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="11 Aug 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
-11 Aug 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_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,
@@ -732,6 +741,7 @@ 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,
@@ -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_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

@@ -96,6 +96,7 @@ Package, Description, Doc page, Example, Library
 "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
@@ -112,7 +113,7 @@ 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)
 
@@ -134,6 +135,7 @@ Package, Description, Doc page, Example, Library
 "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
@@ -148,6 +150,7 @@ 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-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
@@ -694,6 +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:]
@@ -1342,7 +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
@@ -1556,7 +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
@@ -1745,12 +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
@@ -1785,8 +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
 
@@ -1824,8 +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
@@ -2155,11 +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:]
@@ -2673,13 +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
@@ -662,27 +662,25 @@ 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)
+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
+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, but
-we cannot provide support for those.
+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
 
@@ -922,7 +920,7 @@ CPUs and KNLs; the KOKKOS package builds for CPUs (OpenMP), GPUs
 Makefile.intel_cpu
 Makefile.intel_phi
 Makefile.kokkos_omp
-Makefile.kokkos_cuda
+Makefile.kokkos_cuda_mpi
 Makefile.kokkos_phi
 Makefile.omp
 Makefile.opt :ul
@@ -1095,7 +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:
 
@@ -1107,18 +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
@@ -1137,7 +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
@@ -1149,6 +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_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
@@ -235,14 +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".
+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
@@ -359,10 +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

@@ -135,10 +135,10 @@ GPUs, or Phi.
 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, and
+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
@@ -159,7 +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):
 
@@ -167,11 +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/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/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

doc/src/fix_efield.txt

@@ -124,6 +124,11 @@ can include the 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 due to the electric field.
 
+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 adding its forces. Default is the outermost level.

doc/src/fix_eos_table_rx.txt

@@ -7,6 +7,7 @@
 :line
 
 fix eos/table/rx command :h3
+fix eos/table/rx/kk command :h3
 
 [Syntax:]
 
@@ -152,6 +153,29 @@ no      0.93 0.00 0.000 -1.76 :pre
 
 :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_external.txt

@@ -131,6 +131,11 @@ 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 interactions computed by the
+external program 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 stored by this fix

