdpd"_pair_meso.html
+
+[Default:] none
+
+:line
+
+:link(Li2015a)
+[(Li2015)] Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143:
+014101 (2015).  DOI: 10.1063/1.4923254
+

doc/src/compute_temp_uef.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,Section_commands.html#comm)
+
+:line
+
+compute temp/uef command :h3
+
+[Syntax:]
+
+compute ID group-ID temp/uef :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+temp/uef = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all temp/uef 
+compute 2 sel temp/uef :pre
+
+[Description:]
+
+This command is used to compute the kinetic energy tensor in 
+the reference frame of the applied flow field when
+"fix nvt/uef"_fix_nh_uef.html" or
+"fix npt/uef"_fix_nh_uef.html" is used.
+It is not necessary to use this command to compute the scalar
+value of the temperature. A "compute temp"_compute_temp.html 
+may be used for that purpose.
+
+Output information for this command can be found in the
+documentation for "compute temp"_compute_temp.html.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF package. It is only enabled if 
+LAMMPS was built with that package. See the 
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+This command can only be used when "fix nvt/uef"_fix_nh_uef.html 
+or "fix npt/uef"_fix_nh_uef.html is active.
+
+[Related commands:]
+
+"compute temp"_compute_temp.html,
+"fix nvt/uef"_fix_nh_uef.html,
+"compute pressure/uef"_compute_pressure_uef.html
+
+
+[Default:] none

doc/src/compute_voronoi_atom.txt

@@ -217,7 +217,7 @@ This compute is part of the VORONOI package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-It also requiers you have a copy of the Voro++ library built and
+It also requires you have a copy of the Voro++ library built and
 installed on your system.  See instructions on obtaining and
 installing the Voro++ software in the src/VORONOI/README file.
 

doc/src/computes.txt

@@ -30,6 +30,7 @@ Computes :h1
    compute_displace_atom
    compute_dpd
    compute_dpd_atom
+   compute_edpd_temp_atom
    compute_erotate_asphere
    compute_erotate_rigid
    compute_erotate_sphere
@@ -64,6 +65,7 @@ Computes :h1
    compute_pe_atom
    compute_plasticity_atom
    compute_pressure
+   compute_pressure_uef
    compute_property_atom
    compute_property_chunk
    compute_property_local
@@ -95,6 +97,7 @@ Computes :h1
    compute_sna_atom
    compute_stress_atom
    compute_tally
+   compute_tdpd_cc_atom
    compute_temp
    compute_temp_asphere
    compute_temp_body
@@ -112,6 +115,7 @@ Computes :h1
    compute_temp_region_eff
    compute_temp_rotate
    compute_temp_sphere
+   compute_temp_uef
    compute_ti
    compute_torque_chunk
    compute_vacf

doc/src/dihedral_fourier.txt

@@ -7,6 +7,7 @@
 :line
 
 dihedral_style fourier command :h3
+dihedral_style fourier/intel command :h3
 dihedral_style fourier/omp command :h3
 
 [Syntax:]

doc/src/dump_cfg_uef.txt

@@ -0,0 +1,53 @@
+ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+dump cfg/uef command :h3
+
+[Syntax:]
+
+dump ID group-ID cfg/uef N file mass type xs ys zs args :pre
+
+ID = user-assigned name for the dump :ulb,l
+group-ID = ID of the group of atoms to be dumped :l
+N = dump every this many timesteps :l
+file = name of file to write dump info to :l
+args = same as args for "dump custom"_dump.html :pre
+
+:ule
+
+[Examples:]
+
+dump 1 all cfg/uef 10 dump.*.cfg mass type xs ys zs
+dump 2 all cfg/uef 100 dump.*.cfg mass type xs ys zs id c_stress :pre
+
+[Description:]
+
+This command is used to dump atomic coordinates in the
+reference frame of the applied flow field when 
+"fix nvt/uef"_fix_nh_uef.html or
+"fix npt/uef"_fix_nh_uef.html or is used. Only the atomic 
+coordinates and frame-invariant scalar quantities 
+will be in the flow frame. If velocities are selected
+as output, for example, they will not be in the same
+reference frame as the atomic positions.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF package. It is only enabled if
+LAMMPS was built with that package. See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+This command can only be used when "fix nvt/uef"_fix_nh_uef.html
+or "fix npt/uef"_fix_nh_uef.html is active.
+
+[Related commands:]
+
+"dump"_dump.html,
+"fix nvt/uef"_fix_nh_uef.html
+
+[Default:] none

