patch 29Jun18

fix typo in python module

.github/CODEOWNERS

@@ -9,13 +9,49 @@ lib/kokkos/*          @stanmoore1
 lib/molfile/*         @akohlmey
 lib/qmmm/*            @akohlmey
 lib/vtk/*             @rbberger
+lib/kim/*             @ellio167
 
-# packages
-src/KOKKOS            @stanmoore1
-src/USER-CGSDK        @akohlmey
-src/USER-COLVARS      @giacomofiorin
-src/USER-OMP          @akohlmey
-src/USER-QMMM         @akohlmey
+# whole packages
+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
+src/USER-DPD/*        @timattox
+src/USER-INTEL/*      @wmbrownintel
+src/USER-MANIFOLD/*   @Pakketeretet2
+src/USER-MEAMC/*      @martok
+src/USER-MOFFF/*      @hheenen
+src/USER-MOLFILE/*    @akohlmey
+src/USER-NETCDF/*     @pastewka
+src/USER-PHONON/*     @lingtikong
+src/USER-OMP/*        @akohlmey
+src/USER-QMMM/*       @akohlmey
+src/USER-REAXC/*      @hasanmetin
+src/USER-TALLY/*      @akohlmey
+src/USER-UEF/*        @danicholson
+src/USER-VTK/*        @rbberger
+
+# individual files in packages
+src/GPU/pair_vashishta_gpu.*        @andeplane
+src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
+src/MANYBODY/pair_vashishta_table.* @andeplane
+src/USER-MISC/fix_bond_react.*      @jrgissing
+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-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()
@@ -123,43 +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)
-
-if(ENABLE_BODY AND ENABLE_POEMS)
-  message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time")
-endif()
+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()
@@ -170,28 +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}'))"
@@ -201,16 +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)
@@ -218,113 +284,194 @@ 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/v1.0.1.tar.gz
-      URL_MD5 5137e28cb1a64444bd571c98c98a6eee
+      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 REQUIRED)
+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/v1.9.5.tar.gz
+      URL_MD5 9f66efc128da33039e30659f36fc6d00
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+      )
+    ExternalProject_get_property(kim_build INSTALL_DIR)
+    set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
+    set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
+    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})
@@ -333,6 +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}_${MATH_LIBRARIES})
@@ -350,25 +500,16 @@ RegisterStyles(${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})
 
@@ -377,12 +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
@@ -403,40 +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
                          ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
@@ -453,7 +591,7 @@ if(ENABLE_USER-OMP)
     include_directories(${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 ${LAMMPS_LIB_BINARY_DIR}/kokkos)
   add_definitions(-DLMP_KOKKOS)
@@ -489,7 +627,7 @@ if(ENABLE_KOKKOS)
   RegisterNBinStyle(${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)
@@ -502,7 +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}")
@@ -516,7 +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
                            ${USER-INTEL_SOURCES_DIR}/intel_buffers.h
@@ -540,7 +705,10 @@ if(ENABLE_USER-INTEL)
     include_directories(${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
@@ -563,8 +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)
@@ -637,7 +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)
@@ -673,60 +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/Developer/developer.tex

@@ -449,15 +449,15 @@ Writing fixes is a flexible way of extending LAMMPS.  Users can
 implement many things using fixes:
 
 \begin{itemize}
-\item changing particles attributes (positions, velocities, forces, etc.). 
+\item changing particles attributes (positions, velocities, forces, etc.).
 Example: FixFreeze.
 \item reading/writing data. Example: FixRestart.
 \item implementing boundary conditions. Example: FixWall.
-\item saving information about particles for future use (previous positions, 
+\item saving information about particles for future use (previous positions,
 for instance). Example: FixStoreState.
 \end{itemize}
 
-All fixes are derived from class Fix and must have constructor with the 
+All fixes are derived from class Fix and must have constructor with the
 signature: FixMine(class LAMMPS *, int, char **).
 
 Every fix must be registered in LAMMPS by writing the following lines
@@ -478,7 +478,7 @@ included in the file "style\_fix.h". In case if you use LAMMPS make,
 this file is generated automatically - all files starting with prefix
 fix\_ are included, so call your header the same way. Otherwise, don<6F>t
 forget to add your include into "style\_fix.h".
- 
+
 Let's write a simple fix which will print average velocity at the end
 of each timestep. First of all, implement a constructor:
 