doc/src/fix_latte.txt

@@ -0,0 +1,210 @@
+"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 latte command :h3
+
+[Syntax:]
+
+fix ID group-ID latte peID :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+latte = style name of this fix command
+peID = NULL or ID of compute used to calculate per-atom energy :ul
+
+[Examples:]
+
+fix dftb all latte NULL :pre
+
+[Description:]
+
+This fix style is a wrapper on the self-consistent charge transfer
+density functional based tight binding (DFTB) code LATTE. If you
+download and build LATTE, it can be called as a library by LAMMPS via
+this fix to run dynamics or perform energy minimization using DFTB
+forces and energies computed by LATTE.
+
+LATTE is principally developed and supported by Marc Cawkwell and
+co-workers at Los Alamos National Laboratory (LANL).  See the full
+list of contributors in the src/LATTE/README file.
+
+To use this fix, the LATTE program needs to be compiled as a library
+and linked with LAMMPS.  LATTE can be downloaded (or cloned) from
+"https://github.com/lanl/LATTE"_https://github.com/lanl/LATTE.
+Instructions on how to download and build LATTE on your system can be
+found in the lib/latte/README.  Note that you can also use the "make
+lib-latte" command from the LAMMPS src directory to automate this
+process.
+
+Once LAMMPS is built with the LATTE package, you can run the example
+input scripts for molecular dynamics or energy minimization that are
+found in examples/latte.
+
+A step-by-step tutorial can be follwed at: "LAMMPS-LATTE
+tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS
+
+The {peID} argument is not yet supported by fix latte, so it must be
+specified as NULL.  Eventually it will be used to enable LAMMPS to
+calculate a Coulomb potential as an alternative to LATTE performing
+the calculation.
+
+:line
+
+LATTE is a code for performing self-consistent charge transfer
+tight-binding (SC-TB) calculations of total energies and the forces
+acting on atoms in molecules and solids. This tight-binding method is
+becoming more and more popular and widely used in chemistry,
+biochemistry, material science, etc.  
+
+The SC-TB formalism is derived from an expansion of the Kohn-Sham
+density functional to second order in charge fluctuations about a
+reference charge of overlapping atom-centered densities and bond
+integrals are parameterized using a Slater-Koster tight-binding
+approach. This procedure, which usually is referred to as the DFTB
+method has been described in detail by ("Elstner"_#Elstner) and
+("Finnis"_#Finnis2) and coworkers. 
+
+The work of the LATTE developers follows that of Elstner closely with
+respect to the physical model.  However, the development of LATTE is
+geared principally toward large-scale, long duration, microcanonical
+quantum-based Born-Oppenheimer molecular dynamics (QMD) simulations.
+One of the main bottlenecks of an electronic structure calculation is
+the solution of the generalized eigenvalue problem which scales with
+the cube of the system size O(N^3).
+
+The Theoretical and Computer sciences divisions at Los Alamos National
+Laboratory have accumulated large experience addressing this issue by
+calculating the density matrix directly instead of using
+diagonalization. We typically use a recursive sparse Fermi-operator
+expansion using second-order spectral projection functions
+(SP2-algorithm), which was introduced by Niklasson in 2002
+("Niklasson2002"_#Niklasson2002), ("Rubensson"_#Rubensson),
+("Mniszewski"_#Mniszewski).  When the matrices involved in the
+recursive expansion are sufficiently sparse, the calculation of the
+density matrix scales linearly as a function of the system size O(N).
+
+Another important feature is the extended Lagrangian framework for
+Born-Oppenheimer molecular dynamics (XL-BOMD)
+("Niklasson2008"_#Niklasson2008) ("Niklasson2014"_#Niklasson2014),
+("Niklasson2017"_#Niklasson2017) that allows for a drastic reduction
+or even a complete removal of the iterative self-consistent field
+optimization.  Often only a single density matrix calculation per
+molecular dynamics time step is required, yet total energy stability
+is well maintained.  The SP2 and XL-BOMD techniques enables stable
+linear scaling MD simulations with a very small computational
+overhead.  This opens a number of opportunities in many different
+areas of chemistry and materials science, as we now can simulate
+larger system sizes and longer time scales
+("Cawkwell2012"_#Cawkwell2012), ("Negre2016"_#Negre2016).
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the potential energy computed by LATTE to the 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 LATTE DFTB contribution 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
+fix is "extensive".
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The DFTB forces computed by LATTE via this fix are imposed during an
+energy minimization, invoked by the "minimize"_minimize.html command.
+
+NOTE: If you want the potential energy associated with the DFTB
+forces to be included in the total potential energy of the system (the
+quantity being minimized), you MUST enable the
+"fix_modify"_fix_modify.html {energy} option for this fix.
+
+[Restrictions:]
+
+This fix is part of the LATTE 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.
+
+You must use metal units, as set by the "units"_units command to use
+this fix.
+
+LATTE does not currently compute per-atom energy or per-atom virial
+contributions.  So they will not show up as part of the calculations
+performed by the "compute pe/atom"_compute_pe_atom.html or "compute
+stress/atom"_compute_stress_atom.html commands.
+
+Currently, LAMMPS must be run in serial or as a single MPI task, to
+use this fix.  This is typically not a bottleneck, since LATTE will be
+doing 99% or more of the work to compute quantum-accurate forces.
+
+NOTE: NEB calculations can be done using this fix using multiple
+replicas and running LAMMPS in parallel.  However, each replica must
+be run on a single MPI task.  For details, see the "neb"_neb.html
+command and -partition command-line explained in "Section
+2.6"_Section_start.html#start_6 of the manual.
+
+[Related commands:] none
+
+[Default:] none
+
+:line
+
+:link(Elstner)
+[(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner,
+M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
+7260 (1998).
+
+:link(Elstner1)
+[(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner,
+M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
+7260 (1998).
+
+:link(Finnis2)
+[(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van
+Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998).
+
+:link(Mniszewski)
+[(Mniszewski)] S. M. Mniszewski, M. J. Cawkwell, M. E. Wall,
+J. Mohd-Yusof, N. Bock, T. C.  Germann, and A. M. N. Niklasson,
+J. Chem. Theory Comput., 11, 4644 (2015).
+
+:link(Niklasson2002)
+[(Niklasson2002)] A. M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002).
+
+:link(Rubensson)
+[(Rubensson)] E. H. Rubensson, A. M. N. Niklasson, SIAM
+J. Sci. Comput. 36 (2), 147-170, (2014).
+
+:link(Niklasson2008)
+[(Niklasson2008)] A. M. N. Niklasson, Phys. Rev. Lett., 100, 123004
+(2008).
+
+:link(Niklasson2014)
+[(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys.,
+141, 164123, (2014).
+
+:link(Niklasson2017)
+[(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
+
+:link(Cawkwell2012)
+[(Cawkwell2012)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
+(17), 174308 (2012).
+
+:link(Negre2016)
+[(Negre2016)] C. F. A. Negre, S. M. Mniszewski, M. J. Cawkwell,
+N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp.,
+12, 3063 (2016).

