patch 29Jun18

fix typo in python module

.github/CODEOWNERS

@@ -16,6 +16,7 @@ src/COMPRESS/*        @akohlmey
 src/GPU/*             @ndtrung81
 src/KOKKOS/*          @stanmoore1
 src/KIM/*             @ellio167
+src/LATTE/*           @cnegre
 src/USER-CGDNA/*      @ohenrich
 src/USER-CGSDK/*      @akohlmey
 src/USER-COLVARS/*    @giacomofiorin
@@ -43,3 +44,14 @@ src/USER-MISC/*_grem.*              @dstelter92
 
 # tools
 tools/msi2lmp/*       @akohlmey
+
+# cmake
+cmake/*               @junghans @rbberger
+
+# python
+python/*              @rbberger
+
+# docs
+doc/utils/*/*         @rbberger
+doc/Makefile          @rbberger
+doc/README            @rbberger

README

@@ -25,7 +25,7 @@ The LAMMPS distribution includes the following files and directories:
 README			   this file
 LICENSE			   the GNU General Public License (GPL)
 bench			   benchmark problems
-couple			   code coupling examples using LAMMPS as a library
+cmake			   CMake build system
 doc			   documentation
 examples		   simple test problems
 lib			   libraries LAMMPS can be linked with

cmake/CMakeLists.txt

@@ -2,15 +2,16 @@
 # CMake build system
 # This file is part of LAMMPS
 # Created by Christoph Junghans and Richard Berger
-cmake_minimum_required(VERSION 3.1)
+cmake_minimum_required(VERSION 2.8.12)
 
-project(lammps)
+project(lammps CXX)
 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)
+get_filename_component(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src ABSOLUTE)
+get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib ABSOLUTE)
+get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 
-#To not conflict with old Makefile build system, we build everything here
+
+# To avoid conflicts with the conventional 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})
@@ -23,13 +24,23 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
   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)
+# check for files auto-generated by make-based buildsystem
+# this is fast, so check for it all the time
+message(STATUS "Running check for auto-generated files from make-based build system")
+file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
+list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h)
+foreach(_SRC ${SRC_AUTOGEN_FILES})
+  get_filename_component(FILENAME "${_SRC}" NAME)
+  if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME})
+    message(FATAL_ERROR "\n########################################################################\n"
+                          "Found header file(s) generated by the make-based build system\n"
+                          "\n"
+                          "Please run\n"
+                          "make -C ${LAMMPS_SOURCE_DIR} purge\n"
+                          "to remove\n"
+                          "########################################################################")
+  endif()
+endforeach()
 
 ######################################################################
 # compiler tests
@@ -41,28 +52,80 @@ if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
 endif()
 
+# GNU compiler features
+if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+  option(ENABLE_COVERAGE "Enable code coverage" OFF)
+  mark_as_advanced(ENABLE_COVERAGE)
+  if(ENABLE_COVERAGE)
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+  endif()
+  option(ENABLE_SANITIZE_ADDRESS "Enable address sanitizer" OFF)
+  mark_as_advanced(ENABLE_SANITIZE_ADDRESS)
+  if(ENABLE_SANITIZE_ADDRESS)
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address")
+  endif()
+  option(ENABLE_SANITIZE_UNDEFINED "Enable undefined behavior sanitizer" OFF)
+  mark_as_advanced(ENABLE_SANITIZE_UNDEFINED)
+  if(ENABLE_SANITIZE_UNDEFINED)
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=undefined")
+  endif()
+  option(ENABLE_SANITIZE_THREAD "Enable thread sanitizer" OFF)
+  mark_as_advanced(ENABLE_SANITIZE_THREAD)
+  if(ENABLE_SANITIZE_THREAD)
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=thread")
+  endif()
+endif()
+
 ########################################################################
 # User input options                                                   #
 ########################################################################
-option(BUILD_SHARED_LIBS "Build shared libs" OFF)
-if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
-  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+option(BUILD_EXE "Build lmp binary" ON)
+if(BUILD_EXE)
+  set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
+  mark_as_advanced(LAMMPS_MACHINE)
+  if(LAMMPS_MACHINE)
+    set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
+  endif()
 endif()
+
+option(BUILD_LIB "Build LAMMPS library" OFF)
+if(BUILD_LIB)
+  option(BUILD_SHARED_LIBS "Build shared library" OFF)
+  if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
+    set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+  endif()
+  set(LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
+  mark_as_advanced(LIB_SUFFIX)
+  if(LIB_SUFFIX)
+    set(LIB_SUFFIX "_${LIB_SUFFIX}")
+  endif()
+endif()
+
+if(NOT BUILD_EXE AND NOT BUILD_LIB)
+  message(FATAL_ERROR "You need to at least enable one of two following options: BUILD_LIB or BUILD_EXE")
+endif()
+
+option(DEVELOPER_MODE "Enable developer mode" OFF)
+mark_as_advanced(DEVELOPER_MODE)
+option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 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 QUIET)
+option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
+if(BUILD_MPI)
   find_package(MPI REQUIRED)
-  include_directories(${MPI_C_INCLUDE_PATH})
+  include_directories(${MPI_CXX_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()
+  enable_language(C)
   file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
   add_library(mpi_stubs STATIC ${MPI_SOURCES})
   include_directories(${LAMMPS_SOURCE_DIR}/STUBS)
@@ -83,12 +146,6 @@ if(LAMMPS_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)
@@ -96,26 +153,23 @@ 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-BOCS 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
+  KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ REAX REPLICA RIGID SHOCK SPIN SNAP
+  SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
+  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-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
   USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 foreach(PKG ${DEFAULT_PACKAGES})
-  option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
+  option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
-  option(ENABLE_${PKG} "Build ${PKG} Package" OFF)
+  option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
 macro(pkg_depends PKG1 PKG2)
-  if(ENABLE_${PKG1} AND NOT ENABLE_${PKG2})
+  if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
     message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
   endif()
 endmacro()
@@ -123,39 +177,51 @@ 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)
+pkg_depends(CORESHELL KSPACE)
 
 ######################################################
 # 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)
+if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_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
+if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM)
+  enable_language(C)
 endif()
 
-if(ENABLE_USER-OMP OR ENABLE_KOKKOS OR ENABLE_USER-INTEL)
+find_package(OpenMP QUIET)
+option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
+if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
   find_package(OpenMP REQUIRED)
   set (CMAKE_C_FLAGS "${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(PKG_KSPACE)
+  option(FFT_SINGLE "Use single precision FFT instead of double" OFF)
+  set(FFTW "FFTW3")
+  if(FFT_SINGLE)
+    set(FFTW "FFTW3F")
+    add_definitions(-DFFT_SINGLE)
+  endif()
+  find_package(${FFTW} QUIET)
+  if(${FFTW}_FOUND)
+    set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package")
+  else()
+    set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package")
+  endif()
+  set_property(CACHE FFT PROPERTY STRINGS KISSFFT ${FFTW} MKL)
   if(NOT FFT STREQUAL "KISSFFT")
     find_package(${FFT} REQUIRED)
-    add_definitions(-DFFT_${FFT})
+    if(NOT FFT STREQUAL "FFTW3F")
+      add_definitions(-DFFT_FFTW)
+    else()
+      add_definitions(-DFFT_${FFT})
+    endif()
     include_directories(${${FFT}_INCLUDE_DIRS})
     list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
   endif()
@@ -166,28 +232,23 @@ if(ENABLE_KSPACE)
   endif()
 endif()
 
-if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP OR ENABLE_LATTE)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   find_package(LAPACK)
   if(NOT LAPACK_FOUND)
     enable_language(Fortran)
-    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)
+    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
     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)
+if(PKG_PYTHON)
   find_package(PythonInterp REQUIRED)
   find_package(PythonLibs REQUIRED)
   add_definitions(-DLMP_PYTHON)
   include_directories(${PYTHON_INCLUDE_DIR})
   list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
-  if(BUILD_SHARED_LIBS)
+  if(BUILD_LIB AND BUILD_SHARED_LIBS)
     if(NOT PYTHON_INSTDIR)
       execute_process(COMMAND ${PYTHON_EXECUTABLE}
         -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
@@ -197,16 +258,25 @@ if(ENABLE_PYTHON)
   endif()
 endif()
 
-find_package(JPEG)
-if(JPEG_FOUND)
+find_package(JPEG QUIET)
+option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
+if(WITH_JPEG)
+  find_package(JPEG REQUIRED)
   add_definitions(-DLAMMPS_JPEG)
   include_directories(${JPEG_INCLUDE_DIR})
   list(APPEND LAMMPS_LINK_LIBS ${JPEG_LIBRARIES})
 endif()
 
-find_package(PNG)
-find_package(ZLIB)
+find_package(PNG QUIET)
+find_package(ZLIB QUIET)
 if(PNG_FOUND AND ZLIB_FOUND)
+  option(WITH_PNG "Enable PNG support" ON)
+else()
+  option(WITH_PNG "Enable PNG support" OFF)
+endif()
+if(WITH_PNG)
+  find_package(PNG REQUIRED)
+  find_package(ZLIB REQUIRED)
   include_directories(${PNG_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS})
   list(APPEND LAMMPS_LINK_LIBS ${PNG_LIBRARIES} ${ZLIB_LIBRARIES})
   add_definitions(-DLAMMPS_PNG)
@@ -214,85 +284,131 @@ endif()
 
 find_program(GZIP_EXECUTABLE gzip)
 find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
-if(GZIP_FOUND)
+option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND})
+if(WITH_GZIP)
+  if(NOT GZIP_FOUND)
+    message(FATAL_ERROR "gzip executable not found")
+  endif()
   add_definitions(-DLAMMPS_GZIP)
 endif()
 
 find_program(FFMPEG_EXECUTABLE ffmpeg)
 find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
-if(FFMPEG_FOUND)
+option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND})
+if(WITH_FFMPEG)
+  if(NOT FFMPEG_FOUND)
+    message(FATAL_ERROR "ffmpeg executable not found")
+  endif()
   add_definitions(-DLAMMPS_FFMPEG)
 endif()
 
-if(ENABLE_VORONOI)
-  find_package(VORO REQUIRED) #some distros
+if(PKG_VORONOI)
+  option(DOWNLOAD_VORO "Download voro++ (instead of using the system's one)" OFF)
+  if(DOWNLOAD_VORO)
+    include(ExternalProject)
+    ExternalProject_Add(voro_build
+      URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
+      URL_MD5 2338b824c3b7b25590e18e8df5d68af9
+      CONFIGURE_COMMAND "" BUILD_IN_SOURCE 1 INSTALL_COMMAND "" 
+      )
+    ExternalProject_get_property(voro_build SOURCE_DIR)
+    set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a)
+    set(VORO_INCLUDE_DIRS ${SOURCE_DIR}/src)
+    list(APPEND LAMMPS_DEPS voro_build)
+  else()
+    find_package(VORO)
+    if(NOT VORO_FOUND)
+      message(FATAL_ERROR "VORO not found, help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+    endif()
+  endif()
   include_directories(${VORO_INCLUDE_DIRS})
   list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
 endif()
 
-if(ENABLE_LATTE)
-  find_package(LATTE QUIET)
-  if(NOT LATTE_FOUND)
+if(PKG_LATTE)
+  option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF)
+  if(DOWNLOAD_LATTE)
     message(STATUS "LATTE not found - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(latte_build
-      URL https://github.com/lanl/LATTE/archive/v1.1.1.tar.gz
-      URL_MD5 cb86f1d2473ce00aa61ff6a023154b03
+      URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
+      URL_MD5 bed76e7e76c545c36dd848a8f1fd35eb
       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)
+  else()
+    find_package(LATTE)
+    if(NOT LATTE_FOUND)
+      message(FATAL_ERROR "LATTE not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
+    endif()
   endif()
-  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
 endif()
 
-if(ENABLE_USER-MOLFILE)
+if(PKG_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)
+if(PKG_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)
+if(PKG_USER-SMD)
+  option(DOWNLOAD_Eigen3 "Download Eigen3 (instead of using the system's one)" OFF)
+  if(DOWNLOAD_Eigen3)
+    include(ExternalProject)
+    ExternalProject_Add(Eigen3_build
+      URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz 
+      URL_MD5 1a47e78efe365a97de0c022d127607c3
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+    )
+    ExternalProject_get_property(Eigen3_build SOURCE_DIR)
+    set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
+    list(APPEND LAMMPS_DEPS Eigen3_build)
+  else()
+    find_package(Eigen3)
+    if(NOT Eigen3_FOUND)
+      message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_Eigen3=ON to download it")
+    endif()
+  endif()
   include_directories(${EIGEN3_INCLUDE_DIR})
 endif()
 
-if(ENABLE_USER-QUIP)
+if(PKG_USER-QUIP)
   find_package(QUIP REQUIRED)
-  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES})
 endif()
 
-if(ENABLE_USER-QMMM)
+if(PKG_USER-QMMM)
+  message(WARNING "Building QMMM with CMake is still experimental")
   find_package(QE REQUIRED)
   include_directories(${QE_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES})
 endif()
 
-if(ENABLE_USER-VTK)
+if(PKG_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 QUIET)
-  if(NOT KIM_FOUND)
-    message(STATUS "KIM not found - we will build our own")
+if(PKG_KIM)
+  option(DOWNLOAD_KIM "Download kim-api (instead of using the system's one)" OFF)
+  if(DOWNLOAD_KIM)
     include(ExternalProject)
     ExternalProject_Add(kim_build
-      URL https://github.com/openkim/kim-api/archive/v1.9.4.tar.gz
-      URL_MD5 f4d35a1705eed46d64c7c0ab448ff3e0
+      URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
+      URL_MD5 9f66efc128da33039e30659f36fc6d00
       BUILD_IN_SOURCE 1
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
       )
@@ -300,41 +416,62 @@ if(ENABLE_KIM)
     set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
     set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
     list(APPEND LAMMPS_DEPS kim_build)
+  else()
+    find_package(KIM)
+    if(NOT KIM_FOUND)
+      message(FATAL_ERROR "KIM not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
+    endif()
   endif()
   list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
   include_directories(${KIM_INCLUDE_DIRS})
 endif()
 
-if(ENABLE_MSCG)
+if(PKG_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
-        ${MSCG_TARBALL} SHOW_PROGRESS) #EXPECTED_MD5 cannot be due due to master
+  option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
+  if(DOWNLOAD_MSCG)
+    include(ExternalProject)
+    if(NOT LAPACK_FOUND)
+      set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
+    endif()
+    ExternalProject_Add(mscg_build
+      URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
+      URL_MD5 8c45e269ee13f60b303edd7823866a91
+      SOURCE_SUBDIR src/CMake
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ${EXTRA_MSCG_OPTS}
+      BUILD_COMMAND make mscg INSTALL_COMMAND ""
+      )
+    ExternalProject_get_property(mscg_build BINARY_DIR)
+    set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)
+    ExternalProject_get_property(mscg_build SOURCE_DIR)
+    set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src)
+    list(APPEND LAMMPS_DEPS mscg_build)
+    if(NOT LAPACK_FOUND)
+      file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS})
+      add_dependencies(mscg_build linalg)
+    endif()
+  else()
+    find_package(MSCG)
+    if(NOT MSCG_FOUND)
+      message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
     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})
+  list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
+  include_directories(${MSCG_INCLUDE_DIRS})
+endif()
+
+if(PKG_COMPRESS)
+  find_package(ZLIB REQUIRED)
+  include_directories(${ZLIB_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
 endif()
 
