patch 22Sep17

Enhance Kokkos communication logic

.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 +1,717 @@
+########################################
+# 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 ${SRC_STYLE_FILES})
+endif()
+
+enable_language(CXX)
+
+######################################################################
+# compiler tests
+# these need ot be done early (before further tests).
+#####################################################################
+include(CheckCCompilerFlag)
+
+########################################################################
+# User input options                                                   #
+########################################################################
+option(BUILD_SHARED_LIBS "Build shared libs" OFF)
+if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
+  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+endif()
+include(GNUInstallDirs)
+
+set(LAMMPS_LINK_LIBS)
+set(LAMMPS_DEPS)
+set(LAMMPS_API_DEFINES)
+option(ENABLE_MPI "Build MPI version" OFF)
+if(ENABLE_MPI)
+  find_package(MPI REQUIRED)
+  include_directories(${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-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})
+add_dependencies(lammps ${LAMMPS_DEPS})
+set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${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/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/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="22 Sep 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
+22 Sep 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,
@@ -732,6 +738,7 @@ 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 +757,7 @@ 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 +783,7 @@ 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 +845,7 @@ 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,
@@ -868,6 +878,7 @@ 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,
@@ -892,8 +903,8 @@ 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,
@@ -927,8 +938,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "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/alloy (gkiot)"_pair_eam.html,
+"eam/fs (gkiot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
 "gauss (go)"_pair_gauss.html,
 "gayberne (gio)"_pair_gayberne.html,
@@ -942,9 +953,9 @@ 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 (kio)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (giko)"_pair_charmm.html,
+"lj/charmm/coul/long (gkio)"_pair_charmm.html,
 "lj/charmm/coul/msm"_pair_charmm.html,
 "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
 "lj/charmmfsw/coul/long"_pair_charmm.html,
@@ -990,7 +1001,7 @@ 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,
@@ -1024,6 +1035,7 @@ 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 +1053,8 @@ 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 +1088,7 @@ 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)

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
@@ -694,6 +696,65 @@ 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
+
+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 +1403,7 @@ 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 +1617,7 @@ 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 +1806,12 @@ 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 +1846,8 @@ 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 +1885,8 @@ 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 +2216,47 @@ 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:]

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

@@ -29,8 +29,10 @@ Bond Styles: fene, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod :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, 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
 
@@ -359,10 +361,14 @@ 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_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/commands.txt

@@ -92,6 +92,7 @@ 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_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/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
@@ -95,6 +96,7 @@ Computes :h1
    compute_sna_atom
    compute_stress_atom
    compute_tally
+   compute_tdpd_cc_atom
    compute_temp
    compute_temp_asphere
    compute_temp_body

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_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"_#Finnis) 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(Finnis)
+[(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(Niklasson2014)
+[(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
+
+:link(Niklasson2012)
+[(Niklasson2017)] 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_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_rigid.txt

@@ -703,6 +703,11 @@ 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:]

doc/src/fix_wall_ees.txt

@@ -50,17 +50,17 @@ fix ees_cube all wall/region/ees myCube 1.0 1.0 2.5 :pre
 Fix {wall/ees} bounds the simulation domain on one or more of its
 faces with a flat wall that interacts with the ellipsoidal atoms in the
 group by generating a force on the atom in a direction perpendicular to
-the wall and a torque parallel with the wall.  The energy of
+the wall and a torque parallel with the wall.  The energy of
 wall-particle interactions E is given by:
 
 :c,image(Eqs/fix_wall_ees.jpg)
 
 Introduced by Babadi and Ejtehadi in "(Babadi)"_#BabadiEjtehadi. Here,
 {r} is the distance from the particle to the wall at position {coord},
-and Rc is the {cutoff} distance at which the  particle and wall no
-longer interact. Also,  sigma_n is the distance between center of
-ellipsoid and the nearest point of its surface to the wall  The energy
-of the wall (see the image below).
+and Rc is the {cutoff} distance at which the particle and wall no
+longer interact. Also, sigma_n is the distance between center of
+ellipsoid and the nearest point of its surface to the wall. The energy
+of the wall is:
 
 :c,image(JPG/fix_wall_ees_image.jpg)
 
@@ -68,21 +68,22 @@ Details of using this command and specifications are the same as
 fix/wall command. You can also find an example in USER/ees/ under
 examples/ directory.
 