doc/src/fix_modify.txt

@@ -14,10 +14,11 @@ fix_modify fix-ID keyword value ... :pre
 
 fix-ID = ID of the fix to modify :ulb,l
 one or more keyword/value pairs may be appended :l
-keyword = {temp} or {press} or {energy} or {respa} or {dynamic/dof} :l
+keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} :l
   {temp} value = compute ID that calculates a temperature
   {press} value = compute ID that calculates a pressure
   {energy} value = {yes} or {no}
+  {virial} value = {yes} or {no}
   {respa} value = {1} to {max respa level} or {0} (for outermost level)
   {dynamic/dof} value = {yes} or {no}
     yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre
@@ -52,11 +53,10 @@ define their own compute by default, as described in their
 documentation.  Thus this option allows the user to override the
 default method for computing P.
 
-For fixes that calculate a contribution to the potential energy of the
-system, the {energy} keyword will include that contribution in
-thermodynamic output of potential energy.  This is because the {energy
-yes} setting must be specified to include the fix's global or per-atom
-energy in the calculation performed by the "compute
+The {energy} keyword can be used with fixes that support it.
+{energy yes} adds a contribution to the potential energy of the
+system. The fix's global and per-atom
+energy is included in the calculation performed by the "compute
 pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html
 commands.  See the "thermo_style"_thermo_style.html command for info
 on how potential energy is output.  For fixes that tally a global
@@ -69,6 +69,25 @@ are using it when performing an "energy minimization"_minimize.html
 and if you want the energy and forces it produces to be part of the
 optimization criteria.
 
+The {virial} keyword can be used with fixes that support it.
+{virial yes} adds a contribution to the virial of the
+system. The fix's global and per-atom
+virial is included in the calculation performed by the "compute
+pressure"_compute_pressure.html or
+"compute stress/atom"_compute_stress_atom.html
+commands.  See the "thermo_style"_thermo_style.html command for info
+on how pressure is output. 
+
+NOTE: You must specify the {virial yes} setting for a fix if you
+are doing "box relaxation"_fix_box_relax.html and
+if you want virial contribution of the fix to be part of the
+relaxation criteria, although this seems unlikely.
+
+NOTE: This option is only supported by fixes that explicitly say
+so. For some of these (e.g. the
+"fix shake"_fix_shake.html command) the default setting is
+{virial yes}, for others it is {virial no}.
+
 For fixes that set or modify forces, it may be possible to select at
 which "r-RESPA"_run_style.html level the fix operates via the {respa}
 keyword. The RESPA level at which the fix is active can be selected.
@@ -111,4 +130,4 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html
 [Default:]
 
 The option defaults are temp = ID defined by fix, press = ID defined
-by fix, energy = no, respa = 0.
+by fix, energy = no, virial = different for each fix style, respa = 0.

doc/src/fix_mvv_dpd.txt

@@ -0,0 +1,97 @@
+"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 mvv/dpd command :h3
+fix mvv/edpd command :h3
+fix mvv/tdpd command :h3
+
+[Syntax:]
+
+fix ID group-ID mvv/dpd lambda :pre
+fix ID group-ID mvv/edpd lambda :pre
+fix ID group-ID mvv/tdpd lambda :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+mvv/dpd, mvv/edpd, mvv/tdpd = style name of this fix command
+lambda = (optional) relaxation parameter (unitless) :ul
+
+[Examples:]
+
+fix 1 all mvv/dpd
+fix 1 all mvv/dpd 0.5
+fix 1 all mvv/edpd
+fix 1 all mvv/edpd 0.5
+fix 1 all mvv/tdpd
+fix 1 all mvv/tdpd 0.5 :pre
+
+[Description:]
+
+Perform time integration using the modified velocity-Verlet (MVV)
+algorithm to update position and velocity (fix mvv/dpd), or position,
+velocity and temperature (fix mvv/edpd), or position, velocity and
+concentration (fix mvv/tdpd) for particles in the group each timestep.
+
+The modified velocity-Verlet (MVV) algorithm aims to improve the
+stability of the time integrator by using an extrapolated version of
+the velocity for the force evaluation:
+
+:c,image(Eqs/fix_mvv_dpd.jpg)
+
+where the parameter <font size="4">&lambda;</font> depends on the
+specific choice of DPD parameters, and needs to be tuned on a
+case-by-case basis.  Specification of a {lambda} value is opttional.
+If specified, the setting must be from 0.0 to 1.0.  If not specified,
+a default value of 0.5 is used, which effectively reproduces the
+standard velocity-Verlet (VV) scheme.  For more details, see
+"Groot"_#Groot2.
+
+Fix {mvv/dpd} updates the position and velocity of each atom.  It can
+be used with the "pair_style mdpd"_pair_meso.html command or other
+pair styles such as "pair dpd"_pair_dpd.html.
+
+Fix {mvv/edpd} updates the per-atom temperature, in addition to
+position and velocity, and must be used with the "pair_style
+edpd"_pair_meso.html command.
+
+Fix {mvv/tdpd} updates the per-atom chemical concentration, in
+addition to position and velocity, and must be used with the
+"pair_style tdpd"_pair_meso.html command.
+
+: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.
+
+[Related commands:]
+
+"pair_style mdpd"_pair_meso.html, "pair_style edpd"_pair_meso.html,
+"pair_style tdpd"_pair_meso.html
+
+[Default:]
+
+The default value for the optional {lambda} parameter is 0.5.
+
+:line
+
+:link(Groot2)
+[(Groot)] Groot and Warren, J Chem Phys, 107: 4423-4435 (1997).  DOI:
+10.1063/1.474784
+