@@ -487,11 +487,11 @@ of each timestep. First of all, implement a constructor:
 FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
 : Fix(lmp, narg, arg)
 {
-  if (narg < 4) 
+  if (narg < 4)
       error->all(FLERR,"Illegal fix print command");
- 
+
   nevery = atoi(arg[3]);
-  if (nevery <= 0) 
+  if (nevery <= 0)
       error->all(FLERR,"Illegal fix print command");
 }
   \end{verbatim}
@@ -545,7 +545,7 @@ void FixPrintVel::end_of_step()
 {
   // for add3, scale3
   using namespace MathExtra;
-  
+
   double** v = atom->v;
   int nlocal = atom->nlocal;
   double localAvgVel[4]; // 4th element for particles count
@@ -559,7 +559,7 @@ void FixPrintVel::end_of_step()
   MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
   scale3(1.0 / globalAvgVel[3], globalAvgVel);
   if (comm->me == 0) {
-    printf("\%e, \%e, \%e\n", 
+    printf("\%e, \%e, \%e\n",
       globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
   }
 }
@@ -607,14 +607,15 @@ this situation there are several methods which should be implemented:
 
 \begin{itemize}
 \item \verb|double memory_usage| - return how much memory fix uses
-\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays 
+\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays
   in your fix
-\item \verb|void copy_arrays(int i, int j)| - copy i-th per-particle information 
-  to j-th. Used when atoms sorting is performed
+\item \verb|void copy_arrays(int i, int j, int delflag)| - copy i-th per-particle
+  information to j-th. Used when atoms sorting is performed. if delflag is set
+  and atom j owns a body, move the body information to atom i.
 \item \verb|void set_arrays(int i)| - sets i-th particle related information to zero
 \end{itemize}
 
-Note, that if your class implements these methods, it must call add calls of 
+Note, that if your class implements these methods, it must call add calls of
 add\_callback and delete\_callback to constructor and destructor:
 
 \begin{center}
@@ -654,7 +655,7 @@ void FixSavePos::grow_arrays(int nmax)
     memory->grow(this->x, nmax, 3, "FixSavePos:x");
 }
 
-void FixSavePos::copy_arrays(int i, int j)
+void FixSavePos::copy_arrays(int i, int j, int delflag)
 {
     memcpy(this->x[j], this->x[i], sizeof(double) * 3);
 }
@@ -670,7 +671,7 @@ int FixSavePos::pack_exchange(int i, double *buf)
   buf[m++] = x[i][0];
   buf[m++] = x[i][1];
   buf[m++] = x[i][2];
-  
+
   return m;
 }
 

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="30 Mar 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
-30 Mar 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,
@@ -684,6 +698,7 @@ package"_Section_start.html#start_3.
 "addtorque"_fix_addtorque.html,
 "atc"_fix_atc.html,
 "ave/correlate/long"_fix_ave_correlate_long.html,
+"bond/react"_fix_bond_react.html,
 "colvars"_fix_colvars.html,
 "dpd/energy (k)"_fix_dpd_energy.html,
 "drude"_fix_drude.html,
@@ -823,6 +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,
@@ -851,6 +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,
@@ -1016,6 +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,
@@ -1211,7 +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
@@ -1565,15 +1572,6 @@ This operation is not allowed. :dd
 
 This operation is not allowed. :dd
 
-{Cannot use -cuda on and -kokkos on together} :dt
-
-This is not allowed since both packages can use GPUs. :dd
-
-{Cannot use -cuda on without USER-CUDA installed} :dt
-
-The USER-CUDA package must be installed via "make yes-user-cuda"
-before LAMMPS is built. :dd
-
 {Cannot use -kokkos on without KOKKOS installed} :dt
 
 Self-explanatory. :dd
@@ -1597,11 +1595,6 @@ solver/pair style. :dd
 
 This is a current restriction of this command. :dd
 
-{Cannot use GPU package with USER-CUDA package enabled} :dt
-
-You cannot use both the GPU and USER-CUDA packages
-together.  Use one or the other. :dd
-
 {Cannot use Kokkos pair style with rRESPA inner/middle} :dt
 
 Self-explanatory. :dd
@@ -8252,12 +8245,6 @@ Self-explanatory. :dd
 The package command cannot be used afer a read_data, read_restart, or
 create_box command. :dd
 
-{Package cuda command without USER-CUDA package enabled} :dt
-
-The USER-CUDA package must be installed via "make yes-user-cuda"
-before LAMMPS is built, and the "-c on" must be used to enable the
-package. :dd
-
 {Package gpu command without GPU package installed} :dt
 
 The GPU package must be installed via "make yes-gpu" before LAMMPS is
@@ -10230,22 +10217,6 @@ it in different ways. :dd
 
 Self-explanatory. :dd
 
-{USER-CUDA mode requires CUDA variant of min style} :dt
-
-CUDA mode is enabled, so the min style must include a cuda suffix. :dd
-
-{USER-CUDA mode requires CUDA variant of run style} :dt
-
-CUDA mode is enabled, so the run style must include a cuda suffix. :dd
-
-{USER-CUDA package does not yet support comm_style tiled} :dt
-
-Self-explanatory. :dd
-
-{USER-CUDA package requires a cuda enabled atom_style} :dt
-
-Self-explanatory. :dd
-
 {Unable to initialize accelerator for use} :dt
 