-The prefactor {epsilon} can be thought of as an
-effective Hamaker constant with energy units for the strength of the
-ellipsoid-wall interaction.  More specifically, the {epsilon} pre-factor
-= 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon
-* sigma_a * sigma_b * sigma_c, where epsilon is the LJ parameters for
-the constituent LJ particles and sigma_a, sigma_b, and sigma_c are radii
-of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number
+The prefactor {epsilon} can be thought of as an
+effective Hamaker constant with energy units for the strength of the
+ellipsoid-wall interaction.  More specifically, the {epsilon} pre-factor
+= 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon
+* sigma_a * sigma_b * sigma_c, where epsilon is the LJ parameters for
+the constituent LJ particles and sigma_a, sigma_b, and sigma_c are radii
+of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number
 density of the constituent particles, in the wall and ellipsoid
 respectively, in units of 1/volume.
 
 NOTE: You must insure that r is always bigger than sigma_n for
-all particles in the group, or LAMMPS will generate an error.  This
+all particles in the group, or LAMMPS will generate an error.  This
 means you cannot start your simulation with particles touching the wall
-position {coord} (r = sigma_n) or with particles penetrating the wall (0 =< r < sigma_n) or with particles on the wrong side of the
-wall (r < 0). 
+position {coord} (r = sigma_n) or with particles penetrating the wall
+(0 =< r < sigma_n) or with particles on the wrong side of the
+wall (r < 0).
 
 
 Fix {wall/region/ees} treats the surface of the geometric region defined
@@ -93,7 +94,7 @@ Other details of this command are the same as for the "fix
 wall/region"_fix_wall_region.html command.  One may also find an example
 of using this fix in the examples/USER/misc/ees/ directory.
 
-[Restrictions:] 
+[Restrictions:]
 
 This fix is part of the USER-MISC package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making

doc/src/fix_wall_region.txt

@@ -15,7 +15,7 @@ fix ID group-ID wall/region region-ID style epsilon sigma cutoff :pre
 ID, group-ID are documented in "fix"_fix.html command
 wall/region = style name of this fix command
 region-ID = region whose boundary will act as wall
-style = {lj93} or {lj126} or {colloid} or {harmonic}
+style = {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic}
 epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
 sigma = size factor for wall-particle interaction (distance units)
 cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :ul
@@ -112,6 +112,10 @@ For style {lj126}, the energy E is given by the 12/6 potential:
 
 :c,image(Eqs/pair_lj.jpg)
 
+For style {wall/lj1043}, the energy E is given by the 10/4/3 potential:
+
+:c,image(Eqs/fix_wall_lj1043.jpg)
+
 For style {colloid}, the energy E is given by an integrated form of
 the "pair_style colloid"_pair_colloid.html potential:
 
@@ -128,49 +132,8 @@ surface no longer interact.  The energy of the wall potential is
 shifted so that the wall-particle interaction energy is 0.0 at the
 cutoff distance.
 