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
-include(CheckIncludeFile)
+include(CheckIncludeFileCXX)
 foreach(HEADER math.h)
-  check_include_file(${HEADER} FOUND_${HEADER})
+  check_include_file_cxx(${HEADER} FOUND_${HEADER})
   if(NOT FOUND_${HEADER})
     message(FATAL_ERROR "Could not find needed header - ${HEADER}")
   endif(NOT FOUND_${HEADER})
@@ -343,6 +480,9 @@ endforeach(HEADER)
 set(MATH_LIBRARIES "m" CACHE STRING "math library")
 mark_as_advanced( MATH_LIBRARIES )
 include(CheckLibraryExists)
+if (CMAKE_VERSION VERSION_LESS "3.4")
+  enable_language(C) # check_library_exists isn't supported without a c compiler before v3.4
+endif()
 foreach(FUNC sin cos)
   check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
   if(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
@@ -360,25 +500,16 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
 ##############################################
 # add sources of enabled packages
 ############################################
-foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES})
+foreach(PKG ${DEFAULT_PACKAGES})
   set(${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()
+  # check for package files in src directory due to old make system
+  DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
 
-  foreach(PKG_FILE in ${${PKG}_HEADERS})
-      get_filename_component(FNAME ${PKG_FILE} NAME)
-      DetectAndRemovePackageHeader(${LAMMPS_SOURCE_DIR}/${FNAME})
-  endforeach()
-
-  if(ENABLE_${PKG})
+  if(PKG_${PKG})
     # detects styles in package and adds them to global list
     RegisterStyles(${${PKG}_SOURCES_DIR})
 
@@ -387,12 +518,23 @@ foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES})
   endif()
 endforeach()
 
+# dedicated check for entire contents of accelerator packages
+foreach(PKG ${ACCEL_PACKAGES})
+  set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
+
+  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
+  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
+
+  # check for package files in src directory due to old make system
+  DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
+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_${SIMPLE_LIB})
+  if(PKG_${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
@@ -413,40 +555,26 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
   endif()
 endforeach()
 
-if(ENABLE_USER-AWPMD)
+if(PKG_USER-AWPMD)
   target_link_libraries(awpmd ${LAPACK_LIBRARIES})
 endif()
 
-if(ENABLE_USER-ATC)
+if(PKG_USER-ATC)
   target_link_libraries(atc ${LAPACK_LIBRARIES})
 endif()
 
-if(ENABLE_USER-H5MD)
+if(PKG_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)
+if(PKG_USER-OMP)
     set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
     set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
                          ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
@@ -463,7 +591,7 @@ if(ENABLE_USER-OMP)
     include_directories(${USER-OMP_SOURCES_DIR})
 endif()
 
-if(ENABLE_KOKKOS)
+if(PKG_KOKKOS)
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
   set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
   add_definitions(-DLMP_KOKKOS)
@@ -499,7 +627,7 @@ if(ENABLE_KOKKOS)
   RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
   RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
 
-  if(ENABLE_USER-DPD)
+  if(PKG_USER-DPD)
     get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
     list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
     RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
@@ -512,7 +640,7 @@ if(ENABLE_KOKKOS)
   include_directories(${KOKKOS_PKG_SOURCES_DIR})
 endif()
 
-if(ENABLE_OPT)
+if(PKG_OPT)
     set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
     set(OPT_SOURCES)
     set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
@@ -526,7 +654,34 @@ if(ENABLE_OPT)
     include_directories(${OPT_SOURCES_DIR})
 endif()
 
-if(ENABLE_USER-INTEL)
+if(PKG_USER-INTEL)
+    if(NOT DEVELOPER_MODE)
+      if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+        message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler")
+      endif()
+      if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
+        message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
+      endif()
+    endif()
+    option(INJECT_KNL_FLAG "Inject flags for KNL build" OFF)
+    if(INJECT_KNL_FLAG)
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xMIC-AVX512")
+    endif()
+    option(INJECT_INTEL_FLAG "Inject OMG fast flags for USER-INTEL" ON)
+    if(INJECT_INTEL_FLAG AND CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost")
+      endif()
+      include(CheckCXXCompilerFlag)
+      foreach(_FLAG -qopenmp -qno-offload -fno-alias -ansi-alias -restrict -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high)
+        check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG})
+        if(COMPILER_SUPPORTS${_FLAG})
+          set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_FLAG}")
+        endif()
+      endforeach()
+    endif()
     set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
     set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h
                            ${USER-INTEL_SOURCES_DIR}/intel_buffers.h
@@ -550,7 +705,10 @@ if(ENABLE_USER-INTEL)
     include_directories(${USER-INTEL_SOURCES_DIR})
 endif()
 
-if(ENABLE_GPU)
+if(PKG_GPU)
+    if (CMAKE_VERSION VERSION_LESS "3.1") 
+      message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
+    endif()
     set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
     set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
                     ${GPU_SOURCES_DIR}/fix_gpu.h
@@ -573,8 +731,7 @@ if(ENABLE_GPU)
       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)
+      set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g.  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)
@@ -647,7 +804,7 @@ if(ENABLE_GPU)
       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 -D_${GPU_PREC} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
       target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
 
       list(APPEND LAMMPS_LINK_LIBS gpu)
@@ -683,60 +840,157 @@ GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})
 include_directories(${LAMMPS_SOURCE_DIR})
 include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 
+######################################
+# Generate lmpinstalledpkgs.h
+######################################
+set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")
+set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] =  {\n")
+foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+    if(PKG_${PKG})
+        set(temp "${temp}  \"${PKG}\",\n")
+    endif()
+endforeach()
+set(temp "${temp}  NULL\n};\n#endif\n\n")
+message(STATUS "Generating lmpinstalledpkgs.h...")
+file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" )
+execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h")
+
 ###########################################
 # Actually add executable and lib to build
 ############################################
-add_library(lammps ${LIB_SOURCES})
-target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
-if(LAMMPS_DEPS)
-  add_dependencies(lammps ${LAMMPS_DEPS})
+get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
+list (FIND LANGUAGES "Fortran" _index)
+if (${_index} GREATER -1)
+  list(APPEND LAMMPS_LINK_LIBS ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
-set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
-if(BUILD_SHARED_LIBS)
-  set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
-  install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-  install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
-  configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
-  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+list(REMOVE_DUPLICATES LAMMPS_LINK_LIBS)
+if(BUILD_LIB)
+  add_library(lammps ${LIB_SOURCES})
+  target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
+  if(LAMMPS_DEPS)
+    add_dependencies(lammps ${LAMMPS_DEPS})
+  endif()
+  set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LIB_SUFFIX})
+  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 ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY)
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+  endif()
+else()
+  list(APPEND LMP_SOURCES ${LIB_SOURCES})
 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)
+if(BUILD_EXE)
+  add_executable(lmp ${LMP_SOURCES})
+  if(BUILD_LIB)
+    target_link_libraries(lmp lammps)
+  else()
+    target_link_libraries(lmp ${LAMMPS_LINK_LIBS})
+    if(LAMMPS_DEPS)
+      add_dependencies(lmp ${LAMMPS_DEPS})
+    endif()
+  endif()
+  
+  set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
+  install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
+  if(ENABLE_TESTING)
+    add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
+  endif()
 endif()
 
-##################################
+###############################################################################
+# Testing
+#
+# Requires latest gcovr (for GCC 8.1 support):#
+# pip install git+https://github.com/gcovr/gcovr.git
+###############################################################################
+if(ENABLE_COVERAGE)
+    find_program(GCOVR_BINARY gcovr)
+    find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
+
+    if(GCOVR_FOUND)
+        get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
+
+        add_custom_target(
+            gen_coverage_xml
+            COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Generating XML Coverage Report..."
+        )
+
+        add_custom_target(
+            gen_coverage_html
+            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Generating HTML Coverage Report..."
+        )
+    endif()
+endif()
+
+###############################################################################
 # Print package summary
-##################################
-foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
-  if(ENABLE_${PKG})
+###############################################################################
+foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
+  if(PKG_${PKG})
     message(STATUS "Building package: ${PKG}")
   endif()
 endforeach()
 
 string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
+get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
+include(FeatureSummary)
+feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND)
 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}}")
+       Version      ${CMAKE_CXX_COMPILER_VERSION}
+   C++ Flags        ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
+   Defines          ${CPPFLAGS}")
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
-if(LANGUAGES MATCHES ".*Fortran.*")
+list (FIND LANGUAGES "Fortran" _index)
+if (${_index} GREATER -1)
   message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER} 
            Type     ${CMAKE_Fortran_COMPILER_ID}
+           Version  ${CMAKE_Fortran_COMPILER_VERSION}
    Fortran Flags    ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
 endif()
-message(STATUS "Linker flags:
+list (FIND LANGUAGES "C" _index)
+if (${_index} GREATER -1)
+  message(STATUS "C Compiler ${CMAKE_C_COMPILER} 
+     Type     ${CMAKE_C_COMPILER_ID}
+     Version  ${CMAKE_C_COMPILER_VERSION}
+     C Flags  ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
+endif()
+if(CMAKE_EXE_LINKER_FLAGS)
+  message(STATUS "Linker flags:
    Executable      ${CMAKE_EXE_LINKER_FLAGS}")
+  endif()
 if(BUILD_SHARED_LIBS)
-  message(STATUS "Shared libries  ${CMAKE_SHARED_LINKER_FLAGS}")
+  message(STATUS "Shared libraries  ${CMAKE_SHARED_LINKER_FLAGS}")
 else()
-  message(STATUS "Static libries  ${CMAKE_STATIC_LINKER_FLAGS}")
+  message(STATUS "Static libraries  ${CMAKE_STATIC_LINKER_FLAGS}")
 endif()
 message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
-
+if(BUILD_MPI)
+  message(STATUS "Using mpi with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}")
+endif()
+if(PKG_GPU)
+  message(STATUS "GPU Api: ${GPU_API}")
+  if(GPU_API STREQUAL "CUDA")
+    message(STATUS "GPU Arch: ${GPU_ARCH}")
+  elseif(GPU_API STREQUAL "OpenCL")
+    message(STATUS "OCL Tune: ${OCL_TUNE}")
+  endif()
+  message(STATUS "GPU Precision: ${GPU_PREC}")
+endif()
+if(PKG_KOKKOS)
+  message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
+endif()
+if(PKG_KSPACE)
+  message(STATUS "Using ${FFT} as FFT")
+endif()

cmake/Modules/FindFFTW2.cmake

@@ -1,22 +0,0 @@
-# - 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/FindFFTW3F.cmake

@@ -0,0 +1,25 @@
+# - Find fftw3f
+# Find the native FFTW3F headers and libraries.
+#
+#  FFTW3F_INCLUDE_DIRS - where to find fftw3f.h, etc.
+#  FFTW3F_LIBRARIES    - List of libraries when using fftw3f.
+#  FFTW3F_FOUND        - True if fftw3f found.
+#
+
+find_package(PkgConfig)
+
+pkg_check_modules(PC_FFTW3F fftw3f)
+find_path(FFTW3F_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3F_INCLUDE_DIRS})
+
+find_library(FFTW3F_LIBRARY NAMES fftw3f HINTS ${PC_FFTW3F_LIBRARY_DIRS})
+
+set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY})
+set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set FFTW3F_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(FFTW3F DEFAULT_MSG FFTW3F_LIBRARY FFTW3F_INCLUDE_DIR)
+
+mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY )

cmake/Modules/FindMSCG.cmake

@@ -0,0 +1,22 @@
+# - Find mscg
+# Find the native MSCG headers and libraries.
+#
+#  MSCG_INCLUDE_DIRS - where to find mscg.h, etc.
+#  MSCG_LIBRARIES    - List of libraries when using mscg.
+#  MSCG_FOUND        - True if mscg found.
+#
+
+find_path(MSCG_INCLUDE_DIR mscg.h PATH_SUFFIXES mscg)
+
+find_library(MSCG_LIBRARY NAMES mscg)
+
+set(MSCG_LIBRARIES ${MSCG_LIBRARY})
+set(MSCG_INCLUDE_DIRS ${MSCG_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set MSCG_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(MSCG DEFAULT_MSG MSCG_LIBRARY MSCG_INCLUDE_DIR)
+
+mark_as_advanced(MSCG_INCLUDE_DIR MSCG_LIBRARY )

cmake/Modules/StyleHeaderUtils.cmake

@@ -45,14 +45,10 @@ function(FindStyleHeadersExt path style_class extension headers sources)
 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)
+    if(ARGC GREATER 2)
+        list(REMOVE_AT ARGV 0 1)
+        foreach(FNAME ${ARGV})
             get_filename_component(FNAME ${FNAME} NAME)
             set(temp "${temp}#include \"${FNAME}\"\n")
         endforeach()
@@ -107,35 +103,6 @@ function(RegisterStyles search_path)
     FindStyleHeaders(${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  ${sources})
@@ -181,3 +148,21 @@ function(GenerateStyleHeaders output_path)
     GenerateStyleHeader(${output_path} READER     reader    ) # read_dump
     GenerateStyleHeader(${output_path} REGION     region    ) # domain
 endfunction(GenerateStyleHeaders)
+
+function(DetectBuildSystemConflict lammps_src_dir)
+  if(ARGC GREATER 1)
+    list(REMOVE_AT ARGV 0)
+    foreach(SRC_FILE ${ARGV})
+        get_filename_component(FILENAME ${SRC_FILE} NAME)
+        if(EXISTS ${lammps_src_dir}/${FILENAME})
+            message(FATAL_ERROR "\n########################################################################\n"
+                                  "Found package(s) installed by the make-based build system\n"
+                                  "\n"
+                                  "Please run\n"
+                                  "make -C ${lammps_src_dir} no-all purge\n"
+                                  "to uninstall\n"
+                                  "########################################################################")
+        endif()
+    endforeach()
+  endif()
+endfunction(DetectBuildSystemConflict)

cmake/pkgconfig/liblammps.pc.in

@@ -13,6 +13,6 @@ Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
 URL: http://lammps.sandia.gov
 Version:
 Requires:
-Libs: -L${libdir} -llammps@LAMMPS_MACHINE@
+Libs: -L${libdir} -llammps@LIB_SUFFIX@@
 Libs.private: -lm
 Cflags: -I${includedir} @LAMMPS_API_DEFINES@