 There was a problem initializing an accelerator for the gpu package :dd
@@ -10494,10 +10465,6 @@ Must use remap v option with fix deform with this pair style. :dd
 
 If fix deform is used, the remap v option is required. :dd
 
-{Using suffix cuda without USER-CUDA package enabled} :dt
-
-Self-explanatory. :dd
-
 {Using suffix gpu without GPU package installed} :dt
 
 Self-explanatory. :dd

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_intro.txt

@@ -526,14 +526,14 @@ and efforts.
 Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM, USER-TALLY, and COMPRESS packages
 Roy Pollock (LLNL), Ewald and PPPM solvers
 Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package
-Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
+Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential (superseded by USER-MEAMC)
 Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
 Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
 Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
 Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
-Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages
+Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA (obsoleted by KOKKOS) and KOKKOS packages
 Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
-Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
+Christoph Kloss (JKU), Christoph.Kloss at jku.at, LIGGGHTS fork for granular models and granular/fluid coupling
 Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
 Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
 Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul

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)
 
@@ -122,6 +123,7 @@ Package, Description, Doc page, Example, Library
 Package, Description, Doc page, Example, Library
 "USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
 "USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
+"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
 "USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
 "USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
 "USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
@@ -1414,6 +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:]
@@ -1625,6 +1659,43 @@ examples/USER/awpmd :ul
 
 :line
 
+USER-BOCS package :link(USER-BOCS),h4
+
+[Contents:]
+
+This package provides "fix bocs"_fix_bocs.html, a modified version
+of "fix npt"_fix_nh.html which includes the pressure correction to
+the barostat as outlined in:
+
+N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that 
+accurately describe the structure, pressure, and compressibility of
+molecular liquids," J. Chem. Phys. 143, 243148 (2015).
+
+[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
+
+[Install or un-install:]
+
+make yes-user-bocs
+make machine :pre
+
+make no-user-bocs
+make machine :pre
+
+[Supporting info:]
+
+The USER-BOCS user package for LAMMPS is part of the BOCS software package:
+"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS
+
+See the following reference for information about the entire package:
+
+Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
+"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
+J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
+
+Example inputs are in the examples/USER/bocs folder.
+
+:line
+
 USER-CGDNA package :link(USER-CGDNA),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/bond_oxdna.txt

@@ -51,9 +51,11 @@ The coefficients in the above example have to be kept fixed and cannot be change
 Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
-A technical report with more information on the model, the structure of the input file,
-the setup tool and the performance of the LAMMPS-implementation of oxDNA
-can be found "here"_PDF/USER-CGDNA-overview.pdf.
+
+Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation. 
+The article contains more information on the model, the structure of the input file, the setup tool
+and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
 
 :line
 
@@ -72,6 +74,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 :line
 
+:link(Henrich2)
+[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
 :link(oxdna_fene)
 [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
 

doc/src/compute_ackland_atom.txt

@@ -10,19 +10,29 @@ compute ackland/atom command :h3
 
 [Syntax:]
 
-compute ID group-ID ackland/atom :pre
+compute ID group-ID ackland/atom keyword/value :pre
 
-ID, group-ID are documented in "compute"_compute.html command
-ackland/atom = style name of this compute command :ul
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+ackland/atom = style name of this compute command :l
+
+zero or more keyword/value pairs may be appended :l
+keyword = {legacy} :l
+  {legacy} yes/no = use ({yes}) or do not use ({no}) legacy ackland algorithm implementation :pre
+:ule
 
 [Examples:]
 
-compute 1 all ackland/atom :pre
+compute 1 all ackland/atom
+compute 1 all ackland/atom legacy yes :pre
 
 [Description:]
 
 Defines a computation that calculates the local lattice structure
 according to the formulation given in "(Ackland)"_#Ackland.
+Historically, LAMMPS had two, slightly different implementations of
+the algorithm from the paper. With the {legacy} keyword, it is
+possible to switch between the pre-2015 ({legacy yes}) and post-2015
+implemention ({legacy no}). The post-2015 variant is the default.
 
 In contrast to the "centro-symmetry
 parameter"_compute_centro_atom.html this method is stable against
@@ -66,7 +76,8 @@ integers defined above.
 
 "compute centro/atom"_compute_centro_atom.html
 
-[Default:] none
+[Default:]
+The keyword {legacy} defaults to {no}.
 