-For the {lj93} and {lj126} styles, {epsilon} and {sigma} are the usual
-Lennard-Jones parameters, which determine the strength and size of the
-particle as it interacts with the wall.  Epsilon has energy units.
-Note that this {epsilon} and {sigma} may be different than any
-{epsilon} or {sigma} values defined for a pair style that computes
-particle-particle interactions.
-
-The {lj93} interaction is derived by integrating over a 3d
-half-lattice of Lennard-Jones 12/6 particles.  The {lj126} interaction
-is effectively a harder, more repulsive wall interaction.
-
-For the {colloid} style, {epsilon} is effectively a Hamaker constant
-with energy units for the colloid-wall interaction, {R} is the radius
-of the colloid particle, {D} is the distance from the surface of the
-colloid particle to the wall (r-R), and {sigma} is the size of a
-constituent LJ particle inside the colloid particle.  Note that the
-cutoff distance Rc in this case is the distance from the colloid
-particle center to the wall.
-
-The {colloid} interaction is derived by integrating over constituent
-LJ particles of size {sigma} within the colloid particle and a 3d
-half-lattice of Lennard-Jones 12/6 particles of size {sigma} in the
-wall.
-
-For the {wall/harmonic} style, {epsilon} is effectively the spring
-constant K, and has units (energy/distance^2).  The input parameter
-{sigma} is ignored.  The minimum energy position of the harmonic
-spring is at the {cutoff}.  This is a repulsive-only spring since the
-interaction is truncated at the {cutoff}
-
-NOTE: For all of the styles, you must insure that r is always > 0 for
-all particles in the group, or LAMMPS will generate an error.  This
-means you cannot start your simulation with particles on the region
-surface (r = 0) or with particles on the wrong side of the region
-surface (r < 0).  For the {wall/lj93} and {wall/lj126} styles, the
-energy of the wall/particle interaction (and hence the force on the
-particle) blows up as r -> 0.  The {wall/colloid} style is even more
-restrictive, since the energy blows up as D = r-R -> 0.  This means
-the finite-size particles of radius R must be a distance larger than R
-from the region surface.  The {harmonic} style is a softer potential
-and does not blow up as r -> 0, but you must use a large enough
-{epsilon} that particles always reamin on the correct side of the
-region surface (r > 0).
+For a full description of these wall styles, see fix_style
+"wall"_fix_wall.html
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
@@ -182,6 +145,11 @@ fix to add the energy of interaction between atoms and the 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.

doc/src/fixes.txt

@@ -33,6 +33,7 @@ Fixes :h1
    fix_drude
    fix_drude_transform
    fix_dpd_energy
+   fix_dpd_source
    fix_dt_reset
    fix_efield
    fix_ehex
@@ -71,6 +72,7 @@ Fixes :h1
    fix_move
    fix_mscg
    fix_msst
+   fix_mvv_dpd
    fix_neb
    fix_nh
    fix_nh_eff

doc/src/lammps.book

@@ -21,6 +21,7 @@ Section_python.html
 Section_errors.html
 Section_history.html
 
+tutorial_bash_on_windows.html
 tutorial_drude.html
 tutorial_github.html
 tutorial_pylammps.html
@@ -115,6 +116,7 @@ suffix.html
 tad.html
 temper.html
 temper_grem.html
+temper_npt.html
 thermo.html
 thermo_modify.html
 thermo_style.html
@@ -156,6 +158,7 @@ fix_controller.html
 fix_deform.html
 fix_deposit.html
 fix_dpd_energy.html
+fix_dpd_source.html
 fix_drag.html
 fix_drude.html
 fix_drude_transform.html
@@ -197,6 +200,7 @@ fix_momentum.html
 fix_move.html
 fix_mscg.html
 fix_msst.html
+fix_mvv_dpd.html
 fix_neb.html
 fix_nh.html
 fix_nh_eff.html
@@ -315,6 +319,7 @@ compute_dipole_chunk.html
 compute_displace_atom.html
 compute_dpd.html
 compute_dpd_atom.html
+compute_edpd_temp_atom.html
 compute_erotate_asphere.html
 compute_erotate_rigid.html
 compute_erotate_sphere.html
@@ -380,6 +385,7 @@ compute_smd_vol.html
 compute_sna_atom.html
 compute_stress_atom.html
 compute_tally.html
+compute_tdpd_cc_atom.html
 compute_temp.html
 compute_temp_asphere.html
 compute_temp_body.html
@@ -457,6 +463,7 @@ pair_mdf.html
 pair_meam.html
 pair_meam_spline.html
 pair_meam_sw_spline.html
+pair_meso.html
 pair_mgpt.html
 pair_mie.html
 pair_momb.html
@@ -644,4 +651,3 @@ USER/atc/man_unfix_flux.html
 USER/atc/man_unfix_nodes.html
 USER/atc/man_write_atom_weights.html
 USER/atc/man_write_restart.html
-

doc/src/package.txt

@@ -335,7 +335,8 @@ from the USER-INTEL package is not used, then the LRT setting is
 ignored and no extra threads are generated. Enabling LRT will replace
 the "run_style"_run_style.html with the {verlet/lrt/intel} style that
 is identical to the default {verlet} style aside from supporting the
-LRT feature.
+LRT feature. This feature requires setting the preprocessor flag
+-DLMP_INTEL_USELRT in the makefile when compiling LAMMPS.
 