cmake/presets/all_off.cmake

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

cmake/presets/all_on.cmake

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

cmake/presets/manual_selection.cmake

@@ -0,0 +1,69 @@
+set(PKG_ASPHERE OFF CACHE BOOL "" FORCE)
+set(PKG_BODY OFF CACHE BOOL "" FORCE)
+set(PKG_CLASS2 OFF CACHE BOOL "" FORCE)
+set(PKG_COLLOID OFF CACHE BOOL "" FORCE)
+set(PKG_COMPRESS OFF CACHE BOOL "" FORCE)
+set(PKG_CORESHELL OFF CACHE BOOL "" FORCE)
+set(PKG_DIPOLE OFF CACHE BOOL "" FORCE)
+set(PKG_GPU OFF CACHE BOOL "" FORCE)
+set(PKG_GRANULAR OFF CACHE BOOL "" FORCE)
+set(PKG_KIM OFF CACHE BOOL "" FORCE)
+set(PKG_KOKKOS OFF CACHE BOOL "" FORCE)
+set(PKG_KSPACE OFF CACHE BOOL "" FORCE)
+set(PKG_LATTE OFF CACHE BOOL "" FORCE)
+set(PKG_LIB OFF CACHE BOOL "" FORCE)
+set(PKG_MANYBODY OFF CACHE BOOL "" FORCE)
+set(PKG_MC OFF CACHE BOOL "" FORCE)
+set(PKG_MEAM OFF CACHE BOOL "" FORCE)
+set(PKG_MISC OFF CACHE BOOL "" FORCE)
+set(PKG_MOLECULE OFF CACHE BOOL "" FORCE)
+set(PKG_MPIIO OFF CACHE BOOL "" FORCE)
+set(PKG_MSCG OFF CACHE BOOL "" FORCE)
+set(PKG_OPT OFF CACHE BOOL "" FORCE)
+set(PKG_PERI OFF CACHE BOOL "" FORCE)
+set(PKG_POEMS OFF CACHE BOOL "" FORCE)
+set(PKG_PYTHOFF OFF CACHE BOOL "" FORCE)
+set(PKG_QEQ OFF CACHE BOOL "" FORCE)
+set(PKG_REAX OFF CACHE BOOL "" FORCE)
+set(PKG_REPLICA OFF CACHE BOOL "" FORCE)
+set(PKG_RIGID OFF CACHE BOOL "" FORCE)
+set(PKG_SHOCK OFF CACHE BOOL "" FORCE)
+set(PKG_SNAP OFF CACHE BOOL "" FORCE)
+set(PKG_SRD OFF CACHE BOOL "" FORCE)
+set(PKG_VOROFFOI OFF CACHE BOOL "" FORCE)
+
+set(PKG_USER OFF CACHE BOOL "" FORCE)
+set(PKG_USER-ATC OFF CACHE BOOL "" FORCE)
+set(PKG_USER-AWPMD OFF CACHE BOOL "" FORCE)
+set(PKG_USER-BOCS OFF CACHE BOOL "" FORCE)
+set(PKG_USER-CGDNA OFF CACHE BOOL "" FORCE)
+set(PKG_USER-CGSDK OFF CACHE BOOL "" FORCE)
+set(PKG_USER-COLVARS OFF CACHE BOOL "" FORCE)
+set(PKG_USER-DIFFRACTIOFF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-DPD OFF CACHE BOOL "" FORCE)
+set(PKG_USER-DRUDE OFF CACHE BOOL "" FORCE)
+set(PKG_USER-EFF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-FEP OFF CACHE BOOL "" FORCE)
+set(PKG_USER-H5MD OFF CACHE BOOL "" FORCE)
+set(PKG_USER-INTEL OFF CACHE BOOL "" FORCE)
+set(PKG_USER-LB OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MANIFOLD OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MEAMC OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MESO OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MGPT OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MISC OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE)
+set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-OMP OFF CACHE BOOL "" FORCE)
+set(PKG_USER-PHOFFOFF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
+set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
+set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)
+set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE)
+set(PKG_USER-SMD OFF CACHE BOOL "" FORCE)
+set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE)
+set(PKG_USER-SPH OFF CACHE BOOL "" FORCE)
+set(PKG_USER-TALLY OFF CACHE BOOL "" FORCE)
+set(PKG_USER-UEF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-VTK OFF CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

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

cmake/presets/std.cmake

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

cmake/presets/std_nolib.cmake

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

cmake/presets/user.cmake

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

doc/Makefile

@@ -9,6 +9,7 @@ TXT2RST       = $(VENV)/bin/txt2rst
 ANCHORCHECK   = $(VENV)/bin/doc_anchor_check
 
 PYTHON        = $(shell which python3)
+VIRTUALENV     = virtualenv
 HAS_PYTHON3    = NO
 HAS_VIRTUALENV = NO
 
@@ -16,7 +17,13 @@ ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
 HAS_PYTHON3 = YES
 endif
 
+ifeq ($(shell which virtualenv-3 >/dev/null 2>&1; echo $$?), 0)
+VIRTUALENV     = virtualenv-3
+HAS_VIRTUALENV = YES
+endif
+
 ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
+VIRTUALENV     = virtualenv
 HAS_VIRTUALENV = YES
 endif
 
@@ -158,7 +165,7 @@ $(VENV):
 	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@( \
-		virtualenv -p $(PYTHON) $(VENV); \
+		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip install Sphinx; \
 		pip install sphinxcontrib-images; \

doc/src/Eqs/dihedral_table_cut.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+        f(\theta) & = & K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
+        f(\theta) & = & K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
+\end{eqnarray*}
+
+\end{document}
+

doc/src/Eqs/fix_integration_spin_stdecomposition.tex

@@ -0,0 +1,40 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm,tikz}
+\usetikzlibrary{automata,arrows,shapes,snakes}
+\begin{document}
+\begin{varwidth}{50in}
+\begin{tikzpicture}
+
+%Global
+\node (v1) at (0,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ };
+\node (s1) at (0,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ };
+\node (r)  at (0,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{r} \leftarrow \bm{r}+L_r.\Delta t$ };
+\node (s2) at (0,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ };
+\node (v2) at (0,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ };
+
+\draw[line width=2pt, ->] (v1) -- (s1);
+\draw[line width=2pt, ->] (s1) -- (r);
+\draw[line width=2pt, ->] (r) -- (s2);
+\draw[line width=2pt, ->] (s2) -- (v2);
+
+%Spin
+\node (s01) at (6,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ };
+\node (sN1) at (6,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$};
+\node (sN)  at (6,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N} \leftarrow \bm{s}_{\rm N}+L_{s_{\rm N}}.\Delta t/2$ };
+\node (sN2) at (6,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$};
+\node (s02) at (6,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ };
+
+\draw[line width=2pt,dashed, ->] (s01) -- (sN1);
+\draw[line width=2pt, ->] (sN1) -- (sN);
+\draw[line width=2pt, ->] (sN) -- (sN2);
+\draw[line width=2pt,dashed, ->] (sN2) -- (s02);
+
+%from Global to Spin
+\draw[line width=2pt, dashed, ->] (s1) -- (s01.west);
+\draw[line width=2pt, dashed, ->] (s1) -- (s02.west);
+
+\end{tikzpicture}
+\end{varwidth}
+\end{document}

doc/src/Eqs/fix_langevin_spin_sLLG.tex

@@ -0,0 +1,14 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \frac{d \vec{s}_{i}}{dt} = \frac{1}{\left(1+\lambda^2 \right)} \left( \left(
+    \vec{\omega}_{i} +\vec{\eta} \right) \times \vec{s}_{i} + \lambda\, \vec{s}_{i}
+  \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right) \right), \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/force_spin_aniso.tex

@@ -0,0 +1,11 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{H}_{aniso}  = -\sum_{{ i}=1}^{N} K_{an}(\bm{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2, \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/force_spin_zeeman.tex

@@ -0,0 +1,11 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{H}_{zeeman} = -\mu_{B}\mu_0\sum_{i=0}^{N}g_{i} \vec{s}_{i} \cdot \vec{H}_{ext} \nonumber 
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_entropy.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+
+$$
+   s_S^i=-2\pi\rho k_B \int\limits_0^{r_m} \left [ g(r) \ln g(r) - g(r) + 1 \right ] r^2 dr ,
+$$
+
+\end{document}

doc/src/Eqs/pair_entropy2.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+
+$$
+   g_m^i(r) = \frac{1}{4 \pi \rho r^2} \sum\limits_{j} \frac{1}{\sqrt{2 \pi \sigma^2}} e^{-(r-r_{ij})^2/(2\sigma^2)} ,
+$$
+
+\end{document}

doc/src/Eqs/pair_entropy3.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+
+$$
+  \bar{s}_S^i  = \frac{\sum_j s_S^j + s_S^i}{N + 1} ,
+$$
+
+\end{document}

doc/src/Eqs/pair_spin_dmi_interaction.tex

@@ -0,0 +1,16 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{H}_{dm} = -\sum_{{ i,j}=1,i\neq j}^{N} 
+    \left( \vec{e}_{ij} \times \vec{D} \right)
+    \cdot\left(\vec{s}_{i}\times \vec{s}_{j}\right), 
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}
+    \vec{D}\left(r_{ij}\right) 
+    {\rm ~and~}  \vec{D}\left(r_{ij}\right) = \vec{e}_{ij} \times \vec{D}  

doc/src/Eqs/pair_spin_exchange_forces.tex

@@ -0,0 +1,14 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{F}^{i} = \sum_{j}^{Neighbor} \frac{\partial {J} \left(r_{ij} \right)}{
+    \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{r}_{ij}  
+    ~~{\rm and}~~ \vec{\omega}^{i} = \frac{1}{\hbar} \sum_{j}^{Neighbor} {J} 
+    \left(r_{ij} \right)\,\vec{s}_{j} \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_exchange_function.tex

@@ -0,0 +1,13 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d}  \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d}  \right)^2 \right) e^{-\left( \frac{r_{ij}}{d}  
+    \right)^2 }\Theta (R_c - r_{ij}) \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_exchange_interaction.tex

@@ -0,0 +1,11 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{H}_{exchange} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_me_forces.tex

@@ -0,0 +1,13 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{F}^{i} = -\sum_{j}^{Neighbor} \left( \vec{s}_{i}\times \vec{s}_{j} \right)
+    \times \vec{E} ~~{\rm and}~~ \vec{\omega}^{i} = -\frac{1}{\hbar} 
+    \sum_{j}^{Neighbor} \vec{s}_j \times \left(\vec{E}\times r_{ij} \right),\nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_me_interaction.tex

@@ -0,0 +1,12 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times\vec{D}(r_{ij}) ~~{\rm and}~~
+    \vec{F}_i = -\sum_{j}^{Neighb} \frac{\partial D(r_{ij})}{\partial r_{ij}} \left(\vec{s}_{i}\times \vec{s}_{j} \right) \cdot \vec{r}_{ij}, \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_neel_functions.tex

@@ -0,0 +1,13 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{eqnarray}
+    g_1(r_{ij}) &=& g(r_{ij}) + \frac{12}{35} q(r_{ij}) \nonumber \\
+    q_1(r_{ij}) &=& \frac{9}{5} q(r_{ij}) \nonumber \\
+    q_2(r_{ij}) &=& - \frac{2}{5} q(r_{ij}) \nonumber
+  \end{eqnarray}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_neel_interaction.tex

@@ -0,0 +1,16 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \mathcal{H}_{N\acute{e}el}=-\sum_{{ i,j=1,i\neq j}}^N g_1(r_{ij})\left(({\bm e}_{ij}\cdot {\bm s}_{i})({\bm e}_{ij}
+    \cdot {\bm s}_{j})-\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right)
+    +q_1(r_{ij})\left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3}\right)
+    \left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right)
+    + q_2(r_{ij}) \Big( ({\bm e}_{ij}\cdot {\bm s}_{i}) ({\bm e}_{ij}\cdot {\bm s}_{j})^3 + ({\bm e}_{ij}\cdot
+    {\bm s}_{j}) ({\bm e}_{ij}\cdot {\bm s}_{i})^3\Big) \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="11 May 2018 version">
+<META NAME="docnumber" CONTENT="29 Jun 2018 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>
@@ -19,7 +19,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-11 May 2018 version :c,h2
+29 Jun 2018 version :c,h2
 
 Version info: :h3
 

doc/src/Section_commands.txt

@@ -129,6 +129,17 @@ region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
 
 so that you do not have to define (or discard) a temporary variable X.
 
+Additionally, the "immediate" variable expression may be followed by a
+colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
+The format string must be appropriate for a double-precision
+floating-point value.  The format string is used to output the result
+of the variable expression evaluation.  If a format string is not
+specified a high-precision "%.20g" is used as the default.
+
+This can be useful for formatting print output to a desired precion:
+
+print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
+
 Note that neither the curly-bracket or immediate form of variables can
 contain nested $ characters for other variables to substitute for.
 Thus you cannot do this:
@@ -583,6 +594,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "indent"_fix_indent.html,
 "latte"_fix_latte.html,
 "langevin (k)"_fix_langevin.html,
+"langevin/spin"_fix_langevin_spin.hmtl,
 "lineforce"_fix_lineforce.html,
 "momentum (k)"_fix_momentum.html,
 "move"_fix_move.html,
@@ -606,6 +618,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "nve/line"_fix_nve_line.html,
 "nve/noforce"_fix_nve_noforce.html,
 "nve/sphere (o)"_fix_nve_sphere.html,
+"nve/spin"_fix_nve_spin.html,
 "nve/tri"_fix_nve_tri.html,
 "nvt (iko)"_fix_nh.html,
 "nvt/asphere (o)"_fix_nvt_asphere.html,
@@ -618,6 +631,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "planeforce"_fix_planeforce.html,
 "poems"_fix_poems.html,
 "pour"_fix_pour.html,
+"precession/spin"_fix_precession_spin.html,
 "press/berendsen"_fix_press_berendsen.html,
 "print"_fix_print.html,
 "property/atom (k)"_fix_property_atom.html,
@@ -824,6 +838,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "sna/atom"_compute_sna_atom.html,
 "snad/atom"_compute_sna_atom.html,
 "snav/atom"_compute_sna_atom.html,
+"spin"_compute_spin.html,
 "stress/atom"_compute_stress_atom.html,
 "temp (k)"_compute_temp.html,
 "temp/asphere"_compute_temp_asphere.html,
@@ -852,6 +867,7 @@ package"_Section_start.html#start_3.
 "dpd"_compute_dpd.html,
 "dpd/atom"_compute_dpd_atom.html,
 "edpd/temp/atom"_compute_edpd_temp_atom.html,
+"entropy/atom"_compute_entropy_atom.html,
 "fep"_compute_fep.html,
 "force/tally"_compute_tally.html,
 "heat/flux/tally"_compute_tally.html,
@@ -1017,6 +1033,10 @@ KOKKOS, o = USER-OMP, t = OPT.
 "snap (k)"_pair_snap.html,
 "soft (go)"_pair_soft.html,
 "sw (giko)"_pair_sw.html,
+"spin/dmi"_pair_spin_dmi.html,
+"spin/exchange"_pair_spin_exchange.html,
+"spin/magelec"_pair_spin_magelec.html,
+"spin/neel"_pair_spin_neel.html,
 "table (gko)"_pair_table.html,
 "tersoff (giko)"_pair_tersoff.html,
 "tersoff/mod (gko)"_pair_tersoff_mod.html,
@@ -1212,7 +1232,8 @@ package"_Section_start.html#start_3.
 "nharmonic (o)"_dihedral_nharmonic.html,
 "quadratic (o)"_dihedral_quadratic.html,
 "spherical (o)"_dihedral_spherical.html,
-"table (o)"_dihedral_table.html :tb(c=4,ea=c)
+"table (o)"_dihedral_table.html,
+"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
 
 :line
 

doc/src/Section_errors.txt

@@ -803,6 +803,13 @@ lo value must be less than the hi value for all 3 dimensions. :dd
 The box command cannot be used after a read_data, read_restart, or
 create_box command. :dd
 
+{BUG: restartinfo=1 but no restart support in pair style} :dt
+
+The pair style has a bug, where it does not support reading
+and writing information to a restart file, but does not set
+the member variable restartinfo to 0 as required in that case. :dd
+
+
 {CPU neighbor lists must be used for ellipsoid/sphere mix.} :dt
 
 When using Gay-Berne or RE-squared pair styles with both ellipsoidal and

doc/src/Section_howto.txt

@@ -36,7 +36,8 @@ This section describes how to perform common tasks using LAMMPS.
 6.24 "Setting parameters for the kspace_style pppm/disp command"_#howto_24
 6.25 "Polarizable models"_#howto_25
 6.26 "Adiabatic core/shell model"_#howto_26
-6.27 "Drude induced dipoles"_#howto_27 :all(b)
+6.27 "Drude induced dipoles"_#howto_27
+6.28 "Magnetic spins"_#howto_28 :all(b)
 
 The example input scripts included in the LAMMPS distribution and
 highlighted in "Section 7"_Section_example.html also show how to
@@ -2906,6 +2907,54 @@ with a Coulomb pair style. It may be useful to use {coul/long/cs} or
 similar from the CORESHELL package if the core and Drude particle come
 too close, which can cause numerical issues.
 