 :line
 

doc/src/compute_displace_atom.txt

@@ -15,7 +15,7 @@ compute ID group-ID displace/atom :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 displace/atom = style name of this compute command :l
 zero or more keyword/arg pairs may be appended :l
-keyword = {refresh} :
+keyword = {refresh} :l
   {replace} arg = name of per-atom variable :pre
 
 :ule

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_heat_flux.txt

@@ -26,14 +26,16 @@ compute myFlux all heat/flux myKE myPE myStress :pre
 
 Define a computation that calculates the heat flux vector based on
 contributions from atoms in the specified group.  This can be used by
-itself to measure the heat flux into or out of a reservoir of atoms,
-or to calculate a thermal conductivity using the Green-Kubo formalism.
+itself to measure the heat flux through a set of atoms (e.g. a region
+between two thermostatted reservoirs held at different temperatures),
+or to calculate a thermal conductivity using the equilibrium
+Green-Kubo formalism.
 
-See the "fix thermal/conductivity"_fix_thermal_conductivity.html
-command for details on how to compute thermal conductivity in an
-alternate way, via the Muller-Plathe method.  See the "fix
-heat"_fix_heat.html command for a way to control the heat added or
-subtracted to a group of atoms.
+For other non-equilibrium ways to compute a thermal conductivity, see
+"this section"_Section_howto.html#howto_20.  These include use of the
+"fix thermal/conductivity"_fix_thermal_conductivity.html command for
+the Muller-Plathe method.  Or the "fix heat"_fix_heat.html command
+which can add or subtract heat from groups of atoms.
 
 The compute takes three arguments which are IDs of other
 "computes"_compute.html.  One calculates per-atom kinetic energy

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_sna_atom.txt

@@ -161,9 +161,9 @@ function.
 
 The keyword {bzeroflag} determines whether or not {B0}, the bispectrum
 components of an atom with no neighbors, are subtracted from
-the calculated bispectrum components. This optional keyword is only
-available for compute {sna/atom}, as {snad/atom} and {snav/atom}
-are unaffected by the removal of constant terms.
+the calculated bispectrum components. This optional keyword 
+normally only affects compute {sna/atom}. However, when
+{quadraticflag} is on, it also affects {snad/atom} and {snav/atom}.
 
 The keyword {quadraticflag} determines whether or not the
 quadratic analogs to the bispectrum quantities are generated.
@@ -230,13 +230,18 @@ are 30, 90, and 180, respectively. With {quadratic} value=1,
 the numbers of columns are 930, 2790, and 5580, respectively.
 
 If the {quadratic} keyword value is set to 1, then additional
-columns are appended to each per-atom array, corresponding to
+columns are generated, corresponding to
 the products of all distinct pairs of  bispectrum components. If the
 number of bispectrum components is {K}, then the number of distinct pairs
-is  {K}({K}+1)/2. These are output in subblocks of  {K}({K}+1)/2 columns, using the same
-ordering of sub-blocks as was used for the bispectrum
-components. Within each sub-block, the ordering is upper-triangular,
-(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K})
+is  {K}({K}+1)/2.
+For compute {sna/atom} these columns are appended to existing {K} columns.
+The ordering of quadratic terms is upper-triangular,
+(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}).
+For computes {snad/atom} and {snav/atom} each set of {K}({K}+1)/2
+additional columns is inserted directly after each of sub-block
+of linear terms i.e. linear and quadratic terms are contiguous.
+So the nesting order from inside to outside is bispectrum component,
+linear then quadratic, vector/tensor component, type.
 
 These values can be accessed by any command that uses per-atom values
 from a compute as input.  See "Section