 The {balance} keyword sets the fraction of "pair
 style"_pair_style.html work offloaded to the coprocessor for split

doc/src/pair_airebo.txt

@@ -7,10 +7,13 @@
 :line
 
 pair_style airebo command :h3
+pair_style airebo/intel command :h3
 pair_style airebo/omp command :h3
 pair_style airebo/morse command :h3
+pair_style airebo/morse/intel command :h3
 pair_style airebo/morse/omp command :h3
 pair_style rebo command :h3
+pair_style rebo/intel command :h3
 pair_style rebo/omp command :h3
 
 [Syntax:]

doc/src/pair_charmm.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style lj/charmm/coul/charmm command :h3
+pair_style lj/charmm/coul/charmm/intel command :h3
 pair_style lj/charmm/coul/charmm/omp command :h3
 pair_style lj/charmm/coul/charmm/implicit command :h3
 pair_style lj/charmm/coul/charmm/implicit/omp command :h3

doc/src/pair_dpd.txt

@@ -36,7 +36,7 @@ pair_coeff 1 1 1.0 1.0 :pre
 [Description:]
 
 Style {dpd} computes a force field for dissipative particle dynamics
-(DPD) following the exposition in "(Groot)"_#Groot.
+(DPD) following the exposition in "(Groot)"_#Groot1.
 
 Style {dpd/tstat} invokes a DPD thermostat on pairwise interactions,
 which is equivalent to the non-conservative portion of the DPD force
@@ -196,7 +196,7 @@ langevin"_fix_langevin.html, "pair_style srp"_pair_srp.html
 
 :line
 
-:link(Groot)
+:link(Groot1)
 [(Groot)] Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
 
 :link(Afshar)

doc/src/pair_dpd_fdt.txt

@@ -8,6 +8,7 @@
 
 pair_style dpd/fdt command :h3
 pair_style dpd/fdt/energy command :h3
+pair_style dpd/fdt/energy/kk command :h3
 
 [Syntax:]
 
@@ -125,6 +126,29 @@ significantly larger timesteps to be taken.
 
 :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:]
 
 These commands are part of the USER-DPD package.  They are only

doc/src/pair_eam.txt

@@ -14,6 +14,7 @@ pair_style eam/omp command :h3
 pair_style eam/opt command :h3
 pair_style eam/alloy command :h3
 pair_style eam/alloy/gpu command :h3
+pair_style eam/alloy/intel command :h3
 pair_style eam/alloy/kk command :h3
 pair_style eam/alloy/omp command :h3
 pair_style eam/alloy/opt command :h3
@@ -21,6 +22,7 @@ pair_style eam/cd command :h3
 pair_style eam/cd/omp command :h3
 pair_style eam/fs command :h3
 pair_style eam/fs/gpu command :h3
+pair_style eam/fs/intel command :h3
 pair_style eam/fs/kk command :h3
 pair_style eam/fs/omp command :h3
 pair_style eam/fs/opt command :h3

doc/src/pair_exp6_rx.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style exp6/rx command :h3
+pair_style exp6/rx/kk command :h3
 
 [Syntax:]
 
@@ -147,6 +148,31 @@ This style does not support the pair_modify tail option for adding long-range
 tail corrections to energy and pressure for the A,C terms in the
 pair interaction.
 