doc/src/fix_neb.txt

@@ -93,7 +93,7 @@ intermediate replica with the previous and the next image:
 
 Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
 
-Note that in this case the specified {Kspring) is in force/distance
+Note that in this case the specified {Kspring} is in force/distance
 units.
 
 With a value of {ideal}, the spring force is computed as suggested in
@@ -105,7 +105,7 @@ where RD is the "reaction coordinate" see "neb"_neb.html section, and
 RDideal is the ideal RD for which all the images are equally spaced.
 I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where
 I is the replica number).  The meanDist is the average distance
-between replicas.  Note that in this case the specified {Kspring) is
+between replicas.  Note that in this case the specified {Kspring} is
 in force units.
 
 Note that the {ideal} form of nudging can often be more effective at

doc/src/fix_nh.txt

@@ -393,32 +393,36 @@ thermostatting and barostatting.
 :line
 
 These fixes compute a temperature and pressure each timestep.  To do
-this, the fix creates its own computes of style "temp" and "pressure",
-as if one of these two sets of commands had been issued:
+this, the thermostat and barostat fixes create their own computes of
+style "temp" and "pressure", as if one of these sets of commands had
+been issued:
 
+For fix nvt:
 compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp :pre
 
+For fix npt and fix nph:
 compute fix-ID_temp all temp
 compute fix-ID_press all pressure fix-ID_temp :pre
 
-See the "compute temp"_compute_temp.html and "compute
-pressure"_compute_pressure.html commands for details.  Note that the
-IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
-+ underscore + "press".  For fix nvt, the group for the new computes
-is the same as the fix group.  For fix nph and fix npt, the group for
-the new computes is "all" since pressure is computed for the entire
-system.
+For fix nvt, the group for the new temperature compute is the same as
+the fix group.  For fix npt and fix nph, the group for both the new
+temperature and pressure compute is "all" since pressure is computed
+for the entire system.  In the case of fix nph, the temperature
+compute is not used for thermostatting, but just for a kinetic-energy
+contribution to the pressure.  See the "compute
+temp"_compute_temp.html and "compute pressure"_compute_pressure.html
+commands for details.  Note that the IDs of the new computes are the
+fix-ID + underscore + "temp" or fix_ID + underscore + "press".
 
 Note that these are NOT the computes used by thermodynamic output (see
 the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
-and {thermo_press}.  This means you can change the attributes of this
+and {thermo_press}.  This means you can change the attributes of these
 fix's temperature or pressure via the
-"compute_modify"_compute_modify.html command or print this temperature
-or pressure during thermodynamic output via the "thermo_style
-custom"_thermo_style.html command using the appropriate compute-ID.
-It also means that changing attributes of {thermo_temp} or
-{thermo_press} will have no effect on this fix.
+"compute_modify"_compute_modify.html command.  Or you can print this
+temperature or pressure during thermodynamic output via the
+"thermo_style custom"_thermo_style.html command using the appropriate
+compute-ID.  It also means that changing attributes of {thermo_temp}
+or {thermo_press} will have no effect on this fix.
 