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_bocs.txt

@@ -0,0 +1,112 @@
+<"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 bocs command :h3
+
+[Syntax:]
+
+fix  ID group-ID bocs keyword values ... :pre
+
+keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}
+  {temp} values = Tstart Tstop Tdamp
+  {cgiso} values = Pstart Pstop Pdamp
+  {basis set}
+    {analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
+    {linear_spline} values = input_filename
+    {cubic_spline} values = input_filename :pre
+:ule
+
+[Examples:]
+
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre
+ 
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre
+
+thermo_modify press 1_press :pre
+
+
+[Description:]
+
+These commands incorporate a pressure correction as described by 
+Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK
+barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .
+The first half of the command mimics a standard fix npt command:
+
+fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre
+
+The two differences are replacing {npt} with {bocs}, and replacing 
+{iso}/{aniso}/{etc} with {cgiso}.
+The rest of the command details what form you would like to use for 
+the pressure correction equation. The choices are: {analytic}, {linear_spline}, 
+or {cubic_spline}. 
+
+With either spline method, the only argument that needs to follow it 
+is the name of a file that contains the desired pressure correction 
+as a function of volume. The file should be formatted so each line has:
+
+Volume_i, PressureCorrection_i :pre
+
+Note both the COMMA and the SPACE separating the volume's 
+value and its corresponding pressure correction. The volumes in the file 
+should be uniformly spaced. Both the volumes and the pressure corrections 
+should be provided in the proper units, e.g. if you are using {units real}, 
+the volumes should all be in cubic angstroms, and the pressure corrections 
+should all be in atomspheres. Furthermore, the table should start/end at a 
+volume considerably smaller/larger than you expect your system to sample 
+during the simulation. If the system ever reaches a volume outside of the 
+range provided, the simulation will stop.
+
+With the {analytic} option, the arguments are as follows:
+
+... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre
+
+Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you 
+are using {units real}, {V_avg} should be in cubic angstroms, and the 
+coefficients should all be in atmospheres * cubic angstroms.
+
+[Restrictions:]
+
+As this is computing a (modified) pressure, group-ID should be {all}.
+
+The pressure correction has only been tested for use with an isotropic 
+pressure coupling in 3 dimensions.   
+
+By default, LAMMPS will still report the normal value for the pressure
+if the pressure is printed via a {thermo} command, or if the pressures
+are written to a file every so often. In order to have LAMMPS report the
+modified pressure, you must include the {thermo_modify} command given in 
+the examples. For the last argument in the command, you should put 
+XXXX_press, where XXXX is the ID given to the fix bocs command (in the
+example, the ID of the fix bocs command is 1 ).
+
+This fix is part of the USER-BOCS 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:]
+
+For more details about the pressure correction and the entire BOCS software 
+package, visit the "BOCS package on github"_bocsgithub and read the release 
+paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .
+
+
+:link(bocsgithub,https://github.com/noid-group/BOCS)
+
+:line
+
+:link(bocs-Dunn1)
+[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015).
+
+:link(bocs-Martyna)
+[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).
+
+:link(bocs-Dunn2)
+[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).
+
+
+