+: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/pair_hybrid.txt

@@ -10,6 +10,7 @@ pair_style hybrid command :h3
 pair_style hybrid/omp command :h3
 pair_style hybrid/overlay command :h3
 pair_style hybrid/overlay/omp command :h3
+pair_style hybrid/overlay/kk command :h3
 
 [Syntax:]
 

doc/src/pair_meso.txt

@@ -0,0 +1,277 @@
+"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
+
+pair_style edpd command :h3
+pair_style mdpd command :h3
+pair_style mdpd/rhosum command :h3
+pair_style tdpd command :h3
+
+[Syntax:]
+
+pair_style style args :pre
+
+style = {edpd} or {mdpd} or {mdpd/rhosum} or {tdpd} :ulb,l
+args = list of arguments for a particular style :l
+  {edpd} args = cutoff seed
+    cutoff = global cutoff for eDPD interactions (distance units)
+    seed = random # seed (integer) (if <= 0, eDPD will use current time as the seed)
+  {mdpd} args = T cutoff seed
+    T = temperature (temperature units)
+    cutoff = global cutoff for mDPD interactions (distance units)
+    seed = random # seed (integer) (if <= 0, mDPD will use current time as the seed)
+  {mdpd/rhosum} args = 
+  {tdpd} args = T cutoff seed
+    T = temperature (temperature units)
+    cutoff = global cutoff for tDPD interactions (distance units)
+    seed = random # seed (integer) (if <= 0, tDPD will use current time as the seed) :pre
+:ule
+
+[Examples:]
+
+pair_style edpd 1.58 9872598
+pair_coeff * * 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58
+pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10
+pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00 :pre
+
+pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 65689
+pair_coeff 1 1 mdpd/rhosum  0.75
+pair_coeff 1 1 mdpd -40.0 25.0 18.0 1.0 0.75 :pre
+
+pair_style tdpd 1.0 1.58 935662
+pair_coeff * * 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 
+pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 :pre
+
+[Description:]
+
+The {edpd} style computes the pairwise interactions and heat fluxes
+for eDPD particles following the formulations in
+"(Li2014_JCP)"_#Li2014_JCP and "Li2015_CC"_#Li2015_CC. The time
+evolution of an eDPD particle is governed by the conservation of
+momentum and energy given by
+
+:c,image(Eqs/pair_edpd_gov.jpg)
+
+where the three components of <font size="4">F<sub>i</sub></font>
+including the conservative force <font
+size="4">F<sub>ij</sub><sup>C</sup></font>, dissipative force <font
+size="4">F<sub>ij</sub><sup>D</sup></font> and random force <font
+size="4">F<sub>ij</sub><sup>R</sup></font> are expressed as
+
+:c,image(Eqs/pair_edpd_force.jpg)
+
+in which the exponent of the weighting function <font
+size="4"><i>s</i></font> can be defined as a temperature-dependent
+variable. The heat flux between particles accounting for the
+collisional heat flux <font size="4">q<sup>C</sup></font>, viscous
+heat flux <font size="4">q<sup>V</sup></font>, and random heat flux
+<font size="4">q<sup>R</sup></font> are given by
+
+:c,image(Eqs/pair_edpd_heat.jpg)
+
+where the mesoscopic heat friction <font size="4">&kappa;</font> is given by 
+
+:c,image(Eqs/pair_edpd_kappa.jpg)
+
+with <font size="4">&upsilon;</font> being the kinematic
+viscosity. For more details, see Eq.(15) in "(Li2014_JCP)"_#Li2014_JCP.
+
+The following coefficients must be defined in eDPD system for each
+pair of atom types via the "pair_coeff"_pair_coeff.html command as in
+the examples above.
+
+A (force units) 
+gamma (force/velocity units)
+power_f (positive real)
+cutoff (distance units)
+kappa (thermal conductivity units)
+power_T (positive real)
+cutoff_T (distance units)