+:line
+
+6.28 Magnetic spins :link(howto_28),h4
+
+Classical magnetic spin simualtions can be performed via the SPIN
+package.  The algrorithmic and implementation details are described in
+"Tranchida"_#Tranchida7.
+
+The model representents the simulation of atomic magnetic spins
+coupled to lattice vibrations. The dynamics of those magnetic spins
+can be used to simulate a broad range a phenomena related to
+magneto-elasticity, or or to study the influence of defects on the
+magnetic properties of materials.
+
+The magnetic spins are interacting with each others and with the 
+lattice via pair interactions. Typically, the magnetic exchange 
+interaction can be defined using the 
+"pair/spin/exchange"_pair_spin_exchange.html command. This exchange
+applies a magnetic torque to a given spin, considering the orientation
+of its neighboring spins and their relative distances. 
+It also applies a force on the atoms as a function of the spin 
+orientations and their associated inter-atomic distances. 
+ 
+The command "fix precession/spin"_fix_precession_spin.html allows to
+apply a constant magnetic torque on all the spins in the system. This
+torque can be an external magnetic field (Zeeman interaction), or an
+uniaxial magnetic anisotropy. 
+
+A Langevin thermostat can be applied to those magnetic spins using 
+"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat 
+can be coupled to another Langevin thermostat applied to the atoms 
+using "fix langevin"_fix_langevin.html in order to simulate 
+thermostated spin-lattice system. 
+
+The magnetic Gilbert damping can also be applied using "fix 
+langevin/spin"_fix_langevin_spin.html. It allows to either dissipate 
+the thermal energy of the Langevin thermostat, or to perform a 
+relaxation of the magnetic configuration toward an equilibrium state.
+
+All the computed magnetic properties can be outputed by two main 
+commands. The first one is "compute spin"_compute_spin.html, that 
+enables to evaluate magnetic averaged quantities, such as the total 
+magnetization of the system along x, y, or z, the spin temperature, or
+the magnetic energy. The second command is "compute 
+property/atom"_compute_property_atom.html. It enables to output all the
+per atom magnetic quantities. Typically, the orientation of a given 
+magnetic spin, or the magnetic force acting on this spin.
+
 :line
 :line
 
@@ -2957,3 +3006,7 @@ Phys, 79, 926 (1983).
 
 :link(howto-Lamoureux)
 [(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
+
+:link(Tranchida7)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, 
+arXiv preprint arXiv:1801.10233, (2018).

doc/src/Section_packages.txt

@@ -114,6 +114,7 @@ Package, Description, Doc page, Example, Library
 "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_style snap"_pair_snap.html, snap, -
+"SPIN"_#SPIN, magnetic atomic spin dynamics, "Section 6.6.28"_Section_howto.html#howto_28, SPIN, -
 "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)
 
@@ -1415,6 +1416,38 @@ examples/snap :ul
 
 :line
 
+SPIN package :link(SPIN),h4
+
+[Contents:]
+
+Model atomic magnetic spins classically, coupled to atoms moving in
+the usual manner via MD.  Various pair, fix, and compute styles.
+
+[Author:] Julian Tranchida (Sandia).
+
+[Install or un-install:]
+
+make yes-spin
+make machine :pre
+
+make no-spin
+make machine :pre
+
+[Supporting info:]
+
+src/SPIN: filenames -> commands
+"Section 6.28"_Section_howto.html#howto_28
+"pair_style spin/dmi"_pair_spin_dmi.html
+"pair_style spin/exchange"_pair_spin_exchange.html
+"pair_style spin/magelec"_pair_spin_magelec.html
+"pair_style spin/neel"_pair_spin_neel.html
+"fix nve/spin"_fix_nve_spin.html
+"fix precession/spin"_fix_precession_spin.html
+"compute spin"_compute_spin.html
+examples/SPIN :ul
+
+:line
+
 SRD package :link(SRD),h4
 
 [Contents:]

doc/src/atom_style.txt

@@ -15,7 +15,7 @@ atom_style style args :pre
 style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
         {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
+        {sphere} or {spin} 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
@@ -38,6 +38,7 @@ atom_style full
 atom_style body nparticle 2 10
 atom_style hybrid charge bond
 atom_style hybrid charge body nparticle 2 5
+atom_style spin
 atom_style template myMols 
 atom_style tdpd 2 :pre
 
@@ -89,6 +90,7 @@ quantities.
 {peri} | mass, volume | mesocopic Peridynamic models |
 {smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
 {sphere} | diameter, mass, angular velocity | granular models |
+{spin} | magnetic moment | system with magnetic particles |
 {template} | template index, template atom | small molecules with fixed topology |
 {tri} | corner points, angular momentum | rigid bodies |
 {wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
@@ -175,6 +177,9 @@ used for calculating the field variables (e.g. stress and deformation)
 and a contact radius for calculating repulsive forces which prevent
 individual physical bodies from penetrating each other.
 
+For the {spin} style, a magnetic spin is associated to each atom.
+Those spins have a norm (their magnetic moment) and a direction.
+
 The {wavepacket} style is similar to {electron}, but the electrons may
 consist of several Gaussian wave packets, summed up with coefficients
 cs= (cs_re,cs_im).  Each of the wave packets is treated as a separate
@@ -312,6 +317,8 @@ 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.
 
+The {spin} style is part of the SPIN package.
+
 The {wavepacket} style is part of the USER-AWPMD package for the
 "antisymmetrized wave packet MD method"_pair_awpmd.html.
 

doc/src/compute_entropy_atom.txt

@@ -0,0 +1,130 @@
+"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 entropy/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID entropy/atom sigma cutoff keyword value ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :l
+entropy/atom = style name of this compute command :l
+sigma = width of gaussians used in the g(r) smoothening :l
+cutoff = cutoff for the g(r) calculation :l
+one or more keyword/value pairs may be appended :l
+keyword = {avg} or {local}
+  {avg} values = {yes} or {no} cutoff2
+    {yes} = average the pair entropy over neighbors
+    {no} = do not average the pair entropy over neighbors
+    cutoff2 = cutoff for the averaging over neighbors
+  {local} values = {yes} or {no} = use the local density around each atom to normalize the g(r) :pre
+:ule
+
+[Examples:]
+
+compute 1 all entropy/atom 0.25 5.
+compute 1 all entropy/atom 0.25 5. avg yes 5.
+compute 1 all entropy/atom 0.125 7.3 avg yes 5.1 local yes :pre
+
+[Description:]
+
+Define a computation that calculates the pair entropy fingerprint for
+each atom in the group. The fingerprint is useful to distinguish between
+ordered and disordered environments, for instance liquid and solid-like 
+environments, or glassy and crystalline-like environments. Some 
+applications could be the identification of grain boundaries, a 
+melt-solid interface, or a solid cluster emerging from the melt. 
+The advantage of this parameter over others is that no a priori 
+information about the solid structure is required.
+
+This parameter for atom i is computed using the following formula from
+"(Piaggi)"_#Piaggi and "(Nettleton)"_#Nettleton ,
+
+:c,image(Eqs/pair_entropy.jpg)
+
+where r is a distance, g(r) is the radial distribution function of atom 
+i and rho is the density of the system. The g(r) computed for each 
+atom i can be noisy and therefore it is smoothened using:
+
+:c,image(Eqs/pair_entropy2.jpg)
+
+where the sum in j goes through the neighbors of atom i, and sigma is a
+parameter to control the smoothening.
+
+The input parameters are {sigma} the smoothening parameter, and the
+{cutoff} for the calculation of g(r). 
+
+If the keyword {avg} has the setting {yes}, then this compute also
+averages the parameter over the neighbors  of atom i according to:
+
+:c,image(Eqs/pair_entropy3.jpg)
+
+where the sum j goes over the neighbors of atom i and N is the number
+of neighbors. This procedure provides a sharper distinction between
+order and disorder environments. In this case the input parameter 
+{cutoff2} is the cutoff for the averaging over the neighbors and 
+must also be specified.
+
+If the {avg yes} option is used, the effective cutoff of the neighbor
+list should be {cutoff}+{cutoff2} and therefore it might be necessary 
+to increase the skin of the neighbor list with:
+
+neighbor skin bin :pre
+
+See "neighbor"_neighbor.html for details.
+
+If the {local yes} option is used, the g(r) is normalized by the 
+local density around each atom, that is to say the density around each 
+atom  is the number of neighbors within the neighbor list cutoff divided 
+by the corresponding volume. This option can be useful when dealing with 
+inhomogeneus systems such as those that have surfaces.
+
+Here are typical input parameters for fcc aluminum (lattice 
+constant 4.05 Angstroms),
+
+compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 :pre
+
+and for bcc sodium (lattice constant 4.23 Angstroms),
+
+compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 :pre
+
+
+[Output info:]
+
+By default, this compute calculates the pair entropy value for each
+atom as 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 pair entropy values have units of the Boltzmann constant. They are 
+always negative, and lower values (lower entropy) correspond to more
+ordered environments.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"compute cna/atom"_compute_cna_atom.html
+"compute centro/atom"_compute_centro_atom.html
+
+[Default:]
+
+The default values for the optional keywords are avg = no and local = no.
+
+:line
+
+:link(Piaggi)
+[(Piaggi)] Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017).
+
+:link(Nettleton)
+[(Nettleton)] Nettleton and Green, J Chem Phys, 29, 6 (1958).

doc/src/compute_property_atom.txt

@@ -19,6 +19,7 @@ input = one or more atom attributes :l
                         x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
                         vx, vy, vz, fx, fy, fz,
                         q, mux, muy, muz, mu,
+			sp, spx, spy, spz, fmx, fmy, fmz,
                         radius, diameter, omegax, omegay, omegaz,
                         angmomx, angmomy, angmomz,
                         shapex,shapey, shapez,
@@ -46,6 +47,9 @@ input = one or more atom attributes :l
       q = atom charge
       mux,muy,muz = orientation of dipole moment of atom
       mu = magnitude of dipole moment of atom
+      sp = atomic magnetic spin moment
+      spx, spy, spz = direction of the atomic magnetic spin
+      fmx, fmy, fmz = magnetic force
       radius,diameter = radius,diameter of spherical particle
       omegax,omegay,omegaz = angular velocity of spherical particle
       angmomx,angmomy,angmomz = angular momentum of aspherical particle
@@ -82,7 +86,8 @@ input = one or more atom attributes :l
 
 compute 1 all property/atom xs vx fx mux
 compute 2 all property/atom type
-compute 1 all property/atom ix iy iz :pre
+compute 1 all property/atom ix iy iz 
+compute 3 all property/atom sp spx spy spz :pre
 
 [Description:]
 
@@ -152,6 +157,10 @@ The vector or array values will be in whatever "units"_units.html the
 corresponding attribute is in, e.g. velocity units for vx, charge
 units for q, etc.
 
+For the spin quantities, sp is in the units of the Bohr magneton, spx,
+spy, and spz are adimentional quantities, and fmx, fmy and fmz are 
+given in rad.THz. 
+
 [Restrictions:] none
 
 [Related commands:]

doc/src/compute_spin.txt

@@ -0,0 +1,78 @@
+"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 spin command :h3
+
+[Syntax:]
+
+compute ID group-ID compute/spin :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+compute/spin = style name of this compute command :ul
+
+[Examples:]
+
+compute out_mag all compute/spin :pre
+
+[Description:]
+
+Define a computation that calculates magnetic quantities for a system 
+of atoms having spins.
+
+This compute calculates 6 magnetic quantities.
+
+The three first quantities are the x,y and z coordinates of the total magnetization.
+
+The fourth quantity is the norm of the total magnetization.
+
+The fifth quantity is the magnetic energy. 
+
+The sixth one is referred to as the spin temperature, according
+to the work of "(Nurdin)"_#Nurdin1. 
+  
+The simplest way to output the results of the compute spin calculation
+is to define some of the quantities as variables, and to use the thermo and
+thermo_style commands, for example:
+
+compute out_mag		all compute/spin :pre
+
+variable mag_z      	equal c_out_mag\[3\]
+variable mag_norm	equal c_out_mag\[4\]
+variable temp_mag      	equal c_out_mag\[6\] :pre
+
+thermo          	10
+thermo_style    	custom step v_mag_z v_mag_norm v_temp_mag :pre
+
+This serie of commands evaluates the total magnetization along z, the norm of 
+the total magnetization, and the magnetic temperature. Three variables are 
+assigned to those quantities. The thermo and thermo_style commands print them 
+every 10 timesteps.
+
+
+[Output info:]
+
+The array values are "intensive".  The array values will be in
+metal units ("units"_units.html).
+
+[Restrictions:] 
+
+The {spin} compute is part of the SPIN package.
+This compute is only enabled if LAMMPS was built with this package.
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+The atom_style has to be "spin" for this compute to be valid.
+
+[Related commands:] none
+
+
+[Default:] none
+
+:line
+
+:link(Nurdin1)
+[(Nurdin)] Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000)
+

doc/src/computes.txt

@@ -31,6 +31,7 @@ Computes :h1
    compute_dpd
    compute_dpd_atom
    compute_edpd_temp_atom
+   compute_entropy_atom
    compute_erotate_asphere
    compute_erotate_rigid
    compute_erotate_sphere
@@ -95,6 +96,7 @@ Computes :h1
    compute_smd_ulsph_stress
    compute_smd_vol
    compute_sna_atom
+   compute_spin
    compute_stress_atom
    compute_tally
    compute_tdpd_cc_atom

doc/src/create_bonds.txt

@@ -37,8 +37,8 @@ keyword = {special} :l
 
 create_bonds many all all 1 1.0 1.2
 create_bonds many surf solvent 3 2.0 2.4
-create_bond single/bond 1 1 2
-create_bond single/angle 5 52 98 107 special no :pre
+create_bonds single/bond 1 1 2
+create_bonds single/angle 5 52 98 107 special no :pre
 