doc/src/dump_modify.txt

@@ -15,8 +15,9 @@ dump_modify dump-ID keyword values ... :pre
 dump-ID = ID of dump to modify :ulb,l
 one or more keyword/value pairs may be appended :l
 these keywords apply to various dump styles :l
-keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
-  {append} arg = {yes} or {no} or {at} N
+keyword = {append} or {at} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
+  {append} arg = {yes} or {no}
+  {at} arg = N
     N = index of frame written upon first dump
   {buffer} arg = {yes} or {no}
   {element} args = E1 E2 ... EN, where N = # of atom types
@@ -141,13 +142,18 @@ and {dcd}.  It also applies only to text output files, not to binary
 or gzipped or image/movie files.  If specified as {yes}, then dump
 snapshots are appended to the end of an existing dump file.  If
 specified as {no}, then a new dump file will be created which will
-overwrite an existing file with the same name.  If the {at} option is present
-({netcdf} only), then the frame to append to can be specified.  Negative values
-are counted from the end of the file.  This keyword can only take effect if the
-dump_modify command is used after the "dump"_dump.html command, but before the
-first command that causes dump snapshots to be output, e.g. a "run"_run.html or
-"minimize"_minimize.html command.  Once the dump file has been opened, this
-keyword has no further effect.
+overwrite an existing file with the same name.
+
+:line
+
+The {at} keyword only applies to the {netcdf} dump style.  It can only
+be used if the {append yes} keyword is also used.  The {N} argument is
+the index of which frame to append to.  A negative value can be
+specified for {N}, which means a frame counted from the end of the
+file.  The {at} keyword can only be used if the dump_modify command is
+before the first command that causes dump snapshots to be output,
+e.g. a "run"_run.html or "minimize"_minimize.html command.  Once the
+dump file has been opened, this keyword has no further effect.
 
 :line
 

doc/src/dump_netcdf.txt

@@ -25,7 +25,8 @@ args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule
 
 dump 1 all netcdf 100 traj.nc type x y z vx vy vz
 dump_modify 1 append yes at -1 thermo yes
-dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre
+dump 1 all netcdf/mpiio 1000 traj.nc id type x y z
+dump 1 all netcdf 1000 traj.*.nc id type x y z :pre
 
 [Description:]
 
@@ -73,4 +74,3 @@ section for more info.
 [Related commands:]
 
 "dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
-

doc/src/fix.txt

@@ -193,6 +193,7 @@ of "this page"_Section_commands.html#cmd_5.
 "halt"_fix_halt.html - terminate a dynamics run or minimization
 "heat"_fix_heat.html - add/subtract momentum-conserving heat
 "indent"_fix_indent.html - impose force due to an indenter
+"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
 "langevin"_fix_langevin.html - Langevin temperature control
 "lineforce"_fix_lineforce.html - constrain atoms to move in a line
 "momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms

doc/src/fix_addforce.txt

@@ -139,6 +139,11 @@ forces added by this fix in a consistent manner.  I.e. there is a
 decrease in potential energy when atoms move in the direction of the
 added force.
 
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the contribution due to the added forces on atoms to the
+system's virial as part of "thermodynamic output"_thermo_style.html.
+The default is {virial no}
+
 The "fix_modify"_fix_modify.html {respa} option is supported by this
 fix. This allows to set at which level of the "r-RESPA"_run_style.html
 integrator the fix is adding its forces. Default is the outermost

doc/src/fix_bond_create.txt

@@ -150,10 +150,9 @@ atoms.  Note that adding a single bond always adds a new 1st neighbor
 but may also induce *many* new 2nd and 3rd neighbors, depending on the
 molecular topology of your system.  The "extra special per atom"
 parameter must typically be set to allow for the new maximum total
-size (1st + 2nd + 3rd neighbors) of this per-atom list.  There are 3
+size (1st + 2nd + 3rd neighbors) of this per-atom list.  There are 2
 ways to do this.  See the "read_data"_read_data.html or
-"create_box"_create_box.html or "special_bonds extra" commands for
-details.
+"create_box"_create_box.html commands for details.
 
 NOTE: Even if you do not use the {atype}, {dtype}, or {itype}
 keywords, the list of topological neighbors is updated for atoms

doc/src/fix_cmap.txt

@@ -97,6 +97,11 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this
 fix to add the potential "energy" of the CMAP interactions system's
 potential energy as part of "thermodynamic output"_thermo_style.html.
 
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the contribution due to the interaction between atoms to
+the system's virial as part of "thermodynamic output"_thermo_style.html.
+The default is {virial yes}
+
 This fix computes a global scalar which can be accessed by various
 "output commands"_Section_howto.html#howto_15.  The scalar is the
 potential energy discussed above.  The scalar value calculated by this

doc/src/fix_deform.txt

@@ -86,11 +86,16 @@ Change the volume and/or shape of the simulation box during a dynamics
 run.  Orthogonal simulation boxes have 3 adjustable parameters
 (x,y,z).  Triclinic (non-orthogonal) simulation boxes have 6
 adjustable parameters (x,y,z,xy,xz,yz).  Any or all of them can be
-adjusted independently and simultaneously by this command.  This fix
-can be used to perform non-equilibrium MD (NEMD) simulations of a
-continuously strained system.  See the "fix
+adjusted independently and simultaneously by this command.  
+
+This fix can be used to perform non-equilibrium MD (NEMD) simulations
+of a continuously strained system.  See the "fix
 nvt/sllod"_fix_nvt_sllod.html and "compute
-temp/deform"_compute_temp_deform.html commands for more details.
+temp/deform"_compute_temp_deform.html commands for more details.  Note
+that simulation of a continuously extended system (extensional flow)
+can be modeled using the "USER-UEF
+package"_Section_packages.html#USER-UEF and its "fix
+commands"_fix_nh_uef.html.
 