+optional keyword = power or kappa :ul
+
+The keyword {power} or {kappa} is optional. Both "power" and "kappa"
+require 4 parameters <font size="4">c<sub>1</sub>, c<sub>2</sub>,
+c<sub>4</sub>, c<sub>4</sub></font> showing the temperature dependence
+of the exponent <center><font size="4"> <i>s</i>(<i>T</i>) =
+power_f*(1+c<sub>1</sub>*(T-1)+c<sub>2</sub>*(T-1)<sup>2</sup>
++c<sub>3</sub>*(T-1)<sup>3</sup>+c<sub>4</sub>*(T-1)<sup>4</sup>)</font></center>
+and of the mesoscopic heat friction <center><font size="4">
+<i>s<sub>T</sub>(T)</i> =
+kappa*(1+c<sub>1</sub>*(T-1)+c<sub>2</sub>*(T-1)<sup>2</sup>
++c<sub>3</sub>*(T-1)<sup>3</sup>+c<sub>4</sub>*(T-1)<sup>4</sup>)</font></center>
+If the keyword {power} or {kappa} is not specified, the eDPD system
+will use constant power_f and kappa, which is independent to
+temperature changes.
+
+:line
+
+The {mdpd/rhosum} style computes the local particle mass density rho
+for mDPD particles by kernel function interpolation.
+
+The following coefficients must be defined for each pair of atom types
+via the "pair_coeff"_pair_coeff.html command as in the examples above.
+
+cutoff (distance units) :ul
+
+:line
+
+The {mdpd} style computes the many-body interactions between mDPD
+particles following the formulations in
+"(Li2013_POF)"_#Li2013_POF. The dissipative and random forces are in
+the form same as the classical DPD, but the conservative force is
+local density dependent, which are given by
+
+:c,image(Eqs/pair_mdpd_force.jpg)
+
+where the first term in <font size="4">F<sup>C</sup></font> with a
+negative coefficient A < 0 stands for an attractive force within an
+interaction range <font size="4">r<sub>c</sub></font>, and the second
+term with B > 0 is the density-dependent repulsive force within an
+interaction range <font size="4">r<sub>d</sub></font>.
+
+The following coefficients must be defined for each pair of atom types via the
+"pair_coeff"_pair_coeff.html command as in the examples above.
+
+A (force units)
+B (force units)
+gamma (force/velocity units)
+cutoff_c (distance units)
+cutoff_d (distance units) :ul
+
+:line
+
+The {tdpd} style computes the pairwise interactions and chemical
+concentration fluxes for tDPD particles following the formulations in
+"(Li2015_JCP)"_#Li2015_JCP.  The time evolution of a tDPD particle is
+governed by the conservation of momentum and concentration given by
+
+:c,image(Eqs/pair_tdpd_gov.jpg)
+
+where the three components of <font size="4">F<sub>i</sub></font>
+including the conservative force <font
+size="4">F<sub>ij</sub><sup>C</sup></font>, dissipative force <font
+size="4">F<sub>ij</sub><sup>D</sup></font> and random force <font
+size="4">F<sub>ij</sub><sup>R</sup></font> are expressed as
+
+:c,image(Eqs/pair_tdpd_force.jpg)
+
+The concentration flux between two tDPD particles includes the Fickian
+flux <font size="4">Q<sub>ij</sub><sup>D</sup></font> and random flux
+<font size="4">Q<sub>ij</sub><sup>R</sup></font>, which are given by
+
+:c,image(Eqs/pair_tdpd_flux.jpg)
+
+where the parameters kappa and epsilon determine the strength of the
+Fickian and random fluxes. <font size="4"><i>m</i><sub>s</sub></font>
+is the mass of a single solute molecule.  In general, <font
+size="4"><i>m</i><sub>s</sub></font> is much smaller than the mass of
+a tDPD particle <font size="4"><i>m</i></font>. For more details, see
+"(Li2015_JCP)"_#Li2015_JCP.
+
+The following coefficients must be defined for each pair of atom types via the 
+"pair_coeff"_pair_coeff.html command as in the examples above.
+
+A (force units)
+gamma (force/velocity units)
+power_f (positive real)