doc/src/fix_bond_react.txt

@@ -0,0 +1,332 @@
+"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 bond/react command :h3
+
+[Syntax:]
+
+fix ID group-ID bond/react common_keyword values ...
+  react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+  react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+  react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+  ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
+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} :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
+  template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l
+  template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
+  map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l
+  zero or more individual keyword/value pairs may be appended to each react argument :l
+  individual_keyword = {prob} or {stabilize_steps} :l
+    {prob} values = fraction seed
+      fraction = initiate reaction with this probability if otherwise eligible
+      seed = random number seed (positive integer)
+    {stabilize_steps} value = timesteps
+      timesteps = number of timesteps to apply internally created nve/limit.html :pre
+:ule
+
+[Examples:]
+
+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 :pre
+
+molecule mol1 pre_reacted_rxn1.txt
+molecule mol2 post_reacted_rxn1.txt
+molecule mol3 pre_reacted_rxn2.txt
+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 # set thermostat after bond/react :pre
+
+[Description:]
+
+Initiate complex covalent bonding (topology) changes. These topology
+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,
+atom-types, or atomic charges.
+
+Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
+pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
+determine bonding changes a priori. Rather, it uses a distance-based
+probabilistic criteria to effect predetermined topology changes in
+simulations using standard force fields.
+
+This fix was created to facilitate the dynamic creation of polymeric,
+amorphous or highly-crosslinked systems. A suggested workflow for
+using this fix is: 1) identify a reaction to be simulated 2) build a
+molecule template of the reaction site before the reaction has
+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.
+
+Only one 'fix bond/react' command can be used at a time. Multiple
+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.
+
+The {stabilization} keyword enables reaction site stabilization.
+Reaction site stabilization is performed by including reacting atoms
+in an internally created fix "nve/limit"_fix_nve_limit.html time
+integrator for a set number of timesteps given by the
+{stabilize_steps} keyword. While reacting atoms are being time
+integrated by the internal nve/limit, they are prevented from being
+involved in any new reactions. The {xmax} value keyword should
+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. 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.
+
+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:
+
+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
+atom pair must be identified. Second, the topology surrounding the
+bonding atom pair must match the topology of the pre-reaction
+template. If both these conditions are met, the reaction site is
+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.
+
+The pre-reacted molecule template is specified by a molecule command.
+This molecule template file contains a sample reaction site and its
+surrounding topology. As described below, the bonding atom pairs of
+the pre-reacted template are specified by atom ID in the map file. The
+pre-reacted molecule template should contain as few atoms as possible
+while still completely describing the topology of all atoms affected
+by the reaction. For example, if the force field contains dihedrals,
+the pre-reacted template should contain any atom within three bonds of
+reacting atoms.
+
+Some atoms in the pre-reacted template that are not reacting may have
+missing topology with respect to the simulation. For example, the
+pre-reacted template may contain an atom that would connect to the
+rest of a long polymer chain. These are referred to as edge atoms, and
+are also specified in the map file.
+
+Note that some care must be taken when a building a molecule template
+for a given simulation. All atom types in the pre-reacted template
+must be the same as those of a potential reaction site in the
+simulation. A detailed discussion of matching molecule template atom
+types with the simulation is provided on the "molecule"_molecule.html
+command page.
+
+The post-reacted molecule template contains a sample of the reaction
+site and its surrounding topology after the reaction has occurred. It
+must contain the same number of atoms as the pre-reacted template. A
+one-to-one correspondence between the atom IDs in the pre- and
+post-reacted templates is specified in the map file as described
+below. Note that during a reaction, an atom, bond, etc. type may
+change to one that was previously not present in the simulation. These
+new types must also be defined during the setup of a given simulation.
+A discussion of correctly handling this is also provided on the
+"molecule"_molecule.html command page.
+
+The map file is a text document with the following format:
+
+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':
+
+N {equivalences} = # of atoms N in the reaction molecule templates
+N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template :pre
+
+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.
+
+A sample map file is given below:
+
+:line
+
+# this is a map file :pre
+
+2 edgeIDs
+7 equivalences :pre
+
+BondingIDs :pre
+
+3
+5 :pre
+
+EdgeIDs :pre
+
+1
+7 :pre
+
+Equivalences :pre
+
+1   1
+2   2
+3   3
+4   4
+5   5
+6   6
+7   7 :pre
+
+:line
+
+Once a reaction site has been successfully identified, data structures
+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}
+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
+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
+can allow for the possibility of one or more reverse reactions.
+
+The optional keywords deal with the probability of a given reaction
+occurring as well as the stable equilibration of each reaction site as
+it occurs.
+
+The {prob} keyword can affect whether an eligible reaction actually
+occurs. The fraction setting must be a value between 0.0 and 1.0. A
+uniform random number between 0.0 and 1.0 is generated and the
+eligible reaction only occurs if the random number is less than the
+fraction.
+
+The {stabilize_steps} keyword allows for the specification of how many
+timesteps a reaction site is stabilized before being returned to the
+overall system thermostat.
+
+In order to produce the most physical behavior, this 'reaction site
+equilibration time' should be tuned to be as small as possible while
+retaining stability for a given system or reaction step. After a
+limited number of case studies, this number has been set to a default
+of 60 timesteps. Ideally, it should be individually tuned for each fix
+reaction step. Note that in some situations, decreasing rather than
+increasing this parameter will result in an increase in stability.
+
+A few other considerations:
+
+It may be beneficial to ensure reacting atoms are at a certain
+temperature before being released to the overall thermostat. For this,
+you can use the internally-created dynamic group named
+"bond_react_MASTER_group." For example, adding the following command
+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 :pre
+
+NOTE: This command must be added after the fix bond/react command, and
+will apply to all reactions.
+
+Computationally, each timestep this fix operates, it loops over
+neighbor lists (for bond-forming reactions) and computes distances
+between pairs of atoms in the list. It also communicates between
+neighboring processors to coordinate which bonds  are created and/or
+removed. All of these operations increase the cost of a timestep. Thus
+you should be cautious about invoking this fix too frequently.
+
+You can dump out snapshots of the current bond topology via the dump
+local command.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+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
+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
+this fix are "intensive".
+
+These is 1 quantity for each react argument:
+
+(1) cumulative # of reactions occurred :ul
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-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:]
+
+"fix bond/create"_fix_bond_create.html, "fix
+bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
+"dump local"_dump.html, "special_bonds"_special_bonds.html
+
+[Default:]
+
+The option defaults are stabilization = no, stabilize_steps = 60
+
+:line
+
+: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_drude.txt

@@ -154,7 +154,7 @@ Note: The temperature thermostating the core-Drude particle pairs
 should be chosen low enough, so as to mimic as closely as possible the
 self-consistent minimization. It must however be high enough, so that
 the dipoles can follow the local electric field exerted by the
-neighbouring atoms. The optimal value probably depends on the
+neighboring atoms. The optimal value probably depends on the
 temperature of the centers of mass and on the mass of the Drude
 particles.
 

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_modify.txt

@@ -14,14 +14,16 @@ fix_modify fix-ID keyword value ... :pre
 
 fix-ID = ID of the fix to modify :ulb,l
 one or more keyword/value pairs may be appended :l
-keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} :l
+keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} or {bodyforces} :l
   {temp} value = compute ID that calculates a temperature
   {press} value = compute ID that calculates a pressure
   {energy} value = {yes} or {no}
   {virial} value = {yes} or {no}
   {respa} value = {1} to {max respa level} or {0} (for outermost level)
   {dynamic/dof} value = {yes} or {no}
-    yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre
+    yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
+  {bodyforces} value = {early} or {late}
+    early/late = compute rigid-body forces/torques early or late in the timestep :pre
 :ule
 
 [Examples:]
@@ -84,9 +86,8 @@ if you want virial contribution of the fix to be part of the
 relaxation criteria, although this seems unlikely.
 