 Like other fixes that perform thermostatting, fix nvt and fix npt can
 be used with "compute commands"_compute.html that calculate a

doc/src/fix_nh_uef.txt

@@ -0,0 +1,228 @@
+<"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 nvt/uef command :h3
+fix npt/uef command :h3
+
+[Syntax:]
+
+fix ID group-ID style_name erate edot_x edot_y temp Tstart Tstop Tdamp keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+style_name = {nvt/uef} or {npt/uef} :l
+{Tstart}, {Tstop}, and {Tdamp} are documented in the "fix npt"_fix_nh.html command :l
+{edot_x} and {edot_y} are the strain rates in the x and y directions (1/(time units)) :l
+one or more keyword/value pairs may be appended :l
+keyword = {ext} or {strain} or {iso} or {x} or {y} or {z} or {tchain} or {pchain} or {tloop} or {ploop} or {mtk}
+  {ext} value = {x} or {y} or {z} or {xy} or {yz} or {xz} = external dimensions
+    sets the external dimensions used to calculate the scalar pressure
+  {strain} values = e_x e_y = initial strain
+    usually not needed, but may be needed to resume a run with a data file.
+  {iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, {mtk} keywords
+    documented by the "fix npt"_fix_nh.html command :pre
+:ule
+
+[Examples:]
+
+fix uniax_nvt all nvt/uef temp 400 400 100 erate 0.00001 -0.000005
+fix biax_nvt all nvt/uef temp 400 400 100 erate 0.000005 0.000005
+fix uniax_npt all npt/uef temp 400 400 300 iso 1 1 3000 erate 0.00001 -0.000005 ext yz
+fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000 :pre
+
+[Description:]
+
+This fix can be used to simulate non-equilibrium molecular dynamics
+(NEMD) under diagonal flow fields, including uniaxial and biaxial
+flow.  Simulations under continuous extensional flow may be carried
+out for an indefinite amount of time.  It is an implementation of the
+boundary conditions from "(Dobson)"_#Dobson, and also uses numerical
+lattice reduction as was proposed by "(Hunt)"_#Hunt. The lattice
+reduction algorithm is from "(Semaev)"_Semaev. The fix is intended for
+simulations of homogeneous flows, and integrates the SLLOD equations
+of motion, originally proposed by Hoover and Ladd (see "(Evans and
+Morriss)"_#Sllod).  Additional detail about this implementation can be
+found in "(Nicholson and Rutledge)"_#Nicholson.
+
+Note that NEMD simulations of a continuously strained system can be
+performed using the "fix deform"_fix_deform.html, "fix
+nvt/sllod"_fix_nvt_sllod.html, and "compute
+temp/deform"_compute_temp_deform.html commands.
+
+The applied flow field is set by the {eps} keyword. The values
+{edot_x} and {edot_y} correspond to the strain rates in the xx and yy
+directions.  It is implicitly assumed that the flow field is
+traceless, and therefore the strain rate in the zz direction is eqal
+to -({edot_x} + {edot_y}).
+
+NOTE: Due to an instability in the SLLOD equations under extension,
+"fix momentum"_fix_momentum.html should be used to regularly reset the
+linear momentum.
+
+The boundary conditions require a simulation box that does not have a
+consistent alignment relative to the applied flow field. Since LAMMPS
+utilizes an upper-triangular simulation box, it is not possible to
+express the evolving simulation box in the same coordinate system as
+the flow field.  This fix keeps track of two coordinate systems: the
+flow frame, and the upper triangular LAMMPS frame. The coordinate
+systems are related to each other through the QR decomposition, as is
+illustrated in the image below.
+
+:c,image(JPG/uef_frames.jpg)
+
+During most molecular dynamics operations, the system is represented
+in the LAMMPS frame. Only when the positions and velocities are
+updated is the system rotated to the flow frame, and it is rotated
+back to the LAMMPS frame immediately afterwards. For this reason, all
+vector-valued quantities (except for the tensors from
+"compute_pressure/uef"_compute_pressure_uef.html and
+"compute_temp/uef"_compute_temp_uef.html) will be computed in the
+LAMMPS frame. Rotationally invariant scalar quantities like the
+temperature and hydrostatic pressure are frame-invariant and will be
+computed correctly. Additionally, the system is in the LAMMPS frame
+during all of the output steps, and therefore trajectory files made
+using the dump command will be in the LAMMPS frame unless the
+"dump_cfg/uef"_dump_cfg_uef.html command is used.
+
+:line
+
+Temperature control is achieved with the default Nose-Hoover style
+thermostat documented in "fix npt"_fix_nh.html. When this fix is
+active, only the peculiar velocity of each atom is stored, defined as
+the velocity relative to the streaming velocity. This is in contrast
+to "fix nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame
+velocity, and removes the contribution from the streaming velocity in
+order to compute the temperature.
+