+cutoff (distance units)
+cutoff_CC (distance units)
+kappa_i (diffusivity units)
+epsilon_i (diffusivity units)
+power_cc_i (positive real) :ul
+
+The last 3 values must be repeated Nspecies times, so that values for
+each of the Nspecies chemical species are specified, as indicated by
+the "I" suffix.  In the first pair_coeff example above for pair_style
+tdpd, Nspecies = 1.  In the second example, Nspecies = 2, so 3
+additional coeffs are specified (for species 2).
+
+:line
+
+[Example scripts]
+
+There are example scripts for using all these pair styles in
+examples/USER/meso.  The example for an eDPD simulation models heat
+conduction with source terms analog of periodic Poiseuille flow
+problem. The setup follows Fig.12 in "(Li2014_JCP)"_#Li2014_JCP. The
+output of the short eDPD simulation (about 2 minutes on a single core)
+gives a temperature and density profiles as
+
+:c,image(JPG/examples_edpd.jpg)
+
+The example for a mDPD simulation models the oscillations of a liquid
+droplet started from a liquid film. The mDPD parameters are adopted
+from "(Li2013_POF)"_#Li2013_POF.  The short mDPD run (about 2 minutes
+on a single core) generates a particle trajectory which can
+be visualized as follows.
+
+:c,image(JPG/examples_mdpd_first.jpg,JPG/examples_mdpd.gif)
+:c,image(JPG/examples_mdpd_last.jpg)
+
+The first image is the initial state of the simulation.  If you
+click it a GIF movie should play in your browser.  The second image
+is the final state of the simulation.
+
+The example for a tDPD simulation computes the effective diffusion
+coefficient of a tDPD system using a method analogous to the periodic
+Poiseuille flow.  The tDPD system is specified with two chemical
+species, and the setup follows Fig.1 in
+"(Li2015_JCP)"_#Li2015_JCP. The output of the short tDPD simulation
+(about one and a half minutes on a single core) gives the
+concentration profiles of the two chemical species as
+
+:c,image(JPG/examples_tdpd.jpg)
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+The styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} do not support
+mixing. Thus, coefficients for all I,J pairs must be specified explicitly.
+
+The styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} do not support
+the "pair_modify"_pair_modify.html shift, table, and tail options.
+
+The styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} do not write
+information to "binary restart files"_restart.html. Thus, you need
+to re-specify the pair_style and pair_coeff commands in an input script
+that reads a restart file.
+
+[Restrictions:]
+
+The pair styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} are 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_coeff"_pair_coeff.html, "fix mvv/dpd"_fix_mvv_dpd.html, 
+"fix mvv/edpd"_fix_mvv_dpd.html, "fix mvv/tdpd"_fix_mvv_dpd.html,
+"fix edpd/source"_fix_dpd_source.html, "fix tdpd/source"_fix_dpd_source.html, 
+"compute edpd/temp/atom"_compute_edpd_temp_atom.html, 
+"compute tdpd/cc/atom"_compute_tdpd_cc_atom.html
+
+[Default:] none
+
+:line
+
+:link(Li2014_JCP)
+[(Li2014_JCP)] Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys,
+265: 113-127 (2014).  DOI: 10.1016/j.jcp.2014.02.003.
+
+:link(Li2015_CC)
+[(Li2015_CC)] Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040
+(2015).  DOI: 10.1039/C5CC01684C.
+
+:link(Li2013_POF)
+[(Li2013_POF)] Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013).
+DOI: 10.1063/1.4812366.
+
+:link(Li2015_JCP)
+[(Li2015_JCP)] Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys,
+143: 014101 (2015).  DOI: 10.1063/1.4923254.