 [Description:]
 

doc/src/dihedral_table_cut.txt

@@ -0,0 +1,205 @@
+"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
+
+dihedral_style table/cut command :h3
+
+[Syntax:]
+
+dihedral_style table/cut style Ntable :pre
+
+style = {linear} or {spline} = method of interpolation
+Ntable = size of the internal lookup table :ul
+
+[Examples:]
+
+dihedral_style table/cut spline 400
+dihedral_style table/cut linear 1000
+dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
+dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2 :pre
+
+[Description:]
+
+The {table/cut} dihedral style creates interpolation tables of length
+{Ntable} from dihedral potential and derivative values listed in a
+file(s) as a function of the dihedral angle "phi".  In addition, an
+analytic cutoff that is quadratic in the bond-angle (theta) is applied
+in order to regularize the dihedral interaction.  The dihedral table
+files are read by the "dihedral_coeff"_dihedral_coeff.html command.
+
+The interpolation tables are created by fitting cubic splines to the
+file values and interpolating energy and derivative values at each of
+{Ntable} dihedral angles. During a simulation, these tables are used
+to interpolate energy and force values on individual atoms as
+needed. The interpolation is done in one of 2 styles: {linear} or
+{spline}.
+
+For the {linear} style, the dihedral angle (phi) is used to find 2
+surrounding table values from which an energy or its derivative is
+computed by linear interpolation.
+
+For the {spline} style, cubic spline coefficients are computed and
+stored at each of the {Ntable} evenly-spaced values in the
+interpolated table.  For a given dihedral angle (phi), the appropriate
+coefficients are chosen from this list, and a cubic polynomial is used
+to compute the energy and the derivative at this angle.
+
+The following coefficients must be defined for each dihedral type via
+the "dihedral_coeff"_dihedral_coeff.html command as in the example
+above.
+
+style (aat)
+cutoff prefactor
+cutoff angle1
+cutoff angle2
+filename
+keyword :ul
+
+The cutoff dihedral style uses a tabulated dihedral interaction with a 
+cutoff function:
+
+:c,image(Eqs/dihedral_table_cut.jpg)
+
+The cutoff specifies an prefactor to the cutoff function.  While this value
+would ordinarily equal 1 there may be situations where the value should change.
+
+The cutoff angle1 specifies the angle (in degrees) below which the dihedral
+interaction is unmodified, i.e. the cutoff function is 1.
+
+The cutoff function is applied between angle1 and angle2, which is the angle at
+which the cutoff function drops to zero.  The value of zero effectively "turns
+off" the dihedral interaction.
+
+The filename specifies a file containing tabulated energy and
+derivative values. The keyword specifies a section of the file.  The
+format of this file is described below.
+
+:line
+
+The format of a tabulated file is as follows (without the
+parenthesized comments).  It can begin with one or more comment
+or blank lines.
+
+# Table of the potential and its negative derivative  :pre
+
+DIH_TABLE1                   (keyword is the first text on line)
+N 30 DEGREES                 (N, NOF, DEGREES, RADIANS, CHECKU/F)
+                             (blank line)
+1 -168.0 -1.40351172223 0.0423346818422
+2 -156.0 -1.70447981034 0.00811786522531
+3 -144.0 -1.62956100432 -0.0184129719987
+...
+30 180.0 -0.707106781187 0.0719306095245 :pre
+
+# Example 2: table of the potential. Forces omitted :pre
+
+DIH_TABLE2
+N 30 NOF CHECKU testU.dat CHECKF testF.dat :pre
+
+1 -168.0 -1.40351172223
+2 -156.0 -1.70447981034
+3 -144.0 -1.62956100432
+...
+30 180.0 -0.707106781187 :pre
+
+A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections. The first line begins with a keyword which
+identifies the section. The line can contain additional text, but the
+initial text must match the argument specified in the
+"dihedral_coeff"_dihedral_coeff.html command. The next line lists (in
+any order) one or more parameters for the table. Each parameter is a
+keyword followed by one or more numeric values.
+
+Following a blank line, the next N lines list the tabulated values. On
+each line, the 1st value is the index from 1 to N, the 2nd value is
+the angle value, the 3rd value is the energy (in energy units), and
+the 4th is -dE/d(phi) also in energy units). The 3rd term is the
+energy of the 4-atom configuration for the specified angle.  The 4th
+term (when present) is the negative derivative of the energy with
+respect to the angle (in degrees, or radians depending on whether the
+user selected DEGREES or RADIANS).  Thus the units of the last term
+are still energy, not force. The dihedral angle values must increase
+from one line to the next.
+
+Dihedral table splines are cyclic.  There is no discontinuity at 180
+degrees (or at any other angle).  Although in the examples above, the
+angles range from -180 to 180 degrees, in general, the first angle in
+the list can have any value (positive, zero, or negative).  However
+the {range} of angles represented in the table must be {strictly} less
+than 360 degrees (2pi radians) to avoid angle overlap.  (You may not
+supply entries in the table for both 180 and -180, for example.)  If
+the user's table covers only a narrow range of dihedral angles,
+strange numerical behavior can occur in the large remaining gap.
+
+[Parameters:]
+
+The parameter "N" is required and its value is the number of table
+entries that follow. Note that this may be different than the N
+specified in the "dihedral_style table"_dihedral_style.html command.
+Let {Ntable} is the number of table entries requested dihedral_style
+command, and let {Nfile} be the parameter following "N" in the
+tabulated file ("30" in the sparse example above).  What LAMMPS does
+is a preliminary interpolation by creating splines using the {Nfile}
+tabulated values as nodal points.  It uses these to interpolate as
+needed to generate energy and derivative values at {Ntable} different
+points (which are evenly spaced over a 360 degree range, even if the
+angles in the file are not).  The resulting tables of length {Ntable}
+are then used as described above, when computing energy and force for
+individual dihedral angles and their atoms.  This means that if you
+want the interpolation tables of length {Ntable} to match exactly what
+is in the tabulated file (with effectively nopreliminary
+interpolation), you should set {Ntable} = {Nfile}.  To insure the
+nodal points in the user's file are aligned with the interpolated
+table entries, the angles in the table should be integer multiples of
+360/{Ntable} degrees, or 2*PI/{Ntable} radians (depending on your
+choice of angle units).
+
+The optional "NOF" keyword allows the user to omit the forces
+(negative energy derivatives) from the table file (normally located in
+the 4th column).  In their place, forces will be calculated
+automatically by differentiating the potential energy function
+indicated by the 3rd column of the table (using either linear or
+spline interpolation).
+
+The optional "DEGREES" keyword allows the user to specify angles in
+degrees instead of radians (default).
+
+The optional "RADIANS" keyword allows the user to specify angles in
+radians instead of degrees.  (Note: This changes the way the forces
+are scaled in the 4th column of the data file.)
+
+The optional "CHECKU" keyword is followed by a filename.  This allows
+the user to save all of the the {Ntable} different entries in the
+interpolated energy table to a file to make sure that the interpolated
+function agrees with the user's expectations.  (Note: You can
+temporarily increase the {Ntable} parameter to a high value for this
+purpose.  "{Ntable}" is explained above.)
+
+The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
+It is followed by a filename, and it allows the user to check the
+interpolated force table.  This option is available even if the user
+selected the "NOF" option.
+
+Note that one file can contain many sections, each with a tabulated
+potential. LAMMPS reads the file section by section until it finds one
+that matches the specified keyword.
+
+[Restrictions:]
+
+This dihedral style can only be used if LAMMPS was built with the
+USER-MISC package.  See the "Making LAMMPS"_Section_start.html#start_3
+section for more info on packages.
+
+[Related commands:]
+
+"dihedral_coeff"_dihedral_coeff.html, "dihedral_style table"_dihedral_table.html
+
+[Default:] none
+
+:link(dihedralcut-Salerno)
+[(Salerno)] Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).

doc/src/dihedrals.txt

@@ -19,6 +19,7 @@ Dihedral Styles :h1
    dihedral_quadratic
    dihedral_spherical
    dihedral_table
+   dihedral_table_cut
    dihedral_zero
    dihedral_charmm
    dihedral_class2

doc/src/dump_modify.txt

@@ -15,7 +15,7 @@ dump_modify dump-ID keyword values ... :pre
 dump-ID = ID of dump to modify :ulb,l
 one or more keyword/value pairs may be appended :l
 these keywords apply to various dump styles :l
-keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
+keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
   {append} arg = {yes} or {no}
   {at} arg = N
     N = index of frame written upon first dump
@@ -37,6 +37,8 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
   {image} arg = {yes} or {no}
   {label} arg = string
     string = character string (e.g. BONDS) to use in header of dump local file
+  {maxfiles} arg = Fmax
+    Fmax = keep only the most recent {Fmax} snapshots (one snapshot per file)
   {nfile} arg = Nf
     Nf = write this many files, one from each of Nf processors
   {pad} arg = Nchar = # of characters to convert timestep to
@@ -364,6 +366,20 @@ e.g. BONDS or ANGLES.
 
 :line
 
+The {maxfiles} keyword can only be used when a '*' wildcard is
+included in the dump file name, i.e. when writing a new file(s) for
+each snapshot.  The specified {Fmax} is how many snapshots will be
+kept.  Once this number is reached, the file(s) containing the oldest
+snapshot is deleted before a new dump file is written.  If the
+specified {Fmax} <= 0, then all files are retained.
+
+This can be useful for debugging, especially if you don't know on what
+timestep something bad will happen, e.g. when LAMMPS will exit with an
+error.  You can dump every timestep, and limit the number of dump
+files produced, even if you run for 1000s of steps.
+
+:line
+
 The {nfile} or {fileper} keywords can be used in conjunction with the
 "%" wildcard character in the specified dump file name, for all dump
 styles except the {dcd}, {image}, {movie}, {xtc}, and {xyz} styles
@@ -470,7 +486,7 @@ to respond to the call from the dump command, and update the
 appropriate reference positions.  This is done be defining an
 "atom-style variable"_variable.html, {check} in this example, which
 calculates a Boolean value (0 or 1) for each atom, based on the same
-criterion used by dump_modify thresh.  
+criterion used by dump_modify thresh.
 
 See the "compute displace/atom"_compute_displace_atom.html command for
 more details, including an example of how to produce output that
@@ -584,13 +600,13 @@ included.)
 
 region foo sphere 10 20 10 15
 variable inregion atom rmask(foo)
-dump_modify ... thresh v_inregion |^ LAST
+dump_modify ... thresh v_inregion |^ LAST :pre
 
 This will dump atoms which crossed the boundary of the spherical
 region since the last dump.
 
 variable charge atom "(q > 0.5) || (q < -0.5)"
-dump_modify ... thresh v_charge |^ LAST
+dump_modify ... thresh v_charge |^ LAST :pre
 
 This will dump atoms whose charge has changed from an absolute value
 less than 1/2 to greater than 1/2 (or vice versa) since the last dump.
@@ -901,6 +917,7 @@ flush = yes
 format = %d and %g for each integer or floating point value
 image = no
 label = ENTRIES
+maxifiles = -1
 nfile = 1
 pad = 0
 pbc = no

doc/src/fix_adapt.txt

@@ -205,6 +205,14 @@ a bond coefficient over time, very similar to how the {pair} keyword
 operates. The only difference is that now a bond coefficient for a
 given bond type is adapted.
 
+A wild-card asterisk can be used in place of or in conjunction with
+the bond type argument to set the coefficients for multiple bond types.
+This takes the form "*" or "*n" or "n*" or "m*n".  If N = the number of
+atom types, then an asterisk with no numeric values means all types
+from 1 to N.  A leading asterisk means all types from 1 to n (inclusive).
+A trailing asterisk means all types from n to N (inclusive).  A middle
+asterisk means all types from m to n (inclusive).
+
 Currently {bond} does not support bond_style hybrid nor bond_style
 hybrid/overlay as bond styles. The only bonds that currently are
 working with fix_adapt are

doc/src/fix_bond_react.txt

@@ -20,14 +20,15 @@ ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb
 bond/react = style name of this fix command :l
 zero or more common keyword/value pairs may be appended directly after 'bond/react' :l
 these apply to all reaction specifications (below) :l
-common_keyword = {stabilization}
-  {stabilization} values = group-ID xmax
-    group-ID = user-assigned ID of an internally-created dynamic group that excludes reacting atoms, and can be used by a subsequent time integration fix such as nvt, npt, or nve (cannot be 'all')
-  {xmax} value = distance
-    distance = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator
-react = mandatory argument indicating new reaction specification
-  react-ID = user-assigned name for the reaction
-  react-group-ID = only atoms in this group are available for the reaction
+common_keyword = {stabilization} :l
+  {stabilization} values = {no} or {yes} {group-ID} {xmax}
+    {no} = no reaction site stabilization
+    {yes} = perform reaction site stabilization
+      {group-ID} = user-assigned ID for all non-reacting atoms (group created internally)
+      {xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre
+react = mandatory argument indicating new reaction specification :l
+  react-ID = user-assigned name for the reaction :l
+  react-group-ID = only atoms in this group are available for the reaction :l
   Nevery = attempt reaction every this many steps :l
   Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l
   Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
@@ -47,7 +48,7 @@ react = mandatory argument indicating new reaction specification
 
 molecule mol1 pre_reacted_topology.txt
 molecule mol2 post_reacted_topology.txt
-fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt
+fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
 
 molecule mol1 pre_reacted_rxn1.txt
 molecule mol2 post_reacted_rxn1.txt
@@ -56,12 +57,12 @@ molecule mol4 post_reacted_rxn2.txt
 fix 5 all bond/react stabilization yes nvt_grp .03 &
   react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
   react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
-fix 6 nvt_grp nvt temp 300 300 100 # system-wide thermostat must be defined after bond/react :pre
+fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre
 
 [Description:]
 
 Initiate complex covalent bonding (topology) changes. These topology
-changes will be referred to as "reactions" throughout this
+changes will be referred to as 'reactions' throughout this
 documentation. Topology changes are defined in pre- and post-reaction
 molecule templates and can include creation and deletion of bonds,
 angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
@@ -81,10 +82,10 @@ occurred 3) build a molecule template of the reaction site after the
 reaction has occurred 4) create a map that relates the
 template-atom-IDs of each atom between pre- and post-reaction molecule
 templates 5) fill a simulation box with molecules and run a simulation
-with fix/bond react.
+with fix bond/react.
 
 Only one 'fix bond/react' command can be used at a time. Multiple
-reactions can be simultaneously applied by specifying multiple 'react'
+reactions can be simultaneously applied by specifying multiple {react}
 arguments to a single 'fix bond/react' command. This syntax is
 necessary because the 'common keywords' are applied to all reactions.
 
@@ -99,10 +100,11 @@ typically be set to the maximum distance that non-reacting atoms move
 during the simulation.
 
 The group-ID set using the {stabilization} keyword should be a
-previously unused group-ID. The fix bond/react command creates a
-"dynamic group"_group.html of this name that excludes reacting atoms.
-This dynamic group-ID should then be used by a subsequent system-wide
-time integrator, as shown in the second example above. It is currently
+previously unused group-ID. It cannot be specified as 'all'. The fix
+bond/react command creates a "dynamic group"_group.html of this name
+that includes all non-reacting atoms. This dynamic group-ID should
+then be used by a subsequent system-wide time integrator such as nvt,
+npt, or nve, as shown in the second example above. It is currently
 necessary to place the time integration command after the fix
 bond/react command due to the internal dynamic grouping performed by
 fix bond/react.
@@ -111,9 +113,9 @@ NOTE: The internally created group currently applies to all atoms in
 the system, i.e. you should generally not have a separate thermostat
 which acts on the 'all' group.
 
-The following comments pertain to each 'react' argument:
+The following comments pertain to each {react} argument:
 
-A check for possible new reaction sites is performed every Nevery
+A check for possible new reaction sites is performed every {Nevery}
 timesteps.
 
 Two conditions must be met for a reaction to occur. First a bonding
@@ -124,20 +126,20 @@ modified to match the post-reaction template.
 
 A bonding atom pair will be identified if several conditions are met.
 First, a pair of atoms within the specified react-group-ID of type
-typei and typej must separated by a distance between Rmin and Rmax. It
-is possible that multiple bonding atom pairs are identified: if the
-bonding atoms in the pre-reacted template are not 1-2, 1-3, or 1-4
-neighbors, the closest bonding atom partner is set as its bonding
-partner; otherwise, the farthest potential partner is chosen. Then, if
-both an atomi and atomj have each other as their nearest bonding
-partners, these two atoms are identified as the bonding atom pair of
-the reaction site. Once this unique bonding atom pair is identified
-for each reaction, there could two or more reactions that involve a
-given atom on the same timestep. If this is the case, only one such
-reaction is permitted to occur. This reaction is chosen randomly from
-all potential reactions. This capability allows e.g. for different
-reaction pathways to proceed from identical reaction sites with
-user-specified probabilities.
+typei and typej must separated by a distance between {Rmin} and
+{Rmax}. It is possible that multiple bonding atom pairs are
+identified: if the bonding atoms in the pre-reacted template are not
+1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
+its bonding partner; otherwise, the farthest potential partner is
+chosen. Then, if both an atomi and atomj have each other as their
+nearest bonding partners, these two atoms are identified as the
+bonding atom pair of the reaction site. Once this unique bonding atom
+pair is identified for each reaction, there could two or more
+reactions that involve a given atom on the same timestep. If this is
+the case, only one such reaction is permitted to occur. This reaction
+is chosen randomly from all potential reactions. This capability
+allows e.g. for different reaction pathways to proceed from identical
+reaction sites with user-specified probabilities.
 