 NOTE: This option is only supported by fixes that explicitly say
-so. For some of these (e.g. the
-"fix shake"_fix_shake.html command) the default setting is
-{virial yes}, for others it is {virial no}.
+so. For some of these (e.g. the "fix shake"_fix_shake.html command)
+the default setting is {virial yes}, for others it is {virial no}.
 
 For fixes that set or modify forces, it may be possible to select at
 which "r-RESPA"_run_style.html level the fix operates via the {respa}
@@ -120,6 +121,28 @@ compute to calculate temperature.  See the "compute_modify
 dynamic/dof"_compute_modify.html command for a similar way to insure
 correct temperature normalization for those thermostats.
 
+The {bodyforces} keyword determines whether the forces and torques
+acting on rigid bodies are computed {early} at the post-force stage of
+each timestep (right after per-atom forces have been computed and
+communicated among processors), or {late} at the final-integrate stage
+of each timestep (after any other fixes have finished their post-force
+tasks).  Only the rigid-body integration fixes use this option, which
+includes "fix rigid"_fix_rigid.html and "fix
+rigid/small"_fix_rigid.html, and their variants, and also "fix
+poems"_fix_poems.html.
+
+The default is {late}.  If there are other fixes that add forces to
+individual atoms, then the rigid-body constraints will include these
+forces when time-integrating the rigid bodies.  If {early} is
+specified, then new fixes can be written that use or modify the
+per-body force and torque, before time-integration of the rigid bodies
+occurs.  Note however this has the side effect, that fixes such as
+"fix addforce"_fix_addforce.html, "fix setforce"_fix_setforce.html,
+"fix spring"_fix_spring.html, which add forces to individual atoms
+will have no effect on the motion of the rigid bodies if they are
+specified in the input script after the fix rigid command.  LAMMPS
+will give a warning if that is the case.
+
 [Restrictions:] none
 
 [Related commands:]
@@ -130,4 +153,5 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html
 [Default:]
 
 The option defaults are temp = ID defined by fix, press = ID defined
-by fix, energy = no, virial = different for each fix style, respa = 0.
+by fix, energy = no, virial = different for each fix style, respa = 0,
+bodyforce = late.

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_poems.txt

@@ -106,12 +106,18 @@ off, and there is only a single fix poems defined.
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 No information about this fix is written to "binary restart
-files"_restart.html.  None of the "fix_modify"_fix_modify.html options
-are relevant to this fix.  No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15.  No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+files"_restart.html.  
+
+The "fix_modify"_fix_modify.html {bodyforces} option is supported by
+this fix style to set whether per-body forces and torques are computed
+early or late in a timestep, i.e. at the post-force stage or at the
+final-integrate stage, respectively.
+
+No global or per-atom quantities are stored by this fix for access by
+various "output commands"_Section_howto.html#howto_15.  No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
 
 [Restrictions:]
 

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_reax_bonds.txt

@@ -34,6 +34,8 @@ written to {filename} on timesteps that are multiples of {Nevery},
 including timestep 0.  For time-averaged chemical species analysis,
 please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
 
+The specified group-ID is ignored by this fix.
+
 The format of the output file should be reasonably self-explanatory.
 The meaning of the column header abbreviations is as follows:
 

doc/src/fix_restrain.txt

@@ -24,10 +24,12 @@ keyword = {bond} or {angle} or {dihedral} :l
     atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
     Kstart,Kstop = restraint coefficients at start/end of run (energy units)
     theta0 = equilibrium angle theta (degrees)
-  {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
+  {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value
     atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
     Kstart,Kstop = restraint coefficients at start/end of run (energy units)
-    phi0 = equilibrium dihedral angle phi (degrees) :pre
+    phi0 = equilibrium dihedral angle phi (degrees)
+    keyword/value = optional keyword value pairs. supported keyword/value pairs:
+      {mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre
 :ule
 
 [Examples:]
@@ -155,11 +157,13 @@ associated with the restraint is
 with the following coefficients:
 
 K (energy)
-n = 1
+n (multiplicity, >= 0)
 d (degrees) = phi0 + 180 :ul
 
-K and phi0 are specified with the fix.  Note that the value of n is
-hard-wired to 1.  Also note that the energy will be a minimum when the
+K and phi0 are specified with the fix.  Note that the value of the
+dihedral multiplicity {n} is set by default to 1. You can use the
+optional {mult} keyword to set it to a different positive integer.
+Also note that the energy will be a minimum when the
 current dihedral angle phi is equal to phi0.
 
 :line
@@ -183,10 +187,17 @@ added forces to be included in the total potential energy of the
 system (the quantity being minimized), you MUST enable the
 "fix_modify"_fix_modify.html {energy} option for this fix.
 