+Pressure control is achieved using the default Nose-Hoover barostat
+documented in "fix npt"_fix_nh.html. There are two ways to control the
+pressure using this fix. The first method involves using the {ext}
+keyword along with the {iso} pressure style. With this method, the
+pressure is controlled by scaling the simulation box isotropically to
+achieve the average pressure only in the directions specified by
+{ext}.  For example, if the {ext} value is set to {xy}, the average
+pressure (Pxx+Pyy)/2 will be controlled.
+
+This example command will control the total hydrostatic pressure under
+uniaxial tension:
+
+fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz :pre
+
+This example command will control the average stress in compression
+directions, which would typically correspond to free surfaces under
+drawing with uniaxial tension:
+
+fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy :pre
+
+The second method for pressure control involves setting the normal
+stresses using the {x}, {y} , and/or {z} keywords. When using this
+method, the same pressure must be specified via {Pstart} and {Pstop}
+for all dimensions controlled. Any choice of pressure conditions that
+would cause LAMMPS to compute a deviatoric stress are not permissible
+and will result in an error. Additionally, all dimensions with
+controlled stress must have the same applied strain rate. The {ext}
+keyword must be set to the default value ({xyz}) when using this
+method.
+
+For example, the following commands will work:
+
+fix f3 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 y 1 1 5 erate -0.5 -0.5
+fix f4 all npt/uef temp 0.7 0.7 0.5 z 1 1 5 erate 0.5 0.5 :pre
+
+The following commands will not work:
+
+fix f5 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 1 1 5 erate -0.5 -0.5
+fix f6 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 2 2 5 erate 0.5 0.5 :pre
+
+:line
+
+These fix computes a temperature and pressure each timestep.  To do
+this, it creates its own computes of style "temp/uef" and
+"pressure/uef", as if one of these two sets of commands had been
+issued:
+
+compute fix-ID_temp group-ID temp/uef
+compute fix-ID_press group-ID pressure/uef fix-ID_temp :pre
+
+compute fix-ID_temp all temp/uef
+compute fix-ID_press all pressure/uef fix-ID_temp :pre
+
+See the "compute temp/uef"_compute_temp_uef.html and "compute
+pressure/uef"_compute_pressure_uef.html commands for details.  Note
+that the IDs of the new computes are the fix-ID + underscore + "temp"
+or fix_ID + underscore + "press".
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+The fix writes the state of all the thermostat and barostat variables,
+as well as the cumulative strain applied, to "binary restart
+files"_restart.html.  See the "read_restart"_read_restart.html command
+for info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+NOTE: It is not necessary to set the {strain} keyword when resuming a
+run from a restart file. Only for resuming from data files, which do
+not contain the cumulative applied strain, will this keyword be
+necessary.
+
+This fix can be used with the "fix_modify"_fix_modify.html {temp} and
+{press} options. The temperature and pressure computes used must be of
+type {temp/uef} and {pressure/uef}.
+
+This fix computes the same global scalar and vecor quantities as "fix
+npt"_fix_nh.html.
+
+The fix is not invoked during "energy minimization"_minimize.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.
+
+Due to requirements of the boundary conditions, when the {strain}
+keyword is set to zero (or unset), the initial simulation box must be
+cubic and have style triclinic. If the box is initially of type ortho,
+use "change_box"_change_box.html before invoking the fix.
+
+NOTE: When resuming from restart files, you may need to use "box tilt
+large"_box.html since lammps has internal criteria from lattice
+reduction that are not the same as the criteria in the numerical
+lattice reduction algorithm.
+
+[Related commands:]
+
+"fix nvt"_fix_nh.html, "fix nvt/sllod"_fix_nvt_sllod.html, "compute
+temp/uef"_compute_temp_uef.html, "compute
+pressure/uef"_compute_pressure_uef.html, "dump
+cfg/uef"_dump_cfg_uef.html
+
+[Default:]
+
+The default keyword values specific to this fix are exy = xyz, strain
+= 0 0.  The remaining defaults are the same as for {fix
+npt}_fix_nh.html except tchain = 1.  The reason for this change is
+given in "fix nvt/sllod"_fix_nvt_sllod.html.
+
+:line
+
+:link(Dobson)
+[(Dobson)] Dobson, J Chem Phys, 141, 184103 (2014).
+
+:link(Hunt)
+[(Hunt)] Hunt, Mol Simul, 42, 347 (2016).
+
+:link(Semaev)
+[(Semaev)] Semaev, Cryptography and Lattices, 181 (2001).
+
+:link(Sllod)
+[(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984).
+
+:link(Nicholson)
+[(Nicholson and Rutledge)] Nicholson and Rutledge, J Chem Phys, 145,
+244903 (2016).