 The pre-reacted molecule template is specified by a molecule command.
 This molecule template file contains a sample reaction site and its
@@ -175,77 +177,43 @@ A discussion of correctly handling this is also provided on the
 
 The map file is a text document with the following format:
 
-Format of the map file
+A map file has a header and a body. The header of map file the
+contains one mandatory keyword and one optional keyword. The mandatory
+keyword is 'equivalences' and the optional keyword is 'edgeIDs':
 
-A map file has a header and a body. The header appears first. The
-first line of the header is always skipped; it typically contains a
-description of the file.  Lines can have a trailing comment starting
-with '#' that is ignored. If the line is blank (only whitespace after
-comment is deleted), it is skipped. If the line contains a header
-keyword, the corresponding value(s) is read from the line. If it
-doesn't contain a header keyword, the line begins the body of the
-file.
+N {equivalences} = # of atoms N in the reaction molecule templates
+N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template :pre
 
-The header contains one mandatory keyword and one optional keyword.
-The mandatory keyword is 'equivalences' and the optional keyword is
-'edgeIDs.' These specify the number of atoms in the pre- and
-post-reacted templates and the number of edge atoms in pre-reacted
-template, respectively.
-
-The body contains two mandatory sections and one optional section. The
-first section begins with the keyword 'BondingIDs' and lists the atom
-IDs of the bonding atom pair in the pre-reacted molecule template. The
-second mandatory section begins with the keyword 'Equivalences' and
-lists a one-to-one correspondence between atom IDs of the pre- and
-post-reacted templates. The optional section begins with the keyword
-'EdgeIDs' and list the atom IDs of edge atoms in the pre-reacted
+The body of the map file contains two mandatory sections and one
+optional section. The first mandatory section begins with the keyword
+'BondingIDs' and lists the atom IDs of the bonding atom pair in the
+pre-reacted molecule template. The second mandatory section begins
+with the keyword 'Equivalences' and lists a one-to-one correspondence
+between atom IDs of the pre- and post-reacted templates. The first
+column is an atom ID of the pre-reacted molecule template, and the
+second column is the corresponding atom ID of the post-reacted
+molecule template. The optional section begins with the keyword
+'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
 molecule template.
 
-Format of the header of the map file
-
-These are the recognized header keywords. Header lines can come in any
-order. The value(s) are read from the beginning of the line. Thus the
-keyword 'equivalences' should be in a line like "25 equivalences."
-
-equivalences = # of atoms in the pre- and post-reacted molecule
-templates edgeIDs = # of edge atoms in the pre-reacted molecule template :pre
-
-The edgeIDs keyword is optional.
-
-Format of the body of the map file
-
-These are the section keywords for the body of the file.
-
-BondingIDs, EdgeIDs = list of atom IDs of bonding and edge atoms in
-the pre-reacted molecule template
-
-Equivalences = a two column list where the first column is an atom ID
-of the pre-reacted molecule template, and the second column is the
-corresponding atom ID of the post-reacted molecule template
-
-The bondingIDs section will always contain two atom IDs, corresponding
-to the bonding atom pairs of the pre-reacted map file. The
-Equivalences section will contain as many rows as there are atoms in
-the pre- and post-reacted molecule templates. The edgeIDs section is
-optional, but would contain an atom ID for each edge atom in the
-pre-reacted molecule template.
-
 A sample map file is given below:
 
 :line
 
-# This is a map file :pre
+# this is a map file :pre
 
 2 edgeIDs
 7 equivalences :pre
 
 BondingIDs :pre
 
-3 5 :pre
+3
+5 :pre
 
 EdgeIDs :pre
 
-1 7 :pre
+1
+7 :pre
 
 Equivalences :pre
 
@@ -264,13 +232,13 @@ within LAMMPS that store bond topology are updated to reflect the
 post-reacted molecule template. All force fields with fixed bonds,
 angles, dihedrals or impropers are supported.
 
-A few capabilities to note: 1) You may specify as many 'react'
+A few capabilities to note: 1) You may specify as many {react}
 arguments as desired. For example, you could break down a complicated
 reaction mechanism into several reaction steps, each defined by its
-own 'react' argument. 2) While typically a bond is formed or removed
+own {react} argument. 2) While typically a bond is formed or removed
 between the bonding atom pairs specified in the pre-reacted molecule
 template, this is not required. 3) By reversing the order of the pre-
-and post- reacted molecule templates in another 'react' argument, you
+and post- reacted molecule templates in another {react} argument, you
 can allow for the possibility of one or more reverse reactions.
 
 The optional keywords deal with the probability of a given reaction
@@ -304,7 +272,7 @@ you can use the internally-created dynamic group named
 would thermostat the group of all atoms currently involved in a
 reaction:
 
-fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre
 
 NOTE: This command must be added after the fix bond/react command, and
 will apply to all reactions.
@@ -324,10 +292,11 @@ local command.
 [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.
+files"_restart.html, aside from internally-created per-atom
+properties. None of the "fix_modify"_fix_modify.html options are
+relevant to this fix.
 
-This fix computes one statistic for each 'react' argument that it
+This fix computes one statistic for each {react} argument that it
 stores in a global vector, of length 'number of react arguments', that
 can be accessed by various "output
 commands"_Section_howto.html#howto_15. The vector values calculated by
@@ -359,5 +328,5 @@ The option defaults are stabilization = no, stabilize_steps = 60
 
 :line
 
-:link(Gissinger) [(Gissinger)] Gissinger, Jensen and Wise, Polymer,
-128, 211 (2017).
+:link(Gissinger)
+[(Gissinger)] Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).

doc/src/fix_dt_reset.txt

@@ -19,7 +19,9 @@ Tmin = minimum dt allowed which can be NULL (time units)
 Tmax = maximum dt allowed which can be NULL (time units)
 Xmax = maximum distance for an atom to move in one timestep (distance units)
 zero or more keyword/value pairs may be appended
-keyword = {units} :ul
+keyword = {emax} or {units} :ul
+  {emax} value = Emax
+    Emax = maximum kinetic energy change for an atom in one timestep (energy units)
   {units} value = {lattice} or {box}
     lattice = Xmax is defined in lattice units
     box = Xmax is defined in simulation box units :pre
@@ -27,12 +29,17 @@ keyword = {units} :ul
 [Examples:]
 
 fix 5 all dt/reset 10 1.0e-5 0.01 0.1
-fix 5 all dt/reset 10 0.01 2.0 0.2 units box :pre
+fix 5 all dt/reset 10 0.01 2.0 0.2 units box
+fix 5 all dt/reset 5 NULL 0.001 0.5 emax 30 units box :pre
 
 [Description:]
 
 Reset the timestep size every N steps during a run, so that no atom
-moves further than Xmax, based on current atom velocities and forces.
+moves further than the specified {Xmax} distance, based on current
+atom velocities and forces.  Optionally an additional criterion is
+imposed by the {emax} keyword, so that no atom's kinetic energy
+changes by more than the specified {Emax}.
+
 This can be useful when starting from a configuration with overlapping
 atoms, where forces will be large.  Or it can be useful when running
 an impact simulation where one or more high-energy atoms collide with
@@ -48,7 +55,12 @@ current velocity and force.  Since performing this calculation exactly
 would require the solution to a quartic equation, a cheaper estimate
 is generated.  The estimate is conservative in that the atom's
 displacement is guaranteed not to exceed {Xmax}, though it may be
-smaller.
+smaller. 
+
+In addition if the {emax} keyword is used, the specified {Emax} value
+is enforced as a limit on how much an atom's kinetic energy can
+change.  If the timestep required is even smaller than for the {Xmax}
+displacement, then the smaller timestep is used.
 
 Given this putative timestep for each atom, the minimum timestep value
 across all atoms is computed.  Then the {Tmin} and {Tmax} bounds are
@@ -87,4 +99,5 @@ minimization"_minimize.html.
 
 [Default:]
 
-The option defaults is units = lattice.
+The option defaults are units = lattice, and no emax kinetic energy
+limit.

doc/src/fix_langevin_spin.txt

@@ -0,0 +1,102 @@
+"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 langevin/spin command :h3
+
+[Syntax:]
+
+fix ID group-ID langevin/spin T Tdamp seed :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+langevin/spin = style name of this fix command :l
+T = desired temperature of the bath (temperature units, K in metal units) :l
+Tdamp = transverse magnetic damping parameter (adim) :l
+seed = random number seed to use for white noise (positive integer) :l
+:ule
+
+[Examples:]
+
+fix 2 all langevin/spin 300.0 0.01 21 :pre
+
+[Description:]
+
+Apply a Langevin thermostat as described in "(Mayergoyz)"_#Mayergoyz1 to the 
+magnetic spins associated to the atoms. 
+Used with "fix nve/spin"_fix_nve_spin.html, this command performs 
+Brownian dynamics (BD). 
+A random torque and a transverse dissipation are applied to each spin i according to
+the following stochastic differential equation:
+
+:c,image(Eqs/fix_langevin_spin_sLLG.jpg)
+
+with lambda the transverse damping, and eta a random verctor.
+This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG) 
+equation.
+
+The components of eta are drawn from a Gaussian probability law. Their amplitude 
+is defined as a proportion of the temperature of the external thermostat T (in K 
+in metal units).
+
+More details about this implementation are reported in "(Tranchida)"_#Tranchida2.
+
+Note: due to the form of the sLLG equation, this fix has to be defined just
+before the nve/spin fix (and after all other magnetic fixes). 
+As an example:
+
+fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0
+fix 2 all langevin/spin 300.0 0.01 21 
+fix 3 all nve/spin lattice yes :pre
+
+is correct, but defining a force/spin command after the langevin/spin command
+would give an error message. 
+
+Note: The random # {seed} must be a positive integer.  A Marsaglia random
+number generator is used.  Each processor uses the input seed to
+generate its own unique seed and its own stream of random numbers.
+Thus the dynamics of the system will not be identical on two runs on
+different numbers of processors.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  Because the state of the random number generator
+is not saved in restart files, this means you cannot do "exact"
+restarts with this fix, where the simulation continues on the same as
+if no restart had taken place.  However, in a statistical sense, a
+restarted simulation should produce the same behavior.
+
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:]
+
+The {langevin/spin} fix is part of the SPIN package.
+This style is only enabled if LAMMPS was built with this package.
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+The numerical integration has to be performed with {fix nve/spin}
+when {fix langevin/spin} is enabled. 
+
+This fix has to be the last defined magnetic fix before the time
+integration fix (e.g. {fix nve/spin}). 
+
+[Related commands:]
+
+"fix nve/spin"_fix_nve_spin.html, "fix precession/spin"_fix_precession_spin.html
+
+[Default:] none
+
+:line
+
+:link(Mayergoyz1)
+[(Mayergoyz)] I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009)
+
+:link(Tranchida2)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, 
+arXiv preprint arXiv:1801.10233, (2018).

doc/src/fix_nve_spin.txt

@@ -0,0 +1,76 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix nve/spin command :h3
+
+[Syntax:]
+
+fix ID group-ID nve/spin keyword values :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+nve/spin = style name of this fix command :l
+keyword = {lattice} :l
+  {lattice} value = {no} or {yes} :pre
+:ule
+
+[Examples:]
+
+fix 3 all nve/spin lattice yes
+fix 1 all nve/spin lattice no :pre
+
+[Description:]
+
+Perform a symplectic integration for the spin or spin-lattice system.
+
+The {lattice} keyword defines if the spins are integrated on a lattice 
+of fixed atoms (lattice = no), or if atoms are moving (lattice = yes).
+
+By default (lattice = yes), a spin-lattice integration is performed.
+
+The {nve/spin} fix applies a Suzuki-Trotter decomposition to 
+the equations of motion of the spin lattice system, following the scheme:
+
+:c,image(Eqs/fix_integration_spin_stdecomposition.jpg)
+
+according to the implementation reported in "(Omelyan)"_#Omelyan1.
+
+A sectoring method enables this scheme for parallel calculations. 
+The implementation of this sectoring algorithm is reported 
+in "(Tranchida)"_#Tranchida1.
+
+:line
+
+[Restrictions:]
+
+This fix style can only be used if LAMMPS was built with the
+SPIN package. See the "Making LAMMPS"_Section_start.html#start_3
+section for more info on packages.
+
+To use the spin algorithm, it is necessary to define a map with 
+the atom_modify command. Typically, by adding the command:
+
+atom_modify map array :pre
+
+before you create the simulation box. Note that the keyword "hash"
+instead of "array" is also valid.
+
+[Related commands:]
+
+"atom_style spin"_atom_style.html, "fix nve"_fix_nve.html
+
+[Default:] none
+
+:line
+
+:link(Omelyan1)
+[(Omelyan)] Omelyan, Mryglod, and Folk. Phys. Rev. Lett. 
+86(5), 898. (2001).
+
+:link(Tranchida1)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
+arXiv preprint arXiv:1801.10233, (2018).

doc/src/fix_precession_spin.txt

@@ -0,0 +1,87 @@
+"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 precession/spin command :h3
+
+[Syntax:]
+
+fix ID group precession/spin style args :pre
+
+ID, group are documented in "fix"_fix.html command :ulb,l
+precession/spin = style name of this fix command :l
+style = {zeeman} or {anisotropy} :l
+  {zeeman} args = H x y z 
+    H = intensity of the magnetic field (in Tesla)
+    x y z = vector direction of the field
+  {anisotropy} args = K x y z
+    K = intensity of the magnetic anisotropy (in eV)
+    x y z = vector direction of the anisotropy :pre
+:ule
+
+[Examples:]
+
+fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0
+fix 1 all precession/spin anisotropy 0.001 0.0 0.0 1.0 
+fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre
+
+[Description:]
+
+Impose a force torque to each magnetic spin in the group.
+
+Style {zeeman} is used for the simulation of the interaction 
+between the magnetic spins in the defined group and an external 
+magnetic field:
+
+:c,image(Eqs/force_spin_zeeman.jpg)
+
+with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T 
+in metal units). 
+
+Style {anisotropy} is used to simulate an easy axis or an easy plane 
+for the magnetic spins in the defined group: 
+
+:c,image(Eqs/force_spin_aniso.jpg)
+
+with n defining the direction of the anisotropy, and K (in eV) its intensity. 
+If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
+
+In both cases, the choice of (x y z) imposes the vector direction for the force. 
+Only the direction of the vector is important; it's length is ignored.  
+
+Both styles can be combined within one single command line. 
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+By default, the energy associated to this fix is not added to the potential 
+energy of the system. 
+The "fix_modify"_fix_modify.html {energy} option is supported by this fix 
+to add this magnetic potential energy to the potential energy of the system, 
+
+fix             1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix_modify      1 energy yes :pre
+
+This fix computes a global scalar which can be accessed by various 
+"output commands"_Section_howto.html#howto_15. 
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+[Restrictions:]
+
+The {precession/spin} style is part of the SPIN package. 
+This style is only enabled if LAMMPS was built with this package, and
+if the atom_style "spin" was declared. 
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"atom_style spin"_atom_style.html
+
+[Default:] none

doc/src/fix_rigid.txt

@@ -241,19 +241,17 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you
 want.  Thus you should be careful to use a fix group that only
 includes atoms you want to be part of rigid bodies.
 