-This fix computes a global scalar, which can be accessed by various
-"output commands"_Section_howto.html#howto_15.  The scalar is the
-potential energy for all the restraints as discussed above. The scalar
-value calculated by this fix is "extensive".
+This fix computes a global scalar and a global vector of length 3, which
+can be accessed by various "output commands"_Section_howto.html#howto_15.
+The scalar is the total potential energy for {all} the restraints as
+discussed above. The vector values are the sum of contributions to the
+following individual categories:
+
+1 = bond energy
+2 = angle energy
+3 = dihedral energy :ul
+
+The scalar and vector values calculated by this fix are "extensive".
 
 No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.

doc/src/fix_rigid.txt

@@ -223,10 +223,10 @@ via several options.
 
 NOTE: With the {rigid/small} styles, which require that {bodystyle} be
 specified as {molecule} or {custom}, you can define a system that has
-no rigid bodies initially.  This is useful when you are using the {mol}
-keyword in conjunction with another fix that is adding rigid bodies
-on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
-"fix pour"_fix_pour.html.
+no rigid bodies initially.  This is useful when you are using the
+{mol} keyword in conjunction with another fix that is adding rigid
+bodies on-the-fly as molecules, such as "fix deposit"_fix_deposit.html
+or "fix pour"_fix_pour.html.
 
 For bodystyle {single} the entire fix group of atoms is treated as one
 rigid body.  This option is only allowed for the {rigid} styles.
@@ -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
@@ -742,6 +740,11 @@ used to calculate the instantaneous pressure tensor.  Note that the 2
 NVT rigid fixes do not use any external compute to compute
 instantaneous temperature.
 
+The "fix_modify"_fix_modify.html {bodyforces} option is supported by
+all rigid styles to set whether per-body forces and torques are
+computed early or late in a timestep, i.e. at the post-force stage or
+at the final-integrate stage or the timestep, respectively.
+
 The 2 NVE rigid fixes compute a global scalar which can be accessed by
 various "output commands"_Section_howto.html#howto_15.  The scalar
 value calculated by these fixes is "intensive".  The scalar is the

doc/src/fixes.txt

@@ -20,9 +20,11 @@ Fixes :h1
    fix_ave_time
    fix_aveforce
    fix_balance
+   fix_bocs
    fix_bond_break
    fix_bond_create
    fix_bond_swap
+   fix_bond_react
    fix_box_relax
    fix_cmap
    fix_colvars
@@ -59,6 +61,7 @@ Fixes :h1
    fix_langevin
    fix_langevin_drude
    fix_langevin_eff
+   fix_langevin_spin
    fix_latte
    fix_lb_fluid
    fix_lb_momentum
@@ -97,6 +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
@@ -112,6 +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

@@ -135,8 +135,10 @@ fix_ave_histo.html
 fix_ave_time.html
 fix_aveforce.html
 fix_balance.html
+fix_bocs.html
 fix_bond_break.html
 fix_bond_create.html
+fix_bond_react.html
 fix_bond_swap.html
 fix_box_relax.html
 fix_cmap.html
@@ -174,6 +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
@@ -211,6 +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
@@ -227,6 +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
@@ -315,6 +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
@@ -379,6 +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
@@ -504,6 +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
@@ -580,6 +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_kolmogorov_crespi_z.txt

@@ -38,7 +38,7 @@ This shift is achieved by the last term in the equation for {Vij} above.
 This potential is intended for interactions between two layers of graphene.
 Therefore, to avoid interaction between layers in multi-layered materials,
 each layer should have a separate atom type and interactions should only
-be computed between atom types of neighbouring layers.
+be computed between atom types of neighboring layers.
 
 The parameter file (e.g. CC.KC), is intended for use with metal
 "units"_units.html, with energies in meV. An additional parameter, {S},

doc/src/pair_oxdna.txt

@@ -71,9 +71,11 @@ the temperature coefficients have to be matched to the one used in the fix.
 Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
-A technical report with more information on the model, the structure of the input file,
-the setup tool and the performance of the LAMMPS-implementation of oxDNA
-can be found "here"_PDF/USER-CGDNA-overview.pdf.
+
+Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation. 
+The article contains more information on the model, the structure of the input file, the setup tool 
+and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
 
 :line
 
@@ -92,6 +94,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 :line
 
+:link(Henrich1)
+[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
 :link(Sulc1)
 [(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
 

doc/src/pair_oxdna2.txt

@@ -77,9 +77,11 @@ the temperature coefficients have to be matched to the one used in the fix.
 Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
-A technical report with more information on the model, the structure of the input file,
-the setup tool and the performance of the LAMMPS-implementation of oxDNA
-can be found "here"_PDF/USER-CGDNA-overview.pdf.
+
+Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation. 
+The article contains more information on the model, the structure of the input file, the setup tool 
+and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
 
 :line
 
@@ -98,6 +100,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 :line
 
+:link(Henrich)
+[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
 :link(Sulc2)
 [(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
 

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).