doc/src/fix_nve_dot.txt

@@ -44,7 +44,7 @@ A technical report with more information on this integrator can be found
 [Restrictions:]
 
 These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
+"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/fix_nve_dotc_langevin.txt

@@ -24,7 +24,8 @@ keyword = {angmom} :l
 
 [Examples:]
 
-fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
+fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 
+fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre
 
 [Description:]
 
@@ -78,7 +79,9 @@ a Gaussian random number) for speed.
 :line
 
 {Tstart} and {Tstop} have to be constant values, i.e. they cannot
-be variables.
+be variables. If used together with the oxDNA force field for 
+coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
+corresponds to T = 300 K.  
 
 The {damp} parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 0.03
@@ -89,6 +92,10 @@ viscosity of the solvent, i.e. a small relaxation time implies a
 hi-viscosity solvent and vice versa.  See the discussion about gamma
 and viscosity in the documentation for the "fix
 viscous"_fix_viscous.html command for more details.
+Note that the value 78.9375 in the second example above corresponds 
+to a diffusion constant, which is about an order of magnitude larger 
+than realistic ones. This has been used to sample configurations faster
+in Brownian dynamics simulations. 
 
 The random # {seed} must be a positive integer. A Marsaglia random
 number generator is used.  Each processor uses the input seed to
@@ -115,12 +122,12 @@ A technical report with more information on this integrator can be found
 [Restrictions:]
 
 These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
+"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]
 
-"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,
+"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, "bond_style oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
 
 [Default:] none
 

doc/src/fix_qeq.txt

@@ -90,9 +90,14 @@ file specified by {qfile}.  The file has the following format
 ...
 Ntype chi eta gamma zeta qcore :pre
 
-There is one line per atom type with the following parameters.
+There have to be parameters given for every atom type. Wildcard entries
+are possible using the same syntax as elsewhere in LAMMPS
+(i.e., n*m, n*, *m, *). Later entries will overwrite previous ones.
+Empty lines or any text following the pound sign (#) are ignored.
+Each line starts with the atom type followed by five parameters.
 Only a subset of the parameters is used by each QEq style as described
-below, thus the others can be set to 0.0 if desired.
+below, thus the others can be set to 0.0 if desired, but all five
+entries per line are required.
 
 {chi} = electronegativity in energy units
 {eta} = self-Coulomb potential in energy units

doc/src/fix_rhok.txt

@@ -0,0 +1,56 @@
+"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 rhok command :h3
+
+fix ID group-ID rhok nx ny nz K a :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+nx, ny, nz = k-vektor of collective density field
+K = spring constant of bias potential
+a = anchor point of bias potential :ul
+
+[Examples:]
+
+fix bias all rhok 16 0 0 4.0 16.0
+fix 1 all npt temp 0.8 0.8 4.0 z 2.2 2.2 8.0
+# output of 4 values from fix rhok: U_bias rho_k_RE  rho_k_IM  |rho_k|
+thermo_style custom step temp pzz lz f_bias f_bias\[1\] f_bias\[2\] f_bias\[3\] :pre
+
+[Description:]
+
+The fix applies a force to atoms given by the potential
+
+:c,image(Eqs/fix_rhok.jpg)
+
+as described in "(Pedersen)"_#Pedersen.
+
+This field, which biases configurations with long-range order, can be
+used to study crystal-liquid interfaces and determine melting
+temperatures "(Pedersen)"_#Pedersen.
+
+An example of using the interface pinning method is located in the
+{examples/USER/misc/rhok} directory.
+
+[Restrictions:]
+
+This fix is part of the MISC 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:]
+
+"thermo_style"_thermo_style.html
+
+[Default:] none
+
+:line
+
+:link(Pedersen)
+[(Pedersen)] Pedersen, J. Chem. Phys., 139, 104102 (2013).
+

doc/src/fix_rigid.txt

@@ -26,6 +26,9 @@ style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {
 bodystyle = {single} or {molecule} or {group} :l
   {single} args = none
   {molecule} args = none
+  {custom} args = {i_propname} or {v_varname}
+    i_propname = an integer property defined via fix property/atom
+    v_varname  = an atom-style or atomfile-style variable 
   {group} args = N groupID1 groupID2 ...
     N = # of groups
     groupID1, groupID2, ... = list of N group IDs :pre
@@ -80,6 +83,16 @@ fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
 fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
 fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
 fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 :pre
+
+variable bodyid atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)
+fix 1 clump rigid custom v_bodyid :pre
+
+variable bodyid atomfile bodies.txt
+fix 1 clump rigid custom v_bodyid :pre
+
+fix 0 all property/atom i_bodyid
+read_restart data.rigid fix 0 NULL Bodies
+fix 1 clump rigid/small custom i_bodyid :pre
 	
 [Description:]
 
@@ -100,7 +113,7 @@ of a biomolecule such as a protein.
 