-Bodystyle {custom} is similar to bodystyle {molecule}, however some
-custom properties are used to group atoms into rigid bodies. The
-special case for molecule/body ID = 0 is not available. Possible
-custom properties are an integer property associated with atoms through
-"fix property/atom"_fix_property_atom.html or an atom style variable
-or an atomfile style variable. For the latter two, the variable value
-will be rounded to an integer and then rigid bodies defined from
-those values.
-
-For bodystyle {group}, each of the listed groups is treated as a
-separate rigid body.  Only atoms that are also in the fix group are
-included in each rigid body.  This option is only allowed for the
-{rigid} styles.
+Bodystyle {custom} is similar to bodystyle {molecule} except that it
+is more flexible in using other per-atom properties to define the sets
+of atoms that form rigid bodies.  An integer vector defined by the
+"fix property/atom"_fix_property_atom.txt command can be used.  Or an
+"atom-style or atomfile-style variable"_variable.html can be used; the
+floating-point value produced by the variable is rounded to an
+integer.  As with bondstyle {molecule}, each set of atoms in the fix
+groups with the same integer value is treated as a different rigid
+body.  Since fix property/atom vectors and atom-style variables
+produce values for all atoms, you should be careful to use a fix group
+that only includes atoms you want to be part of rigid bodies.
 
 NOTE: To compute the initial center-of-mass position and other
 properties of each rigid body, the image flags for each atom in the

doc/src/fixes.txt

@@ -61,6 +61,7 @@ Fixes :h1
    fix_langevin
    fix_langevin_drude
    fix_langevin_eff
+   fix_langevin_spin
    fix_latte
    fix_lb_fluid
    fix_lb_momentum
@@ -99,6 +100,7 @@ Fixes :h1
    fix_nve_manifold_rattle
    fix_nve_noforce
    fix_nve_sphere
+   fix_nve_spin
    fix_nve_tri
    fix_nvk
    fix_nvt_asphere
@@ -114,6 +116,7 @@ Fixes :h1
    fix_planeforce
    fix_poems
    fix_pour
+   fix_precession_spin
    fix_press_berendsen
    fix_print
    fix_property_atom

doc/src/lammps.book

@@ -176,6 +176,7 @@ fix_ipi.html
 fix_langevin.html
 fix_langevin_drude.html
 fix_langevin_eff.html
+fix_langevin_spin.html
 fix_latte.html
 fix_lb_fluid.html
 fix_lb_momentum.html
@@ -213,6 +214,7 @@ fix_nve_line.html
 fix_nve_manifold_rattle.html
 fix_nve_noforce.html
 fix_nve_sphere.html
+fix_nve_spin.html
 fix_nve_tri.html
 fix_nvk.html
 fix_nvt_asphere.html
@@ -229,6 +231,7 @@ fix_pimd.html
 fix_planeforce.html
 fix_poems.html
 fix_pour.html
+fix_precession_spin.html
 fix_press_berendsen.html
 fix_print.html
 fix_property_atom.html
@@ -317,6 +320,7 @@ compute_displace_atom.html
 compute_dpd.html
 compute_dpd_atom.html
 compute_edpd_temp_atom.html
+compute_entropy_atom.html
 compute_erotate_asphere.html
 compute_erotate_rigid.html
 compute_erotate_sphere.html
@@ -381,6 +385,7 @@ compute_smd_ulsph_strain_rate.html
 compute_smd_ulsph_stress.html
 compute_smd_vol.html
 compute_sna_atom.html
+compute_spin.html
 compute_stress_atom.html
 compute_tally.html
 compute_tdpd_cc_atom.html
@@ -506,6 +511,10 @@ pair_sph_lj.html
 pair_sph_rhosum.html
 pair_sph_taitwater.html
 pair_sph_taitwater_morris.html
+pair_spin_dmi.html
+pair_spin_exchange.html
+pair_spin_magelec.html
+pair_spin_neel.html
 pair_srp.html
 pair_sw.html
 pair_table.html
@@ -582,6 +591,7 @@ dihedral_opls.html
 dihedral_quadratic.html
 dihedral_spherical.html
 dihedral_table.html
+dihedral_table_cut.html
 dihedral_zero.html
 
 lammps_commands_improper.html

doc/src/molecule.txt

@@ -98,19 +98,20 @@ molecule (header keyword = inertia).
 NOTE: The molecule command can be used to define molecules with bonds,
 angles, dihedrals, imporopers, or special bond lists of neighbors
 within a molecular topology, so that you can later add the molecules
-to your simulation, via one or more of the commands listed above.  If
-such molecules do not already exist when LAMMPS creates the simulation
-box, via the "create_box"_create_box.html or
-"read_data"_read_data.html command, when you later add them you may
-overflow the pre-allocated data structures which store molecular
-topology information with each atom, and an error will be generated.
-Both the "create_box"_create_box.html command and the data files read
-by the "read_data"_read_data.html command have "extra" options which
+to your simulation, via one or more of the commands listed above.
+Since this topology-related information requires that suitable storage
+is reserved when LAMMPS creates the simulation box (e.g. when using
+the "create_box"_create_box.html command or the
+"read_data"_read_data.html command) suitable space has to be reserved
+so you do not overflow those pre-allocated data structures when adding
+molecules later.  Both the "create_box"_create_box.html command and
+the "read_data"_read_data.html command have "extra" options which
 insure space is allocated for storing topology info for molecules that
 are added later.
 
-The format of an individual molecule file is similar to the data file
-read by the "read_data"_read_data.html commands, and is as follows.
+The format of an individual molecule file is similar but
+(not identical) to the data file read by the "read_data"_read_data.html
+commands, and is as follows.
 
 A molecule file has a header and a body.  The header appears first.
 The first line of the header is always skipped; it typically contains
@@ -455,7 +456,11 @@ of SHAKE clusters.
 
 :line
 
-[Restrictions:] none
+[Restrictions:]
+
+This command must come after the simulation box is define by a
+"read_data"_read_data.html, "read_restart"_read_restart.html, or
+"create_box"_create_box.html command.
 
 [Related commands:]
 

doc/src/pair_born.txt

@@ -12,12 +12,14 @@ pair_style born/omp command :h3
 pair_style born/gpu command :h3
 pair_style born/coul/long command :h3
 pair_style born/coul/long/cs command :h3
+pair_style born/coul/long/cs/gpu command :h3
 pair_style born/coul/long/gpu command :h3
 pair_style born/coul/long/omp command :h3
 pair_style born/coul/msm command :h3
 pair_style born/coul/msm/omp command :h3
 pair_style born/coul/wolf command :h3
 pair_style born/coul/wolf/cs command :h3
+pair_style born/coul/wolf/cs/gpu command :h3
 pair_style born/coul/wolf/gpu command :h3
 pair_style born/coul/wolf/omp command :h3
 pair_style born/coul/dsf command :h3

doc/src/pair_coul.txt

@@ -20,6 +20,7 @@ pair_style coul/dsf/kk command :h3
 pair_style coul/dsf/omp command :h3
 pair_style coul/long command :h3
 pair_style coul/long/cs command :h3
+pair_style coul/long/cs/gpu command :h3
 pair_style coul/long/omp command :h3
 pair_style coul/long/gpu command :h3
 pair_style coul/long/kk command :h3

doc/src/pair_gw.txt

@@ -95,9 +95,9 @@ This pair style can only be used via the {pair} keyword of the
 
 [Restrictions:]
 
-This pair style is part of the USER-MISC package. It is only enabled
-if LAMMPS was built with that package.  See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+This pair style is part of the MANYBODY package. It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
 
 This pair style requires the "newton"_newton.html setting to be "on"
 for pair interactions.
@@ -117,4 +117,5 @@ appropriate units if your simulation doesn't use "metal" units.
 :line
 
 :link(Gao)
-[(Gao)] Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
+[(Gao)] Gao and Weber, Nuclear Instruments and Methods in Physics
+Research B 191 (2012) 504.

doc/src/pair_ilp_graphene_hbn.txt

@@ -23,15 +23,15 @@ pair_coeff * * ilp/graphene/hbn  BNCH.ILP B N C :pre
 pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
 pair_coeff  * * rebo                 CH.airebo   NULL NULL C
 pair_coeff  * * tersoff              BNC.tersoff B    N    NULL
-pair_coeff  * * ilp/graphene/hbn     BNCH.ILP    B    N    C :pre
+pair_coeff  * * ilp/graphene/hbn     BNCH.ILP    B    N    C
 pair_coeff  1 1 coul/shield 0.70
 pair_coeff  1 2 coul/shield 0.69498201415576216335
-pair_coeff  2 2 coul/shield 0.69
+pair_coeff  2 2 coul/shield 0.69 :pre
 
 [Description:]
 
 The {ilp/graphene/hbn} style computes the registry-dependent interlayer
-potential (RDILP) potential as described in "(Leven)"_#Leven and
+potential (ILP) potential as described in "(Leven)"_#Leven and
 "(Maaravi)"_#Maaravi2. The normals are calculated in the way as described
 in "(Kolmogorov)"_#Kolmogorov2.
 
@@ -61,13 +61,13 @@ NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP),
 are fitted with taper function by setting the cutoff equal to 16.0
 Angstrom.  Using different cutoff or taper function should be careful.
 
-NOTE: Two parameter files (BNCH.ILP and BNCH-old.ILP) are presented,
-BNCH-old.ILP contains the parameters published in "(Leven)"_#Leven and
-"(Maaravi)"_#Maaravi2, which is only suitable for long-range
-interaction. The parameters in BNCH.ILP provides a good description both
-for short- and long-range interaction. This is useful for simulations in
-the high pressure (small interlayer distances) regime. The comparison of
-two sets of parameters can be found in "(Ouyang)"_#Ouyang.
+NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials
+are presented in "(Ouyang)"_#Ouyang1. These parameters provide a good description
+in both short- and long-range interaction regime, while the old ILP parameters
+published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2 are only suitable for
+long-range interaction regime. This feature is essential for simulations in
+high-pressure regime (i.e., the interlayer distance smaller than the equilibrium distance).
+The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
 
 This potential must be used in combination with hybrid/overlay.
 Other interactions can be set to zero using pair_style {none}.
@@ -101,12 +101,12 @@ units, if your simulation does not use {metal} units.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html
-"pair_none"_pair_none.html
-"pair_style hybrid/overlay"_pair_hybrid.html
-"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html
-"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html
-"pair_style pair_coul_shield"_pair_coul_shield.html
+"pair_coeff"_pair_coeff.html,
+"pair_none"_pair_none.html,
+"pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html,
+"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html,
+"pair_style pair_coul_shield"_pair_coul_shield.html.
 
 [Default:] tap_flag = 1
 
@@ -121,5 +121,5 @@ units, if your simulation does not use {metal} units.
 :link(Kolmogorov2)
 [(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
 
-:link(Ouyang)
-[(Ouyang)] W. Ouyang, D. Mandelli, O. Hod, M. Urbakh, In preparation.
+:link(Ouyang1)
+[(Ouyang)] W. Ouyang, D. Mandelli,  M. Urbakh, O. Hod, arXiv:1806.09555 (2018).

doc/src/pair_kolmogorov_crespi_full.txt

@@ -27,7 +27,7 @@ pair_coeff * * kolmogorov/crespi/full  CC.KC      C C :pre
 
 [Description:]
 
-The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi
+The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi (KC)
 interaction potential as described in "(Kolmogorov)"_#Kolmogorov1.
 No simplification is made,
 
@@ -51,6 +51,15 @@ and {rcut} are included in the parameter file. {S} is designed to
 facilitate scaling of energies. {rcut} is designed to build the neighbor
 list for calculating the normals for each atom pair.
 
+NOTE: A new set of parameters of KC potential for hydrocarbons (CH.KC)
+is presented in "(Ouyang)"_#Ouyang2. The parameters in CH.KC provides
+a good description in both short- and long-range interaction regime,
+while the original parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1
+are only suitable for long-range interaction regime. 
+This feature is essential for simulations in high-pressure regime
+(i.e., the interlayer distance smaller than the equilibrium distance).
+The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang2.
+
 This potential must be used in combination with hybrid/overlay.
 Other interactions can be set to zero using pair_style {none}.
 
@@ -83,11 +92,11 @@ units.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html
-"pair_none"_pair_none.html
-"pair_style hybrid/overlay"_pair_hybrid.html
-"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html
-"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html
+"pair_coeff"_pair_coeff.html,
+"pair_none"_pair_none.html,
+"pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
+"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
 
 [Default:] tap_flag = 0
 
@@ -95,3 +104,6 @@ units.
 
 :link(Kolmogorov1)
 [(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
+
+:link(Ouyang2)
+[(Ouyang)] W. Ouyang, D. Mandelli,  M. Urbakh, O. Hod, arXiv:1806.09555 (2018).

doc/src/pair_reaxc.txt

@@ -47,13 +47,14 @@ the "(Aktulga)"_#Aktulga paper. The {reax/c} style was initially
 implemented as a stand-alone C code and is now integrated into LAMMPS
 as a package.
 
-The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that is
-derived from the {reax/c} style. The Kokkos version can run on GPUs and
-can also use OpenMP multithreading. For more information about the Kokkos package,
-see "Section 4"_Section_packages.html#kokkos and "Section 5.3.3"_accelerate_kokkos.html.
-One important consideration when using the {reax/c/kk} style is the choice of either
-half or full neighbor lists. This setting can be changed using the Kokkos "package"_package.html
-command.
+The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that
+is derived from the {reax/c} style. The Kokkos version can run on GPUs
+and can also use OpenMP multithreading. For more information about the
+Kokkos package, see "Section 4"_Section_packages.html#kokkos and
+"Section 5.3.3"_accelerate_kokkos.html.  One important consideration
+when using the {reax/c/kk} style is the choice of either half or full
+neighbor lists. This setting can be changed using the Kokkos
+"package"_package.html command.
 
 The {reax/c} style differs from the "pair_style reax"_pair_reax.html
 command in the lo-level implementation details.  The {reax} style is a
@@ -80,9 +81,8 @@ parameterizations for different classes of materials.  You can submit
 a contact request at the Materials Computation Center (MCC) website
 "https://www.mri.psu.edu/materials-computation-center/connect-mcc"_https://www.mri.psu.edu/materials-computation-center/connect-mcc,
 describing the material(s) you are interested in modeling with ReaxFF.
-They can tell
-you what is currently available or what it would take to create a
-suitable ReaxFF parameterization.
+They can tell you what is currently available or what it would take to
+create a suitable ReaxFF parameterization.
 
 The {cfile} setting can be specified as NULL, in which case default
 settings are used. A control file can be specified which defines
@@ -120,28 +120,31 @@ assign to each atom will be used for computing the electrostatic
 interactions in the system.
 See the "fix qeq/reax"_fix_qeq_reax.html command for details.
 