doc/src/pair_multi_lucy_rx.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style multi/lucy/rx command :h3
+pair_style multi/lucy/rx/kk command :h3
 
 [Syntax:]
 
@@ -200,6 +201,29 @@ This pair style can only be used via the {pair} keyword of the
 
 :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/pair_oxdna.txt

@@ -20,20 +20,24 @@ pair_coeff * * style2 args :pre
 
 style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
 
-style2 = {oxdna/stk}
-args = list of arguments for these two particular styles :ul
+style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
+args = list of arguments for these particular styles :ul
 
-  {oxdna2/stk} args = T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-    T = temperature (oxDNA units, 0.1 = 300 K) :pre
+  {oxdna/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
+    T = temperature (oxDNA units, 0.1 = 300 K) 
+  {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
+    eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre 
 
 [Examples:]
 
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/stk     seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
 
@@ -44,10 +48,11 @@ for coarse-grained modelling of DNA. The effective interaction between the nucle
 excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
 and coaxial stacking interaction {oxdna/coaxstk} as well
 as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
-opposite strands.
+opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
+are supported "(Sulc)"_#Sulc1.
 
-The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
-in the above example. The individual potentials consist of products of modulation factors,
+The exact functional form of the pair styles is rather complex.
+The individual potentials consist of products of modulation factors,
 which themselves are constructed from a number of more basic potentials
 (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
 We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
@@ -55,9 +60,10 @@ for a detailed description of the oxDNA force field.
 
 NOTE: These pair styles have to be used together with the related oxDNA bond style
 {oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients
+"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients
 in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).
+Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example)
+and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).
 When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
 or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
 the temperature coefficients have to be matched to the one used in the fix.
@@ -86,7 +92,11 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 :line
 
+:link(Sulc1)
+[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
 :link(Ouldridge-DPhil1)
 [(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+
 :link(Ouldridge1)
 [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

doc/src/pair_oxdna2.txt

@@ -21,11 +21,15 @@ pair_coeff * * style2 args :pre
 
 style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh} :ul
 
-style2 = {oxdna2/stk} or {oxdna2/dh}
-args = list of arguments for these two particular styles :ul
+style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
+args = list of arguments for these particular styles :ul
 
-  {oxdna2/stk} args = T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+  {oxdna2/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
     T = temperature (oxDNA units, 0.1 = 300 K)
+  {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
+    eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
   {oxdna2/dh} args = T rhos qeff
     T = temperature (oxDNA units, 0.1 = 300 K)
     rhos = salt concentration (mole per litre)
@@ -35,10 +39,10 @@ args = list of arguments for these two particular styles :ul
 
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/stk     seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815 :pre
@@ -50,7 +54,8 @@ for coarse-grained modelling of DNA. The effective interaction between the nucle
 excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
 and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
 as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
-opposite strands.
+opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
+are supported "(Sulc)"_#Sulc2.
 
 The exact functional form of the pair styles is rather complex.
 The individual potentials consist of products of modulation factors,
@@ -61,9 +66,10 @@ and  "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force fi
 
 NOTE: These pair styles have to be used together with the related oxDNA2 bond style
 {oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna2/fene"_bond_oxdna.html). Almost all coefficients
+"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
 in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients
+Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example),
+the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients 
 after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
 e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
 the temperature coefficients have to be matched to the one used in the fix.
@@ -92,6 +98,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 :line
 
+:link(Sulc2)
+[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
 :link(Snodin)
 [(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
 

doc/src/pair_snap.txt

@@ -10,8 +10,7 @@ pair_style snap command :h3
 
 [Syntax:]
 
-pair_style snap
-:pre
+pair_style snap :pre
 
 [Examples:]
 
@@ -20,17 +19,16 @@ pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre
 
 [Description:]
 
-Pair style {snap} computes interactions
-using the spectral neighbor analysis potential (SNAP)
-"(Thompson)"_#Thompson20142. Like the GAP framework of Bartok et al.
-"(Bartok2010)"_#Bartok20102, "(Bartok2013)"_#Bartok2013
-which uses bispectrum components
+Pair style {snap} computes interactions using the spectral
+neighbor analysis potential (SNAP) "(Thompson)"_#Thompson20142.
+Like the GAP framework of Bartok et al. "(Bartok2010)"_#Bartok20102,
+"(Bartok2013)"_#Bartok2013 which uses bispectrum components
 to characterize the local neighborhood of each atom
 in a very general way. The mathematical definition of the
 bispectrum calculation used by SNAP is identical
 to that used by "compute sna/atom"_compute_sna_atom.html.
 In SNAP, the total energy is decomposed into a sum over
-atom energies. The energy of atom {i } is
+atom energies. The energy of atom {i} is
 expressed as a weighted sum over bispectrum components.
 
 :c,image(Eqs/pair_snap.jpg)

doc/src/pair_table_rx.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style table/rx command :h3
+pair_style table/rx/kk command :h3
 
 [Syntax:]
 
@@ -223,6 +224,29 @@ This pair style can only be used via the {pair} keyword of the
 
 :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/pairs.txt

@@ -58,6 +58,7 @@ Pair Styles :h1
    pair_meam
    pair_meam_spline
    pair_meam_sw_spline
+   pair_meso
    pair_mgpt
    pair_mie
    pair_momb