 Example of small rigid bodies are patchy nanoparticles, such as those
 modeled in "this paper"_#Zhang1 by Sharon Glotzer's group, clumps of
-granular particles, lipid molecules consiting of one or more point
+granular particles, lipid molecules consisting of one or more point
 dipoles connected to other spheroids or ellipsoids, irregular
 particles built from line segments (2d) or triangles (3d), and
 coarse-grain models of nano or colloidal particles consisting of a
@@ -203,11 +216,11 @@ most one rigid body.  Which atoms are in which bodies can be defined
 via several options.
 
 NOTE: With the {rigid/small} styles, which require that {bodystyle} be
-specified as {molecule}, you can define a system that has no rigid
-bodies initially.  This is useful when you are using the {mol} keyword
-in conjunction with another fix that is adding rigid bodies on-the-fly
-as molecules, such as "fix deposit"_fix_deposit.html or "fix
-pour"_fix_pour.html.
+specified as {molecule} or {custom}, you can define a system that has
+no rigid bodies initially.  This is useful when you are using the {mol}
+keyword in conjunction with another fix that is adding rigid bodies
+on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
+"fix pour"_fix_pour.html.
 
 For bodystyle {single} the entire fix group of atoms is treated as one
 rigid body.  This option is only allowed for the {rigid} styles.
@@ -222,6 +235,15 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you
 want.  Thus you should be careful to use a fix group that only
 includes atoms you want to be part of rigid bodies.
 
+Bodystyle {custom} is similar to bodystyle {molecule}, however some
+custom properties are used to group atoms into rigid bodies. The
+special case for molecule/body ID = 0 is not available. Possible
+custom properties are an integer property associated with atoms through
+"fix property/atom"_fix_property_atom.html or an atom style variable
+or an atomfile style variable. For the latter two, the variable value
+will be rounded to an integer and then rigid bodies defined from
+those values.
+
 For bodystyle {group}, each of the listed groups is treated as a
 separate rigid body.  Only atoms that are also in the fix group are
 included in each rigid body.  This option is only allowed for the
@@ -703,6 +725,11 @@ NVT, NPT, NPH rigid styles to add the energy change induced by the
 thermostatting to the 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 keeping the objects rigid to the
+system's virial as part of "thermodynamic output"_thermo_style.html.
+The default is {virial yes}
+
 The "fix_modify"_fix_modify.html {temp} and {press} options are
 supported by the 4 NPT and NPH rigid styles to change the computes
 used to calculate the instantaneous pressure tensor.  Note that the 2

doc/src/fix_rx.txt

@@ -7,6 +7,7 @@
 :line
 
 fix rx command :h3
+fix rx/kk command :h3
 
 [Syntax:]
 
@@ -182,6 +183,29 @@ read_data    data.dpd fix foo_SPECIES NULL Species
 
 :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_saed_vtk.txt

@@ -37,8 +37,8 @@ keyword = {file} or {ave} or {start} or {file} or {overwrite}:l
 compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
 compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo :pre
 
-fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
-fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
+fix 1 all saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+fix 2 all saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
 
 [Description:]
 

doc/src/fix_shake.txt

@@ -186,6 +186,11 @@ to 1 and recompiling LAMMPS.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the contribution due to keeping the constraints to the
+system's virial as part of "thermodynamic output"_thermo_style.html.
+The default is {virial yes}
+
 No information about these fixes is written to "binary restart
 files"_restart.html.  None of the "fix_modify"_fix_modify.html options
 are relevant to these fixes.  No global or per-atom quantities are

doc/src/fix_shardlow.txt

@@ -7,6 +7,7 @@
 :line
 
 fix shardlow command :h3
+fix shardlow/kk command :h3
 
 [Syntax:]
 
@@ -52,6 +53,29 @@ 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_smd.txt

@@ -101,6 +101,11 @@ See the "read_restart"_read_restart.html command for info on how to
 re-specify a fix in an input script that reads a restart file, so that
 the operation of the fix continues in an uninterrupted fashion.
 
+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 level.

doc/src/fix_wall.txt

@@ -7,6 +7,7 @@
 :line
 
 fix wall/lj93 command :h3
+fix wall/lj93/kk command :h3
 fix wall/lj126 command :h3
 fix wall/lj1043 command :h3
 fix wall/colloid command :h3
@@ -251,6 +252,11 @@ fix to add the energy of interaction between atoms and each wall to
 the 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 and each wall 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 level.
@@ -277,6 +283,31 @@ the total potential energy of the system (the quantity being
 minimized), you MUST enable the "fix_modify"_fix_modify.html {energy}
 option for this fix.
 
+: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:] none
 
 [Related commands:]