-Using the optional keyword {lgvdw} with the value {yes} turns on
-the low-gradient correction of the ReaxFF/C for long-range
-London Dispersion, as described in the "(Liu)"_#Liu_2011 paper. Force field
+Using the optional keyword {lgvdw} with the value {yes} turns on the
+low-gradient correction of the ReaxFF/C for long-range London
+Dispersion, as described in the "(Liu)"_#Liu_2011 paper. Force field
 file {ffield.reax.lg} is designed for this correction, and is trained
 for several energetic materials (see "Liu"). When using lg-correction,
 recommended value for parameter {thb} is 0.01, which can be set in the
 control file.  Note: Force field files are different for the original
-or lg corrected pair styles, using wrong ffield file generates an error message.
+or lg corrected pair styles, using wrong ffield file generates an
+error message.
 
 Using the optional keyword {enobonds} with the value {yes}, the energy
 of atoms with no bonds (i.e. isolated atoms) is included in the total
 potential energy and the per-atom energy of that atom.  If the value
-{no} is specified then the energy of atoms with no bonds is set to zero.
-The latter behavior is usual not desired, as it causes discontinuities
-in the potential energy when the bonding of an atom drops to zero.
+{no} is specified then the energy of atoms with no bonds is set to
+zero.  The latter behavior is usual not desired, as it causes
+discontinuities in the potential energy when the bonding of an atom
+drops to zero.
 
 Optional keywords {safezone} and {mincap} are used for allocating
-reax/c arrays.  Increasing these values can avoid memory problems, such
-as segmentation faults and bondchk failed errors, that could occur under
-certain conditions. These keywords aren't used by the Kokkos version, which
-instead uses a more robust memory allocation scheme that checks if the sizes of
-the arrays have been exceeded and automatically allocates more memory.
+reax/c arrays.  Increasing these values can avoid memory problems,
+such as segmentation faults and bondchk failed errors, that could
+occur under certain conditions. These keywords aren't used by the
+Kokkos version, which instead uses a more robust memory allocation
+scheme that checks if the sizes of the arrays have been exceeded and
+automatically allocates more memory.
 
 The thermo variable {evdwl} stores the sum of all the ReaxFF potential
 energy contributions, with the exception of the Coulombic and charge
@@ -153,7 +156,8 @@ This pair style tallies a breakdown of the total ReaxFF potential
 energy into sub-categories, which can be accessed via the "compute
 pair"_compute_pair.html command as a vector of values of length 14.
 The 14 values correspond to the following sub-categories (the variable
-names in italics match those used in the original FORTRAN ReaxFF code):
+names in italics match those used in the original FORTRAN ReaxFF
+code):
 
 {eb} = bond energy
 {ea} = atom energy
@@ -340,8 +344,8 @@ reax"_pair_reax.html
 
 [Default:]
 
-The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no, safezone = 1.2,
-mincap = 50.
+The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no,
+safezone = 1.2, mincap = 50.
 
 :line
 

doc/src/pair_spin_dmi.txt

@@ -0,0 +1,66 @@
+"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 spin/dmi command :h3
+
+[Syntax:]
+
+pair_style spin/dmi cutoff :pre
+
+cutoff = global cutoff pair (distance in metal units) :ulb,l
+
+:ule
+	
+[Examples:]
+
+pair_style spin/dmi 4.0
+pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0	
+pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre
+
+[Description:]
+
+Style {spin/dmi} computes the Dzyaloshinskii-Moriya (DM) interaction
+between pairs of magnetic spins: 
+
+:c,image(Eqs/pair_spin_dmi_interaction.jpg)
+
+where si and sj are two neighboring magnetic spins of two particles, 
+eij = (ri - rj)/|ri-rj| is the normalized separation vector between the 
+two particles, and D is the DM vector defining the intensity and the 
+sign of the interaction.
+
+Examples and more explanations about this interaction and its parametrization are 
+reported in "(Tranchida)"_#Tranchida5.
+
+From this DM interaction, each spin i will be submitted to a magnetic torque
+omega and its associated atom to a force F (for spin-lattice calculations only). 
+
+More details about the derivation of these torques/forces are reported in
+"(Tranchida)"_#Tranchida5.
+
+:line
+
+[Restrictions:]
+
+All the {pair/spin} styles are part of the SPIN package. 
+These styles are only enabled if LAMMPS was built with this package, and
+if the atom_style "spin" was declared. 
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, 
+"pair_eam"_pair_eam.html,
+
+[Default:] none
+
+:line
+
+:link(Tranchida5)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
+arXiv preprint arXiv:1801.10233, (2018).

doc/src/pair_spin_exchange.txt

@@ -0,0 +1,82 @@
+"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 spin/exchange command :h3
+
+[Syntax:]
+
+pair_style spin/exchange cutoff :pre
+
+cutoff = global cutoff pair (distance in metal units) :ulb,l
+
+:ule
+
+[Examples:]
+
+pair_style spin/exchange 4.0
+pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
+pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 :pre
+
+[Description:]
+
+Style {spin/exchange} computes the exchange interaction between 
+pairs of magnetic spins:
+
+:c,image(Eqs/pair_spin_exchange_interaction.jpg)
+
+where si and sj are two neighboring magnetic spins of two particles, 
+rij = ri - rj is the inter-atomic distance between the two particles,
+and J(rij) is a function defining the intensity and the sign of the exchange 
+interaction.
+
+This function is defined as:
+
+:c,image(Eqs/pair_spin_exchange_function.jpg)
+
+where a, b and d are the three constant coefficients defined in the associated
+"pair_coeff" command.
+
+The coefficients a, b, and d need to be fitted so that the function above matches with
+the value of the exchange interaction for the N neighbor shells taken into account.
+
+Examples and more explanations about this function and its parametrization are reported
+in "(Tranchida)"_#Tranchida3.
+
+From this exchange interaction, each spin i will be submitted 
+to a magnetic torque omega, and its associated atom can be submitted to a
+force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html),
+such as:
+
+:c,image(Eqs/pair_spin_exchange_forces.jpg)
+
+with h the Planck constant (in metal units).
+
+More details about the derivation of these torques/forces are reported in
+"(Tranchida)"_#Tranchida3.
+
+:line
+
+[Restrictions:]
+
+All the {pair/spin} styles are part of the SPIN package. 
+These styles are only enabled if LAMMPS was built with this package, and
+if the atom_style "spin" was declared. 
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, 
+"pair_eam"_pair_eam.html,
+
+[Default:] none
+
+:line
+
+:link(Tranchida3)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
+arXiv preprint arXiv:1801.10233, (2018).

doc/src/pair_spin_magelec.txt

@@ -0,0 +1,73 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style spin/me command :h3
+
+[Syntax:]
+
+pair_style spin/me cutoff :pre
+
+cutoff = global cutoff pair (distance in metal units) :ulb,l
+
+:ule
+
+[Examples:]
+
+pair_style spin/me 4.5
+pair_coeff * * me 4.5 0.00109 1.0 1.0 1.0 :pre
+
+[Description:]
+
+Style {spin/me} computes a magneto-electric interaction between
+pairs of magnetic spins. According to the derivation reported in
+"(Katsura)"_#Katsura1, this interaction is defined as: 
+
+:c,image(Eqs/pair_spin_me_interaction.jpg)
+
+where si and sj are neighboring magnetic spins of two particles,
+eij = (ri - rj)/|ri-rj| is the normalized separation vector between the
+two particles, and E is an electric polarization vector.
+The norm and direction of E are giving the intensity and the
+direction of a screened dielectric atomic polarization (in eV).
+
+From this magneto-electric interaction, each spin i will be submitted
+to a magnetic torque omega, and its associated atom can be submitted to a
+force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html),
+such as:
+
+:c,image(Eqs/pair_spin_me_forces.jpg)
+
+with h the Planck constant (in metal units).
+
+More details about the derivation of these torques/forces are reported in
+"(Tranchida)"_#Tranchida4.
+
+:line
+
+[Restrictions:]
+
+All the {pair/spin} styles are part of the SPIN package.
+These styles are only enabled if LAMMPS was built with this package, and
+if the atom_style "spin" was declared.
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
+"pair_spin_exchange"_pair_spin_exchange.html, "pair_eam"_pair_eam.html,
+
+[Default:] none
+
+:line
+
+:link(Katsura1)
+[(Katsura)] H. Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005)
+
+:link(Tranchida4)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson, 
+arXiv preprint arXiv:1801.10233, (2018).

doc/src/pair_spin_neel.txt

@@ -0,0 +1,81 @@
+"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 spin/neel command :h3
+
+[Syntax:]
+
+pair_style spin/neel cutoff :pre
+
+cutoff = global cutoff pair (distance in metal units) :ulb,l
+
+:ule
+	
+[Examples:]
+
+pair_style spin/neel 4.0
+pair_coeff * * neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
+pair_coeff 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0 :pre
+
+[Description:]
+
+Style {spin/neel} computes the Neel pair anisotropy model 
+between pairs of magnetic spins: 
+
+:c,image(Eqs/pair_spin_neel_interaction.jpg)
+
+where si and sj are two neighboring magnetic spins of two particles, 
+rij = ri - rj is the inter-atomic distance between the two particles,
+eij = (ri - rj)/|ri-rj| is their normalized separation vector 
+and g1, q1 and q2 are three functions defining the intensity of the
+dipolar and quadrupolar contributions, with:
+
+:c,image(Eqs/pair_spin_neel_functions.jpg)
+
+With the functions g(rij) and q(rij) defined and fitted according to the same
+Bethe-Slater function used to fit the exchange interaction: 
+
+:c,image(Eqs/pair_spin_exchange_function.jpg)
+
+where a, b and d are the three constant coefficients defined in the associated 
+"pair_coeff" command.   
+
+The coefficients a, b, and d need to be fitted so that the function above matches with 
+the values of the magneto-elastic constant of the materials at stake. 
+
+Examples and more explanations about this function and its parametrization are reported 
+in "(Tranchida)"_#Tranchida6. More examples of parametrization will be provided in 
+future work.
+
+From this DM interaction, each spin i will be submitted to a magnetic torque
+omega and its associated atom to a force F (for spin-lattice calculations only). 
+
+More details about the derivation of these torques/forces are reported in
+"(Tranchida)"_#Tranchida6.
+
+:line
+
+[Restrictions:]
+
+All the {pair/spin} styles are part of the SPIN package. 
+These styles are only enabled if LAMMPS was built with this package, and
+if the atom_style "spin" was declared. 
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, 
+"pair_eam"_pair_eam.html,
+
+[Default:] none
+
+:line
+
+:link(Tranchida6)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
+arXiv preprint arXiv:1801.10233, (2018).

doc/src/pair_sw.txt

@@ -192,8 +192,8 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]
 
 This pair style is part of the MANYBODY 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.
+if LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
 
 This pair style requires the "newton"_newton.html setting to be "on"
 for pair interactions.

doc/src/pairs.txt

@@ -97,6 +97,10 @@ Pair Styles :h1
    pair_sph_rhosum
    pair_sph_taitwater
    pair_sph_taitwater_morris
+   pair_spin_dmi
+   pair_spin_exchange
+   pair_spin_magelec
+   pair_spin_neel
    pair_srp
    pair_sw
    pair_table

doc/src/variable.txt

@@ -296,17 +296,24 @@ list of runs (e.g. 1000) without having to list N strings in the input
 script.
 
 For the {string} style, a single string is assigned to the variable.
-The only difference between this and using the {index} style with a
-single string is that a variable with {string} style can be redefined.
-E.g. by another command later in the input script, or if the script is
-read again in a loop.
+Two differences between this this and using the {index} style exist:
+a variable with {string} style can be redefined, e.g. by another command later
+in the input script, or if the script is read again in a loop. The other
+difference is that {string} performs variable substitution even if the
+string parameter is quoted.
 
 For the {format} style, an equal-style variable is specified along
 with a C-style format string, e.g. "%f" or "%.10g", which must be
 appropriate for formatting a double-precision floating-point value.
-This allows an equal-style variable to be formatted specifically for
-output as a string, e.g. by the "print"_print.html command, if the
-default format "%.15g" has too much precision.
+The default format is "%.15g".  This variable style allows an
+equal-style variable to be formatted precisely when it is evaluated.
+
+If you simply wish to print a variable value with desired precision to
+the screen or logfile via the "print"_print.html or "fix
+print"_fix_print.html commands, you can also do this by specifying an
+"immediate" variable with a trailing colon and format string, as part
+of the string argument of those commands.  This is explained in
+"Section 3.2"_Section_commands.html#cmd_2.
 
 For the {getenv} style, a single string is assigned to the variable
 which should be the name of an environment variable.  When the

examples/COUPLE/lammps_quest/lmpqst.cpp

@@ -6,10 +6,10 @@
 //         in.lammps = LAMMPS input script
 //         in.quest = Quest input script
 
-#include "mpi.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
 #include "stdint.h"
 
 #include "many2one.h"

examples/COUPLE/lammps_spparks/lmpspk.cpp

@@ -7,10 +7,10 @@
 //         Sfactor = multiplier on strain effect
 //         in.spparks = SPPARKS input script
 
-#include "mpi.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
 
 #include "lammps_data_write.h"
 #include "many2many.h"

examples/COUPLE/library/error.cpp

@@ -1,6 +1,6 @@
 #include <mpi.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cstdio>
+#include <cstdlib>
 #include "error.h"
 
 /* ---------------------------------------------------------------------- */

examples/COUPLE/library/files.cpp

@@ -1,5 +1,5 @@
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
 #include "files.h"
 
 #define MAXLINE 256

examples/COUPLE/library/irregular.cpp

@@ -1,6 +1,6 @@
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
 #include "irregular.h"
 #include "memory.h"
 #include "error.h"

examples/COUPLE/library/lammps_data_write.cpp

@@ -1,6 +1,6 @@
 #include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
 #include "lammps_data_write.h"
 #include "memory.h"
 #include "error.h"

examples/COUPLE/library/lammps_data_write.h

@@ -1,7 +1,7 @@
 #ifndef LAMMPS_DATA_WRITE_H
 #define LAMMPS_DATA_WRITE_H
 
-#include <stdio.h>
+#include <cstdio>
 #include "send2one.h"
 
 class LAMMPSDataWrite : public Send2One {

examples/COUPLE/library/many2many.cpp

@@ -1,6 +1,6 @@
 #include <mpi.h>
-#include <stdlib.h>
-#include <stdio.h>
+#include <cstdlib>
+#include <cstdio>
 #include "many2many.h"
 #include "irregular.h"
 #include "memory.h"

examples/COUPLE/library/many2one.cpp

@@ -1,6 +1,6 @@
-#include "mpi.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <cstdio>
+#include <cstdlib>
 #include "many2one.h"
 #include "memory.h"
 

examples/COUPLE/library/memory.cpp

@@ -1,6 +1,6 @@
 #include <mpi.h>
-#include <stdlib.h>
-#include <stdio.h>
+#include <cstdlib>
+#include <cstdio>
 #include "memory.h"
 #include "error.h"
 

examples/COUPLE/library/one2many.cpp

@@ -1,5 +1,5 @@
 #include <mpi.h>
-#include <stdlib.h>
+#include <cstdlib>
 #include "one2many.h"
 #include "memory.h"
 

examples/COUPLE/library/send2one.cpp

@@ -1,6 +1,6 @@
-#include "mpi.h"
-#include "stdlib.h"
-#include "stdio.h"
+#include <mpi.h>
+#include <cstdlib>
+#include <cstdio>
 #include "send2one.h"
 #include "memory.h"
 #include "error.h"

examples/COUPLE/multiple/multiple.cpp

@@ -23,10 +23,10 @@
 //         Tdelta = incremental temperature for each of N runs
 // See README for compilation instructions
 
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "mpi.h"
+#include <mpi.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
 
 #include "lammps.h"         // these are LAMMPS include files
 #include "input.h"