 For the {x}, {y}, {z} parameters, the associated dimension cannot be
 shrink-wrapped.  For the {xy}, {yz}, {xz} parameters, the associated

doc/src/fix_dpd_energy.txt

@@ -7,6 +7,7 @@
 :line
 
 fix dpd/energy command :h3
+fix dpd/energy/kk command :h3
 
 [Syntax:]
 
@@ -46,6 +47,29 @@ examples/USER/dpd directory.
 
 :line
 
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 This command is part of the USER-DPD package.  It is only enabled if

doc/src/fix_dpd_source.txt

@@ -0,0 +1,101 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix edpd/source command :h3
+fix tdpd/source command :h3
+
+[Syntax:]
+
+fix ID group-ID edpd/source keyword values ...
+fix ID group-ID tdpd/source cc_index keyword values ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+edpd/source or tdpd/source = style name of this fix command :l
+index (only specified for tdpd/source) = index of chemical species (1 to Nspecies) :l
+keyword = {sphere} or {cuboid} :l
+  {sphere} values = cx,cy,cz,radius,source
+    cx,cy,cz = x,y,z center of spherical domain (distance units)
+    radius = radius of a spherical domain (distance units)
+    source = heat source or concentration source (flux units, see below)
+  {cuboid} values = cx,cy,cz,dLx,dLy,dLz,source
+    cx,cy,cz = x,y,z lower left corner of a cuboid domain (distance units)
+    dLx,dLy,dLz = x,y,z side length of a cuboid domain (distance units)
+    source = heat source or concentration source (flux units, see below) :pre
+:ule
+
+[Examples:]
+
+fix 1 all edpd/source sphere 0.0 0.0 0.0 5.0 0.01
+fix 1 all edpd/source cuboid 0.0 0.0 0.0 20.0 10.0 10.0 -0.01
+fix 1 all tdpd/source 1 sphere 5.0 0.0 0.0 5.0 0.01
+fix 1 all tdpd/source 2 cuboid 0.0 0.0 0.0 20.0 10.0 10.0 0.01 :pre
+
+[Description:]
+
+Fix {edpd/source} adds a heat source as an external heat flux to each
+atom in a spherical or cuboid domain, where the {source} is in units
+of energy/time.  Fix {tdpd/source} adds an external concentration
+source of the chemical species specified by {index} as an external
+concentration flux for each atom in a spherical or cuboid domain,
+where the {source} is in units of mole/volume/time.
+
+This command can be used to give an additional heat/concentration
+source term to atoms in a simulation, such as for a simulation of a
+heat conduction with a source term (see Fig.12 in "(Li2014)"_#Li2014b)
+or diffusion with a source term (see Fig.1 in "(Li2015)"_#Li2015b), as
+an analog of a periodic Poiseuille flow problem.
+
+If the {sphere} keyword is used, the {cx,cy,cz,radius} defines a
+spherical domain to apply the source flux to.
+
+If the {cuboid} keyword is used, the {cx,cy,cz,dLx,dLy,dLz} defines a
+cuboid domain to apply the source flux to.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various "output
+commands"_Section_howto.html#howto_15.  No parameter of this fix can
+be used with the {start/stop} keywords of the "run"_run.html command.
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-MESO package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+Fix {edpd/source} must be used with the "pair_style
+edpd"_pair_meso.html command.  Fix {tdpd/source} must be used with the
+"pair_style tdpd"_pair_meso.html command.
+
+[Related commands:]
+
+"pair_style edpd"_pair_meso.html, "pair_style tdpd"_pair_meso.html,
+"compute edpd/temp/atom"_compute_edpd_temp_atom.html, "compute
+tdpd/cc/atom"_compute_tdpd_cc_atom.html
+
+[Default:] none
+
+:line
+
+:link(Li2014b)
+[(Li2014)] Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis,
+"Energy-conserving dissipative particle dynamics with
+temperature-dependent properties", J. Comput. Phys., 265: 113-127
+(2014). DOI: 10.1016/j.jcp.2014.02.003
+
+:link(Li2015b)
+[(Li2015)] Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis,
+"Transport dissipative particle dynamics model for mesoscopic
+advection-diffusion-reaction problems", J. Chem. Phys., 143: 014101
+(2015).  DOI: 10.1063/1.4923254